基于网络药理学联合加权基因共表达网络分析探究雷公藤治疗系统性红斑狼疮的免疫作用机制

Explore the immune mechanism of Tripterygium wilfordii Hook.f.in treatment of systemic lupus erythematosus based on network pharmacology combined with WGCNA

目的运用网络药理学联合加权基因共表达网络分析(WGCNA)探究雷公藤治疗系统性红斑狼疮(systemic lupus erythematosus,SLE)的潜在作用机制。方法利用TCMSP数据库检索雷公藤的主要活性成分,并挖掘活性成分相关靶点,通过GEO平台下载SLE相关基因芯片GSE65391,使用R软件limma包进行差异分析,并运用WGCNA筛选出的模块基因作为疾病靶点基因。R软件Venn Diagram包进行交集分析并可视化。利用ADEx平台对交集靶点基因的表达情况进行Meta分析。采用R软件clusterProfiler包对交集靶点基因进行基因本体论(GO)功能富集和京都基因与基因组百科全书(KEGG)信号通路富集分析。采用Cytoscape软件进行“药物–活性成分–共同靶点”网络的构建与分析。将交集靶点基因上传至STRING数据库,把结果数据导入至Cytoscape软件构建蛋白相互作用(PPI)网络并筛选核心靶点基因。表达量分析、PPI分析、诊断效能分析被用于展示核心靶点基因的作用与临床价值。采用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。利用R软件并通过CIBERSORT算法对样本的免疫细胞分布进行计算。结果共筛选出有效活性成分50个,成分相关靶点690个,WGCNA关联模块基因1215个;KEGG通路分析,主要涉及Toll样受体等信号通路;筛选出山柰酚、雷公藤甲素、triptofordin B1、异落叶松脂素4个核心成分和SIRT1核心靶点基因。分子对接结果显示,山柰酚和雷公藤甲素与SIRT1具有稳定的结合能力。免疫浸润分析结果显示,SIRTI主要通过抑制中性粒细胞发挥抗SLE作用。结论雷公藤可能从抗炎、调节免疫细胞功能等多方面发挥对SLE的治疗作用,为雷公藤治疗SLE提供了研究思路和理论支撑。

Objective To explore the effect and potential mechanism of Tripterygium wilfordii Hook.f.in treatment of systemic lupus erythematosus(SLE)by network pharmacology combined with WGCNA.Methods The TCMSP database was used to retrieve the main active ingredients of Tripterygium wilfordii Hook.f.,and the active ingredient-related targets were mined through the database.The gene chip GSE65391 related to SLE was downloaded from the GEO platform,and the limma package of R software was used for differential analysis,and the module genes selected by WGCNA were used as disease target genes.R software Venn Diagram package for intersection analysis visualization.ADEx platform was used to perform Meta-analysis on the expression of intersection target genes.R software clusterProfiler package was used to perform gene ontology(GO)functional enrichment analysis and Kyoto encyclopedia of genes and genomes(KEGG)signaling pathway enrichment analysis for intersection target genes.Cytoscape software was used to construct and analyze the“drug-active ingredient-common target”network.The intersection target genes were uploaded to STRING database,and the result data were imported into Cytoscape software to construct protein interaction network(PPI)and screen the core target genes.Expression analysis,protein interaction analysis,and diagnostic efficiency analysis were used to demonstrate the role and clinical value of core target genes.PyMOL software was used to verify the molecular docking between core active components and core target genes.R software and CIBERSORT algorithm were used to calculate the distribution of immune cells.Results A total of 50 active components,690 component-related targets,and 1215 WGCNA association module genes were screened out.KEGG pathway analysis mainly involved Toll-like receptors and other signaling pathways.Four core components including kaempferol,triptolide,triptofordin B1,isocolonin,and SIRT1 core target genes were screened.The molecular docking results showed that kaempferol and reaginin had stable binding ability to SIRT1.The results of immune infiltration analysis showed that SIRTI exerted anti-SLE effect mainly by inhibiting neutrophils.Conclusion In this study,we found that Tripterygium wilfordii Hook.f.may exert its therapeutic effects on SLE from various aspects such as anti-inflammation and regulation of immune cell function,which provides research ideas and theoretical support for the treatment of SLE with Tripterygium wilfordii Hook.f..