Identification and analysis of potential key genes in osteonecrosis of the femoral head based on miRNA-mRNA regulatory network

doi:10.12307/2022.357

Abstract

Abstract: BACKGROUND: MicroRNAs (miRNAs) have been confirmed to be involved in the pathogenesis, prevention, and treatment of osteonecrosis of the femoral head. However, the mechanism is not yet elucidated.
OBJECTIVE: To screen miRNA-mRNA regulatory pairs related to osteonecrosis of the femoral head, to explain its potential mechanism, based on microarray data in the GEO database.
METHODS: The miRNA microarray dataset (GSE89587) and mRNA microarray dataset (GSE74089) were retrieved from NCBI GEO database. Then, we identified the differentially expressed miRNAs and mRNAs for each dataset by the Limma package in R software. Potential downstream targets of these differentially expressed miRNAs were predicted using miRDB, miRTarbase, and TargetScan databases. Based on the relationship among miRNA and mRNA, the miRNA-mRNA regulatory network was visualized using Cytoscape. Next, gene ontology function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of target genes in the regulatory network were carried out by clusterProfiler package in R software. Protein-protein interaction network was constructed by using the Search Tool for the Retrival of Interacting Genes/Protein (STRING) database.
RESULTS AND CONCLUSION: In total, 23 differentially expressed miRNAs, including 10 upregulated (e.g., hsa-miR-4325, hsa-miR-3654) and 13 downregulated miRNAs (e.g., hsa-miR-4680-5p, hsa-miR-4711-3p), were identified. Totally 3992 differentially expressed mRNAs, including 2503 upregulated (e.g., TGFBI, AMTN) and 1489 downregulated (e.g., MSMP, FLJ35424) mRNAs, were screened by the Limma package in R software. 255 miRNA downstream target genes predicted co-existed in miRDB, miRTarbase, and TargetScan databases, and 10 miRNAs (e.g., hsa-miR-3920, hsa-miR-3675-5p) and 34 mRNAs (e.g., MAPK6, SP1 ) were sorted out to construct regulatory networks. These screened targets mainly were significantly enriched in the regulation of mRNA stability and transforming growth factor-β signaling pathway and autophagy. DDX3X, HNRNPC, and SP1 were analyzed as the hub genes in protein-protein interactions, which may be the target genes for osteonecrosis of the femoral head. In summary, the miRNA-mRNA regulatory network constructed in this study clarifies that miR-4725-3p may target ONFH by inhibiting SP1-mediated transforming growth factor-β signaling pathway, providing a strong data support and research direction for the prevention and treatment of ONFH.

Key words: osteonecrosis of the femoral head, GEO database, differentially expressed gene, regulatory network, miRNA-mRNA, gene, protein, bioinformatics

CLC Number:

Liang Xuezhen, Xie Guoxin, Li Jiacheng, Wen Mingtao, Xu Bo, Li Gang. Identification and analysis of potential key genes in osteonecrosis of the femoral head based on miRNA-mRNA regulatory network[J]. Chinese Journal of Tissue Engineering Research, 2022, 26(11): 1720-1727.

Figures/Tables 12

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