Comprehensive phosphoproteomic profiling of？the？signaling network in？mesenchymal stem cells upon？dimethyl fumarate treatment

Abstract

Mesenchymal stem cells (MSCs), recognized as a promising candidate for treating degenerative diseases, have garnered significant attention from scientists in recent decades. However, a notable concern associated with MSCs is their low stability and viability. In a previous study, we found that dimethyl fumarate (DMF) at 10 μM concentration can enhance the proliferation of MSCs and increase their stability. In this research, we performed protein extraction and digestion on both MSCs and DMF-treated MSCs, subsequently enriching phosphorylated peptides using TiO2 and identifying them through nanoLC-MS/MS, with data analysis carried out using MaxQuant and Perseus. The results revealed 837 phosphorylated peptides, of which 559 exhibited elevated expression levels in DMF-treated MSCs compared to untreated MSCs. These 837 and 559 phosphopeptides corresponded to 466 and 340 phosphoproteins, respectively. Furthermore, network analysis of 559 upregulated phosphopeptides using Reactome identified RNA Binding Motif Protein 39 as a potentially crucial protein in mediating cellular responses, potentially influencing RNA processing events and contributing to the regulation of gene expression. This study underscores the significant impact of DMF treatment on the phosphoproteome of MSCs. Further investigations into these identified pathways could illuminate novel therapeutic strategies and enhance the clinical efficacy of MSC-based treatments.