吉林大学学报(医学版) ›› 2022, Vol. 48 ›› Issue (6): 1535-1545.doi: 10.13481/j.1671-587X.20220620

• 临床研究 • 上一篇    下一篇

基于房颤中circRNA-miRNA-mRNA网络构建和免疫细胞浸润的生物信息学分析

范吉林1,朱婷婷2,田晓玲2,刘思佳3,苏静3,张世亮3()   

  1. 1.山东中医药大学第一临床医学院,山东 济南 250014
    2.滨州医学院附属医院神经外科,山东 滨州 256600
    3.山东中医药大学附属医院心病科,山东 济南 250014
  • 收稿日期:2021-11-23 出版日期:2022-11-28 发布日期:2022-12-07
  • 通讯作者: 张世亮 E-mail:zhangshiliangsd@126.com
  • 作者简介:范吉林(1993-),男,山东省德州市人,在读博士研究生,主要从事中西医结合治疗心血管疾病方面的研究。
  • 基金资助:
    科技部“十三五”重大专项重大新药创制项目(2017ZX09301003)

Bioinformatics analysis based on circRNA-miRNA-mRNA network construction and immune cell infiltration in atrial fibrillation

Jilin FAN1,Tingting ZHU2,Xiaoling TIAN2,Sijia LIU3,Jing SU3,Shiliang ZHANG3()   

  1. 1.First College of Clinical Medical Sciences,Shandong University of Traditional Chinese Medicine,Jinan 250014,China
    2.Department of Neurosurgery,Affiliated Hospital,Binzhou Medical College,Binzhou 256600,China
    3.Department of Cardiology,Affiliated Hospital,Shandong University of Traditional Chinese Medicine,Jinan 250014,China
  • Received:2021-11-23 Online:2022-11-28 Published:2022-12-07
  • Contact: Shiliang ZHANG E-mail:zhangshiliangsd@126.com

摘要:

目的 采用生物信息学方法挖掘公共数据库,构建房颤(AF)的内源性RNA(ceRNA)免疫调节网络,了解AF的发生发展机制。 方法 从基因表达数据库(GEO)中下载AF患者和健康对照者环状RNA(circRNA)(GSE129409)、微小RNA(miRNA)(GSE28594)和mRNA(GSE41177)基因表达数据。采用R软件中的“limma”数据包鉴定出差异表达的circRNA、miRNA和mRNA,并通过相关数据库进行可视化展示。通过ENCORI、circBank、TargetScan和miRDB数据库预测差异表达的circRNA、miRNA和mRNA之间的调控关系,并基于circRNA-miRNA对和miRNA-mRNA对构建ceRNA调控网络。采用DAVID数据库对差异表达mRNA(DEmRNA)进行基因本体论(GO)和京都基因和基因组百科全书(KEGG)富集分析以注释其功能。采用受试者工作特征(ROC)曲线筛选最佳基因特征并计算ROC曲线下面积(AUC)。采用CIBERSORT软件分析AF中免疫细胞浸润情况。 结果 共鉴定出103个差异circRNAs、37个差异miRNAs和296个mRNAs(|log2(FC)|>1且P<0.05)。其中预测出与差异表达的circRNA相结合的miRNA 589个,将预测得到miRNA与差异表达miRNA(DEmiRNA)取交集获得9个miRNAs,预测出差异表达miRNA的靶基因3 000个,将预测得到的靶基因与差异表达基因(DEGs)取交集获得32个差异基因。最终,建立了1个由7个circRNAs、5个miRNAs和19个mRNAs组成的circRNA-miRNA-mRNA网络。ceRNA网络中的差异基因主要富集在蛋白质降解、细胞的胞吐作用和蛋白酪氨酸激酶活性等生物过程中。KEGG富集分析,DEGs主要富集在趋化因子信号通路、刺猬信号通路、T淋巴细胞受体信号通路和细胞-细胞因子相互作用等信号通路中。ROC曲线,MAL2、STT3B、SHISA3、ZBTB41、CPNE4、EPHA7、hsa_circ_0006562、hsa_circ_0024957、hsa-miR-199a-5p和hsa-miR-142-3p等具有预测AF的潜在价值(AUC>0.8)。 结论 构建 circRNA-miRNA-mRNA网络为AF中RNA相互作用机制研究提供依据, circRNA可能是AF的潜在治疗靶点。

关键词: 房颤, 基因表达数据库, 免疫浸润, 环状RNA, T淋巴细胞

Abstract:

Objective To mine the public databases by using bioinformatics methods and construct the competitive endogenous RNA(ceRNA) immune regulatory network of atrial fibrillation (AF), and to understand the mechanism of occurrence and development of AF. Methods The gene expression data of circular RNA (circRNA)(GSE129409), micro RNA (miRNA) (GSE28594) and mRNA(GSE41177) in the AF patients and healthy controls were downloaded from Gene Expression Omnibus(GEO).The differentially expressed circRNA, miRNA, and mRNA were discovered using the “limma” Data package in R software, and were then visualized by using the pertinent databases. The regulatory relationships between the differentially expressed circRNA, miRNA and mRNA were predicted by ENCORI,circBank,TargetScan and miRDB Databases, and the ceRNA regulatory networks were constructed based on the circRNA-miRNA pairs and the miRNA-mRNA pairs.The DAVID database was used for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of differentially expressed mRNA(DEmRNA) to annotate its functions. The best gene characteristics were screened by receiver operating characteristic curve (ROC) curve and the area under curve(AUC) was calculated. CIBERSORT software was used to analyze the infiltration of the immune cells in AF. Results A total of 103 differential circRNAs, 37 differential miRNAs,and 296 mRNAs were identified (|log2(FC)|>1 and P<0.05), among them 589 miRNAs were predicted to bind to the differentially expressed circRNAs, 9 miRNAs were obtained by intersecting the predicted miRNAs with differentially expressed miRNA(DEmiRNA), 3 000 target genes of differentially expressed miRNAs were predicted, and 32 differential genes were obtained by intersecting the predicted target genes with differentially expressed genes (DEGs). Finally,7 circRNAs,5 miRNAs,and 19 mRNAs were assembled into a circRNA-miRNA-mRNA network. The differential genes in the ceRNA network were mainly enriched in the biological processes such as protein degradation, cytosolic spitting action of cells, and protein tyrosine kinase activity.The KEGG enrichment analysis results showed that the DEGs were mainly enriched in the signaling pathways such as chemokine signaling pathway, hedgehog signaling pathway, T lymphocyte receptor signaling pathway and cell-cytokine interaction. The ROC curve results showed that MAL2, STT3B, SHISA3, ZBTB41, CPNE4, EPHA7, hsa_circ_0006562 hsa_circ_0024957, hsa-miR-199a-5p,and hsa-miR-142-3p were identified as the viable candidates for predicting AF (AUC>0.8). Conclusion The construction of circRNA-miRNA-mRNA network provides a basis for the study of RNA interaction mechanism in AF,and circRNA may be a potential therapeutic target of AF.

Key words: Atrial fibrillation, Gene Expression Omnibus, Immune infiltration, Circular RNA, T lymphocytes

中图分类号: 

  • R541.75