title: Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer.
abstract: Beginning with precursor lesions, aberrant DNA methylation marks the entire spectrum of prostate cancer progression. We mapped the global DNA methylation patterns in select prostate tissues and cell lines using MethylPlex-next-generation sequencing (M-NGS). Hidden Markov model-based next-generation sequence analysis identified ∼68,000 methylated regions per sample. While global CpG island (CGI) methylation was not differential between benign adjacent and cancer samples, overall promoter CGI methylation significantly increased from ~12.6% in benign samples to 19.3% and 21.8% in localized and metastatic cancer tissues, respectively (P-value < 2 × 10(-16)). We found distinct patterns of promoter methylation around transcription start sites, where methylation occurred not only on the CGIs, but also on flanking regions and CGI sparse promoters. Among the 6691 methylated promoters in prostate tissues, 2481 differentially methylated regions (DMRs) are cancer-specific, including numerous novel DMRs. A novel cancer-specific DMR in the WFDC2 promoter showed frequent methylation in cancer (17/22 tissues, 6/6 cell lines), but not in the benign tissues (0/10) and normal PrEC cells. Integration of LNCaP DNA methylation and H3K4me3 data suggested an epigenetic mechanism for alternate transcription start site utilization, and these modifications segregated into distinct regions when present on the same promoter. Finally, we observed differences in repeat element methylation, particularly LINE-1, between ERG gene fusion-positive and -negative cancers, and we confirmed this observation using pyrosequencing on a tissue panel. This comprehensive methylome map will further our understanding of epigenetic regulation in prostate cancer progression.
authors: Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
authors: Jung H
authors: JH
authors: Kim
authors: Saravana M
authors: SM
authors: Dhanasekaran
authors: John R
authors: JR
authors: Prensner
authors: Xuhong
authors: X
authors: Cao
authors: Daniel
authors: D
authors: Robinson
authors: Shanker
authors: S
authors: Kalyana-Sundaram
authors: Christina
authors: C
authors: Huang
authors: Sunita
authors: S
authors: Shankar
authors: Xiaojun
authors: X
authors: Jing
authors: Matthew
authors: M
authors: Iyer
authors: Ming
authors: M
authors: Hu
authors: Lee
authors: L
authors: Sam
authors: Catherine
authors: C
authors: Grasso
authors: Christopher A
authors: CA
authors: Maher
authors: Nallasivam
authors: N
authors: Palanisamy
authors: Rohit
authors: R
authors: Mehra
authors: Hal D
authors: HD
authors: Kominsky
authors: Javed
authors: J
authors: Siddiqui
authors: Jindan
authors: J
authors: Yu
authors: Zhaohui S
authors: ZS
authors: Qin
authors: Arul M
authors: AM
authors: Chinnaiyan
mesh_terms: D045744:Cell Line, Tumor; D018899:CpG Islands; D019175:DNA Methylation; D004273:DNA, Neoplasm / Q000235:genetics; D057890:Epigenomics; D004847:Epithelial Cells / Q000378:metabolism; D020869:Gene Expression Profiling; D015723:Gene Library; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008297:Male; D008390:Markov Chains; D009362:Neoplasm Metastasis; D020411:Oligonucleotide Array Sequence Analysis; D016133:Polymerase Chain Reaction; D011401:Promoter Regions, Genetic; D011467:Prostate / Q000378:metabolism; D011471:Prostatic Neoplasms / Q000235:genetics* / Q000378:metabolism; D017423:Sequence Analysis, RNA; D024363:Transcription Initiation Site
chemical_list: D004273:DNA, Neoplasm