基于生物信息学分析早期液体复苏改善脓毒症休克的核心基因及通路

Identification of hub genes and key pathways in the early therapy of septic shock based on bioinformatics analysis

目的通过生物信息学分析鉴定脓毒症休克早期的潜在核心基因及通路。方法基因表达谱GSE110487数据集从基因表达综合数据库下载,使用R项目的DESeq2软件包鉴定差异基因。构建《京都基因与基因组百科全书》(Kyoto Encyclopedia of Genes and Genomes,KEGG)和《基因本体论》(Gene Ontology,GO)分析,使用clusterProfiler程序包研究途径和生物过程。使用ggnetwork软件包对蛋白质–蛋白质相互作用(proteinprotein interaction,PPI)网络进行映射,并使用Cytoscape软件进行分子复合物检测(molecular complex detection,MCODE)分析以进一步研究差异基因的相互作用。结果在接受早期液体复苏治疗后出现不同反应性脓毒症休克患者中共鉴定出468个差异基因,包括255个上调基因和213个下调基因,通过对差异基因进行KEGG和GO富集分析,发现表达上调的基因涉及的生物过程主要与免疫过程有关,而表达下调的基因则涉及与有机含氮化合物有关的生物过程、多细胞有机体生物过程以及离子转运有关。经PPI网络构建和MCODE分析,从这些差异基因中筛选出23个核心基因,除CD28、CD3D、CD8B、CD8A、CD160、CXCR6、CCR3、CCR8、CCR9、TLR3、EOMES、GZMB、PTGDR2、CXCL8、GZMA、FASLG、GPR18、PRF1、IDO1等表达上调基因通过各种免疫过程参与早期脓毒症休克的改善外,CNR1、GPER1、TMIGD3、GRM2等表达下调的基因在早期液体复苏改善脓毒症休克中也有显著变化。KEGG通路富集分析和GO功能分析显示差异基因富集的信号通路与细胞因子与细胞因子受体的相互作用、自然杀伤细胞介导的细胞毒性、造血细胞谱、T淋巴细胞受体信号传导途径、磷脂酶D信号通路、细胞黏附分子等有关。结论T淋巴细胞、自然杀伤细胞等淋巴细胞及相关的细胞因子、趋化因子等参与的免疫过程在脓毒症休克的早期治疗中起着重要作用,CD160、CNR1、GPER1、GRM2等核心基因可能是治疗早期脓毒症休克的新靶点。

Objective To identify potential hub genes and key pathways in the early period of septic shock via bioinformatics analysis.Methods The gene expression profile GSE110487 dataset was downloaded from the Gene Expression Omnibus database.Differentially expressed genes were identified by using DESeq2 package of R project.Then Kyoto Encyclopedia of Genes and Genomes(KEGG)and Gene Ontology(GO)analyses were constructed to investigated pathways and biological processes using clusterProfiler package.Subsequently,protein-protein interaction(PPI)network was mapped using ggnetwork package and the molecular complex detection(MCODE)analysis was implemented to further investigate the interactions of differentially expressed genes using Cytoscape software.Results A total of 468differentially expressed genes were identified in septic shock patients with different responses who accepted early supportive hemodynamic therapy,including 255 upregulated genes and 213 downregulated genes.The results of GO and the KEGG pathway enrichment analysis indicated that these up-regulated genes were highly associated with the immunerelated biological processes,and the down-regulated genes are involved in biological processes related to organonitrogen compound,multicellular organismal process,ion transport.Finally,a total of 23 hub genes were identified based on PPI and the subcluster analysis through MCODE software plugin in Cytoscape,which included 19 upregulated hub genes,such as CD28,CD3D,CD8B,CD8A,CD160,CXCR6,CCR3,CCR8,CCR9,TLR3,EOMES,GZMB,PTGDR2,CXCL8,GZMA,FASLG,GPR18,PRF1,IDO1,and additional 4 downregulated hub genes,such as CNR1,GPER1,TMIGD3,GRM2.KEGG pathway enrichment analysis and GO functional annotation showed that differentially expressed genes were primarily associated with the items related to cytokine-cytokine receptor interaction,natural killer cell mediated cytotoxicity,hematopoietic cell lineage,T cell receptor signaling pathway,phospholipase D signaling pathway,cell adhesion molecules,viral protein interaction with cytokine and cytokine receptor,primary immunodeficiency,graftversus-host disease,type 1 diabetes mellitus.Conclusions Some lymphocytes such as T cells and natural killer cells,cytokines and chemokines participate in the immune process,which plays an important role in the early treatment of septic shock,and CD160,CNR1,GPER1,and GRM2 may be considered as new biomarkers.