Functional characterization of BAP1 mutations in genome edited cholangiocarcinoma organoids: role in cell death and drug responses

Cholangiocarcinoma (CCA) is a genetically heterogeneous malignancy of the bile ducts with limited effective treatments and variable chemotherapeutic responses. BRCA1-associated protein 1 (BAP1), a tumor suppressor gene frequently mutated in CCA, encodes a nuclear deubiquitinating enzyme involved in chromatin remodeling and cell death regulation. In this study, we investigated the role of BAP1 mutations in programmed cell death and drug response using patient-derived and prime-edited CCA organoids (CCAOs). BAP1-mutant organoids exhibited impaired activation of apoptosis and necroptosis, as evidenced by reduced cleaved caspase-3 and pMLKL expression. Transcriptomic analysis revealed BAP1-dependent gene expression changes including enrichment of pathways related to stress response, ion transport, and metabolic detoxification. Interesting, BAP1 mutant CCAOs showed enhanced sensitivity to sorafenib, a multikinase inhibitor commonly used in biliary tract cancer. These findings highlight BAP1 as a modulator of cell death and a potential predictive biomarker for sorafenib response in CCA, with implications for personalized therapy design.