miR-124 and miR-203 are epigenetically silenced tumor-suppressive microRNAs in hepatocellular carcinoma

Abstract

MicroRNAs (miRNAs) are a class of small non-coding RNAs that, in general, negatively regulate gene expression. They have been identified in various tumor types, showing that different sets of miRNAs are usually deregulated in different cancers. Some miRNA genes harboring CpG islands undergo methylation-mediated silencing, a characteristic of many tumor suppressor genes. To identify such miRNAs in hepatocellular carcinoma (HCC), we first examined the methylation status of 43 loci containing CpG islands around 39 mature miRNA genes in a panel of HCC cell lines and non-cancerous liver tissues as controls. Among 11 miRNA genes frequently methylated in HCC cell lines but not in non-cancerous liver tissues, three miRNA genes, i.e. miR-124, miR-203 and miR-375, were selected as silenced miRNAs through CpG-island methylation by comparing methylation and expression status and evaluating restored expression after treatment with 5-aza-2'-deoxycytidine. In primary tumors of HCC with paired non-tumorous liver tissues, only miR-124 and miR-203 showed frequent tumor-specific methylation, and their expression status was inversely correlated with methylation status. Ectopic expression of miR-124 or miR-203 in HCC cells lacking their expression inhibited cell growth, with direct downregulation of possible targets, cyclin-dependent kinase 6 (CDK6), vimentin (VIM), SET and MYND domain containing 3 (SMYD3) and IQ motif containing GTPase activating protein 1 (IQGAP1) or ATP-binding cassette, subfamily E, member 1 (ABCE1), respectively. Our results suggest that miR-124 and miR-203 are novel tumor-suppressive miRNAs for HCC epigenetically silenced and activating multiple targets during hepatocarcinogenesis.

The expression of miR-124 increases in aged skin to cause cell senescence and it decreases in squamous cell carcinoma

“…The current authors previously reported that the miR-124 expression was down-regulated in cutaneous SCC (14), which results in the overexpression of ERK as a target molecule and subsequent cell proliferation. miR-124 was also reported to be involved in the carcinogenesis of various cancers such as glioblastoma, gastric cancer, hepatocellular cancer, breast cancer, and prostate cancer (15)(16)(17)(18)(19), indicating that miR-124 is a key miRNA in carcinogenesis.…”

Epigenetic regulation mechanisms of microRNA expression

“…Remarkably, using regioneR (48), which assesses the relation between genomic regions using a permutation test, we observed that a higher proportion of miRNA genes than expected by chance is embedded in CpG islands susceptible to methylation (189 of 1881; z-score = 46.13; number of permutations = 1000; p-value = 0.0009, Figure 1B and C, Table 1 and shown in red in Figure 1A), which might explain why certain miRNAs are more prone to be epigenetically regulated by methylation than others. Furuta et al (49) studied the methylation grade of CpG islands close to 39 miRNA genes in hepatocellular carcinoma cell lines and found that miR-124-1, miR-124-3, miR-203 and miR-375, which were completely embedded in a CpG island, underwent methylation-mediated silencing ( Figure 2A). miRNAs can be classified into two broad categories according to their genomic region: intergenic and intragenic (50,51).…”

The biological regulation of ABCE1

“…As shown in previous findings, miRNA levels seem to be lower in tumors than normal tissues. ABCE1 gene has been implied to be a novel possible target for miR-203, inferring that hypermethylationmediated silencing of tumor-suppressive miRNAs induces the increased expression of ABCE1 gene, contributing to the pathogenesis of hepatocellular carcinoma (HCC) (44). RNase L has been shown to have an impact on the pathogenesis of prostate cancer.…”