WO2005013893A2 - Cancer related genes - Google Patents

Abstract

Method for assaying potential therapeutic agents, such as antitumor agents, based on their modulation of the expression of specified genes, especially genes mapping to the short arm of chromosome 20, or their ability to inhibit or other wise counteract the activity of mutated or truncated polypeptides encoded by said genes, are disclosed, along with methods for diagnosing cancerous, or potentially cancerous, conditions as a result of the mutation and/or disruption of said genes. Also disclosed are the sequences of genes whose dis-regulation is correlated with the development of the cancerous state.

Description

CANCER RELATED GENES

This application claims priority of U.S. Provisional Application 60/489,733, filed 24 July 2003, the disclosure of which is hereby incorporated by reference in its entirety.

FIELD OF THE INVENTION

The present invention relates to genes whose disruption and/or change in expression is useful to distinguish cancerous from non-cancerous tissue and serve as potential therapeutic targets and diagnostic markers.

BACKGROUND OF THE INVENTION

Chromosomal abnormalities have been identified in most cancer cells. Conventional chromosome banding techniques allow for the detection of specific chromosomal defects in tumor cells but interpretation of the banding pattern is sometimes difficult, particularly when complex chromosomal rearrangements or subtle abnormalities are present. In recent years, new techniques, such as CGH (Comparative Genomic Hybridization) and SKY (spectral karyotyping), based on fluorescent in situ hybridization (FISH) have been developed to overcome the limitations of conventional chromosome banding. CGH measures intensities of fluorescently labeled tumor DNA and normal DNA following hybridization to normal chromosomes. SKY utilizes a cocktail of combinatorially labeled human chromosome probes with distinct spectral signatures that identifies each chromosome. A probe set of 24 differentially labeled human chromosomes is hybridized to tumor chromosomes in an effort to identify numerical and structural chromosomal abnormalities in the tumor cell. SKY is particularly useful for identifying subtle and obscure chromosome rearrangements, such as translocations or exchanges of chromosome material, that are not recognized or easily defined by conventional banding techniques. Chromosomal regions involved in such rearrangements contain genes that, when disrupted, may become dis-regulated and be significant to the method of tumor initiation or progression.

SKY analysis of two colon cancer cell lines, SW480 and SW620, has been reported by Melcher et al (Cytogenet Cell Genet 88:145-52 (2000)). Among many chromosomal rearrangements present in SW480 and SW620, the authors revealed two translocations between chromosomes 5 and 20. In accordance with the present invention, the derivative chromosome 5 of Melcher et al have breakpoints that are close to breakpoints of the present disclosure but the derivative chromosome 20 have completely different breakpoints and, therefore, the translocation was not previously recognized as reciprocal.

G-banded analysis of SW480 and SW620 was reported by Gagos et al (Cancer Genet Cytogenet 90:157-65 (1996)), wherein the translocation between chromosome 5 and 20 was recognized, with breakpoints close to those described herein. However, the translocation was not reported as being reciprocal. Conversely, in accordance with the present disclosure, an identical exchange of material between chromosomes 5 and 20 was found following the identification of a balanced, reciprocal translocation (5;20) and this translocation was retained in the cell. Thus, although translocations between chromosome 5 and 20 in cell lines SW480 and SW620 have been reported, they were not heretofore recognized as reciprocal. The present invention utilizes the first characterization of the breakpoint and discloses BAG clones contained in the chromosome 20 breakpoint region.

BRIEF SUMMARY OF THE INVENTION In one aspect the present invention relates to a method for identifying a gene-modulating agent, comprising: (a) contacting a test compound with a cell expressing a gene corresponding to a polynucleotide that comprises a nucleotide sequence selected from SEQ ID NO: 1-1363 and under conditions supporting such expression, and (b) detecting a change in expression of said gene as a result of said contacting, wherein said change in expression indicates gene modulating activity, thereby identifying said test compound as a gene modulating agent.

Such method can employ recombinant cells as well as non- recombinant cells.

In another as, the present invention relates to a method for identifying an anti-neoplastic agent compπsing contacting a cancerous cell with a test compound found to have gene modulating activity in a method of the invention and under conditions supporting growth of said cell and detecting a change in the growth of said cancerous cell as a result of said contacting thereby identifying said test compound as an anti-neoplastic agent.

In a further aspect, the present invention relates to a method for detecting the cancerous status of a cell, comprising contacting DNA from said cell with an oligonucleotide probe comprising a sequence of contiguous nucleotides of a polynucleotide having a nucleotide sequence selected from SEQ ID NO: 1-1363 and determining decreased hybridization thereof when compared to hybridization of said probe to DNA of a normal cell of the same tissue type. One embodiment of such method comprises contacting DNA from said cell with an oligonucleotide probe comprising the nucleotide sequence of BAC RP11-788G24.

In an additional embodiment, the present invention encompasses a method for detecting the cancerous status of a cell, comprising detecting in a cell a polypeptide that is a truncated form of a polypeptide encoded by a gene corresponding to a polynucleotide that comprises a nucleotide sequence selected from SEQ ID NO: 1-1363

In an additional aspect, the present invention relates to a method for treating cancer comprising contacting a cancerous cell with an agent having gene modulating activity in a method of the invention and in an amount effective to cause a reduction in cancerous activity of said cell. In a preferred embodiment, the cell is a colon cell.

In a further aspect, the present invention relates to a method for detecting cancer or a disposition toward developing cancer comprising detecting in a sample from a patient a decrease in expression of a gene corresponding to a polynucleotide comprising a nucleotide sequence selected from SEQ ID NO: 1-1363 .

In a yet further aspect, the present invention relates to a method for determining the likelihood of success of cancer therapy in a patient, comprising monitoring in a patient undergoing cancer therapy the expression of a gene corresponding to a polypeptide having a sequence of SEQ ID NO:

1364-1398 wherein an decrease in said expression prior to completion of said cancer therapy is indicative of a likelihood of success of said cancer therapy.

In a still further aspect, the present invention relates to a method for preventing progression to metastasis in a cancer cell comprising introducing into a cancer cell one or more copies of a gene corresponding to a polynucleotide comprising a nucleotide sequence selected from SEQ ID NO:

1-1363. In a yet still further aspect, the present invention relates to a method for treating cancer in a patient comprising administering to a patient afflicted therewith an effective amount of a vector comprising one or more genes corresponding to a polynucleotide comprising a nucleotide sequence selected from SEQ ID NO: 1-1363 and wherein said vector transduces non-metastatic primary tumor cells.

The present invention also contemplates an isolated oligonucleotide probe comprising a first portion comprising a contiguous genomic nucleotide sequence selected from chromosome 5q and a second portion comprising a contiguous genomic nucleotide sequence selected from chromosome 20p and wherein said probe is useful for determining a t(5;20) translocation event.

The present invention also contemplates a method for determining the occurrence of a t(5;20) translocation event in a cell, comprising: (a) contacting a t(5;20) sensitive oligonucleotide probe with a target

DNA molecule from a cell under conditions supporting hybridization of said probe to said DNA and wherein said t(5;20) sensitive oligonucleotide probe comprises a first portion comprising a contiguous genomic nucleotide sequence selected from chromosome 5q and a second portion comprising a contiguous genomic nucleotide sequence selected from chromosome 20p; (b) determining hybridization of said probe to said target DNA molecule, wherein said hybridization indicates the occurrence of a t(5;20) translocation event in said target DNA molecule thereby determining the occurrence of a t(5;20) translocation event in said cell. The present invention also contemplates a method for determining the occurrence of a t(5;20) translocation event in a cell, comprising: (a) contacting DNA from a cell with a first oligonucleotide primer that hybridizes to a DNA strand from chromosome 5 and a second oligonucleotide primer that hybridizes to a DNA strand from chromosome 20 under conditions supporting said hybridization and under conditions supporting amplification of said hybridized DNA when said first and second oligonucleotide primers hybridize to opposite strands of the same duplex DNA; (b) determining amplification of said hybridized DNA; wherein said amplification indicates the presence of a duplex DNA molecule that hybridizes to both said first and second primers thereby determining the occurrence of a t(5;20) translocation event in said cell.

SEQUENCE LISTING ON CD-ROM ONLY

The sequences disclosed herein as SEQ ID NO: 1-1398 in the sequence listing are contained on compact disc (CD-ROM) only (denoted as Filename: Avalon 199 (1 ,173 kB), 4 copies of which appear on discs denoted Copy 1 , Copy 2, Copy 3 and CRF, and which discs were generated on 22 July 2004), which accompanies this application and the contents of said CD-ROMs are hereby incorporated by reference in their entirety. These sequence numbers also appear in Table 1 where all sequences are referred to as consecutive Sequence ID Nos. for reference. DEFINITIONS

As used herein, the following terms have their indicated definitions, unless specifically stated otherwise.

The term "percent identity" or "percent identical," when referring to a sequence, means that a sequence is compared to a claimed or described sequence after alignment of the sequence to be compared (the "Compared Sequence") with the described or claimed sequence (the "Reference Sequence"). The Percent Identity is then determined according to the following formula:

Percent Identity = 100 [1-(C/R)]

wherein C is the number of differences between the Reference Sequence and the Compared Sequence over the length of alignment between the Reference Sequence and the Compared Sequence wherein (i) each base or amino acid in the Reference Sequence that does not have a corresponding aligned base or amino acid in the Compared Sequence and (ii) each gap in the Reference Sequence and (iii) each aligned base or amino acid in the Reference Sequence that is different from an aligned base or amino acid in the Compared Sequence, constitutes a difference; and R is the number of bases or amino acids in the Reference Sequence over the length of the alignment with the Compared Sequence with any gap created in the Reference Sequence also being counted as a base or amino acid.

If an alignment exists between the Compared Sequence and the

Reference Sequence for which the percent identity as calculated above is about equal to or greater than a specified minimum Percent Identity then the Compared Sequence has the specified minimum percent identity to the

Reference Sequence even though alignments may exist in which the hereinabove calculated Percent Identity is less than the specified Percent Identity.

As used herein, the terms "portion," "segment," and "fragment," when used in relation to polypeptides, refer to a continuous sequence of residues, such as amino acid residues, which sequence forms a subset of a larger sequence. For example, if a polypeptide were subjected to treatment with any of the common endopeptidases, such as trypsin or chymotrypsin, the oligopeptides resulting from such treatment would represent portions, segments or fragments of the starting polypeptide. When used in relation to a polynucleotides, such terms refer to the products produced by treatment of said polynucleotides with any of the common endonucleases, or any stretch of polynucleotides that could be synthetically synthesized. As used herein, the term "DNA segment" or "DNA sequence" refers to a DNA polymer, in the form of a separate fragment or as a component of a larger DNA construct, which has been derived from DNA, and may include both single stranded and duplex sequences. Such segments are provided in the form of an open reading frame uninterrupted by internal non-translated sequences, or introns, which are typically present in eukaryotic genes.

The term "coding region" refers to that portion of a gene which either naturally or normally codes for the expression product of that gene in its natural genomic environment, i.e., the region coding in vivo for the native expression product of the gene.

The term "nucleotide sequence" refers to a heteropolymer of deoxyribonucleotides. Generally, DNA segments encoding the proteins provided by this invention are assembled from cDNA fragments and short oligonucleotide linkers, or from a series of oligonucleotides, to provide a synthetic gene which is capable of being expressed in a recombinant transcriptional unit comprising regulatory elements derived from a microbial or viral operon. The term "expression product" means that polypeptide or protein that is the natural translation product of the gene and any nucleic acid sequence coding equivalents resulting from genetic code degeneracy and thus coding for the same amino acid(s).

The term "fragment," when referring to a coding sequence, means a portion of DNA comprising less than the complete coding region whose expression product retains essentially the same biological function or activity as the expression product of the complete coding region.

The term "test compound" refers to an agent, such as a chemical agent, for example, a small organic compound, whose activity in increasing or decreasing the expression, including transcription, of a gene or polynucleotide, as disclosed herein, is to be evaluated using one or ore of the screening methods of the invention. This term also refers to a chemical agent that is to be evaluated for activity in increasing or decreasing the activity of a polypeptide disclosed herein, or a polypeptide encoded by a polynucleotide or gene disclosed herein and includes a change in the synthesis of such polypeptide. Such a test compound may also operate by binding to the polynucleotide, or gene, or polypeptide whose activity is to be determined in the presence of said test compound. Such evaluation of expression and/or activity will normally be ascertained in the presence and absence of said test compound, with a positive result being denoted as one where the expression or activity is changed, preferably by at least 10%, more preferably by at least 25%, most preferably by at least 50%, when said test compound is present relative to when said test compound is not present. For example, if the transcription of a gene disclosed herein is reduced by at least 10% in terms of the rate or amount of RNA produced under transcription-supporting conditions when a cell containing the gene is contacted with a test compound, versus transcription when the test compound is not present, then the test compound is said to modulate transcription, or expression, of the gene. DETAILED SUMMARY OF THE INVENTION

In one aspect the present invention relates to a set of genes that have been localized within human chromosome 20, especially in the 20p11.2 region, in particular genes that corresponds to a polynucleotide comprising a nucleotide sequence of SEQ ID NO: 1-1363, and which map to the region of translocation. Breakage and translocation of these genes has been correlated with cancer occurrence in cell lines exhibiting such translocation, especially of colon. Thus, disruption of one or more of said genes correlates with the cancerous state, especially colon cancer. The presence of such genes may be indicative of a predilection for development of a cancerous state. Where the genes are disrupted, mutated, and/or translocated, a cancerous condition is indicated for the cells involved. In accordance therewith, reduced gene expression, or non-expression, is observed. Thus, expression of such a gene, or genes, is reduced in cancerous cells as compared to non-cancerous cells, from a specific organ or tissue.

In accordance with the present invention, the cell lines SW480 and SW620, derived from primary and metastatic colon tumors, respectively, in the same patient, were used to identify a reciprocal translocation involving chromosomes 5 and 20 [t(5;20)(q15;p11.2)]. As used herein, the term "primary tumor" refers to a tumor located within the site of tumor formation (here, the colon) and which has not yet metastasized to other locations (for example, the liver, lymph nodes, etc.). The term "metastatic tumor" refers to a tumor at least some of whose cells have metastasized, or spread, to other tissues or organs and "metastatic cells" are cells capable of such spreading.

Cytogenetic (chromosomal) characterization of SW480 and SW620 by spectral karyotyping (SKY) showed that the balanced translocation is the only structural abnormality common to both cell lines. Bacterial artificial chromosome (BAG) clones were used to identify the translocation breakpoint on chromosome 20. The breakpoint on chromosome 20 is consistent in both cell lines. The breakpoint region harbors a gene, or genes, that when dis- regulated by translocation contribute to the development or progression of cancer, especially colon cancer, in a patient. Thus, the same translocation occurs in both cell lines.

In accordance therewith, a BAG clone that identifies the translocation breakpoint on chromosome 20 in SW480 and SW620 (herein denoted RP11- 788G24) The genes identified are as follows:

Genes and Genbank ESTs: (SEQ ID NO: 1-1264)

Genes and Genbank ESTs have been identified and mapped in the region of the translocation

Predicted genes: (SEQ ID NO: 1265-1363 ) (See Table 1) Predicted genes have not been mapped onto the genome but have been identified using computer algorithms.

Predicted Proteins (SEQ ID NO: 1364-1398 ) (See Table 1)

Predicted proteins have been identified using computer algorithms from the genes, Genbank ESTs and predicted transcripts in the region of the translocation and/or deletion. A gene list is presented in Table 1 with SEQ NOs.

The present invention relates to a set of genes that are dis-regulated

(i.e., under-expressed or not expressed, due primarily to breakage and/or translocation) genes in cancer cell lines and have been localized to chromosome region 20p11.2 (the short arm of chromosome 20). These have been identified through a combination of SKY, expression analysis and Reverse Transcriptase-Polymerase Chain Reaction (RT-PCR). Such genes are both markers and potential therapeutic targets for cancer, in particular colon malignancies. In accordance with the present invention, a number of genes have been localized to a portion of chromosome 20, especially the short arm (or p arm) of the chromosome, possibly to a particular portion of such p arm, wherein said gene corresponds to a polynucleotide comprising a nucleotide sequence of SEQ ID NO: 1-1363 (wherein the latter sequences represent predicted genes and predicted proteins).

The procedures used to identify the genes disclosed herein may be summarized as follows: for SKY analysis, based on detailed molecular cytogenetic characterizations, the following data sets are generated, which may include regions/chromosomal aberrations reported in the public domain as well as unique regions/chromosomal aberrations not previously known. Initially, there is generated a map of chromosomal regions involved in a chromosome rearrangement (i.e., dis-regulation, due primarily to translocation/transposition and/or deletion) for a representative cancer cell line or tumor type (e.g. colon) that can be recognized as a pattern/signature for a given tumor. This can be compared with the patterns of losses versus no losses between clinical samples (e.g. colon xenografts) and cell lines (e.g., colon) of matched Stages and Grades to determine a pattern of losses and correlate this with the incidence, type and stage or grade of cancer in a tissue and/or cell type. Then a comparison of the patterns of losses between primary colon tumor cell lines (e.g., SW480 lines) and metastatic colon tumor cell lines (e.g., SW620) can be made.

In accordance with the present invention, for SKY analysis, data sets were generated according to the following steps: 1. Identification and development of a database of novel chromosomal rearrangements in cancer cell lines. 2. Identification of novel translocations involving specific chromosomes or chromosomal regions 3. Reconciliation of SKY and CGH analysis on the same cell line as a verification of the combined findings.

Combining genomic DNA analysis of losses due to dis-regulation (i.e., translocations) in the tumor cell lines/clinical samples with cDNA expression analysis from matched tumor types displayed on a genome template from the Golden Path genome browser using Spotfire analysis. A pattern of gene expression on a U-95 Affymetrix chip set obtained via the Gene Logic's GeneExpress database was used to generate differential gene expression profiles between sample sets containing normal and malignant tissues from colon cell lines. A Spotfire visualization tool was used to generate a list of all the genes that are present in the Golden Path within the clustered regions of losses to generate the gene sets to include in the high throughput integrated transcriptional profiling or HITS platform. The resulting genes are those whose sequences are presented as SEQ ID NO: 1-1363. Thus, dis-regulation is identified as down-regulation of such genes, or of genes corresponding to such genes, or gene sequences. Such down regulation is readily identified as a decrease in mRNA transcripts as a result of the translocation and/or deletion of such gene, or genes.

In accordance with the present invention, under-expression of cellular genes is conveniently monitored in model cellular systems using cell lines (such as is used in the example below), primary cells, or tissue samples maintained in growth media. For different purposes, these may be treated with compounds at one or more different concentrations to assay for modulating agents. Thus, cellular RNAs were isolated from the cells or cultures as an indicator of selected gene expression. The cellular RNAs were then divided and subjected to analysis that detected the presence and/or quantity of specific RNA transcripts, which transcripts were then amplified for detection purposes using standard methodologies, such as reverse transcriptase polymerase chain reaction (RT-PCR). The levels of specific RNA transcripts, including their presence or absence, were determined. When used for identification of modulating agents, such as anti-neoplastic agents, a metric is derived for the type and degree of response of the treated sample compared to control samples.

In accordance with the foregoing, the genes identified as being in the region of the identified translocation on chromosome 20 are localized in and around the 20p11.2 region (short arm of chromosome 20). In particular, such genes include genes that correspond to a polynucleotide comprising a nucleotide sequence of SEQ ID NO: 1-1363.

These genes may be utilized to characterize the cancerous, or non- cancerous, status of cells and tissues. The methods of the invention may be used with a variety of cell lines or with primary samples from tumors maintained in vitro under suitable culture conditions for varying periods of time, or in situ in suitable animal models.

The genes disclosed herein are expressed at levels in cancer cells that are different from the expression levels in non-cancer cells, presumably due to the identified translocation. These genes (SEQ ID NO: 1-1363) are dis- regulated in cancer cells relative to non-cancer cells of corresponding tissues, especially of colon. Thus, if the point of translocation is located in a critical control element, a number of different genes may be affected by such dis- regulation. If the gene comprising the break point is an enhancer sequence, then one or more genes otherwise enhanced will now be down-regulated. If the gene comprising the break point encodes a transcription factor, effects on other related genes will be observed. If the gene comprising the break point normally directs down-regulation of other genes, those genes will be up- regulated (i.e., over-expressed) as a result of such dis-regulation. In one aspect, the present invention relates to a 1. A method for identifying a gene modulating agent, comprising: (a) contacting a test compound with a cell expressing a gene corresponding to a polynucleotide that comprises a nucleotide sequence selected from SEQ ID NO: 1-1363 and under conditions supporting such expression, and (b) detecting a change in expression of said gene as a result of said contacting, wherein said change in expression indicates gene modulating activity, thereby identifying said test compound as a gene modulating agent.

In a preferred embodiment, the change in expression is a decrease in expression. Such contacting may occur either in vitro or in vivo and may involve an in situ gene, such as in a cell, or an isolated chromosome 20, or a portion thereof, or an isolated gene sequence, including one that retains all regulatory elements or which may be wild type, or truncated, or mutated, or otherwise disrupted in a manner similar to that of the corresponding gene as present in a cancerous cell. In one embodiment, the test compound prevents binding of RNA polymerase to said promoter region. In other embodiments, the test compound decreases expression by decreasing transcription or by a detected decrease in synthesis of a polypeptide, preferably wherein the polypeptide comprises an amino acid sequence selected from SEQ ID NO: 1364-1398. In another preferred embodiment, the test compound binds to a polypeptide encoded by a gene disclosed herein, preferably wherein said agent is an antibody.

In another preferred embodiment, the compound binds to a promoter region of said gene, most preferably wherein said compound prevents binding of RNA polymerase to said promoter region, thereby inhibiting and/or preventing transcription of said polynucleotide and thus expression thereof. Such compound may inhibit and/or prevent transcription by binding to the polynucleotide and preventing transcription, such as by an RNA polymerase. Where the compound binds to a promoter region of the polynucleotide, such binding alone may prevent transcription by preventing binding of the polymerase to the promoter region. This is especially the case where the compound binds to the promoter irreversibly, although such binding need not be irreversible in order to decrease expression of the polynucleotide or gene. Alternatively, the compound may bind, reversibly or irreversibly, preferably irreversibly, to some other region of the gene or polynucleotide and effectively shut down continued transcription where the latter process has already begun. In addition, such compound may bind to a portion of the gene or polynucleotide, especially where transcription is occurring in vivo, such as within a cell, that otherwise serves as a binding site for a transcription factor, or other DNA binding protein, that facilitates expression of the gene. Further, such compound may act by binding to an enhancer region and thereby prevent stimulation of increased expression of the gene whose expression is to be modulated, preferably decreased.

Such chemical agents serve to work against the cancerous process in that they retard expression of genes that would otherwise initiate and/or facilitate the development of primary tumors, or progression to a metastatic state. In the present case, where a translocation has occurred, the portion of the disrupted gene that retains the expression-initiating sites, such as the promoter, and working together with one or more enhancer regions, as well as retained transcription factors, can operate to produce a truncated, or otherwise mutated, expression product at both the RNA and polypeptide levels. Such truncated, or otherwise mutated, expression products can then lead to development of primary cancers and/or progression to the metastatic state. By curtailing such expression of such mutated or truncated genes, where, as here, said gene disruption has been correlated with the cancerous status of the cell, these chemical agents act as anti-neoplastic agents (i.e., agents that inhibit or prevent cancer, and/or inhibit or prevent progression to metastasis, or other cancerous progression). Thus, using the gene sequences disclosed herein for screening for such compounds is useful in finding antineoplastic agents. In general, the agents identified by such screening methods will have the effect of inhibiting and/or preventing formation of truncated, or otherwise mutated, expression products of one or more disrupted genes. The agents identified according to the screening methods of the invention may act at the transcriptional (RNA synthesis) or translational (polypeptide synthesis) levels, and may even work to present binding of an RNA transcript to a ribosome.

In other preferred embodiments of the present invention, the genes and/or polynucleotides to be used as targets in the screening methods of the invention comprises a nucleotide sequence of SEQ ID NO: 1-1363, as where these cDNA sequences are incorporated into a polynucleotide, for example, a polynucleotide that also comprises a promoter sequence, especially one characteristic of the translocated gene, and may also include other regulatory elements. Thus, the agents identified according to the screening methods of the invention have a high order of likelihood of disrupting transcription of the native gene. Such sequences can likewise be used to identify genomic sequences present in a cell, such as a cancerous cell, that retain all of the regulatory sequences, such as promoter and enhancer sequences, involved in transcription of the native genes. Thus, where the screening methods of the invention are carried out using cancerous cells, agents are readily identified that bind to such regulatory regions to inhibit and/or prevent transcription.

In any of the screening methods of the invention, the agent to be screened may be contacted within a cell that contains said polynucleotide, or contacted with such cell where cell contact works through a second messenger to modulate gene expression. In a preferred embodiment, said cell is a recombinant cell, or said cell is a cancerous cell, either primary or metastatic, especially where the cell is of the cell line selected from the group consisting of SW480 and SW620. The expression of the gene sequences identified herein can be measured using methods well known in the art, such as monitoring expression of RNA transcripts formed from the gene sequences. Other methods useful in measuring a change in expression of the genes disclosed herein include measuring a change in the amount or rate of synthesis of a polypeptide encoded by said gene, preferably an increase in synthesis of said polypeptide. Where the gene exhibits a mutation, said mutation inducing or advancing the course of a cancerous condition, a decrease in expression of said mutated gene is desirable and useful anti-neoplastic agents are those that induce such decreased expression. Where the mutated gene produces a mutated gene product, for example, a truncated, or otherwise mutated, polypeptide caused by the breakage or deletion of a portion of the gene, useful anti-neoplastic agents are those that counteract, or nullify completely, the physiological effects of said truncated, or otherwise mutated, protein. Such agent may include an antibody or antibody therapeutic.

In accordance with the present invention, one such polypeptide may be a truncated form of the other and thus the sequence of one may be identical to a portion of the other. Such is the case where a truncated, or shortened, polypeptide is encoded and expressed by a gene containing a breakpoint and translocation, , and thus encodes only a portion of the polypeptide encoded by such gene where the deletion or translocation has not occurred. Such truncated polypeptide is therefore produced in a cancerous cell, where the translocation is related to the cancerous condition. Therapeutic agents that act to reduce the activity, or other effects, of such a truncated polypeptide find use in ameliorating, preventing, or otherwise counteracting the cancerous state of a cell or tissue.

The method of the invention can thus be utilized to identify antineoplastic agents useful in treatment of cancerous conditions. Such activity can be further modified by first identifying such an agent using an assay as already described and further contacting such agent with a cancerous cell, followed by monitoring of the status of said cell, or cells. A change in status indicative of successful anti-neoplastic activity may include a decrease in the rate of replication of the cancerous cell(s), a decrease in the total number of progeny cells that can be produced by said cancerous cell(s), or a decrease in the number of times said cancerous cell(s) can replicate, or the death of said cancerous cell(s), especially where said cells are colon cells. Anti-neoplastic agents may also be identified using recombinant cells suitably engineered to contain and express the cancer-related genes disclosed herein. In one such embodiment, a recombinant cell is formed using standard technology and then utilized in the assays disclosed herein. Methods of forming such recombinant cells are well known in the literature. See, for example, Sambrook, et al., Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor, N.Y., (1989), Wu et al, Methods in Gene Biotechnology (CRC Press, New York, NY, 1997), and Recombinant Gene Expression Protocols, in Methods in Molecular Biology, Vol. 62, (Tuan, ed., Humana Press, Totowa, NJ, 1997), the disclosures of which are hereby incorporated by reference.

The present invention also relates to a method for detecting the cancerous status of a cell, comprising detecting decreased copy number and/or expression in said cell of at least one gene that maps to the long arm of chromosome 20, in particular a gene corresponding to a polynucleotide that comprises a nucleotide sequence of SEQ ID NO: 1-1363. Such decreased expression may be readily monitored by comparison to that of otherwise normal cells having the same genes. Decreased expression of these genes is indicative of the cancerous state, as markers of predictive value, detection (using Immunohistochemistry localization of antibodies to the gene), prognostic value, diagnostic or improved/custom therapeutic management and pharmacodynamic markers to follow survival after therapy. The present invention further relates to a method for detecting a cancer-linked gene comprising the steps of contacting a compound identified as having gene modulating activity, especially expression-inhibiting activity, for a gene corresponding to a polynucleotide that comprises a nucleotide sequence selected from SEQ ID NO: 1-1363 with a cell expressing a test gene and detecting modulation, such as decreased expression, of such test gene relative to when said compound is not present, or said contacting does not occur, or has not occurred, thereby identifying said test gene as a cancer- related gene.

In accordance therewith, the present invention also relates to a method for detecting the cancerous status of a cell, comprising contacting DNA from said cell with an oligonucleotide probe comprising a sequence of at least 15 contiguous nucleotides identical to an oligonucleotide having a nucleotide sequence selected from SEQ ID NO: 1-1363 and determining decreased hybridization thereof when compared to hybridization of said probe to DNA of a normal cell of the same tissue type, preferably wherein said tissue is colon. A useful probe may be a duplicate of an oligonucleotide taken from SEQ ID NO: 1-1363, or a structure complementary to such oligonucleotide and which hybridizes to a segment of SEQ ID NO: 1-1363.

For use herein, the probes may be of long or short length, and even probes as short as 15 or 20 contiguous nucleotides in length may suffice, preferably at least 25 contiguous nucleotides in length, more preferably at least 50 contiguous nucleotides in length, even more preferably at least 80 contiguous nucleotides in length and most preferably at least 100 contiguous nucleotides in length.

In an alternative embodiment, the present invention relates to a method for detecting the cancerous status of a cell, comprising contacting DNA from a test cell with an oligonucleotide probe comprising the nucleotide sequence of

BAC RP11-788G24 whereby complete hybridization, or hybridization under conditions of high stringency, indicates the presence of an unbroken gene sequence and thus the presence of a cancerous condition is contra-indicated..

The present invention also relates to a method for treating cancer comprising contacting a cancerous cell with an agent identified as having gene modulating activity using one or more of the screening methods of the invention and in an amount effective to cause a reduction in cancerous activity of said cell, preferably wherein the cell is a colon cell. In a preferred embodiment, such agent was first identified as having anti-neoplastic activity using one of the screening methods of the invention. In a preferred embodiment, the cancerous cell is contacted in vivo, preferably in an animal afflicted with cancer. In other preferred embodiments, said reduction in cancerous activity is a decrease in the rate of proliferation of said cancerous cell, or said reduction in cancerous activity is the death of said cancerous cell.

The present invention also relates to a method for determining the likelihood of success of cancer therapy in a patient, comprising monitoring in a patient undergoing cancer therapy the expression of a gene encoding a polypeptide having a sequence of SEQ ID NO: 1364-1398, or any polypeptide encoded by a polynucleotide comprising a sequence of SEQ ID NO: 1-1363, wherein an decrease in said expression prior to completion of said cancer therapy is indicative of a likelihood of success of said cancer therapy. In a preferred embodiment thereof, the gene comprises a sequence of SEQ ID NO: 1-1363. In a most preferred embodiment, the cancer is a cancer of colon

The molecular links to cancer disclosed herein relate to the production of primary tumors, especially of colon, involving a translocation in the long arm of one copy of chromosome 5 (the q arm) with the short arm of chromosome 20 (the p arm) wherein said translocation is reciprocal. . Thus, because cancer, are linked to specific molecular genetic rearrangements in chromosome 20, the results of these rearrangements is to produce defective expression of the gene, or genes, involved and thereby produce a defective (i.e., mutated or truncated) product (RNA and/or polypeptide). In addition, the affected gene, or genes, may not be expressed at all, such as in the case of the deletion. Thus, the effects of such genetic abnormality can be ameliorated using techniques of gene therapy, such as where a defective, gene is replaced (via gene replacement therapy) with a properly functioning version of the missing, or disrupted, gene.

The genes disclosed herein, corresponding to the cDNA sequences of SEQ ID NO: 1-1363, represent genes mapped to the affected regions of chromosome 5 and thus are candidates for use in gene replacement therapy. Such therapy can involve replacement of cancerous cells with normal cells, or the use of vectors to insert whole copies of the missing, or disrupted, genes into a cancerous cell, either in vitro or in vivo, and thereby make-up for the genetic deletion and/or disruption. For example, where deletion in one copy of chromosome 5 leads to metastasis, and a patient is known to have a primary tumor, especially of colon, that may not be subject to complete removal, or treatment by other means, said patient is a candidate for gene replacement therapy whereby a vector comprising one or more of the genes, whose cDNAs are represented by SEQ ID NO: 1-1363, is used to insert whole and/or properly functioning copies of said genes into said patient. The copies of the genes inserted into the vectors may be native genes, or cDNAs, so long as the genes are expressed after the vectors transduce the potentially metastatic cells. Among the vectors most useful for this procedure are retroviral vectors, adeno-associated vectors, and the like.

The present invention further relates to a method for treating cancer in a patient comprising administering to a patient afflicted therewith an effective amount of a vector comprising one or more genes corresponding to a polynucleotide comprising a nucleotide sequence selected from SEQ ID NO: 1-1363 and wherein said vector transduces non-metastatic primary tumor cells. In a preferred embodiment the cells are colon cells. In other preferred embodiments, said treating cancer is the inhibition of metastasis. In a preferred embodiment, such vector is a retroviral vector.

In one such embodiment, the present invention includes a method for treating cancer in a patient comprising administering to a patient afflicted therewith an effective amount of a vector comprising the nucleotide sequence of BAG RP11-788G24 and wherein said vector transduces non-metastatic primary tumor cells. In a preferred embodiment thereof, the cells are colon cells.

As noted, the genes useful in the assay methods include genes mapping within the 20p region, in particular genes having a nucleotide sequence corresponding to one of the polynucleotides having the sequence of SEQ ID NO: 1- 1363 (i.e., a gene that encodes the same RNA, such as the same messenger RNA, whose corresponding cDNA is one of the sequences of SEQ ID NO: 1- ). The genes useful in the methods of the invention further include genes encoding RNAs whose corresponding cDNA is at least 90% identical to a sequence selected from SEQ ID NO: 1-1363 , preferably at least about 95% identical to such a sequence, more preferably at least about 98% identical to such sequence and most preferably one comprising that sequence are specifically contemplated by all of the methods of the present invention.

The sequences disclosed herein may be genomic in nature and thus represent the sequence of an actual gene, such as a human gene, or may be a cDNA sequence derived from a messenger RNA (mRNA) and thus represent contiguous exonic sequences derived from a corresponding genomic sequence or they may be wholly synthetic in origin for purposes of detecting. As described in the Example, the expression of these cancer- related genes is determined from the relative expression levels of the RNA complement of a cancerous cell relative to a normal (i.e., non-cancerous) cell. Because of the processing that may take place in transforming the initial RNA transcript into the final mRNA, the sequences disclosed herein may represent less than the full genomic sequence. They may also represent sequences derived from ribosomal and transfer RNAs. Consequently, the genes present in the cell (and representing the genomic sequences) and the sequences disclosed herein, which are mostly cDNA sequences, may be identical or may be such that the cDNAs contain less than the full genomic sequence. Such genes and cDNA sequences are still considered corresponding sequences because they both encode similar RNA sequences. Thus, by way of non- limiting example only, a gene that encodes an RNA transcript, which is then method into a shorter mRNA, is deemed to encode both such RNAs and therefore encodes an RNA complementary to (using the usual Watson-Crick complementarity rules), or that would otherwise be encoded by, a cDNA (for example, a sequence as disclosed herein). Thus, the sequences disclosed herein correspond to genes contained in the cancerous or normal cells used to determine relative levels of expression because they represent the same sequences or are complementary to RNAs encoded by these genes. Such genes also include different alleles and splice variants that may occur in the cells used in the methods of the invention.

The genes of the invention "correspond to" a polynucleotide having a sequence of SEQ ID NO: 1-1363 if the gene encodes an RNA (processed or unprocessed, including naturally occurring splice variants and alleles) that is at least 90% identical, preferably at least 95% identical, most preferably at least 98% identical to, and especially identical to, an RNA that would be encoded by, or be complementary to, such as by hybridization with, a polynucleotide having the indicated sequence. In addition, genes including sequences at least 90% identical to a sequence selected from SEQ ID NO: 1-

1363, preferably at least about 95% identical to such a sequence, more preferably at least about 98% identical to such sequence and most preferably comprising such sequence are specifically contemplated by all of the methods of the present invention as being genes that correspond to these sequences.

In addition, sequences encoding the same proteins as any of these sequences, regardless of the percent identity of such sequences, are also specifically contemplated by any of the methods of the present invention that rely on any or all of said sequences, regardless of how they are otherwise described or limited. Thus, any such sequences are available for use in carrying out any of the methods disclosed according to the invention. Such sequences also include any open reading frames, as defined herein, present within any of the sequences of SEQ ID NO: 1-1363 .

The present invention also finds use as a means of diagnosing the presence of cancer in a patient, as where a sample of cancerous tissues or cells, or tissues or cells suspected of being cancerous, based on the detection of decreased expression, including decreased copy number, of one or more of the genes identified according to the invention. Such decreased expression can be determined by any of the means described herein. In one such embodiment, the elevated expression, as compared to normal cells and/or tissues of the same organ, is determined by measuring the relative rates of transcription of RNA, such as by production of corresponding cDNAs and then analyzing the resulting DNA using probes developed from the gene sequences of SEQ ID NO: 1-1363. Thus, the levels of cDNA produced by use of reverse transcriptase with the full RNA complement of a cell suspected of being cancerous produces a corresponding amount of cDNA that can then be amplified using the polymerase chain reaction, or some other means, such as rolling circle amplification, to determine the relative levels of resulting cDNA and, thereby, the relative levels of gene expression.

For RNA analysis, the latter may be isolated from samples in a variety of ways, including lysis and denaturation with a phenolic solution containing a chaotropic agent (e.g., triazol) followed by isopropanol precipitation, ethanol wash, and resuspension in aqueous solution; or . lysis and denaturation followed by isolation on solid support, such as a Qiagen resin and reconstitution in aqueous solution; or lysis and denaturation in non-phenolic, aqueous solutions followed by enzymatic conversion of RNA to DNA template copies. Steady state RNA levels for a given type of cell or tissue may have to be ascertained prior to employment of the methods of the invention but such is well within the skill of those in the art and will not be further described in detail herein.

Aberrant expression may be determined using agents that selectively bind to, and thereby detect, the presence of expression products of the genes disclosed herein. For example, an antibody, possibly a suitably labeled antibody, such as where the antibody is bound to a fluorescent or radiolabel, may be generated against a polypeptide encoded by a gene as disclosed herein, and said antibody will then react with, binding either selectively or specifically, to said polypeptide. Such antibody binding, including the relative extent of such binding in samples derived from suspected cancerous, as opposed to otherwise non-cancerous, cells and tissues, can then be used as a measure of the extent of expression of the cancer-related genes identified herein.

In employing the methods of the invention, it should be borne in mind that gene expression indicative of a cancerous state need not be characteristic of every cell found to be cancerous. Thus, the methods disclosed herein are useful for detecting the presence of a cancerous condition within a tissue where less than all cells exhibit the translocation, or deletion, pattern identified in accordance with the invention.

An isolated oligonucleotide probe comprising a first portion comprising a contiguous genomic nucleotide sequence selected from chromosome 5q and a second portion comprising a contiguous genomic nucleotide sequence selected from chromosome 20p and wherein said probe is useful for determining a t(5;20) translocation event. The present invention also contemplates an isolated oligonucleotide probe comprising a first portion comprising a contiguous genomic nucleotide sequence selected from chromosome 5q and a second portion comprising a contiguous genomic nucleotide sequence selected from chromosome 20p and wherein said probe is useful for determining a t(5;20) translocation event. In one embodiment, such oligonucleotide probe comprises at least 15 contiguous nucleotides selected from a sequence of SEQ ID NO: 1-1363, preferably at least 25 such contiguous nucleotides, more preferably at least 50 such contiguous nucleotides and most preferably at least 100 such contiguous nucleotides.

Such probes find use in determining the occurrence of a t(5;20) translocation event in a cell, such as by a method comprising: (a) contacting a t(5;20) sensitive oligonucleotide probe with a target DNA molecule from a cell under conditions supporting hybridization of said probe to said DNA and wherein said t(5;20) sensitive oligonucleotide probe comprises a first portion comprising a contiguous genomic nucleotide sequence selected from chromosome 5q and a second portion comprising a contiguous genomic nucleotide sequence selected from chromosome 20p; (b) determining hybridization of said probe to said target DNA molecule, wherein said hybridization indicates the occurrence of a t(5;20) translocation event in said target DNA molecule thereby determining the occurrence of a t(5;20) translocation event in said cell.

The aforementioned probes are useful in such methods.

Such methods may also employ primers for amplification as a means of determining such translocation event. Thus, the present invention also encompasses a method for determining the occurrence of a t(5;20) translocation event in a cell, comprising: (a) contacting DNA from a cell with a first oligonucleotide primer that hybridizes to a DNA strand from chromosome 5 and a second oligonucleotide primer that hybridizes to a DNA strand from chromosome 20 under conditions supporting said hybridization and under conditions supporting amplification of said hybridized DNA when said first and second oligonucleotide primers hybridize to opposite strands of the same duplex DNA; (b) determining amplification of said hybridized DNA; wherein said amplification indicates the presence of a duplex DNA molecule that hybridizes to both said first and second primers thereby determining the occurrence of a t(5;20) translocation event in said cell.

In a preferred embodiment, the conditions supporting amplification in step (a) are the conditions promoting the polymerase chain reaction, preferably wherein said cell is an interphase cell or a dividing cell, and most preferably where the primers are selected from the sequences of SEQ ID NO:

1-1363.

The present invention includes cancer modulating agents that are themselves either polypeptides, or small chemical entities, that affect the cancerous process, including initiation, suppression or facilitation of tumor growth, either in vivo or ex vivo. Such agents may also be antibodies that react with one or more polypeptides encoded by a gene as disclosed herein.

In keeping with the disclosure herein, the present invention also relates to a method for treating cancer comprising contacting a cancerous cell with an agent having activity against an expression product encoded by a gene corresponding to a polynucleotide that comprises a nucleotide sequence selected from SEQ ID NO: 1-1363. The method of the present invention includes embodiments of the above-recited method wherein said cancer cell is contacted in vivo as well as ex vivo, preferably wherein said agent comprises a portion, or is part of an overall molecular structure, having affinity for said expression product. In one such embodiment, said portion having affinity for said expression product is an antibody. In one embodiment of the present invention, a chemical agent, such as a protein or other polypeptide, is joined to an agent, such as an antibody, having affinity for an expression product of a cancerous cell, such as a polypeptide or protein encoded by a gene related to the cancerous method, especially a gene sequence corresponding to one of the cDNA sequences of SEQ ID NO: 1-1363 . In a specific embodiment, said expression product acts as a therapeutic target for the affinity portion of said anticancer agent and where, after binding of the affinity portion of such agent to the expression product, the anti-cancer portion of said agent acts against said expression product so as to neutralize its effects in initiating, facilitating or promoting tumor formation and/or growth. In a separate embodiment of the present invention, binding of the agent to said expression product may, without more, have the effect of deterring cancer promotion, facilitation or growth, especially where the presence of said expression product is related, either intimately or only in an ancillary manner, to the development and growth of a tumor. Thus, where the presence of said expression product (such as a mutated or truncated polypeptide) is essential to tumor initiation and/or growth, binding of said agent to said expression product will have the effect of negating said tumor promoting activity. In one such embodiment, said agent is an apoptosis- inducing agent that induces cell suicide, thereby killing the cancer cell and halting tumor growth.

Many cancers contain chromosomal rearrangements, which typically represent translocations, amplifications, or deletions of specific regions of genomic DNA. A recurrent chromosomal rearrangement that is associated with a specific stage and type of cancer always affects a gene (or possibly genes) that play a direct and critical role in the initiation or progression of the disease. Many of the known oncogenes or tumor suppressor genes that play direct roles in cancer have either been initially identified based upon their positional cloning from a recurrent chromosomal rearrangement or have been demonstrated to fall within a rearrangement subsequent to their cloning by other methods.

The present invention also relates to a method that comprises a method for producing a product comprising identifying an agent, including generating test data, according to one of the disclosed methods for identifying such an agent (i.e., the therapeutic agents identified according to the assay procedures disclosed herein) wherein said product is the data collected with respect to said agent as a result of said identification method, or assay, and wherein said data is sufficient to convey the chemical character and/or structure and/or properties of said agent. For example, the present invention specifically contemplates a situation whereby a user of an assay of the invention may use the assay to screen for compounds having the desired enzyme modulating activity and, having identified the compound, then conveys that information (i.e., information as to structure, dosage, etc) to another user who then utilizes the information to reproduce the agent and administer it for therapeutic or research purposes according to the invention. For example, the user of the assay (user 1) may screen a number of test compounds without knowing the structure or identity of the compounds (such as where a number of code numbers are used the first user is simply given samples labeled with said code numbers) and, after performing the screening method, using one or more assay methods of the present invention, then imparts to a second user (user 2), verbally or in writing or some equivalent fashion, sufficient information to identify the compounds having a particular modulating activity (for example, the code number with the corresponding results). This transmission of information from user 1 to user 2 is specifically contemplated by the present invention. In accordance with the foregoing, the present invention encompasses a method for producing test data with respect to the gene modulating activity of a compound comprising: (a) contacting a compound with a cell containing a polynucleotide comprising a nucleotide sequence corresponding to a gene whose expression is increased in a cancerous cell over that in a non-cancerous cell and under conditions wherein said polynucleotide is being expressed, (b) determining a change in expression of polynucleotides as a result of said contacting, and (c) producing test data with respect to the gene modulating activity of said compound based on a decrease in the expression of the determined gene whose expression is otherwise increased in a cancerous cell over that in a non-cancerous cell indicating gene modulating activity. It should be cautioned that, in carrying out the procedures of the present invention as disclosed herein, any reference to particular buffers, media, reagents, cells, culture conditions and the like are not intended to be limiting, but are to be read so as to include all related materials that one of ordinary skill in the art would recognize as being of interest or value in the particular context in which that discussion is presented. For example, it is often possible to substitute one buffer system or culture medium for another and still achieve similar, if not identical, results. Those of skill in the art will have sufficient knowledge of such systems and methodologies so as to be able, without undue experimentation, to make such substitutions as will optimally serve their purposes in using the methods and procedures disclosed herein.

The present invention will now be further described by way of the following non-limiting example. In applying the disclosure of the example, it should be kept clearly in mind that other and different embodiments of the methods disclosed according to the present invention will no doubt suggest themselves to those of skill in the relevant art. EXAMPLE

Cells that express one or more of the genes selected from those that correspond to SEQ ID NO: 1-1363 are grown to a density of 10⁵ cells/cm² in Leibovitz's L-15 medium supplemented with 2 mM L-glutamine (90%) and 10% fetal bovine serum. The cells are collected after treatment with 0.25% trypsin, 0.02% EDTA at 37°C for 2 to 5 minutes. The trypsinized cells are then diluted with 30 ml growth medium and plated at a density of 50,000 cells per well in a 96 well plate (200 μl/well). The following day, cells are treated with either compound buffer alone, or compound buffer containing a chemical agent to be tested, for 24 hours. The media is then removed, the cells lysed and the RNA recovered using the RNAeasy reagents and protocol obtained from Qiagen. RNA is quantitated and 10 ng of sample in 1 μl are added to 24 μl of Taqman reaction mix containing 1X PCR buffer, RNAsin, reverse transcriptase, nucleoside triphosphates, amplitaq gold, Tween 20, glycerol, bovine serum albumin (BSA) and specific PCR primers and probes for a reference gene (18S RNA) and a test gene (Gene X). Reverse transcription is then carried out at 48°C for 30 minutes. The sample is then applied to a Perkin Elmer 7700 sequence detector and heat denatured for 10 minutes at 95°C. Amplification is performed through 40 cycles using 15 seconds annealing at 60°C followed by a 60 second extension at 72°C and 30 second denaturation at 95°C. Data files are then captured and the data analyzed with the appropriate baseline windows and thresholds. The quantitative difference between the target and reference genes is then calculated and a relative expression value determined for all of the samples used. This procedure is then repeated for each of the target genes in a given signature, or characteristic, set and the relative expression ratios for each pair of genes is determined (i.e., a ratio of expression is determined for each target gene versus each of the other genes for which expression is measured, where each gene's absolute expression is determined relative to the reference gene for each compound, or chemical agent, to be screened). The samples are then scored and ranked according to the degree of alteration of the expression profile in the treated samples relative to the control. The overall expression of the set of genes relative to the controls, as modulated by one chemical agent relative to another, is also ascertained. Chemical agents having the most effect on a given gene, or set of genes, are considered the most anti-neoplastic.

In a preferred embodiment of such a method, the cell is an SW480 or SW620 cell.

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Claims

WHAT IS CLAIMED IS:

1. A method for identifying a gene modulating agent, comprising: (a) contacting a test compound with a cell expressing a gene corresponding to a polynucleotide that comprises a nucleotide sequence selected from SEQ ID NO: 1-1363 and under conditions supporting such expression, and (b) detecting a change in expression of said gene as a result of said contacting, wherein said change in expression indicates gene modulating activity, thereby identifying said test compound as a gene modulating agent.

2. The method of claim 1 wherein said gene comprises a nucleotide sequence of SEQ ID NO: 1-1363.

3. The method of claim 1 wherein said change in expression is a decrease in expression.

4. The method of claim 1 wherein said cell is a recombinant cell.

5. The method of claim 1 wherein said cell is a cancerous cell.

6. The method of claim 5 wherein said cell is of the cell line selected from the group consisting of SW480 and SW620.

7. The method of claim 6 wherein said compound binds to a promoter region of said gene.

8. The method of claim 7 wherein said compound prevents binding of RNA polymerase to said promoter region.

9. The method of claim 4 wherein said agent decreases expression by decreasing transcription.

10. The method of claim 3 wherein said decrease in expression is detected as a decrease in synthesis of a polypeptide.

11. The method of claim 10 wherein said polypeptide comprises an amino acid sequence selected from SEQ ID NO: 1364-1398.

12. The method of claim 1 wherein said test compound binds to a polypeptide encoded by said gene.

13. The method of claim 12 wherein said agent is an antibody.

14. A method for identifying an anti-neoplastic agent comprising contacting a cancerous cell with a test compound found to have gene modulating activity in the method of claim 1 and under conditions supporting growth of said cell and detecting a change in the growth of said cancerous cell as a result of said contacting thereby identifying said test compound as an anti-neoplastic agent.

15. The method of claim 14 wherein said change in growth is a decrease in the rate of replication of said cancerous cell.

16. The method of claim 14 wherein said change in growth is a decrease in the total number of progeny cells that can be produced by said cancerous cell.

17. The method of claim 14 wherein said change in growth is a decrease in the number of times said cancerous cell can replicate.

18. The method of claim 14 wherein said change in growth is the death of said cancerous cell.

19. A method for detecting the cancerous status of a cell, comprising contacting DNA from said cell with an oligonucleotide probe comprising a sequence of at least 15 contiguous nucleotides of a polynucleotide having a nucleotide sequence selected from SEQ ID NO: 1-1363 and determining decreased hybridization thereof when compared to hybridization of said probe to DNA of a normal cell of the same tissue type.

20. The method of claim 19 wherein said tissue is colon.

21. The method of claim 19 wherein said probe is at least 20 contiguous nucleotides in length.

22. The method of claim 19 wherein said probe is at least 25 contiguous nucleotides in length.

23. The method of claim 19 wherein said probe is at least 50 contiguous nucleotides in length.

24. The method of claim 19 wherein said probe is at least 80 contiguous nucleotides in length.

25. The method of claim 19 wherein said probe is at least 100 contiguous nucleotides in length.

26. A method for detecting the cancerous status of a cell, comprising contacting DNA from said cell with an oligonucleotide probe comprising the nucleotide sequence of BAG RP11-788G24 .

27. A method for detecting the cancerous status of a cell, comprising detecting in a cell a polypeptide that is a truncated form of a polypeptide encoded by a gene corresponding to a polynucleotide that comprises a nucleotide sequence selected from SEQ ID NO: 1-1363

28. A method for treating cancer comprising contacting a cancerous cell with an agent having gene modulating activity in the method of claim 1 and in an amount effective to cause a reduction in cancerous activity of said cell.

29. The method of claim 28 wherein said cell is a colon cell.

30. The method of claim 28 wherein said agent was first identified as having gene modulating activity using the method of claim 1.

31. A method for detecting cancer or a disposition toward developing cancer comprising detecting in a sample from a patient a decrease in expression of a gene corresponding to a polynucleotide comprising a nucleotide sequence selected from SEQ ID NO: 1-1363.

32. The method of claim 31 wherein said decrease in expression is a decrease in copy number of the gene.

33. The method of claim 31 wherein said gene comprises a nucleotide sequence of SEQ ID NO: 1-1363 .

34. The method of claim 31 wherein said cell is a colon cell.

35. The method of claim 31 wherein said agent was first identified as having anti-neoplastic activity using the method of claim 17.

36. A method for determining the likelihood of success of cancer therapy in a patient, comprising monitoring in a patient undergoing cancer therapy the expression of a gene corresponding to a polypeptide having a sequence of SEQ ID NO: 1-1363 wherein an decrease in said expression prior to completion of said cancer therapy is indicative of a likelihood of success of said cancer therapy.

37. The method of claim 36 wherein said gene comprises a sequence of SEQ ID NO: 1-1363 .

38. The method of claim 36 wherein said cancer is a cancer of colon

39. A method for preventing progression to metastasis in a cancer cell comprising introducing into a cancer cell one or more copies of a gene corresponding to a polynucleotide comprising a nucleotide sequence selected from SEQ ID NO: 1-1363.

40. A method for treating cancer in a patient comprising administering to a patient afflicted therewith an effective amount of a vector comprising one or more genes corresponding to a polynucleotide comprising a nucleotide sequence selected from SEQ ID NO: 1-1363 and wherein said vector transduces non-metastatic primary tumor cells.

41. The method of claim 40 wherein said cells are colon cells.

42. The method of claim 40 wherein said treating cancer is the inhibition of metastasis.

43. The method of claim 40 wherein said vector is a retrovirus.

44. A method for treating cancer in a patient comprising administering to a patient afflicted therewith an effective amount of a vector comprising the nucleotide sequence of one or more BAG RP11-788G24 and wherein said vector transduces non-metastatic primary tumor cells.

45. The method of claim 44 wherein said cells are colon cells.

46. The method of claim 44 wherein said vector is a retrovirus.

47. A method for producing test data with respect to the gene modulating activity of a compound comprising: (a) contacting a compound with a cell containing a polynucleotide comprising a nucleotide sequence corresponding to a gene whose expression is increased in a cancerous cell over that in a non-cancerous cell and under conditions wherein said polynucleotide is being expressed, (b) determining a change in expression of polynucleotides as a result of said contacting, and (c) producing test data with respect to the gene modulating activity of said compound based on a decrease in the expression of the determined gene whose expression is otherwise increased in a cancerous cell over that in a non-cancerous cell indicating gene modulating activity.

48. An isolated oligonucleotide probe comprising a first portion comprising a contiguous genomic nucleotide sequence selected from chromosome 5q and a second portion comprising a contiguous genomic nucleotide sequence selected from chromosome 20p and wherein said probe is useful for determining a t(5;20) translocation event.

49. The isolated oligonucleotide probe of claim 48 wherein said probe comprises at least 15 contiguous nucleotides selected from a sequence of SEQ ID NO: 1-1363.

50. The isolated oligonucleotide probe of claim 48 wherein said probe comprises at least 25 contiguous nucleotides selected from a sequence of SEQ ID NO: 1-1363.

51. The isolated oligonucleotide probe of claim 48 wherein said probe comprises at least 50 contiguous nucleotides selected from a sequence of SEQ ID NO: 1-1363.

52. The isolated oligonucleotide probe of claim 48 wherein said probe comprises at least 100 contiguous nucleotides selected from a sequence of

SEQ ID NO: 1-1363.

53. A method for determining the occurrence of a t(5;20) translocation event in a cell, comprising: (a) contacting a t(5;20) sensitive oligonucleotide probe with a target

DNA molecule from a cell under conditions supporting hybridization of said probe to said DNA and wherein said t(5;20) sensitive oligonucleotide probe comprises a first portion comprising a contiguous genomic nucleotide sequence selected from chromosome 5q and a second portion comprising a contiguous genomic nucleotide sequence selected from chromosome 20p; (b) determining hybridization of said probe to said target DNA molecule, wherein said hybridization indicates the occurrence of a t(5;20) translocation event in said target DNA molecule thereby determining the occurrence of a t(5;20) translocation event in said cell.

54. The method of claim 53 wherein said probe is the probe of claim 48, 49, 50, 51, or 52.

55. A method for determining the occurrence of a t(5;20) translocation event in a cell, comprising: (a) contacting DNA from a cell with a first oligonucleotide primer that hybridizes to a DNA strand from chromosome 5 and a second oligonucleotide primer that hybridizes to a DNA strand from chromosome 20 under conditions supporting said hybridization and under conditions supporting amplification of said hybridized DNA when said first and second oligonucleotide primers hybridize to opposite strands of the same duplex DNA; (b) determining amplification of said hybridized DNA; wherein said amplification indicates the presence of a duplex DNA molecule that hybridizes to both said first and second primers thereby determining the occurrence of a t(5;20) translocation event in said cell.

56. The method of claim 55 wherein the conditions supporting amplification in step (a) are the conditions promoting the polymerase chain reaction.

57. The method of claim 55 wherein said cell is an interphase cell.

58. The method of claim 55 wherein said cell is a dividing cell.

59. The method of claim 55 wherein said primers are selected from the sequences of SEQ ID NO: 1-1363.