加权重基因共表达网络分析识别慢性肾脏病足细胞损伤关键节点基因MAGI2

Identification of podocyte damagerelated MAGI2 gene by weighted gene co-expression network analysis in chronic Kidney disease

目的通过加权基因共表达网络分析(WGCNA)识别慢性肾脏病(CKD)足细胞损伤相关的基因模块与关键基因。方法从基因表达综合数据库(GEO)中下载包含足细胞损伤体外模型及CKD患者肾小球组份的表达谱GSE66107、GSE93798、GSE30528、GSE32591 4个数据集。利用R软件包做数据预处理并选取错误发现率(FDR)<0.05及差异倍数≥1.5作为差异表达基因(DEG);结合数据集GSE993395(133例CKD患者肾小球样本)用WGCNA进行模块化分析并对模块内基因进行功能注释(GO),根据GO结果和含有文献报道的足细胞标准基因(PSG)情况确定足细胞损伤相关模块,根据模块内基因连接度(Kwithin)挑选枢纽(hub)基因;利用Cytoscape软件及插件Cluego构建足细胞损伤相关模块基因的加权共表达网络。结果 4个数据集共得到趋势一致的DEG 7 957个,其中15个DEG在4个数据集中均有差异(co DEG)。GSE993395中包含的4 031个DEG被用于WGCNA分析;最终得到12个基因模块,其中green模块包含最多的co DEG和PSG,进一步通过Kwithin发现其中同时作为co DEG和PSG的MAGI2基因是其hub基因之一。结论WGCNA表达网络分析方法是一个高效的系统生物学方法,应用该方法发现CKD时关键节点基因MAGI2在足细胞损伤中可能起到重要作用。

Objective To screen podocyte damage related critical genes in chronic kidney disease （CKD） patients by weighted gene co-expression network analysis （WGCNA）. Methods Podocyte damage related database of GSE66107, GSE93798, GSE30528, GSE32591 were explored from gene expression GEO database. The R software package was used for data pre-processing. Differentially expressed genes （DEG） were identified for those with FDR 〈 0.05 and fold change ≥ 1.5. DEG in GSE993395 data was analyzed by WGCNA. According to the functional annotation of Gene Ontology （GO） and the podocyte standard gene （PSG） which were reported in literatures, the podocyte injury-associated modules were defined, and the hub gene is selected according to the average connectivity degree of the module （Kwithin）. Then Cytoscape software and plugin Clugo was utilized for network visualization. Results Totally 7957 DEGs were picked out by comparing the expressed data of normal subject and podocyte or glomerulus under typical damage conditions, including 15 DEG that were differently expressed in 4 GSEs. About 4031 DEGs were screened by WGCNA, and 12 gene modules were identified. Green module contained most coDEGs or PSGs, which was suggested as podocyte injury-assosiated module. Furthermore, MAGI2 gene was one of the hub genes that was coDEG and PSG. Conclusions WGCNA is an efficient system for screening of target genes; MAGI2 may play an important role in podocyte damage in CKD.