基于整合药理学和转录组学的肝细胞癌和胆管癌共同差异miRNA调控网络构建及相关中药预测分析

Construction of Common Differential miRNA Regulatory Network of Hepatocellular Carcinoma and Cholangiocarcinoma and Prediction Analysis of Related Traditional Chinese Medicine Based on Integrated Pharmacology and Transcriptomics

目的:利用整合药理学和转录组学方法,构建肝细胞癌与胆管癌共同差异微RNA(miRNA)调控网络,并对关键靶点进行中药预测分析。方法:从GEO数据库获取肝细胞癌、胆管癌芯片数据集,借助在线分析工具GEO_(2)R分析出差异表达miRNA(DEMs)并对其取交集,得到共同DEMs,分别运用FunRich和miRNet软件预测上游转录因子及下游靶基因,并利用DAVID数据库对靶基因进行基因本体(GO)功能富集分析和京都基因与基因组百科全书(KEGG)通路富集分析。借助STRING数据库和Cytoscape 3.9.1软件筛选关键基因(hubGenes)并构建miRNA-hubGenes网络。运用UALCAN、Kaplan Meier-plotter和Coremin Medical数据库对关键基因进行差异表达、总体生存率及相关中药预测分析。结果:肝细胞癌筛选出14个DEMs,胆管癌筛选出104个DEMs, miR-199a-5p为两者共同DEMs,涉及28个上调转录因子,166个下游靶基因;富集分析结果显示,这些靶基因参与肿瘤细胞凋亡、增殖、间质转变和迁移等生物过程,主要通过癌症通路、FoxO信号通路、丝裂原激活的蛋白激酶信号通路以及磷脂酰肌醇3激酶-蛋白激酶B信号通路发挥作用;核心靶点关联中药性味偏微寒,主归肝经,关联最为密切的中药为丹参。结论:miR-199a-5p是肝细胞癌与胆管癌之间重要调控miRNA,丹参干预关键基因出现频次较多,与研究报道基本相符,可为后续肝胆癌机制研究和临床应用提供依据与参考。

OBJECTIVE:To construct the common differential miRNA regulatory network for hepatocellular carcinoma and cholangiocarcinoma based on integrated pharmacology and transcriptomics,and to perform traditional Chinese medicine prediction analysis on the key targets.METHODS:The hepatocellular carcinoma and cholangiocarcinoma chip datasets were obtained from the GEO database.The differentially expressed miRNA(DEMs)were analyzed and intersected to obtain the common DEMs with the online analysis tool GEO_(2)R.The software of FunRich and miRNet were used to predict upstream transcription factors and downstream target genes.Gene ontology analysis(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment analysis of target genes were performed by using DAVID database.STRING database and Cytoscape 3.9.1 software were used to screen key genes(hubGenes)and construct miRNA-hubGenes network.UALCAN,Kaplan Meier-plotter and Coremin Medical databases were used to analyze the differential expression of key genes,overall survival rate and related traditional Chinese medicine prediction analysis.RESULTS:Totally 14 DEMs were screened from hepatocellular carcinoma,and 104 DEMs were screened from cholangiocarcinoma.miR-199a-5p was the common DEMs of the two,involving 28 up-regulated transcription factors and 166 downstream target genes.Enrichment analysis showed that these target genes were involved in the biological processes of tumor cell apoptosis,proliferation,mesenchymal transition and migration,mainly through the cancer pathway,FoxO signaling pathway,mitogen-activated protein kinase signaling pathway and PI3K-Akt signaling pathway.The core target associated with the medicinal taste was slightly cold,mainly attributed to the liver channel,and the most closely associated Chinese medicine was Radix Salviae.CONCLUSIONS:miR-199a-5p is an important regulatory miRNA between hepatocellular carcinoma and cholangiocarcinoma,and the occurrence of key genes of Radix Salviae intervention is more frequent,which is basically consistent with the research reports,and provides basis and reference for the subsequent mechanism research and clinical application of hepatobiliary carcinoma.