CA2530350A1 - Digital cell - Google Patents
Digital cell Download PDFInfo
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- CA2530350A1 CA2530350A1 CA002530350A CA2530350A CA2530350A1 CA 2530350 A1 CA2530350 A1 CA 2530350A1 CA 002530350 A CA002530350 A CA 002530350A CA 2530350 A CA2530350 A CA 2530350A CA 2530350 A1 CA2530350 A1 CA 2530350A1
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- Prior art keywords
- cell
- profile
- parameter
- stimulus
- support
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Classifications
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- G—PHYSICS
- G01—MEASURING; TESTING
- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
- G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
- G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
- G01N33/5005—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12M—APPARATUS FOR ENZYMOLOGY OR MICROBIOLOGY; APPARATUS FOR CULTURING MICROORGANISMS FOR PRODUCING BIOMASS, FOR GROWING CELLS OR FOR OBTAINING FERMENTATION OR METABOLIC PRODUCTS, i.e. BIOREACTORS OR FERMENTERS
- C12M41/00—Means for regulation, monitoring, measurement or control, e.g. flow regulation
- C12M41/48—Automatic or computerized control
Abstract
It is intended to provide a method and system for carrying out data production with respect to the actual status of cells as a profile. It is also intended to provide a system and method for presenting time-lapse and/or real-time information of cell interior directly or as it is from the viewpoint of complex system. It is further intended to provide a method of presenting a digital cell. Thus, there is provided a method of producing profile data relating to cell information, comprising the step (a) of arranging cells in immobilized form on a support and the step (b) of monitoring over time biological factors on or inside the cells or an aggregate thereof, thereby producing profile data of the cells. Furthermore, there is provided a method of producing a digital cell, comprising procuring experimental data by the use of the above method.
Description
DESCRIPTION
' Dz~zTAZ cE~~
TECHNICAT~ FIELD
Ar007 The present invention lies in the field of technology of analysing a cell. More specifically, the present invention is related to a method for providing a profile of a cell in a consistent environment, a system therefor, and data obtained by such technology and data sequence technology related thereto, as well as digital cell technology. The detailed description of the invention is provided as follows.
BACKGROUND ART
The survival of organisms depends on their ability 'to perceive and respond to extra-cellular signals .
At the molecular level, signals are perceived and transmitted through networks of interacting proteins or the like, that act cooperatively to maintain cellular homeostasis and regu~.ate activities ~.ike growth, division and differentiation. Infox~xnation transfer through biologics.l signaling networks is mediated largely by protein-protein interact~.ons that can assemble and disassemble dynamically in response to signals, creating transient circuits that link external events to specific internal outputs, such as changes in gene expression.
Numerous strategies have been developed to map the Az007 protein,protein interactions that underlie these networks.
These studies have Collectively provided a wealth of data delineating genome-wide protein-protein interactions for Saeeharomyces cervis.iae and other organisms. While S powerful, these approaches have provided only a partial picture and are likely to overlook many interactions that are context dependent, forming only in the presence of their appropriate signals.
The disruption of protein-protein interactions either by mutation or small-molecules can create biological fulcrums that enable small perturbations of a signaling network to elicit large changes in cellular phenotype.
However, not all protein-protein interactions in a given signal~.ng pathway are likely to possess this power. As such, complementary strategies that aim to identify regulatory protein-protein interactions by artificially introducing proteins or peptides into cells which compete with and titrate-out the endogenous regulatory interactions, thereby disrupting the normal circuits that connect external signals to ce~.lular responses, are of interest.
By combining this strategy with funatianal assays, such as the activation of a gene in response to a signal, screens for functional interference can be used to identify peptides that perturb regulatory protein-protein interactions.
This strategy, often referred to as dominant--interfering or dominant-negative genetics, has been successfully employed in several model organisms where high-throughput screening methods are easily applied, and to a lesser extent xn mammals, which have traditionally been less amenable to
' Dz~zTAZ cE~~
TECHNICAT~ FIELD
Ar007 The present invention lies in the field of technology of analysing a cell. More specifically, the present invention is related to a method for providing a profile of a cell in a consistent environment, a system therefor, and data obtained by such technology and data sequence technology related thereto, as well as digital cell technology. The detailed description of the invention is provided as follows.
BACKGROUND ART
The survival of organisms depends on their ability 'to perceive and respond to extra-cellular signals .
At the molecular level, signals are perceived and transmitted through networks of interacting proteins or the like, that act cooperatively to maintain cellular homeostasis and regu~.ate activities ~.ike growth, division and differentiation. Infox~xnation transfer through biologics.l signaling networks is mediated largely by protein-protein interact~.ons that can assemble and disassemble dynamically in response to signals, creating transient circuits that link external events to specific internal outputs, such as changes in gene expression.
Numerous strategies have been developed to map the Az007 protein,protein interactions that underlie these networks.
These studies have Collectively provided a wealth of data delineating genome-wide protein-protein interactions for Saeeharomyces cervis.iae and other organisms. While S powerful, these approaches have provided only a partial picture and are likely to overlook many interactions that are context dependent, forming only in the presence of their appropriate signals.
The disruption of protein-protein interactions either by mutation or small-molecules can create biological fulcrums that enable small perturbations of a signaling network to elicit large changes in cellular phenotype.
However, not all protein-protein interactions in a given signal~.ng pathway are likely to possess this power. As such, complementary strategies that aim to identify regulatory protein-protein interactions by artificially introducing proteins or peptides into cells which compete with and titrate-out the endogenous regulatory interactions, thereby disrupting the normal circuits that connect external signals to ce~.lular responses, are of interest.
By combining this strategy with funatianal assays, such as the activation of a gene in response to a signal, screens for functional interference can be used to identify peptides that perturb regulatory protein-protein interactions.
This strategy, often referred to as dominant--interfering or dominant-negative genetics, has been successfully employed in several model organisms where high-throughput screening methods are easily applied, and to a lesser extent xn mammals, which have traditionally been less amenable to
2 these types of screens. One advantage of dominant-negative strategies is that such strategies can pinpoint the functionally relevant protein-protein interaction"fulcrum points" and thereby expose the small number of nodes within the larger web of a protein networl~ that are susceptible to functional modulation by external agents. As such, the results of such strategi~s can provide vital information about the regulatory components that define a particular pathway and can allow the eluaidatzon of key protein-protein interactions suitable for targeting by drug screening programs.
The difficulty in transfecting cells or producing transgenic organisms hinders the progression of development of dominant negative screening in mammals. To overcame this problem, high--efficiency retrovirus transfection has been developed. Although this retrovirus transfection is potent, it is necessary to produce DNA to be packaged into viral. intermediates, and therefore, the applicability of this technique islimited. Alternatively, high-density transfection arrays or Cell arrays are being developed, and the use thereof is proposed.
Rasetta 2npharmatics has proposed using cellular information, as a profile in some patent applications (Japanese 1~CT National Phase laid-Open Publication No. : 2003-505038 ~ Japanese PCT National Phase Laid-Open Publication No.: 2003 - 505022 . Japanese PCT
National Phase Laid-Open Publication No.: 2002 - 533701:
Japanese PCT National. Phase Zaid-Dpen Publication No. : 2002
The difficulty in transfecting cells or producing transgenic organisms hinders the progression of development of dominant negative screening in mammals. To overcame this problem, high--efficiency retrovirus transfection has been developed. Although this retrovirus transfection is potent, it is necessary to produce DNA to be packaged into viral. intermediates, and therefore, the applicability of this technique islimited. Alternatively, high-density transfection arrays or Cell arrays are being developed, and the use thereof is proposed.
Rasetta 2npharmatics has proposed using cellular information, as a profile in some patent applications (Japanese 1~CT National Phase laid-Open Publication No. : 2003-505038 ~ Japanese PCT National Phase Laid-Open Publication No.: 2003 - 505022 . Japanese PCT
National Phase Laid-Open Publication No.: 2002 - 533701:
Japanese PCT National. Phase Zaid-Dpen Publication No. : 2002
3 -533700 ~ Japanese PCT National Phase Laid~Open Publication No.: 2002 - 533699f Japanese PCT National Phase Laid-Open Publication No.: 2002-528095 : Japanese PCT National Phase Laid-Open Publication No.: 2002 - 526757 ~ Japanese PC's National Phase Laid-Open Publication No.: 2002-51802 1 Japanese PCT National Phase Laid-Open Publication No.: 2002 -518003 ~ Japanese PCT National Phase Laid-Open Publication No.: 2002 -514804~Japanese PCT National Phase Laid-Open Publication No. : 2002-514773 : Japanese PCT Nat~,anal Phase Laid-Open Publication No. : 2002-514437) . In such a profile, information from separate cells is processed as a group of separate pieces of information, but not continuous information. Therefore, this technique is limited in that information analysis is nat conducted on a single tthe same) cell. Particularly, in this technique, analy$is is conducted only at one specific time point before and after a certain change, and a series of temporal changes in a point (gene) are not analyzed.
Recent advances in profiling techniques ha~sre led to accurate measurement v~ cellular components, and thus, profiling of cel7.ular information (e.g., Schena et al., 1995, "Quantitativr~ monitoring of gEne expression patterns with a cvznplementary DNA microarray", Science 270:467-470;
Lockhart et al., 1996, "Expression monitoring by hybridization to high-density oJ.igonucleotide arrays", Nature Biotechnology 14 : 1675,1.680: Hlanchard et al. , 1.996, "Sequence to array: Pxobing the genomE's secrets", Nature Biotechnology 14:1649; and US 5,569,588). FQr organ~.sms whose genome is entirely known, it is possib~.e to analyze
Recent advances in profiling techniques ha~sre led to accurate measurement v~ cellular components, and thus, profiling of cel7.ular information (e.g., Schena et al., 1995, "Quantitativr~ monitoring of gEne expression patterns with a cvznplementary DNA microarray", Science 270:467-470;
Lockhart et al., 1996, "Expression monitoring by hybridization to high-density oJ.igonucleotide arrays", Nature Biotechnology 14 : 1675,1.680: Hlanchard et al. , 1.996, "Sequence to array: Pxobing the genomE's secrets", Nature Biotechnology 14:1649; and US 5,569,588). FQr organ~.sms whose genome is entirely known, it is possib~.e to analyze
4 the transcripts of all genes in a cell. In the case of other organisms, for which the amount of known genomic information is increasing, a number of genes in a cell can be simultaneously monitored.
As array technology advances, arrays also have been utilized in the field of drug screening (e. g., Marton et al., "Drug target validation and identification of secondary drug target effects using Microarrays", Nat. Med., 1998 Nov, 4 (I1) :1293-301: and Gray et al. , 1998, "Exploiting chemical libraries, structure, and genomics in the search for.kinase inhibitors", Science, 281:533-538). Analysis using profiles (e.g., US Patent No. 5,777,888) and clustering of profiles provides information about conditions of cells, transplantation, target molecules and drug candidates, and/or the relevant functions, efficacy and toxicity of drugs. These techniques can be used to determine a common profile which represents ideal drug activity and disease conditions. Comparing profiles assists in detecting diseases in patients at an early stage, and provides prediction of improved clinical outcomes for patients who have been diagnosed as having a disease.
However, to date, there has been no technique which can provide information about the same cell in the true sense. In the above-described techniques, data is obtained as average for a group of heterologous cel~.s.
Analyses and evaluations based on such data lack accuracy.
Therefore, there is an increasing demand for a method of providing information at the cellular level.
As array technology advances, arrays also have been utilized in the field of drug screening (e. g., Marton et al., "Drug target validation and identification of secondary drug target effects using Microarrays", Nat. Med., 1998 Nov, 4 (I1) :1293-301: and Gray et al. , 1998, "Exploiting chemical libraries, structure, and genomics in the search for.kinase inhibitors", Science, 281:533-538). Analysis using profiles (e.g., US Patent No. 5,777,888) and clustering of profiles provides information about conditions of cells, transplantation, target molecules and drug candidates, and/or the relevant functions, efficacy and toxicity of drugs. These techniques can be used to determine a common profile which represents ideal drug activity and disease conditions. Comparing profiles assists in detecting diseases in patients at an early stage, and provides prediction of improved clinical outcomes for patients who have been diagnosed as having a disease.
However, to date, there has been no technique which can provide information about the same cell in the true sense. In the above-described techniques, data is obtained as average for a group of heterologous cel~.s.
Analyses and evaluations based on such data lack accuracy.
Therefore, there is an increasing demand for a method of providing information at the cellular level.
5 An object of the present invention is to provide a method for obtaining information, profiles or data of a cell.
Another object of the present invention is to provide a method for obtaining information and data relating to cell status in a consistent environment, and a method and system for accurately presenting such data. In particular, a particular purpose of the present invention is to provide a system and a method for directly or as such infvxmation of a cell in a consistent environment in terms of complex system information, and providing such data and data sequencing technology per se. Another vbj ect of the present invention is to provide a dig~.tal cell and uses thereof.
SUMMARY OF THE INVENTTON
The above-mentioned objects have been achieved or solved by immobilizing a cell onto a substrate, monitoring a biological agent, or a collection thereof, on or in a cell over time to produce cell profile data. As such, sequential collection of data from a cell has been enabled, and production of a digital cell has been achieved.
The above~mentioned object has further been achieved or solved by providing a substrate locating a plurality of cells in a consistent environment. Such a substrate has been provided by immobilizing a cell onto a substrate by means of for example, a salt or an actin-like substance, preferably both a salt and an actin-like substance. As such, the present invention allows one to collect cell profile
Another object of the present invention is to provide a method for obtaining information and data relating to cell status in a consistent environment, and a method and system for accurately presenting such data. In particular, a particular purpose of the present invention is to provide a system and a method for directly or as such infvxmation of a cell in a consistent environment in terms of complex system information, and providing such data and data sequencing technology per se. Another vbj ect of the present invention is to provide a dig~.tal cell and uses thereof.
SUMMARY OF THE INVENTTON
The above-mentioned objects have been achieved or solved by immobilizing a cell onto a substrate, monitoring a biological agent, or a collection thereof, on or in a cell over time to produce cell profile data. As such, sequential collection of data from a cell has been enabled, and production of a digital cell has been achieved.
The above~mentioned object has further been achieved or solved by providing a substrate locating a plurality of cells in a consistent environment. Such a substrate has been provided by immobilizing a cell onto a substrate by means of for example, a salt or an actin-like substance, preferably both a salt and an actin-like substance. As such, the present invention allows one to collect cell profile
6 data from cells of the same type, located in a consistent environment, simultaneously under the same conditions.
Accordingly, the present invention provides the following:
1. A method for producing profile data relating to information of a cell in a consistent environment, said method comprising the steps of:
a) locating a plurality of cells to a support which is capable of maintaining the cells in a consistent environment; and b) monitoring a biological agent, or a collection thereof, on or in the cell to produce the profile data for the cell.
2. A method according to Item 1, whexein the biological agent is a nucleic acid molecule or a molecule derived from the nucleic acid molecule.
3. A method according to Item 1, wherein the cell is immobilized to the support by a composition compzising a) a complex with a positively charged substance and a negatively charged substance: and b) a salt.
4. A method according to Item 1 wherein the cell is provided with an actin-like substance.
5. A method according to Item 1, wherein the cell is immobilized to the support by a composition comprising a) a complex with a positively charged substance and a
Accordingly, the present invention provides the following:
1. A method for producing profile data relating to information of a cell in a consistent environment, said method comprising the steps of:
a) locating a plurality of cells to a support which is capable of maintaining the cells in a consistent environment; and b) monitoring a biological agent, or a collection thereof, on or in the cell to produce the profile data for the cell.
2. A method according to Item 1, whexein the biological agent is a nucleic acid molecule or a molecule derived from the nucleic acid molecule.
3. A method according to Item 1, wherein the cell is immobilized to the support by a composition compzising a) a complex with a positively charged substance and a negatively charged substance: and b) a salt.
4. A method according to Item 1 wherein the cell is provided with an actin-like substance.
5. A method according to Item 1, wherein the cell is immobilized to the support by a composition comprising a) a complex with a positively charged substance and a
7 negatively charged substance: and b) a salt, and is provided with an actin-like substance.
6. A method according to Item 1 wherein the biological agent is selected from the group consisting of a nucleic acid molecule, a protein, a saccahride, a lipid, a low molecular weight molecule, and a complex thereof.
7. A method according to Item 1, wherein the cell is cultured at least abaut three days before the step of monitoring.
6. A method according to Item 1 wherein the biological agent is selected from the group consisting of a nucleic acid molecule, a protein, a saccahride, a lipid, a low molecular weight molecule, and a complex thereof.
7. A method according to Item 1, wherein the cell is cultured at least abaut three days before the step of monitoring.
8. A method according to Item 1, wherein the biological agent comprises a nucleic acid molecule encoding a gene.
9. A method according to Item 1, wherein the profile comprises a profile for gene expression.
10. A method according to Item 1, wherezn the profile comprises a profile of an apoptosis signal.
11. A method according to Item 1 wherein the profile is a profile of a stress signal.
12. A method according to Item 1 wherein the profile is a profile of the localization of a molecule.
13 . A method according to Item 12 wherein the molecule is detected by means selected from the group consisting of fluorescence, phosphorescence, radioactivity, and a combination thereof.
14. A method according to Item 1 wherein the profile comprises a variation in cell morphology.
15. A method according to Ttem l wherein the profile comprises a profile of promoter activity.
16. A method according to Item 1, wherein said profile comprises a profile of a promoter dependent vn a specific drug.
17. A method according to Item 1 wherein said profile comprises a profile of a promoter dependent on a specific drug, wherein said method further comprises the step of administering the specific drug.
18. A method according to Item 1 further comprising the step of'sub~ecting the cell to a foreign agent.
19. A method according to Item 18, wherein said foreign agent comprises an RNAi.
20. A method according to Item 18, wherein said foreign agent comprises a chemical not present in a biological body.
21. A method according to Item 1, wherein said profile comprises a profile of an intermolecular interaction.
22. A method according to Item 18, wherein said foreign agent comprises a ligand for~a receptor of said cell.
23. A method according to Item 1, wherein said profile comprises a profile of an interaction between a receptor and' a ligand.
24 . A method according to Item 1, wherein said profile is of a cellular form, and said method further comprises the step of giving to said cell a stimulus selected from the group consisting of overexpression, underexpression or knockdown of a gene, addition of a foreign agent and a change in the environment.
25. A method according to Item 1, wherein said profile comprises a profile of interaction between molecules present in said cell.
26. A method according to Item 1, further comprising the step of conducting vbeervation using a technology selected from the group consisting of two-hybrid method, FRET and BRET.
27. A method according to Item 1, wherein said profile comprises a profile of interaction between molecules present in said cell, wherein the method further comprises the step of conducting observation using a technology selected from the group consisting of two-hybrid method, FRET and BRET.
28. A method according to Item 1, wherein said cell is located on said support in an array format.
29. A method according to Item 1, wherein said cell is located on said support in an array format, and each of said plurality of cells are located at a space of 1 mm at maximum.
30. A method according to Ttem 1, wherein said profile is obtained in real-time.
31. A method according to Item 1 further comprising the step of immobilizing said cell to a solid support.
32. A method according to Item 1, wherein said data comprises information relating to said profile.
33. A method according to Iteml wherein said data comprises information relating to conditions during said monitoring.
39 . A method according Item 1 wherein said data comprises information relating to the status of said cell.
35. A method according to Ttem 1 wherein said biological agent to be monitored comprises at least two types of biological agent.
36. A method according to Item 1 wherein said biological agent to be monitored comprises at least three types of biological agent.
37. A method according to Item 1 wherein said biological agent to be monitored comprises at least eight types of biological agents:
36. A method according to Item 1 further comprising the step of arbitrarily selecting a biological agent.
39. A method according to Item 1 wherein said cell is selected from the group consisting of a stem cell and a somatic cell.
40. A method according to Item 1 wherein said support comprises a solid support.
41. A method according to Item 1 wherein said support comprises a substrate.
42. A method according to Item 1 wherein said biological agent is a nucleic acid molecule, and said cell is transfected with said nucleic acid molecule.
43. A method according to Item 42, wherein said transfection is conducted on a solid phase or in a liquid phase.
44. A method according to Item 42, wherein said transfection is conducted on a solid support.
45. A method according to Item 1, further comprising the step of comparing a phase of said profile.
46. A method according to Item 1, further comprising the step of subtracting a control profile from the profile of said cell.
47. A method according to Ttem 1 further comprising the step of processing the profile with a mathematical processing method selected from signal processing and multivariant analysis methods.
48. A method for presenting profile data relating to information of a cell in a consistent environment, comprising the steps of:
a) locating a plurality of cells on a support which is capable of maintaining the cells in a consistent environment;
b) monitoring a biological agent, or a collection thereof, on or in the cell to produce the profile data for the cell; and c) presenting the data.
49. A method according to Item 48, wherein said step of presenting is conducted in real-time.
50. A method according to Item 48, wherein said step of presenting is conducted such that visual detection is enabled.
51. A method according to Ttem 4B, wherein said step of presenting is conducted such that auditory detection is enabled.
52. A method for determining the state of a cell in a consistent environment, comprising the steps of:
a) locating a plurality of cells on a support Which is capable of maintaining the cells in a consistent environment: b) monitoring a biological agent, or a collection thereof, on or in the cell to produce the profile , data for the cell; and c) determining the state of said cell from said data.
53. A method according to Item 52, further comprising the step of correlating said profile and the state of said cell in advance.
54. A method according to Item 52, wherein said ee~.l comprises a cell for which the state thereof is known.
55. A method according to Item 52, wherein there are at least two types of said biological agent.
56. A method according to Item 52, further comprising the step of arbitrarily selecting said biological agent.
57. A method according to Item 52, wherein said data is produced in real-time.
58. A method according to Ttem 52, wherein said status is selected from the group consisting of differentiation state, undifferentiation state, cellular response to a foreign agent, cellular cycle and growth state.
59. A method according to Item 52, wherein said cell is selected from the group consisting of a stem cell and a somatic cell.
60. A method according to Item 52, wherein said solid support comprises a substrate.
61. A method according to Item S2, wherein said biological agent is a nucleic acid molecule, and said cell is transfected with said nucleic acid molecule.
62. A method according to Item 61, wherein said transfection is conducted on a solid phase or in a liquid phase.
63 . A method according to Item 52, wherein said biological agent has the capability of binding a different biological agent.
64. A method according to Item 52, wherein said step of determination c) comprises comparing the phases of said profile.
65. A method according to Item 52, wherein said step of determination c) comprises obtaining the difference between said profile and a control profile.
66. A method according to Item 52, wherein said step of determination c) comprises a mathematical processing method selected from the group consisting of signal processing and multivariate analysis methods.
67 . A method for correlating a foreign agent and a cellular response to the foreign agent, comprising the steps of:
a) subjecting a cell to a foreign agent on a support capable of maintaining a plurality of cell in a consistent environment;
b) monitoring a biological agent or a collection thereof on or in the cell to produce the profile data for the cell; and c) correlating the foreign agent and the profile.
68. A method according to Item 68, wherein said cell is immobilized on said support.
69. A method according to Item 69, further comprising the step of using at least two of said foreign agents to obtain profiles of each of the foreign agents.
70. A method according to Item 67, further comprising the step of classifying at least two of said profiles to classify foreign agents corresponding to the profiles.
71. A method according to Item 70, wherein said profile is presented in real-time.
72. A method according to Item 67, wherein said cell is cultured on an array.
73. A method according to Item 67, wherein the monitoring of said profile in step (b) comprises obtaining image data from said array.
74. A method according to Item 67, wherein said correlation between said foreign agent and said profile in step (c) is a step of identifying the identity or difference of the phase of said profile.
75. A method according to Item 67, wherein said foreign agent is selected from the group consisting of temperature changes, humidity changes, electromagnetic waves, potential difference, visible light, infrared light, ultraviolet light, X-rays, chemical substances, pressure, gravity changes, gas partial pressure and osmotic pressure.
76. A method according to Item 75, wherein said chemical substance is a biological molecule, a chemically synthesized substance or a culture medium.
77 . A method according to Item 7 6, wherein said biological molecule is selected from the group consisting of a nucleic acid, a protein, a lipid, a sugar, a proteolipid, a lipoprotein, a glycoprotein and a proteoglycan.
7 B . A method according to Item 7 6, wherein said biological molecule comprises at least vne biological molecule selected from the group consisting of a hormone, a cytokine, a cell adhesion factor and an extracellular matrix protein.
79. A method according to Item 75, wherein said chemical substance is an agonist or antagonist of a receptor.
80. Amethod for identifying an unidentified foreign agent given to a cell, from the profile of said cell, comprising the steps of:
a) subjecting a cell on a support capable of maintaining a plurality of cells in a~consistent environment, to a plurality of known foreign agents b) monitoring a biological agent, or a collection thereof, on .or in the cell over time to produce the profile data for the cell in response to each of the known foreign agents to produce profile data for the cell;
c) correlating each of the known foreign agents and each of the profiles:
d) subjecting the cell to an unidentified foreign agent:
e) monitoring a biological agent, or a collection thereof, on or in the cell subj ected to the unknown foreign agent over time to obtain the profile of the cell relating to the unidentified foreign agent;
f) determining the profile corresponding to the profile obtained in step e) amongst the~profiles obtained in step b):
g) determining that the unidentified foreign agent is the known foreign agent corresponding to the profile which has been determined in step f).
81. A method for identifying an unidentified foreign agent ' 18 given to a cell, from the profile of the cell, comprising the steps of a) providing data relating to a correlation between a known foreign agent, and a profile of the cell corresponding to the known foreign agent, with respect to a biological agent, or a collection thereof, on or in the cell;
b) subjecting the cell to an unidentified foreign agent;
c) monitoring the biological agent, or the collection thereof, on or in the cell over time to produce a profile of the cell;
d) determining the profile corresponding to the profile obtained in step c) amongst the profiles provided in step a); and a ) determining that the unidentified foreign agent is the known foreign agent corresponding to the determined profile.
82. A method for obtaining a profile re~.ating to information of a cell in a consistent environment, comprising the steps of:
a) locating a plurality of cells to a support which is capable of maintaining the cells in a consistent environment; and b) monitoring a biological agent, or a collection thereof, on or in the cell over time to produce the profile data for the cell.
83. A storage medium on which data produced by a method according to Item l, is stored.
84. A storage medium according to Item 83, wherein said storage medium further comprises data of at least one information relating to one selected from the group consisting of information relating to conditions under said monitoring, information relating to said profile, information relating to the state of said cell and information relating to the biological agent.
85. A storage medium accozding to Item 84, wherein the data is stored in a format which links a plurality of the data to each other.
86. A storage medium according to Item 84, wherein the data is stored in a format which has links per said cell.
87. Data produced by a method according to Item 1.
B8. A transmission medium comprising data produced by a method according to Item 1.
89. A system for producing profile data relating to information of a cell in a consistent environment, said method comprising:
a) a support which is capable of maintaining the cell in a consistent environment;
b) means for monitoring a biological agent, or a collection thereof, on or in the cell to produce the profile data for the cell: and c) means for producing profile data for the cell from a signal obtained from the means for monitoring.
90. A system according to Item 89, further comprising a plurality of cells, and the plurality of cells are immobilized on to the support.
91. A system according to Item 90, wherein said support is attached at least one substance selected from the group consisting of a salt and an actin-like substance.
92. A system according to Item 89, wherein said means for monitoring comprises at least one means selected from the group consisting of optical microscopes, fluorescence microscopes, phase-contrast microscopes, reading devices using a laser source, means using surface plasmon resonance (SPR) imaging, electric signals, chemical or biochemical markers singly or in combination, radiation, confocal microscopes, nonconfocal microscopes, differential interference microscopes, stereoscopic microscopes, video monitors and infrared cameras.
93. A system for presenting profile data relating to information of a cell in a consistent environment, comprising:
a) a support which is capable of maintaining the cell in a consistent environment;
b) means for monitoring a biological agent, or a collection thereof, on or in the cell to produce the profile data for the cell;
c) means for producing profile data for the cell from a signal obtained from the means for monitoring: and d) means for presenting the data.
94. A system according to Item 93, further comprising a plurality of cells, wherein the plurality vf.cells are immobilized on to the support.
95. A system according to Item 93, wherein said support is attached at least one substance selected from the group consisting of a salt and an actin-like substance.
96. A system according to Item 93, wherein said means for monitoring comprises at least one means selected from the group consisting of optical microscopes, fluorescence microscopes, phase-contrast microscopes, reading devices using a laser source, means using surface plasmon resonance (SPR) imaging, electric signals, chemical or biochemical markers singly or in combination, radiation, confocal microscopes, nonconfocal microscopes, differential interference microscopes, stereoscopic microscopes, video monitors and infrared cameras.
97. A system according to Item 93, wherein said means for presenting data is a display.
98. A system according to Item 93, wherein said means for presenting data is a speaker.
99. A system for determining the state of a cell in a consistent environment, comprising a) a support which is capable of maintaining the cell in a consistent environment:
b) means for monitoring a biological agent, or a collection thereof, on or in the cell to produce the profile data for the cell:
c) means for producing profile data for the cell from a signal obtained from the means for monitoring: and d) means for determining the state of said cell from said data.
100. A system for correJ.ating a foreign agent and a cellular response to the foreign agent, comprising:
a) a support capable of maintaining a plurality of cells in a consistent environment:
b) means for subjecting the cells to a foreign agent;
c) monitoring a biological agent, or a collection thereof, on or in the cells to produce the profile data for the cells;
d) means for producing profile data for the cells from a signal obtained from the means for monitoring: and e) means for correlating the foreign agent and the profile.
101. A system for identifying an unidentified foreign agent given to a cell, from the pxofile of said cell, comprising:
a) a support capable of maintaining a plurality of cells in a consistent environment;
b) means for subjecting the cells to a known foreign agent:
e) means for monitoring a biological agent, or a collection thereof, on or in a cell over time;
d) means for obtaining the profile data for the cell in response to each of known foreign agents to produce profile data for the cell;
e) means for correlating each of the known foreign agents and each of the profiles;
f) means for subjecting the cells to an unknown foreign agent;
g) means for comparing the profile of the known foreign agent obtained with means d) , and the profile of the unknown foreign agent to determine a profile corresponding to the profile of the unknown foreign agent amongst the profiles of the known foreign agents, wherein said determined unidentified foreign agent is the known foreign agent for which the determined profile corresponds to.
102 . A system for identifying an unidentified foreign agent given to a cell, from the profile of the cell, comprising:
a) a storage medium having stored data relating to a correlation between a known foreign agent, and a profile of the cell corresponding to the known foreign agent, with respect to a biological agent, or a collection thereof, on or in the cell,;
b) means for subjecting the cell to an unidentified foreign agent:
c) a support which is capable of maintaining a plurality of cells in a consistent environment:
d) means for monitoring the biological agent or the collection thereof on or in the cell over time to produce a profile of~the cell;
e) means for obtaining the profile of the cell from a signal obtained from the means for monitoring; and f ) means fvr determining the profile corresponding to the prafile obtained relating to the unidentified foreign agent amongst the profiles stored in storage medium a), wherein the unidentified foreign agent is the known foreign agent for which the determined profile corresponds to.
103. A support capable of immobilizing a plurality of cells and maintaining the cells in a consistent environment.
104. A support according to Item 103, wherein the cells on the support are located in an array format.
105. A support according to Item 103 comprising a complex of a positively charged substance and a negatively charged substance: a salt: yr an actin-like substance.
106. A support according to Item 103 comprising a complex of a positively charged substance and a negatively charged substance: a salt: arid an act~.n-like substance.
107. A support according to Item 103, wherein said item is capable of being located within a space of 1 mm or less at maximum.
108. A support according to Item 103, further comprising a cell immobilized thereon.
109. A support according to Ttem 103, further comprising a biological agent immobilized thereon.
110. A support according to item 109, wherein two or more types of said biological agent are immobilized thereon.
111. A support according to Item 103, wherein a cell and a biological agent are immobilized thereon.
112. A support according to Item 103, wherein a salt: a complex between~a positively charged substance and a negatively charged substance; and an actin-like substance are immobilized thereon together With a cell and a biological agent.
113. A support according to Item 103, wherein a salt; a complex between a positively charged substance and a negatively charged substance; and an actin-like substance are immobslized thereon together with a cell and a biological agent, in an array format.
114 . A support. according to Item 104, wherein a salt, a gene introduction reagent, and an actin-like substance, a nucleic acid molecule, and a cell are immobilized thereon in an array format.
115. . A support according to Ttem 114, wherein the salt is selected from the group consisting of calcium chloride, sodium hydrogen phosphate, sodium hydrogen carbonate, sodium pyruvate, HEPES, calcium chloride, sodium chloride, potassium chloride, magnesium sulfide, iron nitrate, amino acids, and vitamins.
17.6. A support according to Item 114, wherein the gene introduction reagent is selected from the group consisting of cationic polymers, cationic lipids, polyamine-based reagents, polyimine-based reagents, calcium phosphate, oligofectamine and oligofecter.
117. A support according to Item 114, wherein the actin-like substance comprises at least one protein selected from the group consisting of fibronectin, laminin, and vitronectin, or a variant or fragment thereof.
118. A support according to Item 114, wherein the nucleic acid molecule comprises a sequence encoding a protein selected from the group consisting of cytokines, hormones, cell adhesion molecules, cytoskeleton proteins and enzymes.
119. A support according to Item 114, wherein the cell comprises a cell selected from the group consisting of an animal cell, an insect cell, a plant cell, a bacterial cell and a fungal cell.
120. A support according to Item 114 wherein material of said support comprises material selected from the group consisting of glass, silica and plastics.
121. A method for producing a support comprising a plurality of cells immobilized thereon and capable of maintaining the cells in a consistent environment, comprising the steps of:
A) providing a support; and B) immobilizing a cell to the support using a complex comprising of a salt, a positively-charged substance and a negatively-charged substance.
122. A method according to Item 121, wherein said step of immobilizing comprises immobilizing a mixture of the salt, a gene introduction reagent as the positively-charged substance, , an actin-like substance, a nucleic acid molecule as the negatively-charged substance, and the cell in an array format.
123. A method according to Item 121, wherein said step o~
immobilizing comprises a printing step.
124. A method according to Item 121, wherein the step of providing the support comprises the step of producing the support from a support material.
125. An apparatus for producing a suppozt comprising a plu~cality of cells immobilized thereon and capable of maintaining the cells in a consistent environment, comprising:
A) means for providing a support: and H) means for immobilizing a cell to the support using a complex comprising a salt, a positively-charged substance and a negatively-charged substance.
126. An apparatus according to Item 125, wherein said means for immobilizing comprises means for printing.
127. An apparatus according to Item 125, wherein the means for providing the support comprises means for shaping the support from a support material.
128 . A method for producing a digital cell, comprising the steps of:
a) obtaining a cell parameter specifying a cell of experimental interest:
b) obtaining an environment parameter specifying an environment under which the cell specified by the cell parameter is cultured:
c) obtaining a stimulus parameter specifying a stimulus to be given to the cell specified by the cell parameter;
d) obtaining a stimulus response result showing a result which the cell specified by the cell parameter responds to the stimulus specified by the stimulus parameter under the environment specified by the environment parameter;
e) producing an experimental data for the cell, by correlating the cell parameter, the environment parameter, the stimulus parameter and the stimulus response result;
and f) optionally repeating steps a) through e) to produce at least one collection of experimental data for the cell, and to provide the at least one collection of experimental data as a digital cell.
129. A method according to Item 12B, wherein the environment parameter comprises a parameter indicating culture medium in which the cell is cultured, and a parameter showing the conditions of the culture medium.
130. A method according to Item 128, wherein the stimulus parameter comprises a parameter showing a reporter and a parameter showing a chemical stimulus.
131. A method according to Item 128, Wherein said stimulus response result comprises profile data far the cell obtained by monitoring a biological agent, or a collection thereof, on or in the cell aver time.
132 . A method according to Item 128, further comprising the step of storing the digital cell to a database.
133. An apparatus for producing a digital cell, comprising:
a) means for obtaining a cell parameter specifying a cell of experimental interest:
b) means for obtaining an environment parameter specifying an environment under which the cell specified by the cell parameter is cultured c) means for obtaining a stimulus parameter specifying a stimulus to be given to the cell specified by the cell parameter:
d) means for obtaining a stimulus response result showing a result-which the cell specified by the cell parameter responds to the stimulus specified by the stimulus parameter under the environment specified by the environment parameter;
e) means for producing an experimental data for the cell, by correlating the cell parameter, the environment parameter, the stimulus parameter and the stimulus response result; and f) means for providing at least one collection of experimental data as a digital cell; by optionally repeating steps performed by the means a) through e) to produce at least one collection of experimental data for the cell.
134. A method for providing a service which reproduces an experimental result of an actual cell using a digital cell by means of a computer system comprising a service requester and a service provider, comprising the steps of:
preparing a database having at least one digital cell stored thereon, wherein the at least one digital cell is expressed as a collection of at least one experimental data of a cell of experimental interest, wherein each of the at least one experimental data comprises a cell parameter specifying the cell, an environment parameter specifying an envizonment under which the cell specified by the cell parameter is cultured, a stimulus parameter specifying a stimulus to be given to the cell specifiied by the cell parameter, and a stimulus response result showing a result which the cell specified by the cell parameter responds to the stimulus specified by the stimulus parameter under the environment specified by the environment parameter:
receiving the cell parameter, the environment parameter and the stimulus parameter by the service requester to produce a request comprising the cell parameter, the environment parameter and the stimulus parameter;
providing the request to the service provider by the service requester;
searching the database in response to the reguest by the service provider to determine whether or not there is the stimulus response result relating to the cell parameter, the environment parameter and the stimulus parameter included in the request, in the database;
providing the stimulus response result to the service requester by the service provider, when it is determined that the stimulus response result relating to the cell parameter, the environment parameter and the stimulus parameter included in the request exists in the database;
and presenting the stimulus response result by the service requester.
135. A method for providing a service for reproducing an experimental result of an actual cell using a digital cell, by means of a computer system comprising a service requester and a plurality of service providers, comprising the steps of preparing a plurality of databases, each having at least one digital cell stored thereon, wherein the at least one digital cell is expressed as a collection of at least one experimental data of a cell of experimental interest, wherein each of the at least one experimental data comprises a cell parameter specifying the cell, an environment parameter specifying an environment under which the cell specified by the cell parameter is cultured, a stimulus parameter specifying a stimulus to be given to the cell specified by the cell parameter, and a stimulus response result showing a result which the cell specified by the cell parameter responds to the stimulus specified by the stimulus parameter under the environment specified by the environment parameter;
pz~eparing a service registry which stores at least one service capable of being provided by the plurality of service providers;
receiving the cell parameter, the environment parameter and the stimulus parameter by the service requester to produce a request comprising the cell parameter, the environment parameter and the stimulus parameter searching the service registry in response to the request by the service requester to determine whether or not there exists a service provider capable of providing a service for the request amongst the plurality of service providers;
providing the request to the service provider by the service requester when it is determined that a service provider capable of providing a service of the request amongst the plurality of service providers exists;
searching the database in response tv the request by the service provider to determine whether or not there is the stimulus response result relating to the cell parameter, the environment parameter and the stimulus parameter included in the request in the database;
providing the stimulus response result to the service requester by the service provider, when it is determined that the stimulus response result relating to the cell parameter, the environment parameter and the stimulus parameter included in the reguest exists in the database;
and presenting the stimulus response result by the service requester.
135. A computer system for providing a service which reproduces an experimental result of an actual cell using a digital cell, comprising:
a service requester being composed such that it can have access to a database having at least one digital cell stored thereon, each of the at least one digital cell is expressed as a collection of at least one experimental data of a cell of experimental interest, wherein each of the at least one experimental data comprises a cell parameter specifying the cell, an environment parameter specifying an environment under which the cell specified by the cell parameter is cultured, a stimulus parameter specifying a stimulus to be given to the cell specified by the cell parameter, and a stimulus response result showing a result which the cell specified by the cell parameter responds to the stimulus specified by the stimulus parameter under the environment specified by the environment parameter: and a service provider requesting a service desired by a user:
Wherein the service requester comprises:
means for receiving the cell parameter, the environment parameter and the stimulus parameter to produce a request comprising the cell parameter, the environment
39 . A method according Item 1 wherein said data comprises information relating to the status of said cell.
35. A method according to Ttem 1 wherein said biological agent to be monitored comprises at least two types of biological agent.
36. A method according to Item 1 wherein said biological agent to be monitored comprises at least three types of biological agent.
37. A method according to Item 1 wherein said biological agent to be monitored comprises at least eight types of biological agents:
36. A method according to Item 1 further comprising the step of arbitrarily selecting a biological agent.
39. A method according to Item 1 wherein said cell is selected from the group consisting of a stem cell and a somatic cell.
40. A method according to Item 1 wherein said support comprises a solid support.
41. A method according to Item 1 wherein said support comprises a substrate.
42. A method according to Item 1 wherein said biological agent is a nucleic acid molecule, and said cell is transfected with said nucleic acid molecule.
43. A method according to Item 42, wherein said transfection is conducted on a solid phase or in a liquid phase.
44. A method according to Item 42, wherein said transfection is conducted on a solid support.
45. A method according to Item 1, further comprising the step of comparing a phase of said profile.
46. A method according to Item 1, further comprising the step of subtracting a control profile from the profile of said cell.
47. A method according to Ttem 1 further comprising the step of processing the profile with a mathematical processing method selected from signal processing and multivariant analysis methods.
48. A method for presenting profile data relating to information of a cell in a consistent environment, comprising the steps of:
a) locating a plurality of cells on a support which is capable of maintaining the cells in a consistent environment;
b) monitoring a biological agent, or a collection thereof, on or in the cell to produce the profile data for the cell; and c) presenting the data.
49. A method according to Item 48, wherein said step of presenting is conducted in real-time.
50. A method according to Item 48, wherein said step of presenting is conducted such that visual detection is enabled.
51. A method according to Ttem 4B, wherein said step of presenting is conducted such that auditory detection is enabled.
52. A method for determining the state of a cell in a consistent environment, comprising the steps of:
a) locating a plurality of cells on a support Which is capable of maintaining the cells in a consistent environment: b) monitoring a biological agent, or a collection thereof, on or in the cell to produce the profile , data for the cell; and c) determining the state of said cell from said data.
53. A method according to Item 52, further comprising the step of correlating said profile and the state of said cell in advance.
54. A method according to Item 52, wherein said ee~.l comprises a cell for which the state thereof is known.
55. A method according to Item 52, wherein there are at least two types of said biological agent.
56. A method according to Item 52, further comprising the step of arbitrarily selecting said biological agent.
57. A method according to Item 52, wherein said data is produced in real-time.
58. A method according to Ttem 52, wherein said status is selected from the group consisting of differentiation state, undifferentiation state, cellular response to a foreign agent, cellular cycle and growth state.
59. A method according to Item 52, wherein said cell is selected from the group consisting of a stem cell and a somatic cell.
60. A method according to Item 52, wherein said solid support comprises a substrate.
61. A method according to Item S2, wherein said biological agent is a nucleic acid molecule, and said cell is transfected with said nucleic acid molecule.
62. A method according to Item 61, wherein said transfection is conducted on a solid phase or in a liquid phase.
63 . A method according to Item 52, wherein said biological agent has the capability of binding a different biological agent.
64. A method according to Item 52, wherein said step of determination c) comprises comparing the phases of said profile.
65. A method according to Item 52, wherein said step of determination c) comprises obtaining the difference between said profile and a control profile.
66. A method according to Item 52, wherein said step of determination c) comprises a mathematical processing method selected from the group consisting of signal processing and multivariate analysis methods.
67 . A method for correlating a foreign agent and a cellular response to the foreign agent, comprising the steps of:
a) subjecting a cell to a foreign agent on a support capable of maintaining a plurality of cell in a consistent environment;
b) monitoring a biological agent or a collection thereof on or in the cell to produce the profile data for the cell; and c) correlating the foreign agent and the profile.
68. A method according to Item 68, wherein said cell is immobilized on said support.
69. A method according to Item 69, further comprising the step of using at least two of said foreign agents to obtain profiles of each of the foreign agents.
70. A method according to Item 67, further comprising the step of classifying at least two of said profiles to classify foreign agents corresponding to the profiles.
71. A method according to Item 70, wherein said profile is presented in real-time.
72. A method according to Item 67, wherein said cell is cultured on an array.
73. A method according to Item 67, wherein the monitoring of said profile in step (b) comprises obtaining image data from said array.
74. A method according to Item 67, wherein said correlation between said foreign agent and said profile in step (c) is a step of identifying the identity or difference of the phase of said profile.
75. A method according to Item 67, wherein said foreign agent is selected from the group consisting of temperature changes, humidity changes, electromagnetic waves, potential difference, visible light, infrared light, ultraviolet light, X-rays, chemical substances, pressure, gravity changes, gas partial pressure and osmotic pressure.
76. A method according to Item 75, wherein said chemical substance is a biological molecule, a chemically synthesized substance or a culture medium.
77 . A method according to Item 7 6, wherein said biological molecule is selected from the group consisting of a nucleic acid, a protein, a lipid, a sugar, a proteolipid, a lipoprotein, a glycoprotein and a proteoglycan.
7 B . A method according to Item 7 6, wherein said biological molecule comprises at least vne biological molecule selected from the group consisting of a hormone, a cytokine, a cell adhesion factor and an extracellular matrix protein.
79. A method according to Item 75, wherein said chemical substance is an agonist or antagonist of a receptor.
80. Amethod for identifying an unidentified foreign agent given to a cell, from the profile of said cell, comprising the steps of:
a) subjecting a cell on a support capable of maintaining a plurality of cells in a~consistent environment, to a plurality of known foreign agents b) monitoring a biological agent, or a collection thereof, on .or in the cell over time to produce the profile data for the cell in response to each of the known foreign agents to produce profile data for the cell;
c) correlating each of the known foreign agents and each of the profiles:
d) subjecting the cell to an unidentified foreign agent:
e) monitoring a biological agent, or a collection thereof, on or in the cell subj ected to the unknown foreign agent over time to obtain the profile of the cell relating to the unidentified foreign agent;
f) determining the profile corresponding to the profile obtained in step e) amongst the~profiles obtained in step b):
g) determining that the unidentified foreign agent is the known foreign agent corresponding to the profile which has been determined in step f).
81. A method for identifying an unidentified foreign agent ' 18 given to a cell, from the profile of the cell, comprising the steps of a) providing data relating to a correlation between a known foreign agent, and a profile of the cell corresponding to the known foreign agent, with respect to a biological agent, or a collection thereof, on or in the cell;
b) subjecting the cell to an unidentified foreign agent;
c) monitoring the biological agent, or the collection thereof, on or in the cell over time to produce a profile of the cell;
d) determining the profile corresponding to the profile obtained in step c) amongst the profiles provided in step a); and a ) determining that the unidentified foreign agent is the known foreign agent corresponding to the determined profile.
82. A method for obtaining a profile re~.ating to information of a cell in a consistent environment, comprising the steps of:
a) locating a plurality of cells to a support which is capable of maintaining the cells in a consistent environment; and b) monitoring a biological agent, or a collection thereof, on or in the cell over time to produce the profile data for the cell.
83. A storage medium on which data produced by a method according to Item l, is stored.
84. A storage medium according to Item 83, wherein said storage medium further comprises data of at least one information relating to one selected from the group consisting of information relating to conditions under said monitoring, information relating to said profile, information relating to the state of said cell and information relating to the biological agent.
85. A storage medium accozding to Item 84, wherein the data is stored in a format which links a plurality of the data to each other.
86. A storage medium according to Item 84, wherein the data is stored in a format which has links per said cell.
87. Data produced by a method according to Item 1.
B8. A transmission medium comprising data produced by a method according to Item 1.
89. A system for producing profile data relating to information of a cell in a consistent environment, said method comprising:
a) a support which is capable of maintaining the cell in a consistent environment;
b) means for monitoring a biological agent, or a collection thereof, on or in the cell to produce the profile data for the cell: and c) means for producing profile data for the cell from a signal obtained from the means for monitoring.
90. A system according to Item 89, further comprising a plurality of cells, and the plurality of cells are immobilized on to the support.
91. A system according to Item 90, wherein said support is attached at least one substance selected from the group consisting of a salt and an actin-like substance.
92. A system according to Item 89, wherein said means for monitoring comprises at least one means selected from the group consisting of optical microscopes, fluorescence microscopes, phase-contrast microscopes, reading devices using a laser source, means using surface plasmon resonance (SPR) imaging, electric signals, chemical or biochemical markers singly or in combination, radiation, confocal microscopes, nonconfocal microscopes, differential interference microscopes, stereoscopic microscopes, video monitors and infrared cameras.
93. A system for presenting profile data relating to information of a cell in a consistent environment, comprising:
a) a support which is capable of maintaining the cell in a consistent environment;
b) means for monitoring a biological agent, or a collection thereof, on or in the cell to produce the profile data for the cell;
c) means for producing profile data for the cell from a signal obtained from the means for monitoring: and d) means for presenting the data.
94. A system according to Item 93, further comprising a plurality of cells, wherein the plurality vf.cells are immobilized on to the support.
95. A system according to Item 93, wherein said support is attached at least one substance selected from the group consisting of a salt and an actin-like substance.
96. A system according to Item 93, wherein said means for monitoring comprises at least one means selected from the group consisting of optical microscopes, fluorescence microscopes, phase-contrast microscopes, reading devices using a laser source, means using surface plasmon resonance (SPR) imaging, electric signals, chemical or biochemical markers singly or in combination, radiation, confocal microscopes, nonconfocal microscopes, differential interference microscopes, stereoscopic microscopes, video monitors and infrared cameras.
97. A system according to Item 93, wherein said means for presenting data is a display.
98. A system according to Item 93, wherein said means for presenting data is a speaker.
99. A system for determining the state of a cell in a consistent environment, comprising a) a support which is capable of maintaining the cell in a consistent environment:
b) means for monitoring a biological agent, or a collection thereof, on or in the cell to produce the profile data for the cell:
c) means for producing profile data for the cell from a signal obtained from the means for monitoring: and d) means for determining the state of said cell from said data.
100. A system for correJ.ating a foreign agent and a cellular response to the foreign agent, comprising:
a) a support capable of maintaining a plurality of cells in a consistent environment:
b) means for subjecting the cells to a foreign agent;
c) monitoring a biological agent, or a collection thereof, on or in the cells to produce the profile data for the cells;
d) means for producing profile data for the cells from a signal obtained from the means for monitoring: and e) means for correlating the foreign agent and the profile.
101. A system for identifying an unidentified foreign agent given to a cell, from the pxofile of said cell, comprising:
a) a support capable of maintaining a plurality of cells in a consistent environment;
b) means for subjecting the cells to a known foreign agent:
e) means for monitoring a biological agent, or a collection thereof, on or in a cell over time;
d) means for obtaining the profile data for the cell in response to each of known foreign agents to produce profile data for the cell;
e) means for correlating each of the known foreign agents and each of the profiles;
f) means for subjecting the cells to an unknown foreign agent;
g) means for comparing the profile of the known foreign agent obtained with means d) , and the profile of the unknown foreign agent to determine a profile corresponding to the profile of the unknown foreign agent amongst the profiles of the known foreign agents, wherein said determined unidentified foreign agent is the known foreign agent for which the determined profile corresponds to.
102 . A system for identifying an unidentified foreign agent given to a cell, from the profile of the cell, comprising:
a) a storage medium having stored data relating to a correlation between a known foreign agent, and a profile of the cell corresponding to the known foreign agent, with respect to a biological agent, or a collection thereof, on or in the cell,;
b) means for subjecting the cell to an unidentified foreign agent:
c) a support which is capable of maintaining a plurality of cells in a consistent environment:
d) means for monitoring the biological agent or the collection thereof on or in the cell over time to produce a profile of~the cell;
e) means for obtaining the profile of the cell from a signal obtained from the means for monitoring; and f ) means fvr determining the profile corresponding to the prafile obtained relating to the unidentified foreign agent amongst the profiles stored in storage medium a), wherein the unidentified foreign agent is the known foreign agent for which the determined profile corresponds to.
103. A support capable of immobilizing a plurality of cells and maintaining the cells in a consistent environment.
104. A support according to Item 103, wherein the cells on the support are located in an array format.
105. A support according to Item 103 comprising a complex of a positively charged substance and a negatively charged substance: a salt: yr an actin-like substance.
106. A support according to Item 103 comprising a complex of a positively charged substance and a negatively charged substance: a salt: arid an act~.n-like substance.
107. A support according to Item 103, wherein said item is capable of being located within a space of 1 mm or less at maximum.
108. A support according to Item 103, further comprising a cell immobilized thereon.
109. A support according to Ttem 103, further comprising a biological agent immobilized thereon.
110. A support according to item 109, wherein two or more types of said biological agent are immobilized thereon.
111. A support according to Item 103, wherein a cell and a biological agent are immobilized thereon.
112. A support according to Item 103, wherein a salt: a complex between~a positively charged substance and a negatively charged substance; and an actin-like substance are immobilized thereon together With a cell and a biological agent.
113. A support according to Item 103, wherein a salt; a complex between a positively charged substance and a negatively charged substance; and an actin-like substance are immobslized thereon together with a cell and a biological agent, in an array format.
114 . A support. according to Item 104, wherein a salt, a gene introduction reagent, and an actin-like substance, a nucleic acid molecule, and a cell are immobilized thereon in an array format.
115. . A support according to Ttem 114, wherein the salt is selected from the group consisting of calcium chloride, sodium hydrogen phosphate, sodium hydrogen carbonate, sodium pyruvate, HEPES, calcium chloride, sodium chloride, potassium chloride, magnesium sulfide, iron nitrate, amino acids, and vitamins.
17.6. A support according to Item 114, wherein the gene introduction reagent is selected from the group consisting of cationic polymers, cationic lipids, polyamine-based reagents, polyimine-based reagents, calcium phosphate, oligofectamine and oligofecter.
117. A support according to Item 114, wherein the actin-like substance comprises at least one protein selected from the group consisting of fibronectin, laminin, and vitronectin, or a variant or fragment thereof.
118. A support according to Item 114, wherein the nucleic acid molecule comprises a sequence encoding a protein selected from the group consisting of cytokines, hormones, cell adhesion molecules, cytoskeleton proteins and enzymes.
119. A support according to Item 114, wherein the cell comprises a cell selected from the group consisting of an animal cell, an insect cell, a plant cell, a bacterial cell and a fungal cell.
120. A support according to Item 114 wherein material of said support comprises material selected from the group consisting of glass, silica and plastics.
121. A method for producing a support comprising a plurality of cells immobilized thereon and capable of maintaining the cells in a consistent environment, comprising the steps of:
A) providing a support; and B) immobilizing a cell to the support using a complex comprising of a salt, a positively-charged substance and a negatively-charged substance.
122. A method according to Item 121, wherein said step of immobilizing comprises immobilizing a mixture of the salt, a gene introduction reagent as the positively-charged substance, , an actin-like substance, a nucleic acid molecule as the negatively-charged substance, and the cell in an array format.
123. A method according to Item 121, wherein said step o~
immobilizing comprises a printing step.
124. A method according to Item 121, wherein the step of providing the support comprises the step of producing the support from a support material.
125. An apparatus for producing a suppozt comprising a plu~cality of cells immobilized thereon and capable of maintaining the cells in a consistent environment, comprising:
A) means for providing a support: and H) means for immobilizing a cell to the support using a complex comprising a salt, a positively-charged substance and a negatively-charged substance.
126. An apparatus according to Item 125, wherein said means for immobilizing comprises means for printing.
127. An apparatus according to Item 125, wherein the means for providing the support comprises means for shaping the support from a support material.
128 . A method for producing a digital cell, comprising the steps of:
a) obtaining a cell parameter specifying a cell of experimental interest:
b) obtaining an environment parameter specifying an environment under which the cell specified by the cell parameter is cultured:
c) obtaining a stimulus parameter specifying a stimulus to be given to the cell specified by the cell parameter;
d) obtaining a stimulus response result showing a result which the cell specified by the cell parameter responds to the stimulus specified by the stimulus parameter under the environment specified by the environment parameter;
e) producing an experimental data for the cell, by correlating the cell parameter, the environment parameter, the stimulus parameter and the stimulus response result;
and f) optionally repeating steps a) through e) to produce at least one collection of experimental data for the cell, and to provide the at least one collection of experimental data as a digital cell.
129. A method according to Item 12B, wherein the environment parameter comprises a parameter indicating culture medium in which the cell is cultured, and a parameter showing the conditions of the culture medium.
130. A method according to Item 128, wherein the stimulus parameter comprises a parameter showing a reporter and a parameter showing a chemical stimulus.
131. A method according to Item 128, Wherein said stimulus response result comprises profile data far the cell obtained by monitoring a biological agent, or a collection thereof, on or in the cell aver time.
132 . A method according to Item 128, further comprising the step of storing the digital cell to a database.
133. An apparatus for producing a digital cell, comprising:
a) means for obtaining a cell parameter specifying a cell of experimental interest:
b) means for obtaining an environment parameter specifying an environment under which the cell specified by the cell parameter is cultured c) means for obtaining a stimulus parameter specifying a stimulus to be given to the cell specified by the cell parameter:
d) means for obtaining a stimulus response result showing a result-which the cell specified by the cell parameter responds to the stimulus specified by the stimulus parameter under the environment specified by the environment parameter;
e) means for producing an experimental data for the cell, by correlating the cell parameter, the environment parameter, the stimulus parameter and the stimulus response result; and f) means for providing at least one collection of experimental data as a digital cell; by optionally repeating steps performed by the means a) through e) to produce at least one collection of experimental data for the cell.
134. A method for providing a service which reproduces an experimental result of an actual cell using a digital cell by means of a computer system comprising a service requester and a service provider, comprising the steps of:
preparing a database having at least one digital cell stored thereon, wherein the at least one digital cell is expressed as a collection of at least one experimental data of a cell of experimental interest, wherein each of the at least one experimental data comprises a cell parameter specifying the cell, an environment parameter specifying an envizonment under which the cell specified by the cell parameter is cultured, a stimulus parameter specifying a stimulus to be given to the cell specifiied by the cell parameter, and a stimulus response result showing a result which the cell specified by the cell parameter responds to the stimulus specified by the stimulus parameter under the environment specified by the environment parameter:
receiving the cell parameter, the environment parameter and the stimulus parameter by the service requester to produce a request comprising the cell parameter, the environment parameter and the stimulus parameter;
providing the request to the service provider by the service requester;
searching the database in response to the reguest by the service provider to determine whether or not there is the stimulus response result relating to the cell parameter, the environment parameter and the stimulus parameter included in the request, in the database;
providing the stimulus response result to the service requester by the service provider, when it is determined that the stimulus response result relating to the cell parameter, the environment parameter and the stimulus parameter included in the request exists in the database;
and presenting the stimulus response result by the service requester.
135. A method for providing a service for reproducing an experimental result of an actual cell using a digital cell, by means of a computer system comprising a service requester and a plurality of service providers, comprising the steps of preparing a plurality of databases, each having at least one digital cell stored thereon, wherein the at least one digital cell is expressed as a collection of at least one experimental data of a cell of experimental interest, wherein each of the at least one experimental data comprises a cell parameter specifying the cell, an environment parameter specifying an environment under which the cell specified by the cell parameter is cultured, a stimulus parameter specifying a stimulus to be given to the cell specified by the cell parameter, and a stimulus response result showing a result which the cell specified by the cell parameter responds to the stimulus specified by the stimulus parameter under the environment specified by the environment parameter;
pz~eparing a service registry which stores at least one service capable of being provided by the plurality of service providers;
receiving the cell parameter, the environment parameter and the stimulus parameter by the service requester to produce a request comprising the cell parameter, the environment parameter and the stimulus parameter searching the service registry in response to the request by the service requester to determine whether or not there exists a service provider capable of providing a service for the request amongst the plurality of service providers;
providing the request to the service provider by the service requester when it is determined that a service provider capable of providing a service of the request amongst the plurality of service providers exists;
searching the database in response tv the request by the service provider to determine whether or not there is the stimulus response result relating to the cell parameter, the environment parameter and the stimulus parameter included in the request in the database;
providing the stimulus response result to the service requester by the service provider, when it is determined that the stimulus response result relating to the cell parameter, the environment parameter and the stimulus parameter included in the reguest exists in the database;
and presenting the stimulus response result by the service requester.
135. A computer system for providing a service which reproduces an experimental result of an actual cell using a digital cell, comprising:
a service requester being composed such that it can have access to a database having at least one digital cell stored thereon, each of the at least one digital cell is expressed as a collection of at least one experimental data of a cell of experimental interest, wherein each of the at least one experimental data comprises a cell parameter specifying the cell, an environment parameter specifying an environment under which the cell specified by the cell parameter is cultured, a stimulus parameter specifying a stimulus to be given to the cell specified by the cell parameter, and a stimulus response result showing a result which the cell specified by the cell parameter responds to the stimulus specified by the stimulus parameter under the environment specified by the environment parameter: and a service provider requesting a service desired by a user:
Wherein the service requester comprises:
means for receiving the cell parameter, the environment parameter and the stimulus parameter to produce a request comprising the cell parameter, the environment
34 Azoo~
parameter and the stimulus parameter; and means for provide-rig the request to the service provider, and wherein the service provider comprises:
means for searching the database in response to the request by the ser~rice provider tv determine whether or not there is the stimulus response result relating to the cell parameter, the environment parameter and the stimulus parameter included in the request ir: the database;
and means for providing the stimulus response result tv the service requester by the service provider, when it determined that the stimulus response result relating to the cell parameter, the environment parameter ~.5 and the stimulus parameter included in the request exists i.n the database:
wherein the serv~.ce requester further comprises means for presenting the stimulus response result by the service requester.
137. A computer system according to Item 136 wherein the service requester is a Web browser which the user operates, and the service provider is a Web server linked to the service requester via the Internet.
138. A computer system according to Item 136, wherein the service requester provides the request to the service provider in a format described in XML language.
139. A computer system according to Item 136, wherein the ser~crice provider provides the stimulus response result to the service requester in a format described in XML language .
~,4p. A computer system for providing a service which reproduces an experimental result of an actual cell using a digital cell, comprising:
a plurality of service providers, each composed such that the pJ.urality of service providers can have access to a database having at least one digital cell stvz~ed thereon, each of the at least one digital cell is expressed as a collection of at least one experimental data of a ceJ.l of experimental interest, wherex:x each of the at least one experzmenf.al data comprises a cell parameter specifying the cell, an environment parameter specifying an environment under which the cell specified by the Dell paramEter is cultured, a stimulus parameter specifying a stimulus to be given to the cell specified by the cell parameter, and a stiznu~,us response result showing a result which the cell specified by the cell parameter responds to the stimulus specified by the stimulus parameter under the environment specified by the environment parameter;
a service registry which stores at least one service which the plurality of service providers can provide; and a service provider requesting a service desired by a user:
wherein the service requester comprises:
means for receiving the cell parameter, the environment parameter and the stimulus parameter to produce a request comprising the cell parameter, the environment parameter and the st~.mulus parameter means for searching the service registry in response to the request by the service requester to determine whether or not there exists a service provider capable of providing a service of the request amongst the plurality of service providers and means for providing the request to the service provider by the service requester when it is determined that there exists a service provider capable of providing a service of the request amongst the plural~.ty of service providers, wherein each of the plurality of service providers comprises:
means for searching the database in response to the request by the service provider to determ~.ne whether or not there is the stimulus response result relating to the cell parameter, the environment parameter and the stimulus parameter included in the request in the database;
and means for providing the stimulus response result to the service requester by the service provider, when ~.t is determined that the stimulus response result relating to the cell parameter, the environment parameter and the stimulus parameter included in the request exists in the database;
wherein the service requester further comprises means for presenting the stimulus respoz~se result by the service requester.
141. A computer system according to Ttem 140, wherein the service requester is a Web server connected to a Web brow$ex which the user operates via the Internet, and each of the plurality of service providers is a rnieb server connected to the service requester via the Internet.
142. A computer system according to Item 140, wherein the service requester provides the request to the service prov~.der in a format described in ~NtL language.
143. A computer system according to Ttem 140, wherein the service provider provides the stimulus response result to the service requester in a format described in XML language.
144. A method for producing the profile data relating information of a cell, comprising the steps of:
a) immobilizing and locating a cell an a support; and b) monitoring a biological agent, or a collection thereof, on or in the cell to produce the profile data for the ceJ.Z .
145. A method according to Item 144, wherein the biological agent is a nucleic acid molecule or a molecule derived from the nucleic acid molecule.
146. A method according to Item 144, wherein the cell is immobilized to the support by a composition comprising a) a complex with a positively charged substance and a negat~.vely charged substance; and b) a salt.
147. A method according to Item x.44 wh.erein the cell is provided with an actin--like substance.
~1Z0~7 14~. 1~ method according to rtem 7.44, wherein the cell is immobilized f.o the support by a composition comprising a) a complex w~.th a positively charged substance and a negatively charged substance: and b) a salt, and is provided with an actin-like substance.
149. A method according to Item 144 wherein the biological agent is selected from the group consisting of a nucleic 7.4 acid molecule, a protein, a saccharide, a lipid, a low molecu~.e, and a complex thereof.
150. A method according to Item x94, wherein the cell is cultured for at least about three day's before the step of monitoring.
151. A method according to Ttem 144, wherein the biological agent comprises a nucleic acid molecule encoding a gene.
152. A method according to Item 144, wherein the profile Comprises a prvfi.le of gene expression.
153. A method accord~.ng to Item 144, wherein the profile comprises a profile of an, apoptosis signal.
z5 154. A method according to Item 144 wherein the profile is a profile of a stress signal.
155. A method according to Item 144 wherein the profile is a profile of the localization of a molecule.
Azaa7 156. A method according to Item 155 wherein the molecule is detected by means selected from the group consisting of fluorescence, phosphorescence, radioactiv~.ty', and a combination thereof.
157. A method according to Item 144 wherein the profile comprises a variation of cell morpholac~y.
158. A method according to Item 144 wherein the profile comprises a profile of promoters.
159. A method .according to Ztem 144, wherein said profile comprises a profile of a promoter dependent on a specific drug.
160. A method according to Item x.44 wherein said profile comprises a profile of a promoter dependent on a specific drug, wherein said method further comprises the step of administering the specific drug.
16x. A method according to Item 144 further comprising the step of subjecting the cell to a foreign agent.
162. A method according to Item 161, wherein said foreign agent comprises an RNAi.
163. A method according to Item 161, wherein said foreign agent comprises a chemical not present. in a biological k~ody, ~0 164. A method according to Ztem 144, wherein said pzofile comprises a profile of intermolecular interaction.
165. A method according to Ttem 161, wherein said foxeign agent comprises a ligand for a receptor of said cell.
166. A method according to Item 144, wherein said profile comprises a profile of an interaction between a receptor and a ligand.
la 167 _ A method according to Item X44, wherein said profile is a cellular form, and said method fuxther oC~mprises the step of giving to said cell a stimulus selected from the group consisting of overexpression, underexpressiOn or knockdown of a gene, addition of a foreign agent and a change in the environment.
158 _ A method according to Item 144, wherein said profile comprises a profile of interaction between molecules present in said cell.
16$. A method according to Item 144, further comprising the step of conducting observation using a technology selected from the group consisting of twvuhybrid method, FRET and BRET.
170. A method according to Item 144, wherein said profa.le comprises a profile of interaction between molecules present in said cell, wherein the method further comprises the step of conducting observation using a technology se~.~cted from the group consisting of two-hybrid method, FRET and BRET.
173.. A method according to Item 144, wherein said cell is located on said support in an array format.
172. A method according to stem 144, wherein said cell. is located on said support in an array format, and each of said plurality of cells are located at a space of 1 mm at maximum.
to 173. A method according to Item 7.44, wherein said profile is obtained at real time.
174 . A method according to Item 144 further comprising the 7.5 step of immobilizing said cell to a solid support.
175. A method according to Item 144, wherein said data comprises information relating to said profile.
20 176. A method according to Item 144 wherein said data comprises information relating to conditions during said monitoring.
177. A method according Ttem 144 wherein said data 25 comprises ~.nfvrmativn relating to the state of said cell.
178 . A method according to Item 144 wherein said biolog~.cal agent to be monitored comprises at least two types of biological agent.
x79. Amethod according to Item 144 wherein said biological agent to be monitored ovmprises at least three types of biological agent.
180. A method according to item 144 wherein said biological agent to be monitored comprises at least eight types of biological agent.
181. A method according to Ttem 144 further comprising the step of arbitrarily selecting a biological agent.
182. A method according to 'item 144 whexein said cell is selected from the group consisting of a stem cell and a somatic cell.
x.83. A method aGCOrding to Item 144 wherein said support comprises a solid support.
184. A method according to ztem 144 wherein said support comprises a substrate.
X85. A method according to Ttem 144 wherein said biological agent is a nuoleio acid molecule, and said cell is transfected with said nucleic acid molecule.
186. A method according to Item 185, wherein said transfeGtion is conducted an a solid phase or in a liquid phase.
187. A method according to Item 185, wherein said transtection is conducted on a solid support.
1$$ . A method according to Item 144, further comprising the step of comparing a phase of said profile.
189. Rmethod according to rtem 144, further comprising the step of subtracting a control profile from the profi7.e of said cell.
190 . A method according to Item 144 further comprising the step of processing the profile with a mathematical processznc~ method selected from Signal processing and multivariant analysis methods.
Hereinafter, the present invention will be described by way of preferred embodiments. rt will be understand by those skilled in the axt that the embodiments of the present invention can be appropriately made or carried out based an the description of the present specification and the accompanying drawings, and common~.y used techniques well known in the art. fhe function and effect of the present invention can be easily recognized by those skilJ.ed in the art. .
The present invention pra~rides consecutive information (profile) data relating to the state of a cell.
The present invention provides information and data (in particular consecutive information and consecutive profile) relating to the state of a cell in a Consistent environment, in a reproducible manzxer. According to the Azpp7 present invention, ~, method and a system fax presenting such data in an accurate manner are provided. Specifically, it should be surprising a effect to be able tc~ provide a system and a method for information at the cellular level. in a consistent environment in terms of a complex system as such or in a direct manner, and to be able to provide such data and technology fvr aligning such data per se. The present invention further attains the effect of providing a digital cell based on actual, live data and the use thexeof, which have not been conventionally possible prior to the present invention.
As such, according to the present invention, it is possible to determine the state of cells by observing a surprisingly small. number of factors. Therefore, the present invention is applicable to diagnosis, prevention, and treatment . The present invention is also applicable to the fields of food, cosmetics, agriculture, environmental engineering, and the like. Reproduction of a live experiment on a computer system attains the effect of enabling education and research in the field of biotechnology.
BRIEF DESCRIPTION OF THE DRAWING$
Figure 1 shows the results of experiments in which various. actin-like substances and HEK293 cells were used, where gelatsn was used as a control.. Figure 1 shows 34 the effect of each adhesion substance (HEK cell) with respect to transfeati.ar~ efficiency. The HEK cells were transfected with pEGFf~-N1 using an Effectene reagent.
Figure 2 shows exemplary transfection S efficiencies when fibronectin fragments were used.
Figure 3 shows exemplary tranafection efficiencies when fibronectin fragments were used.
Figure ~ shows a summary of the results presented ire. Figures 2 and 3.
Figure 5 shows the results of an example in which transfection effic~.ency was studied for various cells.
Figure 6 shows the results of traxzsfecta.an when various plates were used.
F~.r~uxe 7 shows the results of transfection when various plates were used at a fibronectin concentration of 0, D.27, 0.53, D.B, 1.07, and 1.33 (ug/uL).
Figure 8 provides exemplary photographs showing cell adhesion profiles in the presence or absence t~f fibronectin.
Figure 9 shows exemplary cross-sectional photographs of cell adhesion profiles ~.z~ the presence or absence of fibronectin. Cross-sections of human ~4 6 mesenchymal stem cells (hMSC) were observed using a confoaal laser scanning microscope. hMSC were stained with SYT061 (blue fluorescence) and Texas red - X phall.oidin (red fluorescence) and fixed with 9~ PFA. Blue fluorescence (nuclei: SYT061) and red fluorescence (nuc~.ei: Texas red -- X phalloidin) were obtained using a confocal lasex microscope (ZSM5~.0, Carl Zeiss Co. , Ltd. , pin hole size=1. 0, image interval=0.4).
Figure ~0 shows transition of nueleax surface area. Relative nuclear surface area was determined by cross-sections of hMSC observed with canfocal laser scanning microscopy, hMSC was fixed with 4~ PFA.
1S figure 11 shows the results of an exemplary transfeotion experiment when a transfection array chip was constructed and used.
Figure 12 shows exemplary contam~.nation between each spot on an array.
Figure 13 shows an experiment in which spatially-spaced DNA was taken into cells after the solid phase transfection of the pxesent invention in Example 4.
Figure i3A schematically shows a method for producing a solid phase transfection array (SPTA). This figure shows the mEthodology of a solid transfection.
3Q Figuxe x3H shows the resu~,ts of a so~.id phase transfection. A HEK293 cell line was used to produce a SPTA.
Green colored portions indicate transfected adherent sells.
According to this result, the method of the present invention can be used to produce a group of cells separated spatially and transfected with different genes. As such, Figure I,3A-a, as a whole, depicts schematically the procedure of transfection (SPTA7. Figure 13A depicts the outlines of SPTA determination, and Figure 138 depicts a result of SPTA using 8EK293 cell straa.n. The bar indicates 3mm.
Figure 13C shows the diffexez~.Ge between conventional liquid phase transfection and SPTA.
Figure 14 shows the results of comparison of liquid phase transfectzon a.nd SPTA.
Figure 14A shows the results of experiments where S cell lines were measured with respect to GFP
intensity/mm2. Transfection efficiency was determined as fluorescence intensity per unit area.
Figure 148 shows fluorescent images of celJ.s expressing EGFP corresponding to the data presented in Figuxe i4A. White circular regions therein were regions in which plasmid D1VA Was fixed. In other regivz~s, cells were also fixed in solid phase, however, cells expressi.nc~ EGFP
were not observed. The white bar indicates 500 Eun.
Fluorescent photographs of EGFP expressing cells corresponding to Figure 14A are shown with respect to the five types of cells per measured fluorescence/mm2. White circles correspond to plasmid DNA priz7.ted regions . Outside these regions, cells express EGFP. Further, regions other than the printed regions are attached cells.
Figure ~.~C shows an exemplary transfection method of the present invention.
Figure 14D shows an exemplary transfection method of the present invention.
Figure 15 shows the xesults of coating a chip, whereby cross contam~.nation was reduced.
7. 5 Figure 15 shows the results of liquid phase transfection and SPTA using HEK293 cells, HeZa cells, NIT3T3 cells (also referred to as "3T3"), HepG2 cells, and hMSCs.
Transfection efficiency was determined by GFP intensity.
Transfection efficiency of hMSC depending on the N/P
ratio used is shown in Figure 15A. In the phase of pxior liquid phase transfection (Figuxe 158, upper panel), hMSC
cells were dead and in the case of SPTA, cell morphology was normal (Figure 15H, lower panel).
Figure 16 shows cross contamination between each spot. A nucleic acid mixture containing fibronectin having a predetermined concentration was fixed to a chap coated with APS or PZT~ (poly-L-lysine) . Cell transfection was performed on the chip. Substantially no cross contamination was observed (upper and middle rows). In contrast, significant cross contamination of fixed nucleic acids was observed on an uncoated chip (lower row).
Figure 16C shawl a correlation relationship between the types of substances contained in a mixture used for fixation of nucleic acid and the cell adhesion rate.
The graph presented in Figure 1f shows an increase in the proportion of adherent cells over time. A longer time is required for cell adhesion when the slope of the graph is shal~.ow than when the slope of the graph is steep.
Figure 16D is an enlarged graph which is presented in Figure 16C.
Figure i'~ shows an exemplary configuration of a computer which was used to perform the method of the present invention.
Figure 18 depicts an example of a mathematical analysis method of the present invention. Profiles of promoters shown in Figure 18A (average of pNEF~Im-d2EGFP/negative control) and Figure 18H (a~crerage of pERE-d2EGFP/negat~.ve control ) are obtained by measuring the fluorescent intensity thereof over time. These profiles have been normalized using the autologous fluorescence of either the cell or medium used. Thereafter, in order to compare amplitude of the reporter expression fluctuat~.on, an amplitude ~ 5 or more ( TH>=5 ) was determined to have change in expression fluctuation state. Further, differentiation induction was divided into the following sections: start of differentiation induction,. early stage (0-17.5 hours), and late stage (17.5-31.5 hours) and total stages (0-31.5 hours); and those observed with a variation in expression of an amplitude of 5 or more (TH>=5) were defined as (+) and those with an amplitude of less than 5 were defined as (-). Based on these definitions, the profiles of A and B
were evaluated as shown in the lower tables of Figures 1.8A
and 18~. Tn the table, when extracting any number of reporters, (A+B+ ... n) have been infiegrated with respect to n types of wave forms and the sum is divided by n to form the average wave form and if variations beyond the threshold, such variations were deemed as being "changed".
Figure 18H depicts another example o~ a mathematical analysis according to the present invention.
When a reporter i9 extracted (A+$-~ , . , n) , n types of wave types are integratEd, and the sum is divided by n to produce an average wave form, which was deemed as being a change of the variation above a threshold. The left hand panel of Figure Z8H depicts the integration of two reporter profiles arid draws the average wave form in red or with solid squares.
Those with 5 or more variations of the average profile were deemed to be expression variations for evaluation. As a result, evaluation can be Conducted for variation of the two extracted reporters, as shown in the table herein.
Figure 19 depicts exemplary plasmids containing promoters used in the present invention and an analysis Az007 according to the present invention. Seventeen types of transcriptional factors shown in the left hand panel of figure 19 were used as a reporter uz~der the conditions o:f vr>teoblast differentiation and maintenance of an undifferentiated mesenChymal stem cell, and the expression prof~.le thereof have been obtained over time (figure 19, right handed panel) . From these seventeen types of profiles, any number of profiles have been extracted and evaluated by the method as previously described in Figure 18, taking 1.0 the change in amplitude of the response profile of each transcriptional factor as a standard.
Figure 20 depicts an example of mathematical ana~.ysis at the early stage of induction of differentiation.
By changing the combination arbitrarily ext ratted in the early differentiation induction stage, results as shown in Figure 20 have been obtained. Any number~of reporters were extracted from the reporter group consisting of seventeen species, and caxculated for the average profile according to the method shown in figure ~.8. mhose hav~.r~g five or more var~.ation widths are the results evaluated with the evaluation windows 0-31.5, 0-17.5 and 17.5-31.5. Each extraction condition has se~srenteen extraction patterns, except for where the seventeen extraction pattern has only one way of extraction. Amongst these combinations, Figure ~D shows the ratio in which variation is found therein, including the table and graph included therein. This analysis allows confzxmation of differentiation after fifteen hours although it is not possible to understand the very early stages of differentiation. The number of extraction where 100 ~ change is found for variation is eight or more in this instance.
Figure 21 depiots an example of a mathematical analytical result at the undifferentiation maintenance stage. As in Figure 20, similar results as shown in the graphs have been obtained when a combination arbitrarily extracted under conditions to maintain undifferentiatiori.
Comparing the results with the stage of differentiation induction, as in Fzgure 20, the results are dramatically different. Based on this comparison, ~.t is believed that it is possible to determine whether a cell is moving in the direction of cell differentiation induction, or instead maintaining an undifferentiated state.
Figure 22 schematically shows a cocktail party process.
Figure 23 shows an exempJ.ary construct of a gene transcription switch reporter used in a transfection plasmid of the present invention.
Figure ~4 shows exemplary construction of a set of transcription factor reporters.
Figure 25 shows the results of exemplary assays using transcription factor reporters.
Figure 25 shows an example of measurements of transcriptional activity in the bone differentiation process, , taken in a time-series manner.
Figure 27 shows an example of the oscillation phenomenon and phase analyses of transcriptional acti~crity.
Figure 28 shows a protocol of siRNA experiment.
Figure 29A shows the result$ of the siRNA
experiments . The upper panel shows the results of hMSC, and the lower panel show$ the results of HeLa cells. The numexals show the conce~xtrations (~eg/~L) of the siRNA used.
The xesults obtained w~.th the anti-GFP siRNA are shown an the left hand side, anal the right hand side shows the results with the scramble szRNAs.
Figure 298 shows the effects of siRNA when solid transfection, (pCl2) was conducted on a collagen IV coating.
Figure 298(A) shows PC~.2 cells cotransfected with EGFP
vector and anti-EGFP s~.RNA. As shown, it was obser~cred that only HcRed was coloxed, and green signals derived from pEGFQ-N1 were suppressed. On the other hand, Figure 29S (~3) shows an example using scramble siRNA. As shown, green fluorescence was observed and thus the effects obsexved in Figure 29H(:1,) are due to the effects of RNAi. figures showing the relative f~.uorescence intensities in Figures 29B (~) and 298 (8) , are summari zed in figure 29B (C) . The y axis indicates relative intensity. It can be seen that effects induced by EGFP were almost completely suppressed.
Figure 29C depicts results and graphs summarizing the abo~sr'e. The left-hand panel is a phatagraph comparing EGFP RNAi and scramble (mock) RNRi when changing the ratio of RNAi and pRNA. As shown, EGFP RNA. showed inhibitory effects, whereas scramble RNAi did not exert such effects. This is shown in the right-hand panel, togethex with DsRed2. Experimental cond~.tions were in accordance with those described herein. As a result, red (DsRed derived szgnal) and green (EGFP derived signal) were found to be in proportion With the effect of RNAi.
Figure ~9D depicts an exemplary chip used in the RNAi reporter. When using RNAi as input signals and cointroducing a gene product capable of transmittl.ng signals, such as EGF and the lzke, together with a nuc~.eic acid encoding a gene of interest (including a promotez~), observation of such signal transm~.ssion as output allows extraction of cell information.
Figure 29E shows an exemplary experiment using a variety of reporters (pAPI-EGFP, pApl(PMA)-EGFP, pCRE-EGFP, pE2F-EGFP, pERE-EGFQ, pGAS-EGFP, pGRE-EGFP, pHSE-EGFP, pISRE-EGFP, pMyc-EGFP, pNFAT--EGFP, pNFkB-EGFL~, pRARE-EGFP, pRb-EGFP, pSTST3-EGFf, pSRE-EGFP, pTRE-EGFP, pp53-EGFP, pCREH-sensor, plkB-sensor, pp53-sensor, pCasapase3-sensor); the is-element sequez~ce was purchased from Clontech using a plasmid vector produced by recombining a fluorescence protein gene).
Figure 30 shows changes in the profile when using tetracycline dependent promoters.
Figure 31 shows expression when using tetracycline dependent promoters and tetracycline independent promoters.
Figure 318 shows an exemplary result of analys~.s using a transfected microarray with respect to the effects of tyrosine kznase RNAi on neurons.
Figure 31C depicts responses to retinoic acid (RA) and nerve growth factor (NGF) by a variety of tyrosine kinases. Inhibition percent by siRNA is shown.
Figure 31D depicts an example of a signaling pathway obtained as a resu~.t of an analysis.
Figure 31E shows the results obtained by the above-mentioned analysis. It shows a general analysis of the tyrosine k~.nases responsible for human neuron differentiation. Classification is conducted by determining whether it is dvpaminergic neuron, chvlinergic neuron, or both, or neither. It can be concluded by the analysis that there is high possibility that those tyrosine kinases relating to both types of neuron axe involved in neuron projective formation.
Figure 31F depicts an example of real-time monitoring of transcription regulation of apoptosis in a HeLa cell. The left handed panel shows the result over time, and the right handed panel shows the result of a signaling Azoo~
pathway based on the analysts thereof.
Figure 3Z depicts an example of a system configuration.
Figure 33A depicts an example of a digital cell according to the present invention.
Figure 33~ depicts another example of a digital ~.0 cell. according to the present invention.
Figure 34 depicts an example of a,method for producing a digital cell according to the present invention.
Figure 35 depicts an example of a configuration of computer system 3501 which provides a service reproducing an experimental result obtained using an actual cell using the digital cell.
Figure 3G d~:picts an example of procedures of a process which provides a service reproducing an experimental resu3.t obtained using an actual cell using the digital cell.
Figure 3T depicts an example of input interface for inputting cell parameters, environment parameters and stimulus parameters into service requester 3510.
Figure 38 depicts an example of configurations of computer system 3801 for providing a service of reproducing an experimental result against an actual cell using the digital cell.
Figure 39 depicts an example of procedures of a process for providing a service of reproducing an experimental result against an actual cell using the digital cell.
DESCL~IPTZON OF SEQUENGE LTSTING
SEQ TD NO. 1: nucleic acid seguenee encoding : a fibronectin (human) SEQ ID NO. : an amino acid sequence of 2:
fibronectin (human) SEQ ID NO. 3: nucleic acid sequence encoding : a vitronectin (mo use) 5EQ rD NO. : an amino acid sequence of 4:
vitronectin (mo use) SEQ ID NO 5: nucleic acid sequence enGOding _ : a laminin (mouse a,-chain) SEQ ID NO. 6:
: an amino acid sequence of lam~.n~.n (mouse a,-chain) SEQ TD NO. 7: nucleic acid sequence encoding : a laminin (mouse ~i-chain) SEQ ID NO. 8:
: an amino acid sequence of laminin (mouse ~3~chain) SEQ ID N0. 9: nucleic acid sequence encoding : a laminin (mouse y~-chain) SEQ ID N4. : : an amino acid sequence of Azoo7 laminin (mouse y-chain) SEQ ID NO.: 11: an alaino acid sequence of fibronectin (bovine) SEQ ID NO.: 12: siRNA used in the Examples SEQ ID NO.: ~.3: mouse olfactory receptor T7 (heptanal-sensitive) nucleic acid (Genbank AccESSion No. AF106007) SEQ ID NO.: 14: amino acid sequence of the protein encoded by the nucleic acid set forth in SEQ ID~
NO.: 13 SEQ I37 NO: 15: nucleic acid encoding the murine olfactory receptor S1 (mc9/bc9-equi-sensitive) (Genbank Accession Number AF121972) SEQ ID NO: ~.6: amino acid sequence of the protein encoded by the nucleic acid set forth in SEQ ID NO: 15 SEQ ID NO: 17: nucleic acid encoding the murine o~.factory receptor S50 (cc9-sensitive) (Genbank Accession Number AF121980) SEQ ID NO: 1 B : amino acid sequence of the protein 24 encoded by the nucleic acid set forth in SEQ ID NO: 17 SEQ ID NO: 19: nucleic acid encoding the murine olfactory receptor S19 (nnc9/mh9/bc9-equi-sensitive) (Genbank Accession Number AF~.21976) SEQ ID NQ: 20: amino acid sequence of the protein encoded by the nucleic acid set forth in SEQ ID NO: 19 SEQ TD NO: 21: nucleic acid encoding the murine pR23 (lyraJ.-sensitive) (only coding region of Genbank Accession Number X92969) SEQ ID NO: 22 : amino acid sequence of the protein encoded by the nucleic acid set fprth in SEQ 2D No: 21 SEQ ID NO: 23: nucleic acid encoding the marine olfactory receptor mOR-EV (vanillin-sensitive) (Genbank Accession Number AB061229) SEQ ID NO: 24 : amino acid sequence of the protein encoded by the nucleic acid set foxth in SEQ ID NO: 23 SEQ ID NO: 25: nucleic acid encodis~.g the mur~.ne olfactory receptor or37a (Genbank Accession Number A~133424) SEQ ID NO: 26: amino acid sequence of the protein encoded by the nucleic acid set forth in SEQ ID NO: 25 SEQ ID NO: 27: nucleic acid encoding the marine olfactory receptor C6 (G~:nbank Accession Number AF102523) SEQ ID NO: 28 : amino acid sequence of the protein encoded by the nucleic acid set forth in SEQ ID NO: 27 SEQ ID NO: 29: nucleic acid encoding the marine olfactory receptor FS (Genbank Accession Number AF102531) SEQ ID NO: 30: amino acid sequence of the protein encoded by the nucleic acid set forth in SEQ ID N4: 29 SEQ zD NO: 31: nucleic acid encodzz~g the muxine olfactory receptor S6 (Genbank Accession Number AF121974) SEQ ID NO: 32: amino acid sequence of the protein encoded by the nucleic acid set foxth in SEQ ID NO: 31 SEQ ID NO: 33: nucleic acid encoding the marine olfactory receptor 51.8 (Genbank Accession Number AF121975) SEQ ID NO: 34 : amino acid sequence of the protein encoded by the nucleic acid set forth in SEQ TD NO: 33 5EQ ZD NO: 35: nucleic acid encoding the marine olfactory receptor S25 (Genbank Accession Number AF121977) SEQ ID NO: 36: amino acid sequence of the protein encoded by the nucleic acid set forth in SEQ ZD NO: 35 SEQ ID NO: 37: nucleic acid encoding the murine olfactory receptor S46 (Genbank Accession Number AF121979) SEQ ID NO: 3B : amino acid sequence of the protein encoded by the nucleic acid set forth in SEQ ID NO: 37 SEQ ID NO: 39: nucleic acid encoding the a subunit of murine G-coupled protein (Genbank Accession Number M3677B) 5EQ ID NO: 40 : amino acid sequence of the protein encoded by the nucXeic acid set forth i.n SEQ ID NO: 39 SEQ ID NO: 41: nucleic acid encoding the subunit o~ murine G-coupled pxotein (Genbank Accession Number MB7286) 5EQ ID NO: 42 : amino acid sequence of the protein encoded by the nucleic acid set forth in SEQ ID N0: 41 5EQ TD NO: 43: nucleic acid encoding the subunit of murine G~coupled protein (Genbank Accession Number U37527) SEQ ID NO: 44 : amino acid sequence of the protein encoded by the nucleic acid set forth in SEQ TD N0: 43 ZO SEQ ID NO: 45: nucleic acid encoding the epidermal growth factor receptor (Genbank Accession Number BC023729) SEQ zD NO: 46: amino acid sequence of the protein encoded by ~.he nucleic acid set forth in SEQ rl~ NO: 45 SEQ ID NO: 47: the sequence of siRNA used in Example 9 SEQ ID No: 4$ : the sequence of scrambled RNA used in Example 9 BEST MODE FOR CARRYING OUT THE INVENTION
Az007 Hereinafter, the present invention will be described, it should be understood throughout the present specification that articles for a singular form (e.g. , "a", "an", "the", etc. in English) include the concept of their plurality unless otherwise mentioned. It should be also understood that the terms as used herein have definitions typically used in the art unless otherwise mentioned.
Accordingly, un~.ess otherwise defined, all technical and scientific terms used hErein shall. have the same meaning as generally understood by those skilled in the art to which the present invention pertains. If there is any inconsistency, the present specification precedes, including definitions.
(Definition o~ terms) Terms particularly used herein are defined as follows .
(Cellular Biology) The: term "cell" is herein used in its broadest sense in the art, referring to a structural unit of the tissue of a. multicellular organism, which is capable of seJ.f replicating, has genetic information and a mechanism for expressing it, and is surrounded by a membrane structure which isolates the cell from the outside. Cells used herein may be either naturally-occurring cells or artificially modified cells (e. g., fusion cells, genetically modified cells, ete.), as long as the cell has a chemical receptor or is capable of having such a chemical receptor introduced therein. Exax,nples of cell sources include, but axe not limited to, a single~cell culture; the embryo, blood, or body tissue of normally-grown transgenic animals; a mixture of cells derived from normally-grown cell lines: and the like.
As used herein, the term "digital cell" refers to a collection of at least one experimental data on a cell of experimental. interest. These experimental data correlate the experimental conditions and the experimental results of an example conducted against an actual cell. The digital cell is constituted such thafi once an experimental condition is given, the experimental result related to said experimental condition wzll be reproduced. The digital cell contemplated by the present invention comprises any cell which is amenable to an experiment. It should be understood that the description with respect to all the (living) cells described herein can be applied to a digital cell according to the present invention, as long as such description is applicable to the digital cell.
Using digital cells of the present invention allows reproduction of an experimental result of an experiment conducted using an actual cell, in a computer system. As such, the present invention allow research institutes, educational organizations and individuals having no experimental facilities, to conduct educatiaz7~ and advanced research relat~.nc~ to a cell. As a result, business entities in different fields will be able to start business in this field, which has not been possible to date.
Azoo~
Cells used herein may be derived from any organism (e. g., any unicellular organism (e. g., bacteria and yeast) or any multicellular organisms(e.g., animals (e. g., vertebrates and ~.nvertebrates), plants (e. g., monocotyledons and dicotyledons, etc.)). For example, cells used herein are derived from a vertebrate (e. g., Myxiniformes, Petronyzor~.~.formes, Chondri.chthyes, Osteichthyes, amphibian, reptilian, avian, mammalian, etc.), more preferably mammalian (e. g., monotremata, marsupialia, edentate, dermoptera, ch~.roptera, carnivore, insectivore, proboscides, perissodactyla, axtiodacty~.a, tubuJ.identata, pholidota, sirenia, cetacean, primates, rodentia, lagomorpha, eto.). In one embodiment, cells dErived from primates (e. g., chimpanzee, Japanese monkey, human) are used. Particularly, without lzm~.tation, cells derived from a human are used. The above-described cells may be either stem cells or somatic cells . Also, the cells may be adherent calls, suspended cells, tissue forming cells, and mixtures thereof. The cells may be used fox 2~ transplantation.
Any organ may be targetEd by the present invention. A tissue or cell targeted by the present invention may be derived from any organ. As used herein, the tern "lorgan" refers to a morphologically independent structure, localized to a particular portion of an individual organism, in which a certa~-n function is performed. In multicellular organisms (e. g., animals, plants), an organ consists of several tissues spatially arranged in a particular manner, each tissue being composed ~4 ~Iao~
of a number of cells . An example of such an organ includes an organ relating to the vasculax system. In one embodiment, organs targeted by the? present invention include, but are not limited to, skin, blood vessels, cornea, kidney, heart, liver, umbilical cord, intestine, nr~rve, lung, placenta, pancxeas, brain, peripheral limbs, retina, and the l~.ke.
As used herein, cells differentiated from a pluripotent cell o~ the presEnt invention i.nciude, but are not limited to:
epidermal cells, pancreatic parenchyma) cells, pancreatic duct cells, hepatic cells, blood cells, cardiac muscle calls, skeletal muscle cells, osteoblasts, skeletal myoblasts, neurons, vascular endothelial cells, pigment cells, smooth muscle cells, fat cells, bone cells, cartilage cells, and the like.
As used herein, the term "tissue" refers to an aggregate of cells having substantially the same function and/or form in a multicellu~.ar organism. "Tissue" is typically an aggregate of cells of the same or~.gin, but may be an aggregate of cells of different origins as long as the cells have the same function and/or form. Therefore, when stem cells of the present invention are used to regenerate tissue, the tissue may be composed of an aggregate of cells of two or more different origins. Typical~.y, a tissue constitutes a part of an organ. Animal tissues are separated into epithelial tissue, connective tissue, muscular tissue, nervous tissue, and the like, on a morphologica3., functional, or developmental bas~.s. plant tissues are roughly separated into meristematic tissue and permanent tissue, according to the developmental stage of AI00?
the cells constituting the tissue. Alternatively, tissues may be separated into single tissues and composite tissues according to the type of cells constituting the tissue.
Thus, tissues are separated into various categories.
As used herein, the term "stem cell" refers to a cell capable of self replication and pluripatenoy.
Typically, stem cells can regenerate an inaured tissue.
Stem cells used herein may be, 'but are not limited to, embryonic stem (ES) cells or tissue stem cells (also called tissular stem cells, tissue-specific stem cells, or somatic stem cells). A stem cell may be an artificially produced cell (e. g., fusion cells, reprogrammed cells, or the like used herein) , as long as it has the above-described abilities.
Embryonic stem cells are pluripatent stem cells derived from early embryos. An embryonic stem cell was first established in 1981, and has been applied to the production of knockout mice since 1989. In 1998, a human embryonic stem cell was established, which is currently becoming available for zegenerative medicine. Tissue stem cells have a relatively limited level of differentiation, unlike embryonic stem cells. Tissue stem cells are present in tissues and have an undifferentiated intracellular structure. Tissue stem cells have.a higher nueleusJcytoplasm ratio and have few intracellular organelles. Most tissue stem cElls have pluripotency, a long cell cycle, and proliferative ability beyond the life of the individual. As used herein, stern cells may preferably be embryonic stem cells, though tissue stem cells may also lie employed, depending an the 3p circumstance.
~zao~
Tissue stem cells are separated into categories of sites from which the sells are derived, such as the dermal system, the digestive system, the bone marrow system, the S nervous system, and the like. Tissue stem cells in the dermal system include epidermal stem cells, hair follicle stem cells, and the like. Tissue stem sells in the digestive system include pancreatic (common) stem cells, liver stem ce~.l.s, and the like. Tissue stem cells ~.n the bone marrow system include hematopoietic stem cells, mesenchymal stem cells, and the like. Tissue stem cells in the nervous system include neural stem cells, retinal stem sells, and the lake.
As used herein, the term "somatic cell" refers to any cell other than a germ cell, such as an egg, a sperm, or the like, which does not transfer its DNA to the next generation. Typically, somatic ce~.~.s ha~cre limited or no pluripotency. Somatic cells used herein may be naturally-occurring or genetically modified.
The origin of a stem cell is categorized into the ectoderm, endoderm, or mesoderm. Stem cells of ectodermal origin are mostly present in the brain, including neural stem cel~.s . stem cells of endodermal origin are mostly present in bone marrow, including blood vessel stem cells, hematopoietic stem cells, mesenchymal stem cells, and the like. Stem cells of mesoderm origin are mostly present in organs, including liver stem cells, pancreatic stem cells, and the like. Somatic cells may be herein derived from any germ layer. Preferably, somatic cells, Ar007 such as lymphocytes, spleen cells or testis-derived cells, may be used.
As used herein, the term "isolated" means that naturally accompanying material is at least reduced, or preferably substantially completely eliminated, in the normal environment. Therefore, the term "isolated cell"
refers to a cel.J. substantially free from other accompanying substances (e. g., other cells, proteins, nucleic acids, etc.) in the natural environment. The term "isolated" in relation to nucleic acids or polypeptides means that, for example, the nucleic acids or the polypeptides are substantially free from cellular substances or culture media when they arc pzoduced by recombinant p~tA techniques;
ox precursory chemical substances or other chemical substances when they are chemically synthesized. isolated nucleic acids are preferably free from sequences that naturally flank the nucleic acid within an organism from which the nucleic acid is derived (i.e., sequences positioned at the 5' terminus and the 3~ terminus of the nucleic acid).
As used herein, the term "established" in relation to cells refers to a state of a cell in which a particular property (pluripotency) of the cell is maintained and the cell undergoes stable proliferation under culture conditions. Therefore, established stem cells maintain pluripotency.
As used herein, the term "differentiated cell."
Ar007 refers to a cell having a specza~.ized function and form (e. g. , muscle cells, neurons, etc.). Unlike stem cells, di.fferent~.ated cel.7.s knave no or little pluripotency.
Examples of differentiated cells include epidermic cells, pancreatic parenchymal cells, pancreatic duct cells, hepatic cells, blood cells, cardiac muscle cells, skeletal muscle cells, osteoblasts, skeletal myoblasts, neurons, vascular endothelial cells, pigment cells, smooth muscle cells, fat cells, bone Dells, cartilage Cells, and the like.
As used herein, the term "state" refers to a condition concernirzg varzous parameters of a cell. (e. g~, cell cycle, response to an external factor, signal transduction, gene expression, gene transcription, etc.).
Examples of such a state include, but are not limited to, differentiated states, undifferentiated states, responses to external factors, Cell cycles, growth states, and the like.
As used herein, the terms "differentiation" or "cell differentiation" refers to a phenomenon where two or more types of cells having qualitative differences in form and/or function occur in a daughter cell population derived from the division of a single cell. Therefore, "differentiation" includes a process during which a population (family tree) of cells, which do not originally have a specific detectable feature, acquire a feature, such as the production of a specific protein, or the like. At present, cell differentiation is generally considered to be a state of a cell in which a specific group of genes in the genome are expressed, Cell differentiation can be identified by searching for intracellular br extracellular agents or conditions which elicit the above-desc~cibed state of gene expression. Differentiated cells are stable in principle. Particularly, animal cells which have been differentiated once rarely re-d~.fferentiate into other types of cells.
As used herein, the term "pluxipotency" refers to a nature of a cell, i . a . , an ability to differentiate into one or more, preferably two or more, tissues or organs. Therefore, the terms "pluripotent" and "undifferentiated" axe herein used interchangeably unless otherwise mentioned. Typically, the pluripotency of a cell is limited duxing development, and in an adult, cells constituting a tissue or organ rarely differentiate into different cells, that is, the pluripotenGy is usually lost. Particularly, epithelial cells resist altering into other types of epithelia. cells.
Such alteration typically occurs in pathological conditions, and is called metaplasia, However, mesenchymal cells tend to easily undergo metaplasia, i.e., alter to other mesenchymal cells, with relativexy simple stimuli.
Therefore, mesenchymal cells have a high level of ~5 pluripotency. Embryonic stem ceZ~.s have pluripotency.
Tissue stem cells have pluripotency. Thus, the term "pluripotency" may include the concept of tat~.potency. An example of an in vitro assay for determining whether or not a cell has pluripatency, includes, but is not limited to, culturing undex conditions for inducing the formation and Azao~
differentiation of embryoid bodies. Examples of an in vivo assay fox detexmi~ning the presence or absence of pluripotency, include, but are not limited to, implantation of a cell into an immunodeficient mouse so as to form teratoma, inj action of a cell into a blastocyst so as to form a chimeric embryo, implantation of a cell into a tissue of an organism (e. g., injection of a call into ascites) so as to undergo proliferation, and the like. As used herein, one type of pluripotency is "totipotency", which refers to the ability to be differentiated into all kinds of cells which constitute an organism. The idea of pluripotency encompasses totipotency. An example of a tatipotent cell is a fertilized ovum. An ability to be differentiated into only one type of cell is called "unipotency".
(Biochemistry arid Molecul~.r Biology) As used herein, the term "agent" may refer to any substance or element as long as an intended ob j eat can be achieved (e. g:, energy, such as ionizing radiation, radiation, light, acoustic waves, and the like). Examples of such a substance include, but are not limited to, proteins, polypeptides, oligopeptides, peptides, palynuoleotides, oligonucleotides, nucleotides, nucleic acids (e.g., DNA
such as cDNA, genomic DNA and the like, or RNA such as ml~Nl~, RNAi and the like), polysaccharides, oligosaccharides, lipids, low molecular weight oxgan~.c molecules (e. g., hormones, ligands, information transduction substances, low molecular weight organic molecules, molecules synthesized by combinatorial chemistry, law moJ.ecular weight molecules usable as medicaments (e, g., low molecular weight molecule ligands, etc.), etc.), and composite molecules thereof . Extez~nal. agents may be used singly or in combination. Examples of an agent specific to a polynucleotide include, but are not limited to, representatively, a polynucleotide having complementarity to the sequence of the polynucleotide with a predetermined sequence homology (e. g., 70~ or more sequence identity), a polypeptide such as a transcriptional agent binding to a promoter region, and the like. Examples of an agent specific to a polypeptide include, but are not limited to, representatively, an antibody specifically directed to the polypeptide or derivatives ox analog$ thereof (e. g., single chain antibody), a specific iigand or receptor when the polypeptide is a receptor or ligand, a substrate when the polypeptide is an enzyme, and the like.
As used hexein the term "biological agent"
refers to an agent relating to s biological organism (for example, a cell). Preferably, an agent present in a cell in a normal state is referred to a biological agent. Such biological agents include, but are not limited to, for example: nucleic acid molecules, proteins, sugaz~s, lipids, metabolites, low molecular weight molecules, and complexes thereof, and agents including time elements and the like.
Alternatively, it should be understood that such biological agents include electric curxent, electric potential (such as membrane potential), pH, osmotic pressuxe and the like in the present invention. T3seful biological agents as used herein include, for example, transcriptional controlling sequence (for example, promoters and the like) , structural Az C! 0'~
genES, and nucleic acids encoding the same. As used herein a "collection" of "biological agents" zefex to a. plurality o~ biological agents (of the same or different types).
Preferably, the collection refers to biological agents which cooperate with each other.
As used herein, the term "gene" refers to an element defining a genetic trait. A gene is typically arranged in a given sequence an a chromosome . A gene whioh 1.0 defines the primary structure of a protein is called a structural gene. A gene which regulates the expression of a structural gene is called a regulatory gene (e. g., promoter). Genes herein include structural genes and regulatory genes unless otherwise specified. 'therefore, the term "cyclin gene" typically includes the structural gene of cyclin and the promoter of cyclin. As used herein, '"gene" may refer to "polynucleotide", "oligonucleotide", "nucleic acid", and "nucleic acid molecule" and/or "protein", "polypeptide", "oligopeptide" and "peptide".
As used herein, "gene product" includes "polynucleotide", "oligonucleotide", "nucleic acid" and "nucleic acid molecule" and/or "protein", "polypeptide", "oligopeptide"
and "peptide",.which are expressed by a genre. Those skilled ~.z~ the art understand what a gene product is, according to the context.
As used herein, the term "homology" in relation to a sequence (e, g. , a nucleic acid sequence, an amino acid sequence, eto. ) ,re~exs '~o the level of identity between two or more gene sequences . Therefore, the greater the homology Az0o7 between two g~.ven genes, the greater the identity or similarity between their sequences. Whether ar nat two genes have homology is determined by comparing their sequences directly or by a hybridization method under stringent conditions. When two gene sequences are directly compared with each othex, these genes have homology if the DNA sequences of the genes have representatively at least 50$ identity, preferably at least 70~ identity, more preferably at least 80~, 90~, 95~, 96~, 97~, 98~, or 99~
identity with each other. As used herein, the term "similarity" in reJ.ation to a sequence (e. g. , a nuc3.eic acid sequence, an amino acid sequence, or the like) refers to the J.evel of identity between two or mere sequences when conservative substitution is regarded as positive 1$ (identical) in the above-descr~.bed homology. Therefore, homology and similarity differ from each other in the presence of conservative substitutions. If no conservative substitutions are present, homology and similarity have the same value.
As used herein, the comparison, of similarity, identity anal homology of an amino acid sequence and a nuleotide sequence is calculated with FAST, a tool for sequence analysis using default parameters.
The terms "protein", "polypeptide", "oligopeptide" arid "peptide" as used her~:zn have the same mearizng and refer to an amino acid polymer having any length.
This polymer may be a straight, branched or cyclic chain.
An amino acid may be a naturally-occurring ox nonnaturally-occurring amino acid, or a vari.arnt amino acid.
The term may include those assembled into a composite of a plurality of polypeptide chains . The term ~l.so includes a naturally-occurring or artificially modified amino acid polymers. Such modification includes, for example, disulfide bond formation, glycosylation, lipidation, acetylatian, phosphorylation, or any other manipulation or modification (e. g., conjugation with a labeling moiety).
This definition encompasses a polypeptide containing at Least one amino acid analog (e. g., nonnaturally-occurring amino acid, etc. ) , a peptide-like compound (e. g., peptoid) , and other variants known in the art, for example. Gene products, such as extracellulax matrix p~cote~.n,s (e. g. , ~ibronectin, etc . ) , are usually in the form of a polypeptide .
The terms "polynucleotide", "oliganucleotide", "nucleic acid molecule" and "nucleic acid" as used herein hav2 the Ss.mr~ meaning and refr~r to a nucleptide pplymer having any length. This term also includes an "OligonuCleotide derivative" or a "polynucleOtide derivative". An "oligonucleotide derivative" or a "polynucleotide derivative" includes a nucleotide derivative, or refers to an oligonucleotide or a polynucleotide having different linkages between nucJ.eotides from typ~.cal ~.i.nkagee, which are interchangeably used. Examples of such an oligonucleoti.de specifically include 2'-0-methyl-ribonucleotide, an oligonucleotide derivative in which a phosphodiester bond in an oligonucleotide is converted to a phosphorothioate bond, an aligonucleatide derivative in Which a phosphodiester bond in an oligonucleotide is converted to a N3' --P5' phvsphoroam~.date bond, an oligonucleotide derivative in which a ribose and a phosphodiester bond in an oligox~ucleotide are converted to a peptide-nucleic acid bond, an oligonucleotide derivative in which uracil in an dligonucleotide is substituted with C-5 propynyl uracil, an aliganucleotide derivative in which uracil in an oligonucleotide is substituted with~C--5 thiazole uracil, an oligonucleotide derivative in which cytosine in an oligonucleotide is substituted with C-5 propynyl cytosine, an oligonucleotide derivative in which cytosine in an oligonucleotide is substituted with phenoxazine-modified cytosine, an oligonuc~leotide derivative in which ribose in 17NA is substituted with 2'-O-propyl ribose, and an oligonucleotide derivative in which ribose in an oligonucleotzde is substituted with 2'-methoxyethoxy ribose. Unless otherwise indicated, a particular nucleic acid sequence also implicitly encompasses conservatively-modified variants thereof (e. g. degenerate codon substitutions) arid complementary sequences as well as the sequence explicitly indicated. Specifically, degenerate codon substitutions may be produced by generat~.rig sequences in which the third positian of one or more selected (or all) codons is substituted with mixed-base and/or deoxyinosine residues (Hatzer et al., Nucleic Acid Res. 19:5081(1991); Qhtsuka et al., J. Biol. Chem.
260:2605-2608 (1985); Rossolini et al., Mol. Cell. Probes 8:91-98(1994)). A gene encoding an extracellular matrix protein (e. g., fibronectin, etc.) or the like xs usually in the form of polynucleotide . A molecule to be transfected is in the form of a polynucleotide.
As used herein, the term "corresponding" amino acid or nucleic acid refers to an amino acid or nucleotide in a given polypeptide or polynucleoti.de molecule, which has, or is anticipated to have, a function similar to .that of a predetermined amino acid or nucleotide in a polypeptide or polynucleotide as a reference for comparison.
Particularly, in the case of enzyme molecules, the term refers to an amino acid which is present at a similar position in an active site and similarly contributes to catalytic activity. For example, in the case of a transcriptional contxdlling sequence of a polynucleotide, it may be a portion similar to that of corresponding artholog in the particular portion of the transcription Controlling sequence.
As used herein, the term "corresponding" gene (e.g., a polypeptide or polynucleotide molecule) refers to a gene in a given species, which has, or is antic~.pated to have, a function similar to that of a predetermined gene in a species as a reference for comparison. When there are a plurality of genes having such a function, the term refers to a gene having the same evolutionary origin. Therefore, a gene Corresponding to a given gene may be an ortholog of 2S the given gene. Thez~efore, genes corresponding to mouse cyclin genes can be found in other anima~.s. Such a corresponding gene can be identified by techniques well known in the art. Therefore, for example, a corresponding gene in a given animal can be found by searching a sequence database of the anima. ( a . g . , human, rat ) using the sequence of a reference gene (e.g., mouse cyclin gene, etc.) as a query sequence.
As used herein, the term "fragment" with respect to a polypeptide or polynucleotide refers to a polypeptide or polynucleotide having a sequence length ranging fxom 1 to n-1 w~.th respect to the full length of the reference polypeptide or polynucleotide (of length n) . The ~.ength of the fragment can be appropriately changed depend~.ng on the purpose. For example, in the case of polypeptides, the lower limit of the length of the fragment includes 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 40, 50 or more amino acids.
Lengths represented by integers which are not herein specified (e.g., 11 and the like) may be appropriate as a lower limit. for example, in the case of polynucleotide$, the lower l~.~mit of the length of the fragment includes 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, ~0, 50, 75, 100 or moxe nucleotides. Lengths represented by integers which axe not herein specified (e. g. , 21 and the like) may be appropriate as a lower limit. As used hexein, the length of polypeptides or polynucleatides can be represented by the number of amino acids or nucleic acids, respectively. However, the above~deecribed numbers are not absolute. The above-described' numbers' as the upper or lower limit are intended to include some greater or smaller numbers (e. g. , t10~) , as ~.ong as the same function ~.s maintained. For this purpose, "about" me~y be herein put ahead of the numbers.
However, it should be understood that the interpretation of numbers is not affected by the presence or absence of "about" in the present specification.
As used herein, the term "bio~.ogical activity"
refers to activity possessed by an agent (e.g., a polynucleotide, a protein, etc.) within an organism, including acti~rit~.es exhibiting vazious functions (e. g., transcription promoting activity, etc.). For example, when a certain factor is an enzyme, the biological activity thereof includes its enzyme activity. In another example, when a certain factor is a ligand, the biological activity thereof includes the binding of the ligand to a receptor corresponding thereto. The above-described biological activity can be measured by teChniques.well--known in the axt.
As used herein, the term "polynucleotides hybridizing under stringent. conditions" refers to conditions commonly used and well known in the art. Such a polynucleotide can be obtained by conducting colony hybridization, plaque hybridization, Southern blot hybridization, or the like, 2~ using a polynucleotide selected from the polynucleotides of the present invention.. Specifically, a filtex on which DNA derived from a Colony or plaque is immobilized is used to conduct hybridization at 65°C i.n the presence of 0.7 to 1.0 M Natal. Thereafter, a 0.1. to 2-fold concentration SSC
(saline-sodium citrate) solution. (2--fold concentration SSC
solution is composed of 150 mM sodium chloride and 15 mM
sodium.citrate) is used to wash the filter at 65°C.
Polynucleotides identified by this method are referred to as "polynucleotides hybridizing under stringent conditions". Hybridization can be conducted in accordance with a method.described in, for example, Molecular Cloning 2nd Ed., Current Protocols in Moledular Biology, Supplement 1-38, DN,A Cloning 1: Core Techniques, A Practical Approach, Second Edition, dxford University Press (1995) , and the like.
Here, sequences hybridizing under stringent Gondit~.ons exclude, preferably, sequences containing only A or T.
"Hybridizable polynucleot~.de" refers to a polynuc.leotide which Can hybridize to other polynucl.eotides under the above-described hybridization conditions. Specifically, the hybridizable polynucleot~.de includes at least a polyr~uc3.eotxde having a homology of at least 60~ to the base sequence of DNA encoding a polypeptide having an amino acid sequence specifically herein disclosed, preferably a polynucleotide having a homology of at least $0~, and more preferably a polynucleotide having a homology of at 3east 95~.
As used herein, the term "salt" has the same meaning as that commonly understood by those skilled in the art, including both inorganic and organic salts. Salts are typically generated by neutralizing reactions between s,cids and bases. Salts inc~.ude NaCl, FizS04, and the like, which are generated by neutralization, and in addition, PbS04, ZnCl2, arid the like, which axe generated by reactions between rc~,etals and acids. The latter salts may not be generated directly by neutralizing reactions, but may be regarded as a product of neutralizing reactions between acids and bases.
Salts may be divided into the following categories : normal salts (salts without any H-groups from acids or w~.thout any OF3-groups from bases, including, for example, NaCl, NHQC1, BO
z~zoo~
CH3COONa, and Na2C03) , acid salts (salts w~.th remaining H-groups from acids, including, for example, NaHC03, KHS04, and CaHPO4 } , and basin salts ( salts with remaining OH-grpups from bases, including, for example, MgCl (OH) and CuCl (OH) ? -S This classification is not very important in the present invention. Examples of preferable Belts include salts constituting media (e.g., calcium chloride, sodium hydrogen phosphate, sodium hydrogen carbonate, sodium pyruvate, HEpES, sodium chloride, potassium chloride, magnesium sulfide, iron nitrate, amino acids, vitamins, etc. ) , salts constituting buffer Ce-g-r calcium chloride, magnesium chloride, sodium hydrogen.phosphate, sodium chloride, etc.}, and the like. These salts are preferable as they have a high affinity for cells and thus are better able to maintain cells in culture. These salts may be used singly or in combination.
Preferably, these salts may be used in combination. This is because a combination of salts tends to have a higher affinityvor cells. Therefore, a plurality of salts (e.g., calcium chloride, magnesium chloride, sodium hydrogen phosphate, and sodium chloride) are preferably contained in a medium, rather than only NaCl or the like. More preferably, all salts suitable for cell culture medium may be added to the medium. Tn. another preferred embodiment, glucose may be added to medium.
As used herein the term "material." or "substance" is used in the broadest meaning as used in the art to refer to any thing that is positively or negatively charged.
Azoo~
As used herein., the term "positively charged substance" encompasses alJ. substances having a posztive charge. Such substances include cationic substances such as cationic polymers, cationic lipids and the like, but are not limited to these. Advantageously, such positively charged substances can form a complex. Such positively charged substances which can form a complex. include, for example, substances having a certain maleaular weight (for example, cata.onic polymers ) and substances which can remain IO insoluble, that is, without being dissolved to a certain extent in a specific solvent such as water, an aqueous solution or the like (for example, cationic lipids), but are not limited to the$e, Preferable positively charged substances include, for example, polyethylene imine, I5 poly-L-lysine, synthetic polypeptides, ax derivatives thereof, but are not limited to these. Positively charged substances include,. for example, biological molecules such as histone and synthetic polypeptides, but are not limited to these, The type of preferable positively charged 20 substances changes in accordance with the type of negatively charged substances, which act as a complex partner to form complexes with the positively charged substances. Tt requzres no specific creativity for those sJ~illed in the art to select a preferable complex partner using technology 25 well knotan in the art. For selecting a preferable complex partner, various parameters are considered including, but not limited to, charge, molecular weight, hydxaphobicity, hydrophilicity, properties of substituents, pH, temperature, salt concentration, pressuxe, and other 30 physical and chemical parameters.
Azao~
As used herein, the term" cationic polymer"
refers to a polymer having a cationic functional group, and encompasses, for example, polyethylene imine, poly-~-lysine, synthetic polypeptides, and derivatives thereof, but is not lin2ited to these.
As used herein, the term" cationic lipid" refers to a lipid having a cationic functional group, and encompasses, for example, phosphatidyl choline, phosphatidyl ethanol amine, phosphatidyl serine, and derivatives thereof, but is not limited to these.
Cationic functional groups include, for example, primary amines, secondary amines, and tertiary amines, but are not lim~.ted to these.
As used herein, the term" negatively charged substance" encompasses all substances having a negative charge. Such substances inc~.ude biological molecular polymers, anion~.C substances such as anionic .lipids, a.r~d the like, but are not limited to these. Advantageously, such negatively charged substances can form a comple~c. Such negatively charged substances which can form a complex include, for example, substances 'having a certain molecular weight (for example, anionic polymers such as DNA) and substances which can remain insoluble, that is, without being dissolved to a certain extent in a specific solvent such as watex, an aqueous solutions or the like (for example, anionic lipids), but are not limited to these. Preferable $3 negatively charged substances include, for example, DNA, RNA, ENA, polypeptides, chemical compounds, and complexes thereof, but are not limited to these. Negatively charged substances include, far example, DNA, RNA, PNA, polypeptides, chema.cal compounds, and comp~.exes thereof, but are x~ot limited to these. The type of preferable negatively charged substances ehanc~es in accordance with the type of positively charged suYsstar~ces, which act as a complex partner to form complexes with the negatively charged substances . It requires na specific creativity for those skilled in the art to select a preferable complex partner using technology well known in the art. For selecting a preferable complex partner, various parameters are considered as described above with regard to negatively charged substances.
As used herein, the term "anionic polymer"
encompasses polymers having an anionic functional group, and includes, for example, DNA, RNA, PNA, polypeptides, chemical compounds, arid compl~:xes thereof, but is not limited to these.
fis used herein, the term" anionic lipid"
encompasses lipids having an anionic functional r~roup, and include, for example, phosphatid~.c acid, phosphatidyl serine, but is not limited to these.
Anionic functional groups include, for example, carboxylic groups and phosphoric acid groups, but are not limited to these.
The type of charge of a target substance can be converted by adding a part of a substituent or the like having a positive charge or a negative Charge to the target substance.
Tn the case where a preferable complex partner has the same type of charge as that of the target substance, formation of a complex can be promoted by converting the type o~ charge of either the complex partner or the target substance.
As used herein, the term "complex" refers to two or more substances which directly or indirectly interact with each other and as a result, act as if they were one substance as a whole, As used herein, the term "complex partner" used for a certain member forming a complex refers to another member interacting with the certain member directly or i.ndi.rectly, As used herein, the condition for forming a complex changes in accordance with the type of complex partner. Such a condition can be easily understood by tho$e skilled in the art. Those skilled in the art can easily form a complex from any complex partners (for example, a positively charged substance and a negatively charged substance) using a technique well known in the art.
As used herein, when a complex of positively and negatively charged substances is used, eithef ox' both thereof znay be identical to a biological agent.
As used herein, the term" immobxlxzation" used for a solid-phase support refers to a state in which a substance as a subject of immobilization (e. g. , a biological molecule) is held an the support for at least a certain time period, or an act-of p~.acing the substance into such a state .
As such, in the case where the condition is changed after the substance is ~.mmobilized on the solid-phase support (for 10~ example, the substance is immersed in another solvent) , the substance may be released from the immobilization state.
As used herein; the term "cell affinity" refers to a property of a substance that when the substance is placed in an interactable state with a cell (e. g. germ cell, animal Dell, yeast, plant cell ) or an obj ect containing a cell ( a .
g., tissue, organs, biological organisms), the substance does not have any adverse influence on the cell or the abject containing the cell. Preferably, substances having cell affinity may be substances w~.t~x which a cell interacts as a priority, but axe not ximited to these . According to the present invent~.on, the substance to be immobilized (e. g., positively charged substances and/or negatively charged substances) preferably have cell affinity, but cell affinity is not absolutely. necessary. It was unexpeeted7.y found that when fihe substance to be immobilized has cell.
affinity, the cell affinity of the substance is maintained or improved when the substance is immobilized according to the present zz~vention. In light of the past situation where a substance having cell affinity does not neCesSaxily ,~Taa7 maintain its cell affinity when immobilized on a solid-phase support, the effect of the present invention is enormous.
As used herein, the term "probe" ref~:rs to a substance for use in searching, which is used in a biological experiment, such as in vitro and/or zn viva screening or the like, including, but not limited to, for example, a nucleic acid molecule having a specific base sequence or a peptide containing a specific amino acid sequence.
Examples of a nucleic ac~.d molecule as a common probe include one having a nucleic acid sequence having a length of at least 8 contiguous nucleotides, which is homologous or complementary to the nucleic acid sequence of a gene of interest . Such a nucleic acid sequence may be preferably a nucleic acid sequence having a length of at least 9~contiguous nucleotides, more preferably a length of at least 10 contiguous nucleotides, and even more preferably a length of at least 1I contiguous nucleotides, a length of at least 12 contiguous nucleotid~s, a length of at least 13 contiguous nucleotides, a length of at least 14 contiguous nucleotides, a length of at least 15 contiguous nucleotides, a length of at least 20 contiguous nucleotides, a length of at .least 25 contiguous nucleotides, a length of at least 30 contiguous nucleotides, a length of at least 40 contiguous nucleotides, or a length of at least 50 contiguous nucleotides . A nucleic acid sequence used as a probe includes a nucleic acid sequence having at least 7a~
homology to the above-described sequence, more pxefexably at least 80~, and even more preferably at least 9Q~ or at least 95~.
As used herein, the term "search" indicates that a given nucleic acid sequence is utilized to find other nucleic acid base sequences having a specific function and/or property either electronically or,biologically, or using other methods. Examples of an elec~,roniC search include, but are not limited to, BhAST (Altschul et al.., J. Mnl. Biol. 215:4x3-41p 0,990) ) , FASfA (Pearson & Lipman, Proc. Natl. Acad. Sci., USA 85:2444-2448 (1988) ), the Smith and Watex~zcian method ( Smith and Waterman, J. Mol . Biol.
147:195~197 (1981)), and the Needleman and Wunsch method (Needleman and Wunsch, J. Mol. Biol. 48:443-453 (1970)), and the like. examples of a biological search include, but are not limited to, a macroarzay in which genomie DNA is attached to a nylon membrane or the like or a microarray (microassay) in which genomio DNA ~.s attached to a glass plate under stringent hybridization conditions, PCR, in situ hybridization, and the like.
As used herein, the term "primer" refers to a substance required for the initiation of a reaction o~ a macromolecule compound to~ be synthesized, in a macromolecule synthesis enzymatic rec~ctivn. In a reaction for synthesizing a nucleic acid molecule, a nucleic acid molecule (e.g., DNA, RNA., or the like) which is complementary to part of a macromolecule compound to be synthesized may be used.
A nucleic acid molecule which is Qrdinaxily used as a primer includes one that has a nucleic acid sequence having a length of at least 8 contiguous nucleotides, which is complementary to the nucleic acid sequence of a gene of interest. Such a nucleic acid sequence preferably has a length of at least 9 contiguous nucleotides, more preferably a length of at least 10 contiguous nucleotides, even more preferably a length of at least 11 contiguous nucleotides, a length of at least 12 contiguous nucleotides, a length of at least 13 contiguous nucleota.des, a length of at least 14 contiguous nucleotides, a length of at least 15 contiguous nucleotides, a length of at least 16 contiguous nucleotides, a length of at least 17 contiguous nucleotides, a length of at least 18 contiguous nucleotides, a length of at least 19 contiguous nucleotides, a length of at least 20 contiguous 7.5 nucleotides, a length of at least 25 contiguous nucleotides, a length of at least 30 contiguous nucleotides, a length of at least 40 contiguous nucleotides, and a length of at least 50 contiguous nucleotides. A nucleic acid sequence used as a primer includES a nucleic acid sequence having at least 70% homology to the above-described sequence, more preferably at least 80%, e~cren more preferably at least 90~, and most preferably at least 9S% . An appropriate sequence as a primer may vary depending on the property of the sequence to be synthesized (amplified) . Those skilled in the art can design an appropriate primer depending on the sequence of interest. Such primer design is well known in the art and may be performed manually or using a computer program (e.g., LA9ERGENE, Primer Select., DNAStar).
As used herein, the term "epitope" refers to az~
antigenic determinant. Therefore, the term "epitope"
includes a set of amino acid residues which axe involved in recognition by a particular immunoglobulin, or in the context of T cells, those residues necessary for recognition by the T cell receptor proteins and/or Major Histocampatibility Complex (MiiC) receptors. This term is also used interchangeably With "antigenic determinant" or "antigenic determinant site". In the field of immunology, ~.n vivo or in vitro, an epitope is the features of a molecule (e. g., primary, secondary and tertiary peptide structure, and charge) that form a site recognized by an ~.mmunoglobulin, T cell receptor or HLA molecule. An epitope including a peptide comprises 3 or more amino acids in a spatial conformation which is unique to the epitope. Generally, an epitope consists of at least 5 such amino acids, and more ordinarily, coz~sists of at least 6, 7, 8, 9 or 7.0 such amino acids. The greater the length of an epitope, the more the similarity of the epitope to the original peptide, i.e., longer epitopes are generally preferable. This is not 2Q necessarily the case when the conformation is taken into account. Methods of determining the spatial conformation of amino acids are known in the art, and include, for example, X-ray crystallogxaph,y and 2-~dimensional nuclear magnetic reavnance spectroscopy, furthermore, the identification of epitopes in a given protein is readily accomplished using techniques well known in the art . See, also, Geysen et al . , Proc. Natl. Acad. Sci. LISA (1984) 81: 3998 (general method of rapidly synthesizizxg peptides to determine the location of immunogen~.G epitopes in a given antigen); U. S. Patent No. 4,708,871 (procedures for identifying and chemically synthesizing epitapes of antigens): and Geysers et al., Molecular immunology (1986) 23: 709 (fiechnique for identifying peptides with high affinity for a given antibody) . Antibodies that recognize the same epitope can be identified in a simple immunoassay. Thus, methods for detexma.n~.ng epitopes including a peptide are well known in the art. Such an epitope can be determined using a well-known, common technique by those skilled in the art if the primary nucleic acid or amino acid sequence of the epitope is provided.
Therefore, an epitope including a peptide requires a sequence having a length of at least 3 amino acids, preferably at least 4 amino acids, more preferably at least 5 amino acids, at least 6 amino acids, at least 7 amino acids, at least 8 amino acids, at least 9 amino acids, at least 10 amino acids, at least 15 amino acids, at .east 20 amino acids, and 25 amino acids. Epitopes may be linear or conformational.
As used herein, the term "agent binding specifically to" a certain nucleic acid molecu~.e or polypeptide refers to an agent which has a level of binding to the nucleic acid molecule or polypept~,de equal to or higher than a level of binding to other nucleic acid molecules or polypeptides. E~amplea of such an agent inc~.ude, but are not limited to, when a target is a nucleic acid molecule, a nucleic acid molecule having a . complementary sequence of a nucleic acid molecule of interest, a polypeptide capable of binding to a nucleic acid sequence of interest (e. g., a transcription agent, etc.), and the like, and when a target is a po~.ypeptide, an antibody, a single chain antibody, either of a pair of a receptor and a ligand, either of a pair of an enzyme and a substrate, and the like, As used herein, the term "antibody" encompasses polyclonal antibodies, monoclonal antibodies, human antibodies, humanized antibodies, polyfunctional antibodies, chimeric antibodies, and anti-idiotype antibodies, and fragments thereof (e.g., F(ab')2 and Fab fragments), and other .recombinant conjugates. These antibodies may be fused with an enzyme (e. g., alkaline phosphatase, horseradish peroxidase, d,-galactosidase, and the like) vza a covalent bond or by recombination.
As used herein, the term "monoclonal antibody"
refers to an antibody composition having a group of homologous antibodies. 'this term is not limited by the 2Q production manner thereof. This term encompasses all immunoglobulin molecules and Fab molecules, F (ab' ) 2 fragments, Fv fragments, and other molecules having an immunological binding property of the original monoclonal antibody molecule. Methods for producing polyclonal antibodies and monoclonal ant~.bodies are well known in the art, and will be more sufficiently described below.
Monoclonal antibodies are prepared by usiri$ the standard technique well known in the art (e.g., Kohler and Milstein, Nature (1975) 256:495) or a modification thereof (e. g., Buck et al. f1982) In Vitro 18:377).
Representatively, a mouse or rat is immunized with a protein bound to a protein carrier, and boasted. Subsequently, the spleen (and optionally several large lymph nodes) is removed and dissociated into a single cell suspension. zf desired, the spleen cells may be screened (after removal of nonspecifically adherent cells) by applying the cell suspension to a plate or well coated with a protein antigen.
7.0 H--cells that express membrane-bound immunoglobulin specific far the antigen bind to the plate, and are not rinsed away with the rest of the suspension. Resulting H-cells, ox all dissociated spleen cells, are then induced to fuse with myeloma cells to form hybridomas . The hybridomas are used to produce monoclonal antibodies.
As used herein, the term "antigren" refers to any substrate to whzch an antibody molecule may specifically bind. As used herein, the term "immunogen" refers to an antigen capable of initiating activation of the antigen-specific immune response of a lymphocyte.
Tn a given protein molecule, a given amino acid may be substituted with another amino aoid in a structurally important region, such as a cationic region or a substrate molecule binding site, without a clear reduction or lose of interactive binding ability. A given biological function of a protein is defined by the interactive ability or other property of the protein. Therefore, a particular amino acid substitution may be performed in an amino acid Asaa~
sequence, or at the DNA sequence level, to produce a protein which maintains the original property after the substitution. Therefore, various modifications of peptides as disclosed herein and DNA encoding such peptides may be performed without clear losses of biological activity.
Wh~:z~ the above-described modifications are designed, the hydrophobicity indioes of amino acids may be 1a taken into consideration. Thr~ hydrophobic amino acid indices play an important role in providing a protein with an interactive biological function, which is generally recognized in the art (Yyte, J. and Doolittle, R. F. , J. Mol.
Biol. 157(1):105-132, 1982), The hydrophobic property of an amino acid contributes to the secondary structure of a protein and then regulates interactions between the protein and other molecules (e. g., enzymes, substrates, receptors, DNA, antibodies, antigens, etc _ ) . Each amino acid is given a hydrophobicity index based on the hydrophobicity and 24 charge properties thereof as follows: isoleucine (+4.5);
valine (+4.2); leucine (+3.8); phenylalanine (+2.$);
cysteine/cystine (+2.5); methionine (+1.9); alanine (+1.8); glycine (-~a.9); threonine (-0.7); serine (-0.8);
tryptophan (-0.9); tyrosine (-1.~); proline (-1. f);
hist~.d~.ne (-3.2) ; g.lutamic acid (-3.5) : glutamine (-3.5) ;
aspartic acid (-3. 5) ; asparagine (-~.5) ; lysine (-3. 9) ; and arginine (-4.5).
Tt is well k~xown that if a given amino acid is substituted with another amino acid having a similar Ax007 hydrophobic~.ty index, the resultant protein may still have a biological, function similar to that of the original protein (e. g. , a protein having an equivalent enzymatic activity) .
For such an amino acid substitution, the hydrophobicity index is preferably with~.n ~2, more preferably within t1, and even more preferably within X0.5. It is understood in the art that such an amino acid substitu'~ion based on hydrophobicity is efficient.
Hydrophilicity may also be considered for conservative substitution, As described in US Patent No. 4, 554, x01., amino acid residues are given the following hydrophilicity indices: arginine (+3.0); lysine (+3.0);
aspartic acid (+3.01); glutamic acid (+3.Ot1): serine (+0.3); asparagine (+0.2); c~lutamine (+0.2); glycine (0);
threonine (-0.4): proline (-0.5~1); alanine (-0.5)t histidine (-0.5); cysteine (-1.0); methionine (-1.3);
valine (-1.5); leucine (-1.8); isoleucine (-1.8); tyrosine (-2. 3) ; phenylalanine (-~2.5) ; and tryptophan (-3. 4) . zt .is understood that an amino acid may be substituted with another amino acid which has a similar hydrophilicity index and can stzll provide a biological equivalent. For such an amino acid substitution, the hydrophilicity index is preferably within t2, mare preferably t l, and even more preferably t0.5.
(Profile and its relevant techniques) As used herein, the term "Qrofile" in relation to a cell refers to a set of measuremezlts of the biological state of the cell. Particularly, the term "profile of a A~007 cell" refers to a set of discxete ar continuous values obtained by quantitatively measuring a level. of a "cellular component". A level of a cellular component includes the expression .level, of a gene, the transcription level of a gene (the activity level of a transcription control sequence) , the amount of mRNA encoding a specific gene, and the expression level of a protein in ba.o~.og~.cal systems.
The level o~ each cellular component, such as the expression level of mRNA and/or protein, is known tv alter in xesponse to treatment with drugs or cellular biolag~.cal perturbation or vibration. Therefore, the measurement o~ a plurality of "cellular components" generates a large amount of information about the effects of stimuli on the biological state of a cell, Therefore, the profi3.e is mare and more important in the analysis of cello. Mammalian oe~.~,s contain about 30,000 or more cellular components. Therefore, the profile of an individual cell is usual~.y complicated. A
profile in a prEdetermined state of a b~.ological system may often be measured after stimulating the biological system.
Such stimulation is performed under experimental or environmental conditions associated with the biological system, Examples of a stimulus include exposure of a biological system to a drug candidate, introduction of an exogenous gene, passage of time, deletion of a gene from the system, alteration of culture conditions, and the like.
The wide range measurement of cellular components (i.e., profiles of gene replicat~.on, or transcription, protein expression, and response to stimuli) has a high level of utility including comparison and investigation of the effects of drugs, diagnosis of diseases, and Qptimization of drug administration to patients as well as investigation of cells. Further, profiles are useful for basic life science research. Such profile data may be produced and presented as data in a variety of forIaats. Such formats include, but are not limited to: a function between a numerical value and a period of time, a graphic format, a image format and the like. Accordingly, data relating to a profile may also be called "profile data" as used rierein.
Such data production rnay readily be carried oufi by us~.ng a computer. Coding of an appropriate program may also be carried out by using well known technology in the art.
In the cell analysis of the pxesent application, as regards to information derived from a cell or a substance interacting with the cell, a variety of processes and means fo~c detection may be used- Such process and means for detect~.vn include, but are not l~.mited to: those using visual inspection, optical microscopes,fluarescence microscopes, reading appazatus using a laser l~.ght source, surface plasmon resonance (SPR) imaging, electric signal, chemical and biochemical. markers, or a combination thereof.
As used herein, the term "time,lapse profile"
in relation to a certain, cell refers to a profile which indicates time-lapse changes in a parameter relating to the cell. Examples of a time-lapse profi~.e include, but are not limited for a time-lapse profile of transcription levels, a time-lapse prof~.le of expression levels (translation levels), a time-lapse profile of signal transduction, a time-lapse profile of neural potential, and the like. A
Ax007 time-lapse profile may be produced by continuously recording a certain parameter (e.g., a signal caused by a label associated with s. transcription level). Time-lapse measurement may mean continuous measurezrient. wherefore, the term "time-lapse profile" as used herein may also be referred to as "continuous profile". , As used herein the ~.erm "information" of a cell refers to those acting to direct an object as a whale by binding a number of elements present in the cell. A
collection of information can be said to constitute a digital cell.
As used.herein, the term "state" refers to a condition eonoexx~ing various parameters of a cell (e. g., cell cycle, response to an extexnal factor, signal transduction, gene expression, gene transcription, etc.}.
Examples of such a state include, but are not limited to, differentiated states, undifferentiated states, responses to external factors, cell cycles, growth states, and the like. The responsiveness or resistance of an organism of interest with respect to the following parameters of the, particuJ.axly, environment of the organism may be used herein as a measure of the state c~f the organism: temperature, humidity (e. g., absolute humidity, relative humidity, etc.), pH, salt concentration (e.g. , the concentration of all salts or a particulax salt), nutrients (e.g., the amount of carbohydrate, etc.}, metals (e.g., the amount or concentration of all metals or a particular metal (e. g., a heavy metal, etc.}), gas (e. g., the amount of all gases or a particular gas), organic solvent (e.g., the amount of all organic solvents or a particular organic solvent (e. g. , ethanol, etc.)), pressure (e. g., local or global pressure, etc.), atmospheric pressure, viscosity, flow rate (e. g., the flow rate of a medium in Which an organism is present, etc. ) , light i.nterzs~.ty (e. g. , the quantity of light having a particular wavelength, etc.), light wavelength (e. g., visible light, ultraviolet light, infrared lzght, etc.), electromagnetic waves, z~adiation, gravity, tension, acoustic waves, organisms other than an organism of interest (e. g., paras~.tes, pathogenic bacteria, etc.), chemicals (e. g., pharmaceuticals, etc.), antibiotics, naturally-occurz~ing substances, metal stresses, physical stresses, and the like.
As used herein, the term "environment" (or "Umgeb~xng" in German) in relation to an entity refers to a circumstance which surrounds the entity. In an ezwironznent, various components and quantities of state are recognized, which are called environmental factors.
Examples of environmental factors include the .above-described parameters. Environmental factors are typically roughly divided into non~biologiGal environmental factors and biological environmental factors.
Non-biological environmental factors (inorganic environment factors) may be divided into physical factors and chemical factors, or alternatively, climatic factors and soil factors. Various environmental factors do not always act on organisms independently, but may be associated with one another, Therefore, environment factors may be herein observed one by one or as a whole {a whole of various parameters) . It has been believed that it was difficult to maintain such an environment in a consistent state. This is particularly the case since it has been difficult to maintain cells and to immobilize cells, and to introduce substances such as nucleic acids into a cell. The present invention has also~solved at least one of these problems.
As used herein the term "consistent environment" refers tv substantially all of the circumstances surrounding a cell of interest. Accordingly, as long as a cell Gan grow or differentiate in a similar manner, such environments are deemed to be consistent environments. Ac used herein, a consistent environment refers to an environment where the parameters are the same except for a specific stimulus {for exampxe, an external stimulus).
Examples of such an environment include at least one factor, as a parameter, selected ~rorn the group consisting of temperature, humidity, pH, salt concentration, 24 nutrients, metal, gas, organic salvant, pressure, atmospheric pressure, viscosity, flow rate, light intensity, light wavelength, electromagnetic waves, radiation, gravity, tension, acoustic waves, organisms (e. g., parasites, etc.) other than the organism, chemical agents, antibiotics, natural substances, mental stress, s.nd physical stress, and any combination thereof.
Examples of temperature include, but are not limited to, high temperature, low temperature, very high temperature (e.g., 95°C, etc. ) , very low temperature (e.g., 1. 0 0 Az007 -80°C, etc. ) , a wide range of temperature (e. g. , 150 to --270°C, etc.), and the like.
Examples of humidity include, but are not limited to, a relative humidity of ~.00~, ~ relative humidity of 0$, an arbitrary point from 0% to 100, and the like.
Examples of pH include, but are not limited to, an arbitrary point from 0 to 14, and the like.
Examples of salt concentration include, but are not limited to, a NaCl concentration (e.g., 3~, etc.), an az~bitrary point of other salt concentrations from 0 to 7.00, and the like.
Examples of nutrients include, but are not limited to, proteins, glucose, lipids, vitamins, inorganic salts, and the like.
2p Examples of metals include, 3~ut are not limited to, heavy metals (e. g. , mercury, cadmium, etc. ) , lead, gold, uranium, silver, and the like.
Examples of gas include, but are not limited to, oxygen, nitrogen, carbon dioxide, carbon monoxide, and a mixture thereof, and the like.
Examples of organic solvents include, but are not limited to, ethanol, methanol, xylene, propanol, and the like.
Examples of pressure include, but are not limited to, an arbitrary point from 0 to 10 ton/cm2, and the like.
Examples of atmospheric pressure include, but are not limited to, an arbitrary point from 0 to 100 atmospheric pressure, and the like, Examples of viscosity include, but are not limited to the viscosity of any fluid (e. g. , water, glycerol, etc.) or a mixture thereof, and the like.
Examples of flow rate include, but are not limited to an arbitrary po~.nt from 0 to the velocity of light .
Examples of light intensity include, but are not ~.i.mzted to, a point between darkness and the level of sunlight.
Examples of light wa~relength include, but are not limited to visiY~le light, ultraviolet light (U'Sl-A, UV-B, UV-C, etc.), infrared light (far infrared light, near infrared light, eto.), and the like.
Examples of electromagnetic waves include ones having an arbitrary wavelength.
Examples of radi~tioz~ inc~.ude ones having an arbitrary intensity.
Examples of gravity include, but are not limited to, an arbitrary gravity on the Earth or an arbitrary point from zero gravity to the gravity on the Earth, or an arbitrary gravity greater than or equal to a gravity on the Earth.
Examples of tension include ones having an arbitrary strength.
0 Examples of acoustic waves include ones having an arbitrary intensity and wavelength.
Examples of organisms other than an organism of int~:rest include, but are not limited to, parasites, pathogenic bactexia, znsects, nematodes, and the like.
Examples of chemicals include, but are not limited to hydrochloric acid, sulfuric acid, sodium hydroxide, and the like.
2d Examples of antibiotics include, but are not limited to, penicillin, kaz~amyein, streptomycin, quinoline, and the like.
Examples of naturally-occurring substances ~.nczut~e, but are nat limited to, puffer toxin, snake venom, alkaloid, and the like.
Examples of znenta~. stress include, but are not 30 limited to starvation, population dez~sity, confined spaces, high places, and the like.
ExampJ.es of physical stress include, but are not limited to vibration, noise, electricity, impact, a.nd the like.
As used herein when referring to a digital cell of the present invention, the envi.rt~nment is presented as an "environment parameter". Such. environment parameters include, but are not limited to, medium (type, composition) , pH, temger~.ture, moisture, COZ concentration, concentration, the presence or absence of an antibiotic, the presence or absence of a particular nutrient and the like.
As used herein the term "stimulant" refers to an acting agent which cau$es or inducES expression or enhancement of a specific living action given to a cell from outside. Stimuli include, but are not limited to: a physical stimulus, a chemical stimulus, a biologioal stimulus, a biochemical stimulus, and the like. Physical stimuli include, but axe not limited to: for example, light, electric waves, electric current, pressure, sound (vibration) and the like. Chemical stimuli include but are not limited to: for example, stimuli from chemicals such as antibiotics, nutrients, vitamins, metals, ions, acids, alkalis, salts, buffers and the like. Biological stimuli include, but are not limited to: for example, the existence of another organism such as the existence of a paras~.tic organism or the density of a cell. population and the like.
AIO~~
Biochemical stimuli include, but are not limited to the existence of cell signaling transduction agents, and the like.
S As used herein, when the digital cell of the present invention is used, a stimulus is presented as a "stimulus parameter". A stimulus parameter corresponding to those in response to any stimulus as described herein may be used.
As used herein, it should be understood that the stimulus parameter includes agents for transducing a stimulus such as a reporter and the like. Such reporters include, but are not limited to: for example, on-off regulation of expression against an e~ntibiotic, a transcription-controlling sequence, radioactivity, fluorophores and the like.
As used herein the term "response" to a stimulus refers to any response of a cell to a stimulus such as a change in cell morphology, change in metabolism, change in other cellular behaviors, change in signal transduction and the like. Therefore, for example, results of experiments using the digital cell of the present invention may be recorded as cell dynamics data. Alternatively, when using the above xeporter, the result of such a response to the stimulus may be raw data of the reporter, or data transformed from the data of the reporter.
As used herein, the term "transcription control sequence" refers to a sequence which can regulate the transcrxptx.on Revel of a gene . Such a sequence is at least two nucleotides in length. Examples of such a sequence include, but are not limited to, promoters, enhancers, silencer, terminators, sequences flanking other genomic structural genes, genomic sequences other than exons, sequences within ex4ns, and the like. A transcription control sequence used herein is not related to a particular type. Rather, important information about a transcription control sequence is time-.apse fluctuation. Such fluefiuation is referred to as a process (changes in a state of a cell). Therefore, such a transcription control sequence may be herein arbitrarily selected. Such a transcription control sequence rnay include those whioh are not conventionally used as markers. Preferably, a transcription control sequence has the ability to bind to a txanscx~ipt~.on factoz~.
As used herein, the term "transcription factor"
refers to a factor which regulates the process of transcription of a gene. The term "transcription factor"
mainly indicates a factor which regulates a transcz~i.pti.oz~
in~.t~.ation reaction. TransariQtion factors are roughly divided into the following groups: basic transcription factors rEquired for placing an RNA polymerise into a promoter region on DNA; and transcription regulatory factors which bind to cis-acting elements present upstream or downstream of a transcription region to regulate the synthesis initiation frequency of RNA.
Basic transcription factors are prepared depending on the type of RNA polymerise. A TATA-binding protein is believed to be common to all transcription systems .
1.06 Although there are a number of types of transcription factors, a typical transcription factor consists of a portion structurally required for binding to DNA and a portion required for activat~.ng yr suppressing transcription.
Factors which have a DNA~binding portion and can bind to ois~acting elements are collectively referred to as trans-acting factors.
A portion required for acti~crating ox suppressing transcription is involved in interaction with other transcription factors or basic transoxiption factors.
Such a portion is believed to play a role in regulating transcription via a structural change in DNA or a transcription initiating complex. Transcription regulatory factors are div~.ded into several groups or families according to the structural properties of these portions, including factors which play an important role in the development yr differentiation of a cell..
~xamp~.es of such a transcription factor include, but are not limited to, STATI, STAT2, STAT3, GAS, NEAT, Myc, APl, CREB, NFxB, E2F, Rb, p53, RUNX1, RUNX2, RUNX3, Nkx-2, CF2-ZZ, Skn-1, SRY, HFH-2, Oct-1, Oct-3, $ox-5, HNF-3b, PPARY, and the like.
As used herein,. the term "terminator" refers to a sequence which is located downstream of a protein-encoding region of a gene and whi.Ch is involved in the termination of transGript~.on when DNA is transcribed into mRNA, and the addition of a paly-A sequence. It is known that a terminator ~. 0'7 contr~.butes to the stability of mRNA, and has an influence on the J.evel of gene ~xpr~:ssian.
As used herein, the term "promoter" refers to a base sequence which determines the initiation site o~
transcription of a gene and is a DNA region which directly regulatesthe frequency of transcription. Transcription is started by RNA polymerase binding to a promoter. A promoter region is usually located within about 2 kbp upstream of the first exon of a putative protein coding zegion.
Therefore, it is possible to estimate a promoter region by predicting a protein coding region in a genomic base sequence using DNA analysis software. A putative promoter region is usually located upstream of a structural gene, but is dependent an the structural gene, i . a . , a putative promoter region may be looated downstream of a structural gene.
Preferably, a putative promoter region is located within about 2 kbp upstream of the translation initiation site o~
the first exon. Such promoters ~.riCl.ude, but are not limited to constitutive promoters, specific promoters and induCti~cre promoters and the like.
As used herein, the term "enhancer" refers to a sequence which is used so as to enhance the expression efficiency of a gene of interest. One or more enhancers may be used, ox~ no enhancer may be used.
As used herein, the term "silencer" refers to a sequence which has a function of suppressing and arresting the expression of a gene. Any silencer which has such a Azp07 functian may be herein used. No silencer may be used.
As used herein, the term "operably linked"
indicates that a desired sequence is located such that expression (operation) thereof is under control of a transcription and translation regulatory sequence (e. g., a promoter, an enhancer, and the like) or a translation regulatory sequence . Tn order for a promoter to be operably lznked to a gene, typically, the promoter is located immediately upstream of the gene. A promoter is not necessarily adjacent to e~ structural gene.
Sequences flanking other genome structural genes, genomic sequences other than axons, and sequences within axons may also be herein used. For example, in addition to the above-described sequences having specific names, structural gene-flanking sequences are thought to be involved fn the cantro3. of transcription in terms of "processes". Therefore, such flanking sequences are also included in transcription control sequences. Genomic sequences other than axons and sequences within axons are also expected to be involved in the control of transcription in terms of "processes". Therefore, genomic sequences other than axons and sequences within axons are also included in transcription control sequences.
As used herein, the term "RNAi" is an abbreviation of RNA interference and refers to a phenomenon where an agent for causing RNAi, such as double-stz~anded ~0 RNA (also called dsRNA) , is introduced into cells and mRNA
homologous thereto is specifically degraded, so that the synthesis of gene products is suppressed, and techniques using the phenomenon. As used herein, RNAi may have the same meaning as that of an agent which causes RNAi.
As used herein, the term "an agent causing RNRi"
refers to any agent capable of causing RNAi . As used herein, "an agent causing RNAi of a tlene" indicates that the agent causes RNAi relating to the gene and that the effect of RNAi is achieved (e. g., suppression of expression of the gene, and the like). Examples of such an agent causing RNAi include, but are not limited to, a sequence having at least about '70~ homology to the nucleic acid sequence of a target gene or a sequence hybridizable thereto under stringent conditioz~s, RNA containing a double-stranded portion having a length of at least 10 nucleotides or variants thereof.
Here, this agent may be preferably DNA containing a 3' protruding end, and mare preferably the 3' protruding end has a length of 2 or more nucleotides (e.g., 2-9 nucleotides in length).
Though not wishing to be bound by any theory, a mechanism which causes RNAi is considered to be as follows .
When a molecule which causes RNAi, such as dsRNA, is introduced into a cell, an RNaseIII-like nuclease having a helicase domain (called dicer) cleaves the molecule at about 20 base pair intervals from the 3' terminus in the presence of AmP in the case where the RNA is relatively long (e. g., 40 or more base pairs). As used herein, the term "siRNA" is an abbreviation of short interfering RNA and Azao~
refers to short double-stranded RNA of 10 or more base pairs which are artificially chemically synthesized or b~.ochemically synthesized, synthesized by an organism, or produced by double-stxanded RNA of about 40 or more basE
pairs being degraded within the organism. siRNA typically has a structure comprising 5'-phosphate and 3'-OH, where the ~' terminus projects by about 2 bases. A specific protein is bound to siRNA to form RISC
(RNA-induced-silencing-complex). this complex recognizes and binds to mRNA having the same sequence as that of siRNA
and cleaves mRNA at the middlE of siRNA due to RNaseIZI-like enzymatic activity. It is preferable that the relationship between the sequence of siRNA and the sequence of mRNA to be cleaved as a target is a 1a0% match. However, base mutations at a site away from the middle of siRNA do not completely remove the cleavage activity by RNA,, leaving parti.aJ. acti~rity, while base mutations in the middle of siRNA
have a laxge influence and the mRNA cleavage activity by RNAi is considerabJ.y lowered. By utilizing such a nature, only mRNA having a mutation can be specifically degraded.
Specifically, siRNA in which the mutation is provided in the middle thereof is synthesized and is introduced into a cell. Therefore, in the present invention, siRNA per se, as well as an agent capable of producing siRNA (e. g., representatively dsRNA of about 40 or more base pairs) can be used as an agent capable of eliciting RNAi.
Also, though not w~.shing to be bound by any theory, apart from the above--described pathway, the antisense strand of siRNA binds to mRNA and siRNA functions Azoo~
as a px~.mer for RNA-dependent RNA polymerase (RdRP) , sa that dsRNA is synthesized. This dsRNA is a substrate for a dicer again, leading to production of new siRNA. It is intended that such a reaction is amplified. Therefore, in the present invention, siRNA per se, as well as an agent capable of producing siRNA are useful. xn fact, in insects and the like, for example, 35 dsRNA molecules aan substantially completely degrade 1,000 or more cop~:es of intracellular mRNA, and therefore, it will be understood that siRNA per se, as well as an agent capable of producing siRNA, is useful .
Tn the present invention, double-stranded RNA
having a length of about 20 bases (e. g., representatively about 21 to 23 bases) or less than about 20 bases, called siRNA, Can be used. Expression of siRNA in cells can suppress expression of a pathogenic gene targeted by the siRNA. Therefore, siRNA can be used far the treatment, prophylaxis, prognosis, and the like of diseases.
The siRNA of the present invention may be in any form as long as it can elicit RNAi.
In another embodiment, an agent capable of causing RNAi may have a short hairpin structure having a sticky portion at the 3' terminus (shRNA~ short hairpin RNA) .
As used herein, the term "shRNA" refers to a molecule of about 20 or more base pairs ~.n which a single-stranded RNA
partially contains a palindramic base sequence and forms a double-strand structure therein (i.e., a hairpin structure). shRNA can be artificially chemically AIOa7 synthesized. Alternatively, shRNA can be produced by linking sense and antisense strands of a DNA sequence in reverse directions and synthesizing RNA in vitro with T7 RNA polymerase using the DNA as a template. Though not wishing to be bound by any theory, it should be understood that after shRNA is introduced into a cell, the shRNA is degraded in the cell to a length of about 20 bass (e. g., representatively 21, 22, 23 bases) , and causes RNAi as with siRNA, leading to the treatment effects of the present invention. It should be understood that such an effect is exhibited in a wide range of organisms, such as insects, plants, animals (including mammals), and the like. Thus, shRNA elicits RNAx as with siRNA and therefore can be used as an effective component of the present invention. shRNA
may preferably have a 3' protz~uding end. The length of the double-stranded portion is not particularly limited, but is preferably about 10 or more nucleotides, and more preferably about 20 or more nucleotides. Here, the 3' protruding end may be preferably DNA, more preferably DNA
of at least 2 nucleotides ~.n length, and even more preferably DNA of 2~4 nucleotides in length.
An agent capable of causing RNAi used in the present invention may be artificially synthesized (chemically or biochemically) or naturally occurring.
There is substantially no difference there between in terms of the effect of the present invention. A chemically synthesized agent is preferably purified by liquid chromatography or the like.
An agent capable of causing RNAi used in the present invention can be produced .z.n vitro. In this synthesis system, '~7 RNA polymerase and T7 promoter are used to synthesize antisense and sense RNAs from template DNA.
These RNAs are annealed and thereafter introduced ~.nto a cell. In this case, RNAi is caused via the above-described mechanism, thereby achieving the effect of the present invention. Here, for example, the introduction of RNA into cell can be carried out using a calcium phosphate method.
Another example of an agent capable of causing RNAi according to the present invent~.on is a single-stranded nuclEic acid hybridizable to mRNA, or all nucleic acid analogs thereof_ Such agents are useful for the method and composition of the present invention.
As used herein, the term "time-lapse" means any action or phenomenon that is related to the passage of time.
As used herein, the term "monitor" refers to the measurement of a state of a cell using at least one parameter as a measure (e.g., a labeling signal attrilauted to transcription, etc.). Preferably, monitoring is performed using a device, such as a detector, a measuring instrument, or the like. More preferably, such a device is connected to a computer for recording and/ax processing data.
Monitoring may comprise the step of obtaining image data of a solid phase support (e. g., an array, a plate, etc.), As used herein, the term "rea3. time" means that a certain state is substantially s~.multaneously displayed in another form (e. g., as an image on a display or a graph with processed data) . In such a Case, the "real time" lags behind an actual event by the time required far data processing. Such a time lag is included in the scope of "real time" if it is substant~.ally negligible. Such a time lag may be typically within 10 seconds, and preferably within 1 second, w~.thout limitation. A time lag exceedinr~
seconds may be included in the scope of "real. time".
As used herein, the determination of a state of a cell can be performed using various methods . Exampl~s of such methods include, but are not limited to, mathematical processing (e. g., signal processing, multivariate analysis, etc.), empirical processing, phase changes, and the like.
As used herein, the term "difference" refers to a result of mathematical processing in which a value of a control profile (e. g., without a stimulus) is subtracted from a certain profile.
As used herein, the term "phase" in relation to a time-lapse profile refers to a result of a determination of whether the profile is positive or negative with xespect to a reference point (typically 0) , which is expressed with + or -, and also refers to analysis based on such a result.
As used hexezn, the term "correlate" or "correlation" in relat~.on to a profile (e.g., a time-.apse profile, etc.) and a state of a cell refers to an act of Azoa~
associating the profile or particular information about changes, with the state of the cell. A relationship between them is referred to as "correlation" yr a "correlation relationship". Conventionally, it was substantially impossible to associate a profile (e. g., a time-lapse profile, etc.) with a state of a cell. No relationship between them was known. The present invention has an advantageous effect of performing such a correlation.
As used here~.n, correlat~.on can be perfoz-~ned by associating at least one profile (e. g. , a time-lapse profile, etc. ) or changes therein, with a state of a cell, a tissue, an organ or an organism (e , g. , drug resistance, etc. ) . For example, a profile (e.g., a time-lapse profile, etc.) or changes therein is quantitatively or qualitatively associated with at least onE parameter indicating a state of a cell. A small number of profiles (e. g., time-lapse profile, etc. ) may be used for corxr~xat~.ozz as long as correlation can be performed, typically including, without l~.mxtation, 1, preferably 2, and more preferably 3. The present invention demonstrated that at least 2, preferably at least 3, profiles (e. g. , a time-lapsE profile, etc. ) are sufficient for specifying substantially all cells. Such an effect could not be expected by conventional profiling ar assays which use point observation, and can be said to be realized by the present invention. At least one profile (e.g., a time-.apse profile, etc.) may be subjected to mathematical processing by utilizing a matrix to associate the profile with a state of a cell. zn one preferred embodiment, at least 8 profiles (e. g. , a time-lapse profile, Az007 etc.) may be advantageously used. By observing increases or decrease9 in 6 profiles, 256 results can be theoretically obtained, based on which abaut 300 types of cells constituting an organism can be substantially distinguished from one another. zn this context, it may be more advantageous to use at least 9 or 10 structures as profiles.
On the other hand, by using the technology of the present invention, it is possible to substantially understand the state of a cell, merely by selecting any single biological agent and obtaining the profile data thereof.
Examples of a specific method for correlation include, but are not limited to, signal processing (e. g., wavelet analysis, etc.), multivariate analysix (e. g., cluster analys~.s, etc.), and the like.
Gorrelation may be performed in advance or may be performed at the time of detarm~.n,ativn of cells using a control.
As used herein, the term "external factor" in relation to a cell refers to a factor which is not usually present zn the cell (e.g., a substance, energy, etc.). As used herein, the term "factor" may refez to any substance or element as long as an intended object can be achieved (e. g. , energy, such as ionizing rad~.ation, radiation, light, acoustic waves, and the like) . Examples of such a substance include, but axe not limited to, proteins, polypeptides, oligopeptides, peptides, polynucleotides, vligonucleotides, nucleotides, nucleic acids (e.g., DNA
Azoo~
such as cDNA, genomio DNA and the like, or RNA such as mRNA, RNAi and the like), polysaccharides, oligosacchaz~.des, lipids, low molecular weight organic moleculr~s (e. g., hormones, ligands, information transduction substances, S low molecular weight oxganic molecules, molecules synthesized by combinatorial chemistry, low molecular weight molecules usable as medicaments (e. g., low molecular weight molecule ligands, etc.), etc.), and composite molecules thereof. External factors may be used'singly or in combination. Examples of eon external factor as used herein include, but are not limited to, temperature changes, humidity changes, electromagnetic wave, potential difference, visible light, ~.nfrarEd light, ultraviolet light, X--rays, chemical substances, pressure, gravity changes, gas partial pxessure, osmotio pressure, and the like. In one embodiment, an external factor may be a biological molecule or a chemically synthesized substance.
As used herein, the term "biological molecule"
refers to molecules relating to an organism and aggregations thereof. As used herein, the term "biolpg~.cal" or "organism" refers to a biological organism, including, but being not limited to, an animal, a plant, a. fungus, a virus, and the like. Biological molecules include molecules extracted from an organism and aggregations thereof, though the present invention is not limited to this. Any molecule capab~.e of affecting an organism and aggregations thereof fall within the defin~.tion of a biological molecule.
Therefore, low molecular weight molecules (e.g., low molecular weight molecule ligands, etc.), capable of being A~007 used as medicaments fall within the definition of a biological molecule as long as an effect on an organism is intended. Examples of such a biological molecule inciude, but are not limited to, proteins, polypept~.des, oligopeptides, peptides, polynucleotides, oligonucleotides, nucleotides, nucleic acids (e.g., DNA
such as cDNA and genomic DNA; RNA such as mRNA), polysaccharides, oligosaccharides, lipids, low molecular we~.ght molecules (e. g., hormones, ligands, information transmitting substances, ~.ow molecular weight organic molecules, etc.), and composite molecules thereof and aggregations thereof (e. g., glycolipids, glycoproteins, lipoproteins, etc.), and the like. A biological molecule may include a cell itself or a portion of tissue as long as it is intended to be introduced into a cell. typically, a biological molecule may be a nucleic acid, a protein, a lipid, a sugar, a proteolipid, a lipoprotein, a glycoprotein, a proteoglycan, or the like. Preferably, a bialQgiCa~.
molecule may include a n,ucleie acid (DNA or RNA) or a protein.
In another preferred embodiment, a biological molecule is a nucleic acid (e.g., genomic DNA or eDNA, or DNA synthesized by PCR or the ~.~.ke). In another preferred embodiment, a biological molecule may be a protein. Qreferably, such a biological molecule may be a hormone or a cytokine.
As used herein, the term "chemiGal~.y synthesized substance" or "chEmical" refers to any substance which may be synthesized by using typical chemical techniques . Such synthesis techniques are well known in the art. Those ak~.lled in the art can produce chemically 13.9 synthesized substances by combining such techniques as appropriate.
The term "cytokine" is used he=rein in the broadest sense in the art and refers to a physiologically active substance which is produced by a cell and acts on the same or a different cell. Cytokines are generally proteins or polypeptides hav~.ng a function of controlling an immune response, regulating the endoczine system, regulating the nervous system, acting against a tumor, acting against a virus, regulating cell growth, regulating ce~.~. di.ffereTitiation, or the like. Cytokines are used herein in the form of a protein or a nuc7.eic ac~.d or in othex forms. In actual practice, cytokines are typically proteins. The terms "growth factor" refers to a substance which promotes or controls cell growth. Growth factors are also called "proliferation factors" or "development factors". Growth factors may be added to cell or tissue culture medium, subst~.tuting for serum macromolecules . It has been revealed that a number of growth f actors have 3 function of controlling diffierentiation in addition to a function of promoting cell growth. Examples of cytokines representatively include, but are not limited to, intexJ.eukins, chernokines, hematopoietic factors (e. g., colony stimulating factors), tumor necrosis factor, and interferons. Representative e~tamples of growth factors include, but are not limited to, platelet-derived growth factor (PDGF), epidermal growth factor tEGF), fibroblast growth factor (FGF) , hepatocyte growth factor (IiGF) , endothelial ce~.l growth factor (VEGF), cardiotrophin, and Azoo~
the like, which have proliferative activity.
The term "hormone" is herein used in its broadest sense in the art, referring to a physiological organic compound which is produced in a particular organ ax cell of an animal or plant, and has a physiological effect on an organ apart from the site producing the compound.
Examples of such a hormone include, but are not limited to, growth hormones, sex hormones, thyroid hormones, and the like. The scope of hormones may overlap partially w~.th that of cytokines.
As used herein, the term "actin-like substance"
refers to a substance which interacts directly or indirectly with actin within cells to alter the form or state of actin.
ExampJ.es of such a substance include, but are not ~.~.mited to, extracellular matrix proteins (e. g., fibranectin, vitronectin, laminin, etc.), and the like. Such actin-like substances include substances identified by the following assays. As used herein, interaction with actin is evaluated by visualizing actin with an actin staining reagent (Molecular Probes, Texas Red-X phalloidin) or the like, followed by m~.croscopic inspection to observe and determine actin aggregation, actin reoanstruction or an improvement ~5 in cellular outgrowth xate. Such evaluation stay be performed quantitatively or qualitatively. Actin-like substances are herein utilized so as to increase transfectian efficiency. An actin-like substance used herein is der~.ved from any organism, including, for example, mammals, such as human, mouse, bovine, and the like.
As used hez~ein, the terms "cell adhesion agent", "cell adhesion molecule", "adhesion agent" and "adhesion molecule" are used interchangeablx to refer to a molecule capable of mediating the joining of two or more cells (cell adhesion) or adhesion between a substrate and a cell. In general, cell adhesion molecules are divided into two groups: molecules involved in cell-cell adhesion (~.ntercellular adhesion) (cell-cell adhesion molecules) x0 and molecules involved in cell-extracellular matrix adhesion (cell-substrate adhesion) (cell-substrate adhesion mplecules) . For a method of the present invention, either type of molecule is useful and can be effectively used. Therefore, cell adhesion molecules herein include a substrate protein and a cellular protein (e. g., integrin, etc.) involved in cell-substrate adhesion. A maleCUle other than a protein can fall. within the concept of a cell adhesion molecule as lung as it can mediate cell adhesion.
Fox cell-cell adhesion, cadherin, a number of molecules belonging in an immunot~lobu~.in superfamily (NCAM, L1, ICAM, fasciclin II, III, etc. ) , selectin, and the J.ike are knawn, each of which is knQwTa to connect cell membranes via e~ specific molecular reaction.
~n the other hand, a major cell adhesion molecule functioning for cell-substrate adhesion is integrin, which recognizes and binds to various proteins contained in extracellular matrices. These cell adhesi.an molecules are all located on cell membranes arid can be regarded as a type cf xeceptor (cell adhesion receptor).
Therefore, receptors present on cell. membranes can also be used in a method of the present invention. Examples of such a receptor include, but are not limited to, ac-integrin, ~-integrin, CD44, syndecan, aggrecan, and the like.
Techniques for cell adhesion are well known as described above and as described in, for example, "Saibogaimatorikkusu -Rinsho keno Oyo- CExtracellular matrix -Clinical Applications-], Medical. Review.
It can be determined whether or not a certain molecule is a cell adhesion molecule, by an assay, such as biochemical quantification (an SDS-PAGE method, a labeled-collagen method, etc.), immunologiCal quantification (an enzyme antibody method, a fluorescent antibody method, an immunohistologieal study, etc.), a PDR
method, a hybridization method, or the like, in which a positive reaction is detected. Examples of such a cell adhesion molecule include, but are not limited to, collagen, integrin, fibronectin, laminin, vitronectin, fibrinogen, immunoglobulin superfamily members (e. g., CD2, CD4, CD8, ICMI, ICAM2, VCAM1) , selectin, cadherin, and the like. Most of these cell adhesion molecules transmit an auxiliary signal for cell activation into a cell due to intercellular interaction as well as cell adhesion. It can be determined Whether or not such an auxiliary signal can be transmitted into a. cell, by an assay, such as biochemical quantification (an SDS-PAGE method, a labeled-collagen me'~hod, etc.), immunological quantification (an enzyme azrtibody method, a fluorescent antibody method, an ~.mmunohistological study, Azoo~
etc.), a PDR method, a hybridization method, yr the like, in which a positive reaction is detected.
Examples of cell adhesion molecules include, but are not limited to, immunoglobulin superfamily molecules (LFA-3, ICAM-1, CD2, CD4, CDB, ICMl, ICAM2, VCAMl, etc.); integrin family molecules (LFA-1, Mac-1, gpIIbIIIa, p150, p95, VLAI, VLA2, VLA3, VLA4, VLA5, VLA6, etc.);
selectin family molecules (L-seleetin, E-selectin, P-selectin, etc.), and the like.
As used hexe~.zx, the term "extrace~.lu~.ax matrix protein" refers to a protein constituting an "extracellular matrix". As used herein, the term "extracellular matrix"
(ECM) is also called "extracellular substrate" and has the same meaning as commonly used in the art, and refers to a substance existing between somatic cells no matter whether the cells are epithelial cells or non-epithelia.J. ceJ.J.s .
Extracellular matrices are involved in suppoxt~.ng tissue as well as in internal environmental structures essential for survival of all somatic cells . Extracellular matrices are generally produced from connective tissue cells. Some extraeellular matrices are secreted from cells possessing basal membrane, such as epithelial cells or endothelial 2S cells. Extracellular matrices are roughly divided into fibrous components and matrices filling there between.
Fibrous components include collagen f~.bexs and eXastin fibers. A basic component of matrices is glycosaminoglycan (acidic mucopolysaccharide), most of which is bound to non-collagenous protein to form a polymer of a proteoglycan AI ~ 0'7 (acidic mucapolysaccharide-pxotein complex}. In addition, matrices include glycoproteins, such as laminin of basal membrane, microfibrils around elastin fibers, fibers, fibronectins on cell surfaces, and the like. Specifically differentiated tissue hoe the same basic structure. For example, in hyaline cartilage, chondroblasts characteristically produce a large amount of cartilage matrices including proteoglycans. In bones, osteoblasts produce bone matrices which cause calcification. Examples of extracel~.ular matrices for use in the present invention include, but are not limited to, collagen, elastin, proteaglycan, glycosaminaglycan, fibronectin, laminin, elastic fiber, collagen fiber, and the like.
As used herein, the term "receptor" refers to a molecule which is present on cells, within nuclei, or the like, and is capable of binding to an extracellular ox intracellular agent where the binding mediates signal txansduction. Receptors are typically in the form of pxoteins. The binding partner of a receptor is usually ~ceferred to as a ligand.
As u$ed herein, the term "agonist" refers to an agent which binds to the receptor of a certain biologica~.ly acting substance (e.g., ligand, etc.), and has the same or similar function as the function of the substance.
As used herein, the term "antagonist" refers to a factor which competitively binds to the receptor of a certain biologically acting substance (ligand}, and does not produce a physiological action via the receptor.
Antagonists include antagonist drugs, blockers, inhibitors, and the like.
(Devices and solid phase supports) As used herein, the term "device" refers to a part which can constitute the whole or a, portion of an appaxatu9, and comprises a support (Preferably, a solid phase support) and a taxget substance oarr~.ed thereon.
Examples of such a device include, but are not limited to, chips, arrays, microtiter plates, cell culture plates, Petri dishes, films, beads, and the like.
As used herein, the team "support" refers to a I5 material which can fix a substance, such as a biological molecule. Such a support znay be made from a.ny fixing material which has a capability of binding to a biological molecule as used herein via covalent or noncovalent bonds, or which may be induced to have such r~ capability.
examples of materials used for supports include any material capable of forming a solid surface, such as, without limitation, glass, silica, silicon, ceramics, silicon dioxide, plast~.cs, metals (including alloys), naturally-occurring and synthetic polymers (e. g., polystyrene, cellulose, chitosan, dextran, and nylon), and the like _ A support may be formed of layers made of a plurality of materials . Foz~ example, a support may be made of an inorganic insulating material, such as glass, quartz glass, alumina, sapphire, forsterite, silicon oxide, silicon carbide, silicon nitride, or the like. A support may be made of an organic material, such as polyethylene, ethylene, polypropylene, palyisobutylene, polyethylene terephthalate, unsaturated polyester, fluorine-containing resin, polyvinyl chloride, polyvinylidene chloride, palyvi.nyl acetate, polyvinyl alcohol, polyvinyl acetal, acrylic resin, polyacrylanitrile, polystyrene, acetal resin, polycarbonate, polyamide, phenol resin, urea resin, epoxy resin, melamine resin, styrene--acrylonitrile copolymer, acrylonitrile-butadiene-styrene copolymer, silicone resin, polyphenylene oxide, polysulfone, and the like. Also in the present inventzvn, nitrocellulose film, nylon film, PVDF film, or the like, which are used in blotting, may be used as a material for a support. When a material Z5 constituting a support is in the solid phase, such as a support is herein particularly referred to as a "solid phase support" . A solid phase support may be herein in the form of a plate, a microwell plate, a ch~.p, a glass slide, a film, beads, a mefial (surface), or the like. A support may be 24 uncoated or may be coated.
As used herein, the term "liquid phase" has the same meanings as are commonly understood by those skilled in the: art, typically referring to a state in solution.
As used herein, the term "solid phase" has the same meanings as are commonly understood by those skilled in the art, typically referring to a solid state . As used herein, liquid and solid may be collectively referred to as a "fluid".
As used herein, the term "substrate" refers to a material (preferably, so~.~.d) whioh is used to construct a chip ar array according to the present invention.
Therefore, substrates are inoluded in the concept of plates .
Such a substrate may be made from any solid material which h~.s a capability of binding to a biological molecule as used herein via covalent or noncovalent bonds, or which may be induced to have such a capability.
Examples of materials used far plates and substrates include ariy material capable of forming a solid surface, such as, without limitation, glass, silica, silicon, cerama.cs, silicon di.ox~.de, plastics, metals (including alloys), naturally-occurring and synthetic polymers (e. g., polystyrene, cellulose, chitosan, dextran, and nylon) , and the like. A support may be formed of layers made of a plurality of materials. Far example, a support may be made of an inorganic insulating material, such as glass, quarts glass, alumina, sapphire, forsterite, silicon oxide, silicon carbide, silicon nitride, or the like. A
support may be made of an organic material, such as polyethylene, ethylene, polypropylene, polyisobutylene, polyethylene terephthalate, unsaturated polyester, fluorine-containing resin, polyvinyl ahlaride, polyvinylidene chloride, polyvinyl acetate, polyvinyl alcohol, polyvinyl acetal, acrylic resin, polyacrylonitrile, polystyrene, acetal resin, polycarbonate, polyamide, phenol resin, urea resin, epoxy resin, melamine resin, styrene-acrylonitrile copolymer, acrylonitrile-butadiene-styrene copolymer, silicone resin, polyphenylen~: oxide, polysulfone, and the like. A material preferable as a substrate varies depending on various parameters such as a measuring device, and can be selected from the above-described various materials as appropriate riy those skilled in the art . For transfection arrays, glass slides are preferable. Preferably, such a substrate may be coated with a substance or have a coating.
1O As used herein, the term "coating" in relation to a solid phase support or substrate refers to an act of forming a film of a material on a surface of the solid phase support or substrate, and also refers to a film itself.
Coating is performed for variaus purposes, such as, for example, improvement in the quality of a solid phase support and substrate (e. g., elongation of life span., improvement in resistance to hostile environment, such as resistance to acids, etc. ) , an improvement in affinity to a substance integrated with a solid phase support or substrate, and the like. Various materials may be used for such coating, including, without limitation, biological substances (e. g., DNA, RNA, protein, lipid, etc.), polymers (e. g., poly-Z-xysine, MAS (avai~.able from Matsunami Glass, Kish.iwada, Japan) , and hydrophobic fluorine resin) , silane (APS (e. g. , 'y-aminopropyl silane, etc. ) ) , metals (e. g. , gold, etc.), in addition to the above-described solid phase support and substrate. The selection of such materials is within the technical scope of those skilled in the art and thus can be performed using techniques well known in the art. Tn one preferred embodiment, such a coating may be advantageously made of poly-L-lysine, silane (e. g., epoxy silane or mercaptosilane, APS (y-aminopropyl silane) , etc. ) , MAS, hydrophobic fluorine resin, a metal (e. g. , gold, etc. ) .
Such a material may be preferably a substance suitable for cells or objects containing cells (e. g. , organisms, organs, etc. ) .
As used herein, the terms "chip" or "microchip"
are used interchangeably to refer to a micro-integrated circuit which has versatile functions and constitutes a portion of a system. Examples of a chip include, but are not limitEd to, DNA ch~.ps, protein chips, and the like.
As used herein, the term "array" refers to substrate (e.g., a chip, etc.) which has a pattexn of a composition containing at least one (e. g., 1000 or more, etc.) taxget substance (e. g., DNA, proteins, transfection mixtures, etc.), which are arrayed. Among arrays, patterned substrates having a small size (e.g., 10x10 mm, etc.) are particularly ~eeferred to as m~.croarrays. The teams "microarray" and "array" are used interchangeably.
Therefore, a patterned substrate having a larger size than that which is described above may be referred to as a microarray. For example, an array comprises a set of desired transfection mixtuxes fixed to a solid phase surface or a film thereof . An arxay preferably comprises at least 102 antibodies of the same or different types, more preferably at least 7.03, even more preferably at least 10°, and still even more preferably at least 105. These antibodi~:s aze placed on a surface of up to 125x80 m~, more preferably 10x10 mm. An array includes, but is not limited to, a 9~--well microtiter plate, a 384-well microtiter plate, a microtiter plate the size of a glass slide, and the like.
A composition to be fixed may contain one or a plurality of types of target substances. Such a number of target substance types may be in the range of from one to the number of spots, including, without limitation, about 10, about 100, about 500, and about 1,000.
As described above, any number of target substances (e.g., proteins, such as antibodies) may be provided on a solid phase surface or film, typically including no more than 108 biological molecules per substrate; in another embodiment no more than 10' biological molecules, no more than 106 biological molecules, no more than 105 biological molecules, no more than 10' biological molecules, no mare than 103 biological molecules, or no more than lOZ biological molecules. A composition containing more than 108 biological molecule target substances may be provided on a substrate. In these cases, the size of a substrate is preferably small. Particularly, the size of a spot of a composition containing target substances (e.g., proteins such as antibodiesy may be as small as the size of a s~.ng7.e bza~.og~.oal molecule (e. g. , 1. to 2 nm order) .
Zn some cases, the minimum area of a substrate may be determined based on the number of biological molecules on a substrate. A composition containing target substances, which are intended to be introduced into cells, are herein typically arrayed on and fixed via covalent bonds or physical interaction to a substrate in the form of spots having a size of 0.01 mm to 10 mm.
"Spots" of biological molecules may be provided on an array. As used herein, the term "spot" refers to a certain set of compositions containing target substances.
As used herein, the term "spotting" refers to an act of preparing a spot of a composition containing a certain target substance on a substrate or plate. Spotting may be performed by any method, for example, pipetting or the like, or alternatively, by using an automatic device. These methods are well known in the art.
As used hexein, the term "address" refers to a unique position on a substrate, which may be distinguished from other unique positions. Addresses are appropriately associated with spots. Addresses can have any distinguishable shape such that substances at each address may be distinguished from substances at other addresses (e . g. , optically) . A shape defining an address may be, for example, without limitatipn, a circle, an ellipse, a square, a rectangle, or an irregular shape. Therefore, the term "address" is used to indicate an abstract concept, while the term "spot" is used to indicate a specific concept.
Unless it is necessary to distinguish them from each other, the terms "address" and "spot" may be herein used interchangeably.
The size of each address particularly depends on the size of the substrate, the number of addresses on the substrate, the amount of a composition containing target substances and/ox a~railable reagents, the size of microparticles, and the level of resolution required for any method used for the array. The size of each address ~Ct~ty be, for example, in the range of from 1-2 nm to several centimeters, though the address may have any size suited to an array.
The spatial arrangement and shape which define an address axe designed so that the micraarray ~.s suited to a particular application. Addresses may be densely arranged or sQar~sely distributed, or subgrouped into a desired pattern appropriate for a particular type of material to be analyzed.
Microarrays are widely reviewed in, for example, "Genomu Kino Kenkyu Purotokoru [Genomic Function Research Protocol] tJikken Igaku Bessatsu [Special. Issue of Experimental Medicine] , Posuto Genomu J'idai no Jikken Koza 1 [Lecture 1 oz~ ExQerimentation in Post-genome Era) , "Genomu Ikagaku to koxekarano Genomu Iryo [Genome Medical Science and Futuristic Genome Therapy (,Tikken Igaku Zokan [Special Tssue of Experimental Medicine]), and the like.
A vast amount of data can be obtained from a microarray. Therefore, data analysis software is important for facilitating correspondence between clones and spots, data analysis, and the like. Such software may be attached to various detection systems (e. g., Ermolaeva G. et al., (1998) I~at. Genet., 20: 19-23). The format of such a database includes, for example, GATC (genetio analysis technology Consortium) proposed by Affymetrix.
M~.cromachining for arrays is described in, for example, Campbell, S.A. (1996), "The Science and Engineering of Microelectronic Fabrication", Oxford University Press; taut, P.V. (1996), "Micromicroarray Fabrication: a Practical Guide to Semiconductor Processing", Semiconductor Services; Madou, M.J. (7.997), "Fundamentals of Microfabrication", CRC1 5 Press; Rai--Choudhury, P.
(1997), "Handbook of Microlithography, Micxomachining, &
Microfabrication: Microlithography": a.n;d the like, portions related thereto of which are herein incorporated by reference.
~.5 ( Detection) In cell analysis or determination in the present invention, various detection methods and means Can, be used as gong as they can be used to detect information attributed to a cell or a substance interacting therewith. Examples of such detection methods and means a,ncJ.ude, but are not limited to, visual inspection, optical microscopes, confocal microscopes, reading devices using a laser light source, surface plasmon resonance (SPR) imaging, electric signals, chemical ox biochemical markers, which may be used singly or i.n combination. Examples of such a detecting device ~.nclude, but are not limited to, fluorescence analyzing devices, spectrophotometers, scintillation counters, CCD, luminometers, and the like. Any means capable of detecting a biological molecule may be used.
13~
As used herein, the term "marker" refers to a biological agent for indicating a level or frequency of a substance or state of interest. Examples of such a marker include, but are.not limited to, nucleic acids encoding a gene, gene products, metabolic products, receptors, ligands, antibodies, and the like.
Therefore, es used herein, the term "marker" in relation to a state of a cell refers to an agent (e. g., ligands, antibodies, complementary nucleic acids, etc.) interacting with intracellular factorsindicating the state of the cell (e. g., nucleic acids encoding a gene, gene products (e. g., mRNA, proteins, posttxarzscriptionally modified proteins, etc.), metabolic products, receptors, ~.5 etc. ) in addition to transcription control factors. In the present invention, such a marker may be used to produce a time-lapse profile which is in turn analyzed. Such a marker may preferably interact with a factor of interest . As used herein, the term "specificity" in relation to a marker refers to a property of the marker which interacts with a molecule of interest to a significantly higher extent than with similar molecules. Such a marker is herein preferably present within cells or may be present outside cells.
As used here~.n, the term "label" refers to a factor which distinguishes a molecule or substance of interest from others (e. g., substances, energy, electromagnetic waves, etc. ) . Examples of ~.abeling methods include, but are no't limited to, RI (radioisotope) methods, fluorescence methods, biotinylation methods, Aroa~
chemoluminance methods, and the like. When the above-described nucJ.eic acid fragments and complementary oligonucleatides ale labeled by fluorescence methods, fluorescent substances having different fluorescence emission maximum wavelengths are used for labeling. The difference between each fluorescence emission maximum wavelength may be preferably 10 nm or more. Any fluorescent substance which can bind to a base portion of a nucleic acid may be used, preferably including a cyanine dye (e.g., Cy3 1Q and Cy5 in the Cy Dye'r°~ series, etc. ) , a rhodamine 6G reagent, N-acetoxy-N2-acetyl amino fluorine (AAF), AAIF (iodine dexivati~cre of AAF) , and the like. Examples ~ of fluorescent substaz~aes having a difference in fluorescence emiss.ian maximum wavelength of 10 nm c~x more include a combination 7.5 of Cy5 and a rhodamine 6G reagent, a combination of Cy3 and fluorescein, a combination of a rhodamin,e ~G reagent and fluorescein, and the like. Zn the present invention, such a label can be used to alter a sample of interest so that the sample can be detected by detecting means. Such 20 alteration i.s known in the art. Those skilled in the art can perform such alteration using a method appropriate for c~ label and a sample of interest.
As used herein, the term "i.nteraction" refers 25 to, without limitation, hydrophobic interactions, hydrophilic interactions, hydrogen bonds, 'fan der Waals forces, ionic interactions, nonionic interaotioz~s, electrostatic interactions, and the like.
30 As used herein, the term "interaction level" in Ax007 relation to interaction between two substances (e. g., cells, etc.) refers to the extent or frequency of interaction between the two substances. Such an interaction level can be measured by methods well known in the art . For example, the number of cells which are fixed and actually perform an interaction is counted directly or indirectly (e.g., the intensity of reflected light), for example, without limitation, by using an optical microscope, a fluorer>cenee microscope, a phase-contrs.st microscope, or the ~.ike, or alternatively by staining celJ.s w~.th a markex, an antibody, a fluorescent label ox' the like specific thereto and measuring the intensity thereof. Such a level can be displayed directly from a marker or indirectly via a label.
eased on the measured value of such a level, the number or frequency of genes, which are actually transcribed or expressed in a certain spot, can be calculated.
(Presentation and display) As used herein, the terms "display" and "presentation" are used interchangeably to refer to an act of providing a profile obtained by a method of the present invention, or information derived therefrom, directly or indirectly, or in an information-processed form. Examples of such displayed forms include, but are not limited to, various methods, such as graphs, photographs, tables, animations, and the like. Such techniques are described in, for example, METHOD5 IN CELL BIOLOGY, VOL. 56, ed. 1998, pp:185-215, ~lHigh-Resolution Multimode Digital Microscope System (Sluder & Wolf, Salmon) , which discusses application software far automating a microscope and controlling a camera and the design of a hardware device comprising an automated optical microscope, a camera, and a Z-axis focusing device, which can be used herein. Image acquisition by a camera is described in detail in, for example, Inoue and Spring, Video Microscopy, 2d. Edition, 1997, which is herein incorporated by reference.
Real time display can also be performed using techniques well known in the art. ~'or example, after a7.~.
images are obtained and stored~in a semi-permanent memory, or substantially at the same t~.me as when an image ~.s obtained, the image can be processed with appropriate application software to obtain processed data. For example, data may be processed by a method for playing back a sequence of images without interruption, a method for displaying images in real time, or a method for displaying images as a "movie" showing irradiating lzght as changes or continuation on a focal plane.
Tn another embodiment, application software for measurement and presentation typically includes software for setting conditions for applying stimuli or condit~.oris for recording detected signals . With such a measurement and presentation application, a computer can have a means for applying a stimulus to cell$ and a means for processing signals detected from cells, and in addition, can Control an optically observing means (a STT camera and an image filing device) and/or a cell culturing means.
Hy inputting conditions for stimulation on a Azoo~
parameter setting screen using a keyboard, a touch panel, a mouse, or the J.zke, ifi is possible to set the desired complex conditions for stimulation. In addition, various conditions, such as a temperature for cell culture, pH, and the like, can be set using a keyboard, a mouse, or the like.
A display screen displays a time-lapse profile detected from a ceJ.l or information derived therefrom in real time or after,recording. In addition, another recorded profile or information derived therefrom of a ce~.~. can be displayed while being superimposed with a microscopic image of the cell. In addition to recorded information, measurement parameters in xecording (stimulation conditions, recording cøndit~.ons, display conditions, process conditi.ans, various conditions for cep s, temperature, pH, etc.) can be displayed in real t~.me. The present invention may be equipped with a function of issuing an alarm when a temperature or pH departs from the tolerable range.
On a data analysis screen, it is possible to set conditions for various mathematical analyses, such as Fourier transformation, cluster analysis, FFT analysis, coherence analysis, correlation analysis, and the like.
The pxesent invention may be equipped w~.th a function of temporarily displaying a profile, a function of displaying typography, or the like. The results of these analyses can be displayed while being superimposed with microscopic images stored in a recording medium.
(Gene introduction) Any technique may be used here~.n fox introduction of a nucleic acid molecule into cells, including, for example, transformation, transduction, transfection, and the like. In the present invention, transfection is preferable.
As used herein, the term "transfection" refers to an act of performing gene introduction or transfection by culturing Cells with genomic DNA, plr~smid DNA, vir2~1 DNA, vixal FtNA or the like in a substantially naked farm (excluding viral particles), ox adding such a genetic material into cell suspension to allow the cells to take in the genetic material . A 'gene introduced by transfection is typically expressed within cells in a temporary manner or may be incorporated into cells in a permanent manner.
Such a nucleic acid molecule introduction technique is well known in the art and com~tonly used, and is described in, for example, Ausubel F.A. et al., editors, (1988), Current Protocols in Molecular Eiology, Wiley, New York, NY; 5ambrook J. et al. (1987) Molecular Cloning: A
Laboratory Manual, 2nd Ed. and its 3rd Ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY; Special issue, Jikken Igaku jExperimentaX Medicine] "Experimental Methods for Gene introduction & Expreas~.on Analysis", Yodo-sha, 1997; and the like. Gene introduction can be confirmed by method as described herein, such as Northern blotting analysis and Western blotting analysis, or other weJ.l~-known, cammc~n or routine techniques .
~. 4 0 When a gene is mentioned herein, the term "vector" or "recombinant vector" refers to ~. vector transferring a polynucleotide sequence of interest to a target cell. Such a vector is capable of self-replication or incorporation into a chromosome in a host cell (e. g., a prokaryotic cell., yeast, an animal cell, a plant cell, an insect cell, an individual animal, and an individual plant, etc.), and contains a promoter at a site suitable for transcription of a polynucleotide of the present ~.nv~nt~.on.
A vector suitable for performing cloning is referred to as a "cloning vector". Such a cloning vector ordinarily contains a multiple cloning site containing a plurality of restxlct~.on sites. Restriction enzyme sites and multiple 7~5 cloning sites as described above are well known in the art and can be used as appropriate by those skilled in the art depending on the purpose in accordance with publications described herein (e. g., Sambrook et al., supra).
As used hexeiz~, the term "expression vector"
refers to a nuczeic acid sequence comprising a structural gene and a promoter for regulating expression thereof, and in addition, various regulatory elements in a state that aJ.~.ows them to operate within host cells. The regulatory element may include, preferably, terminators, selectable markers such as drug-resistance genes, and enhancers.
Examples of "recombinant vectors" for prokaryotic cells include, but are not limited to, pcDNA3 (+) , pEluescript-SK (+/-) , pGEM-T, pEF-BOS, pEGFP , pHAT, pUCl8, A~ao7 pFT-DEST~42GATEWAY (Tnvitrogen), and the like.
Examples of "recombinant vectors" for animal cells include, but are not limited to, pcDNAT/Amp, pcDNAI, pCDMB (all commercially available from Funakoshi ) , pAGE107 [Japanese paid-Open Publication No. 3-229 (Invitrogen), pAGE103 [J. Biochem. , 101, 1307 (1987 ) ] , pAMo, pAMoA [J. Biol.
Chem., 268, 22782-22787(1993)], a retrovirus expression vector based on a murine stem cell virus (MSCV), pEF-BOS, pEGFP, and the like.
Examples of recombinant vectors for plant cells include, but are not ~.imited to, pPCVZCEn4HPT, pCGN1S48, pCGNl549, pBI221, p8I121, and the like.
Any of the above-described methods ~or introducing DNA into cells can be used as a vector introduction method, including, for example, txansfection, transduction, transformation, and the like (e. g., a calcium phosphate method; a liposome method, a DEAF dextran method, an electroporation method, a particle gun (gene gun) method, and the like), a lipofection method, a spheroplast method (Pros. Natl. Acad. Sci. USA, $4, 1929(1978)), a lithium acetate method (J. Bactexiol., 153, 163(1983); and Proc.
Natl. Acad. Sci. USA, 75, 1929(1978)), and the like.
As used herein, the term "operably linked"
indicates that, a desired sequence is located such that expression (operation). thereof is under contxol of a transexiption and translation regulatory sequence (e. g., a promoter, an enhancer, and the like) or a translation regulatory sequence . In order for a pxomoter to be operably linked to a gene, typically, the promoter is located immediately upstream of the gene. A promoter is not necessarily adjacent to a structural gene.
As 'used herein, the term "gene introduction reagent" refers to a reagent which is used in a gene introduction method so as to enhance introduction efficiency. Examples of such a gene introduction reagent include, but are not limited to, cationic polymers, cationic lipids, polyamine-based reagents, pvlyimine-based reagents, calcium phosphate, and the like. Specific examples of a reagent used in transfection include reagents available from various sources, such as, without limitation, Effectene Transfection Reagent (cat. no. 301.425, Qiagen, CA) , TransFast~ Transfection Reagent (E2431, Promega, WI) , Tfx~-20 Reagent (E2391, Promega, WI), SuperFeGt Transfeetion Reagent (301305, Qiagen, CA), PolyFect Transfection Reagent (301105, Qiagen, CA), LipofectAMINE
X000 Reagent (11668-019, Tnvitrogen corporation, CA), JetPEZ (x4) cone. (101-30, Polyplus-transfection, France) and ExGen 500 (R0511, Fermentas Inc., MD), and the like.
Gene expression (e. g., mRNA expression, pvlypeptide expression) may be "detected" or "quantified"
by an apprdpr~.ate method, including mRt~A measurement and immunological measurement methods. Examples of molecular biological measurement methods include Northern blotting methods, dot blotting methods, PCR methods, and the like.
Azaa~
Examples of immunological measurement methods include EZISA
methods, RIA methods, fluorescent antibody methods, fnTestern blotting methods, immunohistologieal staining methods, and the like, where a microtiter plate may be used. Examples of quantification methods include ELISA methods, RIA
methods, and the like. A gene analysis method using an array (e. g. , a DNA array, a protein array, etc. ) may be used. The DNA array is widely reviewed in Saibo-Kogaku [Cell Engineering] , special issur~, "DNA Microarray arid Up-to-date PCR Method", edited by Shujun-sha. The protein array is described in detail in Nat Genet. 2002 Dec; 32 Suppl:526-32.
Examples of methods for analyzing gene expression include, but are not limited to, RT-PCR methods, RACE methods, SSC~
methods, immunopreeipitation methods, two-hybrid systems, in vitro translation methods, and the like, in addition to the above-described techniques. Other analysis methods are described iri, for example, "Genome Analysis Experimental Method, Yusuke Nakamura's Lab-Manual, edited by Yusuke Nakamura, Yodosha (2x02), and the like. All of the above-described publications are herein incorporated by reference.
As used herein, the term "expression level"
refers to the amount of a polypeptide or mRNA expressed in a sub~eot cell. The term "expression level" includes the level of protein expression of a polypeptide evaluated by cony appropriate method using an antibody, including immunological measurement methods (e. g., an ELISA method, an RIA method, a fluorescent antibody method, a Western blotting method, an immunohistological staining method, and Aioa~
the life, or the mRNA level of expression of a polypeptide evaluated by any appropriate method, includ~.ng molecular biological measurement methods (e. g., a Northern blotting method, a dot blotting method, a PCR method, and the like) .
The term "change in expression level" indicates that an increase or decrease in the protein or mRNA level of expression of a polypeptide evaluated by an appropriate method including the above-described immunological measurement methods or molecular biological measurement methods.
(Screening) As used herein, the term "screening" refers to selection of a target, such as an organism, a subatanGe, or the like, a given specific property of ~.nterest from a population containing a number of elements using a specific operation/evaluation method. For screening, an agent (e. g., an antibody), a polypeptxde or a nucleic acid molecule of the present invention can be used.
As used herein, screening by utilizing an immunological reaction is also referred to as "immunophenotypirig". ~ri th~.s case, azx antibody or a single chain antibody may be used for inununophenotyping a cell line and a biological sample. A transcription or translation product of a gene may be useful as a cell specific marker, or more partieu~.ar~.y, a cell marker which is distinctively expressed in various stages in differentiation and/or maturation of a specific cell type. A monoc~.onal antibody directed to a specific epitope, or a combination of epitopes Azoo7 allows for screening of a yell population expressing a marker.
Various techniques employ monoclonal antibodies to screen for a cell population expressing a marker. Examples of such techniques include, but axe not limited to, magnetic separat~.on using magnetic beads coated with antibodies, "panning" using antibodies attached to a solid matrix ( i . a . , a plate}, flow cytometry, and the like (e. g., OS Patent No. 5, 985, 660; and Morrison et al., Cell, 96: 737-99 (1999) ) .
These techniques may be used to screen cell populations containing undifferentiated cells, which can grow and/or differentiate as seen in human umbilical cord blood or which are treated and modified into an undifferentiated state (e. g., embryonic stem cells, tissue stem cells, etc.).
(Diagnosis}
As used herein, the team "diagnosis" refers to an act of identifying various parameters assoc~.ated with a disease, a disorder, a condition, or the like of a subject and determin~.ng a current state of the disease, the disorder, the cond~.tion, or the like. A method, device, or system of the present invention can be used to analyze a sugar chain structure, a drug resistance level, or the like. Such information can be used to seleot parameters, such as a disease, a disorder, a condit~.on, and a prescription or method for treatment or preventative method fox a subject.
A diagnosis method of the present ~.nvention can use, in principle, a sample which is derived from the body ~rao~
of a subject. Therefore, it is possible for some one which is not a medical practitioner, such as a medical doctor, to deal with such a sample. The present invention is industrially useful.
S
(Therapy) As used herein, the term "therapy" refers to an act of preventing progression of a disease or a disorder, preferably ma~.ntaining the current state of a disease oz a disorder, more preferably alleviating a disease or a disorder, and more preferably e~ct~.nguishing a disease or a disorder.
As used herein, the term "sub j ect" refexs to an organism which is subj ected to the treatment of the present invention. A subject is also referred to as a "patient".
A patient or subject may preferably be a human.
As used herein, the term "cause" or "pathogen"
2d in relation to a disease, a disorder or a condition of a subject refers to an agent associated with the disease, the disorder or the condition (also collective~.y referred to as a "lesion", or "disease damage" in plants), including, without limitation, a causative or pathogenic substance (pathogenic agent), a disease agent, a disease cell, a pathogenic vixus, and the like.
A disease targeted by the present invention may be any disease associated with a pathogenic gene. Examples of such a disease include, but are not limited to, cancer, Azoo~
infectious diseases due to viruses or bacteria, allergy, hypertension, hyperlipemia, diabetes, cardiac diseases, cerebral infarction, dementia, obesity, arteriosclerosis, infertility, mental and nervous diseases, cataract, progeria, hypersensitivity to ultraviolet radiation, and the like.
A disordex targeted by the present invention may be any disorder associated with a pathogenic gene.
Examples of such a disease, disorder or condition include, but are not lim~.ted to, circulatory diseases (anemia (e. g., aplastic anemia (particularly, severe apxastic anemia), renal. anemia, cancerous anemia, secondary anemia, refractory anemia, etc.), cancer or tumors (e. g., leukemia, multiple mye~.oma), etc.);
neurological diseases (dementia, cerebral stroke and sequela thereof, cerebral tumor, spinal injury, etc.);
immunological diseases (T-cell deficiency syndrome, leukemia, etc.); motor organ and the skeletal system diseases (fracture, osteoporosis, luxation of joints, subluxation, sprain, ~.igament injury, osteaarthritis, osteosarcoma, Ewing's sarcoma, osteogenesis imperfecta, osteochondradysplasia, etc.); derznatologic diseases (atrichis,, melanoma, curia malignant lympoma, hemangiosarcoma, histiocytosis, hydroa, pustulosis, dermatitis, eczema, etc.); endocrinologic diseases (hypothalamus/hypophysis diseases, thyroid gland dzseases, accessory thyroid gland (parathyroid) diseases, adrenal cortex/medulla diseases, saccharometabolism abnormality, ~. 4 B
lipid metabolism abnormality, protein metabolism abnormality, nucleic acid metabolism abnormality, inherent metabolic disorders (phenylketonurea, galactosemia, homoeystinuria, maple syrup urine disease), analbuminemia, Jack of ascorbic acid synthetic ability, hyperbilirubinemea, hyperbilirubinuxea, kallikrein defic~.ency, mast cell deficiency, d~.abetes insipidus, vasopressin secretion abnormality, dwarfism, Wolman's disease (acid lipase deficiency, mucopolysaccharidosis VT, etc.); respiratory diseases (pulmonary diseases (e. g., pneumonia, lung cancer, etc.), bronchial diseases, lung cancer, bronchial cancer, etc.); alimentary diseases (esophageal diseases (e. g., esophageal cancer, etc.), stomach/duodenum diseases (e. g., stomach cancer, duodenum cancer, etc.), small intestine 16 diseases/large intestine diseases (e.g., polyps of the colon, colon cancer, rectal cancer, etc.), bile duct diseases, liver diseases (e. g., liver cirrhosis, hepatitis (A, B, C, D, E, etc. ) , fulmiriant hepatitis, chronic hepatitis, primary lever cancer, alcoholic liver disorders, drug induced liver disorders, etc.), pancreatic diseases (acute pancreatetis, chronic pancreatitis, pancreas cancer, cystic pancreas diseases, etc.), peritoneum/abdominal wall/diaphragm diseases (hernia, etc.), Hirschsprung's disease, etc.); urinary diseases (kidney diseases (e. g., renal failure, primary glomerulus diseases, renovascular disorders, tubular function abnormality, interstitial kidney diseases, kidney disorders due to systemic diseases, kidney cancer, etc.), bladder diseases (e. g., cystitis, bladder cancer, etc. ) ; genital diseases (male genital. organ diseases (e. g., male sterility, pxostatomegaly, prostate Azoo~
Cancer, testicular cancer, etc.), female genital organ diseases (e. g., female sterility, ovaxy function disorders, hysteromyama, adenomyosis uteri, uterine cancer, endometriosis, ovarian cancer, villosity diseases, etc.), etc); aixculatory diseases (heart failure, angina pectoris, myocardial infarct, arrhythmia, valvulitis, cardiac musc~.e/pericardium diseases, congenital heart diseases (e. g., atrial aeptal defect, arteria3. canal patency, tetralogy of Fallot, etc.), artery diseases (e. g., arteriosclerosis, aneurysm), vein diseases (e. g., phlebeurysm, etc.), lymphoduct diseases (e. g., lymphedema, etc.), etc.): and the like.
As used herein, the term "cancer" refers to a malignant tumor which has a high level of atypism, grows faster than normal cells, tends to disruptively invade surrounding tissue or metastasize to new body sites or a condition characterized by the presence of such a malignant tumor. In the present invention, Cancer includes, without limitation, solid cancer and hematological cancer.
As used herein, the term "solid cancer" refers to a cancer having a solid shape in contrast to hematological cancer, such as leukemia and the like. Examples of such a solid cancer include, but are not limited to, breast cancer, liver cancer, stomach cancer, lung cancer, head and neck cancer, uterocervical cancer, prostate cancer, retinoblastama, malignant lymphoma, esophagus cancer, brain tumor, asteoncus, and the like.
~. 5 0 As used herein, the term "cancer therapy"
encompasses administration of an anticancer agent (e. g., a chemotherapeutic agent, radiation therapy, etc.) or surgical therapy, such as surgical excision and the l~.ke.
Chemotherapeutic agents used herein are well known in the art and are described in, for example, Shigeru Tsukagoshi et al. editors, "Kogan zai Manuaru [Manual of Anticancer agents)", 2nd ed., ChugaiIgaku sha;
ZO Pharmacology; and Lippincott Tnlilliams & Wil.kins, Tnc.
Examples of such chemotherapeuti.c agents are described below: 1) alkylating agents which alkylate cell components, such as DNA, protein, and the like, to produce cytotoxicity (e. g., cyclophosphamide, busulfan, thiotepa, dacarbazine, etc.); 2) antimetabolites which main~.y inhibit synthesis of nucleic acids (e. g., antifolics (methotrexate, etc.), antipurines (6-mercaptopurine, etc.), antipyrimidines (~luorourasil (5-FU), etc.); 3) DNA topdisomerase inhibitors (e. g., camptothecin and etoposide, each of which inhibits topoisomerases I and II)): 4) tubulin agents which inhibit formation of microtubules arid suppress ce7.l division (vinblastine, vincristine, etc.); 5) platinum dompounds which bind to DNA and proteins to exhibit cytotoxicity (cisplatin, carboplatin, etc.); 6) anticancer antibiotics which bind to DNA to inhibit synthesis of DNA
and RNA (adriamycin, dactinomycin, mitomycin C, bleomycin, etc.); 7) hormone agents which are s.pplicable to hormone-dependent cancer, such as breast cancer, uterus cancer, prostate cancer, and the like (e. g., tamox~.fen, 3Q leuprorelin (LH-RH), etc.); 8) biological formulations Azoa~
(asparaginase effective for asparagine requiring blood malignant tumor, interferon exhibiting direct antitumor action and indirect action by immunopotentiation, etc.);
9) immunostimulants which exhibit cap~bil~.ty of immune response, indirectly leading to antitumox activity (e. g., rentinan which is a polysaccharide derived from shiitake mushroom, bestatin which is a peptide derived from a microorganism, etc.)..
~.0 An "anticancer agent" used herein selectively suppresses the growth of cancerous (tumor) cells, and includes both pharmaceutical agents and radiation therapy.
Such an anticancer agent is well known in the art and described in, for example, Shigeru Tsukagoshi et al. editors, J.S "Kogan zai Manuaru [Manual of Anticancer agents] ", 2nd ed. , ChugaiIgaku sha; Pharmacology: and T~ippincott Williams &
Wilkins, Inc.
As used herein, the term "radiation therapy"
20 refers to a therapy for diseases using ionizing radiation or radioactive substances. Representative examples of radiation therapy include, but axe not limited to, X-ray therapy, y-ray therapy, electrpz~ beam therapy, proton beam therapy, heavy particle beam therapy, neutron capture 25 therapy, and the like. For example, heavy particle beam therapy ~.s preferable. However, hea~ry particle beam therapy requires a large-size device and is not generally used. The above-described radiation therapies are well known in the art and are described in, for example, Sho Kei 30 Zen, "Hoshasenkensa to Chiryo no Kiso: Hoshasen Chiryo to 1a2 A~oo~
Shugakuteki Chi.~ryo CBasics of Radiation Examination and Therapies: Radiation Therapy and Incentive Therapy?", (Shiga Medical School, Radiation): Total digestive system care, Vol. 6, No. 6, gages 79-89, 6-7 (2p02.02). For drug resistance to be identified in the present invention, chemotherapies are typically considered. However, resistance to radiation therapy is also associated with time-lapse profiles. Therefore, radiation therapy is herein encompassed by the concept of pharmaceutical agents.
x0 As used herein, the term "pharmaceutically acceptable carrier" refers to a material for use in production of a medicament, an animal drug or an agricultural chemical, which does not have an adverse effect cn an effective component. Examples of such a pharmaceutically acceptable carrier include, but are not limited to, antioxidants, presexwatives, colorants, flavoring agents, diluents, Emulsifiers, suspending agents, solvents, fillers, bulking agents, buffers, delivery ~rehicles, excipients, agricultural or pharmaceutical ad~uvants, and the like.
The type and amount of a pharmaceutical agent used in a treatment method of the present invention can be easily determined by those skilled in the art based on information obtained by a method of the pzesent invention (e. g . , information about the level of drug resistance, etc. ) and with reference to the puxpose of use, a target disease {type, sevexity, and the like) , the patient's age, weight, sex, and case h~.story, the form or type of the cell, and AI~07 the like. The frequency of the treatment method of the present invention applied to a subject (or patient) is also determined by those skilled in the art with respect to the purpose of use, target disease (type, severity, and the like) , the patient s age, weight, sex, and ease history, the progression of the therapy, and the like. Examples of the frequency include once per day to several months (e. g. , once per week to once per month) . Preferably, administration is performed once per week to once per month with reference to the progression of the therapy.
As used herein, the term "instructions" refers to a description of a tailor made therapy of the present invention for a person who performs administration, such as a medical doctor, a patient, or the like. Instructions state when to administer a medicament of the present invention, such as immediately after or before radiation therapy (e. g. , within 24 hours, etc. ) . The instructions are prepared in accordance with a format defined by an authority 2Q of a country in which the present inventiar~ is practiced (e. g., Health, Labor and Welfare Ministry in Japan, Food and Drug Administration (FDA) in the U.B., and the like), explicitly describing that the instructions are approved by the authority. The instructions are so-cal~.ed package insert and are typically provided in paper media. The instructions are not so limited and may be provided in the form of electronic media (e. g. , web sites, electronic mails, and the like provided on the Internet), In a therapy of the present invention, two or ~. 5 4 more pharmaceutical agents may be used as required.. When two or more pharmaceutical agents are used, these agents may have similar properties or may be derived from similar origins, or alternatively, may have different praperties or may be derived from different origins. A method of the present invention. can be used to obtain infarm~.ti.oz~ about the drug resistance level of a method of administering two Qr more pharmaceutical agents.
J.0 Also, in the present invention, ger~e therapy can be performed based an the resultant information about drug resistance. As used herein, the term "gene therapy" ref$ra to a therapy in Which a nucleic acid, which has been expressed or can be expressed, is administered inta a subj ect . In such an embodiment of the present invention, a protein encoded by a nucleic acid is produced to mec~i.ate a therapeutic effect.
rn the present invention, it will be understood by those skilled in the art that if the result of analysis of a certain specific time-lapse profile is correlated with a state of a cell in a similar organism (e. g., mouse with respect to human, etc.}, the result of an analysis of a corresponding time-lapse profile can be correlated with a state of a cell. This feature a,s supported by, for example, Dobutsu Baiyo Saibo Manuaru [An;imal Culture Cell Manual], Seno, ed., Kyoritsu Shuppan, 1993, which is herein incorporated by reference.
The present invention may be applied to gene therapies . As used herein, the term "gene therapy" refers to a therapy in which a nucl~:ic acid, which has been expressed or can be expressed, is administered into a subject. In such an embodiment of the present irivent~ion, a protein encoded by a nucleic acid is produced to mediate 2~ therapeutic effect.
Az~,y methods for gene therapy available in the art may be used in accordance with the present invention.
Illustrative methods will be described below.
Methods ~ox gene therapy are generally reviewed in, for example, Goldspiel et al., Clinical Pharmacy 12:
488-505(1993); Wu and Wu, Biotherapy 3: 87-95(1991)1 Tolstoshev, Ann. Rev. Pharmacol. Toxicol., 32:
573-596(1993): Mulligan, Science 260: 926-~932(1993)~
Morgan and Anderson, Ann. Rev. Biochem., 62: 191-217 (1993) and May, TIBTECH 11(5}: 1S5-215(1993). Commonly known recombinant DNA techniques used in gene therapy are described in, for example, Ausubel et al. (ed.), Current Protocols in Molecular Biology, ,john Wiley & Sons, NY (1993) and Kriegler, Gene Transfer and E~tpression, A haboratory Manual, Stoekton Press, NY (1990}.
(Basic techniques) Techniques used herein are within the technical scope of the present invention unless otherwise specified.
These techniques are commonly used in the f~.elds of fluidics, micromachining, organic chemistry, biochemistry, genetic engineering, molecular biology, microbiology, genetics, AI~~7 and the~.x xelevant fie~:ds. The techniques are well described in documents described below arid the documents mentioned herein else~rhere.
Mierofabrication is described in, for example, Campbell, S.A. (1996), "The Science and Engineering of Microelectronic Fabrication", Oxford University Press;
Zaut, P.V. (1996), "Micromicroarray Fabxzcation: a Practical Cuide to Semiconductor Processing", Semiconductor Services; Madau, M_J. (1997), " Fundamentals of Microfabrication", CRC1 5 Press; Ra.~-Choudhury, P.
(1997), "Handbook of Microlithography, Micromachining, &
Microfabricatian: Miorolithography". Relevant portions (or possibly the entirety) of each of these publications are herein incorporated by reference.
Molecular biology techniques, bioahemistxy techniques, and microbiology techniques used herein are well known and commonly used in the art, and are described in, for example, SambrQak J. et al. (1989), "Molecular Cloning: A Laboratory Manual", Cold Spring Harbor and its 3xd Bd. (2001): Ausubel, F.M. (1987), "Current Protocols ire Molecular Hiology", Greens Pub. Associates and Wiley-Interscience; Ausubel, F.M_ (1989), "8hort fxotocols in Molecular Biology: A Compendium of Methods from Current Protocols in Molecular Biology", Greens Pub. Associates and Wiley-Interscience; znnis, M.A. (1990), "PCR Protocols:
A Guide to Methods and Applications", Academic Press;
Ausubel, F.M. 0992), "Short Protocols in Molecular Biology: A Compendium of Methods from Current Protocols in Molecular Hic~lagy", Gxeene Pub. Associates: Ausubel, F.M.
( 1995 ) , "Short Protocols ~.n Molecular 'Biology: A
Compendium of Methods from Current Protocols in Molecular Biology", Greene Pub. Associates: Innis, M.A. et al. (1995) , "PCR Strategies", Academic Press; Ausubel, F.M. (1999), "Short Protocols in Molecular Biology: A Compendium of Methods from Current Protocols in MoleGUlar Hiology", TnTzley, and annual. updates; Sninsky, J.J. et al. (1999}, "PCR
Applications. Protocols for Functional Genomics", Academic Press; Speoial issue, Jikken Igaku [Experimental Medicine] "Idenshi Donyu & Hatsugenkaiseki Jikkenho [Experimental Method for Gene introduction & Expression Analysis]", Yodo-sha, 1997; and the like. Relevant portions (ox possibly the entirety) of each of these publications are herein incorporated by reference.
DNA synthesis techniques and nucleic acid chemistry for producing artificially synthesized genes are described in, for examp~,e, Gait, M.J. (1985), "Oligonucleotide Synthesis: A Practical Approach", IRL
Press; Gait, M.J. (7.990), "Oligonucleotide Synthesis: A
Practical Approach", IRL Press; Eckstein, F_ (1991}, "pl~,gonucleotides and Analogues: A Practical Approach", IRL
Press: Adams, R. Z. et al . ( 1992 ) , "The H~.oohemistry of the Nucleic Acids", Chapman & Hall: Shabarova, Z. et al. (Z994) r "Advanced Organic Chemistry of Nucleic Acids", Weinheim;
Blackburn, G.M. et a~.. ( 1996 ) , "Nucleic Acids in Chemistry and Biology", oxford University Press; Hermanson, G.T.
(I996), "BioCon~ugate Techniques", Academic Press; and the 3p like. Relevant portions (or possibly the entixety) of each of these publications are herein incorporated by reference.
(Analysis of co-regulation of gezles ) Mathematical processes used herein can be performed by using well-known techniques described in, for example, Kazuyuki Shimizu, "Seimei Sisutemu Kaiseki notameno Sugaku [Mathematics ~ox Analyzing $iologiaal Syatems~", Corona sha, 1999; and the like. Among these techniques, representative analysis techniques will be described below.
in one embodiment, such a mathematioaJ. process may be regression analysis. ,Examples of regression analysis ~.nclude, but are not limited to, linear regression (e. g., simple regression analysis, multiple regression analysis, robust estimation, etc.), nonlinear estimation, and the like.
In simple regression analysis, n sets of data (x1. Yi) to (xn. Ya? are fitted to yi=axi+b+e~, (i=1, 2, ..., n) where a and b are model parameters, and e1 represents a deviation or an error from the straight line. The parameters a and b are typically determined so that the mean of a sum of squares of the distance between a data point and the straight line is minimal. Zn this case, the rms of the distance is partially differentiated to produce simultaneous linear equations. These equations are solved for a and b which minimize the square errors. Such values are called least square estimates.
Azoo7 Next, a regression line is calculated based on the value obtained by subtracting the mean of all data values from each data value. A regression line represented by:
AE~Xi + $ = EYi is assumed. Further, it is assumed that 8 =d. The mean (xave~
yane) of (x~.. Yi) (i=1, 2, ..., n) is calculated, and the variance of x (sxx) and the covariance of x and y (sxy) are calculated.
The above-described regression line can be represented by:
Y - gave - (sxy/s~) (x - rave) ~
The correlation coefficient rXy is represented by:
rxy = 8xy/~ ( SxysYY~ .
zn thzs case, the relationship ~ei2/n = syy(1 -rxy2) is satisfied. Therefore, as ~ rxy ~ approaches 1, the error is decreased, which means that data can be satisfactorily represented by the r~gression line.
Tn another embodiment, multiple regression analysi9 is used. zz~ this technique, ~r is not a single independent variable, and is considered to be a function of two or more variables, e.g., is represented by:
= ao + alxl + a2x2 + ~ . . + anXrt.
This equation is called a mu~.tiple regression equation. ao and the lzke axe called (partial) regression coefficients. xn multiple regression analysis, a least square method is used and noxmal equations are solved to obtain least square estimates. Evaluatipn can be performed as with single regression analysts.
In another embodiment, robust estimation is used. The least square method is based on the premise that measurement values are not biased and measurement errors have a normal distributions and models have no approximation error. In actual situations, however, there may be errors in measurement. Zn robust estimation, unreliable data is detected and separated as outliers from the great majority of data which are reliable, or is subjected to a statistical pxocess. Such a robust estimation may be utilized herein.
Nonl.~near estimation may also be used herein.
With nonlinear estimation, it is possible to represent a nonlinear model as vector equations which are in turn solved.
Other mathematical processes used herein include principal component analysis, which utilizes two--dimensional data principal component analysis, multi~-dimensional data principal component analysis, singular value decomposition, and generalized inverse matrix. Alternatively, canonical correlation analysis, factor analysis, discrimination analysis, cluster ane~lysis, and the like may be used herein.
(Gene set classification by cluster analysis) for a number of applications, it may be desirable to obtain a set of reference transcription control sequences which axe cooperatively controlled under a wide range of conditions. An embodiment of identifying such a set of reference transcription control sequences is, for example, a clustering algorithm, wrhich is reviewed in, for example, Fukunaga, 1990, "Statistical Pattern ReCOgriition", 2nd ed., Academic Press, San Diego: Anderberg, 1973, "Cluster Analysis for Applications", Academic Press: New York; Everitt, 1974, "Cluster Analysis", London: Heinemann Educ. Books; Hartigan, 1975, "Clustering Algorithms", New York: WilEy; and Sneath and Sokal, 1973, "Numerical Taxonomy", Freeman, A set of transcription control sequences can also be defined based on a transcription control mechanism.
Transcription control sequences having a transcription factor binding site for the same or similar sequences in a regulatory region are likely to be cooperatively regulated.
In a certain embodiment, the regulatory regions of transcription control sequences of interest are compared with dne another using multiple alignment analysis, so that a possible common transcription factor binding site can be determzr~ed (Stormo and Hartzell, 19$9, "Identifying prote~.n binding sites from unaligned DNA fragments", Proc. Natl.
Acad. Sci., 86: 17.$3--1187: Hertz and Stormo, 1995, "Identification of consensus patterns in unaligned DNA and protein sequences : a large--deviation statistical basis for penalizing gaps", Proc. of 3rd Int.l . Conf . on Bioinformatics and Genome Research, Lim and Cantor, ed. , World Scientific Publishing Co. , Ltd. S~.x~gapore, pp.201-216) .
It may be desirable to obtain a set of basic transcription control sequences which s.xe cooperatively regu~.ated under various conditions. With such a set, a method of the present invention can satisfactorily and efficiently carry out determination based an profiles, A
preferable embodiment for identifying such a set of basic transcription control sequences includes a clustering algorithm.
In an embodiment using cluster e~nalysis, the transcription levels of a number of transcription control sequences can be monitored while applying various stimuli to biological samples. A tab7.e of data contain~.ng measurements of the tzanscripta.on levels of transcription control sequences is used in cluster analysis. Tn order to obtain a set of basic transcription control sequences containing transcription control sequences which s~.multaneously vary under various conditions, typically at least two, preferably at least 3, more preferably at least 10, even more preferably more than S0, and most preferably more than 100 stimuli or conditions are used. Cluster analysis ~.s performed for a table of data having mxk dimensions where m is the total number of conditions or stimuli and k is the number of transcription control sequences to be measured.
A number of cluster~.ri,g algorithms are useful ~or clustering analysis. In clustering algorithms, differences or distances between samples are used to foxzri clusters. Zn a certain embodiment, a distance used is a Euclidean distal j~r'~).~ ~~~i-Y~~ ~~ al space:
~Gr r (1) where (x, y) represents a distance between gene X and gene Y (or any other cellular components X and X (e. g., transcription control sequences) ) ; Xi and Yi represent gene expression in response to l stimuli. Euclidean distances may be squared and then multiplied with weighting which are increased with an increase in the distance. Alternatively, a distance reference may be, for example, a distance between transcription co " ~ Y, or a Manhattan distance repress: ~~~ly~ ~ ~ ~~
J l (2) where Xi and Yi represent responses of transcription control 24 sequences or gene expression when l stimuli are applied.
Several other definitions of distance include Chebyshev distance, power distance, and mismatch rate. When dimensional data can be categorized without modifioat~.on, a mismatch rate defined as z (x, y) = (the number of X~,~Yi) /l may be used in a method of the present invention. Such a method is particularly useful in terms of cellular responses _ Another useful definition of distance is I=1-r where r is a correlation coefficient of response vectors X and Y, e.g., a normalized inner prpduct X~Y/IXIIYI. Specifically, an ~0 inner product X~Y is defined by:
Aroo~
X~~'~~,Xrx (3) .
filso, ~ X ~ _ (X~X) l~z and ~ Y ~ -- (Y-Y) lea .
Most preferably, a distance reference is suited to a biological problem in order to identify cellular components (e. g., transcription control sequences, etc.) which are simultaneously changed and/or simultaneously regulated. ~'~~ ~~~~~-~--~ ~ ~ ~ ° ~~-~ a ~mlarly preferred embodiment, ~'Y I=1-x having a correlation cc ~ ~ ted inner product _ 1 of genes X c ~ ' ~r 2 ~' ~ Vx uch a preferred embodiment, x j (4) where QicX~ and a~~Y~ represent standard errors in measurement of genes X and Y in experiment i.
The above-described normalized and weighted inner products (correlation coefficients) are constrained between values +~1 (two response vectors are completely correlated, i . a . , the two vectors are essentially the same) and -~. (two response vectors are not correlated or da not have the same orientation (i.e., opposing orientations)).
These correlation coefficients are particularly preferable in an embodiment of the pxesent invention which tries to detect a set or clustex of cellular components (e. g., transcription cantral sequences, etc.) having the same sign Or respOnBe.
In another embodiment, it is preferable to identify a set or cluster of cellular components (e. g., S transcription control sequences, etc.) which simultaneously regulate the same biological response or pathway or are involved in such regulation, or have similar or non-correlated rESponses. In such a embodiment, it is preferable to use the absolute value of either the above-described normalized or weighted inner product, i.e., girl as a correlation coefficient.
Tn still another embodiment, the relationship between cellular components (e. g., transcription control sequences, etc.), which are simultaneously regulated and/or simultaneously changed, are more complicated, e.g., a number of biozogical pathways (e. g., signal transduction pathways, etc.) are involved with the same cellular component (e. g., a transcription control sequence, etc.) so that different results may be obtained. In such an embodiment, it is preferable to use a correlation coefficient r=r~°h~'g~? which can identify cellular components (other transcription control sectuences as controls which are not invoa ~ y aneously changed and/or sin ~ ; Xi ;y~ A correlation coefficient t' ' f ~~~, is particularly useful for t iX
l (5) .
Various cluster linkage methods are useful in a method of the present invention.
Examples of~sueh a technique include a simple linkage method, a nearest neighbor method, and the like.
In these techniques, a d~.stance between the two closest samples is measured. Alternatively, in a complete linkage method, Which may be herein used, a maximum distance between two samples in different clusters za measured. This technique is particularly useful when genes or other cellular components naturally farm separate "clumps".
Alternatively, the mean of non-weighted pairs is used to define the mean distance of all sample pairs in xS two different clustexs. This technique is also useful in clustering genes or other cellular components which naturally form separate "clumps" . Finally, a weighted pair mean techz~~.que is also available. This technique is the same as a non-weighted pair mean technique, except that in the farmer, the size of each cluster is used as a weight.
This technique is particularly useful in an embodiment in which it is suspected that the size of a cluster of transcription control sequences or the like varies considerably (Sneath and Sokal, 1973, "Numerical taxonomy", San Francisco : W . H. Freeman & Co. ) . Other cluster l~.rrl~age methods, such as, for example, non-weighted and weighted pair group centroid and ~nTard's method, are also useful in several embodiments of the present invention. See, for example, Ward, 1953, J. Am. Stat. Assn., 58: 2361 and Hartigan, 1975, "Clustering algorithms", New York: Wiley.
In a certain preferred embodiment, cluster analysis can be performed using a well-known hclust technique (e. g., see a well-known procedure in "hclust"
available from Program S-Plus, MathSoft, Inc., Cambxxdge, MA ) .
According to the present invention, it was found that even if the versatility of stimuli to a clustering set is increased, a state of a cell can be substantially elucidated by analyzing typically at least two, preferably at least 3, profiles using a method of the present invention.
Stimulation conditions include treatment with a pharmaceutical agent in different concentxatidns, different measurement times after treatment, response to genetic mutations in various genes, a combination of tz~eatment 4f a pharmaceutical agent and mutation, and changes in growth conditions (temperature, density, calcium concentration, etc.).
As used herein, the term "significantly different" in relation to two statistics means that the two statistics are different from each other with a statistical significance. In an embodiment of the present invention, data of a set of experiments assessing the responses of cellular components can be randomized by a Monte Carlo method to define an objective test.
In a certain embodiment, an objective test can be defined by the following technique. pk~, represents a Azoo~
response of a component k in experiment i. II~~y represents a random permutation of the indices of experiments. Next, pxnti? is calculated for s number of different random permutation9 (about 100 to 1, 000) , For each branch of the original tree and each permutation:
(1) hierarchical clustering is performed using the same algorithm as that which has been used for the original data which is not permutated (in this ease, "hclust"); and (2) an imprcwement f in classification in total variance abo ' '' ' ' ' ' n transition is made from on ~_ l ~ ~,~xr~~ J~~~~~l (~>
where Dk is the square of the distance reference (mean) of component k with respect to the center of a o~-uster to which component k belongs. Superscript 1 or 2 ind~.cates the center of all branches or the center of the more preferable cluster of the two subclusters. The distance function D
used in this Clustering technique has a considerable degree of freedom. In these examples, D~~.--r, where r is a correlation coefficient of one response with respect to another response of a component appearing in a set of experiments (or of the mean cluster response).
Specifically, an obi ective statistical test can be preferably used to determine the statistical reliability of grouping an~r clustering methods or algorithms.
Preferably, similar tests can be appla-ed to both x69 Azao7 hierarchical and nonhiers.xchical clustering methods. The compactness of a cluster is quantitatively defined as, for example, the mean of squares of the distances of elements in the cluster from the "mean of the cluster", or mare preferably, the inverse o~ the mean of squares of the distances of elements from the mean of the cluster. The mean of a spec~.f~.c cluster is generally defined as the mean of response vectors of all elements in the c~.uster. However, in a specific embodiment (e.g., the de~i.nition of the mean of the cluster is doubtful) , for example, the absolute values of normalized or weighted inner products are used to evaluate the distance function of a clustering algorithm (1.e., I=1-~r~). Typically, the above-described definition of the mean may raise a problem in an embodiment in which response vectors have opposing directions so that the mean of the cluster as defined above is zero. Therefore, in such an embodiment, a different definition is preferably selected for the compactness of a cluster, far example, without limitation, the mean of squares of the distances of all pairs of elements in a cluster. Alternatively, the compactness of a cluster may be defined as the mean of distances between each element ( a . g . , a cellular component ) of a c7.uster and another element of the cluster (or more preferably the inverse of the mean distance).
Other definitions, which may be used in statistical techniques used in the present invention, are obvious to those skilled in the art.
rn another embodiment, a profile of the present invention can be analy2ed using signal processing techniques. In these signal processing techniques, a oorrelat.ion funatzon is defined, a correlation coefficient is calcuJ.ated, an autocorrelation function and a cross-correlation funot~.on; are defined, and these functions are weighted where the sum of the weights is equal to 1.
Thereby, moving averages can be obtained.
In signal processing, it a.s important to consider a time domain and a frequency domain. Rhythm often plays an important role in dynamic characteristic analysis for natural phenomena, part~.cularly life and organisms . If a certain time function f(t) satisfies the following condition, the function is called a periodic function:
f (t) - f (t~-T) .
At time 0, the function takes a value of f (0) .
The function takes a value o~ f(0) at time T again after taking various values after time 0. Such a function is called a periodic function. Such a function includes a sine wave. T is called a period. The function has one cycle per time T. Alterx~atzvely, this feature may be represented by 1/T which means the number of cycles per unit time (cycles/time) without loss of the informat~.on. The concept represented by the number of cycles per unit time is called frequency. If the frequency is represented by f, f is represented by:
f=1/T.
~z0o7 Thus, the frequency is an inverse of the time.
The 'time is dealt in a time domain, while the frequency is dealt in a frequency domain. The frequency may be represented in an electrical engineering manner. For example, the frequency is represented by angular measure where one pexiod corresponds to 360° or 2~ radians. zn this case, f (cycles/ sec) is converted to 2xf (radians/sec), which is generally represented by cu (=2~f) and is caZ~.ed angu~.ar frequency.
Now, a sine wave is compared with a cosine wave.
The cosine wave is obtained by translating the sine wave by 90° or.~/2 radians. The sine wave may be represented by the delayed cosine wave. This time delay is called phase.
For example, when a pure cosine wave has a phase of 0, a sine wave has a phase of 90°. When a sine wave is added tv a cosine wave, the amplitude of the resultant wave is increased by a factor of ~2 and the phase is ~/4.
Tn such analysis, fourier series and frequency analysis may be available. In addition, Fpux~.er transformation, discrete Fvurier transformation, and power spectrum may be s,vailable. In Fourier expansion, techniques, such as wavelet transformation and the like, may be available. These techniques are well known in the art and are described in, for example, Xukzo Shimizu, "Seimei Sisutemu Kaiseki notameno Sugaku [Mathematics for analyzing life systems]", Corpna sha, (1999); and Yasuhiro Ishikawa, "Rinsho Igaku notameno Ueburetto Kaiseki [Wavelet analysis for clinical medicine]", Igaku Shuppan.
(Description of preferred embod~.ments) Hereinafter, the present invention will be described by way of embodiments. The embodiments described below are provided only for illustrative purposes.
Accordingly, the scope of the present invention is not limited by the embodiments except as by the appended claims.
In one aspect, the present invention provides a method for representing a state of a cell. The method comprises the steps of: a) obtaining a time-lapse profile of the ce~.l by time-lapse monitoring of a gez'ie state (e.g., the expression of a gene (transcription, trans~.ation, etc. ) , etc. ) associated with at least one gene selected from genes derived from the cell: and b) presenting the time-lapse profile. For example, the profile of the intensity of a signal obtained by monitoring is aub~ected to interval different~.ation, thereby obtaining a function of changes which can be in turn displayed. In this case, preferably, for example a constitutive promoter or the lzke, which is assumed to be changed, can be used as a reference to obtain a difference, thereby obtaining a time-lapse profile. The present invention is not limited to this.
Time-lapse profiles may be displayed using any method, for example, they may be visually displayed using a display device (e.g., an x axis showing time while the y axis shows signal intensity), or alternatively, may be displayed as a table of numerical values. Alternatively, signal intensity may be displayed as optical intensity_ Furthermore, profiles may be presented by means of sound.
preferably, cells are fixed to a solid phase support (e.g., an array, a plate, a mi.crotiter plate, eto. ) when they are monitored. Such fixation can be carr~.ed out using techniques known in the art or teChrii.quea as described herein. Fixation or immobilization of a cell allows systematic investigation thereof.
Tn a preferred embodiment, such a time-lapse profile may be presented in real time. The real time presentation may contain a time lag to some extent if it is performed substantially in real time. A tolerable time lag is, for example, 10 seconds at maximum, and more preferably ~. second at maximum, though the tolerable time lag depends on the required level of real time (simultaneity).
Tn another aspect, the present invention provides a method for determining a state of a celJ.. Such determination of the cellular state is achieved by monitoring changes in a transcriptional state of a transcription control factor, which are not conventionally observed. Therefore, the method of the present invention for determining the cellular state allows determination of various states which cannot be conventionally observed.
Such a method comprises the steps of: a) obtaining a t~.me-lapse profile of the cell by time-lapse mon~.tox~.ng of a transcriptional state associated with at least one biological agent selected from. a biological agent group derived from the cell; and b) determining the state of the cell based on the time--lapse profile of the transcription level.
Preferably, cells are fixed to a solid phase support (e. g. , an array, a plate, a microtiter plate, etc. ) when they are monitored. Such fixation can be carried out using techniques known in the art or techniques as described herein.
In a preferred embodiment, advantageously, the cellular state determination method of the present invention may further comprise correlating the time-lapse profile with the state of the cell before obtaining the time-lapse profile. Alternatively, such correlation information may be provided fxom l~nown information. Such a correlating step may be performed at every determining step or correlation information may be stored in a database and used as required.
In a preferred embod~.ment, the transcription control sequence may be, without limitation, a promoter, an enhancer, a silencer, anothex flanking sequence of a structural gene in a genome, and a genomic sequence other than axons. A pxaznvter is preferable. This is because a transcription level can be directly measured, and the state of transcription directly reflects the state of a cell. Zn a particular embodiment, the transcription control sequences may include constitutive promoters, specific promoters, inducible promoters, and the like.
In certain embodiments, any promoter may be used. The present invention is characterised in that any type of promoter can be used. According to the method of the present invention, profiles can be analyzed from a viewpoint of "procession". Therefore, it is possible to determine a state of a cell using any promoter or any set of promoters.
Such determination cannot be achieved by conventional techniques. The present invention is highly useful since the present invention achieves what cannot be achieved by conventional techniques.
In a preferred embodiment, at least two biological agents (far example, transcriptional control sequence) are monitored. Hy observing at least two ba.o~.ogical agents, 80~ of the states of a cell can be typically identified. More preferably, at least 3 biological agents are monitored. By observing at least three biological agents, at least 90~ of the states of a cell can be typically identified. Tn a most preferred embodiment, at least 8 biological agents are monitored. Hy observing at least 8 biological agents, substantially all of the states of a cell can be typically identified. Thus, although any biological agents are selected, substantially all of the states of a cell can be determined by selecting and monitoring a small number of biological agents, as described above . This feature has not been cc~nventzonally expected. The method of the present invention is simpler, more precise and more accurate than conventional 1'7 6 AI~07 determination methods in which observation is made at time points and resultant data is statistically processed as heterologous groups.
Therefore, the determins.tion method of thr~
present invention preferably further comprises arbitrarily seJ.ecting at least one b~.ological agent from s biological agent group before monitaxlnc~. An important feature of the present invention is such that a biological agent, which does not exhibit specificity when intrestigated from poa.nt to point, oan be used. Further, the present invention allows accurate reflection of the resultant data to the state of a cell of interest, since data linearly measured data under a consistent environment can be used. Such accurate data cannot be obtained conventionally.
Zn a preferred embodiment, such a time-lapse profile obtained in the present intrention may be presented in real time_ Alternatively, in the present invention, data may be obtained in a real tune mariner. The real time presentation may contain a time lag to some extent if it is performed substantially in real time. A tolerable time lag is, fox example, 10 seconds at maximum, and more preferably 1 second at maximum, though the toXorable time lag depends on the rewired 7.e'v'el of real time (simultaneity) .
As used herein, the term "real time" means that the real time presentation may contain a time lag to some extent if it is performed substantially in real time. A tolerable time lag is, for example, 10 seconds at maximum, and more preferably 1 second at maximum, though the tolerable time lag depends on the required level of real time (simultaneity) .
For example, the level of real time may be preferably 30 seconds at maximum, or even longer in the case of, far example, therapies required for real time diagnosis.
In a particular preferable embodiment, states determined by the cellular state determination method of the present invention includes, for example, differentiated states, undifferentiated states, cellular responses to external factors, cell Cycles, growth states, and the like.
More speci.fi.cally, such a state includes, for example, without limitation, a response of a cancer cell to an anticancer agent, drug resistance, a response tc~ a biological clock, a differentiated state of a stem cell. (e. g. , a mesenchymal stem cell, a neural stem cell, etc.), an undifferentiated state of a purified stem cell (e.g., an embz~yonic stem cell, etc. ) , a change in cellular morphology, a state of cellul~.r migration, intracellular loca~.ization of a molecule, production of a secxeted substance, and the 20' like.
Therefore, in a preferred embodiment, a cell assessed by the cellular state determination method of the present invention includes, for example, without limitation, a stem ceJ.l ox a somatic cell, or a mixture thereof.
Alternatively, such a cell includes an adherent cell, a suspended cell, a tissue forming cell, and a mixtuxe thexeof .
Tn a preferred embodiment, the cellular state determination method of the present invention may be x78 A~~~7 pezfox-med upon a cell fixed on a substrate which is a solid phase support . In such a case, the solid phase support is called a chip. When cells axe arrayed on the substrate, the substrate is also called an array.
In a particularly preferred embodiment of the cellular state determination method of the present invention, advantageously, when a b~.o~.ogical agent (for example, a transcription control sequence) used for determination is a nucleic acid molecule, such a nucleic acid molecule may be operably linked to a reporter gene sequence and may be transfected into a cell. In this case, the transcription letrel of the transcription control sequence can be measured as a signal from the reporter gene.
Such transfection may be performed in the solid phase or in the liquid phase. For transfection, a techniquE
for increasing the efficiency of introduction of a target substance into a cell may be used. zn the present invention, a target substance (e. g., DNA, RNA, a polypeptide, a sugar Chain, or a composite substance thereof, etc. ) , which cannot be substantially introduced into cells under typical conditions, is presented (preferably, contacted) along with an actin-like substance, such as fibronectin, to a cell, thereby making it possible to efficiency introduce the target substance into cells. Therefore, the transfection method comprises the steps of: A) providing a target substance (i.e., DNA comprising a transcription control sequence) and B) providing an actin-like substance (e. g., fibronectin), wherein the order of steps of A) and B) is not particularly limitEd, and C) contacting the target substance and the actin-like substance with the cell. The target substance and the actin-like substance may be provided together or separately. The actin-like acting substance may be used as described in detail above for the composition of the present invention, for increasing the efficiency of introduction of a target substance into a cell.
Such a technique can be carried out as appropriate based on the present specification by those skilled in the art.
Therefore, the actin-like substance may be used in a manner which is described in detail above for the composition of the present invention for increasing the efficiency of introduction of a target substance into a cell _ Preferably, the actin-like acting substance may be an extracell.ular matrix protein (e. g., fibroneCtin, vitranectin, laminin, etc.. ) or a ~crariant thereof. More preferably, fibronectin or a variant or fragment thereof may be used.
Tn one embodiment, a transcription control sequence used in the present invention may be oapable of binding to a transcription factor. Examples of such a transcription factor include, but are not lim~.ted to, ISRE, RARE, STAT3, GAS, NFAT, MIC, Afl, SRE, GRE, CRE, NflCg, ERE, 2S TRE, E2F, ~tb, p53, and the like. These transcription factors are commercially available from BD Biosciences Clonetech, CA, USA. ISRE is related to STAT1/2_ RARE is related to retinoic acid. STAT3 is related to the Contxol of differentiation. GRE is related td the metabolism of sugar. CRE is related to cAMP. THE is related to thyroid hormone. E2F is related to cell cycle, p53 is related to G1 check point. Therefore, such information can be used to determine a state of a cell.
g In a preferred embodiment, the determination step of b) of the present invention comprises comparing the phases of the time-lapse profiles . Phases can be calculated by those skilled in the art using general techniques as described here~.n above and techniques described in the examples below.
In another preferred embodiment, the determination step of b) of the present invention comprises calculating a difference between the time-lapse profile of the cell and a control profile. The difference sari be calculated by those skilled in the art using general techniques as described herein above and techniques described in Examples below.
In another preferred embodiment, the determination step of b) of the present invention comprises a mathematical process selected from the group consisting of signal processing and multivariate analysis. Such a mathematical process can be easily carried out by those 2S skilled in the art based on the description of the present specification.
In another aspect, the present invention provides a method for correlating an external factor with 3d a cellular response to the external factor. The method AI 0 0'T
comprises the steps of: a) exposing a plurality of cells to an external factor on a support capable of retaining the cells in a consistent environment: b) monitoring a transcriptionax state relating to at least one of a transcriptional factor group present on or Within the cells over time to generate profile data for the Dells; and c) correlating the external factor with the profile.
Any external factor to be correlated in the present invention may. be used. Such an external factor is preferably directly or indirectly applicable to a cell. A
method for applying such an external factor is well known in the art, depending on the type of the external factor used. When a substance is used, the substance is dissolved into a solvent, and the resultant solution is added to a medium containing a cell.
"The correlation method of the present invention may utilize the production mEthod of profiles as described hereinabove.
A variety of methods can be provided for correlating a foreign agent and a pxofile in the method of correlation of the present invention, rn brief, profiles obtained when a foreign agent is applied to a cell, are patternized, and if there is little difference between the patternized profiles, it can be inferred that the particular foreign agent has been applied to the cells.
Preferably, a cell may be monitored in an 1,82 Azoo~
immobilized state t~o a solid support such as an array, a plate, a microtiterplate and the like. Such a method for immobilization can be conducted based an anx known methodology ~.n the art or the methods desardbed herein.
In a preferred embodiment, a correlation method of the present invention may further comprise using at least two external factors to obtain a profile for each external factor. In certain embodiments, at least three, or at least faun, mare preferably at least ten such foreign agents may be used but the present invention is not limited thereto.
Moxe preferably, the correlation step may fuxther compxise dividing at least two prof~.les into categories and c~.assify~.ng the external factoxs corresponding to the respective profiles into the categories. Such categorization may be readily conducted by those skilled in the art based on the description of the present specification. Such categorization or classification allows correlation and identification of an unknown foreign agent by means of the method of the present invention.
In a preferred embodiment, a transcription control sequence used in the present invention may be, without limitation, a promoter, an enhancer, a silencer, other flanking sequences of structural genes in geriomes, and genomic sequences other than axons. A promotex is preferable, s~.nce the transcr~.ption level. can ~e directly measuxed.
In a particular embodiment, transcription control sequences used in the present inver~tion may be constitutive promoters, specific promoters, inducible promoters, and the like. The present invention is characterized in that any type of promoter can be used.
According to the method of the present invent~.on, pxof~.~.es can be analyzed from a viewpoint of "process" ar "procession" .
Therefore, ~.t is possible to determine a state of a ce~.Z
using any promoter or any set of promoters. Such determination cannot be achieved by conventional techniques.
The present invention is highly useful since the present invention achieves what cannot be achieved by conventional.
techniques.
In 'a preferred embodiment, at least two transcription control sequences are monitored. By observing at least two transcription control sequences, at least B0~ of the states of a cell can be typically identified.
Moxe preferably, at least 3 transcription control sEquences are monitored. Hy observing at least three transcription control sequencES, at least 90~ of the states v~ a Cell Gan be typically identified. In a most preferred embodiment, at least 8 transcription control sequences are monitored.
By observing at least 8 transcription control sequences, substantially all of the states of a cell can be typically identified. Thus, although any transcription control sequences are selected, substantially all of the states of a cell can be determined by selecting and monitvrzng s small number of transcription control sequences as described 18 ~1 above. This feature has not been conventionally expected.
The method of the present invention is simpler, more precise and more accurate than conventional determination methods in which observation is made at time points and resultant data is statistically processed as hetero~ogous groups.
Therefore, the determination method of the present invention preferably further comprises arbitrarily selecting at least one transcription control sequence from a group of transcription control sequences before monitoring. An important feature of the present invention is such that a transcription control sequence, Which does not exhibit specificity when investigated from point to point, can be used.
In a preferred embodiment, such a time-lapse profi~.e may be presented in reaz time. The zeal time presentation may contain a time lag to some extent if it is performed substantia~.ly in real time. A tolerable time lag. is, for example, 14 seconds at maximum, and more preferably ~. second at maximum, though the tolErable time lag depends on the required level of real time (simultaneity) .
For example, in the case of environment measurement requiring zeal time idez7aification of external factors, the tolerable time lag may be, for example, 1 sec at maximum, 0.1 sec at maximum, or the like. Alternatively, after data is stored on a storage medium at real time, profiles may be pz~esented corresponding to the data based on the stored data, with some time lag.
In a preferred embodiment, in the correlation step of c) cf the present invention, the phase of the time-lapse pr4file may be used as information about the time-lapse pxofile in order to correlate the external factor with the time-lapse profile. The phase is represented by plus or minus depending an the signal intensity at a certain time. Even using such a simplified method, a cell or an external factor can be identified, thus demonstrating the precision cf the method of the present invention.
to Preferably, in the method of the pxesent invention, cells are advantageously cultured on an array.
This is because a number of cells can be simultaneously observed. Preferably, when a cell is immobilized on a solid support such as an array, a salt may be us~d.
In a preferred embodiment, the step of monitoring the transcription level over time may comprise obtaining image data from the array. This is because image data can be subjected to visual inspection and a human (particularly, a person skilled in the art, such as a medical practitioner or the like) can easi~.y examine image data with his/her eyes.
In a preferred embodiment of the present invention, the step of correlating the external factor with the time-lapse prof~.J.e may comprise distinguishing the phases of the time-lapse pxofiles. As described above, phase is a simple parameter, and its information processing is simple. Thus, cells can be well a. denti.fied by such simple AI 0 0'7 information processing.
In a preferred embodiment, examples of an extexnal factor to be identified by the method of the present invention include, but are nvt limited to, a temperature change, a humidity change, an electromagnetic wave, a potential difference, visible light, infrared light, ultraviolet light, X-ray, a chemical substance, a pressure, a gravity change, a gas partial pressure, an osmotic pressure, and the like. These factors cannot be satisfactorily identified by conventional methods. By using the cell determination method of the present invention which places an importance on "procession", an influence of a factor on a cell Can be well examined.
In a particularly preferred embodiment, an external factor to be identified by the method of the pxeserlt invention may be a chemical substance. Bxamples of such a chemical substance include, but are not limited to, biological molecules, chemical compound, media, and the like.
Examples of biological molecules znc~.ude, lout are not limited to, nucleic acids, proteins, lipids, sugars, proteolipids, lipoproteins, glycoproteins, proteoglycans, and the like. These biological molecules are known to have an influence on oz~ganisms. Unknown biological molecules are also highly likely to have an influence on organisms and are considered to be important targets for Study.
3~
Particularly preferably, hormones, cytakine, cell adhesion factors, extracellular matrices, receptor agonists, receptor antagonists, and the like, which are expected to have an influence on cells, are used as biological molecules to be investigated.
In another aspect, the present invention provides a method for inferring an unidentified external factor given to a cell based on a time-lapse profile of the cell. The method comprises the steps of: a) exposing the cell to a plurality of known external factors; b) obtaining a time-lapse profile of the cell for each known external factor by time-lapse monitoring of a transcription level associated with at least one bivlogica~. agent selected from the group consisting of biological agents derived from the cell.: c) correlating the known external factors with the respective time-lapse profiles; d) exposing the cell to the unidentified external factor; e) obtaining a time-lapse profile of the unidentified external factor by time--lapse monitoring of the transcription level of the selected biological. agent; f) determining a profile corresponding to the time-lapse profile obtained in the step of e) from the time-lapse pro~iXes obtained in the step of b); and g) determining that the unidentified external factor is the known external factor corresponding to the profile determined in the step of f).
In the method of the present invention, the step of exposing a cell to external factors can be performed as described above herein or as illustrated in the examples described below. The step of obtaining a time-lapse profile can be performed as described above herein or as illustrated in the examples described below. The correlation step can be performed as described above herein or as illustrated in the examples described below. After information about all known external factors has been obtained, an unidentified external factor issimilarly monitored. These pieces of information are compared to determine whether or not the unidentified external factor is a known one. If the profile of an unidentified fs.ctor fully matches the profile of a known factor, these two factors can be determined as being identical. Also, if the profile of an unidentified factor substantially matches the profile of a known factor, these two factors can be determined to be identical. Such determination depends on the information quantity and quality of the known external factor. Such determination can be easily carried out by those skilled in the art considering various elements.
Tn another aspect, the present invention provides a method for inferring an unidentified external factor given to a cell based on a time-lapse profile of the cell. The method comprises: a) providing data relating to a correlation relationship between known external factors ,and time-lapse profiles of the cell in response to the known external factors, in relation to at least one promoter selected from promoters present in the sell; b) exposing the cell to the unidentified external factor: c) obtaining a time-lapse profile of the cell by time--lapse monitoring of a transcription level associated with the selected I$9 promoter; d) determining a profile corresponding to the time-lapse profile obtained in the step of c) from the time-lapse profiles obtained in the step of a); and e) determining that the unidentified external factor is the known external factor corresponding to the profile determined in the step of d).
Exposure to external factors, profi.Ze generation, correlation, and the like can be carried out using techniques as described herein above or as illustrated in the examples below.
Zn another aspect, the present ~.rivention provides a system for presenting a state of a cell. The system comprises: a) means for obtaining a time-lapse profile of the cell by time-~Zapse monitoring of a transcription level associated with at least one transcription control sequence selected from the group consisting of transcription control sequences derived trom the call: and b) means for presenting the time-lapse profile.
An exemplary system canfigura'tion is presented in figure 32.
A configuration of a computer or system for implementing the cellular state presenting method of the present invention is shown in Figure 17, figure 17 shows an exemplary configuration of a computer 500 for executing the ce~.lular state presenting method of the pre&ent invention. An exemplary system configuration is presented in Figure 32, The computer 500 comprises an input section 501, a CPU 502, an output section 503, a memory 509, and a bus 505.
The input section 501, the CPU 502, the output section 503, and the memory 509 are connected via a bus 505 _ The input section 501 and the output section 503 axe connected to an I/O device 506_ An outline of a process for presenting a state of a cell, which is executed by the computer 500, will be described below_ A program for executing the cellular State presenting method (hereinafter referred to as a "cellular state presenting program") is stored in, for example, the memory 502. Alternatively, each component of the cellular state presenting program may be stored in any type of recording medium, such as a floppy disk, MO, CD-ROM, CD-R, DVD-ROM, or the like separately or together. Alternatively, the program may be stored in an application server. The cellular state presenting program stored in such a recording medium is loaded via the I /O device 506 ( a . g _ , a disk drive, a network (e.g., the Tnternet)) to the memory 504 of the computer 500. The CPU 502 executes the cellular state presenting program, so that the computer 500 functions as a device for performing the cellular state presenting method of the present irivezntion.
Information about a cell or the like is znput via the input section 501 as we~.l as profile data obtained.
Known information may be input as appropriate.
The CPU 502 generates display data based on the information about profile data and cells through the input section 50i, and stored the display data into the memory 504.
Thereafter, the CPU 502 may store the information in the memory 504. Thereafter, the output section 503 outputs a cellular state selected by the CPU 502 as display data. The output data is output through the I/O device 506.
In another aspect, the present. invention provides a system for determining a state of a cell. The system comprisES: a) means for obtaining a time-lapse profile of the cell by time-lapse monitoring of a transcription level associated with at least one biological agent se,~ected from the group consisting of biological agents derived fxom the Cell; and b) means for determining the state of the cell based on the time-.apse profi~.e. An exemplary system configuration is presented in Figure 3Z.
A configuration of a computer or system for implementing the cellular state determining method of the present invention is shown in Figure 17. Figure 17 shows an exemp~.a,x~y configuration of a computer 500 for executing the cellular state determining method of the present invention. An exemplary system configuration is presented in Figure 32.
The computer 500 comprises an input section 501, 3p a CPU 502, an output section 503, a memory 504, and a bus 505.
The input section 501, the CPU 502, the output section 503, and the memory 504 are connected via a bus 505. The input section 50l arid the output section 503 are connected to an I/0 device 506.
An outline of a process for determining a state of a cell, which is executed by the computer 500, will be described below.
A program for executing the cellular state determining method (hereinafter referred to as a "cellular state determining program") is stored in, for example, the memory 50Z . Alternati~srely, each component of the cellular state determining program may be stored in any type of recording medium, such as a floppy disk, M0, CD-RpM, CD-R, DVD-ROM, or the like, separately or t4gether.
Alternatively, the program may be stored in an application server. The cellular state determining program stored in such a recording medium is loaded via the T/O device 506 (e, g. , a disk drive, a network (e. g. , the Internet) ) to the memory 50~4 of the computer 500. The CPU 502 executes the cellular state presenting program, so that the computer 500 functions as a device fvr performing the celluJ,ax state determining method of the present invention.
Information about a cell or the like is input via the input sectzon 501, as well as profzle data obtained.
Known information may be input as appropriate.
The CPU 502 determxz~es a state of a cell based on the information about profile data and cells input through the input section 501, generates the results as determination result data, and stores the determination result data in the memory 504. Thereafter, the CPU 502 may store the information in the memory 5G4. Thereafter, the output section 503 outputs a cellular state seleoted by the CPU 502 as detez~ni,nation result data. The output data is output through the I/O devise 506.
Tn another aspect, the present invention provides a system for correlating an external factor with a response of a cell to the external factor. 'Ihe system comprises: a) means for exposing the cell to the external factor; b) means for obtaining a time-lapse profile of the cell by time-lapse monitoring of a transcription level associated with at least one promoter selected from the group consisting of promoters derived from the cell; and c) means for correlating the external factor with the time--lapse profile. Such a system can be implemented using a computer as with the above-described systems. An exemplary system configuration is presented in Figure 32.
In another aspect, the present invention provides a system for inferring an unidentified external factor given to a cell based on a time-lapse profile. The system comprising: a) means for exposing the cell to a plurality of known external factors; b) means for obtaining a time-lapse profile of the cell for each known external factor. by time-lapse monitoring of a transcription level associated with at least one biological agent selected from the group consisting of biological agents deri~red from the cell; c) means for correlating the known external factors with the respective time-lapse profiles; d) means for exposing the cell to the un~.dentif~.ed external factor;
e) means for obtaining a timg--lapse profile of the unidentified external factor by time-lapse manztvr~.ng of the transcription level of the selected transcription control sequence: f) means for determining a profile corresponding to the time-lapse profile obtained in the 7.a means of e) from the time-lapse profiles obtained in the means of b); and g) means for determining that the unidentified external. factor is the known external factor corresponding to the profile determined in the means of f ) .
Such a system can be ~.mpl.emented using a computer as with the above-described systems. An exemplary system configuration is presented in figure 32.
In another aspect, the present invention provides a system for inferr~.ng an unidentified external factor given to a cell based on a time-lapse profile, comprising: a) means for providing data relating to a correlation relationship between known external factors and time-lapse profiles of the cell in response to the known exte~cns~l factors, in relation to at least one biological agent selected from biological agents present in the cell;
b) means for exposing the ce~.l. to the unidentified external factor; c) means for obtaining a time-lapse profile of the cell by time-lapse monitoring of a transcription level associated with the selected transcription cantxoJ.
30. sequence; d) means for determining a profile corresponding to the time-lapse profi~:e obtained in the means of c) from the time-lapse profiles obtained in the means of a); and e) determining that the unidentified external ~aGtar is the known external factor corresponding to the profile determined ~.n the means of d) . Such a s~sstem can be implemented using a computer as with the above-dascribad systems. An exemplary system configuration is presented in Figure 3Z.
When the present invention is prpvided in the form of a system as described above, each constituent elem~nt thereof can be implemented as with the detailed or preferred embodiments of the method 4f the present invention.
Preferred embodiments of such a system can be easily selected by those skilled in the art and can be made or carried vut by those skilled in the az~t based on the present specification. An exemplary system configuration is presented in Figure 32.
In another aspect, the present in~rention provides a computer recordable recording medium recording a program for executing a process for presenting a state of a cell to a computer. The recording medium records at least a program far executing the procedures vf:
a) obtaining a time-lapse profile of the cell by time-lapse monitoring of a txa~nsoription level associated with at least one biological agent selected from the group consisting of biological agents derived from the cell; and b) presenting the time-lapse profile.
~. 9 6 Az007 In another aspect, the present invention provides a computer recordable recording medium recording a program for executing a process for determining a state of a cell. to a computer. The recording medium records at least a program for executing the praceduxes of:
a) obtaining a time-lapse profile of the cell by time-lapse monitoring of a transcription level associated with at least one biological agent selected from the group consisting of biological agents derived from the cell; and b) determining the state of the oell based on the time-lapse profile of the transcript~.Qn level.
In another aspect, the present invention provides a computer xecordable recozding medium recording a program for executing a process far correlating an external factor with a response of a cell to the external factor.
The recording medium records at least a program for executing the procedures of: a) exposing the cell to the external factor; by obtaining a time-lapse profile of the cell by time-lapse monitoring of a transcription level associated with at least one transcri.pt~.on control factor selected ~rom the group consisting of transcription control factors derived from the cell: and c) correlating the external factor with the time-lapse profile.
In another aspect, the present invention provides a computer recordable recording medium recording a program for exeGUting a process for inferring an unidentif~.ed external factor given to a cell based on a time-lapse profile. The recording medium records at least Azoo~
a program for executing the procedures of: a) exposing the cell to a plurality of known external factors: b) obtaining a time-lapse profile of the cell for each known external factor by time-lapse monitoring of a transcription J.evel associated with at least one transcription control factor selected from the group consisting of transcription control factors derived from the cell; c) carrelatix~g the known external factors with the respective time-lapse profiles:
d) exposing the cell to the unidentified external factor:
e) obtaining a time-lapse profile of the unidentified external factor by time--lapse rnanitoring of the transcription level of the selected transcz~iptian control sequence; f) determining a profile corresponding to the time-lapse profile obtained in the procedure of e) from the time-lapse profiles obtained in the procedure of b); and g) determining that the unidentified external factor is the known external factor corresponding to the profile determined in the procedure of f), In another aspect, the present invention provides a camputer recordable recording medium recording a program for executing a process for inferring an unidentified external factor given to a cell based an a time-lapse profile, The recording medium records at least a pxagram for executing the procedures of: a) providing data relating to a correlation relationship between known external fadtaxs and time-lapse profiles of the cell in response to the known external factors, in relation to at least one transcription control sequence selected from transcription control. sequences present in the cell:
AI00~
b) exposing the cell to the unidentified external factor;
c) obtaining a time-lapse profile of the cell by time-lapse monitoring of a transcription level associated with the selected transcription control sequence; d) determining a profile corresponding to the time-lapse profile obtained in the procedure of c) from the time-lapse profiles obtai~.ed in the procedure of a); and e) determining that the unidentified external factor is the known external factor corresponding to the profile determined in the procedure of d) .
When thG present invention is provided in the form of a z~ecord~.ng medium as described above, each const~.tuent element thereof can be implemented as wai.th the detaa.~.ed o~ preferred embodiments of the method of the present invention. Qreferred embodiments of such a recording medium can be easily selected by those skilled in the art and can be made or carried out by those skilled in the art based on the present specification.
In another aspect, the present invention provides a program for executing a process for presenting a state of a cell to a computer. The program executes the procedures of: a) obtaining a time-lapse profile of the cell by time-lapse monitoring ofi a transcription level associated with at least one biological agent selected from the group consisting of biological agents derived from the cell: and b) presenting the time--lapse profile.
Tn another aspect, the present invention provides a program for executing a process for determining a state of a cell to a avmputer _ The program executes the procedures of: a) obtaining ~ time-lapse profile of the cell by time-lapse monitoring of a transcription level associated with at lEast one biological agent selected from the group consisting of biological agents derived from the cells and b) determining the state of the cell based on the time-lapse profile of the transcription level.
In another aspect, the present invention provides a program for executing a process for correlating an external factor with a response of a cell to the external f~Ctor_ The program executes the procedures of:
a) exposing the cell to the external factor; b) obtaining a time-lapse profile of the cell by time-lapse monitoring of a transcription level associated With at least one transcription control factor selected from the group consisting of transcription control factors derived from the cell: and c) correlating the external factor With the time-lapse profile.
Tn another aspect, the present invention provides a program for executing a process for inferring an unidentified external factor given to a cell based on a time-lapse profile. The pz~ogram executes the procedures of: a) exposing the cell to a plurality of known external factors; b) obtaining a time-lapse profile of the cell for each known external factor by time-lapse monitoring of a transcription level associated with a.t least one transcxiptivn control factor selected from the group A~007 consisting of transcription control factors derived from the cell.: c) correlating the known external factors with the respective time-lapse profa.les; d) exposing the cell to the unidentif~.ed external factor: e) obtaining a time-lapse profile of the unidentified external factor by time-lapse monitoring of the transcription le~'el of the selected transcription control sequr~nce; f) determining a profile corresponding to the time--lapse profile obtained in the procedure of e) from the time-lapse profiles obtained 20 in the procedure of b): and g) determining that the unidentified external factor is the known external factor corresponding to the profile determined in the procedure of f ) .
In another aspect, the present invention pro~rides a program for executing a process for inferring an unidentified external factor given to a cell based on a time-lapse profile. The program executes the procedures of: a) providing data relating to a correlation relationship between known external factors and time-lapse profiles of the cell. in response to the known external factors, in relation to at least one transcription control sequence selected from transcription control sequences present in the cell; b) exposing the cell to the unidentified external factor; c) obtaining a time-lapse profile of the cell by time-lapse monitoring of a transcription ~.evel associated with the selected transcription control sequence; d) determining a profile corresponding to the time-lapse profile obtained in the procedure of c) from the time-lapse profiles obtained in the procedure of a)f arid e) determining that the unidentified external factor is the known external factor corresponding to the profile determined in the procedure of d).
S When the present invention is provided in the form of a pragrarn as described above, each constituent e~.ement thereof can be implemented as with the detailed or preferred embodiments of the method of the present invention.
Preferred embodiments of such a program oan be eas~.3.y selected by those skilled in the art and can be made or carried out by those skilled in the art based on the present specification. Description formats of such a program are well known to those skilled in the art and include, for example, the C+~language, and the like.
In another aspect, the present invention provides a method and system for diagnosing a subject. The diagnosis method comprises the steps of: a) obtaining a time-J.apse profile of the cell by time-lapse monitoring of ~0 a transcription level associated with at least one transcription control sequence selected from the group consisting of transcription control sequences derived from the cell; b) determining the state of the cell based an the time-lapse profile of the transcription level; and c) determining a condition, disorder or disease of a subject based on the state of the cell. The diagnosa,s method is provided in the form of a system, the system of the present invention comprises: a) means for obtaining a time-lapse profile of the cell by time-lapse monitoring of a transcription level associated with at least one transcription control sequence selected from the group consisting of txar~scription control sequences derived from the cell.; b) means for determining the state of the cell based on the time-lapse profile of the transcription level;
and c) means for determining a condition, disorder or disease of a subject based on the state of the cell. The present invent~.on is applicable to tailor-made disgnvses and therapies, such as drug resistance, selection o~
apprvpxiate anticancer agents, selection of appropriate transplant cells, and the like. Preferably, the diagnosis method of the present invention may be provided as a therapeutic or preventative method comprising the step of treating a subject with a therapy or preventative method selected based on the xesu~.t of diagnosis. In another preferred eznbvdiment, the diagnosis system of the present invention may be provided as a therapeutic or pre~erentative system comprising means for treating a subj ect with a therapy or preventative method, selected based on the result of diagnosis. An exemplary system configuration is shown in Figure 32.
A configuration of a computer or system for implementing the diagnosis method and system of the present ~.nvention is shown in Figure 17. Figure 17 shows an exemplary configuration of a computer 500 fox executing the cellular state determining method of the present invention.
An exemplary system configuration is shown in Figure 32.
The computer 5d0 comprises an input section 501, a CPU 502, an output section 503, a memory 504, and a bus 505 .
The input section 50~, the CPU 502, the output section 503, and the memory 504 are connected via a bus 5a5:. The znput section 501 and the output section 503 are connected to an T/O device 506.
An outJ.a.ne of a correlation process, which is executed by the computer 500, will be described below.
A program for executing the correlation method and/or selection of treatment or preventative method (hereinafter referred to as a "correlation program" and a "selection program", respectively) is stored in, for example, the memory 502. Alternatively, the correlation program and the selection program may be stared in ~.ny type of recording medium, such as a floppy disk, MO, CD~ROM, CD-R, DVD-ROM, or the like, separately or together.
Alternatively, the programs may be stored in an application server. The correlation program and the selection program stored in such a recording medium are loaded via the I/p device 506 (e.g., a disk drive, a network (e.g., the Internet)) to the memory 504 of the computer 500. The CPU 502 executes the correlation program and the selection program, so that the computer 500 functions as a device for performing the correlation method and the selection method of the present invention.
The result of analysis of a time-lapse profile (e.g., phase, etc. ) and infoxznat~.on about a ce7.~. ox the like are input via the input section 501. Secondary information about a condition, disorder or disease to be correlated with 2p4 a time-lapse profile and information about treatment and/or preventative methods may be input as required.
The CPU 5t~2 correlates information about a time-lapse profile with a state of a cell or a condition, disorder or disease of a subject and a preventative or therapeutic method as required, based on the in.formgtion input through the input section 501, and stares correlation data into the memory 50~. Thereafter, the CPU 502 may store the information in the memory 504 , Thereafter, the output section S03 outputs information about a state of a cell or a condition, disorder or disease of a subject and a preventative or thexapeutic m~ahQd as required, Which has been selected by the CPU 502 as diagnostic information. The output data i.s output through the I/O device 506.
(Generation of data) In one aspect, the present invention provides a method for generating profile data of information of a cell.. The method comprises the steps of: a) providing and fixing the cell to a support: and b? monitoring a biological agent or an aggregation of biological agents on or writhin the cell over time to genexate data an the profile of the cell. In this aspect, the pxesent invention is characterized in that the cell is fixed to substantially the same site of the support so that infox-mation oari be continuously (e_g., in a time-lapse manner, etc.) obtained from the same cell. Thereby, ~.t is possible to monitor a biological agent and an aggregation of biological agents over time. The time-lapse monitoring makes it possible to ~1r007 obtain.a profile of a cell and construct a digital cell.
Tv fix a cell to a support, a fixing agent, such as a salt or the like, may be used for tYie support i.r1 the present invention. A combination of a salt, a complex of a positively charged substance and a negatively charged substance, and a cell may f ix the cell to the support . Any salt may be used in the present ln~rention. Examples of such a salt include, but axe not limited ta, calcium chloride, sodium l~ydro~gen phosphate, sodium hydrogen carbonate, sodium pyruvate, HEPE9,,sodium chloride, potassium chloride, magnesium sulfide, iron nitrate, amino acids, vitamins, and the like. Examples of the above-described combination of a positi~rely charged substance and a negatively charged substance include, but are not limited to, complexes of a negatively charged substance selected from the group consisting of DNA, RNA, 1?NA, a polypeptide, a chemical compound, and a complex thexeof and a positively charged substance selected from the group consis'~ing of a cationic polymer, a cationic lipid, a cationic polyamino acid, and a complex thereof . In a preferred embodiment of the present invention, a biological agent of interest may be a nucleic acid molecule or a molecule derived from such a nucleic acid molecule. This is b~;cau$e most nucleic acid molecules carry genetic information, from which cellular information can be obtained.
In another aspect, the pxesent invention relates to data obtained by a method comprising the steps of: a) providing and fixing the ce~~ to a support: and b)~ monitoring a biological agent or an aggregation of Azoo~
biological agents on or within the cell over txxne to generate data of the profile of the cell_ Such data is Qbtained by the method which is not conventionallx av'ail.abl.e, and is thus novel. Therefore, the present invention provides a recording medium storing such data zn another aspect, the present invention relates to a method for generating profile data of infdrrnatlon of a plurality of cells in a consistent environment. The method comprises the steps of:
a) providing a plurality of cells on a support which can ma~.ntain a consistent environment; and b) monitoring a biological agent or an aggregation of biological agents on or within the cells over time to generate praf~.le data for the cells. zn this aspect, the pxesent invention is characterized in that profile data or information for a plurality of sells in a consistent environment can be obtained. Techniques for providing such an environment z5 also within the scope of the present invention. To provide a consistent environment for a plurality of cells, a fixing agent, such as a salt or the like, may be used fox the support in the present invention. A comb~.z~ation of a salt, a complex of a positively charged substance and a negatively charged substance, and cel7.s may fix the cells to the support. Any salt may be used in the present invention. Examples of such a salt include, but are not limited ta, calcium chloride, sodium hydrogen phosphate, sodit~nt hydxogezx carbonate, sodium pyruvate, HEPES, radium chloride, potassium chloride, magnesium sulfide, iron nitxate, amino acids, vitamins, and the ~.il~e. Examples of the above-described combination of a positively charged substance and a negat~.vely charged substance include, but are not limited to, complexes of a negativeJ.y charged substance selected from the group consisting of DNA, RNA, PNA, a polypeptide, a chemical compound, and a complex thereof and a positively charged substance selected from the group consisting of a cationic polymer, a cationic lipid, a cationic polyamino acid and a complex thereof . In a preferred embodiment of the present invention, a biological agent of interest may be a nucleic acid molecule or a molecule derived Exam such a nucleic acid molecule . This is because most nucleic acid molecules carry genetic information, from which cellular information can be obtained.
In a preferred embodiment, an actin-like acting substance is preferably provided to the cells in the method of the presEnt invention. The actin-like acting Substance acts on actin within the cells to de~arzn the internal cytaskeletan to facilitate introduction of an external factor into the cells. The presence of such an actin-like acting substance makes it possible tc investigate an influence of an external factor of interest on the cells.
In one embodiment, a biological agent targeted by the present invention is at least one factor selected from the group consisting of nucleic acids, proteins, sugar chains, lipids, law molecular weight molecules, and composite molecules thereof.
zn a preferred embodiment, cells targeted by the present invention are preferably cultured for a certaix'r period of time without stimulation before monitoring. This procedure is performed for the purpose of synchronizing the target calls. The period of time required for synchronization is, for example, advantageously at least one day, more preferably at least two days, even more preferably at least 3 days, and still even more preferably at least 5 days. It should b~ noted that as the period of time for culture is increased, the necessity of maintaining the culture conditions increases. In the synchronization procedure, the same medium is preferably supplied to cells.
Therefore, the culture medium is preferably consistent or at least changed in a consistent manner. To achieve this, a means for causing convection in the medium may be 1S preferably provided and used.
In a more preferred embodiment, a biological agent provided to a cell in the present invention may comprise a nucleic acid molecule encoding a gene. The nucleic acid molecule encoding a gene is preferably transfected into a cell. Preferably, such a biological agent may be provided along with a tranrsfection reagent (gene introduction reagent). More preferably, the nucleic acid molecule encoding a gene may be provided to a cell along with a gene introduction reag~:nt and an actin-like acting substance. Tn this case, the cell is preferably provided with a complex of a salt, a positively charged substance, and a negatively charged substance (in this case, a nucle~.c acid molecule and a gene introduction reagent). Thus, the cell and the target molecule are fixed on a support. In addition, this technique makes it possible to allow separate biological agents (e , g . , nuc~.eic ac~.d molecules ) to be separately introduced into cel~.s without a partition. As substantially no partition is used, a pl.uraZ~.ty of cells can be mon~.toxed in substantially a consistent environment.
Further, different biological agents can be introduced into a cell, thereby making it possible to obtain a profile of a state of the cell affected by the biological agents. Such a profile can be stored as data. Such data may be stored in a certain standard format, and therefore, can be reproduced and compared. Thus, the present invention has an effect which is not achieved by canventional bzo~.vg~.cal assays. Such data, once obtained and stored in such a standard format, can be extracted and used far various purposes and a number of times. For example, researchers can perform "virtual experiments" to conduct various analyses under the same conditions While taking into consideration diffErences in a substantially infinite number of parameters. In addition, since virtual experiments and the results thereof are stored in a raw data format, undergraduate and graduate students, who otherwise spend mast of their schaa~l life doing laboratory work, can receive education in data analysis in the true sense. mhe above-described cellular profile data can be easily standardized, thereby making it possible to do research based on data which may have been obtained by e~tperiments under the same Conditions aver the world. Such data may be distributed irz a standardized form. Such a standardized form may be readable to typical computers (e.g., computers having a commonly available OS, such as Windows, Mac, UNTX, LINtIX, or the like) . Data produced in the present invention may include generated cellular profile data, information about experimental conditions used in data generation, information about cells, information about environments, and the like.
In a preferred embodiment, a profile targeted by the present invention may include a profile of gene expression, a profile of an apoptotic signal, a profile of a stress signal, a profile of the localization of a molecule (preferably, the molecule is labeled with a fluorescent, phosphorescent, yr radioactive substance, or a combination.
thereof), a profile of changes in cellular morphology, a profile of a promoter, a profile of a promoter dependent on a specific pharmaceutical agent (e. g., antibiotics, liganda, toxins, nutrients, vitamins, hormones, cytokines, etc.), a profile of an intermolecular interaction, and the like. In an embodiment in which the present invention targets a profile of a promoter dependent on a specific pharmaceutical agent, it is preferable that the present invention may further comprise administering the specific pharmaceutical agent.
rn a preferred embodiment, the present 2S invention may further comprise providing an external stimulus to the cell. Such an external stimulus may or may not be a biological agent . The extsraal factor may be any factor and ~.ncludes, without limitation, substances or other eJ.ements (e. g., energy, such as ionizzng radiation, radiation, light, acoustic wares, and the like).
In one embodiment, an external factor used ix~
the present invention may be RNAi. RNAi can be used to substantially suppress an arbitrary gene. It is possible to produce RNAi for all existing genes and investigate the effect of RNAi on the genes. RNAi can be created by techniques well known in the art.
In anothex embodiment, an external factor of the present invention may comprise a chemical substance which does not exist in organisms . By providing such a chemical substance which does not exist in organisms, it is possible to collect a variety of information. Once collected, such data can be reused. Therefore, assuming that a chemical substance which does not exist in organisms is not substantially available, if data can be obtained once for such a chemical substance in accordance with the present invention, research can continue without worrying about the availability of such a chemical substance.
In one embodiment, an external factor targeted by the present invention may comprise a ligand to a cellular receptor. By analyzing a ligand, it is possible to study various signal transduction pathways. Therefore, in such a case, a profile obtained according to the present invention may be a profile of receptor-ligand interactions.
In a preferred embodiment pf the present in~rentian, a pro:~i~.e of cellular morphology may be obtained.
in this case, a method of the present invention may further comprise applying a stimulus to a cell which may be selected from the group consisting of overexprESSion of a genE, underexpression of a gene, knock down of a gez~e, addition of an external factor, and a change in an environment.
rn a preferred embodiment, a profile obtained according to the present invention may be a profiJ.e of interactions between molecules present within a cell. Such an intermolecular interaction includes, but is not limited to, interaction between molecules present in a signal transduction pathway, interaction between a receptor and a ligand, interaction between a transcription factor and a transcription factor sequence, and the like.
In another preferred embodiment, a profile obtained according to the present invezxtion may be a profile of interaction between molecules present in a cell. In this case, a method of the present invention may further comprise obsexwing a cell using a technique selected from the group consisting of a two--hybrid method, FRET, and HRET. The two-hybrid method detects intermolecular interaction within a cell_ Specifically, this technique is described in, for example, Protein-Protein Tnteractions, A MOLECULAR
CLONING MIaI~TUAL, Edited by Erica Gvlernis, Cold Spring Fiabor Laboratory Press, Cold Spring Harbor, New York (this document also describes FRET). FRET is a technique for detecting inter- or intro-molecular resonance energy shift as a fluorescent wavelength, and zs described in, fox example, Protein-Protein Interactions (supra): and Miyaws.ki A., Visualization of the spatial and temporal dynam~.cs of intracellular signaling, Dev. Cell, 2003 Mar; 4 (3) :295-305.
BRET is an intermolecular interaction assay system and is described, for example, 8oute N. , The use of resonance energy transfer in high-throughput screening: BRET versus E'RET, Trends Pharmacol Sci., 2002 Aug; 23(8):351-4.
Tn a preferred embodiment, cells targeted by the present invention are preferabJ.y arranged on a support in a pattern of an array. In this case, preferably, a plurality 1p of cells targeted by the present invention may be spaced at intervals of 1.0 Grn at maximum, more preferably 1 cm at maximum, even more preferably 1 mm at maximum, and most preferably 0.1 mm at maximum. The cells need to be spaced at minimum intervals. Such intervals may be preferably set so that substantially no interaction occurs.
In one embodiment, a profile obtained according to the present invention may or may rzot be obtained in real time. A real time profile may be advantageous. GThen simultaneity is important, it is important to obta3.n a profile in real time. Alternatively, when a profile is intended to be stored, the profile is not necessarily obtained in real time.
In. an additional embodiment, the present invention further comprises fixing a cell to a solid phase support. In this case, the cell is fixed to the solid phase support along with a salt, a complex, an actin-like acting substarzce, or the like.
Tn one embodiment, data generated according to the present invenaion may contain information about a profile. In. a preferred embodiment, data generated according to the present invention may contain information about conditions for monitoring, information about a cellular state, information about an external factor, inforznat~.an about an environment, and the like.
In a preferred embodiment, at least two biological agents may be preferably monitored in the pxesent invention, mare preferably at least 3 biological agents, and even more preferably at least 8 biological agents.
Alternatively, all b~.ological agents in a certain specific category (e. g., all ol~actary receptors, all gustatory receptors, etc.) may be preferably monitored.
Alternatively, in another preferred embodiment, the present invention may further comprise arbztxarily selecting the above-described biological agents.
In a preferred embodiment, a cell targeted by the present invention may be selected from the group consisting of stem cells and somatic cells.
Tn one embodiment, a support used in the present invention is preferab~.y a solid phase support. This is because cells are easily faxed to such a support. Such a solid phase support may be made a~ any material known in the art. The support may be in the foxm of a substrate.
In one embodiment of the pxesent invention, the above-described biological agent may be a nucleic acid and the above-described cell may be trans~ected with the nucleic acid. Hy transfecting the cell with the nucleic acid, an inf~.uence of the nucleic acid on the cell can be collected in real time or in a standardized storable format into data or a profile. This cannot be achieved by conventional techniques. In a preferred embodiment, transfection may be performed in solid a phase or in a liquid phase. More preferably, transfection may be advantageously performed in a solid phase . This is because data collection and standardization or normalization can be more easily carried out.
1.5 In a preferred embodiment of the present invention, a profile may be subjected to a process selected from the group consisting of phase comparison, calculation of a difference ~xom a control profile, signal processing, and multivariate analysis. Data processed in such a manner may fall within the scope of the present invention.
In another aspect, the present invention provides a method for presenting profile data of information about a plurality of cells in a consistent environment. The method comprises the steps of: a} providing a plurality of cells on a support capable of reta~.ning the cells in a consis~.ent environment; b} monitoring a biological agent or an aggregation of biologicaX agents on or within the celxs over t~.me to generate profi7.e data for the cells; and c} presenting the data.
The above-described support capable of retaining a plurality of cells in a cansisterit environment can be achieved as~ described elsewhere herein. The step of generating data can be performed as described elsewhere herein. The step of presenting data can be performed as described elsewhere herein. Examples of a method of performing such presentation include, but are not limited to, techniques of using ~raridus sensory means, such as visual means, auditory means, olfactory means, tactile means, gustatory means, and the like. Preferably, a visually presentat~.on means may be used. Such visual means include, without limitation, a computer display and the like.
Preferably, in the presentat~.on method of the present invention, presentation may be performed in real time. Alternatively, storr~d data may be stored and presentation may be delayed. when presentation should b~
performed ~.n real time, data signals may be transferred ~D directly to, for example, a display.
In another aspect, the present invention provides a method for determining states of cells in a consistent environment. The method comprises the steps of:
a) providing a plurality of cells on a support capable of retaining the ce~.ls in a consistent environment:
b) monitox~.ng 'a biological agent or an aggregation of b~.ological agents on or within the cells over time to generate profile data for the cells: and c) determining the 34 states of the cells based on the data.
The above-described support capable of retaining a plurality of cells in a consistent environment can be achieved as described elsewhere herein. The step of S generating data can be performed as described elsewhere herein. The step of determining the states of the cells may be performed by correlating the generated data with information about the cells, or comparing the generated data with standard data. In this case, the data may be statistically processed.
Therefore, in a certain embodiment, th$ present invention may Further comprise correlating a profile obtained according to the present invention with a state of a cell before obtaining the time-lapse profile. To perform determination smoothly, the cells targeted by the pre9ent invention may ad~crantageously include cells whose states are known. It is possible to store data of cells whose states are known, determination can thus be quickly performed by comparir~g data between the known cell and unknown ce~.ls .
During determination, at least two biological agents are preferably present. I~n this case, the plurality of biological agents may belong to heterologous categories (e. g., proteins and nucleic acids, etc.) or homologous categories.
Preferably, the present invention may further comprise arbitrarily selecting a biological agent. Any biological agent can be selected and used to characterize a state of a cell to some extent, and in some cmsea, identification is possible. Thus, the present invention has s.r~ effect which cannot be e~tpected from conventional techniques.
In the determination method of the present invention, data may be preferably generated in real time.
G~hen data is generated in real time, an unknown substance or state of an unknown cell may be determined in real time.
2n the determination method of the present invention, examples of a state of a target cell include, but are not limited to, differentiated states, undifferentiated states, cellular responses to extez~nal factors, cell cycles, growth states, and the J.ike.
A cell, targeted by the present invention may be either a stem ce~,l or a somatic cell. Any somatic cell may be used. A cell may be selected by those skilled in the. art, depending on the purpose of use of the cell.
A solid phase support used in the determination method of the present inv~entifln may comprise a substrate.
In the present invention, such a substrate can be used as a part of a computer system, so that determination can be automated. An exemplary configuration of such a system is shown in Figure 32.
Tn a preferred embodiment, in the determination method of the present invention, the bio~.ogical agent may be a nucleic acid moXecule, and the cell is transfected with the nucleic acid molecule. Transfeatxon may be performed on a solid phase support using any material, but preferably a gene introduction agent, more preferably a salt, an actin-like acting substance, or the like. Transfection may be performed in solid phase or in liquid phase, and preferably in solid phase.
Ln a determination method of the present invention, a target biological agent may be capable of binding to another biological agent. By investigating a biological agent having such a property, a network mechanism in a cell may be elucidated.
In a determination method of the present invention, the determinat~.on step may comprise a mathematical process selected from the group consisting of comparison of phases of profiles, collection of differences from a control profile, signal proces$ing, and multivariate analysis. Such processing techniques are well known in the art and described in detail herein.
In another aspect, the present invention provides a method for correlating an external factor with a cellular response to the external factor. The method compz~ises the steps of: a) exposing a plurality of cells to an external factor on a support capable of retaining the cells in a consistent environment: b) monitor~.ng a biological agent or an aggregation of biological agents on or within the cells over time to generate profile data for the cElls: and c) correlating the external factor with the profile. exposure of the cells to the external factor may be achieved by placing the cells and the external fs.ctor into an environment in which the cexls are contacted with the extexnaJ. factor. For example, when the cells are fixed on the support, the external factor is added to the support to achieve exposure. Techniques for generating and coxxelating data are also well known in the art, and may 3.~ be used singly or in combination. Preferably, atatistioal processes axe performed to generate statistically signi~i.cazat data and information.
In a preferred embodiment, in the Correlation method of the present in~rention, the cells may be fixed on the support. Since the cells are fixed, data can be easily standardized, so that data can be significantly efficiently processed.
In a preferred embodiment, a correlation method of the present invention may further comprise using at 7.east two external factors to obtain a profile fox each external factor. Techniques for obtaining such a profile are well described here~.n.
More preferably, the correlation step may fiurther comprise dividing at least two profiles into categories and classifying the external factoxs corresponding to the xespectxve pxofil~s into the categories. By categorization, data can be processed in a more standardized manner.
3~T007 Zn a preferred embodiment, a profile obtained by the present invention may be presented in real time. When data is intended to be stored, data may riot be particularly presented in real time.
In ~, preferred embodiment, a cell used in the present invention may be cultured on an array. In such a case, therefore, the cell is preferably covered with medium.
Any medium which is commonly used for cells may be used.
zn a preferred embodiment of the present invention, the step of monitoring a profile may comprise obtaining image data from the array. Particularly, when a profile contains visual information (e.g., emission of fluaresaence due to gene expression), the profile can be obtained by capturing image data_ In a correlation method of the present invention, the step of correlating an external f~.ctor with a profile may comprise distinguishing between phases of the profile.
Distinguishing phases of the profile can be achieved only after the present invention provides time-lapse prafz~.es obta~.zxed in a consistent environment .
An external factor targeted by the present invention may be selected from the group consisting of a temperature change, a humidity ohange, an electromagnetic wave, a potential difference, visible light, infrared light, ultraviolet light, X-rays, a Chemical substance, a pressure, a gravity change, a gas partia,z pressure, and an osmotic pressure. Preferably, the chemical substance may be a biological molecule, a chemical compound, or a medium.
Examples of such a biological molecule include, but are not limited to, nucleic acid molecules, proteins, lipids, sugars, prateolipids, lipoproteins, glycoprcteins, proteaglycan,s, and the like. Such a biological molecule may also be, fax example, a hormone, a cytokine, a cell adhesion 7.0 factor, an extracellular matrix, or the like.
Alternatively, the chemical substance may be either a receptor agonist or antagaz~ist.
In another aspect, the present invention relates to a method for identifying an unidentified external factor given to a cell from a profile of the cell. The method comprises the steps of: a) exposing a cell to a plurality of known external factors on a support capable of retaining the cell in a Consistent env~.xozxment; b) monitoring a biological agent ax an aggregation of biological agents on or within the cell over time to generate a profile of the cell to each of the known external factors and to generate profile data for the cell; c) correlating each of the known external factors with each of the profiles; d) exposing the cell to an unidentified external factor; e) monitoring a biological agent or an aggregation of biological agents on or within the cell. exposed to the external factors over time to obtain a profile of the cell with respect to the unidentified external factor; f) determining, from the profiles obtained in the step of b) , a profile cdrrespnnding to the profile obtained the step of e) : and g) determining that the unidentified external factor is the knotan e~tternal factor corresponding to the profile determined in the step of f). Techniques for exposure to external factors, data generation, corzelation, exposure to unidentified external factors, and the like are described elsewhere herein and can be selected as appropriate depending on the purpose by those skilled in the art taking such descriptions into consideration.
Tn another aspect, the pxeserit invention provides a method for ident~.~ying an unidentified external factor given. to a cell from a profile of the cell. The method comprises the steps of: a) providing data relating to a correlation relationship between known external factors and protiles of the cell in response to the known external factors, in relation to a biological agent or an aggregation of biological agents on or within the cell: b) exposing the cell to the unidentified external. fs.ctor; c) monitoring the biological agent or the aggregation of the biological agents on yr within the cell to obtain a profile of the cell:
d) determining, from the profiles provided in the step of a) , a profile corresponding to the profile obtained in the step of c); and e) determining that the unidentified external factor is the known external factor corresponding to the profile def.ermined in the step of d) . Techniques for exposure to externalfactors, data generation, correlation, exposure to unidentified external factors, and the like are described elsewhere herein and can be selected as appropriate depending on the purpose by thc~sa skilled in the art taking such descriptions into consideration.
In another aspect, the present invention provides a method for obtaining a profile relating to ~.nformation for a plurality of cells in a con~i~stent environmez~t. The method comprises the steps of:
a) providing a plurality of cells on a support capable of retaining the cells i.~x a consistent environment; and b) monitoring a biological agent or an aggregation of biological agents on or within the cell over time to generate a profile of the cells. Techniques for exposure to external factors, data generation, correlation, exppsure to unident~.fied external factors, and the like axe described elsewhere herein and can be selected as appropriate, depending on the purpose by those skilled in the art taking such descriptions into consideration.
In another aspect, the present invention relates to a recording medium in which data generated by a method for generating cellular profile data of the present ~.nventian is stored. Data may be stored in any format. Any recording medium may be used. Examples of such a recording medium include, but are not limited to, CD-ROMs, flexible disks, CD-Rs, CD-RWs, MOs, mini disks, DVD-ROMs, DVD-Rs, memory sticks, hard disks, and the like. The present invention also relates to a transmission medium in which data generated by a method for generating cellular profile data of the present invention is stored. Examples of such a transmission medium include, but are not limited to, networks, such as ~.ntranets, the Tnternet, and the like.
A~007 A recording medium or transmission medium of the present invention may further contain data relating to at least dne piece of information selected from the group consisting of information about conditions for the monitoring step, information about the profile, information about the cellular state, and information about the biological agent. Data relating to such information may be stored while being linked to one another. Preferably, the data may be advantageously standardized. Standardized data can be distributed on general distribution pathways. The above-described linkage may be constructed far each cell br for each biological agent, or for both.
Tn another aspect, the present invention relates to data generated by a method for generating cellular profile data of the present invention. Such data canz'~ot be generated by conventional techniques and is thus novel.
In another aspect, the present invention provides a system for generating profile data of information for a plurality of cells in a consistent environment. the system comprises: a) a support capable of retaining a plurality of cells in a consistent environment: b) means for monitoring a biological factor or an aggregation of b~.ological factors on or within the cells over time: and c) means for generating profile data for the cells from a signal obtained fxom the monitoring means. The support capable of retaining cells in a consistent environment can be made by those skilled in the art using a technique first Azoo~
provided by the present invention. Such a technique is attributed to the finding that cells are fixed and arrayed without a partition. Examples of the monitoring means include, but are not limited to, microscopes t a . g . , optical microscopes, fluorescence mi.crascopes, phase-contrast microscopes, etc.), electron microscopes, scanners, naked eyes, infrared cameras, confocal/nonconfocal microscopes, CCD cameras, and the like. An exemplary configuration of such a system is shown in Figure 32.
zn a system of the present invention, the system may riot necessarily contain cells from the start, but preferably may contain cells which are advantageously fixed on a support. Tn such a case, f~.xation is preferably standardized. In addition, the cells are fixed and spaced, for example, wit.haut limitation, at intervals of 1 mm or the like.
In a preferred embodiment, at least one substance selected from the group consisting of salts and actin--like acting substances may be preferably adhered to the support . Hy adhering ce~.ls to the support with a salt or an actin-like acting substance, or preferably with both, fixation of the cells and/or introduction of a substance into the cells can be enhanced.
Examples of the monitoring means used in the system of the present invention include, but axe not limited to, optical microscopes, fluorescence microscopes, phase--contrast microscopes, reading devices using a laser source, means using surface plasmon resonance (SPR) imaging, electric signals, chemical or biochemical markers singly or in combination, radiation, cozxfocal microscopes, nonconfocal microscopes, differential interference microscopes, stereoscopic microscopes, video monitors, infrared cameras, and the lzke. Preferably, a scanner (e.g., a scanner fox scanning a surface of a substrate using a whzte light source ox laser) may be used. The reason a scanner is preferable is that fluorescence can efficiently transmzt 7.0 excited energy and microscopic technology can be easily applied. Further, measurement can be advantageously performed without significant damage to cells. An exemplary configuration of such a system is shown in Figure 32.
rn another aspect, the present invent~.on provides a system for presenting a profile of information for a plurality of cells in a consistent enva.~conment. The system comprises: a) a support capable of retaining a plurality of cells in a consistent environment: b) means for monitoring a biological factor or an aggregation of biological factors on or within the cells over time; c) means for generating profile data for the cells from a signal obtained from the monitoring means; and d) means for presenting the data. The support, the monitoring means, and the data generating means can be made as described elsewhere herein. The means for presenting data can be achieved by techniques well known in the art. Examples of such a data presenting means include, but are not limited to, computer displays, loudspeakers, and the like. An exemplary Azaa7 configuration of such a system is shown in Figure 32.
A presentation system of the present invention may further comprise a plurality of cells, in which the cells are preferably fixed to the support . In such a case, at least one substance selected from the group consisting of salts and actin-like acting substances may be preferably adhered to the support. By adhering cells to the support with a salt or an actin-like acting substance, or preferably with both, fixation of the cells and/or introduction of a substance into the cells can be enhanced.
Any mon~.toring means may be used. Examples of the monitoring means include, but are riot limited to, optical x5 microscopes; fluorescence microscopes; phase microscopes;
reading devices using a laser source; means using surface plasmon resonance (SPR)imaging, electric signals, chemical or biochemical markers singly or in combination; and the like.
zo Any data presenting means may be used, including, without limitation, displays, loudspeakers, and the like.
In another aspect, the present invention 25 pxovides a system for determining a state of a cell. The system comprises: a) a support capable of retaining a plurality of cells in a consistent env~.roxlmen.t: b) means for monitoring a biological factor or an aggregation of biological factors on or within the cells over time: c) means 34 fpr generating data from a signal obtained by the monitoring means; and d) means for extrapolating the state of the cell firom the data. The support, the monitoring means, and the data generating means can be made by these skilled in the art as described elsewhere herein. The means fc~r extrapoXating a state of a cell from data may be produced an,d used by techniques well known in the art. For example, measured data can be compared with standard data for known cells to achieve extrapolation. A device storing a program for such extrapolation or a computer capable of executing 7.0 such a program may be used as the extrapolation means . An exemplary configuration of such a system is shown in Figure 3Z.
In another aspect, the present invention provides a system for correlating an external factor With responses of cells to the external factor. The system comprises: a) a support capable of retaining a plurality of cells in a consistent environment: b) means for exposing the cell to the external factor; c) means for monitox~.ng a biological factor or an aggregation of biological factors on or within the cells over times d) generating profile data for the cells from a signal from the monitoring means ~ and e) means for correlating the externax factor with the profile. The support, the monitoring means, and the data generating means can be made by those skilled in the art as described elsewherE herein. The means for exposing the Dells to the external factor can be designed and carried out as appropriate by those skilled in the art depending on the properties of the external factor_ The Correlation means can employ a recording medium storing a program for correlation or a computer capable of executing such a program.
Preferably, a system of the present invention comprises a plurality of cells. An exemp~.ary configuration of such a system is. shown in figure 32.
In another aspect, the present invention provides a system for identifying an unidentified external factor given to a cell based on a profile of the cell. The system comprises: a) a support capable of retaining a plurality of cells in a consistent environment: b) means far exposing the cell to one or mare known external factors;
c) means for monitoring a biological factor or an aggregation of biological factors on or within the cells over time; d) means for obts.ining a profile of the cell with respect to each of the known external factors to generate profile data for the cell; e) means fax correlating each of the known external factors with each profile: f) means for exposing the cell to the unidentified external factor;
g) means for comparing the profiles of the known external factors obtained by thr~ means of d) with the profile of the unidentified external factor to determine a profile of the unidentified external factor from the profiles of the known external factors, wherein the determined unidentified external factor is the known external factor corresponding to the determined profile. The support, the exposure means, the monitoring means, the data generating means, and the correlation means, and the other exposure means can be made and carried out as appropriate by those skilled in the apt as described elsewhere herein. The means for determining a corresponding profile can also be made and carried out by utilizing a retarding medium storing a program capable of executing such a determination process and a computer capable of executing such ~ program. Preferably, a system of the present invention comprises a plurality of cells.
An exemplary configuration, of such a system is shown in E'igure 32.
In another aspect, the present invention provides a system for identifying an unidentified external factor given to a cell based on a profile of the cell. The system comprises: a) a recording medium storing providing data relating to a correlation relationship between known external fetters and profiles of the Cell irr response to the known external factors, in relation to a biological ~.5 factor or an aggregation of biological factors an or within the cell; b) means for exposing the cell to the unidentified external factor: c)a support capable of retaining a plurality of cells in a consistent environment ; d)means for monitoring a biological factor or an aggregation of b~.alagical factors on or within the cells over time; e) means for obtaining a profile of the cell from a signal obtained by the monitoring means; f ) means for determining, from the profiles stored in the recording medium of a.), a profile corresponding to the profile obtained with respect to the unidentified external factor, wherein the determined unidentified external factor is the known external factor corresponding to the detex~mirled profile. The support, the exposure means, the monitoring means, the data generating means, and the correlation means, and the other exposure means can be made and carried out as appropriate by thane Azoo7 skilled in the art as described elsewhere herein. The means for determining a corresponding profile can also be made and carried out by utilizing ~ recording medium storing a program capable of executing such a determination process and a computer capable of executing such a program.
Preferably, a system of the present invention comprises a plurality of cells. An exempxary configuration of such a system is shown in Figure 32, In another aspect, the present invention relates to a support capable of maintaining a consistent en~criror~,ment for a plurality of cells. Such a support was first provided by the present invention. By utilizing such a support, a plurality oP cells can be analyzed in a consistent environment.
Preferably, cells are arranged on a support in the form of an array. This is because standardized analysis can be achieved. In this case, the support. may preferably comprise a salt or an actin-like acting substance. More preferably, the support may advantageously comprise a complex of a positively charged substance and a negatively charged substance. This is because cells can be easily fixed to the support using such a complex. Actin-like acting substances are preferable when the interior of cells is analyzed, since the actin-like acting substances increase the efficiency of introduction of external factors into cells. Therefore, in a preferred embodiment of the present invention, the support may comprise a salt arid an actin-like act~.ng substance, and more preferab~.y may comprise a complex of a positively charged substance and a negatively charged substance.
A support of the present in~erentiori i~5 characterized in that, cells may be provided and spaced at intervals of 1 mm. In the case of such ~.nterva~.s, it is not conventionally possible to provide an environment without a partition. wherefore, the present invention has a remarkable effect, as well as practicability, applicability and utility.
In a preferred embodiment, a support of the present invention may comprise a cell fixed thereto. In a more preferred embodiment, a support of the present invention may comprise a biological factor fixed thereto.
In a preferred embodiment, at least two biological factors may be fixed to the support. Such biological factors may be factors selectEd from the group consisting of nucleic acid molecules, proteins, sugars, lipids, metabolites, low molecular weight molecules, and complexes thereof, and fsctors containing physical elements and/or temporal elements.
In a more preferred embodiment, a cell and a biological factor may be fixed to a support of the present invention in a mixed manner. The biological factor and the cell may be provided so that they aan interact with each other. Such interaction may vaxy depend~.ng on the biological factor. According to the propert~.es of the biological factor, those skilled in the art can understand 23~
how the biological factor interacts with the cell and where the biological~factor~is positioned so as to interact with the cell .
In a preferred embodiment, a salt, a complex of a positively charged substance and a negatively charged substance, and an actin-like acting substance are fixed along with a cell and a biological factor to a support of the present invention.
Zn a more preferred embodiment, a salt, a complex of a positively charged substance and a negatively charged substance, and an actin-like acting substance are fixed along with a cell and a biological factor to a support of the present invention in the form of an array. With such a structure, a cell chip capable of generating the profile data of a cell can be provided. The support has a structure in which a salt, a complex of a positively charged substance az~d a negatively chs.rged substance, and an actin-like acting substance are fixed along with a cell and a biological factor in the form of an array. Such a support is also called a "transfection array".
Examples of a salt used in the support of the 2S present invention include, but are not limited to, calcium chloride, sodium hydrogen phosphate, sodium hydrogen.
carbonate, sodium pyruvate, HEPES, sodium chloride, potassium chloride, magnesium sulfide, iron nitrat~, amino acids, vitamins, and the like. A preferable salt is, for 3Q example, without limitation, sodium chloride or the like.
Examples of a gene introduction agent used in the support of the present invention include, but are not limited to, cationic polymers, cati.onie lipids, polyamine-based reagents, polyimine-based reagents, caJ.cium phosphate, oligofectarnin, and oligofectors and the like. preferably the gene ~.ntroduction reagents used may be preferably, but are not limited to lipofectamines, oligofectamines and oligofectors.
Examples of an actin-like acting substance used in the support of the present invention include, but are not limited to, fibronectin, laminin, ,sritronectin, and the like. A preferable actin-like acting substance is, for examp~.e, without limitation, fibronectin.
Examples of a nucleic acid molecule used in the support of the present invention include, but are not limited to, nucleic acid molecules comprising transaript~.on control sequences (e. g., promoters, enhancers, etc.}, gene coding sequences, genomic sequEnces containing nontranslation regions, nucleic acid sequences encoded by the genome of a host (a fluorescent protein gene, E. coli/yeast self-replication origins, a GAh4 domain, etc. ) , and the like.
preferable nucleic acid molecules include, but are not limited to, transcription control sequences (e. g., promoters, enhancers, etc.), gene coding sequences, genomic sequences conta~.nirig nontranslation regions, and the like.
Examples of a cell used in the support of the present invention include, but are not limited to, stem cells, established cell lines, primary culture cells, insect cells, bacterial cells, and the like. Preferable cells include, but are not limited to, stem cells, established cell lines, primary culture cells, and the like.
Examples of a material for a support of the present invention include, but are not limited to, glass, silica, plastics, and the like. Preferable materials include, but are not limited to, the above, described materials with coating.
In another aspect, the present invention provides a method for producing a support comprising a 1S p~.urality of cells fixed thereto and capable of maintaining a consistent environment for the cells. The method comprises the steps of: A) providing the support; and B) fixing the cells via a salt and a complex of a positively charged substance and a negatively charged substance onto the support. The step of providing a support may be achieved by ob'~aining a commercially available support or molding a support material. A support material may be preparEd by mixing starting materiaJ.s for the material as required. The fixing step can be carried out by using techna.ques known 2S in the art. Examples of such fixing techniques include, but are not limited to, an ink jet printing technique, a pin array technique, a stamping technique, and the like. These techniques are well known and can be performed as appropriate by those sk~.l,led ~.n the art _ Tn a preferred embodiment, the fixing step in the present invention may comprise fixing a mixture of the salt, the complex of a gene introduction agent and an actin-like acting substance (positively charged substances) arid a nucleic acid molecule (a negatively charged substance), and the cell in the form of an array.
Such a fixing step may be achieved by printing techniques .
In another aspect, the present invention provides a device for producing a support oaxnprising a plurality of cells fixed thereto and capable of maintaining a consistent environment for the cells. The device comprises : A) means for providing the support: and B) means fpr fixing the cells via a salt and a complex of a positively charged substance and a negatively charged substance onto the support. The support may be obtained using means which can perform the above-described methods. Examples of such means incl.udE, but are not limited to, a support moJ.di.ng means, a material tormulating.means (e.g., a mixing means) , and the like. The molding means can employ techniques well known in the art. The fixing means may comprise a printing means. As such a printing means, commercially available ink jet printers can be used.
2b (l7igital Cell) As used herein the term "digital cell" refers to a collection of at least one experimental data corresponding to a cell of experimental interest . Such experimental data is a correlation between the conditions used for the experiments aa~xducted on an actual cell in the real world, and the experimental results thereof. The digital cell is composed suoh that when an experimental candition is given, an experimental result relating to the experimental.
condition will be reproduced.
By using the digital cell, expexixnental results conducted az~ an actual cell can be reproduced an a computer system. This allows institutions or indiv~.duals having no experimental facilities to conduct cutting-edge studies relating to a cell. As a result, it allows the introduction of business entities having a primary interest in disciplines other than that of the present technical art, which could not been achieved to date, prior to the disclosure of the present invention.
Figure 33A depicts an example of data structure of a digita.J. cell. This example represents a digital cell by a collection of three experimental data A1, A2 and A3 relating to cell A.
Each of experimental data A1, A2 and A3, comprises cell parameter, environment parameter and stimulus parameter as parameters indiaatirig experimental conditions, and stimulus response result as an experimental result.
As used herein, the cell parameter specifies a cell of experimental interest. The environment parameter specifies an environment under which the ael~. specified by the cell parameter is cultured. The stimulus parameter specifies a stimulus given to the cell specified by the cell parameter. The stimulus response result shows a result which the cell specified by the cell parameter responded to the stimulus specified by the stimulus parameter under the environment specified lay the envzrorunent parameter.
Experimental data A1 shows that cell A was cultured in a medium called "L~MEM", under the culture condition of pH "7", temperature "37" degree Celsius, COZ
concentration "5" %, arid a stimulus consisting of a reporter called "Tet-OFF GMV EGF" or "MCV EGFP" and a chemical stimulus (agent) "Doxycycene" is given thereto to obtain a stimulus response result. The stimulus response result is represented by "cell dynamic data 1" and "reporter measurement data 1".
Expexzmental data A2 shows that cell A was cultured in a medium called "DMEM", under the culture condition of pH "7", temperature "37" degree Celsius, COz concentration "5" ~, and a stimulus consisting of a reporter called "c-Los" and a chemical stimulus (agent) "P5C833" is given thereto to obtain a stimulus response resu7.t. The stzznul.us xespon.se result is represented by "cell dynamic data 2" and "reporter measurement data 2".
Experimental data A3 shows that cell A was cultured in a medium called "DMEM", under the culture condition of pH "5", temperature "39" degree CelCius, GOZ
concentration "4" ~, and a stimulus cons~.sting of a reporter called "CRAB" and a chemical stimulus (agent) "Vindecine"
is given thereto to obtain a stimulus response result . The stimulus response resu3.t is represented by "cell dynamic data 3" and "reporter measurement data 3".
As such, parameters indicating experimental conditions (a cell parameter, an environment parameter and a stimulus parameter) and a stimulus response result showzng an experimental result are correlated. Such correlatzvn and data correlated thereby are called experimental data.
The digital cell is provided as a collection of at least one experimental data an a cell of experimental interest.
Figure 338 shows another example of data structure of the diga.tal cell. This example shows the layered structure of the data structure shown in Figure 33A.
As such, layering the structure of the data structure of the digital Gell allows expression of the same content with less data than the data structure shown in Figure 33A.
In the examples of figures 33A and 33B, correlation has bean presented by a unidirectional link (arrows in the Figures) between the parameter showing the experimental conditions and experimental results. Iiawever, methodsof correlation are not limited thereto. Any methods of correlation may be used herein.
(Production of a digital cell) Figure 34 shows an example of the procedure of a process of producing a digital cell. This procedure may be implemented by any type of computer_ Step 5340.: Cell parameters specifying a cell of experimental interest are obtained. CeXI parameters can be obtained by, for example, receiving cel 1 parameters inputted by a user into a computer. Alternatively, data outputted from an experimental apparatus ma y be obtained by collection ox analysis of the same in an automatic manner by a computer to obtain cell parameters.
Step 53402: Environment parameters specifying an environment under which the cell specified by the cell parameters is cultured, are obtained. The environment parameters are obtained by xeoe,iving, by a computer, environment parameters inputted by a user, for example.
Alternatively, environment parameters may be obtained by automatically collecting or analyzing data outputted from an experimental apparatus (for example, sensors measuring experimental environment and the like) and the li.ke, by a computer. The environment parameters include, for example, parameters representing a medium fox Culturing a cell and a parameter representing conditions for such culture.
Parameters of such culture conditions include for example, pH, ~.emperature, Ca2 concentration of the medium, and the like.
Step 53403: Stimulus parameter specifying a stimulus to be given to a cell specified by the cell parameter. A
stimulus parameter is obteained by, for example, receiving, by a computer, a stimulus parameter inputted by a user.
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Z~lternatively, a stimulus parameter may be obtained by automatically collecting or analyzing, by a computer, data outputted by an experimental apparatus. Such a stimulus parameter may comprise, for example, a parameter representing a reporter and a parameter zepresenting a chemical stimulus.
Stop 53404: A st~.mu~.us response result showing the xesult ~.n xesponse to a stimulus by the stimulus parameter, by a cell specified by the cell parameter under the orivirozsrnent spea~.fied by the environment parameter, is obtained. The stimulus response result is obtained by automatically collecting or analyzing data outputted from an experimental apparatus such as monitoring apparatus for monitoring the course of experiments.
Step 53405: The cell parameter, the environment parameter, the stimulus parameter and the stimulus response result are correlated with each other. This correlation allows production of an experimental data against a cell of experimental interest. Such a correlation is conducted by linking in a single direction shown in Figure 33A.
However, methods correlation is not limited to such.
Step 5340: Steps 53401 through 53405 are repeated as necessary. This allows production of at least one experimental data against a cell of experimenfial interest . The collection of at least one experimental data is pxovided as a digital cell.
The computer implementing the process for producing a digital cell, functions as an apparatus or device for producing a digital cell. The digital cell producEd is stored on, for example, a database which can be accessed by the computer.
As such, provision of a digita 1 sell of a collection of at 'least one experimental data, is only possible by the present inventors by providing and developing technologies for locating a plurality of cells on a substrate under a consistent environment.
Conventionally, in the prior art, it was not possible to maintain a plurality of cells under a consistent environment, and thus the experimental conditions have not been reliable, and thus no significance is found when accumulating experimental data bEtween experiments. T-~s such, the "production of a digital cell" is a real advance in technology which is feasible for the first time through the technological inno~cra~tion of the present inventors.
(Provision of a method of reproducing experimental results against an actual cell) Figure 85 depicts an example of a configuration of computer system 3501 which provides a service reproducing an experimental result obtained using an actual cell using the digital cell.
Computer system 3501 comprises service requester 3510 requesting a service desired by a user, and service provider 3520 providing the des~.red service in 2~4 response to the request.
~1r007 Computer system 3501 may comprise a plurality of service requesters 3510.
Service provider 3520 is configured so as to be capable of accessing database 3522 with at least one digital cell stored thereon. A database structure of the digital cell stored on database 3522 is shown in, for example, Figures 33A and 338. Database 3522 may be provided inside service provider 3520, yr may be located outside service provider 3520.
Sexvice provider 3520 may be configured so as to be capable of accessing a plura7.ity of databases stored thereon with respect to at least one digital cell.
Service requester 35x0 and service provider 3520 may independently be any type of computer.
Service requester 3510 and service provider 3520 are connected to each other via network 3530. Network 3530 may be any type of network, but in view of fEasibility of connection or cost, most prefexabl~r, the network is the Internet.
When network 3530 is the Intexnet, service requester 3510 may be a Web browser operatEd by a user, and service provider 3520 may be a Web server connected to service requester via the Intexnet. Such a configuration alJ.ows any user across the entire world easy access to service provider 3520.
Figure 36 depicts an example of process for providing a service of reproducing an experimental result against an actual cell using a digital cell. This process may be implemented by cooperating service requester 3510 and service provider 3520.
Step S3601: Service requester 3510 receives cell and environment parameters and prnduoes request comprising the cell parameter, the environment parameter and the stimulus parameter. The request is described in, for example, XML.
Step 53602: Service request 3510 provides the request to service provider 3520.
Step 53603: Service provider 3520 searches for database 3522 in response to the request, to determine whether or not there is a stimulus response result relating to the cell parameter, the.envixonxnent parameter and the stimulus parameter included z.n the request in database 3522.
Step 53604: when it is determined that there exists a stimulus response result relating to the cexl parameter, the environment parameter and the stimulus parameter included in the request in database 3522, service provider 320 prQVi.des sexvice requester 3510 with the stimulus response result. The stimulus response result is described in, for example, XML.
Step 53605: Service requester 3510 displays the stimulus response result provided by service provider 3520.
If it is determined there is no stimulus response result relating to the cell parameter, the environment parameter and the stimulus parameter irioluded in the requested ~.n database 3522, service provider 3520 provides service requester 3510 with a result of "no hit", for ~. 0 example .
Procedures as shown in Figure 36 may be processed in a single computer. For example, a single computer program in a single computer may be used for implementing the procedures of steps 53601 through S3605 shown in Figure 36.
In this case, such a single computer functions as an apparatus having the caznbined functions of service requester 3510 and service providEr 3520.
Figure 37 depicts an example of input interface fpr inputting a cell parameter, an environment parameter and a stimulus parameter to service 3510. Zn this example, these parameters are inputted by inputting these parameters as texts by a user ~.nto a desired region.
Any number of methods may be employed as a method far inputting these parameters into service requester 3510.
For example, these parameters may be inputted by choosing these parameters from a menu ( such as, pu~.l-down menu, pop~-up menu and the like) by a user.
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Service requester 3510 may employ any embodiment for displaying the stimulus response result.
For example, service requester 35x0 may display the stimulus response result on a display screen, or may output the stimulus response xesult to a printer. Service requester 3510 may display the stimulus response result us~.r~g a still image or display the stimulus response result using movie display.
The stimulus response result may ~.zxcluda profile data of a cell obtained by mon~.toring a biological agent or a collection thereof on or in a cell over time.
In such a case, for example, the profile data of a cell shown in Figure 19 may be displayed by service requester 3510 as the stimulus response result.
As such, according to computer system 3510, it is now possible to provide a service of reproducing an experimental result for an actual celz using the digital cell. ~1s such, it is possible to conduct an advanced search relating to a cell even by a research organization or an individual without experimental facilities.
Figure 38 depicts an example of configurations of computer system 3801 for providing a serv~.oe of reproducing an experimental result against an actual cell using the digitax cell.
Computer system 3801 comprises service requester 3810 requesting a service desired 3~y a user; a plurality of service prov3.ders 382013$20N: and setvica registry 3$40 with registration of at least one service which can be provided by a plux~aiity of service providers 382013$20N, wherein N is an a~iy integer of two or more.
Computer system 3801 may include a plurality of service requesters 3810. Service provider 38201 is configured so as to be capable of accessing database 38221 at least Qne digital cell stored thereon. A data structure of a digital cell stored on database 38221 is as shown in Figures 33A and 33H. Database 3822 may be provided in service provider 38201 or outside service provider 3820, wherein 1 = 1, 2, N.
Service provider 38201 may be configured to be capable of accessing a plurality of databases with at least one digital cell each stored thereon.
Service registry 3840 is configured to be capable of accessing database 3842 with data stored thereon representing services being capable of being prQVided by service providers 38201 to 3820N. Database 3842 may be provided in service registry or outside service registry 3840. Storing data representing sexv~.ces on database 3842 allows registration of services to service registry 3840.
Formats of data stored on database 3842 are preferably pre-normalized. Storage of data to database 3842 may be performed manually by a firm managing service registry 3840 or by transmitting data from service providers 38201 to 3820N
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via network 383D to service registry 384p.
Each service requester 3810, service provider 3820 1 to 3620N and service registry 3840 may be any type of computer.
Each of service providers 382D1 to 3820N is preferably conducted by research parried out by any of organizations, firms or any other corporation possessing experimental faCZlities which conducts research vz'1 an actual cell. Each of servipe requester 3810 and service registry 3840 is preferably condupted by any of organizations, f~.rms or any other corporat~.on (for example, an association for promoting digital cells) managing provision of s~:rvices of reproducing experimental results against an actual cell using the digital cell. Further, in order to secure the quality of services reg~.stered to service registry 3840, it is preferable to oblige such an o~cganization which manages serva.ce providers 38201 to 3820N to satisfy a predetermined standard.
Service requester 3810, service provider 38201 to 3820N and sexv~.ce registry 3840 are connected via network 383D. Network 3830 is of any type but most preferably, in 2S view of ease of connection and cost, is 'the Internet.
When network 3830 is the Internet, service requester 38.0 xnay be a Web server connected to a Web browser operated by a user via the Internet. Each of 3820138217N may be a Web servex connected to service requester 3810 via the Azoo~
Internet. In this case, service requester 3810 functions as portal or Website interrelaying to a Web browser operated by a user and a Web server of service provider 38201. This configuration allows easy access to serv~.ce providerB of 38201 to 3820N by users all over the world, and it is now possible for research institutes andlvr firms all over the world to participate in the business of providing th~ service of reproducing experimental results against an actual cell using a digital cell.
Figure 3g depicts an example of a .process for providing a service of reproducing an experimental result against an actual cell using the digital Cell. This procedure is implemented by cooperating serv~.ce requester 3810 and service providers 38201 with 3820N.
Step 53910: Service requester 3810 receives a cell parameter, an environment parameter, and a stimulus parameter, and produces d. request comprising such a cell parameter, an environment parameter, and a stimulus parameter. Such a request is described in, for r~~rample, XMT.~ .
Step 53902: Service requester 3810 searches service registry 3840 responding to the request, and determines whethex ar not there exists a service provider 3820f which can provide a service of the requester amongst sexvice provides 3820 to 3820N, wherein 1 is any ~.nteger of x to N.
Service providers 38201 to 3820~a may employ any type of method for register services which can be provided by service providers 38201 to 3820N on service registry 3840.
For example, when service provider 38201 is capable of providing a service of reproducing ari experimental result against cell A, then cell parameters specifying cell A and addresses (for example, URi~ and the like) specifying the locations of service provider 3$201 may be stored on database 3842. Far example, zf service provider 38202 can provide services of reproducing cells B and C, then cell parameters specifying cell A and addresses (for example, URh and the like) specifying the locations of service provider 38202 may be stored on database 3$42. Alternatively, when service provider can provide the service of reproducing experimental results satisfying specific experimental conditions agaiz~st cell D, then parameters such as environment parameters and stimulus parameters specifying the experimental conditions and addresses (for example, a URL and the like) specifying the locations of service provider 38203 may be stored on database 3842.
Step 53903: If there exists a service provider 38201 which can provide a service of the requester, amongst service providers 38201 to 3820, such service requester 3810 provides service provider 38201 with the request. The location of service provider 3$20 may be specified by referring t.o database 3842 of service registry 3940.
Step S3904: service provider 38201 searches database 38221 in response to the request, and determines whether ox not there exists the stimulus response result relating to the cell parameter, the environment parameter and the stimuJ.us parameter included in the request in database 38221.
Step 53905: If determined that there exists a stimulus response result relating to the cell parameter, the environment parameter and the stimulus parameter included in the request in database 38221, service prov~.der 3B20~ provides service requester 3810 With the stimulus response result. The stimulus response result is described in, for example, XML.
Step 53906: service requester 3810 displays stimulus response result prpvided by service provider 38201.
If determined that there is no stimulus response result relatzng to the cell parameter, environment parameter and stimulus parameter containr~d in the request ~.n database 3822, service provider 38201 wrill provide serv~.ce requester 3810 w~.th, for example, the result of "no hit" .
As described above, any number of methodologies may be employed as a method for inputt~.ng a cell parameter, an environment parameter and a stimulus parameter to service requester 3810, and further any forms may be employed as a form of displaying stimuXus response result by service requester 3810.
As such, according to computer system 3810, it is possible to provide a ser,crice of reproducing an experimental result against an actual cell using the digital cell. This allows research institutes or individual having no experimental facilities to pexform advanced research activities relating to a cell. Further, according to computer system 3801, registration of services capable of being provided by a plurality of service providers $$20i to 3820N, provides opportunities to participate in the business 1.0 of providing the service of reproducing experimental results against an actual cell using the digital cell to research organizations or fixrns all over the world.
All patents, published patent applications and publications cited herein are incorporated by reference as if set forth fully herein.
The preferred embodiments of the pxesent invention have been heretofore described far a better understanding of the present invention. Hereinafter, the present invention will be described by way of examples.
Examples described below are provided only for illu8trative purposes . Accordingly, the scope of the present invention is not limited except as by the appended claims . According to the examples below, it will be understood that those skilled in the art can select cells, supports, biological agents, salts, positively charged substances, negatively chaxged substances, actin-like acting substances, and the like, as appropriate, and can make or carry out the present invention.
EXAMPLES
Hereinafter, the present invention will be described in greater detail by Way of examples, though the present invention is not limited to the examples below.
Reagents, supports, and the like~are commerciaJ.J.y avaiXable from Sigma (St. Louis, USA) , Wako Pure Chemical industries (Osaka, Japan), Matsunami Glass (Kishiwada, Japan) unless otherwise specified.
(Example 1: Reagents) formulations below were prepared ~.n Exempla 1.
As candidates for an actin-like acting substance, various extracellular matrix proteins and variants or fragments thereof were prepared in Example I, as listed below. Fibronectin and the like were commercially available. Fragments and variants were obtained by genetic engineering techniques:
1) fibronectin (~SEQ ID NO.: 11);
2) fibronectin 29 kDa fragment;
~) fibroneotxn 43 kDa fragment:
4) fibronectin 72 kDa fragment:
5) fibronectin variant (SEQ zD NO. : 11, alanine at 152 was substituted with leucine);
6) ProNectin F (Sanyo Chemical Industries, Kyoto, Japan);
7) ProNectin L (Sanyp Chemical Industries);
8 ) ProNectin Plus ( Sanyo Chezn,icaJ. Zndustrias ) ;
9) laminin (SEQ TD NO.: 6);
) RGD peptide ( tr~.peptide ) ;
11) RGD-containing 30kDa peptide;
12) 5 amigo acids of laminin (IKVAV, SEQ zD NO.: 28); and 5 13) gelatin.
Plasmids were prepared as DNA for transfection.
Q~.asmids, pEGFP-N1 and pDsRed2--N1 (bath from BD Biosciences, Clontech, CA, U5A) were used. In these plasmids, gene 10 Expression was under the control of cytomegalovirus (CMV) .
The plasmid DNA was amplified in E. coli (XL1 blue, St rat gene, TX, USA) and the amplified plasmid DNA was used as a oomp~.ex partner. The DNA was dissolved in distilled watex free from DNa.se and RNase .
The following transfection reagents were used:
Effectene Transfeotic~n Reagent (cat. no. 301425, Qiagen, CA) , TransFast~ Transfection Reagent (E2431, Promega, WI ) , Tfx~~20 Reagent (E2391, Promega, WI), SuperFect Transfection Reagent (301305, Qiagen, CA), PolyFeot Transfection Reagent (301105, Qiagen, CA), I,ipofectAMINE
2000 Reagent (11668-019, Tntritrogen corporation, CA), JetPEI (x4) conc. (101-30, Polyplus-transfection, France), and ExGen 500 (R0511, Fermentas Inc., MD). These transfection reagents were added to the above-described DNA
and actin-like acting substances in advance, or complexes thereof with the DNA were produced in advanoe.
The thus-obtained solution was used in assays using transfection arrays described below.
(Example 2: Transfection array - Demonstration using meaenchymal stem cells) In Example 2, an improvement in the transfection efficiency in solid phase was observed. The protocol used in Example 2 will be described below.
(Protocol) The final concentration of DNA was adjusted to 1 ~g/~L. An actin-like acting substance was preserved as a stock having a concentration of 10 pg/~.L in ddHzO. Ail dilutions were made using PBS, ddHzO, or Dulbecco' s MEM. A
series of dilutions, for example, 0.2 ~tg/~L, 0.27 ~.eg/~,~,L, 0.4 ~g/~.t.L, 0.53 E.~,g/'~.L, 0.6 ~i.g/J.I.L, 0.8 ~.tg/~L, 1.0 ~.g/~L, 1.07 ~g/~.L, 1.33 ~tg/).iL, and the like, were formulated.
Transfeetion reagents were used in accordance with instructions provided by each manufacturer.
Plasmid DNA was removed from a glycerol stock and amplified zz~ x.00 mL L--amp overnight. Qiaprep Miniprep or Qiagen Plasmid Purification Maxi was used to purify DNA
in accordance with a standard protocol provided by the manufacturer.
In Example 2, the following 5 cells were used to confirm an effect: human mesenchymal stem cell (hM~Cs, PT-2501, Cambrex BioScience ~nTalkersville, Inc. , MD) : human embryonic renal cell (HEK293, RCB1637, RTKEN Cell Eank, JPN); NIH3T3-3 cell (RCB0150, RIKEN Cell Bank, JPN); HeLa cell (RC80007, RIKEN Cell 8ank,JPN)~ and HepG2(RCH1648, RIKEN Cell Bank, JPN) . These cells were cultured in DMEM/10%
IFS containing L-glut and pen/strep.
(Dilutzan and DNA spats) Transfectian reagents and DNA were mixed to form a DNA-transfection reagent complex. Formation of the complex requires a certain period of time. Therefore, the mi~rture was spotted onto a solid phase support (e.g., a poly-L-lysine slide) using an arrayer. In Example 2, as a solid phase support, an APS slide, a MAS slide, and an uncoated slide were used as well as a poly-L-lysine slide.
These slides are available from Matsunami Glass (Kishiwada, Japan) or the like.
For complex formation and spat fixation, the slides were dried overnight in a vacuum dryer. Drying was performed for a duration in the range of 2 hours to 1 week.
2p Although the actin-like acting substance might be used during the complex formation, it was aXsa used immediately before spotting in Example 2.
(formulation of mixed solution and application to solid phase supports) 300 ~L of DNA concentrated buffer (EC buffer) + 16 ~ of an enhancer were mixed in an Eppendorf tube. The mixture was mixed with a vortex, followed by incubation for 5 minutes. 50' ~L of a transfectiari reagent (EffeCtene, etc.) was added to the mixture, followed by mixing by A=007 pipetting. To apply ~a transfection reagent, an annular wax barrier was formed.around the spots on the slide_ 3~6 ~L
of the mixture was added to the spot region surrounded by the wax, followed by incubation at room temperature fox 10 to 20 minutes. Thereby, the fixation to the support was manually aohiwsred.
(D~.stribution of cells) Next, a protocol for adding cells will be described. Cells were distributed far transfection. The distribution was typically performed by reduced-pressure suction in a hood. A slide was placed on a dish, and a solution containing cells was added to the dish for transfection. The~cells were distributed as follows.
The gxowing cells were distributed to a concentration of 10' aells/25 mL. The cells were plated on the slide in a 100x100x15 mm squaxed Petri dish or a 100 mm (radius) x xS mm circular dish. Transfectian eras conducted for about 40 hours. This period of time corresponded to about 2 cell cycles. The slide was treated for immunofluorescence.
(Evaluation of gene introduction) gene introduction was evaluated by detection using, for example, immunofluorescence, fluorescence microscope examination, laser scanning, radioactive labels, and sensitive films, or amulsion.
When an expressed protein to be visualized is a fluorescent protein, such a protein can be observed with a fluorescence microscope and a photograph thereof can be taken. Far large-sized expression arrays, slides may be scanned using a laser scanner for storage of data. If an expressed protein can be detected using fluorescent antibodies, an immunofluorescence protocol can be successively performed. 2f detect~.on is based on radioactivity, the slide may be adhered as described above, and autoradiography using film or emulsion can be performed to detect radioactivity.
(Laser scanning and Quantification of fluorescence intensity) To quantify transfection efficiency, the present inventors use a DNA microarray scanner (GezIeTAC
UC4x4, Genomic Solutions Inc., MT). Total fluorescence intensity (arbitrary unit) was measured, and thereafter, fluorescence intensity per unit surface area Was calculated.
(Cross-sectional observation by confocal scanning microscope) Cells were seeded on tissue culture dishes at a final concentration of 1x105 cells/well. arid cultured in appropriate medium (Human Mesenchymal Cell Basal Medium (MSCGM BulletKit PT-3001, Cambrex BioScience Walkersville, Inc., MD). After fixation of the cell layer with 4%
paraformaldehyde solution, SYTO and Texas Red-X phalloidin (Molecular Probes Inc . , OR, USA) was added to the Cell. ~.ayex for observation of nuclei and F-actin. The samp~.es emitting light due to gene products and the stained samples were observed with a confocal laser microscope (t~SM510: Carl Zeiss Co. , T~td. , pin hole szze=Chl=123 ~,am, Ch2=108 Elm, image interval = 0.4) to obtain cross sectional views.
(Results) Figure 1 shows the results of experiments in which various actin-like acting substances and HEK293 cells were used where gelatin was usEd as a control.
~. 0 As can be seen from the results, whereas transfection was not very successful in a system using gelatin, transfection took place to a significant ~.evel in systems using fibronectin, ProNectin (ProNectin F, ProNectin L, ProNectin Plus) which is a variant of fibronectin, and laminin. Therefore, it was demonstrated that these molecules significantly increased transfection efficiency. Use of the RGD peptide alone exhibited substantially no effect.
figures Z and 3 show transfection efficiency when fibronectin fragments were used. Figure ~4 shows the summary of the results. 29 kDa and 72 kDa fragments exhibited a significant level of transfection activity, while a 43 kDa fragment had activity but its level was low.
Therefore, ~.t was suggested that an amino acid sequence contained in the 29 kDa fragment played a role in an increase in transfection efficiency. Substantially no contam~.nation wasp found in the case of the 29 kDa fragment, while contamination was observed in the case of the other two fragments (43 kDa and 72 kDa) . Therefor, only the 29 kDa dvrnain may be preferably used as an actin-like acting substance. When only the RGD peptide was used, increased transfection efficiency was not exhibited. The 29-kDa peptide therefore exhibited activity with respect to enhancing transfection efficiency. Such a system with an additional 6 amino acids of laminin (higher molecular weight) exhibited transfection activity. Therefore, these peptide sequences may also play an important role in increased transfection efficiency, without limitation. In such a case, a molecular weight of at least 5 kDa, preferably at least 10 kDa, and more preferably at least 15 kDa may be requ~.red for an increase in transfection efficiency.
Next, Figure 5 shows the result of studies on the transfection efficiency of cells. In Figure 5, HEK293 cells, HeLa cells, and 3T3 cells, which were conventionally transfectable, and HepG2 cells and mesenchymal stem cells (MSC) which were conventionally believed to be substantially impassible to tran9fect, were used to show the effect o~ the transfeCtion me'~hod of the present invention. The vertical. axis represents the intensity of GFP.
In Figure 5, the transfection method of the present invention using a solid phase support was compared with a conventional liquid phase transfection method. The conventional liquid phase transfection method was conducted in accordance with a protocol recommended by the kit manufacturer.
~ 62 Ax007 As can be seen from Figure.5, transfection efficiency compaxable to HeT~a and 3f3 was achieved in HepG2 cells and mesenchymal stem cells (MSC) which were conventionally believed to be substant~.ally impossible to transfect, as well as HEK293 cells, HeLa cells, and 3T3 cells, which wexe conventionally txansfectable. Such an effect was not aohie~red by conventional transfection systems . The present invention was the first to provide a system which can increase transfection efficiency for substantially all cells and can provide practicable transfection to all cells _ By using solid phase conditions, cross contamination was significantly reduced. Therefore, it was demonstrated that the present invention using a solid phase support is 1.5 appropriate for production of an integrated bioarray.
Next, Figure 6 shows the results of transfection when various plates Were used. As can be seen from the xesults of figure 6, when coating was provided, contamination was reduced as compared with when coating was not provided and transfection efficiency was increased.
Next, Figure 7 shows the results of transfection where the concentration of fibroneotin was 0, 0.27, 0.53, 0.8, 1.07, and 1.33 (~g/~L for each). In Figure 7, slides coated with PLL (poly-L-lysine), APS and uncoated slides were shown.
As can be seen from the results of Figure 7, transfection efficiency was ~.ncreased with an increase in fibronectin concentration. Note that in the case of PLL
coating and the absence of coating, the transfection efficiency reached a phateau at a fibronectin concentration of more than 0.53 ~g/~.~.L. In the case of APS, it was found that the effect was further increased at a fibxen.ectin concentration of more than of 1.07 ~g/~L.
Next, Figure 8 shows photographs indicating cell adhesion profiles i.n the presence or absence of fibronectin. Figure 9 shows cross-sectional photographs.
It was revealed that the morphology of adherent cells were .significantly different (Figure 8) . The full extension of cells was found for the initial 3 hours of culture iri the presence of f~.branectin, while extension was limited in the absence of fibronectin (Figure 9). Considering the behavior of filaments (Figure 9) and the results of the time-lapse observation, it was considered that an actin-like acting substance, such as fibronectin, af.tached to a solid phase support had an influence on the shape and orientation of actin filaments, and the efficiency of introduction d~ a substance into a cell, such as transfection efficiency yr the like, was thus increased. Specifically, actin filaments quickly change their location in the presence of fibronectin, and disappear from the cytoplasmxc space under the nucleus as the cell extends. It is considered that actin depletion in the perinucleax space, which is induced by an actin-like acting substance, such as fibronectin, allows the transport of a target substance, such as DNA or the like, into cells or nuclei. Though not wishing to be bound by any thevx~y, the reason is considered Ar007 to be that the viscosity of cytoplasm is reduced and positively charged DNA particles are prevented from being trapped by. negatively charged actin filaments.
Additionally, it is considered that the surface area of the S nucleus is significantly increased in the presence of fibronectin (Figure 10), possibly facilitating the transfer of a target substance, such as DNA or the like, into nuclei.
(Example ~: Application to bioarrays) Next, larger-scale experiments were conducted to determine whether or not the above-described effect was demonstrated when arrays were used.
(Experimental protocols) (Cell S4uroe~, culture media, and culture conditions) In this example, five different c~:ll lines wexe used: human mesenchymal stem cells (hMSCs, PT-2501, Cambrex BiaScience Walkersville, Tnc,, MD), human embryonic kidney ce~.l HEK293 (RCB1637, RIKEN Cell Bank, JPN), NZI~3T3-3 (RC80150, RIKEN Cell Bank, JPN), HeZa (RCB0007, RIKEN Cell Bank, JPN), and HepG2 (RCB164B, RIKEN Cell Bank, JPN). In the case of human MSCs, cells were maintained in commercialized Human Mesenchymal Cell Basal. Medium (MSCGM
aul.letKit PT-3001, Cambrex BioScience'Walkersville, inc., MD) . In case of HEK293, NzH5T3-3, HeLa and FiepG2, cells were maintained in Dulbecco's Modified Eagles Medium (DMEM, high glucose 4.5 g/L with L-Glut amine and sodium pyruvate~
14246-25, Naka.lai Tesque, JPN} with 10~ fetal bovine serum Az007 (FBS, 29-167-54, Lot No. 2025F, Dainippon Pharmaceutical CO_ , LTD. , JPN) . All cells were cultivated in a contxo7.led incubator at 37°C in 5~ COz. In experiments involving hMSCs, we used hMSCs of less than five passages, in order to avoid phenotypic changes.
(Plasmids and Transfection reagents) To evaluate the efficiency of transfection, the pEGFP-N1 and pDsRed2-Nl vectors (cat. no. 6085--1, 6973-~., BD Biosciences Clontech, CA) were used. Both genes' expressions were under the control of cytomegalovirus (CMV) promoter. Transfected cells continuously expressed EGFP or DsRed2, respectiveJ.y. Plasm~.d DNAS were amplified using Escherichia coli, XI,~.-blue strain (200249, Stratagene, TX) , and purified by EndoFree Plasmid Kit (EndoFxee Qlasznid Maxi Kit 12362, QIAGEN, CA). In all cases, plasmid DNA was dissolved in DNase and RNase free water. Transfection reagents were obtained as below: Effectene Transfection Reagent (cat. no.301425, Qiagen, CA), TransFast~
Transfection Reagent (E2431, Promega, WI) , Tfx~-20 Reagent (E2391, Promega,~ WI), SuperFeat Transfection Reagent (301305, Qiagen, CA), PolyFect Transfection Reagent (301105, Qiagen, CA), LipofectAMINE 2000 Reagent (11668-019, Invitrogen corporation, CA), JetPEr (x4) conc. (101-30, Polyplus-transfection, France), and ExGen 500 (R0511, Fermentas Inc., MD).
(Solid-Phase Transfection Array (SPTA) production) The detail of protocols for 'reverse A20o7 transfection' are described in the web site, 'Reverse Transfection HomEpage' (http://staffs.wi.mit.edu/sabatini~ublic/reverse trans fe~t~.on.htm) or J. Ziauddin,.D. M. 5abatinz, Nature, 411, 2001, 107; and R.W. Zu, S.N. Eailey, D.M. Sabatini, Trends in Cell Biology, Vol. 12, No. 10, 485. In our solid phase transfection (SPTA method) , three types of glass slides were studied (silanized glass slidesi APS slides, and poly-h-lysine coated glass slides: PLZ slides, and MAS
coated slides; Matsunami Glass, JPN) with a 48 square pattern (3 mm x 3 mm) separated by a hydrophobic fluoride resin coating.
(Plasmid DNA printing solution preparation) Two different ways to produce a SPTA were developed. The main differences reside in the preparation of the plasmid DNA printing solution.
(Method A) In the case of using Effectene Transfection Reagent, the printing solution contained plasmid DNA and cell adhesiozl molecules (bovine plasma fibronectin (cat.
no. 16042-47., Nakalai Tesque, JPN) , dissolved in ultra-pure water at a concentration of 4 mg/mL). The abo~cre solution was applied on the surface of the slide using an ink~et printer (synQUAD~, Cartesian Technologies, InC., CA) or manually, using a 0.5 to 30 ~,L tip. This printed slide was dried up over 15 minutes at room temperature in a safety-cabinet. Before transfeCtzon, total Effecterie reagent was gently poured on the DNJ~r-printed glass slide Alpa~
and incubated for 15 minutes at. room temperature. The e~tcess Effectene solution was removed from the glass slide using a vacuum aspirator and dried up at room temperature fox 15 minutes in a safety-cabinet. The DNA-printed glass slide obtained was set in the bottom of a 100-mm culture dish and approximately 25 m~, of cell suspension (2 to 4x104 cells/m~) was gently poured into the dish. Then, the dish was transferred to the incubator at 37°C in 5% COZ and incubated for 2 ar 3 days.
(Method B) Iri case of other transfection reagdnts (TransFastT~°, TfxTM-20, SuperFect, PolyFect, LipofectAMINE
2000, JetPEI (x4 ) conc. , or ExGen) , plasmid DNA, fibroneCt~.n, and the transfection reagent were mixed homogeneously in a x.5--mL micro-tube according to the ratios i~xdicated in the manufacturer s instructions and incubated at room temperature for 15 minutes before print~.~ng on a chip. The printing solution was applied onto the surface of the glass-slzde using an inkjet printer or a 0.5- to 10-~tL tip.
The pz~~.nted glass-slide was completely dried up at room temperature over 10 minutes in a safety-cabinet. The pz~inted glass-slide was placed in the bottom of a 100--z~un culture dish and approximately 3 mL of sell suspension (2 to ~ixl0° cel~.s/mL) was added and incubated at room temperature over 15 minutes in a safety-cabinet. After incubation, fresh medium was poured gently into the dish.
Then, the dish was transferred to an incubator at 37°C in 5% C02 and incubated for 2 to 3 days. After incubation, using fluorescence microscopy (IX-71, Olympus PROMARKETING, INC., use Azoa~
~7PN) , we obaer~red the transfectants, based on their expression of enhanced fluorescent proteins ( EFP, EGFP and DsRed2). Phase cantrast images were taken with the same microscope. In both protocols, calls were fixed using a paraformaldehyde (PFA) fixation method (4~ PFA in PBS, treatment time was 10 minutes at room tEmpe raturE).
(Laser scanning and fluorescence intensity quantification) In order to quantify the transfection efficiency, we used a DNA micro-array scanner (~eneTAC UC4x4, Genomic SoJ.utaans Znc., MI). The total fluorescence intensity (arbitrary units) was measured, and thereafter, the fluorescence intensity per surface area was calculated.
(Results) (Fibronectin-supported localized transfection) A transfeetion array chap was constructed as shown in Figure 11. The transfection array chip was constructed by microprinting a cell cultivation medium solution containing fibronectin and DNA/transfectian reagent onto a poly L lysine (PLL) coated g lass slide.
Various cells were used for this example. The cells were cultivated under typical cell aulti~ration conditions . As they adhered to the glass slide, the cells ef~i.ciently incorporated and expressed the genes corresponding to the DNA printed at a given position on the array. As compared to conventional transfe ction methods Az007 (e. g., cationic lipid or cationic polymer-mediated transfection), the efficiency of transfection using the method of the present invention was high in all the cells tested. Importantly, it was found that tissue stem cells, such as HepG2 and hMSC, which were conventionally believed to resist transfection, were efficiently transfeCted. hMSC
was transfected at an efficiency 40 or more times higher than that of conventional techniques. Tn addition, high spatial localization, which is required for high-density arrays, was achieved (low cross contamination between adjacent spats on the array). This was confirmed by production of a checkered pattern array of EGFP and Ds--Red.
hMSC cultivated on this array expressed the corresponding f~.uarescent proteins with virtually total. space resolution.
The result is shown in Fa.gure 12. As can be seen from Figure l2, i.t was found that there was little cross contamination. Based on the study of the role of the individual components of the printed mixture, transfection efficiency can be optimized.
(Solid-phase transfection array of human mesenchymal stem cells) The capacity of human Mesenchymal Stem Cells (hMSC) to differentiate into various kinds of cel~.s is particularly intriguing in studies which target tissue regeneration and renewal. In particular, the genetic analysis of transformation of these cells has attracted attention with expectation of understanding of a factor that controls the pluripotency of hMSC. In conventional hMSC
studies, it is not possible to perform transtection with desired genet~.c materials.
Azoo7 (solid-phase transfection array of human mesenchymal stem cells) The capacity of human Mesenchymal Stem Cells (hMSC) to differentiate into various kinds of cells is particularly intriguing in studies which target tissue regeneration and renewal. In particular, the genetic analysis of transformation of these cells has attracted 1.0 attention with expectation of understanding a factor that controls the pluripotency of hMSC. In canventional hMSC
studies, it is not possible to per~arm transfection with desired genetic materia~.s.
To achieve this, conventional methods include either a viral vector technique or electroporation. The present inventors developed a complex-salt system, which could be used to achieve solid phase transfection which makes it possible to obtain high transfeotian effiaa,ency to various cell lines (including hM$C) and special localization in high-density arxays. Are outline of solid phase tzansfection is shown in Figure 19A.
It was demonstrated that solid phase transfection can be used to achieve a "transfection patch"
capable of being used for in vivo gene delivery and a solid phase transfection array (SPTA) for high-throughput genetic function research on hMSC.
Although a number of standard techniques are 271.
available for transfeoting mammalian cells, it is known that it is inconvenient and difficult to introduce genetic material into hMSC as compared with cell lfines, such as HEK293, HeLa, and the like. Conventional ~rira~, vector delivery and electroporation techniques are both ~.mportant.
However, these techniques have the following inconveniences: potential toxicity (for the virus technique); difficulty in high,throughput analysis at the g~nomic scale; and limited appl.i.cations in vivo studies (for electroporation?.
The present inventors develop~d a so7.~.d phase support fixed system which can be eas~.ly fixed to a solid phase support and has sustained-release capability and cell affinity, whereby most of the above-described drawbacks could be overcome.
An example of the results of the above-described experiment is shown in Figure 138. The present inventors used our microprinting technique to fix a mixture of a selected genetic material, a transfection reagent, an appropriate cell adhesion molecule, and a salt onto a solid support. By culturing cells on a support having such a mixture fixed thereonto, the gene contained in the mixture was taken in by the cultured ceJ.ls . 1~s a resu~.t, it became possible to facilitate support-adherent ce 11s to take ire DNA spatially separated therefrom (Figure 138).
As a result of this example, several important effects were achieved: high transfection efficiency (thereby making it possible to study a group of cells on a statistically significant scale)] low cross contamination between regions having different DNA molecules (thereby making it possible to study the effects of different genes separately); the extended survival of transfected cells;
high-throughput, compatible and simple detecting procedure.
SPTA having these features sexves as an appxdpriate baeis for further studies.
To achieve the above-described objects, the present inventors studied five different cell dines (HEK293, HeLa, NIH3T3, HepG2 and hMSC) as described above with both our methodology (transfection in a solid phase system) (see Figures 13A and 13C) and conventional liquid-phase transfection under a series of transfection conditions.
Cross contamination was eva7.uated for both systems as follows. In the case of SPTA, we printed DNA's encoding a red fluorescent protein (RFP) and a green fluorescent protein (GFP) on glass supports in a checked pattern. In the Case of experiments including conventional liquid phase transfectian (where cells to be transfected cannot be spatially separated Exam one another spontaneously) , a DNA
encoding GFP was used. Several transfection reagents were evaluated: four liquid transfection reagexlts (Effectene, TransFast~, Tfx~-20, LopofectAMrNE 2000) , two pol~ra.mine (SuperFect, PolyFect), and two polyimine (JetPEI (x4) and ExGen 500 ) .
Transfecti.on efficiency: transfection efficiency was determined as total Fluorescence intensity per unit area (Figure 14A and Figure 14B (images)). The results of liquid phase optimal for cell lines used were obtained using different transfection reagents (see Figures ~.4C to 14D). Next, these efficient transfection reagents were used to optimize a solid phase protocol.
Several tendencies were observed. For CeJ.l lines which are readily transfectable (e. g., HER293, HeLa, NIH3T3, etc.), the transfection efficiency observed in the solid phase protocol was slightly superior to, but essentially simixar to, that of the standard liquid phase protocol (Figure 14A
to 7.4D) .
However, for cells which are difficult to transfect (e. g., hMBC, HepG2, etc.), we observed that transfection efficiency was increased up to 40 fold while the features of the cells were retained under conditians optimized to the SPTA methodology (see the above-described protocol and Figures 14C and 14D). in the case of hMSC
(Figures 15A and 15B) , the best conditions included use of a polyethylene imine (P~Iy transfection reagent. As expected, important factorsfor achieving high txansfection efficiency are the charge balance (N/P ratio) between the number of nitrogen atoms (N) in the polymer and the number of phosphate residues (P) in plasmid DNA, and DNA
concentration. Generally, increases in the N/P ratio and the concentration lead to an increase in transfection efficiency. We also observed a significant reduction in the survival rate of hMSC cells in liquid phase transfection experiments where the DNA concentration was high and the N/P ratio was high. Because of these two opposing factors, Az0o7 the liquid phase transfection of hMSC had a relatively low cell survival rate (N/P ratio >10) , In the case of the SPTA
protocol, however, a considerably high N/P ratio Mixed to the solid support) and DNA concentration were tolerable (probably attributable to the effect of the solid support stabilizing cell membranes). while the cell surv~.va~, rate and the cellular state were not significantly affected.
Therefore, this is probably responsible for the dramatic improvement in transfection efficiency. It was found that the N/P rat~.o of 10 was optimal for SPTA, and a sufficient transfection level. was provided while minimizing cytotoxicity. Another reason for the increase in txansfection efficiency observed in the case of the SPTA
protocol is that a high local ratio of the DNA concentration to the transfection reagent concentration was achieved (th~.s leads to cell death in liquid phase transfection expeximents).
The coating agent used is crucial to achieving of high transfection efficiency on Chips. It was found that when a glass chip is used, PZL provided best results both for transfection efficiency and cross contamination (described below). When fibronectin coating was not used, few transfectants were observed (all the other experimental condit~.ons were retained unchanged). Although it's function is not completely established, fibronectin probably plays a rule ~.n a.ccelerating the cell adhesion process (data not shown), and thus limits the time which permits the diffusion of DNA released from the surface.
Low cross contamination: apart from the higher transfection efficiency observed in the SPTA protocol, an important advantage of the technique of the present invention is the provision of an array of separated cells, in which selected genes are expressed in the separate posit~.ons. The present inventars printed JetPEI (see the "Experimental protocols" section) and two different reporter genes (RFP and GFP) mixed with fibronectin on glass surface coated with fibronectin. The resultant transfection chip was subjected to appropriate cell culture.
Expressed GFP and RFP were localized in regions in which corresponding cDNA had been spotted, under experimental conditions which had been found to be best. substantially no cross contamination was observed (Figures ~61~ to l6D).
In the absence of fibronectin or PZL, however, cross contamination which hinders solid phase transfection was observed, and the transfection efficiency was significantly lower (see Figure 6). This result demonstrated the hypothesis that the relative proportion of p~.asmid DNA, which was released from the cell adhesion and the support surface, is an important factor in high transfection efficiency and high cross contamination.
Another cause of cross contamination may be 'the mobility of transfected cells on a solid support. The present ~.nventors measured both the rate of cell adhesion (Figure 16C) and the diffusion rate of plasmid DNA on several supports. As a result, substantially no DNA diffusion occurred under optimum conditioz'zs. I~iowever, a considerable amount of plasmid DNA diffused under high cross Ax007 contamination conditions until cell adhesion was completed, so that plasmid DNA was depleted froze the solid phase surface.
This established technique ~.s of particular importance in the context of cost-effective high-throughput gene function screening. Indeed, the small amounts of transfection reagent and DNA required, as well as the possible automatizatian of the entire process (from plasmid isolation to detection) increase the utility of the above presented method.
In conclusion, the present invention hag successfully realized a hMSC transfection array in a system Z5 using complex-salt. V~ith this technique, it will be possible to achieve high-throughput studies using solid phase transfection, such as the elucidation of the genetic mechanism underpinning the differentiation of pluripotent stem Cells. The detailed mechanism of the solid phase transfection as well as methodologies for the use of this technology for high throughput, real time gene expression monitoring can be applied for various purposes.
(Example 4: Mathematical analysis) Next, time--lapse profiles were produced based on data obtained using the techniques described in Examples 2 and~3.
(Induction of differentiation) Each reporter was fixed to a solid phase support and cultured in undifferentiated mesenchymaZ stem cell maintenance medium (MSCGM, PT--3001, PT-3238, PT-4105, Cambre~, BioWhittaker, USA) for two days. Thereafter, the medium was replaced~with differentiation-inducing medium (hMSC Differentiation, PT-3002, PT-4120, Cambz~ex, BiaWhittaker, U5A). The response profile of each reporter was measured.
(Mathematical analysis technique) 7.p A mathematical analysis technique us~ad herein is shown in Figures 18a and l8B ;18-1 to 18-2).
(Transcription factors used herein) As shown in Figures 19 and 24, plasmids (commercially available from Clontech), in which 17 transcription factors (ISRE, RARE, STAT3, GAS, NFAT, MZC, API, SRE, GRE, CRE, NF~cB, ERE, TRE, E2F; Rb, p53 ) Wexe operably linked to GFP, were used to observe the differentiation of mesenchymal stem cells into osteoblasts. The resultant time-lapse profiles are shown in Figure 19. Reporters for the transcription factors were constructed as shown in Figuxe 23.
An assay was conducted using the reporters for the transcription factoxs under control conditions (sells, suppJ.emental factors, culture conditions, etc.) published by Clontech.
The results are shown in Figure 2b. It wad demonstrated that when Compared only to DNA in this manner, most of the transcription factors were induced when inducing agents were added.
Next, the activity of the transcription factors was measured over tzme in the course of induct~.on of differentiation into bone. Tn this case, time-lapse profiles, which were obtained during the induction of differentiation under the above-described conditions, were compared with each other. The time-lapse profiles were obtained as follows. Each reporter gene was introduced into mesenchymal stem cells by a solid phase transfection method.
The cells were cultured in undifferentiated state maintenance medium for two days . Thereafter, the medium was replaced with osteoblaet d~.fferentiation medium. This time point was referred to as the osteoblast differentiation start time. Supplement factors were added at concentrations recommended for the asteob~.ast differentiation medium. The other culture conditions were in accordance With Cambrex's instructions.
The results are shown in Figure 26. The profile pattern on the left of Figure 26 was obtained 10 hours to hours after replacement of the medium. The profile pattern on the right of Figure 26 was obtained 5 to 6 days 25 after replacement of the medium. Thus, it was demonstrated that the pattern significantly charged over time. The phases of the pxofzJ.es were calculated using a formula shown in Figure 27 and the results were summarized in a tabl~ to the right of Figure 27. As can be seen, the inversion of 30 the phase of the profile was deeply associated With differentiation for ISRE, RARE, STAT3, GRE, CRE, TRE, E2F, and p53. Therefore, it was demonstrated that by examining the phase, changes in process, i.e., the occurrence of transcription control, could be detectEd.
5~
(Arbitrary combination of reporters) ~iext, it was demonstrated that digferentiation could be identified using an arbitrary combination of promoters for which data was extx~aGted at the initial stage of induction of differentiation. Briefly, the analysis was conducted as shown in Figure 20.
The results are shown in Figure 20. This analysis revealed that although differentiation could not be detected at its very initial stage (potentially due to noise), but could be confirmed about 15 hours after induction of differentiation. Tn tha.s example, when data was extracted for 8 or more promoters, differentiation could be detected at a detection rate of 100. When data was extracted for 3 promoters, differentiation could be detected at a detection rate of more than 90~. When data was extracted for two promoters, differentiation could be detected at a detection rate of 88~. when data was extracted for one promoter, differentiation could be detected at a detection rate of 82~. Thus, it was revealed that one, two or at least three promoters are sufficient for determination or identification of the state of cells.
(Maintenance of undifferentiated state) Next, the maintenance of undifferentiated state Azoa~
was analyzed using an arb~.trary combination of transcription control sequences for which data was extracted. Analysis was conducted as described in Figure 20.
The results are shown in Figure 2t. As is ~.argely different fz~om the results of induction of differentiation, by comparing the profiles of the transcription control sequences with one another, it could xa be determined whether or not stem cells were induced into differentiation or remained undifferentiated. Such s, determination could be achieved using at least one transcription control sequence. The determination of the state of cells using such a small number of transcription control sequences cannot be achieved by conventional techniques. It can be said that the present invention achieved an exceXlent effect.
Hy analyzing a cellular process in such a fashion, the formation of cellular functions can be described as a cocktail party process as shown in Figure 22.
G~lith such a process description, the present invention mads it possible to ana~.yze the progression of a cellular response to drugs and the progression of the induction of differentiation,.
(Example 5 Anticancer agent) In this example, cisplatin was used as an exemplary anticancer agent and was mixed into the medium of exposed cells. The concentration of the anticancer agent was selected as appropriate, such as 1 ~tM, 5 ~M, 10 E1M, and the like, to observe the xeaction of the cells. Cisplatin~
was applied to cells resistant ox sensitive to the anticancer agent. Time-lapse observation was conducted to produce profiles as in the above-described examples . As a result, it was revealed that time-lapse profiles varied depending on the difference in cisplatin concentxstian and resistance/sensitivity.
(Example 6: RNAi) The present Example demonstrated that it was possible to obtain a profile relating to gene knockdown effect using a cell was ~.mmobilized as described in ExamplE
1, RNAi was used as a biological agent. The following was used as RNAi for experimentation. Gene expression inhibition methods using riboaymes and siRNA and the like allows obtaining profiles of response reactions in a cell for which gene expression inhibition is conducted using the s acne .
RNAi: those sequences available at the URL:
http://.www.nippongene.jp/pages/products/sirna/review/
were used (for example, Control siRNA duplex).
(RNAi transfectivn) First, it was confirmed whether the siRNA could achieve knockdown effects. Synthesis of siRNA
5'-AAGCAGCAGGACUUCUUC,AAG-3' (SEQ ID NO: 2) corresponding to EGFP was perfozrned to prepare an arxay substrate as described herein above in the Examples. The preparation of array substrate using siRNA instead of nucleic acid molecules zno7.uding promoter sequences was performed.
Transfection using these axray substrates confirmed Effective inhibition of expxess~.on of a target gene. The protocols thereof are presented a.n Figure ~8.
(Results) Figure 2~A shows the effects of target gene inhibition by siRNA. Expression of the target gene has actually been inhibited. The result$ using this gel may be stored so a prof~.J.e ire any data format.
Next, results of siRNA are stored as a prafi7.e data (image data of xIFF format having resolution at the level of 5 um/pixel or less). As such, the results of siRNA may be stored as a profile data. Such a format is not limited to those specifically presented in this Example, but those skilled in the art may employ any type of formats.
(Figure ~: AppZioations uszng siRNA and a transfection m~.croarray of PC7.2 cells on a collagen IV coated chip) Next, the present Example conducted a gene expression inhibition experiment using siRNA. The present Example evaluated whether or not the present invention functions by observing whether or not siRNAs against EGFP
can specifically inhibit the expression of the EGFP as an indicator.
Using the conditions described in Example 7, transfection of PC~.2 was conducted on an array coated with collagen IV. In lieu of the gene used in ExampJ.e 7, the following cond~.tion9 were usEd:
0.75 ng of an expression vector (pEGFP-N1}, HcRed (avai3.able from HD Clontech) were each spotted on a single, specific spot of the array. Thereafter, 16.5 ng of siRNA
( available from Dharmacon, taxget sequence : 5' -GGC TAC GTC
CAG GAG CGC ACC -3' (5EQ Z17 N0:47)=a) or scrambled siRNA (available from Dharznacon. target sequence: 5' -gCg CgC
TTT gTA ggA TTC g-3' (SEQ zD NO: 48 ) =b) were also spotted.
Figure 298 shows fi.he xesults. As shown in Figure 29 8(A), in the case of PC12 cells co-transfected ~.5 with EGFP vector and anti-EGFP siRNA, it was observed that only signals from HcRed were detected, and the green signal which should be derived from pEGFP--N1 had been inhibited.
On the other hand, as shown in Figure 29 B (8) , in the case of scrambled siRNA, green fluorescence was been observed and thus it was confirmed that the effects seen in Figure a9 8(A) is the result of RNAi. Rela'~ive zritensities of the fluorescence in Figures 298(A) and 298(Hy are shown in E'igure 29S(C) . y-axis is shown with relative luminance. It can be seen that the effect by EGFP is substantially completely inhibited.
Figure 29C shows a result and graph summarizing the above. The left-hand panel shows a photograph comparing an EGFP RNAi and a scrambled (Mack} RNAi. As shown in the figure, the use of RNAi of EGFP showed and inhibitory effect, whexeas the use of scrambled RNAi did nvt show such an inhibitory effect. The right-hand panel shows the same together with DsRed2. Experimental conditions are similar to the above Examples. As a result, red (signal derived from DsRed) and gxeen (signal derived from EGFP) were presented in the proportion of the effects of RNAi.
Figure 2~1~ shows an illustrative drawing of a chip using an RNAi reporter. When using RNA, as an input signal, and introducing a nucleic acid encoding both a gene product capable of signaling such as EGF and the like, and a gene of interest (a.ncluding a promoter) as an output, observation of the'signaling as the output allows one to produce cellular information.
3. 5 Figure 29E shows an exemplary experiments using a vaxiety of reporters ( pAPl-EGFP, pAPI(PMA)-EGFP, pCRE-EGFP, pE2F-EGFP, pERE-EGFP, pGAS-EGFP, pGRE-EGFP, pHSE-EGFP, pISRE-EGFp, pMyc-EGFP, pNFAT--EGFP, pNFkB-EGFP, pRARE-EGFP, pRb-EGFP, pSTST3-EGFP, pSRE-~EGFP, pTRE-EGFP, pp53-EGFP, pCREH-sensor, pIkB-sensox, pp53-sensor, pCasapase3-sensor; cis-element sequence was commercialJ.y available from Clontech; these axe plasmid vectors produced by recombining a fluorescent protein gene) . As such, the system of the present invention will function regardless of the types of reporters used.
(Example 7: Regulation of gene expression using a tetracycline-dependent promotex) As described in the Examples 1-3, it was Azoa7 demonstrated that a tetracycline-dependent promoter could be used to produce a profile showing how gene e~cpression is regulated. The seque:xoea described below were used.
As the tetracycline-dependent promoter (and its gene vector construct), pTet-Off and pTet-On vectors (BD
Hiosciences) were used (see http://www.clontech:com/techinfo/veGtors/cattet.shtm~.).
As a vector, pTRE-d2EGFP (SEQ ID NO.: 29) was used (see http://www.clontech.com/techinfo/vectors/vectorsT-Z/pTl~
E-d2EGFP.shtml). _ (Protocol) pTet-Off and pTet-On (SEQ ID NOS.: 26 and 27, respectively) were printed unto array substrates. Real time measurement was performed on the array substrates to determine whether or not tetracycline regulates gene expression. The results are shown in Figure 30. As shown in Figure 30, a change in gene expression was detected only fox the tetracycline--dependent promoter. Figure 31 is a photograph showing the actual states of expression for the tetracyc~.ine-dependent promoter and the tetracycline-independent promoter. As can be seen, the difference b~aween them is measurable by the naked eye.
(Measurement of profile data) images are taken in real time. Changes in intensity per cell or area are plotted on a graph. The resultant data may be subjected to linear transformation, such as no~.se reduction, and then multivariate analysis, signal processing, ox the like, to obtain profile data. The resultant data is compared between phenomena or cells, thereby making it possible to determine a specific response ar identity for the cells.
(Example 8: Gene expression) Next, nuclezc acid molecules encoding structural genes were used to produce cellular profiles.
In this example, an olfactory receptor I7 (SEQ TD NOS: 13, 14) was used as a structural gene. The protocol used in Examples 1-3 was used.
As a result, as with promoters, it was demonstrated that cellular profiles eou~d be produced by measuring the amount of gene products or the like.
(Example 9: Apoptotic signals) Next, it was investigated that cellular profiles could be produced by monitoring the activation of caspase 3 present within cells. Txansfect.ion and array preparata.on were performed as in the above~described examples.
pCaspase3-Sensor Vector (HD Biosciences Clontech, 1020 East Meadow Circle, Palo Altv, CA 94303: cat.
No. 8185-1) was used to monitor an apoptotic signal from caspase 3.
As a result, as with promoters, it was demonstrated that cellular profiles could be produced by measursng apoptotic signals or the like.
(Example 10: Stress signal) Next, it was investigated whether cellular profiles characterizing stress signals from JNK, ERK, p38 or the like could be produced using transcription factor reporters. Transfection and array preparatior~ were performed as in the above-described examples.
pAPI~-EGFP, pCRE-EGfP, and pSRE-EGFP available from BD Bioscience Clontech were used to monitor stress signals from JNK, ERK, and p38.
As a result, as in the above-described examples, it was demonstrated that cellular profiles could be produced by measuring stress signals.
(Example 11: Localization of molecules) Next, it was demonstrated that a gene of interest could be fused with a. fluorescent protein so that the expression profile of the gene product and the cellular localization of the gene product could be visualized.
GFP, RFP, CFP and BFP, were used a$ fluore8cerit proteins and cloned KIAA cDNA libraries c~x the like were used as genes of interest to produce gene constructs. These materials are specifically d~:scribed below:
cloned KIAA eDNA ~KIAA=Kazusa DNA Research Institute, Kazusa, Chiba, Japan): and cDNA libraries commercially available from Tnvitrogen.
Transfection and array preparation were performed as in the above-described examples.
The expression of cloned KIAA, ~CZAA~.474, was monitored to produce a profile of the expression and investigate the localizd.tion of the expression product.
As a result, as iz~ the above-described examples, it was demanstrated that intentionally constructed gene constructs could be used to produce cellular profiles for target characteristics.
(Example 12: Changes in cellular morphology) Next, it was demonstrated that cellular profiles characterizing cellular morphology could be.
produced by expressing or knaGking out genes or adding substances (glycerophosphate as a chemical substance and dexamethasone as a Cytokine) . Cellular morphology, such as multinucleated cells, cellular outgrowth, outgrowth pxQ~jections, and the like, was measured and analyzed as three-dimensional data.
xhe specific sequences of the introduced nucleic acid molecules are described below:
Cloned KIAA (supra); and RNAi fox transcription factors (C9FA-7., AP1) .
2$9 Transfection and array preparation were performed as in the abdwe-described examp~.es.
Mesenchymal stem cells as used in the above-described examples were used to monitor the morphology of Dells which were induced to be differentiated into osteoblasts.
As a result, as in the above-described e~tamples, it was demonstrated that intentionally constructed gene constructs could be used to produce cellular profiles for target characteristics. Event descriptors can be produced based on the profile data using the process as used in the above-described examples.
(Example 13: Intermolecular interaction) Next, it was demonstrated that cellular profiles could be produced by using a technique such as a two-hybrid system, FRET, BRET, or the like.
fhe specific sequences of the introduced nucleic acid molecules are described below:
olfactory receptors (SEQ xD NOS: 13 to 38) ; and G proteins (SEQ ID NOS: 39 to 44).
Transfection and array preparation were performed as in the above-described examples.
Alao~
The dissociation of the olfactory receptor and G protein was monitored through induction of a scented substance, which was captured as changes in fluorescent wavelength. Tn this manner, cells were monitored.
The two-hybrid system, FRET, and BRET were specifically performed as follows.
The two-hybrid system was available from Clontech (http://www.Glontech.co.jp/product/catalog/0070030a6.sh tml) _ FRET and BRET were performed using devices ava~,lable from Herthold Japan.
As a result, as in the above-described examples, it was demonstrated that intentionally constructed gene constructs could be used in a two-hybrid system, FRET, HRET, or the like, to produce cellular profiles.
(EXAMPLE 14: Receptor-Zigand) Next, it was demonstrated that a cellular profile can be produced by employing the interaction between a xeceptor and its ligand as an indicator. it is useful for network formation in a cell, to obtain interactive information betweezx a receptor protein present in the cell membrane or nuclear membrane, or the like, and a ligand thereto.
In the present Example, the following was prepared:
(Cell adhesion molecules) A variety of extracellular matrix protein and variants and fragments thereof were prepared as candidates for cell adhesion molecules. What was prepared in the present Example is as follows . Gell adhesion molecules were commercially available.
1) ProNectin F (Sanyo Chemical Industries, Kyoto, Japan):
2) ProNectin L (Sazlyo Chemical Industries=
3) ProNectin Plus (Sanyo Chemical Industries):
4)~fibronectin (SEQ ID NO.: 2);
5) gelatin.
Plasmids were prepared as DNA for transfection.
Plasmids, pEGFP-N1 and pDsRed2~-Nl (both from HD Hia~ci.ences, Clontech, CA, USA) were used. In these plasxriids, gene expression was under the control of cyt4megalovirus (CMV).
The plasmi.d DNA was amplified in E. coli (XLl blue, Stratgene, TX, USA) and the amplified plasmid DNA was used as a complex partner. The DNA was dissolved in distilled water free from DNase and RNase.
The following tx~ansfection reagents were used:
Effectene Transfection Reagent (cat. no. 301425, Qiagen, CA) , TransFastm°' Transfection Reagent (E2431, Promega, WI) , TfxT~'-20 Reagent (E2391, Promega, WI), SuperFect Transfeotion Reagent (301305, Qiagen, CA), PolyFect Transfectivn Reagent (301105, Qiagen, CA), ZipofectAMINE
2000 Reagent (11668-019, zzwitrogen corporation, CA), Azoo7 JetPEI (x4) cons. (101-30, Polyplus~transfection, France), and ExGen 50b (R0511, Fermentas Inc., MD). These transfection reagents were added to the above-described DNA
and actin-like acting substance in advance or comp3.exes thereof with the DNA were produced in advance.
The thus-obtained solution Was used in assays using transfection arrays described below. Next, transfection effects ozx a solid phage were observed. The protocols therefor are descra.bed below:
(Protocol) The final concentration of DNA was adjusted to 1 ugJ~th. A cell adhesion molecule was preserved as a stuck having a concentration of 10 ~g/~L in ddH20. All dilutions were made using PBS, ddHzO, or Dulbecca' s MEM. A series of dilutions, for example, 0.2 ~,g/~~.L, 0.27 ~g/~L, 0.4 ~g/N.L, 0 . 53 E.v.g/~,L, 0 . 6 ~.lg/~L, 0 . $ ~.l.g/~,iL, 1. 0 ~.~g/~.tL, 1. 07 ~x.g/~L, 1.33 ~.g/~.L, and the like, were formulated.
Transfection reagents were used in accordance with instructions provided by each manufacturer.
Plasmid DNA was remo~red from a glycerol stock and amplified in 100 mL L-amp overnight. Qiaprep Miniprep or Qiagen Plasmid Purification Maxi was used to purify DNP~
in accordance with a standard protocol provided by the manufacturer.
In the present Example, the following five cells were used to confirm an effect : human mesenchymal stem cell.
(hMSCs, PT-2501, Cambrex BioScience walkersville, Inc., Mn) ; human embryonic renal cell (HEK293, RCH1637, RIKEN Cell Bank, JPN): NIH3T3-3 cell (RCB0150, RIKEN Cell Bank, JPN);
S HeZa cell (RCB0007, RIKEN Cell Hank, JPN) ; and HepG2 (RCH1648, RIIiEN Cell Hank, JPN) . These ce7.ls were cultured in DMEM/10~
IFS containing L-gxut and pen/strep.
(Dilution and DNA spots) ~.0 Transfection reagents and DNA were mixed to form a DNA--transfection reagent complex. The complex formation requires a certain period of time. Therefore, the mixture was spotted onto a solid phase support (e. g. , a poly-L-lysine slide) using an arrayer. In the present Example, as a solid 15 phase support, an APS slide, a MAS slide, and an uncoated slide were used, as well as a poJ.y-L-lysine slide. These slides are available from Matsunami Glass (Kishiwada, Japan) or the like.
20 For complex formation and spot fixation, the slides were dried overnight in a vacuum dryer. Drying was performed for a duration in the range of 2 hours to ~. week.
AJ.though the cell adhesion molecule might be 25 used during the complex formation, it was also used immediately befoxe spotting in the present Example.
(Formulation of mixed solution and application to solid phase supports) 30 300 ~tL of DNA concentrated buffer (EC buffer) + 16 p.L of an enhancer were mixed in an Eppendorf tube. The mixture was mixed with a Vortex, followed by incubation for minutes. 50 ~ of a transfection reagent (Effectene, etc.) was added to the mixture, followed by mixing by 5 pipetting. To apply a transfection reagent, an annular wax barrier was formed axound the spots on the slide. 366 ~.tZ
of the mixture was added to the spot region surrounded by the wax, followed by incubation at room temperature for 10 to 20 minutes. Thereby, the fixation to the support waa manually achieved.
(Distribution of cells) Next, a protocol. for adding cells will be described. Cells were distr~.buted for transfection. The distribution wag typically performed by reduced-pressure suction in a hood. A slide was placed on a dish, and a solution containing cells was added to the dish for transfection. The cells were distributed as follows.
The growing cells were seeded at a concentration of 10' oells/25 mL. The cells were plated on the slide in a 100x100x15 mm squared Petri dish or a 100 mm (radius) k ~.S mm circular dish. Transfection was conducted for about 40 hours. This period of time corresponded to about 2 Cell cycles. The slide was treated ~ox immunofluorescence.
(Evaluation of gene introduction) Gene introduction was evaluated by detection using, for example, immunofluorescence, fluorescence microscope examination, laser scanning, xadioaGtive labels, and sensitive films, or emulsion_ 'then an expressed protein to be visualized ins a fluorescent protein, suoh a protein can be observed with S a fluorescence microscope and a photograph thereof can be taken. For larga~s~.zed expression arrays, slides may be scanned using a laser scanner for storage of data. If an expressed protein can be detected using specific fluorescence in the case of calcium, a protocol specific for detection of a specific fluorescence can be successively performed to detect signals. If an expressed protein can be detected using fluorescence antibodies, an immunofluorescence protocol can be successively performed.
(user scanning and Quantification of fluorescence intensity) To quantify transfection effic~.ency, the present inventors used a DNA microarray scanner (GeneTAC
UC4xA, Genom.ic Solutions Inc., MTV. Total fluorescence intensity (arbitrary units) was measured, and thereafter, fluorescence intensity per unit surface area was calculated.
(Cross-sectional observation by confocal scanning microscope) Cells were seeded on tissue culture dishes at a final concentration of 1x10 cells/well and cultured in appropriate medium (Human Mesenchymal Cell Baaal Medium (MSCGM BulletKit PT-3001, Cambrex BioScience Walkersville, Inc., MD). After fixation of the cell ~.ayer with 4~
paraformaldehyde solution, SYTO and Texas Red-X phalloidin (Ma~.ecul.ax Probes Inc. , OR, USA) was added to the cell. layer far observation of nuclei and F-actin. The samples emitting light due to gene products and the stained samples were observed with a confocal laser microscope (LSM510: Carl Zeiss Co. , Ltd. , pin hole size~Gh2~223 ~.~,m, Ch2~Z08 ~,m, image interval = 0.4} tp obtain Gross sectional views.
Next, an Example, to which the present invention is applied to, is described wherein an olfactory receptor is selected as a typical example of a chemical substance receptox, When a pze~.iminaxy example was implemented, it was proved that transfection arrays can also be used for an olfactory receptor The olfactory receptor expression vector group was spotted per every kind of receptor, on a cover glass, which was made like an array, was secured with screws and the l.zke in d chamber for signal measurement, and cells having an almost homogeneous nature, were cultured thereon.
Regarding a chamber for signal measurement, sample gas was infiroduced into a known structure (Pros. Natl. Aced. Sci.
USA, 96(1999): 4090-4045 and the like). Other devised chambers are also intended. During response measurement, culture medium was passed through the chamber at a constant speed. Culture media was supp~.ied to the chamber for measurement from the apen~.ng of a culture medium supply tube, and a sample gas supplying tube was secured at the position preferably near the liquid level, which is the upper portion of an interval whose boundary is defined by reaching a wall AZ~~7 Which prevents the appxoaGh of culture media over a cover -slip that forms the ceiling of the measurement member, so that sample gas can be supplied to culture medium flowing across the interval. This sample gas supplying tube is preferably made of materials to which lipophilic odor substances such as Teflon and peak,.. and dust are not readily s.dsorbed. The higher effect was obtained in the asztuetion wherein, at the time other than introducing sample gas, sample gas remaining in a tube was removed, and to preferably keep the interior clean, the tube (preferably with a broad opening) could be purged with odorless air by setting a three-way valve in the mid course, or by setting a check valve at a joint of an odorless air supplying tube. However, it was not necessary. The example could also be implemented in the situation wherein, at a time other than when introducing sample gas from outside for an appropriate time such as 0. 5-4 seconds, odorless air was introduced from mid course of a sample gas supplying tube near a opening for collecting gas from outside, the izxterior of the tube was washed therewith, and at the same time, odorless gas was supplied to the culture medium as sample gas to promote the removal of remaining gas in a measu.~ement chamber. A
supporting base for the upper-glass cover slip is made of a water repellent opaque plastic such as Teflon. A width 2S of flow channel, where culture medium flows, is about 2-fold of a width of an array, and the array is disposed in the center of the flow channel. Regarding a culture medium supplying tube and an overflow culture medium sucking tube, a portion several millimeters from the opening at the side of the measuz~ement chamber is made using mater~.als which PsI~~7 have high hydrophilicity and are difficult to deform, such as stainless steel. The upper portion of the supporting base of the upper glass cover-slip where culture medium flows, from the openings of both tubes to an array, was coated, or covered with a pieces of lens paper and the like ~.n o~dex to provide sufficient hydrophilicity. Negative pressure for suction was adjusted at the grade such that measurements were not affected by. vibration from sound generated by aspiration culture.
Generally, response measurement could be implemented 2 days after the gene introduced by the vector was expressed. Since an upper glass cover-sl.~.p was required only at the time of measurement, it was riot required to install it during culture until the gene was expressed.
Therefore, the Example could be implemented, adding an upper glass cover slip integxsted with a wall which prevents leakage of culture medium, and a supporting base for the upper glass cover slip, to a chamber for measurement, when setting a chamber for measurement of a change in fluorescence measured by an apparatus after the gene expressed. The Example could also be imp~.emented in the situation wherein culture medium was exchanged without using a culture medium supply tube and an overflow culture suction line tube during culture until the gene was expressed. An amount of about lOml of culture medium was.supplied and exchanged at the frequency of .about once per several hours t4 one day, only during the time tissue culture was performed.
The size of odor response could be optically AToo~
measured using a two-dimensional image sensor such as a sensitive video camera, with a calcium ion sensitive fluorescent dye fura-2 and the like absorbed into the cell.
The measurement interval preferably has time resolution which can evaluate time ~an~stants of build-up and recovery of response of about 1/3-1 second. However, if average response time curve or its theoretical formula had been obtained, actual change was estimated from measurement results at 5 points with 5--second-intervals, 5, 10, 15, 20, ZO and 25 seconds after stimulation. The obtained estimates of the time constant of the response sts.rting time, response build-up time, and response recovery time was set as an index, and evaluation could be made as to whether a signal was induced by odor, or generated by spontaneous activity of 1S a cell, or other abnormalities.
In this Example, the response of an expressed olfactory receptor in olfactory receptor neuron was studied by measuring the change in fluorescence intensity of calcium 20 sensitive fluorescent. dye, Decrease of fluorescence intensity (downward change) corresponds to the response of an olfactory receptor. Odor molecules were added to the culture at the concentration indicated above them as stimulation source, and administered to a cell during the 25 time indicated by a bar (~ or 2 seconds) . As understood from this example, responses measured simultaneously in a simultaneously adjusted cell have high intercommunity in response time characteristics, response threshold concentration corresponding to different stimulatipn per 30 GeIJ., arid relative value of response amplitude. However, Aloo~
cells adjusted at a different times show some differences.
These results show that the highest measurement reliability can be obtained by measuring odor response using a sensor arrayed to a size that allows a homogeneous adm~.~istxat~.oz7, of sample gas, providing the same adjustment conditions.
(Example 7.5: Application to neuron differentiation) Next, experiments similar to those of Example 14 have been conducted with neurons to analyze the effects of tyrosine kinase RNAi with a transfection microarray. The exemplified drawings are shown in Figure 318.
As shown in Figure 318, network analysis can be Conducted by taking photographs of signal represented by a reporter and collecting information thereon.
Figure 31~ shows the responses of retinoic acid (RA) and nerve growth factor (NGF) to a variety of tyrosine kinases. Inhibition ~S by siRNA is shown.
Figure 31D depicts an exemplary drawing of a signal transduction pathway obtained as a xesult of analysis.
Figure 31E shows results obtained by the above-mentioned analysis. Classification has been made regardless of whethex the subject cells were dopaminergic neurons, cholinergic neuron, both, ox n,oithar. It oan be concluded that those kinases relating to both. cell types have high probability of relating to nerve projection ~a~.
formation.
(Example ~.6~: Data prcduGtion) Data produced in Examples 5-15 can be analyzed using a mathematical analysis with an appropriate modification as described in Example 4. Such data have been presented in a variety of formats.
(Example 17: Production of a digital cell) Data produced in Examples 5-15 and additional data produced using the protocols described therein were used to produce a digital cell. In order to produce digital cells, parameters fox data produced in these Examples have been extracted, and medium, pfi, temperature, Cpz concentration, and the J.ike have been used as environment parameters. Database production may be performed using, for example, a spreadsheet software such as Excel~'M available from Microsoft, or a database software such as Access'' also available from Microsoft. Next, as cell parameters, a database including cell species such as those used in Examples 5-15 can be used. ~ variety of stimulus parameters such as a vaxiety of chemical stimuli, (for example, including a variety of growth factors or cytokines such as HGF, FGF, PDGF, VEGF, CSF and the like) can be input to produce cell dynamics data, measurement data of reporters such as fluorescence intensity and the like. As such, a database constituting digital cell can be produced_ Such examples are shown in Figures 33A and 335.
(Example 18: Use of digital cells: ~n ejltco live experiments) The digital cells produced in Example 17 have been used to conduct experiments on a computer. In the present Example, a mesenchymal stem cell is used to study which agents are differentiation agents. In the case of Figure 33~r, cell A is selected as cell (for example, mesenohymal stem cell or the like)_ Further, DMEM is selected as a medium, pH 7 . 4 is selected as the ~pH, 3'7 degree Celsius is selected as the temperature, 5~ ie selected as the COZ concentration. Moreover, a variety of chemical stimuli such as growth factors or cytak~.nes such as HGF, FGF, FDGF, VEGF, and CSF are selected. With respect to such a variety of chemical stimuli, concentrations are also appropriately selected, such as 1nM to lmM. Combinations of these two or three thereof are also selected as a variety of chemical stimuli. Depending these combination and concentration, data regarding responses with respect to how a mesenchymal stem cell responds is output . As an output, cell dynamic is included. From such cell dynamic, it is confirmed that the mesenchymal stem cell is differentiated (e.g. to bone marrow or adipocyte or the like) or not. If morphology is not sufficient, combinations between transcriptional factors and EGF as reporters are used to output further measurement data _ As such, it can be conf~.xmed whether ox not a mesenchyma~. stem cell is differentiated to which e~ Specific differentiated cell. Us~.ng the present method, one can specify a chemical stimulus which induces differentiation to a specific differentiated cell.
(Example 19: Use of digital cells - education by .in silico live experiments In sil.ico live experiments described in Example 1$ axe conducted during school education. In this example, the experimental theme as described above is given to a student .
The student selects a variety of parameters from a database of a given digital cells. fhe student composes his/her own research based.or~ the data selected. The student submits the composed research. results as assignment/report. As such, education to a student can be conducted without using a live experimental system.
(Example 20: provision of a digital service) A database of the digital cell may be provided as an external service. Databases produced in Example 18 may use those embodiment described in Figure 35. As such, the configuration of computer system 3501 providing a service reproducing experimental results to an actual cell using the digital cells is shown, Computer system 3501 comprises service requester 3510 requesting services desired by a user, and sexvzce provider 3520 providing a determined service in response to the request . Users such as research inst~.tutes, educational organizations or institutions request desired services. Service provider
parameter and the stimulus parameter; and means for provide-rig the request to the service provider, and wherein the service provider comprises:
means for searching the database in response to the request by the ser~rice provider tv determine whether or not there is the stimulus response result relating to the cell parameter, the environment parameter and the stimulus parameter included in the request ir: the database;
and means for providing the stimulus response result tv the service requester by the service provider, when it determined that the stimulus response result relating to the cell parameter, the environment parameter ~.5 and the stimulus parameter included in the request exists i.n the database:
wherein the serv~.ce requester further comprises means for presenting the stimulus response result by the service requester.
137. A computer system according to Item 136 wherein the service requester is a Web browser which the user operates, and the service provider is a Web server linked to the service requester via the Internet.
138. A computer system according to Item 136, wherein the service requester provides the request to the service provider in a format described in XML language.
139. A computer system according to Item 136, wherein the ser~crice provider provides the stimulus response result to the service requester in a format described in XML language .
~,4p. A computer system for providing a service which reproduces an experimental result of an actual cell using a digital cell, comprising:
a plurality of service providers, each composed such that the pJ.urality of service providers can have access to a database having at least one digital cell stvz~ed thereon, each of the at least one digital cell is expressed as a collection of at least one experimental data of a ceJ.l of experimental interest, wherex:x each of the at least one experzmenf.al data comprises a cell parameter specifying the cell, an environment parameter specifying an environment under which the cell specified by the Dell paramEter is cultured, a stimulus parameter specifying a stimulus to be given to the cell specified by the cell parameter, and a stiznu~,us response result showing a result which the cell specified by the cell parameter responds to the stimulus specified by the stimulus parameter under the environment specified by the environment parameter;
a service registry which stores at least one service which the plurality of service providers can provide; and a service provider requesting a service desired by a user:
wherein the service requester comprises:
means for receiving the cell parameter, the environment parameter and the stimulus parameter to produce a request comprising the cell parameter, the environment parameter and the st~.mulus parameter means for searching the service registry in response to the request by the service requester to determine whether or not there exists a service provider capable of providing a service of the request amongst the plurality of service providers and means for providing the request to the service provider by the service requester when it is determined that there exists a service provider capable of providing a service of the request amongst the plural~.ty of service providers, wherein each of the plurality of service providers comprises:
means for searching the database in response to the request by the service provider to determ~.ne whether or not there is the stimulus response result relating to the cell parameter, the environment parameter and the stimulus parameter included in the request in the database;
and means for providing the stimulus response result to the service requester by the service provider, when ~.t is determined that the stimulus response result relating to the cell parameter, the environment parameter and the stimulus parameter included in the request exists in the database;
wherein the service requester further comprises means for presenting the stimulus respoz~se result by the service requester.
141. A computer system according to Ttem 140, wherein the service requester is a Web server connected to a Web brow$ex which the user operates via the Internet, and each of the plurality of service providers is a rnieb server connected to the service requester via the Internet.
142. A computer system according to Item 140, wherein the service requester provides the request to the service prov~.der in a format described in ~NtL language.
143. A computer system according to Ttem 140, wherein the service provider provides the stimulus response result to the service requester in a format described in XML language.
144. A method for producing the profile data relating information of a cell, comprising the steps of:
a) immobilizing and locating a cell an a support; and b) monitoring a biological agent, or a collection thereof, on or in the cell to produce the profile data for the ceJ.Z .
145. A method according to Item 144, wherein the biological agent is a nucleic acid molecule or a molecule derived from the nucleic acid molecule.
146. A method according to Item 144, wherein the cell is immobilized to the support by a composition comprising a) a complex with a positively charged substance and a negat~.vely charged substance; and b) a salt.
147. A method according to Item x.44 wh.erein the cell is provided with an actin--like substance.
~1Z0~7 14~. 1~ method according to rtem 7.44, wherein the cell is immobilized f.o the support by a composition comprising a) a complex w~.th a positively charged substance and a negatively charged substance: and b) a salt, and is provided with an actin-like substance.
149. A method according to Item 144 wherein the biological agent is selected from the group consisting of a nucleic 7.4 acid molecule, a protein, a saccharide, a lipid, a low molecu~.e, and a complex thereof.
150. A method according to Item x94, wherein the cell is cultured for at least about three day's before the step of monitoring.
151. A method according to Ttem 144, wherein the biological agent comprises a nucleic acid molecule encoding a gene.
152. A method according to Item 144, wherein the profile Comprises a prvfi.le of gene expression.
153. A method accord~.ng to Item 144, wherein the profile comprises a profile of an, apoptosis signal.
z5 154. A method according to Item 144 wherein the profile is a profile of a stress signal.
155. A method according to Item 144 wherein the profile is a profile of the localization of a molecule.
Azaa7 156. A method according to Item 155 wherein the molecule is detected by means selected from the group consisting of fluorescence, phosphorescence, radioactiv~.ty', and a combination thereof.
157. A method according to Item 144 wherein the profile comprises a variation of cell morpholac~y.
158. A method according to Item 144 wherein the profile comprises a profile of promoters.
159. A method .according to Ztem 144, wherein said profile comprises a profile of a promoter dependent on a specific drug.
160. A method according to Item x.44 wherein said profile comprises a profile of a promoter dependent on a specific drug, wherein said method further comprises the step of administering the specific drug.
16x. A method according to Item 144 further comprising the step of subjecting the cell to a foreign agent.
162. A method according to Item 161, wherein said foreign agent comprises an RNAi.
163. A method according to Item 161, wherein said foreign agent comprises a chemical not present. in a biological k~ody, ~0 164. A method according to Ztem 144, wherein said pzofile comprises a profile of intermolecular interaction.
165. A method according to Ttem 161, wherein said foxeign agent comprises a ligand for a receptor of said cell.
166. A method according to Item 144, wherein said profile comprises a profile of an interaction between a receptor and a ligand.
la 167 _ A method according to Item X44, wherein said profile is a cellular form, and said method fuxther oC~mprises the step of giving to said cell a stimulus selected from the group consisting of overexpression, underexpressiOn or knockdown of a gene, addition of a foreign agent and a change in the environment.
158 _ A method according to Item 144, wherein said profile comprises a profile of interaction between molecules present in said cell.
16$. A method according to Item 144, further comprising the step of conducting observation using a technology selected from the group consisting of twvuhybrid method, FRET and BRET.
170. A method according to Item 144, wherein said profa.le comprises a profile of interaction between molecules present in said cell, wherein the method further comprises the step of conducting observation using a technology se~.~cted from the group consisting of two-hybrid method, FRET and BRET.
173.. A method according to Item 144, wherein said cell is located on said support in an array format.
172. A method according to stem 144, wherein said cell. is located on said support in an array format, and each of said plurality of cells are located at a space of 1 mm at maximum.
to 173. A method according to Item 7.44, wherein said profile is obtained at real time.
174 . A method according to Item 144 further comprising the 7.5 step of immobilizing said cell to a solid support.
175. A method according to Item 144, wherein said data comprises information relating to said profile.
20 176. A method according to Item 144 wherein said data comprises information relating to conditions during said monitoring.
177. A method according Ttem 144 wherein said data 25 comprises ~.nfvrmativn relating to the state of said cell.
178 . A method according to Item 144 wherein said biolog~.cal agent to be monitored comprises at least two types of biological agent.
x79. Amethod according to Item 144 wherein said biological agent to be monitored ovmprises at least three types of biological agent.
180. A method according to item 144 wherein said biological agent to be monitored comprises at least eight types of biological agent.
181. A method according to Ttem 144 further comprising the step of arbitrarily selecting a biological agent.
182. A method according to 'item 144 whexein said cell is selected from the group consisting of a stem cell and a somatic cell.
x.83. A method aGCOrding to Item 144 wherein said support comprises a solid support.
184. A method according to ztem 144 wherein said support comprises a substrate.
X85. A method according to Ttem 144 wherein said biological agent is a nuoleio acid molecule, and said cell is transfected with said nucleic acid molecule.
186. A method according to Item 185, wherein said transfeGtion is conducted an a solid phase or in a liquid phase.
187. A method according to Item 185, wherein said transtection is conducted on a solid support.
1$$ . A method according to Item 144, further comprising the step of comparing a phase of said profile.
189. Rmethod according to rtem 144, further comprising the step of subtracting a control profile from the profi7.e of said cell.
190 . A method according to Item 144 further comprising the step of processing the profile with a mathematical processznc~ method selected from Signal processing and multivariant analysis methods.
Hereinafter, the present invention will be described by way of preferred embodiments. rt will be understand by those skilled in the axt that the embodiments of the present invention can be appropriately made or carried out based an the description of the present specification and the accompanying drawings, and common~.y used techniques well known in the art. fhe function and effect of the present invention can be easily recognized by those skilJ.ed in the art. .
The present invention pra~rides consecutive information (profile) data relating to the state of a cell.
The present invention provides information and data (in particular consecutive information and consecutive profile) relating to the state of a cell in a Consistent environment, in a reproducible manzxer. According to the Azpp7 present invention, ~, method and a system fax presenting such data in an accurate manner are provided. Specifically, it should be surprising a effect to be able tc~ provide a system and a method for information at the cellular level. in a consistent environment in terms of a complex system as such or in a direct manner, and to be able to provide such data and technology fvr aligning such data per se. The present invention further attains the effect of providing a digital cell based on actual, live data and the use thexeof, which have not been conventionally possible prior to the present invention.
As such, according to the present invention, it is possible to determine the state of cells by observing a surprisingly small. number of factors. Therefore, the present invention is applicable to diagnosis, prevention, and treatment . The present invention is also applicable to the fields of food, cosmetics, agriculture, environmental engineering, and the like. Reproduction of a live experiment on a computer system attains the effect of enabling education and research in the field of biotechnology.
BRIEF DESCRIPTION OF THE DRAWING$
Figure 1 shows the results of experiments in which various. actin-like substances and HEK293 cells were used, where gelatsn was used as a control.. Figure 1 shows 34 the effect of each adhesion substance (HEK cell) with respect to transfeati.ar~ efficiency. The HEK cells were transfected with pEGFf~-N1 using an Effectene reagent.
Figure 2 shows exemplary transfection S efficiencies when fibronectin fragments were used.
Figure 3 shows exemplary tranafection efficiencies when fibronectin fragments were used.
Figure ~ shows a summary of the results presented ire. Figures 2 and 3.
Figure 5 shows the results of an example in which transfection effic~.ency was studied for various cells.
Figure 6 shows the results of traxzsfecta.an when various plates were used.
F~.r~uxe 7 shows the results of transfection when various plates were used at a fibronectin concentration of 0, D.27, 0.53, D.B, 1.07, and 1.33 (ug/uL).
Figure 8 provides exemplary photographs showing cell adhesion profiles in the presence or absence t~f fibronectin.
Figure 9 shows exemplary cross-sectional photographs of cell adhesion profiles ~.z~ the presence or absence of fibronectin. Cross-sections of human ~4 6 mesenchymal stem cells (hMSC) were observed using a confoaal laser scanning microscope. hMSC were stained with SYT061 (blue fluorescence) and Texas red - X phall.oidin (red fluorescence) and fixed with 9~ PFA. Blue fluorescence (nuclei: SYT061) and red fluorescence (nuc~.ei: Texas red -- X phalloidin) were obtained using a confocal lasex microscope (ZSM5~.0, Carl Zeiss Co. , Ltd. , pin hole size=1. 0, image interval=0.4).
Figure ~0 shows transition of nueleax surface area. Relative nuclear surface area was determined by cross-sections of hMSC observed with canfocal laser scanning microscopy, hMSC was fixed with 4~ PFA.
1S figure 11 shows the results of an exemplary transfeotion experiment when a transfection array chip was constructed and used.
Figure 12 shows exemplary contam~.nation between each spot on an array.
Figure 13 shows an experiment in which spatially-spaced DNA was taken into cells after the solid phase transfection of the pxesent invention in Example 4.
Figure i3A schematically shows a method for producing a solid phase transfection array (SPTA). This figure shows the mEthodology of a solid transfection.
3Q Figuxe x3H shows the resu~,ts of a so~.id phase transfection. A HEK293 cell line was used to produce a SPTA.
Green colored portions indicate transfected adherent sells.
According to this result, the method of the present invention can be used to produce a group of cells separated spatially and transfected with different genes. As such, Figure I,3A-a, as a whole, depicts schematically the procedure of transfection (SPTA7. Figure 13A depicts the outlines of SPTA determination, and Figure 138 depicts a result of SPTA using 8EK293 cell straa.n. The bar indicates 3mm.
Figure 13C shows the diffexez~.Ge between conventional liquid phase transfection and SPTA.
Figure 14 shows the results of comparison of liquid phase transfectzon a.nd SPTA.
Figure 14A shows the results of experiments where S cell lines were measured with respect to GFP
intensity/mm2. Transfection efficiency was determined as fluorescence intensity per unit area.
Figure 148 shows fluorescent images of celJ.s expressing EGFP corresponding to the data presented in Figuxe i4A. White circular regions therein were regions in which plasmid D1VA Was fixed. In other regivz~s, cells were also fixed in solid phase, however, cells expressi.nc~ EGFP
were not observed. The white bar indicates 500 Eun.
Fluorescent photographs of EGFP expressing cells corresponding to Figure 14A are shown with respect to the five types of cells per measured fluorescence/mm2. White circles correspond to plasmid DNA priz7.ted regions . Outside these regions, cells express EGFP. Further, regions other than the printed regions are attached cells.
Figure ~.~C shows an exemplary transfection method of the present invention.
Figure 14D shows an exemplary transfection method of the present invention.
Figure 15 shows the xesults of coating a chip, whereby cross contam~.nation was reduced.
7. 5 Figure 15 shows the results of liquid phase transfection and SPTA using HEK293 cells, HeZa cells, NIT3T3 cells (also referred to as "3T3"), HepG2 cells, and hMSCs.
Transfection efficiency was determined by GFP intensity.
Transfection efficiency of hMSC depending on the N/P
ratio used is shown in Figure 15A. In the phase of pxior liquid phase transfection (Figuxe 158, upper panel), hMSC
cells were dead and in the case of SPTA, cell morphology was normal (Figure 15H, lower panel).
Figure 16 shows cross contamination between each spot. A nucleic acid mixture containing fibronectin having a predetermined concentration was fixed to a chap coated with APS or PZT~ (poly-L-lysine) . Cell transfection was performed on the chip. Substantially no cross contamination was observed (upper and middle rows). In contrast, significant cross contamination of fixed nucleic acids was observed on an uncoated chip (lower row).
Figure 16C shawl a correlation relationship between the types of substances contained in a mixture used for fixation of nucleic acid and the cell adhesion rate.
The graph presented in Figure 1f shows an increase in the proportion of adherent cells over time. A longer time is required for cell adhesion when the slope of the graph is shal~.ow than when the slope of the graph is steep.
Figure 16D is an enlarged graph which is presented in Figure 16C.
Figure i'~ shows an exemplary configuration of a computer which was used to perform the method of the present invention.
Figure 18 depicts an example of a mathematical analysis method of the present invention. Profiles of promoters shown in Figure 18A (average of pNEF~Im-d2EGFP/negative control) and Figure 18H (a~crerage of pERE-d2EGFP/negat~.ve control ) are obtained by measuring the fluorescent intensity thereof over time. These profiles have been normalized using the autologous fluorescence of either the cell or medium used. Thereafter, in order to compare amplitude of the reporter expression fluctuat~.on, an amplitude ~ 5 or more ( TH>=5 ) was determined to have change in expression fluctuation state. Further, differentiation induction was divided into the following sections: start of differentiation induction,. early stage (0-17.5 hours), and late stage (17.5-31.5 hours) and total stages (0-31.5 hours); and those observed with a variation in expression of an amplitude of 5 or more (TH>=5) were defined as (+) and those with an amplitude of less than 5 were defined as (-). Based on these definitions, the profiles of A and B
were evaluated as shown in the lower tables of Figures 1.8A
and 18~. Tn the table, when extracting any number of reporters, (A+B+ ... n) have been infiegrated with respect to n types of wave forms and the sum is divided by n to form the average wave form and if variations beyond the threshold, such variations were deemed as being "changed".
Figure 18H depicts another example o~ a mathematical analysis according to the present invention.
When a reporter i9 extracted (A+$-~ , . , n) , n types of wave types are integratEd, and the sum is divided by n to produce an average wave form, which was deemed as being a change of the variation above a threshold. The left hand panel of Figure Z8H depicts the integration of two reporter profiles arid draws the average wave form in red or with solid squares.
Those with 5 or more variations of the average profile were deemed to be expression variations for evaluation. As a result, evaluation can be Conducted for variation of the two extracted reporters, as shown in the table herein.
Figure 19 depicts exemplary plasmids containing promoters used in the present invention and an analysis Az007 according to the present invention. Seventeen types of transcriptional factors shown in the left hand panel of figure 19 were used as a reporter uz~der the conditions o:f vr>teoblast differentiation and maintenance of an undifferentiated mesenChymal stem cell, and the expression prof~.le thereof have been obtained over time (figure 19, right handed panel) . From these seventeen types of profiles, any number of profiles have been extracted and evaluated by the method as previously described in Figure 18, taking 1.0 the change in amplitude of the response profile of each transcriptional factor as a standard.
Figure 20 depicts an example of mathematical ana~.ysis at the early stage of induction of differentiation.
By changing the combination arbitrarily ext ratted in the early differentiation induction stage, results as shown in Figure 20 have been obtained. Any number~of reporters were extracted from the reporter group consisting of seventeen species, and caxculated for the average profile according to the method shown in figure ~.8. mhose hav~.r~g five or more var~.ation widths are the results evaluated with the evaluation windows 0-31.5, 0-17.5 and 17.5-31.5. Each extraction condition has se~srenteen extraction patterns, except for where the seventeen extraction pattern has only one way of extraction. Amongst these combinations, Figure ~D shows the ratio in which variation is found therein, including the table and graph included therein. This analysis allows confzxmation of differentiation after fifteen hours although it is not possible to understand the very early stages of differentiation. The number of extraction where 100 ~ change is found for variation is eight or more in this instance.
Figure 21 depiots an example of a mathematical analytical result at the undifferentiation maintenance stage. As in Figure 20, similar results as shown in the graphs have been obtained when a combination arbitrarily extracted under conditions to maintain undifferentiatiori.
Comparing the results with the stage of differentiation induction, as in Fzgure 20, the results are dramatically different. Based on this comparison, ~.t is believed that it is possible to determine whether a cell is moving in the direction of cell differentiation induction, or instead maintaining an undifferentiated state.
Figure 22 schematically shows a cocktail party process.
Figure 23 shows an exempJ.ary construct of a gene transcription switch reporter used in a transfection plasmid of the present invention.
Figure ~4 shows exemplary construction of a set of transcription factor reporters.
Figure 25 shows the results of exemplary assays using transcription factor reporters.
Figure 25 shows an example of measurements of transcriptional activity in the bone differentiation process, , taken in a time-series manner.
Figure 27 shows an example of the oscillation phenomenon and phase analyses of transcriptional acti~crity.
Figure 28 shows a protocol of siRNA experiment.
Figure 29A shows the result$ of the siRNA
experiments . The upper panel shows the results of hMSC, and the lower panel show$ the results of HeLa cells. The numexals show the conce~xtrations (~eg/~L) of the siRNA used.
The xesults obtained w~.th the anti-GFP siRNA are shown an the left hand side, anal the right hand side shows the results with the scramble szRNAs.
Figure 298 shows the effects of siRNA when solid transfection, (pCl2) was conducted on a collagen IV coating.
Figure 298(A) shows PC~.2 cells cotransfected with EGFP
vector and anti-EGFP s~.RNA. As shown, it was obser~cred that only HcRed was coloxed, and green signals derived from pEGFQ-N1 were suppressed. On the other hand, Figure 29S (~3) shows an example using scramble siRNA. As shown, green fluorescence was observed and thus the effects obsexved in Figure 29H(:1,) are due to the effects of RNAi. figures showing the relative f~.uorescence intensities in Figures 29B (~) and 298 (8) , are summari zed in figure 29B (C) . The y axis indicates relative intensity. It can be seen that effects induced by EGFP were almost completely suppressed.
Figure 29C depicts results and graphs summarizing the abo~sr'e. The left-hand panel is a phatagraph comparing EGFP RNAi and scramble (mock) RNRi when changing the ratio of RNAi and pRNA. As shown, EGFP RNA. showed inhibitory effects, whereas scramble RNAi did not exert such effects. This is shown in the right-hand panel, togethex with DsRed2. Experimental cond~.tions were in accordance with those described herein. As a result, red (DsRed derived szgnal) and green (EGFP derived signal) were found to be in proportion With the effect of RNAi.
Figure ~9D depicts an exemplary chip used in the RNAi reporter. When using RNAi as input signals and cointroducing a gene product capable of transmittl.ng signals, such as EGF and the lzke, together with a nuc~.eic acid encoding a gene of interest (including a promotez~), observation of such signal transm~.ssion as output allows extraction of cell information.
Figure 29E shows an exemplary experiment using a variety of reporters (pAPI-EGFP, pApl(PMA)-EGFP, pCRE-EGFP, pE2F-EGFP, pERE-EGFQ, pGAS-EGFP, pGRE-EGFP, pHSE-EGFP, pISRE-EGFP, pMyc-EGFP, pNFAT--EGFP, pNFkB-EGFL~, pRARE-EGFP, pRb-EGFP, pSTST3-EGFf, pSRE-EGFP, pTRE-EGFP, pp53-EGFP, pCREH-sensor, plkB-sensor, pp53-sensor, pCasapase3-sensor); the is-element sequez~ce was purchased from Clontech using a plasmid vector produced by recombining a fluorescence protein gene).
Figure 30 shows changes in the profile when using tetracycline dependent promoters.
Figure 31 shows expression when using tetracycline dependent promoters and tetracycline independent promoters.
Figure 318 shows an exemplary result of analys~.s using a transfected microarray with respect to the effects of tyrosine kznase RNAi on neurons.
Figure 31C depicts responses to retinoic acid (RA) and nerve growth factor (NGF) by a variety of tyrosine kinases. Inhibition percent by siRNA is shown.
Figure 31D depicts an example of a signaling pathway obtained as a resu~.t of an analysis.
Figure 31E shows the results obtained by the above-mentioned analysis. It shows a general analysis of the tyrosine k~.nases responsible for human neuron differentiation. Classification is conducted by determining whether it is dvpaminergic neuron, chvlinergic neuron, or both, or neither. It can be concluded by the analysis that there is high possibility that those tyrosine kinases relating to both types of neuron axe involved in neuron projective formation.
Figure 31F depicts an example of real-time monitoring of transcription regulation of apoptosis in a HeLa cell. The left handed panel shows the result over time, and the right handed panel shows the result of a signaling Azoo~
pathway based on the analysts thereof.
Figure 3Z depicts an example of a system configuration.
Figure 33A depicts an example of a digital cell according to the present invention.
Figure 33~ depicts another example of a digital ~.0 cell. according to the present invention.
Figure 34 depicts an example of a,method for producing a digital cell according to the present invention.
Figure 35 depicts an example of a configuration of computer system 3501 which provides a service reproducing an experimental result obtained using an actual cell using the digital cell.
Figure 3G d~:picts an example of procedures of a process which provides a service reproducing an experimental resu3.t obtained using an actual cell using the digital cell.
Figure 3T depicts an example of input interface for inputting cell parameters, environment parameters and stimulus parameters into service requester 3510.
Figure 38 depicts an example of configurations of computer system 3801 for providing a service of reproducing an experimental result against an actual cell using the digital cell.
Figure 39 depicts an example of procedures of a process for providing a service of reproducing an experimental result against an actual cell using the digital cell.
DESCL~IPTZON OF SEQUENGE LTSTING
SEQ TD NO. 1: nucleic acid seguenee encoding : a fibronectin (human) SEQ ID NO. : an amino acid sequence of 2:
fibronectin (human) SEQ ID NO. 3: nucleic acid sequence encoding : a vitronectin (mo use) 5EQ rD NO. : an amino acid sequence of 4:
vitronectin (mo use) SEQ ID NO 5: nucleic acid sequence enGOding _ : a laminin (mouse a,-chain) SEQ ID NO. 6:
: an amino acid sequence of lam~.n~.n (mouse a,-chain) SEQ TD NO. 7: nucleic acid sequence encoding : a laminin (mouse ~i-chain) SEQ ID NO. 8:
: an amino acid sequence of laminin (mouse ~3~chain) SEQ ID N0. 9: nucleic acid sequence encoding : a laminin (mouse y~-chain) SEQ ID N4. : : an amino acid sequence of Azoo7 laminin (mouse y-chain) SEQ ID NO.: 11: an alaino acid sequence of fibronectin (bovine) SEQ ID NO.: 12: siRNA used in the Examples SEQ ID NO.: ~.3: mouse olfactory receptor T7 (heptanal-sensitive) nucleic acid (Genbank AccESSion No. AF106007) SEQ ID NO.: 14: amino acid sequence of the protein encoded by the nucleic acid set forth in SEQ ID~
NO.: 13 SEQ I37 NO: 15: nucleic acid encoding the murine olfactory receptor S1 (mc9/bc9-equi-sensitive) (Genbank Accession Number AF121972) SEQ ID NO: ~.6: amino acid sequence of the protein encoded by the nucleic acid set forth in SEQ ID NO: 15 SEQ ID NO: 17: nucleic acid encoding the murine o~.factory receptor S50 (cc9-sensitive) (Genbank Accession Number AF121980) SEQ ID NO: 1 B : amino acid sequence of the protein 24 encoded by the nucleic acid set forth in SEQ ID NO: 17 SEQ ID NO: 19: nucleic acid encoding the murine olfactory receptor S19 (nnc9/mh9/bc9-equi-sensitive) (Genbank Accession Number AF~.21976) SEQ ID NQ: 20: amino acid sequence of the protein encoded by the nucleic acid set forth in SEQ ID NO: 19 SEQ TD NO: 21: nucleic acid encoding the murine pR23 (lyraJ.-sensitive) (only coding region of Genbank Accession Number X92969) SEQ ID NO: 22 : amino acid sequence of the protein encoded by the nucleic acid set fprth in SEQ 2D No: 21 SEQ ID NO: 23: nucleic acid encoding the marine olfactory receptor mOR-EV (vanillin-sensitive) (Genbank Accession Number AB061229) SEQ ID NO: 24 : amino acid sequence of the protein encoded by the nucleic acid set foxth in SEQ ID NO: 23 SEQ ID NO: 25: nucleic acid encodis~.g the mur~.ne olfactory receptor or37a (Genbank Accession Number A~133424) SEQ ID NO: 26: amino acid sequence of the protein encoded by the nucleic acid set forth in SEQ ID NO: 25 SEQ ID NO: 27: nucleic acid encoding the marine olfactory receptor C6 (G~:nbank Accession Number AF102523) SEQ ID NO: 28 : amino acid sequence of the protein encoded by the nucleic acid set forth in SEQ ID NO: 27 SEQ ID NO: 29: nucleic acid encoding the marine olfactory receptor FS (Genbank Accession Number AF102531) SEQ ID NO: 30: amino acid sequence of the protein encoded by the nucleic acid set forth in SEQ ID N4: 29 SEQ zD NO: 31: nucleic acid encodzz~g the muxine olfactory receptor S6 (Genbank Accession Number AF121974) SEQ ID NO: 32: amino acid sequence of the protein encoded by the nucleic acid set foxth in SEQ ID NO: 31 SEQ ID NO: 33: nucleic acid encoding the marine olfactory receptor 51.8 (Genbank Accession Number AF121975) SEQ ID NO: 34 : amino acid sequence of the protein encoded by the nucleic acid set forth in SEQ TD NO: 33 5EQ ZD NO: 35: nucleic acid encoding the marine olfactory receptor S25 (Genbank Accession Number AF121977) SEQ ID NO: 36: amino acid sequence of the protein encoded by the nucleic acid set forth in SEQ ZD NO: 35 SEQ ID NO: 37: nucleic acid encoding the murine olfactory receptor S46 (Genbank Accession Number AF121979) SEQ ID NO: 3B : amino acid sequence of the protein encoded by the nucleic acid set forth in SEQ ID NO: 37 SEQ ID NO: 39: nucleic acid encoding the a subunit of murine G-coupled protein (Genbank Accession Number M3677B) 5EQ ID NO: 40 : amino acid sequence of the protein encoded by the nucXeic acid set forth i.n SEQ ID NO: 39 SEQ ID NO: 41: nucleic acid encoding the subunit o~ murine G-coupled pxotein (Genbank Accession Number MB7286) 5EQ ID NO: 42 : amino acid sequence of the protein encoded by the nucleic acid set forth in SEQ ID N0: 41 5EQ TD NO: 43: nucleic acid encoding the subunit of murine G~coupled protein (Genbank Accession Number U37527) SEQ ID NO: 44 : amino acid sequence of the protein encoded by the nucleic acid set forth in SEQ TD N0: 43 ZO SEQ ID NO: 45: nucleic acid encoding the epidermal growth factor receptor (Genbank Accession Number BC023729) SEQ zD NO: 46: amino acid sequence of the protein encoded by ~.he nucleic acid set forth in SEQ rl~ NO: 45 SEQ ID NO: 47: the sequence of siRNA used in Example 9 SEQ ID No: 4$ : the sequence of scrambled RNA used in Example 9 BEST MODE FOR CARRYING OUT THE INVENTION
Az007 Hereinafter, the present invention will be described, it should be understood throughout the present specification that articles for a singular form (e.g. , "a", "an", "the", etc. in English) include the concept of their plurality unless otherwise mentioned. It should be also understood that the terms as used herein have definitions typically used in the art unless otherwise mentioned.
Accordingly, un~.ess otherwise defined, all technical and scientific terms used hErein shall. have the same meaning as generally understood by those skilled in the art to which the present invention pertains. If there is any inconsistency, the present specification precedes, including definitions.
(Definition o~ terms) Terms particularly used herein are defined as follows .
(Cellular Biology) The: term "cell" is herein used in its broadest sense in the art, referring to a structural unit of the tissue of a. multicellular organism, which is capable of seJ.f replicating, has genetic information and a mechanism for expressing it, and is surrounded by a membrane structure which isolates the cell from the outside. Cells used herein may be either naturally-occurring cells or artificially modified cells (e. g., fusion cells, genetically modified cells, ete.), as long as the cell has a chemical receptor or is capable of having such a chemical receptor introduced therein. Exax,nples of cell sources include, but axe not limited to, a single~cell culture; the embryo, blood, or body tissue of normally-grown transgenic animals; a mixture of cells derived from normally-grown cell lines: and the like.
As used herein, the term "digital cell" refers to a collection of at least one experimental data on a cell of experimental. interest. These experimental data correlate the experimental conditions and the experimental results of an example conducted against an actual cell. The digital cell is constituted such thafi once an experimental condition is given, the experimental result related to said experimental condition wzll be reproduced. The digital cell contemplated by the present invention comprises any cell which is amenable to an experiment. It should be understood that the description with respect to all the (living) cells described herein can be applied to a digital cell according to the present invention, as long as such description is applicable to the digital cell.
Using digital cells of the present invention allows reproduction of an experimental result of an experiment conducted using an actual cell, in a computer system. As such, the present invention allow research institutes, educational organizations and individuals having no experimental facilities, to conduct educatiaz7~ and advanced research relat~.nc~ to a cell. As a result, business entities in different fields will be able to start business in this field, which has not been possible to date.
Azoo~
Cells used herein may be derived from any organism (e. g., any unicellular organism (e. g., bacteria and yeast) or any multicellular organisms(e.g., animals (e. g., vertebrates and ~.nvertebrates), plants (e. g., monocotyledons and dicotyledons, etc.)). For example, cells used herein are derived from a vertebrate (e. g., Myxiniformes, Petronyzor~.~.formes, Chondri.chthyes, Osteichthyes, amphibian, reptilian, avian, mammalian, etc.), more preferably mammalian (e. g., monotremata, marsupialia, edentate, dermoptera, ch~.roptera, carnivore, insectivore, proboscides, perissodactyla, axtiodacty~.a, tubuJ.identata, pholidota, sirenia, cetacean, primates, rodentia, lagomorpha, eto.). In one embodiment, cells dErived from primates (e. g., chimpanzee, Japanese monkey, human) are used. Particularly, without lzm~.tation, cells derived from a human are used. The above-described cells may be either stem cells or somatic cells . Also, the cells may be adherent calls, suspended cells, tissue forming cells, and mixtures thereof. The cells may be used fox 2~ transplantation.
Any organ may be targetEd by the present invention. A tissue or cell targeted by the present invention may be derived from any organ. As used herein, the tern "lorgan" refers to a morphologically independent structure, localized to a particular portion of an individual organism, in which a certa~-n function is performed. In multicellular organisms (e. g., animals, plants), an organ consists of several tissues spatially arranged in a particular manner, each tissue being composed ~4 ~Iao~
of a number of cells . An example of such an organ includes an organ relating to the vasculax system. In one embodiment, organs targeted by the? present invention include, but are not limited to, skin, blood vessels, cornea, kidney, heart, liver, umbilical cord, intestine, nr~rve, lung, placenta, pancxeas, brain, peripheral limbs, retina, and the l~.ke.
As used herein, cells differentiated from a pluripotent cell o~ the presEnt invention i.nciude, but are not limited to:
epidermal cells, pancreatic parenchyma) cells, pancreatic duct cells, hepatic cells, blood cells, cardiac muscle calls, skeletal muscle cells, osteoblasts, skeletal myoblasts, neurons, vascular endothelial cells, pigment cells, smooth muscle cells, fat cells, bone cells, cartilage cells, and the like.
As used herein, the term "tissue" refers to an aggregate of cells having substantially the same function and/or form in a multicellu~.ar organism. "Tissue" is typically an aggregate of cells of the same or~.gin, but may be an aggregate of cells of different origins as long as the cells have the same function and/or form. Therefore, when stem cells of the present invention are used to regenerate tissue, the tissue may be composed of an aggregate of cells of two or more different origins. Typical~.y, a tissue constitutes a part of an organ. Animal tissues are separated into epithelial tissue, connective tissue, muscular tissue, nervous tissue, and the like, on a morphologica3., functional, or developmental bas~.s. plant tissues are roughly separated into meristematic tissue and permanent tissue, according to the developmental stage of AI00?
the cells constituting the tissue. Alternatively, tissues may be separated into single tissues and composite tissues according to the type of cells constituting the tissue.
Thus, tissues are separated into various categories.
As used herein, the term "stem cell" refers to a cell capable of self replication and pluripatenoy.
Typically, stem cells can regenerate an inaured tissue.
Stem cells used herein may be, 'but are not limited to, embryonic stem (ES) cells or tissue stem cells (also called tissular stem cells, tissue-specific stem cells, or somatic stem cells). A stem cell may be an artificially produced cell (e. g., fusion cells, reprogrammed cells, or the like used herein) , as long as it has the above-described abilities.
Embryonic stem cells are pluripatent stem cells derived from early embryos. An embryonic stem cell was first established in 1981, and has been applied to the production of knockout mice since 1989. In 1998, a human embryonic stem cell was established, which is currently becoming available for zegenerative medicine. Tissue stem cells have a relatively limited level of differentiation, unlike embryonic stem cells. Tissue stem cells are present in tissues and have an undifferentiated intracellular structure. Tissue stem cells have.a higher nueleusJcytoplasm ratio and have few intracellular organelles. Most tissue stem cElls have pluripotency, a long cell cycle, and proliferative ability beyond the life of the individual. As used herein, stern cells may preferably be embryonic stem cells, though tissue stem cells may also lie employed, depending an the 3p circumstance.
~zao~
Tissue stem cells are separated into categories of sites from which the sells are derived, such as the dermal system, the digestive system, the bone marrow system, the S nervous system, and the like. Tissue stem cells in the dermal system include epidermal stem cells, hair follicle stem cells, and the like. Tissue stem sells in the digestive system include pancreatic (common) stem cells, liver stem ce~.l.s, and the like. Tissue stem cells ~.n the bone marrow system include hematopoietic stem cells, mesenchymal stem cells, and the like. Tissue stem cells in the nervous system include neural stem cells, retinal stem sells, and the lake.
As used herein, the term "somatic cell" refers to any cell other than a germ cell, such as an egg, a sperm, or the like, which does not transfer its DNA to the next generation. Typically, somatic ce~.~.s ha~cre limited or no pluripotency. Somatic cells used herein may be naturally-occurring or genetically modified.
The origin of a stem cell is categorized into the ectoderm, endoderm, or mesoderm. Stem cells of ectodermal origin are mostly present in the brain, including neural stem cel~.s . stem cells of endodermal origin are mostly present in bone marrow, including blood vessel stem cells, hematopoietic stem cells, mesenchymal stem cells, and the like. Stem cells of mesoderm origin are mostly present in organs, including liver stem cells, pancreatic stem cells, and the like. Somatic cells may be herein derived from any germ layer. Preferably, somatic cells, Ar007 such as lymphocytes, spleen cells or testis-derived cells, may be used.
As used herein, the term "isolated" means that naturally accompanying material is at least reduced, or preferably substantially completely eliminated, in the normal environment. Therefore, the term "isolated cell"
refers to a cel.J. substantially free from other accompanying substances (e. g., other cells, proteins, nucleic acids, etc.) in the natural environment. The term "isolated" in relation to nucleic acids or polypeptides means that, for example, the nucleic acids or the polypeptides are substantially free from cellular substances or culture media when they arc pzoduced by recombinant p~tA techniques;
ox precursory chemical substances or other chemical substances when they are chemically synthesized. isolated nucleic acids are preferably free from sequences that naturally flank the nucleic acid within an organism from which the nucleic acid is derived (i.e., sequences positioned at the 5' terminus and the 3~ terminus of the nucleic acid).
As used herein, the term "established" in relation to cells refers to a state of a cell in which a particular property (pluripotency) of the cell is maintained and the cell undergoes stable proliferation under culture conditions. Therefore, established stem cells maintain pluripotency.
As used herein, the term "differentiated cell."
Ar007 refers to a cell having a specza~.ized function and form (e. g. , muscle cells, neurons, etc.). Unlike stem cells, di.fferent~.ated cel.7.s knave no or little pluripotency.
Examples of differentiated cells include epidermic cells, pancreatic parenchymal cells, pancreatic duct cells, hepatic cells, blood cells, cardiac muscle cells, skeletal muscle cells, osteoblasts, skeletal myoblasts, neurons, vascular endothelial cells, pigment cells, smooth muscle cells, fat cells, bone Dells, cartilage Cells, and the like.
As used herein, the term "state" refers to a condition concernirzg varzous parameters of a cell. (e. g~, cell cycle, response to an external factor, signal transduction, gene expression, gene transcription, etc.).
Examples of such a state include, but are not limited to, differentiated states, undifferentiated states, responses to external factors, Cell cycles, growth states, and the like.
As used herein, the terms "differentiation" or "cell differentiation" refers to a phenomenon where two or more types of cells having qualitative differences in form and/or function occur in a daughter cell population derived from the division of a single cell. Therefore, "differentiation" includes a process during which a population (family tree) of cells, which do not originally have a specific detectable feature, acquire a feature, such as the production of a specific protein, or the like. At present, cell differentiation is generally considered to be a state of a cell in which a specific group of genes in the genome are expressed, Cell differentiation can be identified by searching for intracellular br extracellular agents or conditions which elicit the above-desc~cibed state of gene expression. Differentiated cells are stable in principle. Particularly, animal cells which have been differentiated once rarely re-d~.fferentiate into other types of cells.
As used herein, the term "pluxipotency" refers to a nature of a cell, i . a . , an ability to differentiate into one or more, preferably two or more, tissues or organs. Therefore, the terms "pluripotent" and "undifferentiated" axe herein used interchangeably unless otherwise mentioned. Typically, the pluripotency of a cell is limited duxing development, and in an adult, cells constituting a tissue or organ rarely differentiate into different cells, that is, the pluripotenGy is usually lost. Particularly, epithelial cells resist altering into other types of epithelia. cells.
Such alteration typically occurs in pathological conditions, and is called metaplasia, However, mesenchymal cells tend to easily undergo metaplasia, i.e., alter to other mesenchymal cells, with relativexy simple stimuli.
Therefore, mesenchymal cells have a high level of ~5 pluripotency. Embryonic stem ceZ~.s have pluripotency.
Tissue stem cells have pluripotency. Thus, the term "pluripotency" may include the concept of tat~.potency. An example of an in vitro assay for determining whether or not a cell has pluripatency, includes, but is not limited to, culturing undex conditions for inducing the formation and Azao~
differentiation of embryoid bodies. Examples of an in vivo assay fox detexmi~ning the presence or absence of pluripotency, include, but are not limited to, implantation of a cell into an immunodeficient mouse so as to form teratoma, inj action of a cell into a blastocyst so as to form a chimeric embryo, implantation of a cell into a tissue of an organism (e. g., injection of a call into ascites) so as to undergo proliferation, and the like. As used herein, one type of pluripotency is "totipotency", which refers to the ability to be differentiated into all kinds of cells which constitute an organism. The idea of pluripotency encompasses totipotency. An example of a tatipotent cell is a fertilized ovum. An ability to be differentiated into only one type of cell is called "unipotency".
(Biochemistry arid Molecul~.r Biology) As used herein, the term "agent" may refer to any substance or element as long as an intended ob j eat can be achieved (e. g:, energy, such as ionizing radiation, radiation, light, acoustic waves, and the like). Examples of such a substance include, but are not limited to, proteins, polypeptides, oligopeptides, peptides, palynuoleotides, oligonucleotides, nucleotides, nucleic acids (e.g., DNA
such as cDNA, genomic DNA and the like, or RNA such as ml~Nl~, RNAi and the like), polysaccharides, oligosaccharides, lipids, low molecular weight oxgan~.c molecules (e. g., hormones, ligands, information transduction substances, low molecular weight organic molecules, molecules synthesized by combinatorial chemistry, law moJ.ecular weight molecules usable as medicaments (e, g., low molecular weight molecule ligands, etc.), etc.), and composite molecules thereof . Extez~nal. agents may be used singly or in combination. Examples of an agent specific to a polynucleotide include, but are not limited to, representatively, a polynucleotide having complementarity to the sequence of the polynucleotide with a predetermined sequence homology (e. g., 70~ or more sequence identity), a polypeptide such as a transcriptional agent binding to a promoter region, and the like. Examples of an agent specific to a polypeptide include, but are not limited to, representatively, an antibody specifically directed to the polypeptide or derivatives ox analog$ thereof (e. g., single chain antibody), a specific iigand or receptor when the polypeptide is a receptor or ligand, a substrate when the polypeptide is an enzyme, and the like.
As used hexein the term "biological agent"
refers to an agent relating to s biological organism (for example, a cell). Preferably, an agent present in a cell in a normal state is referred to a biological agent. Such biological agents include, but are not limited to, for example: nucleic acid molecules, proteins, sugaz~s, lipids, metabolites, low molecular weight molecules, and complexes thereof, and agents including time elements and the like.
Alternatively, it should be understood that such biological agents include electric curxent, electric potential (such as membrane potential), pH, osmotic pressuxe and the like in the present invention. T3seful biological agents as used herein include, for example, transcriptional controlling sequence (for example, promoters and the like) , structural Az C! 0'~
genES, and nucleic acids encoding the same. As used herein a "collection" of "biological agents" zefex to a. plurality o~ biological agents (of the same or different types).
Preferably, the collection refers to biological agents which cooperate with each other.
As used herein, the term "gene" refers to an element defining a genetic trait. A gene is typically arranged in a given sequence an a chromosome . A gene whioh 1.0 defines the primary structure of a protein is called a structural gene. A gene which regulates the expression of a structural gene is called a regulatory gene (e. g., promoter). Genes herein include structural genes and regulatory genes unless otherwise specified. 'therefore, the term "cyclin gene" typically includes the structural gene of cyclin and the promoter of cyclin. As used herein, '"gene" may refer to "polynucleotide", "oligonucleotide", "nucleic acid", and "nucleic acid molecule" and/or "protein", "polypeptide", "oligopeptide" and "peptide".
As used herein, "gene product" includes "polynucleotide", "oligonucleotide", "nucleic acid" and "nucleic acid molecule" and/or "protein", "polypeptide", "oligopeptide"
and "peptide",.which are expressed by a genre. Those skilled ~.z~ the art understand what a gene product is, according to the context.
As used herein, the term "homology" in relation to a sequence (e, g. , a nucleic acid sequence, an amino acid sequence, eto. ) ,re~exs '~o the level of identity between two or more gene sequences . Therefore, the greater the homology Az0o7 between two g~.ven genes, the greater the identity or similarity between their sequences. Whether ar nat two genes have homology is determined by comparing their sequences directly or by a hybridization method under stringent conditions. When two gene sequences are directly compared with each othex, these genes have homology if the DNA sequences of the genes have representatively at least 50$ identity, preferably at least 70~ identity, more preferably at least 80~, 90~, 95~, 96~, 97~, 98~, or 99~
identity with each other. As used herein, the term "similarity" in reJ.ation to a sequence (e. g. , a nuc3.eic acid sequence, an amino acid sequence, or the like) refers to the J.evel of identity between two or mere sequences when conservative substitution is regarded as positive 1$ (identical) in the above-descr~.bed homology. Therefore, homology and similarity differ from each other in the presence of conservative substitutions. If no conservative substitutions are present, homology and similarity have the same value.
As used herein, the comparison, of similarity, identity anal homology of an amino acid sequence and a nuleotide sequence is calculated with FAST, a tool for sequence analysis using default parameters.
The terms "protein", "polypeptide", "oligopeptide" arid "peptide" as used her~:zn have the same mearizng and refer to an amino acid polymer having any length.
This polymer may be a straight, branched or cyclic chain.
An amino acid may be a naturally-occurring ox nonnaturally-occurring amino acid, or a vari.arnt amino acid.
The term may include those assembled into a composite of a plurality of polypeptide chains . The term ~l.so includes a naturally-occurring or artificially modified amino acid polymers. Such modification includes, for example, disulfide bond formation, glycosylation, lipidation, acetylatian, phosphorylation, or any other manipulation or modification (e. g., conjugation with a labeling moiety).
This definition encompasses a polypeptide containing at Least one amino acid analog (e. g., nonnaturally-occurring amino acid, etc. ) , a peptide-like compound (e. g., peptoid) , and other variants known in the art, for example. Gene products, such as extracellulax matrix p~cote~.n,s (e. g. , ~ibronectin, etc . ) , are usually in the form of a polypeptide .
The terms "polynucleotide", "oliganucleotide", "nucleic acid molecule" and "nucleic acid" as used herein hav2 the Ss.mr~ meaning and refr~r to a nucleptide pplymer having any length. This term also includes an "OligonuCleotide derivative" or a "polynucleOtide derivative". An "oligonucleotide derivative" or a "polynucleotide derivative" includes a nucleotide derivative, or refers to an oligonucleotide or a polynucleotide having different linkages between nucJ.eotides from typ~.cal ~.i.nkagee, which are interchangeably used. Examples of such an oligonucleoti.de specifically include 2'-0-methyl-ribonucleotide, an oligonucleotide derivative in which a phosphodiester bond in an oligonucleotide is converted to a phosphorothioate bond, an aligonucleatide derivative in Which a phosphodiester bond in an oligonucleotide is converted to a N3' --P5' phvsphoroam~.date bond, an oligonucleotide derivative in which a ribose and a phosphodiester bond in an oligox~ucleotide are converted to a peptide-nucleic acid bond, an oligonucleotide derivative in which uracil in an dligonucleotide is substituted with C-5 propynyl uracil, an aliganucleotide derivative in which uracil in an oligonucleotide is substituted with~C--5 thiazole uracil, an oligonucleotide derivative in which cytosine in an oligonucleotide is substituted with C-5 propynyl cytosine, an oligonucleotide derivative in which cytosine in an oligonucleotide is substituted with phenoxazine-modified cytosine, an oligonuc~leotide derivative in which ribose in 17NA is substituted with 2'-O-propyl ribose, and an oligonucleotide derivative in which ribose in an oligonucleotzde is substituted with 2'-methoxyethoxy ribose. Unless otherwise indicated, a particular nucleic acid sequence also implicitly encompasses conservatively-modified variants thereof (e. g. degenerate codon substitutions) arid complementary sequences as well as the sequence explicitly indicated. Specifically, degenerate codon substitutions may be produced by generat~.rig sequences in which the third positian of one or more selected (or all) codons is substituted with mixed-base and/or deoxyinosine residues (Hatzer et al., Nucleic Acid Res. 19:5081(1991); Qhtsuka et al., J. Biol. Chem.
260:2605-2608 (1985); Rossolini et al., Mol. Cell. Probes 8:91-98(1994)). A gene encoding an extracellular matrix protein (e. g., fibronectin, etc.) or the like xs usually in the form of polynucleotide . A molecule to be transfected is in the form of a polynucleotide.
As used herein, the term "corresponding" amino acid or nucleic acid refers to an amino acid or nucleotide in a given polypeptide or polynucleoti.de molecule, which has, or is anticipated to have, a function similar to .that of a predetermined amino acid or nucleotide in a polypeptide or polynucleotide as a reference for comparison.
Particularly, in the case of enzyme molecules, the term refers to an amino acid which is present at a similar position in an active site and similarly contributes to catalytic activity. For example, in the case of a transcriptional contxdlling sequence of a polynucleotide, it may be a portion similar to that of corresponding artholog in the particular portion of the transcription Controlling sequence.
As used herein, the term "corresponding" gene (e.g., a polypeptide or polynucleotide molecule) refers to a gene in a given species, which has, or is antic~.pated to have, a function similar to that of a predetermined gene in a species as a reference for comparison. When there are a plurality of genes having such a function, the term refers to a gene having the same evolutionary origin. Therefore, a gene Corresponding to a given gene may be an ortholog of 2S the given gene. Thez~efore, genes corresponding to mouse cyclin genes can be found in other anima~.s. Such a corresponding gene can be identified by techniques well known in the art. Therefore, for example, a corresponding gene in a given animal can be found by searching a sequence database of the anima. ( a . g . , human, rat ) using the sequence of a reference gene (e.g., mouse cyclin gene, etc.) as a query sequence.
As used herein, the term "fragment" with respect to a polypeptide or polynucleotide refers to a polypeptide or polynucleotide having a sequence length ranging fxom 1 to n-1 w~.th respect to the full length of the reference polypeptide or polynucleotide (of length n) . The ~.ength of the fragment can be appropriately changed depend~.ng on the purpose. For example, in the case of polypeptides, the lower limit of the length of the fragment includes 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 40, 50 or more amino acids.
Lengths represented by integers which are not herein specified (e.g., 11 and the like) may be appropriate as a lower limit. for example, in the case of polynucleotide$, the lower l~.~mit of the length of the fragment includes 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, ~0, 50, 75, 100 or moxe nucleotides. Lengths represented by integers which axe not herein specified (e. g. , 21 and the like) may be appropriate as a lower limit. As used hexein, the length of polypeptides or polynucleatides can be represented by the number of amino acids or nucleic acids, respectively. However, the above~deecribed numbers are not absolute. The above-described' numbers' as the upper or lower limit are intended to include some greater or smaller numbers (e. g. , t10~) , as ~.ong as the same function ~.s maintained. For this purpose, "about" me~y be herein put ahead of the numbers.
However, it should be understood that the interpretation of numbers is not affected by the presence or absence of "about" in the present specification.
As used herein, the term "bio~.ogical activity"
refers to activity possessed by an agent (e.g., a polynucleotide, a protein, etc.) within an organism, including acti~rit~.es exhibiting vazious functions (e. g., transcription promoting activity, etc.). For example, when a certain factor is an enzyme, the biological activity thereof includes its enzyme activity. In another example, when a certain factor is a ligand, the biological activity thereof includes the binding of the ligand to a receptor corresponding thereto. The above-described biological activity can be measured by teChniques.well--known in the axt.
As used herein, the term "polynucleotides hybridizing under stringent. conditions" refers to conditions commonly used and well known in the art. Such a polynucleotide can be obtained by conducting colony hybridization, plaque hybridization, Southern blot hybridization, or the like, 2~ using a polynucleotide selected from the polynucleotides of the present invention.. Specifically, a filtex on which DNA derived from a Colony or plaque is immobilized is used to conduct hybridization at 65°C i.n the presence of 0.7 to 1.0 M Natal. Thereafter, a 0.1. to 2-fold concentration SSC
(saline-sodium citrate) solution. (2--fold concentration SSC
solution is composed of 150 mM sodium chloride and 15 mM
sodium.citrate) is used to wash the filter at 65°C.
Polynucleotides identified by this method are referred to as "polynucleotides hybridizing under stringent conditions". Hybridization can be conducted in accordance with a method.described in, for example, Molecular Cloning 2nd Ed., Current Protocols in Moledular Biology, Supplement 1-38, DN,A Cloning 1: Core Techniques, A Practical Approach, Second Edition, dxford University Press (1995) , and the like.
Here, sequences hybridizing under stringent Gondit~.ons exclude, preferably, sequences containing only A or T.
"Hybridizable polynucleot~.de" refers to a polynuc.leotide which Can hybridize to other polynucl.eotides under the above-described hybridization conditions. Specifically, the hybridizable polynucleot~.de includes at least a polyr~uc3.eotxde having a homology of at least 60~ to the base sequence of DNA encoding a polypeptide having an amino acid sequence specifically herein disclosed, preferably a polynucleotide having a homology of at least $0~, and more preferably a polynucleotide having a homology of at 3east 95~.
As used herein, the term "salt" has the same meaning as that commonly understood by those skilled in the art, including both inorganic and organic salts. Salts are typically generated by neutralizing reactions between s,cids and bases. Salts inc~.ude NaCl, FizS04, and the like, which are generated by neutralization, and in addition, PbS04, ZnCl2, arid the like, which axe generated by reactions between rc~,etals and acids. The latter salts may not be generated directly by neutralizing reactions, but may be regarded as a product of neutralizing reactions between acids and bases.
Salts may be divided into the following categories : normal salts (salts without any H-groups from acids or w~.thout any OF3-groups from bases, including, for example, NaCl, NHQC1, BO
z~zoo~
CH3COONa, and Na2C03) , acid salts (salts w~.th remaining H-groups from acids, including, for example, NaHC03, KHS04, and CaHPO4 } , and basin salts ( salts with remaining OH-grpups from bases, including, for example, MgCl (OH) and CuCl (OH) ? -S This classification is not very important in the present invention. Examples of preferable Belts include salts constituting media (e.g., calcium chloride, sodium hydrogen phosphate, sodium hydrogen carbonate, sodium pyruvate, HEpES, sodium chloride, potassium chloride, magnesium sulfide, iron nitrate, amino acids, vitamins, etc. ) , salts constituting buffer Ce-g-r calcium chloride, magnesium chloride, sodium hydrogen.phosphate, sodium chloride, etc.}, and the like. These salts are preferable as they have a high affinity for cells and thus are better able to maintain cells in culture. These salts may be used singly or in combination.
Preferably, these salts may be used in combination. This is because a combination of salts tends to have a higher affinityvor cells. Therefore, a plurality of salts (e.g., calcium chloride, magnesium chloride, sodium hydrogen phosphate, and sodium chloride) are preferably contained in a medium, rather than only NaCl or the like. More preferably, all salts suitable for cell culture medium may be added to the medium. Tn. another preferred embodiment, glucose may be added to medium.
As used herein the term "material." or "substance" is used in the broadest meaning as used in the art to refer to any thing that is positively or negatively charged.
Azoo~
As used herein., the term "positively charged substance" encompasses alJ. substances having a posztive charge. Such substances include cationic substances such as cationic polymers, cationic lipids and the like, but are not limited to these. Advantageously, such positively charged substances can form a complex. Such positively charged substances which can form a complex. include, for example, substances having a certain maleaular weight (for example, cata.onic polymers ) and substances which can remain IO insoluble, that is, without being dissolved to a certain extent in a specific solvent such as water, an aqueous solution or the like (for example, cationic lipids), but are not limited to the$e, Preferable positively charged substances include, for example, polyethylene imine, I5 poly-L-lysine, synthetic polypeptides, ax derivatives thereof, but are not limited to these. Positively charged substances include,. for example, biological molecules such as histone and synthetic polypeptides, but are not limited to these, The type of preferable positively charged 20 substances changes in accordance with the type of negatively charged substances, which act as a complex partner to form complexes with the positively charged substances. Tt requzres no specific creativity for those sJ~illed in the art to select a preferable complex partner using technology 25 well knotan in the art. For selecting a preferable complex partner, various parameters are considered including, but not limited to, charge, molecular weight, hydxaphobicity, hydrophilicity, properties of substituents, pH, temperature, salt concentration, pressuxe, and other 30 physical and chemical parameters.
Azao~
As used herein, the term" cationic polymer"
refers to a polymer having a cationic functional group, and encompasses, for example, polyethylene imine, poly-~-lysine, synthetic polypeptides, and derivatives thereof, but is not lin2ited to these.
As used herein, the term" cationic lipid" refers to a lipid having a cationic functional group, and encompasses, for example, phosphatidyl choline, phosphatidyl ethanol amine, phosphatidyl serine, and derivatives thereof, but is not limited to these.
Cationic functional groups include, for example, primary amines, secondary amines, and tertiary amines, but are not lim~.ted to these.
As used herein, the term" negatively charged substance" encompasses all substances having a negative charge. Such substances inc~.ude biological molecular polymers, anion~.C substances such as anionic .lipids, a.r~d the like, but are not limited to these. Advantageously, such negatively charged substances can form a comple~c. Such negatively charged substances which can form a complex include, for example, substances 'having a certain molecular weight (for example, anionic polymers such as DNA) and substances which can remain insoluble, that is, without being dissolved to a certain extent in a specific solvent such as watex, an aqueous solutions or the like (for example, anionic lipids), but are not limited to these. Preferable $3 negatively charged substances include, for example, DNA, RNA, ENA, polypeptides, chemical compounds, and complexes thereof, but are not limited to these. Negatively charged substances include, far example, DNA, RNA, PNA, polypeptides, chema.cal compounds, and comp~.exes thereof, but are x~ot limited to these. The type of preferable negatively charged substances ehanc~es in accordance with the type of positively charged suYsstar~ces, which act as a complex partner to form complexes with the negatively charged substances . It requires na specific creativity for those skilled in the art to select a preferable complex partner using technology well known in the art. For selecting a preferable complex partner, various parameters are considered as described above with regard to negatively charged substances.
As used herein, the term "anionic polymer"
encompasses polymers having an anionic functional group, and includes, for example, DNA, RNA, PNA, polypeptides, chemical compounds, arid compl~:xes thereof, but is not limited to these.
fis used herein, the term" anionic lipid"
encompasses lipids having an anionic functional r~roup, and include, for example, phosphatid~.c acid, phosphatidyl serine, but is not limited to these.
Anionic functional groups include, for example, carboxylic groups and phosphoric acid groups, but are not limited to these.
The type of charge of a target substance can be converted by adding a part of a substituent or the like having a positive charge or a negative Charge to the target substance.
Tn the case where a preferable complex partner has the same type of charge as that of the target substance, formation of a complex can be promoted by converting the type o~ charge of either the complex partner or the target substance.
As used herein, the term "complex" refers to two or more substances which directly or indirectly interact with each other and as a result, act as if they were one substance as a whole, As used herein, the term "complex partner" used for a certain member forming a complex refers to another member interacting with the certain member directly or i.ndi.rectly, As used herein, the condition for forming a complex changes in accordance with the type of complex partner. Such a condition can be easily understood by tho$e skilled in the art. Those skilled in the art can easily form a complex from any complex partners (for example, a positively charged substance and a negatively charged substance) using a technique well known in the art.
As used herein, when a complex of positively and negatively charged substances is used, eithef ox' both thereof znay be identical to a biological agent.
As used herein, the term" immobxlxzation" used for a solid-phase support refers to a state in which a substance as a subject of immobilization (e. g. , a biological molecule) is held an the support for at least a certain time period, or an act-of p~.acing the substance into such a state .
As such, in the case where the condition is changed after the substance is ~.mmobilized on the solid-phase support (for 10~ example, the substance is immersed in another solvent) , the substance may be released from the immobilization state.
As used herein; the term "cell affinity" refers to a property of a substance that when the substance is placed in an interactable state with a cell (e. g. germ cell, animal Dell, yeast, plant cell ) or an obj ect containing a cell ( a .
g., tissue, organs, biological organisms), the substance does not have any adverse influence on the cell or the abject containing the cell. Preferably, substances having cell affinity may be substances w~.t~x which a cell interacts as a priority, but axe not ximited to these . According to the present invent~.on, the substance to be immobilized (e. g., positively charged substances and/or negatively charged substances) preferably have cell affinity, but cell affinity is not absolutely. necessary. It was unexpeeted7.y found that when fihe substance to be immobilized has cell.
affinity, the cell affinity of the substance is maintained or improved when the substance is immobilized according to the present zz~vention. In light of the past situation where a substance having cell affinity does not neCesSaxily ,~Taa7 maintain its cell affinity when immobilized on a solid-phase support, the effect of the present invention is enormous.
As used herein, the term "probe" ref~:rs to a substance for use in searching, which is used in a biological experiment, such as in vitro and/or zn viva screening or the like, including, but not limited to, for example, a nucleic acid molecule having a specific base sequence or a peptide containing a specific amino acid sequence.
Examples of a nucleic ac~.d molecule as a common probe include one having a nucleic acid sequence having a length of at least 8 contiguous nucleotides, which is homologous or complementary to the nucleic acid sequence of a gene of interest . Such a nucleic acid sequence may be preferably a nucleic acid sequence having a length of at least 9~contiguous nucleotides, more preferably a length of at least 10 contiguous nucleotides, and even more preferably a length of at least 1I contiguous nucleotides, a length of at least 12 contiguous nucleotid~s, a length of at least 13 contiguous nucleotides, a length of at least 14 contiguous nucleotides, a length of at least 15 contiguous nucleotides, a length of at least 20 contiguous nucleotides, a length of at .least 25 contiguous nucleotides, a length of at least 30 contiguous nucleotides, a length of at least 40 contiguous nucleotides, or a length of at least 50 contiguous nucleotides . A nucleic acid sequence used as a probe includes a nucleic acid sequence having at least 7a~
homology to the above-described sequence, more pxefexably at least 80~, and even more preferably at least 9Q~ or at least 95~.
As used herein, the term "search" indicates that a given nucleic acid sequence is utilized to find other nucleic acid base sequences having a specific function and/or property either electronically or,biologically, or using other methods. Examples of an elec~,roniC search include, but are not limited to, BhAST (Altschul et al.., J. Mnl. Biol. 215:4x3-41p 0,990) ) , FASfA (Pearson & Lipman, Proc. Natl. Acad. Sci., USA 85:2444-2448 (1988) ), the Smith and Watex~zcian method ( Smith and Waterman, J. Mol . Biol.
147:195~197 (1981)), and the Needleman and Wunsch method (Needleman and Wunsch, J. Mol. Biol. 48:443-453 (1970)), and the like. examples of a biological search include, but are not limited to, a macroarzay in which genomie DNA is attached to a nylon membrane or the like or a microarray (microassay) in which genomio DNA ~.s attached to a glass plate under stringent hybridization conditions, PCR, in situ hybridization, and the like.
As used herein, the term "primer" refers to a substance required for the initiation of a reaction o~ a macromolecule compound to~ be synthesized, in a macromolecule synthesis enzymatic rec~ctivn. In a reaction for synthesizing a nucleic acid molecule, a nucleic acid molecule (e.g., DNA, RNA., or the like) which is complementary to part of a macromolecule compound to be synthesized may be used.
A nucleic acid molecule which is Qrdinaxily used as a primer includes one that has a nucleic acid sequence having a length of at least 8 contiguous nucleotides, which is complementary to the nucleic acid sequence of a gene of interest. Such a nucleic acid sequence preferably has a length of at least 9 contiguous nucleotides, more preferably a length of at least 10 contiguous nucleotides, even more preferably a length of at least 11 contiguous nucleotides, a length of at least 12 contiguous nucleotides, a length of at least 13 contiguous nucleota.des, a length of at least 14 contiguous nucleotides, a length of at least 15 contiguous nucleotides, a length of at least 16 contiguous nucleotides, a length of at least 17 contiguous nucleotides, a length of at least 18 contiguous nucleotides, a length of at least 19 contiguous nucleotides, a length of at least 20 contiguous 7.5 nucleotides, a length of at least 25 contiguous nucleotides, a length of at least 30 contiguous nucleotides, a length of at least 40 contiguous nucleotides, and a length of at least 50 contiguous nucleotides. A nucleic acid sequence used as a primer includES a nucleic acid sequence having at least 70% homology to the above-described sequence, more preferably at least 80%, e~cren more preferably at least 90~, and most preferably at least 9S% . An appropriate sequence as a primer may vary depending on the property of the sequence to be synthesized (amplified) . Those skilled in the art can design an appropriate primer depending on the sequence of interest. Such primer design is well known in the art and may be performed manually or using a computer program (e.g., LA9ERGENE, Primer Select., DNAStar).
As used herein, the term "epitope" refers to az~
antigenic determinant. Therefore, the term "epitope"
includes a set of amino acid residues which axe involved in recognition by a particular immunoglobulin, or in the context of T cells, those residues necessary for recognition by the T cell receptor proteins and/or Major Histocampatibility Complex (MiiC) receptors. This term is also used interchangeably With "antigenic determinant" or "antigenic determinant site". In the field of immunology, ~.n vivo or in vitro, an epitope is the features of a molecule (e. g., primary, secondary and tertiary peptide structure, and charge) that form a site recognized by an ~.mmunoglobulin, T cell receptor or HLA molecule. An epitope including a peptide comprises 3 or more amino acids in a spatial conformation which is unique to the epitope. Generally, an epitope consists of at least 5 such amino acids, and more ordinarily, coz~sists of at least 6, 7, 8, 9 or 7.0 such amino acids. The greater the length of an epitope, the more the similarity of the epitope to the original peptide, i.e., longer epitopes are generally preferable. This is not 2Q necessarily the case when the conformation is taken into account. Methods of determining the spatial conformation of amino acids are known in the art, and include, for example, X-ray crystallogxaph,y and 2-~dimensional nuclear magnetic reavnance spectroscopy, furthermore, the identification of epitopes in a given protein is readily accomplished using techniques well known in the art . See, also, Geysen et al . , Proc. Natl. Acad. Sci. LISA (1984) 81: 3998 (general method of rapidly synthesizizxg peptides to determine the location of immunogen~.G epitopes in a given antigen); U. S. Patent No. 4,708,871 (procedures for identifying and chemically synthesizing epitapes of antigens): and Geysers et al., Molecular immunology (1986) 23: 709 (fiechnique for identifying peptides with high affinity for a given antibody) . Antibodies that recognize the same epitope can be identified in a simple immunoassay. Thus, methods for detexma.n~.ng epitopes including a peptide are well known in the art. Such an epitope can be determined using a well-known, common technique by those skilled in the art if the primary nucleic acid or amino acid sequence of the epitope is provided.
Therefore, an epitope including a peptide requires a sequence having a length of at least 3 amino acids, preferably at least 4 amino acids, more preferably at least 5 amino acids, at least 6 amino acids, at least 7 amino acids, at least 8 amino acids, at least 9 amino acids, at least 10 amino acids, at least 15 amino acids, at .east 20 amino acids, and 25 amino acids. Epitopes may be linear or conformational.
As used herein, the term "agent binding specifically to" a certain nucleic acid molecu~.e or polypeptide refers to an agent which has a level of binding to the nucleic acid molecule or polypept~,de equal to or higher than a level of binding to other nucleic acid molecules or polypeptides. E~amplea of such an agent inc~.ude, but are not limited to, when a target is a nucleic acid molecule, a nucleic acid molecule having a . complementary sequence of a nucleic acid molecule of interest, a polypeptide capable of binding to a nucleic acid sequence of interest (e. g., a transcription agent, etc.), and the like, and when a target is a po~.ypeptide, an antibody, a single chain antibody, either of a pair of a receptor and a ligand, either of a pair of an enzyme and a substrate, and the like, As used herein, the term "antibody" encompasses polyclonal antibodies, monoclonal antibodies, human antibodies, humanized antibodies, polyfunctional antibodies, chimeric antibodies, and anti-idiotype antibodies, and fragments thereof (e.g., F(ab')2 and Fab fragments), and other .recombinant conjugates. These antibodies may be fused with an enzyme (e. g., alkaline phosphatase, horseradish peroxidase, d,-galactosidase, and the like) vza a covalent bond or by recombination.
As used herein, the term "monoclonal antibody"
refers to an antibody composition having a group of homologous antibodies. 'this term is not limited by the 2Q production manner thereof. This term encompasses all immunoglobulin molecules and Fab molecules, F (ab' ) 2 fragments, Fv fragments, and other molecules having an immunological binding property of the original monoclonal antibody molecule. Methods for producing polyclonal antibodies and monoclonal ant~.bodies are well known in the art, and will be more sufficiently described below.
Monoclonal antibodies are prepared by usiri$ the standard technique well known in the art (e.g., Kohler and Milstein, Nature (1975) 256:495) or a modification thereof (e. g., Buck et al. f1982) In Vitro 18:377).
Representatively, a mouse or rat is immunized with a protein bound to a protein carrier, and boasted. Subsequently, the spleen (and optionally several large lymph nodes) is removed and dissociated into a single cell suspension. zf desired, the spleen cells may be screened (after removal of nonspecifically adherent cells) by applying the cell suspension to a plate or well coated with a protein antigen.
7.0 H--cells that express membrane-bound immunoglobulin specific far the antigen bind to the plate, and are not rinsed away with the rest of the suspension. Resulting H-cells, ox all dissociated spleen cells, are then induced to fuse with myeloma cells to form hybridomas . The hybridomas are used to produce monoclonal antibodies.
As used herein, the term "antigren" refers to any substrate to whzch an antibody molecule may specifically bind. As used herein, the term "immunogen" refers to an antigen capable of initiating activation of the antigen-specific immune response of a lymphocyte.
Tn a given protein molecule, a given amino acid may be substituted with another amino aoid in a structurally important region, such as a cationic region or a substrate molecule binding site, without a clear reduction or lose of interactive binding ability. A given biological function of a protein is defined by the interactive ability or other property of the protein. Therefore, a particular amino acid substitution may be performed in an amino acid Asaa~
sequence, or at the DNA sequence level, to produce a protein which maintains the original property after the substitution. Therefore, various modifications of peptides as disclosed herein and DNA encoding such peptides may be performed without clear losses of biological activity.
Wh~:z~ the above-described modifications are designed, the hydrophobicity indioes of amino acids may be 1a taken into consideration. Thr~ hydrophobic amino acid indices play an important role in providing a protein with an interactive biological function, which is generally recognized in the art (Yyte, J. and Doolittle, R. F. , J. Mol.
Biol. 157(1):105-132, 1982), The hydrophobic property of an amino acid contributes to the secondary structure of a protein and then regulates interactions between the protein and other molecules (e. g., enzymes, substrates, receptors, DNA, antibodies, antigens, etc _ ) . Each amino acid is given a hydrophobicity index based on the hydrophobicity and 24 charge properties thereof as follows: isoleucine (+4.5);
valine (+4.2); leucine (+3.8); phenylalanine (+2.$);
cysteine/cystine (+2.5); methionine (+1.9); alanine (+1.8); glycine (-~a.9); threonine (-0.7); serine (-0.8);
tryptophan (-0.9); tyrosine (-1.~); proline (-1. f);
hist~.d~.ne (-3.2) ; g.lutamic acid (-3.5) : glutamine (-3.5) ;
aspartic acid (-3. 5) ; asparagine (-~.5) ; lysine (-3. 9) ; and arginine (-4.5).
Tt is well k~xown that if a given amino acid is substituted with another amino acid having a similar Ax007 hydrophobic~.ty index, the resultant protein may still have a biological, function similar to that of the original protein (e. g. , a protein having an equivalent enzymatic activity) .
For such an amino acid substitution, the hydrophobicity index is preferably with~.n ~2, more preferably within t1, and even more preferably within X0.5. It is understood in the art that such an amino acid substitu'~ion based on hydrophobicity is efficient.
Hydrophilicity may also be considered for conservative substitution, As described in US Patent No. 4, 554, x01., amino acid residues are given the following hydrophilicity indices: arginine (+3.0); lysine (+3.0);
aspartic acid (+3.01); glutamic acid (+3.Ot1): serine (+0.3); asparagine (+0.2); c~lutamine (+0.2); glycine (0);
threonine (-0.4): proline (-0.5~1); alanine (-0.5)t histidine (-0.5); cysteine (-1.0); methionine (-1.3);
valine (-1.5); leucine (-1.8); isoleucine (-1.8); tyrosine (-2. 3) ; phenylalanine (-~2.5) ; and tryptophan (-3. 4) . zt .is understood that an amino acid may be substituted with another amino acid which has a similar hydrophilicity index and can stzll provide a biological equivalent. For such an amino acid substitution, the hydrophilicity index is preferably within t2, mare preferably t l, and even more preferably t0.5.
(Profile and its relevant techniques) As used herein, the term "Qrofile" in relation to a cell refers to a set of measuremezlts of the biological state of the cell. Particularly, the term "profile of a A~007 cell" refers to a set of discxete ar continuous values obtained by quantitatively measuring a level. of a "cellular component". A level of a cellular component includes the expression .level, of a gene, the transcription level of a gene (the activity level of a transcription control sequence) , the amount of mRNA encoding a specific gene, and the expression level of a protein in ba.o~.og~.cal systems.
The level o~ each cellular component, such as the expression level of mRNA and/or protein, is known tv alter in xesponse to treatment with drugs or cellular biolag~.cal perturbation or vibration. Therefore, the measurement o~ a plurality of "cellular components" generates a large amount of information about the effects of stimuli on the biological state of a cell, Therefore, the profi3.e is mare and more important in the analysis of cello. Mammalian oe~.~,s contain about 30,000 or more cellular components. Therefore, the profile of an individual cell is usual~.y complicated. A
profile in a prEdetermined state of a b~.ological system may often be measured after stimulating the biological system.
Such stimulation is performed under experimental or environmental conditions associated with the biological system, Examples of a stimulus include exposure of a biological system to a drug candidate, introduction of an exogenous gene, passage of time, deletion of a gene from the system, alteration of culture conditions, and the like.
The wide range measurement of cellular components (i.e., profiles of gene replicat~.on, or transcription, protein expression, and response to stimuli) has a high level of utility including comparison and investigation of the effects of drugs, diagnosis of diseases, and Qptimization of drug administration to patients as well as investigation of cells. Further, profiles are useful for basic life science research. Such profile data may be produced and presented as data in a variety of forIaats. Such formats include, but are not limited to: a function between a numerical value and a period of time, a graphic format, a image format and the like. Accordingly, data relating to a profile may also be called "profile data" as used rierein.
Such data production rnay readily be carried oufi by us~.ng a computer. Coding of an appropriate program may also be carried out by using well known technology in the art.
In the cell analysis of the pxesent application, as regards to information derived from a cell or a substance interacting with the cell, a variety of processes and means fo~c detection may be used- Such process and means for detect~.vn include, but are not l~.mited to: those using visual inspection, optical microscopes,fluarescence microscopes, reading appazatus using a laser l~.ght source, surface plasmon resonance (SPR) imaging, electric signal, chemical and biochemical. markers, or a combination thereof.
As used herein, the term "time,lapse profile"
in relation to a certain, cell refers to a profile which indicates time-lapse changes in a parameter relating to the cell. Examples of a time-lapse profi~.e include, but are not limited for a time-lapse profile of transcription levels, a time-lapse prof~.le of expression levels (translation levels), a time-lapse profile of signal transduction, a time-lapse profile of neural potential, and the like. A
Ax007 time-lapse profile may be produced by continuously recording a certain parameter (e.g., a signal caused by a label associated with s. transcription level). Time-lapse measurement may mean continuous measurezrient. wherefore, the term "time-lapse profile" as used herein may also be referred to as "continuous profile". , As used herein the ~.erm "information" of a cell refers to those acting to direct an object as a whale by binding a number of elements present in the cell. A
collection of information can be said to constitute a digital cell.
As used.herein, the term "state" refers to a condition eonoexx~ing various parameters of a cell (e. g., cell cycle, response to an extexnal factor, signal transduction, gene expression, gene transcription, etc.}.
Examples of such a state include, but are not limited to, differentiated states, undifferentiated states, responses to external factors, cell cycles, growth states, and the like. The responsiveness or resistance of an organism of interest with respect to the following parameters of the, particuJ.axly, environment of the organism may be used herein as a measure of the state c~f the organism: temperature, humidity (e. g., absolute humidity, relative humidity, etc.), pH, salt concentration (e.g. , the concentration of all salts or a particulax salt), nutrients (e.g., the amount of carbohydrate, etc.}, metals (e.g., the amount or concentration of all metals or a particular metal (e. g., a heavy metal, etc.}), gas (e. g., the amount of all gases or a particular gas), organic solvent (e.g., the amount of all organic solvents or a particular organic solvent (e. g. , ethanol, etc.)), pressure (e. g., local or global pressure, etc.), atmospheric pressure, viscosity, flow rate (e. g., the flow rate of a medium in Which an organism is present, etc. ) , light i.nterzs~.ty (e. g. , the quantity of light having a particular wavelength, etc.), light wavelength (e. g., visible light, ultraviolet light, infrared lzght, etc.), electromagnetic waves, z~adiation, gravity, tension, acoustic waves, organisms other than an organism of interest (e. g., paras~.tes, pathogenic bacteria, etc.), chemicals (e. g., pharmaceuticals, etc.), antibiotics, naturally-occurz~ing substances, metal stresses, physical stresses, and the like.
As used herein, the term "environment" (or "Umgeb~xng" in German) in relation to an entity refers to a circumstance which surrounds the entity. In an ezwironznent, various components and quantities of state are recognized, which are called environmental factors.
Examples of environmental factors include the .above-described parameters. Environmental factors are typically roughly divided into non~biologiGal environmental factors and biological environmental factors.
Non-biological environmental factors (inorganic environment factors) may be divided into physical factors and chemical factors, or alternatively, climatic factors and soil factors. Various environmental factors do not always act on organisms independently, but may be associated with one another, Therefore, environment factors may be herein observed one by one or as a whole {a whole of various parameters) . It has been believed that it was difficult to maintain such an environment in a consistent state. This is particularly the case since it has been difficult to maintain cells and to immobilize cells, and to introduce substances such as nucleic acids into a cell. The present invention has also~solved at least one of these problems.
As used herein the term "consistent environment" refers tv substantially all of the circumstances surrounding a cell of interest. Accordingly, as long as a cell Gan grow or differentiate in a similar manner, such environments are deemed to be consistent environments. Ac used herein, a consistent environment refers to an environment where the parameters are the same except for a specific stimulus {for exampxe, an external stimulus).
Examples of such an environment include at least one factor, as a parameter, selected ~rorn the group consisting of temperature, humidity, pH, salt concentration, 24 nutrients, metal, gas, organic salvant, pressure, atmospheric pressure, viscosity, flow rate, light intensity, light wavelength, electromagnetic waves, radiation, gravity, tension, acoustic waves, organisms (e. g., parasites, etc.) other than the organism, chemical agents, antibiotics, natural substances, mental stress, s.nd physical stress, and any combination thereof.
Examples of temperature include, but are not limited to, high temperature, low temperature, very high temperature (e.g., 95°C, etc. ) , very low temperature (e.g., 1. 0 0 Az007 -80°C, etc. ) , a wide range of temperature (e. g. , 150 to --270°C, etc.), and the like.
Examples of humidity include, but are not limited to, a relative humidity of ~.00~, ~ relative humidity of 0$, an arbitrary point from 0% to 100, and the like.
Examples of pH include, but are not limited to, an arbitrary point from 0 to 14, and the like.
Examples of salt concentration include, but are not limited to, a NaCl concentration (e.g., 3~, etc.), an az~bitrary point of other salt concentrations from 0 to 7.00, and the like.
Examples of nutrients include, but are not limited to, proteins, glucose, lipids, vitamins, inorganic salts, and the like.
2p Examples of metals include, 3~ut are not limited to, heavy metals (e. g. , mercury, cadmium, etc. ) , lead, gold, uranium, silver, and the like.
Examples of gas include, but are not limited to, oxygen, nitrogen, carbon dioxide, carbon monoxide, and a mixture thereof, and the like.
Examples of organic solvents include, but are not limited to, ethanol, methanol, xylene, propanol, and the like.
Examples of pressure include, but are not limited to, an arbitrary point from 0 to 10 ton/cm2, and the like.
Examples of atmospheric pressure include, but are not limited to, an arbitrary point from 0 to 100 atmospheric pressure, and the like, Examples of viscosity include, but are not limited to the viscosity of any fluid (e. g. , water, glycerol, etc.) or a mixture thereof, and the like.
Examples of flow rate include, but are not limited to an arbitrary po~.nt from 0 to the velocity of light .
Examples of light intensity include, but are not ~.i.mzted to, a point between darkness and the level of sunlight.
Examples of light wa~relength include, but are not limited to visiY~le light, ultraviolet light (U'Sl-A, UV-B, UV-C, etc.), infrared light (far infrared light, near infrared light, eto.), and the like.
Examples of electromagnetic waves include ones having an arbitrary wavelength.
Examples of radi~tioz~ inc~.ude ones having an arbitrary intensity.
Examples of gravity include, but are not limited to, an arbitrary gravity on the Earth or an arbitrary point from zero gravity to the gravity on the Earth, or an arbitrary gravity greater than or equal to a gravity on the Earth.
Examples of tension include ones having an arbitrary strength.
0 Examples of acoustic waves include ones having an arbitrary intensity and wavelength.
Examples of organisms other than an organism of int~:rest include, but are not limited to, parasites, pathogenic bactexia, znsects, nematodes, and the like.
Examples of chemicals include, but are not limited to hydrochloric acid, sulfuric acid, sodium hydroxide, and the like.
2d Examples of antibiotics include, but are not limited to, penicillin, kaz~amyein, streptomycin, quinoline, and the like.
Examples of naturally-occurring substances ~.nczut~e, but are nat limited to, puffer toxin, snake venom, alkaloid, and the like.
Examples of znenta~. stress include, but are not 30 limited to starvation, population dez~sity, confined spaces, high places, and the like.
ExampJ.es of physical stress include, but are not limited to vibration, noise, electricity, impact, a.nd the like.
As used herein when referring to a digital cell of the present invention, the envi.rt~nment is presented as an "environment parameter". Such. environment parameters include, but are not limited to, medium (type, composition) , pH, temger~.ture, moisture, COZ concentration, concentration, the presence or absence of an antibiotic, the presence or absence of a particular nutrient and the like.
As used herein the term "stimulant" refers to an acting agent which cau$es or inducES expression or enhancement of a specific living action given to a cell from outside. Stimuli include, but are not limited to: a physical stimulus, a chemical stimulus, a biologioal stimulus, a biochemical stimulus, and the like. Physical stimuli include, but axe not limited to: for example, light, electric waves, electric current, pressure, sound (vibration) and the like. Chemical stimuli include but are not limited to: for example, stimuli from chemicals such as antibiotics, nutrients, vitamins, metals, ions, acids, alkalis, salts, buffers and the like. Biological stimuli include, but are not limited to: for example, the existence of another organism such as the existence of a paras~.tic organism or the density of a cell. population and the like.
AIO~~
Biochemical stimuli include, but are not limited to the existence of cell signaling transduction agents, and the like.
S As used herein, when the digital cell of the present invention is used, a stimulus is presented as a "stimulus parameter". A stimulus parameter corresponding to those in response to any stimulus as described herein may be used.
As used herein, it should be understood that the stimulus parameter includes agents for transducing a stimulus such as a reporter and the like. Such reporters include, but are not limited to: for example, on-off regulation of expression against an e~ntibiotic, a transcription-controlling sequence, radioactivity, fluorophores and the like.
As used herein the term "response" to a stimulus refers to any response of a cell to a stimulus such as a change in cell morphology, change in metabolism, change in other cellular behaviors, change in signal transduction and the like. Therefore, for example, results of experiments using the digital cell of the present invention may be recorded as cell dynamics data. Alternatively, when using the above xeporter, the result of such a response to the stimulus may be raw data of the reporter, or data transformed from the data of the reporter.
As used herein, the term "transcription control sequence" refers to a sequence which can regulate the transcrxptx.on Revel of a gene . Such a sequence is at least two nucleotides in length. Examples of such a sequence include, but are not limited to, promoters, enhancers, silencer, terminators, sequences flanking other genomic structural genes, genomic sequences other than exons, sequences within ex4ns, and the like. A transcription control sequence used herein is not related to a particular type. Rather, important information about a transcription control sequence is time-.apse fluctuation. Such fluefiuation is referred to as a process (changes in a state of a cell). Therefore, such a transcription control sequence may be herein arbitrarily selected. Such a transcription control sequence rnay include those whioh are not conventionally used as markers. Preferably, a transcription control sequence has the ability to bind to a txanscx~ipt~.on factoz~.
As used herein, the term "transcription factor"
refers to a factor which regulates the process of transcription of a gene. The term "transcription factor"
mainly indicates a factor which regulates a transcz~i.pti.oz~
in~.t~.ation reaction. TransariQtion factors are roughly divided into the following groups: basic transcription factors rEquired for placing an RNA polymerise into a promoter region on DNA; and transcription regulatory factors which bind to cis-acting elements present upstream or downstream of a transcription region to regulate the synthesis initiation frequency of RNA.
Basic transcription factors are prepared depending on the type of RNA polymerise. A TATA-binding protein is believed to be common to all transcription systems .
1.06 Although there are a number of types of transcription factors, a typical transcription factor consists of a portion structurally required for binding to DNA and a portion required for activat~.ng yr suppressing transcription.
Factors which have a DNA~binding portion and can bind to ois~acting elements are collectively referred to as trans-acting factors.
A portion required for acti~crating ox suppressing transcription is involved in interaction with other transcription factors or basic transoxiption factors.
Such a portion is believed to play a role in regulating transcription via a structural change in DNA or a transcription initiating complex. Transcription regulatory factors are div~.ded into several groups or families according to the structural properties of these portions, including factors which play an important role in the development yr differentiation of a cell..
~xamp~.es of such a transcription factor include, but are not limited to, STATI, STAT2, STAT3, GAS, NEAT, Myc, APl, CREB, NFxB, E2F, Rb, p53, RUNX1, RUNX2, RUNX3, Nkx-2, CF2-ZZ, Skn-1, SRY, HFH-2, Oct-1, Oct-3, $ox-5, HNF-3b, PPARY, and the like.
As used herein,. the term "terminator" refers to a sequence which is located downstream of a protein-encoding region of a gene and whi.Ch is involved in the termination of transGript~.on when DNA is transcribed into mRNA, and the addition of a paly-A sequence. It is known that a terminator ~. 0'7 contr~.butes to the stability of mRNA, and has an influence on the J.evel of gene ~xpr~:ssian.
As used herein, the term "promoter" refers to a base sequence which determines the initiation site o~
transcription of a gene and is a DNA region which directly regulatesthe frequency of transcription. Transcription is started by RNA polymerase binding to a promoter. A promoter region is usually located within about 2 kbp upstream of the first exon of a putative protein coding zegion.
Therefore, it is possible to estimate a promoter region by predicting a protein coding region in a genomic base sequence using DNA analysis software. A putative promoter region is usually located upstream of a structural gene, but is dependent an the structural gene, i . a . , a putative promoter region may be looated downstream of a structural gene.
Preferably, a putative promoter region is located within about 2 kbp upstream of the translation initiation site o~
the first exon. Such promoters ~.riCl.ude, but are not limited to constitutive promoters, specific promoters and induCti~cre promoters and the like.
As used herein, the term "enhancer" refers to a sequence which is used so as to enhance the expression efficiency of a gene of interest. One or more enhancers may be used, ox~ no enhancer may be used.
As used herein, the term "silencer" refers to a sequence which has a function of suppressing and arresting the expression of a gene. Any silencer which has such a Azp07 functian may be herein used. No silencer may be used.
As used herein, the term "operably linked"
indicates that a desired sequence is located such that expression (operation) thereof is under control of a transcription and translation regulatory sequence (e. g., a promoter, an enhancer, and the like) or a translation regulatory sequence . Tn order for a promoter to be operably lznked to a gene, typically, the promoter is located immediately upstream of the gene. A promoter is not necessarily adjacent to e~ structural gene.
Sequences flanking other genome structural genes, genomic sequences other than axons, and sequences within axons may also be herein used. For example, in addition to the above-described sequences having specific names, structural gene-flanking sequences are thought to be involved fn the cantro3. of transcription in terms of "processes". Therefore, such flanking sequences are also included in transcription control sequences. Genomic sequences other than axons and sequences within axons are also expected to be involved in the control of transcription in terms of "processes". Therefore, genomic sequences other than axons and sequences within axons are also included in transcription control sequences.
As used herein, the term "RNAi" is an abbreviation of RNA interference and refers to a phenomenon where an agent for causing RNAi, such as double-stz~anded ~0 RNA (also called dsRNA) , is introduced into cells and mRNA
homologous thereto is specifically degraded, so that the synthesis of gene products is suppressed, and techniques using the phenomenon. As used herein, RNAi may have the same meaning as that of an agent which causes RNAi.
As used herein, the term "an agent causing RNRi"
refers to any agent capable of causing RNAi . As used herein, "an agent causing RNAi of a tlene" indicates that the agent causes RNAi relating to the gene and that the effect of RNAi is achieved (e. g., suppression of expression of the gene, and the like). Examples of such an agent causing RNAi include, but are not limited to, a sequence having at least about '70~ homology to the nucleic acid sequence of a target gene or a sequence hybridizable thereto under stringent conditioz~s, RNA containing a double-stranded portion having a length of at least 10 nucleotides or variants thereof.
Here, this agent may be preferably DNA containing a 3' protruding end, and mare preferably the 3' protruding end has a length of 2 or more nucleotides (e.g., 2-9 nucleotides in length).
Though not wishing to be bound by any theory, a mechanism which causes RNAi is considered to be as follows .
When a molecule which causes RNAi, such as dsRNA, is introduced into a cell, an RNaseIII-like nuclease having a helicase domain (called dicer) cleaves the molecule at about 20 base pair intervals from the 3' terminus in the presence of AmP in the case where the RNA is relatively long (e. g., 40 or more base pairs). As used herein, the term "siRNA" is an abbreviation of short interfering RNA and Azao~
refers to short double-stranded RNA of 10 or more base pairs which are artificially chemically synthesized or b~.ochemically synthesized, synthesized by an organism, or produced by double-stxanded RNA of about 40 or more basE
pairs being degraded within the organism. siRNA typically has a structure comprising 5'-phosphate and 3'-OH, where the ~' terminus projects by about 2 bases. A specific protein is bound to siRNA to form RISC
(RNA-induced-silencing-complex). this complex recognizes and binds to mRNA having the same sequence as that of siRNA
and cleaves mRNA at the middlE of siRNA due to RNaseIZI-like enzymatic activity. It is preferable that the relationship between the sequence of siRNA and the sequence of mRNA to be cleaved as a target is a 1a0% match. However, base mutations at a site away from the middle of siRNA do not completely remove the cleavage activity by RNA,, leaving parti.aJ. acti~rity, while base mutations in the middle of siRNA
have a laxge influence and the mRNA cleavage activity by RNAi is considerabJ.y lowered. By utilizing such a nature, only mRNA having a mutation can be specifically degraded.
Specifically, siRNA in which the mutation is provided in the middle thereof is synthesized and is introduced into a cell. Therefore, in the present invention, siRNA per se, as well as an agent capable of producing siRNA (e. g., representatively dsRNA of about 40 or more base pairs) can be used as an agent capable of eliciting RNAi.
Also, though not w~.shing to be bound by any theory, apart from the above--described pathway, the antisense strand of siRNA binds to mRNA and siRNA functions Azoo~
as a px~.mer for RNA-dependent RNA polymerase (RdRP) , sa that dsRNA is synthesized. This dsRNA is a substrate for a dicer again, leading to production of new siRNA. It is intended that such a reaction is amplified. Therefore, in the present invention, siRNA per se, as well as an agent capable of producing siRNA are useful. xn fact, in insects and the like, for example, 35 dsRNA molecules aan substantially completely degrade 1,000 or more cop~:es of intracellular mRNA, and therefore, it will be understood that siRNA per se, as well as an agent capable of producing siRNA, is useful .
Tn the present invention, double-stranded RNA
having a length of about 20 bases (e. g., representatively about 21 to 23 bases) or less than about 20 bases, called siRNA, Can be used. Expression of siRNA in cells can suppress expression of a pathogenic gene targeted by the siRNA. Therefore, siRNA can be used far the treatment, prophylaxis, prognosis, and the like of diseases.
The siRNA of the present invention may be in any form as long as it can elicit RNAi.
In another embodiment, an agent capable of causing RNAi may have a short hairpin structure having a sticky portion at the 3' terminus (shRNA~ short hairpin RNA) .
As used herein, the term "shRNA" refers to a molecule of about 20 or more base pairs ~.n which a single-stranded RNA
partially contains a palindramic base sequence and forms a double-strand structure therein (i.e., a hairpin structure). shRNA can be artificially chemically AIOa7 synthesized. Alternatively, shRNA can be produced by linking sense and antisense strands of a DNA sequence in reverse directions and synthesizing RNA in vitro with T7 RNA polymerase using the DNA as a template. Though not wishing to be bound by any theory, it should be understood that after shRNA is introduced into a cell, the shRNA is degraded in the cell to a length of about 20 bass (e. g., representatively 21, 22, 23 bases) , and causes RNAi as with siRNA, leading to the treatment effects of the present invention. It should be understood that such an effect is exhibited in a wide range of organisms, such as insects, plants, animals (including mammals), and the like. Thus, shRNA elicits RNAx as with siRNA and therefore can be used as an effective component of the present invention. shRNA
may preferably have a 3' protz~uding end. The length of the double-stranded portion is not particularly limited, but is preferably about 10 or more nucleotides, and more preferably about 20 or more nucleotides. Here, the 3' protruding end may be preferably DNA, more preferably DNA
of at least 2 nucleotides ~.n length, and even more preferably DNA of 2~4 nucleotides in length.
An agent capable of causing RNAi used in the present invention may be artificially synthesized (chemically or biochemically) or naturally occurring.
There is substantially no difference there between in terms of the effect of the present invention. A chemically synthesized agent is preferably purified by liquid chromatography or the like.
An agent capable of causing RNAi used in the present invention can be produced .z.n vitro. In this synthesis system, '~7 RNA polymerase and T7 promoter are used to synthesize antisense and sense RNAs from template DNA.
These RNAs are annealed and thereafter introduced ~.nto a cell. In this case, RNAi is caused via the above-described mechanism, thereby achieving the effect of the present invention. Here, for example, the introduction of RNA into cell can be carried out using a calcium phosphate method.
Another example of an agent capable of causing RNAi according to the present invent~.on is a single-stranded nuclEic acid hybridizable to mRNA, or all nucleic acid analogs thereof_ Such agents are useful for the method and composition of the present invention.
As used herein, the term "time-lapse" means any action or phenomenon that is related to the passage of time.
As used herein, the term "monitor" refers to the measurement of a state of a cell using at least one parameter as a measure (e.g., a labeling signal attrilauted to transcription, etc.). Preferably, monitoring is performed using a device, such as a detector, a measuring instrument, or the like. More preferably, such a device is connected to a computer for recording and/ax processing data.
Monitoring may comprise the step of obtaining image data of a solid phase support (e. g., an array, a plate, etc.), As used herein, the term "rea3. time" means that a certain state is substantially s~.multaneously displayed in another form (e. g., as an image on a display or a graph with processed data) . In such a Case, the "real time" lags behind an actual event by the time required far data processing. Such a time lag is included in the scope of "real time" if it is substant~.ally negligible. Such a time lag may be typically within 10 seconds, and preferably within 1 second, w~.thout limitation. A time lag exceedinr~
seconds may be included in the scope of "real. time".
As used herein, the determination of a state of a cell can be performed using various methods . Exampl~s of such methods include, but are not limited to, mathematical processing (e. g., signal processing, multivariate analysis, etc.), empirical processing, phase changes, and the like.
As used herein, the term "difference" refers to a result of mathematical processing in which a value of a control profile (e. g., without a stimulus) is subtracted from a certain profile.
As used herein, the term "phase" in relation to a time-lapse profile refers to a result of a determination of whether the profile is positive or negative with xespect to a reference point (typically 0) , which is expressed with + or -, and also refers to analysis based on such a result.
As used hexezn, the term "correlate" or "correlation" in relat~.on to a profile (e.g., a time-.apse profile, etc.) and a state of a cell refers to an act of Azoa~
associating the profile or particular information about changes, with the state of the cell. A relationship between them is referred to as "correlation" yr a "correlation relationship". Conventionally, it was substantially impossible to associate a profile (e. g., a time-lapse profile, etc.) with a state of a cell. No relationship between them was known. The present invention has an advantageous effect of performing such a correlation.
As used here~.n, correlat~.on can be perfoz-~ned by associating at least one profile (e. g. , a time-lapse profile, etc. ) or changes therein, with a state of a cell, a tissue, an organ or an organism (e , g. , drug resistance, etc. ) . For example, a profile (e.g., a time-lapse profile, etc.) or changes therein is quantitatively or qualitatively associated with at least onE parameter indicating a state of a cell. A small number of profiles (e. g., time-lapse profile, etc. ) may be used for corxr~xat~.ozz as long as correlation can be performed, typically including, without l~.mxtation, 1, preferably 2, and more preferably 3. The present invention demonstrated that at least 2, preferably at least 3, profiles (e. g. , a time-lapsE profile, etc. ) are sufficient for specifying substantially all cells. Such an effect could not be expected by conventional profiling ar assays which use point observation, and can be said to be realized by the present invention. At least one profile (e.g., a time-.apse profile, etc.) may be subjected to mathematical processing by utilizing a matrix to associate the profile with a state of a cell. zn one preferred embodiment, at least 8 profiles (e. g. , a time-lapse profile, Az007 etc.) may be advantageously used. By observing increases or decrease9 in 6 profiles, 256 results can be theoretically obtained, based on which abaut 300 types of cells constituting an organism can be substantially distinguished from one another. zn this context, it may be more advantageous to use at least 9 or 10 structures as profiles.
On the other hand, by using the technology of the present invention, it is possible to substantially understand the state of a cell, merely by selecting any single biological agent and obtaining the profile data thereof.
Examples of a specific method for correlation include, but are not limited to, signal processing (e. g., wavelet analysis, etc.), multivariate analysix (e. g., cluster analys~.s, etc.), and the like.
Gorrelation may be performed in advance or may be performed at the time of detarm~.n,ativn of cells using a control.
As used herein, the term "external factor" in relation to a cell refers to a factor which is not usually present zn the cell (e.g., a substance, energy, etc.). As used herein, the term "factor" may refez to any substance or element as long as an intended object can be achieved (e. g. , energy, such as ionizing rad~.ation, radiation, light, acoustic waves, and the like) . Examples of such a substance include, but axe not limited to, proteins, polypeptides, oligopeptides, peptides, polynucleotides, vligonucleotides, nucleotides, nucleic acids (e.g., DNA
Azoo~
such as cDNA, genomio DNA and the like, or RNA such as mRNA, RNAi and the like), polysaccharides, oligosacchaz~.des, lipids, low molecular weight organic moleculr~s (e. g., hormones, ligands, information transduction substances, S low molecular weight oxganic molecules, molecules synthesized by combinatorial chemistry, low molecular weight molecules usable as medicaments (e. g., low molecular weight molecule ligands, etc.), etc.), and composite molecules thereof. External factors may be used'singly or in combination. Examples of eon external factor as used herein include, but are not limited to, temperature changes, humidity changes, electromagnetic wave, potential difference, visible light, ~.nfrarEd light, ultraviolet light, X--rays, chemical substances, pressure, gravity changes, gas partial pxessure, osmotio pressure, and the like. In one embodiment, an external factor may be a biological molecule or a chemically synthesized substance.
As used herein, the term "biological molecule"
refers to molecules relating to an organism and aggregations thereof. As used herein, the term "biolpg~.cal" or "organism" refers to a biological organism, including, but being not limited to, an animal, a plant, a. fungus, a virus, and the like. Biological molecules include molecules extracted from an organism and aggregations thereof, though the present invention is not limited to this. Any molecule capab~.e of affecting an organism and aggregations thereof fall within the defin~.tion of a biological molecule.
Therefore, low molecular weight molecules (e.g., low molecular weight molecule ligands, etc.), capable of being A~007 used as medicaments fall within the definition of a biological molecule as long as an effect on an organism is intended. Examples of such a biological molecule inciude, but are not limited to, proteins, polypept~.des, oligopeptides, peptides, polynucleotides, oligonucleotides, nucleotides, nucleic acids (e.g., DNA
such as cDNA and genomic DNA; RNA such as mRNA), polysaccharides, oligosaccharides, lipids, low molecular we~.ght molecules (e. g., hormones, ligands, information transmitting substances, ~.ow molecular weight organic molecules, etc.), and composite molecules thereof and aggregations thereof (e. g., glycolipids, glycoproteins, lipoproteins, etc.), and the like. A biological molecule may include a cell itself or a portion of tissue as long as it is intended to be introduced into a cell. typically, a biological molecule may be a nucleic acid, a protein, a lipid, a sugar, a proteolipid, a lipoprotein, a glycoprotein, a proteoglycan, or the like. Preferably, a bialQgiCa~.
molecule may include a n,ucleie acid (DNA or RNA) or a protein.
In another preferred embodiment, a biological molecule is a nucleic acid (e.g., genomic DNA or eDNA, or DNA synthesized by PCR or the ~.~.ke). In another preferred embodiment, a biological molecule may be a protein. Qreferably, such a biological molecule may be a hormone or a cytokine.
As used herein, the term "chemiGal~.y synthesized substance" or "chEmical" refers to any substance which may be synthesized by using typical chemical techniques . Such synthesis techniques are well known in the art. Those ak~.lled in the art can produce chemically 13.9 synthesized substances by combining such techniques as appropriate.
The term "cytokine" is used he=rein in the broadest sense in the art and refers to a physiologically active substance which is produced by a cell and acts on the same or a different cell. Cytokines are generally proteins or polypeptides hav~.ng a function of controlling an immune response, regulating the endoczine system, regulating the nervous system, acting against a tumor, acting against a virus, regulating cell growth, regulating ce~.~. di.ffereTitiation, or the like. Cytokines are used herein in the form of a protein or a nuc7.eic ac~.d or in othex forms. In actual practice, cytokines are typically proteins. The terms "growth factor" refers to a substance which promotes or controls cell growth. Growth factors are also called "proliferation factors" or "development factors". Growth factors may be added to cell or tissue culture medium, subst~.tuting for serum macromolecules . It has been revealed that a number of growth f actors have 3 function of controlling diffierentiation in addition to a function of promoting cell growth. Examples of cytokines representatively include, but are not limited to, intexJ.eukins, chernokines, hematopoietic factors (e. g., colony stimulating factors), tumor necrosis factor, and interferons. Representative e~tamples of growth factors include, but are not limited to, platelet-derived growth factor (PDGF), epidermal growth factor tEGF), fibroblast growth factor (FGF) , hepatocyte growth factor (IiGF) , endothelial ce~.l growth factor (VEGF), cardiotrophin, and Azoo~
the like, which have proliferative activity.
The term "hormone" is herein used in its broadest sense in the art, referring to a physiological organic compound which is produced in a particular organ ax cell of an animal or plant, and has a physiological effect on an organ apart from the site producing the compound.
Examples of such a hormone include, but are not limited to, growth hormones, sex hormones, thyroid hormones, and the like. The scope of hormones may overlap partially w~.th that of cytokines.
As used herein, the term "actin-like substance"
refers to a substance which interacts directly or indirectly with actin within cells to alter the form or state of actin.
ExampJ.es of such a substance include, but are not ~.~.mited to, extracellular matrix proteins (e. g., fibranectin, vitronectin, laminin, etc.), and the like. Such actin-like substances include substances identified by the following assays. As used herein, interaction with actin is evaluated by visualizing actin with an actin staining reagent (Molecular Probes, Texas Red-X phalloidin) or the like, followed by m~.croscopic inspection to observe and determine actin aggregation, actin reoanstruction or an improvement ~5 in cellular outgrowth xate. Such evaluation stay be performed quantitatively or qualitatively. Actin-like substances are herein utilized so as to increase transfectian efficiency. An actin-like substance used herein is der~.ved from any organism, including, for example, mammals, such as human, mouse, bovine, and the like.
As used hez~ein, the terms "cell adhesion agent", "cell adhesion molecule", "adhesion agent" and "adhesion molecule" are used interchangeablx to refer to a molecule capable of mediating the joining of two or more cells (cell adhesion) or adhesion between a substrate and a cell. In general, cell adhesion molecules are divided into two groups: molecules involved in cell-cell adhesion (~.ntercellular adhesion) (cell-cell adhesion molecules) x0 and molecules involved in cell-extracellular matrix adhesion (cell-substrate adhesion) (cell-substrate adhesion mplecules) . For a method of the present invention, either type of molecule is useful and can be effectively used. Therefore, cell adhesion molecules herein include a substrate protein and a cellular protein (e. g., integrin, etc.) involved in cell-substrate adhesion. A maleCUle other than a protein can fall. within the concept of a cell adhesion molecule as lung as it can mediate cell adhesion.
Fox cell-cell adhesion, cadherin, a number of molecules belonging in an immunot~lobu~.in superfamily (NCAM, L1, ICAM, fasciclin II, III, etc. ) , selectin, and the J.ike are knawn, each of which is knQwTa to connect cell membranes via e~ specific molecular reaction.
~n the other hand, a major cell adhesion molecule functioning for cell-substrate adhesion is integrin, which recognizes and binds to various proteins contained in extracellular matrices. These cell adhesi.an molecules are all located on cell membranes arid can be regarded as a type cf xeceptor (cell adhesion receptor).
Therefore, receptors present on cell. membranes can also be used in a method of the present invention. Examples of such a receptor include, but are not limited to, ac-integrin, ~-integrin, CD44, syndecan, aggrecan, and the like.
Techniques for cell adhesion are well known as described above and as described in, for example, "Saibogaimatorikkusu -Rinsho keno Oyo- CExtracellular matrix -Clinical Applications-], Medical. Review.
It can be determined whether or not a certain molecule is a cell adhesion molecule, by an assay, such as biochemical quantification (an SDS-PAGE method, a labeled-collagen method, etc.), immunologiCal quantification (an enzyme antibody method, a fluorescent antibody method, an immunohistologieal study, etc.), a PDR
method, a hybridization method, or the like, in which a positive reaction is detected. Examples of such a cell adhesion molecule include, but are not limited to, collagen, integrin, fibronectin, laminin, vitronectin, fibrinogen, immunoglobulin superfamily members (e. g., CD2, CD4, CD8, ICMI, ICAM2, VCAM1) , selectin, cadherin, and the like. Most of these cell adhesion molecules transmit an auxiliary signal for cell activation into a cell due to intercellular interaction as well as cell adhesion. It can be determined Whether or not such an auxiliary signal can be transmitted into a. cell, by an assay, such as biochemical quantification (an SDS-PAGE method, a labeled-collagen me'~hod, etc.), immunological quantification (an enzyme azrtibody method, a fluorescent antibody method, an ~.mmunohistological study, Azoo~
etc.), a PDR method, a hybridization method, yr the like, in which a positive reaction is detected.
Examples of cell adhesion molecules include, but are not limited to, immunoglobulin superfamily molecules (LFA-3, ICAM-1, CD2, CD4, CDB, ICMl, ICAM2, VCAMl, etc.); integrin family molecules (LFA-1, Mac-1, gpIIbIIIa, p150, p95, VLAI, VLA2, VLA3, VLA4, VLA5, VLA6, etc.);
selectin family molecules (L-seleetin, E-selectin, P-selectin, etc.), and the like.
As used hexe~.zx, the term "extrace~.lu~.ax matrix protein" refers to a protein constituting an "extracellular matrix". As used herein, the term "extracellular matrix"
(ECM) is also called "extracellular substrate" and has the same meaning as commonly used in the art, and refers to a substance existing between somatic cells no matter whether the cells are epithelial cells or non-epithelia.J. ceJ.J.s .
Extracellular matrices are involved in suppoxt~.ng tissue as well as in internal environmental structures essential for survival of all somatic cells . Extracellular matrices are generally produced from connective tissue cells. Some extraeellular matrices are secreted from cells possessing basal membrane, such as epithelial cells or endothelial 2S cells. Extracellular matrices are roughly divided into fibrous components and matrices filling there between.
Fibrous components include collagen f~.bexs and eXastin fibers. A basic component of matrices is glycosaminoglycan (acidic mucopolysaccharide), most of which is bound to non-collagenous protein to form a polymer of a proteoglycan AI ~ 0'7 (acidic mucapolysaccharide-pxotein complex}. In addition, matrices include glycoproteins, such as laminin of basal membrane, microfibrils around elastin fibers, fibers, fibronectins on cell surfaces, and the like. Specifically differentiated tissue hoe the same basic structure. For example, in hyaline cartilage, chondroblasts characteristically produce a large amount of cartilage matrices including proteoglycans. In bones, osteoblasts produce bone matrices which cause calcification. Examples of extracel~.ular matrices for use in the present invention include, but are not limited to, collagen, elastin, proteaglycan, glycosaminaglycan, fibronectin, laminin, elastic fiber, collagen fiber, and the like.
As used herein, the term "receptor" refers to a molecule which is present on cells, within nuclei, or the like, and is capable of binding to an extracellular ox intracellular agent where the binding mediates signal txansduction. Receptors are typically in the form of pxoteins. The binding partner of a receptor is usually ~ceferred to as a ligand.
As u$ed herein, the term "agonist" refers to an agent which binds to the receptor of a certain biologica~.ly acting substance (e.g., ligand, etc.), and has the same or similar function as the function of the substance.
As used herein, the term "antagonist" refers to a factor which competitively binds to the receptor of a certain biologically acting substance (ligand}, and does not produce a physiological action via the receptor.
Antagonists include antagonist drugs, blockers, inhibitors, and the like.
(Devices and solid phase supports) As used herein, the term "device" refers to a part which can constitute the whole or a, portion of an appaxatu9, and comprises a support (Preferably, a solid phase support) and a taxget substance oarr~.ed thereon.
Examples of such a device include, but are not limited to, chips, arrays, microtiter plates, cell culture plates, Petri dishes, films, beads, and the like.
As used herein, the team "support" refers to a I5 material which can fix a substance, such as a biological molecule. Such a support znay be made from a.ny fixing material which has a capability of binding to a biological molecule as used herein via covalent or noncovalent bonds, or which may be induced to have such r~ capability.
examples of materials used for supports include any material capable of forming a solid surface, such as, without limitation, glass, silica, silicon, ceramics, silicon dioxide, plast~.cs, metals (including alloys), naturally-occurring and synthetic polymers (e. g., polystyrene, cellulose, chitosan, dextran, and nylon), and the like _ A support may be formed of layers made of a plurality of materials . Foz~ example, a support may be made of an inorganic insulating material, such as glass, quartz glass, alumina, sapphire, forsterite, silicon oxide, silicon carbide, silicon nitride, or the like. A support may be made of an organic material, such as polyethylene, ethylene, polypropylene, palyisobutylene, polyethylene terephthalate, unsaturated polyester, fluorine-containing resin, polyvinyl chloride, polyvinylidene chloride, palyvi.nyl acetate, polyvinyl alcohol, polyvinyl acetal, acrylic resin, polyacrylanitrile, polystyrene, acetal resin, polycarbonate, polyamide, phenol resin, urea resin, epoxy resin, melamine resin, styrene--acrylonitrile copolymer, acrylonitrile-butadiene-styrene copolymer, silicone resin, polyphenylene oxide, polysulfone, and the like. Also in the present inventzvn, nitrocellulose film, nylon film, PVDF film, or the like, which are used in blotting, may be used as a material for a support. When a material Z5 constituting a support is in the solid phase, such as a support is herein particularly referred to as a "solid phase support" . A solid phase support may be herein in the form of a plate, a microwell plate, a ch~.p, a glass slide, a film, beads, a mefial (surface), or the like. A support may be 24 uncoated or may be coated.
As used herein, the term "liquid phase" has the same meanings as are commonly understood by those skilled in the: art, typically referring to a state in solution.
As used herein, the term "solid phase" has the same meanings as are commonly understood by those skilled in the art, typically referring to a solid state . As used herein, liquid and solid may be collectively referred to as a "fluid".
As used herein, the term "substrate" refers to a material (preferably, so~.~.d) whioh is used to construct a chip ar array according to the present invention.
Therefore, substrates are inoluded in the concept of plates .
Such a substrate may be made from any solid material which h~.s a capability of binding to a biological molecule as used herein via covalent or noncovalent bonds, or which may be induced to have such a capability.
Examples of materials used far plates and substrates include ariy material capable of forming a solid surface, such as, without limitation, glass, silica, silicon, cerama.cs, silicon di.ox~.de, plastics, metals (including alloys), naturally-occurring and synthetic polymers (e. g., polystyrene, cellulose, chitosan, dextran, and nylon) , and the like. A support may be formed of layers made of a plurality of materials. Far example, a support may be made of an inorganic insulating material, such as glass, quarts glass, alumina, sapphire, forsterite, silicon oxide, silicon carbide, silicon nitride, or the like. A
support may be made of an organic material, such as polyethylene, ethylene, polypropylene, polyisobutylene, polyethylene terephthalate, unsaturated polyester, fluorine-containing resin, polyvinyl ahlaride, polyvinylidene chloride, polyvinyl acetate, polyvinyl alcohol, polyvinyl acetal, acrylic resin, polyacrylonitrile, polystyrene, acetal resin, polycarbonate, polyamide, phenol resin, urea resin, epoxy resin, melamine resin, styrene-acrylonitrile copolymer, acrylonitrile-butadiene-styrene copolymer, silicone resin, polyphenylen~: oxide, polysulfone, and the like. A material preferable as a substrate varies depending on various parameters such as a measuring device, and can be selected from the above-described various materials as appropriate riy those skilled in the art . For transfection arrays, glass slides are preferable. Preferably, such a substrate may be coated with a substance or have a coating.
1O As used herein, the term "coating" in relation to a solid phase support or substrate refers to an act of forming a film of a material on a surface of the solid phase support or substrate, and also refers to a film itself.
Coating is performed for variaus purposes, such as, for example, improvement in the quality of a solid phase support and substrate (e. g., elongation of life span., improvement in resistance to hostile environment, such as resistance to acids, etc. ) , an improvement in affinity to a substance integrated with a solid phase support or substrate, and the like. Various materials may be used for such coating, including, without limitation, biological substances (e. g., DNA, RNA, protein, lipid, etc.), polymers (e. g., poly-Z-xysine, MAS (avai~.able from Matsunami Glass, Kish.iwada, Japan) , and hydrophobic fluorine resin) , silane (APS (e. g. , 'y-aminopropyl silane, etc. ) ) , metals (e. g. , gold, etc.), in addition to the above-described solid phase support and substrate. The selection of such materials is within the technical scope of those skilled in the art and thus can be performed using techniques well known in the art. Tn one preferred embodiment, such a coating may be advantageously made of poly-L-lysine, silane (e. g., epoxy silane or mercaptosilane, APS (y-aminopropyl silane) , etc. ) , MAS, hydrophobic fluorine resin, a metal (e. g. , gold, etc. ) .
Such a material may be preferably a substance suitable for cells or objects containing cells (e. g. , organisms, organs, etc. ) .
As used herein, the terms "chip" or "microchip"
are used interchangeably to refer to a micro-integrated circuit which has versatile functions and constitutes a portion of a system. Examples of a chip include, but are not limitEd to, DNA ch~.ps, protein chips, and the like.
As used herein, the term "array" refers to substrate (e.g., a chip, etc.) which has a pattexn of a composition containing at least one (e. g., 1000 or more, etc.) taxget substance (e. g., DNA, proteins, transfection mixtures, etc.), which are arrayed. Among arrays, patterned substrates having a small size (e.g., 10x10 mm, etc.) are particularly ~eeferred to as m~.croarrays. The teams "microarray" and "array" are used interchangeably.
Therefore, a patterned substrate having a larger size than that which is described above may be referred to as a microarray. For example, an array comprises a set of desired transfection mixtuxes fixed to a solid phase surface or a film thereof . An arxay preferably comprises at least 102 antibodies of the same or different types, more preferably at least 7.03, even more preferably at least 10°, and still even more preferably at least 105. These antibodi~:s aze placed on a surface of up to 125x80 m~, more preferably 10x10 mm. An array includes, but is not limited to, a 9~--well microtiter plate, a 384-well microtiter plate, a microtiter plate the size of a glass slide, and the like.
A composition to be fixed may contain one or a plurality of types of target substances. Such a number of target substance types may be in the range of from one to the number of spots, including, without limitation, about 10, about 100, about 500, and about 1,000.
As described above, any number of target substances (e.g., proteins, such as antibodies) may be provided on a solid phase surface or film, typically including no more than 108 biological molecules per substrate; in another embodiment no more than 10' biological molecules, no more than 106 biological molecules, no more than 105 biological molecules, no more than 10' biological molecules, no mare than 103 biological molecules, or no more than lOZ biological molecules. A composition containing more than 108 biological molecule target substances may be provided on a substrate. In these cases, the size of a substrate is preferably small. Particularly, the size of a spot of a composition containing target substances (e.g., proteins such as antibodiesy may be as small as the size of a s~.ng7.e bza~.og~.oal molecule (e. g. , 1. to 2 nm order) .
Zn some cases, the minimum area of a substrate may be determined based on the number of biological molecules on a substrate. A composition containing target substances, which are intended to be introduced into cells, are herein typically arrayed on and fixed via covalent bonds or physical interaction to a substrate in the form of spots having a size of 0.01 mm to 10 mm.
"Spots" of biological molecules may be provided on an array. As used herein, the term "spot" refers to a certain set of compositions containing target substances.
As used herein, the term "spotting" refers to an act of preparing a spot of a composition containing a certain target substance on a substrate or plate. Spotting may be performed by any method, for example, pipetting or the like, or alternatively, by using an automatic device. These methods are well known in the art.
As used hexein, the term "address" refers to a unique position on a substrate, which may be distinguished from other unique positions. Addresses are appropriately associated with spots. Addresses can have any distinguishable shape such that substances at each address may be distinguished from substances at other addresses (e . g. , optically) . A shape defining an address may be, for example, without limitatipn, a circle, an ellipse, a square, a rectangle, or an irregular shape. Therefore, the term "address" is used to indicate an abstract concept, while the term "spot" is used to indicate a specific concept.
Unless it is necessary to distinguish them from each other, the terms "address" and "spot" may be herein used interchangeably.
The size of each address particularly depends on the size of the substrate, the number of addresses on the substrate, the amount of a composition containing target substances and/ox a~railable reagents, the size of microparticles, and the level of resolution required for any method used for the array. The size of each address ~Ct~ty be, for example, in the range of from 1-2 nm to several centimeters, though the address may have any size suited to an array.
The spatial arrangement and shape which define an address axe designed so that the micraarray ~.s suited to a particular application. Addresses may be densely arranged or sQar~sely distributed, or subgrouped into a desired pattern appropriate for a particular type of material to be analyzed.
Microarrays are widely reviewed in, for example, "Genomu Kino Kenkyu Purotokoru [Genomic Function Research Protocol] tJikken Igaku Bessatsu [Special. Issue of Experimental Medicine] , Posuto Genomu J'idai no Jikken Koza 1 [Lecture 1 oz~ ExQerimentation in Post-genome Era) , "Genomu Ikagaku to koxekarano Genomu Iryo [Genome Medical Science and Futuristic Genome Therapy (,Tikken Igaku Zokan [Special Tssue of Experimental Medicine]), and the like.
A vast amount of data can be obtained from a microarray. Therefore, data analysis software is important for facilitating correspondence between clones and spots, data analysis, and the like. Such software may be attached to various detection systems (e. g., Ermolaeva G. et al., (1998) I~at. Genet., 20: 19-23). The format of such a database includes, for example, GATC (genetio analysis technology Consortium) proposed by Affymetrix.
M~.cromachining for arrays is described in, for example, Campbell, S.A. (1996), "The Science and Engineering of Microelectronic Fabrication", Oxford University Press; taut, P.V. (1996), "Micromicroarray Fabrication: a Practical Guide to Semiconductor Processing", Semiconductor Services; Madou, M.J. (7.997), "Fundamentals of Microfabrication", CRC1 5 Press; Rai--Choudhury, P.
(1997), "Handbook of Microlithography, Micxomachining, &
Microfabrication: Microlithography": a.n;d the like, portions related thereto of which are herein incorporated by reference.
~.5 ( Detection) In cell analysis or determination in the present invention, various detection methods and means Can, be used as gong as they can be used to detect information attributed to a cell or a substance interacting therewith. Examples of such detection methods and means a,ncJ.ude, but are not limited to, visual inspection, optical microscopes, confocal microscopes, reading devices using a laser light source, surface plasmon resonance (SPR) imaging, electric signals, chemical ox biochemical markers, which may be used singly or i.n combination. Examples of such a detecting device ~.nclude, but are not limited to, fluorescence analyzing devices, spectrophotometers, scintillation counters, CCD, luminometers, and the like. Any means capable of detecting a biological molecule may be used.
13~
As used herein, the term "marker" refers to a biological agent for indicating a level or frequency of a substance or state of interest. Examples of such a marker include, but are.not limited to, nucleic acids encoding a gene, gene products, metabolic products, receptors, ligands, antibodies, and the like.
Therefore, es used herein, the term "marker" in relation to a state of a cell refers to an agent (e. g., ligands, antibodies, complementary nucleic acids, etc.) interacting with intracellular factorsindicating the state of the cell (e. g., nucleic acids encoding a gene, gene products (e. g., mRNA, proteins, posttxarzscriptionally modified proteins, etc.), metabolic products, receptors, ~.5 etc. ) in addition to transcription control factors. In the present invention, such a marker may be used to produce a time-lapse profile which is in turn analyzed. Such a marker may preferably interact with a factor of interest . As used herein, the term "specificity" in relation to a marker refers to a property of the marker which interacts with a molecule of interest to a significantly higher extent than with similar molecules. Such a marker is herein preferably present within cells or may be present outside cells.
As used here~.n, the term "label" refers to a factor which distinguishes a molecule or substance of interest from others (e. g., substances, energy, electromagnetic waves, etc. ) . Examples of ~.abeling methods include, but are no't limited to, RI (radioisotope) methods, fluorescence methods, biotinylation methods, Aroa~
chemoluminance methods, and the like. When the above-described nucJ.eic acid fragments and complementary oligonucleatides ale labeled by fluorescence methods, fluorescent substances having different fluorescence emission maximum wavelengths are used for labeling. The difference between each fluorescence emission maximum wavelength may be preferably 10 nm or more. Any fluorescent substance which can bind to a base portion of a nucleic acid may be used, preferably including a cyanine dye (e.g., Cy3 1Q and Cy5 in the Cy Dye'r°~ series, etc. ) , a rhodamine 6G reagent, N-acetoxy-N2-acetyl amino fluorine (AAF), AAIF (iodine dexivati~cre of AAF) , and the like. Examples ~ of fluorescent substaz~aes having a difference in fluorescence emiss.ian maximum wavelength of 10 nm c~x more include a combination 7.5 of Cy5 and a rhodamine 6G reagent, a combination of Cy3 and fluorescein, a combination of a rhodamin,e ~G reagent and fluorescein, and the like. Zn the present invention, such a label can be used to alter a sample of interest so that the sample can be detected by detecting means. Such 20 alteration i.s known in the art. Those skilled in the art can perform such alteration using a method appropriate for c~ label and a sample of interest.
As used herein, the term "i.nteraction" refers 25 to, without limitation, hydrophobic interactions, hydrophilic interactions, hydrogen bonds, 'fan der Waals forces, ionic interactions, nonionic interaotioz~s, electrostatic interactions, and the like.
30 As used herein, the term "interaction level" in Ax007 relation to interaction between two substances (e. g., cells, etc.) refers to the extent or frequency of interaction between the two substances. Such an interaction level can be measured by methods well known in the art . For example, the number of cells which are fixed and actually perform an interaction is counted directly or indirectly (e.g., the intensity of reflected light), for example, without limitation, by using an optical microscope, a fluorer>cenee microscope, a phase-contrs.st microscope, or the ~.ike, or alternatively by staining celJ.s w~.th a markex, an antibody, a fluorescent label ox' the like specific thereto and measuring the intensity thereof. Such a level can be displayed directly from a marker or indirectly via a label.
eased on the measured value of such a level, the number or frequency of genes, which are actually transcribed or expressed in a certain spot, can be calculated.
(Presentation and display) As used herein, the terms "display" and "presentation" are used interchangeably to refer to an act of providing a profile obtained by a method of the present invention, or information derived therefrom, directly or indirectly, or in an information-processed form. Examples of such displayed forms include, but are not limited to, various methods, such as graphs, photographs, tables, animations, and the like. Such techniques are described in, for example, METHOD5 IN CELL BIOLOGY, VOL. 56, ed. 1998, pp:185-215, ~lHigh-Resolution Multimode Digital Microscope System (Sluder & Wolf, Salmon) , which discusses application software far automating a microscope and controlling a camera and the design of a hardware device comprising an automated optical microscope, a camera, and a Z-axis focusing device, which can be used herein. Image acquisition by a camera is described in detail in, for example, Inoue and Spring, Video Microscopy, 2d. Edition, 1997, which is herein incorporated by reference.
Real time display can also be performed using techniques well known in the art. ~'or example, after a7.~.
images are obtained and stored~in a semi-permanent memory, or substantially at the same t~.me as when an image ~.s obtained, the image can be processed with appropriate application software to obtain processed data. For example, data may be processed by a method for playing back a sequence of images without interruption, a method for displaying images in real time, or a method for displaying images as a "movie" showing irradiating lzght as changes or continuation on a focal plane.
Tn another embodiment, application software for measurement and presentation typically includes software for setting conditions for applying stimuli or condit~.oris for recording detected signals . With such a measurement and presentation application, a computer can have a means for applying a stimulus to cell$ and a means for processing signals detected from cells, and in addition, can Control an optically observing means (a STT camera and an image filing device) and/or a cell culturing means.
Hy inputting conditions for stimulation on a Azoo~
parameter setting screen using a keyboard, a touch panel, a mouse, or the J.zke, ifi is possible to set the desired complex conditions for stimulation. In addition, various conditions, such as a temperature for cell culture, pH, and the like, can be set using a keyboard, a mouse, or the like.
A display screen displays a time-lapse profile detected from a ceJ.l or information derived therefrom in real time or after,recording. In addition, another recorded profile or information derived therefrom of a ce~.~. can be displayed while being superimposed with a microscopic image of the cell. In addition to recorded information, measurement parameters in xecording (stimulation conditions, recording cøndit~.ons, display conditions, process conditi.ans, various conditions for cep s, temperature, pH, etc.) can be displayed in real t~.me. The present invention may be equipped with a function of issuing an alarm when a temperature or pH departs from the tolerable range.
On a data analysis screen, it is possible to set conditions for various mathematical analyses, such as Fourier transformation, cluster analysis, FFT analysis, coherence analysis, correlation analysis, and the like.
The pxesent invention may be equipped w~.th a function of temporarily displaying a profile, a function of displaying typography, or the like. The results of these analyses can be displayed while being superimposed with microscopic images stored in a recording medium.
(Gene introduction) Any technique may be used here~.n fox introduction of a nucleic acid molecule into cells, including, for example, transformation, transduction, transfection, and the like. In the present invention, transfection is preferable.
As used herein, the term "transfection" refers to an act of performing gene introduction or transfection by culturing Cells with genomic DNA, plr~smid DNA, vir2~1 DNA, vixal FtNA or the like in a substantially naked farm (excluding viral particles), ox adding such a genetic material into cell suspension to allow the cells to take in the genetic material . A 'gene introduced by transfection is typically expressed within cells in a temporary manner or may be incorporated into cells in a permanent manner.
Such a nucleic acid molecule introduction technique is well known in the art and com~tonly used, and is described in, for example, Ausubel F.A. et al., editors, (1988), Current Protocols in Molecular Eiology, Wiley, New York, NY; 5ambrook J. et al. (1987) Molecular Cloning: A
Laboratory Manual, 2nd Ed. and its 3rd Ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY; Special issue, Jikken Igaku jExperimentaX Medicine] "Experimental Methods for Gene introduction & Expreas~.on Analysis", Yodo-sha, 1997; and the like. Gene introduction can be confirmed by method as described herein, such as Northern blotting analysis and Western blotting analysis, or other weJ.l~-known, cammc~n or routine techniques .
~. 4 0 When a gene is mentioned herein, the term "vector" or "recombinant vector" refers to ~. vector transferring a polynucleotide sequence of interest to a target cell. Such a vector is capable of self-replication or incorporation into a chromosome in a host cell (e. g., a prokaryotic cell., yeast, an animal cell, a plant cell, an insect cell, an individual animal, and an individual plant, etc.), and contains a promoter at a site suitable for transcription of a polynucleotide of the present ~.nv~nt~.on.
A vector suitable for performing cloning is referred to as a "cloning vector". Such a cloning vector ordinarily contains a multiple cloning site containing a plurality of restxlct~.on sites. Restriction enzyme sites and multiple 7~5 cloning sites as described above are well known in the art and can be used as appropriate by those skilled in the art depending on the purpose in accordance with publications described herein (e. g., Sambrook et al., supra).
As used hexeiz~, the term "expression vector"
refers to a nuczeic acid sequence comprising a structural gene and a promoter for regulating expression thereof, and in addition, various regulatory elements in a state that aJ.~.ows them to operate within host cells. The regulatory element may include, preferably, terminators, selectable markers such as drug-resistance genes, and enhancers.
Examples of "recombinant vectors" for prokaryotic cells include, but are not limited to, pcDNA3 (+) , pEluescript-SK (+/-) , pGEM-T, pEF-BOS, pEGFP , pHAT, pUCl8, A~ao7 pFT-DEST~42GATEWAY (Tnvitrogen), and the like.
Examples of "recombinant vectors" for animal cells include, but are not limited to, pcDNAT/Amp, pcDNAI, pCDMB (all commercially available from Funakoshi ) , pAGE107 [Japanese paid-Open Publication No. 3-229 (Invitrogen), pAGE103 [J. Biochem. , 101, 1307 (1987 ) ] , pAMo, pAMoA [J. Biol.
Chem., 268, 22782-22787(1993)], a retrovirus expression vector based on a murine stem cell virus (MSCV), pEF-BOS, pEGFP, and the like.
Examples of recombinant vectors for plant cells include, but are not ~.imited to, pPCVZCEn4HPT, pCGN1S48, pCGNl549, pBI221, p8I121, and the like.
Any of the above-described methods ~or introducing DNA into cells can be used as a vector introduction method, including, for example, txansfection, transduction, transformation, and the like (e. g., a calcium phosphate method; a liposome method, a DEAF dextran method, an electroporation method, a particle gun (gene gun) method, and the like), a lipofection method, a spheroplast method (Pros. Natl. Acad. Sci. USA, $4, 1929(1978)), a lithium acetate method (J. Bactexiol., 153, 163(1983); and Proc.
Natl. Acad. Sci. USA, 75, 1929(1978)), and the like.
As used herein, the term "operably linked"
indicates that, a desired sequence is located such that expression (operation). thereof is under contxol of a transexiption and translation regulatory sequence (e. g., a promoter, an enhancer, and the like) or a translation regulatory sequence . In order for a pxomoter to be operably linked to a gene, typically, the promoter is located immediately upstream of the gene. A promoter is not necessarily adjacent to a structural gene.
As 'used herein, the term "gene introduction reagent" refers to a reagent which is used in a gene introduction method so as to enhance introduction efficiency. Examples of such a gene introduction reagent include, but are not limited to, cationic polymers, cationic lipids, polyamine-based reagents, pvlyimine-based reagents, calcium phosphate, and the like. Specific examples of a reagent used in transfection include reagents available from various sources, such as, without limitation, Effectene Transfection Reagent (cat. no. 301.425, Qiagen, CA) , TransFast~ Transfection Reagent (E2431, Promega, WI) , Tfx~-20 Reagent (E2391, Promega, WI), SuperFeGt Transfeetion Reagent (301305, Qiagen, CA), PolyFect Transfection Reagent (301105, Qiagen, CA), LipofectAMINE
X000 Reagent (11668-019, Tnvitrogen corporation, CA), JetPEZ (x4) cone. (101-30, Polyplus-transfection, France) and ExGen 500 (R0511, Fermentas Inc., MD), and the like.
Gene expression (e. g., mRNA expression, pvlypeptide expression) may be "detected" or "quantified"
by an apprdpr~.ate method, including mRt~A measurement and immunological measurement methods. Examples of molecular biological measurement methods include Northern blotting methods, dot blotting methods, PCR methods, and the like.
Azaa~
Examples of immunological measurement methods include EZISA
methods, RIA methods, fluorescent antibody methods, fnTestern blotting methods, immunohistologieal staining methods, and the like, where a microtiter plate may be used. Examples of quantification methods include ELISA methods, RIA
methods, and the like. A gene analysis method using an array (e. g. , a DNA array, a protein array, etc. ) may be used. The DNA array is widely reviewed in Saibo-Kogaku [Cell Engineering] , special issur~, "DNA Microarray arid Up-to-date PCR Method", edited by Shujun-sha. The protein array is described in detail in Nat Genet. 2002 Dec; 32 Suppl:526-32.
Examples of methods for analyzing gene expression include, but are not limited to, RT-PCR methods, RACE methods, SSC~
methods, immunopreeipitation methods, two-hybrid systems, in vitro translation methods, and the like, in addition to the above-described techniques. Other analysis methods are described iri, for example, "Genome Analysis Experimental Method, Yusuke Nakamura's Lab-Manual, edited by Yusuke Nakamura, Yodosha (2x02), and the like. All of the above-described publications are herein incorporated by reference.
As used herein, the term "expression level"
refers to the amount of a polypeptide or mRNA expressed in a sub~eot cell. The term "expression level" includes the level of protein expression of a polypeptide evaluated by cony appropriate method using an antibody, including immunological measurement methods (e. g., an ELISA method, an RIA method, a fluorescent antibody method, a Western blotting method, an immunohistological staining method, and Aioa~
the life, or the mRNA level of expression of a polypeptide evaluated by any appropriate method, includ~.ng molecular biological measurement methods (e. g., a Northern blotting method, a dot blotting method, a PCR method, and the like) .
The term "change in expression level" indicates that an increase or decrease in the protein or mRNA level of expression of a polypeptide evaluated by an appropriate method including the above-described immunological measurement methods or molecular biological measurement methods.
(Screening) As used herein, the term "screening" refers to selection of a target, such as an organism, a subatanGe, or the like, a given specific property of ~.nterest from a population containing a number of elements using a specific operation/evaluation method. For screening, an agent (e. g., an antibody), a polypeptxde or a nucleic acid molecule of the present invention can be used.
As used herein, screening by utilizing an immunological reaction is also referred to as "immunophenotypirig". ~ri th~.s case, azx antibody or a single chain antibody may be used for inununophenotyping a cell line and a biological sample. A transcription or translation product of a gene may be useful as a cell specific marker, or more partieu~.ar~.y, a cell marker which is distinctively expressed in various stages in differentiation and/or maturation of a specific cell type. A monoc~.onal antibody directed to a specific epitope, or a combination of epitopes Azoo7 allows for screening of a yell population expressing a marker.
Various techniques employ monoclonal antibodies to screen for a cell population expressing a marker. Examples of such techniques include, but axe not limited to, magnetic separat~.on using magnetic beads coated with antibodies, "panning" using antibodies attached to a solid matrix ( i . a . , a plate}, flow cytometry, and the like (e. g., OS Patent No. 5, 985, 660; and Morrison et al., Cell, 96: 737-99 (1999) ) .
These techniques may be used to screen cell populations containing undifferentiated cells, which can grow and/or differentiate as seen in human umbilical cord blood or which are treated and modified into an undifferentiated state (e. g., embryonic stem cells, tissue stem cells, etc.).
(Diagnosis}
As used herein, the team "diagnosis" refers to an act of identifying various parameters assoc~.ated with a disease, a disorder, a condition, or the like of a subject and determin~.ng a current state of the disease, the disorder, the cond~.tion, or the like. A method, device, or system of the present invention can be used to analyze a sugar chain structure, a drug resistance level, or the like. Such information can be used to seleot parameters, such as a disease, a disorder, a condit~.on, and a prescription or method for treatment or preventative method fox a subject.
A diagnosis method of the present ~.nvention can use, in principle, a sample which is derived from the body ~rao~
of a subject. Therefore, it is possible for some one which is not a medical practitioner, such as a medical doctor, to deal with such a sample. The present invention is industrially useful.
S
(Therapy) As used herein, the term "therapy" refers to an act of preventing progression of a disease or a disorder, preferably ma~.ntaining the current state of a disease oz a disorder, more preferably alleviating a disease or a disorder, and more preferably e~ct~.nguishing a disease or a disorder.
As used herein, the term "sub j ect" refexs to an organism which is subj ected to the treatment of the present invention. A subject is also referred to as a "patient".
A patient or subject may preferably be a human.
As used herein, the term "cause" or "pathogen"
2d in relation to a disease, a disorder or a condition of a subject refers to an agent associated with the disease, the disorder or the condition (also collective~.y referred to as a "lesion", or "disease damage" in plants), including, without limitation, a causative or pathogenic substance (pathogenic agent), a disease agent, a disease cell, a pathogenic vixus, and the like.
A disease targeted by the present invention may be any disease associated with a pathogenic gene. Examples of such a disease include, but are not limited to, cancer, Azoo~
infectious diseases due to viruses or bacteria, allergy, hypertension, hyperlipemia, diabetes, cardiac diseases, cerebral infarction, dementia, obesity, arteriosclerosis, infertility, mental and nervous diseases, cataract, progeria, hypersensitivity to ultraviolet radiation, and the like.
A disordex targeted by the present invention may be any disorder associated with a pathogenic gene.
Examples of such a disease, disorder or condition include, but are not lim~.ted to, circulatory diseases (anemia (e. g., aplastic anemia (particularly, severe apxastic anemia), renal. anemia, cancerous anemia, secondary anemia, refractory anemia, etc.), cancer or tumors (e. g., leukemia, multiple mye~.oma), etc.);
neurological diseases (dementia, cerebral stroke and sequela thereof, cerebral tumor, spinal injury, etc.);
immunological diseases (T-cell deficiency syndrome, leukemia, etc.); motor organ and the skeletal system diseases (fracture, osteoporosis, luxation of joints, subluxation, sprain, ~.igament injury, osteaarthritis, osteosarcoma, Ewing's sarcoma, osteogenesis imperfecta, osteochondradysplasia, etc.); derznatologic diseases (atrichis,, melanoma, curia malignant lympoma, hemangiosarcoma, histiocytosis, hydroa, pustulosis, dermatitis, eczema, etc.); endocrinologic diseases (hypothalamus/hypophysis diseases, thyroid gland dzseases, accessory thyroid gland (parathyroid) diseases, adrenal cortex/medulla diseases, saccharometabolism abnormality, ~. 4 B
lipid metabolism abnormality, protein metabolism abnormality, nucleic acid metabolism abnormality, inherent metabolic disorders (phenylketonurea, galactosemia, homoeystinuria, maple syrup urine disease), analbuminemia, Jack of ascorbic acid synthetic ability, hyperbilirubinemea, hyperbilirubinuxea, kallikrein defic~.ency, mast cell deficiency, d~.abetes insipidus, vasopressin secretion abnormality, dwarfism, Wolman's disease (acid lipase deficiency, mucopolysaccharidosis VT, etc.); respiratory diseases (pulmonary diseases (e. g., pneumonia, lung cancer, etc.), bronchial diseases, lung cancer, bronchial cancer, etc.); alimentary diseases (esophageal diseases (e. g., esophageal cancer, etc.), stomach/duodenum diseases (e. g., stomach cancer, duodenum cancer, etc.), small intestine 16 diseases/large intestine diseases (e.g., polyps of the colon, colon cancer, rectal cancer, etc.), bile duct diseases, liver diseases (e. g., liver cirrhosis, hepatitis (A, B, C, D, E, etc. ) , fulmiriant hepatitis, chronic hepatitis, primary lever cancer, alcoholic liver disorders, drug induced liver disorders, etc.), pancreatic diseases (acute pancreatetis, chronic pancreatitis, pancreas cancer, cystic pancreas diseases, etc.), peritoneum/abdominal wall/diaphragm diseases (hernia, etc.), Hirschsprung's disease, etc.); urinary diseases (kidney diseases (e. g., renal failure, primary glomerulus diseases, renovascular disorders, tubular function abnormality, interstitial kidney diseases, kidney disorders due to systemic diseases, kidney cancer, etc.), bladder diseases (e. g., cystitis, bladder cancer, etc. ) ; genital diseases (male genital. organ diseases (e. g., male sterility, pxostatomegaly, prostate Azoo~
Cancer, testicular cancer, etc.), female genital organ diseases (e. g., female sterility, ovaxy function disorders, hysteromyama, adenomyosis uteri, uterine cancer, endometriosis, ovarian cancer, villosity diseases, etc.), etc); aixculatory diseases (heart failure, angina pectoris, myocardial infarct, arrhythmia, valvulitis, cardiac musc~.e/pericardium diseases, congenital heart diseases (e. g., atrial aeptal defect, arteria3. canal patency, tetralogy of Fallot, etc.), artery diseases (e. g., arteriosclerosis, aneurysm), vein diseases (e. g., phlebeurysm, etc.), lymphoduct diseases (e. g., lymphedema, etc.), etc.): and the like.
As used herein, the term "cancer" refers to a malignant tumor which has a high level of atypism, grows faster than normal cells, tends to disruptively invade surrounding tissue or metastasize to new body sites or a condition characterized by the presence of such a malignant tumor. In the present invention, Cancer includes, without limitation, solid cancer and hematological cancer.
As used herein, the term "solid cancer" refers to a cancer having a solid shape in contrast to hematological cancer, such as leukemia and the like. Examples of such a solid cancer include, but are not limited to, breast cancer, liver cancer, stomach cancer, lung cancer, head and neck cancer, uterocervical cancer, prostate cancer, retinoblastama, malignant lymphoma, esophagus cancer, brain tumor, asteoncus, and the like.
~. 5 0 As used herein, the term "cancer therapy"
encompasses administration of an anticancer agent (e. g., a chemotherapeutic agent, radiation therapy, etc.) or surgical therapy, such as surgical excision and the l~.ke.
Chemotherapeutic agents used herein are well known in the art and are described in, for example, Shigeru Tsukagoshi et al. editors, "Kogan zai Manuaru [Manual of Anticancer agents)", 2nd ed., ChugaiIgaku sha;
ZO Pharmacology; and Lippincott Tnlilliams & Wil.kins, Tnc.
Examples of such chemotherapeuti.c agents are described below: 1) alkylating agents which alkylate cell components, such as DNA, protein, and the like, to produce cytotoxicity (e. g., cyclophosphamide, busulfan, thiotepa, dacarbazine, etc.); 2) antimetabolites which main~.y inhibit synthesis of nucleic acids (e. g., antifolics (methotrexate, etc.), antipurines (6-mercaptopurine, etc.), antipyrimidines (~luorourasil (5-FU), etc.); 3) DNA topdisomerase inhibitors (e. g., camptothecin and etoposide, each of which inhibits topoisomerases I and II)): 4) tubulin agents which inhibit formation of microtubules arid suppress ce7.l division (vinblastine, vincristine, etc.); 5) platinum dompounds which bind to DNA and proteins to exhibit cytotoxicity (cisplatin, carboplatin, etc.); 6) anticancer antibiotics which bind to DNA to inhibit synthesis of DNA
and RNA (adriamycin, dactinomycin, mitomycin C, bleomycin, etc.); 7) hormone agents which are s.pplicable to hormone-dependent cancer, such as breast cancer, uterus cancer, prostate cancer, and the like (e. g., tamox~.fen, 3Q leuprorelin (LH-RH), etc.); 8) biological formulations Azoa~
(asparaginase effective for asparagine requiring blood malignant tumor, interferon exhibiting direct antitumor action and indirect action by immunopotentiation, etc.);
9) immunostimulants which exhibit cap~bil~.ty of immune response, indirectly leading to antitumox activity (e. g., rentinan which is a polysaccharide derived from shiitake mushroom, bestatin which is a peptide derived from a microorganism, etc.)..
~.0 An "anticancer agent" used herein selectively suppresses the growth of cancerous (tumor) cells, and includes both pharmaceutical agents and radiation therapy.
Such an anticancer agent is well known in the art and described in, for example, Shigeru Tsukagoshi et al. editors, J.S "Kogan zai Manuaru [Manual of Anticancer agents] ", 2nd ed. , ChugaiIgaku sha; Pharmacology: and T~ippincott Williams &
Wilkins, Inc.
As used herein, the term "radiation therapy"
20 refers to a therapy for diseases using ionizing radiation or radioactive substances. Representative examples of radiation therapy include, but axe not limited to, X-ray therapy, y-ray therapy, electrpz~ beam therapy, proton beam therapy, heavy particle beam therapy, neutron capture 25 therapy, and the like. For example, heavy particle beam therapy ~.s preferable. However, hea~ry particle beam therapy requires a large-size device and is not generally used. The above-described radiation therapies are well known in the art and are described in, for example, Sho Kei 30 Zen, "Hoshasenkensa to Chiryo no Kiso: Hoshasen Chiryo to 1a2 A~oo~
Shugakuteki Chi.~ryo CBasics of Radiation Examination and Therapies: Radiation Therapy and Incentive Therapy?", (Shiga Medical School, Radiation): Total digestive system care, Vol. 6, No. 6, gages 79-89, 6-7 (2p02.02). For drug resistance to be identified in the present invention, chemotherapies are typically considered. However, resistance to radiation therapy is also associated with time-lapse profiles. Therefore, radiation therapy is herein encompassed by the concept of pharmaceutical agents.
x0 As used herein, the term "pharmaceutically acceptable carrier" refers to a material for use in production of a medicament, an animal drug or an agricultural chemical, which does not have an adverse effect cn an effective component. Examples of such a pharmaceutically acceptable carrier include, but are not limited to, antioxidants, presexwatives, colorants, flavoring agents, diluents, Emulsifiers, suspending agents, solvents, fillers, bulking agents, buffers, delivery ~rehicles, excipients, agricultural or pharmaceutical ad~uvants, and the like.
The type and amount of a pharmaceutical agent used in a treatment method of the present invention can be easily determined by those skilled in the art based on information obtained by a method of the pzesent invention (e. g . , information about the level of drug resistance, etc. ) and with reference to the puxpose of use, a target disease {type, sevexity, and the like) , the patient's age, weight, sex, and case h~.story, the form or type of the cell, and AI~07 the like. The frequency of the treatment method of the present invention applied to a subject (or patient) is also determined by those skilled in the art with respect to the purpose of use, target disease (type, severity, and the like) , the patient s age, weight, sex, and ease history, the progression of the therapy, and the like. Examples of the frequency include once per day to several months (e. g. , once per week to once per month) . Preferably, administration is performed once per week to once per month with reference to the progression of the therapy.
As used herein, the term "instructions" refers to a description of a tailor made therapy of the present invention for a person who performs administration, such as a medical doctor, a patient, or the like. Instructions state when to administer a medicament of the present invention, such as immediately after or before radiation therapy (e. g. , within 24 hours, etc. ) . The instructions are prepared in accordance with a format defined by an authority 2Q of a country in which the present inventiar~ is practiced (e. g., Health, Labor and Welfare Ministry in Japan, Food and Drug Administration (FDA) in the U.B., and the like), explicitly describing that the instructions are approved by the authority. The instructions are so-cal~.ed package insert and are typically provided in paper media. The instructions are not so limited and may be provided in the form of electronic media (e. g. , web sites, electronic mails, and the like provided on the Internet), In a therapy of the present invention, two or ~. 5 4 more pharmaceutical agents may be used as required.. When two or more pharmaceutical agents are used, these agents may have similar properties or may be derived from similar origins, or alternatively, may have different praperties or may be derived from different origins. A method of the present invention. can be used to obtain infarm~.ti.oz~ about the drug resistance level of a method of administering two Qr more pharmaceutical agents.
J.0 Also, in the present invention, ger~e therapy can be performed based an the resultant information about drug resistance. As used herein, the term "gene therapy" ref$ra to a therapy in Which a nucleic acid, which has been expressed or can be expressed, is administered inta a subj ect . In such an embodiment of the present invention, a protein encoded by a nucleic acid is produced to mec~i.ate a therapeutic effect.
rn the present invention, it will be understood by those skilled in the art that if the result of analysis of a certain specific time-lapse profile is correlated with a state of a cell in a similar organism (e. g., mouse with respect to human, etc.}, the result of an analysis of a corresponding time-lapse profile can be correlated with a state of a cell. This feature a,s supported by, for example, Dobutsu Baiyo Saibo Manuaru [An;imal Culture Cell Manual], Seno, ed., Kyoritsu Shuppan, 1993, which is herein incorporated by reference.
The present invention may be applied to gene therapies . As used herein, the term "gene therapy" refers to a therapy in which a nucl~:ic acid, which has been expressed or can be expressed, is administered into a subject. In such an embodiment of the present irivent~ion, a protein encoded by a nucleic acid is produced to mediate 2~ therapeutic effect.
Az~,y methods for gene therapy available in the art may be used in accordance with the present invention.
Illustrative methods will be described below.
Methods ~ox gene therapy are generally reviewed in, for example, Goldspiel et al., Clinical Pharmacy 12:
488-505(1993); Wu and Wu, Biotherapy 3: 87-95(1991)1 Tolstoshev, Ann. Rev. Pharmacol. Toxicol., 32:
573-596(1993): Mulligan, Science 260: 926-~932(1993)~
Morgan and Anderson, Ann. Rev. Biochem., 62: 191-217 (1993) and May, TIBTECH 11(5}: 1S5-215(1993). Commonly known recombinant DNA techniques used in gene therapy are described in, for example, Ausubel et al. (ed.), Current Protocols in Molecular Biology, ,john Wiley & Sons, NY (1993) and Kriegler, Gene Transfer and E~tpression, A haboratory Manual, Stoekton Press, NY (1990}.
(Basic techniques) Techniques used herein are within the technical scope of the present invention unless otherwise specified.
These techniques are commonly used in the f~.elds of fluidics, micromachining, organic chemistry, biochemistry, genetic engineering, molecular biology, microbiology, genetics, AI~~7 and the~.x xelevant fie~:ds. The techniques are well described in documents described below arid the documents mentioned herein else~rhere.
Mierofabrication is described in, for example, Campbell, S.A. (1996), "The Science and Engineering of Microelectronic Fabrication", Oxford University Press;
Zaut, P.V. (1996), "Micromicroarray Fabxzcation: a Practical Cuide to Semiconductor Processing", Semiconductor Services; Madau, M_J. (1997), " Fundamentals of Microfabrication", CRC1 5 Press; Ra.~-Choudhury, P.
(1997), "Handbook of Microlithography, Micromachining, &
Microfabricatian: Miorolithography". Relevant portions (or possibly the entirety) of each of these publications are herein incorporated by reference.
Molecular biology techniques, bioahemistxy techniques, and microbiology techniques used herein are well known and commonly used in the art, and are described in, for example, SambrQak J. et al. (1989), "Molecular Cloning: A Laboratory Manual", Cold Spring Harbor and its 3xd Bd. (2001): Ausubel, F.M. (1987), "Current Protocols ire Molecular Hiology", Greens Pub. Associates and Wiley-Interscience; Ausubel, F.M_ (1989), "8hort fxotocols in Molecular Biology: A Compendium of Methods from Current Protocols in Molecular Biology", Greens Pub. Associates and Wiley-Interscience; znnis, M.A. (1990), "PCR Protocols:
A Guide to Methods and Applications", Academic Press;
Ausubel, F.M. 0992), "Short Protocols in Molecular Biology: A Compendium of Methods from Current Protocols in Molecular Hic~lagy", Gxeene Pub. Associates: Ausubel, F.M.
( 1995 ) , "Short Protocols ~.n Molecular 'Biology: A
Compendium of Methods from Current Protocols in Molecular Biology", Greene Pub. Associates: Innis, M.A. et al. (1995) , "PCR Strategies", Academic Press; Ausubel, F.M. (1999), "Short Protocols in Molecular Biology: A Compendium of Methods from Current Protocols in MoleGUlar Hiology", TnTzley, and annual. updates; Sninsky, J.J. et al. (1999}, "PCR
Applications. Protocols for Functional Genomics", Academic Press; Speoial issue, Jikken Igaku [Experimental Medicine] "Idenshi Donyu & Hatsugenkaiseki Jikkenho [Experimental Method for Gene introduction & Expression Analysis]", Yodo-sha, 1997; and the like. Relevant portions (ox possibly the entirety) of each of these publications are herein incorporated by reference.
DNA synthesis techniques and nucleic acid chemistry for producing artificially synthesized genes are described in, for examp~,e, Gait, M.J. (1985), "Oligonucleotide Synthesis: A Practical Approach", IRL
Press; Gait, M.J. (7.990), "Oligonucleotide Synthesis: A
Practical Approach", IRL Press; Eckstein, F_ (1991}, "pl~,gonucleotides and Analogues: A Practical Approach", IRL
Press: Adams, R. Z. et al . ( 1992 ) , "The H~.oohemistry of the Nucleic Acids", Chapman & Hall: Shabarova, Z. et al. (Z994) r "Advanced Organic Chemistry of Nucleic Acids", Weinheim;
Blackburn, G.M. et a~.. ( 1996 ) , "Nucleic Acids in Chemistry and Biology", oxford University Press; Hermanson, G.T.
(I996), "BioCon~ugate Techniques", Academic Press; and the 3p like. Relevant portions (or possibly the entixety) of each of these publications are herein incorporated by reference.
(Analysis of co-regulation of gezles ) Mathematical processes used herein can be performed by using well-known techniques described in, for example, Kazuyuki Shimizu, "Seimei Sisutemu Kaiseki notameno Sugaku [Mathematics ~ox Analyzing $iologiaal Syatems~", Corona sha, 1999; and the like. Among these techniques, representative analysis techniques will be described below.
in one embodiment, such a mathematioaJ. process may be regression analysis. ,Examples of regression analysis ~.nclude, but are not limited to, linear regression (e. g., simple regression analysis, multiple regression analysis, robust estimation, etc.), nonlinear estimation, and the like.
In simple regression analysis, n sets of data (x1. Yi) to (xn. Ya? are fitted to yi=axi+b+e~, (i=1, 2, ..., n) where a and b are model parameters, and e1 represents a deviation or an error from the straight line. The parameters a and b are typically determined so that the mean of a sum of squares of the distance between a data point and the straight line is minimal. Zn this case, the rms of the distance is partially differentiated to produce simultaneous linear equations. These equations are solved for a and b which minimize the square errors. Such values are called least square estimates.
Azoo7 Next, a regression line is calculated based on the value obtained by subtracting the mean of all data values from each data value. A regression line represented by:
AE~Xi + $ = EYi is assumed. Further, it is assumed that 8 =d. The mean (xave~
yane) of (x~.. Yi) (i=1, 2, ..., n) is calculated, and the variance of x (sxx) and the covariance of x and y (sxy) are calculated.
The above-described regression line can be represented by:
Y - gave - (sxy/s~) (x - rave) ~
The correlation coefficient rXy is represented by:
rxy = 8xy/~ ( SxysYY~ .
zn thzs case, the relationship ~ei2/n = syy(1 -rxy2) is satisfied. Therefore, as ~ rxy ~ approaches 1, the error is decreased, which means that data can be satisfactorily represented by the r~gression line.
Tn another embodiment, multiple regression analysi9 is used. zz~ this technique, ~r is not a single independent variable, and is considered to be a function of two or more variables, e.g., is represented by:
= ao + alxl + a2x2 + ~ . . + anXrt.
This equation is called a mu~.tiple regression equation. ao and the lzke axe called (partial) regression coefficients. xn multiple regression analysis, a least square method is used and noxmal equations are solved to obtain least square estimates. Evaluatipn can be performed as with single regression analysts.
In another embodiment, robust estimation is used. The least square method is based on the premise that measurement values are not biased and measurement errors have a normal distributions and models have no approximation error. In actual situations, however, there may be errors in measurement. Zn robust estimation, unreliable data is detected and separated as outliers from the great majority of data which are reliable, or is subjected to a statistical pxocess. Such a robust estimation may be utilized herein.
Nonl.~near estimation may also be used herein.
With nonlinear estimation, it is possible to represent a nonlinear model as vector equations which are in turn solved.
Other mathematical processes used herein include principal component analysis, which utilizes two--dimensional data principal component analysis, multi~-dimensional data principal component analysis, singular value decomposition, and generalized inverse matrix. Alternatively, canonical correlation analysis, factor analysis, discrimination analysis, cluster ane~lysis, and the like may be used herein.
(Gene set classification by cluster analysis) for a number of applications, it may be desirable to obtain a set of reference transcription control sequences which axe cooperatively controlled under a wide range of conditions. An embodiment of identifying such a set of reference transcription control sequences is, for example, a clustering algorithm, wrhich is reviewed in, for example, Fukunaga, 1990, "Statistical Pattern ReCOgriition", 2nd ed., Academic Press, San Diego: Anderberg, 1973, "Cluster Analysis for Applications", Academic Press: New York; Everitt, 1974, "Cluster Analysis", London: Heinemann Educ. Books; Hartigan, 1975, "Clustering Algorithms", New York: WilEy; and Sneath and Sokal, 1973, "Numerical Taxonomy", Freeman, A set of transcription control sequences can also be defined based on a transcription control mechanism.
Transcription control sequences having a transcription factor binding site for the same or similar sequences in a regulatory region are likely to be cooperatively regulated.
In a certain embodiment, the regulatory regions of transcription control sequences of interest are compared with dne another using multiple alignment analysis, so that a possible common transcription factor binding site can be determzr~ed (Stormo and Hartzell, 19$9, "Identifying prote~.n binding sites from unaligned DNA fragments", Proc. Natl.
Acad. Sci., 86: 17.$3--1187: Hertz and Stormo, 1995, "Identification of consensus patterns in unaligned DNA and protein sequences : a large--deviation statistical basis for penalizing gaps", Proc. of 3rd Int.l . Conf . on Bioinformatics and Genome Research, Lim and Cantor, ed. , World Scientific Publishing Co. , Ltd. S~.x~gapore, pp.201-216) .
It may be desirable to obtain a set of basic transcription control sequences which s.xe cooperatively regu~.ated under various conditions. With such a set, a method of the present invention can satisfactorily and efficiently carry out determination based an profiles, A
preferable embodiment for identifying such a set of basic transcription control sequences includes a clustering algorithm.
In an embodiment using cluster e~nalysis, the transcription levels of a number of transcription control sequences can be monitored while applying various stimuli to biological samples. A tab7.e of data contain~.ng measurements of the tzanscripta.on levels of transcription control sequences is used in cluster analysis. Tn order to obtain a set of basic transcription control sequences containing transcription control sequences which s~.multaneously vary under various conditions, typically at least two, preferably at least 3, more preferably at least 10, even more preferably more than S0, and most preferably more than 100 stimuli or conditions are used. Cluster analysis ~.s performed for a table of data having mxk dimensions where m is the total number of conditions or stimuli and k is the number of transcription control sequences to be measured.
A number of cluster~.ri,g algorithms are useful ~or clustering analysis. In clustering algorithms, differences or distances between samples are used to foxzri clusters. Zn a certain embodiment, a distance used is a Euclidean distal j~r'~).~ ~~~i-Y~~ ~~ al space:
~Gr r (1) where (x, y) represents a distance between gene X and gene Y (or any other cellular components X and X (e. g., transcription control sequences) ) ; Xi and Yi represent gene expression in response to l stimuli. Euclidean distances may be squared and then multiplied with weighting which are increased with an increase in the distance. Alternatively, a distance reference may be, for example, a distance between transcription co " ~ Y, or a Manhattan distance repress: ~~~ly~ ~ ~ ~~
J l (2) where Xi and Yi represent responses of transcription control 24 sequences or gene expression when l stimuli are applied.
Several other definitions of distance include Chebyshev distance, power distance, and mismatch rate. When dimensional data can be categorized without modifioat~.on, a mismatch rate defined as z (x, y) = (the number of X~,~Yi) /l may be used in a method of the present invention. Such a method is particularly useful in terms of cellular responses _ Another useful definition of distance is I=1-r where r is a correlation coefficient of response vectors X and Y, e.g., a normalized inner prpduct X~Y/IXIIYI. Specifically, an ~0 inner product X~Y is defined by:
Aroo~
X~~'~~,Xrx (3) .
filso, ~ X ~ _ (X~X) l~z and ~ Y ~ -- (Y-Y) lea .
Most preferably, a distance reference is suited to a biological problem in order to identify cellular components (e. g., transcription control sequences, etc.) which are simultaneously changed and/or simultaneously regulated. ~'~~ ~~~~~-~--~ ~ ~ ~ ° ~~-~ a ~mlarly preferred embodiment, ~'Y I=1-x having a correlation cc ~ ~ ted inner product _ 1 of genes X c ~ ' ~r 2 ~' ~ Vx uch a preferred embodiment, x j (4) where QicX~ and a~~Y~ represent standard errors in measurement of genes X and Y in experiment i.
The above-described normalized and weighted inner products (correlation coefficients) are constrained between values +~1 (two response vectors are completely correlated, i . a . , the two vectors are essentially the same) and -~. (two response vectors are not correlated or da not have the same orientation (i.e., opposing orientations)).
These correlation coefficients are particularly preferable in an embodiment of the pxesent invention which tries to detect a set or clustex of cellular components (e. g., transcription cantral sequences, etc.) having the same sign Or respOnBe.
In another embodiment, it is preferable to identify a set or cluster of cellular components (e. g., S transcription control sequences, etc.) which simultaneously regulate the same biological response or pathway or are involved in such regulation, or have similar or non-correlated rESponses. In such a embodiment, it is preferable to use the absolute value of either the above-described normalized or weighted inner product, i.e., girl as a correlation coefficient.
Tn still another embodiment, the relationship between cellular components (e. g., transcription control sequences, etc.), which are simultaneously regulated and/or simultaneously changed, are more complicated, e.g., a number of biozogical pathways (e. g., signal transduction pathways, etc.) are involved with the same cellular component (e. g., a transcription control sequence, etc.) so that different results may be obtained. In such an embodiment, it is preferable to use a correlation coefficient r=r~°h~'g~? which can identify cellular components (other transcription control sectuences as controls which are not invoa ~ y aneously changed and/or sin ~ ; Xi ;y~ A correlation coefficient t' ' f ~~~, is particularly useful for t iX
l (5) .
Various cluster linkage methods are useful in a method of the present invention.
Examples of~sueh a technique include a simple linkage method, a nearest neighbor method, and the like.
In these techniques, a d~.stance between the two closest samples is measured. Alternatively, in a complete linkage method, Which may be herein used, a maximum distance between two samples in different clusters za measured. This technique is particularly useful when genes or other cellular components naturally farm separate "clumps".
Alternatively, the mean of non-weighted pairs is used to define the mean distance of all sample pairs in xS two different clustexs. This technique is also useful in clustering genes or other cellular components which naturally form separate "clumps" . Finally, a weighted pair mean techz~~.que is also available. This technique is the same as a non-weighted pair mean technique, except that in the farmer, the size of each cluster is used as a weight.
This technique is particularly useful in an embodiment in which it is suspected that the size of a cluster of transcription control sequences or the like varies considerably (Sneath and Sokal, 1973, "Numerical taxonomy", San Francisco : W . H. Freeman & Co. ) . Other cluster l~.rrl~age methods, such as, for example, non-weighted and weighted pair group centroid and ~nTard's method, are also useful in several embodiments of the present invention. See, for example, Ward, 1953, J. Am. Stat. Assn., 58: 2361 and Hartigan, 1975, "Clustering algorithms", New York: Wiley.
In a certain preferred embodiment, cluster analysis can be performed using a well-known hclust technique (e. g., see a well-known procedure in "hclust"
available from Program S-Plus, MathSoft, Inc., Cambxxdge, MA ) .
According to the present invention, it was found that even if the versatility of stimuli to a clustering set is increased, a state of a cell can be substantially elucidated by analyzing typically at least two, preferably at least 3, profiles using a method of the present invention.
Stimulation conditions include treatment with a pharmaceutical agent in different concentxatidns, different measurement times after treatment, response to genetic mutations in various genes, a combination of tz~eatment 4f a pharmaceutical agent and mutation, and changes in growth conditions (temperature, density, calcium concentration, etc.).
As used herein, the term "significantly different" in relation to two statistics means that the two statistics are different from each other with a statistical significance. In an embodiment of the present invention, data of a set of experiments assessing the responses of cellular components can be randomized by a Monte Carlo method to define an objective test.
In a certain embodiment, an objective test can be defined by the following technique. pk~, represents a Azoo~
response of a component k in experiment i. II~~y represents a random permutation of the indices of experiments. Next, pxnti? is calculated for s number of different random permutation9 (about 100 to 1, 000) , For each branch of the original tree and each permutation:
(1) hierarchical clustering is performed using the same algorithm as that which has been used for the original data which is not permutated (in this ease, "hclust"); and (2) an imprcwement f in classification in total variance abo ' '' ' ' ' ' n transition is made from on ~_ l ~ ~,~xr~~ J~~~~~l (~>
where Dk is the square of the distance reference (mean) of component k with respect to the center of a o~-uster to which component k belongs. Superscript 1 or 2 ind~.cates the center of all branches or the center of the more preferable cluster of the two subclusters. The distance function D
used in this Clustering technique has a considerable degree of freedom. In these examples, D~~.--r, where r is a correlation coefficient of one response with respect to another response of a component appearing in a set of experiments (or of the mean cluster response).
Specifically, an obi ective statistical test can be preferably used to determine the statistical reliability of grouping an~r clustering methods or algorithms.
Preferably, similar tests can be appla-ed to both x69 Azao7 hierarchical and nonhiers.xchical clustering methods. The compactness of a cluster is quantitatively defined as, for example, the mean of squares of the distances of elements in the cluster from the "mean of the cluster", or mare preferably, the inverse o~ the mean of squares of the distances of elements from the mean of the cluster. The mean of a spec~.f~.c cluster is generally defined as the mean of response vectors of all elements in the c~.uster. However, in a specific embodiment (e.g., the de~i.nition of the mean of the cluster is doubtful) , for example, the absolute values of normalized or weighted inner products are used to evaluate the distance function of a clustering algorithm (1.e., I=1-~r~). Typically, the above-described definition of the mean may raise a problem in an embodiment in which response vectors have opposing directions so that the mean of the cluster as defined above is zero. Therefore, in such an embodiment, a different definition is preferably selected for the compactness of a cluster, far example, without limitation, the mean of squares of the distances of all pairs of elements in a cluster. Alternatively, the compactness of a cluster may be defined as the mean of distances between each element ( a . g . , a cellular component ) of a c7.uster and another element of the cluster (or more preferably the inverse of the mean distance).
Other definitions, which may be used in statistical techniques used in the present invention, are obvious to those skilled in the art.
rn another embodiment, a profile of the present invention can be analy2ed using signal processing techniques. In these signal processing techniques, a oorrelat.ion funatzon is defined, a correlation coefficient is calcuJ.ated, an autocorrelation function and a cross-correlation funot~.on; are defined, and these functions are weighted where the sum of the weights is equal to 1.
Thereby, moving averages can be obtained.
In signal processing, it a.s important to consider a time domain and a frequency domain. Rhythm often plays an important role in dynamic characteristic analysis for natural phenomena, part~.cularly life and organisms . If a certain time function f(t) satisfies the following condition, the function is called a periodic function:
f (t) - f (t~-T) .
At time 0, the function takes a value of f (0) .
The function takes a value o~ f(0) at time T again after taking various values after time 0. Such a function is called a periodic function. Such a function includes a sine wave. T is called a period. The function has one cycle per time T. Alterx~atzvely, this feature may be represented by 1/T which means the number of cycles per unit time (cycles/time) without loss of the informat~.on. The concept represented by the number of cycles per unit time is called frequency. If the frequency is represented by f, f is represented by:
f=1/T.
~z0o7 Thus, the frequency is an inverse of the time.
The 'time is dealt in a time domain, while the frequency is dealt in a frequency domain. The frequency may be represented in an electrical engineering manner. For example, the frequency is represented by angular measure where one pexiod corresponds to 360° or 2~ radians. zn this case, f (cycles/ sec) is converted to 2xf (radians/sec), which is generally represented by cu (=2~f) and is caZ~.ed angu~.ar frequency.
Now, a sine wave is compared with a cosine wave.
The cosine wave is obtained by translating the sine wave by 90° or.~/2 radians. The sine wave may be represented by the delayed cosine wave. This time delay is called phase.
For example, when a pure cosine wave has a phase of 0, a sine wave has a phase of 90°. When a sine wave is added tv a cosine wave, the amplitude of the resultant wave is increased by a factor of ~2 and the phase is ~/4.
Tn such analysis, fourier series and frequency analysis may be available. In addition, Fpux~.er transformation, discrete Fvurier transformation, and power spectrum may be s,vailable. In Fourier expansion, techniques, such as wavelet transformation and the like, may be available. These techniques are well known in the art and are described in, for example, Xukzo Shimizu, "Seimei Sisutemu Kaiseki notameno Sugaku [Mathematics for analyzing life systems]", Corpna sha, (1999); and Yasuhiro Ishikawa, "Rinsho Igaku notameno Ueburetto Kaiseki [Wavelet analysis for clinical medicine]", Igaku Shuppan.
(Description of preferred embod~.ments) Hereinafter, the present invention will be described by way of embodiments. The embodiments described below are provided only for illustrative purposes.
Accordingly, the scope of the present invention is not limited by the embodiments except as by the appended claims.
In one aspect, the present invention provides a method for representing a state of a cell. The method comprises the steps of: a) obtaining a time-lapse profile of the ce~.l by time-lapse monitoring of a gez'ie state (e.g., the expression of a gene (transcription, trans~.ation, etc. ) , etc. ) associated with at least one gene selected from genes derived from the cell: and b) presenting the time-lapse profile. For example, the profile of the intensity of a signal obtained by monitoring is aub~ected to interval different~.ation, thereby obtaining a function of changes which can be in turn displayed. In this case, preferably, for example a constitutive promoter or the lzke, which is assumed to be changed, can be used as a reference to obtain a difference, thereby obtaining a time-lapse profile. The present invention is not limited to this.
Time-lapse profiles may be displayed using any method, for example, they may be visually displayed using a display device (e.g., an x axis showing time while the y axis shows signal intensity), or alternatively, may be displayed as a table of numerical values. Alternatively, signal intensity may be displayed as optical intensity_ Furthermore, profiles may be presented by means of sound.
preferably, cells are fixed to a solid phase support (e.g., an array, a plate, a mi.crotiter plate, eto. ) when they are monitored. Such fixation can be carr~.ed out using techniques known in the art or teChrii.quea as described herein. Fixation or immobilization of a cell allows systematic investigation thereof.
Tn a preferred embodiment, such a time-lapse profile may be presented in real time. The real time presentation may contain a time lag to some extent if it is performed substantially in real time. A tolerable time lag is, for example, 10 seconds at maximum, and more preferably ~. second at maximum, though the tolerable time lag depends on the required level of real time (simultaneity).
Tn another aspect, the present invention provides a method for determining a state of a celJ.. Such determination of the cellular state is achieved by monitoring changes in a transcriptional state of a transcription control factor, which are not conventionally observed. Therefore, the method of the present invention for determining the cellular state allows determination of various states which cannot be conventionally observed.
Such a method comprises the steps of: a) obtaining a t~.me-lapse profile of the cell by time-lapse mon~.tox~.ng of a transcriptional state associated with at least one biological agent selected from. a biological agent group derived from the cell; and b) determining the state of the cell based on the time--lapse profile of the transcription level.
Preferably, cells are fixed to a solid phase support (e. g. , an array, a plate, a microtiter plate, etc. ) when they are monitored. Such fixation can be carried out using techniques known in the art or techniques as described herein.
In a preferred embodiment, advantageously, the cellular state determination method of the present invention may further comprise correlating the time-lapse profile with the state of the cell before obtaining the time-lapse profile. Alternatively, such correlation information may be provided fxom l~nown information. Such a correlating step may be performed at every determining step or correlation information may be stored in a database and used as required.
In a preferred embod~.ment, the transcription control sequence may be, without limitation, a promoter, an enhancer, a silencer, anothex flanking sequence of a structural gene in a genome, and a genomic sequence other than axons. A pxaznvter is preferable. This is because a transcription level can be directly measured, and the state of transcription directly reflects the state of a cell. Zn a particular embodiment, the transcription control sequences may include constitutive promoters, specific promoters, inducible promoters, and the like.
In certain embodiments, any promoter may be used. The present invention is characterised in that any type of promoter can be used. According to the method of the present invention, profiles can be analyzed from a viewpoint of "procession". Therefore, it is possible to determine a state of a cell using any promoter or any set of promoters.
Such determination cannot be achieved by conventional techniques. The present invention is highly useful since the present invention achieves what cannot be achieved by conventional techniques.
In a preferred embodiment, at least two biological agents (far example, transcriptional control sequence) are monitored. Hy observing at least two ba.o~.ogical agents, 80~ of the states of a cell can be typically identified. More preferably, at least 3 biological agents are monitored. By observing at least three biological agents, at least 90~ of the states of a cell can be typically identified. Tn a most preferred embodiment, at least 8 biological agents are monitored. Hy observing at least 8 biological agents, substantially all of the states of a cell can be typically identified. Thus, although any biological agents are selected, substantially all of the states of a cell can be determined by selecting and monitoring a small number of biological agents, as described above . This feature has not been cc~nventzonally expected. The method of the present invention is simpler, more precise and more accurate than conventional 1'7 6 AI~07 determination methods in which observation is made at time points and resultant data is statistically processed as heterologous groups.
Therefore, the determins.tion method of thr~
present invention preferably further comprises arbitrarily seJ.ecting at least one b~.ological agent from s biological agent group before monitaxlnc~. An important feature of the present invention is such that a biological agent, which does not exhibit specificity when intrestigated from poa.nt to point, oan be used. Further, the present invention allows accurate reflection of the resultant data to the state of a cell of interest, since data linearly measured data under a consistent environment can be used. Such accurate data cannot be obtained conventionally.
Zn a preferred embodiment, such a time-lapse profile obtained in the present intrention may be presented in real time_ Alternatively, in the present invention, data may be obtained in a real tune mariner. The real time presentation may contain a time lag to some extent if it is performed substantially in real time. A tolerable time lag is, fox example, 10 seconds at maximum, and more preferably 1 second at maximum, though the toXorable time lag depends on the rewired 7.e'v'el of real time (simultaneity) .
As used herein, the term "real time" means that the real time presentation may contain a time lag to some extent if it is performed substantially in real time. A tolerable time lag is, for example, 10 seconds at maximum, and more preferably 1 second at maximum, though the tolerable time lag depends on the required level of real time (simultaneity) .
For example, the level of real time may be preferably 30 seconds at maximum, or even longer in the case of, far example, therapies required for real time diagnosis.
In a particular preferable embodiment, states determined by the cellular state determination method of the present invention includes, for example, differentiated states, undifferentiated states, cellular responses to external factors, cell Cycles, growth states, and the like.
More speci.fi.cally, such a state includes, for example, without limitation, a response of a cancer cell to an anticancer agent, drug resistance, a response tc~ a biological clock, a differentiated state of a stem cell. (e. g. , a mesenchymal stem cell, a neural stem cell, etc.), an undifferentiated state of a purified stem cell (e.g., an embz~yonic stem cell, etc. ) , a change in cellular morphology, a state of cellul~.r migration, intracellular loca~.ization of a molecule, production of a secxeted substance, and the 20' like.
Therefore, in a preferred embodiment, a cell assessed by the cellular state determination method of the present invention includes, for example, without limitation, a stem ceJ.l ox a somatic cell, or a mixture thereof.
Alternatively, such a cell includes an adherent cell, a suspended cell, a tissue forming cell, and a mixtuxe thexeof .
Tn a preferred embodiment, the cellular state determination method of the present invention may be x78 A~~~7 pezfox-med upon a cell fixed on a substrate which is a solid phase support . In such a case, the solid phase support is called a chip. When cells axe arrayed on the substrate, the substrate is also called an array.
In a particularly preferred embodiment of the cellular state determination method of the present invention, advantageously, when a b~.o~.ogical agent (for example, a transcription control sequence) used for determination is a nucleic acid molecule, such a nucleic acid molecule may be operably linked to a reporter gene sequence and may be transfected into a cell. In this case, the transcription letrel of the transcription control sequence can be measured as a signal from the reporter gene.
Such transfection may be performed in the solid phase or in the liquid phase. For transfection, a techniquE
for increasing the efficiency of introduction of a target substance into a cell may be used. zn the present invention, a target substance (e. g., DNA, RNA, a polypeptide, a sugar Chain, or a composite substance thereof, etc. ) , which cannot be substantially introduced into cells under typical conditions, is presented (preferably, contacted) along with an actin-like substance, such as fibronectin, to a cell, thereby making it possible to efficiency introduce the target substance into cells. Therefore, the transfection method comprises the steps of: A) providing a target substance (i.e., DNA comprising a transcription control sequence) and B) providing an actin-like substance (e. g., fibronectin), wherein the order of steps of A) and B) is not particularly limitEd, and C) contacting the target substance and the actin-like substance with the cell. The target substance and the actin-like substance may be provided together or separately. The actin-like acting substance may be used as described in detail above for the composition of the present invention, for increasing the efficiency of introduction of a target substance into a cell.
Such a technique can be carried out as appropriate based on the present specification by those skilled in the art.
Therefore, the actin-like substance may be used in a manner which is described in detail above for the composition of the present invention for increasing the efficiency of introduction of a target substance into a cell _ Preferably, the actin-like acting substance may be an extracell.ular matrix protein (e. g., fibroneCtin, vitranectin, laminin, etc.. ) or a ~crariant thereof. More preferably, fibronectin or a variant or fragment thereof may be used.
Tn one embodiment, a transcription control sequence used in the present invention may be oapable of binding to a transcription factor. Examples of such a transcription factor include, but are not lim~.ted to, ISRE, RARE, STAT3, GAS, NFAT, MIC, Afl, SRE, GRE, CRE, NflCg, ERE, 2S TRE, E2F, ~tb, p53, and the like. These transcription factors are commercially available from BD Biosciences Clonetech, CA, USA. ISRE is related to STAT1/2_ RARE is related to retinoic acid. STAT3 is related to the Contxol of differentiation. GRE is related td the metabolism of sugar. CRE is related to cAMP. THE is related to thyroid hormone. E2F is related to cell cycle, p53 is related to G1 check point. Therefore, such information can be used to determine a state of a cell.
g In a preferred embodiment, the determination step of b) of the present invention comprises comparing the phases of the time-lapse profiles . Phases can be calculated by those skilled in the art using general techniques as described here~.n above and techniques described in the examples below.
In another preferred embodiment, the determination step of b) of the present invention comprises calculating a difference between the time-lapse profile of the cell and a control profile. The difference sari be calculated by those skilled in the art using general techniques as described herein above and techniques described in Examples below.
In another preferred embodiment, the determination step of b) of the present invention comprises a mathematical process selected from the group consisting of signal processing and multivariate analysis. Such a mathematical process can be easily carried out by those 2S skilled in the art based on the description of the present specification.
In another aspect, the present invention provides a method for correlating an external factor with 3d a cellular response to the external factor. The method AI 0 0'T
comprises the steps of: a) exposing a plurality of cells to an external factor on a support capable of retaining the cells in a consistent environment: b) monitoring a transcriptionax state relating to at least one of a transcriptional factor group present on or Within the cells over time to generate profile data for the Dells; and c) correlating the external factor with the profile.
Any external factor to be correlated in the present invention may. be used. Such an external factor is preferably directly or indirectly applicable to a cell. A
method for applying such an external factor is well known in the art, depending on the type of the external factor used. When a substance is used, the substance is dissolved into a solvent, and the resultant solution is added to a medium containing a cell.
"The correlation method of the present invention may utilize the production mEthod of profiles as described hereinabove.
A variety of methods can be provided for correlating a foreign agent and a pxofile in the method of correlation of the present invention, rn brief, profiles obtained when a foreign agent is applied to a cell, are patternized, and if there is little difference between the patternized profiles, it can be inferred that the particular foreign agent has been applied to the cells.
Preferably, a cell may be monitored in an 1,82 Azoo~
immobilized state t~o a solid support such as an array, a plate, a microtiterplate and the like. Such a method for immobilization can be conducted based an anx known methodology ~.n the art or the methods desardbed herein.
In a preferred embodiment, a correlation method of the present invention may further comprise using at least two external factors to obtain a profile for each external factor. In certain embodiments, at least three, or at least faun, mare preferably at least ten such foreign agents may be used but the present invention is not limited thereto.
Moxe preferably, the correlation step may fuxther compxise dividing at least two prof~.les into categories and c~.assify~.ng the external factoxs corresponding to the respective profiles into the categories. Such categorization may be readily conducted by those skilled in the art based on the description of the present specification. Such categorization or classification allows correlation and identification of an unknown foreign agent by means of the method of the present invention.
In a preferred embodiment, a transcription control sequence used in the present invention may be, without limitation, a promoter, an enhancer, a silencer, other flanking sequences of structural genes in geriomes, and genomic sequences other than axons. A promotex is preferable, s~.nce the transcr~.ption level. can ~e directly measuxed.
In a particular embodiment, transcription control sequences used in the present inver~tion may be constitutive promoters, specific promoters, inducible promoters, and the like. The present invention is characterized in that any type of promoter can be used.
According to the method of the present invent~.on, pxof~.~.es can be analyzed from a viewpoint of "process" ar "procession" .
Therefore, ~.t is possible to determine a state of a ce~.Z
using any promoter or any set of promoters. Such determination cannot be achieved by conventional techniques.
The present invention is highly useful since the present invention achieves what cannot be achieved by conventional.
techniques.
In 'a preferred embodiment, at least two transcription control sequences are monitored. By observing at least two transcription control sequences, at least B0~ of the states of a cell can be typically identified.
Moxe preferably, at least 3 transcription control sEquences are monitored. Hy observing at least three transcription control sequencES, at least 90~ of the states v~ a Cell Gan be typically identified. In a most preferred embodiment, at least 8 transcription control sequences are monitored.
By observing at least 8 transcription control sequences, substantially all of the states of a cell can be typically identified. Thus, although any transcription control sequences are selected, substantially all of the states of a cell can be determined by selecting and monitvrzng s small number of transcription control sequences as described 18 ~1 above. This feature has not been conventionally expected.
The method of the present invention is simpler, more precise and more accurate than conventional determination methods in which observation is made at time points and resultant data is statistically processed as hetero~ogous groups.
Therefore, the determination method of the present invention preferably further comprises arbitrarily selecting at least one transcription control sequence from a group of transcription control sequences before monitoring. An important feature of the present invention is such that a transcription control sequence, Which does not exhibit specificity when investigated from point to point, can be used.
In a preferred embodiment, such a time-lapse profi~.e may be presented in reaz time. The zeal time presentation may contain a time lag to some extent if it is performed substantia~.ly in real time. A tolerable time lag. is, for example, 14 seconds at maximum, and more preferably ~. second at maximum, though the tolErable time lag depends on the required level of real time (simultaneity) .
For example, in the case of environment measurement requiring zeal time idez7aification of external factors, the tolerable time lag may be, for example, 1 sec at maximum, 0.1 sec at maximum, or the like. Alternatively, after data is stored on a storage medium at real time, profiles may be pz~esented corresponding to the data based on the stored data, with some time lag.
In a preferred embodiment, in the correlation step of c) cf the present invention, the phase of the time-lapse pr4file may be used as information about the time-lapse pxofile in order to correlate the external factor with the time-lapse profile. The phase is represented by plus or minus depending an the signal intensity at a certain time. Even using such a simplified method, a cell or an external factor can be identified, thus demonstrating the precision cf the method of the present invention.
to Preferably, in the method of the pxesent invention, cells are advantageously cultured on an array.
This is because a number of cells can be simultaneously observed. Preferably, when a cell is immobilized on a solid support such as an array, a salt may be us~d.
In a preferred embodiment, the step of monitoring the transcription level over time may comprise obtaining image data from the array. This is because image data can be subjected to visual inspection and a human (particularly, a person skilled in the art, such as a medical practitioner or the like) can easi~.y examine image data with his/her eyes.
In a preferred embodiment of the present invention, the step of correlating the external factor with the time-lapse prof~.J.e may comprise distinguishing the phases of the time-lapse pxofiles. As described above, phase is a simple parameter, and its information processing is simple. Thus, cells can be well a. denti.fied by such simple AI 0 0'7 information processing.
In a preferred embodiment, examples of an extexnal factor to be identified by the method of the present invention include, but are nvt limited to, a temperature change, a humidity change, an electromagnetic wave, a potential difference, visible light, infrared light, ultraviolet light, X-ray, a chemical substance, a pressure, a gravity change, a gas partial pressure, an osmotic pressure, and the like. These factors cannot be satisfactorily identified by conventional methods. By using the cell determination method of the present invention which places an importance on "procession", an influence of a factor on a cell Can be well examined.
In a particularly preferred embodiment, an external factor to be identified by the method of the pxeserlt invention may be a chemical substance. Bxamples of such a chemical substance include, but are not limited to, biological molecules, chemical compound, media, and the like.
Examples of biological molecules znc~.ude, lout are not limited to, nucleic acids, proteins, lipids, sugars, proteolipids, lipoproteins, glycoproteins, proteoglycans, and the like. These biological molecules are known to have an influence on oz~ganisms. Unknown biological molecules are also highly likely to have an influence on organisms and are considered to be important targets for Study.
3~
Particularly preferably, hormones, cytakine, cell adhesion factors, extracellular matrices, receptor agonists, receptor antagonists, and the like, which are expected to have an influence on cells, are used as biological molecules to be investigated.
In another aspect, the present invention provides a method for inferring an unidentified external factor given to a cell based on a time-lapse profile of the cell. The method comprises the steps of: a) exposing the cell to a plurality of known external factors; b) obtaining a time-lapse profile of the cell for each known external factor by time-lapse monitoring of a transcription level associated with at least one bivlogica~. agent selected from the group consisting of biological agents derived from the cell.: c) correlating the known external factors with the respective time-lapse profiles; d) exposing the cell to the unidentified external factor; e) obtaining a time-lapse profile of the unidentified external factor by time--lapse monitoring of the transcription level of the selected biological. agent; f) determining a profile corresponding to the time-lapse profile obtained in the step of e) from the time-lapse pro~iXes obtained in the step of b); and g) determining that the unidentified external factor is the known external factor corresponding to the profile determined in the step of f).
In the method of the present invention, the step of exposing a cell to external factors can be performed as described above herein or as illustrated in the examples described below. The step of obtaining a time-lapse profile can be performed as described above herein or as illustrated in the examples described below. The correlation step can be performed as described above herein or as illustrated in the examples described below. After information about all known external factors has been obtained, an unidentified external factor issimilarly monitored. These pieces of information are compared to determine whether or not the unidentified external factor is a known one. If the profile of an unidentified fs.ctor fully matches the profile of a known factor, these two factors can be determined as being identical. Also, if the profile of an unidentified factor substantially matches the profile of a known factor, these two factors can be determined to be identical. Such determination depends on the information quantity and quality of the known external factor. Such determination can be easily carried out by those skilled in the art considering various elements.
Tn another aspect, the present invention provides a method for inferring an unidentified external factor given to a cell based on a time-lapse profile of the cell. The method comprises: a) providing data relating to a correlation relationship between known external factors ,and time-lapse profiles of the cell in response to the known external factors, in relation to at least one promoter selected from promoters present in the sell; b) exposing the cell to the unidentified external factor: c) obtaining a time-lapse profile of the cell by time--lapse monitoring of a transcription level associated with the selected I$9 promoter; d) determining a profile corresponding to the time-lapse profile obtained in the step of c) from the time-lapse profiles obtained in the step of a); and e) determining that the unidentified external factor is the known external factor corresponding to the profile determined in the step of d).
Exposure to external factors, profi.Ze generation, correlation, and the like can be carried out using techniques as described herein above or as illustrated in the examples below.
Zn another aspect, the present ~.rivention provides a system for presenting a state of a cell. The system comprises: a) means for obtaining a time-lapse profile of the cell by time-~Zapse monitoring of a transcription level associated with at least one transcription control sequence selected from the group consisting of transcription control sequences derived trom the call: and b) means for presenting the time-lapse profile.
An exemplary system canfigura'tion is presented in figure 32.
A configuration of a computer or system for implementing the cellular state presenting method of the present invention is shown in Figure 17, figure 17 shows an exemplary configuration of a computer 500 for executing the ce~.lular state presenting method of the pre&ent invention. An exemplary system configuration is presented in Figure 32, The computer 500 comprises an input section 501, a CPU 502, an output section 503, a memory 509, and a bus 505.
The input section 501, the CPU 502, the output section 503, and the memory 509 are connected via a bus 505 _ The input section 501 and the output section 503 axe connected to an I/O device 506_ An outline of a process for presenting a state of a cell, which is executed by the computer 500, will be described below_ A program for executing the cellular State presenting method (hereinafter referred to as a "cellular state presenting program") is stored in, for example, the memory 502. Alternatively, each component of the cellular state presenting program may be stored in any type of recording medium, such as a floppy disk, MO, CD-ROM, CD-R, DVD-ROM, or the like separately or together. Alternatively, the program may be stored in an application server. The cellular state presenting program stored in such a recording medium is loaded via the I /O device 506 ( a . g _ , a disk drive, a network (e.g., the Tnternet)) to the memory 504 of the computer 500. The CPU 502 executes the cellular state presenting program, so that the computer 500 functions as a device for performing the cellular state presenting method of the present irivezntion.
Information about a cell or the like is znput via the input section 501 as we~.l as profile data obtained.
Known information may be input as appropriate.
The CPU 502 generates display data based on the information about profile data and cells through the input section 50i, and stored the display data into the memory 504.
Thereafter, the CPU 502 may store the information in the memory 504. Thereafter, the output section 503 outputs a cellular state selected by the CPU 502 as display data. The output data is output through the I/O device 506.
In another aspect, the present. invention provides a system for determining a state of a cell. The system comprisES: a) means for obtaining a time-lapse profile of the cell by time-lapse monitoring of a transcription level associated with at least one biological agent se,~ected from the group consisting of biological agents derived fxom the Cell; and b) means for determining the state of the cell based on the time-.apse profi~.e. An exemplary system configuration is presented in Figure 3Z.
A configuration of a computer or system for implementing the cellular state determining method of the present invention is shown in Figure 17. Figure 17 shows an exemp~.a,x~y configuration of a computer 500 for executing the cellular state determining method of the present invention. An exemplary system configuration is presented in Figure 32.
The computer 500 comprises an input section 501, 3p a CPU 502, an output section 503, a memory 504, and a bus 505.
The input section 501, the CPU 502, the output section 503, and the memory 504 are connected via a bus 505. The input section 50l arid the output section 503 are connected to an I/0 device 506.
An outline of a process for determining a state of a cell, which is executed by the computer 500, will be described below.
A program for executing the cellular state determining method (hereinafter referred to as a "cellular state determining program") is stored in, for example, the memory 50Z . Alternati~srely, each component of the cellular state determining program may be stored in any type of recording medium, such as a floppy disk, M0, CD-RpM, CD-R, DVD-ROM, or the like, separately or t4gether.
Alternatively, the program may be stored in an application server. The cellular state determining program stored in such a recording medium is loaded via the T/O device 506 (e, g. , a disk drive, a network (e. g. , the Internet) ) to the memory 50~4 of the computer 500. The CPU 502 executes the cellular state presenting program, so that the computer 500 functions as a device fvr performing the celluJ,ax state determining method of the present invention.
Information about a cell or the like is input via the input sectzon 501, as well as profzle data obtained.
Known information may be input as appropriate.
The CPU 502 determxz~es a state of a cell based on the information about profile data and cells input through the input section 501, generates the results as determination result data, and stores the determination result data in the memory 504. Thereafter, the CPU 502 may store the information in the memory 5G4. Thereafter, the output section 503 outputs a cellular state seleoted by the CPU 502 as detez~ni,nation result data. The output data is output through the I/O devise 506.
Tn another aspect, the present invention provides a system for correlating an external factor with a response of a cell to the external factor. 'Ihe system comprises: a) means for exposing the cell to the external factor; b) means for obtaining a time-lapse profile of the cell by time-lapse monitoring of a transcription level associated with at least one promoter selected from the group consisting of promoters derived from the cell; and c) means for correlating the external factor with the time--lapse profile. Such a system can be implemented using a computer as with the above-described systems. An exemplary system configuration is presented in Figure 32.
In another aspect, the present invention provides a system for inferring an unidentified external factor given to a cell based on a time-lapse profile. The system comprising: a) means for exposing the cell to a plurality of known external factors; b) means for obtaining a time-lapse profile of the cell for each known external factor. by time-lapse monitoring of a transcription level associated with at least one biological agent selected from the group consisting of biological agents deri~red from the cell; c) means for correlating the known external factors with the respective time-lapse profiles; d) means for exposing the cell to the un~.dentif~.ed external factor;
e) means for obtaining a timg--lapse profile of the unidentified external factor by time-lapse manztvr~.ng of the transcription level of the selected transcription control sequence: f) means for determining a profile corresponding to the time-lapse profile obtained in the 7.a means of e) from the time-lapse profiles obtained in the means of b); and g) means for determining that the unidentified external. factor is the known external factor corresponding to the profile determined in the means of f ) .
Such a system can be ~.mpl.emented using a computer as with the above-described systems. An exemplary system configuration is presented in figure 32.
In another aspect, the present invention provides a system for inferr~.ng an unidentified external factor given to a cell based on a time-lapse profile, comprising: a) means for providing data relating to a correlation relationship between known external factors and time-lapse profiles of the cell in response to the known exte~cns~l factors, in relation to at least one biological agent selected from biological agents present in the cell;
b) means for exposing the ce~.l. to the unidentified external factor; c) means for obtaining a time-lapse profile of the cell by time-lapse monitoring of a transcription level associated with the selected transcription cantxoJ.
30. sequence; d) means for determining a profile corresponding to the time-lapse profi~:e obtained in the means of c) from the time-lapse profiles obtained in the means of a); and e) determining that the unidentified external ~aGtar is the known external factor corresponding to the profile determined ~.n the means of d) . Such a s~sstem can be implemented using a computer as with the above-dascribad systems. An exemplary system configuration is presented in Figure 3Z.
When the present invention is prpvided in the form of a system as described above, each constituent elem~nt thereof can be implemented as with the detailed or preferred embodiments of the method 4f the present invention.
Preferred embodiments of such a system can be easily selected by those skilled in the art and can be made or carried vut by those skilled in the az~t based on the present specification. An exemplary system configuration is presented in Figure 32.
In another aspect, the present in~rention provides a computer recordable recording medium recording a program for executing a process for presenting a state of a cell to a computer. The recording medium records at least a program far executing the procedures vf:
a) obtaining a time-lapse profile of the cell by time-lapse monitoring of a txa~nsoription level associated with at least one biological agent selected from the group consisting of biological agents derived from the cell; and b) presenting the time-lapse profile.
~. 9 6 Az007 In another aspect, the present invention provides a computer recordable recording medium recording a program for executing a process for determining a state of a cell. to a computer. The recording medium records at least a program for executing the praceduxes of:
a) obtaining a time-lapse profile of the cell by time-lapse monitoring of a transcription level associated with at least one biological agent selected from the group consisting of biological agents derived from the cell; and b) determining the state of the oell based on the time-lapse profile of the transcript~.Qn level.
In another aspect, the present invention provides a computer xecordable recozding medium recording a program for executing a process far correlating an external factor with a response of a cell to the external factor.
The recording medium records at least a program for executing the procedures of: a) exposing the cell to the external factor; by obtaining a time-lapse profile of the cell by time-lapse monitoring of a transcription level associated with at least one transcri.pt~.on control factor selected ~rom the group consisting of transcription control factors derived from the cell: and c) correlating the external factor with the time-lapse profile.
In another aspect, the present invention provides a computer recordable recording medium recording a program for exeGUting a process for inferring an unidentif~.ed external factor given to a cell based on a time-lapse profile. The recording medium records at least Azoo~
a program for executing the procedures of: a) exposing the cell to a plurality of known external factors: b) obtaining a time-lapse profile of the cell for each known external factor by time-lapse monitoring of a transcription J.evel associated with at least one transcription control factor selected from the group consisting of transcription control factors derived from the cell; c) carrelatix~g the known external factors with the respective time-lapse profiles:
d) exposing the cell to the unidentified external factor:
e) obtaining a time-lapse profile of the unidentified external factor by time--lapse rnanitoring of the transcription level of the selected transcz~iptian control sequence; f) determining a profile corresponding to the time-lapse profile obtained in the procedure of e) from the time-lapse profiles obtained in the procedure of b); and g) determining that the unidentified external factor is the known external factor corresponding to the profile determined in the procedure of f), In another aspect, the present invention provides a camputer recordable recording medium recording a program for executing a process for inferring an unidentified external factor given to a cell based an a time-lapse profile, The recording medium records at least a pxagram for executing the procedures of: a) providing data relating to a correlation relationship between known external fadtaxs and time-lapse profiles of the cell in response to the known external factors, in relation to at least one transcription control sequence selected from transcription control. sequences present in the cell:
AI00~
b) exposing the cell to the unidentified external factor;
c) obtaining a time-lapse profile of the cell by time-lapse monitoring of a transcription level associated with the selected transcription control sequence; d) determining a profile corresponding to the time-lapse profile obtained in the procedure of c) from the time-lapse profiles obtai~.ed in the procedure of a); and e) determining that the unidentified external factor is the known external factor corresponding to the profile determined in the procedure of d) .
When thG present invention is provided in the form of a z~ecord~.ng medium as described above, each const~.tuent element thereof can be implemented as wai.th the detaa.~.ed o~ preferred embodiments of the method of the present invention. Qreferred embodiments of such a recording medium can be easily selected by those skilled in the art and can be made or carried out by those skilled in the art based on the present specification.
In another aspect, the present invention provides a program for executing a process for presenting a state of a cell to a computer. The program executes the procedures of: a) obtaining a time-lapse profile of the cell by time-lapse monitoring ofi a transcription level associated with at least one biological agent selected from the group consisting of biological agents derived from the cell: and b) presenting the time--lapse profile.
Tn another aspect, the present invention provides a program for executing a process for determining a state of a cell to a avmputer _ The program executes the procedures of: a) obtaining ~ time-lapse profile of the cell by time-lapse monitoring of a transcription level associated with at lEast one biological agent selected from the group consisting of biological agents derived from the cells and b) determining the state of the cell based on the time-lapse profile of the transcription level.
In another aspect, the present invention provides a program for executing a process for correlating an external factor with a response of a cell to the external f~Ctor_ The program executes the procedures of:
a) exposing the cell to the external factor; b) obtaining a time-lapse profile of the cell by time-lapse monitoring of a transcription level associated With at least one transcription control factor selected from the group consisting of transcription control factors derived from the cell: and c) correlating the external factor With the time-lapse profile.
Tn another aspect, the present invention provides a program for executing a process for inferring an unidentified external factor given to a cell based on a time-lapse profile. The pz~ogram executes the procedures of: a) exposing the cell to a plurality of known external factors; b) obtaining a time-lapse profile of the cell for each known external factor by time-lapse monitoring of a transcription level associated with a.t least one transcxiptivn control factor selected from the group A~007 consisting of transcription control factors derived from the cell.: c) correlating the known external factors with the respective time-lapse profa.les; d) exposing the cell to the unidentif~.ed external factor: e) obtaining a time-lapse profile of the unidentified external factor by time-lapse monitoring of the transcription le~'el of the selected transcription control sequr~nce; f) determining a profile corresponding to the time--lapse profile obtained in the procedure of e) from the time-lapse profiles obtained 20 in the procedure of b): and g) determining that the unidentified external factor is the known external factor corresponding to the profile determined in the procedure of f ) .
In another aspect, the present invention pro~rides a program for executing a process for inferring an unidentified external factor given to a cell based on a time-lapse profile. The program executes the procedures of: a) providing data relating to a correlation relationship between known external factors and time-lapse profiles of the cell. in response to the known external factors, in relation to at least one transcription control sequence selected from transcription control sequences present in the cell; b) exposing the cell to the unidentified external factor; c) obtaining a time-lapse profile of the cell by time-lapse monitoring of a transcription ~.evel associated with the selected transcription control sequence; d) determining a profile corresponding to the time-lapse profile obtained in the procedure of c) from the time-lapse profiles obtained in the procedure of a)f arid e) determining that the unidentified external factor is the known external factor corresponding to the profile determined in the procedure of d).
S When the present invention is provided in the form of a pragrarn as described above, each constituent e~.ement thereof can be implemented as with the detailed or preferred embodiments of the method of the present invention.
Preferred embodiments of such a program oan be eas~.3.y selected by those skilled in the art and can be made or carried out by those skilled in the art based on the present specification. Description formats of such a program are well known to those skilled in the art and include, for example, the C+~language, and the like.
In another aspect, the present invention provides a method and system for diagnosing a subject. The diagnosis method comprises the steps of: a) obtaining a time-J.apse profile of the cell by time-lapse monitoring of ~0 a transcription level associated with at least one transcription control sequence selected from the group consisting of transcription control sequences derived from the cell; b) determining the state of the cell based an the time-lapse profile of the transcription level; and c) determining a condition, disorder or disease of a subject based on the state of the cell. The diagnosa,s method is provided in the form of a system, the system of the present invention comprises: a) means for obtaining a time-lapse profile of the cell by time-lapse monitoring of a transcription level associated with at least one transcription control sequence selected from the group consisting of txar~scription control sequences derived from the cell.; b) means for determining the state of the cell based on the time-lapse profile of the transcription level;
and c) means for determining a condition, disorder or disease of a subject based on the state of the cell. The present invent~.on is applicable to tailor-made disgnvses and therapies, such as drug resistance, selection o~
apprvpxiate anticancer agents, selection of appropriate transplant cells, and the like. Preferably, the diagnosis method of the present invention may be provided as a therapeutic or preventative method comprising the step of treating a subject with a therapy or preventative method selected based on the xesu~.t of diagnosis. In another preferred eznbvdiment, the diagnosis system of the present invention may be provided as a therapeutic or pre~erentative system comprising means for treating a subj ect with a therapy or preventative method, selected based on the result of diagnosis. An exemplary system configuration is shown in Figure 32.
A configuration of a computer or system for implementing the diagnosis method and system of the present ~.nvention is shown in Figure 17. Figure 17 shows an exemplary configuration of a computer 500 fox executing the cellular state determining method of the present invention.
An exemplary system configuration is shown in Figure 32.
The computer 5d0 comprises an input section 501, a CPU 502, an output section 503, a memory 504, and a bus 505 .
The input section 50~, the CPU 502, the output section 503, and the memory 504 are connected via a bus 5a5:. The znput section 501 and the output section 503 are connected to an T/O device 506.
An outJ.a.ne of a correlation process, which is executed by the computer 500, will be described below.
A program for executing the correlation method and/or selection of treatment or preventative method (hereinafter referred to as a "correlation program" and a "selection program", respectively) is stored in, for example, the memory 502. Alternatively, the correlation program and the selection program may be stared in ~.ny type of recording medium, such as a floppy disk, MO, CD~ROM, CD-R, DVD-ROM, or the like, separately or together.
Alternatively, the programs may be stored in an application server. The correlation program and the selection program stored in such a recording medium are loaded via the I/p device 506 (e.g., a disk drive, a network (e.g., the Internet)) to the memory 504 of the computer 500. The CPU 502 executes the correlation program and the selection program, so that the computer 500 functions as a device for performing the correlation method and the selection method of the present invention.
The result of analysis of a time-lapse profile (e.g., phase, etc. ) and infoxznat~.on about a ce7.~. ox the like are input via the input section 501. Secondary information about a condition, disorder or disease to be correlated with 2p4 a time-lapse profile and information about treatment and/or preventative methods may be input as required.
The CPU 5t~2 correlates information about a time-lapse profile with a state of a cell or a condition, disorder or disease of a subject and a preventative or therapeutic method as required, based on the in.formgtion input through the input section 501, and stares correlation data into the memory 50~. Thereafter, the CPU 502 may store the information in the memory 504 , Thereafter, the output section S03 outputs information about a state of a cell or a condition, disorder or disease of a subject and a preventative or thexapeutic m~ahQd as required, Which has been selected by the CPU 502 as diagnostic information. The output data i.s output through the I/O device 506.
(Generation of data) In one aspect, the present invention provides a method for generating profile data of information of a cell.. The method comprises the steps of: a) providing and fixing the cell to a support: and b? monitoring a biological agent or an aggregation of biological agents on or writhin the cell over time to genexate data an the profile of the cell. In this aspect, the pxesent invention is characterized in that the cell is fixed to substantially the same site of the support so that infox-mation oari be continuously (e_g., in a time-lapse manner, etc.) obtained from the same cell. Thereby, ~.t is possible to monitor a biological agent and an aggregation of biological agents over time. The time-lapse monitoring makes it possible to ~1r007 obtain.a profile of a cell and construct a digital cell.
Tv fix a cell to a support, a fixing agent, such as a salt or the like, may be used for tYie support i.r1 the present invention. A combination of a salt, a complex of a positively charged substance and a negatively charged substance, and a cell may f ix the cell to the support . Any salt may be used in the present ln~rention. Examples of such a salt include, but axe not limited ta, calcium chloride, sodium l~ydro~gen phosphate, sodium hydrogen carbonate, sodium pyruvate, HEPE9,,sodium chloride, potassium chloride, magnesium sulfide, iron nitrate, amino acids, vitamins, and the like. Examples of the above-described combination of a positi~rely charged substance and a negatively charged substance include, but are not limited to, complexes of a negatively charged substance selected from the group consisting of DNA, RNA, 1?NA, a polypeptide, a chemical compound, and a complex thexeof and a positively charged substance selected from the group consis'~ing of a cationic polymer, a cationic lipid, a cationic polyamino acid, and a complex thereof . In a preferred embodiment of the present invention, a biological agent of interest may be a nucleic acid molecule or a molecule derived from such a nucleic acid molecule. This is b~;cau$e most nucleic acid molecules carry genetic information, from which cellular information can be obtained.
In another aspect, the pxesent invention relates to data obtained by a method comprising the steps of: a) providing and fixing the ce~~ to a support: and b)~ monitoring a biological agent or an aggregation of Azoo~
biological agents on or within the cell over txxne to generate data of the profile of the cell_ Such data is Qbtained by the method which is not conventionallx av'ail.abl.e, and is thus novel. Therefore, the present invention provides a recording medium storing such data zn another aspect, the present invention relates to a method for generating profile data of infdrrnatlon of a plurality of cells in a consistent environment. The method comprises the steps of:
a) providing a plurality of cells on a support which can ma~.ntain a consistent environment; and b) monitoring a biological agent or an aggregation of biological agents on or within the cells over time to generate praf~.le data for the cells. zn this aspect, the pxesent invention is characterized in that profile data or information for a plurality of sells in a consistent environment can be obtained. Techniques for providing such an environment z5 also within the scope of the present invention. To provide a consistent environment for a plurality of cells, a fixing agent, such as a salt or the like, may be used fox the support in the present invention. A comb~.z~ation of a salt, a complex of a positively charged substance and a negatively charged substance, and cel7.s may fix the cells to the support. Any salt may be used in the present invention. Examples of such a salt include, but are not limited ta, calcium chloride, sodium hydrogen phosphate, sodit~nt hydxogezx carbonate, sodium pyruvate, HEPES, radium chloride, potassium chloride, magnesium sulfide, iron nitxate, amino acids, vitamins, and the ~.il~e. Examples of the above-described combination of a positively charged substance and a negat~.vely charged substance include, but are not limited to, complexes of a negativeJ.y charged substance selected from the group consisting of DNA, RNA, PNA, a polypeptide, a chemical compound, and a complex thereof and a positively charged substance selected from the group consisting of a cationic polymer, a cationic lipid, a cationic polyamino acid and a complex thereof . In a preferred embodiment of the present invention, a biological agent of interest may be a nucleic acid molecule or a molecule derived Exam such a nucleic acid molecule . This is because most nucleic acid molecules carry genetic information, from which cellular information can be obtained.
In a preferred embodiment, an actin-like acting substance is preferably provided to the cells in the method of the presEnt invention. The actin-like acting Substance acts on actin within the cells to de~arzn the internal cytaskeletan to facilitate introduction of an external factor into the cells. The presence of such an actin-like acting substance makes it possible tc investigate an influence of an external factor of interest on the cells.
In one embodiment, a biological agent targeted by the present invention is at least one factor selected from the group consisting of nucleic acids, proteins, sugar chains, lipids, law molecular weight molecules, and composite molecules thereof.
zn a preferred embodiment, cells targeted by the present invention are preferably cultured for a certaix'r period of time without stimulation before monitoring. This procedure is performed for the purpose of synchronizing the target calls. The period of time required for synchronization is, for example, advantageously at least one day, more preferably at least two days, even more preferably at least 3 days, and still even more preferably at least 5 days. It should b~ noted that as the period of time for culture is increased, the necessity of maintaining the culture conditions increases. In the synchronization procedure, the same medium is preferably supplied to cells.
Therefore, the culture medium is preferably consistent or at least changed in a consistent manner. To achieve this, a means for causing convection in the medium may be 1S preferably provided and used.
In a more preferred embodiment, a biological agent provided to a cell in the present invention may comprise a nucleic acid molecule encoding a gene. The nucleic acid molecule encoding a gene is preferably transfected into a cell. Preferably, such a biological agent may be provided along with a tranrsfection reagent (gene introduction reagent). More preferably, the nucleic acid molecule encoding a gene may be provided to a cell along with a gene introduction reag~:nt and an actin-like acting substance. Tn this case, the cell is preferably provided with a complex of a salt, a positively charged substance, and a negatively charged substance (in this case, a nucle~.c acid molecule and a gene introduction reagent). Thus, the cell and the target molecule are fixed on a support. In addition, this technique makes it possible to allow separate biological agents (e , g . , nuc~.eic ac~.d molecules ) to be separately introduced into cel~.s without a partition. As substantially no partition is used, a pl.uraZ~.ty of cells can be mon~.toxed in substantially a consistent environment.
Further, different biological agents can be introduced into a cell, thereby making it possible to obtain a profile of a state of the cell affected by the biological agents. Such a profile can be stored as data. Such data may be stored in a certain standard format, and therefore, can be reproduced and compared. Thus, the present invention has an effect which is not achieved by canventional bzo~.vg~.cal assays. Such data, once obtained and stored in such a standard format, can be extracted and used far various purposes and a number of times. For example, researchers can perform "virtual experiments" to conduct various analyses under the same conditions While taking into consideration diffErences in a substantially infinite number of parameters. In addition, since virtual experiments and the results thereof are stored in a raw data format, undergraduate and graduate students, who otherwise spend mast of their schaa~l life doing laboratory work, can receive education in data analysis in the true sense. mhe above-described cellular profile data can be easily standardized, thereby making it possible to do research based on data which may have been obtained by e~tperiments under the same Conditions aver the world. Such data may be distributed irz a standardized form. Such a standardized form may be readable to typical computers (e.g., computers having a commonly available OS, such as Windows, Mac, UNTX, LINtIX, or the like) . Data produced in the present invention may include generated cellular profile data, information about experimental conditions used in data generation, information about cells, information about environments, and the like.
In a preferred embodiment, a profile targeted by the present invention may include a profile of gene expression, a profile of an apoptotic signal, a profile of a stress signal, a profile of the localization of a molecule (preferably, the molecule is labeled with a fluorescent, phosphorescent, yr radioactive substance, or a combination.
thereof), a profile of changes in cellular morphology, a profile of a promoter, a profile of a promoter dependent on a specific pharmaceutical agent (e. g., antibiotics, liganda, toxins, nutrients, vitamins, hormones, cytokines, etc.), a profile of an intermolecular interaction, and the like. In an embodiment in which the present invention targets a profile of a promoter dependent on a specific pharmaceutical agent, it is preferable that the present invention may further comprise administering the specific pharmaceutical agent.
rn a preferred embodiment, the present 2S invention may further comprise providing an external stimulus to the cell. Such an external stimulus may or may not be a biological agent . The extsraal factor may be any factor and ~.ncludes, without limitation, substances or other eJ.ements (e. g., energy, such as ionizzng radiation, radiation, light, acoustic wares, and the like).
In one embodiment, an external factor used ix~
the present invention may be RNAi. RNAi can be used to substantially suppress an arbitrary gene. It is possible to produce RNAi for all existing genes and investigate the effect of RNAi on the genes. RNAi can be created by techniques well known in the art.
In anothex embodiment, an external factor of the present invention may comprise a chemical substance which does not exist in organisms . By providing such a chemical substance which does not exist in organisms, it is possible to collect a variety of information. Once collected, such data can be reused. Therefore, assuming that a chemical substance which does not exist in organisms is not substantially available, if data can be obtained once for such a chemical substance in accordance with the present invention, research can continue without worrying about the availability of such a chemical substance.
In one embodiment, an external factor targeted by the present invention may comprise a ligand to a cellular receptor. By analyzing a ligand, it is possible to study various signal transduction pathways. Therefore, in such a case, a profile obtained according to the present invention may be a profile of receptor-ligand interactions.
In a preferred embodiment pf the present in~rentian, a pro:~i~.e of cellular morphology may be obtained.
in this case, a method of the present invention may further comprise applying a stimulus to a cell which may be selected from the group consisting of overexprESSion of a genE, underexpression of a gene, knock down of a gez~e, addition of an external factor, and a change in an environment.
rn a preferred embodiment, a profile obtained according to the present invention may be a profiJ.e of interactions between molecules present within a cell. Such an intermolecular interaction includes, but is not limited to, interaction between molecules present in a signal transduction pathway, interaction between a receptor and a ligand, interaction between a transcription factor and a transcription factor sequence, and the like.
In another preferred embodiment, a profile obtained according to the present invezxtion may be a profile of interaction between molecules present in a cell. In this case, a method of the present invention may further comprise obsexwing a cell using a technique selected from the group consisting of a two--hybrid method, FRET, and HRET. The two-hybrid method detects intermolecular interaction within a cell_ Specifically, this technique is described in, for example, Protein-Protein Tnteractions, A MOLECULAR
CLONING MIaI~TUAL, Edited by Erica Gvlernis, Cold Spring Fiabor Laboratory Press, Cold Spring Harbor, New York (this document also describes FRET). FRET is a technique for detecting inter- or intro-molecular resonance energy shift as a fluorescent wavelength, and zs described in, fox example, Protein-Protein Interactions (supra): and Miyaws.ki A., Visualization of the spatial and temporal dynam~.cs of intracellular signaling, Dev. Cell, 2003 Mar; 4 (3) :295-305.
BRET is an intermolecular interaction assay system and is described, for example, 8oute N. , The use of resonance energy transfer in high-throughput screening: BRET versus E'RET, Trends Pharmacol Sci., 2002 Aug; 23(8):351-4.
Tn a preferred embodiment, cells targeted by the present invention are preferabJ.y arranged on a support in a pattern of an array. In this case, preferably, a plurality 1p of cells targeted by the present invention may be spaced at intervals of 1.0 Grn at maximum, more preferably 1 cm at maximum, even more preferably 1 mm at maximum, and most preferably 0.1 mm at maximum. The cells need to be spaced at minimum intervals. Such intervals may be preferably set so that substantially no interaction occurs.
In one embodiment, a profile obtained according to the present invention may or may rzot be obtained in real time. A real time profile may be advantageous. GThen simultaneity is important, it is important to obta3.n a profile in real time. Alternatively, when a profile is intended to be stored, the profile is not necessarily obtained in real time.
In. an additional embodiment, the present invention further comprises fixing a cell to a solid phase support. In this case, the cell is fixed to the solid phase support along with a salt, a complex, an actin-like acting substarzce, or the like.
Tn one embodiment, data generated according to the present invenaion may contain information about a profile. In. a preferred embodiment, data generated according to the present invention may contain information about conditions for monitoring, information about a cellular state, information about an external factor, inforznat~.an about an environment, and the like.
In a preferred embodiment, at least two biological agents may be preferably monitored in the pxesent invention, mare preferably at least 3 biological agents, and even more preferably at least 8 biological agents.
Alternatively, all b~.ological agents in a certain specific category (e. g., all ol~actary receptors, all gustatory receptors, etc.) may be preferably monitored.
Alternatively, in another preferred embodiment, the present invention may further comprise arbztxarily selecting the above-described biological agents.
In a preferred embodiment, a cell targeted by the present invention may be selected from the group consisting of stem cells and somatic cells.
Tn one embodiment, a support used in the present invention is preferab~.y a solid phase support. This is because cells are easily faxed to such a support. Such a solid phase support may be made a~ any material known in the art. The support may be in the foxm of a substrate.
In one embodiment of the pxesent invention, the above-described biological agent may be a nucleic acid and the above-described cell may be trans~ected with the nucleic acid. Hy transfecting the cell with the nucleic acid, an inf~.uence of the nucleic acid on the cell can be collected in real time or in a standardized storable format into data or a profile. This cannot be achieved by conventional techniques. In a preferred embodiment, transfection may be performed in solid a phase or in a liquid phase. More preferably, transfection may be advantageously performed in a solid phase . This is because data collection and standardization or normalization can be more easily carried out.
1.5 In a preferred embodiment of the present invention, a profile may be subjected to a process selected from the group consisting of phase comparison, calculation of a difference ~xom a control profile, signal processing, and multivariate analysis. Data processed in such a manner may fall within the scope of the present invention.
In another aspect, the present invention provides a method for presenting profile data of information about a plurality of cells in a consistent environment. The method comprises the steps of: a} providing a plurality of cells on a support capable of reta~.ning the cells in a consis~.ent environment; b} monitoring a biological agent or an aggregation of biologicaX agents on or within the celxs over t~.me to generate profi7.e data for the cells; and c} presenting the data.
The above-described support capable of retaining a plurality of cells in a cansisterit environment can be achieved as~ described elsewhere herein. The step of generating data can be performed as described elsewhere herein. The step of presenting data can be performed as described elsewhere herein. Examples of a method of performing such presentation include, but are not limited to, techniques of using ~raridus sensory means, such as visual means, auditory means, olfactory means, tactile means, gustatory means, and the like. Preferably, a visually presentat~.on means may be used. Such visual means include, without limitation, a computer display and the like.
Preferably, in the presentat~.on method of the present invention, presentation may be performed in real time. Alternatively, storr~d data may be stored and presentation may be delayed. when presentation should b~
performed ~.n real time, data signals may be transferred ~D directly to, for example, a display.
In another aspect, the present invention provides a method for determining states of cells in a consistent environment. The method comprises the steps of:
a) providing a plurality of cells on a support capable of retaining the ce~.ls in a consistent environment:
b) monitox~.ng 'a biological agent or an aggregation of b~.ological agents on or within the cells over time to generate profile data for the cells: and c) determining the 34 states of the cells based on the data.
The above-described support capable of retaining a plurality of cells in a consistent environment can be achieved as described elsewhere herein. The step of S generating data can be performed as described elsewhere herein. The step of determining the states of the cells may be performed by correlating the generated data with information about the cells, or comparing the generated data with standard data. In this case, the data may be statistically processed.
Therefore, in a certain embodiment, th$ present invention may Further comprise correlating a profile obtained according to the present invention with a state of a cell before obtaining the time-lapse profile. To perform determination smoothly, the cells targeted by the pre9ent invention may ad~crantageously include cells whose states are known. It is possible to store data of cells whose states are known, determination can thus be quickly performed by comparir~g data between the known cell and unknown ce~.ls .
During determination, at least two biological agents are preferably present. I~n this case, the plurality of biological agents may belong to heterologous categories (e. g., proteins and nucleic acids, etc.) or homologous categories.
Preferably, the present invention may further comprise arbitrarily selecting a biological agent. Any biological agent can be selected and used to characterize a state of a cell to some extent, and in some cmsea, identification is possible. Thus, the present invention has s.r~ effect which cannot be e~tpected from conventional techniques.
In the determination method of the present invention, data may be preferably generated in real time.
G~hen data is generated in real time, an unknown substance or state of an unknown cell may be determined in real time.
2n the determination method of the present invention, examples of a state of a target cell include, but are not limited to, differentiated states, undifferentiated states, cellular responses to extez~nal factors, cell cycles, growth states, and the J.ike.
A cell, targeted by the present invention may be either a stem ce~,l or a somatic cell. Any somatic cell may be used. A cell may be selected by those skilled in the. art, depending on the purpose of use of the cell.
A solid phase support used in the determination method of the present inv~entifln may comprise a substrate.
In the present invention, such a substrate can be used as a part of a computer system, so that determination can be automated. An exemplary configuration of such a system is shown in Figure 32.
Tn a preferred embodiment, in the determination method of the present invention, the bio~.ogical agent may be a nucleic acid moXecule, and the cell is transfected with the nucleic acid molecule. Transfeatxon may be performed on a solid phase support using any material, but preferably a gene introduction agent, more preferably a salt, an actin-like acting substance, or the like. Transfection may be performed in solid phase or in liquid phase, and preferably in solid phase.
Ln a determination method of the present invention, a target biological agent may be capable of binding to another biological agent. By investigating a biological agent having such a property, a network mechanism in a cell may be elucidated.
In a determination method of the present invention, the determinat~.on step may comprise a mathematical process selected from the group consisting of comparison of phases of profiles, collection of differences from a control profile, signal proces$ing, and multivariate analysis. Such processing techniques are well known in the art and described in detail herein.
In another aspect, the present invention provides a method for correlating an external factor with a cellular response to the external factor. The method compz~ises the steps of: a) exposing a plurality of cells to an external factor on a support capable of retaining the cells in a consistent environment: b) monitor~.ng a biological agent or an aggregation of biological agents on or within the cells over time to generate profile data for the cElls: and c) correlating the external factor with the profile. exposure of the cells to the external factor may be achieved by placing the cells and the external fs.ctor into an environment in which the cexls are contacted with the extexnaJ. factor. For example, when the cells are fixed on the support, the external factor is added to the support to achieve exposure. Techniques for generating and coxxelating data are also well known in the art, and may 3.~ be used singly or in combination. Preferably, atatistioal processes axe performed to generate statistically signi~i.cazat data and information.
In a preferred embodiment, in the Correlation method of the present in~rention, the cells may be fixed on the support. Since the cells are fixed, data can be easily standardized, so that data can be significantly efficiently processed.
In a preferred embodiment, a correlation method of the present invention may further comprise using at 7.east two external factors to obtain a profile fox each external factor. Techniques for obtaining such a profile are well described here~.n.
More preferably, the correlation step may fiurther comprise dividing at least two profiles into categories and classifying the external factoxs corresponding to the xespectxve pxofil~s into the categories. By categorization, data can be processed in a more standardized manner.
3~T007 Zn a preferred embodiment, a profile obtained by the present invention may be presented in real time. When data is intended to be stored, data may riot be particularly presented in real time.
In ~, preferred embodiment, a cell used in the present invention may be cultured on an array. In such a case, therefore, the cell is preferably covered with medium.
Any medium which is commonly used for cells may be used.
zn a preferred embodiment of the present invention, the step of monitoring a profile may comprise obtaining image data from the array. Particularly, when a profile contains visual information (e.g., emission of fluaresaence due to gene expression), the profile can be obtained by capturing image data_ In a correlation method of the present invention, the step of correlating an external f~.ctor with a profile may comprise distinguishing between phases of the profile.
Distinguishing phases of the profile can be achieved only after the present invention provides time-lapse prafz~.es obta~.zxed in a consistent environment .
An external factor targeted by the present invention may be selected from the group consisting of a temperature change, a humidity ohange, an electromagnetic wave, a potential difference, visible light, infrared light, ultraviolet light, X-rays, a Chemical substance, a pressure, a gravity change, a gas partia,z pressure, and an osmotic pressure. Preferably, the chemical substance may be a biological molecule, a chemical compound, or a medium.
Examples of such a biological molecule include, but are not limited to, nucleic acid molecules, proteins, lipids, sugars, prateolipids, lipoproteins, glycoprcteins, proteaglycan,s, and the like. Such a biological molecule may also be, fax example, a hormone, a cytokine, a cell adhesion 7.0 factor, an extracellular matrix, or the like.
Alternatively, the chemical substance may be either a receptor agonist or antagaz~ist.
In another aspect, the present invention relates to a method for identifying an unidentified external factor given to a cell from a profile of the cell. The method comprises the steps of: a) exposing a cell to a plurality of known external factors on a support capable of retaining the cell in a Consistent env~.xozxment; b) monitoring a biological agent ax an aggregation of biological agents on or within the cell over time to generate a profile of the cell to each of the known external factors and to generate profile data for the cell; c) correlating each of the known external factors with each of the profiles; d) exposing the cell to an unidentified external factor; e) monitoring a biological agent or an aggregation of biological agents on or within the cell. exposed to the external factors over time to obtain a profile of the cell with respect to the unidentified external factor; f) determining, from the profiles obtained in the step of b) , a profile cdrrespnnding to the profile obtained the step of e) : and g) determining that the unidentified external factor is the knotan e~tternal factor corresponding to the profile determined in the step of f). Techniques for exposure to external factors, data generation, corzelation, exposure to unidentified external factors, and the like are described elsewhere herein and can be selected as appropriate depending on the purpose by those skilled in the art taking such descriptions into consideration.
Tn another aspect, the pxeserit invention provides a method for ident~.~ying an unidentified external factor given. to a cell from a profile of the cell. The method comprises the steps of: a) providing data relating to a correlation relationship between known external factors and protiles of the cell in response to the known external factors, in relation to a biological agent or an aggregation of biological agents on or within the cell: b) exposing the cell to the unidentified external. fs.ctor; c) monitoring the biological agent or the aggregation of the biological agents on yr within the cell to obtain a profile of the cell:
d) determining, from the profiles provided in the step of a) , a profile corresponding to the profile obtained in the step of c); and e) determining that the unidentified external factor is the known external factor corresponding to the profile def.ermined in the step of d) . Techniques for exposure to externalfactors, data generation, correlation, exposure to unidentified external factors, and the like are described elsewhere herein and can be selected as appropriate depending on the purpose by thc~sa skilled in the art taking such descriptions into consideration.
In another aspect, the present invention provides a method for obtaining a profile relating to ~.nformation for a plurality of cells in a con~i~stent environmez~t. The method comprises the steps of:
a) providing a plurality of cells on a support capable of retaining the cells i.~x a consistent environment; and b) monitoring a biological agent or an aggregation of biological agents on or within the cell over time to generate a profile of the cells. Techniques for exposure to external factors, data generation, correlation, exppsure to unident~.fied external factors, and the like axe described elsewhere herein and can be selected as appropriate, depending on the purpose by those skilled in the art taking such descriptions into consideration.
In another aspect, the present invention relates to a recording medium in which data generated by a method for generating cellular profile data of the present ~.nventian is stored. Data may be stored in any format. Any recording medium may be used. Examples of such a recording medium include, but are not limited to, CD-ROMs, flexible disks, CD-Rs, CD-RWs, MOs, mini disks, DVD-ROMs, DVD-Rs, memory sticks, hard disks, and the like. The present invention also relates to a transmission medium in which data generated by a method for generating cellular profile data of the present invention is stored. Examples of such a transmission medium include, but are not limited to, networks, such as ~.ntranets, the Tnternet, and the like.
A~007 A recording medium or transmission medium of the present invention may further contain data relating to at least dne piece of information selected from the group consisting of information about conditions for the monitoring step, information about the profile, information about the cellular state, and information about the biological agent. Data relating to such information may be stored while being linked to one another. Preferably, the data may be advantageously standardized. Standardized data can be distributed on general distribution pathways. The above-described linkage may be constructed far each cell br for each biological agent, or for both.
Tn another aspect, the present invention relates to data generated by a method for generating cellular profile data of the present invention. Such data canz'~ot be generated by conventional techniques and is thus novel.
In another aspect, the present invention provides a system for generating profile data of information for a plurality of cells in a consistent environment. the system comprises: a) a support capable of retaining a plurality of cells in a consistent environment: b) means for monitoring a biological factor or an aggregation of b~.ological factors on or within the cells over time: and c) means for generating profile data for the cells from a signal obtained fxom the monitoring means. The support capable of retaining cells in a consistent environment can be made by those skilled in the art using a technique first Azoo~
provided by the present invention. Such a technique is attributed to the finding that cells are fixed and arrayed without a partition. Examples of the monitoring means include, but are not limited to, microscopes t a . g . , optical microscopes, fluorescence mi.crascopes, phase-contrast microscopes, etc.), electron microscopes, scanners, naked eyes, infrared cameras, confocal/nonconfocal microscopes, CCD cameras, and the like. An exemplary configuration of such a system is shown in Figure 32.
zn a system of the present invention, the system may riot necessarily contain cells from the start, but preferably may contain cells which are advantageously fixed on a support. Tn such a case, f~.xation is preferably standardized. In addition, the cells are fixed and spaced, for example, wit.haut limitation, at intervals of 1 mm or the like.
In a preferred embodiment, at least one substance selected from the group consisting of salts and actin--like acting substances may be preferably adhered to the support . Hy adhering ce~.ls to the support with a salt or an actin-like acting substance, or preferably with both, fixation of the cells and/or introduction of a substance into the cells can be enhanced.
Examples of the monitoring means used in the system of the present invention include, but axe not limited to, optical microscopes, fluorescence microscopes, phase--contrast microscopes, reading devices using a laser source, means using surface plasmon resonance (SPR) imaging, electric signals, chemical or biochemical markers singly or in combination, radiation, cozxfocal microscopes, nonconfocal microscopes, differential interference microscopes, stereoscopic microscopes, video monitors, infrared cameras, and the lzke. Preferably, a scanner (e.g., a scanner fox scanning a surface of a substrate using a whzte light source ox laser) may be used. The reason a scanner is preferable is that fluorescence can efficiently transmzt 7.0 excited energy and microscopic technology can be easily applied. Further, measurement can be advantageously performed without significant damage to cells. An exemplary configuration of such a system is shown in Figure 32.
rn another aspect, the present invent~.on provides a system for presenting a profile of information for a plurality of cells in a consistent enva.~conment. The system comprises: a) a support capable of retaining a plurality of cells in a consistent environment: b) means for monitoring a biological factor or an aggregation of biological factors on or within the cells over time; c) means for generating profile data for the cells from a signal obtained from the monitoring means; and d) means for presenting the data. The support, the monitoring means, and the data generating means can be made as described elsewhere herein. The means for presenting data can be achieved by techniques well known in the art. Examples of such a data presenting means include, but are not limited to, computer displays, loudspeakers, and the like. An exemplary Azaa7 configuration of such a system is shown in Figure 32.
A presentation system of the present invention may further comprise a plurality of cells, in which the cells are preferably fixed to the support . In such a case, at least one substance selected from the group consisting of salts and actin-like acting substances may be preferably adhered to the support. By adhering cells to the support with a salt or an actin-like acting substance, or preferably with both, fixation of the cells and/or introduction of a substance into the cells can be enhanced.
Any mon~.toring means may be used. Examples of the monitoring means include, but are riot limited to, optical x5 microscopes; fluorescence microscopes; phase microscopes;
reading devices using a laser source; means using surface plasmon resonance (SPR)imaging, electric signals, chemical or biochemical markers singly or in combination; and the like.
zo Any data presenting means may be used, including, without limitation, displays, loudspeakers, and the like.
In another aspect, the present invention 25 pxovides a system for determining a state of a cell. The system comprises: a) a support capable of retaining a plurality of cells in a consistent env~.roxlmen.t: b) means for monitoring a biological factor or an aggregation of biological factors on or within the cells over time: c) means 34 fpr generating data from a signal obtained by the monitoring means; and d) means for extrapolating the state of the cell firom the data. The support, the monitoring means, and the data generating means can be made by these skilled in the art as described elsewhere herein. The means fc~r extrapoXating a state of a cell from data may be produced an,d used by techniques well known in the art. For example, measured data can be compared with standard data for known cells to achieve extrapolation. A device storing a program for such extrapolation or a computer capable of executing 7.0 such a program may be used as the extrapolation means . An exemplary configuration of such a system is shown in Figure 3Z.
In another aspect, the present invention provides a system for correlating an external factor With responses of cells to the external factor. The system comprises: a) a support capable of retaining a plurality of cells in a consistent environment: b) means for exposing the cell to the external factor; c) means for monitox~.ng a biological factor or an aggregation of biological factors on or within the cells over times d) generating profile data for the cells from a signal from the monitoring means ~ and e) means for correlating the externax factor with the profile. The support, the monitoring means, and the data generating means can be made by those skilled in the art as described elsewherE herein. The means for exposing the Dells to the external factor can be designed and carried out as appropriate by those skilled in the art depending on the properties of the external factor_ The Correlation means can employ a recording medium storing a program for correlation or a computer capable of executing such a program.
Preferably, a system of the present invention comprises a plurality of cells. An exemp~.ary configuration of such a system is. shown in figure 32.
In another aspect, the present invention provides a system for identifying an unidentified external factor given to a cell based on a profile of the cell. The system comprises: a) a support capable of retaining a plurality of cells in a consistent environment: b) means far exposing the cell to one or mare known external factors;
c) means for monitoring a biological factor or an aggregation of biological factors on or within the cells over time; d) means for obts.ining a profile of the cell with respect to each of the known external factors to generate profile data for the cell; e) means fax correlating each of the known external factors with each profile: f) means for exposing the cell to the unidentified external factor;
g) means for comparing the profiles of the known external factors obtained by thr~ means of d) with the profile of the unidentified external factor to determine a profile of the unidentified external factor from the profiles of the known external factors, wherein the determined unidentified external factor is the known external factor corresponding to the determined profile. The support, the exposure means, the monitoring means, the data generating means, and the correlation means, and the other exposure means can be made and carried out as appropriate by those skilled in the apt as described elsewhere herein. The means for determining a corresponding profile can also be made and carried out by utilizing a retarding medium storing a program capable of executing such a determination process and a computer capable of executing such ~ program. Preferably, a system of the present invention comprises a plurality of cells.
An exemplary configuration, of such a system is shown in E'igure 32.
In another aspect, the present invention provides a system for identifying an unidentified external factor given to a cell based on a profile of the cell. The system comprises: a) a recording medium storing providing data relating to a correlation relationship between known external fetters and profiles of the Cell irr response to the known external factors, in relation to a biological ~.5 factor or an aggregation of biological factors an or within the cell; b) means for exposing the cell to the unidentified external factor: c)a support capable of retaining a plurality of cells in a consistent environment ; d)means for monitoring a biological factor or an aggregation of b~.alagical factors on or within the cells over time; e) means for obtaining a profile of the cell from a signal obtained by the monitoring means; f ) means for determining, from the profiles stored in the recording medium of a.), a profile corresponding to the profile obtained with respect to the unidentified external factor, wherein the determined unidentified external factor is the known external factor corresponding to the detex~mirled profile. The support, the exposure means, the monitoring means, the data generating means, and the correlation means, and the other exposure means can be made and carried out as appropriate by thane Azoo7 skilled in the art as described elsewhere herein. The means for determining a corresponding profile can also be made and carried out by utilizing ~ recording medium storing a program capable of executing such a determination process and a computer capable of executing such a program.
Preferably, a system of the present invention comprises a plurality of cells. An exempxary configuration of such a system is shown in Figure 32, In another aspect, the present invention relates to a support capable of maintaining a consistent en~criror~,ment for a plurality of cells. Such a support was first provided by the present invention. By utilizing such a support, a plurality oP cells can be analyzed in a consistent environment.
Preferably, cells are arranged on a support in the form of an array. This is because standardized analysis can be achieved. In this case, the support. may preferably comprise a salt or an actin-like acting substance. More preferably, the support may advantageously comprise a complex of a positively charged substance and a negatively charged substance. This is because cells can be easily fixed to the support using such a complex. Actin-like acting substances are preferable when the interior of cells is analyzed, since the actin-like acting substances increase the efficiency of introduction of external factors into cells. Therefore, in a preferred embodiment of the present invention, the support may comprise a salt arid an actin-like act~.ng substance, and more preferab~.y may comprise a complex of a positively charged substance and a negatively charged substance.
A support of the present in~erentiori i~5 characterized in that, cells may be provided and spaced at intervals of 1 mm. In the case of such ~.nterva~.s, it is not conventionally possible to provide an environment without a partition. wherefore, the present invention has a remarkable effect, as well as practicability, applicability and utility.
In a preferred embodiment, a support of the present invention may comprise a cell fixed thereto. In a more preferred embodiment, a support of the present invention may comprise a biological factor fixed thereto.
In a preferred embodiment, at least two biological factors may be fixed to the support. Such biological factors may be factors selectEd from the group consisting of nucleic acid molecules, proteins, sugars, lipids, metabolites, low molecular weight molecules, and complexes thereof, and fsctors containing physical elements and/or temporal elements.
In a more preferred embodiment, a cell and a biological factor may be fixed to a support of the present invention in a mixed manner. The biological factor and the cell may be provided so that they aan interact with each other. Such interaction may vaxy depend~.ng on the biological factor. According to the propert~.es of the biological factor, those skilled in the art can understand 23~
how the biological factor interacts with the cell and where the biological~factor~is positioned so as to interact with the cell .
In a preferred embodiment, a salt, a complex of a positively charged substance and a negatively charged substance, and an actin-like acting substance are fixed along with a cell and a biological factor to a support of the present invention.
Zn a more preferred embodiment, a salt, a complex of a positively charged substance and a negatively charged substance, and an actin-like acting substance are fixed along with a cell and a biological factor to a support of the present invention in the form of an array. With such a structure, a cell chip capable of generating the profile data of a cell can be provided. The support has a structure in which a salt, a complex of a positively charged substance az~d a negatively chs.rged substance, and an actin-like acting substance are fixed along with a cell and a biological factor in the form of an array. Such a support is also called a "transfection array".
Examples of a salt used in the support of the 2S present invention include, but are not limited to, calcium chloride, sodium hydrogen phosphate, sodium hydrogen.
carbonate, sodium pyruvate, HEPES, sodium chloride, potassium chloride, magnesium sulfide, iron nitrat~, amino acids, vitamins, and the like. A preferable salt is, for 3Q example, without limitation, sodium chloride or the like.
Examples of a gene introduction agent used in the support of the present invention include, but are not limited to, cationic polymers, cati.onie lipids, polyamine-based reagents, polyimine-based reagents, caJ.cium phosphate, oligofectarnin, and oligofectors and the like. preferably the gene ~.ntroduction reagents used may be preferably, but are not limited to lipofectamines, oligofectamines and oligofectors.
Examples of an actin-like acting substance used in the support of the present invention include, but are not limited to, fibronectin, laminin, ,sritronectin, and the like. A preferable actin-like acting substance is, for examp~.e, without limitation, fibronectin.
Examples of a nucleic acid molecule used in the support of the present invention include, but are not limited to, nucleic acid molecules comprising transaript~.on control sequences (e. g., promoters, enhancers, etc.}, gene coding sequences, genomic sequEnces containing nontranslation regions, nucleic acid sequences encoded by the genome of a host (a fluorescent protein gene, E. coli/yeast self-replication origins, a GAh4 domain, etc. ) , and the like.
preferable nucleic acid molecules include, but are not limited to, transcription control sequences (e. g., promoters, enhancers, etc.), gene coding sequences, genomic sequences conta~.nirig nontranslation regions, and the like.
Examples of a cell used in the support of the present invention include, but are not limited to, stem cells, established cell lines, primary culture cells, insect cells, bacterial cells, and the like. Preferable cells include, but are not limited to, stem cells, established cell lines, primary culture cells, and the like.
Examples of a material for a support of the present invention include, but are not limited to, glass, silica, plastics, and the like. Preferable materials include, but are not limited to, the above, described materials with coating.
In another aspect, the present invention provides a method for producing a support comprising a 1S p~.urality of cells fixed thereto and capable of maintaining a consistent environment for the cells. The method comprises the steps of: A) providing the support; and B) fixing the cells via a salt and a complex of a positively charged substance and a negatively charged substance onto the support. The step of providing a support may be achieved by ob'~aining a commercially available support or molding a support material. A support material may be preparEd by mixing starting materiaJ.s for the material as required. The fixing step can be carried out by using techna.ques known 2S in the art. Examples of such fixing techniques include, but are not limited to, an ink jet printing technique, a pin array technique, a stamping technique, and the like. These techniques are well known and can be performed as appropriate by those sk~.l,led ~.n the art _ Tn a preferred embodiment, the fixing step in the present invention may comprise fixing a mixture of the salt, the complex of a gene introduction agent and an actin-like acting substance (positively charged substances) arid a nucleic acid molecule (a negatively charged substance), and the cell in the form of an array.
Such a fixing step may be achieved by printing techniques .
In another aspect, the present invention provides a device for producing a support oaxnprising a plurality of cells fixed thereto and capable of maintaining a consistent environment for the cells. The device comprises : A) means for providing the support: and B) means fpr fixing the cells via a salt and a complex of a positively charged substance and a negatively charged substance onto the support. The support may be obtained using means which can perform the above-described methods. Examples of such means incl.udE, but are not limited to, a support moJ.di.ng means, a material tormulating.means (e.g., a mixing means) , and the like. The molding means can employ techniques well known in the art. The fixing means may comprise a printing means. As such a printing means, commercially available ink jet printers can be used.
2b (l7igital Cell) As used herein the term "digital cell" refers to a collection of at least one experimental data corresponding to a cell of experimental interest . Such experimental data is a correlation between the conditions used for the experiments aa~xducted on an actual cell in the real world, and the experimental results thereof. The digital cell is composed suoh that when an experimental candition is given, an experimental result relating to the experimental.
condition will be reproduced.
By using the digital cell, expexixnental results conducted az~ an actual cell can be reproduced an a computer system. This allows institutions or indiv~.duals having no experimental facilities to conduct cutting-edge studies relating to a cell. As a result, it allows the introduction of business entities having a primary interest in disciplines other than that of the present technical art, which could not been achieved to date, prior to the disclosure of the present invention.
Figure 33A depicts an example of data structure of a digita.J. cell. This example represents a digital cell by a collection of three experimental data A1, A2 and A3 relating to cell A.
Each of experimental data A1, A2 and A3, comprises cell parameter, environment parameter and stimulus parameter as parameters indiaatirig experimental conditions, and stimulus response result as an experimental result.
As used herein, the cell parameter specifies a cell of experimental interest. The environment parameter specifies an environment under which the ael~. specified by the cell parameter is cultured. The stimulus parameter specifies a stimulus given to the cell specified by the cell parameter. The stimulus response result shows a result which the cell specified by the cell parameter responded to the stimulus specified by the stimulus parameter under the environment specified lay the envzrorunent parameter.
Experimental data A1 shows that cell A was cultured in a medium called "L~MEM", under the culture condition of pH "7", temperature "37" degree Celsius, COZ
concentration "5" %, arid a stimulus consisting of a reporter called "Tet-OFF GMV EGF" or "MCV EGFP" and a chemical stimulus (agent) "Doxycycene" is given thereto to obtain a stimulus response result. The stimulus response result is represented by "cell dynamic data 1" and "reporter measurement data 1".
Expexzmental data A2 shows that cell A was cultured in a medium called "DMEM", under the culture condition of pH "7", temperature "37" degree Celsius, COz concentration "5" ~, and a stimulus consisting of a reporter called "c-Los" and a chemical stimulus (agent) "P5C833" is given thereto to obtain a stimulus response resu7.t. The stzznul.us xespon.se result is represented by "cell dynamic data 2" and "reporter measurement data 2".
Experimental data A3 shows that cell A was cultured in a medium called "DMEM", under the culture condition of pH "5", temperature "39" degree CelCius, GOZ
concentration "4" ~, and a stimulus cons~.sting of a reporter called "CRAB" and a chemical stimulus (agent) "Vindecine"
is given thereto to obtain a stimulus response result . The stimulus response resu3.t is represented by "cell dynamic data 3" and "reporter measurement data 3".
As such, parameters indicating experimental conditions (a cell parameter, an environment parameter and a stimulus parameter) and a stimulus response result showzng an experimental result are correlated. Such correlatzvn and data correlated thereby are called experimental data.
The digital cell is provided as a collection of at least one experimental data an a cell of experimental interest.
Figure 338 shows another example of data structure of the diga.tal cell. This example shows the layered structure of the data structure shown in Figure 33A.
As such, layering the structure of the data structure of the digital Gell allows expression of the same content with less data than the data structure shown in Figure 33A.
In the examples of figures 33A and 33B, correlation has bean presented by a unidirectional link (arrows in the Figures) between the parameter showing the experimental conditions and experimental results. Iiawever, methodsof correlation are not limited thereto. Any methods of correlation may be used herein.
(Production of a digital cell) Figure 34 shows an example of the procedure of a process of producing a digital cell. This procedure may be implemented by any type of computer_ Step 5340.: Cell parameters specifying a cell of experimental interest are obtained. CeXI parameters can be obtained by, for example, receiving cel 1 parameters inputted by a user into a computer. Alternatively, data outputted from an experimental apparatus ma y be obtained by collection ox analysis of the same in an automatic manner by a computer to obtain cell parameters.
Step 53402: Environment parameters specifying an environment under which the cell specified by the cell parameters is cultured, are obtained. The environment parameters are obtained by xeoe,iving, by a computer, environment parameters inputted by a user, for example.
Alternatively, environment parameters may be obtained by automatically collecting or analyzing data outputted from an experimental apparatus (for example, sensors measuring experimental environment and the like) and the li.ke, by a computer. The environment parameters include, for example, parameters representing a medium fox Culturing a cell and a parameter representing conditions for such culture.
Parameters of such culture conditions include for example, pH, ~.emperature, Ca2 concentration of the medium, and the like.
Step 53403: Stimulus parameter specifying a stimulus to be given to a cell specified by the cell parameter. A
stimulus parameter is obteained by, for example, receiving, by a computer, a stimulus parameter inputted by a user.
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Z~lternatively, a stimulus parameter may be obtained by automatically collecting or analyzing, by a computer, data outputted by an experimental apparatus. Such a stimulus parameter may comprise, for example, a parameter representing a reporter and a parameter zepresenting a chemical stimulus.
Stop 53404: A st~.mu~.us response result showing the xesult ~.n xesponse to a stimulus by the stimulus parameter, by a cell specified by the cell parameter under the orivirozsrnent spea~.fied by the environment parameter, is obtained. The stimulus response result is obtained by automatically collecting or analyzing data outputted from an experimental apparatus such as monitoring apparatus for monitoring the course of experiments.
Step 53405: The cell parameter, the environment parameter, the stimulus parameter and the stimulus response result are correlated with each other. This correlation allows production of an experimental data against a cell of experimental interest. Such a correlation is conducted by linking in a single direction shown in Figure 33A.
However, methods correlation is not limited to such.
Step 5340: Steps 53401 through 53405 are repeated as necessary. This allows production of at least one experimental data against a cell of experimenfial interest . The collection of at least one experimental data is pxovided as a digital cell.
The computer implementing the process for producing a digital cell, functions as an apparatus or device for producing a digital cell. The digital cell producEd is stored on, for example, a database which can be accessed by the computer.
As such, provision of a digita 1 sell of a collection of at 'least one experimental data, is only possible by the present inventors by providing and developing technologies for locating a plurality of cells on a substrate under a consistent environment.
Conventionally, in the prior art, it was not possible to maintain a plurality of cells under a consistent environment, and thus the experimental conditions have not been reliable, and thus no significance is found when accumulating experimental data bEtween experiments. T-~s such, the "production of a digital cell" is a real advance in technology which is feasible for the first time through the technological inno~cra~tion of the present inventors.
(Provision of a method of reproducing experimental results against an actual cell) Figure 85 depicts an example of a configuration of computer system 3501 which provides a service reproducing an experimental result obtained using an actual cell using the digital cell.
Computer system 3501 comprises service requester 3510 requesting a service desired by a user, and service provider 3520 providing the des~.red service in 2~4 response to the request.
~1r007 Computer system 3501 may comprise a plurality of service requesters 3510.
Service provider 3520 is configured so as to be capable of accessing database 3522 with at least one digital cell stored thereon. A database structure of the digital cell stored on database 3522 is shown in, for example, Figures 33A and 338. Database 3522 may be provided inside service provider 3520, yr may be located outside service provider 3520.
Sexvice provider 3520 may be configured so as to be capable of accessing a plura7.ity of databases stored thereon with respect to at least one digital cell.
Service requester 35x0 and service provider 3520 may independently be any type of computer.
Service requester 3510 and service provider 3520 are connected to each other via network 3530. Network 3530 may be any type of network, but in view of fEasibility of connection or cost, most prefexabl~r, the network is the Internet.
When network 3530 is the Intexnet, service requester 3510 may be a Web browser operatEd by a user, and service provider 3520 may be a Web server connected to service requester via the Intexnet. Such a configuration alJ.ows any user across the entire world easy access to service provider 3520.
Figure 36 depicts an example of process for providing a service of reproducing an experimental result against an actual cell using a digital cell. This process may be implemented by cooperating service requester 3510 and service provider 3520.
Step S3601: Service requester 3510 receives cell and environment parameters and prnduoes request comprising the cell parameter, the environment parameter and the stimulus parameter. The request is described in, for example, XML.
Step 53602: Service request 3510 provides the request to service provider 3520.
Step 53603: Service provider 3520 searches for database 3522 in response to the request, to determine whether or not there is a stimulus response result relating to the cell parameter, the.envixonxnent parameter and the stimulus parameter included z.n the request in database 3522.
Step 53604: when it is determined that there exists a stimulus response result relating to the cexl parameter, the environment parameter and the stimulus parameter included in the request in database 3522, service provider 320 prQVi.des sexvice requester 3510 with the stimulus response result. The stimulus response result is described in, for example, XML.
Step 53605: Service requester 3510 displays the stimulus response result provided by service provider 3520.
If it is determined there is no stimulus response result relating to the cell parameter, the environment parameter and the stimulus parameter irioluded in the requested ~.n database 3522, service provider 3520 provides service requester 3510 with a result of "no hit", for ~. 0 example .
Procedures as shown in Figure 36 may be processed in a single computer. For example, a single computer program in a single computer may be used for implementing the procedures of steps 53601 through S3605 shown in Figure 36.
In this case, such a single computer functions as an apparatus having the caznbined functions of service requester 3510 and service providEr 3520.
Figure 37 depicts an example of input interface fpr inputting a cell parameter, an environment parameter and a stimulus parameter to service 3510. Zn this example, these parameters are inputted by inputting these parameters as texts by a user ~.nto a desired region.
Any number of methods may be employed as a method far inputting these parameters into service requester 3510.
For example, these parameters may be inputted by choosing these parameters from a menu ( such as, pu~.l-down menu, pop~-up menu and the like) by a user.
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Service requester 3510 may employ any embodiment for displaying the stimulus response result.
For example, service requester 35x0 may display the stimulus response result on a display screen, or may output the stimulus response xesult to a printer. Service requester 3510 may display the stimulus response result us~.r~g a still image or display the stimulus response result using movie display.
The stimulus response result may ~.zxcluda profile data of a cell obtained by mon~.toring a biological agent or a collection thereof on or in a cell over time.
In such a case, for example, the profile data of a cell shown in Figure 19 may be displayed by service requester 3510 as the stimulus response result.
As such, according to computer system 3510, it is now possible to provide a service of reproducing an experimental result for an actual celz using the digital cell. ~1s such, it is possible to conduct an advanced search relating to a cell even by a research organization or an individual without experimental facilities.
Figure 38 depicts an example of configurations of computer system 3801 for providing a serv~.oe of reproducing an experimental result against an actual cell using the digitax cell.
Computer system 3801 comprises service requester 3810 requesting a service desired 3~y a user; a plurality of service prov3.ders 382013$20N: and setvica registry 3$40 with registration of at least one service which can be provided by a plux~aiity of service providers 382013$20N, wherein N is an a~iy integer of two or more.
Computer system 3801 may include a plurality of service requesters 3810. Service provider 38201 is configured so as to be capable of accessing database 38221 at least Qne digital cell stored thereon. A data structure of a digital cell stored on database 38221 is as shown in Figures 33A and 33H. Database 3822 may be provided in service provider 38201 or outside service provider 3820, wherein 1 = 1, 2, N.
Service provider 38201 may be configured to be capable of accessing a plurality of databases with at least one digital cell each stored thereon.
Service registry 3840 is configured to be capable of accessing database 3842 with data stored thereon representing services being capable of being prQVided by service providers 38201 to 3820N. Database 3842 may be provided in service registry or outside service registry 3840. Storing data representing sexv~.ces on database 3842 allows registration of services to service registry 3840.
Formats of data stored on database 3842 are preferably pre-normalized. Storage of data to database 3842 may be performed manually by a firm managing service registry 3840 or by transmitting data from service providers 38201 to 3820N
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via network 383D to service registry 384p.
Each service requester 3810, service provider 3820 1 to 3620N and service registry 3840 may be any type of computer.
Each of service providers 382D1 to 3820N is preferably conducted by research parried out by any of organizations, firms or any other corporation possessing experimental faCZlities which conducts research vz'1 an actual cell. Each of servipe requester 3810 and service registry 3840 is preferably condupted by any of organizations, f~.rms or any other corporat~.on (for example, an association for promoting digital cells) managing provision of s~:rvices of reproducing experimental results against an actual cell using the digital cell. Further, in order to secure the quality of services reg~.stered to service registry 3840, it is preferable to oblige such an o~cganization which manages serva.ce providers 38201 to 3820N to satisfy a predetermined standard.
Service requester 3810, service provider 38201 to 3820N and sexv~.ce registry 3840 are connected via network 383D. Network 3830 is of any type but most preferably, in 2S view of ease of connection and cost, is 'the Internet.
When network 3830 is the Internet, service requester 38.0 xnay be a Web server connected to a Web browser operated by a user via the Internet. Each of 3820138217N may be a Web servex connected to service requester 3810 via the Azoo~
Internet. In this case, service requester 3810 functions as portal or Website interrelaying to a Web browser operated by a user and a Web server of service provider 38201. This configuration allows easy access to serv~.ce providerB of 38201 to 3820N by users all over the world, and it is now possible for research institutes andlvr firms all over the world to participate in the business of providing th~ service of reproducing experimental results against an actual cell using a digital cell.
Figure 3g depicts an example of a .process for providing a service of reproducing an experimental result against an actual cell using the digital Cell. This procedure is implemented by cooperating serv~.ce requester 3810 and service providers 38201 with 3820N.
Step 53910: Service requester 3810 receives a cell parameter, an environment parameter, and a stimulus parameter, and produces d. request comprising such a cell parameter, an environment parameter, and a stimulus parameter. Such a request is described in, for r~~rample, XMT.~ .
Step 53902: Service requester 3810 searches service registry 3840 responding to the request, and determines whethex ar not there exists a service provider 3820f which can provide a service of the requester amongst sexvice provides 3820 to 3820N, wherein 1 is any ~.nteger of x to N.
Service providers 38201 to 3820~a may employ any type of method for register services which can be provided by service providers 38201 to 3820N on service registry 3840.
For example, when service provider 38201 is capable of providing a service of reproducing ari experimental result against cell A, then cell parameters specifying cell A and addresses (for example, URi~ and the like) specifying the locations of service provider 3$201 may be stored on database 3842. Far example, zf service provider 38202 can provide services of reproducing cells B and C, then cell parameters specifying cell A and addresses (for example, URh and the like) specifying the locations of service provider 38202 may be stored on database 3$42. Alternatively, when service provider can provide the service of reproducing experimental results satisfying specific experimental conditions agaiz~st cell D, then parameters such as environment parameters and stimulus parameters specifying the experimental conditions and addresses (for example, a URL and the like) specifying the locations of service provider 38203 may be stored on database 3842.
Step 53903: If there exists a service provider 38201 which can provide a service of the requester, amongst service providers 38201 to 3820, such service requester 3810 provides service provider 38201 with the request. The location of service provider 3$20 may be specified by referring t.o database 3842 of service registry 3940.
Step S3904: service provider 38201 searches database 38221 in response to the request, and determines whether ox not there exists the stimulus response result relating to the cell parameter, the environment parameter and the stimuJ.us parameter included in the request in database 38221.
Step 53905: If determined that there exists a stimulus response result relating to the cell parameter, the environment parameter and the stimulus parameter included in the request in database 38221, service prov~.der 3B20~ provides service requester 3810 With the stimulus response result. The stimulus response result is described in, for example, XML.
Step 53906: service requester 3810 displays stimulus response result prpvided by service provider 38201.
If determined that there is no stimulus response result relatzng to the cell parameter, environment parameter and stimulus parameter containr~d in the request ~.n database 3822, service provider 38201 wrill provide serv~.ce requester 3810 w~.th, for example, the result of "no hit" .
As described above, any number of methodologies may be employed as a method for inputt~.ng a cell parameter, an environment parameter and a stimulus parameter to service requester 3810, and further any forms may be employed as a form of displaying stimuXus response result by service requester 3810.
As such, according to computer system 3810, it is possible to provide a ser,crice of reproducing an experimental result against an actual cell using the digital cell. This allows research institutes or individual having no experimental facilities to pexform advanced research activities relating to a cell. Further, according to computer system 3801, registration of services capable of being provided by a plurality of service providers $$20i to 3820N, provides opportunities to participate in the business 1.0 of providing the service of reproducing experimental results against an actual cell using the digital cell to research organizations or fixrns all over the world.
All patents, published patent applications and publications cited herein are incorporated by reference as if set forth fully herein.
The preferred embodiments of the pxesent invention have been heretofore described far a better understanding of the present invention. Hereinafter, the present invention will be described by way of examples.
Examples described below are provided only for illu8trative purposes . Accordingly, the scope of the present invention is not limited except as by the appended claims . According to the examples below, it will be understood that those skilled in the art can select cells, supports, biological agents, salts, positively charged substances, negatively chaxged substances, actin-like acting substances, and the like, as appropriate, and can make or carry out the present invention.
EXAMPLES
Hereinafter, the present invention will be described in greater detail by Way of examples, though the present invention is not limited to the examples below.
Reagents, supports, and the like~are commerciaJ.J.y avaiXable from Sigma (St. Louis, USA) , Wako Pure Chemical industries (Osaka, Japan), Matsunami Glass (Kishiwada, Japan) unless otherwise specified.
(Example 1: Reagents) formulations below were prepared ~.n Exempla 1.
As candidates for an actin-like acting substance, various extracellular matrix proteins and variants or fragments thereof were prepared in Example I, as listed below. Fibronectin and the like were commercially available. Fragments and variants were obtained by genetic engineering techniques:
1) fibronectin (~SEQ ID NO.: 11);
2) fibronectin 29 kDa fragment;
~) fibroneotxn 43 kDa fragment:
4) fibronectin 72 kDa fragment:
5) fibronectin variant (SEQ zD NO. : 11, alanine at 152 was substituted with leucine);
6) ProNectin F (Sanyo Chemical Industries, Kyoto, Japan);
7) ProNectin L (Sanyp Chemical Industries);
8 ) ProNectin Plus ( Sanyo Chezn,icaJ. Zndustrias ) ;
9) laminin (SEQ TD NO.: 6);
) RGD peptide ( tr~.peptide ) ;
11) RGD-containing 30kDa peptide;
12) 5 amigo acids of laminin (IKVAV, SEQ zD NO.: 28); and 5 13) gelatin.
Plasmids were prepared as DNA for transfection.
Q~.asmids, pEGFP-N1 and pDsRed2--N1 (bath from BD Biosciences, Clontech, CA, U5A) were used. In these plasmids, gene 10 Expression was under the control of cytomegalovirus (CMV) .
The plasmid DNA was amplified in E. coli (XL1 blue, St rat gene, TX, USA) and the amplified plasmid DNA was used as a oomp~.ex partner. The DNA was dissolved in distilled watex free from DNa.se and RNase .
The following transfection reagents were used:
Effectene Transfeotic~n Reagent (cat. no. 301425, Qiagen, CA) , TransFast~ Transfection Reagent (E2431, Promega, WI ) , Tfx~~20 Reagent (E2391, Promega, WI), SuperFect Transfection Reagent (301305, Qiagen, CA), PolyFeot Transfection Reagent (301105, Qiagen, CA), I,ipofectAMINE
2000 Reagent (11668-019, Tntritrogen corporation, CA), JetPEI (x4) conc. (101-30, Polyplus-transfection, France), and ExGen 500 (R0511, Fermentas Inc., MD). These transfection reagents were added to the above-described DNA
and actin-like acting substances in advance, or complexes thereof with the DNA were produced in advanoe.
The thus-obtained solution was used in assays using transfection arrays described below.
(Example 2: Transfection array - Demonstration using meaenchymal stem cells) In Example 2, an improvement in the transfection efficiency in solid phase was observed. The protocol used in Example 2 will be described below.
(Protocol) The final concentration of DNA was adjusted to 1 ~g/~L. An actin-like acting substance was preserved as a stock having a concentration of 10 pg/~.L in ddHzO. Ail dilutions were made using PBS, ddHzO, or Dulbecco' s MEM. A
series of dilutions, for example, 0.2 ~tg/~L, 0.27 ~.eg/~,~,L, 0.4 ~g/~.t.L, 0.53 E.~,g/'~.L, 0.6 ~i.g/J.I.L, 0.8 ~.tg/~L, 1.0 ~.g/~L, 1.07 ~g/~.L, 1.33 ~tg/).iL, and the like, were formulated.
Transfeetion reagents were used in accordance with instructions provided by each manufacturer.
Plasmid DNA was removed from a glycerol stock and amplified zz~ x.00 mL L--amp overnight. Qiaprep Miniprep or Qiagen Plasmid Purification Maxi was used to purify DNA
in accordance with a standard protocol provided by the manufacturer.
In Example 2, the following 5 cells were used to confirm an effect: human mesenchymal stem cell (hM~Cs, PT-2501, Cambrex BioScience ~nTalkersville, Inc. , MD) : human embryonic renal cell (HEK293, RCB1637, RTKEN Cell Eank, JPN); NIH3T3-3 cell (RCB0150, RIKEN Cell Bank, JPN); HeLa cell (RC80007, RIKEN Cell 8ank,JPN)~ and HepG2(RCH1648, RIKEN Cell Bank, JPN) . These cells were cultured in DMEM/10%
IFS containing L-glut and pen/strep.
(Dilutzan and DNA spats) Transfectian reagents and DNA were mixed to form a DNA-transfection reagent complex. Formation of the complex requires a certain period of time. Therefore, the mi~rture was spotted onto a solid phase support (e.g., a poly-L-lysine slide) using an arrayer. In Example 2, as a solid phase support, an APS slide, a MAS slide, and an uncoated slide were used as well as a poly-L-lysine slide.
These slides are available from Matsunami Glass (Kishiwada, Japan) or the like.
For complex formation and spat fixation, the slides were dried overnight in a vacuum dryer. Drying was performed for a duration in the range of 2 hours to 1 week.
2p Although the actin-like acting substance might be used during the complex formation, it was aXsa used immediately before spotting in Example 2.
(formulation of mixed solution and application to solid phase supports) 300 ~L of DNA concentrated buffer (EC buffer) + 16 ~ of an enhancer were mixed in an Eppendorf tube. The mixture was mixed with a vortex, followed by incubation for 5 minutes. 50' ~L of a transfectiari reagent (EffeCtene, etc.) was added to the mixture, followed by mixing by A=007 pipetting. To apply ~a transfection reagent, an annular wax barrier was formed.around the spots on the slide_ 3~6 ~L
of the mixture was added to the spot region surrounded by the wax, followed by incubation at room temperature fox 10 to 20 minutes. Thereby, the fixation to the support was manually aohiwsred.
(D~.stribution of cells) Next, a protocol for adding cells will be described. Cells were distributed far transfection. The distribution was typically performed by reduced-pressure suction in a hood. A slide was placed on a dish, and a solution containing cells was added to the dish for transfection. The~cells were distributed as follows.
The gxowing cells were distributed to a concentration of 10' aells/25 mL. The cells were plated on the slide in a 100x100x15 mm squaxed Petri dish or a 100 mm (radius) x xS mm circular dish. Transfectian eras conducted for about 40 hours. This period of time corresponded to about 2 cell cycles. The slide was treated for immunofluorescence.
(Evaluation of gene introduction) gene introduction was evaluated by detection using, for example, immunofluorescence, fluorescence microscope examination, laser scanning, radioactive labels, and sensitive films, or amulsion.
When an expressed protein to be visualized is a fluorescent protein, such a protein can be observed with a fluorescence microscope and a photograph thereof can be taken. Far large-sized expression arrays, slides may be scanned using a laser scanner for storage of data. If an expressed protein can be detected using fluorescent antibodies, an immunofluorescence protocol can be successively performed. 2f detect~.on is based on radioactivity, the slide may be adhered as described above, and autoradiography using film or emulsion can be performed to detect radioactivity.
(Laser scanning and Quantification of fluorescence intensity) To quantify transfection efficiency, the present inventors use a DNA microarray scanner (GezIeTAC
UC4x4, Genomic Solutions Inc., MT). Total fluorescence intensity (arbitrary unit) was measured, and thereafter, fluorescence intensity per unit surface area Was calculated.
(Cross-sectional observation by confocal scanning microscope) Cells were seeded on tissue culture dishes at a final concentration of 1x105 cells/well. arid cultured in appropriate medium (Human Mesenchymal Cell Basal Medium (MSCGM BulletKit PT-3001, Cambrex BioScience Walkersville, Inc., MD). After fixation of the cell layer with 4%
paraformaldehyde solution, SYTO and Texas Red-X phalloidin (Molecular Probes Inc . , OR, USA) was added to the Cell. ~.ayex for observation of nuclei and F-actin. The samp~.es emitting light due to gene products and the stained samples were observed with a confocal laser microscope (t~SM510: Carl Zeiss Co. , T~td. , pin hole szze=Chl=123 ~,am, Ch2=108 Elm, image interval = 0.4) to obtain cross sectional views.
(Results) Figure 1 shows the results of experiments in which various actin-like acting substances and HEK293 cells were used where gelatin was usEd as a control.
~. 0 As can be seen from the results, whereas transfection was not very successful in a system using gelatin, transfection took place to a significant ~.evel in systems using fibronectin, ProNectin (ProNectin F, ProNectin L, ProNectin Plus) which is a variant of fibronectin, and laminin. Therefore, it was demonstrated that these molecules significantly increased transfection efficiency. Use of the RGD peptide alone exhibited substantially no effect.
figures Z and 3 show transfection efficiency when fibronectin fragments were used. Figure ~4 shows the summary of the results. 29 kDa and 72 kDa fragments exhibited a significant level of transfection activity, while a 43 kDa fragment had activity but its level was low.
Therefore, ~.t was suggested that an amino acid sequence contained in the 29 kDa fragment played a role in an increase in transfection efficiency. Substantially no contam~.nation wasp found in the case of the 29 kDa fragment, while contamination was observed in the case of the other two fragments (43 kDa and 72 kDa) . Therefor, only the 29 kDa dvrnain may be preferably used as an actin-like acting substance. When only the RGD peptide was used, increased transfection efficiency was not exhibited. The 29-kDa peptide therefore exhibited activity with respect to enhancing transfection efficiency. Such a system with an additional 6 amino acids of laminin (higher molecular weight) exhibited transfection activity. Therefore, these peptide sequences may also play an important role in increased transfection efficiency, without limitation. In such a case, a molecular weight of at least 5 kDa, preferably at least 10 kDa, and more preferably at least 15 kDa may be requ~.red for an increase in transfection efficiency.
Next, Figure 5 shows the result of studies on the transfection efficiency of cells. In Figure 5, HEK293 cells, HeLa cells, and 3T3 cells, which were conventionally transfectable, and HepG2 cells and mesenchymal stem cells (MSC) which were conventionally believed to be substantially impassible to tran9fect, were used to show the effect o~ the transfeCtion me'~hod of the present invention. The vertical. axis represents the intensity of GFP.
In Figure 5, the transfection method of the present invention using a solid phase support was compared with a conventional liquid phase transfection method. The conventional liquid phase transfection method was conducted in accordance with a protocol recommended by the kit manufacturer.
~ 62 Ax007 As can be seen from Figure.5, transfection efficiency compaxable to HeT~a and 3f3 was achieved in HepG2 cells and mesenchymal stem cells (MSC) which were conventionally believed to be substant~.ally impossible to transfect, as well as HEK293 cells, HeLa cells, and 3T3 cells, which wexe conventionally txansfectable. Such an effect was not aohie~red by conventional transfection systems . The present invention was the first to provide a system which can increase transfection efficiency for substantially all cells and can provide practicable transfection to all cells _ By using solid phase conditions, cross contamination was significantly reduced. Therefore, it was demonstrated that the present invention using a solid phase support is 1.5 appropriate for production of an integrated bioarray.
Next, Figure 6 shows the results of transfection when various plates Were used. As can be seen from the xesults of figure 6, when coating was provided, contamination was reduced as compared with when coating was not provided and transfection efficiency was increased.
Next, Figure 7 shows the results of transfection where the concentration of fibroneotin was 0, 0.27, 0.53, 0.8, 1.07, and 1.33 (~g/~L for each). In Figure 7, slides coated with PLL (poly-L-lysine), APS and uncoated slides were shown.
As can be seen from the results of Figure 7, transfection efficiency was ~.ncreased with an increase in fibronectin concentration. Note that in the case of PLL
coating and the absence of coating, the transfection efficiency reached a phateau at a fibronectin concentration of more than 0.53 ~g/~.~.L. In the case of APS, it was found that the effect was further increased at a fibxen.ectin concentration of more than of 1.07 ~g/~L.
Next, Figure 8 shows photographs indicating cell adhesion profiles i.n the presence or absence of fibronectin. Figure 9 shows cross-sectional photographs.
It was revealed that the morphology of adherent cells were .significantly different (Figure 8) . The full extension of cells was found for the initial 3 hours of culture iri the presence of f~.branectin, while extension was limited in the absence of fibronectin (Figure 9). Considering the behavior of filaments (Figure 9) and the results of the time-lapse observation, it was considered that an actin-like acting substance, such as fibronectin, af.tached to a solid phase support had an influence on the shape and orientation of actin filaments, and the efficiency of introduction d~ a substance into a cell, such as transfection efficiency yr the like, was thus increased. Specifically, actin filaments quickly change their location in the presence of fibronectin, and disappear from the cytoplasmxc space under the nucleus as the cell extends. It is considered that actin depletion in the perinucleax space, which is induced by an actin-like acting substance, such as fibronectin, allows the transport of a target substance, such as DNA or the like, into cells or nuclei. Though not wishing to be bound by any thevx~y, the reason is considered Ar007 to be that the viscosity of cytoplasm is reduced and positively charged DNA particles are prevented from being trapped by. negatively charged actin filaments.
Additionally, it is considered that the surface area of the S nucleus is significantly increased in the presence of fibronectin (Figure 10), possibly facilitating the transfer of a target substance, such as DNA or the like, into nuclei.
(Example ~: Application to bioarrays) Next, larger-scale experiments were conducted to determine whether or not the above-described effect was demonstrated when arrays were used.
(Experimental protocols) (Cell S4uroe~, culture media, and culture conditions) In this example, five different c~:ll lines wexe used: human mesenchymal stem cells (hMSCs, PT-2501, Cambrex BiaScience Walkersville, Tnc,, MD), human embryonic kidney ce~.l HEK293 (RCB1637, RIKEN Cell Bank, JPN), NZI~3T3-3 (RC80150, RIKEN Cell Bank, JPN), HeZa (RCB0007, RIKEN Cell Bank, JPN), and HepG2 (RCB164B, RIKEN Cell Bank, JPN). In the case of human MSCs, cells were maintained in commercialized Human Mesenchymal Cell Basal. Medium (MSCGM
aul.letKit PT-3001, Cambrex BioScience'Walkersville, inc., MD) . In case of HEK293, NzH5T3-3, HeLa and FiepG2, cells were maintained in Dulbecco's Modified Eagles Medium (DMEM, high glucose 4.5 g/L with L-Glut amine and sodium pyruvate~
14246-25, Naka.lai Tesque, JPN} with 10~ fetal bovine serum Az007 (FBS, 29-167-54, Lot No. 2025F, Dainippon Pharmaceutical CO_ , LTD. , JPN) . All cells were cultivated in a contxo7.led incubator at 37°C in 5~ COz. In experiments involving hMSCs, we used hMSCs of less than five passages, in order to avoid phenotypic changes.
(Plasmids and Transfection reagents) To evaluate the efficiency of transfection, the pEGFP-N1 and pDsRed2-Nl vectors (cat. no. 6085--1, 6973-~., BD Biosciences Clontech, CA) were used. Both genes' expressions were under the control of cytomegalovirus (CMV) promoter. Transfected cells continuously expressed EGFP or DsRed2, respectiveJ.y. Plasm~.d DNAS were amplified using Escherichia coli, XI,~.-blue strain (200249, Stratagene, TX) , and purified by EndoFree Plasmid Kit (EndoFxee Qlasznid Maxi Kit 12362, QIAGEN, CA). In all cases, plasmid DNA was dissolved in DNase and RNase free water. Transfection reagents were obtained as below: Effectene Transfection Reagent (cat. no.301425, Qiagen, CA), TransFast~
Transfection Reagent (E2431, Promega, WI) , Tfx~-20 Reagent (E2391, Promega,~ WI), SuperFeat Transfection Reagent (301305, Qiagen, CA), PolyFect Transfection Reagent (301105, Qiagen, CA), LipofectAMINE 2000 Reagent (11668-019, Invitrogen corporation, CA), JetPEr (x4) conc. (101-30, Polyplus-transfection, France), and ExGen 500 (R0511, Fermentas Inc., MD).
(Solid-Phase Transfection Array (SPTA) production) The detail of protocols for 'reverse A20o7 transfection' are described in the web site, 'Reverse Transfection HomEpage' (http://staffs.wi.mit.edu/sabatini~ublic/reverse trans fe~t~.on.htm) or J. Ziauddin,.D. M. 5abatinz, Nature, 411, 2001, 107; and R.W. Zu, S.N. Eailey, D.M. Sabatini, Trends in Cell Biology, Vol. 12, No. 10, 485. In our solid phase transfection (SPTA method) , three types of glass slides were studied (silanized glass slidesi APS slides, and poly-h-lysine coated glass slides: PLZ slides, and MAS
coated slides; Matsunami Glass, JPN) with a 48 square pattern (3 mm x 3 mm) separated by a hydrophobic fluoride resin coating.
(Plasmid DNA printing solution preparation) Two different ways to produce a SPTA were developed. The main differences reside in the preparation of the plasmid DNA printing solution.
(Method A) In the case of using Effectene Transfection Reagent, the printing solution contained plasmid DNA and cell adhesiozl molecules (bovine plasma fibronectin (cat.
no. 16042-47., Nakalai Tesque, JPN) , dissolved in ultra-pure water at a concentration of 4 mg/mL). The abo~cre solution was applied on the surface of the slide using an ink~et printer (synQUAD~, Cartesian Technologies, InC., CA) or manually, using a 0.5 to 30 ~,L tip. This printed slide was dried up over 15 minutes at room temperature in a safety-cabinet. Before transfeCtzon, total Effecterie reagent was gently poured on the DNJ~r-printed glass slide Alpa~
and incubated for 15 minutes at. room temperature. The e~tcess Effectene solution was removed from the glass slide using a vacuum aspirator and dried up at room temperature fox 15 minutes in a safety-cabinet. The DNA-printed glass slide obtained was set in the bottom of a 100-mm culture dish and approximately 25 m~, of cell suspension (2 to 4x104 cells/m~) was gently poured into the dish. Then, the dish was transferred to the incubator at 37°C in 5% COZ and incubated for 2 ar 3 days.
(Method B) Iri case of other transfection reagdnts (TransFastT~°, TfxTM-20, SuperFect, PolyFect, LipofectAMINE
2000, JetPEI (x4 ) conc. , or ExGen) , plasmid DNA, fibroneCt~.n, and the transfection reagent were mixed homogeneously in a x.5--mL micro-tube according to the ratios i~xdicated in the manufacturer s instructions and incubated at room temperature for 15 minutes before print~.~ng on a chip. The printing solution was applied onto the surface of the glass-slzde using an inkjet printer or a 0.5- to 10-~tL tip.
The pz~~.nted glass-slide was completely dried up at room temperature over 10 minutes in a safety-cabinet. The pz~inted glass-slide was placed in the bottom of a 100--z~un culture dish and approximately 3 mL of sell suspension (2 to ~ixl0° cel~.s/mL) was added and incubated at room temperature over 15 minutes in a safety-cabinet. After incubation, fresh medium was poured gently into the dish.
Then, the dish was transferred to an incubator at 37°C in 5% C02 and incubated for 2 to 3 days. After incubation, using fluorescence microscopy (IX-71, Olympus PROMARKETING, INC., use Azoa~
~7PN) , we obaer~red the transfectants, based on their expression of enhanced fluorescent proteins ( EFP, EGFP and DsRed2). Phase cantrast images were taken with the same microscope. In both protocols, calls were fixed using a paraformaldehyde (PFA) fixation method (4~ PFA in PBS, treatment time was 10 minutes at room tEmpe raturE).
(Laser scanning and fluorescence intensity quantification) In order to quantify the transfection efficiency, we used a DNA micro-array scanner (~eneTAC UC4x4, Genomic SoJ.utaans Znc., MI). The total fluorescence intensity (arbitrary units) was measured, and thereafter, the fluorescence intensity per surface area was calculated.
(Results) (Fibronectin-supported localized transfection) A transfeetion array chap was constructed as shown in Figure 11. The transfection array chip was constructed by microprinting a cell cultivation medium solution containing fibronectin and DNA/transfectian reagent onto a poly L lysine (PLL) coated g lass slide.
Various cells were used for this example. The cells were cultivated under typical cell aulti~ration conditions . As they adhered to the glass slide, the cells ef~i.ciently incorporated and expressed the genes corresponding to the DNA printed at a given position on the array. As compared to conventional transfe ction methods Az007 (e. g., cationic lipid or cationic polymer-mediated transfection), the efficiency of transfection using the method of the present invention was high in all the cells tested. Importantly, it was found that tissue stem cells, such as HepG2 and hMSC, which were conventionally believed to resist transfection, were efficiently transfeCted. hMSC
was transfected at an efficiency 40 or more times higher than that of conventional techniques. Tn addition, high spatial localization, which is required for high-density arrays, was achieved (low cross contamination between adjacent spats on the array). This was confirmed by production of a checkered pattern array of EGFP and Ds--Red.
hMSC cultivated on this array expressed the corresponding f~.uarescent proteins with virtually total. space resolution.
The result is shown in Fa.gure 12. As can be seen from Figure l2, i.t was found that there was little cross contamination. Based on the study of the role of the individual components of the printed mixture, transfection efficiency can be optimized.
(Solid-phase transfection array of human mesenchymal stem cells) The capacity of human Mesenchymal Stem Cells (hMSC) to differentiate into various kinds of cel~.s is particularly intriguing in studies which target tissue regeneration and renewal. In particular, the genetic analysis of transformation of these cells has attracted attention with expectation of understanding of a factor that controls the pluripotency of hMSC. In conventional hMSC
studies, it is not possible to perform transtection with desired genet~.c materials.
Azoo7 (solid-phase transfection array of human mesenchymal stem cells) The capacity of human Mesenchymal Stem Cells (hMSC) to differentiate into various kinds of cells is particularly intriguing in studies which target tissue regeneration and renewal. In particular, the genetic analysis of transformation of these cells has attracted 1.0 attention with expectation of understanding a factor that controls the pluripotency of hMSC. In canventional hMSC
studies, it is not possible to per~arm transfection with desired genetic materia~.s.
To achieve this, conventional methods include either a viral vector technique or electroporation. The present inventors developed a complex-salt system, which could be used to achieve solid phase transfection which makes it possible to obtain high transfeotian effiaa,ency to various cell lines (including hM$C) and special localization in high-density arxays. Are outline of solid phase tzansfection is shown in Figure 19A.
It was demonstrated that solid phase transfection can be used to achieve a "transfection patch"
capable of being used for in vivo gene delivery and a solid phase transfection array (SPTA) for high-throughput genetic function research on hMSC.
Although a number of standard techniques are 271.
available for transfeoting mammalian cells, it is known that it is inconvenient and difficult to introduce genetic material into hMSC as compared with cell lfines, such as HEK293, HeLa, and the like. Conventional ~rira~, vector delivery and electroporation techniques are both ~.mportant.
However, these techniques have the following inconveniences: potential toxicity (for the virus technique); difficulty in high,throughput analysis at the g~nomic scale; and limited appl.i.cations in vivo studies (for electroporation?.
The present inventors develop~d a so7.~.d phase support fixed system which can be eas~.ly fixed to a solid phase support and has sustained-release capability and cell affinity, whereby most of the above-described drawbacks could be overcome.
An example of the results of the above-described experiment is shown in Figure 138. The present inventors used our microprinting technique to fix a mixture of a selected genetic material, a transfection reagent, an appropriate cell adhesion molecule, and a salt onto a solid support. By culturing cells on a support having such a mixture fixed thereonto, the gene contained in the mixture was taken in by the cultured ceJ.ls . 1~s a resu~.t, it became possible to facilitate support-adherent ce 11s to take ire DNA spatially separated therefrom (Figure 138).
As a result of this example, several important effects were achieved: high transfection efficiency (thereby making it possible to study a group of cells on a statistically significant scale)] low cross contamination between regions having different DNA molecules (thereby making it possible to study the effects of different genes separately); the extended survival of transfected cells;
high-throughput, compatible and simple detecting procedure.
SPTA having these features sexves as an appxdpriate baeis for further studies.
To achieve the above-described objects, the present inventors studied five different cell dines (HEK293, HeLa, NIH3T3, HepG2 and hMSC) as described above with both our methodology (transfection in a solid phase system) (see Figures 13A and 13C) and conventional liquid-phase transfection under a series of transfection conditions.
Cross contamination was eva7.uated for both systems as follows. In the case of SPTA, we printed DNA's encoding a red fluorescent protein (RFP) and a green fluorescent protein (GFP) on glass supports in a checked pattern. In the Case of experiments including conventional liquid phase transfectian (where cells to be transfected cannot be spatially separated Exam one another spontaneously) , a DNA
encoding GFP was used. Several transfection reagents were evaluated: four liquid transfection reagexlts (Effectene, TransFast~, Tfx~-20, LopofectAMrNE 2000) , two pol~ra.mine (SuperFect, PolyFect), and two polyimine (JetPEI (x4) and ExGen 500 ) .
Transfecti.on efficiency: transfection efficiency was determined as total Fluorescence intensity per unit area (Figure 14A and Figure 14B (images)). The results of liquid phase optimal for cell lines used were obtained using different transfection reagents (see Figures ~.4C to 14D). Next, these efficient transfection reagents were used to optimize a solid phase protocol.
Several tendencies were observed. For CeJ.l lines which are readily transfectable (e. g., HER293, HeLa, NIH3T3, etc.), the transfection efficiency observed in the solid phase protocol was slightly superior to, but essentially simixar to, that of the standard liquid phase protocol (Figure 14A
to 7.4D) .
However, for cells which are difficult to transfect (e. g., hMBC, HepG2, etc.), we observed that transfection efficiency was increased up to 40 fold while the features of the cells were retained under conditians optimized to the SPTA methodology (see the above-described protocol and Figures 14C and 14D). in the case of hMSC
(Figures 15A and 15B) , the best conditions included use of a polyethylene imine (P~Iy transfection reagent. As expected, important factorsfor achieving high txansfection efficiency are the charge balance (N/P ratio) between the number of nitrogen atoms (N) in the polymer and the number of phosphate residues (P) in plasmid DNA, and DNA
concentration. Generally, increases in the N/P ratio and the concentration lead to an increase in transfection efficiency. We also observed a significant reduction in the survival rate of hMSC cells in liquid phase transfection experiments where the DNA concentration was high and the N/P ratio was high. Because of these two opposing factors, Az0o7 the liquid phase transfection of hMSC had a relatively low cell survival rate (N/P ratio >10) , In the case of the SPTA
protocol, however, a considerably high N/P ratio Mixed to the solid support) and DNA concentration were tolerable (probably attributable to the effect of the solid support stabilizing cell membranes). while the cell surv~.va~, rate and the cellular state were not significantly affected.
Therefore, this is probably responsible for the dramatic improvement in transfection efficiency. It was found that the N/P rat~.o of 10 was optimal for SPTA, and a sufficient transfection level. was provided while minimizing cytotoxicity. Another reason for the increase in txansfection efficiency observed in the case of the SPTA
protocol is that a high local ratio of the DNA concentration to the transfection reagent concentration was achieved (th~.s leads to cell death in liquid phase transfection expeximents).
The coating agent used is crucial to achieving of high transfection efficiency on Chips. It was found that when a glass chip is used, PZL provided best results both for transfection efficiency and cross contamination (described below). When fibronectin coating was not used, few transfectants were observed (all the other experimental condit~.ons were retained unchanged). Although it's function is not completely established, fibronectin probably plays a rule ~.n a.ccelerating the cell adhesion process (data not shown), and thus limits the time which permits the diffusion of DNA released from the surface.
Low cross contamination: apart from the higher transfection efficiency observed in the SPTA protocol, an important advantage of the technique of the present invention is the provision of an array of separated cells, in which selected genes are expressed in the separate posit~.ons. The present inventars printed JetPEI (see the "Experimental protocols" section) and two different reporter genes (RFP and GFP) mixed with fibronectin on glass surface coated with fibronectin. The resultant transfection chip was subjected to appropriate cell culture.
Expressed GFP and RFP were localized in regions in which corresponding cDNA had been spotted, under experimental conditions which had been found to be best. substantially no cross contamination was observed (Figures ~61~ to l6D).
In the absence of fibronectin or PZL, however, cross contamination which hinders solid phase transfection was observed, and the transfection efficiency was significantly lower (see Figure 6). This result demonstrated the hypothesis that the relative proportion of p~.asmid DNA, which was released from the cell adhesion and the support surface, is an important factor in high transfection efficiency and high cross contamination.
Another cause of cross contamination may be 'the mobility of transfected cells on a solid support. The present ~.nventors measured both the rate of cell adhesion (Figure 16C) and the diffusion rate of plasmid DNA on several supports. As a result, substantially no DNA diffusion occurred under optimum conditioz'zs. I~iowever, a considerable amount of plasmid DNA diffused under high cross Ax007 contamination conditions until cell adhesion was completed, so that plasmid DNA was depleted froze the solid phase surface.
This established technique ~.s of particular importance in the context of cost-effective high-throughput gene function screening. Indeed, the small amounts of transfection reagent and DNA required, as well as the possible automatizatian of the entire process (from plasmid isolation to detection) increase the utility of the above presented method.
In conclusion, the present invention hag successfully realized a hMSC transfection array in a system Z5 using complex-salt. V~ith this technique, it will be possible to achieve high-throughput studies using solid phase transfection, such as the elucidation of the genetic mechanism underpinning the differentiation of pluripotent stem Cells. The detailed mechanism of the solid phase transfection as well as methodologies for the use of this technology for high throughput, real time gene expression monitoring can be applied for various purposes.
(Example 4: Mathematical analysis) Next, time--lapse profiles were produced based on data obtained using the techniques described in Examples 2 and~3.
(Induction of differentiation) Each reporter was fixed to a solid phase support and cultured in undifferentiated mesenchymaZ stem cell maintenance medium (MSCGM, PT--3001, PT-3238, PT-4105, Cambre~, BioWhittaker, USA) for two days. Thereafter, the medium was replaced~with differentiation-inducing medium (hMSC Differentiation, PT-3002, PT-4120, Cambz~ex, BiaWhittaker, U5A). The response profile of each reporter was measured.
(Mathematical analysis technique) 7.p A mathematical analysis technique us~ad herein is shown in Figures 18a and l8B ;18-1 to 18-2).
(Transcription factors used herein) As shown in Figures 19 and 24, plasmids (commercially available from Clontech), in which 17 transcription factors (ISRE, RARE, STAT3, GAS, NFAT, MZC, API, SRE, GRE, CRE, NF~cB, ERE, TRE, E2F; Rb, p53 ) Wexe operably linked to GFP, were used to observe the differentiation of mesenchymal stem cells into osteoblasts. The resultant time-lapse profiles are shown in Figure 19. Reporters for the transcription factors were constructed as shown in Figuxe 23.
An assay was conducted using the reporters for the transcription factoxs under control conditions (sells, suppJ.emental factors, culture conditions, etc.) published by Clontech.
The results are shown in Figure 2b. It wad demonstrated that when Compared only to DNA in this manner, most of the transcription factors were induced when inducing agents were added.
Next, the activity of the transcription factors was measured over tzme in the course of induct~.on of differentiation into bone. Tn this case, time-lapse profiles, which were obtained during the induction of differentiation under the above-described conditions, were compared with each other. The time-lapse profiles were obtained as follows. Each reporter gene was introduced into mesenchymal stem cells by a solid phase transfection method.
The cells were cultured in undifferentiated state maintenance medium for two days . Thereafter, the medium was replaced with osteoblaet d~.fferentiation medium. This time point was referred to as the osteoblast differentiation start time. Supplement factors were added at concentrations recommended for the asteob~.ast differentiation medium. The other culture conditions were in accordance With Cambrex's instructions.
The results are shown in Figure 26. The profile pattern on the left of Figure 26 was obtained 10 hours to hours after replacement of the medium. The profile pattern on the right of Figure 26 was obtained 5 to 6 days 25 after replacement of the medium. Thus, it was demonstrated that the pattern significantly charged over time. The phases of the pxofzJ.es were calculated using a formula shown in Figure 27 and the results were summarized in a tabl~ to the right of Figure 27. As can be seen, the inversion of 30 the phase of the profile was deeply associated With differentiation for ISRE, RARE, STAT3, GRE, CRE, TRE, E2F, and p53. Therefore, it was demonstrated that by examining the phase, changes in process, i.e., the occurrence of transcription control, could be detectEd.
5~
(Arbitrary combination of reporters) ~iext, it was demonstrated that digferentiation could be identified using an arbitrary combination of promoters for which data was extx~aGted at the initial stage of induction of differentiation. Briefly, the analysis was conducted as shown in Figure 20.
The results are shown in Figure 20. This analysis revealed that although differentiation could not be detected at its very initial stage (potentially due to noise), but could be confirmed about 15 hours after induction of differentiation. Tn tha.s example, when data was extracted for 8 or more promoters, differentiation could be detected at a detection rate of 100. When data was extracted for 3 promoters, differentiation could be detected at a detection rate of more than 90~. When data was extracted for two promoters, differentiation could be detected at a detection rate of 88~. when data was extracted for one promoter, differentiation could be detected at a detection rate of 82~. Thus, it was revealed that one, two or at least three promoters are sufficient for determination or identification of the state of cells.
(Maintenance of undifferentiated state) Next, the maintenance of undifferentiated state Azoa~
was analyzed using an arb~.trary combination of transcription control sequences for which data was extracted. Analysis was conducted as described in Figure 20.
The results are shown in Figure 2t. As is ~.argely different fz~om the results of induction of differentiation, by comparing the profiles of the transcription control sequences with one another, it could xa be determined whether or not stem cells were induced into differentiation or remained undifferentiated. Such s, determination could be achieved using at least one transcription control sequence. The determination of the state of cells using such a small number of transcription control sequences cannot be achieved by conventional techniques. It can be said that the present invention achieved an exceXlent effect.
Hy analyzing a cellular process in such a fashion, the formation of cellular functions can be described as a cocktail party process as shown in Figure 22.
G~lith such a process description, the present invention mads it possible to ana~.yze the progression of a cellular response to drugs and the progression of the induction of differentiation,.
(Example 5 Anticancer agent) In this example, cisplatin was used as an exemplary anticancer agent and was mixed into the medium of exposed cells. The concentration of the anticancer agent was selected as appropriate, such as 1 ~tM, 5 ~M, 10 E1M, and the like, to observe the xeaction of the cells. Cisplatin~
was applied to cells resistant ox sensitive to the anticancer agent. Time-lapse observation was conducted to produce profiles as in the above-described examples . As a result, it was revealed that time-lapse profiles varied depending on the difference in cisplatin concentxstian and resistance/sensitivity.
(Example 6: RNAi) The present Example demonstrated that it was possible to obtain a profile relating to gene knockdown effect using a cell was ~.mmobilized as described in ExamplE
1, RNAi was used as a biological agent. The following was used as RNAi for experimentation. Gene expression inhibition methods using riboaymes and siRNA and the like allows obtaining profiles of response reactions in a cell for which gene expression inhibition is conducted using the s acne .
RNAi: those sequences available at the URL:
http://.www.nippongene.jp/pages/products/sirna/review/
were used (for example, Control siRNA duplex).
(RNAi transfectivn) First, it was confirmed whether the siRNA could achieve knockdown effects. Synthesis of siRNA
5'-AAGCAGCAGGACUUCUUC,AAG-3' (SEQ ID NO: 2) corresponding to EGFP was perfozrned to prepare an arxay substrate as described herein above in the Examples. The preparation of array substrate using siRNA instead of nucleic acid molecules zno7.uding promoter sequences was performed.
Transfection using these axray substrates confirmed Effective inhibition of expxess~.on of a target gene. The protocols thereof are presented a.n Figure ~8.
(Results) Figure 2~A shows the effects of target gene inhibition by siRNA. Expression of the target gene has actually been inhibited. The result$ using this gel may be stored so a prof~.J.e ire any data format.
Next, results of siRNA are stored as a prafi7.e data (image data of xIFF format having resolution at the level of 5 um/pixel or less). As such, the results of siRNA may be stored as a profile data. Such a format is not limited to those specifically presented in this Example, but those skilled in the art may employ any type of formats.
(Figure ~: AppZioations uszng siRNA and a transfection m~.croarray of PC7.2 cells on a collagen IV coated chip) Next, the present Example conducted a gene expression inhibition experiment using siRNA. The present Example evaluated whether or not the present invention functions by observing whether or not siRNAs against EGFP
can specifically inhibit the expression of the EGFP as an indicator.
Using the conditions described in Example 7, transfection of PC~.2 was conducted on an array coated with collagen IV. In lieu of the gene used in ExampJ.e 7, the following cond~.tion9 were usEd:
0.75 ng of an expression vector (pEGFP-N1}, HcRed (avai3.able from HD Clontech) were each spotted on a single, specific spot of the array. Thereafter, 16.5 ng of siRNA
( available from Dharmacon, taxget sequence : 5' -GGC TAC GTC
CAG GAG CGC ACC -3' (5EQ Z17 N0:47)=a) or scrambled siRNA (available from Dharznacon. target sequence: 5' -gCg CgC
TTT gTA ggA TTC g-3' (SEQ zD NO: 48 ) =b) were also spotted.
Figure 298 shows fi.he xesults. As shown in Figure 29 8(A), in the case of PC12 cells co-transfected ~.5 with EGFP vector and anti-EGFP siRNA, it was observed that only signals from HcRed were detected, and the green signal which should be derived from pEGFP--N1 had been inhibited.
On the other hand, as shown in Figure 29 B (8) , in the case of scrambled siRNA, green fluorescence was been observed and thus it was confirmed that the effects seen in Figure a9 8(A) is the result of RNAi. Rela'~ive zritensities of the fluorescence in Figures 298(A) and 298(Hy are shown in E'igure 29S(C) . y-axis is shown with relative luminance. It can be seen that the effect by EGFP is substantially completely inhibited.
Figure 29C shows a result and graph summarizing the above. The left-hand panel shows a photograph comparing an EGFP RNAi and a scrambled (Mack} RNAi. As shown in the figure, the use of RNAi of EGFP showed and inhibitory effect, whexeas the use of scrambled RNAi did nvt show such an inhibitory effect. The right-hand panel shows the same together with DsRed2. Experimental conditions are similar to the above Examples. As a result, red (signal derived from DsRed) and gxeen (signal derived from EGFP) were presented in the proportion of the effects of RNAi.
Figure 2~1~ shows an illustrative drawing of a chip using an RNAi reporter. When using RNA, as an input signal, and introducing a nucleic acid encoding both a gene product capable of signaling such as EGF and the like, and a gene of interest (a.ncluding a promoter) as an output, observation of the'signaling as the output allows one to produce cellular information.
3. 5 Figure 29E shows an exemplary experiments using a vaxiety of reporters ( pAPl-EGFP, pAPI(PMA)-EGFP, pCRE-EGFP, pE2F-EGFP, pERE-EGFP, pGAS-EGFP, pGRE-EGFP, pHSE-EGFP, pISRE-EGFp, pMyc-EGFP, pNFAT--EGFP, pNFkB-EGFP, pRARE-EGFP, pRb-EGFP, pSTST3-EGFP, pSRE-~EGFP, pTRE-EGFP, pp53-EGFP, pCREH-sensor, pIkB-sensox, pp53-sensor, pCasapase3-sensor; cis-element sequence was commercialJ.y available from Clontech; these axe plasmid vectors produced by recombining a fluorescent protein gene) . As such, the system of the present invention will function regardless of the types of reporters used.
(Example 7: Regulation of gene expression using a tetracycline-dependent promotex) As described in the Examples 1-3, it was Azoa7 demonstrated that a tetracycline-dependent promoter could be used to produce a profile showing how gene e~cpression is regulated. The seque:xoea described below were used.
As the tetracycline-dependent promoter (and its gene vector construct), pTet-Off and pTet-On vectors (BD
Hiosciences) were used (see http://www.clontech:com/techinfo/veGtors/cattet.shtm~.).
As a vector, pTRE-d2EGFP (SEQ ID NO.: 29) was used (see http://www.clontech.com/techinfo/vectors/vectorsT-Z/pTl~
E-d2EGFP.shtml). _ (Protocol) pTet-Off and pTet-On (SEQ ID NOS.: 26 and 27, respectively) were printed unto array substrates. Real time measurement was performed on the array substrates to determine whether or not tetracycline regulates gene expression. The results are shown in Figure 30. As shown in Figure 30, a change in gene expression was detected only fox the tetracycline--dependent promoter. Figure 31 is a photograph showing the actual states of expression for the tetracyc~.ine-dependent promoter and the tetracycline-independent promoter. As can be seen, the difference b~aween them is measurable by the naked eye.
(Measurement of profile data) images are taken in real time. Changes in intensity per cell or area are plotted on a graph. The resultant data may be subjected to linear transformation, such as no~.se reduction, and then multivariate analysis, signal processing, ox the like, to obtain profile data. The resultant data is compared between phenomena or cells, thereby making it possible to determine a specific response ar identity for the cells.
(Example 8: Gene expression) Next, nuclezc acid molecules encoding structural genes were used to produce cellular profiles.
In this example, an olfactory receptor I7 (SEQ TD NOS: 13, 14) was used as a structural gene. The protocol used in Examples 1-3 was used.
As a result, as with promoters, it was demonstrated that cellular profiles eou~d be produced by measuring the amount of gene products or the like.
(Example 9: Apoptotic signals) Next, it was investigated that cellular profiles could be produced by monitoring the activation of caspase 3 present within cells. Txansfect.ion and array preparata.on were performed as in the above~described examples.
pCaspase3-Sensor Vector (HD Biosciences Clontech, 1020 East Meadow Circle, Palo Altv, CA 94303: cat.
No. 8185-1) was used to monitor an apoptotic signal from caspase 3.
As a result, as with promoters, it was demonstrated that cellular profiles could be produced by measursng apoptotic signals or the like.
(Example 10: Stress signal) Next, it was investigated whether cellular profiles characterizing stress signals from JNK, ERK, p38 or the like could be produced using transcription factor reporters. Transfection and array preparatior~ were performed as in the above-described examples.
pAPI~-EGFP, pCRE-EGfP, and pSRE-EGFP available from BD Bioscience Clontech were used to monitor stress signals from JNK, ERK, and p38.
As a result, as in the above-described examples, it was demonstrated that cellular profiles could be produced by measuring stress signals.
(Example 11: Localization of molecules) Next, it was demonstrated that a gene of interest could be fused with a. fluorescent protein so that the expression profile of the gene product and the cellular localization of the gene product could be visualized.
GFP, RFP, CFP and BFP, were used a$ fluore8cerit proteins and cloned KIAA cDNA libraries c~x the like were used as genes of interest to produce gene constructs. These materials are specifically d~:scribed below:
cloned KIAA eDNA ~KIAA=Kazusa DNA Research Institute, Kazusa, Chiba, Japan): and cDNA libraries commercially available from Tnvitrogen.
Transfection and array preparation were performed as in the above-described examples.
The expression of cloned KIAA, ~CZAA~.474, was monitored to produce a profile of the expression and investigate the localizd.tion of the expression product.
As a result, as iz~ the above-described examples, it was demanstrated that intentionally constructed gene constructs could be used to produce cellular profiles for target characteristics.
(Example 12: Changes in cellular morphology) Next, it was demonstrated that cellular profiles characterizing cellular morphology could be.
produced by expressing or knaGking out genes or adding substances (glycerophosphate as a chemical substance and dexamethasone as a Cytokine) . Cellular morphology, such as multinucleated cells, cellular outgrowth, outgrowth pxQ~jections, and the like, was measured and analyzed as three-dimensional data.
xhe specific sequences of the introduced nucleic acid molecules are described below:
Cloned KIAA (supra); and RNAi fox transcription factors (C9FA-7., AP1) .
2$9 Transfection and array preparation were performed as in the abdwe-described examp~.es.
Mesenchymal stem cells as used in the above-described examples were used to monitor the morphology of Dells which were induced to be differentiated into osteoblasts.
As a result, as in the above-described e~tamples, it was demonstrated that intentionally constructed gene constructs could be used to produce cellular profiles for target characteristics. Event descriptors can be produced based on the profile data using the process as used in the above-described examples.
(Example 13: Intermolecular interaction) Next, it was demonstrated that cellular profiles could be produced by using a technique such as a two-hybrid system, FRET, BRET, or the like.
fhe specific sequences of the introduced nucleic acid molecules are described below:
olfactory receptors (SEQ xD NOS: 13 to 38) ; and G proteins (SEQ ID NOS: 39 to 44).
Transfection and array preparation were performed as in the above-described examples.
Alao~
The dissociation of the olfactory receptor and G protein was monitored through induction of a scented substance, which was captured as changes in fluorescent wavelength. Tn this manner, cells were monitored.
The two-hybrid system, FRET, and BRET were specifically performed as follows.
The two-hybrid system was available from Clontech (http://www.Glontech.co.jp/product/catalog/0070030a6.sh tml) _ FRET and BRET were performed using devices ava~,lable from Herthold Japan.
As a result, as in the above-described examples, it was demonstrated that intentionally constructed gene constructs could be used in a two-hybrid system, FRET, HRET, or the like, to produce cellular profiles.
(EXAMPLE 14: Receptor-Zigand) Next, it was demonstrated that a cellular profile can be produced by employing the interaction between a xeceptor and its ligand as an indicator. it is useful for network formation in a cell, to obtain interactive information betweezx a receptor protein present in the cell membrane or nuclear membrane, or the like, and a ligand thereto.
In the present Example, the following was prepared:
(Cell adhesion molecules) A variety of extracellular matrix protein and variants and fragments thereof were prepared as candidates for cell adhesion molecules. What was prepared in the present Example is as follows . Gell adhesion molecules were commercially available.
1) ProNectin F (Sanyo Chemical Industries, Kyoto, Japan):
2) ProNectin L (Sazlyo Chemical Industries=
3) ProNectin Plus (Sanyo Chemical Industries):
4)~fibronectin (SEQ ID NO.: 2);
5) gelatin.
Plasmids were prepared as DNA for transfection.
Plasmids, pEGFP-N1 and pDsRed2~-Nl (both from HD Hia~ci.ences, Clontech, CA, USA) were used. In these plasxriids, gene expression was under the control of cyt4megalovirus (CMV).
The plasmi.d DNA was amplified in E. coli (XLl blue, Stratgene, TX, USA) and the amplified plasmid DNA was used as a complex partner. The DNA was dissolved in distilled water free from DNase and RNase.
The following tx~ansfection reagents were used:
Effectene Transfection Reagent (cat. no. 301425, Qiagen, CA) , TransFastm°' Transfection Reagent (E2431, Promega, WI) , TfxT~'-20 Reagent (E2391, Promega, WI), SuperFect Transfeotion Reagent (301305, Qiagen, CA), PolyFect Transfectivn Reagent (301105, Qiagen, CA), ZipofectAMINE
2000 Reagent (11668-019, zzwitrogen corporation, CA), Azoo7 JetPEI (x4) cons. (101-30, Polyplus~transfection, France), and ExGen 50b (R0511, Fermentas Inc., MD). These transfection reagents were added to the above-described DNA
and actin-like acting substance in advance or comp3.exes thereof with the DNA were produced in advance.
The thus-obtained solution Was used in assays using transfection arrays described below. Next, transfection effects ozx a solid phage were observed. The protocols therefor are descra.bed below:
(Protocol) The final concentration of DNA was adjusted to 1 ugJ~th. A cell adhesion molecule was preserved as a stuck having a concentration of 10 ~g/~L in ddH20. All dilutions were made using PBS, ddHzO, or Dulbecca' s MEM. A series of dilutions, for example, 0.2 ~,g/~~.L, 0.27 ~g/~L, 0.4 ~g/N.L, 0 . 53 E.v.g/~,L, 0 . 6 ~.lg/~L, 0 . $ ~.l.g/~,iL, 1. 0 ~.~g/~.tL, 1. 07 ~x.g/~L, 1.33 ~.g/~.L, and the like, were formulated.
Transfection reagents were used in accordance with instructions provided by each manufacturer.
Plasmid DNA was remo~red from a glycerol stock and amplified in 100 mL L-amp overnight. Qiaprep Miniprep or Qiagen Plasmid Purification Maxi was used to purify DNP~
in accordance with a standard protocol provided by the manufacturer.
In the present Example, the following five cells were used to confirm an effect : human mesenchymal stem cell.
(hMSCs, PT-2501, Cambrex BioScience walkersville, Inc., Mn) ; human embryonic renal cell (HEK293, RCH1637, RIKEN Cell Bank, JPN): NIH3T3-3 cell (RCB0150, RIKEN Cell Bank, JPN);
S HeZa cell (RCB0007, RIKEN Cell Hank, JPN) ; and HepG2 (RCH1648, RIIiEN Cell Hank, JPN) . These ce7.ls were cultured in DMEM/10~
IFS containing L-gxut and pen/strep.
(Dilution and DNA spots) ~.0 Transfection reagents and DNA were mixed to form a DNA--transfection reagent complex. The complex formation requires a certain period of time. Therefore, the mixture was spotted onto a solid phase support (e. g. , a poly-L-lysine slide) using an arrayer. In the present Example, as a solid 15 phase support, an APS slide, a MAS slide, and an uncoated slide were used, as well as a poJ.y-L-lysine slide. These slides are available from Matsunami Glass (Kishiwada, Japan) or the like.
20 For complex formation and spot fixation, the slides were dried overnight in a vacuum dryer. Drying was performed for a duration in the range of 2 hours to ~. week.
AJ.though the cell adhesion molecule might be 25 used during the complex formation, it was also used immediately befoxe spotting in the present Example.
(Formulation of mixed solution and application to solid phase supports) 30 300 ~tL of DNA concentrated buffer (EC buffer) + 16 p.L of an enhancer were mixed in an Eppendorf tube. The mixture was mixed with a Vortex, followed by incubation for minutes. 50 ~ of a transfection reagent (Effectene, etc.) was added to the mixture, followed by mixing by 5 pipetting. To apply a transfection reagent, an annular wax barrier was formed axound the spots on the slide. 366 ~.tZ
of the mixture was added to the spot region surrounded by the wax, followed by incubation at room temperature for 10 to 20 minutes. Thereby, the fixation to the support waa manually achieved.
(Distribution of cells) Next, a protocol. for adding cells will be described. Cells were distr~.buted for transfection. The distribution wag typically performed by reduced-pressure suction in a hood. A slide was placed on a dish, and a solution containing cells was added to the dish for transfection. The cells were distributed as follows.
The growing cells were seeded at a concentration of 10' oells/25 mL. The cells were plated on the slide in a 100x100x15 mm squared Petri dish or a 100 mm (radius) k ~.S mm circular dish. Transfection was conducted for about 40 hours. This period of time corresponded to about 2 Cell cycles. The slide was treated ~ox immunofluorescence.
(Evaluation of gene introduction) Gene introduction was evaluated by detection using, for example, immunofluorescence, fluorescence microscope examination, laser scanning, xadioaGtive labels, and sensitive films, or emulsion_ 'then an expressed protein to be visualized ins a fluorescent protein, suoh a protein can be observed with S a fluorescence microscope and a photograph thereof can be taken. For larga~s~.zed expression arrays, slides may be scanned using a laser scanner for storage of data. If an expressed protein can be detected using specific fluorescence in the case of calcium, a protocol specific for detection of a specific fluorescence can be successively performed to detect signals. If an expressed protein can be detected using fluorescence antibodies, an immunofluorescence protocol can be successively performed.
(user scanning and Quantification of fluorescence intensity) To quantify transfection effic~.ency, the present inventors used a DNA microarray scanner (GeneTAC
UC4xA, Genom.ic Solutions Inc., MTV. Total fluorescence intensity (arbitrary units) was measured, and thereafter, fluorescence intensity per unit surface area was calculated.
(Cross-sectional observation by confocal scanning microscope) Cells were seeded on tissue culture dishes at a final concentration of 1x10 cells/well and cultured in appropriate medium (Human Mesenchymal Cell Baaal Medium (MSCGM BulletKit PT-3001, Cambrex BioScience Walkersville, Inc., MD). After fixation of the cell ~.ayer with 4~
paraformaldehyde solution, SYTO and Texas Red-X phalloidin (Ma~.ecul.ax Probes Inc. , OR, USA) was added to the cell. layer far observation of nuclei and F-actin. The samples emitting light due to gene products and the stained samples were observed with a confocal laser microscope (LSM510: Carl Zeiss Co. , Ltd. , pin hole size~Gh2~223 ~.~,m, Ch2~Z08 ~,m, image interval = 0.4} tp obtain Gross sectional views.
Next, an Example, to which the present invention is applied to, is described wherein an olfactory receptor is selected as a typical example of a chemical substance receptox, When a pze~.iminaxy example was implemented, it was proved that transfection arrays can also be used for an olfactory receptor The olfactory receptor expression vector group was spotted per every kind of receptor, on a cover glass, which was made like an array, was secured with screws and the l.zke in d chamber for signal measurement, and cells having an almost homogeneous nature, were cultured thereon.
Regarding a chamber for signal measurement, sample gas was infiroduced into a known structure (Pros. Natl. Aced. Sci.
USA, 96(1999): 4090-4045 and the like). Other devised chambers are also intended. During response measurement, culture medium was passed through the chamber at a constant speed. Culture media was supp~.ied to the chamber for measurement from the apen~.ng of a culture medium supply tube, and a sample gas supplying tube was secured at the position preferably near the liquid level, which is the upper portion of an interval whose boundary is defined by reaching a wall AZ~~7 Which prevents the appxoaGh of culture media over a cover -slip that forms the ceiling of the measurement member, so that sample gas can be supplied to culture medium flowing across the interval. This sample gas supplying tube is preferably made of materials to which lipophilic odor substances such as Teflon and peak,.. and dust are not readily s.dsorbed. The higher effect was obtained in the asztuetion wherein, at the time other than introducing sample gas, sample gas remaining in a tube was removed, and to preferably keep the interior clean, the tube (preferably with a broad opening) could be purged with odorless air by setting a three-way valve in the mid course, or by setting a check valve at a joint of an odorless air supplying tube. However, it was not necessary. The example could also be implemented in the situation wherein, at a time other than when introducing sample gas from outside for an appropriate time such as 0. 5-4 seconds, odorless air was introduced from mid course of a sample gas supplying tube near a opening for collecting gas from outside, the izxterior of the tube was washed therewith, and at the same time, odorless gas was supplied to the culture medium as sample gas to promote the removal of remaining gas in a measu.~ement chamber. A
supporting base for the upper-glass cover slip is made of a water repellent opaque plastic such as Teflon. A width 2S of flow channel, where culture medium flows, is about 2-fold of a width of an array, and the array is disposed in the center of the flow channel. Regarding a culture medium supplying tube and an overflow culture medium sucking tube, a portion several millimeters from the opening at the side of the measuz~ement chamber is made using mater~.als which PsI~~7 have high hydrophilicity and are difficult to deform, such as stainless steel. The upper portion of the supporting base of the upper glass cover-slip where culture medium flows, from the openings of both tubes to an array, was coated, or covered with a pieces of lens paper and the like ~.n o~dex to provide sufficient hydrophilicity. Negative pressure for suction was adjusted at the grade such that measurements were not affected by. vibration from sound generated by aspiration culture.
Generally, response measurement could be implemented 2 days after the gene introduced by the vector was expressed. Since an upper glass cover-sl.~.p was required only at the time of measurement, it was riot required to install it during culture until the gene was expressed.
Therefore, the Example could be implemented, adding an upper glass cover slip integxsted with a wall which prevents leakage of culture medium, and a supporting base for the upper glass cover slip, to a chamber for measurement, when setting a chamber for measurement of a change in fluorescence measured by an apparatus after the gene expressed. The Example could also be imp~.emented in the situation wherein culture medium was exchanged without using a culture medium supply tube and an overflow culture suction line tube during culture until the gene was expressed. An amount of about lOml of culture medium was.supplied and exchanged at the frequency of .about once per several hours t4 one day, only during the time tissue culture was performed.
The size of odor response could be optically AToo~
measured using a two-dimensional image sensor such as a sensitive video camera, with a calcium ion sensitive fluorescent dye fura-2 and the like absorbed into the cell.
The measurement interval preferably has time resolution which can evaluate time ~an~stants of build-up and recovery of response of about 1/3-1 second. However, if average response time curve or its theoretical formula had been obtained, actual change was estimated from measurement results at 5 points with 5--second-intervals, 5, 10, 15, 20, ZO and 25 seconds after stimulation. The obtained estimates of the time constant of the response sts.rting time, response build-up time, and response recovery time was set as an index, and evaluation could be made as to whether a signal was induced by odor, or generated by spontaneous activity of 1S a cell, or other abnormalities.
In this Example, the response of an expressed olfactory receptor in olfactory receptor neuron was studied by measuring the change in fluorescence intensity of calcium 20 sensitive fluorescent. dye, Decrease of fluorescence intensity (downward change) corresponds to the response of an olfactory receptor. Odor molecules were added to the culture at the concentration indicated above them as stimulation source, and administered to a cell during the 25 time indicated by a bar (~ or 2 seconds) . As understood from this example, responses measured simultaneously in a simultaneously adjusted cell have high intercommunity in response time characteristics, response threshold concentration corresponding to different stimulatipn per 30 GeIJ., arid relative value of response amplitude. However, Aloo~
cells adjusted at a different times show some differences.
These results show that the highest measurement reliability can be obtained by measuring odor response using a sensor arrayed to a size that allows a homogeneous adm~.~istxat~.oz7, of sample gas, providing the same adjustment conditions.
(Example 7.5: Application to neuron differentiation) Next, experiments similar to those of Example 14 have been conducted with neurons to analyze the effects of tyrosine kinase RNAi with a transfection microarray. The exemplified drawings are shown in Figure 318.
As shown in Figure 318, network analysis can be Conducted by taking photographs of signal represented by a reporter and collecting information thereon.
Figure 31~ shows the responses of retinoic acid (RA) and nerve growth factor (NGF) to a variety of tyrosine kinases. Inhibition ~S by siRNA is shown.
Figure 31D depicts an exemplary drawing of a signal transduction pathway obtained as a xesult of analysis.
Figure 31E shows results obtained by the above-mentioned analysis. Classification has been made regardless of whethex the subject cells were dopaminergic neurons, cholinergic neuron, both, ox n,oithar. It oan be concluded that those kinases relating to both. cell types have high probability of relating to nerve projection ~a~.
formation.
(Example ~.6~: Data prcduGtion) Data produced in Examples 5-15 can be analyzed using a mathematical analysis with an appropriate modification as described in Example 4. Such data have been presented in a variety of formats.
(Example 17: Production of a digital cell) Data produced in Examples 5-15 and additional data produced using the protocols described therein were used to produce a digital cell. In order to produce digital cells, parameters fox data produced in these Examples have been extracted, and medium, pfi, temperature, Cpz concentration, and the J.ike have been used as environment parameters. Database production may be performed using, for example, a spreadsheet software such as Excel~'M available from Microsoft, or a database software such as Access'' also available from Microsoft. Next, as cell parameters, a database including cell species such as those used in Examples 5-15 can be used. ~ variety of stimulus parameters such as a vaxiety of chemical stimuli, (for example, including a variety of growth factors or cytokines such as HGF, FGF, PDGF, VEGF, CSF and the like) can be input to produce cell dynamics data, measurement data of reporters such as fluorescence intensity and the like. As such, a database constituting digital cell can be produced_ Such examples are shown in Figures 33A and 335.
(Example 18: Use of digital cells: ~n ejltco live experiments) The digital cells produced in Example 17 have been used to conduct experiments on a computer. In the present Example, a mesenchymal stem cell is used to study which agents are differentiation agents. In the case of Figure 33~r, cell A is selected as cell (for example, mesenohymal stem cell or the like)_ Further, DMEM is selected as a medium, pH 7 . 4 is selected as the ~pH, 3'7 degree Celsius is selected as the temperature, 5~ ie selected as the COZ concentration. Moreover, a variety of chemical stimuli such as growth factors or cytak~.nes such as HGF, FGF, FDGF, VEGF, and CSF are selected. With respect to such a variety of chemical stimuli, concentrations are also appropriately selected, such as 1nM to lmM. Combinations of these two or three thereof are also selected as a variety of chemical stimuli. Depending these combination and concentration, data regarding responses with respect to how a mesenchymal stem cell responds is output . As an output, cell dynamic is included. From such cell dynamic, it is confirmed that the mesenchymal stem cell is differentiated (e.g. to bone marrow or adipocyte or the like) or not. If morphology is not sufficient, combinations between transcriptional factors and EGF as reporters are used to output further measurement data _ As such, it can be conf~.xmed whether ox not a mesenchyma~. stem cell is differentiated to which e~ Specific differentiated cell. Us~.ng the present method, one can specify a chemical stimulus which induces differentiation to a specific differentiated cell.
(Example 19: Use of digital cells - education by .in silico live experiments In sil.ico live experiments described in Example 1$ axe conducted during school education. In this example, the experimental theme as described above is given to a student .
The student selects a variety of parameters from a database of a given digital cells. fhe student composes his/her own research based.or~ the data selected. The student submits the composed research. results as assignment/report. As such, education to a student can be conducted without using a live experimental system.
(Example 20: provision of a digital service) A database of the digital cell may be provided as an external service. Databases produced in Example 18 may use those embodiment described in Figure 35. As such, the configuration of computer system 3501 providing a service reproducing experimental results to an actual cell using the digital cells is shown, Computer system 3501 comprises service requester 3510 requesting services desired by a user, and sexvzce provider 3520 providing a determined service in response to the request . Users such as research inst~.tutes, educational organizations or institutions request desired services. Service provider
35.0 providing commercial service provides appropriate data to the research institutes, educational organizations or institutions upon request. For the purpose of school education, for exs.mple, a particular data base only directed to a particular cell or parameters or the like may Ioe of service target.
so As such, it is demonstrated that the digital cell of the present invention can be used to pro~ride services.
Although certain preferred embodiments have been described herein, it is not intended that such embodiments be construed as limitations on the scope of the invention except as set forth in the appended claims.
Various other modifications and equivalents will be apparent to and can be readily made by those skilled in the art, after reading the description herein, without departing from the scope and spirit of this invention. All patents, published patent applications and publications cited hexei.n axe incorporated by reference as if set forth fully herein.
INDUSTRIAL APPLICABILITY
According to the present invention, it is possible to determine the state of cells by observing a surprisingly small numbex of factors. Therefore, the gz~esent invention is applicable to diagnosis, prevention, and treatment . The present invention is also applicable to the fields of food, cosmetics, agriculture, environmental engineering, and the like. As live experiments can be reproduced on a computer, education and research in the field of biotechnolog~r can be conducted on such a computer, which is industrially applicable.
SEQUENCE LISTING
<110~ National Institute of Advanced Industrial Science and Technology, Masato M1YAKE, Tomoaki YOSHIKAWA, Jun MIYAKE
Cy20~ Digital cell C130> A1007PCT
<150~ JP 2003-181915 Clb1> 2003-8-25 C150~ JP 2003~-2894fi9 C151~ 2003-B-7 <160~ 48 <170> Patentln version 3.1 C2y0~ 1 C212> DNA
<2137 Homo saplens C2z0>
<221> CDS
<222~ (1 ) . . (1929) C223> flbronectin 3 C400> 1 atg att agg ggt ccg ggg ccc ggg ctg ctg ctg ctg gcc gtc cag tgc 48 Met Leu Arg Gly Pro Gly Pro Gty Leu Leu Leu Leu Aia Val Gln Cys ctg ggg aca gcg gtg ccc tcc acg Bga goo tog aag agc sag agg cag 86
so As such, it is demonstrated that the digital cell of the present invention can be used to pro~ride services.
Although certain preferred embodiments have been described herein, it is not intended that such embodiments be construed as limitations on the scope of the invention except as set forth in the appended claims.
Various other modifications and equivalents will be apparent to and can be readily made by those skilled in the art, after reading the description herein, without departing from the scope and spirit of this invention. All patents, published patent applications and publications cited hexei.n axe incorporated by reference as if set forth fully herein.
INDUSTRIAL APPLICABILITY
According to the present invention, it is possible to determine the state of cells by observing a surprisingly small numbex of factors. Therefore, the gz~esent invention is applicable to diagnosis, prevention, and treatment . The present invention is also applicable to the fields of food, cosmetics, agriculture, environmental engineering, and the like. As live experiments can be reproduced on a computer, education and research in the field of biotechnolog~r can be conducted on such a computer, which is industrially applicable.
SEQUENCE LISTING
<110~ National Institute of Advanced Industrial Science and Technology, Masato M1YAKE, Tomoaki YOSHIKAWA, Jun MIYAKE
Cy20~ Digital cell C130> A1007PCT
<150~ JP 2003-181915 Clb1> 2003-8-25 C150~ JP 2003~-2894fi9 C151~ 2003-B-7 <160~ 48 <170> Patentln version 3.1 C2y0~ 1 C212> DNA
<2137 Homo saplens C2z0>
<221> CDS
<222~ (1 ) . . (1929) C223> flbronectin 3 C400> 1 atg att agg ggt ccg ggg ccc ggg ctg ctg ctg ctg gcc gtc cag tgc 48 Met Leu Arg Gly Pro Gly Pro Gty Leu Leu Leu Leu Aia Val Gln Cys ctg ggg aca gcg gtg ccc tcc acg Bga goo tog aag agc sag agg cag 86
Claims (144)
1. A method for producing profile data relating to information of a cell in a consistent environment, said method comprising the steps of:
a) locating a plurality of cells to a support which is capable of maintaining the cells in a consistent environment; and b) monitoring a biological agent or a collection thereof on or in the cell to produce the profile data for the cell.
a) locating a plurality of cells to a support which is capable of maintaining the cells in a consistent environment; and b) monitoring a biological agent or a collection thereof on or in the cell to produce the profile data for the cell.
2. A method according to Claim 1, wherein the biological agent is a nucleic acid molecule or a molecule derived from the nucleic acid molecule.
3. A method according to Claim 1, wherein the cell is immobilized to the support by a composition comprising a) a complex with a positively charged substance and a negatively charged substance; and b) a salt.
4. A method according to Claim 1 wherein the cell is provided with an actin-like substance.
5. A method according to Claim 1, wherein the cell is immobilized to the support by a composition comprising a) a complex with a positively charged substance and a negatively charged substance; and b) a salt, and is provided with an actin-like acting substance.
6. A method according to Claim 1 wherein the biological agent is selected from the group consisting of a nucleic acid molecule, a protein, a saccharide, a lipid, a low molecular weight molecule, and a complex thereof.
7. A method according to Claim 1, wherein the cell is cultured at least about three days before the step of monitoring.
8. A method according to Claim 1, wherein the biological agent comprises a nucleic acid molecule encoding a gene.
9. A method according to Claim 1, wherein the profile comprises a profile for gene expression.
10. A method according to Claim 1, wherein the profile comprises a profile of an apoptosis signal.
11. A method according to Claim 1 wherein the profile is a profile of a stress signal.
12. A method according to Claim 1 wherein the profile is a profile of the localization of a molecule.
13. A method according to Claim 12 wherein the molecule is detected by means selected from the group consisting of fluorescence, phosphorescence, radioactivity, and a combination thereof.
14. A method according to Claim 1 wherein the profile comprises a variation in cell morphology.
15. A method according to Claim 1 wherein the profile comprises a profile of promoter activity.
16. A method according to Claim 1, wherein said profile comprises a profile of a promoter dependent on a specific drug.
17. A method according to Claim 1 wherein said profile comprises a profile of a promoter dependent on a specific drug, wherein said method further comprises the step of administering the specific drug.
18. A method according to Claim 1 further comprising the step of subjecting the cell to a foreign agent.
19. A method according to Claim 18, wherein said foreign agent comprises an RNAi.
20. A method according to Claim 18, wherein said foreign agent comprises a chemical not present in a biological body.
21. A method according to Claim 1, wherein said profile comprises a profile of an intermolecular interaction.
22. A method according to Claim 18, wherein said foreign agent comprises a ligand for a receptor of said cell.
23. A method according to Claim 1, wherein said profile comprises a profile of an interaction between a receptor and a ligand.
24. A method according to Claim 1, wherein said profile is of a cellular form, and said method further comprises the step of giving to said cell a stimulus selected from the group consisting of overexpression, underexpression or knockdown of a gene, addition of a foreign agent and a change in the environment.
25. A method according to Claim 1, wherein said profile comprises a profile of interaction between molecules present in said cell.
26. A method according to Claim 1, further comprising the step of conducting observation using a technology selected from the group consisting of two-hybrid method, FRET and BRET.
27. A method according to Claim 1, wherein said profile comprises a profile of interaction between molecules present in said cell, wherein the method further comprises the step of conducting observation using a technology selected from the group consisting of two-hybrid method, FRET and BRET.
28. A method according to Claim 1, wherein said cell is located on said support in an array format.
29. A method according to Claim 1, wherein said cell is located on said support in an array format, and each of said plurality of cells are located at a space of 1 mm at maximum.
30. A method according to Claim 1, wherein said profile is obtained in real time.
31. A method according to Claim 1 further comprising the step of immobilizing said cell to a solid support.
32. A method according to Claim 1, wherein said data comprises information relating to said profile.
33. A method according to Claim 1 wherein said data comprises information relating to conditions during said monitoring.
34. A method according Claim 1 wherein said data comprises information relating to the state of said cell.
35. A method according to Claim 1 wherein said biological agent to be monitored comprises at least two types of biological agent.
36. A method according to Claim 1 wherein said biological agent to be monitored comprises at least three types of biological agent.
37. A method according to Claim 1 wherein said biological agent to be monitored comprises at least eight types of biological agents.
38. A method according to Claim 1 further comprising the step of arbitrarily selecting a biological agent.
39. A method according to Claim 1 wherein said cell is selected from the group consisting of a stem cell and a somatic cell.
40. A method according to Claim 1 wherein said support comprises a solid support.
41. A method according to Claim 1 wherein said support comprises a substrate.
42. A method according to Claim 1 wherein said biological agent is a nucleic acid molecule, and said cell is transfected with said nucleic acid molecule.
43. A method according to Claim 42, wherein said transfection is conducted on a solid phase or in a liquid phase.
44. A method according to Claim 42 wherein said transfection is conducted on a solid support.
45. A method according to Claim 1, further comprising the step of comparing a phase of said profile.
46. A method according to Claim 1, further comprising the step of subtracting a control profile from the profile of said cell.
47. A method according to Claim 1 further comprising the step of processing the profile with a mathematical processing method from signal processing and multivariant analysis methods.
48. A method for presenting profile data relating to information of a cell in a consistent environment, comprising the steps of:
a) locating a plurality of cells on a support which is capable of maintaining the cells in a consistent environment;
b) monitoring a biological agent or a collection thereof on or in the cell to produce the profile data for the cell; and c) presenting the data.
a) locating a plurality of cells on a support which is capable of maintaining the cells in a consistent environment;
b) monitoring a biological agent or a collection thereof on or in the cell to produce the profile data for the cell; and c) presenting the data.
49. A method according to Claim 48, wherein said step of presenting is conducted in real-time.
50. A method according to Claim 48, wherein said step of presenting is conducted such that visual detection is enabled.
51. A method according to Claim 48, wherein said step of presenting is conducted such that auditory detection is enabled.
52. A method for determining the state of a cell in a consistent environment, comprising the steps of:
a) locating a plurality of cells on a support which is capable of maintaining the cells in a consistent environment: b) monitoring a biological agent or a collection thereof on or in the cell to produce the profile data for the cell; and c) determining the state of said cell from said data.
a) locating a plurality of cells on a support which is capable of maintaining the cells in a consistent environment: b) monitoring a biological agent or a collection thereof on or in the cell to produce the profile data for the cell; and c) determining the state of said cell from said data.
53. A method according to Claim 52, further comprising the step of correlating said profile and the state of said cell in advance.
54. A method according to Claim 52, wherein said cell comprises a cell for which the state thereof is known.
55. A method according to Claim 52, wherein there are at least two types of said biological agent.
56. A method according to Claim 52, further comprising the step of arbitrarily selecting said biological agent.
57. A method according to Claim 52, wherein said data is produced in real-time.
56. A method according to Claim 52, wherein said status is selected from the group consisting of differentiation state, undifferentiation state, cellular response to a foreign agent, cellular cycle and growth state.
59. A method according to Claim 52, wherein said cell is selected from the group consisting of a stem cell and a somatic cell.
60. A method according to Claim 52, wherein said solid support comprises a substrate.
61. A method according to Claim 52, wherein said biological agent is a nucleic acid molecule, and said cell is transfected with said nucleic acid molecule.
62. A method according to Claim 61, wherein said transfection is conducted on a solid phase or in a liquid phase.
63. A method according to Claim 52, wherein said biological agent has the capability of binding a different biological agent.
64. A method according to Claim 52, wherein said step of determination c) comprises comparing the phases of said profile.
65. A method according to Claim 52, wherein said step of determination c) comprises obtaining the difference between said profile and a control profile.
66. A method according to Claim 52, wherein said step of determination c) comprises a mathematical processing method selected from the group consisting of signal processing and multivariate analysis methods.
67. A method for correlating a foreign agent and a cellular response to the foreign agent, comprising the steps of:
a) subjecting a cell to a foreign agent an a support capable of maintaining a plurality of cell in a consistent environment;
b) monitoring a biological agent or a collection thereof an dr in the cell to produce the profile data for the cell; and c) correlating the foreign agent and the profile.
a) subjecting a cell to a foreign agent an a support capable of maintaining a plurality of cell in a consistent environment;
b) monitoring a biological agent or a collection thereof an dr in the cell to produce the profile data for the cell; and c) correlating the foreign agent and the profile.
68. A method according to Claim 68, wherein said cell is immobilized on said support.
69. A method according to Claim 69, further comprising the step of using at least two of said foreign agents to obtain profiles of each of the foreign agents.
70 . A method according to Claim 67, further comprising the step of classifying at least two of said profiles to classify foreign agents corresponding to the profiles.
71. A method according to Claim 70, wherein said profile is presented in real-time.
72. A method according to Claim 67, wherein said cell is cultured on an array.
73. A method according to Claim 67, wherein the monitoring of said profile in step (b) comprises obtaining image data from said array.
74. A method according to Claim 67, wherein said correlation between said foreign agent and said profile in step (c) is a step of identifying the identity or difference of the phase of said profile.
75. A method according to Claim 67, wherein said foreign agent is selected from the group consisting of temperature changes, humidity changes, electromagnetic wave, potential difference, visible light, infrared light, ultraviolet light, X-rays, chemical substances, pressure, gravity changes, gas partial pressure and osmotic pressure.
76. A method according to Claim 75, wherein said chemical substance is a biological molecule, a chemically synthesized substance or a culture medium
77. A method according to Claim 76, wherein said biological molecule is selected from the group consisting of a nucleic acid, a protein, a lipid, a sugar, a proteolipid, a lipoprotein, a glycoprotein and a proteoglycan.
78. A method according to Claim 76, wherein said biological molecule comprises at least one biological molecule selected from the group consisting of a hormone, a cytokine, a cell adhesion factor and a extracellular matrix protein.
79. A method according to Claim 75, wherein said chemical substance is an agonist or antagonist of a receptor.
80. A method for identifying an unidentified foreign agent given to a cell, from the profile of said cell, comprising the steps of:
a) subjecting a cell on a support capable of maintaining a plurality of cell in a consistent environment to a plurality of known foreign agents;
b) monitoring a biological agent or a collection thereof on or in the cell over time to produce the profile data for the cell in response to each of known foreign agents to produce profile data for the cell;
c) correlating each of the known foreign agents and each of the profiles;
d) subjecting the cell to an unidentified foreign agent;
e) monitoring a biological agent or a collection thereof on or in the cell subjected to the unknown foreign agent over time to obtain the profile of the cell relating to the unidentified foreign agent;
f) determining the profile corresponding to the profile obtained in step e) amongst the profiles obtained in step b);
g) determining that the unidentified foreign agent is the known foreign agent corresponding to the profile which has been determined in step f).
a) subjecting a cell on a support capable of maintaining a plurality of cell in a consistent environment to a plurality of known foreign agents;
b) monitoring a biological agent or a collection thereof on or in the cell over time to produce the profile data for the cell in response to each of known foreign agents to produce profile data for the cell;
c) correlating each of the known foreign agents and each of the profiles;
d) subjecting the cell to an unidentified foreign agent;
e) monitoring a biological agent or a collection thereof on or in the cell subjected to the unknown foreign agent over time to obtain the profile of the cell relating to the unidentified foreign agent;
f) determining the profile corresponding to the profile obtained in step e) amongst the profiles obtained in step b);
g) determining that the unidentified foreign agent is the known foreign agent corresponding to the profile which has been determined in step f).
81. A method for identifying an unidentified foreign agent given to a cell, from the profile of the cell, comprising the steps of:
a) providing data relating to correlation between a known foreign agent, and a profile of the cell corresponding to the known foreign agent, with respect to a biological agent or a collection thereof on or in the cell;
b) subjecting the cell to an unidentified foreign agent;
c) monitoring the biological agent or the collection thereof on or in the cell over time to produce a profile of the cell;
d) determining the profile corresponding to the profile obtained in step c) amongst the profiles provided in step a); and e) determining that the unidentified foreign agent is the known foreign agent corresponding to the determined profile.
a) providing data relating to correlation between a known foreign agent, and a profile of the cell corresponding to the known foreign agent, with respect to a biological agent or a collection thereof on or in the cell;
b) subjecting the cell to an unidentified foreign agent;
c) monitoring the biological agent or the collection thereof on or in the cell over time to produce a profile of the cell;
d) determining the profile corresponding to the profile obtained in step c) amongst the profiles provided in step a); and e) determining that the unidentified foreign agent is the known foreign agent corresponding to the determined profile.
82. A method for obtaining a profile relating to information of a cell in a consistent environment, comprising the steps of:
a) locating a plurality of cells to a support which is capable of maintaining the cells in a consistent environment; and b) monitoring a biological agent or a collection thereof on or in the cell over time to produce the profile data for the cell.
a) locating a plurality of cells to a support which is capable of maintaining the cells in a consistent environment; and b) monitoring a biological agent or a collection thereof on or in the cell over time to produce the profile data for the cell.
83. A storage medium on which data produced by a method according to Claim 1, is stored.
84. A storage medium according to Claim 83, wherein said storage medium further comprises data of at least one information relating to one selected from the group consisting of information relating to conditions under said monitoring, information relating to said profile, information relating to the state of said cell and information relating to the biological agent.
85. A storage medium according to Claim 84, wherein the data is stored in a format which links a plurality of the data to each other.
86. A storage medium according to Claim 84, wherein the data is stored in a format which has links per said cell.
87. Data produced by a method according to Claim 1.
88. A transmission medium comprising data produced by a method according to Claim 1.
89. A system for producing profile data relating to information of a cell in a consistent environment, said method comprising:
a) a support which is capable of maintaining the cells in a consistent environment;
b) means for monitoring a biological agent or a collection thereof on or in the cell to produce the profile data for the cell; and c) means for producing profile data for the cell from a signal obtained from the means for monitoring.
a) a support which is capable of maintaining the cells in a consistent environment;
b) means for monitoring a biological agent or a collection thereof on or in the cell to produce the profile data for the cell; and c) means for producing profile data for the cell from a signal obtained from the means for monitoring.
90. A system according to Claim 89, further comprising a plurality of cells, and the plurality of cells are immobilized on to the support.
91. A system according to Claim 90, wherein said support is attached at least one substance selected from the group consisting of a salt and an actin-like acting substance.
92. A system according to Claim 89, wherein said means for monitoring comprises at least one means selected from the group consisting of optical microscopes, fluorescence microscopes, phase-contrast microscopes, reading devices using a laser source, means using surface plasmon resonance (SPR) imaging, electric signals, chemical or biochemical markers singly or in combination, radiation, confocal microscopes, nonconfocal microscopes, differential interference microscopes, stereoscopic microscopes, video monitors and infrared cameras.
93. A system for presenting profile data relating to information of a cell in a consistent environment, comprising:
a) a support which is capable of maintaining the cell in a consistent environment;
b) means for monitoring a biological agent or a collection thereof on or in the cell to produce the profile data fog the cell;
c) means for producing profile data for the cell from a signal obtained from the means for monitoring; and d) means for presenting the data.
a) a support which is capable of maintaining the cell in a consistent environment;
b) means for monitoring a biological agent or a collection thereof on or in the cell to produce the profile data fog the cell;
c) means for producing profile data for the cell from a signal obtained from the means for monitoring; and d) means for presenting the data.
94. A system according to Claim 93, further comprising a plurality of cells, wherein the plurality of cells are immobilized on to the support.
95. A system according to Claim 93, wherein said support is attached at least one substance selected from the group consisting of a salt and an actin-like acting substance.
96. A system according to Claim 93, wherein said means for monitoring comprises at least one means selected from the group consisting of optical microscopes, fluorescence microscopes, phase-contrast microscopes, reading devices using a laser source, means using surface plasmon resonance (SPR) imaging, electric signals, chemical or biochemical markers singly or in combination, radiation, confocal microscopes, nonconfocal microscopes, differential interference microscopes, stereoscopic microscopes, video monitors and infrared cameras.
97. A system according to Claim 93, wherein said means for presenting data is a display.
98. A system according to Claim 93, wherein said means for presenting data is a speaker.
99. A system for determining the state of a cell in a consistent environment, comprising a) a support which is capable of maintaining the cell in a consistent environment;
b) means for monitoring a biological agent or a collection thereof an or in the cell to produce the profile data for the cell;
c) means for producing profile data for the cell from a signal obtained from the means for monitoring; and d) means for determining the state of said cell from said data.
b) means for monitoring a biological agent or a collection thereof an or in the cell to produce the profile data for the cell;
c) means for producing profile data for the cell from a signal obtained from the means for monitoring; and d) means for determining the state of said cell from said data.
100. A system for correlating a foreign agent and a cellular response to the foreign agent, comprising:
a) a support capable of maintaining a plurality of cell in a consistent environment;
b) means for subjecting a foreign agent;
c) monitoring a biological agent or a collection thereof on or in the cell to produce the profile data for the cell;
d) means for producing profile data for the cell from a signal obtained from the means for monitoring; and e) means for correlating the foreign agent and the profile.
a) a support capable of maintaining a plurality of cell in a consistent environment;
b) means for subjecting a foreign agent;
c) monitoring a biological agent or a collection thereof on or in the cell to produce the profile data for the cell;
d) means for producing profile data for the cell from a signal obtained from the means for monitoring; and e) means for correlating the foreign agent and the profile.
101. A system for identifying an unidentified foreign agent given to a cell, from the profile of said cell, comprising:
a) a support capable of maintaining a plurality of cell in a consistent environment;
b) means for subjecting a known foreign agent;
a) means for monitoring a biological agent or a collection thereof on or in a cell over time;
d) means for obtaining the profile data for the cell in response to each of known foreign agents to produce profile data for the cell;
e) means for correlating each of the known foreign agents and each of the profiles;
f) means for subjecting the cells to an unknown foreign agent;
g) means for comparing the profile of the known foreign agent obtained with means d), and the profile of the unknown foreign agent to determine a profile corresponding to the profile of the unknown foreign agent amongst the profiles of the known foreign agents, wherein said determined unidentified foreign agent is the known foreign agent for which the determined profile corresponds to.
a) a support capable of maintaining a plurality of cell in a consistent environment;
b) means for subjecting a known foreign agent;
a) means for monitoring a biological agent or a collection thereof on or in a cell over time;
d) means for obtaining the profile data for the cell in response to each of known foreign agents to produce profile data for the cell;
e) means for correlating each of the known foreign agents and each of the profiles;
f) means for subjecting the cells to an unknown foreign agent;
g) means for comparing the profile of the known foreign agent obtained with means d), and the profile of the unknown foreign agent to determine a profile corresponding to the profile of the unknown foreign agent amongst the profiles of the known foreign agents, wherein said determined unidentified foreign agent is the known foreign agent for which the determined profile corresponds to.
102. A system for identifying an unidentified foreign agent given to a cell, from the profile of the cell, comprising:
a) a storage medium having stored data relating to a correlation between a known foreign agent, and a profile of the cell corresponding to the known foreign agent, with respect to a biological agent or a collection thereof on or in the cell;
b) means for subjecting the cell to an unidentified foreign agent;
c) a support which is capable of maintaining a plurality of cells in a consistent environment;
d) means for monitoring the biological agent or the collection thereof on or in the cell over time to produce a profile of the cell;
e) means for obtaining the profile of the cell from a signal obtained from the means for monitoring; and f) means for determining the profile corresponding to the profile obtained relating to the unidentified foreign agent amongst the profiles stored in the storage medium a) , wherein the unidentified foreign agent is the known foreign agent for which the determined profile corresponds to.
a) a storage medium having stored data relating to a correlation between a known foreign agent, and a profile of the cell corresponding to the known foreign agent, with respect to a biological agent or a collection thereof on or in the cell;
b) means for subjecting the cell to an unidentified foreign agent;
c) a support which is capable of maintaining a plurality of cells in a consistent environment;
d) means for monitoring the biological agent or the collection thereof on or in the cell over time to produce a profile of the cell;
e) means for obtaining the profile of the cell from a signal obtained from the means for monitoring; and f) means for determining the profile corresponding to the profile obtained relating to the unidentified foreign agent amongst the profiles stored in the storage medium a) , wherein the unidentified foreign agent is the known foreign agent for which the determined profile corresponds to.
103. A support capable of immobilizing a plurality of cells and maintaining the cells in a consistent environment.
104. A support according to Claim 103, wherein the cells on the support are located in an array format.
105. A support according to Claim 103 comprising a complex of a positively charged substance and a negatively charged substance; a salt; or an actin-like acting substance.
106. A support according to Claim 103 comprising a complex of a positively charged substance and a negatively charged substance; a salt; and an actin-like acting substance.
107. A support according to Claim 103, wherein said claim is capable of being located within a space of 1 mm or less at maximum.
108. A support according to Claim 103, further comprising a cell immobilized thereon.
109. A support according to Claim 103, further comprising a biological agent immobilized thereon.
110. A support according to claim 109, wherein two or more types of said biological agent are immobilized thereon.
111. A support according to Claim 103, wherein a cell and a biological agent are immobilized thereon.
112. A support according to Claim 103, wherein a salt; a complex between a positively charged substance and a negatively charged substance; and an actin-like acting substance are immobilized thereon together with a cell and a biological agent.
113. A support according to Claim 103, wherein a salt; a complex between a positively charged substance and a negatively charged substances and an actin-like acting substance are immobilized thereon together with a cell and a biological agent, in an array format.
114. A support according to Claim 104, wherein a salt, a gene introduction reagent, and an actin-like acting substance, a nucleic and molecule, and a cell are immobilized thereon in an array format.
115. A support according to Claim 114, wherein the salt is selected from the group consisting of calcium chloride, sodium hydrogen phosphate, sodium hydrogen carbonate, radium pyruvate, HEPES, calcium chloride, sodium chloride, potassium chloride, magnesium sulfide, iron nitrate, amino acids, and vitamins.
116. A support according to Claim 114, wherein the gene introduction reagent is selected from the group consisting of cationic polymers, cationic lipids, polyamine-based reagents, polyimine-based reagents, calcium phosphate, oligofectamine and oligofecter.
117. A support according to Claim 114, wherein the actin-like acting substance comprises at least one protein selected from the group consisting of fibronectin, laminin, and vitronectin, or a variant or fragment thereof.
118. A support according to Claim 114, wherein the nucleic acid molecule comprises a sequence encoding a protein selected from the group consisting of cytokines, hormones, cell adhesion molecules, cytoskeleton proteins and enzymes.
119. A support according to Claim 114, wherein the cell comprises a cell selected from the group consisting of an animal cell, an insect cell, a plant cell, a bacterial cell and a fungal cell.
120. A support according to Claim 114 wherein material of said support comprises material selected from the group consisting of glass, silica and plastics.
121. A method for producing a support comprising a plurality of cells immobilized thereon and capable of maintaining the cells in a consistent environment, comprising the steps of:
A) providing a support; and B) immobilizing a cell to the support using a complex comprising a salt, a positively-charged substance and a negatively-charged substance.
A) providing a support; and B) immobilizing a cell to the support using a complex comprising a salt, a positively-charged substance and a negatively-charged substance.
122. A method according to Claim 121, wherein said step of immobilizing comprises immobilizing a mixture of the salt, a gene introduction reagent, as the positively-charged substance , an actin-like acting substance, a nucleic acid molecule as the negatively-charged substance, and the cell in an array format.
123. A method according to Claim 121, said step of immobilizing comprises a printing step.
124. A method according to Claim 121, wherein the step of providing the support comprises the step of producing the support from a support material.
125. An apparatus for producing a support comprising a plurality of cells immobilized thereon and capable of maintaining the cells in a consistent environment, comprising:
A) means for providing a support; and B) means for immobilizing a cell to the support using a complex comprising a salt, a positively-charged substance and a negatively-charged substance.
A) means for providing a support; and B) means for immobilizing a cell to the support using a complex comprising a salt, a positively-charged substance and a negatively-charged substance.
126. An apparatus according to Claim 125, wherein said means for immobilizing comprises means for printing.
127. An apparatus according to Claim 225, whereon the means for providing the support comprises means for shaping the support from a support material.
128. A method for producing a digital cell, comprising the steps of:
a) obtaining a cell parameter specifying a cell of experimental interest;
b) obtaining an environment parameter specifying an environment under which the cell specified by the cell parameter is cultured;
c) obtaining a stimulus parameter specifying a stimulus to be given to the cell specified by the cell parameter;
d) obtaining a stimulus response result showing a result which the cell specified by the cell parameter responds to the stimulus specified by the stimulus parameter under the environment specified by the environment parameter;
e) producing an experimental data for the cell, by correlating the cell parameter, the environment parameter, the stimulus parameter and the stimulus response result;
and f) optionally repeating steps a) through e) to produce at least one collection of experimental data for the cell, and to provide the at least one collection of experimental data as a digital cell.
a) obtaining a cell parameter specifying a cell of experimental interest;
b) obtaining an environment parameter specifying an environment under which the cell specified by the cell parameter is cultured;
c) obtaining a stimulus parameter specifying a stimulus to be given to the cell specified by the cell parameter;
d) obtaining a stimulus response result showing a result which the cell specified by the cell parameter responds to the stimulus specified by the stimulus parameter under the environment specified by the environment parameter;
e) producing an experimental data for the cell, by correlating the cell parameter, the environment parameter, the stimulus parameter and the stimulus response result;
and f) optionally repeating steps a) through e) to produce at least one collection of experimental data for the cell, and to provide the at least one collection of experimental data as a digital cell.
129. A method according to Claim 128, wherein the environment parameter comprises a parameter indicating culture medium in which the cell is cultured, and a parameter showing the conditions of the culture medium.
130. A method according to Claim 128, wherein the stimulus parameter comprises a parameter showing a reporter and a parameter showing a chemical stimulus.
131. A method according to Claim 128, wherein said stimulus response result comprises profile data for the cell obtained by monitoring a biological agent or a collection thereof on or in the cell over time.
132. A method according to Claim 128, further comprising the step of storing the digital cell to a database.
133. An apparatus for producing a digital cell, comprising:
a) means for obtaining a cell parameter specifying a cell of experimental interest;
b) means for obtaining an environment parameter specifying an environment under which the cell specified by the cell parameter is cultured;
c) means for obtaining a stimulus parameter specifying a stimulus to be given to the cell specified by the cell parameter;
d) means for obtaining a stimulus response result showing a result which the cell specified by the cell parameter responds to the stimulus specified by the stimulus parameter under the environment specified by the environment parameter;
e) means for producing an experimental data for the cell, by correlating the cell parameter, the environment parameter, the stimulus parameter and the stimulus response result; and f ) means for providing at least one collection of experimental data as a digital cell, by optionally repeating steps performed by the means a) through e) to produce at least one collection of experimental data for the cell.
a) means for obtaining a cell parameter specifying a cell of experimental interest;
b) means for obtaining an environment parameter specifying an environment under which the cell specified by the cell parameter is cultured;
c) means for obtaining a stimulus parameter specifying a stimulus to be given to the cell specified by the cell parameter;
d) means for obtaining a stimulus response result showing a result which the cell specified by the cell parameter responds to the stimulus specified by the stimulus parameter under the environment specified by the environment parameter;
e) means for producing an experimental data for the cell, by correlating the cell parameter, the environment parameter, the stimulus parameter and the stimulus response result; and f ) means for providing at least one collection of experimental data as a digital cell, by optionally repeating steps performed by the means a) through e) to produce at least one collection of experimental data for the cell.
134. A method for providing a service which reproduces an experimental result of an actual cell using a digital cell by means of a computer system comprising service a requester axed a service provider, comprising the steps of:
preparing a database having at least one digital cell stored thereon, wherein the at least one digital cell is expressed as a collection of at least one experimental data of a cell of experimental interest, wherein each of the at least one experimental data comprises a cell parameter specifying the cell, an environment parameter specifying an environment under which the cell specified by the cell parameter is culture, a stimulus parameter specifying a stimulus to be given to the cell specified by the cell parameter, and a stimulus response result showing a result which the cell specified by the cell parameter responds to the stimulus specified by the stimulus parameter under the environment specified by the environment parameter;
receiving the cell parameter, the environment parameter and the stimulus parameter by the service requester to produce a request comprising the cell parameter, the environment parameter and the stimulus parameter;
providing the request to the service provider by the service requester;
searching the database in response to the request by the service provider to determine whether or not there is the stimulus response result relating to the cell parameter, the environment parameter and the stimulus parameter included in the request, in the database:
providing the stimulus response result to the service requester by the service provider, when it is determined that the stimulus response result relating to the cell parameter, the environment parameter and the stimulus parameter included in the request exists in the database:
and presenting the stimulus response result by the service requester.
preparing a database having at least one digital cell stored thereon, wherein the at least one digital cell is expressed as a collection of at least one experimental data of a cell of experimental interest, wherein each of the at least one experimental data comprises a cell parameter specifying the cell, an environment parameter specifying an environment under which the cell specified by the cell parameter is culture, a stimulus parameter specifying a stimulus to be given to the cell specified by the cell parameter, and a stimulus response result showing a result which the cell specified by the cell parameter responds to the stimulus specified by the stimulus parameter under the environment specified by the environment parameter;
receiving the cell parameter, the environment parameter and the stimulus parameter by the service requester to produce a request comprising the cell parameter, the environment parameter and the stimulus parameter;
providing the request to the service provider by the service requester;
searching the database in response to the request by the service provider to determine whether or not there is the stimulus response result relating to the cell parameter, the environment parameter and the stimulus parameter included in the request, in the database:
providing the stimulus response result to the service requester by the service provider, when it is determined that the stimulus response result relating to the cell parameter, the environment parameter and the stimulus parameter included in the request exists in the database:
and presenting the stimulus response result by the service requester.
135. A method for providing a service for reproducing an experimental, result of an actual cell using a digital cell, by means of a computer system comprising a service requester and a plurality of service providers, comprising the steps of:
preparing a plurality of databases, each having at least one digital. cell stored thereon, wherein the at least one digital cell is expressed as a collection of at least one experimental. data of a cell of experimental interest, wherein each of the at least one experimental data comprises a cell parameter specifying the cell, an environment parameter specifying an environment under which the cell specified by the cell parameter is culture, a stimulus parameter specifying a stimulus to be given to the cell specified by the cell parameter, and a stimulus response result showing a result which the cell specified by the cell parameter responds to the stimulus specified by the stimulus parameter under the environment specified by the environment parameter;
preparing a service registry which stores at least one service capable of being provided by the plurality of service providers;
receiving the cell parameter, the environment parameter and the stimulus parameter by the service requester to produce a request comprising the cell parameter, the environment parameter and the stimulus parameter;
searching the service registry in response to the request by the service requester to determine whether as not there exists a service provider capable of providing a service for the request amongst the plurality of service providers;
providing the request to the service provider by the service requester when it is determined that a service provider capable of providing a service of the request amongst the plurality of service providers exists;
searching the database in response to the request by the service provider to determine whether or not there is the stimulus response result relating to the cell parameter, the environment parameter and the stimulus parameter included in the request in the database;
providing the stimulus response result to the service requester by the service provider, when it is determined that the stimulus response result relating to the cell parameter, the environment parameter and the stimulus parameter included in the request exists in the database;
and presenting the stimulus response result by the service requester.
preparing a plurality of databases, each having at least one digital. cell stored thereon, wherein the at least one digital cell is expressed as a collection of at least one experimental. data of a cell of experimental interest, wherein each of the at least one experimental data comprises a cell parameter specifying the cell, an environment parameter specifying an environment under which the cell specified by the cell parameter is culture, a stimulus parameter specifying a stimulus to be given to the cell specified by the cell parameter, and a stimulus response result showing a result which the cell specified by the cell parameter responds to the stimulus specified by the stimulus parameter under the environment specified by the environment parameter;
preparing a service registry which stores at least one service capable of being provided by the plurality of service providers;
receiving the cell parameter, the environment parameter and the stimulus parameter by the service requester to produce a request comprising the cell parameter, the environment parameter and the stimulus parameter;
searching the service registry in response to the request by the service requester to determine whether as not there exists a service provider capable of providing a service for the request amongst the plurality of service providers;
providing the request to the service provider by the service requester when it is determined that a service provider capable of providing a service of the request amongst the plurality of service providers exists;
searching the database in response to the request by the service provider to determine whether or not there is the stimulus response result relating to the cell parameter, the environment parameter and the stimulus parameter included in the request in the database;
providing the stimulus response result to the service requester by the service provider, when it is determined that the stimulus response result relating to the cell parameter, the environment parameter and the stimulus parameter included in the request exists in the database;
and presenting the stimulus response result by the service requester.
136. A computer system for providing a service which reproduces an experimental result of an actual cell using a digital cell, comprising:
a service requester being composed such that it van have access to a database having at least one digital cell stored thereon, each of the at least one digital cell is expressed as a collection of at least one experimental data of a cell of experimental interest, wherein each of the at least one experimental data comprises a cell parameter specifying the cell, an environment parameter specifying an environment under which the cell specified by the cell parameter is cultured, a stimulus parameter specifying a stimulus to be given to the cell specified by the cell parameter, and a stimulus response result showing a result which the cell specified by the cell parameter responds to the stimulus specified by the stimulus parameter under the environment specified by the environment parameter; and a service provider requesting a service desired by a user;
wherein the service requester comprises:
means for receiving the cell parameter, the environment parameter and the stimulus parameter to produce a request comprising the cell parameter, the environment parameter and the stimulus parameter; and means for providing the request to the service provider, and wherein the service provider comprises:
means for searching the database in response to the request by the service provider to determine whether or not there is the stimulus response result relating to the cell parameter, the environment parameter and the stimulus parameter included in the request in the database;
and means for providing the stimulus response result to the service requester by the service provider, when it determined that the stimulus response result relating to the cell parameter, the environment parameter and the stimulus parameter included in the request exists in the database;
wherein the service requester further comprises means for presenting the stimulus response result by the service requester.
a service requester being composed such that it van have access to a database having at least one digital cell stored thereon, each of the at least one digital cell is expressed as a collection of at least one experimental data of a cell of experimental interest, wherein each of the at least one experimental data comprises a cell parameter specifying the cell, an environment parameter specifying an environment under which the cell specified by the cell parameter is cultured, a stimulus parameter specifying a stimulus to be given to the cell specified by the cell parameter, and a stimulus response result showing a result which the cell specified by the cell parameter responds to the stimulus specified by the stimulus parameter under the environment specified by the environment parameter; and a service provider requesting a service desired by a user;
wherein the service requester comprises:
means for receiving the cell parameter, the environment parameter and the stimulus parameter to produce a request comprising the cell parameter, the environment parameter and the stimulus parameter; and means for providing the request to the service provider, and wherein the service provider comprises:
means for searching the database in response to the request by the service provider to determine whether or not there is the stimulus response result relating to the cell parameter, the environment parameter and the stimulus parameter included in the request in the database;
and means for providing the stimulus response result to the service requester by the service provider, when it determined that the stimulus response result relating to the cell parameter, the environment parameter and the stimulus parameter included in the request exists in the database;
wherein the service requester further comprises means for presenting the stimulus response result by the service requester.
137. A computer system according to Claim 136 wherein the service requester is a Web browser which the user operates, and the service provider is a web server linked to the service requester via the Internet.
138. A computer system according to Claim 136, wherein the service requester provides the request to the service provider in a format described in XML language.
139. A computer system according to Claim 136, wherein the service provider provides the stimulus response result to the service requester in a format described in XML language.
140. A computer system for providing a service which reproduces an experimental result of an actual cell using a digital cell, comprising:
a plurality of service providers, each composed such that the plurality of service providers can have access to a database having at least one digital cell stored thereon, each of the at least one digital cell is expressed as a collection of at least one experimental data of a cell of experimental interest, wherein each of the at least one experimental data comprises a cell parameter specifying the cell, an environment parameter specifying an environment under which the cell specified by the cell parameter is cultured, a stimulus parameter specifying a stimulus to be given to the cell specified by the cell parameter, and a stimulus response result showing a result which the cell specified by the cell parameter responds to the stimulus specified by the stimulus parameter under the environment specified by the environment parameter;
a service registry which stores at least one service which the plurality of service providers can provide; and a service provider requesting a service desired by a user:
wherein the service requester comprises:
means for receiving the cell parameter, the environment parameter and the stimulus parameter to produce a request comprising the cell parameter, the environment parameter and the stimulus parameter;
means for searching the service registry in response to the request by the service requester to determine whether or not there exists a service provider capable of providing a service of the request amongst the plurality of service providers and means for providing the request to the service provider by the service requester when it is determined that there exists a service provider capable of providing a service of the request amongst the plurality of service providers, wherein each of the plurality of service providers comprises:
means for searching the database in response to the request by the service provider to determine whether or not there is the stimulus response result relating to the cell parameter, the environment parameter and the stimulus parameter included in the request in the database;
and means for providing the stimulus response result to the service requester by the service provider, when it is determined that the stimulus response result relating to the cell parameter, the environment parameter and the stimulus parameter included in the request exists in the database;
wherein the service requester further comprises means for presenting the stimulus response result by the service requester.
a plurality of service providers, each composed such that the plurality of service providers can have access to a database having at least one digital cell stored thereon, each of the at least one digital cell is expressed as a collection of at least one experimental data of a cell of experimental interest, wherein each of the at least one experimental data comprises a cell parameter specifying the cell, an environment parameter specifying an environment under which the cell specified by the cell parameter is cultured, a stimulus parameter specifying a stimulus to be given to the cell specified by the cell parameter, and a stimulus response result showing a result which the cell specified by the cell parameter responds to the stimulus specified by the stimulus parameter under the environment specified by the environment parameter;
a service registry which stores at least one service which the plurality of service providers can provide; and a service provider requesting a service desired by a user:
wherein the service requester comprises:
means for receiving the cell parameter, the environment parameter and the stimulus parameter to produce a request comprising the cell parameter, the environment parameter and the stimulus parameter;
means for searching the service registry in response to the request by the service requester to determine whether or not there exists a service provider capable of providing a service of the request amongst the plurality of service providers and means for providing the request to the service provider by the service requester when it is determined that there exists a service provider capable of providing a service of the request amongst the plurality of service providers, wherein each of the plurality of service providers comprises:
means for searching the database in response to the request by the service provider to determine whether or not there is the stimulus response result relating to the cell parameter, the environment parameter and the stimulus parameter included in the request in the database;
and means for providing the stimulus response result to the service requester by the service provider, when it is determined that the stimulus response result relating to the cell parameter, the environment parameter and the stimulus parameter included in the request exists in the database;
wherein the service requester further comprises means for presenting the stimulus response result by the service requester.
141. A computer system according to Claim 140, wherein the service requester is a Web server connected to a Web browser which the user operates via the Internet, and each of the plurality of service providers is a Web server connected to the service requester via the Internet.
142. A computer system according to Claim 140, wherein the service requester provides the request to the service provider in a format described in XML language.
143. A computer system according to Claim 140, wherein the service provider provides the stimulus response result to the service requester in a format described in XML language.
144. A method for producing the profile data relating information of a cell, comprising the steps of:
a) immobilizing and locating a cell on a support; and b) monitoring a biological agent or a collection thereof on or in the cell to produce the profile data for the cell.
a) immobilizing and locating a cell on a support; and b) monitoring a biological agent or a collection thereof on or in the cell to produce the profile data for the cell.
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| CA2530350A1 (en) * | 2003-06-25 | 2005-03-10 | National Institute Of Advanced Industrial Science And Technology | Digital cell |
| US20050149546A1 (en) * | 2003-11-03 | 2005-07-07 | Prakash Vipul V. | Methods and apparatuses for determining and designating classifications of electronic documents |
| US7519565B2 (en) * | 2003-11-03 | 2009-04-14 | Cloudmark, Inc. | Methods and apparatuses for classifying electronic documents |
| US8862582B2 (en) * | 2007-11-15 | 2014-10-14 | At&T Intellectual Property I, L.P. | System and method of organizing images |
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| US10083275B2 (en) | 2012-12-13 | 2018-09-25 | International Business Machines Corporation | Stable genes in comparative transcriptomics |
| US10542961B2 (en) | 2015-06-15 | 2020-01-28 | The Research Foundation For The State University Of New York | System and method for infrasonic cardiac monitoring |
| US11205103B2 (en) | 2016-12-09 | 2021-12-21 | The Research Foundation for the State University | Semisupervised autoencoder for sentiment analysis |
| JP2018100903A (en) * | 2016-12-20 | 2018-06-28 | パナソニックＩｐマネジメント株式会社 | Resin determination method and apparatus |
| CN117597452A (en) * | 2021-06-29 | 2024-02-23 | 富士胶片株式会社 | Method for producing cell mathematical model, cell mathematical model production program, cell mathematical model production device, method for determining cell mathematical model, cell mathematical model determination program, and cell mathematical model determination device |
| CN113759196B (en) * | 2021-09-08 | 2022-09-13 | 山东大学 | High-voltage electrical equipment experimental device and experimental method thereof |
| WO2023190139A1 (en) * | 2022-03-30 | 2023-10-05 | 富士フイルム株式会社 | Construction method, construction device, and construction program |
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