Identification of typical miRNAs and target genes in hepatocellular carcinoma by DNA microarray technique

The purpose of this study was to identify featured miRNAs of hepatocellular carcinoma (HCC) by comparing normal and cancer cell line samples and find potential utility as biomarkers for early diagnosis and treatment of HCC.

We downloaded the gene expression profile GSE41077 from Gene Expression Omnibus database which included 6 HCC cell lines samples and 2 controls. Differentially expressed miRNAs were identified by multtest package in R language after the data normalization. The selected differentially expressed miRNAs were further analyzed using bioinformatics methods. Target genes of these miRNAs were predicted using miRTarBase and miRecords databases. STRING software was used to construct the interaction network of target genes. Finally, we made module analysis by using Cytoscape software and its plugins--MCODE and BiNGO.

A total of 40 differentially expressed miRNAs were identified and the remarkably down-regulated miRNA was hsa-miR-122 which included 29 high confident target genes. The interaction network of target genes was constructed among 629 interaction pairs. Four functional modules in the network were obtained, from which EGLN3, ALDOA, NCAM1 and AACS were the high confident target genes, respectively. Genes in the modules most related to biological functions of signal transmission, regulation of macromolecule metabolic process.

Low level of expression of hsa-miR-122 in HCC cell line is consistent with the existed previous studies. It is not only confirm the importance role of such miRNA in HCC cells, but also provide important help in identifying specific biomarker of HCC cells.