生物信息学方法分析炎症性肠病诱导结直肠癌发生过程的基因调控机制  

Bioinformatics Analysis of Gene Regulation Mechanism of Inflammatory Bowel Disease Induced Colorectal Cancer

作　　者：萧文泽 赵力 Xiao Wenze;Zhao Li(Department of Rheumatology and Immunology,Fudan University Pudong Medical Center,Shanghai 201399,China;Department of Rheumatology and Immunology,Huashan Hospital Affiliated to Fudan University,Shanghai 200040,China)

机构地区：[1]上海市浦东医院,复旦大学附属浦东医院风湿免疫科,上海201399 [2]上海华山医院,复旦大学附属华山医院风湿免疫科,上海200040

出　　处：《华中科技大学学报（医学版）》2019年第5期537-543,共7页Acta Medicinae Universitatis Scientiae et Technologiae Huazhong

基　　金：浦东新区科技发展基金资助项目（No.PKJ2018-Y36）;复旦大学附属浦东医院浦菁计划资助项目（No.PJ201502)

摘　　要：目的探究炎症性肠病相关结直肠癌发生发展过程中的基因调控机制。方法提取GEO数据库GSE6731(炎症性肠病芯片)、GSE21250(结直肠癌芯片)数据集,采用R语言分别获取炎症性肠病与结直肠癌相对于健康对照人群的差异表达基因。取两组差异基因交集定义为炎症性肠病诱导结直肠癌的风险基因,进一步进行功能富集分析,并绘制蛋白互作网络。随后基于TCGA数据库,利用GEPIA网页工具分析风险基因与结直肠癌患者生存期的关系,利用LinkedOmics工具分析风险基因在TNM各子集的表达水平。通过蛋白质免疫印迹(Western blot)及荧光定量PCR(qRT-PCR)实验在临床标本中验证生物信息学分析结果。结果在炎症性肠病组获得223个差异表达基因,在结直肠癌组中获得1037个差异表达基因,两组交叉的差异表达基因为35个,定义为风险基因。进一步针对风险基因进行功能富集,发现外泌体为其主要功能注释,蛋白互作分析中ABCB1、CXCL12位于互作网络中心。生存期分析中发现了7个与结直肠癌生存期相关的风险基因,TNM子集分析中发现F2RL1在各分期中呈阶梯状下降。qRT-PCR和Western blot实验验证了F2RL1在临床标本中的表达水平。结论炎症性肠病诱导结直肠癌发生发展与多个基因及其下游机制相关,该研究提示ABCB1、CXCL12、F2RL1是具有诊断与治疗意义的新靶点。Objective To explore the mechanism of gene regulation in inflammatory bowel disease(IBD)induced colorectal development.Methods GEO database GSE6731(inflammatory bowel disease data)and GSE21250(colorectal cancer data)were extracted by R Software to obtain differentially expressed genes(DEGs)of patients with inflammatory bowel disease(IBD)and colorectal cancer(CRC) compared with healthy controls.The intersection of DEGs between the two groups was defined as the risk gene of IBD induced CRC.The functional enrichment was further studied and the protein interaction network was drawn.Then,based on TCGA database,the relationship between risk genes and survival time was analyzed by GEPIA web page tool,and the expression level of risk genes in each subset of TNM was analyzed by LinkedOmics web tool.Results Totally,223 DEGs were obtained in IBD group,1037 DEGs were obtained in CRC group and 35 of them were defined as risk genes.Furthermore,in the functional enrichment of risk genes,it was found that exosomes were the main functional annotations.In protein interaction analysis,ABCB1 and CXCL12 were located in the center of the interaction network.Seven risk genes associated with colorectal cancer survival were identified in survival analysis.In TNM subset analysis,F2 RL1 decreased stepwise in all stages.Finally,we verified the expression of F2 RL1 in clinical specimens through experiments.Conclusion Inflammatory bowel disease induced colorectal cancer is associated with various genes and downstream mechanisms,among which ABCB1,CXCL12 and F2 RL1 are new targets with diagnostic and therapeutic significance.

关 键 词：炎症性肠病 结直肠癌 生物信息学 

分 类 号：R735.34[医药卫生—肿瘤]