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Identifying hepatocellular carcinoma-related hub genes by bioinformatics analysis and CYP2C8 is a potential prognostic biomarker

Li, Chuanfei, Zhou, Di, Jiang, Xiaoling, Liu, Minhui, Tang, Hui, Mei, Zhechuan
Gene 2019 v.698 pp. 9-18
bioinformatics, biomarkers, computer software, gene expression, gene expression regulation, gene ontology, genes, genomics, hepatoma, immunohistochemistry, liver, patients, protein-protein interactions, quantitative polymerase chain reaction, reverse transcriptase polymerase chain reaction
Hepatocellular carcinoma (HCC) is one type of the most common malignancies. However, the underlying molecular mechanisms involved in the development of HCC remain unknown. To identify the candidate genes in the progression of HCC, gene expression profiles GSE14520, GSE54236, GSE57957 and GSE64041 were downloaded from the Gene Expression Omnibus database (GEO). A total of 405 tumor and 399 para-carcinoma samples from patients with HCC were examined to identify the differentially expressed genes (DEGs), followed by function enrichment analyses including Gene Ontology (GO) functions and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. A total of 78 DEGs were screened, including 62 downregulated genes and 16 upregulated genes. Subsequently, the protein-protein interaction network (PPI) was constructed using the Search Tool for Retrieval of Interacting Genes (STRING) database. The module analysis and Hub genes validation were performed using Cytoscape software. Hierarchical clustering of hub genes was evaluated using UCSC Cancer Genomics Browser. Survival analyses of Hub genes were performed using Kaplan Meier Plotter database. Genes specifically expressed in the liver were analyzed using GENEVESTIGATOR database. CYP2C8 was identified as one of the most promising molecules among all the candidate genes. The expression profile of CYP2C8 in HCC was analyzed using ONCOMINE and UALCAN database. The expression levels of CYP2C8 in HCC samples and hepatoma cells were verified using reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and immunohistochemistry analysis. In summary, DEGs and hub genes were identified in the present study, which provides novel insight on the development of HCC. CYP2C8 was downregulated in HCC and could be a potential prognostic biomarker.