创伤性脑损伤后基因表达谱数据的权重基因共表达网络分析

Weighted correlation network analysis of gene expression profiling data after traumatic brain injury

目的通过对创伤性脑损伤(TBI)后脑组织的基因表达谱数据进行权重基因共表达网络分析(WGCNA),筛选具有重要意义的基因集,并明确其涉及的功能及信号通路,为TBI的机制研究和治疗提供参考。方法在基因表达数据库(GEO)中下载大鼠TBI基因表达谱数据GSE2871,将全部47个大鼠脑组织样本的8799个基因的表达情况进行WGCNA分析;计算选择β加权软阈值后,对全部基因构建无向加权基因网络,识别具有高度绝对相关性的基因集;从数据库中获取样本信息并计算样本特征与模块间的相关性,选取与损伤程度及取样部位相关的模块进行基因本体(GO)分析和京都基因与基因组百科全书(KEGG)通路分析,从而获悉上述关键模块中基因涉及的生物学过程和通路;计算关键模块内基因的模块相关度和性状相关度,进而遴选关键模块中的核心基因。结果将GSE2871表达谱数据库中的所有大鼠脑组织样本和基因纳入WGCNA,共得出22个模块,分别标记为模块A~V。其中模块E、G、T、U与取样部位显著相关,模块E和模块G同时与损伤程度显著相关;GO分析和KEGG通路分析提示,与损伤程度和取样部位均显著相关的模块E、G中的基因主要参与白细胞迁移、细胞趋化及各种免疫反应调控等相关生物学过程,涉及抗原处理与呈递、细胞因子-细胞因子受体相互作用及白细胞介素(IL)-17信号等信号通路。与取样部位显著相关的模块T、U主要参与低氧反应、细胞代谢、细胞膜离子通道调控和信号传导等生物学过程,涉及神经退行性疾病信号通路、核糖体、自噬、神经活性的配体-受体相互作用等信号通路;Tuba1b/1c、Ifitm3、Cebpd、Nfkbia、Serinc3、Pmpcb、Cyp4a8等为上述关键模块的核心基因。结论与大鼠TBI显著相关的基因主要参与免疫激活、炎症反应、能量代谢异常、钙离子通道失调、自噬异常及细胞凋亡等病理生理环节。

Objective To screen important genes and characterize their functions and signaling pathways by weighted gene co-expression network analysis(WGCNA)on the gene expression profile of brain tissue after traumatic brain injury(TBI)so as to provide a reference for the mechanism research and treatment of TBI.Methods The rat TBI gene expression profile GSE2871 was downloaded from the Gene Expression Omnibus(GEO).The expression profile of 8799 genes of all 47 rat brain tissue samples was analyzed by WGCNA.After calculating and selecting theβ-weighted soft threshold,undirected weighted gene network was constructed to identify gene sets with a high degree of correlation.Sample information was obtained from the database to calculate the correlation between each trait of the samples and modules.Gene ontology(GO)analysis and KEGG pathway analysis were performed for the genes in modules related to injury severity and sampling side in order to unvail the biological processes and pathways involved.The gene-module correlation and gene-trait correlation in these key modules were calculated and hub genes were selected.Results All the rat brain tissue samples and genes in GSE2871 were included in the WGCNA analysis.A total of 22 modules were obtained,which were marked as modules A to V.Modules E,G,T and U were significantly associated with the sampling side.Modules E and G were significantly related to injury severity.GO analysis and KEGG pathway analysis indicated that the genes in modules E and G with significant relation to injury severity and sampling side were mainly implicated in leukocyte migration,cell chemotaxis,various immune response regulation,etc.The involved pathways included antigen processing and presentation pathways,cell factor-cytokine receptor interaction,interleukin-17 signaling pathway,etc.While modules T and U with significant relation to the sampling side were mainly implicated in hypoxia response,cell metabolism,cell membrane ion channel regulation,signal transduction,etc.The pathways involved were neurodegenerative disease signaling pathways,ribosomes,autophagy,neuroactive ligand-receptor interactions,etc.Among the key modules significantly relating to traits,Tuba1b/1c,Ifitm3,Cebpd,Nfkbia,Serinc3,Pmpcb and Cyp4a8 were selected as hub genes of the above key modules.Conclusion The genes significantly relating to rat TBI are mainly involved in pathophysiological links such as immune activation,inflammatory response,abnormal energy metabolism,calcium channel disorders,abnormal autophagy and cell apoptosis.