Abstract
AIMS AND OBJECTIVES: This study aimed to identify immunologically relevant transcriptomic and proteomic biomarkers in hepatocellular carcinoma (HCC) and to characterize their B-cell epitopes for potential integration into nanomaterial-based biosensors and immunomodulatory platforms for early diagnosis and targeted therapy. METHODS: We conducted a comprehensive multi-omics analysis by integrating transcriptomic (TCGA-LIHC) and proteomic data to identify differentially expressed genes (DEGs) in HCC. Protein-protein interaction networks and pathway enrichment were used to prioritize hub genes. Five candidate biomarkers, RFC2, HSP90AB1, YWHAZ, CYP2E1, and ADH4, were selected for qRT-PCR and serum ELISA validation in clinical cohorts comprising 85 HCC patients and 50 healthy controls. B-cell epitope prediction was performed using BepiPred 2.0 and validated through synthetic peptide-based ELISA in the same cohort to assess immunoreactivity. Diagnostic performance was evaluated using ROC curve analysis. RESULTS: RFC2, HSP90AB1, and YWHAZ were significantly upregulated (|log2FC|>0.2) and showed high serological expression, whereas CYP2E1 and ADH4 were consistently downregulated. Predicted B-cell epitopes from RFC2, HSP90AB1, and YWHAZ exhibited strong immunoreactivity (AUC>0.84), indicating their diagnostic potential. Enrichment analysis revealed that upregulated DEGs were involved in cell cycle and mitotic progression, while downregulated genes were linked to immune suppression and metabolic dysfunction. These validated immunogenic epitopes offer promising anchors for nanomaterial-functionalized biosensors, such as gold nanoparticle-conjugated ELISA, graphene-based electrochemical platforms, and peptide-coated quantum dots, for ultrasensitive and multiplexed HCC detection. CONCLUSION: By integrating transcriptomic and proteomic screening with epitope-level validation, we identified a novel panel of immunogenic biomarkers suitable for nanomaterial-enabled diagnostics in HCC. These findings support the translational potential of peptide-nano scaffold conjugates in developing minimally invasive, immune-responsive biosensing and therapeutic tools tailored for early-stage liver cancer management.