基于生物信息学分析和实验验证鉴定肝癌中与侵袭转移相关的 microRNAs。

Identification of invasion-metastasis-associated microRNAs in hepatocellular carcinoma based on bioinformatic analysis and experimental validation.

机构信息

Program of Innovative Cancer Therapeutics, Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, College of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou, 310003, China.

Key Laboratory of Organ Transplantation, Hangzhou, 310003, Zhejiang, China.

出版信息

J Transl Med. 2018 Sep 29;16(1):266. doi: 10.1186/s12967-018-1639-8.

DOI:10.1186/s12967-018-1639-8

PMID:30268144

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC6162949/

Abstract

BACKGROUND

Hepatocellular carcinoma (HCC) is one of the most lethal cancer, mainly attributing to its high tendency to metastasis. Vascular invasion provides a direct path for solid tumor metastasis. Mounting evidence has demonstrated that microRNAs (miRNAs) are related to human cancer onset and progression including invasion and metastasis.

METHODS

In search of invasion-metastasis-associated miRNAs in HCC, microarray dataset GSE67140 was downloaded from the Gene Expression Omnibus database. Differentially expressed miRNAs (DE-miRNAs) were obtained by R software package and the potential target genes were predicted by miRTarBase. The database for annotation, visualization and integrated discovery (DAVID) was introduced to perform functional annotation and pathway enrichment analysis for these potential targets of DE-miRNAs. Protein-protein interaction (PPI) network was established by STRING database and visualized by Cytoscape software. The effects of the miR-494-3p and miR-126-3p on migration and invasion of HCC cell lines were evaluated by conducting wound healing assay and transwell assay.

RESULTS

A total of 138 DE-miRNAs were screened out, including 57 upregulated miRNAs and 81 downregulated miRNAs in human HCC tumors with vascular invasion compared with human HCC tumors without vascular invasion. 762 target genes of the top three upregulated and downregulated miRNAs were predicted, and they were involved in HCC-related pathways, such as pathway in cancer, focal adhesion and MAPK signaling pathway. In the PPI network, the top 10 hub nodes with higher degrees were identified as hub genes, such as TP53 and MYC. Through constructing the miRNA-hub gene network, we found that most of hub genes could be potentially modulated by miR-494-3p and miR-126-3p. Of note, miR-494-3p and miR-126-3p was markedly upregulated and downregulated in HCC cell lines and tissues, respectively. In addition, overexpression of miR-494-3p could significantly promote HCC migration and invasion whereas overexpression of miR-126-3p exerted an opposite effect.

CONCLUSIONS

Targeting miR-494-3p and miR-126-3p may provide effective and promising approaches to suppress invasion and metastasis of HCC.

摘要

背景

肝细胞癌 (HCC) 是最致命的癌症之一，主要归因于其高转移倾向。血管侵犯为实体瘤转移提供了直接途径。越来越多的证据表明，微小 RNA (miRNA) 与人类癌症的发生和进展有关，包括侵袭和转移。

方法

为了寻找与 HCC 侵袭转移相关的 miRNA，从基因表达综合数据库中下载了微阵列数据集 GSE67140。通过 R 软件包获得差异表达 miRNA (DE-miRNA)，并通过 miRTarBase 预测潜在靶基因。引入数据库注释、可视化和综合发现 (DAVID) 对这些 DE-miRNA 的潜在靶基因进行功能注释和通路富集分析。通过 STRING 数据库建立蛋白质-蛋白质相互作用 (PPI) 网络，并通过 Cytoscape 软件可视化。通过划痕愈合试验和 Transwell 试验评估 miR-494-3p 和 miR-126-3p 对 HCC 细胞系迁移和侵袭的影响。

结果

共筛选出 138 个 DE-miRNA，包括血管侵犯的 HCC 肿瘤与无血管侵犯的 HCC 肿瘤相比，有 57 个上调 miRNA 和 81 个下调 miRNA。预测了前三种上调和下调 miRNA 的 762 个靶基因，这些靶基因参与了 HCC 相关通路，如癌症通路、粘着斑和 MAPK 信号通路。在 PPI 网络中，确定了前 10 个具有较高度数的枢纽节点为枢纽基因，如 TP53 和 MYC。通过构建 miRNA-枢纽基因网络，我们发现大多数枢纽基因可能被 miR-494-3p 和 miR-126-3p 潜在调节。值得注意的是，miR-494-3p 和 miR-126-3p 在 HCC 细胞系和组织中分别显著上调和下调。此外，miR-494-3p 的过表达可显著促进 HCC 迁移和侵袭，而 miR-126-3p 的过表达则产生相反的效果。