miRNAs as cell-intrinsic epigenetic regulators in muscle in type 2 diabetes

miRNAs are important metabolic regulators and are altered at both the cellular and secreted levels in diseases, including type 2 diabetes (T2D). However, to what extent these alterations are in response to factors in the in vivo milieu or are cell-intrinsic remains unclear. Here we used a disease-in-a-dish model in which iPSCs from T2D patients and controls were differentiated into myoblasts (iMyos), and their cellular and secreted miRNAs were profiled. We found that iMyos from T2D donors exhibit cell-intrinsic alterations in miRNA expression and secretion in small extracellular vesicles (sEVs)/exosomes. Integrating miRNA-predicted targets with transcriptomic and proteomic data revealed that miRNAs altered in T2D iMyos were associated with coordinated changes in their predicted targets, but with a much greater impact on protein than on mRNA levels. This effect was validated by miRNA overexpression in control iMyos. The upregulated miRNAs targeted pathways related to aerobic respiration, membrane trafficking, and RNA metabolism. Even more marked changes were observed in sEV-associated miRNAs secreted by T2D iMyos, indicative of T2D-associated effects on miRNA sorting and release. Target genes of secreted miRNAs altered in T2D iMyos were enriched in metabolic pathways including insulin signaling and mitochondrial metabolism. Consistent with this, sEVs derived from control iMyos increased glucose uptake and mitochondrial function in recipient human white adipocytes, whereas sEVs from T2D iMyos did not. Thus, in T2D, muscle exhibits cell-intrinsic alterations in expression and secretion of miRNAs, which function as epigenetic regulators of protein expression locally, as well as potentially in distal tissues.