UBE4B-mediated ubiquitination and degradation of VPS35 differentially regulate cancer cell behaviors in a context-dependent manner

Vacuolar protein sorting 35 (VPS35) is a core component of the retromer complex. Dysfunction of VPS35 has been linked to the pathogenesis of Parkinson’s disease (PD), with the D620N point mutation identified as a causative factor in familial PD. However, the role of VPS35 in cancer progression and its post-translational modifications remains poorly understood. In this study, we demonstrate that the ubiquitin E3 ligase ubiquitin conjugation factor E4 B (UBE4B) mediates the ubiquitination of VPS35, catalyzing the formation of K48-linked polyubiquitin chains, which target VPS35 for degradation. We show that the VPS35 D620N mutant, along with most non-small cell lung cancer (NSCLC)-associated mutants, is similarly degraded by UBE4B, mirroring wild-type VPS35. Analysis of the Clinical Proteomic Tumor Analysis Consortium (CPTAC) and International Cancer Proteogenome Consortium (ICPC) databases revealed that UBE4B is upregulated in many cancers—particularly in lung and breast cancers—while VPS35 expression is correspondingly downregulated, suggesting an inverse correlation between the two proteins in these malignancies. Notably, the D620N mutation is absent in patients with NSCLC, underscoring distinct molecular mechanisms in lung cancer and PD. Further experiments indicated that UBE4B promotes proliferation and migration in H1299 and H125 cells, whereas VPS35 (including the D620N mutant) suppresses these processes. Intriguingly, UBE4B enhances apoptosis in a p53-dependent manner, while VPS35 has minimal impact on cancer cell apoptosis. In neuroblastoma cells, however, the UBE4B–VPS35 axis exhibits opposing roles: UBE4B inhibits, while VPS35 promotes, proliferation and migration. Our findings highlight UBE4B-mediated ubiquitination of VPS35 as a novel regulatory mechanism in cancer progression, providing new insights into the context-dependent roles of the UBE4B–VPS35 axis across different cancer types.