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
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U.S. Patent Feb. 15, 2011 Sheet 3 of 218 US 7,890.267 B2
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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
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1 115OOk 1 1151 Ok 1 1152Ok 1 1153Ok
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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:
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14 15 16 HTS: 4 2 SEARCH RESULTS FOR QUERY
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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
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PPFA3 CDS2
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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. 3A U.S. Patent Feb. 15, 2011 Sheet 15 of 218 US 7,890.267 B2
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U.S. Patent Feb. 15, 2011 Sheet 17 of 218 US 7,890.267 B2
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U.S. Patent Feb. 15, 2011 Sheet 18 of 218 US 7,890.267 B2
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U.S. Patent Feb. 15, 2011 Sheet 20 of 218 US 7,890.267 B2
55639k 5564Ok 55641k 55642k 55643k 55644k g-H----H-----H-----H------He-----H- Entrez genes NM_003600 STK6 serine/threonine protein kinases"
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U.S. Patent Feb. 15, 2011 Sheet 23 of 218 US 7,890.267 B2
551 12.5k 55113k 55113.5k 55114k Entrez genes NM 012346 NUP62: nucleoporin 62kDa NM 016553 NUP62: nucleoporin 62kDa -- NM 153718 NUP62: nucleoporin 62kDa &xt:^x-awwww.xxxx.7%xxxxessex&sixaxissaxwssex.assassssss NM 153719 NUP62: nucleoporin.62kDa NM 172374
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U.S. Patent Feb. 15, 2011 Sheet 24 of 218 US 7,890.267 B2
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Fig. 4B-3 U.S. Patent Feb. 15, 2011 Sheet 30 of 218 US 7,890.267 B2
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129380k 129381k 129382k 129383K 129384k 129385k 129386k 129387k 129388k 129389k Entrez genes NM_002417 MKl67:antigen identified by monoolonal antibody K1-67 - --- Sequence Tagged Sites SHGC-6421 Recombination rate (eH/Hb) 2 SNP coverage/5Kb o H O CEU:dprino O
U.S . Patent Feb. 15, 2011 Sheet 32 of 218 US 7,890.267 B2
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SHOWING 76.35 kbp FROM chr14, POSITIONS 101,764,930 TO 101,841,283 (RAGE)
10177Ok 101780k 101790k 101800k 101810k 10182Ok 101830k 101840k Genotyped SNPs rS2236493 S974350 +) 1. (A 42677(+ G OO A. OO Sg O s (+S 1 e G SO T TYR T 5 1129 (i. O) (EUCHBPTYRis A CE CHBPTYR
ENTREZ GENES NM O14226 RAGE: MAPK/MAK/MRKOVERLAPPNGKNASE Fig. 4D U.S. Patent Feb. 15, 2011 Sheet 34 of 218 US 7,890.267 B2
U.S. Patent Feb. 15, 2011 Sheet 35 of 218 US 7,890.267 B2
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Entrez genes NM_000321 RB1: retinoblastoma 1
Fig. 5A-2 U.S. Patent Feb. 15, 2011 Sheet 36 of 218 US 7,890.267 B2
GENOTYPE AND ALLELE FREQUENCIES FORPTEN rs122551.99 ANDTP53 rs9897559 SNPS IN DIFFERENTETHNIC GROUPS 0.3 PTEN HETEROZYGOTE TP53 rs 12255199 FREQUENCY rS9897.559 O.25 HETEROZYGOTE ALLELE FREQUENCY FREQUENCY ALLELE FREQUENCY O 52 O .1 HOMOZYGOTE HOMOZYGOTE FREQUENCY FREQUENCY 0.05
CEU CHBJPT YRI POPULATIONS Fig.5B U.S. Patent Feb. 15, 2011 Sheet 37 Of 218 US 7,890.267 B2
GENOTYPE AND ALLELE FREOUENCIES FOR RB1 rs9535024 AND rS2804089 SNPS INDIFFERENTETHNIC GROUPS O.6 y7 RB1 RB1 rS953.5024 rS2804089 ALLELE 0.5 - HETEROZYGOTE FREQUENCY ALLELE FREQUENCY 1. FREQUENCY 0.4 HETEROZYGOTE /7 FREQUENCY O.3 HETEROZYGOTE FREQUENCY 0.2 HETEROZYGOTE 1. FREQUENCY
"tO 1727 AZZ 1272 Maa 12/27 YZy CEU CHBJPT YR POPULATIONS Fig.5C
GENOTYPE AND ALLELE FREOUENCIES FOR RB1 rs2804088 AND rS2156910 SNPS IN DIFFERENTETHNIC GROUPS 0.6 RB1 RB1 1s2804088AEE rS2156910 0.5HETEOZYGOTEFREQUENCY FREQUENCY HETEROZYGOTEFREQUENCY FREQUENCYALLELE 0.4
0.3 Eg: HETEROZYGOTE
FREQUENCY 0.2 "I CEUCHBJPTYRI POPULATIONS Fig.5D
U.S. Patent Feb. 15, 2011 Sheet 39 Of 218 US 7,890.267 B2
GENOTYPE AND ALLELE FREOUENCIES FOR hERT SNP rS6882O77 INDIFFERENTETHNIC GROUPS rS6882O77 O.5 1.7 O.45 HETEROZYGOTE ALLELE 0.4 FREQUENCY FREOUENCY O.35 O.3 O.25 0.2 1 HOMOZYGOTE O.15 FREQUENCY 0.1 O.05 - U - O CEU CHBJPT YR POPULATIONS Fig.5F
GENOTYPE AND ALLELE FREQUENCIES OF THE AKT1 SNP rS4375597 INDIFFERENTETHNIC GROUPS rS437.5597 - 41 O HETEROZYGOTE FREQUENCY ALLELE O.35 FREQUENCY O. 3 O.25 O. 2 O.15 HOMOZYGOTE O. FREQUENCY O.05 22 277 f3 4.27 E O CEU CHBJPT YR POPULATIONS Fig.5G U.S. Patent Feb. 15, 2011 Sheet 40 of 218 US 7,890.267 B2
Metastasis-free survival of 97 early-stage breast cancer patients with distinct expression profiles of the 5-gene 14q32 locus signature -- Worst prognosis --- Bad prognosis -- Poor prognosis 5 O -- Intermediate prognosis ki------Good prognosis PC O.OOO1
O 50 100 150 2OO TIME, MONTHS Fig.6A
Relapse-free survival of prostate cancer patients with distinct expression profiles of the 14d32 locus 8-genesignature
-- Worst prognosis --- Poor prognosis Intermediate prognosis -- Cure P (O.OOO1
O 25 50 75 100 125 TIME AFTERRP, MONTHS Fig.6B U.S. Patent Feb. 15, 2011 Sheet 41 of 218 US 7,890.267 B2
Metastasis-free survival of 97 breast cancer patients with distinct expression profiles of the 6-gene signature from 100 most variable loci 100 -- 5-year survival: 0% s Median Survival: 16mo e 75 ---- 5-year survival: 24% a Median Survival: 38mo 2 50 -- 5-year survival: 60% 5 -- 5-year survival: 79% 25 -- 5-year survival: 100% O O 50 100 150 200 P (0.0001 TIME, MONTHS Fig. 6C
Relapse-free survival of prostate cancer patients with distinct expression profiles of the 14-gene signature from 100 most variable loci
-- Worst prognosis --- Poor prognosis -- Intermediate prognosis -- Cure
P < O.OOO1
O 25 50 75 100 125 TIME AFTERRP, MONTHS Fig. 6D U.S. Patent Feb. 15, 2011 Sheet 42 of 218 US 7,890.267 B2
Metastasis-free survival of 97 early stagebreast Cancer patients with distinct expression profiles of the 10-gene SNP-based signature 100 -- Worst prognosis
s D 75 - Bad prognosis 2 "... -- Poor prognosis H 50 ...r- 1. -- Intermediate prognosis 2 25 -- Cure O 50 100 150 200 PC 0.0001 TIME MONTHS Fig. 6E
Relapse-free survival of 79 prostate cancer patients with distinct expression profiles of the 17-gene SNP-based signature
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s- ---- Worst s 75 -- Bad es -- PPOOr 1. 50 -- Intermediate 2 25 r-- Cure A O P< O.OOO1 O 25 50 75 100 125 TIME AFTERRP, MONTHS Fig. 6F U.S. Patent Feb. 15, 2011 Sheet 43 of 218 US 7,890.267 B2
Metastasis-free survival of 97 early stage breast cancer patients with distinct expression profiles of the 4-gene SNP signature
100 -- Worst ---- Poor 75 -- Intermediate
50 in El dissa -- Cure
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75 -- Bad prognosis -- Poor prognosis 50 line all-alt
-- Cure 25 P ( 0.0001
O 25 50 75 1 OO 125 TIME AFTERRP, MONTHS Fig. 6H U.S. Patent Feb. 15, 2011 Sheet 44 of 218 US 7,890.267 B2
Metastasis-free survival of 97 early stage breast cancer patients with distinct expression profiles of the 27-gene SNP-based signature 100 -- Worst prognosis s --- Bad prognosis gS 75 -- Poor prognosis 50 r -- Intermediate prognosis 1. in an in a an an 2 25 -- Cure O P < O.OOO1 O 50 100 150 2OO TIME, MONTHS Fig. 6l
Relapse-free survival of 79 prostate cancer patients with distinct expression profiles of the 27-gene SNP-based signature -- Worst prognosis s- --- Bad prognosis 2 -- Poor prognosis O -- Intermediate prognosis 2 t -- Cure ?h- P<0.0001 O 25 50 75 100 125 TIME MONTHS Fig. 6J U.S. Patent Feb. 15, 2011 Sheet 45 of 218 US 7,890.267 B2
Metastasis-free survival of 97 early stage breast cancer patients with distinct expression profiles of the SNP-based 11-gene signature 100 -- Worst prognosis
- --- Bad prognosis s 75 -- Poor prognosis 50 Intermediate prognosis H ---L------2. -- Cure L 9 25 P< O.OOO1 A. O 50 100 150 200 TIME MONTHS Fig. 6K
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1 OO -- Worst prognosis - s 2 75 - le Poor prognosis 2 t 50 -- Cure t
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Relapse-free survival of prostate cancer patients with distinct expression profiles of the 32-transcripts proteomics-based signature 100 -- Worst ss 75 --- Bad ? Poor D 2 50 -- Good l -- Cure 2 25 P<0.0001
O O 25 50 75 100 125 TIME AFTERRP, MONTHS Fig.6M
Relapse-free survival of 286 early stage breast cancer patients with distinct expression profiles of the 24-transcript proteomics-based signature
-- Worst --- Bad -- POOr -- Intermediate -- Good --- Cure P < 0.0001
O 50 100 150 2OO TIME MONTHS Fig. 6N U.S. Patent Feb. 15, 2011 Sheet 47 of 218 US 7,890.267 B2
Relapse-free survival of prostate cancer patients with distinct expression profiles of the 11-gene BM-1 pathway signature - 1 OO s 75 - POOR PROGNOSIS s -- INTERMEDIATE PROGNOSIS 50 -- GOOD PROGNOSS Z 2 25 P < O.OOO1
h O O 25 50 75 100 125 TIME AFTERRP, MONTHS Fig. 7A
Relapse-free Survival of prostate cancer patients with distinct expression profiles of the 11-gene Myc pathway signature 100 - s 75 -- POOR PROGNOSIS S -- INTERMEDIATE PROGNOSIS 50 -- GOOD PROGNOSIS 2. l 2 25 P< O.OOO1 I C O O 25 50 75 100 125 TIME AFTERRP, MONTHS Fig. 7B U.S. Patent Feb. 15, 2011 Sheet 48 of 218 US 7,890.267 B2
Relapse-free survival of 79 prostate cancer patients with distinct expression patterns of the 14-gene Her2/Neu pathway signature 100 - -- WORST PROGNOSIS e 75 -- BAD PROGNOSS g role POOR PROGNOSIS 2 50 -- INTERMEDIATE PROGNOSIS y -- CURE
A- 25 P < O.OOO
O -- O 25 50 75 1 OO 125 TIME AFTERRP, MONTHS Fig. 7C
Relapse-free Survival of 79 prostate cancer patients with distinct expression patterns of the BMI1:MYC:Her2/Neu network signatures 1 OO s -- WORST PROGNOSIS is 75 -- POOR PROGNOSIS 2 50 -- INTERMEDIATE PROGNOSIS 2 -- CURE U 25 P < O.OOO1 A O O 25 50 75 1OO 125 TIME AFTERRP, MONTHS Fig. 7D U.S. Patent Feb. 15, 2011 Sheet 49 of 218 US 7,890.267 B2
Metastasis-free Survival of breast cancer patients with distinct expression profiles of the 11-gene BM-1 pathway signature 1 OO - C s 75 - POOR PROGNOSIS g -- INTERMEDIATE PROGNOSIS 50 -- GOOD PROGNOSIS 2 - 25 P < O.OOO1 C O O 50 1 OO 150 200 TIME, MONTHS Fig. 7E
Metastasis-free Survival of breast cancer patients with distinct expression profiles of the 11-gene Myc pathway signature 1 OO - s s 75 - POOR PROGNOSIS g -- INTERMEDIATE PROGNOSIS 50 -- GOOD PROGNOSIS 2. i.L 25 P ( 0.0001 a O O 50 1 OO 150 200 TIME, MONTHS Fig. 7F U.S. Patent Feb. 15, 2011 Sheet 50 Of 218 US 7,890.267 B2
Metastasis-free Survival of breast cancer patients with distinct expression profiles of the 14-gene Her2/neu pathway signature 100 90 8O -- GOOD PROGNOSS 70 -- POOR PROGNOSIS 6O PC O.OOO1 50 40 30 O 50 1OO 150 2OO TIME, MONTHS Fig. 7G
Metastasis-free survival of 97 breast cancer patients with distinct expression patterns of the BMI1:MyC:Her2/neu network signatures
milliam 3 GOOD SIGNATURES
-- 2 GOOD SIGNATURES
-- ONE GOOD SIGNATURE
- ONE POOR SIGNATURE
-- 2 POOR SIGNATURES
-- 3 POOR SIGNATURES
1OO 150 200 TIME, MONTHS Fig. 7H U.S. Patent Feb. 15, 2011 Sheet 51 of 218 US 7,890.267 B2
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Relapse-free survival of prostate cancer patients with distinct expression patterns of the 8-signature CTO algorithm
100 ii. : : -- Therapy failure &C 75 É -- Cure z 50 P < 0.0001 2 25 L A O O 25 50 75 1 OO 125 TIME AFTERRP, MONTHS Fig. 8B
Metastasis-free survival of 97 early stage breast cancer patients with distinct expression profiles of the 10-signature CTO algorithm
- 100 s -- Poor prognosis is 75 D 50 -- Cure 1. 25 P < 0.0001
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Cytoplasmic AMACR and nuclear pé3 expression in parental PC-3 human prostate carcinoma cells 2OO 18O 160 140 120 100 8O s 60 40 20 O 50 100 150 200 250
Cytoplasmic AMACR and nuclear pé3 expression in PC-3-32 human prostate carcinoma metastasis
precursor cells 200
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50 U.S. Patent Feb. 15, 2011 Sheet 65 of 218 US 7,890.267 B2
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U.S. Patent Feb. 15, 2011 Sheet 71 Of 218 US 7,890.267 B2
PC-3-32 - PC-3
BM-1 and ubiH2A nuclear expression in PC-3-32 human prostate carcinoma metastasis precursor Cells 140
O 5O 1 OO 150 200 250 BMI1 BM-1 and ubiH2A nuclear expression in PC-3
human prostate carcinoma cells
O 50 1 OO 150 200 250 BMI1
Fig. 21-1 U.S. Patent Feb. 15, 2011 Sheet 72 Of 218 US 7,890.267 B2 ? PC-3-32 - PC-3
Ezh2 and H3metK27 expression in PC-3-32 human prostate carcinoma metastasis precursor cells
O O 1 OO 15O 200 25O 3OO 3metK27 Ezh2 and H3metK27 expression in parental PC-3 human prostate carcinoma cells 140 120 1 OO 8O 60 s 40 20 O O SO 1 OO 150 200 250 300 3metK27 Fig. 21-2 U.S. Patent Feb. 15, 2011 Sheet 73 Of 218 US 7,890.267 B2
PC-3-32 - PC-3 U.S. Patent Feb. 15, 2011 Sheet 74 of 218 US 7,890.267 B2
RT-PCR analysis of the BMI1 siRNA-mediated gene silencing in PC-3-32 cells. B, BMI1 & L. luciferase siRNA Fig. 22A-2 U.S. Patent Feb. 15, 2011 Sheet 75 Of 218 US 7,890.267 B2
/ Specificity of the BM-1 siRNA-mediated gene silencing in PC-3-32 human prostate carcinoma metastasis precursor cells 0. 2
p = 9.03535E-09 -1.2 - -To-T------
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6 O 40 20- P= 1.1E-59 p14E-92 O 1 O 20 30 40 50 60 DBM-1 siRNA72 EZLUCFERASE siRNA 72 Y -- Fig. 22A-3 U.S. Patent Feb. 15, 2011 Sheet 76 of 218 US 7,890.267 B2
siRna mediated BM-1 silencing diminishes survival of human prostate carcinoma metastasis precursor Cells subjected to anoikis 45 40 35 3O Pat OOOOO9 25 2O 15 1 O 5 LUCIFERASE BM-1
siRna mediated BMI-1 increases apoptosis of human prostate carcinoma metastasis precursor cells subjected to anoikis 60 50 40 P = 0.00002 30 2O 10
LUCFERASE BM-1
Fig. 22A-4 U.S. Patent Feb. 15, 2011 Sheet 77 of 218 US 7,890.267 B2
pC-3 pc-3-32 Ezh2 siRNA Luc SiRNA
Fig. 22B-1 Specificity of the EZH2 siRNA-mediated gene silencing in PC-3-32 human prostate carcinoma metastasis precursor cells 9 ol0.1 p=0.325 p=0.973 p=0,386 p=0.978 le U O rter es 2-2-1-2-6 7-2-1 2 p=0,1104 p=0743 p=0.691 O -0.05
>< -0.15 L G -0.2 SP -0.25 CQD -0.3 p=1.16347F-08 -035 is a s's 'e's is s is g g s is S. S. ss H- - is st S2 S2 Fig. 22B-2
30 cyci. 35 cycl. RT-PCR analysis of the Ezh2 siRNA-mediated gene silencing in E. L. E . PC-3-32 cells. E, Ezh2 siRNA; EZH2 Luciferase siRNA. KAAO962 Fig. 22B-3 U.S. Patent Feb. 15, 2011 Sheet 78 of 218 US 7,890.267 B2
siRna-mediated EZH2 silencing diminishes Survival of human prostate carcinoma metastasis precursor cells subjected to anoikis
luciferase EZH2
siRna-mediated EZH2 silencing increases apoptosis in human prostate carcinoma cells Subjected to anoikis 60
luciferase EZH2
Fig. 22B-4
U.S. Patent Feb. 15, 2011 Sheet 80 of 218 US 7,890.267 B2
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BM1 SiRNA 120 DAYS Luc siRNA 44-50 DAYS Ezh25iRNA 120 DAYS
PROSTATES PROSTATES Fig.24B-1 U.S. Patent Feb. 15, 2011 Sheet 83 of 218 US 7,890.267 B2
Survival of mice bearing orthotopolic PC-3-GFP-39 human prostate carcinoma xenografts treated with BM-1 siRNA or Control LUC siRNA 100 2 -- LUC siRNA D 75 -- BM-1 siRNA 2 50 Logrank test:
- O O 25 50 75 1 OO TIME, DAYS
Survival of mice bearing orthotopoic PC-3-GFP-39 human prostate carcinoma xenografts treated with Ezh2 siRNA or control LUC siRNA 100 2 -- LUC siRNA D 75 -- Ezh2zh2 SisiRNA 2 50 Logrank test:
l
l O O 25 50 75 100 TIME, DAYS Fig.24B-2 U.S. Patent Feb. 15, 2011 Sheet 84 of 218 US 7,890.267 B2
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U.S. Patent Feb. 15, 2011 Sheet 86 of 218 US 7,890.267 B2
Relapse-free survival of prostate cancer patients 100 - C 2 75 -- HIGHT/N RATIO D 50 -- LOWT/NRATIO Z 25 P = 0.0256 A O O 1 O 20 30 40 50 60 70 TIME AFTERRP, MONTHS Fig. 26A
Relapse-free survival of prostate cancer patients 100 S& 75 BM-1 HIGH 50 -- BM-1 LOW 2 25 P < 0.0001 Q O O 25 50 75 100 125 TIME AFTERRP, MONTHS Fig. 26B U.S. Patent Feb. 15, 2011 Sheet 87 Of 218 US 7,890.267 B2
Relapse-free survival of prostate cancer patients 100
s2 75 -- Ezh2 HIGH D 50 - Ezh2 LOW Z 25 P = 0.0092 A O O 25 50 75 1 OO 125 TIMEAFTERRP, MONTHS Fig.26C
Relapse-free survival of prostate cancer patients 100 s -- POOR PROGNOSIS s 75 BM 1/Ezh2 HIGH 2 -- GOOD PROGNOSIS 50 BM1/Ezh2 LOW LL 2 25 P < O.OOO1 1. A O O 25 5O 75 100 125 TIME AFTERRP, MONTHS Fig. 26D U.S. Patent Feb. 15, 2011 Sheet 88 of 218 US 7,890.267 B2
Relapse-free survival of prostate cancer patients stratified into sub-groups using 8 covariate cancertherapy outcome algorithm 100 - -- TOP 20% s s 75 -- 296 - 4096 g -- 41% - 6096 2 50 -- 61% - 80% t -- 81% - 100% 25 A- P < O.OOO1 O O 25 5O 75 100 125 TIME AFTERRP, MONTHS
Percentile rank 1-20%. 21-40%. 41-60% 61-80% 81-1 OO96 Number of censored subjects 3 5 8 10 16 Number od deaths/events 12 11 8 6 O 5-year Survival 20% 44% 61.96 63% 100% Median survival 18 43.2 67.4 Undefined Undefined Fig. 26E U.S. Patent Feb. 15, 2011 Sheet 89 of 218 US 7,890.267 B2
Breast cancer data set of 286 patients with early-stage LN negative disease Breast Cancer CTOP Signatures (Affymetrix Chip-Based Algorithm) 11-gene BMI1-pathway signature 11-gene MYC-pathway signature 14-gene Her2/neu-pathway signature 7-gene 14q32-locus signature 7-gene SNP-based signature (BrCa97 Table98 Genes) 27-gene SNP-based signature (Cheung Nature 2005) 5-gene Suz12-pathway signature 27-gene SNP-based signature (Table 9 Nature 2005) 6-gene 100-Variable loci signature 18-gene SNP-based signature (Table 10 Nature 2005) 24-gene proteomics-based signature 25-gene Beta-catenin-pathway signature 14-gene Src-pathway signature 20-gene Ras-pathway signature 34(25)-gene cell line-based signature 32-gene CCND1-pathway signature 27-gene E2F3-pathway signature
7-gene SNP-based signature (BrCa97 Table98 Genes) Coeff. BrCal 286 RAGE 205130 at -1.7499 BRF1 215676 at 0.8222 GHG3 211430s 0.3997 COLEC 11 219873 at 0.3786 EDAR 220048 at 1.3155 ERCC6 207347 at -2.3444 CEACAM1 206576 s. -0.7468 6-gene 100-Variable loci signature Coeff. BrCal 286 KIAAO449 204411 at -0. 1919 RNF5 209111 at 2.1163 RPP30 203436 at -1.2727 GNAS1 200780 x -0.052 EPB41 L2 201719 s 0.6852 SLC25A16 209910 at 0.5759 27-gene SNP-based signature (Cheung Nature 2005) Coeff. BrCal 286 DDX17 208151 x -0.7691 CAP-1A 203337 x O.3413 16 209827 s. -0.6075 S100A13 202598 at 0.2455 SMARCB1 206532 at -0.2408 WAMP8 202546 at - 1,3839 TM7SF3 217974 at -0.1247 ZNF85 206572 x -1.7358
Fig.27-1 U.S. Patent Feb. 15, 2011 Sheet 90 Of 218 US 7,890.267 B2
CG-96 217276 x 0.3412 CG-96 202938 x O. 1377 CGI-96 214243 s. -0.96.17 CG-96 217284 x 0.3492 CGI-96 202937 x 0.518 EIF3S8 200647 x 0.3886 CTBP1 203392 s. -0.6149 RPS26 217753 s. -0.3595 CTSH 202295 s -0.5336 GSTM2 204418 x -O.7323 GSTM1 204550 x 0.2581 CPNE1 206918 s 0.0047 AA827892 65588 at O.2572 CSTB 201201 at 2.0975 LRAP (LOC641219759 at 0.0842 HLA-DRB2 2094.80 at 0.1356 PSPHL 205048 st -0.0519 POMZP3 204148 s. -0.316 RF5 205469 st -0.5652 18-gene SNP-based signature (Table 10 Nature 2005) Coeff. BrCal 286 LCT 206945 at -0.2548 CDH12 219656 at 0.4552 PMCHL1 217123 x 0.2418 CD36 209554 at -0.1737 CD36 206488 s. -0.3618 CD36 209555 s 0.2745 PMS2L5 214757 at -O.O757 WBSCR 16 221247 s -O.O3 ARNT2 202986 at O.O.478 TGAE 205055 at O,6221 HSA277841 218896 s. 0.808 CAMKK 207359 at O.5355 CAMKK 210787 s. 0.4013 P2RX1 210401 at -0.2664 LARGE 204414 at -0.1886 HEPH 203903 s 0.6079 HEPH 203902 at -0.3O33 MAOB 204041 at -0, 1906 27-gene SNP-based signature (Table 9 Nature 2005) Coeff. BrCal 286 THEA 214763 at 13178 THEA 216103 at -0.6966 FY 204997 at -0.0208 COLEC 1 219873 at 0.3336 ALMS1 214707 x -0.738 ALMS1 214221 at 0.1.192 ALMS1 214220 s. -0.6032
U.S. Patent Feb. 15, 2011 Sheet 91. Of 218 US 7,890.267 B2
/ EDAR 220048 at 19277 FXR1 201637 s. 100.58 MCF2L2 215112 x 0.2093 SLC30A9 202614 at 0.701 ADH1B 209612 s. -0.4537 ADH1B 209613 s. O. 1297 SLC39A4 219215 s 0.6118 ERCC6 207347 at 0.155 NEUROG3 207965 at -O.399 F2 205754 at -0, 1212 HERC1 218306 s. O.2901 ZNF646 204876 at - 14154 ZNF646 214226 at 0.9969 FUT6 21 1885 x -O.O897 FUT6 211882 x 0.4409 FUT6 210399 x O.78O2 FUT6 211465 x - 18658 CEACAM1 206576 s. -0.797 GNB1 220762 s. O.5006 EDA2R 221399 at -0.4436 5-gene Suz12-pathway signature Coeff. BrCal 286 SMARCA4 213720 s 18143 SMARCA4 212520 s. - 15726 FLJ10350 217943 s 0.5446 PG7 200704 at 18815 KAAO794 217 100 s. -1. 1788
11-gene MYC-pathway signature Coeff.BrCal 286 201257 x at -0.5513 202614 at -0.044 203560 at 0.7248 218215 s at -0.5977 203728 at -0.2553 201939 at -0.3067 202645 s at -0,5774 204687 at - 13927 201463 s at -0.5314 208822 s at 0.5336 201493 s at -0.3513
11-gene MYC-pathway signature HG-U133A Log 10 FC Log 10 FC MYC PrCa RPS3A 201257 x 93480 at 1.727812 O.761176 SC30A9 202614 at 97920 at 101219 0.4983.11
U.S. Patent Feb. 15, 2011 Sheet 92 of 218 US 7,890.267 B2
GGH 203560 at 93575 at 0.686355 0.320146 NR1H2 218215 s 101981 at 0.632576 0.385606 BAK1 203728 at 104710 at 0.317336 0.222716 PLK2 201939 at 92310 at 0.2894.02 0.193125 MEN1 202645 s 102783 at 0.182033 0.184691 DKFZP564O08 204687 at 100547 at -0.50616 -0.24304 TALDO1 201463 s 95120 at -0.54782 -0.29667 DAP3 208822 s 103999 at -0.57915 -0.24797 PUM2 201493 s.103833 at -1.11837 -0.50786 PUM2 216221s 103833 at -1.11837 -0.50786 Relapse-free survival of 286 breast cancer patients with early Stage LN negative disease and distinct expression profiles of the 11-gene MYC-pathway signature 110 milm S 100 --- E63r 90 -- INTERMEDIATE 2 80 GOOD
it 70 'lluulu- CURE 60 uuuLill--- P < O.OOO1 50 40 O 50 100 150 200 Fig 27-4 TIME, MONTHS 32-gene CCND1-pathway signature HGU133/ Coeff. BrCal 286 HSPG2 201654 s -0.1094 HSPG2 201655 s 2.1647 RPS6KA1 203379 at -1.9011 AXN1 212849 at -0.5451 EVX1 207914 x 0.3491 MT2A 212185 x 0.1073 MT2A 212859 x -0.3585 LOR 207720 at 0.1258 GNA2 201040 at -0.1148 KF22 216969 s 0.3857 KF22 202183 s -0.1592 HADH2 202282 at 0.9952 RAB31 217764 s 2.5208 RAB31 217762 s -0.7709 RAB31 217763 s -1.1503 LTBR 203005 at 1.3203 HSPA1B 202581 at 0.3912 HSPH1 206976 s 19668 HSPH1 208744 x -0.4138 HSPA1A 200799 at 0.2274 HSPA1A 200800s -0.0017 ASNS 205047 s 1,4163 U.S. Patent Feb. 15, 2011 Sheet 93 Of 218 US 7,890.267 B2
LGALS3BP 200923 at -0.3446 PPD 204185 x 0.9434 PPD 204186 s -0.5779 EFNA1 202023 at 0.2104 HEXA 201765 s -1.3534 HEXA 215155 at -0.4056 TGFB1 203084 at -0.5546 TGFB1 203085 s 0.6784 MADH3 205397 x 0.7286 MADH3 205398 s -0.319 Relapse-free survival of 286 early-stage LN negative breast cancer patients with distinct expression profiles of the 32-gene CCND1-pathway signature s -- WORST 2 -- BAD 2 --- POOR 2 -- INTERMEDIATE m - GOOD Zt P<0.0001
50 100 150 200 TIME, MONTHS 34(25)-gene cell line-based signature Coeff. BrCal 286 AP2B1 200612 s. -10816 AP2B1 200615 s 1.6081 MCM6 201930 at 0.3501 EXT1 201995 at 13101 GSTM3 202554 st -0,2405 AKAP2 202760 s. - 1, 1881 OXCT 202780 at 0.2495 DCK 203302 at 0.6672 ALDH4A1 203722 at 0.372 CDC42BPA 203794 at O. 1411 KNTC2 204162 at - 12649 FL1 204406 at -0.0036 MELK 204825 at 14,495 CCNE2 205034 at 16436 FGF18 206986 at -0,0909 FGF18 206987 x 0.4006 TGFB3 209747 at -0.4338 FLT1 210287 s. -0.1881 FGF18 211029 x 0.1789 FGF-18 211485 s O.O139
U.S. Patent Feb. 15, 2011 Sheet 94 of 218 US 7,890.267 B2
ALDH4A1 211552 s. -O. 1629 BBC3 211692 s. 0.0438 CCNE2 211814 s O. 1238 CDC42BPA 213595 s 0.1262 FGF18 214284 st 0.0294 GMPS 214431 at 0.1271 CDC42BPA 214464 at 0.6559 CDC42BPA 215296 at 0.4751 DC13 218447 at 12131 SCUBE2 219197 s. 0.3124 ECT2 219787 s. -0.9872 C2OOfA-6 219958 at 0.5044 DAP-3 220997 s. 0.2623 FLT1 222033 s. 1313
Relapse-free Survival of 286 early-stage LN negative breast cancer patients with distinct expression profiles of the 34-gene cell line-based signature -- WORST --BAD 75 --- POOR -- INTERMEDIATE 1 Tu -- INTERMEDIATE 2
re------INTERMEDIATE 3
s -- GOOD --- CURE O 50 1 OO 150 200 TIME MONTHS 25-gene Beta-catenin-pathway signature Coeff. BrCal 286 CBX3 200037 s. 17813 EPRS 200842 s. 18719 A4321.96 201865 x -0.241 NR3C1 201866 s 12031 TRIM14 203147 s - 15688 C6orf56 204047 s -0.694 FUSP1 206095 s 0.3975 SFRS6 206108 s. 0.6177 NRD1 208709 st 0.6567 KAAO217 208953 at -0.5185 CSPG6 209259 st 1.0769 SMG1 210057 at 0.4366 COL13A1 211343 s 1, 1768 KAA0323 212356 at 0.6172
U.S. Patent Feb. 15, 2011 Sheet 95 of 218 US 7,890.267 B2
JMJO2B 212495 at 0.203 KIAA1033 212794 s -1.3719 KIAA1033 212795 at 0.7128 NEK1 213331 s -0.7198 KIAAO779 213349 at -0.3565 RPS11 213350 at -1.0971 FUSP1 213594 x 0.5765 BE503392 213637 at 0.2659 RPESP 214725 at 0.1129 C20orfA2 218796 at -0.1837 THOC2 222122 s -0.2331 Relapse-free survival of 286 early-stage LN negative breast cancer patients with distinct expression profiles of the 25-gene Wnt/B-catenin pathway signature s100ts ------L--- -- FATAL s -- WORST is 75 --BAD V --POOR 50 --INTERMEDIATE 25 -- CURE P < O.OOO1 O 50 100 150 200 TIME, MONTHS
14-gene Src-pathway signature Coeff. BrCa 286 TEB4 201736 s 0.8939 DMTF1 203301 s 1.6743 ZNF-U69274. 204847 at 2.1594 FLU21940 205836 s -1.4425 RRM2 209773 s 0.6683 RRM2 201890 at 0.3395 MARK3 202569 s -2.1484 TRRAP 202642 s. 0.2057 TNFAIP3 202644 s -1.0438 HSPH1 206976 s 1.0417 JMJD2B 212495 at -0.16 MRPS6 213167 s. 0.3007 RPS19 213414 s -1.2665 FANCL 218397 at 0.3961
U.S. Patent Feb. 15, 2011 Sheet 96 of 218 US 7,890.267 B2
Relapse-free Survival of 286 early-stage LN negative breast cancer patients with distinct expression profiles of the 14-gene SrC-pathway signature
-- WORST --BAD
Tululu ill-l-al-ul --- POOR Lulua-lulu -- INTERMEDIATE -- GOOD 25 P< O.OOO1 50 100 150 200 TIME MONTHS
20-gene Ras-pathway signature Coeff. BrCal 286 MDH1 200978 at 3.04.92 TPR3 201188 s 0.7269 PRNP 201300 s. O9827 TEA1 2014.46 s - 16523 DAF 201925 s 0.37.17 SDC4 202071 at 0.5599 CYP1B1 202437 s 0.2349 SKP2 203626 s O.6175 DTR 203821 at -0.148 DNAJC6 204721 s -0.0014 MBNL2 205017 s. -0.1515 HOXC6 206858 s. 15603 LGALS8 210732 s. O4054 DPA 213250 at O.2367 HNRPH1 213472 at O. 1255 PMS2L6 214756 x -1.2514 MGC 12518 215239 x - 1.1785 GJB3 215243 s. -1.8933 PMS2L6 215667 x -O,2554 TA1 217164 at 0.6719
U.S. Patent Feb. 15, 2011 Sheet 97 of 218 US 7,890.267 B2
Relapse-free survival of 286 early-stage LN negative breast cancer patients with distinct expression profiles of the 20-gene RaS-pathway signature 100 -- WORST 2 --BAD 75 --- POOR 7 50 -- INTERMEDIATE - GOOD 1, 25 P < 0.0001 Qu) ; O O 50 1 OO 150 200 TIME MONTHS
24-gene proteomics-based signature Coeff.BrCal 286 RAN 200749 at 2.2157 STMN1 200783 s -1.4252 PRSS8 202525 at -0.5833 AMACR 209424 is 1.4373 SMARCC2 201321 s 3.2232 TGA5 201389 at 2.0463 STK6 208079 s 1.8921 AMACR 209425 at -2.7739 CDKN2A 209644 x 1.2597 NEXN 212847 at 2.3007 TRAF3IP2 21541.1 s 0.6156 AMACR 217113 at -1.0155 UBE2I 208760 at 1.2075 UBE2I 211008 s 0.4531 UBE2I 213536 s -0.7147 PDLM5 213684 s -0.4287 TGFB11 209651 at 2.5214 MAPKAPK3 202788 at -1.62 PDLM5 203243 s 0.9864 EZH2 203358 s 0.635 ACTA1 203872 at -0.5586 MMP23A 207118 s -0.241 CASP7 207181 s -19609 NEXN 214093 s -1.9885
Fig.27-9 U.S. Patent Feb. 15, 2011 Sheet 98 of 218 US 7,890.267 B2
11-gene BMI1-pathway signature 11-gene BMI1-pathway signature Coeff. Broa 286 210560 at 0.0092 Gbx2 210560 at 212022 s at 1088 K67 212022 s at 21471.0 s at 15138 Cyclin B1 214710s at 216277 at 0.2118 BUB1 216277 at 204162 at -0.7901 HEC 204162 at 216964 at -0.3928 KIAA 1063 216964 at 202473 x at - 13438 HCFC1 202473 x at 205215 at 0.4783 RNF2 205215 at 209442 x at 0.0465 ANK3 209442 x at 203638 s at 0.5148 FGFR2 203638 s at 208228s at -0.0694 FGFR2 208228 s at 209616 s at 0.1831 CES 209616 s at
Relapse-free survival of 286 breast cancer patientsWITH early stage LN negative disease and distinct expression profiles of the 11-gene BMI1-pathway signature
--BAD y --POOR uuuuu. -- INTERMEDIATE W. "ill.its. Llull J -- CURE 50 P<0.0001 25
O 50 100 150 2OO TIME, MONTHS 14-gene Her2/neu-pathway signature 14-gene Her2/neu-pathway signature Coeff. BrCal 286 203373 at -0.8698 STATI2 203373 at 202677 at 0.6695 RASA 202677 at 201063 at -0.3836 RCN1 201063 at 220286 at 0.1774 FLJ20313 220286 at 212211 at -0.6679 KIAA0697 212211 at 218859 s at -0.6124 HDCMC28218859 s at 205420 at 0.8886 PEX7 205420 at 204485 s at 0.4887 TOM1L1 204485 s at 204010 s at -0.3749 KRAS2 204010 s at 204256 at 15795 MGC5487 204256 at 210868 s at -0.696 MGC5487 210868 s at 213457 at 0.9886 MASL1 213457 at 219534 x at 0.3154 CDKN1C 219534 x at 219533 at -0.2943 CDKN1C 219533 at Fig.27-10 U.S. Patent Feb. 15, 2011 Sheet 99 of 218 US 7,890.267 B2
Relapse-free survival of 286 breast cancer patients with early-stage LN negative disease and distinct expression profiles of the 14-gene Her2/neu-pathway signature - 100 --BAD s --POOR 2 75 -- INTERMEDIATE D - -- GOOD ? 50 Lulti-- -- CURE 2 t 25 P < 0.0001 LL A O O 50 100 150 200 TIME, MONTHS
7-gene 14q32-locus signature Coeff. BrCal 286 GBP1 202105 at -2.261 PLAA 209532 at 0.7378 XPC 209375 at -1.2898 NDUFB2 222090 at -0.0686 SNRPB2 208821 at 0.6476 NDUFB2 221894 at 0.1476 SNRPB2 213175 s -0.9471 Survival of 286 breast cancer patients with early stage LN negative disease and distinct expression profiles of the 7-gene 14q32 locus signature
3. --BAD 2 --POOR 2 75 4. -- INTERMEDIATE O l bulu un LLULL.L.L -- GOOD
? 50 ---L------CURE t2. 25 P<0.0001 ? LL a- 0 O 50 100 150 200 TIME, MONTHS Fig.27-11