Recurrent Variations in DNA Methylation in Human Pluripotent Stem Cells and Their Differentiated Derivatives

Center for Regenerative Medicine, Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
Cell stem cell (Impact Factor: 22.27). 05/2012; 10(5):620-34. DOI: 10.1016/j.stem.2012.02.013
Source: PubMed


Human pluripotent stem cells (hPSCs) are potential sources of cells for modeling disease and development, drug discovery, and regenerative medicine. However, it is important to identify factors that may impact the utility of hPSCs for these applications. In an unbiased analysis of 205 hPSC and 130 somatic samples, we identified hPSC-specific epigenetic and transcriptional aberrations in genes subject to X chromosome inactivation (XCI) and genomic imprinting, which were not corrected during directed differentiation. We also found that specific tissue types were distinguished by unique patterns of DNA hypomethylation, which were recapitulated by DNA demethylation during in vitro directed differentiation. Our results suggest that verification of baseline epigenetic status is critical for hPSC-based disease models in which the observed phenotype depends on proper XCI or imprinting and that tissue-specific DNA methylation patterns can be accurately modeled during directed differentiation of hPSCs, even in the presence of variations in XCI or imprinting.

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    • "Tissue-specific silencing of paternal Gsa most likely takes place after 11 weeks postfertilization and after tissue differentiation (Turan et al., 2014; Zheng et al., 2001). A genome-wide DNA methylation revealed the maintenance of GNAS methylation in hiPSCs with culture , although hypermethylation and hypomethylation were also observed (Nazor et al., 2012). "
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    ABSTRACT: Data from the literature indicate that genomic imprint marks are disturbed in human pluripotent stem cells (PSCs). GNAS is an imprinted locus that produces one biallelic (Gsα) and four monoallelic (NESP55, GNAS-AS1, XLsα, and A/B) transcripts due to differential methylation of their promoters (DMR). To document imprinting at the GNAS locus in PSCs, we studied GNAS locus DMR methylation and transcript (NESP55, XLsα, and A/B) expression in human embryonic stem cells (hESCs) and human induced pluripotent stem cells (hiPSCs) derived from two human fibroblasts and their progenies. Results showed that (1) methylation at the GNAS locus DMRs is DMR and cell line specific, (2) changes in allelic transcript expression can be independent of a change in allele-specific DNA methylation, and (3) interestingly, methylation at A/B DMR is correlated with A/B transcript expression. These results indicate that these models are valuable to study the mechanisms controlling GNAS methylation, factors involved in transcript expression, and possibly mechanisms involved in the pathophysiology of pseudohypoparathyroidism type 1B.
    Stem Cell Reports 09/2014; 3(3):432-43. DOI:10.1016/j.stemcr.2014.07.002
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    • "Serial cell passage in vitro is known to change the methylation profiles of cultured cells [30]–[32]. We confirmed this finding in this study as we observed hyper-methylation in in vitro samples compared to PTs and progressive hyper-methylation with serial passage in vitro. "
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    ABSTRACT: In vitro and in vivo models are widely used in cancer research. Characterizing the similarities and differences between a patient's tumor and corresponding in vitro and in vivo models is important for understanding the potential clinical relevance of experimental data generated with these models. Towards this aim, we analyzed the genomic aberrations, DNA methylation and transcriptome profiles of five parental tumors and their matched in vitro isolated glioma stem cell (GSC) lines and xenografts generated from these same GSCs using high-resolution platforms. We observed that the methylation and transcriptome profiles of in vitro GSCs were significantly different from their corresponding xenografts, which were actually more similar to their original parental tumors. This points to the potentially critical role of the brain microenvironment in influencing methylation and transcriptional patterns of GSCs. Consistent with this possibility, ex vivo cultured GSCs isolated from xenografts showed a tendency to return to their initial in vitro states even after a short time in culture, supporting a rapid dynamic adaptation to the in vitro microenvironment. These results show that methylation and transcriptome profiles are highly dependent on the microenvironment and growth in orthotopic sites partially reverse the changes caused by in vitro culturing.
    PLoS ONE 04/2014; 9(4):e94045. DOI:10.1371/journal.pone.0094045
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    • "Various trials and studies have been performed to overcome immune rejection from allogeneic hES derived tissues such as neurons or blood cell transplantation [21, 22]. Again, iPSC is competent enough to perform human disease modeling and tissue regeneration for cell transplantation [15, 23]. "
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    ABSTRACT: Induced pluripotent stem cell (iPSC) technology has shown us great hope to treat various human diseases which have been known as untreatable and further endows personalized medicine for future therapy without ethical issues and immunological rejection which embryonic stem cell (hES) treatment has faced. It has been agreed that iPSCs knowledge can be harnessed from disease modeling which mimics human pathological development rather than trials utilizing conventional rodent and cell lines. Now, we can routinely generate iPSC from patient specific cell sources, such as skin fibroblast, hair follicle cells, patient blood samples and even urine containing small amount of epithelial cells. iPSC has both similarity and dissimilarity to hES. iPSC is similar enough to regenerate tissue and even full organism as ES does, however what we want for therapeutic advantage is limited to regenerated tissue and lineage specific differentiation. Depending on the lineage and type of cells, both tissue memory containing (DNA rearrangement/epigenetics) and non-containing iPSC can be generated. This makes iPSC even better choice to perform disease modeling as well as cell based therapy. Tissue memory containing iPSC from mature leukocytes would be beneficial for curing cancer and infectious disease. In this review, the benefit of iPSC for translational approaches will be presented.
    Blood Research 03/2014; 49(1):7-14. DOI:10.5045/br.2014.49.1.7
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Questions & Answers about this publication

  • Jeanne F Loring added an answer in DNA Methylation:
    The Cancer Genome Atlas (TCGA) and Illumina Human Methylation CpG Island Identifiers
    I am examining the TCGA Methylation (Glioblastoma multiforme) dataset, to assess whether we can use it as a means for identification of potential biomarkers for clinical development. The issue I have is that we, ourselves, don't (at least yet) run our own chips here, nor have we done any Illumina assay chip designs.

    Is there a readily-available public reference-list database that I've missed, which will allow me to bridge from the Illumina Human Methylation 27/450 CG# identifier codes back to standard NCBI Gene/RefSeq? I recall that, in the early days of TaqMan assay development, the exact targets of the SNP assays were all proprietary, and the marriage of those assays to Illumina sequence identifiers was sometimes challenging, if one needed to identify actual targets to assess biological plausibility/relevance...
    Jeanne F Loring
    If you're interested in a non-cancer dataset, we have Illumina gene expression array data and 450K methylation data linked in our paper on human pluripotent stem cells: