#RSAA2026 Identification of Key Hub Genes in Hepatocellular Carcinoma via Integrated Bioinformatics Analysis and Stringent PPI Network Filtering

Abstract

Hepatocellular Carcinoma (HCC) remains one of the most aggressive malignancies with complex molecular mechanisms. This study aims to identify key hub genes involved in HCC progression through an integrated bioinformatics approach. The datasets were retrieved from the Gene Expression Omnibus (GEO) database and Differentially expressed genes (DEGs) were analyzed with GEO2R. The Protein-Protein Interaction (PPI) networks were constructed using the STRING and Cytoscape. Topological analysis was performed using the CytoHubba to identify the top 10 hub genes based on their connectivity scores. Functional enrichment analyses (GO and KEGG) were performed to elucidate the biological roles of these proteins. Three independent GEO datasets identified a total of 1,778 DEGs. After mapping these genes to the STRING database, only 1,736 DEGs were successfully recognized. To ensure high-confidence interactions, the network was filtered using a stringent interaction score threshold of ≥ 0.999, resulting in a core subset of 300 genes. Gene Ontology (GO) enrichment analysis of these genes revealed significant involvement in the regulation of apoptotic processes (Biological Process), association with the cyclin D2-CDK4 and Bcl-2 family protein complexes (Cellular Component), and high activity in BH3 domain binding and DNA-binding transcription activator activity (Molecular Function). Subsequent pathway analysis via ShinyGO prioritized the “Pathways in Cancer” category, from which 26 genes were curated for further refinement. Finally, topological analysis using CytoHubba identified 10 key hub genes: CDK4, TP53, FOS, HSP90AA1, AR, BCL2L1, FOXO1, BCL2, ESR1, and CDKN2A, which serve as the primary drivers in HCC interaction network. The findings highlight a specific cluster of hub genes that drive hepatocarcinogenesis. Those 10 genes may serve as robust candidate biomarkers for the diagnosis and prognosis of Hepatocellular Carcinoma.