Genome-scale DNA methylation pattern profiling of human bone marrow mesenchymal stem cells in long-term culture.
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 ≥ 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.
Department of Molecular and Life Sciences, Hanyang University, Ansan 426-791, Korea.
Mi Ran
MR
Choi
Yong-Ho
YH
In
Jungsun
J
Park
Taesung
T
Park
Kyoung Hwa
KH
Jung
Jin Choul
JC
Chai
Mi Kyung
MK
Chung
Young Seek
YS
Lee
Young Gyu
YG
Chai
D001854:Bone Marrow Cells / Q000378:metabolism*; D019175:DNA Methylation; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D006801:Humans; D059630:Mesenchymal Stem Cells / Q000378:metabolism*; D035683:MicroRNAs; D058977:Molecular Sequence Annotation; D061251:Primary Cell Culture; D011401:Promoter Regions, Genetic; D015203:Reproducibility of Results; D015398:Signal Transduction; D059506:Telomere Shortening
D035683:MicroRNAs