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(12) Patent Application Publication (10) Pub. No.: US 2013/0022974 A1 Chinnaiyan Et Al

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(12) Patent Application Publication (10) Pub. No.: US 2013/0022974 A1 Chinnaiyan Et Al US 2013 0022974A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2013/0022974 A1 Chinnaiyan et al. (43) Pub. Date: Jan. 24, 2013 (54) DNA METHYLATION PROFILES IN CANCER Publication Classification (75) Inventors: Arul M. Chinnaiyan, Plymouth, MI (51) Int. Cl. (US); Mohan Saravana Dhanasekaran, Ann Arbor, MI (US); Jung Kim, CI2O I/68 (2006.01) Northville, MI (US) (52) U.S. Cl. ...................................................... 435/6.11 (73) Assignee: THE REGENTS OF THE UNIVERSITY OF MICHIGAN, Ann (57) ABSTRACT Arbor, MI (US) (21) Appl. No.: 13/523,545 The present invention relates to compositions and methods (22) Filed: Jun. 14, 2012 for cancer diagnosis, research and therapy, including but not limited to, cancer markers. In particular, the present invention Related U.S. Application Data relates to methylation levels of genes (e.g., in CGI islands of (60) Provisional application No. 61/498,296, filed on Jun. the promoter regions) as diagnostic markers and clinical tar 17, 2011. gets for prostate cancer. Patent Application Publication Jan. 24, 2013 Sheet 1 of 30 US 2013/0022974 A1 Figure 1 A SS 838 s & S&s&&xis&3:38 a. a. a. a. a. a. a. a. a. 888& R is Patent Application Publication Jan. 24, 2013 Sheet 2 of 30 US 2013/0022974 A1 &- 3838; iiirage::c Benign Adja Patent Application Publication Jan. 24, 2013 Sheet 3 of 30 US 2013/0022974 A1 Figure 3 N = 6619 tique TSS Else.” (6077 Unique Reiseg Genes) t S S SS &S .S. SMyy Na3S S Nd: - alie Nic23 Ci (pg islands Cin 5'Shore of CpG islands On 3 Shore of CpG islands On Non-CpG islancis Patent Application Publica US 2013/0022974 A1 ty?un81 Patent Application Publication Jan. 24, 2013 Sheet 6 of 30 US 2013/0022974 A1 Figure 6 A RASSF1 Chr3:50,342,221-50,353,371 B RASSE1 Š H3K4methylation 2 Swariants 1 & 4 Variant2 8 DNA methylation 2 O giwariant 3 PrEC NCap swariants 1 & 4 swariant 2 swariant 3 Variant 3 C LNCaPDMSO LNCaP 5-AZA Variant 3 NCP RACE (i. lili 1 1a 2 1, 3 5 8 Exons Svariants 1-4 Š H3K4methylation Evariants 5-8, & 8 DNA methylation ( So 2 2 as PrEC LNCaP 2 4 3 Evariants 5-8 2 ( -82 is LNCaP 5 RACE F 2 0 a2345678siclilill 2134567 Exons Patent Application Publication Jan. 24, 2013 Sheet 7 of 30 US 2013/0022974 A1 Figure 7 H3K4 + Methylation SS S X X S r O S. -N4 C O L r 8S38S8Š8Š ŠCpG islands Methylated Regions -1500 ISS 1500 bp H3K4 Binding Regions S Patent Application Publication Jan. 24, 2013 Sheet 8 of 30 US 2013/0022974 A1 Figure 8 A S. SS &Š xxxssssssssssssss Š. SS-Sysis: Patent Application Publication US 2013/0022974 A1 ..…–.….§. "…………. =.–ž§'___.…. ? §'====,(,,)–---- |~~~~ •=(-)_—___| :. |T????? |r=: :L. .¿?????????????? ……………………………...……… . 6?un814 er,????ae Patent Application Publication Jan. 24, 2013 Sheet 10 of 30 US 2013/0022974 A1 Figure 10 A Raw Counts associated with Chromosome 21 8, 8... 3,338......... g i:8:::::::::::::::::::::::::::::::: ----------------------------------------. 8. $38: & 3: X s & n ce - N s ce U S C O O O O O O s o C A- s c U S.) is: 2 a. R4=0.8556 x's ---------- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - warra-aaluka - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -'. ... : :-----'-:::::::::s'--::::::'. : SSC 38, 8: S: 388 FE 8: $8 8: 3 x: S.S. 88 - 8:3 LNCaP 400 bp Cut v1 PrEC 400bp Cut v1 Correlation by Raw Counts Correlation by Raw Counts B Peaks associated with Total CpG islands &..is . 338..... ....... 18:08cir. 18torio Q S H 8,838w -s d U 8 & 8 CP is ...---------------------------------------------------------- C O O O S st ?h n s s O ?h 4 2.368.----------...} : (iii.........i............................................................... - $828: a sist sixto PrEC 400bp Cut v1 Correlation by Peak Height Correlation by Peak Height Patent Application Publication Jan. 24, 2013 Sheet 11 of 30 US 2013/0022974 A1 Figure 11 A NCar vs. PEC PC NCa S.SEx&SR 99 SS 2 SS: Š CDKN2A 8 C4 & ES5 8 : Pf FOXSE & iOSKE S. AfiOXC: S AFEXA2 Cai SCX7 FOXC: Sa-i-A12 Sa-rra Sa-n-2 FOXA2 F5. ES MeDP-Seq, M.NGS CGI promoter(13936) CG - Non-Promoter(54572) Patent Application Publication Jan. 24, 2013 Sheet 12 of 30 US 2013/0022974 A1 Figure 12 CpG islands LNCaP PrEC n O . a C t L ŠCpG islands Methylated Regions n = 3,496 Refsed genes -1,500 TSS +1,500 bp 8S Patent Application Publication Jan. 24, 2013 Sheet 13 of 30 US 2013/0022974 A1 Figure 13 -31814918 Scale: chr1: . 31814500mino 31816000 BS-Seq Amplicon ; : BS-Seq-Amplicon No data ; PrEC-MNGS ; : PrEC-MNGS No data 19: LNCap-MNGS LNCaP-MNGS 8.6288 . 35.1599 ifief MeDP LNCap-MeDIP RSSSSsess kwsSSX Repeating Elements by RepeatMasker RepeatMasker: ; : ; ; ; ; ; ; ; ; ; : ; ; ; ; ; ; ENCODEHudson Alpha Methyl-seq TSPAN1 chr1:46418579-46418802 Scale: ; ; ; ; chr1: 46418000: 46419500: BS-Seq-Amplicon BS-Seq-Amplicon No data PrEC-MNGS PrEC-MNGS LNCaP-MNGS &&ss-sesssssssss Repeating Elements by Repeat Masker ENCODE Hudson Alpha Methyl-sed Patent Application Publication Jan. 24, 2013 Sheet 14 of 30 US 2013/0022974 A1 Figure 13 (continued) SPON2 chr4:1156947-1157266; 1157164-1157488 Scale: ; ; ; - 1kb . chr4: 115300 1157000; 1157500; BS-Seq Amplicon BS-Seq-AmpliconN 34.979 PrEC-MNGS 8.43 No data NCaP-MNGS No data No data LNCaP-MeDIP LNCaP-MeDP RefSeq Genes RepeatMaske NCODE Hudson Alpha Methyl-Seq K5521. K5622 : SHC1 chr1:153209107-153209344 Scale . chr1: 153208500 153209000: BS-Sec Amplicon15320950 153210000: BS-Seq-Amplicon ; : Š No data. PrEC-MNGS PrEC-MNGS No data, 19 NCaP-M LNCaP-MNGS 15,682 CBN.aP-MeDIP LNCap-MeDIP 8.1079 RepeatMask Repeating Elements by RepeatMasker ENCODEHudson Alpha Methyl-sed Patent Application Publication Jan. 24, 2013 Sheet 15 of 30 US 2013/0022974 A1 Figure 13 (continued) RASSF1A chr3:50353011-503531.98 Scale 500 bases-------- chr3:3: ; : 50353.000: : 50352500: : BS-Seq-Amplicon 50353500s 50354000: BS-Seq-Amplicon S. No data, PrECMNGS PreC-MNGS No data ; 30.27 LNCaPMNGS LNCap-MNGS 8.05 . SSSS 46.7579 . LN : RefSec. Genes Repeating Elements by Repeat Masker RepeatMasker ENCODEHudson Alpha Methyl-sec Š PPP1R3C Chr10:93382583-93382815 nexeneeeeeeeeeeeeerint- . exexext seesenteresex sextee exextee-sex sexx...exceeeeeeeeeeeexses:S. -... 93382000 93382500 93383000 9338s 500 BS-Seq-Amplicon : BS-Seq-Amplicon No data seeinas PrEC-MNGS No data LNCap-MNGS 112.24 LNCaP-MNGS 12.3884. ; : . 39.2857 LNCap-MeD LNCaP-MeDIP ass Repeating Elements by RepeatMasker ENCODE Hudson Alpha Methyl-seq Patent Application Publication Jan. 24, 2013 Sheet 16 of 30 US 2013/0022974 A1 Figure 13 (continued) NTN4 Chr12:94707434-94.707704 Scale: . 1kbisexists . chr12, 94.706500 94707000 94.707500. 94708000 94708500 ; : BS-Seq-Amplicon BS-Seq-Amplicon No data PrEC-MNGS No data 139,855. LNCaP-MNGS& S : LNCap-MNGS 12.0178. 20.7231, NSSNSS & LNCap-MeDIP RefSeq Genes Repeating Elements by RepeatMasker RepeatMasker ENCODEHudson Alpha Methyl-sed K5621. K5622. s MYC chr8:128815497-128815 710 chrs: 128815500 1288.16000 1 128817000 128317500 1288.18000 128818500 BS-Seq-Amplicon S. BS-Seq-Amplicon: & ‘. No data, . PrEC-MNGS PrEC-MNGS No data i No data: NCaP-MNGS LNCap-MNGS No data No data ; LNCap-MeDIP LNCap-MeDIP No data. : S : RefSeqGenes : SSSSSSSSsass Sass . epeating Elements by R RepeatMasker ; : ; ; ; ; ; ; ; ; ; : ; ; ENCODE Hudson Alpha Methyl-sed K5621 K5622: . Patent Application Publication Jan. 24, 2013 Sheet 17 of 30 US 2013/0022974 A1 Figure 14 LAMC2 chr1:181421688-18142.1931 Scale : : 1kb------------ sess-ses-------------------------------- chr1: 181421000 : 181421500: 181422000: 181422500; ; ; ; ; ; ; ; ; 181423000 BS-Sea-Amplicon ; : : ESSENRicon . q-Amp ; : ; ; ; ; ; ; ; ; : : & : ; ; No data ; : . PrEC-MNGS : : PrEC-MNGS No data. : ; ; ; ; ; ; ; ; ; 43,78. LNCaP-MNGS : 25.8276 : : : . : LNCaP-MeDP RefSeqGenes : 83.88. SSSSess is iss'ssis8 iss-se: :; Repeating Elements by RepeatMasker RepeatMasker M ENCODEHudson Alpha Methylised K5621.K5522 8 : . ; . KCTD1 Chr18:22381178-2238.1550 scalee ... , - r chr18: 22380000 22380500: 22381000 22381500: 22382OOO: 223.82500 22383Coo: BS-Seq-Amplicon: . ;. .: . &S Location ::: : . No data: . PrEc-MNGS PrEC-MNGS 66,9328.No data : LNCap-MNGS incap-MNGs šs. 54.85 . ... s. Se als SSS is RepeatMasker ENCODEHudson Alpha Methyl-sea Patent Application Publication Jan. 24, 2013 Sheet 18 of 30 US 2013/0022974 A1 Figure 14 (continued) CDKN2A Chr0:21960825-2196.1015 . - Soeto.sexes---s-s-s-s-s- : : . :: . ; : : 2196.0500: 2196.1000. 21.961500: BS-Seq-Amplicon . S.BS-Seq-Amplicon : No datas: : . PrEC-MNGS PrEC-MNGS 9.1038. ; : : &S SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS &s.& 78,0998. LNCaP-MeDIP S. eas RepeatMasker N K562. , , , . CALML3 chr10:55.56581-5556830 Scale: . chr10: 5557000 5557500 BS-Seq-Amplicon BS-Seq-AmpliconS. ; No data. ; ; ; ; ; ; ; ; ; : ; ; ; ; ; ; ; ; ; ; PrEC-MNGS PrEC-MNGS . LNCaP-MNGS: . :. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. &. Š: Šs $. m S incapriatip” LNCaP-MeDIP RefSeq Genes Repeating Elements by RepeatMasker RepeatMasker - . ENCODEHudsonAlpha Methyl-seq Patent Application Publication Jan. 24, 2013 Sheet 19 of 30 US 2013/0022974 A1 Figure 14 (continued) CHMP4A chr14:28313174-28313411 Scale 1kbox-ories chr14: 28312500 : 28313000; : BS-Seq-Ampl28313500 gon BS-Sec-Amplicon: Š No datai. PrEC-MNGS PrEC-MNGS No data. 378,726. LNCaP-MNGS LNCap-MNGS 1644. 11,5662. LNCap-MeDIP - epeatMasker RepeatMasker ENCODE Hudson Alpha Methyl-sed 5-112101,503 3. BS-Sed-Amplicon112101500; . 112102000: 112102500 S.PrEC-MNGS LNCap-MNGS & CaP-MeDIP LNCap-MeDIP RefSeq Genes epeating Elements by RepeatMasker ENCODEHudson Alpha Methyl-sea Patent Application Publication Jan. 24, 2013 Sheet 20 of 30 US 2013/0022974 A1 Figure 14 (continued) AOX1 chr2:201158884-201159157 Scales . .1 kb chr2: 201158000: . 201158500: 201159,000 2011595.00 20116000 BS-Seq Amplicon . : : : . BS-Sed-Amplicon : No data, "PENN65 : PrEC-MNGS No data, 180.991. LNCaP-MNGS LNCaP-MNGS SSSSSSSSSSSSSSSS RSSR'ss: SSSSSSSS-S-S- Repeating Elements by Repeat Masker RepeatMasker m ENCODE Hudson Alpha Methyl-seq K5621 . ; : : ::S . K5522 E: AMT chr3:49434492-49434742 Scale 1kbsesssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssss chr3: . 19434000 49.434500i 49435000 49435500 BS-Seq Amplicon ; : : BS-Seq-AmpliconŠ: ; : 8 .
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