SOX9 and TNFAIP3 dysregulation in HCV-associated HCC after DAA therapy: insights into post-viral oncogenic memory

Abstract

BACKGROUND: Hepatitis C virus (HCV) is a leading cause of chronic liver disease and hepatocellular carcinoma (HCC). Despite the high efficacy of direct-acting antivirals (DAAs) in eradicating HCV, HCC may still develop after sustained virological response (SVR), suggesting that HCV may leave behind lasting epigenetic and immunological alterations that sustain oncogenic risk. OBJECTIVES: This study aimed to investigate the expression profiles of SOX9, TNFAIP3, and FOSL2 in peripheral blood mononuclear cells (PBMCs) and liver tissues from HCV-related HCC patients and to explore, through in silico analyses, their molecular and immunological roles in HCV-driven hepatocarcinogenesis. METHODOLOGY: Gene expression was quantified in PBMCs and liver tissues using RT-qPCR. Receiver operating characteristic (ROC) curve analyses assessed diagnostic potential. In silico analyses evaluated protein-protein interactions, gene-gene networks, epigenetic modifications, and correlations with immune cell infiltration and immunomodulatory molecules using publicly available datasets. RESULTS: SOX9, TNFAIP3, and FOSL2 were identified as interconnected regulators within NF-κB and TGF-β pathways, enriched in inflammatory and infection-related processes, and epigenetically modulated via promoter hypermethylation and histone remodeling. Their expression strongly correlated with macrophages, T cells, dendritic cells, and key immune modulators. RT-qPCR validation confirmed overexpression of SOX9 and TNFAIP3 in PBMCs and liver tissues from HCV-HCC patients, with PBMC levels closely reflecting tissue expression, and ROC analyses highlighted their potential as non-invasive biomarkers. CONCLUSIONS: SOX9 and TNFAIP3 emerge as key mediators linking persistent epigenetic alterations with immune remodeling in HCV-related HCC, and as potential non-invasive biomarkers for evaluation of HCC risk and post-DAA surveillance. CLINICAL TRIAL NUMBER: Not applicable.