Abstract LB-096: Chromatin alterations in human prostate cancer

Whole human genome is packed into chromatin, which is dynamically remodeled. Chromatin structure has been extensively studied with cell lines, but information about chromatin structure in tissue context is lacking. We present genome-wide chromatin accessibility analysis of clinical tissue samples using transposase-accessible chromatin sequencing (ATAC-seq). Our sample cohort consist 11 benign prostatic hyperplasia (BPH), 16 primary prostate cancer (PC), and 11 castration resistant prostate cancer (CRPC) samples. We identified 23,307 to 136,104 regions of accessible chromatin per sample using MACS2 peak calling. Utilizing a peak unification method resulted in a unified set of 178,333 high confidence peaks across sample set. To find out which loci are differentially accessible during disease progression, we further compared normalized ATAC-seq signal between sample groups across the genome. We identified 4747 and 9445 differentially accessible regions (DARs) for BPH to PC and PC to CRPC comparison, respectively. Out of these, in 2961 and 6652 chromatin was opening and in 1786 and 2793 chromatin was closing in respective comparison. Using DARs, we observe clear separation of the sample groups. Earlier, we have characterized this cohort using DNA, RNA and DNA methylation sequencing as well as SWATH proteomics. Using these data and the same analysis approach as with DARs, we identified 2061 and 2723 differentially methylated regions (DMRs) in BPH to PC and PC to CRPC comparisons, respectively. We compared locations of DARs and DMRs and found out that these occur in different loci overlapping only in 27 and 35 loci in respective comparisons. When integrated with gene expression data, the chromatin accessibility correlated (|coefficient| g 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-096.