Abstract 4840: DNA methylation patterns and transcript isoform regulation in prostate cancer
Authors: Dhanasekaran Saravana Mohan , Kim Jung (Julie) H. , Prensner John , Cao Xuhong , Robinson Daniel , Kalyana-Sundaram Shanker , Shankar Sunita , Jing Xiaojun , Iyer Matthew , Sam Lee , Hu Ming , Grasso Catherine , Maher Christopher , Palanisamy Nallasivam , Mehra Rohit , Huang Christina , Siddiqui Javed , Yu Jindan , Qin Zhaohui , Chinnaiyan Arul 
Published: June 2012

Abstract
In cancer, the genome undergoes global DNA methylation changes, which contributes to disease progression. We mapped the global DNA methylation patterns in prostate tissues and cells (n=19) from fifty nanograms of genomic DNA. The methylated regions enriched by Methylplex technology, were subjected -Next Generation Sequencing (M-NGS). A total of 28 lanes of next generation sequencing yielded approximately 530 million sequence reads. The reads uniquely mapped to human genome were analyzed by H-Peak program to identify 1.8 million methylated regions from the 28 runs. While twenty percent of all CpG islands (CGIs) (68,508) were methylated in tissues, the promoter CGI methylation gradually increased from ∼12.6% in benign samples to 19.3% and 21.8% in localized and metastatic cancer tissues. However surprisingly, the total methylation events in intergenic/intronic regions between benign adjacent and cancer tissues were largely comparable. We found distinct patterns in promoter methylation around transcription start sites where methylation occurred directly on the CGIs, flanking regions and on CGI sparse promoters. Among the 6,691 methylated promoters in prostate tissues, 2481 differentially methylated regions (DMRs) were cancer specific and several previously studied targets were among them. A novel cancer specific DMR in WFDC2 promoter showed 77% methylation in cancer (17/22), 100% methylation in transformed prostate cell lines (6/6), none in the benign tissues (0/10) and normal PrEC cells. Integration of LNCaP DNA methylation and H3K4me3 data suggested a role for DNA methylation in alternate transcription start site utilization. Specifically, we detail the regulation of RASSF1, a gene previously reported to be silenced through DNA methylation in PCa and NDRG2. We show that variant-1 of RASSF1, but not variant-2 or -3, is specifically silenced in LNCaP through promoter methylation, and normal cells do not exhibit this phenomenon. Treatment with 5-Aza-2-deoxycytidine preferentially induced re-expression of variant-1 of RASSF1 in LNCaP, confirming transcriptional regulation of this isoform through DNA methylation. The methylated promoters lacking CGIs showed sparse H3K4me3 modification, interestingly methylated promoters containing CGIs showed a mutually exclusive H3K4me3/DNA methylation marks. Finally, we observed a difference in the methylation of LINE-1 elements between transcription factor ERG positive and negative cancers. The comprehensive methylome map presented here will further our understanding of epigenetic regulation of the prostate cancer genome.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4840. doi:10.1158/1538-7445.AM2011-4840