Potential targets and clinical value of miR-490-5p in hepatocellular carcinoma: a study based on TCGA, qRT-PCR and bioinformatics analyses.

ABSTRACT

OBJECTIVE: To explore potential targets and clinical value of miR-490-5p in the oncogenesis and progression of hepatocellular carcinoma (HCC). METHODS: Clinical value of miR-490-5p was accessed through The Cancer Genome Atlas (TCGA) and qRT-PCR analyses. Potential target mRNAs of miR-490-5p were predicted by bioinformatics methods and were annotated as Gene Ontology (GO) function analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) signaling pathway analysis, and Protein-Protein Interaction (PPI) network analysis. RESULTS: miR-490 expression in HCC tissues was lower compared with normal control tissues based on TCGA and down regulation of miR-490-5p was verified by qRT-PCR (P<0.0001). Both miR-490 and miR-490-5p had moderate ability to diagnose HCC tissues from noncancerous tissues. Moreover, lower miR-490 level predicted poorer overall survival in patients with HCC (P=0.0063). One hundred and eighty-four mRNAs were selected as potential targets of miR-490-5p by overlap with 4,090 prediction genes and 1,478 differentially expressed genes (DEGs). Gene Ontology (GO) function analysis showed that the most significant terms were vasculature development, endoplasmic reticulum, and protein binding in biological process (BP), cellular component (CC), and molecular function (MF). In KEGG signaling pathway analysis, the statistically significant terms were lysosome, focal adhesion, glioma. In PPI network analysis, SRC, SRP9, PDGFRB, RPL28, and RPS23 were identified as the hub genes. CONCLUSION: miR-490-5p is down-regulated in HCC and may be a prospectively diagnostic and prognostic biomarker. Moreover, miR-490-5p might directly target SRC, SRP9, PDGFRB, RPL28, or RPS23 and play an important role in HCC.