基于加权基因共表达网络分析筛选结肠癌关键长链非编码RNA及其竞争性内源RNA网络构建

Screening of key long non-coding RNA and construction of competing endogenous RNA network in colon cancer based on weighted gene co-expression network analysis

目的通过加权基因共表达网络分析(WGCNA)方法筛选与结肠癌可能相关的长链非编码RNA(lncRNA),并构建其竞争性内源RNA(ceRNA)网络,为进一步探索结肠癌的机制提供依据。方法在GEO数据库下载结肠癌GSE126092的数据信息,获得差异表达lncRNA。下载癌症基因组图谱(TCGA)数据库中结肠癌组织及结肠正常组织lncRNA的表达数据,通过WGCNA方法筛选出与结肠癌相关性最高的模块,与GEO差异表达lncRNA取交集筛选出结肠癌关键lncRNA,进一步构建这些lncRNA相关的ceRNA网络,对靶mRNA进行基因本位(GO)功能分析和京都基因与基因组百科全书(KEGG)富集分析。结果共筛选出6个在结肠癌组织和正常组织中具有差异表达的lncRNA:锌指NFX1结构1反义RNA1(ZFAS1),β1,3-半乳糖基转移酶5反义RNA1(B3GALT5-AS1),细胞色素P450家族1亚家族B成员1反义RNA1(CYP1B1-AS1),二肽基肽酶样10反义RNA1(DPP10-AS1),VPS9包含域1反义RNA1(VPS9D1-AS1)和细胞周期蛋白依赖性激酶抑制因子2B反义RNA1(CDKN2B-AS1),并构建了其相关ceRNA网络。GO功能分析结果显示,生物功能主要集中在DNA模板转录调控、RNA聚合酶Ⅱ基因启动子的转录调控和RNA聚合酶Ⅱ启动子转录负向调控等;细胞功能主要集中在细胞核、突触、神经细胞体、突触后密集区和微管相关复合体;分子功能主要集中在核酸结合、金属离子结合、DNA结合等。KEGG富集分析结果显示,基因主要富集在癌症蛋白聚糖、磷脂酰肌醇-3-羟激酶(PI3K)-蛋白激酶B(AKT)信号通路、Rap1信号通路和局部粘连等。结论本研究通过WGCNA分析方法筛选出可能与结肠癌相关的lncRNA,并构建了其相关的ceRNA调控网络,可供后续实验验证。

Objective To screen long non-coding RNA(lncRNA)that may be associated with colon cancer by weighted gene co-expression network analysis(WGCNA),and construct its competing endogenous RNA(ceRNA)network,which provides a basis for further exploring the mechanism of colon cancer.Method The data information of colon cancer GSE126092 was downloaded from the GEO database,and the differentially expressed lncRNA was obtained.The expression data of lncRNA in colon cancer tissue and normal colon tissue from The Cancer Genome Atlas(TCGA)database were downloaded.The module with the highest correlation with colon cancer was screened by the WGCNA method,and the key lncRNA of colon cancer were screened by intersection with GEO differentially expressed lncRNA,and the ceRNA network related to these lncRNA was further constructed.Target mRNA were subjected to Gene Ontology(GO)functional analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG)enrichment analysis.Result A total of 6 lncRNA with differential expression between colon cancer tissues and normal tissues were screened out,these lncRNA included zinc finger NFX1-type containing 1 antisense RNA 1(ZFAS1),beta-1,3-galactosyltransferase 5 antisense RNA 1(B3GALT5-AS1),cytochrome P450 family 1 subfamily B member 1 antisense RNA 1(CYP1B1-AS1),dipeptidyl peptidase like 10 antisense RNA 1(DPP10-AS1),VPS9 domain containing 1 antisense RNA 1(VPS9D1-AS1),and cyclin dependent kinase inhibitor 2B antisense RNA 1(CDKN2B-AS1).According to the foregoing results,their related ceRNA network was also constructed.The results of GO functional analysis showed that the biological functions were mainly concentrated in the transcriptional regulation of the DNA template,the transcriptional regulation of RNA polymerase II gene promoter,and the negative regulation of RNA polymerase II promoter transcription.Cellular functions were primarily enriched in the nucleus,synapses,nerve cell bodies,postsynaptic densities,and microtubule-associated complexes.Molecular functions mainly focused on nucleic acid binding,metal ion binding,DNA binding,etc.The results of KEGG enrichment analysis showed that genes were mainly enriched in cancer proteoglycan,phosphatidylinositol 3-hydroxy kinase(PI3K)-protein kinase B(AKT)signaling pathway,Rap1 signaling pathway,and local adhesion,etc.Conclusion In this study,lncRNA that may be related to colon cancer were screened out by the WGCNA,and their related ceRNA regulatory network was constructed.This model could be verified by subsequent experiments.