Oligonucleotides for cancer diagnosis

Abstract

The present invention provides sets of oligonucleotides corresponding to genes encoding proteins involved in protein synthesis and/or stability or genes encoding proteins involved in the regulation of defense and/or chromatin remodeling for use in preparing transcript patterns particularly for cancer diagnosis. The invention also extends to such sets and kits containing such sets as well as related method reliant on analysis of marker polypeptides encoded by the genes to develop characteristic expression profiles.

1 - 47 . (canceled) 
     
     
         48 . A method of preparing a standard gene transcript pattern characteristic of a cancer or stage thereof in an organism comprising at least the steps of:
 a) isolating mRNA from the cells of a sample of one or more organisms having the cancer or stage thereof, which isolated mRNA may optionally be reverse transcribed to cDNA;   b) hybridizing the mRNA or cDNA of step (a) to a set of oligonucleotide probes specific for said cancer or stage thereof in an organism and sample thereof corresponding to the organism and sample thereof under investigation, wherein said set comprises at least 10 oligonucleotides, wherein each of said at least 10 oligonucleotides is selected from an oligonucleotide listed in Table 2 or 3, or derived from a sequence described in Table 2 or 3, or a complementary sequence thereof, and wherein said set contains less than 1000 oligonucleotide probes; and   c) assessing the amount of mRNA or cDNA hybridizing to each of said probes to produce a characteristic pattern reflecting the level of gene expression of genes to which said oligonucleotides bind, in the sample with the cancer or stage thereof, thereby obtaining a standard gene transcript pattern characteristic of a cancer or stage thereof in an organism.   
     
     
         49 . A method of preparing a test gene transcript pattern comprising at least the steps of:
 a) isolating mRNA from the cells of a sample of said test organism, which isolated mRNA may optionally be reverse transcribed to cDNA;   b) hybridizing the mRNA or cDNA of step (a) to a set of oligonucleotides as defined in  claim 48  specific for a cancer or stage thereof in an organism and sample thereof corresponding to the organism and sample thereof under investigation; and   c) assessing the amount of mRNA or cDNA hybridizing to each of said probes to produce said pattern reflecting the level of gene expression of genes to which said oligonucleotides bind, in said test sample, thereby obtaining a test gene transcript pattern.   
     
     
         50 . A method of diagnosing or identifying or monitoring a cancer or stage thereof in an organism, comprising the steps of:
 a) isolating mRNA from the cells of a sample of said organism, which isolated mRNA may optionally be reverse transcribed to cDNA;   b) hybridizing the mRNA or cDNA of step (a) to a set of oligonucleotides specific for said cancer or stage thereof in an organism and sample thereof corresponding to the organism and sample thereof under investigation, wherein each of said at least 10 oligonucleotides is selected from an oligonucleotide listed in Table 2 or 3, or derived from a sequence described in Table 2 or 3, or a complementary sequence thereof, and wherein said set contains less than 1000 oligonucleotide probes;   c) assessing the amount of mRNA or cDNA hybridizing to each of said probes to produce a characteristic pattern reflecting the level of gene expression of genes to which said oligonucleotides bind, in said sample; and   d) comparing said pattern to a standard diagnostic pattern prepared according to the method of  claim 48  using a sample from an organism corresponding to the organism and sample under investigation to determine the presence of said cancer or a stage thereof in the organism under investigation.   
     
     
         51 . The method as claimed in  claim 48 , wherein each oligonucleotide probe is selected from an oligonucleotide listed in Table 2, or derived from a sequence described in Table 2, or a complementary sequence thereof. 
     
     
         52 . The method as claimed in  claim 48 , wherein each oligonucleotide probe is selected from an oligonucleotide listed in Table 3, or derived from a sequence described in Table 3, or a complementary sequence thereof. 
     
     
         53 . The method as claimed in  claim 48 , wherein said set additionally comprises one or more oligonucleotide probes selected from an oligonucleotide listed in Table 4, or derived from a sequence described in Table 4, or a complementary sequence thereof. 
     
     
         54 . The method as claimed in  claim 48 , wherein the oligonucleotide derived from a sequence disclosed in Table 2, 3 or 4 is a part of a gene described by its Accession number in Table 2, 5 or 6, respectively, or a complementary sequence thereof. 
     
     
         55 . The method as claimed in  claim 53 , wherein the oligonucleotide derived from a sequence disclosed in Table 2, 3 or 4 is a part of a gene described by its Accession number in Table 2, 5 or 6, respectively, or a complementary sequence thereof. 
     
     
         56 . The method as claimed in  claim 48 , wherein said set consists of from 10 to 500 probes. 
     
     
         57 . The method as claimed in  claim 48 , wherein said set of probes are immobilized on one or more solid supports. 
     
     
         58 . The method as claimed in  claim 48 , wherein said sample is peripheral blood. 
     
     
         59 . The method as claimed in  claim 48 , wherein said cancer is stomach, lung, breast, prostate gland, bowel, skin, colon or ovary cancer. 
     
     
         60 . The method as claimed in  claim 48 , wherein said organism is a mammal. 
     
     
         61 . The method as claimed in  claim 48 , wherein at least one of said probes in said set is suitable for diagnosing, identifying or monitoring at least two of said cancers or stages hereof. 
     
     
         62 . The method of diagnosing or identifying or monitoring as claimed in  claim 50 , wherein said diagnosing, identifying or monitoring of two or more cancers or stages thereof in an organism, wherein said test pattern produced in step c) of the diagnostic method is compared in step d) to at least two of said standard diagnostic patterns, wherein each standard diagnostic pattern is a pattern generated for a different cancer or stage thereof. 
     
     
         63 . A set of oligonucleotide probes as defined in  claim 48 , wherein said probe set contains less than 500 probes. 
     
     
         64 . A kit comprising a set of oligonucleotide probes as defined in  claim 63  immobilized on one or more solid supports. 
     
     
         65 . A method of preparing a standard gene transcript pattern characteristic of a cancer or stage thereof in an organism comprising at least the steps of:
 a) releasing target polypeptides from a sample of one or more organisms having the cancer or stage thereof;   b) contacting said target polypeptides with one or more binding partners, wherein each binding partner is specific to a marker polypeptide (or a fragment thereof) encoded by the gene to which an oligonucleotide as defined in  claim 48  binds, to allow binding of said binding partners to said target polypeptides, wherein said marker polypeptides are specific for said cancer in an organism and sample thereof corresponding to the organism and sample thereof under investigation; and   c) assessing the target polypeptide binding to said binding partners to produce a characteristic pattern reflecting the level of gene expression of genes which express said marker polypeptides, in the sample with the cancer or stage thereof, thereby obtaining a standard gene transcript pattern characteristic of a cancer or stage thereof in an organism.   
     
     
         66 . A method of preparing a test gene transcript pattern comprising at least the steps of:
 a) releasing target polypeptides from a sample of said test organism;   b) contacting said target polypeptides with one or more binding partners, wherein each binding partner is specific to a marker polypeptide (or a fragment thereof) encoded by the gene to which an oligonucleotide as defined in  claim 48  binds, to allow binding of said binding partners to said target polypeptides, wherein said marker polypeptides are specific for said cancer in an organism and sample thereof corresponding to the organism and sample thereof under investigation; and   c) assessing the target polypeptide binding to said binding partners to produce a characteristic pattern reflecting the level of gene expression of genes which express said marker polypeptides, in said test sample, thereby obtaining a test gene transcript pattern.   
     
     
         67 . A method of diagnosing or identifying or monitoring a cancer or stage thereof in an organism comprising the steps of:
 a) releasing target polypeptides from a sample of said organism;   b) contacting said target polypeptides with one or more binding partners, wherein each binding partner is specific to a marker polypeptide (or a fragment thereof) encoded by the gene to which an oligonucleotide binds, to allow binding of said binding partners to said target polypeptides, wherein said marker polypeptides are specific for said cancer in an organism and sample thereof corresponding to the organism and sample thereof under investigation, and wherein said oligonucleotide is selected from an oligonucleotide listed in Table 2 or 3, or derived from a sequence described in Table 2 or 3, or a complementary sequence thereof; and   c) assessing the target polypeptide binding to said binding partners to produce a characteristic pattern reflecting the level of gene expression of genes which express said marker polypeptides in said sample; and   d) comparing said pattern to a standard diagnostic pattern prepared according to the method of  claim 65  using a sample from an organism corresponding to the organism and sample under investigation to determine the degree of correlation indicative of the presence of said cancer or a stage thereof in the organism under investigation.   
     
     
         68 . The method as claimed in  claim 59 , wherein said cancer is breast cancer. 
     
     
         69 . The method as claimed in  claim 60 , wherein said organism is a human. 
     
     
         70 . The set of oligonucleotide probes as claimed in  claim 63 , wherein said set additionally comprises one or more oligonucleotide probes selected from an oligonucleotide listed in Table 4, or derived from a sequence described in Table 4, or a complementary sequence thereof. 
     
     
         71 . The set of oligonucleotide probes as claimed in  claims 63 , wherein the oligonucleotide derived from a sequence disclosed in Table 2, 3 or 4 is a part of a gene described by its Accession number in Table 2, 5 or 6, respectively, or a complementary sequence thereof. 
     
     
         72 . The method as claimed in  claim 48 , wherein said set of oligonucleotides is randomly selected from the oligonucleotides listed in Table 2 or 3, wherein each oligonucleotide may be replaced with an oligonucleotide derived from said Table 2 or 3 oligonucleotide, with an oligonucleotide with a complementary sequence or with a functionally equivalent oligonucleotide. 
     
     
         73 . The method as claimed in  claim 49 , wherein said set of oligonucleotides is randomly selected from the oligonucleotides listed in Table 2 or 3, wherein each oligonucleotide may be replaced with an oligonucleotide derived from said Table 2 or 3 oligonucleotide, with an oligonucleotide with a complementary sequence or with a functionally equivalent oligonucleotide. 
     
     
         74 . The method as claimed in  claim 50 , wherein said set of oligonucleotides is randomly selected from the oligonucleotides listed in Table 2 or 3, wherein each oligonucleotide may be replaced with an oligonucleotide derived from said Table 2 or 3 oligonucleotide, with an oligonucleotide with a complementary sequence or with a functionally equivalent oligonucleotide. 
     
     
         75 . The method as claimed in  claim 48  wherein said set comprises all of the oligonucleotides listed in Table 2 or 3, wherein each oligonucleotide may be replaced with an oligonucleotide derived from said Table 2 or 3 oligonucleotide, with an oligonucleotide with a complementary sequence or with a functionally equivalent oligonucleotide. 
     
     
         76 . The method as claimed in  claim 49  wherein said set comprises all of the oligonucleotides listed in Table 2 or 3, wherein each oligonucleotide may be replaced with an oligonucleotide derived from said Table 2 or 3 oligonucleotide, with an oligonucleotide with a complementary sequence or with a functionally equivalent oligonucleotide. 
     
     
         77 . The method as claimed in  claim 50  wherein said set comprises all of the oligonucleotides listed in Table 2 or 3, wherein each oligonucleotide may be replaced with an oligonucleotide derived from said Table 2 or 3 oligonucleotide, with an oligonucleotide with a complementary sequence or with a functionally equivalent oligonucleotide. 
     
     
         78 . The method as claimed in  claim 72 , wherein said set additionally comprises all of the oligonucleotides listed in Table 4 wherein each oligonucleotide may be replaced with an oligonucleotide derived from said Table 4 oligonucleotide, with an oligonucleotide with a complementary sequence or with a functionally equivalent oligonucleotide. 
     
     
         79 . The method as claimed in  claim 73 , wherein said set additionally comprises all of the oligonucleotides listed in Table 4 wherein each oligonucleotide may be replaced with an oligonucleotide derived from said Table 4 oligonucleotide, with an oligonucleotide with a complementary sequence or with a functionally equivalent oligonucleotide. 
     
     
         80 . The method as claimed in  claim 74 , wherein said set additionally comprises all of the oligonucleotides listed in Table 4 wherein each oligonucleotide may be replaced with an oligonucleotide derived from said Table 4 oligonucleotide, with an oligonucleotide with a complementary sequence or with a functionally equivalent oligonucleotide. 
     
     
         81 . The method as claimed in  claim 75 , wherein said set additionally comprises all of the oligonucleotides listed in Table 4 wherein each oligonucleotide may be replaced with an oligonucleotide derived from said Table 4 oligonucleotide, with an oligonucleotide with a complementary sequence or with a functionally equivalent oligonucleotide. 
     
     
         82 . The method as claimed in  claim 76 , wherein said set additionally comprises all of the oligonucleotides listed in Table 4 wherein each oligonucleotide may be replaced with an oligonucleotide derived from said Table 4 oligonucleotide, with an oligonucleotide with a complementary sequence or with a functionally equivalent oligonucleotide. 
     
     
         83 . The method as claimed in  claim 77 , wherein said set additionally comprises all of the oligonucleotides listed in Table 4 wherein each oligonucleotide may be replaced with an oligonucleotide derived from said Table 4 oligonucleotide, with an oligonucleotide with a complementary sequence or with a functionally equivalent oligonucleotide.