VDAC1 and VDAC2 as prognostic biomarkers and therapeutic targets in hepatocellular carcinoma

Background: Voltage-dependent anion channels (VDACs) are mitochondrial outer membrane proteins regulating metabolism, apoptosis, and immune responses, but their clinical value in hepatocellular carcinoma (HCC) remains incomplete. This study aimed to clarify whether VDAC1 and VDAC2 serve as prognostic biomarkers and potential therapeutic targets in HCC by comprehensively analyzing their expression patterns, prognostic value, regulatory mechanisms, immune associations, and functional roles through multi-omics approaches and in vitro validation. Methods: Transcriptomic and clinical data from The Cancer Genome Atlas (TCGA) database (33 cancer types) were analyzed to evaluate VDAC1 and VDAC2 expression, diagnostic performance, and prognostic significance using receiver operating characteristic (ROC), Kaplan-Meier, and Cox regression, with nomogram construction for recurrence prediction. Validation was performed using Gene Expression Omnibus (GEO) database (GSE14520) and the Human Protein Atlas. Genetic and epigenetic regulation, including mutations, copy number variations, and promoter methylation, were assessed for prognostic impact via cBioPortal, Gene Set Cancer Analysis (GSCA), and UALCAN (an interactive TCGA-based analysis portal). Immune associations, including tumor-infiltrating cells and immune evasion potential, were examined using TIMER2.0, CIBERSORTx, and Tumor Immune Dysfunction and Exclusion (TIDE). Functional relevance was tested in Hep3B and PLC cells through Small interfering RNA (siRNA)-mediated knockdown, with assays of proliferation, apoptosis, Ferroptosis, migration, and epithelial–mesenchymal transition. Results: VDAC1 and VDAC2 were significantly upregulated in HCC and independently predicted poorer overall survival. VDAC1 had a stronger prognostic impact in advanced-stage patients, while VDAC2 retained predictive value in early-stage tumors. Both accurately distinguished tumors from normal tissues. Multi-omics analyses revealed distinct regulation: VDAC1 was driven by copy number gain and promoter hypermethylation, whereas VDAC2 was largely independent of these alterations, suggesting post-transcriptional control. High expression correlated with immunosuppressive cell infiltration and elevated immune evasion scores, with immune context modulating prognostic effects. Functional experiments confirmed that silencing either genos inhibited cell proliferation, promoted apoptosis, reduced migration, and differentially affected ferroptosis. Conclusions: VDAC1 and VDAC2 are prognostic biomarkers and therapeutic targets in HCC, with genetic and immune interactions jointly influencing outcomes, supporting their potential for patient risk stratification and targeted or immune-based therapies.