A Temporal Chromatin Signature in Human Embryonic Stem Cells Identifies Regulators of Cardiac Development

Department of Pathology, University of Washington, Seattle, WA 98109, USA
Cell (Impact Factor: 32.24). 09/2012; 151(1):221-32. DOI: 10.1016/j.cell.2012.08.027
Source: PubMed


Directed differentiation of human embryonic stem cells (ESCs) into cardiovascular cells provides a model for studying molecular mechanisms of human cardiovascular development. Although it is known that chromatin modification patterns in ESCs differ markedly from those in lineage-committed progenitors and differentiated cells, the temporal dynamics of chromatin alterations during differentiation along a defined lineage have not been studied. We show that differentiation of human ESCs into cardiovascular cells is accompanied by programmed temporal alterations in chromatin structure that distinguish key regulators of cardiovascular development from other genes. We used this temporal chromatin signature to identify regulators of cardiac development, including the homeobox gene MEIS2. Using the zebrafish model, we demonstrate that MEIS2 is critical for proper heart tube formation and subsequent cardiac looping. Temporal chromatin signatures should be broadly applicable to other models of stem cell differentiation to identify regulators and provide key insights into major developmental decisions.

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Available from: Hans Reinecke, Sep 28, 2015
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    • "We found that concentrations lower than 50 ng/ml activin A did not markedly influence mesoderm specification (supplementary material Fig. S2). Based on previous work on directed differentiation from hESCs, we have established that mesoderm is specified on day 2 of differentiation (Paige et al., 2010, 2012; Palpant et al., 2013). At this time point, analysis of Venus activity showed that differentiation with A 100 caused significantly lower activity of endogenous Wnt/β-catenin signaling than A 50 (Fig. 1A-C). "
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    ABSTRACT: During vertebrate development, mesodermal fate choices are regulated by interactions between morphogens such as activin/nodal, BMPs and Wnt/β-catenin that define anterior-posterior patterning and specify downstream derivatives including cardiomyocyte, endothelial and hematopoietic cells. We used human embryonic stem cells to explore how these pathways control mesodermal fate choices in vitro. Varying doses of activin A and BMP4 to mimic cytokine gradient polarization in the anterior-posterior axis of the embryo led to differential activity of Wnt/β-catenin signaling and specified distinct anterior-like (high activin/low BMP) and posterior-like (low activin/high BMP) mesodermal populations. Cardiogenic mesoderm was generated under conditions specifying anterior-like mesoderm, whereas blood-forming endothelium was generated from posterior-like mesoderm, and vessel-forming CD31(+) endothelial cells were generated from all mesoderm origins. Surprisingly, inhibition of β-catenin signaling led to the highly efficient respecification of anterior-like endothelium into beating cardiomyocytes. Cardiac respecification was not observed in posterior-derived endothelial cells. Thus, activin/BMP gradients specify distinct mesodermal subpopulations that generate cell derivatives with unique angiogenic, hemogenic and cardiogenic properties that should be useful for understanding embryogenesis and developing therapeutics. © 2015. Published by The Company of Biologists Ltd.
    Development 07/2015; 128(19). DOI:10.1242/dev.117010 · 6.46 Impact Factor
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    • "Data are shown as mean ± SEM. See also Figure S6 and Table S3. Figure 7. Epigenetic Regulation Underlying the PDE Expression Pattern in DCM iPSC-CMs and DCM Heart Tissues (A) Designing of ChIP primers in PDE2A gene structure based on key active and repressive histone marker regions of ESCs and ESC-CMs (Paige et al., 2012). (B and C) ChIP-qPCR measurement of histone marker modification levels at region 1 (B) and region 2 (C) of PDE2A gene in iPSC and iPSC-CM cells from both Ctrl and DCM group (*p < 0.05 in two-way ANOVA) (Holm-Sidak method). "
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    ABSTRACT: β-adrenergic signaling pathways mediate key aspects of cardiac function. Its dysregulation is associated with a range of cardiac diseases, including dilated cardiomyopathy (DCM). Previously, we established an iPSC model of familial DCM from patients with a mutation in TNNT2, a sarcomeric protein. Here, we found that the β-adrenergic agonist isoproterenol induced mature β-adrenergic signaling in iPSC-derived cardiomyocytes (iPSC-CMs) but that this pathway was blunted in DCM iPSC-CMs. Although expression levels of several β-adrenergic signaling components were unaltered between control and DCM iPSC-CMs, we found that phosphodiesterases (PDEs) 2A and PDE3A were upregulated in DCM iPSC-CMs and that PDE2A was also upregulated in DCM patient tissue. We further discovered increased nuclear localization of mutant TNNT2 and epigenetic modifications of PDE genes in both DCM iPSC-CMs and patient tissue. Notably, pharmacologic inhibition of PDE2A and PDE3A restored cAMP levels and ameliorated the impaired β-adrenergic signaling of DCM iPSC-CMs, suggesting therapeutic potential. Copyright © 2015 Elsevier Inc. All rights reserved.
    Cell stem cell 06/2015; 17(1). DOI:10.1016/j.stem.2015.04.020 · 22.27 Impact Factor
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    • "Since the study of human development is hampered by limited access to human tissues, particularly of the embryonic stage, understanding cell-lineage-specific differentiation of human ESCs provides an alternative. Indeed, a recent study utilized such a system to investigate human cardiac lineage specification (Paige et al., 2012). Therefore, it is possible that a comprehensive transcriptome characterization of the different developmental stages of endoderm and pancreatic cell lineages would generate a rich resource for understanding the regulatory networks of cell lineage specification and provide additional insights into the mechanism of beta cell differentiation. "
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    ABSTRACT: Long non-coding RNAs (lncRNAs) regulate diverse biological processes, including cell lineage specification. Here, we report transcriptome profiling of human endoderm and pancreatic cell lineages using purified cell populations. Analysis of the data sets allows us to identify hundreds of lncRNAs that exhibit differentiation-stage-specific expression patterns. As a first step in characterizing these lncRNAs, we focus on an endoderm-specific lncRNA, definitive endoderm-associated lncRNA1 (DEANR1), and demonstrate that it plays an important role in human endoderm differentiation. DEANR1 contributes to endoderm differentiation by positively regulating expression of the endoderm factor FOXA2. Importantly, overexpression of FOXA2 is able to rescue endoderm differentiation defects caused by DEANR1 depletion. Mechanistically, DEANR1 facilitates FOXA2 activation by facilitating SMAD2/3 recruitment to the FOXA2 promoter. Thus, our study not only reveals a large set of differentiation-stage-specific lncRNAs but also characterizes a functional lncRNA that is important for endoderm differentiation. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.
    Cell Reports 04/2015; 123(1). DOI:10.1016/j.celrep.2015.03.008 · 8.36 Impact Factor
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