Analysis of androgen receptor signaling and DNA methylation dynamics in prostate biology

DNA methylation is an epigenetic modification that contributes to stable gene silencing by interfering with the ability of transcriptional regulators to bind to DNA and, when found at high density, by recruiting methylation-specific repressor proteins. Published data reveal that hormone stimulation of certain nuclear receptors (i.e. the estrogen receptor and the glucocorticoid receptor) induces rapid, dynamic changes in DNA methylation patterns alongside transcriptional responses at a subset of target loci, over time. However, the ability of androgen receptor (AR) to dynamically regulate gene transcription is relatively under-studied and its role in the regulation of DNA methylation patterns remains to be elucidated. The purpose of this study is to establish that AR regulates gene transcription in a dynamic, DNA methylation-dependent manner in normal, non-transformed prostate epithelial cells. It was demonstrated at select target genes in normal prostate cells that hormone stimulated AR activity correlates with dynamic changes in nascent gene expression, inversely in phase with changes in DNA methylation patterns. Furthermore, it was shown dynamic recruitment of AR and RNA Polymerase II to these regions, as well as the recruitment of proteins involved in the DNA demethylation process: TET1 and TDG.;As a second goal of this study, it was hypothesized that AR target genes that display dynamic DNA methylation patterns in normal cells are susceptible to aberrant DNA methylation in cancer, as aberrant DNA methylation is a well-established characteristic of cancer cells. Using patient prostate cancer samples, we show that DNA methylation of AR target genes is increased in castrate-recurrent disease, as compared to androgen stimulated prostate cancer. Increased aberrant methylation in prostate cancer was further validated in the Cancer Genome Atlas (TCGA) prostate adenocarcinoma cohort; further, methylated genes were significantly down-regulated, as measured by gene expression profiling in TCGA and Oncomine. In silico analyses of AR binding in androgen-dependent and androgen-independent prostate cancer cell lines also revealed that the AR cistrome in these cell lines are observed to be moderately methylated in vivo. Further, genes that are dynamically regulated by AR in normal cells are observed to be aberrantly methylated in prostate cancer. Collectively, these findings establish that AR activity induces transient changes in DNA methylation patterns in prostate biology, which may have direct relevance to prostate tumorigenesis and contribute to the aberrant methylation patterns found in prostate cancer.