2024, Vol. 28 ›› Issue (36): 5811-5816

Bioinformatics analysis of m6A-associated genes in steroid-induced osteonecrosis of the femoral head

Linghu Xitao1, Gui Jiaqi2, Liang Zhuozhi2, Wa Qingde1, Huang Shuai2   

Abstract: BACKGROUND: m6A modification has been confirmed to play an important role in the occurrence and development of osteonecrosis of the femoral head; however, the role of m6A modification patterns in steroid-induced osteonecrosis of the femoral head remains unknown.
OBJECTIVE: Bioinformatics analysis was performed based on the Gene Expression Omnibus (GEO) database to analyze the differential expression of the m6A gene in steroid-induced osteonecrosis of the femoral head, predict the downstream targeted miRNAs, and investigate the potential pathogenesis.
METHODS: Expressing profiles of mRNA data of steroid-induced osteonecrosis of the femoral head were downloaded from GEO database (GSE123568). Differentially expressed genes (DEGs), Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed using the R software. After obtaining these differentially methylated m6A genes (m6A-DEGs), we analyzed GO function and KEGG pathway enrichment and compared the correlation among the m6A-DEGs typing according to gene expression. The protein-protein interaction network and core gene subnetwork of m6A-DEGs were constructed using Cytoscape software. The m6A-DEGs-associated potential miRNAs were predicted using the TargetScan, miRTarBase, and miRBD databases. Simultaneously, ChIPBase and hTFtarget databases were used to predict potential transcription factors of seven core genes, then m6A-miRNA and transcription factor-m6A regulatory networks were constructed separately. Finally, the expression levels of the seven core m6A-DEGs were verified by using the GSE74089 dataset.
RESULTS AND CONCLUSION: (1) A total of 2 460 common DEGs were screened out from datasets, among which 1 455 genes were upregulated and 1 005 genes were downregulated. (2) A total of 14 m6A-DEGs were identified in the datasets. Among them, 11 m6A-DEGs were up-regulated and 3 m6A-DEGs were down-regulated. Differential gene expression was considered significant for m6A-DEGs in steroid-induced osteonecrosis of the femoral head (P < 0.05). Spearman correlation analysis showed a significant correlation between m6A-DEGs. (3) GO and KEGG enrichment analysis showed that m6A-DEGs were mainly enriched in myeloid cell differentiation and development, immune and cytokine receptor activity, osteoclast differentiation, AMPK signaling pathway and interleukin-17 signaling pathway. (4) The seven core genes of m6A-DEGs contained YTHDF3, YTHDF1, YTHDF2, ALKBH5, METTL3, HNRNPA2B1, and HNRNPC. A total of 44 miRNAs overlapping were detected in the miRTarBase, miRDB, and TargetScan databases. Totally 79 transcription factors overlapping were found in the ChIPBase and hTFtarget databases. (5) The expression levels of six core m6A-DEGs in the GSE74089 dataset were consistent with those in the GSE123568 dataset. (6) These findings confirm that the seven m6A-DEGs identified through bioinformatics techniques play a regulatory role in the expression of various miRNAs, transcription factors, AMPK, and interleukin-17 signaling pathways, and these genes have a significant impact on the differentiation and development of bone marrow cells as well as osteoclast differentiation in steroid-induced osteonecrosis of the femoral head. Consequently, these findings offer data support and establish a research direction for future investigations into the pathogenesis and targeted therapeutic strategies for steroid-induced osteonecrosis of the femoral head.

Key words: steroid-induced osteonecrosis of the femoral head, m6A methylation, microRNA, transcription factor, bioinformatics, differentially expressed gene, gene regulatory network, core gene