BAP1 and USP1 cooperate to regulate FANCD2 stability and cell proliferation in mesothelioma cells

BRCA1-associated protein 1 (BAP1) is frequently inactivated in pleural mesothelioma and functions as a tumor suppressor through its deubiquitinating activity. In this study, we investigated the context-dependent interplay between BAP1 and ubiquitin-specific protease 1 (USP1) in mesothelioma cells, focusing on their roles in regulating FANCD2, cell proliferation, and DNA damage responses. Genetic suppression of USP1 selectively inhibited cell proliferation in BAP1-deficient mesothelioma cells, whereas reintroduction of wild-type BAP1 rescued this growth defect; notably, a catalytically inactive BAP1 mutant failed to do so, indicating that BAP1 deubiquitinase activity is required for this compensation. In contrast, depletion of FANCD2 suppressed cell proliferation irrespective of BAP1 status, underscoring the essential role of FANCD2 in mesothelioma cell survival. Although both BAP1 and USP1 were capable of deubiquitinating FANCD2 in vitro, USP1 suppression in mesothelioma cells did not provide clear biochemical evidence of altered FANCD2 ubiquitination. Instead, USP1 knockdown was associated with reduced FANCD2 transcript and protein levels, without markedly affecting FANCD2 mRNA stability. At the cellular level, USP1 depletion impaired FANCD2 focus formation and reduced its colocalization with γ-H2AX in BAP1-deficient cells, consistent with defective DNA damage signaling. Despite these changes, homologous recombination (HR) efficiency was largely preserved, whereas non-homologous end joining activity was modestly increased upon USP1 suppression. Consistent with these in vitro findings, USP1 knockdown suppressed tumor growth in an intrathoracic xenograft model. Collectively, our results indicate that BAP1 and USP1 appear to regulate FANCD2 through distinct, context-dependent mechanisms, with USP1 primarily influencing FANCD2 expression and BAP1 modulating FANCD2 function at the post-translational level. Together, these findings identify USP1 as a context-dependent therapeutic vulnerability in BAP1-deficient mesothelioma and support a working model in which USP1-dependent maintenance of FANCD2 function becomes critical in the absence of functional BAP1.