基于生物信息学和分子对接分析肺动脉高压的关键基因及靶向中药筛选

Analysis of Key Genes in Pulmonary Hypertension and Screening of Targeted Chinese Herbal Medicines Based on Bioinformatics and Molecular Docking

目的通过生物信息学分析筛选肺动脉高压(Pulmonaryhypertension,PH)的关键基因,进而预测治疗PH的潜在中药。方法从GEO数据库筛选下载原始数据集芯片GSE113439,运用GEO2R在线分析工具进行差异分析得到差异表达基因(Differentially expressed genes,DEGs),应用DAVID数据库对DEGs进行GO功能富集分析和KEGG pathway通路富集分析,运用STRING11.5数据库构建DEGs蛋白互作网络(PPI),利用Cytoscape软件及其附带插件从PPI网络中得到可视化子网络图和核心基因,通过Coremine Medical数据库得到作用于核心基因的且收录于《中华人民共和国药典(2020版)》的潜在中药,借助中药系统药理学数据库与分析平台(TCMSP)和Uniprot在线数据库得到中药成分和靶标蛋白等信息,并运用Cytoscape软件构建中药-活性成分-靶点网络图,最后将中药有效成分与关键基因的受体蛋白进行分子对接,通过PyMOL软件进行可视化展示。结果对GSE113439数据集共筛选得到608个DEGs(P<0.05,|Log2FC|>1),其中包括505个上调基因和103个下调基因,这些基因主要涉及炎症反应、蛋白磷酸化、RNA聚合酶Ⅱ启动子转录的正调控和细胞分裂等生物学过程,与真核生物核糖体的生物发生、肌动蛋白细胞骨架的调节、核质转运等通路有关,共筛选得到十个关键基因,分别为NUSAP1、DLGAP5、NVAPG、CENPF、TOP2A、KIF11、ASPM、CEP55、CENPE和KIF20A,进一步预测治疗PH的潜在中药有:枳壳、枳实、香橼、青蒿、川贝母、高良姜、黄芩,最后将中药有效成分luteolin(木犀草素)和quercetin(槲皮素)与受体蛋白1ZXM进行分子对接。结论基于生物信息学分析得到关键DEGs进而筛选预测出具有治疗PH的靶向中药,为今后的临床和科研提供依据。

Objective To screen the key genes of pulmonary hypertension by bioinformatics analysis and then predict the potential Chinese herbal medicines for the treatment of pulmonary hypertension.Methods The original dataset GSE113439 was selected and downloaded from the GEO database.GEO2R online was used to identify the differentially expressed genes(DEGs).DAVID was used for the gene ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment analyses on the DEGs.The protein-protein interaction(PPI)network of DEGs was constructed by STRING11.5.Cytoscape and its plug-ins were used to obtain the visual subnetworks and core genes.The potential Chinese herbal medicines acting on core genes and included in the Pharmacopoeia of the People′s Republic of China(2020 Edition)were retrieved from Coremine Medical.The active components and target proteins of the Chinese herbal medicines were searched against the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform(TCMSP)and Uniprot online.In addition,Cytoscape was used to construct the“Chinese herbal medicine-active component-target”network.Finally,molecular docking was performed between the active components of Chinese herbal medicines and receptor proteins of key genes,and the results were visualized by PyMOL.Results A total of 608 DEGs(P<0.05,|Log2FC|>1)were screened out,including 505 genes with up-regulated expression and 103 genes with down-regulated expression.These genes were mainly involved in the positive regulation of inflammation,protein phosphorylation,and RNA polymeraseⅡpromoter transcription as well as cell division.They were associated with eukaryotic ribosome biogenesis,actin cytoskeleton regulation,nucleoplasm transport and other pathways.Ten core genes were screened out,including NUSAP1,DLGAP5,NVAPG,CENPF,TOP2A,KIF11,ASPM,CEP55,CENPE,and KIF20A.The potential Chinese herbal medicines predicted for treating pulmonary hypertension were Aurantii Fructus,Aurantii Fructus Immaturus,Citri Fructus,Artemisiae Annuae Herba,Fritillariae Cirrhosae Bulbus,Alpiniae Officinarum Rhizoma,and Scutellariae Radix.Finally,molecular docking results revealed the binding of luteolin and quercetin as the active components of Chinese herbal medicines with the receptor protein 1ZXM.Conclusion This study obtained the core DEGs by bioinformatics tools and screened out targeted Chinese herbal medicines for treating pulmonary hypertension,providing evidence for future clinical practice and scientific research.