The Deubiquitinase USP2 Inhibits Clear Cell Renal Cell Carcinoma by Activating the p53 Signaling Pathway and Inducing Ferroptosis

Background Clear cell renal cell carcinoma (ccRCC) remains lethal in 40% of patients because of intrinsic resistance to VEGF- and immune-targeted therapies. The deubiquitinase (DUB) family has been implicated in tumour–immune crosstalk, but a systems-level portrait and functional driver gene are still lacking. Methods Multi-cohort transcriptomic profiles (TCA-KIRC, n = 528; E-MTAB-1980, n = 101; ICGC-KIRC, n = 91) were integrated to construct a DUB-based prognostic signature. Cell-type deconvolution, single-cell RNA-seq (GSE73121) and in-vitro assays (786-O/A498 cells) were employed to dissect mechanism. USP2–p53 interaction was predicted by AlphaFold-multimer modelling and validated by co-immunoprecipitation. Ferroptosis was quantified by C11-BODIPY 581/591 staining, GSH/GSSG ratio and lipidomics. Results A four-DUB signature (USP2high, USP53high, UCHL1low, USP50low) robustly stratified patients into high- and low-risk groups across all three independent cohorts (hazard ratio = 2.41, 95% CI 1.78–3.25; average 5-year AUC = 0.82). High-risk tumours displayed an immunosuppressive microenvironment with decreased CD8 + cytotoxic T cells and elevated M0 macrophages (p < 0.001). Single-cell analysis localized USP2 expression to malignant epithelial cells. Functionally, USP2 overexpression inhibited proliferation (EdU incorporation ↓54%), migration (wound closure ↓62%) and anchorage-independent growth (soft-agar colonies ↓68%), whereas USP2 knock-out had the opposite effect. Mechanistically, USP2 directly deubiquitinated p53 at Lys120/164, prolonged p53 half-life (t½ ↑2.3-fold) and transcriptionally repressed SLC7A11 and GPX4. This dual action triggered lipid peroxidation accumulation (MDA ↑3.1-fold), GSH depletion (↓58%) and classical ferroptosis that was rescued by Ferrostatin-1 (p < 0.01) but not Z-VAD or necrostatin-1. Orthotopic 786-O xenografts confirmed that USP2 overexpression reduced tumour burden by 72% and synergized with anti-PD-1 to achieve complete responses in 5/8 mice. Conclusions We identify a clinically actionable DUB signature and uncover the USP2–p53–ferroptosis axis as a central tumour-suppressive circuit in ccRCC. Reactivating USP2 or its downstream ferroptotic programme offers a rational strategy to overcome resistance to current VEGF/PD-1 blockade.