基于生物信息学技术对结直肠癌相关lncRNA、miRNA和mRNA的筛选及其部分生物学功能的分析

Screening of colorectal cancer associated lncRNA, miRNA and m RNA based on bioinformatics technology and analysis of their biological functions

目的:筛选TCGA数据库中结直肠癌(CRC)差异表达的lncRNA、miRNA和mRNA,探讨其与CRC预后的关系及相关生物学功能。方法:从TCGA数据库中下载CRC样本的RNA测序(RNA-Seq)数据及miRNA-Seq数据并进行分析,利用R程序筛选出差异表达的lncRNA、miRNA和mRNA。通过miRcode、TargetScan和miRTarbase 3个数据库对差异表达的RNA之间的关系进行分析整合,构建CRC中的lncRNA-miRNA-mRNA ceRNA网络。用Kaplan-Meier法分析ceRNA网络中的lncRNA、miRNA和mRNA表达量与患者生存预后的关系,后用GSEA功能富集分析软件分析出参与CRC发生发展的信号通路。结果:共鉴定出CRC中614个差异表达的lncRNA、244个差异表达的miRNA、12 672个差异表达的mRNA;构建了由139个lncRNA、37个miRNA和228个mRNA组成的ceRNA网络;发现有58个lncRNA、23个miRNA、150个mRNA与CRC的预后相关。GSEA富集分析结果显示,mRNA主要参与Notch、Hedgehog和TGF-β等信号通路。结论:成功构建CRC相关ceRNA网络,并筛选出与CRC预后相关的lncRNA、miRNA和mRNA,为后续深入开展CRC的临床研究及基础实验研究提供有价值的前期基础。

Objective:To screen differentially expressed lncRNA,miRNA and mRNA in colorectal cancer(CRC)in TCGA database,and to explore their relationship with CRC prognosis and related biological functions.Methods:RNA sequencing(RNA-Seq)data and miRNA-Seq data of CRC samples were downloaded from the TCGA database and analyzed,and differentially expressed lncRNA,miRNA and mRNA were screened by R program.The lncRNA-miRNA-mRNA ceRNA network in CRC was constructed by analyzing and integrating the relationships between differentially expressed RNAs through miRcode,TargetScan and miRTarbase databases.Kaplan-Meier method was used to analyze the relationship between the expression of lncRNA,miRNA,mRNA in ceRNA network and the survival prognosis of patients.Finally,the signal pathways involved in the occurrence and development of CRC were analyzed by GSEA functional enrichment analysis software.Results:A total of 614 differentially expressed lncRNAs,244 differentially expressed miRNAs,and 12 672 differentially expressed mRNAs in CRC were identified;a ceRNA network consisting of 139 lncRNAs,37 miRNAs and 228 mRNAs was constructed;It was found that 58 lncRNAs,23 miRNAs,and 150 mRNAs were associated with the prognosis of CRC.The results of GSEA enrichment analysis showed that mRNA was mainly involved in signaling pathways such as Notch,Hedgehog and TGF-β.Conclusion:CRC-related ceRNA network was successfully constructed and lncRNAs,miRNAs and mRNAs associated with CRC prognosis were screened.It provides a valuable preliminary basis for further in-depth clinical research and basic experimental research on CRC.