Exploration of oncogenic cooperation between germline variation and somatic mutation in prostate cancer progression

Prostate carcinoma (PCa) is the most common cancer of men, associated with a still unresolved issue of accurate risk-stratification. While recent advances in omics technologies have provided clues as to how molecular changes shape the onset and progression of PCa, it remains largely unclear whether germline variants and somatic mutations cooperate to contribute to PCa progression and outcome. Thus, we explored whether oncogenic cooperation between regulatory germline variants and somatic driver mutations can help explain why some PCa patients develop a more aggressive phenotype, which may have implications for risk-adapted medical treatment. Here, by employing an integrative functional genomics approach, we identified receptor-type protein-tyrosine phosphatase kappa (PTPRK) as a TMPRSS2::ERG (TE)-modulated gene associated with PCa progression whose expression is controlled by cooperation of the TE-fusion with a regulatory single nucleotide polymorphism (SNP). Analysis of available clinically annotated patient cohorts demonstrated that PTPRK is overexpressed in TE-positive PCa tumors and associated with higher Gleason scores and metastatic disease. TE knockdown in PCa cell lines reduced PTPRK expression, while ectopic overexpression of the fusion in TE-negative PCa cell lines and prostatic epithelium cells induced its expression. Functionally, PTPRK silencing inhibited cellular proliferation, cell cycle progression, and clonogenic growth of PCa cells, which was mirrored by dysregulation of corresponding gene and protein signatures in global transcriptomic and phospho-proteomic analyses after PTPRK knockdown. Analysis of TE ChIP-Seq and Hi-C data from PCa cells highlighted a proximal TE-bound DNA element whose TE-dependent enhancer activity was validated in reporter assays and which could be abrogated by a regulatory SNP. Collectively, our results provide evidence of how exploration of oncogenic cooperation may help to identify novel biomarkers and potentially druggable pathways and highlight the role of the regulatory genome in PCa progression.