Experimental and Molecular Medicine

Korean Society for Biochemistry and Molecular Biongy (생화학분자생물학회)
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Genome-scale DNA methylation pattern profiling of human bone marrow mesenchymal stem cells in long-term culture

  • Choi, Mi Ran (Department of Molecular and Life Sciences, Hanyang University) ;
  • In, Yong-Ho (Medicinal Bioconvergence Research Center, Seoul National University) ;
  • Park, Jungsun (Medicinal Bioconvergence Research Center, Seoul National University) ;
  • Park, Taesung (Interdisciplinary Program in Bioinformatics, Seoul National University) ;
  • Jung, Kyoung Hwa (Department of Molecular and Life Sciences, Hanyang University) ;
  • Chai, Jin Choul (Department of Molecular and Life Sciences, Hanyang University) ;
  • Chung, Mi Kyung (Fertility Center, CHA Gangnam Medical Center, CHA University) ;
  • Lee, Young Seek (Department of Molecular and Life Sciences, Hanyang University) ;
  • Chai, Young Gyu (Department of Molecular and Life Sciences, Hanyang University)
  • Accepted : 2012.06.05
  • Published : 2012.08.31
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Abstract

Human bone marrow mesenchymal stem cells (MSCs) expanded in vitro exhibit not only a tendency to lose their proliferative potential, homing ability and telomere length but also genetic or epigenetic modifications, resulting in senescence. We compared differential methylation patterns of genes and miRNAs between early-passage [passage 5 (P5)] and late-passage (P15) cells and estimated the relationship between senescence and DNA methylation patterns. When we examined hypermethylated genes (methylation peak ${\geq}$ 2) at P5 or P15, 2,739 genes, including those related to fructose and mannose metabolism and calcium signaling pathways, and 2,587 genes, including those related to DNA replication, cell cycle and the PPAR signaling pathway, were hypermethylated at P5 and P15, respectively. There was common hypermethylation of 1,205 genes at both P5 and P15. In addition, genes that were hypermethylated at P5 (CPEB1, GMPPA, CDKN1A, TBX2, SMAD9 and MCM2) showed lower mRNA expression than did those hypermethylated at P15, whereas genes that were hypermethylated at P15 (MAML2, FEN1 and CDK4) showed lower mRNA expression than did those that were hypermethylated at P5, demonstrating that hypermethylation at DNA promoter regions inhibited gene expression and that hypomethylation increased gene expression. In the case of hypermethylation on miRNA, 27 miRNAs were hypermethylated at P5, whereas 44 miRNAs were hypermethylated at P15. These results show that hypermethylation increases at genes related to DNA replication, cell cycle and adipogenic differentiation due to long-term culture, which may in part affect MSC senescence.

Keywords

Acknowledgement

Supported by : National Research Foundation of Korea (NRF)

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