CMA-mediated USP9X degradation promotes SHH medulloblastoma progression by facilitating SUFU ubiquitination

Medulloblastoma (MB) represents the most prevalent malignant paediatric brain tumour, characterised by the sonic Hedgehog molecular subtype (SHH-MB), which is driven by aberrant activation of the SHH signalling cascade. Suppressor of fused (SUFU), a core member of SHH signal transduction, functions as a tumour suppressor by inhibiting the activity of transcription factors glioma-associated oncogene homologue (GLI)-triggered SHH signalling pathway. While ubiquitin-mediated proteasomal degradation of SUFU has been shown to modulate SHH signalling, the regulatory factors involved in SUFU deubiquitination and their specific roles in MB pathogenesis remain largely undefined.

Mass spectrometry and co-immunoprecipitation were employed to identify the interaction between USP9X and SUFU. Clinical correlation analyses were conducted using MB tissue microarrays and publicly available datasets. Ubiquitination assays, functional cell-based experiments, and orthotopic xenograft models were performed to evaluate the biological role of USP9X in SHH-MB. Chaperone-mediated autophagy (CMA) inhibitors were utilised to investigate their regulatory effects on USP9X expression and SHH-MB progression.

Mass spectrometry identified the deubiquitinase ubiquitin-specific protease 9X (USP9X) as a previously unrecognised SUFU-binding partner. Notably, USP9X and SUFU exhibit a positive correlation in a MB tissue array, with both exhibiting low expression levels that are associated with adverse prognostic outcomes. Loss of USP9X in SHH-MB enhances cell proliferation in vitro as well as orthotopic MB xenograft tumourgenicity in vivo. Mechanically, USP9X deubiquitinates and stabilises SUFU, thereby negatively regulating SHH signal transduction. Interestingly, SHH signalling promotes SUFU ubiquitination through CMA-dependent degradation of USP9X protein levels, facilitating pathway activation. Combined inhibition of CMA and SHH pathway had a synergically therapeutic effect on SHH-MB.

These results establish CMA and USP9X as pivotal regulators of SHH medulloblastoma MB progression, emphasising their potential as novel therapeutic targets for medulloblastoma, and combinatorial inhibition of CMA and Smoothened (SMO) may provide a strategy to overcome intrinsic or acquired resistance to SMO monotherapy in SHH-MB.

Deubiquitinase USP9X suppresses SHH Medulloblastoma progression by facilitating SUFU ubiquitination. SHH promotes USP9X degradation through the CMA pathway. Combined inhibition of CMA and SHH pathway had a synergically therapeutic effect on SHH Medulloblastoma.