基于加权基因共表达网络对胎儿生长受限发病机制的分析诊断标记物筛选

Based on weighted gene co-expression network analysis of the pathogenesis of fetal growth restriction and screening of diagnostic markers

目的宫内生长受限(IUGR)发病原因复杂,其发生机制也受多因素影响。文中利用加权基因共表达网络(WGCNA)分析IUGR机制,并寻找可能的诊断标志物。方法从基因表达综合数据库(GEO)下载GSE100415和GSE12216数据集,利用WGCNA分析与IUGR相关的模块,对模块内的基因进行生物学功能(GO)、京都基因与基因组百科全书(KEGG)和疾病本体论(DO)富集分析,并且联合蛋白相互作用(PPI)得出诊断标志物的候选基因。用ROC曲线对候选基因的预测能力进行探索。为进一步验证生物信息学结果,用PT-qPCR检测17例胎儿生长受限胎盘组织和16例正常胎盘组织中的候选基因的表达水平。结果WGCNA共表达网络表明,blue模块与IUGR密切相关,通过筛选blue模块基因得到PKM、LDHA、HK2、PIK3CB、OCRL共5个候选基因。RT-qPCR结果提示胎儿生长受限胎盘组织中HK2、PIK3CB和OCRL的表达水平均显著低于正常胎盘组织(P<0.05)。结论通过WGCNA分析方法,筛选出与IUGR相关的枢纽模块,其中HK2、PIK3CB和OCRL可能作为潜在的诊断标记物。

Objective The pathogenesis of intrauterine growth restriction(IUGR)is complex,and its mechanism is also affected by many factors.We used weighted gene co-expression network analysis(WGCNA)to know the mechanism of IUGR and search for possible diagnostic markers.Methods The datasetsGSE100415 and GSE12216 were downloaded from Gene Expression Database(GEO),WGCNA was used to analyze IUGR related modules,and genes in the modules were analyzed by biological function(GO),Kyoto Encyclopedia of Genes and Genomes(KEGG)and Disease ontology(DO)enrichment analysis.And meanwhile,combined protein interaction(PPI)was used to identify candidate genes for diagnostic markers.The predictive ability of candidate genes was explored by ROC curve.To further validate the bioinformatics results,pT-qPCR was used to detect the expression levels of candidate genes in 17 placental tissues with growth restriction and 16 normal placental tissues.Results The co-expression network of WGCNA showed that blue module was closely related to IUGR.Five candidate genes were obtained by screening blue module genes,including PKM,LDHA,HK2,PIK3CB and OCRL.Rt-qPCR results showed that the expression levels of HK2,PIK3CB and OCRL in fetal growth restriction placenta were significantly lower than those in normal placenta(P<0.05).Conclusion By WGCNA,the hub modules related to IUGR were screened out,among which HK2,PIK3CB and OCRL could be used as potential diagnostic markers.