Absence of somatic copy number alterations in non-neoplastic prostate epithelium

Somatic copy number alterations (CNA) in cancer driver genes are a hallmark of human cancers, but have recently been reported in benign tissues in a handful of organ systems, including the prostate. However, these recent findings may be confounded by technical limitations and challenges in accurately ruling out cancer precursors such as intra-epithelial neoplastic lesions, particularly in frozen tissue. To address this, we used a panel of molecular markers to definitively distinguish benign glands from prostatic intra-epithelial neoplasia (PIN) and invasive cancer in frozen tissue sections, and used this as a guide for laser capture microdissection followed by whole genome sequencing to assess copy number alterations. Our analysis of 171 benign samples from 138 subjects revealed a complete absence of large copy number alterations (LCNA) in benign epithelium, including at key driver genes such as MYC, PTEN, RB1, and APC. In contrast, a significant fraction of PIN exhibited intermediate LCNA levels between benign and cancer. A post-hoc review of these copy number altered PIN lesions indicated that they would have been highly difficult to distinguish morphologically from benign prostate without the use of the panel of molecular markers. These results highlight the importance of rigorous molecular approaches for tissue diagnosis in frozen tissue and suggest that previous reports of CNA in benign prostate may reflect misidentified PIN.