Understanding the mechanisms of prostate cancer (PC) development into castration-resistant prostate cancer (CRPC) is a key factor in finding better diagnostic and treatment tools. Although a number of studies have tried to explain the molecular evolution of CRPC, more refined understanding on molecular mechanisms is still needed for improved patient care. While increasing amounts of genomic aberrations are accumulating in prostate cancer genome during the disease progression, we still lack understanding on the functional impact of the majority of these aberrations or their combinations. Identification of the regulatory regions from tissue samples enables in-depth analysis of regulatory elements and upstream regulators that are driving tumor development. Thus, we can gain detailed understanding of how the genomic alterations reorganize the chromatin and enable the emergence of cancer phenotype.
We have previously characterized a cohort of 60 clinical prostate tissue samples including benign prostatic hyperplasia (BPH), PC, and CRPC with RNA-seq, MeDIP-seq, DNA-seq, small-RNA-seq, and mass spectrometry. To gain insight into the epigenetic regulation during the disease progression, we decided to use assay for transposase-accessible chromatin using sequencing (ATAC-seq). We first developed a method that allows us to use freshly frozen prostate samples as starting material, and performed ATAC-seq for BPH, PC, and CRPC samples from the above-mentioned cohort.
High quality peaks were identified from all the samples, ranging from tens of thousands to over one hundred thousand peaks per sample. Large variation in the chromatin structure was observed across the cohort. Unsupervised clustering based on peak intensities was able to separate the three different sample types into separate clusters with distinct chromatin state profile for each sample cluster. Next we extracted nucleosome signals from the data. This signal is able to illustrate nucleosome occupancy and positioning with high resolution in the areas of open chromatin. We observed organized nucleosome patterns in our BPH samples, but this organization start to fall apart in PC and especially in CRPC samples where nucleosome localization is no longer uniform inside the group. The results imply increased heterogeneity in chromatin structure as a result of disease progression.
Our data show that ATAC-seq data from clinical prostate material are sufficient to separate different sample groups to their own clusters, and it is possible to have detailed information about nucleosome binding in tumor tissues. These data allow us to reveal novel changes in chromatin state and integrate those changes to other features such as gene expression. With these data we aim to connect specific regulatory elements and upstream regulators to cancer phenotypes and genomic alterations. This new layer of information will bring us closer to understanding the mechanisms that drive molecular evolution of CRPC with potential implications in clinical practice for patients suffering from this devastating disease.
Citation Format: Joonas Tuominen, Tomi Häkkinen, Matti Annala, Kati Kivinummi, Teuvo Tammela, Leena Latonen, Kirsi Granberg, Tapio Visakorpi, Matti Nykter. Chromatin state alterations in human prostate cancer progression [abstract]. In: Proceedings of the AACR Special Conference: Prostate Cancer: Advances in Basic, Translational, and Clinical Research; 2017 Dec 2-5; Orlando, Florida. Philadelphia (PA): AACR; Cancer Res 2018;78(16 Suppl):Abstract nr A077.