Differential DNA Methylation Encodes Proliferation and Senescence Programs in Human Adipose-Derived Mesenchymal Stem Cells

Abstract

Adult adipose tissue-derived mesenchymal stem cells (ASCs) constitute a vital population of multipotent cells capable of differentiating into numerous end-organ phenotypes. However, scientific and translational endeavors to harness the regenerative potential of ASCs 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-azacitidine (5-AZA). We describe specific changes to DNA methylation of ASCs, uncovering pathways likely associated with the enhancement of their proliferative capacity. We identified 4,797 differentially methylated regions (FDR < 0.05) associated with 3,625 genes, of which 1,584 DMRs annotated to the promoter region. Gene set enrichment of differentially methylated promoters identified "phagocytosis," "type 2 diabetes," and "metabolic pathways" as disproportionately hypomethylated, whereas "adipocyte differentiation" was the most-enriched pathway among hyper-methylated gene promoters. Weighted coexpression network analysis of DMRs identified clusters associated with cellular proliferation and other developmental programs. Furthermore, the ELK4 binding site was disproportionately hyper-methylated within the promoters of genes associated with AKT signaling. Overall, this study offers numerous preliminary insights into the epigenetic landscape that influences the regenerative capacity of human ASCs.

MiR-200c-3p maintains stemness and proliferative potential in adipose-derived stem cells by counteracting senescence mechanisms

“…ASCs were isolated from abdominal subcutaneous fat liposuction aspirates of five healthy donors who underwent elective plastic surgery. Liposuction aspirates were transferred to the laboratory and processed under sterile conditions within 24 h. Isolation and phenotypic characterization of ASCs were performed as previously described [8]. Briefly, liposuction aspirates were washed extensively with sterile phosphate-buffered saline (PBS) containing 2% penicillin/ streptomycin (PS) and subjected to enzymatic digestion with 0.075% collagenase type I for 30-60 min at 37˚C and 5% CO 2 .…”

“…The replicative senescence is regulated by the p53/p21 pathway, which can be differentially expressed during the in vitro passaging along with the stemness markers [7]. Moreover, there is a plethora of epigenetic-sensitive paths involved in ASC differentiation [8]. Even the immunosuppressive ability of ASCs is cell passage dependent [9].…”

Reconsidering LINE-1’s role in cancer: does LINE-1 function as a reporter detecting early cancer-associated epigenetic signatures?

“…During periods of prolonged proliferation, cells have been observed to deplete their DNA of methylation, an epigenetic mark which generally acts to condense chromatin [ 16 , 26 , 30 ]. Global hypomethylation has also been shown to promote cellular capacity for self-renewal in certain stem cells [ 27 , 28 ]. Whether altered DNA methylation induces or results from cell proliferation, the observation that cancer cells have been found to contain large hypomethylated blocks of DNA encompassing roughly half the genome is well established [ 24 , 25 , 29 ].…”

Clinical epigenetics and restoring of metabolic health in severely obese patients undergoing batriatric and metabolic surgery

“…Obesity has globally reached epidemic proportions, increasing the risk for type 2 diabetes (T2D) and CVDs as major causes of morbidity and mortality worldwide [3]. Advanced epigenomic-based technologies are providing novel insight into the pathogenesis of obesity and CVDs [3][4][5][6][7]. Direct epigenetic marks consist in DNA methylation and histone modification changes occurring as a response to specific environmental exposures, which can affect gene expression programs without modifications in genetic background [8].…”

“…of transcriptional programs underlying oxidative stress, inflammation, and metabolic unbalance which may predispose to obesity [4][5][6][7][8].…”