Genome-wide Long Noncoding RNA and mRNA Expression Profile Reveals Associations Between Inorganic Elements Exposure and Risk of Developing Hepatocellular Carcinoma

Abstract Background The long non-coding RNAs (lncRNA) have been closely associated with the development of hepatocellular carcinoma (HCC). The present study conducted a genome-wide microarray analysis and qPCR validation to gain a comprehensive insight on this issue. Methods Thirty male HCC patients with chronic HBV infection were included in the present study. Primary HCC tissues and normal tissue were collected. Synthesize double stranded complementary DNA from 10 pairs of samples were labeled and hybridized to microarray chip. Further analysis, such as hierarchical clustering analysis, gene ontology (GO) and pathway analysis were performed. In addition, qPCR validation was conducted in all samples. Results The microarray analysis identified 946 upregulated and 571 downregulated lncRNAs, along with 1,720 upregulated and 1,106 downregulated mRNAs. Among them, ENST00000583827.1 (fold change: 21.11) and uc010isf.1 (fold change: 17.76) were the most over- and under-expressed lncRNAs in HCC tissues. As for the mRNAs, KIF20A (fold change: 26.44) and HEPACAM (fold change: 49.56) were the most over- and under-expressed in HCC tissues. GO analysis revealed that the most differentially expressed mRNAs were related with the response of metal ion. Pathway analysis also suggested the most enriched pathway was mineral absorption. Conclusion The subsequent qPCR validation exhibited high consistency with microarray analysis, expect one lncRNA. It also revealed that TCONS_00008984 had 768.94-fold expression level in HCC tissues when compared with normal tissues. TCONS_00008984 has the potential to serve as a diagnostic marker or prognosis indicator. GO and pathway analysis that exposure to inorganic elements may possibly involve with HCC risk.