Integrated Analysis of Bulk RNA Sequencing, eQTL, GWAS, and Single-Cell RNA Sequencing Reveals Key Genes in Hepatocellular Carcinoma

Hepatocellular carcinoma (HCC) poses a continual therapeutic challenge owing to its elevated incidence and unfavourable prognosis, underscoring the critical need for the discovery of new molecular targets for detection and therapy. This work included the analysis of three publically accessible HCC datasets from TCGA and GEO. Instrumental variables (IVs) were derived via expression quantitative trait loci (eQTL) analysis, then followed by two-sample Mendelian randomisation (MR) analysis utilising publically available summary statistics. Key disease-associated genes were identified by assessing odds ratios and connecting them with differentially expressed genes across the datasets. The potential molecular mechanisms of these genes were clarified by functional enrichment analysis, clinical data analysis, single-cell RNA sequencing, GSEA, immune cell infiltration, and immune checkpoint analysis. These findings were then confirmed by Western blotting, immunohistochemistry, and quantitative PCR. By synthesising the outcomes from differential analysis of the databases, we found two genes, SERPING1 and STEAP3, that may be crucial in the beginning and development of HCC. These genes have a role in vital biological pathways and functions, such as metabolic regulation and macrophage activation. The significance of immunological-mediated processes in HCC was further highlighted by CIBERSORT analysis, which revealed a specific pattern of immune cell infiltration and the location of immunological checkpoints in the illness. The findings elucidate the molecular mechanisms of HCC and underscore critical genes implicated in its pathogenesis. SERPING1 and STEAP3 affect tumour cells and modify the tumour microenvironment (TME), indicating that targeting these genes may offer a viable immunotherapeutic approach for HCC in clinical settings.