Pluripotent stem cells escape from senescence-associated DNA methylation changes

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 longterm 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 doxycyclineinducible 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 SADNAm in pluripotent cells may play a central role for their escape from cellular senescence.

A methylome-wide study of aging using massively parallel sequencing of the methyl-CpG-enriched genomic fraction from blood in over 700 subjects

“…These regulatory proteins included transcriptional repressor CTCF, polycomb protein EZH2 and histone 2A member Z. A previous study by Koch et al, using pluripotent stem cells, linked regions of senescence-associated hypomethylation to binding sites for polycomb proteins (49). While we could not access data for all of the polycomb proteins they investigated, both our study and theirs observed focal hypomethylation at EZH2 binding sites.…”

The Polycomb Protein Ezh2 Impacts on Induced Pluripotent Stem Cell Generation

“…iPS cells show high Ezh2 expression (Fig. 1A-D) and also overcome senescence [36]. Therefore, iPS cell generation appears to be linked to high Ezh2 expression.…”

The lncRNA HOTAIR impacts on mesenchymal stem cellsviatriple helix formation

“…Some of these senescence-associated DNAm (SA-DNAm) changes are almost linearly acquired during culture expansion and can therefore be used as biomarker for the state of cellular aging (5–7). Notably, SA-DNAm changes are enriched in developmental genes, such as homeobox genes, and they can be reversed by reprogramming into induced pluripotent stem cells (iPSCs) (4,7,8). This indicates that SA-DNAm changes—and hence also the process of replicative senescence—are somehow regulated, but the underlying mechanism is still unclear.…”