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

Q3 Medicine

中南大学学报(医学版) Pub Date : 2024-04-28 DOI:10.11817/j.issn.1672-7347.2024.230343

Zhi Liu, Zhe Ruan, Haitao Long, Ruibo Zhao, Yong Zhu, Zhangyuan Lin, Peng Chen, Shushan Zhao

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引用次数: 0

Abstract

Objectives: Type H blood vessels are a subtype of bone-specific microvessels (CD31^hiEmcn^hi) 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 1 761 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.

Conclusions: 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.

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通过综合生物信息学方法识别 H 型和 L 型血管内皮细胞中的 ceRNA 网络。

目的：H 型血管是骨特异性微血管（CD31hiEmcnhi）的一种亚型，在血管生成和骨生成的耦合过程中发挥着重要的调节作用。尽管有报道称 H 型血管和 L 型血管在生理和病理骨条件下发挥着不同的作用，但它们的遗传差异仍有待阐明。本研究旨在通过综合生物信息学方法，构建H型和L型血管内皮细胞（ECs）差异表达（DE）关键基因的竞争性内源性RNA（ceRNA）网络：我们从ArrayExpress和Gene Expression Omnibus（GEO）数据库中下载了相关原始数据，并使用Limma R-Bioconductor软件包筛选了H型和L型血管内皮细胞中的DE lncRNAs、DE miRNAs和DE mRNAs。根据它们之间的相互作用构建了一个总的 ceRNA 网络，然后利用蛋白质-蛋白质相互作用（PPI）网络进行细化，以选择上调和下调的关键基因。对这些关键基因进行了富集分析。使用流式细胞仪和实时 RT-PCR 进行随机验证：结果：共鉴定出 1 761 个 DE mRNA、187 个 DE lncRNA 和 159 个 DE miRNA，并根据它们之间的相互作用构建了一个全面的 ceRNA 网络。通过PPI网络筛选出6个上调（Itga5、Kdr、Tjp1、Pecam1、Cdh5和Ptk2）和2个下调（Csf1r和Il10）的关键基因，构建了与这些关键基因相关的ceRNA子网络。上调的关键基因主要富集在血管生成和血管凋亡的负调控中。流式细胞术和实时 RT-PCR 的结果与生物信息学分析一致：本研究根据选定的关键基因，提出了与H型和L型血管内皮细胞上调和下调相关的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的见解。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

中南大学学报(医学版) Medicine-Medicine (all)

CiteScore

1.00

自引率

0.00%

发文量

8237

期刊介绍： Journal of Central South University (Medical Sciences), founded in 1958, is a comprehensive academic journal of medicine and health sponsored by the Ministry of Education and Central South University. The journal has been included in many important databases and authoritative abstract journals at home and abroad, such as the American Medline, Pubmed and its Index Medicus (IM), the Netherlands Medical Abstracts (EM), the American Chemical Abstracts (CA), the WHO Western Pacific Region Medical Index (WPRIM), and the Chinese Science Citation Database (Core Database) (CSCD); it is a statistical source journal of Chinese scientific and technological papers, a Chinese core journal, and a "double-effect" journal of the Chinese Journal Matrix; it is the "2nd, 3rd, and 4th China University Excellent Science and Technology Journal", "2008 China Excellent Science and Technology Journal", "RCCSE China Authoritative Academic Journal (A+)" and Hunan Province's "Top Ten Science and Technology Journals". The purpose of the journal is to reflect the new achievements, new technologies, and new experiences in medical research, medical treatment, and teaching, report new medical trends at home and abroad, promote academic exchanges, improve academic standards, and promote scientific and technological progress.