Emerging roles for the epigenetic modifiers PBRM1 SETD2 and BAP1 in clear cell renal cell carcinoma pathogenesis and prognosis beyond VHL

Clear cell renal cell carcinoma (ccRCC) pathogenesis, which is traditionally centered on VHL inactivation, is critically driven by recurrent mutations in the epigenetic modifier genes PBRM1, SETD2, and BAP1 on chromosome 3p. These mutations define molecular subtypes with distinct clinical outcomes. PBRM1 loss (∼40%), a subunit of the SWI/SNF complex, is linked to a more indolent phenotype and potential sensitivity to antiangiogenic therapy as well as immune checkpoint inhibitor (ICI) resistance. SETD2 mutations (10–15%) cause genomic instability and are associated with aggressive features but may improve the ICI response. BAP1 mutation (10–15%) strongly predicts high-grade tumors, sarcomatoid differentiation, poor survival, and therapy resistance. The mutational status of these genes provides powerful prognostic and emerging predictive biomarkers. Future precision medicine strategies are evolving toward integrated multigene models and novel therapies targeting epigenetic vulnerabilities, such as synthetic lethality approaches and combination therapies, to improve ccRCC management.Furthermore, recent studies reveal that mutations in these epigenetic modifiers profoundly reshape the metabolic network of ccRCC by altering key pathways such as glycolysis, oxidative phosphorylation, and lipid metabolism. This dysregulation of the “epigenetic-metabolic axis” provides a novel mechanism underlying tumor heterogeneity, stemness, and differential treatment responses, opening new avenues for developing combination therapies that target metabolic vulnerabilities.