结直肠癌患者血液外泌体差异表达非编码RNA的筛选及生物信息学分析

Bioinformatic analysis of differentially expressed exosomal non-coding RNAs in patients with colorectal cancer

目的对结直肠癌患者血液外泌体差异表达非编码RNA(ncRNA)进行筛选及功能分析,探索结直肠癌的发病机制,为结直肠癌早期诊断分子标志物的筛选及治疗靶点提供理论依据。方法从exoRBase数据库中选取12例结直肠癌患者和32例正常对照者血液外泌体的RNA-seq数据,利用R软件的Limma包筛选差异表达ncRNA和信使RNA(mRNA),预测其结合的微小RNAs(miRNA),构建竞争内源性RNA(ceRNA)网络,并利用R软件的clusterProfiler包和enrichplot包对差异表达mRNAs进行基因本体论(GO)功能富集和京都基因与基因组百科全书(KEGG)通路富集分析。结果结直肠癌组和正常对照组外泌体差异表达基因筛选,共筛选出125个差异表达mRNAs,其中上调表达117个,下调表达8个;52个差异表达长链非编码RNAs(lncRNAs),均为上调表达;81个差异表达环状RNAs(circRNAs),其中上调表达47个,下调表达34个。预测mRNAs和lncRNAs、circRNAs结合的共同miRNAs,构建miRNAs为中心的ceRNA调控网络,包含16个lncRNAs、13个circRNAs、62个miRNAs和25个mRNAs。差异表达mRNAs主要涉及丝裂原活化蛋白激酶(MAPK)信号通路、胰高血糖素信号通路、Fcγ受体介导的吞噬作用等。结论通过生物信息学方法构建ceRNA调控网络,可揭示差异表达基因调控结直肠癌发生、发展的分子机制,有助于临床上指导结直肠癌的早期诊断和精准治疗。

Objective To screen the differentially expressed non-coding RNAs(ncRNAs)in patients with colorectal cancer.Methods The exosomal RNA-seq data of 12 colorectal cancer patients and 32 normal controls were obtained from exoRBase database.Differentially expressed ncRNAs and messenger RNAs(mRNAs)were screened by Limma package in R software.The shared microRNAs(miRNAs)of differentially expressed long non-coding RNAs(lncRNAs),circular RNAs(circRNAs)and mRNAs were obtained and a competing endogenous RNA(ceRNA)network was developed.Gene Ontology(GO)functional and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment analysis of differentially expressed mRNAs were performed with clusterProfiler and enrichplot package in R software.Results A total of 125 differentially expressed mRNAs(117 up-regulated and 8 down-regulated),52 differentially expressed lncRNAs(all up-regulated),81 differentially expressed circRNAs(47 up-regulated and 34 down-regulated)were identified in blood exosomes of colorectal cancer patients and normal controls.A ceRNA network was developed,including 16 lncRNAs,13 circRNAs,62 miRNAs and 25 mRNAs.The differentially expressed mRNAs were mainly enriched in MAPK signaling pathway,Glucagon signaling pathway and Fc gamma R-mediated phagocytosis.Conclusion We have developed a ceRNA network with bioinformatic tool for exploring the molecular mechanisms of colorectal cancer,and developed a new strategy to guide in the early diagnose and individualized treatment of colorectal cancer.