A systematic investigation based on microRNA-mediated gene regulatory network reveals that dysregulation of microRNA-19a/Cyclin D1 axis confers an oncogenic potential and a worse prognosis in human hepatocellular carcinoma

MicroRNAs (miRNAs) contribute to a wide variety of human diseases by regulating gene expression, leading to imbalances in gene regulatory networks. To discover novel hepatocellular carcinoma (HCC)-related miRNA-target axes and to elucidate their functions, we here performed a systematic investigation combining biological data acquisition and integration, miRNA-target prediction, network construction, functional assay and clinical validation. As a result, a total of 117 HCC differentially expressed miRNAs were identified, and 728 high confident target genes of these miRNAs were collected. Then, the interaction network of target genes was constructed and 221 key nodes with topological importance in the network were identified according to their topological features including degree, node-betweenness, closeness and K-coreness. Among these key nodes, Cyclin D1 had the highest node-betweenness, implying its bottleneck role in the network. Luciferase reporter assay confirmed that miRNA-19a, which was one of HCC downregulated miRNAs, directly targeted Cyclin D1 in HCC cells. Moreover, miR-19a might play inhibitory roles in HCC malignancy via regulating Cyclin D1 expression. Further clinical evidence also highlighted the prognostic potential of miR-19a/Cyclin D1 axis in HCC. In conclusion, this systematic investigation provides a framework to identify featured miRNAs and their target genes which are potent effectors in the occurrence and development of HCC. More importantly, miR-19a/Cyclin D1 axis might have promising applications as a therapeutic target and a prognostic marker for patients with HCC.

微小RNA（microRNAs, miRNAs）通过调控基因表达引发基因调控网络失衡，进而参与多种人类疾病的发生发展。为发掘新型肝细胞癌（hepatocellular carcinoma, HCC）相关miRNA-靶基因轴并阐明其功能，本研究开展了一项系统性研究，整合了生物数据获取与整合、miRNA靶标预测、网络构建、功能实验及临床验证等环节。研究共鉴定出117个HCC差异表达miRNA，并收集到这些miRNA的728个高可信度靶基因。随后构建了靶基因相互作用网络，并根据节点度、节点介数、接近中心性及K核数等拓扑特征，筛选出221个具有拓扑重要性的关键节点。其中，细胞周期蛋白D1（Cyclin D1）的节点介数最高，提示其在网络中发挥瓶颈作用。荧光素酶报告基因实验证实，作为HCC下调miRNA之一的miR-19a，可直接靶向肝癌细胞中的Cyclin D1。此外，miR-19a可能通过调控Cyclin D1的表达，抑制HCC的恶性进展。进一步的临床数据也表明，miR-19a/Cyclin D1轴具备良好的HCC预后评估价值。综上，本系统性研究为鉴定HCC发生发展中发挥关键效应的特征性miRNA及其靶基因提供了研究框架。更为重要的是，miR-19a/Cyclin D1轴有望成为HCC患者的治疗靶点及预后标志物，具备良好的临床应用前景。