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(12) United States Patent (10) Patent No.: US 7,890.267 B2 Glinsky (45) Date of Patent: Feb US0078.90267B2 (12) United States Patent (10) Patent No.: US 7,890.267 B2 Glinsky (45) Date of Patent: Feb. 15, 2011 (54) PROGNOSTIC AND DIAGNOSTIC METHOD driven by the Polycomb Group (PcG) proteins BMI1 and Ezh2:...”. FOR CANCERTHERAPY Proceedings of the American Association for Cancer Research Annual Meeting, 47:984-985. (Abstract only).* (75) Inventor: Gennadi V. Glinsky, Loudonville, NY Raaphorst, F. M. et al. (2000) "Coexpression of BMI-1 and EZH2 (US) polycomb group genes in Reed- Sternberg cells of Hodgkin's dis ease”, American J. Pathology, 157(3): 709-715.* (73) Assignee: Ordway Research Institute, Albany, Veer, Van T L J et al. (2002) "Gene expression profiling predicts NY (US) clinical outcome of breast cancer', Nature, 415(6871): 530-536.* Affymetrix: “GeneChip human genome U95 set'. Data Sheet, (*) Notice: Subject to any disclaimer, the term of this Online 2003, XP0025,04985, retrieved from the Internet: patent is extended or adjusted under 35 URL:http://www.affymetrix.com/support/technical/datasheets/ U.S.C. 154(b) by 714 days. hgu95 datasheet.pdf>. Cheung et al., “Mapping determinants of human gene expression by (21) Appl. No.: 11/732,442 regional and genome-wide association”. Nature, 437: 1365-1369 (22) Filed: Apr. 2, 2007 (2005). Glinsky et al., “Gene expression profiling predicts clinical outcome (65) Prior Publication Data of prostate cancer'. J. Clin. Invest., 113(6):913-923 (2004). Glinsky et al., “Microarray analysis identifies a death-from-cancer US 2009/O 1707 15 A1 Jul. 2, 2009 signature predicting therapy failure in patients with multiple types of cancer, J. Clin. Invest., 115(6): 1503-1521 (2005). Related U.S. Application Data Imai et al., “C421A polymorphism in the human breast cancer resis (60) Provisional application No. 60/875,061, filed on Dec. tance protein gene is associated with low expression of Q141K pro 15, 2006, provisional application No. 60/823,577, tein and low-level drug resistance'. Mol. Cancer Ther. 1(8):611-616 filed on Aug. 25, 2006, provisional application No. (2002). Spielman et al., “Common genetic variants account for differences in 60/822.705, filed on Aug. 17, 2006, provisional appli gene expression among ethnic groups', Nat. Genetics, 39(2):226-231 cation No. 60/787,818, filed on Mar. 31, 2006. (2007). Varambally et al., “Integrative genomic and proteomic analysis of (51) Int. Cl. prostate cancer reveals signature of metastatic progression'. Cancer G06F 7/00 (2006.01) Cell, 8(5):393-406 (2005). (52) U.S. Cl. ............................. 702/19, 702/20; 703/11; 703/13:435/6: 436/501:536/24.5 * cited by examiner (58) Field of Classification Search ....................... None See application file for complete search history. Primary Examiner Mary K Zeman (74) Attorney, Agent, or Firm Ivor R. Elrifi; Mintz, Levin (56) References Cited Cohn Ferris Glovsky and Popeo PC U.S. PATENT DOCUMENTS (57) ABSTRACT 2006, OO73479 A1 4/2006 Frudakis ........................ 435/6 2009/0098538 A1* 4/2009 Glinsky ......................... 435/6 The present invention provides novel methods and kits for FOREIGN PATENT DOCUMENTS diagnosing the presence of cancer within a patient, and for WO WOO1,53834 * 7 2001 determining whether a Subject who has cancer is Susceptible WO WO 2004/O11625 A2 2, 2004 to different types of treatment regimens. The cancers to be WO WO O7,114896 * 10/2007 tested include, but are not limited to, prostate, breast, lung, WO WO 08/021483 * 2/2010 gastric, ovarian, bladder, lymphoma, mesothelioma, WO WO 03/060164 * 7 2010 medulloblastoma, glioma, and AML. Identification of OTHER PUBLICATIONS therapy-resistant patients early in their treatment regimen can lead to a change in therapy in order to achieve a more Suc Mimori et al. 2005, EJSO 31 : 376-380.* cessful outcome. One embodiment of the present invention is Hamer et al. 2002, Hybridoma and Hybridomics).* directed to a method for diagnosing cancer or predicting Berezovska, Olga P. et al. (2006) “Essential role for activation of the cancer-therapy outcome by detecting the expression levels of polycomb group (PcG) protein chromatin silencing pathway in meta static prostate cancer', Cell Cycle 5(16): 1886-1901.* multiple markers in the same cell at the same time, and Bild, Andrea H. et al. (2006) “Oncogenic pathway signatures in scoring their expression as being above a certain threshold, human cancers as a guide to targeted therapies', Nature, 439(7074): wherein the markers are from a particular pathway related to 353-357.* cancer, with the score being indicative or a cancer diagnosis Cao, R. etal. (2005) “Role of Bmi-1 and Ring 1A in H2A ubiquityla or a prognosis for cancer-therapy failure. This method can be tion and hox gene silencing'. Molecular Cell 20(6): 845-854.* used to diagnose cancer or predict cancer-therapy outcomes Glinsky, G.V. et al. (2004) “Classification of human breast cancer for a variety of cancers. The markers can come from any using gene expression profiling as a component of the Survival pre pathway involved in the regulation of cancer, including spe dictor algorithm”. Clinical Cancer Research, 10(7): 2272-2283.* cifically the PCG pathway and the “stemness' pathway. The Glinsky, G.V. et al. (2005) “Death-from-cancer signatures and stem cell contribution to metastatic cancer', Cell Cycle, 4(9): 1171-1175.* markers can be mRNA, microRNA, DNA, or protein. Glinsky, G.V. et al. (2006) “Integrative genomics and proteomics analysis reveals engagement of cooperating oncogenic pathways 2 Claims, 218 Drawing Sheets U.S. Patent Feb. 15, 2011 Sheet 1 of 218 US 7,890.267 B2 DEATH-FROM-CANCER SIGNATURE GENES (GLINSKY et al., JC, 2005) HITS; 3 2 12 SEARCHRESULTS FOR QUERY CCNB1 KNTC2 BUB1 HCFC1 FGFR2 Gbx2 Rnf2 USP22 ANK3 CES1 MK167 BMI1:40 HITS HOMOSAPIENS (HUMAN) GENOME VIEW BUILD 35.1 STATISTICS Fig. 1A U.S. Patent Feb. 15, 2011 Sheet 2 of 218 US 7,890.267 B2 ^ / U.S. Patent Feb. 15, 2011 Sheet 3 of 218 US 7,890.267 B2 <—————————————————————————————————————++——————> U.S. Patent Feb. 15, 2011 Sheet 4 of 218 US 7,890.267 B2 22600k 2261 Ok 22620 k 22630k CEU Phased Haplotypes YRIPhased Haplotypes Heterozygosity/5 Kb 2050 incClf II listasia: corol. Toowoc Cobrod O N-- Fig. 1 B-3 U.S. Patent Feb. 15, 2011 Sheet 5 of 218 US 7,890.267 B2 GENOTYPE AND ALLELE FREQUENCIES OF THE BMI1 ONCOGENESNP rs11012946 INDIFFERENTETHNICGROUPS 0.3 rS1 1 012946 HETEROZYGOTE ALLELE 0.25 FREQUENCY, FREQUENCY O. 2 O 15 HOMOZYGOTE FREQUENCY CEU CHBJPTYR POPULATIONS Fig. 1C GENOTYPE AND ALLELE FREQUENCIES OF THE NEAR-BMI1 ONCOGENESNPS IN DIFFERENTETHNIC GROUPS 0.8 ALLELE ALLELE rS 1 1 0 12952 FREQUENCY rS7099308 FREQUENCY 0.7 -1 0.6 HOMOZYGOTE HOMOZYGOTE >- FREQUENCY FREQUENCY U 0.5 2 D 0.4 SEE 0.3 HETEROZYGOTE HETEROZYGOTE 0.2 -- FREQUENCY FREQUENCY 0.1 O CEU CHBJPTYR POPULATIONS Fig. 1D U.S. Patent Feb. 15, 2011 Sheet 7 of 218 US 7,890.267 B2 ?----···---···«)*^suudpinab U.S. Patent Feb. 15, 2011 Sheet 8 of 218 US 7,890.267 B2 1 115OOk 1 1151 Ok 1 1152Ok 1 1153Ok CEUPhased Haplotypes YRIPhased Haplotypes CHB Phased Haplotypes JPTPhased Haplotypes Heterozygosity/5Kb U.S. Patent Feb. 15, 2011 Sheet 9 of 218 US 7,890.267 B2 HETEROZYGOTE GENOTYPE FREQUENCY INDIFFERENTETHNIC GROUPS FORSNPS OF DEATH-FROM-CANCERSIGNATURE GENES 0. 3 0. 2 J. J. J. EllCEU CHBJPT YR POPULATIONS Fig.1F U.S. Patent Feb. 15, 2011 Sheet 10 of 218 US 7,890.267 B2 HOMOZYGOTE GENOTYPE FREQUENCY INDIFFERENTETHNIC GROUPS FORSNPS OF DEATH-FROM-CANCERSIGNATURE GENES 0.45 0.4 HCFC1 O.35 0.3 BUB1 O.25 CCNB1 0.2 FGFR2 O.15 0.1 KNTC2 O.05 O CEU CHBJPTYR POPULATIONS Fig. 1G ALLELE FREQUENCY INDIFFERENTETHNICGROUPS FOR SNPS OF DEATH-FROM-CANCERSIGNATURE GENES 0.6 HCFC1 BUB1 0.5 CCNB1 FGFR2 0.4 0.3 KNTC2 0.2 0.1 CEUCHBJPTYR POPULATIONS Fig. 1H U.S. Patent Feb. 15, 2011 Sheet 11 of 218 US 7,890.267 B2 PROSTATE CANCER RECURRENCE SIGNATURE GENES (GLINSKY et al., JC, 2004) HTS: U 14 15 16 HTS: 4 2 SEARCH RESULTS FOR QUERY KLF6 Winf$ACHAF1ATCF2 KIAAO476 PPFIA3 CDS2 JUNBFOSER3 TPR1 ZFP36MGC5466:34. HITS HOMOSAPIENS (HUMAN) GENOME VIEWBUILD 35.1 STATISTICS Fig. 2A - GENOTYPE AND ALLELE FREQUENCIES OF THEKLF6 GENESNP rs2388864N DFFERENTETHNIC GROUPS 0.45 ?1 rs2388864 0.4 HETEROZYGOTE ALLELE 0.35 FREQUENCY FREQUENCY 0.3 | - HOMOZYGOTE 0.25 FREOUENCY 0.2 0.15 0.1 0.05 -7E7 F CEU CHBJPTYRI POPULATIONS Fig. 2B U.S. Patent Feb. 15, 2011 Sheet 12 of 218 US 7,890.267 B2 GENOTYPE AND ALLELE FREQUENCIES OF THE Wnt5 GENESNP rs9311564. IN DFFERENTETHNIC GROUPS TCF2 11 rs9311564 rS7209.295 Z CE -FREQUENCY-is 4 -------- o d SE | HOMOZYGOTE SE SE -FREQUENCY SE 2- 27 ft 2 CEU CHBJPT YR CEU CHBJPT YR POPULATIONS POPULATIONS CHAF1A KIAA0476 rS81 12822 rS6695083 >- - U 2 1. 1. O D O O LL SE f La 2f CEU CHBJPT YR CEU CHBJPT YR POPULATIONS POPULATIONS U.S. Patent Feb. 15, 2011 Sheet 13 of 218 US 7,890.267 B2 PPFA3 CDS2 rS 1040 1584 rS61 16661 f Z Z L D d O O L OY I- - CEU CHBJPT YRI CEU CHBJPT YR POPULATIONS POPULATIONS NEAR FOS CHAF1A -n rS8023205 rS1 1668886 - >- 2. U d 2 -1 SE - SE CEU CHBJPT YRI CEU CHBJPT YR POPULATIONS POPULATIONS Fig. 2D U.S. Patent Feb. 15, 2011 Sheet 14 of 218 US 7,890.267 B2 PROSTATE CANCER RECURRENCESIGNATURE GENES (VARAMBALLY et al., CANCER CELL, 2005) 4 + . 6 7 8 9 10 1 1. HTS: 4 14 8 3 5 D - sa - 18 19 20 21 22 X MT NOT PLACED HTS: 8 6 4 16 6 4 8 SEARCHRESULTS FORQUERY:STK6EZH2NUP62 ERBB2IPRALAUBE2IXPO1CDKN2AMSH2 VT1BUBA2SMARCC2 TRIM28 OCLN MCM6 RAN MAPK9ILF3 CSkHADH2STMN1 UHRF1 KPNA2 Cok4 MCM2 RAB27 NEXNKLK3 ACPPPRSS8 MLCKMAP2K4 TRAF3IP2PPP1R12APDLM5 CSRP1 ITGA5FLNACASP7 MMP23AACTA1DLGAP1 MAPKAPK3 BIRC2 CAV2TGFB11 PXNAMACR CRYABCFLAR: 165HTS HOMOSAPIENS (HUMAN) GENOME VIEW BUILD 35.1 STATISTICS -- Fig.
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