Cells Comprising the Prostate Cancer Microenvironment Lack Recurrent Clonal Somatic Genomic Aberrations

Abstract

Prostate cancer-associated stroma (CAS) plays an active role in malignant transformation, tumor progression, and metastasis. Molecular analyses of CAS have demonstrated significant changes in gene expression; however, conflicting evidence exists on whether genomic alterations in benign cells comprising the tumor microenvironment (TME) underlie gene expression changes and oncogenic phenotypes. This study evaluates the nuclear and mitochondrial DNA integrity of prostate carcinoma cells, CAS, matched benign epithelium and benign epithelium-associated stroma by whole genome copy number analyses, targeted sequencing of TP53, and fluorescence in situ hybridization. Comparative genomic hybridization (aCGH) of CAS revealed a copy-neutral diploid genome with only rare and small somatic copy number aberrations (SCNAs). In contrast, several expected recurrent SCNAs were evident in the adjacent prostate carcinoma cells, including gains at 3q, 7p, and 8q, and losses at 8p and 10q. No somatic TP53 mutations were observed in CAS. Mitochondrial DNA (mtDNA) extracted from carcinoma cells and stroma identified 23 somatic mtDNA mutations in neoplastic epithelial cells but only one mutation in stroma. Finally, genomic analyses identified no SCNAs, no loss of heterozygosity (LOH) or copy-neutral LOH in cultured cancer-associated fibroblasts (CAFs), which are known to promote prostate cancer progression in vivo.

Enduring epigenetic landmarks define the cancer microenvironment

“…Here, we generated high-resolution methylome maps of purified CAFs and matched NPFs. We found no evidence of gross genomic alterations in CAFs, similar to other reports (Qiu et al 2008;Bianchi-Frias et al 2016). Instead, CAFs harbor discrete and consistent DNA methylation differences, predominantly at regulatory regions across the genome.…”

“…Initial studies suggested that CAFs acquire genetic aberrations, but no recurrent genome alterations were identified in subsequent reports (Qiu et al 2008;Ashida et al 2012;Bianchi-Frias et al 2016). Here we ask if genome-wide differences in the epigenome underpin the persistent phenotypic differences between CAFs and NPFs.…”

Cellular determinants and microenvironmental regulation of prostate cancer metastasis

“…Despite their metastasis-abetting roles, the stromal cells in primary PCa surprisingly do not seem to sustain prevalent clonal somatic copy-number alterations [57]. The genomes of stromal cells associated with PCa were found to be generally stable and indistinguishable from the benign stroma and benign epithelial cells from the same patient [57], suggesting that molecular mechanisms other than chromosomal aberrations, most likely epigenetic, cause reactive stroma initiation and PCa progression.…”

“…The genomes of stromal cells associated with PCa were found to be generally stable and indistinguishable from the benign stroma and benign epithelial cells from the same patient [57], suggesting that molecular mechanisms other than chromosomal aberrations, most likely epigenetic, cause reactive stroma initiation and PCa progression. For example, IL-6 can contribute to the epigenetic silencing of TGF-β type II receptor ( TGFBR2 ) in adjacent fibroblastic cells, and this loss of prostatic stromal TGF-β signaling was found to mediate the further epigenetic silencing of DNA damage repair and reactive oxygen-metabolism genes [58].…”

Interaction of prostate carcinoma-associated fibroblasts with human epithelial cell lines in vivo

“…Experiments in mouse models demonstrated the potential of stromal mutations to affect tumor evolution (Hill et al, 2005a, b) however while interesting this may not be relevant to human disease. More recently, detailed genetic analysis of CAF by comparative genomic hybridization, DNA sequencing, and microsatellite methods, found no convincing evidence of clonal somatic copy-number alterations in the stromal components of human tumors, leading to a general acceptance that clonal somatic gene changes are not a major route to the formation of tumor stroma associated with human carcinomas (Bianchi-Frias et al, 2016, Campbell et al, 2009, Qiu et al, 2008). …”