Correlation of Hepatocellular Carcinoma Stemness Indices and Clinical Characteristics and Prognosis
Abstract Background Recent studies have shown that cancer stem cell (CSC) is related to the occurrence and development of hepatocellular carcinoma(HCC), but the mechanism has not yet been elucidated. Therefore, it is necessary to explore the relationship between HCC stem cells and the survival time of HCC patients and its mechanism to guide the treatment. Methods We downloaded the RNA-Seq data and clinical information from The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC). The mRNA gene expression-based stemness index (mRNAsi) and DNA methylation-based stemness index (mDNAsi) were calculated through one-class logistic regression (OCLR). By applying the univariable Cox regression analysis, we found that mRNAsi and mRNAsi were significantly correlated with overall survival (OS). Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analysis were used to seek for different genes, and searched for hub genes through protein-protein interaction (PPI) analysis. The spearman’s rank correlation coefficient test was applied to analyze the relationship between these hub genes and the stemness indices. Results The mRNA gene expression-based stemness index (mRNAsi) and DNA methylation-based stemness index (mDNAsi) levels of HCC samples from TCGA and ICGC were significantly negatively related to clinical characteristics and OS. Analysis of differentially expressed genes and PPI revealed that SNAP25, KPT19, GABBR1 and EPCAM were significantly negative correlation with mDNAsi. Conclusion Our new model based on stemness indices-related genes was available for predicting prognosis. The SNAP25, KPT19, GABBR1 and EPCAM were potentially therapeutic targets for HCC patients.