基于 TCGA 数据库构建子宫内膜癌 ceRNA 网络及关键基因的筛选。
Construction of Endometrial Carcinoma ceRNA Network and Screening of Key Genes Based on TCGA Database.
机构信息
Department of Gynecology and Obstetrics, Yantai Affiliated Hospital of Binzhou Medical University, Muping District, Yantai, Shandong 264100, China.
出版信息
Comput Math Methods Med. 2022 Jul 4;2022:1418232. doi: 10.1155/2022/1418232. eCollection 2022.
OBJECTIVE
Long noncoding RNA (lncRNA) has received more and more attention in human tumor research. This study is aimed at clarifying the regulatory network of lncRNAs-microRNAs- (miRNAs-) mRNAs and at determining the relevant targets in the development of endometrial cancers.
METHODS
Download the miRNA, mRNA, and lncRNA expression profile data of endometrial cancer patients from TCGA; use the "DESeq2" package of R software to identify the differential expression of miRNAs, mRNAs, and lncRNAs; construct a network of ceRNA; and perform gene ontology (GO) and Kyoto Encyclopedia of Gene and Genome (KEGG) pathway enrichment assessment on mRNAs in the network of ceRNA; string and Cytoscape 3.7.2 perform PPI assessment on target genes and TOP 10 hub gene screening; Cytoscape 3.7.2 computer program was employed for constructing the lncRNA-miRNA-TOP10 hub mRNA network diagram to determine the signal axis; StarBase database to verify the Top10 hub mRNA expression; the "survival" package in R computer program was implemented to analyze the survival rate of all genes on the lncRNA-miRNA-Top10 hub mRNA network diagram; RT-qPCR to verify the expression level of genes on the signal axis.
RESULTS
1119 differential mRNAs, 14 differential lncRNAs, and 65 differential miRNAs were screened in TCGA; we constructed a ceRNA regulatory network composed of 5 DELs, 7 DEMs, and 90 DEGs; String combined with Cytoscape to screen out Top10 hub genes, namely: LEFTY1, LIN28A, LHX3, ST8SIA3, CEP55, FBXO32, DCN, ANGPTL1, ADRA1A, and KCNMA1; the StarBase database verification results show that ADRA1A, ANGPTL1, FBXO32, KCNMA1, and DCN are downregulated in endometrial cancer tissues; LEFTY1, LIN28A, LHX3, ST8SIA3, and CEP55 are upregulated in endometrial cancer; the constructed lncRNA-miRNA-hub Top10 mRNA network map identified CTD-2314B22, RP11-89 K21/hsa-miR-143, hsa-miR-424/LEFTY1, LIN28A, LHX3, ST8SIA3, and CEP55 signal axis; survival analysis results show that CTD-2314B22, RP11-89 K21, hsa-miR-96, hsa-miR-211, LHX3, ST8SIA3, and DCN are all related to survival; RT-qPCR results indicate CTD-2314B22, RP11-89 K21, LEFTY1, LIN28A, LHX3, ST8SIA3, and CEP55 are upregulated in endometrial cancer cells, and hsa-miR-143 and hsa-miR-424 are downregulated in endometrial cancer cells.
CONCLUSION
From the perspective of the lncRNA-miRNA-mRNA network, our study identified CTD-2314B22, RP11-89 K21/hsa-miR-143, hsa-miR-424/LEFTY1, LIN28A, LHX3, ST8SIA3, and CEP55 signal axis, which can present considerably potent biomarkers and therapeutic targets for treating endometrial cancer.
目的
长链非编码 RNA（lncRNA）在人类肿瘤研究中受到越来越多的关注。本研究旨在阐明 lncRNA-miRNA-mRNA 的调控网络，并确定子宫内膜癌发展过程中的相关靶点。
方法
从 TCGA 下载子宫内膜癌患者的 miRNA、mRNA 和 lncRNA 表达谱数据；使用 R 软件的“DESeq2”包识别 miRNA、mRNA 和 lncRNA 的差异表达；构建 ceRNA 网络；对 ceRNA 网络中的 mRNAs 进行基因本体（GO）和京都基因与基因组百科全书（KEGG）通路富集评估；STRING 和 Cytoscape 3.7.2 对靶基因进行 PPI 评估和 TOP10 枢纽基因筛选；Cytoscape 3.7.2 计算机程序用于构建 lncRNA-miRNA-TOP10 枢纽 mRNA 网络图，以确定信号轴；StarBase 数据库验证 Top10 枢纽 mRNA 表达；R 计算机程序中的“survival”包用于分析 lncRNA-miRNA-TOP10 枢纽 mRNA 网络图上所有基因的生存率；RT-qPCR 验证信号轴上基因的表达水平。
结果
TCGA 筛选出 1119 个差异表达的 mRNAs、14 个差异表达的 lncRNAs 和 65 个差异表达的 miRNAs；构建了一个由 5 个 DELs、7 个 DEMs 和 90 个 DEGs 组成的 ceRNA 调控网络；STRING 结合 Cytoscape 筛选出 TOP10 枢纽基因，即：LEFTY1、LIN28A、LHX3、ST8SIA3、CEP55、FBXO32、DCN、ANGPTL1、ADRA1A 和 KCNMA1；StarBase 数据库验证结果表明，ADRA1A、ANGPTL1、FBXO32、KCNMA1 和 DCN 在子宫内膜癌组织中下调；LEFTY1、LIN28A、LHX3、ST8SIA3 和 CEP55 在子宫内膜癌中上调；构建的 lncRNA-miRNA-枢纽 Top10 mRNA 网络图谱确定了 CTD-2314B22、RP11-89 K21/hsa-miR-143、hsa-miR-424/LEFTY1、LIN28A、LHX3、ST8SIA3 和 CEP55 信号轴；生存分析结果表明，CTD-2314B22、RP11-89 K21、hsa-miR-96、hsa-miR-211、LHX3、ST8SIA3 和 DCN 均与生存相关；RT-qPCR 结果表明，CTD-2314B22、RP11-89 K21、LEFTY1、LIN28A、LHX3、ST8SIA3 和 CEP55 在子宫内膜癌细胞中上调，而 hsa-miR-143 和 hsa-miR-424 在子宫内膜癌细胞中下调。
结论
从 lncRNA-miRNA-mRNA 网络的角度来看，我们的研究确定了 CTD-2314B22、RP11-89 K21/hsa-miR-143、hsa-miR-424/LEFTY1、LIN28A、LHX3、ST8SIA3 和 CEP55 信号轴，这些信号轴可以作为治疗子宫内膜癌的潜在生物标志物和治疗靶点。
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