Identification of ceRNA networks in type H and L vascular endothelial cells through integrated bioinformatics methods
10.11817/j.issn.1672-7347.2024.230343
- VernacularTitle: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
- Author:
Zhi LIU
1
;
Zhe RUAN
;
Haitao LONG
;
Ruibo ZHAO
;
Yong ZHU
;
Zhangyuan LIN
;
Peng CHEN
;
Shushan ZHAO
Author Information
1. 中南大学湘雅医院骨科,长沙 410008
- Keywords:
bone vessels;
type H vascular endothelial cells;
ceRNA network;
bioinformatics
- From:
Journal of Central South University(Medical Sciences)
2024;49(4):562-577
- CountryChina
- Language:Chinese
-
Abstract:
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 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. 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.
