Mechanistically guided therapeutic strategy for BAP1 mutant tumors through protein stability and chromatin modulation.

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Background: Mutations in BAP1 occur across multiple cancers and are associated with aggressive clinical phenotypes and limited therapeutic options. Although BAP1 functions as a deubiquitinase, its role in DNA damage responses and potential therapeutic vulnerabilities remains incompletely studied. We examined how BAP1 mutations affect DNA repair and explored rational combination strategies to target these vulnerabilities. Methods: Quantitative proteomics and ubiquitin profiling identified proteins whose stability is regulated by BAP1. A targeted small molecule screen was performed to discover compounds that selectively reduced survival of BAP1 mutant cells. Selected compounds were evaluated using proliferation, viability and apoptosis assays, DNA repair functional assays, and chromatin structure analyses. Drug synergy was determined using combination index modeling. Preclinical efficacy was assessed in cell-derived and patient-derived xenograft models. Results: BAP1 mutations disrupted the stability of key DNA damage response proteins, impairing damage repair efficiency. Treatment with a selected drug combination led to changes in chromatin structure, further reduced DNA repair capacity, and selectively triggered apoptosis in BAP1 mutant cells. The combination treated induced enhanced cytotoxicity, significantly reduced tumor growth, and improved survival in vivo. These effects were specific to BAP1 mutant models and were not observed in BAP1 wildtype tumors. Conclusions: BAP1 modulates DNA repair through effects on protein stability and chromatin dynamics. Our study identifies a mechanistically guided drug combination that selectively targets BAP1-deficient tumors, providing a foundation for further preclinical and clinical evaluation.