Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer

Jung H. Kim, Saravana M. Dhanasekaran, John R. Prensner, Xuhong Cao, Daniel Robinson, Shanker Kalyana-Sundaram, Christina Huang, Sunita Shankar, Xiaojun Jing, Matthew Iyer, Ming Hu, Lee Sam, Catherine Grasso, Christopher A. Maher, Nallasivam Palanisamy, Rohit Mehra, Hal D. Kominsky, Javed Siddiqui, Jindan Yu, Zhaohui S. QinArul M. Chinnaiyan

Research output: Contribution to journalArticle

130 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)1028-1041
Number of pages14
JournalGenome research
Volume21
Issue number7
DOIs
StatePublished - Jul 1 2011

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

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    Kim, J. H., Dhanasekaran, S. M., Prensner, J. R., Cao, X., Robinson, D., Kalyana-Sundaram, S., Huang, C., Shankar, S., Jing, X., Iyer, M., Hu, M., Sam, L., Grasso, C., Maher, C. A., Palanisamy, N., Mehra, R., Kominsky, H. D., Siddiqui, J., Yu, J., ... Chinnaiyan, A. M. (2011). Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer. Genome research, 21(7), 1028-1041. https://doi.org/10.1101/gr.119347.110