DNA methylation profiling across six histological states of prostate cancer

In spite of its prevalence as one of the world’s leading malignancies, prostate cancer (PCa) continues to evade molecular taxonomic sub-classification. However, gross clinical differences are observed within the umbrella term ‘prostate adenocarcinoma’; the majority of tumors appear indolent in nature, whilst a subset manifest aggressively. Contributing factors towards this resistance to molecular classification are an atypically low mutation frequency and a poorly delineated pathobiology. Conversely, epigenetic changes are evidenced to be amongst the earliest and most-widespread aberrations in PCa . We thus hypothesized that delineating epigenomic alterations during the stepwise progression of PCa would improve our understanding of the disease pathobiology and the molecular underpinning of indolent and aggressive tumors. Herein, we report the first epigenomic roadmap of prostate tumorigenesis, in which we dissected DNA methylation and microRNA expression in enriched epithelial cells across the entire trajectory of PCa, through tumor initiation, primary disease and metastatic dissemination. We provide evidence in support of proliferative inflammatory atrophy (PIA) as a precursor lesion, distinct from high-grade prostatic intraepithelial neoplasia (HGPIN) and show that indolent and aggressive tumors display unique sets of epigenetically dysregulated loci, which we further investigated as potential discriminatory markers. This study also establishes the importance of DNA methylation beyond the gene promoter in human cancer, with pronounced intra- and inter-genic CpG methylation observed. 45 human formalin fixed paraffin embedded prostate samples were analysed. Samples were enriched for epithelial cell population by laser capture microdissection. The chort consisted of 10 benign prostate samples (B), 7 proliferative inflammatory atrophy (PIA), 6 high-grade prostatic intraepithelial neoplasia (HGPIN), 7 indolent primary cancers (PCI), 8 aggressive primary prostate cancers (PCA), and 6 metastatic prostate cancers (PCM). Benign samples were procured from radical cystoprostatecomy from patients with no evidence of prostate cancer. PIA, HGPIN and primary tumours were all obtained from radical prostatectomy cases. PCI was defined as Gleason 6, pT2 disease, with a pre-operative PSA <10 ng/ml and no evidence of biochemical or clinical recurrence (5-year follow-up). PCA was defined as primary Gleason ≥4, pT3 disease, with evidence of biochemical or clinical recurrence. Metastatic lesions were obtained from visceral metastases (liver, adrenal, lymph node and per-aortic), obtained during rapid autopsy. Five samples excluded from the final analysis: PCI06-1, PCI06-2, PBL-1, PBL-2, PBL-3