Pluripotent stem cells escape from senescence-associated DNA methylation changes

Genome Res. 2013 Feb;23(2):248-59. doi: 10.1101/gr.141945.112. Epub 2012 Oct 18.

Abstract

Pluripotent stem cells evade replicative senescence, whereas other primary cells lose their proliferation and differentiation potential after a limited number of cell divisions, and this is accompanied by specific senescence-associated DNA methylation (SA-DNAm) changes. Here, we investigate SA-DNAm changes in mesenchymal stromal cells (MSC) upon long-term culture, irradiation-induced senescence, immortalization, and reprogramming into induced pluripotent stem cells (iPSC) using high-density HumanMethylation450 BeadChips. SA-DNAm changes are highly reproducible and they are enriched in intergenic and nonpromoter regions of developmental genes. Furthermore, SA-hypomethylation in particular appears to be associated with H3K9me3, H3K27me3, and Polycomb-group 2 target genes. We demonstrate that ionizing irradiation, although associated with a senescence phenotype, does not affect SA-DNAm. Furthermore, overexpression of the catalytic subunit of the human telomerase (TERT) or conditional immortalization with a doxycycline-inducible system (TERT and SV40-TAg) result in telomere extension, but do not prevent SA-DNAm. In contrast, we demonstrate that reprogramming into iPSC prevents almost the entire set of SA-DNAm changes. Our results indicate that long-term culture is associated with an epigenetically controlled process that stalls cells in a particular functional state, whereas irradiation-induced senescence and immortalization are not causally related to this process. Absence of SA-DNAm in pluripotent cells may play a central role for their escape from cellular senescence.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Aged
  • Cell Line, Transformed
  • Cells, Cultured
  • Cellular Senescence / genetics*
  • Cellular Senescence / radiation effects
  • DNA Methylation* / radiation effects
  • Epigenesis, Genetic / radiation effects
  • Gamma Rays / adverse effects
  • Humans
  • Induced Pluripotent Stem Cells / metabolism
  • Induced Pluripotent Stem Cells / radiation effects
  • Mesenchymal Stem Cells / metabolism
  • Mesenchymal Stem Cells / radiation effects
  • Middle Aged
  • Models, Biological
  • Pluripotent Stem Cells / metabolism*
  • Pluripotent Stem Cells / radiation effects

Associated data

  • GEO/GSE37065
  • GEO/GSE37066
  • GEO/GSE38806