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WO 2012/174256 A2 20 December 2012 (20.12.2012) P O P C T

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WO 2012/174256 A2 20 December 2012 (20.12.2012) P O P C T (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2012/174256 A2 20 December 2012 (20.12.2012) P O P C T (51) International Patent Classification: (81) Designated States (unless otherwise indicated, for every C12Q 1/68 (2006.0 1) G01N 33/574 (2006.0 1) kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BR, BW, BY, BZ, (21) International Application Number: CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, DO, PCT/US20 12/042483 DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, (22) International Filing Date: HR, HU, ID, IL, IN, IS, JP, KE, KG, KM, KN, KP, KR, 14 June 2012 (14.06.2012) KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, (25) Filing Language: English OM, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SC, SD, (26) Publication Language: English SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (30) Priority Data: 61/498,296 17 June 201 1 (17.06.201 1) US (84) Designated States (unless otherwise indicated, for every kind of regional protection available): ARIPO (BW, GH, (71) Applicant (for all designated States except US): THE RE¬ GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, SZ, TZ, GENTS OF THE UNIVERSITY OF MICHIGAN UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, [US/US]; 1600 Huron Parkway, 2nd Floor, Ann Arbor, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, Michigan 48109-2590 (US). EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, (72) Inventors; and TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, (75) Inventors/Applicants (for US only): CHINNAIYAN, ML, MR, NE, SN, TD, TG). Arul M. [US/US]; 51300 Plymouth Valley Drive, Ply mouth, Michigan 48170 (US). DHANASEKARAN, Mo¬ Published: han Saravana [IN/US]; 1108 Maiden Lane Court, Apt. — without international search report and to be republished 107, Ann Arbor, Michigan 48105 (US). KIM, Jung upon receipt of that report (Rule 48.2(g)) [KR/US]; 43425 Scenic Lane, Northville, Michigan 48167 (US). (74) Agent: ARENSON, Tanya A.; Casimir Jones, S.C., 2275 Deming Way, Suite 310, Middleton, Wisconsin 53562 (US). < © (54) Title: DNA METHYLATION PROFILES IN CANCER (57) Abstract: The present invention relates to compositions and methods for cancer diagnosis, research and therapy, including but not limited to, cancer markers. In particular, the present invention relates to methylation levels of genes (e.g., in CGI islands of the promoter regions) as diagnostic markers and clinical targets for prostate cancer. CROSS REFERENCE TO RELATED APPLICATIONS 5 This application claims priority to U.S. Provisional Application No. 61/498,296, filed June 17, 20 1, which is herein incorporated by reference in its entirety. STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT [0 This invention was made with government support under CA069568, CA! 32874, CA 275 and DA021519 awarded by the National Institutes of Health and BC07023 awarded by the Army edical Research and Material Command. The government has certain rights in the invention. FIELD OF THE INVENTION ί5 The present invention relates to compositions and methods for cancer diagnosis, research and therapy, including but not limited to, cancer markers. In particular, the present invention relates to methylation levels of genes (e.g., in CG islands of the promoter regions) as diagnostic markers and clinical targets for prostate cancer. 0 BACKGROUND OF THE INVENTION A central aim in cancer research is to identify altered genes that are causally implicated in oncogenesis. Several types of somatic mutations have been identified including base substitutions, insertions, deletions, translocations, and chromosomal gains and losses, all of which result in altered activity of an oncogene or tumor suppressor gene. First hypothesized in the early 1900's, there is 5 now compelling evidence for a causal role for chromosomal rearrangements in cancer (Rowley, Nat Rev Cancer : 245 (2001 )). Recurrent chromosomal aberrations were thought to be primarily characteristic of leukemias, lymphomas, and sarcomas. Epithelial tumors (carcinomas), which are much more common and contribute to a relatively large fraction of the morbidity and mortality associated with human cancer, comprise less than 1% of the known, disease-specific chromosomal \ rearrangements (Mitelman, Mutat Res 462: 247 (2000)). While hematological malignancies are often characterized by balanced, disease-specific chromosomal rearrangements, most solid tumors have a plethora of non-specific chromosomal aberrations. It is thought that the karyotypic complexity of solid tumors is due to secondary alterations acquired through cancer evolution or progression. Two primary mechanisms of chromosomal rearrangements have been described. In one mechanism, promoter/enhancer elements of one gene are rearranged adjacent to a proto-oncogene, thus causing altered expression of an oncogenic protein. This type of translocation is exemplified by the apposition of immunoglobulin (IG) and T-ee receptor (TCR) genes to MYC leading to 5 activation of this oncogene in B- and T-cell malignancies, respectively (Rabbitts, Nature 372: 43 (1994)). In the second mechanism, rearrangement results in the fusion of two genes, which produces a fusion protein that may have a new function or altered activity. The prototypic example of this translocation is the BCR-ABL gene fusion in chronic myelogenous leukemia (CM L) (Rowley, Nature 243: 290 (1973); de Klein et a ., Nature 300: 765 (1982)). Importantly, this finding led to the [0 rational development of imatinib mesylate (Gleevec), which successfully targets the BCR-ABL kinase (Deininger et al., Blood 105: 2640 (2005)). Thus, diagnostic methods that specifically identify epithelial tumors are needed. SUMMARY OF THE INVENTION [5 The present invention relates to compositions and methods for cancer diagnosis, research and therapy, including but not limited to, cancer markers. In particular, the present invention relates to methylation levels of genes (e.g., in CGI islands of the promoter regions) as diagnostic markers and clinical targets for prostate cancer. Embodiments of the present invention provide compositions, kits, and methods useful in the detection and screening of prostate cancer. Experiments conducted during the course of development of embodiments of the present invention identified aberent methylation status of certain genes in prostate cancer. Some embodiments of the present invention provide compositons and methods for detecting such aberently methylated genes. Identification of aberently methylated genes finds use in screening, diagnostic and research uses. 15 For example, in some embodiments, the present invention provides compositions, kits and methods of screening for the presence of prostate cancer in a subject, comprising contacting a biological sample from a subject with a reagent for detecting the methylation status of one or more genes (e.g., including but not limited to, WFDC2, MAGI2, MEIS2, NTN4, GPRC5B, C9orfI25, FGFR2, AOX!, VAMPS, C14orf!59, PPP1R3C, S100A16 orAMT&s wel l as one or more of the genes listed in Table 4; and detecting the methylation status of said genes using an in vitro assay, wherein a higher degress of methylation of said genes in said sample relative to the level of methylation in normal prostate cells in indicative of prostate cancer in said subject. In some embodiments, the sample is selected from tissue, blood, plasma, serum, urine, urine supernatant, urine cell pellet, semen, prostatic secretions or prostate cells. In some embodiments, the detecting the level of methyiation is carried out utilizing Methyiplex-Next Generation Sequencing (M-NGS) or another suitable assay. In some embodiments, the cancer is localized prostate cancer or metastatic prostate cancer in some embodiments, the methyiation is detected in the 5' non-coding region (e.g., promoter region) of the gene. In some embodiments expression of genes is decreased when an increased level of methyiation is present. n some embodiments, analysis is conducted using a computer implemented method, and results are displayed to a user using a user interface. In some embodiments, the results of the method are used to determine a treatment course of action. In some embodiments, the treatment course of action (e.g., chemotherapy) is administered. In some embodiments, the method is performed again after treatment and is used to determine whether further treatment is needed and/or administered. Additional embodiments are described herein DESCRIPTION O F THE FIGURES Figure 1 shows characterization of genome-wide methyiation patterns in prostate cells by M- NGS (A) Venn diagram represents a 70% overlap between the regions methylated in LNCaP and PrEC cells. (B) In LNCaP an PrEC, the majority of DNA methyiation occurred in intergenic an intronic regions and the genomic distribution of methyiation peaks was similar. (C) Promoter associated CpG islands displayed 7 fold difference in methyiation between LNCaP and PrEC cells. (D) DNA methyiation in APC, CHMP4A, CALML3, CDKN2A, KCTDl, LAMC2, RASSF1, S C1, TINAGLI and TSPAN1 gene promoters in LNCaP (L) ceils; SPON2 in PrEC (P) cells and a negative control region in C were validated by bisulfite sequencing. Figure 2 shows DNA methyiation pattern in prostate tissues (A) Genome -wide distribution of DNA methyiation in various prostate sample groups analyzed. The majority of methyiation peaks are confined to intergenic and intronic regions similar to cell lines. (B) A gradual increase in percent methyiation with cancer progression among promoter CGLs compared CG s located in other genomic regions was observed. * Pearson's Chi-squared test p-value <2x 0 '6 Figure 3 shows promoter DNA methyiation during prostate cancer progression A total of 6619 gene promoters from 6077 unique RefSeq genes harbored DNA methyiation among the various sample groups analyzed (Normal, Benign Adjacent, PCa or MET).
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