Ubiquitin D regulates MDM2 degradation to enhance p53-driven MHC antigen presentation in cutaneous melanoma

Background While currently available therapies have improved the clinical outcomes of patients with metastatic melanoma (MM), long-term durable response rates remain limited. The therapies have also expanded to treat patients with high-risk primary melanoma (PRM). There is an urgent need to identify markers of treatment resistance and the underlying biological mechanisms in MM and high-risk PRM. Ubiquitin-like modifiers (UBLs) such as ubiquitin D (UBD) control post-translational modifications of functional targets in cancer cells that may shape immune surveillance and immunotherapy resistance. Methods Formalin-fixed paraffin-embedded (FFPE) PRM tissue samples (n = 7) underwent Nanostring GeoMx Digital Spatial Profiling using a whole-transcriptome assay. The findings were validated in functional assays using human PRM and MM cell lines. Independent validation employed bioinformatics analyses (bulk RNA-seq deconvolution, single-cell RNA-Seq, and pathway analyses) across multiple public melanoma datasets. Multiplex immunofluorescence was performed in three independent patient cohorts: 1) nevus, PRM, and MM FFPEs; 2) clinically annotated MM tissue microarray; and 3) MM surgical FFPEs from patients treated with adjuvant immune checkpoint inhibitors (ICI). Results Spatial transcriptomics revealed the upregulation of UBD at the tumor invasive margin in high-risk PRM. Consistent with a TME cytokine–driven mechanism, interferon-γ (IFN-γ) stimulation enhanced UBD expression in melanoma cell lines. Functionally, UBD knockdown decreased major histocompatibility complex class I (MHC-I) and antigen presentation and processing (APP) molecules, increased MDM2 levels, and reduced p53 levels. Co-immunoprecipitation and pharmacologic studies indicated that UBD binds MDM2 and promotes its proteasomal degradation; MDM2 knockdown reversed the reduction in MHC-I and APP molecules mediated by UBD-loss. Clinically, low UBD expression was associated with significantly shorter overall survival in patients with PRM and MM and poorer ICI treatment response in MM patients. Conclusions This study demonstrated that UBD induced by IFN-γ within the TME regulates MDM2 degradation to sustain p53 levels, thereby maintaining MHC-I and APP expression levels. High UBD levels are beneficial in patients with PRM and MM. The UBD-MDM2-p53-MHC-I axis is a critical regulator of antigen presentation and UBD may represent a target to counteract immune evasion and ICI resistance.