US 2005O260639A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2005/0260639 A1 Nakamura et al. (43) Pub. Date: Nov. 24, 2005 (54) METHOD FOR DIAGNOSING PANCREATIC Related U.S. Application Data CANCER (63) Continuation-in-part of application No. PCT/JPO3/ 11817, filed on Sep. 17, 2003. (75) Inventors: Yusuke Nakamura, Yokohama-shi (JP); Toyomasa Katagiri, Shinagawa-ku (60) Provisional application No. 60/555,809, filed on Mar. 24, 2004. Provisional application No. 60/450,889, (JP); Hidewaki Nakagawa, filed on Feb. 28, 2003. Provisional application No. Shinagawa-ku (JP) 60/414,872, filed on Sep. 30, 2002. Publication Classification Correspondence Address: TOWNSEND AND TOWNSEND AND CREW, (51) Int. Cl. .................................................. C12O 1/68 LLP (52) U.S. Cl. .................................................................. 435/6 TWO EMBARCADERO CENTER EIGHTH FLOOR (57) ABSTRACT SAN FRANCISCO, CA 94111-3834 (US) Objective methods for detecting and diagnosing pancreatic cancer (PNC) are described herein. In one embodiment, the (73) Assignees: Oncotherapy Science, Inc., Kawasaki diagnostic method involves determining the expression level shi (JP); The University of Tokyo, Bun of PNC-associated gene that discriminates between PNC kyo-ku (JP) cells and normal cells. The present invention further pro vides methods of Screening for therapeutic agents useful in (21) Appl. No.: 11/090,739 the treatment of pancreatic cancer, methods of treating pancreatic cancer and method of vaccinating a Subject (22) Filed: Mar. 24, 2005 against pancreatic cancer. Patent Application Publication Nov. 24, 2005 Sheet 1 of 16 US 2005/0260639 A1 FG 1 Patent Application Publication Nov. 24, 2005 Sheet 2 of 16 US 2005/0260639 A1 s - to co on S 2 2 O C C C D C C C D C) () () O U O n. O. all all all a ?al all all a fall a Z TUBA 12 : APP 1012 13 : ARHGDB 1212 15: ATDC 1012 16 : ATP1B3 1212 19: BIRC5 1212 22 : BUB1B 12/12 33: CELSR3 9/12 35: CKS1 7112 36 : CKS2 11112 48 : CYP2S1 8/12 54: E2-EPF to six tax xxx 8/12 56 : ELF4 11/12 57 : ENC1 7112 59 : EPHA4 9/12 61 : Evi-1 11/12 63 : FOXM1 11112 73 : GW112 7112 74 : GYS1 10/12 77 : HDGF 10/12 Patent Application Publication Nov. 24, 2005 Sheet 3 of 16 US 2005/0260639 A1 FIG.2-2 s vs N O OC O. V.cN V(Y) VNr. vanLO vsto N- vOO E () () () (d O C C C D cd O c) O O a - A - all all all all all all d. a 2 TUBA 83 : HOXB7 84 : h AD 612 -colony10 12/12 102: KNSL6 10/12 103: KPNB2 10/12 11.5: MMP11 11/12 120: MYBL2 10/12 125: OAS1 t sis an ess 8/12 127: ORP150 fi ass 3% O 412 132: PCON3 141: PPM1B was a w tw. At 3:...at 31 12 12/12 143: PRC1 6/12 149: PSCA , , , , was e ... 9/12 152: PYCR1 O O 155: RBMS1 12/12 157: REGIV as as O - ". 164: S100P 169: SFN 170: SLC12A2 5/12 173: SLC2A1 Patent Application Publication Nov. 24, 2005 Sheet 4 of 16 US 2005/0260639 A1 FG.2-3 - so to a S 2 2 2 CD C C C C C C C D C C D C ( ) O - C - O - O - all a a a Z TUBA 178: SRD5A1 8/12 180: TCEA1 8/12 184: TK1 10/12 188: UBCH10 10/12 196: WHSC1 8/12 198: FLJ10134 8/12 2O3: 5/12 208: KAAO101 12/12 217: KIAA1624 9/12 218: KIAA1808 8/12 225: FLU21504 11112 231: WANGL1 6/12 234: EST 11/12 239: EST 8/12 245: EST - - - - - - 6/12 253: EST 12/12 254: FXYD3 9/12 259: EST u au it 6/12 Patent Application Publication Nov. 24, 2005 Sheet 6 of 16 US 2005/0260639 A1 FG4 Liver Liver meta meta () (+) ANPEP DKFZP586OO223 MMP12 PTMS MYG1 3 ES PASSA MAN1B1 PKM2 EDH2KIAAO668 ZNF282 BZRP . FGG PLOD ; FBL KRT8AS28 EST RP4-751H13 ... YKT6 FLJ13102 EST SDCCAG8 HEXA EMK1 GPRK7 HSPC138 PPP1 CC WAS Patent Application Publication Nov. 24, 2005 Sheet 7 of 16 US 2005/0260639 A1 FIG.5 (A-1) NR4A1 KIAAO469 KIAAO903 GRB10 GP is MTMR1 CSH2 DKFZP761C169 TIMM9 CTSB HSPC164 GOLGA3 BRE SAHBP1 TPD52L2 HSPD1 HSPA1A AARS YME1L1 RALY EST WARS SENP2 MRPL3 MLLT4 CCT6A ARPC3 HSP 105B SHMT2 RPL37A POH1 EST GLS FLJ10803 ... EST - NPD002 GRB14 Patent Application Publication Nov. 24, 2005 Sheet 8 of 16 US 2005/0260639 A1 FIG.5 (A-2) LCAT RAGE ARGBP2 T. E. ATP1A1EST SCAP EIF3S8. SYNGR2 GPRC5C is EST EST BZRP PRSS1 TUFM E. E. OARSSERPNA4 it. GSTM1 CBARA1 HK1 FLOT2 RPS11 LOC51 189 DAG1 PRKACB AGR2 RPL38 TPM3 PSMB4 ATP5O PPP3CA PM5 MAC30 ACO1 DBY EST RPL17 EEF1G RPS2 RPLP1 RPL23A RPL13A CATX-8 CASP4 RPLP2 Patent Application Publication Nov. 24, 2005 Sheet 9 of 16 US 2005/0260639 A1 FIG.5 (B) 4.6 2 30 60 90 Number of discriminating genes (C) -100 Number of discriminating genes o early-recurrent cases 0 late-recurrent cases Patent Application Publication Nov. 24, 2005 Sheet 10 of 16 US 2005/0260639 A1 FG.6 (A) 90d O80d º?Od (B) d.©||9 O9Od O8Od O6Od O9||Od O94,Od Patent Application Publication Nov. 24, 2005 Sheet 11 of 16 US 2005/0260639 A1 FG.7 CDH3 normal pancreatic du Patent Application Publication Nov. 24, 2005 Sheet 12 of 16 US 2005/0260639 A1 FG. 8-1 (A) PCIDH1 Patent Application Publication Nov. 24, 2005 Sheet 13 of 16 US 2005/0260639 A1 FIG.8-2 (C) GPR107 | Patent Application Publication Nov. 24, 2005 Sheet 14 of 16 US 2005/0260639 A1 FIG.9 (A) PCDH1 ACTB (B) PK-45P 41 Os EGFPsi (C) O.6 0.5 0.4 0.3 0.2 0.1 41 Osi EGFP Si Patent Application Publication Nov. 24, 2005 Sheet 15 of 16 US 2005/0260639 A1 FIG.10 Patent Application Publication Nov. 24, 2005 Sheet 16 of 16 US 2005/0260639 A1 FG.11 (B)KLM-1 1003si EGFPsi (C) 10O3Si EGFPSi US 2005/0260639 A1 Nov. 24, 2005 METHOD FOR DIAGNOSING PANCREATIC fusion proteins, has been developed to treat chronic myel CANCER ogenous leukemias wherein constitutive activation of bcr abl tyrosine kinase plays a crucial role in the transformation PRIORITY INFORMATION of leukocytes. Agents of these kinds are designed to Suppress 0001. This application is a continuation-in-part of PCT/ oncogenic activity of specific gene products (Fujita et al., JP2003/011817 (WO 2004/031412), which claims priority Cancer Res 61.7722-6 (2001)). Therefore, gene products to U.S. Provisional Applications Ser. No. 60/414,872, filed commonly up-regulated in cancerous cells may serve as Sep. 30, 2002 and Ser. No. 60/450,889, filed Feb. 28, 2003. potential targets for developing novel anti-cancer agents. This application also claims the benefit of Ser. No. 60/555, 0006. It has been demonstrated that CD8+ cytotoxic T 809 filed Mar. 24, 2004. All of these applications are lymphocytes (CTLs) recognize epitope peptides derived incorporated herein by reference. from tumor-associated antigens (TAAS) presented on MHC Class I molecule, and lyse tumor cells. Since the discovery TECHNICAL FIELD of MAGE family as the first example of TAAS, many other TAAS have been discovered using immunological 0002 The invention relates to methods of diagnosing approaches (Boon, Int J Cancer 54: 177-80 (1993); Boon pancreatic cancer. and van der Bruggen, J Exp Med 183: 725-9 (1996); van der Bruggen et al., Science 254: 1643-7 (1991); Brichard et al., BACKGROUND OF THE INVENTION J Exp Med 178: 489-95 (1993); Kawakami et al., J Exp Med 0.003 Pancreatic cancer has one of the highest mortality 180: 347-52 (1994)). Some of the discovered TAAS are now rates of any malignancy, and the 5-year-Survival rate of in the Stage of clinical development as targets of immuno patients is 4%. 28000 patients with pancreatic cancer are therapy. TAAS discovered so far include MAGE (van der diagnosed each year, and nearly all patients will die of their Bruggen et al., Science 254: 1643-7 (1991)), gp100 disease (1). The poor prognosis of this malignancy is a result (Kawakami et al., J Exp Med 180: 347-52 (1994)), SART of the difficulty of early diagnosis and poor response to (Shichijo et al., J Exp Med 187: 277-88 (1998)), and current therapeutic methods (1, 2). In particular currently no NY-ESO-1 (Chen et al., Proc Natl Acad Sci USA94: 1914-8 tumor markers are identified that allow reliable Screening at (1997)). On the other hand, gene products which had been an early, potentially curative Stage of the disease. demonstrated to be specifically over-expressed in tumor 0004 cDNA microarray technologies have enabled to cells, have been shown to be recognized as targets inducing obtain comprehensive profiles of gene expression in normal cellular immune responses. Such gene products include p53 and malignant cells, and compare the gene expression in (Umano et al., Brit J Cancer 84: 1052-7 (2001)), HER2/neu malignant and corresponding normal cells (Okabe et al., (Tanaka et al., Brit J Cancer 84: 94-9 (2001)), CEA (Nukaya Cancer Res 61:2129-37 (2001); Kitahara et al., Cancer Res et al., Int J Cancer 80: 92-7 (1999)), and so on. 61: 3544-9 (2001); Lin et al., Oncogene 21:4120-8 (2002); 0007. In spite of significant progress in basic and clinical Hasegawa et al., Cancer Res 62:7012-7 (2002)). This research concerning TAAS (Rosenbeg et al., Nature Med 4: approach enables to disclose the complex nature of cancer 321-7 (1998); Mukherji et al., Proc Natl Acad Sci USA 92: cells, and helps to understand the mechanism of carcino 8078-82 (1995); Hu et al., Cancer Res 56: 2479-83 (1996)), genesis.