CA2471967A1

CA2471967A1 - Wt1 antisense oligos for the inhibition of breast cancer

Info

Publication number: CA2471967A1
Application number: CA002471967A
Authority: CA
Inventors: Gabriel Lopez-Berestein; Ana Maria Tari; Pablo Zapata-Benavides
Original assignee: Individual
Current assignee: University of Texas System
Priority date: 2002-01-03
Filing date: 2003-01-03
Publication date: 2003-07-31
Also published as: EP1460898A1; EP1460898A4; US20040043950A1; WO2003061386A1

Abstract

The present invention provides methods for inhibiting the growth of breast cancer cells and methods for treating breast cancers expressing Wilms' Tumor 1 (WT1) gene product using a WT1 antisense oligonucleotide. It further provides methods of predicting breast cancer progression and methods for the screening of candidate substances for activity against breast cancer.

Description

DESCRIPTION
WTl ANTISENSE OLIGOS FOR THE INHIBITION OF BREAST CANCER
BACKGROUND OF THE INVENTION
The present application claims priority to provisional U.S. Patent Application Serial No.
60/345,102 filed January 3, 2002. The entire text of the above referenced applications are incorporated herein by reference and without disclaimer.
1. Field of the Invention The present invention relates generally to the fields of cancer therapy, specifically treatment of breast cancer. More particularly, these treatments involve the use of antisense oligonucleotides against the Wilins' Tumor 1 (WT1) gene, and lipid associated and liposomal formulations thereof.

2. Description of Related Art Breast cancer is the second most common form of cancer among women in the U.S., and the second leading cause of cancer deaths among women. Although several forms of radiation-therapy and chemotherapy are available for the treatment of such cancers, these therapies, especially when used in high doses, have side effects such as killing non-cancerous cells. When used in lower doses, they may not be enough to eradicate the cancer completely. Gene therapy is another form of anti-cancer therapy that has been receiving much attention.
However, for a gene therapy to be effective it is necessary to identify genes and gene products that are involved in the disease and may be targeted for therapy.
Wilms' Tumor is a pediatric kidney cancer arising from pluripotent embryonic renal precursors (Lee et al., 2001). WT1 is a Wilins' Tumor gene that was isolated from chromosome l 1p13 by a positional cloning technique (Call et al., 1990; Gessler et al., 1990). Abnormalities of the WTl gene are found in approximately 10% of patients with Wilms' tumor and the WT1 has been categorized to be a tumor suppressor gene (Haber et al., 1990; Little et al., 1992).
It has been shown that WTl participates in leukemogenesis and all leukemic cells expxess high levels of WT1 expression (moue et al., 1994). It has also been shown that a WT1 antisense ohgomer suppresses and inhibits growth of leul~emia cells (U.S. 6034235;
Yarnagami et al., 1996).
Oji et al., (1999), have determine the role of the Wilms' tumor gene WT1 in tumorigenesis of solid tumors, by examining the expression of the WT1 gene in 34 solid tumor cell lines including four gastric cancer cell lines, five colon cancer cell lines, 15 lung cancer cell lines, four breast cancer cell lines, one germ cell tumor cell line, two ovarian cancer cell lines, one uterine cancer cell line, one thyroid cancer cell line, and one hepatocellular carcinoma cell line. WTl gene expression was detected in three of the four gastric cancer cell lines, all of the five colon cancer cell lines, 12 of the 15 lung cancer cell lines, two of the four breast cancer cell lines, the germ cell tumor cell line, the two ovarian cancer cell lines, the uterine cancer cell line, the thyroid cancer cell line, and the hepatocellular carcinoma cell line.
Furthermore, when a gastric cancer cell line AZ-521, a lung cancer cell line OS3, and an ovarian cancer cell line TYK-nu were treated with WT1 antisense oligomers, the growth of these cells was significantly inhibited in association with a reduction in WT1 protein levels. Thus, there is indication that the WT1 gene plays an oncogenic role in the growth of several types of solid tumors.
It has been recently shown that the expression of high levels of the WT1 mRNA
is associated with invasive breast cancers with poor patient prognosis (Miyoshi et al., 2002).
However, the role of WT1 antisense molecules as possible treatments for breast cancer has not been investigated. As current cancer therapies have only limited therapeutic benefits, especially with regard to breast cancers, there exists a need for a treatment that is specific for different types of breast tumors.
SUMMARY OF THE INVENTION
The present invention overcomes these and other defects in the art and demonstrates that antisense WT1 molecules are effective in inhibiting cancer cell growth in breast cancers expressing the Wilms' Tumor 1 (WT1) gene.
Thus, provided are methods for treating and/or preventing breast cancer. The invention also provides methods for diagnosing breast cancer and methods for screening for substances with activity against breast cancer.
In some embodiments, methods of inhibiting the growth of breast cancer cells expressing a WT1 gene product comprising contacting the cell with an amount of a WT1 antisense molecule effective to inhibit the growth of the breast cancer cell are provided.
An "effective amount" is defined here as an amount of a WT1 antisense molecule that will decrease, reduce, inhibit or otherwise abrogate the growth of a cancer cell, arrest-cell growth, _2_ induce apoptosis, inhibit metastasis, induce tumor necrosis, kill cells or induce cytotoxicity in cancer cells.
In some aspects of these embodiments, the cell may express one or more WTl isoforms and/or one or more adverse oncogenes. The present invention contemplates that the growth of any breast cancer cell expressing a WT1 gene product may be inhibited. Thus, the breast cancer cell may be estrogen negative. Alternatively, the breast cancer cell may be estrogen positive.
In some embodiments, the WT1 antisense molecule may be a double stranded or single stranded DNA. In some specific embodiments, the DNA may be an oligonucleotide wherein the oligonucleotide may be 6 to about 50 bases in length comprising one or more modified bases. In other embodiments, the WT1 antisense molecule may be an RNA.
The antisense molecule may be produced from an expression vector encoding the antisense molecule under the control of a promoter active in the cell.
Any promoter active in a breast cancer cell may be used. However, some non-limiting examples are provided. For example, in some embodiments of the method, one may use a constitutive promoter, such as, a CMV promoter, an RSV promoter, or an SV40 promoter. In other embodiments, the promoter may be a tissue-specific promoter such as leptin gene promoter, IGF binding protein-3 promoter, adenomatous polyposis coli gene promoter. In yet other embodiments, the promoter may be an inducible promoter, for example, Tet-On system, Tet-Off system.
Expression vectors for the expression of antisense molecules as set forth herein are well known to one of skill in the art. In some embodiments, the expression vector may be a non-viral vector and/or a viral vector. Some examples of viral vectors include adenoviral vectors, retroviral vectors, herpesviral vectors, vaccinia viral vectors, adeno-associated viral vectors, lentiviral vectors or polyoma viral vectors.
In some embodiments of the method, the antisense molecule may hybridize to a transcript, a translation initiation site that may comprise 5'-GTCGGAGCCCATTTGCTG-3' (SEQ ID NO:1), a splice site, a genomic sequence, a transcription start site, an intron, an exon, and/or an intron-exon junction.
In other embodiments, the antisense molecule may be associated with one or more lipid molecules. In some specific aspects, the lipid may comprise at least one neutrally charged lipid.
One example of a neutrally charged lipid is dioleoylphosphatidylcholine (DOPC). Other neutrally charged lipids known in the art may also be used. This includes lipids such as phosphatidylcholines, phosphatidylglycerols, and phosphatidylethanolamines.

In yet other aspects, the W'1'1 anhsense molecule may be associated with more than one lipids wherein the lipids on a whole are neutrally charged. For example, the lipid component can comprise a mixture of positively and negatively charged lipids such that the overall charge of the lipid component is neutral.
In yet other embodiments, the antisense molecule may be encapsulated in a liposome. W
some specific embodiments, the liposome may be comprised of at least one or more neutrally charged lipid molecules.
Another embodiment of the invention also provides methods of treating a subject having a breast cancer which express a Wilms' Tumor 1 (WT1) gene product, comprising administering to the subject an amount of an WT1 antisense molecule that is effective to treat the cancer.
The term "treat cancer" is defined as a decrease in cancer cell growth, reduction in cancer cell growth, inhibition or abrogation of growth of a cancer cell, cancer cell growth arrest, induction of apoptosis, killing of cancer cells, inhibition of metastasis, induction of tumor necrosis, and/or induction of cytotoxicity in cancer cells.
In such embodiments, the antisense molecule or. formulations thereof may be administered to the tumor by intratumoral injection. In other embodiments, it may be administered to the tumor vasculature. In some other embodiments, it may be administered locally to the tumor. In yet other embodiments, it may be administered regionally. In other embodiments, it may be administered to the lymphatic system locally or regionally to the tumor.
In yet other embodiments, the antisense molecule or formulations thereof may be administered to the subject having such a tumor by systemic or parenteral methods of administration. This includes among others intravenous, intraarterial, intramuscular, intraperitoneal routes of administration.
The composition may advantageously be delivered to a human patient in a volume of 0.50-10.0 ml per dose, or in an amount of 5-100 mg antisense oligonucleotide per m2 or 5-30 mg antisense oligonucleotide per m2. Thus, one may administer 5 mg/m2, 6mg/m2, 7mg/m2, 8mg/m2, 9mg/m2, lOmg/m2, llmg/ma, l2mg/m2, l3mg/m2, l4mg/m2, l5mg/m2, l6mg/ma, l7mg/m2, l8mg/ma, l9mg/m2, 20mg/m2, 2lmg/m2, 22mg/m2, 23mg/m2, 24mg/m2, 25mg/m2, 26mg/m2, 27mg/m2, 28mg/mz, 29mg/mz, 30mg/m2, 35mg/mz, 40mg/ma, 45mg/m2, SOmg/m2, SSmg/m2, 60mg/ma, 65mg/m2, 70mg/m2, 75mg/m2, 80mg/m2, 85mg/m2, 90mg/m2, 95mg/m2, or 100mg/m2 of a WT1 antisense oligonucleotide. Of course intermediate ranges are also contemplated as useful and this includes ranges such as 10.5 mg/m2, 92 mg/m2, and the like. As will be appreciated by one of skill in the art, the final dose of administration will be determined by a skilled physician depending on the disease status and individual suffering from the disease taKmg mto ettect tactors such as age, sex, and the tn~e. The composition may further be administered multiply, daily, weekly and/or monthly. As an example, it is contemplated that one particular therapeutic regimen the composition may be administered 3 times per week for 8 weeks.
It is also contemplated that the therapeutic methods may further comprise administering to a subject a second breast cancer therapy such as chemotherapy, radiation therapy, immunotherapy, hormonal therapy and/or gene therapy. Such methods are well known to a person of ordinary skill in the art and are also described elsewhere in the specification.
In some embodiments of the invention, the second breast cancer therapy may be provided to the subject prior to the WT1 antisense molecule. In other embodiments, the second breast cancer therapy may be provided to the subject after the WTl antisense molecule. In yet other embodiments, the second breast cancer therapy may be provided to the subject at the same time as said WT1 antisense molecule.
The present invention also provides methods of predicting breast cancer progression in a subject having breast cancer that comprise obtaining a sample from the subject comprising breast cancer tumor cells and assessing expression of one or more isofonns of Wilms' Tumor 1 (WT1) gene product in the cells. In some embodiments, the assessing comprises measuring WT1 protein levels. In other embodiments, the assessing comprises measuring WT1 mRNA levels. In some embodiments, measuring these levels may comprise quantitative immunodetection methods and/or quantitative PCR. All these methods are known to a person of ordinary skill in the art and are also described elsewhere in the specification.
The present invention also provides methods of screening candidate substances for growth inhibitory activity against breast cancer comprising providing a cell that expresses one or more isoforms of the Wilms' Tumor 1 (WT1) gene product, contacting the cell with the candidate substance suspected of inhibiting WT1 and measuring the effect of the candidate substance on the cell wherein a decrease in the amount of WTl gene product in the cell, as compared to a cell not treated with the candidate substance, indicates that the candidate substance has activity against breast cancer. The candidate substance may be a protein, a polypeptide, a nucleic acid and/or a small molecule pharmaceutical. In some embodiments of this method, the measuring may comprise determining the level of a WT1 gene product in the cell andlor determining the level of a WTl gene transcript in the cell and/or determining the level of more than one WT1 gene product and/or determining the level of more than one WTl transcript isoform and/or measuring the level of WTl gene product in a cell not treated with the candidate substance.

"A" or "an" is dehned herein to mean one or more than one. Uther objects, features and advantages of the present invention will become apparent from the following detailed description. It should be understood, however, that the detailed description and the specific examples, while indicating preferred embodiments of the invention, are given by way of illustration only, since various changes and modifications within the spirit and scope of the invention will become apparent to those skilled in the art from this detailed description.
BRIEF DESCRIPTION OF THE DRAWINGS
The following drawings form part of the present specification and are included to further demonstrate certain aspects of the present invention. The invention may be better understood by reference to one or more of these drawings in combination with the detailed description of specific embodiments presented herein.
FIG. 1. Western blot analysis of WTl expression in nuclear extracts of breast cancer cells. Nuclear mitotic apparatus protein (N-UMA) was used as an internal control.
FIGS. ZA, 2B, 2C, and 2D. Growth inhibition of breast cancer cell lines by L-WT1.
FIG. 2A. K562 cells - light bars: L-control; dark bars: L-WT1. FIG. 2B. MDA-MB-453 ( ~ ), and MCF-7 ( O ) cells treated with L-control oligos; MDA-MB-453( ~ ) and MCF-7 ( ) cells treated with L-WT1 oligos. FIG. 2C. Effect of 12 ~,M L-WT1 in 9 breast cancer cell lines. light bars: L-control; dark bars: L-WTl. FIG. 2D. Western blot of WT1 protein expression in MCF-7 and MDA-MB-453 cells exposed to L-WT1 and L-control oligos.
FIG. 3. Reduction in numbers of breast cancer cells by L-WT1. MCF-7 and MDA-MB-453 cells were treated with 12 pM L-WT1 or L-control oligos for 3 days and observed under light microscopy.
FIGS. 4A, 4B, and 4C. Expression of WT1 mRNA isoforms in breast cancer cell lines.
ER-positive cell lines: 1: MCF-7; 2: BT-474; 3: T-47D; 4: MDA-MB-361. ER-negative cell lines: 5: SKBr-3; 6: MDA-MB-231; 7: MDA-MB-453; 8: BT-20; 9: MDA-MB-468, and 10:
K562 leukemic cells. FIG. 4A. Results from a single round of RT-PCR analysis of total WT1 mRNA in breast cancer cell lines. FIG. 4B. Results from nested RT-PCR analysis of the KTS+
and the KTS- isoforms of WT1 mRNA. FIG. 4C. Results from nested RT-PCR
analysis of all 4 isoforms of WT1 mRNA.

DESCRIPTION OF ILLUSTRATIVE EMBODIMENTS
As mentioned above, breast cancer is the second most common form of cancer among women in the U.S., and the second leading cause of cancer deaths among women.
While many therapies exist, these are either insufficient to eradicate the disease or are too toxic or both.
Thus, there is a need to provide improved therapies and to better predict the progression of breast cancer.
I. THE PRESENT INVENTION
The Wilms' Tumor 1 (WT1) gene modulates the expression of several genes involved in mammary glands. The inventors have identified a role for WT1 in the proliferation of breast cancer cells. The present invention provides a therapy that makes use of antisense oligonucleotides to reduce WT1 protein expression and induce growth inhibition of breast cancer cells. A particular method for delivering these antisense molecules is in association with lipids and in some embodiments via liposomes.
Some breast cancer cells are estrogen receptor (ER)-positive and some are ER-negative.
While WT1 is expressed in higher levels in ER-positive cells, liposomal WTl (L-WTl) is effective at inhibiting proliferation of breast cancer cells irrespective of their ER status. In addition, it is contemplated that the L-WT1 will be useful in inhibiting even those cells that have a high level of expression of adverse oncogenes such as EGFR, Her2/neu, and the mutant p53 protein. Thus, this technology holds great promise as a therapeutic agent for the treatment of cancer.
The present invention further contemplates the prediction of breast cancer progression in an individual having breast cancer by assessing expression of one or more isoforms of Wilms' Tumor 1 (WT1) gene product in said cells.
It also contemplates a method of screening a substance for its ability to suppress the WT1 protein expression in a cancer cell thus acting as a potential inhibitor of breast cancer. The invention, in its various embodiments, is described in greater detail below.
II. WILMS' TUMOR GENE (WTl) The chromosome 11p13 Wilms' Tumor susceptibility gene (WT1) appears to play a crucial role in regulating the proliferation and differentiation of nephroblasts and gonadal tissue.
When present in the germline, specific heterozygous dominant-negative mutations are associated with severe abnormalities of renal and sexual differentiation, pointing to the essential role of WT1 for normal genitourinary development.

WTl encodes a protein migrating around SOkDa, which contains two domains W th apparent functional properties: a C-terminal domain that consists of four Cyst-His2 zinc finger domains involved in DNA binding and an N-terminal proline/ glutamine-rich transactivational domain. The zinc finger domains have a high degree of homology to the early growth response 1 and 2 products (Sukhatme et al., 1988; Joseph et al., 1988). The coding sequence is comprised of 10 exons, with each zinc finger encoded by an individual exon. Each of the four zinc finger domains is contained within a separate exon. The genomic structure of the zinc finger domains has been analyzed in which a small deletion has been detected (Haber et al., 1990). The analysis demonstrated that each zinc finger is separated from the next by a short intron.
Two alternative pre-mRNA splicing events give rise to four distinct transcripts or isoforms. Alternative splice I consists of 51 nucleotides, encoding 17 amino acids, including 5 serines and 1 threonine, potential sites of protein phosphorylation. The proline rich amino terminus domain is encoded by the first exon alone, and the 51 nucleotides of alternative splice I
compose exon 5. Splice I is inserted between the proline-rich amino terminus of the predicted protein and the first zinc finger domain.
Alternative splice II, results from the use of a variable splice donor site between exon 9 and 10, leading to the insertion of three amino acids, lysine-threonine-serine (commonly referred to as KTS), between third and fourth zinc finger. This insertion disrupts the critical spacing between these zinc fingers resulting in the loss of DNA binding to the consensus WT1 DNA
binding sequence (Wang et al., 1995).
The presence of two alternative splices in the WT1 trancript may reflect a degree of complexity in gene product function. The molecular mechanisms resulting in alternative mRNA
splicing are poorly understood, but axe thought to reflect both nucleotide sequence information contained in the splice junction, as well as cell type-specific regulatory factors (Breitbart et al., 1987).
Genetic evidence suggests that WT1 mutations, deletions, or imbalances among the different WTl isoforms may alter the transcriptional-regulator function of WT1 leading to developmental abnormalities and possibly cancer (Klamt et al., 1998; Guan et al., 1998; Liu et al., 1999). High expression of WTl has been correlated with poor prognosis and increased drug resistance in acute myeloid leukemia (moue et al., 1994), probably because increased WT1 expression can stimulate the proliferation and block the differentiation of leukemic cells (Yamagami et al., 1996). Therefore, WTl seems to act as both a tumor suppressor gene and an oncogene in certain types of malignancies. Recently, two groups have reported that breast cancer -g_ cells also express WT1 protein, but they did not describe the function of WT1 in breast cancer cells (Silberstein et al., 1997; Loeb et al., 2001).
III. ANTISENSE CONSTRUCTS
The term "antisense" is intended to refer to oligonucleotide or polynucleotide molecules complementary to a portion of a WT1 RNA, or the DNA's corresponding thereto.
"Complementary" oligonucleotides are those which are capable of base-pairing according to the standard Watson-Crick complementarity rules. That is, the larger purines will base pair with the smaller pyrimidines to form combinations of guanine paired with cytosine (G:C) and adenine paired with either thymine (A:T) in the case of DNA, or adenine paired with uracil (A:~ in the case of RNA. liiclusion of less common bases such as inosine, 5-methylcytosine, 6-methyladenine, hypoxanthine and others in hybridizing sequences does not interfere with pairing.
As used herein, the terms "complementary" or "antisense" mean oligonucleotides that are substantially complementary over their entire length and have very few base mismatches. For example, sequences of seven bases in length may be termed complementary when they have a complementary nucleotide for five or six positions out of seven. Naturally, sequences which are "completely complementary" will be sequences which are entirely complementary throughout their entire length and have no base mismatches.
Alternatively, the hybridizing segments may be shorter oligonucleotides. While all or part of the gene sequence may be employed in the context of antisense construction, it is important that the antisense when constructed binds/hybridizes the target sequence and does not face interference from other sequences that may be present in the gene sequence.
Statistically, any sequence 17 bases long should occur only once in the human genome and, therefore, suffice to specify a unique target sequence. Although shorter oligomers are easier to make and increase in vivo accessibility, numerous other factors are involved in determining the specificity of hybridization. Both binding affinity and sequence specificity of an oligonucleotide to its complementary target increases with increasing length. It is contemplated that oligonucleotides of 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45 or 50 base pairs will be used. In the present invention, SEQ ID NO:l is the sequence of the WT1 antisense oligos targeted against the translation initiation site and SEQ m N0:2 is the sequence of the control oligos. One can readily determine whether a given antisense nucleic acid is effective in targeting of the corresponding host cell gene simply by testing the constructs in vitro to determine whether the endogenous gene's function is affected or whether the expression of related genes having complementary sequences is affected.
Targeting double-stranded (ds) DNA with oligonucleotides leads to triple-helix formation; targeting RNA will lead to double-helix formation. Antisense oligonucleotides, when introduced into a target cell, specifically bind to their target oligonucleotide and interfere with transcription, RNA processing, transport, translation and/or stability.
Antisense RNA constructs, or DNA encoding such antisense RNA's, may be employed to inhibit gene transcription or translation or both within a host cell, either in vitf~o or ifa vivo, such as within a host animal, including a human subj ect.
The intracellular concentration of monovalent cation is approximately 160 mM
(10 mM
Na+; 150 mM K~. The intracellular concentration of divalent cation is approximately 20 mM
(18 mM Mgr; 2 mM Cap). The intracellular protein concentration, which would serve to decrease the volume of hybridization and, therefore, increase the effective concentration of nucleic acid species, is 150 mg/ml. Constructs can be tested in vitro under conditions that mimic these in vivo conditions.
Antisense constructs may be designed to hybridize to a WT1 transcript, a translation initiation site, a splice site, a WT1 genomic sequence, a start site, an intron, an exon or an intron- .
exon junction.
Hybridization is a process by which two complementary nucleic acid strands, such as DNA and DNA, RNA and DNA or RNA and RNA, recognize and bind to each other and form a double stranded structure. Intracellular hybridization is the basis of antisense therapy. This involves the administration/delivery of an antisense nucleic acid to a cell where the antisense molecule fords its complementary target-nucleic acid, which may be either DNA
or RNA, and hybridizes to it thereby preventing further transcription or translation of the target-nucleic acid.
In a particular embodiment of the invention, it is contemplated that the most effective antisense constructs for the present invention will include regions complementary to portions of the mRNA start site. One can readily test such constructs simply by testing the constructs i~ vitro to determine whether levels of the target protein are affected. Similarly, detrimental non-specific inhibition of protein synthesis also can be measured by determining target cell viability i~c vitYO.
It is envisioned that hybridization of the antisense oligonucleotides of the present invention to the translation initiation site of mRNA will be the basis of the antisense-gene therapy aimed at WT1 mediated diseases. Intracellular hybridization will prevent the transcription of mRNA and thereby decrease the protein content in the cell to which the antisense oligonucleotide is administered.

Other sequences with lower degrees of homology also are contemplated. ror examp~e, an antisense construct which has limited regions of high homology, but also contains a non-homologous region (e.g., a ribozyme) could be designed. These molecules, though having less than 50% homology, would bind to target sequences under appropriate conditions.
As mentioned above, the oligonucleotides according to the present invention may encode a WTl gene or a portion of that gene that is sufficient to effect antisense inhibition of expression of WT1 protein. These oligonucleotides may be derived from genomic DNA, i.e., cloned directly from the genome of a particular organism. In other embodiments, however, the oligonucleotides may be complementary DNA (cDNA). cDNA is DNA prepared using messenger RNA (mRNA) as template. Thus, a cDNA does not contain any interrupted coding sequences and usually contains almost exclusively the coding regions) for the corresponding protein. In other embodiments, the antisense oligonucleotide may be produced synthetically.
It may be advantageous to combine portions of the genomic DNA with cDNA or synthetic sequences to generate specific constructs. For example, where an intron is desired in the ultimate construct, a genomic clone will need to be used. The cDNA or a synthesized oligonucleotide may provide more convenient restriction sites for the remaining portion of the construct and, therefore, would be used for the rest of the sequence.
In certain embodiments, one may wish to employ antisense constructs which include other elements, for example, those which include C-5 propyne pyrimidines.
Oligonucleotides which contain C-5 propyne analogues of uridine and cytidine have been shown to bind RNA
with high affinity and to be potent antisense inhibitors of gene expression (Wagner et al., 1993).
As an alternative to targeted antisense delivery, targeted ribozymes may be used. The term "ribozyme" refers to an RNA-based enzyme capable of targeting and cleaving particular base sequences in both DNA and RNA. Ribozymes can either be targeted directly to cells, in the form of RNA oligonucleotides incorporating ribozyme sequences, or introduced into the cell as an expression vector encoding the desired ribozyrnal RNA. Ribozymes may be used and applied in much the same way as described for antisense oligonucleotide. Ribozyrne sequences also may be modified in much the same way as described for antisense oligonucleotide.
For example, one could incorporate non-Watson-Crick bases, or make mixed RNA/DNA
oligonucleotides, or modify the phosphodiester backbone.
Alternatively, the antisense oligo- or polynucleotides of the present invention may be provided as mRNA via transcription from expression constructs that carry nucleic acids encoding the oligonucleotides.

A nucleic acid may be made by any technique known to one of ordinary skill in the art, such as for example, chemical synthesis, enzymatic production or biological production. Non-limiting examples of a synthetic nucleic acid (e.g., a synthetic oligonucleotide), include a nucleic acid made by ifa vitro chemically synthesis using phosphotriester, phosphite or phosphoramidite chemistry and solid phase techniques, as described in EP 266,032 incorporated herein by reference, or via deoxynucleoside H-phosphonate intermediates as described by Froehler et al., 1986 and U.S. Patent Serial No. 5,705,629, each incorporated herein by reference. In the methods of the present invention, one or more oligonucleotides may be used.
Various different mechanisms of oligonucleotide synthesis have been disclosed in for example, U.S. Patents.
4,659,774, 4,816,571, 5,141,813, 5,264,566, 4,959,463, 5,428,148, 5,554,744, 5,574,146, 5,602,244, each of which is incorporated herein by reference.
A non-limiting example of an enzymatically produced nucleic acid includes one produced by enzymes in amplification reactions such as PCR~ (see for example, U.S. Patent 4,683,202 and U.S. Patent 4,682,195, each incorporated herein by reference), or the synthesis of an oligonucleotide described in U.S. Patent No. 5,645,897, incorporated herein by reference. A
non-limiting example of a biologically produced nucleic acid includes a recombinant nucleic acid produced (i. e., replicated) in a living cell, such as a recombinant DNA
vector replicated in bacteria (see for example, Sambrook et al. 1989, incorporated herein by reference).
IV. GENETIC CONSTRUCTS
The nucleic acid segments of the present invention, regardless of the length of the coding sequence itself, may be combined with other DNA sequences, such as promoters, enhancers and polyadenylation signals. It will be important to employ a promoter that effectively directs the expression of the DNA segment in the cell type, organism, or even animal, chosen for expression. Throughout this application, the term "expression construct" is meant to include any type of genetic construct containing an antisense product in which part or all of the nucleic acid sequence is capable of being transcribed. Typical expression vectors include bacterial plasmids or phage, such as any of the pUC or BluescriptTM plasmid series or, as discussed further below, viral vectors adapted for use in eukaryotic cells.
A. Promoters In particular embodiments, the antisense oligonucleotide or polynucleotide is part of an expression construct and is under the transcription control of a promoter. A
"promoter" is a control sequence that is a region of a nucleic acid sequence at which initiation and rate of transcription are controlled. It may contain genetic elements at which regulatory proteins and molecules may bind, such as RNA polymerase and other transcription factors, to initiate the specific transcription a nucleic acid sequence. The phrases "operatively positioned,"
"operatively linked," "under control," and "under transcriptional control"
mean that a promoter is in a correct functional location and/or orientation in relation to a nucleic acid sequence to control transcriptional initiation and/or expression of that sequence.
The term promoter will be used here to refer to a group of transcriptional control modules that are clustered around the initiation site for RNA polymerase II. Much of the thinking about how promoters are organized derives from analyses of several viral promoters, including those for the HSV thymidine kinase (tk) and SV40 early transcription units. These studies, augmented by more recent work, have shown that promoters are composed of discrete functional modules, each consisting of approximately 7-20 by of DNA, and containing one or more recognition sites for transcriptional activator or repressor proteins.
At least one module in each promoter functions to position the start site for RNA
synthesis. The best known example of this is the TATA box, but in some promoters lacking a TATA box, such as the promoter for the mammalian terminal deoxynucleotidyl transferase gene and the promoter for the SV40 late genes, a discrete element overlying the start site itself helps to fix the place of initiation.
Additional promoter elements regulate the frequency of transcriptional initiation.
Typically, these are located in the region 30-110 by upstream of the start site, although a number of promoters have recently been shown to contain functional elements downstream of the start site as well. The spacing between promoter elements frequently is flexible, so that promoter function is preserved when elements are inverted or moved relative to one another. In the tk promoter, the spacing between promoter elements can be increased to 50 by apart before activity begins to decline. Depending on the promoter, it appears that individual elements can function either co-operatively or independently to activate transcription.
The particular promoter employed to control the expression of a nucleic acid encoding the antisense oligonucleotides of this invention is not believed to be important, so long as it is capable of directing the expression of the antisense oligonucleotides in the targeted cell. Thus, where a human cell is targeted, it is preferable to position the nucleic acid coding the antisense oligonucleotide described in the invention adjacent to and under the control of a promoter that is capable of being expressed in a human cell. Generally speaking, such a promoter might include either a human or viral promoter.

In various embodiments, the human cytomegalovirus (CMV) immediate early gene promoter, the SV40 early promoter, the Rous sarcoma virus (RSV) long terminal repeat can be used to obtain high-level expression of the antisense oligonucleotides described and contemplated in the present invention. The use of other viral or mammalian cellular or bacterial phage promoters which are well-known in the art to achieve expression of an antisense oligonucleotide of interest is contemplated as well, provided that the levels of expression are sufficient for a given purpose.
Selection of a promoter that is regulated in response to specific physiologic or synthetic signals can permit inducible expression of the WT1 antisense oligonucleotide.
For example, in the case where expression of a transgene or transgenes when a multicistronic vector is utilized, is toxic to the cells in which the vector is produced, it may be desirable to prohibit or reduce expression of one or more of the transgenes. Examples of transgenes that may be toxic to the producer cell line are pro-apoptotic and cytokine genes: Several inducible promoter systems are available for production of viral vectors where the transgene product may be toxic.
The ecdysone system (Invitrogen, Carlsbad, CA) is one such system. This system is designed to allow regulated expression of a gene of interest in mammalian cells. It consists of a tightly regulated expression mechanism that allows virtually no basal level expression of the transgene, but over 200-fold inducibility. The system is based on the heterodimeric ecdysone receptor of D~osophila, and when ecdysone or an analog such as muristerone A
binds to the receptor, the receptor activates a promoter to turn on expression of the downstream transgene high levels of mRNA transcripts are attained. In this system, both monomers of the heterodimeric receptor are constitutively expressed from one vector, whereas the ecdysone-responsive promoter which drives expression of the gene of interest is on another plasmid.
Engineering of this type of system into the gene transfer vector of interest would therefore be useful. Cotransfection of plasmids containing the gene of interest and the receptor monomers in the producer cell line would then allow for the production of the gene transfer vector without expression of a potentially toxic transgene. At the appropriate time, expression of the transgene could be activated with ecdysone or muristeron A.
Another inducible system that would be useful is the Tet-OffrM or Tet-OnTM
system (Clontech, Palo Alto, CA) originally developed by Gossen and Bujard (Gossen and Bujard, 1992; Gossen et al., 1995). This system also allows high levels of gene expression to be regulated in response to tetracycline or tetracycline derivatives such as doxycycline. In the Tet-OnTM system, gene expression is turned on in the presence of doxycycline, whereas in the Tet-OffrM system, gene expression is turned on in the absence of doxycycline.
These systems are based on two regulatory elements derived from the tetracycline resistance operon of E. coli. The tetracycline operator sequence to which the tetracycline repressor binds, and the tetracycline repressor protein. The gene of interest is cloned into a plasmid behind a promoter that has tetracycline-responsive elements present in it. A second plasmid contains a regulatory element called the tetracycline-controlled transactivator, which is composed, in the Tet-OffrM system, of the VP16 domain from the herpes simplex virus and the wild-type tertracycline repressor. Thus in the absence of doxycycline, transcription is constitutively on. In the Tet-OnTM system, the tetracycline repressor is not wild-type and in the presence of doxycycline activates transcription.
For gene therapy vector production, the Tet-OffrM system would be preferable so that the producer cells could be grown in the presence of tetracycline or doxycycline and prevent expression of a potentially toxic transgene, but when the vector is introduced to the patient, the gene expression would be constitutively on.
In some circumstances, it may be desirable to regulate expression of a transgene in a gene therapy vector. For example, different viral promoters with varying strengths of activity may be utilized depending on the level of expression desired. In mammalian cells, the CMV immediate early promoter is often used to provide strong transcriptional activation.
Modified versions' of the CMV promoter that are less potent have also been used when reduced levels of expression of the transgene are desired. When expression of a transgene in hematopoetic cells is desired, retroviral promoters such as the LTRs from MLV or MMTV are often used. Other viral promoters that may be used depending on the desired effect include SV40, RSV
LTR, HIV-1 and HIV-2 LTR, adenovirus promoters such as from the ElA, E2A, or MLP region, AAV
LTR, cauliflower mosaic virus, HSV-TK, and avian sarcoma virus.
Similarly tissue specific promoters may be used to effect transcription in specific tissues or cells so as to reduce potential toxicity or undesirable effects to non-targeted tissues. For example, promoters such as leptin gene promoter (O'Neil et al., 2001), CDH13 (Toyooka et al., 2001), adenomatous polyposis coli (APC) gene promoter (Jin et al., 2001), IGF
binding protein-3 promoter (IGFBP-3) (Walker et al., 2001) may be used to target gene expression in breast cancers.
By employing a promoter with well-known properties, the level and pattern of expression of an antisense oligonucleotide of interest can be optimized.
Further, selection of a promoter that is regulated in response to specific physiologic signals can permit inducible expression of an antisense oligonucleotide. For example, a nucleic acid W der control of the human PAI-1 promoter results in expression inducible by tumor necrosis factor.
Tables 1 and 2 list several elements/promoters which may be employed, in the context of the present invention, to regulate the expression of antisense constructs. This list is not intended to be exhaustive of all the possible elements involved in the promotion of expression but, merely, to be exemplary thereof.
B. Enhancers Enhancers are genetic elements that increase transcription from a promoter located at a distant position on the same molecule of DNA. Enhancers are organized much like promoters.
That is, they are composed of many individual elements, each of which binds to one or more transcriptional proteins. The basic distinction between enhancers and promoters is operational.
An enhancer region as a whole must be able to stimulate transcription at a distance; this need not be true of a promoter region or its component elements. On the other hand, a promoter must have one or more elements that direct initiation of RNA synthesis at a particular site and in a particular orientation, whereas enhancers lack these specificities. Promoters and enhancers are often overlapping and contiguous, often seeming to have a very similar modular organization.
Below is a list of viral promoters, cellular promoters/enhancers and inducible promoters/enhancers that could be used in combination with the nucleic acid encoding an antisense oligonucleotide described in this invention in an expression construct (Table 1 and Table 2). Additionally any promoter/enhancer combination (as per the Eukaryotic Promoter Data Base EPDB) also could be used to drive expression of a nucleic acid according to the present invention. Use of a T3, T7 or SP6 cytoplasmic expression system is another possible embodiment. Eukaryotic cells can support cytoplasmic transcription from certain bacterial promoters if the appropriate bacterial polymerase is provided, either as part of the delivery complex or as an additional genetic expression construct.
Table 1 - Other Promoter/Enhancer Elements Promoter/Enhancer References hnmunoglobulin Heavy ChainBanerji et al., 1983; Gilles et al., 1983; Grosschedl and Baltimore, 1985; Atchinson and Perry, 1986, 1987; Imler et al., 1987; Weinberger et al., 1988;

Kiledjian et al., 1988; Porton et al., 1990 Immunoglobulin Light ChainQueen and Baltimore, 1983; Picard and Schaffner, T-Cell Receptor Luria et al., 1987, Winoto and Baltimore, 1989;

Redondo et al., 1990 HLA DQ ec and DQ (3 Sullivan and Peterlin, 1987 (3-Interferon Goodbourn et al., 1986; Fujita et al., 1987;

Goodbourn and Maniatis, 1985 Interleukin-2 Greene et al., 1989 Promoter/Enhancer References Interleukin-2 Receptor Greene et al., 1989; Lin et al., MHC Class II Koch et al., 1989 MHC Class II HLA-DRa Sherman et al., 1989 ~3-Actin Kawamoto et al., 1988; Ng et al., Muscle Creatine Kinase Jaynes et al., 1988; Horlick and Benfield, 1989;
Johnson et al., 1989a Prealbumin (Transthyretin)Costa et al., 1988 Elastase I Omitz et al., 1987 Metallothionein Karin et al., 1987; Culotta and Hamer, Collagenase Pinkert et al., 1987; Angel et al., Albumin Gene Pinkert et al., 1987, Tronche et al., 1989, 1990 a-Fetoprotein Godbout et al., 1988; Campere and Tilghman, y-Globin Bodine and Ley, 1987; Perez-Stable and Constantini, 1990 (3-Globin Trudel and Constantini, 1987 c-fos Cohen et al., 1987 c-HA-ras Triesman, 1986; Deschamps et al., Insulin Edlund et al., 1985 Neural Cell Adhesion MoleculeHirsch et al., 1990 (NCAM) al-antitrypsin Latimer et al., 1990 H2B (TH2B) Histone Hwang et al., 1990 Mouse or Type I Collagen Ripe et al., 1989 Glucose-Regulated ProteinsChang et al., 1989 (GRP94 and GRP78) Rat Growth Hormone Larsen et al., 1986 Human Serum Amyloid A Edbrooke et al., 1989 (SAA) Troponin I (TN I) Yutzey et al., 1989 Platelet-Derived Growth Pech et al., 1989 Factor Duchenne Muscular DystrophyKlamut et al., 1990 SV40 Banerji et al., 1981; Moreau et al., 1981; Sleigh and Lockett, 1985; Firak and Subramanian, 1986;
Herr and Clarke, 1986; Imbra and Karin, 1986;
Kadesch and Berg, 1986; Wang and Calame, 1986;
Ondek et al., 1987; Kuhl et al., 1987 Schaffiier et al., 1988 Polyoma Swartzendruber and Lehman, 1975;
Vasseur et al., 1980; Katinka et al., 1980, 1981;
Tyndell et al., 1981; Dandolo et al., 1983; deVilliers et al., 1984;
Hen et al., 1986; Satake et al., 1988; Campbell and Villarreal, 1988 Retroviruses Kriegler and Botchan, 1982, 1983;
Levinson et al., 1982; Kriegler et al., 1983, 1984a,b, 1988; Bosze et al., 1986; Miksicek et al., 1986;
Celander and Haseltine, 1987; Thiesen et al., 1988; Celander et al., 1988; Chol et al., 1988; Reisman and Rotter, Promoter/Enhancer References Papilloma Virus Campo et al., 1983; Lusky et al., 1983; Spandidos and Willcie, 1983; Spalholz et al., 1985; Lusky and Botchan, 1986; Cripe et al., 1987;
Gloss et al., 1987; Hirochika et al., 1987, Stephens and Hentschel, 1987; Glu et al., 1988 Hepatitis B Virus Bulla and Siddiqui, 1986; Jameel and Siddiqui, 1986; Shaul and Ben-Levy, 1987; Spandau and Lee, 1988 Human Irnmunodeficiency Muesing et al., 1987; Hauber and Cullan, Virus 1988;

Jakobovits et al., 1988; Feng and Holland, 1988;

Takebe et al., 1988; Rowen et al., 1988; Berkhout et al., 1989; Laspia et al., 1989;
Sharp and Marciniak, 1989; Braddock et al., Cytomegalovirus Weber et al., 1984; Boshart et al., 1985; Foecking and Hofstetter, 1986 Gibbon Ape Leukemia VirusHolbrook et al., 1987; Quinn et al., Table 2 Inducible Elements Element Inducer MT II Phorbol Ester (TPA) Heavy metals MMTV (mouse mammary tumorGlucocorticoids virus) 13-Interferon poly(rT)X
poly(rc) Adenovirus 5 E2 Ela c jun Phorbol Ester (TPA), HzOz Collagenase Phorbol Ester (TPA) Stromelysin Phorbol Ester (TPA), IL-1 SV40 Phorbol Ester (TPA) Murine MX Gene Interferon, Newcastle Disease Virus GRP78 Gene A23187 a-2-Macroglobulin IL-6 Vimentin Serum MHC Class I Gene H-2kB Interferon HSP70 Ela, SV40 Large T Antigen Proliferin Phorbol Ester-TPA

Tumor Necrosis Factor FMA

Thyroid Stimulating HormoneThyroid Hormone a, Gene ~ Insulin E Box ~ Glucose In certain embodiments of this invention, the delivery of a nucleic acid to a cell may be identified ira vitf°o or irz vivo by including a marker in the expression construct. The marker would result in an identifiable change to the transfected cell permitting easy identification of expression. Enzymes such as herpes simplex virus thymidine kinase (t7z) (eulcaryotic) or chloramphenicol acetyltransferase (CAT) (prolcaryotic) may be employed.
C. Polyadenylation Signals Where a cDNA insert is employed, one will typically desire to include a polyadenylation signal to effect proper polyadenylation of the gene transcript. The nature of the polyadenylation signal is not believed to be crucial to the successful practice of the invention, and any such sequence may be employed such as human or bovine growth hormone and SV40 polyadenylation signals. Also contemplated as an element of the expression cassette is a terminator. These elements can serve to enhance message levels and to minimize read through from the cassette into other sequences.
V. LIPID FORMULATIONS
In a particular embodiment of the invention, the antisense oligonucleotides and expression vectors may be associated with a lipid. An oligonucleotide associated with a lipid may be encapsulated in the aqueous interior of a liposome, interspersed within the lipid bilayer of a liposome, attached to a liposome via a linking molecule that is associated with both the liposome and the oligonucleotide, entrapped in a liposome, complexed with a liposome, dispersed in a solution containing a lipid, mixed with a lipid, combined with a lipid, contained as a suspension in a lipid, contained or complexed with a micelle, or otherwise associated with a lipid. The lipid or lipid/oligonucleotide associated compositions of the present invention are not limited to any particular structure in solution. For example, they may be present in a bilayer structure, as micelles, or with a "collapsed" structure. They may also simply be interspersed in a solution, possibly forming aggregates which are not uniform in either size or shape.
Lipids are fatty substances which may be naturally occurnng or synthetic lipids. For example, lipids include the fatty droplets that naturally occur in the cytoplasm as well as the class of compounds which are well known to those of skill in the art which contain long-chain aliphatic hydrocarbons and their derivatives, such as fatty acids, alcohols, amines, amino alcohols, and aldehydes. An example is the lipid dioleoylphosphatidylcholine (DOPC).
Phospholipids may be used for preparing the liposomes according to the present invention and can carry a net positive charge, a net negative charge or are neutral. Diacetyl phosphate can be employed to confer a negative charge on the hposomes, and stearylamme can be used to confer a positive charge on the liposomes. The liposomes can be made of one or more phospholipids.
In a particular embodiment, the lipid material is comprised of a neutrally charged lipid.
A neutrally charged lipid can comprise a lipid without a charge, a substantially uncharged lipid or a lipid mixture with equal number of positive and negative charges.
In one aspect, the lipid component of the composition comprises a neutral lipid. In another aspect, the lipid material consists essentially of neutral lipids which is further defined as a lipid composition containing at least 70% of lipids without a charge. In other aspects, the lipid material may contain at least 80% to 90% of lipids without a charge. In yet other aspects, the lipid material may comprise about 90%, 95%, 96%, 97%, 98%, 99% or 100% lipids without a charge.
In specific aspects, the neutral lipid comprises a phosphatidylcholine, a phosphatidylglycerol, or a phosphatidylethanolamine. In a particular aspect, the phosphatidylcholine comprises DOPC.
In other aspects the lipid component comprises a substantially uncharged lipid. A
substantially uncharged lipid is described herein as a lipid composition that is substantially free of anionic and cationic phospholipids and cholesterol. In yet other aspects the lipid component comprises a mixture of lipids to provide a substantially uncharged lipid.
Thus, the lipid mixture may comprise negatively and positively charged lipids.
Lipids suitable for use according to the present invention can be obtained from commercial sources. For example, dimyristyl phosphatidylcholine ("DMPC") can be obtained from Sigma Chemical Co., dicetyl phosphate ("DCP") is obtained from K & K
Laboratories (Plainview, NY); cholesterol ("Chol") is obtained from Calbiochem-Behring;
dimyristyl phosphatidylglycerol ("DMPG") and other lipids may be obtained from Avanti Polar Lipids, Inc.
(Birmingham, Ala.). Stock solutions of lipids in chloroform or chloroform/methanol can be stored at about -20°C. Preferably, chloroform is used as the only solvent since it is more readily evaporated than methanol.
Phospholipids from natural sources, such as egg or soybean phosphatidylcholine, brain phosphatidic acid, brain or plant phosphatidylinositol, heart cardiolipin and plant or bacterial phosphatidylethanolamine are preferably not used as the primary phosphatide, i.e., constituting 50% or more of the total phosphatide composition, because of the instability and leakiness of the resulting liposomes.

"Liposome" is a generic term encompassing a variety of single and multilamellar lipid vehicles formed by the generation of enclosed lipid bilayers or aggregates.
Liposomes may be characterized as having vesicular structures with a phospholipid bilayer membrane and an imler aqueous medium. Multilamellar liposomes have multiple lipid layers separated by aqueous medium. They form spontaneously when phospholipids are suspended in an excess of aqueous solution. The lipid components undergo self rearrangement before the formation of closed structures and entrap water and dissolved solutes between the lipid bilayers (Ghosh and Bachhawat, 1991). However, the present invention also encompasses compositions that have different structures in solution than the normal vesicular structure. For example, the lipids may assume a micellar structure or merely exist as nonuniform aggregates of lipid molecules. Also contemplated are lipofectamine-nucleic acid complexes.
Liposome-mediated oligonucleotide delivery and expression of foreign DNA ih vitfAo has been very successful. Wong et al. (1980) demonstrated the feasibility of liposome-mediated delivery and expression of foreign DNA in cultured chick embryo, HeLa and hepatoma cells.
Nicolau et al. (1987) accomplished successful liposome-mediated gene transfer in rats after intravenous inj ection.
In certain embodiments of the invention, the lipid may be associated with a hemagglutinating virus (HVJ). This has been shown to facilitate fusion with the cell membrane and promote cell entry of liposome-encapsulated DNA (I~aneda et al., 1989). In other embodiments, the lipid may be complexed or employed in conjunction with nuclear non-histone chromosomal proteins (HMG-1) (Kato et al., 1991). In yet further embodiments, the lipid may be complexed or employed in conjunction with both HVJ and HMG-1. Such expression vectors have been successfully employed in transfer and expression of an oligonucleotide ih vitro and in vivo and thus are applicable for the present invention. Where a bacterial promoter is employed in the DNA construct, it also will be desirable to include within the liposome an appropriate bacterial polymerase.
Liposomes used according to the present invention can be made by different methods.
The size of the liposomes varies depending on the method of synthesis. A
liposome suspended in an aqueous solution is generally in the shape of a spherical vesicle, having one or more concentric layers of lipid bilayer molecules. Each layer consists of a parallel array of molecules represented by the formula XY, wherein X is a hydrophilic moiety and Y is a hydrophobic moiety. In aqueous suspension, the concentric layers are arranged such that the hydrophilic moieties tend to remain in contact with an aqueous phase and the hydrophobic regions tend to self associate. For example, when aqueous phases are present both within and without the nposome, the rapid molecules may form a bilayer, known as a lamella, of the arrangement XY-YX. Aggregates of lipids may form when the hydrophilic and hydrophobic parts of more than one lipid molecule become associated with each other. The size and shape of these aggregates will depend upon many different variables, such as the nature of the solvent and the presence of other compounds in the solution.
Liposomes within the scope of the present invention can be prepared in accordance with known laboratory techniques. A particular method of the invention describes the preparation of liposomes and is described below. Briefly, P-ethoxy oligonucleotides (also referred to as PE
oligos) are dissolved in DMSO and the phospholipids (Avanti Polar Lipids, Alabaster, AL), such as for example the preferred neutral phospholipid dioleoylphosphatidylcholine (DOPC), is dissolved in test-butanol. The lipid is then mixed with the antisense oligonucleotides. In the case of DOPC, the molar ratio of the lipid to the antisense oligos is 20:1.
Tween 20 is added to the lipid:oligo mixture such that Tween 20 is'S% of the combined weight of the lipid and oligo.
Excess tert-butanol is added to this mixture such that the volume of tent-butanol is at least 95%.
The mixture is vortexed, frozen in a dry ice/acetone bath and lyophilized overnight. The lyophilized preparation is stored at -20°C and can be used up to three months. When required the lyophilized liposomes are reconstituted in 0.9% saline. The average diameter of the particles obtained using Tween 20 for encapsulating the lipid with the oligo is 0.7-1.0 ~m in diameter.
Alternatively liposomes can be prepared by mixing liposomal lipids, in a solvent in a container, e.g., a glass, pear-shaped flask. The container should have a volume ten-times greater than the volume of the expected suspension of liposomes. Using a rotary evaporator, the solvent is removed at approximately 40°C under negative pressure. The solvent normally is removed within about 5 min. to 2 hours, depending on the desired volume of the liposomes. The composition can be dried further in a desiccator under vacuum. The dried lipids generally are discarded after about 1 week because of a tendency to deteriorate with time.
Dried lipids can be hydrated at approximately 25-50 mM phospholipid in sterile, pyrogen-free water by shaking until all the lipid film is resuspended. The aqueous liposomes can be then separated into aliquots, each placed in a vial, lyophilized and sealed under vacuum.
In other alternative methods, liposomes can be prepared in accordance with other known laboratory procedures: the method of Bangham et al. (1965), the contents of which are incorporated herein by reference; the method of Gregoriadis (1979), the contents of which are incorporated herein by reference; the method of Deamer and Uster (1983), the contents of which are incorporated by reference; and the reverse-phase evaporation method as described by Szoka _22_ anti Yapahad~opoulos (ly'/~). The aforementioned methods deter m their respectme abilities to entrap aqueous material and their respective aqueous space-to-lipid ratios.
The dried lipids or lyophilized liposomes prepared as described above may be dehydrated and reconstituted in a solution of inhibitory peptide and diluted to an appropriate concentration with an suitable solvent, e.g., DPBS. The mixture is then vigorously shaken in a vortex mixer.
Unencapsulated nucleic acid is removed by centrifugation at 29,000 x g and the liposomal pellets washed. The washed liposomes are resuspended at an appropriate total phospholipid concentration, e.g., about 50-200 mM. The amount of nucleic acid encapsulated can be determined in accordance with standard methods. After determination of the amount of nucleic acid encapsulated in the liposome preparation, the liposomes may be diluted to appropriate concentrations and stored at 4°C until use.
P-ethoxy oligonucleotides, nucleases resistant analogues of phosphodiesters, are preferred because they are stable in serum. Neutral lipids are also preferred and specifically the lipid dioleoylphosphatidylchoine is preferred. However other lipids such as other phosphatidylcholines, phosphatidylglycerols, and phosphatidylethanolamines may also be useful.
In yet another particular method described herein, the nuclease-resistant oligonucleotides and lipids are dissolved in DMSO and t-butanol respectively. The lipid is then mixed with the oligonucleotides in a molar ratio of between about 5:1 to about 100:1, and preferably in a ratio of 20:1. The preferred lipid:oligonucleotide ratio for P-ethoxy oligonucleotides and the lipid dioleoylphosphatidylchoine is 20:1. Tween 20 is then added to the mixture to obtain the ' liposomes. Excess t-butanol is added and the mixture is vortexed, frozen in an acetone/dry-ice bath, and then lyophilized overnight. The preparation is stored at -20°C and may be used within one month of preparation. When required for use the lyophilized liposomal antisense oligonucleotides are reconstituted in 0.9% saline.
In an alternative embodiment, nuclease-resistant oligonucleotides are mixed with lipids in the presence of excess t-butanol. The mixture is vortexed before being frozen in an acetone/dry ice bath. The frozen mixture is then lyophilized and hydrated with Hepes-buffered saline (1 mM
Hepes, 10 mM NaCl, pH 7.5) overnight, and then the liposomes are sonicated in a bath type sonicator for 10 to 15 min. The size of the liposomal-oligonucleotides typically ranges between 200-300 nm in diameter as determined by the submicron particle sizer autodilute model 370 (Nicomp, Santa Barbara, CA).
A pharmaceutical composition comprising the liposomes will usually include a sterile, pharmaceutically acceptable carrier or diluent, such as water or saline solution.

V1. 1VU1V-L1YUSUMAL DEL1VEKY SYSTEMS
The delivery of antisense constructs of the present invention may also be accomplished using expression vectors which may be viral or non-viral in nature.
Retroviruses. The retroviruses are a group of single-straaided RNA viruses characterized by an ability to convert their RNA to double-stranded DNA in infected cells by a process of reverse-transcription (Coffin, 1990). The resulting DNA then stably integrates into cellular chromosomes as a provirus and directs synthesis of viral proteins. The integration results in the retention of the viral gene sequences in the recipient cell and its descendants. The retroviral genome contains three genes - gag, pol, and ehv - that code for capsid proteins, polymerase enzyme, and envelope components, respectively. A sequence found upstream from the gag gene, termed ~I', functions as a signal for packaging of the genome into virions. Two long terminal repeat (LTR) sequences are present at the 5' and 3' ends of the viral genome. These contain strong promoter and enhancer sequences and are also required for integration in the host cell genome (Coffin, 1990).
In order to construct a retroviral vector, a nucleic acid encoding a WTl antisense construct as described in this invention is inserted into the viral genome in the place of certain viral sequences to produce a virus that is replication-defective. In order to produce virions, a packaging cell line containing the gag, pol and env genes but without the LTR
and ~I' components is constructed (Mann et al., 1983). When a recombinant plasmid containing an inserted DNA, together with the retroviral LTR and ~I' sequences, is introduced into this cell line (by calcium phosphate precipitation for example), the ~I' sequence allows the RNA transcript of the recombinant plasmid to be packaged into viral particles, which are then secreted into the culture media (Nicolas and Rubenstein, 1988; Temin, 1986; Mann et al., 1983).
The media containing the recombinant retroviruses is then collected, optionally concentrated, and used for gene transfer. Retroviral vectors are able to infect a broad variety of cell types. However, integration and stable expression require the division of host cells (Paskind et al., 1975).
Adehoviruses. Human adenoviruses are double-stranded DNA tumor viruses with genome sizes of approximate 36 kB. As a model system for eukaryotic gene expression, adenoviruses have been widely studied and well characterized, which makes them an attractive system for development of adenovirus as a gene transfer system. This group of viruses is easy to grow and manipulate, and they exhibit a broad host range iya vitro and ih vivo. In lytically infected cells, adenoviruses are capable of shutting off host protein synthesis, directing cellular machmenes to synthesize large quantities of viral proteins, and producing copious amounts of virus.
The E1 region of the genome includes ElA and E1B which encode proteins responsible for transcription regulation of the viral genome, as well as a few cellular genes. E2 expression, including E2A and E2B, allows synthesis of viral replicative functions, e.g.
DNA-binding protein, DNA polymerase, and a terminal protein that primes replication. E3 gene products prevent cytolysis by cytotoxic T cells and tumor necrosis factor and appear to be important for viral propagation. Functions associated with the E4 proteins include DNA
replication, late gene expression, and host cell shutoff. The late gene products include most of the virion capsid proteins, and these are expressed only after most of the processing of a single primary transcript from the major late promoter has occurred. The major late promoter (MLP) exhibits high efficiency during the late phase of the infection (Stratford-Perncaudet and Perricaudet, 1991).
A small portion of the viral genome appears to be required in cis adenovirus-derived vectors when used in connection with cell lines such as 293 cells. Ad5-transformed human embryonic kidney cell lines (Graham et al., 1977) have been developed to provide the essential viral proteins ira tYans.
Particular advantages of an adenovirus system for expressing and delivering the antisense oligonucleotides of this invention include (i) the structural stability of recombinant adenoviruses;
(ii) the safety of adenoviral administration to humans; and (iii) lack of any known association of adenoviral infection with cancer or malignancies; (iv) the ability to obtain high titers of the recombinant virus; and (v) the high infectivity of adenovirus.
Further advantages of adenovirus vectors over retroviruses include the higher levels of gene expression. Additionally, adenovirus replication is independent of host gene replication, unlike retroviral sequences. Because adenovirus transforming genes in the El region can be readily deleted and still provide efficient expression vectors, oncogenic risk from adenovirus vectors is thought to be negligible (Grunhaus et al., 1992).
In general, adenovirus gene transfer systems are based upon recombinant, engineered adenovirus which is rendered replication-incompetent by deletion of a portion of its genome, such as E1, and yet still retains its competency for infection. Sequences encoding relatively large foreign proteins can be expressed when additional deletions are made in the adenovirus genome. Surprisingly persistent expression of transgenes following adenoviral infection has also been reported.
Qtlae~ l~i~al Vectors as Expression Cosastructs. Other viral vectors may be employed as expression constructs in the present invention. Vectors derived from viruses such as vaccinia virus (Kidgeway, ly~~; Baichwal and ~ugden, 1y~6; C;oupar et al., ly~~) adeno-associated virus (AAV) (Ridgeway, 1988; Baichwal and Sugden, 1986; Hermonat and Muzycska, 1984) lentivirus, polyoma virus and herpes viruses may be employed. They offer several attractive features for various mammalian cells (Friedman et al., 1989; Ridgeway, 1988;
Baichwal and Sugden, 1986; Coupar et al., 1988; Horwich et al., 1990).
With the recent recognition of defective hepatitis B viruses, new insight was gained into .
the structure-function relationship of different viral sequences. Izz vitro studies showed that the virus could retain the ability for helper-dependent packaging and reverse transcription despite the deletion of up to 80% of its genome (Horwich et al., 1990). This suggested that large portions of the genome could be replaced with foreign genetic material. The hepatotropism and persistence (integration) were particularly attractive properties for liver-directed gene transfer. Chang et al.
(1991) introduced the chloramphenicol acetyltransferase (CAT) gene into duck hepatitis B virus genome in the place of the polymerase, surface, and pre-surface coding sequences. It was cotransfected with wild-type virus into an avian hepatoma cell line. Culture media containing high titers of the recombinant virus were used to infect primary duckling hepatocytes. Stable CAT gene expression was detected for at least 24 days after transfection (Chang et al., 1991).
Non-vival Methods. Several non-viral methods for the transfer of expression vectors into cultured mammalian cells also are contemplated in the present invention. These include calcium phosphate precipitation (Graham and van der Eb, 1973; Chen and Okayama, 1987;
Rippe et al., 1990); DEAE-dextran (copal, 1985); electroporation (Tur-Kaspa et al., 1986;
Potter et al., 1984); direct microinjection (Harland and Weintraub, 1985); cell sonication (Fecheimer et al., 1987); gene bombardment using high velocity microprojectiles (Yang et al., 1990); polycations;
and receptor-mediated transfection (Wu and Wu, 1987; Wu and Wu, 1988). Some of these techniques may be successfully adapted for in vivo or ex vivo use.
In one embodiment of the invention, the expression construct may simply consist of naked recombinant vector. Transfer of the construct may be performed by any of the methods mentioned above which physically or chemically permeabilize the cell membrane.
For example, Dubensky et al. (1984) successfully injected polyomavirus DNA in the form of CaP04 precipitates into liver and spleen of adult and newborn mice demonstrating active viral replication and acute infection. Benvenisty and Neshif (1986) also demonstrated that direct intraperitoneal injection of CaP04 precipitated plasmids results in expression of the transfected genes. It is envisioned that DNA encoding an WT1 antisense oligonucleotide construct may also be transferred in a similar manner in vivo.

Another embodiment of the invention for transferring a naked 1~1~A expression vector into cells may involve particle bombardment. This method depends on the ability to accelerate DNA coated microprojectiles to a high velocity allowing them to pierce cell membranes and enter cells without killing them (I~lein et al., 1987). Several devices for accelerating small particles have been developed. One such device relies on a high voltage discharge to generate an electrical current, which in turn provides the motive force (Yang et al., 1990). The microprojectiles used have consisted of biologically inert substances such as tungsten or gold beads.
Selected organs including the liver, skin, and muscle tissue of rats and mice have been bombarded ifz vivo (Yang et al., 1990; Zelenin et al., 1991). This may require surgical exposure of the tissue or cells, to eliminate any intervening tissue between the gun and the target organ.
DNA encoding a WTl antisense oligonucleotide as described in this invention may be delivered via this method.
VII. PHARMACEUTICALS
Where clinical application of liposomes containing antisense oligo- or polynucleotides or expression vectors is undertaken, it will be necessary to prepare the liposome complex as a pharmaceutical composition appropriate for the intended application.
Generally, this will entail preparing a pharmaceutical composition that is essentially free of pyrogens, as well as any other impurities that could be Harmful to humans or animals. One also will generally desire to employ appropriate buffers to render the complex stable and allow for uptake by target cells.
Aqueous compositions of the therapeutic composition of the present invention comprise an effective amount of the antisense expression vector encapsulated in a liposome as discussed above, further dispersed in pharmaceutically acceptable carrier or aqueous medium. Such compositions also are referred to as inocula. The phrases "pharmaceutically"
or "pharmacologically acceptable" refer to compositions that do not produce an adverse, allergic or other untowaxd reaction when administered to an animal, or a human, as appropriate.
As used herein, "pharmaceutically acceptable Garner" includes any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents and the like. The use of such media and agents for pharmaceutical active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active ingredient, its use in the therapeutic compositions is contemplated. Supplementary active ingredients also can be incorporated into the compositions.

Solutions of therapeutic compositions can be prepared in water suitably mixed with a surfactant, such as hydroxypropylcellulose. Dispersions also can be prepared in glycerol, liquid polyethylene glycols, mixtures thereof and in oils. Under ordinary conditions of storage and use, these preparations contain a preservative to prevent the growth of microorganisms.
For human administration, preparations should meet sterility, pyrogenicity, general safety and purity standards as required by FDA Office of Biologics standards. The biological material should be extensively dialyzed to remove undesired small molecular weight molecules and/or lyophilized for more ready formulation into a desired vehicle, where appropriate. The active compounds will then generally be formulated for parenteral administration, e.g., formulated for injection via the intravenous, intramuscular, sub-cutaneous, intralesional, or even intraperitoneal routes. The preparation of an aqueous composition that contains the therapeutic composition as an active component or ingredient will be known to those of skill in the art in light of the present disclosure. Typically, such compositions can be prepared as injectables, either as liquid solutions or suspensions; solid forms suitable for using to prepare solutions or suspensions upon the addition of a liquid prior to injection can also be prepared; and the preparations can also be emulsified.
The pharmaceutical forms suitable for injectable use include sterile aqueous solutions or dispersions; formulations including sesame oil, peanut oil or aqueous propylene glycol; and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersions.
In all cases the form must be sterile and must be fluid to the extent that easy syringability exists.
It must be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms, such as bacteria and fungi.
A therapeutic composition can be formulated into a composition in a neutral or salt form.
Pharmaceutically acceptable salts, include the acid addition salts (formed with the free amino groups of the protein) and which are formed with inorganic acids such as, for example, hydrochloric or phosphoric acids, or such organic acids as acetic, oxalic, tartaric, mandelic, and the like. Salts formed with the free carboxyl groups can also be derived from inorganic bases such as, for example, sodium, potassium, ammonium, calcium, or fernc hydroxides, and such organic bases as isopropylamine, trimethylamine, histidine, procaine and the like.
The carrier can also be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid polyethylene glycol, and the like), suitable mixtures thereof, and vegetable oils. The proper fluidity can be maintained, for example, by the use of a coating, such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants. The prevention of the action of _2g_ microorganisms can be brought about by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, sorbic acid, thimerosal, and the like. In many cases, it will be preferable to include isotonic agents, for example, sugars or sodium chloride. Prolonged absorption of the injectable compositions can be brought about by the use in the compositions of agents delaying absorption, for example, aluminum monostearate and gelatin.
Sterile injectable solutions are prepared by incorporating the active compounds in the required amount in the appropriate solvent with various of the other ingredients enumerated above, as required, followed by filtered sterilization. Generally, dispersions are prepared by incorporating the various sterilized active ingredients into a sterile vehicle which contains the basic dispersion medium and the required other ingredients from those enumerated above. In the case of sterile powders for the preparation of sterile injectable solutions, the preferred methods of preparation are vacuum-drying and freeze-drying techniques which yield a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof.
The therapeutic. compositions of the present invention are advantageously administered in the form of injectable compositions either as liquid solutions or suspensions;
solid forms suitable for solution in, or suspension in, liquid prior to injection may also be prepared. These preparations also may be emulsified. A typical composition for such purpose comprises a pharmaceutically acceptable carrier. For instance, the composition may contain 10 mg, 25 mg, 50 mg or up to about 100 mg of human serum albumin per milliliter of phosphate buffered saline. Other pharmaceutically acceptable can-iers include aqueous solutions, non-toxic.
excipients, including salts, preservatives, buffers and the like.
Examples of non-aqueous solvents are propylene glycol, polyethylene glycol, vegetable oil and injectable organic esters such as ethyloleate. Aqueous carriers include water, alcoholic/aqueous solutions, saline solutions, parenteral vehicles such as sodium chloride, Ringer's dextrose, etc. Intravenous vehicles include fluid and nutrient replenishers.
Preservatives include antimicrobial agents, anti-oxidants, chelating agents and inert gases. The pH and exact concentration of the various components the pharmaceutical composition are adjusted according to well lcnown parameters.
Additional formulations are suitable for oral administration. Oral formulations include such typical excipients as, for example, pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharine, cellulose, magnesium carbonate and the like. The compositions take the form of solutions, suspensions, tablets, pills, capsules, sustained release _29_ formulations or powders. When the route is topical, the form may be a cream, ointment, salve or spray.
The therapeutic compositions of the present invention may include classic pharmaceutical preparations. Administration of therapeutic compositions according to the present invention will be via any common route so long as the target tissue is available via that route. This includes oral, nasal, buccal, rectal, vaginal or topical. Topical administration would be particularly advantageous for the treatment of skin cancers, to prevent chemotherapy-induced alopecia or other dermal hyperproliferative disorder. Alternatively, administration may be by orthotopic, intradermal subcutaneous, intramuscular, intraperitoneal or intravenous injection.
Such compositions would normally be administered as pharmaceutically acceptable compositions that include physiologically acceptable carriers, buffers or other excipients. For treatment of conditions of the lungs, the preferred route is aerosol delivery to the lung. Volume of the aerosol is between about 0.01 ml and 0.5 ml. Similarly, a preferred method for treatment of colon-associated disease would be via enema. Volume of the enema is between about 1 ml and 100 ml.
An effective amount of the therapeutic composition is determined based on the intended goal. The term "unit dose" or "dosage" refers to physically discrete units suitable for use in a subject, each unit containing a predetermined-quantity of the therapeutic composition calculated to produce the desired responses, discussed above, in association with its administration, i. e., the appropriate route and treatment regimen. The quantity to be administered, both according to number of treatments and unit dose, depends on the protection desired.
Precise amounts of the therapeutic composition also depend on the judgment of the practitioner and are peculiar to each individual. Factors affecting the dose include the physical and clinical state of the patient, the route of administration, the intended goal of treatment (alleviation of symptoms versus cure) and the potency, stability and toxicity of the particular therapeutic substance.
Administration of the therapeutic construct of the present invention to a patient will follow general protocols for the administration of chemotherapeutics, taking into account the toxicity, if any, of the vector. It is expected that the treatment cycles would be repeated as necessary. It also is contemplated that various standard therapies, as well as surgical intervention, may be applied in combination with the described treatments.
Depending on the particular cancer to be, administration of therapeutic compositions according to the present invention will be via any common route so long as the target tissue is available via that route. This includes oral, nasal, buccal, rectal, vaginal or topical. Topical administration would be particularly advantageous for treatment of skin cancers. Alternatively, administration will be by orthotopic, intradennal, subcutaneous, intramuscular, intraperitoneal or intravenous injection. Such compositions would normally be administered as pharmaceutically acceptable compositions that include physiologically acceptable carriers, buffers or other excipients.
The treatments may include various "unit doses." Unit dose is defined as containing a predetermined-quantity of the therapeutic composition calculated to produce the desired responses in association with its administration, i.e., the appropriate route and treatment regimen.
The quantity to be administered, and the particular route and formulation, axe within the skill of those in the clinical arts. Also of importance is the subject to be treated, in particular, the state of the subject and the protection desired. A unit dose need not be administered as a single injection but may comprise continuous infusion over a set period of time.
According to the present invention, one may treat the cancer by directly injecting a tumor with the therapeutic composition of the present invention. Alternatively, the tumor may be infused or perfused with the antisense oligonucleotides using any suitable delivery vehicle.
Local or regional administration, with respect to the tumor, also is contemplated. Finally, systemic administration may be performed. Continuous administration also may be applied where appropriate, for example, where a tumor is excised and the tumor bed is treated to eliminate residual, microscopic disease. Delivery via syringe or catherization is preferred. Such continuous perfusion may take place for a period from about 1-2 hours, to about 2-6 hours, to about 6-12 hours, to about 12-24 hours, to about 1-2 days, to about 1-2 wk or longer following the initiation of treatment. Generally, the dose of the therapeutic composition via continuous perfusion will be equivalent to that given by a single or multiple injections, adjusted over a period of time during which the perfusion occurs.
For tumors of > 4 cm, the volume to be administered will be about 4-10 ml (preferably 10 ml), while for tumors of c 4 cm, a volume of about 1-3 ml will be used (preferably 3 ml).
Multiple injections delivered as single dose comprise about 0.1 to about 0.5 ml volumes. The viral particles or protein may advantageously be contacted by administering multiple injections to the tumor, spaced at approximately 1 cm intervals.
In certain embodiments, the tumor being treated may not, at least initially, be resectable.
Treatments with therapeutic compositions may increase the resectability of the tumor due to shrinkage at the margins or by elimination of certain particularly invasive portions. Following treatments, resection may be possible. Additional viral or protein treatments subsequent to resection will serve to eliminate microscopic residual disease at the tumor site.

A typical course of treatment, for a primary tumor or a post-excision tumor bed, will involve multiple doses. Typical primary tumor treatment involves a 6 dose application over a two-week period. The two-week regimen may be repeated one, two, three, four, five, six or more times. During a course of treatment, the need to complete the planned dosings may be re-evaluated.
The preparation of more, or highly, concentrated solutions for direct injection is also contemplated, where the use of DMSO as solvent is envisioned to result in extremely rapid penetration, delivering high concentrations of the active agents to a small area.
For parenteral administration in an aqueous solution, for example, the solution should be suitably buffered if necessary and the liquid diluent first rendered isotonic with sufficient saline or glucose. These particular aqueous solutions are especially suitable for intravenous, intramuscular, subcutaneous and intraperitoneal administration. In this connection, sterile aqueous media which can be employed will be known to those of skill in the art in light of the present disclosure. For example, one dosage could be dissolved in 1 ml of isotonic NaCl solution and either added to 1000 ml of hypodermoclysis fluid or injected at the proposed site of infusion, (see for example, "Remington's Pharmaceutical Sciences" 15th Edition, pages 1035-1038 and 1570-1580). Some variation in dosage will necessarily occur depending on the condition of the subject being treated. The person responsible for administration will, in any event, determine the appropriate dose for the individual subject.
VIII. COMBINATION CANCER THERAPY
To further enhance the efficacy of the therapy provided by the invention, combination therapies are contemplated. Thus, a second therapeutic agent in addition to a WTl antisense oligonucleotide therapy may be used. The second therapeutic agent may be a chemotherapeutic agent, a radiotherapeutic agent, a gene therapeutic agent, a proteiupeptide/polypeptide therapeutic agent, an immunotherapeutic agent, or a hormonal therapeutic agent. Such agents are well known in the art.
As set forth earlier an "effective amount" is defined as an amount of the WTl antisense composition that can decrease, reduce, inhibit or otherwise abrogate the growth of a cancer cell, arrest-cell growth, induce apoptosis, inhibit metastasis, induce tumor necrosis, kill cells or induce cytotoxicity in cells.
The administration of the second therapeutic agent may precede or follow the therapy using an antisense construct by intervals ranging from minutes to days to weeks. In embodiments where the second therapeutic agent and an antisense construct encoding nucleic acid or protein product are administered together, one would generally ensure that a significant period of time did not expire between the time of each delivery. In such instances, it is contemplated that one would administer to a patient both modalities within about 12-24 hours of each other and, more preferably, within about 6-12 hours of each other, with a delay time of only about 12 hours being most preferred. In some situations, it may be desirable to extend the time period for treatment significantly, however, where several days (2, 3, 4, 5, 6 or 7) to several weeks (1, 2, 3, 4, 5, 6, 7 or ~) lapse between the respective administrations.
It also is conceivable that more than one administration of either the second therapeutic agent and an antisense oligonucleotide will be required to achieve complete cancer cure. Various combinations may be employed, where the second therapeutic agent is "A" and the antisense oligonucleotide is "B", as exemplified below:
AB/A B/AB BB/A A/AB B/A/A ABB BBB/A BB/AB
A/ABB AB/AB ABBlA BB/A/A B/AB/A B/A/AB BBB/A
A/A/AB B/A/A/A AB/A/A A/AB/A ABBB B/ABB BB/AB
Other combinations also are contemplated. The exact dosages and regimens of each agent can be suitably altered by those of ordinary skill in the art.
Provided below is a description of some other agents effective in the treatment of cancer.
(i) Radiotherapeutic Agents In some tumor cell lines, levels of antisense oligonucleotide were found to correlate to the sensitivity of cells to ionizing radiation, indicating that antisense therapy restores and/or enhances sensitivity of tumor cells to genotoxic agents. Therefore, additional therapy with radiotherapeutic agents and factors including radiation and waves that induce DNA damage for example, y-irradiation, X-rays, UV-irradiation, microwaves, electronic emissions, radioisotopes, and the like are contemplated. Therapy may be achieved by irradiating the localized tumor site with the above described forms of radiations. It is most likely that all of these factors effect a broad range of damage DNA, on the precursors of DNA, the replication and repair of DNA, and the assembly and maintenance of chromosomes.
Dosage ranges for X-rays range from daily doses of 50 to 200 roentgens for prolonged periods of time (3 to 4 weeks), to single doses of 2000 to 6000 roentgens.
Dosage ranges for radioisotopes vary widely, and depend on the half life of the isotope, the strength and type of radiation emitted, and the uptake by the neoplastic cells.
(ii) Surgery Approximately 60% of persons with cancer will undergo surgery of some type, which includes preventative, diagnostic or staging, curative and palliative surgery.
Curative surgery is a cancer treatment that may be used in conjunction with other therapies, such as the treatment of the present invention, chemotherapy, radiotherapy, hormonal therapy, gene therapy, immunotherapy and/or alternative therapies.
Curative surgery includes resection in which all or part of cancerous tissue is physically removed, excised, and/or destroyed. Tumor resection refers to physical removal of at least part of a tumor. In addition to tumor resection, treatment by surgery includes laser surgery, cryosurgery, electrosurgery, and microscopically controlled surgery (Mohs' surgery). It is further contemplated that the present invention may be used in conjunction with removal of superficial cancers, precancers, or incidental amounts of normal tissue.
Upon excision of part of all of cancerous cells, tissue, or tumor, a cavity may be formed in the body. Treatment may be accomplished by perfusion, direct injection or local application of the area with an additional anti-cancer therapy. Such treatment may be repeated, for example, every 1, 2, 3, 4, 5, 6, or 7 days, or every 1, 2, 3, 4, and 5 weeks or every 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 1 l, or 12 months. These treatments may be of varying dosages as well.
(iii) Chemotherapeutic Agents Agents that damage DNA are chemotherapeutics. These can be, for example, agents that directly cross-link DNA, agents that intercalate into DNA, and agents that lead to chromosomal and mitotic aberrations by affecting nucleic acid synthesis. Agents that directly cross-link nucleic acids, specifically DNA, are envisaged and are exemplified by cisplatin, and other DNA
alkylating agents. Agents that damage DNA also include compounds that interfere with DNA
replication, mitosis, and chromosomal segregation.
Some examples of chemotherapeutic agents include antibiotic chemotherapeutics such as, Doxorubicin, Daunorubicin, Mitomycin (also known as mutamycin and/or mitomycin-C), Actinomycin D (Dactinomycin), Bleomycin, Plicomycin. Plant alkaloids such as Taxol, Vincristine, Vinblastine. Miscellaneous agents such as Cisplatin, VP16, Tumor Necrosis Factor.
Alkylating Agents such as, Carmustine, Melphalan (also known as alkeran, L-phenylalanine mustard, phenylalanine mustard, L-PAM, or L-sarcolysin, is a phenylalanine derivative of nitrogen mustard), Cyclophosphamide, Chlorambucil, Busulfan (also known as myleran), Lomustine. And other agents for example, Cisplatin (CDDP), Carboplatin, Procarbazine, Mechlorethamine, Camptothecin, Ifosfamide, Nitrosurea, Etoposide (VP16), Tamoxifen, Raloxifene, Estrogen Receptor Binding Agents, Gemcitabien, Navelbine, Farnesyl-protein transferase inhibitors, Transplatinum, 5-Fluorouracil, and Methotrexate, Temazolomide (an aqueous form of DTIC), or any analog or derivative variant of the foregoing.
(iv) Immunotherapy Imrnunotherapeutics may be used in conjunction with the therapy contemplated in the present invention. Immunotherapeutics, generally, rely on the use of immune effector cells and molecules to target and destroy cancer cells. The immune effector may be, for example, another antibody specific for some other marker on the surface of a tumor cell. This antibody in itself may serve as an effector of therapy or it may recruit other cells to actually effect cell killing.
This antibody also may be conjugated to a drug or toxin (chemotherapeutic, radionuclide, ricin A
chain, cholera toxin, pertussis toxin, etc.) and serve merely as a targeting agent. Alternatively, the effector may be a lymphocyte carrying a surface molecule that interacts, either directly or indirectly, with a tumor cell target.
In one aspect the immunotherapy can be used to target a tumor cell. Many tumor markers exist and any of these may be suitable for targeting in the context of the present invention. Cormnon tumor markers include carcinoembryonic antigen, prostate specific antigen, urinary tumor associated antigen, fetal antigen, tyrosinase (p97), gp68, TAG-72, HMFG, Sialyl Lewis Antigen, MucA, MucB, PLAP, estrogen receptor, laminin receptor, erb B
and p155.
Alternate immune stimulating molecules also exist including: cytokines such as IL-2, IL-4, IL-12, GM-CSF, gamma-IFN, chemokines such as MIP-1, MCP-1, IL-8 and growth factors such as FLT3ligand.
(a) Passive Immunotherapy A number of different approaches for passive immunotherapy of cancer exist.
They may be broadly categorized into the following: injection of antibodies alone;
injection of antibodies coupled to toxins or chemotherapeutic agents; injection of antibodies coupled to radioactive isotopes; injection of anti-idiotype antibodies; and finally, purging of tumor cells in bone marrow.

(b) Active Immunotherapy In active immunotherapy, an antigenic peptide, polypeptide or protein, or an autologous or allogenic tumor cell composition or "vaccine" is administered, generally with a distinct bacterial adjuvant (Ravindranath & Morton, 1991; Morton & Ravindranath, 1996;
Morton et al., 1992; Mitchell et al., 1990; Mitchell et al., 1993).
(c) Adoptive Immunotherapy In adoptive immunotherapy, the patient's circulating lymphocytes, or tumor infiltrated lymphocytes, are isolated in vitro, activated by lymphokines such as IL-2 or transduced with genes for tumor necrosis, and readministered (Rosenberg et al., 1988; 1989).
To achieve this, one would aclininister to an animal, or human patient, an immunologically effective amount of activated lymphocytes in combination with an adjuvant-incorporated antigenic peptide composition as described herein. The activated lymphocytes will most preferably be the patient's own cells that were earlier isolated from a blood or tumor sample and activated (or "expanded") in vitro.
(v) Gene Therapy The present invention contemplates the use of a variety of different therapeutic transgenes in combination with the antisense therapy of the present invention.
For example, genes encoding a tumor suppressor, an inhibitor of apoptosis, a cell cycle regulatory gene, a toxin, a cytokine, a ribosome inhibitory protein and interferons are contemplated as suitable genes that potentiate the inhibition of cancer cell growth according to the present invention.
(a) Tumor Suppressors The tumor suppressors function to inhibit excessive cellular proliferation.
The inactivation of these genes destroys their inhibitory activity, resulting in unregulated proliferation. It is contemplated that the antisense oligonucleotide may be attached to antibodies that recognize mutant tumor suppressors or wild-type tumor suppressors.
Alternatively, an antisense construct may be linked to all or part of the tumor suppressor.
Exemplary tumor suppressors are p53, p16 and C-CAM which are described below.
High levels of mutant p53 have been found in many cells transformed by chemical carcinogenesis, ultraviolet radiation, and several viruses. The p53 gene is a frequent target of mutational inactivation in a wide variety of human tumors and is already documented to be the most frequently mutated gene in common human cancers. It is mutated in over 50% of human NSCLC (Hollstein et al., 1991) and in a wide spectrum of other tumors. nne p~.~ gene encones a 393-amino acid phosphoprotein that can form complexes with host proteins such as large-T
antigen and E1B. The protein is found in normal tissues and cells, but at concentrations which are minute by comparison with transformed cells or tumor tissue.
Wild-type p53 is recognized as an important growth regulator in many cell types.
Missense mutations are common for the p53 gene and are essential for the transforming ability of the oncogene. A single genetic change prompted by point mutations can create carcinogenic p53. Unlike other oncogenes, however, p53 point mutations are known to occur in at least 30 distinct codons, often creating dominant alleles that produce shifts in cell phenotype without a reduction to homozygosity. Additionally, many of these dominant negative alleles appear to be tolerated in the organism and passed on in the germ line. Various mutant alleles appear to range from minimally dysfunctional to strongly penetrant, dominant negative alleles (Weinberg, 1991).
Another inhibitor of cellular proliferation is p16. The major transitions of the eukaryotic cell cycle are triggered by cyclin-dependent kinases, or CDK's. One CDK, cyclin-dependent kinase 4 (CDK4), regulates progression through the Gl. The activity of this enzyme may be to phosphorylate Rb at late Gl. The activity of CDK4 is controlled by an activating subunit, D-type cyclin, and by an inhibitory subunit, the p 16x4 has been biochemically characterized as a protein that specifically binds to and inhibits CDK4, and thus may regulate Rb phosphorylation (Serrano et al., 1993; Serrano et al., 1995). Since the p16~~4 protein is a CDK4 inhibitor (Serrano, 1993), deletion of this gene may increase the activity of CDK4, resulting in hyperphosphorylation of the Rb protein. p 16 also is known to regulate the function of CDK6.
p16~~4 belongs to a newly described class of CDK-inhibitory proteins that also includes pl6B, p19, p21~''~1, and p27KiPy The p16~~4 gene maps to 9p21, a chromosome region frequently deleted in many tumor types. Homozygous deletions and mutations of the p16~~4 gene are frequent in human tumor cell lines. This evidence suggests that the p16~~4 gene is a tumor suppressor gene. This interpretation has been challenged, however, by the observation that the frequency of the p16~K4 gene alterations is much lower in primary uncultured tumors than in cultured cell lines (Caldas et al., 1994; Cheng et al., 1994;
Hussussian et al., 1994; Kamb et al., 1994; Okamoto et al., 1994; Nobori et al., 1995; Orlow et al., 1994).
Restoration of wild-type p16~K4 function by transfection with a plasmid expression vector reduced colony formation by some human cancer cell lines (Okamoto, 1994).
Other genes that may be employed according to the present invention include Rb, APC, mda-7, DCC, NF-l, NF-2, WT-1, MEN-I, MEN-II, zacl, p73, VHL, MMACIIPTEN, DBCCR-1, FCC, rsk-3, p27, p27/p16 fusions, p21/p27 fusions, anti-thrombotic genes (e.g., COX-1, '1'r'Yl), YCi~, lip, YZr', f°as, myc, neu, raf; ef°b, fins, t~lz, ret, gsp, hst, abl, ElA, p300, genes involved in angiogenesis (e.g., VEGF, FGF, thrombospondin, BAI-1, GDAIF, or their receptors) and MCC.
(b) Regulators of Programmed Cell Death Apoptosis, or programmed cell death, is an essential process for normal embryonic development, maintaining homeostasis in adult tissues, and suppressing carcinogenesis (Kerr et al., 1972). The Bcl-2 family of proteins and ICE-like proteases have been demonstrated to be important regulators and effectors of apoptosis in other systems. The Bcl-2 protein, discovered in association with follicular lynphoma, plays a prominent role in controlling apoptosis and enhancing cell survival in response to diverse apoptotic stimuli (Bakhshi et al., 1985; Cleary and Sklar, 1985; Cleary et al., 1986; Tsujimoto ~et al., 1985; Tsujimoto and Croce, 1986). The evolutionarily conserved Bcl-2 protein now is recognized to be a member of a family of related proteins, which can be categorized as death agonists or death antagonists.
Apo2 ligand (Apo2L, also called TRAIL) is a member of the tumor necrosis factor (TNF) cytokine family. TRAIL activates rapid apoptosis in many types of cancer cells, yet is not toxic to normal cells. TRAIL mRNA occurs in a wide variety of tissues. Most normal cells appear to be resistant to TRAIL's cytotoxic action, suggesting the existence of mechanisms that can protect against apoptosis induction by TRAIL. The first receptor described for TRAIL, called death receptor 4 (DR4), contains a cytoplasmic "death domain"; DR4 transmits the apoptosis .
signal carried by TRAIL. Additional receptors have been identified that bind to TRAIL. One receptor, called DRS, contains a cytoplasmic death domain and signals apoptosis much like DR4.
The DR4 and DRS mRNAs are expressed in many normal tissues and tumor cell lines. Recently, decoy receptors such as DcRl and DcR2 have been identified that prevent TRAIL
from inducing apoptosis through DR4 and DRS. These decoy receptors thus represent a novel mechanism for regulating sensitivity to a pro-apoptotic cytokine directly at the cell's surface. The preferential expression of these inhibitory receptors in normal tissues suggests that TRAIL
may be useful as an anticancer agent that induces apoptosis in cancer cells while sparing normal cells (Marsters et al., 1999).
Subsequent to its discovery, it was shown that Bcl-2 acts to suppress cell death triggered by a variety of stimuli. Also, it now is apparent that there is a family of Bcl-2 cell death regulatory proteins which share in common structural and sequence homologies.
These different family members have been shown to either possess similar functions to Bcl-2 (e.g., BclxL, BcIW, Bcls, Mcl-l, A1, Bfl-1) or counteract Bcl-2 function and promote cell death (e.g., Bax, Bak, Bik, Bim, Bid, Bad, Harakiri). It is contemplated that any of these polypeptides, including TRAIL, or any other polypeptides that induce or promote of apoptosis, may be operatively linked to an antisense construct, or that an antibody recognizing any of these polypeptides may also be attached to an antisense construct.
It will be appreciated by those of skill in the art that monoclonal or polyclonal antibodies specific for proteins that are preferentially expressed in metastatic or nonmetastatic cancer will have utilities in several types of applications. These may include the production of diagnostic kits for use in detecting or diagnosing human cancer. An alternative use would be to link such antibodies to therapeutic agents, such as chemotherapeutic agents, followed by administration to individuals with cancer, thereby selectively targeting the cancer cells for destruction. The skilled practitioner will realize that such uses are within the scope of the present invention.
(c) Interferons Other classes of genes that are contemplated to be inserted into the vectors of the present invention include interferons, interleukins and cytokines. Inteferon-a, interferon-[3, interferon-y, interleukin 1 (IL-1), IL-2, IL-3, IL-4, IL-5, IL-6, IL,-7, IL-8, IL-9, IL-10,1L-11, IL-12, IL-13, IL-14, IL-15, angiostatin, thrombospondin, endostatin, METH-1, METH-2, Flk2/Flt3 ligand, GM-CSF, G-CSF, M-CSF, and tumor necrosis factor (TNF).
(d) Cell Cycle Regulatory Genes In another embodiment, the present invention utilizes an isolated nucleic acid segment comprising a cell cycle regulatory gene operatively linked to an antisense oligonucleotide of the present invention; transferring the nucleic acid segment into a cancer cell to obtain a transfected cell; and maintaining the cancer cell under conditions effective to express the cell cycle regulatory gene; wherein expression of the cell cycle regulatory gene inhibits proliferation of the cancer cell. In the practice of the method, the cell cycle regulatory gene operatively linked to an antisense oligonucleotide may comprise a liposomal or a non-liposomal vector.
In the present invention, it comprises a liposomal vector. Further, the cell cycle regulatory gene may preferably encode Rb, p53, cell cycle dependent kinase, CDK kinase, cyclin or a constitutively active Rb gene product, or an antisense RNA.
(e) Toxin Encoding Genes hi another embodiment, the present invention may be described as a method of inlubiting tumor cell growth comprising the steps of obtaining an isolated nucleic acid segment comprising a toxin encoding gene. The genes may encode TNFoc, gelonin, ricin A Chain, Pseudomonas exotoxin, diphtheria toxin, mitogillin, saporin, ribosome inhibitory protein.
(f) Oncogenes Oncogenes are considered to be genes that, when mutated or activated, sponsor the development of cancer. Therapeutic intervention involves the inhibition of these gene products.
For example, one may provide antisense or ribozymes which inhibit the transcription, processing or translation of an oncogene. Alternatively, single chain antibodies that encode products bind to and inhibit the oncogene can be utilized. Table 3 provides a list of suitable oncogene targets.
Table 3 Geue Source Hunzau Disease Functioh Growth Factors HSTlKS Transfection FGF family member INT 2 MMTV promoter FGF family member Insertion 11VTIlWNTI MMTV promoter Factor-like Insertion SIS Simian sarcoma PDGF B
virus Receptor Tyrosine Kinases ERBBlHER Avian Amplified, deletedEGF/TGF-a/

erythroblastosis squamous cell Amphiregulin/

virus; ALV cancer; Hetacellulin promoter glioblastoma receptor insertion;

amplified human tumors ERBB-2/NEIIlHER- Transfected Amplified breast,Regulated by from rat NDF/

2 Glioblastomas ovarian, gastricHeregulin and cancers EGF-Related factors FMS SM feline sarcoma CSF-1 receptor virus KIT HZ feline sarcoma MGF/Steel receptor virus Hematopoieis TRK Transfection from NGF (nerve growth Gefze Source Husuau Disease Fuuctiotz human colon Factor) receptor cancer MET Transfection Scatter factor/HGF
from human Receptor osteosarcoma RET Translocations Sporadic thyroidOrphan receptor and Tyr point mutations cancer; Kinase familial medullary thyroid cancer;

multiple endocrine neoplasias 2A
and ROS ITRII avian sarcoma Orphan receptor Tyr Virus I~inase PDGF receptor Translocation Chronic TEL(ETS-like Myelomonocytic transcription Leukemia factor)!

PDGF receptor gene Fusion TGF ,l3 receptor Colon carcinoma mismatch mutation target NONRECEPTOR TYROSINE
KINASES
ABI. Abelson MuI.V Chronic Interact with RB, myelogenous RNA

leukemia polymerase, CRK, translocation CBL

with BCR

FPSlFES Avian Fujinami SV;GA

FeSV

LCK MuI.V (marine Src family; T-cell leukemia signaling; interacts virus) promoter CD4/CD8 T-cells insertion SRC Avian Rous Membrane-sarcoma associated Tyr Virus kinase with signaling function;

activated by receptor kinases Gene Source Hufrza~a Disease Fuuctiou YES Avian Y73 virus Src family;
signaling SER/THR PROTEIN KINASES
AKT AKT8 murine Regulated by retrovirus PI(3 )K?;

regulate 70-kd k?

MOS Moloney murine GVBD; cystostatic SV

factor; MAP

kinase kinase PIM 1 Promoter insertion Mouse RAFlMIL 3611 murine SV; Signaling in RAS

MH2 Pathway avian SV

MISCELLANEOUS
CELL SURFACE

APC Tumor suppresser Colon cancer Interacts with catenins DCC Tumor suppresser Colon cancer CAM domains E-cadherin Candidate tumor Breast cancer Extracellular Suppresser homotypic binding;

intracellular interacts with catenins PTClNBCCS Tumor suppresser Nevoid basal 12 transmembrane cell and cancer domain; signals Dsosophilia syndrome (Gorlinethrough Gli homology syndrome) homogue CI to antagonize hedgehog pathway TAN 1 Notch Translocation T-ALI. Signaling?

homologue MISCELLANEOUS
SIGNALING

BCL-2 Translocation B-cell lymphoma Apoptosis CBL Mu Cas NS-1 V Tyrosine-Phosphorylated RING

finger interact Abl CRK CT1010 ASV Adapted SH2/SH3 interact Abl DPC4 Tumor suppresser Pancreatic cancerTGF-(3-related signaling Pathway MAS Transfection and Possible angiotensin Getze Source Hu>zzau Disease Fuuctiou Tumorigenicity Receptor NGK Adaptor SH2/SH3 GUANINE NUCLEOTIDE EXCHANGERS AND BINDING
PROTEINS
BCR Translocated Exchanger;
with protein ABL Kinase in CML

DBL Transfection Exchanger GSP

NF 1 Hereditary tumorTumor suppressorRAS GAP

Suppressor neurofibromatosis OST Transfection Exchanger Harvey-I~irsten,HaRat SV; Ki Point mutations Signal cascade N- in RAS RaSV; many Balb-MoMuSV; human tumors Transfection T~AV Transfection S 112/S 113;

exchanger NUCLEAR PROTEINS AND TRANSCRIPTION FACTORS
BRCAI Heritable suppressorMammary Localization cancer/ovarian unsettled cancer BRCA2 Heritable suppressorMammary cancer Function unknown ERBA Avian thyroid hormone erythroblastosis receptor Virus (transcription) ETS Avian E26 virus DNA binding EVII MuLV promotor AML Transcription factor Insertion FOS FBI/FBR marine 1 transcription osteosarcoma factor viruses with c-JUN

GLI Amplified glioma Glioma Zinc finger;
cubitus interruptus homologue is in hedgehog signaling pathway;

inhibitory link PTC .

and hedgehog HMGI lLIM Translocation Lipoma Gene fusions high t(3:12) mobility group t(12:15) HMGI-C (XT-hook) and transcription factor LIM or acidic Geue Sout~ce Huszzazz DiseaseFuuctiotz domain .IUN ASV-17 Transcription factor AP-1 with FOS

MLLlVHRX + Translocation/fusionAcute myeloid Gene fusion of ELIlMEN ELL with MLL leukemia DNA-Trithorax-like binding and methyl gene transferase MLL

with ELI RNA pol II

elongation factor MYB Avian DNA binding myeloblastosis Virus MYC Avian MC29; Burkitt's lymphomaDNA binding with Translocation MAX partner;
B-cell cyclin Lymphomas; regulation; interact promoter RB?; regulate Insertion avian apoptosis?

leukosis Virus N MYC Amplified Neuroblastoma L-MYC Lung cancer REL Avian NF-~B family transcription factor Retriculoendothelio sis Virus SKI Avian SKV770 Transcription factor Retrovirus T~HL Heritable suppressorVon Hippel-LandauNegative regulator syndrome or elongin;

transcriptional elongation complex WT 1 Wilms' tumor Transcription factor CELL CYCLE/DNA DAMAGE
RESPONSE
ATM Hereditary disorder Ataxia- Protein/lipid kinase telangiectasia homology; DNA

damage response upstream in pathway BCL-2 Translocation Follicular Apoptosis lymphoma FACC Point mutation Fanconi's anemia group Geue Source Husuau Disease Fuuctiou C (predisposition leukemia MDA-7 Fragile site Lung carcinoma Histidine triad-3p14.2 related diadenosine 5 3~~~~-tetraphosphate asymmetric hydrolase 7~.MLIIMutL HNPCC Mismatch repair;

Mutt Homologue hMSH2/MutS HNPCC Mismatch repair;

MutS

Homologue hPMSl HNPCC Mismatch repair;

Mutt Homologue hPMS~ HNPCC Mismatch repair;

Mutt Homologue INK4/1~ITSl Adj acent INK-4BCandidate MTS p 16 CDK inhibitor at 1 9p21; CDI~ suppressor and complexes MLM

melanoma gene INK4BlMTS2 Candidate p15 CDK inhibitor suppressor MDM 2 Amplified Sarcoma Negative regulator p53 p53 Association Mutated >50% Transcription with factor;

SV40 human checkpoint control;

T antigen tumors, includingapoptosis hereditary Li-Fraumeni syndrome PRAD~IBCLl Translocation Parathyroid Cyclin D
with Parathyroid adenoma;

hormone B-CLL

or IgG

RB Hereditary Retinoblastoma; Interact cyclin/cdk;

Retinoblastoma;osteosarcoma; regulate E2F

Association breast transcription with factor many cancer; other DNA virus tumorsporadic Antigens cancers XPA xeroderma Excision repair;

pigmentosum; photo-skin cancer product predisposition recognition;

Geue Source Hurrzau Disease Function zinc finger (g) Other Agents It is contemplated that other agents may be used in combination with the present invention to improve the therapeutic efficacy of treatment. One form of therapy for use in conjunction with chemotherapy includes hyperthermia, which is a procedure in which a patient's tissue is exposed to high temperatures (up to 106°F). External or internal heating devices may be involved in the application of local, regional, or whole-body hyperthermia.
Local hyperthermia involves the application of heat to a small area, such as a tumor. Heat may be generated externally with high-frequency waves targeting a tumor from a device outside the body. Internal heat may involve a sterile probe, including thin, heated wires or hollow tubes filled with warm water, implanted microwave antennae, or radio frequency electrodes.
A patient's organ or a limb is heated for regional therapy, which is accomplished using devices that produce high energy, such as magnets. Alternatively, some of the patient's blood may be removed and heated before being perfused into an area that will be internally heated.
Whole-body heating may also be implemented in cases where cancer has spread throughout the body. Warm-water blankets, hot wax, inductive coils, and thermal chambers may be used for this purpose.
Hormonal therapy may also be used in conjunction with the present invention.
The use of hormones may be employed in the treatment of certain cancers such as breast, prostate, ovarian, or cervical cancer to lower the level or block the effects of certain hormones such as testosterone or estrogen and this often reduces the risk of metastases.
The terms "contacted" and "exposed," when applied to a cell, are used herein to describe the process by which a therapeutic construct or protein and a chemotherapeutic or radiotherapeutic agent are delivered to a target cell or are placed in direct juxtaposition with the target cell. To achieve cell killing or stasis, both agents are delivered to a cell in a combined amount effective to kill the cell or prevent it from dividing.
IX. PROGNOSTIC APPLICATIONS
As described earlier, the WT1 mRNA can be spliced in two different ways leading to the expression of at least four predominant isoforms (Haber et al., 1991). One splicing inserts or removes 17 amino acids in exon 5; the other splicing inserts or removes the 3-amino-acid Lys-Thr-Ser (KTS) in exon 9, located between zinc fingers 3 and 4 (Lee et al., 2001; Wang et al., lyy5). Ail of the resulting bV'1'1 isotorms can positively or negatively regulate gene expression (Klamt et al., 1998). Throughout the application, reference to WT1 will encompass its various isoforms.
The WTl splicing isofonns have different biological activities (Lee et al., 2001). Of the two major splicing products encoded by WT1, the -KTS isoforms have transactivational properties in some genes that are involved in cell growth and differentiation, whereas the +KTS
isoforms have a potential role in RNA processing (Lee et al., 2001). Exon 5 may function as a repressor domain or as an activator domain, depending on which proteins are interacting with WT1 (Richard et al., 2001).
WT1 mRNA is readily detected by Northern (RNA) blot in most Wilms tumor, as well as normal fetal kidney tissue (Haber et al., 1990). With the more sensitive RNA
PCR technique, alternatively spliced WT1 transcripts can be easily demonstrated in all tissues. However, PCR
analysis can only provide an approximate ratio of the various RNA species and due to the positions and sizes of two alternative splices, it cannot be used to distinguish various splicing combinations.
To determine the existence and relative abundance of various forms of the WT1 transcript, an RNase protection assay has been developed which is capable of differentiating each form based on a protected fragment of distinctive length (Haber et al., 1991). The functional role of each WT1 isoform in breast cancer cells such as cell proliferation, sensitivity to estrogens and anti-estrogens, sensitivity to apoptotic and chemotherapeutic stimuli may enable one to determine whether a patient's breast tumor has high expression of a certain WT1 isoform, and may potentially be able to predict what kind of therapy the breast tumor will respond to.
Techniques such as RT-PCR or RNase protection assay may be used to determine the level of expression of a certain WT1 isoform.
The present invention further contemplates that the evaluation of the expression level of one or more isoforms of WT1 gene product in a cancer cell will be useful to effectively predict the efficacy of a cancer therapeutic regimen, to determine whether the patient's cancer will be responsive to a particular cancer therapeutic regimen by analyzing the cancer tissues or cancer cells of a patient and to monitor the progression of breast cancer in a patient. The method of the present invention will involve obtaining a sample from said subject comprising breast cancer cells and assessing expression of one or more isoforms of Wilms' Tumor 1 (WT1) gene product in said cells.
The present invention's prognostic method therefore allows the determination of the need for specific cancer therapeutic regimens based on the expression of WTl in an individual patient.

The expression levels of W'1~1 protein will also be useful in monitoring the effectiveness of a treatment regimen, such as that of the present invention, alone or in conjunction with other cancer therapies as described above. Again, in such a situation the level of expression of WT1 protein will be used to effectively determine and adjust the dosage of a radiation amd/or chemotherapeutic combination regimen. In any event, the methods of the present invention will assist physicians in determining optimal treatment courses and doses for individuals with different tumors of varying malignancy based on the levels of expression of WTl proteins in such tumors.
As described herein, the amount of a WT1 polypeptide/protein and/or mRNA
present within a biological sample or specimen, such as a tissue, a cell(s), blood or serum or plasma sample, any other biological fluid, a biopsy, needle biopsy cores, surgical resection samples, lymph node tissue, or any other clinical sample may be determined by means of a molecular biological assay to determine the level of a nucleic acid that encodes such a polypeptide, or by means of a polypeptide/protein detection assay such as a western blot, northern blot (to quantitate RNA), RNA-PCR or even by means of an immunoassay may be detected and measured or quantified. Such detection and measuring/quantification methods may be used to measure WT1 protein levels or WT1 mRNA levels and such methods are known to one of skill in the art.
In certain embodiments, nucleic acids or polypeptides would be extracted from these samples. Some embodiments would utilize kits containing pre-selected primer pairs or hybridization probes, such as an antisense construct of the present invention.
Antibodies may also be used for this purpose. The amplified nucleic acids or polypeptide would be tested for the presence of a WT1 polypeptide/protein and/or mRNA by any of the detection methods described later in the description or other suitable methods known in the art.
In other embodiments, sample/specimen extracts containing a WT1 polypeptide/protein and/or mRNA would be extracted from a sample and subjected to an immunoassay.
Immunoassays of tissue sections are also possible. Immunoassays that are contemplated useful are well known to one of skill in the art. Kits containing the antibodies to WTl polypeptides would be useful.
In terms of analyzing tissue samples, irrespective of the manner in which the level of a WTl polypeptide/protein and/or mRNA is determined, the prognostic evaluation may generally require the amount of the WT1 product in the tissue sample to be compared to the amount in normal cells, in other patients and/or amounts at an earlier stage of treatment of the same patient.
Comparing the varying levels will allow the characteristics of the particular cancer to be more precisely defined and therefore allow for prescribing a tailor made cancer treatment regimen to a patient.
Thus, it is contemplated that the levels of a WT1 polypeptide/protein and/or mRNA
detected would be compared with statistically valid groups of metastatic, non-metastatic malignant, benign or normal tissue samples; and/or with earlier WT1 levels in the same patient.
The diagnosis and prognosis of the individual patient would be determined by comparison with such groups.
If desired, the cancer prognostic methods of the present invention may be readily combined with other methods in order to provide an even more reliable indication of prognosis.
Various markers of cancer have been proposed to be correlated with metastasis and malignancy.
They are generally classified as cytological, protein or nucleic acid markers.
Any one or more of such methods may thus be combined with those of this invention in order to provide a multi-marker prognostic test. Some examples of tumor markers specific to breast include p27, cyclin E, carcinoembryonic antigen (CEA), mucin associated antigen, tumor polypeptide antigen and breast cancer specific antigen.
Combination. of the present techniques with one or more other diagnostic or prognostic techniques or markers is certainly contemplated. In that many cancers are multifactorial, the use of more than one method or marker is often highly desirable.
A. Prognostic Kits The materials and reagents required for detecting the levels of expression of a WT1 polypeptide/protein and/or mRNA in a cancer cell in a biological sample may be assembled together in a kit.
One set of kits are designed to detect the levels of expression of a WT1 nucleic acid.
Such kits of the invention will generally comprise one or more preselected primers or probes specific for WTl. The antisense constructs of the present invention may be used as hybridization probes or primers. Preferably, the kits will comprise, in suitable container means, one or more nucleic acid probes or primers and means for detecting nucleic acids. In certain embodiments, such as in kits for use in Northern blotting, the means for detecting the nucleic acids may be a label, such as a radiolabel, that is linked to a nucleic acid probe itself.
Preferred kits are those suitable for use in PCRTM which is described later in the specification. In PCRTM kits, two primers will preferably be provided that have sequences from, and that hybridize to, spatially distinct regions of the WTl gene. Preferred pairs of primers for amplifying nucleic acids are selected to amplify the sequences specified herein. Also included in rc:KlM kits may be enzymes suitable for amplifying nucleic acids, including various polymerases (RT, Taq, etc.), deoxynucleotides and buffers to provide the necessary reaction mixture for amplification.
In each case, the kits will preferably comprise distinct containers for each individual reagent and enzyme, as well as for each cancer probe or primer pair. Each biological agent will generally be suitable aliquoted in their respective containers.
The container means of the kits will generally include at least one vial or test tube.
Flasks, bottles and other container means into which the reagents are placed and aliquoted are also possible. The individual containers of the kit will preferably be maintained in close confinement for commercial sale. Suitable larger containers may include injection or blow-molded plastic containers into which the desired vials are retained.
Instructions may be provided with the kit.
In further embodiments, the invention provides immunological kits for use in detecting the levels of expression of WT1 in biological samples, e.g., in cancer cells.
Such kits will generally comprise one or more antibodies that have immunospecificity for WT1 proteins or peptides.
As the anti-WT1 antibodies may be employed to detect WT1 proteins or peptides and' their levels, both of such components may be provided in the kit. The immunodetection kits will thus comprise, in suitable container means, a WT1 protein or peptide, or a first antibody that binds to such a protein or peptide, and an immunodetection reagent.
In other embodiments, it is contemplated that the antibodies will be those that bind to the WT1 antigenic epitopes. MAbs are readily prepared and will often be preferred.
Where proteins or peptides are provided, it is generally preferred that they be highly purified.
In certain embodiments, the WT1 protein or peptide, or the first antibody that binds to the WT1 protein or peptide may be bound to a solid support, such as a column matrix or well of a microtitre plate.
The immunodetection reagents of the kit may take any one of a variety of forms, including those detectable labels that are associated with, or linked to, the given antibody or antigen itself. Detectable labels that are associated with or attached to a secondary binding ligand are also contemplated. Exemplary secondary ligands are those secondary antibodies that have binding affinity for the first antibody or antigen.
Further suitable immunodetection reagents for use in the present kits include the two-component reagent that comprises a secondary antibody that has binding affinity for the first antibody or antigen (generally anti-WT1) along with a third antibody that has binding affinity for the second antibody, wherein the third antibody is linked to a detectable label.
As noted above in the discussion of antibody conjugates, a number of exemplary labels are known in the art and all such labels may be employed in connection with the present invention. Radiolabels, nuclear magnetic spin-resonance isotopes, fluorescent labels and enzyme tags capable of generating a colored product upon contact with an appropriate substrate are suitable examples.
The kits may contain antibody-label conjugates either in fully conjugated form, in the form of intermediates, or as separate moieties to be conjugated by the user of the kit.
The kits may further comprise a suitably aliquoted composition of a WTlantigen whether labeled or unlabeled, as may be used to prepare a standard curve for a detection assay.
The kits of the invention, regardless of type, will generally comprise one or more containers into which the biological agents are placed and, preferably, suitable aliquoted. The components of the kits may be packaged either in aqueous media or in lyophilized form.
The immunodetection kits of the invention, may additionally contain one or more of a variety of other cancer marker antibodies or antigens, if so desired. Such kits could thus provide a panel of cancer markers, as may be better used in testing a variety of patients. By way of example, such additional markers could include, other tumor markers such as breast cancer antigen CA15-3, p53, BR 27.29, HER-2/neu, BRCA-1, and BRCA-2. The container means of the kits will generally include at least one vial, test tube, flask, bottle, or even syringe or other container means, into which the antibody or antigen may be placed, and preferably, suitably aliquoted. Where a second or third binding ligand or additional component is provided, the kit will also generally contain a second, third or other additional container into which this ligand or component may be placed.
The kits of the present invention will also typically include a means for containing the antisense composition, and any other reagent containers in close confinement for commercial sale. Such containers may include injection or blow-molded plastic containers into which the desired vials are retained.
X. SCREENING ASSAYS
The present invention contemplates the screening of compounds for abilities to affect expression or function of isoforms of WT1. Particularly preferred compounds will be those useful in inhibiting the expression of WT1, thus inhibiting the growth of breast cancer cells. In the screening assays of the present invention, the candidate substance may first be screened for basic activity -e.g., binding to a target molecule - and then tested for its ability to inhibit expression, at the cellular, tissue or whole animal level.
The present invention provides methods of screening for candidate substances that show activity against breast cancer. In one embodiment, the present invention is directed to a method of:
(i) providing a cell that expresses one or more isoforms of the Wilms' Tumor 1 (WT1) gene product;
(ii) contacting the cell with the candidate substance suspected of inhibiting WT1; and (iii) measuring the effect of the candidate substance on the cell.
The candidate substance may be a protein, a nucleic acid or a small molecule pharmaceutical. As a result of measurement, a decrease in the amount of one or more WTl isoform gene products or gene transcripts in said cell, as compared to a cell not treated with said candidate substance, indicates that said candidate substance has activity against breast cancer.
In still yet other embodiments, one would look at the effect of a candidate substance on the expression of WTl. This can be done by examining mRNA expression, although the clinical results could be insufficient. A more direct way of assessing expression is by directly examining protein levels, for example, through Western blot or ELISA. An inhibitor according to the present invention may be one which exerts an inhibitory effect on the expression or function of WTl.
As used herein, the term "candidate substance" refers to any molecule that may inhibit growth of cancer cells. The candidate substance may be a protein or fragment thereof, a small molecule inhibitor, or even a nucleic acid molecule. It may prove to be the case that the most useful pharmacological compounds will be compounds that are structurally related to compounds which interact naturally with WTl. Creating and examining the action of such molecules is known as "rational drug design," and include making predictions relating to the structure of target molecules.
The goal of rational drug design is to produce structural analogs of biologically active polypeptides or target compounds. By creating such analogs, it is possible to fashion drugs which are more active or stable than the natural molecules, which have different susceptibility to alteration or which may affect the function of various' other molecules. In one approach, one would generate a three-dimensional structure for a molecule like a WT1, and then design a molecule for its ability to interact with WT1. Alternatively, one could design a partially functional fragment of a WT1 (binding but no activity), thereby creating a competitive inhibitor.
This could be accomplished by x-ray crystallography, computer modeling or by a combination of both approaches.
It also is possible to use antibodies to ascertain the structure of a target compound or inhibitor. In principle, this approach yields a pharmacore upon which subsequent drug design can be based. It is possible to bypass protein crystallography altogether by generating anti idiotypic antibodies to a functional, pharmacologically active antibody. As a mirror image of a mirror image, the binding site of anti-idiotype would be expected to be an analog of the original antigen. The anti-idiotype could then be used to identify and isolate peptides from banks of chemically- or biologically-produced peptides. Selected peptides would then serve as the pharmacore. Anti-idiotypes may be generated using the methods described herein for producing antibodies, using an antibody as the antigen.
On the other hand, one may simply acquire, from various commercial sources, small molecule libraries that are believed to meet the basic criteria for useful drugs in an effort to "brute force" the identification of useful compounds. Screening of such libraries, including combinatorially generated libraries (e.g., peptide libraries), is a rapid and efficient way to screen large number of related (and unrelated) compounds for activity. Combinatorial approaches also lend themselves to rapid evolution of potential drugs by the creation of second, third and fourth generation compounds modeled of active, but otherwise undesirable compounds.
Candidate compounds may include fragments or parts of naturally-occurring compounds or may be found as active combinations of known compounds which are otherwise inactive. It is proposed that compounds isolated from natural sources, such as animals, bacteria, fungi, plant sources, including leaves and bark, and marine samples may be assayed as candidates for the presence of potentially useful pharmaceutical agents. It will be understood that the pharmaceutical agents to be screened could also be derived or synthesized from chemical compositions or man-made compounds. Thus, it is understood that the candidate substance identified by the present invention may be polypeptide, polynucleotide, small molecule inhibitors or any other compounds that may be designed through rational drug design starting from known inhibitors of hypertrophic response.
The candidate substance suspected of inhibiting WT1 expression may be an antisense molecule. In an assay that comprises the screening of such molecules, the cell that expresses one or more isoforms of Wilins' Tumor gene product is contacted with the antisense molecule suspected of inhibiting WT1 expressing cells. The ability of the antisense construct to inhibit the expression of WT1 may be assayed by methods such as measuring the levels of expression of the WT1 gene or measuring the levels of the WT1 gene product in the cell. Other suitable inhibitors include ribozymes, and antibodies (including single chain antibodies).
It will, of course, be understood that all the screening methods of the present invention are useful in themselves notwithstanding the fact that effective candidates may not be found. The invention provides methods for screening for such candidates, not solely methods of finding them.
A. Ifz vitf~o Assays A quick, inexpensive and easy assay to run is a binding assay. Binding of a molecule to a target may, in and of itself, be inhibitory, due to steric, allosteric or charge-charge interactions.
This can be performed in solution or on a solid phase and can be utilized as a first round screen to rapidly eliminate certain compounds before moving into more sophisticated screening assays.
The target may be either free in solution, fixed to a support, expressed in or on the surface of a cell. Either the target or the compound may be labeled, thereby permitting determining of binding. In another embodiment, the assay may measure the inhibition of binding of a target to a natural or artificial substrate or binding partner (such as a WT1).
Competitive binding assays can be performed in which one of the agents (WTl for example) is labeled. Usually, the target will be the labeled species, decreasing the chance that the labeling will interfere with the binding moiety's function. One may measure the amount of free label versus bound label to determine binding or inhibition of binding.
A technique for high throughput screening of compounds is described in WO
84/03564.
Large numbers of small peptide test compounds are synthesized on a solid substrate, such as plastic pins or some other surface. The peptide test compounds are reacted with, for example, a WT1 and washed. Bound polypeptide is detected by various methods.
Purified target, such as a WTl, can be coated directly onto plates for use in the aforementioned drug screening techniques. However, non-neutralizing antibodies to the polypeptide can be used to immobilize the polypeptide to a solid phase. Also, fusion proteins containing a reactive region (preferably a terminal region) may be used to link an active region (e.g., the C-terminus of a WT1) to a solid phase.
B. Isz cyto Assays Various cell lines that express isoforms of WT1 can be utilized for screening of candidate substances. For example, cells containing a WT1 with an engineered indicator can be used to study vanous functional attributes of candidate compounds. In such assays, the compound would be formulated appropriately, given its biochemical nature, and contacted with a target cell.
Molecular analysis may be performed in which the fraction of a WT1 and related genes may be explored. This involves assays such as those for protein expression, enzyme function, substrate utilization, mRNA expression (including differential display of whole cell or polyA
RNA) and others.
XI. QUANTITATING LEVELS OF EXPRESSION OF WT1 The levels of expression of WT1 polypeptide/protein and/or mRNA is a function of the proliferation of breast cancer cells and is thus useful for various purposes such as a prognostic method for determining the breast cancer progression, as a screening method to know whether a candidate substance is able to inhibit cancer by inhibiting the WT1 gene or gene product and also in determining the type of treatment/combination treatment that may be used on a patient depending on the efficacy of the treatment. It may also be used to determine the progress of a patient when treated with an antisense oligonucleotide therapy or to determine what type or dose of the therapeutic regimen are suitable. Therefore, some embodiments of the invention concern.
measuring and/or quantitation and/or estimation of levels of WTl expression.
A. Quantitative PCR
For quantitation of a nucleic acid, reverse transcription (RT) of RNA to cDNA
followed by relative quantitative or semi-quantitative PCRTM (RT-PCRTM) can be used to determine the relative concentrations of specific mRNA species in a series of total cell RNAs isolated from the cancer cells.
By determining that the concentration of a specific mRNA species varies, it is shown that the gene encoding the specific mRNA species is expressed at different levels in different types of cancers.
In PCRTM, the number of molecules of the amplified target DNA increase by a factor approaching two with every cycle of the reaction until some reagent becomes limiting.
Thereafter, the rate of amplification becomes increasingly diminished until there is not an increase in the amplified target between cycles. If one plots a graph on which the cycle number is on the X axis and the log of the concentration of the amplified target DNA
is on the Y axis, one observes that a curved line of characteristic shape is formed by connecting the plotted points.
Beginning with the first cycle, the slope of the line is positive and constant. This is said to be the linear portion of the curve. After some reagent becomes limiting, the slope of the line begins to decrease and eventually becomes zero. At this point the concentration of the amplified target DNA becomes asymptotic to some fixed value. This is said to be the plateau portion of the curve.
The concentration of the target DNA in the linear portion of the PCRTM is directly proportional to the starting concentration of the target before the PCRTM was begun. By determining the concentration of the PCRTM products of the target DNA in PCRTM
reactions that have completed the sane number of cycles and are in their linear ranges, it is possible to determine the relative concentrations of the specific target sequence in the original DNA
mixture.
If the DNA mixtures are cDNAs synthesized from RNAs isolated from different cells, the relative abundances of the specific mRNA from which the target sequence was derived can be determined for the respective tissues or cells. This direct proportionality between the concentration of the PCRTM products and the relative mRNA abundances is only true in the linear range portion of the PCRTM reaction.
The final concentration of the target DNA in the plateau portion of the curve is determined by the availability of reagents in the reaction mix and is independent the original concentration of target DNA. Therefore, the first condition that must be met before the relative abundances of a mRNA species can be determined by RT-PCRTM for a collection of RNA
populations is that the concentrations of the amplified PCRTM products must be sampled when the PCRTM reactions are in the linear portion of their curves.
The second condition that must be met for an RT-PCRTM study to successfully determine the relative abundances of a particular mRNA species is that relative concentrations of the amplifiable cDNAs must be normalized to some independent standard. The goal of an RT-PCRTM study is to determine the abundance of a particular mRNA species relative to the average abundance of all mRNA species in the sample. W such studies, mRNAs for (3-actin, asparagine synthetase and lipocortin II may be used as external and internal standards to which the relative abundance of other mRNAs are compared.
Most protocols for competitive PCRTM utilize internal PCRTM internal standards that are approximately as abundant as the target. Other studies are available that use a more conventional relative quantitative RT-PCRTM with an external standard protocol.

B. Immunodetection Methods In still further embodiments, the present invention concerns immunodetection methods for binding, purifying, removing, quantifying or otherwise generally detecting WT1 gene product. The steps of various useful immunodetection methods have been described in the scientific literature, such as, e.g., Nakamura et al. (1987; incorporated herein by reference).
Immunoassays, in their most simple and direct sense, are binding assays.
Certain preferred immunoassays are the various types of enzyme linked immunosorbent assays (ELISAs), radioimmunoassays (RIA) and immunobead capture assay. Immunohistochemical detection using tissue sections also is particularly useful. However, it will be readily appreciated that detection is not limited to such techniques, and Western blotting, dot blotting, FAGS analyses, and the like also may be used in connection with the present invention.
1. Immunohistochemistry Fresh-frozen and formalin-fixed, paraffin-embedded tissue blocks may be prepared from study by immunohistochemistry (IHC). For example, each tissue block consists of 50 mg of residual "pulverized" tumor. The method of preparing tissue blocks from these particulate specimens has been successfully used in previous IHC studies of various prognostic factors, e.g., in breast, and is well known to those of skill in the art (Brown et al., 1990;
Abbondanzo et al., 1990; Allred et al., 1990).
Briefly, frozen-sections may be prepared by rehydrating 50 ng of frozen "pulverized"
tumor at room temperature in phosphate buffered saline (PBS) in small plastic capsules; pelleting the particles by centrifugation; resuspending them in a viscous embedding medium (OCT);
inverting the capsule and pelleting again by centrifugation; snap-freezing in -70°C isopentane;
cutting the plastic capsule and removing the frozen cylinder of tissue;
securing the tissue cylinder on a cryostat microtome chuck; and cutting 25-50 serial sections containing an average of about 500 remarkably intact tumor cells.
Permanent-sections may be prepared by a similax method involving rehydration of the 50 mg sample in a plastic microfuge tube; pelleting; resuspending in 10% formalin for 4 h fixation;
washing/pelleting; resuspending in warm 2.5% agar; pelleting; cooling in ice water to harden the agar; removing the tissue/agar block from the tube; infiltrating and embedding the block in paraffin; and cutting up to 50 serial permanent sections.

2. FACS
- Fluorescent activated cell sorting, flow cytometry or flow microfluorometry provides the means of scanning individual cells for the presence of an antigen, such as WTl. The method employs instrumentation that is capable of activating, and detecting the excitation emissions of labeled cells in a liquid medium.
FACE is unique in its ability to provide a rapid, reliable, quantitative, and multiparameter analysis on either living or fixed cells. Cells would generally be obtained by biopsy, single cell suspension in blood or culture. FACE analyses would probably be most useful when desiring to analyze a number of cancer antigens at a given time, e.g., to follow an antigen profile during disease progression.
3. Western Blots Western blotting may be used to detect inhibition of proliferation of breast cancer cell lines due to specific inhibition of WT1 protein expression. The antisense construct of the present invention may be used as high-affinity primary reagents for the identification of WT1 gene product immobilized onto a solid support matrix, such as nitrocellulose, nylon or combinations thereof. The technique of western blots is well known to a person of ordinary skill in the art.
XII. EXAMPLES
The following examples are included to demonstrate particular embodiments of the invention. It should be appreciated by those of skill in the art that the techniques disclosed in the examples which follow represent techniques discovered by the inventor to function well in the practice of the invention, and thus can be considered to constitute preferred modes for its practice. However, those of skill in the art should, in light of the present disclosure, appreciate that many changes can be made in the specific embodiments which are disclosed and still obtain a like or similar result without departing from the spirit and scope of the invention.

Materials And Methods Cell Culture The ERa-positive breast cancer cell lines MCF-7, BT-474, T-47D, and MDA-MB-361 (Sutherland et al., 1988; Fitzgerald et al., 1997), and the ERoc-negative breast cancer cell lines SI~Br-3, MDA-MB-231, MDA-MB-453, BT-20, and MDA-MB-468 (Fitzgerald et al., 1997;
Love-Schimenti et al., 1996) were obtained from the American Type Culture Collection (Manassas, VA). They were propagated in DMEM/F12 medium supplemented with 10%
FCS.
The human leukemia cell line K562, chosen as a positive control cell line because of its high expression of WT1 protein (Yamagami et al., 1996), was also obtained from ATCC
and propagated in RPMI 1640 medium supplemented with 10% FCS. All cell lines were incubated in 95% air and 5% C02 at 37 °C.
Western Blotting Western blotting was used to determine the expression levels of WT1 proteins in nuclear extracts from breast cancer and leukemia cell lines since these proteins are known to localize within the nucleus (Dobashi et al., 1997). Protein concentration was determined by using the Bio-Rad DC protein concentration assay. Briefly 50 qg of proteins were subjected to electrophoresis on 12% SDS-polyacrylamide gels and transferred to nitrocellulose membranes.
Immunodetection was done using rabbit antibodies specific for WT1 (C-19) from Santa Cruz Biotechnology (Santa Cruz, CA) and anti-rabbit secondary antibodies conjugated with horseradish peroxidase (Amersham Life Science Inc.). Protein bands were visualized by enhanced chemiluminescence (Kirkegaard ~z Perry Laboratories, Gaithersburg, MD).
Preparation of Liposome-Incorporated Oligonucleotides The following is a brief description of how oligonucleotides may be incorporated in a liposome. For details one may refer to Tari et al. (2000).
The oligonucleotides were radiolabelled with 32P radioisotope and incorporated in DOPC
lipids purchased from Avanti Polar Lipids (Alabaster, AL). DOPC was dissolved in ter-t-butanol at 20mg/ml. Oligonucleotides are dissolved in water or DMSO at ~8mg/ml.
Oligonucleotides are aliquoted and mixed well before adding excess text-butanol. Because DMSO
is present, tert-butanol should be added for at least 95% (v/v) so that the mixture can be well frozen in an acetone/dry ice bath before being lyophilized overnight. The lyophilized preparation is hydrated with 0.9% normal saline at a final oligonucleotide concentration of O.lmM.
WTl Antisense Oligos and Cell Treatment P-ethoxy oligos, purchased from Oligos Etc., Inc. (Wilsonville, OR), were incorporated into DOPC liposomes (Tari et al., 2000). The sequence of the WT1 antisense oligos targeted against the translation initiation site is 5'-GTCGGAGCCCATTTGCTG-3' (SEQ 1D
NO: 1), and the sequence of the control oligos is 5'-GGGCTTTTGAACTCTGCT-3' (SEQ ID NO: 2) (Yamagami et al., 1996). Breast cancer and leukemia cells were plated in 96-well plates (2 x 103 cells per well) in DMEMlFI2 supplemented with 10% FCS and allowed to adhere overnight.
Then various concentrations (0, 3, 6, or 12 ~,M) of liposomal WT1 antisense (L-WT1) and liposomal control (L-control) oligos were added to the cells and incubated for 72 h. Cell growth was determined by using the CellTiter 96 Aqueous nonradioactive proliferation assay (Promega, Madison, WI).
Light Microscopic Evaluation of Cell Growth MCF-7 and MDA-MB-453 cells were seeded in 6-well plates (1.0 x 105 cells per well) in DMEM/F12 medium supplemented with 10% FCS. After 24 h, the cells were treated with 12 ~M L-WT1 or L-control oligos for 3 days, examined under light microscopy at magnification, and photographed with Kodak gold 400 film.
RNA Purification and RT-PCR
Total RNA was prepared from the cell lines by using 1 ml of TRIzoI Reagent (Life Technologies, Gaithersburg, MD) according to the manufacturer's protocol. The pellet of RNA
was dissolved in DEPC-treated-water and quantified by spectrophotometry at 260 nm. cDNA
was created with Superscript II according to the manufacturer's protocol (Gibco BRL). All PCR
reactions were carried out with 5 ~,1 of cDNA, 0.2 mM dNTPs, 100 ng of each primer, 10 mM
Tris-HCl (pH 8.4, 50 mM KCI, 0.01% gelatin, 1.5 mM MgCl2), and 2.5 U of Taq DNA
polymerase. PCR to detect the different WT1 isoforms was performed with primers as described by Brenner et al. (Brenner et al., 1992). The thermal profile involved 35 cycles of denaturation at 94°C for 40 s, primer annealing at 64°C for 30s, and extension at 72°C for 30s. PCR products were subjected to electrophoresis on 2% agarose gels and the reaction products were visualized with ethidium bromide and photographed under UV transillumination.

Expression of WTl Protein in Breast Cancer Cell Lines The endogenous expression of the 52-54 kDa WTl protein in breast cancer cell lines was assessed and K562 leukemic cells were used as positive control. WTl protein was detected in the nuclear extracts of both ER-positive and ER-negative cell lines (FIG. 1).
The results obtained indicate that WT1 protein is vital for the proliferation of breast cancer cells, regardless of whether the cells are ER-positive or ER-negative.
The inventors found no correlation between the basal expression of WTl protein and the inhibitory response to L-WT1. Nor was any correlation evident between inhibition by L-WT1 and the status of p53 protein, as MCF-7 is the only cell line that expresses the wild-type 53 protein (Casey et al., 1991).
Reduction of WTl Protein Expression Leads to Growth Inhibition of Breast Cancer. It was first verified that L-WT1 oligos could inhibit the growth of K562 leukemia cells (Yamagami et al., 1996; Algar et al., 1996) in a dose dependent manner (FIG.
2A). Next, the effect of L-WT1 on MCF-7 cells, an ER-positive cell line with high endogenous WTl expression, and on MDA-MB-453 cells, an ER-negative cell line with low endogenous WT1 expression, was studied. L-WT1 induced dose-dependent growth inhibition in both cell lines (FIG. 2B). Maximal growth inhibition (>90%) was observed at 12 ~,M L-WTl;
therefore, this concentration was used for the subsequent experiments. These findings were further expanded to 7 more breast cancer cell lines, the ER-positive BT-474, T-47D, and MDA-MB-361 and the ER-negative cell lines SKBr-3, MDA-MB-231, BT-20, and MDA-MB-468. L-WT1 inhibited the growth of 8 of the 9 breast cancer cell lines, with greater than 50%
effects in MCF-7, T-47D, and MDA-MB-453 cells (FIG. 2C). Under the same conditions, approximately 50%
growth inhibition was observed in BT-474 and MDA-MB-468 cells while less than 50%
growth inhibition was observed in 1VIDA-MB-361, SKBr-3, and BT-20 cells. No growth inhibition was observed in MDA-MB-231 cells.
Western blotting confirmed that the inhibition of proliferation in MCF-7 and MDA-MB-453 cells was due to specific inhibition of WT1 protein expression (FIG. 2D).
The inventors have detected WT1 mRNA in all cell lines and this contradicts a previous report by Loeb et al. (2001) who found WT1 mRNA in T-47D and MDA-MB-468 cells but not in MCF-7, MDA-MB-231 or SKBr-3 cells. However these investigators used one round of PCR, whereas the inventors subj ected cells to reamplification by using nested PCR.
The inventors' data indicated low but detectable WT1 levels in breast cancer cells, and the reamplification allowed the different WT1 isoforms to be detected as well.
Light Microscopy. Using light microscopy, the inventors observed that L-WT1 reduced the number of MCF-7 and MDA-MB-453 cells as compared with untreated cells (FIG. 3). But L-control did not decrease the number of MCF-7 and MDA-MB-453 cells.
Expression of WTl mRNA Isoforms. RT-PCR was used to determine whether expression of the total WT1 mRNA and its isoforms was associated with the growth inhibition of breast cancer cells. The highest total mRNA expression was detected in T-47D
and MDA-MB-468 cells, since the PCR products of WT1 (857 bp) in these cell lines were detected in the first round of PCR (FIG. 4A). However in the other cell lines, the PCR products of WT1 were not detected until the second round of PCR.
To identify the various WT1 mRNA isoforms, the inevntors first amplified the KTS
region with specific primers to exon 7 and primers to the KTS- or KTS+ areas in exon 9. All cell lines produce two products, but the KTS- isoform was more abundant than the KTS+ isoform (FIG. 4B). To detect exon 5 isoforms, primers to exon 1 and primers to KTS- or KTS+ isoforms were used (FIG. 4C), all four WT1 isoforms were detected in the control K562 cells and in the ER-positive cells. Among the four ER-positive cells, MDA-MB-361 cells had the lowest '' expression of these isoforms. All four isoforms were also detected in two of the five ER-negative cell lines MDA-MB-453 and MDA-MB-468. However, only the exon 5+/KTS+
and exon 5-/KTS- isoforms were detected in the SKBr-3 cells, and only the exon 5+/KTS+ and exon 5+IKTS- isoforms were detected in the BT-20 cells. No PCR products were observed in the MDA-MB-231 cells.
As described earlier in the description, the WT1 splicing isoforms have different:
biological activities (Lee et al., 2001). The KTS- isoforms have transactivational properties in some genes that are involved in cell growth and differentiation, whereas the KTS+ isoforms have a potential role in RNA processing (Lee et al., 2001). Exon 5 may function as a repressor domain or as an activator domain, depending on which proteins are interacting with WT1 (Richard et al., 2001). In the inventors' study, all five cell lines in which L-WT1 led to >_ 50%
growth inhibition contain all four WT1 isoforms. But the two cell lines that were little affected by L-WT1 expressed only two WT1 isoforms, and the one cell line that was not affected by L-WT1 expressed no WT1 isoforms. These data show that the regulation of breast cancer cell growth by WT1 protein may depend on the expression of all four WTl isoforms.
***********************************************************
All of the methods and compositions disclosed and claimed herein can be made and executed without undue experimentation in light of the present disclosure.
While the compositions and methods of this invention have been described in terms of preferred embodiments, it will be apparent to those of skill in the art that variations may be applied to the methods and compositions and in the steps or in the sequence of steps of the method described herein without departing from the concept, spirit and scope of the invention.
More specifically, it will be apparent that certain agents which are both chemically and physiologically related may be substituted for the agents described herein while the same or similar results would be achieved. All such similar substitutes and modifications apparent to those skilled in the art are deemed to be within the spirit, scope and concept of the invention as defined by the appended claims.

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SEQUENCE LISTING
<110> Board of Regents, The University of Texas System BERESTEIN, GABRIEL LOPEZ
TARI, ANA MARIA
ZAPATA-BENAVIDES, PABLO
<120> SEQUENCE LISTING
<110> LOPEZ BERESTEIN, GABRIEL
TARI, ANA MARIA
ZAPATA-BENAVIDES, PABLO
<120> WT1 ANTISENSE OLIGOS FOR THE INHIBITION OF BREAST CANCER
<130> UTFC:730W0 <140> UNKNOWN
<l41> 2003-01-03 <150> 60/345,102 <151> 2002-01-03 <160> 2 <170> PATENTIN VER. 2.1 <210> 1 <211> 18 <2l2> DNA
<2l3> ARTIFICIAL SEQUENCE
<220>
<223> DESCRIPTION OF ARTIFICIAL SEQUENCE: SYNTHETIC
PRIMER
<400> 1 <210> 2 <211> 18 <212> DNA
<213> ARTIFICIAL SEQUENCE
<220>
<223> DESCRIPTION OF ARTTFICIAL SEQUENCE: SYNTHETIC
PRIMER
<400> 2 <140> UNKNOWN
<141> 2003-O1-03 <150> 60/345,102 <151> 2002-O1-03 <160> 2 <170> PatentIn Ver. 2.1

Claims

1. Use of a WT1 antisense molecule for the manufacture of a medicament for therapy of a breast cancer which expresses a Wilms' Tumor 1 (WT1) gene product, said therapy comprising contacting cells of said cancer with an amount of a WT1 antisense molecule effective to inhibit the growth of said cancer cells.

2. The use of claim 1, wherein said WT1 antisense molecule is a DNA.

3. The use of claim 1, wherein said WT1 antisense molecule is an RNA.

4. The use of claim 1, wherein the antisense molecule is produced from an expression vector encoding said antisense under the control of a promoter active in said cell.

5. The use of claim 4, wherein said promoter is a constitutive promoter.

6. The use of claim 5, wherein said constitutive promoter is a CMV promoter, an RSV
promoter, an SV40 promoter.

7. The use of claim 4, wherein said promoter is a tissue specific promoter.

8. The use of claim 7, wherein said tissue specific promoter is leptin gene promoter, IGF
binding protein-3 promoter, adenomatous polyposis coli gene promoter.

9. The use of claim 4, wherein said promoter is an inducible promoter.

10. The use of claim 9, wherein said inducible promoter is Tet-On system, Tet-Off system.

11. The use of claim 1, wherein said breast cancer cell is estrogen receptor-positive.

12. The use of claim 1, wherein said breast cancer cell is estrogen receptor-negative.

13. The use of claim 2, wherein said DNA is an oligonucleotide.

14. The use of claim 13, wherein said oligonucleotide is 6 to about 50 bases in length.

15. The use of claim 13, wherein said oligonucleotide comprises one or more modifed bases.

16. The use of claim 1, wherein said antisense molecule hybridizes to a WT1 transcript.

17. The use of claim 16, wherein said antisense molecule hybridizes to a translation initiation site or a splice site.

18. The use of claim 1, wherein said antisense molecule hybridizes to a WT1 genomic sequence.

19. The use of claim 18, wherein said antisense molecule hybridizes to a transcription start site, an intron, an exon, or an intron-exon junction.

20. The use of claim 2, wherein said DNA is a double-stranded DNA.

21. The use of claim 2, wherein said DNA is a single-stranded DNA.

22. The use of claim 4, wherein said expression vector is a non-viral vector.

23. The use of claim 4, wherein said expression vector is a viral vector.

24. The use of claim 23, wherein said viral vector is selected from the group consisting of adenovirus, retrovirus, herpesvirus, vaccinia virus, adeno-associated virus, lentivirus and polyoma virus.

25. The use of claim 1, wherein said antisense molecule is associated with one or more lipid.

26. The use of claim 25, wherein said antisense molecule is encapsulated in a liposome.

27. The use of claim 25, wherein the lipid comprises at least one neutrally charged lipid.

28. The use of claim 27, wherein said neutrally charged lipid is DOPC.
28.1 The use of claim 25, further defined as comprising more than one lipids wherein the lipids on a whole are neutrally charged.

29. The use of claim 17, wherein said antisense molecule hybridizes to a translation initiation site and comprises 5'-GTCGGAGCCCATTTGCTG-3'.

30. The use of claim 29, wherein said antisense molecule consists of 5'-GTCGGAGCCCATTTGCTG-3'.

31. The use of claim 1, wherein said cell expresses multiple WT1 isoforms.

32. The use of claim 1, wherein said cell expresses one or more adverse oncogene products.

33. Use of a WT1 antisense molecule for the manufacture of a medicament for therapy of a breast tumor which expresses a Wilms' Tumor 1 (WT1) gene product, comprising administering an effective amount of said medicament to the tumor.

34. The use of claim 33, wherein the administering is by intratumoral injection.

35. The use of claim 33, wherein the administering is by injection into the tumor vasculature.

36. The use of claim 33, wherein the administering is locally to said tumor.

37. The use of claim 33, wherein the administering is regionally to said tumor.

38. The use of claim 33, wherein the administering is to the lymphatic system locally or regionally to said tumor.

39. The use of claim 33, further comprising a second breast tumor therapy.

40. The use of claim 39, wherein said second breast tumor therapy is chemotherapy, radiation therapy, immunotherapy, hormonal therapy, or gene therapy.

41. The use of claim 39, wherein said second breast cancer therapy is provided prior to said WT1 antisense molecule.

42. The use of claim 39, wherein said second breast cancer therapy is provided after said WT1 antisense molecule.

43. The use of claim 39, wherein said second breast cancer therapy is provided at the same time as said WT1 antisense molecule.

44. A method of predicting breast cancer progression in a subject having breast cancer comprising:
(a) obtaining a sample from said subject comprising breast cancer tumor cells;
and (b) assessing expression of one or more isoforms of Wilms' Tumor 1 (WT1) gene product in said cells.~

45. The method of claim 44, wherein assessing comprises measuring WT1 protein levels.

46. The method of clam 44, wherein measuring comprises quantitative immunodetection.

47. The method of claim 44, wherein assessing comprises measuring WT1 mRNA
levels.

48. The method of claim 47, wherein measuring comprises quantitative PCR.

49. A method of screening a candidate substance for activity against breast cancer comprising:
(i) providing a cell that expresses one or more isoforms of the Wilms' Tumor 1 (WT1) gene product;
(ii) contacting the cell with the candidate substance suspected of inhibiting WT1; and (iii) measuring the effect of the candidate substance on the cell.
wherein a decrease in the amount of WT1 gene product in said cell, as compared to a cell not treated with said candidate substance, indicates that said candidate substance has activity against breast cancer.

50. The method of claim 49, wherein said candidate substance is a protein, a nucleic acid or a small molecule pharmaceutical.

51. The method of claim 49, wherein measuring comprises determining the level of a WT1 gene product in said cell.

52. The method of claim 49, wherein said cell is a breast cancer cell.