Epigenetic stability, adaptability, and reversibility in human embryonic stem cells

Abstract

The stability of human embryonic stem cells (hESCs) is of critical importance for both experimental and clinical applications. We find that as an initial response to altered culture conditions, hESCs change their transcription profile for hundreds of genes and their DNA methylation profiles for several genes outside the core pluripotency network. After adaption to conditions of feeder-free defined and/or xeno-free culture systems, expression and DNA methylation profiles are quite stable for additional passaging. However, upon reversion to the original feeder-based culture conditions, numerous transcription changes are not reversible. Similarly, although the majority of DNA methylation changes are reversible, highlighting the plasticity of DNA methylation, a few are persistent. Collectively, this indicates these cells harbor a memory of culture history. For culture-induced DNA methylation changes, we also note an intriguing correlation: hypomethylation of regions 500-2440 bp upstream of promoters correlates with decreased expression, opposite to that commonly seen at promoter-proximal regions. Lastly, changes in regulation of G-coupled protein receptor pathways provide a partial explanation for many of the unique transcriptional changes observed during hESC adaptation and reverse adaptation.demethylation | methylcytosine | G-protein-signaling modulator 3 | murine embryonic fibroblast | hypermethylation

Reversal of dopamine system dysfunction in response to high‐fat diet

“…Epigenetic gene regulation, for example through changes in DNA methylation, presents a pathway whereby organisms can readily adapt to environmental challenges. Epigenetic marks can be maintained across the lifespan (39), and in cultured embryonic stem cells, both reversible and persistent patterns of differential DNA methylation were observed in response to changing environmental conditions (40). These data are the first to demonstrate in vivo a dynamic methylation pattern that changes with the presence or absence of an environmental challenge.…”

An epigenetic perspective on the failing heart and pluripotent-derived-cardiomyocytes for cell replacement therapy

“…That is, both murine and human primed ESCs (most hESC lines), relative to naïve cells, exhibit more heterogeneous expression profiles, often have underwent XCI in female lines, have increased de novo methyl transferase expression, increased class II enhancer marks (poised for activation during differentiation), and a non-uniform differentiation propensity Gafni et al, 2013). So although pluripotency is classically tested as the ability of a stem cell to differentiate into all 3 germ layers and more stringently to form a blastocyst chimera, epigenomic differences whether through crude manipulation of the epigenome (Choi et al, 2004;Yoon et al, 2006;Chow et al, 2013b;Horrillo et al, 2013), adjustments to the microenvironment (Horton et al, 2009;Tompkins et al, 2012), or progressive accumulation of epigenetic changes over passaging (Tanasijevic et al, 2009;Tompkins et al, 2012), can all have defining influences on cell fate.…”

Mutation Frequency Dynamics inHPRTLocus in Culture-Adapted Human Embryonic Stem Cells and Induced Pluripotent Stem Cells Correspond to Their Differentiated Counterparts

“…The demonstration of differences in the APE1 locus might shed light on the differences in MFs; however, the available epigenetic data on hESC adaptation are scarce. Nevertheless, Tompkins et al detected epigenetic changes in genes involved in DNA repair pathways, particularly in BER; they found uracil-N-glycosylase to be differentially regulated in adapted hESCs [51]. Moreover, the dose of reprogramming factors appears to affect CNVs [52], indicating a connection between epigenetics and genomic stability.…”