基于网络药理学与GEO差异基因芯片数据分析小白菊内酯治疗宫颈癌的分子机制

Mechanism of parthenolide in treatment of cervical cancer based on network pharmacology and GEO data analysis

目的利用网络药理学结合GEO基因芯片分析的方法以及细胞实验研究小白菊内酯治疗宫颈癌的分子机制。方法首先利用GEO数据库获取宫颈癌芯片数据,再通过R软件获得其差异基因,同时绘制火山图。利用Swiss Target Prediction、SuperPred和HERB数据库收集小白菊内酯的作用靶点。通过GEO差异基因、Malacards、PharmGkb、CTD、DrugBank和DisGeNET数据库收集宫颈癌的疾病靶基因,利用Cytoscape 3.7.2软件制作药物–活性成分–靶点–疾病网络图,通过String数据库和Cytoscape3.7.2软件对交集基因进行蛋白相互作用(PPI)网络富集分析。利用R语言的clusterfiler程序包对小白菊内酯治疗宫颈癌的潜在作用靶标进行基因本体(GO)富集分析和京都基因与基因组百科全书(KEGG)信号通路富集分析。最后,通过人宫颈癌HeLa细胞模型验证小白菊内酯的作用机制。结果获取88个小白菊内酯靶基因,8167个宫颈癌的疾病靶点,26个差异基因,3个在宫颈癌中表达上调,23个在宫颈癌中表达下调。PPI网络以及拓扑分析结果显示,Toll样受体4(TLR4)、前列腺素内过氧化物酶2(PTGS2)、人细胞色素p450家族成员2C9(CYP2C9)、细胞色素P4503A4酶(CYP3A4)、组蛋白脱乙酰基酶2(HDAC2)、溴结构域包含蛋白2(BRD2)和溴结构域包含蛋白4(BRD4)是小白菊内酯治疗宫颈癌的7个核心基因。GO富集分析得出小白菊内酯影响的生物学过程(BP)有452个,包括对外源性刺激的反应、雌激素代谢过程等,作用的细胞组合(CC)有43个,包括组蛋白脱乙酰酶复合物、组蛋白甲基转移酶复合物等,作用的分子功能(MF)有41个;KEGG通路富集分析结果显示小白菊内酯治疗宫颈癌可能涉及药物代谢–细胞色素P450、细胞色素P450对异种物质的代谢及Toll样受体信号通路等信号通路。MTT实验证明,小白菊内酯以剂量相关的方式抑制HeLa细胞的增殖,IC50值为6μmol/L。结论小白菊内酯能够明显抑制Hela细胞增殖,作用机制可能涉及多个靶点和多条通路。

Objective To study the molecular mechanism of parthenolide in treatment of cervical cancer based on network pharmacology combined with GEO gene chip analysis and cell experiment.Methods GEO database was used to obtain cervical cancer chip data,and then R software was used to obtain its differential genes,and the volcano map was drawn at the same time.Swiss Target Prediction,SuperPred,and HERB databases were used to collect the action targets of parthenolide.The target genes of cervical cancer were collected through GEO differential genes,Malacards,PharmGkb,CTD,DrugBank,and DisGeNET databases,and the drug-active ingredient-target-disease network map was made using Cytoscape 3.7.2 software.The protein interaction(PPI)network enrichment analysis of intersection genes was performed using the String database and Cytoscape3.7.2 software.The gene ontology(GO)enrichment analysis and the Kyoto Encyclopedia of Genes and Genomes(KEGG)signaling pathway enrichment analysis of the potential targets of parthenolide in treatment of cervical cancer were conducted using the clusterfiler package in R language.The mechanism of parthenolide was verified by HeLa cell model of human cervical cancer.Results A total of 88 parthenolide target genes,8167 disease targets of cervical cancer,and 26 differentially expressed genes with 3 up-regulated and 23 down-regulated in cervical cancer were chosen.PPI network and topology analysis results show that TLR4,PTGS2,CYP2C9,CYP3A4,HDAC2,BRD2,and BRD4 are the seven core genes of parthenolide in treatment of cervical cancer.GO enrichment analysis showed that there were 452 biological processes(BP)affected by parthenolide,including response to exogenous stimuli and estrogen metabolism,43 cell combinations(CC)affected by parthenolide,including histone deacetylase complex and histone methyltransferase complex,and 41 molecular functions(MF)affected by parthenolide.The results of KEGG pathway enrichment analysis showed that the treatment of cervical cancer by parthenolide may involve drug metabolism,cytochrome P450,cytochrome P450 metabolism of heterogeneous substances and toll-like receptor signaling pathway.MTT assay demonstrated that parthenolide inhibited HeLa cell proliferation in a dose-dependent manner with IC50 of 6μmol/L.Conclusion Parthenolide can significantly inhibit the proliferation of Hela cells,and the mechanism of action may be that parthenolide can treat cervical cancer through multiple targets and multiple pathways.