Genome-Wide DNA Methylation Analysis during Osteogenic Differentiation of Human Bone Marrow Mesenchymal Stem Cells

Abstract

Bone marrow mesenchymal stem cells (BMSCs) nowadays are regarded as promising candidates in cell-based therapy for the regeneration of damaged bone tissues that are either incurable or intractable due to the insufficiency of current therapies. Recent studies suggest that BMSCs differentiate into osteoblasts, and that this differentiation is regulated by some specific patterns of epigenetic modifications, such as DNA methylation. However, the potential role of DNA methylation modification in BMSC osteogenic differentiation is unclear. In this study, we performed a genome-wide study of DNA methylation between the noninduced and induced osteogenic differentiation of BMSCs at day 7. We found that the majority of cytosines in a CpG context were methylated in induced BMSCs. Our results also revealed that, along with the induced osteogenic differentiation in BMSCs, the average genomic methylation levels and CpG methylation in transcriptional factor regions (TFs) were increased, the CpG methylation level of various genomic elements was mainly in the medium-high methylation section, and CpG methylation levels in the repeat element had highly methylated levels. The GO analysis of differentially methylated region- (DMR-) associated genes (DMGs) showed that GO terms, including cytoskeletal protein binding (included in Molecular Function GO terms), skeletal development (included in Biological Process GO terms), mesenchymal cell differentiation (included in Biological Process GO terms), and stem cell differentiation (included in Biological Process), were enriched in the hypermethylated DMGs. Then, the KEGG analysis results showed that the WNT pathway, inositol phosphate metabolism pathway, and cocaine addiction pathway were more correlative with the DMRs during the induced osteogenic differentiation in BMSCs. In conclusion, this study revealed the difference of methylated levels during the noninduced and induced osteogenic differentiation of BMSCs and provided useful information for future works to characterize the important function of epigenetic mechanisms on BMSCs' differentiation.

Dnmt3b ablation impairs fracture repair through upregulation of Notch pathway

“…In addition to Rbpjκ, we recently identified hypomethylation in Cxcl12 gene in Dnmt3b LOF chondrocytes (20), suggesting Dnmt3b LOF could directly modify DNA methylation pattern in chondrocyte maturation-related genes. Findings from other groups also demonstrated that chondrogenic-and osteogenic-related genes could be regulated via alteration of DNA methylation in promoters (41)(42)(43). We thus speculate Dnmt3b LOF leads to progenitor differentiation defect through a combination of an altered Notch pathway and the alteration of DNA methylation in chondrogenic-and osteogenic-specific genes.…”

Shared Genetic and Epigenetic Mechanisms between the Osteogenic Differentiation of Dental Pulp Stem Cells and Bone Marrow Stem Cells

“…RUNX1 involvement in DPSC osteogenesis has not been shown; nevertheless, another member of the RUNX family (RUNX2) could enhance bone deposition and facilitate novel bone formation after transplantation of RUNX2-transfected DPSCs [ 61 ]. Forkhead box protein A1/2 (FOXA1/2) has been reported as hypermethylated in the course of BMSC osteogenesis [ 62 ] and its knockdown promoted BMSC osteodifferentiation [ 63 ], which has still not been reported in DPSCs. Hypoxic conditions are known to promote cell proliferation and enhance the osteogenic differentiation of both BMSC and DPSC by inducing the expression of HIF1A (hypoxia-inducible factor 1-alpha) and upregulating the osteogenic-related genes (e.g., Oct-4, Sox2, c-Myc, RUNX2, and PPAR γ 2) [ 64 – 66 ].…”

Mettl3 Regulates Osteogenic Differentiation and Alternative Splicing of Vegfa in Bone Marrow Mesenchymal Stem Cells

“…While much evidence has demonstrated that the osteogenic differentiation of BMSCs is intimately associated with multiple genetic factors, such as signaling molecules and growth factors, the epigenetic regulatory mechanisms underlying cell differentiation have attracted increasing attention [59,60,61]. Recent evidence has illustrated that epigenetic modifications, such as histone acetylation and DNA methylation, are involved in the cell differentiation process of BMSCs during bone regeneration [62,63]. As another layer of epigenetic regulation (RNA epigenetics), m 6 A modification has recently been reported to play important roles in cell function and the differentiation of embryonic stem cells (ESCs) and various cancer cell types [64,65,66].…”