Bioinformatics analysis to reveal key biomarkers for early and late hepatocellular carcinoma

BACKGROUND: The aim of this study was to find the long non-coding RNAs (lncRNAs) and mRNAs acting as biomarker of early and late hepatocellular carcinoma (HCC). METHODS: The Cancer Genome Atlas (TCGA) dataset was used to identify shared differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEmRNAs) between early and late HCC and normal tissue. Functional annotation and protein-protein interaction network of shared DEmRNAs were performed. Furthermore, DElncRNAs-DEmRNAs co-expression network of early and late HCC were also performed. The expression of selected candidate genes were validated by the quantitative real time polymerase chain reaction (qRT-PCR). RESULTS: A total of 1,201 shared DEmRNAs and 162 shared DElncRNAs were identified in both early and late HCC compared with normal controls. Cell cycle, p53 signaling pathway, retinol metabolism and metabolism of xenobiotics by cytochrome P450 were four significantly enriched pathways. Base on the protein-protein interaction network, CDK1, AURKA, CDC20, PLK1, AURKB, HIST1H2BG, BUB1B, CCNA2, CCNB1 and CDT1 were key protein. CTD-2510F5.4 and HAND2-AS1 were hub lncRNAs in both early and late HCC. Overall, the confirmation results of qRT-PCR were generally consistent with our integrated analysis. CONCLUSIONS: A total of 4 DEmRNAs (CDK1, KIFC1, CENPF and ECM1) and 2 DElncRNAs (CTD-2510F5.4 and HAND2-AS1) were identified as key biomarkers for HCC. This study may contribute to reveal the pathogenesis of early and late HCC and provide new and accurate therapeutic targets for HCC.