Mesenchymal stem cell (MSC)-derived exosomes mediate tissue regeneration in a variety of diseases including ischemic heart injury, liver fibrosis, and cerebrovascular disease. Despite an increasing number of studies reporting the therapeutic effects of MSC exosomes, the underlying molecular mechanisms and their miRNA complement are poorly characterized. Here researchers from SUNY Buffalo profiled microRNA (miRNA) in MSC exosomes and conducted a network analysis to identify the dominant biological processes and pathways modulated by exosomal miRNAs. At a system level, miRNA-targeted genes were enriched for (cardio)vascular and angiogenesis processes in line with observed cardiovascular regenerative effects. Targeted pathways were related to Wnt signaling, pro-fibrotic signaling via TGF-β and PDGF, proliferation, and apoptosis. When tested, MSC exosomes reduced collagen production by cardiac fibroblasts, protected cardiomyocytes from apoptosis, and increased angiogenesis in HUVECs. The intrinsic beneficial effects were further improved by virus-free enrichment of MSC exosomes with network-informed regenerative miRNAs capable of promoting angiogenesis and cardiomyocyte proliferation. The data presented here help define the miRNA landscape of MSC exosomes, establish their biological functions through network analyses at a system level, and provide a platform for modulating the overall phenotypic effects of exosomes.
Processes and pathways targeted by the most abundant miRNAs in MSC exosomes
The 23 most abundant miRNAs contained within MSC exosomes were analyzed using miRDIP to determine the target gene landscape (5,481 genes). Of these, 1,317 were in the top two-thirds in confidence and were further analyzed by PANTHER to identify statistically enriched biological processes and pathways regulated by the target genes. Only GO terms enriched more than one variance above the mean (1.81-fold) and meeting statistical significance (p < 1e-6) were considered likely biological processes and pathways. (A) Enrichment map of biological processes targeted by the top 23 miRNAs in MSC exosomes. Nodes represent the individual genes of significantly enriched biological processes and the miRNAs which target them, connected by the edges. Genes related to the biological processes of vascularization are shown as small red circles, growth-related genes are shown in green circles, and genes with overlapping contributions to vascularization and growth are shown as large red circles. miRNAs targeting similar gene clusters are located in close proximity to one another (e.g., let-7(a,b,i)-5p and hsa-miR-29(a,b)-3p). (B) Enriched biological processes and (C) enriched pathways targeted by the top 23 miRNAs ranked based on significance from high to low. (D) Enrichment map of pathways targeted by the top 23 miRNAs. Nodes represent significantly enriched pathways and the miRNAs which target them.