Methods and kits for diagnosing the prognosis of cancer patients

Abstract

The prognosis of a cancer patient can be determined by analyzing the modulation of expression of specified genes in the tumor tissue. Genes uniquely up-regulated in adult stem cells that can reconstitute the tissue of the tumor are analyzed for up-regulation in the patient's tumor. Up-regulation of a plurality of such genes in the tumor is an indication of good prognosis. Genes uniquely up-regulated in fetal stem cells are analyzed for up-regulation in the patient's tumor. Up-regulation of a plurality of such genes in the tumor are an indication of a poor prognosis. Specific genes are disclosed, the modulation of which, in a patient's prostate cancer tumor, will serve as an indication of prognosis. Patients with a good prognosis are subjected to watchful waiting. Patients with a poor prognosis are aggressively treated. Kits are provided containing a set of affinity reagents that specifically detect expression of the various genes.

We claim: 
     
         1 . A method for determining the prognosis of a cancer patient having a tissue-specific tumor, comprising:
 (a) analyzing the expression levels of a plurality of genes in tumor cells of the cancer patient, which genes are uniquely up-regulated in adult stem cells that have a high capacity of reconstituting the tissue from which the tumor originated, said unique up-regulation being as compared to fully differentiated cells of said tissue;   (b) if expression of a plurality of the genes analyzed is up-regulated in the tumor cells as compared to their expression in normal cells or tumor cells of said tissue in a plurality of other cancer patients having the tissue-specific tumor, a good prognosis for said patient is determined; and   (c) if step (b) determines a good prognosis, adopting a regimen of active surveillance for the patient without taking active steps to remove, reduce or otherwise treat the tumor until symptoms appear or change.   
     
     
         2 . The method according to  claim 1 , wherein said analyzing step is accomplished by assaying for the levels of proteins that are the expression products of said genes. 
     
     
         3 . The method according to  claim 1 , wherein said analyzing step is accomplished by assaying for the levels of RNA transcription from said genes. 
     
     
         4 . The method according to  claim 1 , wherein the tissue-specific tumor is prostate tumor. 
     
     
         5 . The method according to  claim 4 , wherein said plurality of genes in step (a) comprises the KLF4 gene and the JUNB gene and, in step (b), the expression of both of the KLF4 and the JUNB genes must be up-regulated in the prostate tumor cells as compared to their expression in normal prostate cells or prostate tumor cells in a plurality of other prostate tumor patients for a good prognosis to be determined. 
     
     
         6 . A method in accordance with  claim 4 , wherein said step (a) comprises:
 (a) analyzing the expression levels, in the patient's prostate tumor cells, of at least two of the genes selected from the group consisting of JUNB, KLF4, FOXH1, FOS, CLDN4, PADI4, B3GNT5, CDC7, PANK1, UNG, CBR3, and ATF3;   
       and wherein said step (b) comprises:
 (b) if expression of at least two of the genes analyzed is modulated, as compared to their expression in normal prostate cells or in prostate tumor samples from a plurality of other prostate tumor patients, determining a good prognosis, wherein said modulated expression is defined as
 (i) up-regulation in the case of JUNB, KLF4, FOXH1, FOS, CLDN4, PADI4, B3GNT5, CDC7, CBR3, and ATF3, and 
 (ii) down-regulation in the case of PANK1 and UNG. 
 
 
     
     
         7 . The method according to  claim 6 , wherein said analyzing step is performed after surgical removal of, other definitive treatment of, the prostate cancer, and wherein said prognosis is a prognosis of cancer recurrence, and a good prognosis is defined as a decreased likelihood of recurrence or an increased likelihood of no recurrence 
     
     
         8 . The method according to  claim 6 , wherein said analyzing step is performed prior to surgical removal of, other definitive treatment of, the prostate cancer, and wherein said prognosis is a prognosis of cancer progression, and a good prognosis is defined as an increased likelihood that surgery or other definitive treatment will not be necessary unless symptoms appear or change. 
     
     
         9 . A method for determining the prognosis of a cancer patient having a tissue-specific tumor, comprising:
 (a) analyzing the expression levels of a plurality of genes in tumor cells of the cancer patient, which genes are uniquely up-regulated in fetal stem cells that have a high capacity of reconstituting the tissue from which the tumor originated, said unique up-regulation being as compared to fully differentiated cells of said tissue;   (b) if expression of a plurality of the genes analyzed is up-regulated in the tumor cells as compared to their expression in normal cells or tumor cells of said tissue in a plurality of other cancer patients having the tissue-specific tumor, a bad prognosis for said patient is determined; and   (c) if step (b) determines a bad prognosis, taking active steps to remove, reduce or otherwise treat the tumor.   
     
     
         10 . A method in accordance with  claim 9  wherein the tissue-specific tumor is prostate tumor. 
     
     
         11 . A method in accordance with  claim 10 , wherein said step (a) comprises:
 (a) analyzing the expression levels, in the patient's prostate tumor cells, of at least five of the genes selected from the group consisting of ACAT1, ANLN, ARHGDIG, ASPN, BNC1, BRCA1, BUB1B, C13ORF3, C6ORF105, C8ORF34, CASC5, CCNA2, CDKN3, CENPF, CENPI, CHPF, CIT, DEGS1, DIRAS2, DLGAP5, DNAH8, DUSP26, E2F8, EFNA3, ELFN2, EME1, EPHA6, ESPL1, EVPL, FAP, FKBP10, FOLH1, HBE1, HCG_1774568, IGF2BP3, INCENP, IRS4, IVL, KIF11, KIF4A, KIF4B, KRT1, LOC654342, MELK, MKI67, MLF1IP, NCAPG, NCAPG2, NFS1, NOX4, NUSAP1, ONECUT2, PRC1, PRR3, PSAPL1, PSAT1, PTPRR, RACGAP1, RAMP2, RELN, RP11-49G10.8, SCGN, SLC2A13, SLC31A2, SLC35F1, SLC6A10P, SMC2, SYT9, TAS2R10, TEX101, THSD1, TPX2, TSSC1, TTK, UBE2C, UNC13C, USP9Y, UTS2D, WNT4, WT1, ZFP41, AASDHPPT, ACIN1, ACSL5, ACTN1, AHNAK, ANKRA2, ANKRD36, ANDS, ANXA1, ASCC3, B4GALT1, BACE2, BTBD3, C10ORF26, C180RF25, CASP4, CD44, CDK10, CEP110, CHD3, COG4, CTR9, CWF19L2, CYP1B1, CYP27A1, DDHD2, DDX6, DENND2D, DPP4, DYM, EED, EFCAB4B, EPC1, ERAP1, FAM122C, FAM13B, FAM178A, FAS, FBXO21, GALNS, GBP2, GSTM1, HLA-A, HYDIN, IFI16, IL6ST, KIAA0174, KIAA1009, KIAA1328, KLHL2, KRT14, LEPR, LNPEP, LOC652614, LRRK1, MAN2A1, MAP3K1, MBD1, MT1X, MTSS1, MTUS1, NAPG, NRBP2, OGN, PCNX, PDK4, PHACTR2, PHLPP, PI15, PITPNC1, PLAA, PLEKHF2, PRKD3, PSEN1, PSMB8, PSPC1, RAB11FIP2, RBBP7, RBBP8, RBM41, RGS2, RGS22, RND3, RNPC3, RPRD1A, SATB1, SCN7A, SDCCAG10, SETBP1, SH3RF2, SLC15A2, SPG7, SQRDL, SRD5A2, ST6GAL1, SYNCRIP, TNFRSF10D, TNRC6A, TRIM22, ZADH2, ZBTB20, ZNF259, ZNF334, and ZNF532;   
       and wherein said step (b) comprises:
 (b) if expression of at least five of the genes analyzed is modulated, as compared to their expression in normal prostate cells or in prostate tumor samples from a plurality of other prostate tumor patients, determining a poor prognosis, wherein said modulated expression is defined as
 (i) up-regulation in the case of ACAT1, ANLN, ARHGDIG, ASPN, BNC1, BRCA1, BUB1B, C13ORF3, C6ORF105, C8ORF34, CASC5, CCNA2, CDKN3, CENPF, CENPI, CHPF, CIT, DEGS1, DIRAS2, DLGAP5, DNAH8, DUSP26, E2F8, EFNA3, ELFN2, EME1, EPHA6, ESPL1, EVPL, FAP, FKBP10, FOLH1, HBE1, HCG_1774568, IGF2BP3, INCENP, IRS4, IVL, KIF11, KIF4A, KIF4B, KRT1, LOC654342, MELK, MKI67, MLF1IP, NCAPG, NCAPG2, NFS1, NOX4, NUSAP1, ONECUT2, PRC1, PRR3, PSAPL1, PSAT1, PTPRR, RACGAP1, RAMP2, RELN, RP11-49G10.8, SCGN, SLC2A13, SLC31A2, SLC35F1, SLC6A10P, SMC2, SYT9, TAS2R10, TEX101, THSD1, TPX2, TSSC1, TTK, UBE2C, UNC13C, USP9Y, UTS2D, WNT4, WT1 and ZFP41, and 
 (ii) down-regulation in the case of AASDHPPT, ACIN1, ACSL5, ACTN1, AHNAK, ANKRA2, ANKRD36, ANO5, ANXA1, ASCC3, B4GALT1, BACE2, BTBD3, C10ORF26, C180RF25, CASP4, CD44, CDK10, CEP110, CHD3, COG4, CTR9, CWF19L2, CYP1B1, CYP27A1, DDHD2, DDX6, DENND2D, DPP4, DYM, EED, EFCAB4B, EPC1, ERAP1, FAM122C, FAM13B, FAM178A, FAS, FBXO21, GALNS, GBP2, GSTM1, HLA-A, HYDIN, IFI16, IL6ST, KIAA0174, KIAA1009, KIAA1328, KLHL2, KRT14, LEPR, LNPEP, LOC652614, LRRK1, MAN2A1, MAP3K1, MBD1, MT1X, MTSS1, MTUS1, NAPG, NRBP2, OGN, PCNX, PDK4, PHACTR2, PHLPP, PI15, PITPNC1, PLAA, PLEKHF2, PRKD3, PSEN1, PSMB8, PSPC1, RAB11FIP2, RBBP7, RBBP8, RBM41, RGS2, RGS22, RND3, RNPC3, RPRD1A, SATB1, SCN7A, SDCCAG10, SETBP1, SH3RF2, SLC15A2, SPG7, SQRDL, SRD5A2, ST6GAL1, SYNCRIP, TNFRSF10D, TNRC6A, TRIM22, ZADH2, ZBTB20, ZNF259, ZNF334, and ZNF532. 
 
 
     
     
         12 . The method according to  claim 11 , wherein said analyzing step is performed after surgical removal of, other definitive treatment of, the prostate cancer, and wherein said prognosis is a prognosis of cancer recurrence, and a poor prognosis is defined as an increased likelihood of recurrence. 
     
     
         13 . The method according to  claim 11 , wherein said analyzing step is performed prior to surgical removal of, other definitive treatment of, the prostate cancer, wherein said prognosis is a prognosis of cancer progression, and a poor prognosis is defined as an increased likelihood of tumor progression and therefore an increased likelihood of the necessity of tumor excision or other definitive treatment, and wherein step (c) comprises performing surgery on the prostate of the patient. 
     
     
         14 . The method according to  claim 11 , wherein at least 10 of said genes are analyzed in said analyzing step. 
     
     
         15 . The method according to  claim 14 , wherein said determination is of a poor prognosis if at least ten of the genes analyzed manifest said modulated expression. 
     
     
         16 . The method according to  claim 11 , wherein at least 20 of said genes are analyzed in said analyzing step. 
     
     
         17 . The method according to  claim 16 , wherein said determination is of a poor prognosis if at least fifteen of the genes analyzed manifest said modulated expression. 
     
     
         18 . A kit for determining expression of at least five genes selected from the group consisting of ACAT1, ANLN, ARHGDIG, ASPN, BNC1, BRCA1, BUB1B, C13ORF3, C6ORF105, C8ORF34, CASC5, CCNA2, CDKN3, CENPF, CENPI, CHPF, CIT, DEGS1, DIRAS2, DLGAP5, DNAH8, DUSP26, E2F8, EFNA3, ELFN2, EME1, EPHA6, ESPL1, EVPL, FAP, FKBP10, FOLH1, HBE1, HCG_1774568, IGF2BP3, INCENP, IRS4, IVL, KIF11, KIF4A, KIF4B, KRT1, LOC654342, MELK, MKI67, MLF1IP, NCAPG, NCAPG2, NFS1, NOX4, NUSAP1, ONECUT2, PRC1, PRR3, PSAPL1, PSAT1, PTPRR, RACGAP1, RAMP2, RELN, RP11-49G10.8, SCGN, SLC2A13, SLC31A2, SLC35F1, SLC6A10P, SMC2, SYT9, TAS2R10, TEX101, THSD1, TPX2, TSSC1, TTK, UBE2C, UNC13C, USP9Y, UTS2D, WNT4, WT1, ZFP41, AASDHPPT, ACIN1, ACSL5, ACTN1, AHNAK, ANKRA2, ANKRD36, ANO5, ANXA1, ASCC3, B4GALT1, BACE2, BTBD3, C10ORF26, C180RF25, CASP4, CD44, CDK10, CEP110, CHD3, COG4, CTR9, CWF19L2, CYP1B1, CYP27A1, DDHD2, DDX6, DENND2D, DPP4, DYM, EED, EFCAB4B, EPC1, ERAP1, FAM122C, FAM13B, FAM178A, FAS, FBXO21, GALNS, GBP2, GSTM1, HLA-A, HYDIN, IFI16, IL6ST, KIAA0174, KIAA1009, KIAA1328, KLHL2, KRT14, LEPR, LNPEP, LOC652614, LRRK1, MAN2A1, MAP3K1, MBD1, MT1X, MTSS1, MTUS1, NAPG, NRBP2, OGN, PCNX, PDK4, PHACTR2, PHLPP, PI15, PITPNC1, PLAA, PLEKHF2, PRKD3, PSEN1, PSMB8, PSPC1, RAB11FIP2, RBBP7, RBBP8, RBM41, RGS2, RGS22, RND3, RNPC3, RPRD1A, SATB1, SCN7A, SDCCAG10, SETBP1, SH3RF2, SLC15A2, SPG7, SQRDL, SRD5A2, ST6GAL1, SYNCRIP, TNFRSF10D, TNRC6A, TRIM22, ZADH2, ZBTB20, ZNF259, ZNF334, and ZNF532, comprising:
 a set of affinity reagents to specifically detect expression of said at least five genes, wherein said set of affinity reagents contains fewer than 2,501 affinity reagents.   
     
     
         19 . The kit of  claim 18 , further comprising at least one signal producing system that, used in conjunction with at least one of said affinity reagents, generates a signal if said affinity reagent binds to a marker of expression of the gene for which said reagent is specific, the presence of said signal indicating expression of said gene or the level of said signal correlating to the level of expression of said gene. 
     
     
         20 . The kit of  claim 18 , further including at least one signal producing label attached directly or indirectly to the affinity reagent, said signal producing label being selected from the group consisting of a radioactive, enzymatic, hapten, reporter dye or fluorescent label.