Systematic analysis of UBE2D3 and its association with prognosis, tumor microenvironment, and drug sensitivity in renal clear cell carcinoma

Background Dysregulated copper metabolism contributes to kidney renal clear cell carcinoma (KIRC) progression. This study systematically investigated the prognostic and therapeutic implications of copper metabolism-related gene UBE2D3 in KIRC. Methods Utilizing The Cancer Genome Atlas (TCGA)-KIRC transcriptomic data and clinical records (n=530), we analyzed differential expression, survival correlation, and clinical significance of copper metabolism-related genes. UBE2D3 was prioritized based on diagnostic/prognostic value. Functional enrichment, immune infiltration [Cell-Identification By Estimating Relative Subsets Of RNA Transcripts (CIBERSORT), Tumor Immune Estimation Resource (TIMER), Tumor Immune Single-cell Hub 2 (TISCH2)], drug sensitivity (oncoPredict), and molecular docking analyses were performed. UBE2D3 protein expression was validated via immunohistochemistry (IHC) in 9 clinical KIRC specimens. Results UBE2D3 expression was significantly downregulated in KIRC versus normal tissue and inversely correlated with advanced tumor stage/grade (P<0.001). Low UBE2D3 expression predicted poorer overall survival [hazard ratio (HR) =0.67, P=0.002] and served as an independent prognostic factor. UBE2D3 loss associated with altered tumor immune microenvironment, including reduced M1 macrophage infiltration and increased regulatory T cells. Single-cell RNA sequencing confirmed predominant UBE2D3 expression in monocytes/macrophages. Hypermethylation and copy number variation significantly influenced UBE2D3 dysregulation. Drug sensitivity analysis revealed that UBE2D3-low tumors were more responsive to vincristine, bosutinib, and ambazone [median inhibitory concentration difference (IC50 diff.) P<0.01], supported by favorable molecular docking affinities. Conclusions UBE2D3 may function as a tumor suppressor in KIRC, as suggested by its downregulation in advanced stages and correlation with improved survival. Correspondingly, its loss appears to correlate with advanced disease, an immunosuppressive tumor microenvironment (TME), and unfavorable prognosis. This potential role in modulating immune cell dynamics and drug sensitivity positions UBE2D3 as a promising biomarker for prognostication and personalized therapy selection in KIRC.