通过整合的生物信息学方法鉴定H和L型血管内皮细胞中的ceRNA网络  

Identification of ceRNA networks in type H and L vascular endothelial cells through integrated bioinformatics methods

作　　者：刘志 阮哲 龙海涛[1] 赵瑞波[1] 朱勇[1] 林涨源[1] 陈鹏[1,2] 赵树山 LIU Zhi;RUAN Zhe;LONG Haitao;ZHAO Ruibo;ZHU Yong;LIN Zhangyuan;CHEN Peng;ZHAO Shushan(Department of Orthopaedics,Xiangya Hospital,Central South University,Changsha 410008;National Clinical Research Center for Geriatric Disorders,Xiangya Hospital,Central South University,Changsha 410008,China)

机构地区：[1]中南大学湘雅医院骨科,长沙410008 [2]国家老年疾病临床医学研究中心(湘雅医院),长沙410008

出　　处：《中南大学学报（医学版）》2024年第4期562-577,共16页Journal of Central South University ：Medical Science

基　　金：supported by the National Natural Science Foundation (81902222);the Natural Science Foundation of Hunan Province (2020JJ4928),China。

摘　　要：目的:H型血管是一种骨特异性微血管亚型(CD31hiEmcnhi),在成血管-成骨耦联机制中具有重要的调节作用。研究报道H和L型血管在骨骼生理和病理条件下发挥不同的作用,它们之间的遗传差异仍有待阐明。本研究旨在通过整合的生物信息学方法构建H和L型血管内皮细胞中关键差异表达(differential expression,DE)基因的竞争性内源RNA(competitive endogenous RNA,ceRNA)网络。方法:从ArrayExpress和基因表达综合(Gene Expression Omnibus,GEO)数据库中下载相关原始数据,通过Limma R-Bioconductor包筛选H和L型血管间的DE lncRNAs、DE miRNAs和DE mRNAs,构建总ceRNA网络,随后根据蛋白质相互作用(protein-protein interaction,PPI)网络筛选出上调和下调的关键基因,以此精细化ceRNA网络并对关键基因进行富集分析。最后,通过流式细胞术和real time RT-PCR进行随机验证。结果:共鉴定出1 761个DE mRNAs、187个DE lncRNAs和159个DE miRNAs,通过相互作用关系构建总ceRNA网络;通过PPI网络筛选出6个上调(Itga5、Kdr、Tjp1、Pecam1、Cdh5、Ptk2)和2个下调(Csf1r、Il10)的关键基因,并以此构建关键基因相关的ceRNA亚网络。上调的关键基因主要富集在血管生成与血管凋亡的负调控;流式细胞术和real-time RT-PCR的结果与生物信息学分析结果一致。结论:本研究根据所筛选的关键基因提出上调和下调的H型和L型血管内皮细胞相关的ceRNA网络,为H型和L型血管内皮细胞在骨代谢中的调控机制提供了新见解。Objective:Type H blood vessels are a subtype of bone-specific microvessels(CD31hiEmcnhi)that play an important regulatory role in the coupling of angiogenesis and osteogenesis.Despite reports on the distinct roles of type H and L vessels under physiological and pathological bone conditions,their genetic differences remain to be elucidated.This study aims to construct a competitive endogenous RNA(ceRNA)network of key gene for differencial expression(DE)in type H and L vascular endothelial cells(ECs)through integrated bioinformatic methods.Methods:We downloaded relevant raw data from the ArrayExpress and the Gene Expression Omnibus(GEO)database and used the Limma R-Bioconductor package to screen for DE lncRNAs,DE miRNAs,and DE mRNAs between type H and L vascular ECs.A total ceRNA network was constructed based on their interactions,followed by refinement using protein-protein interaction(PPI)networks to select upregulated and downregulated key genes.Enrichment analysis was performed on these key genes.Random validation was conducted using flow cytometry and real-time RT-PCR.Results:A total of 1761 DE mRNAs,187 DE lncRNAs,and 159 DE miRNAs were identified,and a comprehensive ceRNA network was constructed based on their interactions.Six upregulated(Itga5,Kdr,Tjp1,Pecam1,Cdh5,and Ptk2)and 2 downregulated(Csf1r and Il10)key genes were selected via PPI network to construct a subnetwork of ceRNAs related to these key genes.Upregulated key genes were mainly enriched in negative regulation of angiogenesis and vascular apoptosis.Results from flow cytometry and real-time RT-PCR were consistent with bioinformatics analysis.Conclusion:This study proposes a ceRNA network associated with upregulated and downregulated type H and L vascular ECs based on selected key genes,providing new insights into the regulatory mechanisms of type H and L vascular ECs in bone metabolism.

关 键 词：骨骼血管 H型血管内皮细胞 ceRNA网络 生物信息学 

分 类 号：R336[医药卫生—人体生理学]