Differential DNA methylation encodes proliferation and senescence programs in human adipose-derived mesenchymal stem cells

Adipose tissue-derived mesenchymal stem cells (ASC’s) constitute a vital population of multipotent cells capable of differentiating into end-organ tissues. However, scientific endeavors to harness the regenerative potential of ASC’s for regenerative medicine are currently limited by an incomplete understanding of the mechanisms that determine cell-lineage commitment and stemness. In the current study, we used reduced representation bisulfite sequencing (RRBS) analysis to identify epigenetic gene targets and cellular processes that are responsive to 5-azathioprine, a potent inducer of DNA methylation. In this manner, we describe specific changes to DNA methylation of ASCs to identify the critical pathways associated with ASC differentiation  . We identified 4,797 differentially-methylated regions (FDR < 0.05) associated with 3,625 genes. Gene set enrichment analysis of the differentially-methylated target promoters identified phagocytosis, type 2 diabetes mellitus, and metabolic pathways as disproportionately hypomethylated, whereas adipocyte differentiation was the top most-enriched pathway to represent genes with hyper-methylated promoters. Interestingly, ZNF11 and ELK4 gene response elements were identified as genomic features most affected by DNA hypo- and hyper-methylation, respectively. Although further validation is needed, the implications of this pilot analysis provide the basis for understanding how epigenetic mechanisms influence the metabolic phenotype, and ultimately regenerative capacity, of ASC’s.