BAP1-mediated stabilization of SUFU enhances E2F1 activity and promotes colorectal tumorigenesis.

[BACKGROUND] The Hedgehog (Hh) signaling pathway plays a pivotal role in tumorigenesis. SUFU (Suppressor of Fused), a key negative regulator of Hh signaling, also interacts with additional signaling pathways involved in cancer progression. However, its specific function and regulatory mechanisms in colorectal cancer (CRC) remain poorly understood.

[METHODS] Using Co-immunoprecipitation (Co-IP), we identified BAP1 as a candidate deubiquitinating enzyme (DUB) that interacts with SUFU. Western blotting was used to investigate the molecular mechanism by which BAP1 regulates SUFU protein stability. Integration of public databases and immunohistochemical (IHC) staining of CRC patient samples revealed altered expression both BAP1 and SUFU in CRC. Functional assays, including CCK-8 cell proliferation assays and xenograft tumor models, were conducted to evaluate the biological impact of BAP1-SUFU signaling. Furthermore, transcriptomic analyses and rescue experiments were performed to investigate the downstream regulatory mechanisms of the BAP1-SUFU axis in CRC cell proliferation.

[RESULTS] We demonstrated that BAP1 regulates the ubiquitination and protein stability of SUFU via its UCH enzymatic domain. Analysis of CRC clinical samples and public datasets revealed that BAP1 and SUFU are concurrently upregulated in tumor tissues. Functional experiments in vivo confirmed that BAP1 and SUFU promote CRC cell proliferation and clonogenic potential through modulation of the cell cycle. Pharmacological inhibition of BAP1 resulted in reduced SUFU protein levels and significantly suppressed CRC cell proliferation. Rescue experiments further showed that overexpression of SUFU partially restored cell proliferation in the presence of BAP1 inhibition, suggesting a functional dependency. Transcriptomic and mechanistic analyses revealed that disruption of the BAP1-SUFU axis alters cell-cycle transcriptional programs through a Hh-independent mechanism and implicates E2F1 as a downstream regulator, which was confirmed by Western blot and rescue experiments demonstrating its essential role in driving the proliferative phenotype. Moreover, knockdown of BAP1 or SUFU, as well as pharmacological inhibition of BAP1, significantly suppressed tumor growth in xenograft models and reduced E2F1 protein levels, further elucidating the mechanistic basis of this regulatory axis and demonstrating its therapeutic potential in vivo.

[CONCLUSION] These findings highlight the critical role of SUFU in promoting CRC cell proliferation through its regulation by BAP1. Targeting BAP1 enzymatic activity offers a promising therapeutic strategy to modulate SUFU levels and suppress tumor growth. The development of specific BAP1 inhibitors may represent a novel and effective approach to improve outcomes in CRC.

[SUPPLEMENTARY INFORMATION] The online version contains supplementary material available at 10.1186/s12964-025-02627-9.