Epigenetic aberrations in human pluripotent stem cells

Bar, Shiran; Benvenisty, Nissim

doi:10.15252/embj.2018101033

Cited by 85 publications

(71 citation statements)

References 185 publications

(280 reference statements)

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“…One example of this integrated head size as a phenotype to study changes occurring in individuals with ASD and macrocephaly [59,60]. These advantages are often also true for iNs derived from patients [39]; however, unlike iNs, iPSCs can recapitulate different in vivo developmental stages and have a methylation profile which resembles that of ESC [61][62][63][64][65]. It is important to note that iPSC do retain a small fraction of methylation markers from the donor, which can differ between different iterations of reprogramming and can depend on the source of the reprogrammed cells used [62,63,65].…”

Section: In Vitro Options For Studying Human Brain Developmentmentioning

confidence: 99%

“…These advantages are often also true for iNs derived from patients [39]; however, unlike iNs, iPSCs can recapitulate different in vivo developmental stages and have a methylation profile which resembles that of ESC [61][62][63][64][65]. It is important to note that iPSC do retain a small fraction of methylation markers from the donor, which can differ between different iterations of reprogramming and can depend on the source of the reprogrammed cells used [62,63,65]. Additionally, iPSCs tend to have lower genetic stability, sometimes leading to multiple unintended copy number variants (CNV) and single nucleotide variants (SNV), which necessitates whole genome sequencing to validate each line [66].…”

Section: In Vitro Options For Studying Human Brain Developmentmentioning

confidence: 99%

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Human in vitro models for understanding mechanisms of autism spectrum disorder

Gordon

Geschwind

2020

Molecular Autism

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Early brain development is a critical epoch for the development of autism spectrum disorder (ASD). In vivo animal models have, until recently, been the principal tool used to study early brain development and the changes occurring in neurodevelopmental disorders such as ASD. In vitro models of brain development represent a significant advance in the field. Here, we review the main methods available to study human brain development in vitro and the applications of these models for studying ASD and other psychiatric disorders. We discuss the main findings from stem cell models to date focusing on cell cycle and proliferation, cell death, cell differentiation and maturation, and neuronal signaling and synaptic stimuli. To be able to generalize the results from these studies, we propose a framework of experimental design and power considerations for using in vitro models to study ASD. These include both technical issues such as reproducibility and power analysis and conceptual issues such as the brain region and cell types being modeled.Early development as a critical period for ASD susceptibility

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Section: In Vitro Options For Studying Human Brain Developmentmentioning

confidence: 99%

Section: In Vitro Options For Studying Human Brain Developmentmentioning

confidence: 99%

Human in vitro models for understanding mechanisms of autism spectrum disorder

Gordon

Geschwind

2020

Molecular Autism

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“…Table 3). In addition to hESCs, imprinted defects have been broadly associated with hiPSCs (46-48) and are one of the major concerns for the downstream applications of these cells (49,50). A few of the imprinted loci showed no or minor abnormalities (e.g.…”

Section: Human Impliconmentioning

confidence: 99%

“…This creates an epigenetic obstacle for their correct use in disease modelling and their application in regenerative medicine (33,46-49). In contrast to blood samples and primary dermal fibroblast, hESCs and hiPSCs exhibit several imprinting defects consistent with the reports in the literature (Suppl.Table 4)(50). This was exacerbated when hESCs were grown in naïve conditions, where loss of methylation in imprinted regions followed the globally reduced levels of DNA methylation typical of cells grown in these culture conditions (42,44).…”

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confidence: 99%

IMPLICON: an ultra-deep sequencing method to uncover DNA methylation at imprinted regions

Klobučar

Kreibich

Krueger

et al. 2020

Preprint

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Genomic imprinting is an epigenetic phenomenon leading to parental allele-specific expression. Dosage of imprinted genes is crucial for normal development and its dysregulation accounts for several human disorders. This unusual expression pattern is mostly dictated by differences in DNA methylation between parental alleles at specific regulatory elements known as imprinting control regions (ICRs). Although several approaches can be used for methylation inspection, we lack an easy and cost-effective method to simultaneously measure DNA methylation at multiple imprinted regions. Here, we present IMPLICON, a new high-throughput method measuring DNA methylation levels at imprinted regions with base-pair resolution and over 1000-fold coverage. We initially designed IMPLICON to look at ICRs in adult tissues of inbred mice. Then, we validated it in hybrid mice from reciprocal crosses for which we could discriminate methylation profiles in the two parental alleles.Lastly, we developed a human version of IMPLICON and detected imprinting errors in embryonic and induced pluripotent stem cells. We also provide rules and guidelines to adapt this method for investigating the DNA methylation landscape of any set of genomic regions.In summary, IMPLICON is a rapid, cost-effective and scalable method, which could become the gold standard in both imprinting research and diagnostics.(OMIM#105830) syndromes caused by defects in the paternal or maternal chr15q11-q13 region, respectively (13,14).Most imprinted genes are located in clusters throughout the genome, containing a cisacting CpG-rich DNA element referred to as imprinting control region (ICR) (reviewed in (1)). The ICR is epigenetically marked by DNA methylation in a parent-of-origin fashion, which correlates with expression and/or silencing of the surrounding imprinted genes.Deletions of ICRs result in the loss of parental allele-specific expression within an imprinted cluster (15,16). ICRs acquire parental-specific DNA methylation in the germline, which are maintained throughout development and adulthood, resisting the global wave of demethylation and de novo methylation steps during early embryonic development (reviewed in (1,17,18)). The preservation of parental allele-specific methylation at ICRs, also known as germline differentially methylated regions (gDMRs), is fundamental for the correct maintenance of imprinted expression throughout life.Despite their importance, there is currently no robust, cost-effective and highthroughput method to assess the methylation status of ICRs across multiple imprinted regions (Suppl . Table 1; reviewed in (19)). The traditional way of measuring DNA methylation is bisulfite sequencing (20). Bisulfite treatment of DNA results in deamination of unmodified cytosines to uracils, whereas methylated cytosines remain unchanged. This is followed by PCR amplification of a region of interest followed by subcloning and Sanger sequencing. This method is laborious and not cost-effective for multiple samples or viewpoints. Alternatively, bisulfite ...

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“…Epigenetic variance also plays an important role in differentiation bias (Adewumi et al, 2007;Bar and Benvenisty, 2019;Lagarkova et al, 2006). These changes vary from DNA methylation or histone modifications (Gifford et al, 2013;Xie et al, 2013), to chromatin remodelling (Dixon et al, 2015) and X-chromosome inactivation (Geens and Chuva De Sousa Lopes, 2017;Salomonis et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

Constitutional activation of BMP4 and WNT signalling in hESC results in impaired mesendoderm differentiation

Markouli

Deckersberg

Dziedzicka

et al. 2020

Preprint

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We identified a human embryonic stem cell subline that fails to respond to the differentiation cues needed to obtain mesendoderm derivatives, differentiating into trophoblast-like cells instead. RNA-sequencing analysis showed that the subline has hyperactivation of the WNT and BMP4 signalling. Modulation of these pathways with small molecules confirmed them as the cause of the differentiation impairment. While activation of WNT and BMP4 in control cells resulted in a loss of mesendoderm differentiation and induction of trophoblast markers, inhibition of these pathways in the subline restored its ability to differentiate. Karyotyping and exome sequencing analysis did not identify any changes in the genome that could account for the pathway deregulation. These findings add to the increasing evidence that different responses of stem cell lines to differentiation protocols are based on genetic and epigenetic factors, inherent to the line or acquired during cell culture.

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Epigenetic aberrations in human pluripotent stem cells

Cited by 85 publications

References 185 publications

Human in vitro models for understanding mechanisms of autism spectrum disorder

Human in vitro models for understanding mechanisms of autism spectrum disorder

IMPLICON: an ultra-deep sequencing method to uncover DNA methylation at imprinted regions

Constitutional activation of BMP4 and WNT signalling in hESC results in impaired mesendoderm differentiation

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