US20030026800A1

US20030026800A1 - Monoclonal antibodies, antigens and diagnosis and therapy of malignant diseases

Info

Publication number: US20030026800A1
Application number: US09/967,719
Authority: US
Inventors: Britta Hardy; Abraham Novogrodsky
Original assignee: Mor Research Applications Ltd
Current assignee: Mor Research Applications Ltd
Priority date: 1999-03-31
Filing date: 2001-09-28
Publication date: 2003-02-06
Also published as: ATE283289T1; DE69922261T2; BR9917218A; RU2235131C2; ZA200106809B; CN1267452C; CA2367901A1; HUP0200537A2; AU5996599A; US7695715B2; EP1165616A1; US20060099209A1; DE69922261D1; IL145535A; EP1165616B1; JP2003500015A; CN1346371A; AU776464B2; IL145535A0; IL129299A0

Abstract

The invention concerns novel DNA and amino acid sequences of monoclonal antibodies (mAbs) raised against lymphoblastoid cells and peptides to which the mAbs bind to. The invention also concerns diagnostic assays using said antibodies or peptides for detecting individuals with a high probability of having a malignant disease and, at times, for detecting an individual having a specific malignant disease. The invention further concerns pharmaceutical compositions comprising the mAbs or peptides of the invention for use in the treatment of various malignant diseases as well as methods for the treatment of malignant diseases using the mAbs or peptides of the invention.

Description

CROSS-REFERENCE TO RELATED APPLICATION

This application is a continuation of the U.S. National Stage designation of International Application PCT/IL99/00518 filed Sep. 30, 1999, the content of which is expressly incorporated herein by reference thereto.[0001]

FIELD OF THE INVENTION

The present invention concerns novel sequences of monoclonal antibodies, peptidic sequences of antigens to which the monoclonal antibodies bind, as well as diagnostic and therapeutic assays using the monoclonal antibody and peptides.

BACKGROUND OF THE INVENTION

Co-owned PCT Application, Publication No. WO 95/20605, discloses immuno-stimulatory monoclonal antibodies. The antibodies subject of this PCT application were raised against B lymphoblastoid cells and were shown to have an immuno-stimulatory effect. When injected into tumor-bearing animals, these antibodies were also found to elicit an anti-tumor effect.

Cancer diagnosis, under current medical procedures, is typically a multi-step process involving physical examination, use of a variety of imaging techniques, employment of a variety of cancer markers, etc. There is a longfelt need in the art for cancer diagnostic techniques which allow detection of cancer and also determination of the type of cancer which the tested individual is suffering from.

GENERAL DESCRIPTION OF THE INVENTION

The present invention is based on the finding of sequences of monoclonal antibodies against lymphoblastoid cells. The present invention is further based on the finding that the level of binding of these antibodies to T-cells of patients having cancer is different (higher or lower) than the level of binding of these antibodies to T-cells of healthy individuals.

In accordance with one aspect of the invention there is provided a monoclonal antibody having a variable region selected from the group consisting of:

(a) a monoclonal antibody having a heavy chain variable region comprising the amino acid sequence of FIG. 1;

(b) a monoclonal antibody having a Kappa light chain variable region comprising the amino acid sequence of FIG. 2;

(c) a monoclonal antibody having a heavy chain variable region comprising the amino acid sequence of FIG. 1 and the Kappa light chain variable region comprising the amino acid sequence of FIG. 2;

(d) a monoclonal antibody having a heavy chain variable region having at least 70% identity to the amino acid sequence of FIG. 1;

(e) a monoclonal antibody having a light chain variable region having at least 70% identity to the sequence of FIG. 2.

In accordance with the invention, the term “antibody” refers to monoclonal antibodies of any of the classes IgG, IgM, IgD, IgA and IgE. The term refers to whole antibodies or fragments of the antibodies comprising the antigen-binding domain of the antibodies, e.g. antibodies lacking the Fc portion, single chain antibodies, fragments of articles consisting essentially of only the variable antigen-binding domain of the antibody, etc.

In addition the invention also concerns antibodies which bind to an antigen to which any one of the above mAbs specifically binds to i.e. antibodies which have cross reactivity with the above antibodies.

In accordance with one embodiment of the invention, the monoclonal antibody is a chimeric human-mouse antibody, namely a mAb with a constant region derived from a human origin and a variable region derived from mouse. For this purpose, the Kappa light and heavy chain variable regions of the mAb of the invention were PCR cloned and their DNA sequenced. In accordance with yet another embodiment of the invention the antibody is a fully humanized antibody, i.e. both its variable and constant region are derived from a human source.

The term “having at least X percent identity” refers to the percent of amino acid residues that are identical in the two compared sequences when the sequences are optimally aligned. Thus, 70% amino acid sequence identity means that 70% of the amino acids in two or more optimally aligned polypeptide sequences are identical. Preferably, the identity is at least 80%, most preferably at least 90%.

In accordance with an additional aspect of the invention, there are provided mouse hybridoma cell lines which produce any of the mAbs of the invention. The hybridomas may be prepared by any of the methods known in the art (for example, Kohler, G. and Milstein, C., Nature, 256:495-497, (1975)). The supernatant of the hybridoma cell lines are typically screened for antibody binding activity by any one of the methods known in the art such as by enzyme linked immuno sorbent assay (ELISA) or radio immuno assay (RIA). The supernatants are screened for production of mAbs which bind to any of the peptides of the invention (as explained below) or which bind to cells to which they bind, e.g. Daudi cells or T lymphocytes.

DNA sequences which encode any of the amino acid sequences of the heavy chain or light chain of the above mAbs are also encompassed within the scope of the invention. As will no doubt be clear to any man versed in the art, due to the degenerative nature of the genetic code a plurality of nucleic acid sequences may code for the mAb of the invention beyond those shown in FIGS. 1 or 2.

The invention also provides expression vectors such as plasmids having said DNA sequences as well as host cells containing one or more of these expression vectors.

In accordance with another aspect of the invention, there are provided peptidic sequences of a B-cell antigens to which the mAbs of the invention can bind. Searches performed against the non-redundant gene bank database and the EST division determined that these peptidic sequences are novel.

In accordance with this additional aspect of the invention there is provided a peptide selected from the group consisting of:

(a) a peptide having an amino acid sequence as depicted in FIG. 10;

(b) a peptide having an amino acid sequence as depicted in FIG. 11;

(c) a peptide having an amino acid sequence as depicted in FIG. 12;

(d) a peptide having at least 85% identity to any one of the amino acid sequences of the peptides of (a), (b) and (c) above; and

(e) a protein or a peptide comprising one or more of the peptides of (a)-(d) above.

The peptides of the invention may be used for a variety of diagnostic assays, such as, for example, competitive immuno-assays wherein the level of binding of the mAb of the invention to its native antigen, which exists on T-cells is determined. In addition, the peptides may be used for the production of antibodies in immunized animals which antibodies may then be used for any one of the utilities described above and below.

Analogs of all the above peptides also form an additional aspect of the present invention. As will be appreciated by an person versed in the art, the amino acid sequence of the peptides of the invention may be altered, for example, by addition, deletion or conservative or non-conservative substitution of one or more amino acids without substantially altering the antibody binding properties of the peptide

The term “conservative substitution” refers to the substitution of an amino acid in one class by an amino acid of the same class, where a class if defined by common physiochemical amino acid side chain properties and high substitution frequencies in homologous proteins found in nature, as determined, for example, by a standard Dayhoff frequency exchange matrix or BLOSUM matrix. [Six general classes of amino acid side chains have been characterized and include: Class I (Cys); Class II (Ser, Thr, Pro, Ala, Gly); Class III (Asn, Asp, Gln, Glu); Class IV (His, Arg, Lys); Class V (Ile, Leu, Val, Met); and Class VI (Phe, Tyr, Trp). For example, substitution of an Asp for another Class III residue such as Asn, Gln, or Glu, is a conservative substitution. The term “non-conservative substitution” refers to the substitution of an amino acid in one class with an amino acid from another class; for example, substitution of an Ala, a Class II residue, with a Class III residue such as Asp, Asn, Glu, or Gln.

The letters used above (and hereinafter) to denote specific amino acids (aa) are in accordance with the 1-letter amino acid symbols recommend by the IUPAC-IUB Biochemical Nomenclature Commission.

Analogs of the above peptides which fall under the scope of the present invention are such which have substantially the same level of binding to the mAbs of the invention as the peptides depicted in FIGS. 10-12. The level of binding can be determined by any manner known in the art.

The peptides and analogs of the invention may also be chemically modified and such chemically modified peptides and analogues also form a part of the invention. The term “chemically modified” refers to a protein where at least one of its amino acid residues is modified either by natural processes, such as processing or other post-translational modifications, or by chemical modification techniques which are well known in the art. Among the numerous known modifications typical, but not exclusive examples include: acetylation, acylation, amidation, ADP-ribosylation, glycosylation, GPI anchor formation, covalent attachment of a liquid or lipid derivative, methylation, myristylation, pegylation, prenylation, phosphorylation, ubiqutination, or any similar process.

The second finding on which the invention is based is that the mAbs of the invention can bind to a different extent to T-cells obtained from individuals having a malignant disease as compared to the extent of binding of the same mAbs to T-cells of a healthy individual.

Thus, by a further aspect of the present invention an assay is provided for identifying a tested individual with a high probability of having a malignant disease comprising:

(a) obtaining a body fluid sample from said individual;

(b) contacting said sample with at least one mAb of the invention;

(c) determining the extent of binding of said mAbs to T-cells within said sample; and

(d) comparing the extent of (c) to the extent of binding of the mAbs of the invention to T-cells in a sample obtained from a healthy individual; a significant difference between the above two extents of binding indicating that said tested individual has a high probability of having a malignant disease.

In accordance with the invention, the sample obtained from the individual to be tested may be any body fluid which contains a detectable amount of T-cells. Typically, the body fluid sample is a blood or lymph fluid sample. Preferably, before contacting the mAbs of the invention with the obtained sample, the peripheral blood monoclear cells (PBMC) in the sample are separated by any one of the methods known in the art such as by Ficoll Hypaque density centrifugation and the separated cells are then contacted with the tested antibodies.

The term “malignant disease” in accordance with the invention is to be understood as any kind of malignant disease known in the art at any of its stages.

This term also encompasses malignant diseases which are at their early stages and have not yet elicited clinical symptoms. Preferably this term refers to solid tumors.

The term “healthy individual” relates to an individual who does not have a malignant disease, and may also refer to an average level of several individuals or to a level obtained by pooling together body fluids from several individuals. It should be noted that once a standard extent of binding of healthy individuals is established, there is no need to re-establish this standard for every test and the figure established may be used continuously. In accordance with the invention it has been found that in healthy individuals about 25% of CD3 ⁺ T-cells bind to antibodies of the invention.

The term “high probability” means that the assay of the invention is an initial screening assay capable of identifying individuals suspected of having a malignant disease. The fact that the individual detected by the method of the invention has indeed a malignant disease will have to be verified later by utilizing additional techniques known in the art.

The term “extent of binding” relates to the level of binding of the antibody to an antigen present on the T-cell of the tested individual which extent can be determined by any of the methods known in the art for determining binding levels of antibodies such as ELISA or Western Blotting. The extent of binding may be determined using any detection system such as anti-mouse immunoglobulin or fragments thereof linked to a detectable marker. Examples of such detectable markers are a radioactive group, a fluorescent group, an enzyme capable of catalyzing a reaction yielding a detectable product (such as a color reaction), a biotin group capable of being detected by avidin, etc. By a preferred embodiment, the extent of binding of the mAbs of the invention to the T-cells is carried out by double labeling in which the anti T-cell antibody (e.g. anti-CD3 ⁺ antibody) is attached to one kind of fluorescent marker and the mAb of the invention is attached to a second type of fluorescent marker. The extent of binding is then determined using fluorecein activated cell sorter (FACS). The quantitation of the extent of binding is achieved by determining the percent of CD3⁺ T-cells (determined by their binding of anti-CD3⁺ antibodies) which also bind the mAb of the invention.

In accordance with the invention, it was found that the total number of CD3 ⁺ cells in blood samples of individuals having a malignant disease is similar to the number of CD3⁺ cells in blood samples obtained from healthy individuals so that the normalization of the extent of binding of both mAb and CD3⁺ T-cells by using total CD3⁺ binding T-cells both in malignant patients and healthy individuals is valid. However, the percent of the CD3⁺ binding T-cells which also bind the mAb of the invention (hereinafter: “CD3⁺ mAb cells”) in individuals having a malignant disease differs significantly from the percent of CD3⁺ mAb⁺ cells in blood of healthy individuals. The percent of the CD3⁺ mAb⁺ cells in an individual having a malignant disease may either be significantly higher or significantly lower than the percent of CD3⁺ mAb⁺ cells in healthy individuals, depending on the type of the malignant disease.

The extent of binding of a mAb of the invention to a T-cell obtained from a tested individual will be considered to be “significantly different” than the extent of binding to T-cells obtained from a healthy individual when the difference in binding of the mAb is statistically different in a significant degree as determined by any of the statistical methods known in the art (e.g. Students t-Test) which are used in connection with results obtained by the experimental methods mentioned herewith.

The invention not only enables to identify individuals having a high probability of having any type of malignant diseases (where the diseased individual has a different extent of binding of T-cells to mAbs of the invention as compared to a healthy individual) but can also help identify individuals having specific types of cancer by determining whether said extent is higher or lower than the corresponding extent in the healthy individual.

Typically, the percent of binding of the mAbs of the invention to T-cells obtained from healthy individuals is in the range of about 25%, i.e. 25% of the cells expressing the CD3 ⁺ T-cell marker (determined by binding of anti-CD3⁺ antibody to the cells) also bind the mAbs of the invention.

In accordance with the invention, it has been shown that in samples obtained from prostate cancer patients, the percent of CD3 ⁺ T-cells to which the mAbs of the invention bind are in the range of about 50%.

It was further shown that where the CD3 ⁺ T-cells originate from samples obtained from colon or breast carcinoma patients, the percent of the cells which also bind to the mAbs of the invention is about 7% and 10%, respectively.

Thus, in accordance with the present invention it has become possible to determine that there is a high probability that there exists a specific type of cancer in a body fluid sample taken from a tested individual using a simple and single assay based on the extent of binding of the mAbs of the invention to CD3 ⁺ cells present in the body fluid sample. The simplicity of the diagnostic assay of the invention which necessitates use of only one kind of mAb to identify an individual having a certain type of cancer is very useful for wide screening of a population.

Thus, the present invention by another of its aspects provides an assay for identifying a tested individual with a high probability of having a specific malignant disease comprising:

(a) obtaining a body fluid sample from said individual;

(b) contacting said sample with the mAbs of the invention;

(c) determining the extent of binding of said mAbs to T-cells in said sample; and

(d) comparing the extent of binding (c) cells obtained to the extent of binding of the mAbs to T-cells obtained from a healthy individual, the existence of a significant difference in the extents of binding indicating with a high probability that the tested individual has a malignant disease wherein whether the extent of binding to the T-cells from said individual is above or below the extent of the binding of the mAbs in T-cells of healthy individuals, indicates a specific type of malignant disease which the tested individual has with high probability.

In particular, where the extent of binding to the mAb of the invention is significantly higher than in healthy individuals the tested individual has a high probability of having prostate cancer.

Where the extent of binding is significantly lower than the healthy individual, the tested individual has a high probability of having colon or breast cancer.

In accordance with the diagnostic aspect of the invention, compositions comprising the mAbs of the invention may be used for diagnosis to identify individuals with the high probability of having a malignant disease (in general) or for identifying a specific malignant disease the individual is likely to have. The invention therefore provides by another of its aspects, a diagnostic composition comprising mAbs belonging to at least one of the abovementioned antibodies together with a suitable carrier. The carrier may either be a soluble carrier such as any one of the physiological acceptable buffers known in the art (e.g. PBS) or a solid state carrier such as, for example, latex beads.

The present invention also provides kits, e.g. diagnostic assay kits, for utilizing the mAbs of the invention and carrying out the diagnostic assays disclosed above. In one embodiment, the diagnostic kit would conventionally include at least one of the above mAbs in one or more containers, a conjugate of a specific binding partner for the mAb (for example the antigen or analog of the invention), a label capable of producing a detectable signal and directions for its use. The label may be, a priori, bound to the monoclonal antibody or, alternatively, the label may be bound to a carrier molecule which then specifically binds to the mAb. The incubation of the tested sample with the diagnostic reagent composition is for a time sufficient to allow binding of the monoclonal antibodies to the cells.

By a further aspect of the invention, there are provided pharmaceutical compositions comprising, as an active ingredient, one or more of the mAbs of the invention together. Use of said mAbs for the preparation of pharmaceutical preparations for the treatment of various malignant diseases in an individual is also within the scope of the invention.

By yet another aspect the present invention concerns a method of treatment of malignant diseases by administering to an individual in need a therapeutically effective amount of said mAbs. A therapeutically effective amount being an amount capable of alleviating the symptoms of the malignant disease, reducing the symptoms or completely eliminating them.

Pharmaceutical compositions comprising the peptides of the invention also constitute an aspect of the invention. Such compositions may be used, for example, for active immunization of an individual to obtain antibodies which may then bind to the T-cells of the individual and elicit an immune response in the individual.

DETAILED DESCRIPTION OF THE ASPECTS OF THE INVENTION

The main aspects of the invention will now be described with occasional reference to the attached figures. In the following description and figures, the term “BAT antibody” will be used interchangeably with the term “mAbs of the invention”.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 shows the DNA (SEQ ID NO.: 1) and peptide sequences (SEQ ID NO.: 2) of the heavy chain variable region of the mAb of the invention;. [0064]
FIG. 2 shows DNA (SEQ ID NO.: 3) and peptide sequences (SEQ ID NO.: 4) of the Kappa light chain variable region of the mAb of the invention; [0065]
FIG. 3 shows an analysis of the amino acid sequence of the heavy chain variable region of the antibody of the invention (designated “BAT “BAT” defines the amino acid sequence of the BAT antibody V[0066] _Hregion, while “VMS2” defines the amino acid sequence of the germline VMS2/VGK4 germline gene. Where the BAT sequence and the germline sequence are identical the germline sequence is represented by a dot (.); where mismatches occur the different germline residue is shown. The tables below, the sequence on the following pages describe the frequency with which certain amino acids have been seen at a particular residue position both within the Kabat et al., Sequences of proteins of immunological interest, (1991) mouse heavy chain subgroup miscellaneous (Mouse V_HMisc.) and across a larger database of all known mouse V_Hsequences (All Mouse V_H);.
FIG. 4 shows an analysis of the amino acid sequence of the kappa light chain variable region of the antibody of the invention (designated in the FIG. As “BAT”). “Mouse” defines the amino acid sequence of the BAT antibody K[0067] _Kregion, while “Germ” defines the amino acid sequence of the germline H4 germline gene. Where the BAT sequence and the germline sequence are identical the germline sequence is represented by a dot (.); where mismatches occur the different germline residue is shown. The tables below and on the following pages describe the frequency with which certain amino acids have been seen at a particular residue position both within the Kabat mouse heavy chain subgroup VI (Mouse V_KVI) and across a larger database of all known mouse V_Ksequences (All Mouse V_K);
FIG. 5 shows the DNA (SEQ ID NO.: 5) and peptide sequences (SEQ ID NO.: 6) of the Kappa light chain variable regions of the chimeric antibody of the invention; [0068]
FIG. 6 shows the DNA (SEQ ID NO.: 7) and peptide sequences (SEQ ID NO.: 8) of the heavy chain variable region of the chimeric antibody of the invention; [0069]
FIG. 7 shows a schematic representation of the pKN 110 mammalian expression vector used for the expression of the Kappa light chain of the chimeric antibody of the invention; [0070]
FIG. 8 shows a schema tic representation of the pG1D 110 mammalian expression vector used for the expression of the heavy chain of the chimeric antibody of the invention. [0071]
FIG. 9 shows a graphic representation featuring an example of results of an ELISA assay measuring the binding characteristics of the mouse and the γ1/Kappa chimeric antibody of the invention to Daudi cells;. [0072]
FIG. 10 shows the amino acid sequence of peptide 1 (SEQ ID NO.: 9) of the invention; [0073]
FIG. 11 shows the amino acid sequence of peptide 2 (SEQ ID NO.: 10) of the invention; [0074]
FIG. 12 shows the amino acid sequence of peptide 3 (SEQ ID NO.: 11) of the invention; [0075]
FIG. 13 is a schematical representation showing the percent of CD3[0076] ⁺ cells which also bind the mAb of the invention (indicated as “BAT”) as compared to the total number of CD3⁺ cells in blood samples of healthy individuals as determined by FACS analysis;
FIG. 14 shows the percent of CD3[0077] ⁺ cells which also bind the mAb of the invention (indicated as BAT) as compared to the total number of CD3⁺ cells in blood samples taken from patients having colon carcinoma as determined by FACS analysis;
FIG. 15 shows the percent of CD3[0078] ⁺ cells which also bind the mAb of the invention (indicated as BAT) as compared to the total number of CD3⁺ cells in blood samples obtained from patients having breast carcinoma;
FIG. 16 shows the percent of CD3[0079] ⁺ cells which also bind the mAb of the invention (indicated as BAT) as compared to the total number of CD3⁺ cells in blood samples obtained from patients having prostate carcinoma;
FIG. 17 is a schematic representation showing the mean percent of CD3[0080] ⁺ cells which bind the mAb of the invention (indicated as BAT) in healthy individuals as compared to patients having breast carcinoma, colon carcinoma or prostate carcinoma;
FIG. 18 is a photograph of a Western Blot of peptides obtained from T-cells of individuals having prostate cancer, ear, nose and throat (ENT) carcinoma, breast carcinoma or from membranes of Daudi cells. The Blot was incubated with the mAb of the invention and shows an increased amount of antigen in T-cells obtained from patients having prostate carcinoma as compared to an undetectable level of antigen in T-cells obtained from patients having breast carcinoma;[0081]

I. SEQUENCING OF THE MAB

(A) Abbreviations [0082]
Fetal Calf Serum (FCS); ribonucleic acid (RNA); messenger RNA (mRNA); deoxyribonucleic acid (DNA); copy DNA (cDNA) ; polymerase chain reaction (PCR); minute (min); second (sec); Tris-borate buffer (TBE). [0083]
(B) Materials [0084]
Media components and all other tissue culture materials were obtained from Life Technologies (UK). The RNA isolation kit was obtained from Stratagene (USA) while the 1[0085] ^ststrand cDNA synthesis kit was purchased from Pharmacia (UK). All the constituents and equipment for the PCR-reactions, including AmpliTaq® DNA polymerase, were purchased from Perkin Elmer (USA). The TA Cloning® kit was obtained from Invitrogen (USA). Agarose (UltraPure™) was obtained from Life Technologies (UK). The Thermo Sequences™ pre-mixed cycle sequencing kit and the Vistra 725 DNA sequencing machine were both purchased from Amersham (UK). All other molecular biological products were obtained from New England Biolabs (USA).
(C) Experimental Techniques:PCR Cloning and Sequencing of the Mouse BAT Antibody Variable Region Genes [0086]
The mouse BAT hybridoma cell line and the Daudi cell line were successfully transferred to the MRC-CC and both cell lines were grown, in suspension, using RPMI (without glutamine) supplemented with 10% (v/v) FCS, 100 units/ml penicillin, 100 μg/ml streptomycin and 2 mM L-glutamine, 1 mM sodium pyruvate and 12.5 units/ml Nystatin. [0087]
Approximately 10[0088] ⁸of viable cells of the BAT hybridoma cell line were harvested and, from the 10⁸cells, total RNA was isolated using an RNA Isolation kit according to the manufacturers instructions. The kit used a guanidinium thiocyanate phenol-chloroform single step extraction procedure as described by Chromczynski and Sacchi, Anal. Biochem., 162:156, 1987. Also following the manufacturers instructions a 1^stStrand cDNA synthesis kit was employed to produce a single-stranded DNA copy of the BAT hybridoma mRNA using the NotI-(dT)₁₈primer supplied in the kit. Approximately 5 μg of total RNA was used in each 33 μl final reaction volume. The completed reaction mix was then heated to 90° C. for 5 min. to denature the RNA-cDNA duplex and inactivate the reverse transcriptase, before being chilled on ice.
To PCR-amplify the mouse heavy chain variable region gene (V[0089] _Hgene) and the mouse kappa light chain variable region gene (V_Kgene) from the hybridoma cell line the method described by Jones and Bendig, Bio/Technology, 9:8, 1987 was followed. Essentially, two series of degenerate primers, one designed to anneal to the leader sequences of the mouse heavy chain genes (i.e. MHV1-12; Table 1) and one designed to anneal to the leader sequences of mouse kappa light chain genes (i.e. MKV1-11; Table 2) were used, in conjunction with primers designed to anneal to the 5′-end of the appropriate constant region gene, to PCR-clone the murine variable region genes.
Separate PCR-reactions were prepared for each of the degenerate primers with their appropriate constant region primer, in a special PCR-room using specific protocols designed to minimize the possibility of cross-contamination. Amplitaq® DNA polymerase was used to amplify the template cDNA in all cases. The PCR-reaction tubes were than loaded into a Perkin Elmer 480 DNA thermal cycler and cycled (after an initial melt at 94° C. for 1.5 min) at 94° C. for 1 min and 72° C. for 1 min over 25 cycles. At the completion of the last cycle a final extension step at 72° C. for 10 min was carried out before the reactions were cooled to 4° C. Except for between the annealing (50° C.) and extension (72° C.) steps, when an extended ramp time of 2.5 min was used, a 30 sec ramp time between each step of the cycle was employed. [0090]
10 μl aliquots from each PCR-reaction were run on a 1% agarose/TBE (pH 8.8) gel to determine which had produced a PCR-product of the correct size. Those PCR-reactions that did appear to amplify full-length variable region genes were repeated to produce independent PCR-clones and thereby minimize the effect of PCR-errors. 1-6 μ[0091] 1 aliquots of those PCR-products of the correct size were directly cloned into the pCRII™ vector, provided by the TA Cloning® kit, and transformed into INA αF′ competent cells as described in the manufacturers instructions. Colonies containing the plasmid, with a correctly sized insert, were identified by PCR-screening the colonies using the pCRII Forward and pCRII Reverse oliognucleotide primers described in Table 3 below according to the method of Güssow and Clackson, Nucleic Acids Res., 17:4000, 1989
Those putative positive clones identified were double-stranded plasmid DNA sequenced using the Vistra DNA sequencing machine and the Thermo Sequenase™ pre-mixed cycle sequencing kit as described in the manufacturers instructions. [0092]

EXAMPLE 1

Cloning and Sequencing of the Heavy Chain Variable Region of the BAT Antibody

As with all humanization projects, a strict PCT-cloning and sequencing protocol was followed. This was done to minimize the possibility of introducing errors into the wild-type sequences of the mouse VH variable region genes from the BAT hybridoma cell line. Only if all the DNA sequence data from at least two different V[0093] _Hgene clones, from the hybridoma cell line expressing the murine BAT antibody, matched perfectly were the gene sequences accepted as correct.
Three separate PCR-products, each from a different total RNA preparation and subsequent first strand cDNA synthesis reaction, were PCR-cloned and completely DNA sequenced on both strands. Although all twelve heavy chain primers were tested (Table 1), only the MHV9 primer (in conjunction with MHCG3—designed to anneal to the CH[0094] ₁domain of the mouse γ3 heavy chain gene) was PCR-amplified an approximately 460 bp product which was then TA-cloned into the pCRII™ cloning vector (data not shown).
DNA sequence analysis of several individual clones from each of the three PCR-products (each from different 1[0095] ^ststrand synthesis reactions and subsequent PCR-reactions) resulted in the determination of the BAT antibody heavy chain variable region sequence as described in FIG. 1. This sequence was confirmed on both DNA strands for all three PCR-clones studied.

EXAMPLE 2

Cloning and Sequencing of the Kappa Light Chain Variable Region of the BAT Antibody

The single stranded cDNA template, produced via 1[0096] ^ststrand synthesis, was PCR-amplified using a series of kappa light chain degenerate primers (Table 2 below). However, this resulted in the amplification of a number of PCR-products from more than one degenerate primer, suggesting that more than one variable region gene was being transcribed, at least, by the BAT hybridoma cell line.
First, a PCR-product was seen when the MKV2 primer (which, like all of the MKV series of primers, anneals to the 5′ end of the DNA sequence of the kappa light chain signal peptide) and MKC (which is designed to anneal to the 5′ end of the mouse kappa constant region gene) were used together. Previous in-house experience had shown us that the MKV2 primer would PCT-amplify an aberrant mRNA transcript. This aberrant pseudogene was present in all standard fusion partners derived from the original MOPC-21 plasmacytoma cell line and was known as MOPC-21n Deyev, S. M., et al., [0097] Genetica, 85:45, 1991. NO-0 was a cell line which was derived from MOPC-21 line, and it was this line which was used as the fusion partner to produce the BAT hybridoma. Consequently, it was not surprising that a PCR-product was seen when using the MKV2 primer. This product was analyzed and shown to be the non-functional pseudogene (data not shown).
Unusually, another pseudogene, previously identified as being secreted by the related cell line NS-1 Hamlyn, P. H., et al., [0098] Nucl. Acis Res., 9:4485, 1981 and normally PCR-cloned when using the MKV7 primer in conjunction with MKC primer, was not seen in any of the PCR-products so far analyzed. Since the NS-1 and NS-0 cell lines were very closely related, this was a little surprising. However, it also highlighted the confusing nature of kappa light chain transcription that was present in the BAT hybridoma cell line.
Another PCR-clone, which ultimately turned out to be the V[0099] _Kgene of the BAT antibody, was also successfully PCR-amplified from the BAT hybridoma cell line with the primers MKV5 and MKC. Following transformation of the approximately 450 bp product into INVαF′ competent cells, putative positive transformants were identified using the PCR-screening assay and then DNA sequenced.
From sequence analysis of two individual clones of the MKV5 product (each from different [0100] ₁ ^ststrand synthesis reactions and subsequent PCR-reactions) the DNA sequence of the BAT antibody kappa light chain variable region gene was determined (FIG. 2). This sequence was again confirmed on both DNA strands for each clone.

EXAMPLE 3

Sequence Analysis of the Mouse BAT Antibody Variable Regions

The amino acid sequence of the BAT V[0101] _κand V_Hregions were compared to the consensus sequences of murine variable region subgroups that were defined in the Kabat (Supra) database From this analysis the BAT V_Hregion was found to most closely match the consensus sequence of mouse kappa subgroup VI. Similar comparisons of the BAT V_Hregion to the Kabat databasefound that it exhibited the closest match to the consensus sequence of mouse heavy chain subgroup “miscellaneous”.
A comparison of the above BAT antibody variable region sequences to a database of murine germlines, found that the closest germline gene to the BAT V[0102] _Hgene was VMS/VGK4 (FIG. 3), whilst the closest germline gene to the BAT V_κgene was H4 (FIG. 4). As can be seen in FIG. 3, those mismatches that did occur between the BAT V_Hgene and its closest germline gene were, unsurprisingly, predominantly located in the CDR2 and CDR3. There were only three framework changes, and all these were located in FR3. With respect to the BAT V_κgene (FIG. 4), it was again not all together surprising that the majority of mismatches were positioned in the CDRs. The four differences that were located in the FRs were all highly conservative changes, except for the cysteine at position 72 (Kabat numbering) in FR3. Its location immediately adjacent to an important canonical residue (position 71) suggested that the cysteine may have been playing a key role in antigen binding. However, only through modeling the Fv domain could such a supposition be clarified.

Nevertheless, these analyses confirmed that both the V _Hregions and the V_κregions of the mouse BAT variable regions appeared to be typical of mouse variable regions.

TABLE 1


PCR-primers used in the cloning of the
BAT heavy chain variable region gene

Name	Sequence (5′→3′)

MHV5^a (30 mer; SEQ ID NO:12)	ATGGACTCCAGGCTCAATTTAGTTTTCCTT

MHV9^a (30 mer; SEQ ID NO:13)	ATGGATTGGGTGTGGACCTTGCTATTCCTG
	C A

MHCG3^b(21 mer; SEQ ID NO:14)	CAAGGGATAGACAGATGGGGC

TABLE 2


PCR-primers used in the cloning of the
BAT kappa light chain variable region gene

Name	Sequence (5′→3′)

MKV2^a (30 mer; SEQ ID NO:15)	ATGGAGACAGACACACTCCTGCTATGGGTG
	T T

MKV5^a (30 mer; SEQ ID NO:16)	ATGGATTTTCAGGTGCAGATTATCAGCTTC
	A T

MKV6^a (30 mer; SEQ ID NO:17)	ATGAGGTGCCCTGTTCAGTTCCTGGGG
	T TT C G C T A

MKV11^a(30 mer; SEQ ID NO:18)	ATGGAAGCCCCAGCTCAGCTTCTCTTCC

MKC^b (20 mer; SEQ ID NO:19)	ACTGGATGGTGGGAAGATGG

[0105]

TABLE 3

Primers for PCR screening transformed colonies

Name Sequence (5′-43 3′)

pCRII Forward Primer (18 mer; SEQ ID:20) CTAGATGCATGCTCGAGC

pCRII Reverse Primer (21 mer; SEQ ID:21) TACCGAGCTCGGATCCACTAG

II. CONSTRUCTION AND EXPRESSION OF THE CHIMERIC ANTIBODY OF THE INVENTION

(A) Abbreviations [0106]
The following non-SI unit and other abbreviations were used: [0107]
Polymerase chain reaction (PCR); deoxyribonucleic acid (DNA); copy DNA (cDNA); kappa light chain variable region (V[0108] _κ); heavy chain variable region (V_H); minute (min); Tris-borate buffer (TBE); phosphate buffered saline (PBS); room temperature (RT), bovine serum albumin (BSA); hydrochloric acid (HCl); horseradish peroxidase (HRP); low fat milk LFM); hour (hr); percent (%); O-phenylenediamine dihydrochloride (OPD); multiple cloning site (MCS).
(B) Materials [0109]
Media components and all other tissue culture materials were obtained from Life Technologies (UK). The constituents for the PCR-reactions, including AmpliTaq® DNA polymerase, were purchased from Perkin Elmer (USA). However, the TA Cloning® kit and INVαF′ competent cells were obtained from Invitrogen (USA). DH5α competent cells and agarose (UltraPure™) were obtained from Life Technologies (UK). The Thermo Sequenase™ pre-mixed cycle sequencing kit and the Vistra 725 DNA sequencing machine were both purchased from Amersham (UK). The Big Dye™ Terminator Cycle Sequencing Ready Reaction Kit used with the ABI Prism 310 Genetic Analyzer were purchased from PE Applied Biosystems (UK). All other molecular biological products described were obtained either from New England biolabs (USA) or Promega (USA). Nunc-Immuno Plate MaxiSorp™ immunoplates were purchased from Life Technoloiges (UK) while the Coming easy wash ELISA plates were obtained from Coming Laboratory Sciences Company (UK). The goat anti-human IgG (Fc[0110] _γfragment specific) antibody, the goat anti-human kappa light chain/HRP conjugate and the AffinPure goat anti-human IgG (Fc_γfragment specific)/HRP conjugate were obtained from Jackson ImmunoResearch Laboratories Inc. (USA). K-Blue TMB substrate and Red Stop solution were purchased from Neogen Inc. (USA). All other products for the ELISA were obtained from Sigma (UK). Microplate Manager® data analysis software package was purchased from Bio-Rad (UK). The micro-volume stirred ultrafiltration cell and PM30 filter membrane were obtained from Amicon PLC (UK), while the Immunopure® (G) IgG purification kit was purchased from Pierce PLC (UK).
(C) Experimental Techniques [0111]
C1 Construction of chimeric γ1/[0112] _κBAT antibody
The previously isolated mouse kappa light chain variable region (V[0113] _κ) gene (FIG. 1) and heavy chain variable region (V_H) gene (FIG. 2) were modified at the 5′- and 3′-ends, using specifically designed PCR-primers (Table 1), to enable expression of the BAT variable region genes in mammalian cells as part of a chimeric mouse-human antibody. To achieve this separation PCR-reactions were prepared for each variable region gene in a specific PCR-room using specific protocols designed to minimize the possibility of cross-contamination. The plasmids BATV_H-pCR2. 1 and BATV_κ-pCR2. 1 were used as templates and AmpliTaq® DNA polymerase was used t amplify these templates. Primers B8814 and B8815 (Table 4) were used to PCR-modify the BAT V_Hgene while primers C0224 and C0225 (Table 4) were used to PCR-mutate the BAT V_κgene.
The PCR-reaction tubes were cycled (after an initial melt at 94° C. for 3 min) at 94° C. for 50 s, 72° C. for 1 min 30 s over 30 cycles. At the completion of the last cycle a final extension step at 72° C. for 10 min was carried out before the reactions were cooled on ice. 5 μl aliquots from each PCR-reaction were then run on a 1.2% agarose/TBE (pH 8.8) gel to determine which had produced a PCR-product of the correct size. [0114]
1-2 μl aliquots of those PCR-products of the correct size were directly cloned into the pCR2.1™ vector, provided by the TA Cloning® kit, and transformed into INVαF′ competent cells as described in the manufacturers instructions. Colonies containing the plasmid, with a correctly sized insert, were identified by PCR-screening the colonies using the 1212 and 1233 oligonucleotide primers (Table 5) according to the method of Güissow and Clackson (Supra) Those putative positive clones identified were double-stranded plasmid DNA sequenced using both the Vistra DNA sequencing machine and ABI Prism 310 Genetic Analyzer. The Thermo Sequenase™ pre-mixed cycle sequencing kit and the Big Dye™ Terminator Cycle Sequencing Ready Reaction Kit were used as described in the manufacturers instructions with the primers 1212 and 1233 (Table 5). [0115]
Those clones containing the correctly adapted BAT V[0116] _κand V_Hgenes (FIGS. 5 and 6, respectively) were subcloned, as a HindIII-BamHi fragments, into the expression vectors pKN110 (FIG. 7) and pG1D110 (FIG. 8), respectively, to express chimeric light and heavy chains in mammalian cells. The ligated expression vectors (i.e. pKN 110-BATV_κand pG1D110-BATV_H) were then transformed into DH5_α competent cells. Positive clones, containing the correctly constructed expression vectors, were finally identified by restriction digest analysis.
C2 Co-transfection of chimeric γ1/[0117] _κBAT antibody vector DNA into COS cells
The method of Kettleborough et al. was followed to transfect the mammalian expression vectors into COS cells. Briefly, the DNA (10 μg each of the kappa light chain expression vector pKN110-BATV[0118] _κand heavy chain expression vector pG1D110-BATV_H) was added to a 0.70 ml aliquot of 1×10⁷cells/ml in PBS and pulsed at 1900 V, 25 μF capacitance using a Bio-Rad Cene Pulser apparatus. Following a 10 min recovery at RT the electroporated cells were added to 8 ml of DMEM containing 5% FCS and incubated for 72 hr in 5% CO₂at 37° C. After 72 hr incubation, the medium was collected, spun to remove cell debris and analyzed by ELISA for chimeric BAT antibody production.
C3 Quantification of chimeric γ1/[0119] _κantibody via ELISA
Each well of a 96-well Nunc-Immuno Plate MaxiSorp™ immunoplate as first coated with 100 μl aliquots of 0.4 ng/μl goat anti-human IgG (Fc[0120] _γfragment specific) antibody, diluted in PBS and incubated overnight at 4° C. and removed prior to use. 100 μl/well aliquots f the experimental samples (i.e. harvested COS cell supernatants—spun to remove cell debris) and 1:2 sample dilutions, diluted in sample-enzyme conjugate buffer (0.1 M Tris-HCl (pH 7.0), 0.1 M NaCl, 0.02% (v/v) TWEEN-20 and 0.2% (w/v) BSA), were then dispensed onto the immunoplate. In addition, a purified human γ1/_κantibody (1000 ng/μl), which was used as a standard and serially diluted 1:2, and also loaded onto the immunoplate. The immunoplate was incubated at 37° C. for 1 hr before being washed with 200 μl/well of wash buffer (PBS/0.1% (v/v) TWEEN-20) three times. 100 μl of goat anti-human kappa light chain/horseradish peroxidase conjugate, diluted 5000-fold in sample-enzyme conjugate buffer, was added to each well, following which the immunoplate was incubated at 37° C. for 1 hr before it was washed as before. 150 μl aliquots of K-Blue substrate were then added to each well, following which the immunoplate was incubated for 10 min at RT in the dark. The reaction was finally halted by dispensing 50 μl of Red Stop into each well. The optical density at 655 nm was then determined using a Bio-Rad 3550 microplate reader in conjunction with the Microplate Manager® software package.
C4 Purification of the Chimeric BAT Antibody [0121]
The chimeric BAT γ1/[0122] _κantibody was purified from COS cell supernatants in two stages. First, a micro-volume stirred ultrafiltration cell with a PM30 filter membrane was used, according to the manufacturers instructions, to reduce the volume of the raw, non-purified supernatant. Then an Immunopure® (G) IgG purification kit was used to affinity purify the chimeric BAT antibody from the concentrated supernatant, also according to the manufacturers instructions.
C5 Daudi cell ELISA [0123]
The cell ELISA assay was carried out using the Daudi cell cultured from an original stock also by Dr. Hardy (Felsenstein Medical Research Center, Rabin Medical Center, Beilinson Campus, Petach Tikva,49100, Israel). Minor modifications were made to the assay depending upon whether the mouse or the mouse-human chimeric BAT antibody was being analyzed. When assaying the binding affinity of the mouse BAT antibody a goat anti-mouse IgG (Fab specific)/HRP conjugate (diluted 1:15000) was used as the secondary antibody. Conversely, when measuring the affinity of the chimeric BAT antibody AffiniPure goat anti-human IgG (Fc[0124] _γ fragment specific)/HRP conjugate (diluted 1000-fold) was used.
The Daudi cells (2 days after being passaged) were first plated at 10[0125] ⁵cells/well in a 96 well Coming easy wash ELISA plate and then incubated overnight at 37° C. in a dry incubator. The next day, 200 μl of rehydration buffer (PBS containing 10% FCS and 0.05% azide) was added to each well which was then left for a minimum of 1 hr. The rehydration buffer was then decanted off before 50 μl aliquots of various 1:2 serial dilutions of the purified BAT antibody was added to the wells of the plate. The plate was again incubated overnight (at 4° C.), washed twice with 200 μl/well of PBS containing 5% LFM and allowed to dry. 50 μl/well of the HRP conjugated secondary antibody was then added before a series of six different washes (i.e. one wash with PBS containing 5% LFM, three washed with the same buffer supplemented with 0.05% TWEEN-20, followed by a further two washes with the PBS/LFM buffer) were carried out. 200 μl/well of 0.4 mg/ml OPD substrate in 0.05 M citrate buffer (pH 5.0) and 60 mg/ml hydrogen peroxide was then added before the ELISA plate was incubated in the dark and at RT until the color had developed (usually about 30 min). Finally, the reaction was stopped by the addition of 50 μl/well of 2.5 M sulfuric acid and the optical density at 490 nm was then measured using a Bio-Rad 3550 microplate reader in conjunction with the Microplate Manager® software package.
Results [0126]

EXAMPLE 4

Construction of the Chimeric γ1/_κBAT antibody

As with all projects, a strict PCR-cloning and sequencing protocol was followed. This was done to minimize the possibility of introducing errors into the wild-type sequences of the mouse variable region genes during the PCR-modification step. Using the primers C0224 and C0225 (Table 1) the mouse BAT V[0127] _κgene (FIG. 2) was modified via PCR to produce a 418 bp band (data not shown). This PCR-product was ligated into the pCR2.1 plasmid and transformed into INVαF′ competent cells. Similarly, the mouse BAT V_Hgene (FIG. 1 was PCR-mutated using primers B8814 and B8815 (Table 1) to produce a 436 bp band (data not shown). This PCR-product was also ligated into the pCR2.1 plasmid and transformed into INVαF′ competent cells.
Putative positive transformants were then detected using the PCR-screening assay (data not shown) before finally being ds-DNA sequenced on the ABI Prism 310 Genetic Analyzer. FIGS. 3 and 4 show the results of this DNA sequence analysis of the chimeric BAT V[0128] _κgene and BAT V_Hgene, respectively. The analysis was carried out both to confirm their successful mutagenesis and also show the presence of any PCR-errors that may have been introduced into the genes. Only one PCR-reaction was actually carried out for each variable region gene and only two clones from each of these PCR-reactions were eventually DNA sequences to completed.
Nevertheless, this proved sufficient to isolate at least one clone for each modified variable region gene which contained the correct modified DNA sequence. [0129]
The mutated V[0130] _Hand V_κgenes were then subcloned into the appropriate expression vectors, as hindIII/BamHI fragments, to create pKN110-BATV_κ(7.88kb) and pG1D110-BATV_H(7.55 kb), respectively. The fidelity of the expression vectors constructed was then confirmed via restriction enzyme analysis (data not shown). Once co-transfected into COS cells, these vectors wold allow the transient expression of a γ1/_κversion of the chimeric BAT antibody.
In addition, as an extra component to the BAT antibody humanization project, the BAT V[0131] _Hgene was also subcloned, as a HindIII/BamHI fragment, into both the pG3D110 and the pG4D1100 heavy chain expression vectors. These vectors were identical to pG1D110, save for the replacement of the cDNA copy γ1 human constant region genes with either a cDNA copy of the ³γ constant region genes (in the case of pG3D110) or the cDNA of the γ3 constant region genes (in the case of pG3D110) or the cDNA of the γ4 constant region genes (in the case of pG3D110). The construction of these vectors (i.e. pG3D110-BATV_κ, of both γ3/_κand γ4_κversions of the chimeric BAT antibody in COS cells.

EXAMPLE 5

Transient Expression of the Chimeric γ1/_κBAT Antibody

The two vectors pKN110-BATV[0132] _κand pG1D110-BATV_Hwere co-transfected into COS cells in a series of repeated transient expression experiments. After being expressed for 72 hr the mouse-human γ1/_κchimeric BAT antibody was detected in the supernatant of the COS cell co-transfections via the γ1/_κELISA. From these assays the mean concentration of γ1/_κchimeric BAT antibody detected in the media was calculated to be 509±272 ng/ml.
Interestingly, the γ3/[0133] _κand γ4/_κversions of the chimeric BAT antibody appeared to produce significantly greater quantities of antibody following their expression COS cells. Specifically, when pG3D110-BATV_Hand pKN110BATV_κwere co-transfected into COS cells, initial analysis of the supernatant (using the ELISA method described in Section 4.3 and human IgG3/kappa antibody as a standard) measured the expression levels of the chimeric γ3/_κBAT antibody to be 6.7 μg/ml. Moreover, when pG4D110-BATV_HpKN110-BATV_κwere expressed in COS cells, the same ELISA (using human IgG4/kappa antibody as a standard) measured the expression levels of the chimeric γ4/_κBAT antibody to be 8.2 μg/ml.

EXAMPLE 6

Purification of the Chimeric γ1/_κBAT antibody

Harvesting approximately 8 ml per co-transfection, a series of transfections were carried out until 200 ml of COS supernatant had been collected. The volume of this supernatant was then reduced to 15 ml by passing the supernatant through a micro-volume stirred ultrafiltration cell with a PM30 filter membrane—which had a molecular weight cut-off of 30 kDa. [0134]
The Immunopure® (G) IgG purification kit essentially comprised of a 2 ml column of immobilized Protein G column. The antibody was eluted from the column with 6 ml of elution buffer, the eluate of which was collected in 1 ml fractions. The concentration of chimeric γ1/[0135] _κBAT antibody in each fraction was then assayed using the ELISA method described in Section C3. This analysis found that the chimeric antibody was present in Fraction 3 (42.05 μg/ml) and Fraction 4 (20.05 μg/ml), which correspond to a total recovery of 62.1 μg of chimeric γ1/_κBAT antibody. This was stored at −20° C., until its subsequent transfer to Curetech for further analysis.

EXAMPLE 7

Analysis of Daudi Cell Binding by the Chimeric γ1/_κBat antibody

Using the Daudi cell ELISA it was clearly shown that the purified chimeric γ1/ _κBAT antibody bound to Daudi cells. FIG. 9 shows a typical example of one experiment. However, what was less conclusive was the binding of similar concentrations of mouse BAT antibody, in the same ELISA, which appeared to be lower than the chimeric antibody. Nevertheless, since the conjugated secondary antibody used to detect antibody binding to the Daudi cells was different for each antibody construct, no direct comparison of the binding of the two versions can legitimately be made.

TABLE 4


Primers used to PCR-modify the mouse BAT antibody
kappa light chain and heavy chain variable region
genes to allow their expression as part of a
chimeric γ1/₇₈BAT antibody in mammalian cells

Name	Sequence (5′→3′)

C0225 (42 mer; SEQ ID:22)	C C C A A G C T T G C C G C C A C C A T G
	G A T T T T C A G G T G C A G A T T A T C

C0224 (39 mer; SEQ ID NO:23)	C G C G G A T C C A C T C A C G T T T T A
	T T T C C A A C T T T G T C C C C G

B8815 (40 mer; SEQ ID NO:24)	G G A T C C A C T C A C C T G A G G A G A
	C G G T G A C T G A G G T T C C T T G

B8814 (42 mer; SEQ ID NO:25)	A A G C T T G C C G C C A C C A T G G C T
	T G G G T G T G G A C C T T G C T A T T C

TABLE 5


Primers used to PCR screen the transformed colonies and DNA
sequence the PCR-modified variable region genes of the BAT antibody

Name	Sequence (5′→3′)

Huγ1 (17 mer; SEQ ID NO:26)	T T G G A G G A G G G T G C C A G

HCMVi.3s (28 mer; SEQ ID NO:27)	G T C A C C G T C C T T G A C A C G C G T
	C T C G G G A

FOR (18 me; SEQ ID NO:28)	T G T A A A A C G A C G G C C A G T

REV (18 mer; SEQ ID NO:29)	G A A A C A G C T A T G A C C A T G

B6990 (27 mer; SEQ ID NO:30)	C A G C A T A T G T T G A C T C T C C A C
	T G T C G G
B6991 (27 mer; SEQ ID NO:31)	G T C A A C A T A T G C T G A A G A G T T
	C A A G G G

B8809 (18 mer; SEQ ID NO:32)	T G C C A G G T C A A G T G T A A G

B8810 (18 mer; SEQ ID NO:33)	A A G C C A G G T T G G A T G T C C

IV AMINO ACID SEQUENCES OF 3 PEPTIDES TAKEN FROM THE DAUDI B-CELL LYMPHOBLASTOID CELL LINE ANTIGEN TO WHICH THE MABS OF THE INVENTION BIND

Three peptides comprised in the antigenic epitope of the Daudi B lymphoblastoid cells to which the mAbs of the invention bind were sequenced. Their sequence depicted in FIGS. 10, 11 and [0138] 12.
Searches performed against the non-redundant gene bank database and the EST Division yielded no hits when the three peptides were ran as queries using the TBLASTN algorithm (Version 2) with an EXPECT value of 10 and the matrix BLOSUM 62. [0139]
However, since the peptides are small peptides, they were submitted again at a higher EXPECT value to make the search less stringent. The filter was also unmasked for low complexity which can eliminate potentially confounding matches (e.g. hits against proline-rich regions or proly-A tails) from the blast reports, leaving regions whose blast statistics reflect the specificity of their pairwise alignment. The three peptides of the invention did not yield any hit with the gene bank and the EST division database even at a very low stringency. [0140]
Thus, in accordance with the above results, the three above peptides seem to be novel peptides. [0141]

IV DIAGNOSIS OF MALIGNANT DISEASES IN PATIENTS USING THE MAB OF THE INVENTION

Peripheral blood lymphocytes from tested individuals were double-labeled using the anti-CD3 antibody and one of the mAbs of the invention. The percent of CD3[0142] ⁺ cells which bind the mAbs of the invention were determined. In accordance with the invention, it has been shown that the number of the CD3^+mAb ⁺ cells in individuals having a malignant disease differs from the percent of these cells in blood samples obtained from healthy individuals. The fact that there exists a significant difference of the percent of the CD3⁺ cells in the individuals having a malignant disease and whether the difference is above or below the percent of CD3⁺mAb⁺ cells obtained from healthy individuals enables to determine at high probability whether the individual has a malignant disease as well as the specific kind of malignant disease which the tested individual may have.
Typically, human peripheral blood lymphocytes were obtained from 20 ml blood of either a healthy individual or from cancer patients by Ficoll Hypaque density centrifugation. The cells were washed and suspended in PBS containing 0.5% BSA and 0.05% as acid. The samples containing 0.5×10[0143] ⁶cells were used for FACS analysis. First, the cells were incubated with a saturated amount of the mAb of the invention for 45 mins. at 0° C. followed by their incubation with an anti-mouse mAb conjugated to FITC for 30 mins. on ice. After two washes and centrifugation at 1200 rpm cells were incubated with an anti-human CD3 conjugated to PE antibodies for 30 mins. on ice. Following this incubation, the cells were washed twice and the sample is analyzed by a FACS scan (Bectan Dickinson). The results are shown in FIGS. 13 to 17.
As can be seen in FIG. 13, as well as in FIG. 17, the percent of CD3[0144] ⁺ BAT⁺cells (as compared to total CD3⁺ cells) in blood samples obtained from healthy individuals is in the range of about 25%. As seen in FIG. 14, the percent of the CD3⁺ BAT⁺ cells in blood samples obtained from patients having colon carcinoma is substantively lower, as compared to healthy individuals, in the range of about 7%. Similarly, the percent of CD3⁺ BAT⁺ cells in blood samples obtained from patients having breast carcinoma was in the range of about 10% (FIG. 15). These results clearly indicate that colon and breast carcinoma can be identified by the fact that the percent of CD3⁺ BAT⁺ cells is lower as compared to healthy individuals.
The percent of CD3[0145] ⁺ BAT⁺ cells in blood samples obtained from prostate carcinoma patients is significantly higher than the percentagein blood samples of healthy individuals as seen in FIG. 16 and is in the range of about 50%. These results clearly indicate that prostate carcinoma can be identified by the fact that the percent of CD3⁺ BAT⁺ cells is higher a compared to healthy individuals. As seen in FIG. 18, the amount of the antigen to, which the mAb of the invention bind found on T-cells, obtained from prostate carcinoma patients is very high while the antigen is undetectable in T-cells obtained from patients of breast carcinoma.
The above results show that the mAbs of the invention may be used in order to identify an individual suffering from a certain kind of malignant disease. Thus, if a blood sample is obtained from a tested individual and the extent of binding of the mAbs of the invention to CD3[0146] ⁺ cells in the sample is significantly high (in the range of about 50%), there is a very high probability that the tested individual is suffering from prostate cancer. Against this, if the percent of the CD3⁺ cells in the sample is significantly low as compared to healthy individuals (in the range of about 7% or 10%), there is a high probability that the tested individual is suffering from breast or colon carcinoma. Obviously, if the tested individual is a male individual, there is a high probability of his suffering from colon carcinoma.
The above examples are not to be construed as limiting and additional correlations between the percent of CD3[0147] ⁺ cells which bind the mAbs of the invention and other malignant diseases are also within the scope of the invention.
1 33 1 462 DNA Humanus 1 tactagtcga catggcttgg gtgtggacct tgctattcct gatggcagct gcccaaagta 60 tccaagcaca gatccagttg gtgcagtctg gacctgagtt gaagaagcct ggagagacag 120 tcaagatctc ctgcaaggct tctggatata ctttcacaaa ctatggaatg aactgggtga 180 agcaggctcc aggaaagggt ttaaagtgga tgggctggat aaacaccgac agtggagagt 240 caacatatgc tgaagagttc aagggacggt ttgccttctc tttggaaacc tctgccaaca 300 ctgcctattt gcagatcaac aacctcaaca atgaggacac gcctacatat ttctgtgtga 360 gagtcggcta cgatgctttg gactactggg gtcaaggaac ctcagtcacc gtctcctcaa 420 ctacaacaac agccccatct gtctatccct tcccgggttc ca 462 2 136 PRT Humanus 2 Met Ala Trp Val Trp Thr Leu Leu Phe Leu Met Ala Ala Ala Gln Ser 1 5 10 15 Ile Gln Ala Gln Ile Gln Leu Val Gln Ser Gly Pro Glu Leu Lys Lys 20 25 30 Pro Gly Glu Thr Val Lys Ile Ser Cys Lys Ala Ser Gly Tyr Thr Phe 35 40 45 Thr Asn Tyr Gly Met Asn Trp Val Lys Gln Ala Pro Gly Lys Gly Leu 50 55 60 Lys Trp Met Gly Trp Ile Asn Thr Asp Ser Gly Glu Ser Thr Tyr Ala 65 70 75 80 Glu Glu Phe Lys Gly Arg Phe Ala Phe Ser Leu Glu Thr Ser Ala Asn 85 90 95 Thr Ala Tyr Leu Gln Ile Asn Asn Leu Asn Asn Glu Asp Thr Ala Thr 100 105 110 Tyr Phe Cys Val Arg Val Gly Tyr Asp Ala Leu Asp Tyr Trp Gly Gln 115 120 125 Gly Thr Ser Val Thr Val Ser Ser 130 135 3 443 DNA Humanus 3 actagtcgac atggatttac aggtgcagat tatcagcttc ctgctaatca gtgcctcagt 60 cataatgtcc agaggacaaa ttgttctcac ccagtctcca gcaatcatgt ctgcatctcc 120 aggggagaag gtcaccataa cctgcagtgc caggtcaagt gtaagttaca tgcactggtt 180 ccagcagaag ccaggcactt ctcccaaact ctggatttat aggacatcca acctggcttc 240 tggagtccct gctcgcttca gtggcagtgg atctgggacc tcttactgtc tcacaatcag 300 ccgaatggag gctgaagatg ctgccactta ttactgccag caaaggagta gtttcccact 360 cacgttcggc tcggggacaa agttggaaat aaaacgggct gatgctgcac caactgtatc 420 catcttccca ccatccaaga tct 443 4 128 PRT Humanus 4 Met Asp Leu Gln Val Gln Ile Ile Ser Phe Leu Leu Ile Ser Ala Ser 1 5 10 15 Val Ile Met Ser Arg Gly Gln Ile Val Leu Thr Gln Ser Pro Ala Ile 20 25 30 Met Ser Ala Ser Pro Gly Glu Lys Val Thr Ile Thr Cys Ser Ala Arg 35 40 45 Ser Ser Val Ser Tyr Met His Trp Phe Gln Gln Lys Pro Gly Thr Ser 50 55 60 Pro Lys Leu Trp Ile Tyr Arg Thr Ser Asn Leu Ala Ser Gly Val Pro 65 70 75 80 Ala Arg Phe Ser Gly Ser Gly Ser Gly Thr Ser Tyr Cys Leu Thr Ile 85 90 95 Ser Arg Met Glu Ala Glu Asp Ala Ala Thr Tyr Tyr Cys Gln Gln Arg 100 105 110 Ser Ser Phe Pro Leu Thr Phe Gly Ser Gly Thr Lys Leu Glu Ile Lys 115 120 125 5 412 DNA Humanus 5 aagcttgccg ccaccatgga tttacaggtg cagattatca gcttcctgct aatcagtgcc 60 tcagtcataa tgtccagagg acaaattgtt ctcacccagt ctccagcaat catgtctgca 120 tctccagggg agaaggtcac cataacctgc agtgccaggt caagtgtaag ttacatgcac 180 tggttccagc agaagccagg cacttctccc aaactctgga tttataggac atccaacctg 240 gcttctggag tccctgctcg cttcagtggc agtggatctg ggacctctta ctgtctcaca 300 atcagccgaa tggaggctga agatgctgcc acttattact gccagcaaag gagtagtttc 360 ccactcacgt tcggctcggg gacaaagttg gaaataaaac gtgagtggat cc 412 6 128 PRT Humanus 6 Met Asp Leu Gln Val Gln Ile Ile Ser Phe Leu Leu Ile Ser Ala Ser 1 5 10 15 Val Ile Met Ser Arg Gly Gln Ile Val Leu Thr Gln Ser Pro Ala Ile 20 25 30 Met Ser Ala Ser Pro Gly Glu Lys Val Thr Ile Thr Cys Ser Ala Arg 35 40 45 Ser Ser Val Ser Tyr Met His Trp Phe Gln Gln Lys Pro Gly Thr Ser 50 55 60 Pro Lys Leu Trp Ile Tyr Arg Thr Ser Asn Leu Ala Ser Gly Val Pro 65 70 75 80 Ala Arg Phe Ser Gly Ser Gly Ser Gly Thr Ser Tyr Cys Leu Thr Ile 85 90 95 Ser Arg Met Glu Ala Glu Asp Ala Ala Thr Tyr Tyr Cys Gln Gln Arg 100 105 110 Ser Ser Phe Pro Leu Thr Phe Gly Ser Gly Thr Lys Leu Glu Ile Lys 115 120 125 7 436 DNA Humanus 7 aagcttgccg ccaccatggc ttgggtgtgg accttgctat tcctgatggc agctgcccaa 60 agtatccaag cacagatcca gttggtgcag tctggacctg agttgaagaa gcctggagag 120 acagtcaaga tctcctgcaa ggcttctgga tatactttca caaactatgg aatgaactgg 180 gtgaagcagg ctccaggaaa gggtttaaag tggatgggct ggataaacac cgacagtgga 240 gagtcaacat atgctgaaga gttcaaggga cggtttgcct tctctttgga aacctctgcc 300 aacactgcct atttgcagat caacaacctc aacaatgagg acacggctac atatttctgt 360 gtgagagtcg gctacgatgc tttggactac tggggtcaag gaacctcagt caccgtctcc 420 tcaggtgagt ggatcc 436 8 135 PRT Humanus 8 Met Ala Trp Val Trp Thr Leu Leu Phe Leu Met Ala Ala Ala Gln Ser 1 5 10 15 Ile Gln Ala Gln Ile Gln Leu Val Gln Ser Gly Pro Glu Leu Lys Lys 20 25 30 Pro Gly Glu Thr Val Glu Ile Ser Cys Lys Ala Ser Gly Tyr Thr Phe 35 40 45 Thr Asn Tyr Gly Met Asn Trp Val Lys Gln Ala Pro Gly Lys Gly Leu 50 55 60 Lys Trp Met Gly Trp Ile Asn Thr Asp Ser Gly Glu Ser Thr Tyr Ala 65 70 75 80 Glu Glu Phe Lys Gly Arg Phe Ala Phe Ser Leu Glu Thr Ser Ala Asn 85 90 95 Thr Ala Tyr Leu Gln Ile Asn Asn Leu Asn Asn Glu Asp Thr Ala Thr 100 105 110 Tyr Phe Cys Val Arg Val Gly Tyr Asp Ala Leu Asp Tyr Trp Gly Gln 115 120 125 Gly Thr Ser Val Thr Val Ser 130 135 9 9 PRT Humanus 9 Thr Ile Asn Glu Glu Glu Glu Lys Cys 1 5 10 14 PRT Humanus 10 Asn Ser Gly Pro Ser Met Arg Lys Lys Asn Val Ser Ile Gly 1 5 10 11 5 PRT Humanus 11 Ile Pro Asp His Gln 1 5 12 30 DNA artificial sequence PCR-primers used in the cloning of the BAT heavy chain variable region gene 12 atggactcca ggctcaattt agttttcctt 30 13 30 DNA artificial sequence PCR-primers used in the cloning of the BAT heavy chain variable region gene 13 atggattggg tgtggacctt gctattcctg 30 14 21 DNA Artificial Sequence PCR-primers used in the cloning of the BAT heavy chain variable region gene 14 caagggatag acagatgggg c 21 15 30 DNA Artificial Sequence PCR-primers used in the cloning of the BAT kappa light chain variable region gene 15 atggagacag acacactcct gctatgggtg 30 16 30 DNA Artificial Sequence PCR-primers used in the cloning of the BAT kappa light chain variable region gene 16 atggattttc aggtgcagat tatcagcttc 30 17 27 DNA Artificial Sequence PCR-primers used in the cloning of the BAT kappa light chain variable region gene 17 atgaggtgcc ctgttcagtt cctgggg 27 18 28 DNA artificial sequence PCR-primers used in the cloning of the BAT kappa light chain variable region gene 18 atggaagccc cagctcagct tctcttcc 28 19 18 DNA Artificial Sequence PCR-primers used in the cloning of the BAT kappa light chain variable region gene 19 ctagatgcat gctcgagc 18 20 20 DNA Artificial Sequence pCRII Forward Primer 20 actggatggt gggaagatgg 20 21 21 DNA Artificial Sequence pCRII Reverse Primer 21 taccgagctc ggatccacta g 21 22 42 DNA artificial sequence C0225 primer 22 cccaagcttg ccgccaccat ggattttcag gtgcagatta tc 42 23 39 DNA artificial sequence C0224 Primer 23 cgcggatcca ctcacgtttt atttccaact ttgtccccg 39 24 40 DNA artificial sequence B8815 Primer 24 ggatccactc acctgaggag acggtgactg aggttccttg 40 25 42 DNA artificial sequence B8814 Primer 25 aagcttgccg ccaccatggc ttgggtgtgg accttgctat tc 42 26 17 DNA artificial sequence Huy1 Primer 26 ttggaggagg gtgccag 17 27 28 DNA artificial sequence HCMVi.3s primer 27 gtcaccgtcc ttgacacgcg tctcggga 28 28 18 DNA artificial sequence FOR primer 28 tgtaaaacga cggccagt 18 29 18 DNA artificial sequence REV primer 29 gaaacagcta tgaccatg 18 30 27 DNA artificial sequence B6990 primer 30 cagcatatgt tgactctcca ctgtcgg 27 31 27 DNA artificial sequence B6991 primer 31 gtcaacatat gctgaagagt tcaaggg 27 32 18 DNA artificial sequence B8809 primer 32 tgccaggtca agtgtaag 18 33 18 DNA artificial sequence B8810 primer 33 aagccaggtt ggatgtcc 18

Claims

1. A monoclonal antibody comprising a heavy chain variable region having at least 70% identity to the amino acid sequence of FIG. 1; a light chain variable region having at least 70% identity to the amino acid sequence of FIG. 2; or both said heavy chain variable region and said light chain variable region.

2. The monoclonal antibody according to claim 1, wherein said heavy chain variable region comprises of the amino acid sequence of FIG. 1; said light chain variable region comprises of the amino acid sequence of FIG. 2; or both said heavy chain variable region and said light chain variable region comprising FIG. 1 and FIG. 2 correspondingly.

3. A monoclonal antibody, wherein said antibody binds to an antigen to which any one of the monoclonal antibodies of claim 1 specifically bind.

4. The antibody according to claim 1, wherein the antibody is a chimeric human-mouse antibody.

5. A nucleic acid molecule encoding the amino acid sequence of the monoclonal antibody of claim 1.

6. An expression vector having the nucleic acid sequence of claim 5.

7. An expression vector according to claim 6, comprising of plasmid pKN110 or plasmid pG1D110.

8. A cell transfected with the expression vector of claim 6.

9. A hybridoma cell line producing at least one of the monoclonal antibodies of claim 1.

10. A peptide having an amino acid sequence at least 85% identical to the amino acid sequence of the peptides in FIG. 10, FIG. 11, or FIG. 12.

11. The peptide of claim 10, wherein the peptide comprises of the amino acid sequence of the peptide in FIG. 10, FIG. 11, or FIG. 12.

12. A protein or peptide comprising one or more of the peptides of claim 10.

13. A peptide analog of any of the peptides of claim 10, wherein said peptide analog has substantially the same level of binding to a monoclonal antibody comprising a heavy chain variable region having at least 70% identity to the amino acid sequence of FIG. 1, a light chain variable region having at least 70% identity to the amino acid sequence of FIG. 2, or both said heavy chain variable region and said light chain variable region.

14. A method for identifying a tested individual with a high probability of having a malignant disease comprising:

(a) obtaining a body fluid sample from said individual;

(b) contacting said sample with at least one of the monoclonal antibodies of claim 1, or a monoclonal antibody, wherein said antibody binds to an antigen to which any one of the monoclonal antibodies of claim 1 specifically bind;

(c) determining the extent of binding of said monoclonal antibody to T-cells within said sample; and

(d) comparing the extent of (c) to the extent of binding of the monoclonal to T-cells in a sample obtained from a healthy individual, wherein a significant difference between said extents of binding indicate that said tested individual has a high probability of having a malignant disease.

15. The method according to claim 14, wherein before step (b) the peripheral blood mononuclear cells are separated, said separated the peripheral blood mononuclear cells are then contacted in step (c) with said monoclonal antibody.

16. The method according to claim 14, wherein said body fluid is blood.

17. The method according to claim 14, wherein the extent of binding of the monoclonal antibodies obtained from said tested individual is higher than the extent of binding of the same monoclonal antibody to T-cells of healthy individuals.

18. The method according to claim 17, wherein said specific malignant disease is prostate carcinoma.

19. The method according to claim 14, wherein the extent of binding of the monoclonal antibody to T-cells obtained from said tested individual is lower than the extent of binding of the same monoclonal antibody to T-cells of healthy individuals.

20. The method according to claim 19, wherein said specific malignant disease is breast carcinoma or colon carcinoma.

21. A composition comprising at least one monoclonal antibody of claim 1 together with a carrier.

22. A kit comprising at least one monoclonal antibody of claim 1 together with a conjugate of a specific binding partner for said monoclonal antibody, and a label capable of producing a detectable signal.

23. A method for the treatment of a malignant disease comprising administering to an individual in need a therapeutically effect amount of the composition of claim 21.

24. The method according to claim 23, wherein said malignant disease is a solid tumor, prostate carcinoma, breast carcinoma, or colon carcinoma.

25. A composition comprising of a therapeutically effective amount of one or more of the peptides of claim 10, together with a carrier.

26. A method for the treatment of a malignant disease comprising administering to an individual in need a therapeutically effect amount of the composition of claim 25.

27. The method according to claim 26, wherein said malignant disease is a solid tumor, prostate carcinoma, breast carcinoma, or colon carcinoma.