基于WGCNA联合网络药理学探究防己地黄汤治疗类风湿关节炎的作用机制

Mechanism of action of Fangji Dihuang Decoction in treatment of rheumatoid arthritis based on WGCNA combined with network pharmacology

目的 利用网络药理学和加权基因共表达网络分析(WGCNA)方法探讨防己地黄汤治疗类风湿关节炎的分子机制。方法 利用TCMSP、SwissTargetPrediction、HERB数据平台及相关文献检索防己地黄汤的主要活性成分及其相关靶点,通过R软件limma包对GEO平台类风湿关节炎数据集GSE110169进行差异分析。基于WGCNA筛选与疾病相关的基因模块。利用R软件VennDiagram包进行交集靶点分析。通过Cytoscape的cytoHubba插件筛选核心靶点基因。采用Cytoscape软件进行“药物–活性成分–靶点–疾病”网络构建与分析。clusterProfiler包对交集靶点基因进行基因本体论(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。通过PyMOL软件对核心活性成分与核心靶点基因进行分子对接验证;并运用CIBERSOTR进行核心靶点基因的免疫浸润分析。结果 共筛选出有效活性成分129个,相关靶点1 280个,基因芯片差异基因2 091个;筛选出3个与疾病相关的基因模块;获得药物与疾病共同靶点139个;KEGG通路分析显示,主要富集在T细胞受体信号通路、NOD样受体信号通路、Toll样受体信号通路等;筛选出汉黄芩素和槲皮素2个核心成分及肿瘤蛋白53(TP53)和胱氨酸蛋白酶3(CASP3)2个核心靶点基因。分子对接显示,核心成分与核心靶点之间均具有稳定的结合能力;免疫浸润分析表明,核心靶点基因与多数免疫细胞关系密切。结论 防己地黄汤可能从抗炎、调节免疫细胞功能等多方面发挥对类风湿关节炎的治疗作用。

Objective To investigate the molecular mechanism of Fangji Dihuang Decoction in treatment of rheumatoid arthritis based on network pharmacology and WGCNA.Methods The main active ingredients of Fangji Dihuang Decoction and their related targets were retrieved using TCMSP,SwissTargetPrediction,and HERB data platforms.And the difference analysis of GEO platform rheumatoid arthritis dataset GSE110169 was performed by R software limma package.Screening of gene modules associated with diseases based on WGCNA.Intersectional target analysis was performed using the R software VennDiagram package.Core target genes were screened by CytoHubba plugin of Cytoscape.Cytoscape software was used to construct and analyze the “drug-active component-target-disease” network.clusterProfiler package was used for GO and KEGG pathway enrichment analysis of intersectional target genes.Molecular docking of the core active ingredient with the core target genes was verified by PyMOL software,and immunoinfiltration analysis of the core target genes was performed by CIBERSOTR.Results A total of 129 active ingredients,1 280 related targets,and 2 091 differential genes on gene chips were screened,3 disease-related gene modules were screened,and 139 common targets between drugs and diseases were obtained.KEGG pathway analysis showed that they were mainly enriched in T cell receptor signaling pathway,NOD-like receptor signaling pathway,and Toll-like receptor signaling pathway.Two core components of wogonin and quercetin and two core target genes of tumor protein 53(TP53) and cystine protease 3(CASP3) were screened.Molecular docking showed that both core components and core targets had stable binding ability.Immune infiltration analysis showed that the core target genes were closely related to most immune cells.Conclusion Fangji Dihuang Decoction may exert therapeutic effects on rheumatoid arthritis in various aspects,including anti-inflammation and regulation of immune cell function.