Analysis and Identification of Hub Genes in Hepatocellular Carcinoma Based on Weighted Gene Co-expression Network and Cancer Genome Atlas Clinical Data

Abstract

Background Hepatocellular carcinoma (HCC) is the third leading cause of common cancer-related mortality globally, accounting for approximately 90% of all primary liver cancer cases. Its recurrence and mortality rates are high, with the underlying molecular mechanisms remaining unclear. Objective To explore potential molecular mechanisms of HCC and explore novel biomarkers. Methods RNA-seq expression data and clinical information were retrieved from TCGA database, differential gene expression analysis was conducted between normal liver tissue and HCC tissue. Enrichment analysis on the differentially expressed genes was performed. Based on the gene expression data profiles of HCC in TCGA, a co-expression network was established using the WGCNA R package, and weighted gene co-expression network analysis (WGCNA) was performed to select clinically significant modules and screen candidate Hub genes; the candidate Hub genes were further analyzed for significant differential expression in HCC tissues and normal liver tissues, and whether they were significantly correlated with the overall survival and disease-free survival of HCC patients. The Hub genes were conclusively identified, and their protein expression was validated through the Human Protein Atlas database. Results The genetic expression data in this study were obtained from 50 normal liver tissue samples and 373 HCC tissue samples. Through differential gene expression analysis, a total of 7 230 genes differential expression between HCC and normal hepatic tissue, comprising 3 691 up-regulated genes and 3 539 down-regulated genes in HCC were identified. Enrichment analysis showed that the up-regulated differentially expressed genes were mainly involved in cell cycle regulation and mitotic processes; the down-regulated differentially expressed genes were mainly involved in processes such as small molecule metabolism and organic acid metabolism. WGCNA identified 19 gene modules related to the clinical features of HCC patients, the cyan and purple modules were screened by analyzing the relationship between the modules and the clinical features. The first two genes in the cyan module genes that were strongly associated with both overall survival and disease-free survival of patients were VPS45 and FAM189B. In the purple module genes, first two genes that were strongly associated with both overall survival and disease-free survival of patients were CLEC1B and FCN3, respectively; therefore, VPS45, FAM189B, CLEC1B and FCN3 were identified as the final Hub genes. Immunohistochemical staining in the Human Protein Atlas database showed that VPS45 and FAM189B were expressed higher in HCC tissues than in normal liver tissues. FCN3 was expressed in HCC tissues lower than in normal liver tissues, the difference in the expression of CLEC1B between HCC tissues and normal liver tissues was not obvious. Conclusion VPS45, FAM189B, CLEC1B and FCN3 have been preliminary identified as possible novel potential biomarkers for HCC, which may provide a theoretical basis for targeted therapy of HCC.

Keywords

• carcinoma, hepatocellular|weighted gene co-expression network analysis|hub gene|molecular targeted therapy