Early-stage biomarkers identification by integrated genomic analysis in hepatocellular carcinoma

Hepatocellular carcinoma (HCC), a type of liver cancer, ranks as the third-leading cause of death due to the lack of definite biomarkers for early-stage detection. HCC progression occurs by the dysregulation of several genes. Though several studies focus on biomarkers for HCC diagnosis, stage-specific marker identification remains elusive. Hence, the present study aims to identify early-stage biomarkers for the detection of HCC through integrated in silico analysis. The differential gene expression was performed using GEO2R for the datasets (GSE14520, GSE63898, GSE121248, GSE124535, GSE94660, and GSE6764) retrieved from Gene Expression Omnibus (GEO) of patients with cirrhotic liver or HCC. The common differentially expressed gene enrichment analysis was performed using Funrich for Gene ontology (GO) and Kyoto Encyclopedia of Gene and Genomics (KEGG) gene mapping. The Protein-Protein Interaction (PPI) network was performed using the Search Tool for the Retrieval of Interacting Genes (STRING). The hub genes were identified using the CytoHubba plug-in of Cytoscape software. The identified genes were verified for their prognostic value using the Kaplan-Meier plotter and Immunohistochemistry micrographs obtained from the Human Protein Atlas database. An overall of 243 common differentially expressed genes (DEGs) were identified containing 171 upregulated and 72 downregulated genes. With the help of PPI network construction, ten hub genes were identified as CDK1, AURKA, CCNB1, CCNB2, CENPF, CDC20, TOP2A, BUB1, RRM2, and HMMR, which are dysregulated owing to HCC proliferation, tumorigenesis and poor prognosis in patients. These hub genes are suitable waypoints for the diagnosis and targeted therapy against early-stage HCC.