Integrated Expression Profiling And ChIP-seq Analyses Of The Growth Inhibition Response Program Of The Androgen Receptor

The androgen receptor (AR) plays important roles in the development of male phenotype and in different human diseases including prostate cancers. The AR can act either as a promoter or a tumor suppressor depending on cell types. The AR proliferative response program has been well studied, but its prohibitive response program has not yet been thoroughly studied. Previous studies found that PC3cells expressing the wild-type AR inhibit growth and suppress invasion. We applied expression profiling to identify the response program of PC3cells expressing the AR (PC3-AR) under different growth conditions (i.e. with or without androgens and at different concentration of androgens) and then applied the newly developed ChIP-seq technology to identify the AR binding regions in the PC3cancer genome. A surprising finding was that the comparison of MOCK-transfected PC3cells with AR-transfected cells identified3,452differentially expressed genes (two fold cutoff) even without the addition of androgens (i.e. in ethanol control), suggesting that a ligand independent activation or extremely low-level androgen activation of the AR. ChIP-Seq analysis revealed6,629AR binding regions in the cancer genome of PC3cells with an FDR (false discovery rate) cut off of0.05. About22.4%(638of2,849) can be mapped to within2kb of the transcription start site (TSS). Three novel AR binding motifs were identified in the AR binding regions of PC3-AR cells, and two of them share a core consensus sequence CGAGCTCTTC, which together mapped to27.3%of AR binding regions (1,808/6,629). In contrast, only about2.9%(190/6,629) of AR binding sites contains the canonical AR matrix M00481, M00447and M00962(from the Transfac database), which is derived mostly from AR proliferative responsive genes in androgen dependent cells. In addition, we identified four top ranking co-occupancy transcription factors in the AR binding regions, which include TEF1(Transcriptional enhancer factor), GATA (GATA transcription factors), OCT (octamer transcription factors) and PU1(PU.1transcription factor). Our data provide a valuable data set in understanding the molecular basis for growth inhibition response program of the AR in prostate cancer cells, which can be exploited for developing novel prostate cancer therapeutic strategies.