Aberrant expression of epigenetically regulated microRNAs in liver cancer

Abstract

Liver cancer (hepatocellular carcinoma, HCC) is a major malignancy worldwide. Despite definite improvements in the outcome of patients with HCC, the overall prognosis of this cancer is still unsatisfactory because of late presentation and frequent tumor recurrence after surgical resection. New diagnostic and adjuvant treatment modalities are much awaited. MicroRNAs (miRNAs) are a class of small (~22 nt) single-stranded noncoding RNAs widely expressed in eukaryotic cells. miRNAs play an important role in modulating gene expression by promoting mRNA degradation or translational repression. There is mounting evidence that miRNAs are implicated in almost all major physiological processes, including cell proliferation, differentiation, apoptosis, and human carcinogenesis. Epigenetic alterations including aberrant DNA methylation and histone modification are important in regulating chromatin structure and gene expression. In this study, we investigated the role of epigenetic alterations in miRNA deregulation in human HCC. miRNA expression changes of HCC cell lines upon treatment with DNA demethylating agent (5-Aza-dC) and histone deacetylase inhibitor (Trichostatin A, TSA) were compared with stem-loop RT-qPCR based TaqMan low density array. In total, 98 miRNAs were remarkably up-regulated upon 5-Aza-dC/TSA treatment. Among these, 35 miRNA were commonly upregulated by treatment with the epigenetic inhibitors in both cell lines. The majority of these miRNAs was either associated with promoter CpG islands or located on imprinted regions. Expression analysis revealed that these epigenetically regulated miRNAs were frequently deregulated in human HCCs, and their expression pattern was able to distinguish primary HCCs from their corresponding non-tumorous livers. Interestingly, CpG island-associated miRNAs tended to be down-regulated in human HCCs, whereas, miRNAs located on imprinted regions were frequently overexpressed in human HCC samples. Our findings suggest that aberrant epigenetic silencing and loss of imprinting may contribute to miRNA deregulation in human HCC.