颞叶内侧癫痫基因表达的生物信息学分析

Bioinformatics analysis of gene expression in Mesio-temporal lobe epilepsy

目的通过生物信息学方法分析颞叶内侧癫痫(Mesio-temporal lobe epilepsy,MTLE)模型小鼠的海马组织与正常海马组织差异表达的基因,以及其生物学功能、细胞定位、参与的信号通路等,筛选出在MTLE发生发展过程中的关键基因,并挑选关键基因中处于整个调控网络的核心基因(与其它基因关系最密切者),为MTLE的发病机制及其防治研究提供新思路。方法①从基因芯片公共数据库(Gene expression omnibus,GEO)中搜索下载MTLE相关基因芯片数据集(GSE88992),该芯片含有17个癫痫模型小鼠的海马标本[包括8个病例组和9个对照组,其中将通过注射海藻氨酸(Kainic acid,KA;1 nmol/50 nL)获得的MTLE小鼠模型作为病例组,注射生理盐水的小鼠作为平行对照组,在注射后6、12及24 h提取海马标本];②通过GEO2R工具筛选和鉴定出MTLE小鼠的差异表达基因(Differentially expressed genes,DEGs),调整后P值<0.05,|log2(fold-change)|>1作为截断值的标准;③使用Venny2.1.0对上调和下调的差异表达基因分别取交集,筛选出共同差异表达的基因;④利用DAVID在线网站及FUNRICH软件分析基因的信号通路、基因蛋白表达等信息;⑤利用STRING在线网站及Cytoscape软件分析差异基因表达蛋白的相互作用以及挑选出5个与周围基因高度相关性(度值,Degree)的中枢基因,实现蛋白相互作用的可视化及分析核心模块基因。结果①在GEO数据集GSE88992,注射后6、12和24 h的结果中筛选出688、1294和1916个DEGs,分别包括549、797和870个上调基因以及139、497和1046个下调基因;②所有DEGs中,有285个上调的DEGs和46个下调的DEGs,共有331个DEGs在3个结果中共存,提示这331个共表达DEGs具有重要意义;③筛选出DEGs中的核心模块以及挑选出10个核心基因(Il6、Fos、Stat3、Ptgs2、Ccl2、Timp1、Cd44、Icam1、Atf3、Cxcl1),生物信息学分析提示核心模块基因主要富集在细胞质膜与细胞间隙中;涉及的生物学过程集中在中性粒细胞趋化、炎症反应、正向调控ERK1和ERK2级联反应;生物分子功能集中在趋化因子活性、细胞因子活性和趋化因子受体结合等;KEGG信号通路分析DEGs主要参与趋化因子信号通路、细胞因子互作信号通路等信号通路。结论通过生物信息学分析表明MTLE的发病机制错综复杂,是多个基因相互作用的结果,多条信号通路参与了MTLE的发病,对MTLE基因表达的进一步分析有利于揭示其发病机制以及确定新的候选治疗靶点。

Objective To investigate the significant genes in Mesio-temporal lobe epilepsy(MTLE)and explore the molecular mechanism of MTLE.Methods The microarray data of MTLE were downloaded from the Gene Expression Omnibus(GEO)database and analyzed by bioinformatics methods using GEO2R tool,Venny2.1.0,FUNRICH and Cytoscape software,DAVID and String databases.Results Of all the 331 differentially expressed genes(DEGs),46 genes were down-regulated and 285 genes were up-regulated in dataset GSE88992;Furthermore,the core module genes were identified from those DEGs,which were expressed mostly in plasma membrane and extracellular space;The major molecular funtion were chemokine activity,cytokine activity and chemokine receptor binding;The main biological pathways involved neutrophil chemotaxis,inflammatory response and positive regulation of ERK1 and ERK2 cascade;The KEGG analysis showed DEGs enriched in Chemokine signaling pathway,Cytokine-cytokine receptor interaction and Complement and coagulation cascades.In addition,ten hub genes(Il6,Fos,Stat3,Ptgs2,Ccl2,Timp1,Cd44,Icam1,Atf3,Cxcl1)were found to significantly express in the MTLE.Conclusion The pathogenesis of MTLE involves multiple genes,and multiple cell signaling pathways.Thus investigations of these genes may provide valuable insights into the mechanism of MTLE.