Transcriptome-wide m6A Methylation Profiling Reveals Regulatory Networks During Endothelial Differentiation of Bone...

BackgroundMesenchymal stem cell (MSC)-derived endothelial-like cells exhibit enhanced angiogenic potential compared with undifferentiated MSCs. However, the role of N6-methyladenosine (m6A) RNA modification in MSC endothelial differentiation remains unclear.MethodsHuman bone marrow-derived MSCs were isolated and induced toward an endothelial phenotype using cytokine-enriched medium. Endothelial differentiation was evaluated using flow cytometry, western blotting, immunofluorescence staining, tube formation assays, and Dil-Ac-LDL uptake assays. MeRIP-seq and RNA-seq were performed to profile transcriptome-wide m6A methylation and gene expression changes. Bioinformatics analyses, including GO enrichment, KEGG pathway analysis, and protein-protein interaction (PPI) network construction, were conducted to identify key regulatory genes and pathways.ResultsFollowing induction, MSCs exhibited endothelial characteristics, including increased expression of CD31 and CD34, enhanced tube formation ability, and increased Dil-Ac-LDL uptake. Transcriptome-wide analysis identified 16,355 differentially methylated peaks and 2,732 differentially expressed genes, including 1,204 differentially methylated and expressed genes (DMEGs). Functional enrichment analysis revealed that DMEGs were mainly associated with extracellular matrix organization, endothelial differentiation, and cell adhesion. PPI network analysis identified a highly interconnected module, and integrin family genes (ITGA1, ITGAV, ITGA11, ITGB5) and ADAMTS2 were identified as key hub genes.ConclusionsThis study provides a transcriptome-wide landscape of m6A methylation during endothelial differentiation of BM-MSCs and identifies key regulatory pathways and hub genes potentially involved in this process. These findings suggest that m6A-mediated epitranscriptomic regulation plays an important role in MSC endothelial differentiation and angiogenesis.