表达谱芯片和DNA甲基化芯片联合分析筛选克罗恩病发生、发展的分子靶标

Comprehensive Analysis for Microarray Data of Expression Profile and DNA Methylation in Crohn′s Disease

目的 通过生物信息学方法筛选与克罗恩病(CD)发病相关的异常甲基化修饰的差异表达基因。方法 从公共基因表达数据库(GEO)下载CD的表达谱芯片GSE102134和DNA甲基化芯片GSE105798。通过R语言软件对CD表达谱芯片进行差异表达分析,同时对CD的DNA甲基化芯片进行差异甲基化位点分析。筛选异常甲基化修饰的差异表达基因进行功能富集分析。STRING数据库和Cytoscape软件共同构建蛋白相互作用网络,筛选CD的核心基因。最后通过GEO数据库GSE75214和GSE186582验证差异基因表达。结果 采用表达谱芯片分析,共筛选出1315个差异表达基因,其中780个表达上调,535个表达下调。CD组与对照组比较,共发现11066个差异甲基化位点,其中8542个高甲基化位点,2524个低甲基化位点。对差异表达基因和差异甲基化基因进行联合分析,找到55个低甲基化修饰下表达上调的基因,和125个高甲基化修饰下表达上调的基因。GO分析表明异常甲基化修饰的差异表达基因与跨膜转运蛋白活性、细胞顶端组成和有机阴离子转运相关。KEGG信号通路主要为PIK/Akt信号通路、黏附斑和ECM-受体相互作用等。STRING和Cytoscape软件筛选信号通路中的关键基因,并在GSE75214和GSE186582芯片集验证差异基因的表达,结果提示COL4A2、COL4A1、PDGFRB和PYY可能在CD中起重要作用。结论COL4A2、COL4A1、PDGFRB和PYY可能是CD疾病诊断和治疗的潜在靶点。

Objective To find the biomarker and potential therapeutic targets for development of Crohn′s disease(CD) by comprehensive analysis of gene expression and DNA methylation data. Methods The Microarray data of expression profile(GSE102134) and DNA methylation(GSE105798) were obtained from the common Gene Expression Omnibus(GEO). The differentially expressed genes(DEGs) and differentially methylated probes(DMPs) were screened by R language. Then, functional enrichment analyses for aberrantly methylated differentially expressed genes were performed. STRING and Cytoscape were used to construct protein-protein interaction(PPI) network, and core genes of CD were identified. Finally, GSE75214 and GSE186582 were used to verify the expression of differentially expressed genes. Results A total of 1315 DEGs, including 780 up-regulated and 535 down-regulated genes, were screened from microarray data. Besides, 11066 DMPs were obtained from DNA methylation data, of which 8542 were hepermethylation sites and 2524 were hypomethylation sites. Then, we obtained 55 hypomethylatef/highly expressed oncogenes and 125 hypermethylatef/downregulated oncogenes by overlapping the lists of differentially expressed genes and aberrantly methylated genes. GO analysis suggested that these aberrantly methylated expressed genes were mainly involved in active transmembrane transporter activity, apical part of cell and organic anion transport. KEGG enrichment analysis revealed that differential gene were primarily enriched in the PIK-Akt signaling pathway, Focal adhesion and ECM-receptor interaction. Core genes including COL4 A2, COL4 A1, PDGFRB, PYY were identified based on STRING, Cytoscape, GSE75214 and GSE186582 data set. And these genes may play a vital role in CD. Conclusion COL4 A2, COL4 A1, PDGFRB and PYY may function as potential targets for diagnosis and treatment of CD.