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Schacker M, Cheng YH, Eckersley-Maslin M, Snaith RM, Colledge WH. Hypermethylation and reduced expression of Gtl2, Rian and Mirg at the Dlk1-Dio3 imprinted locus as a marker for poor developmental potential of mouse embryonic stem cells. Stem Cell Res 2020; 48:101931. [PMID: 32822966 PMCID: PMC7567021 DOI: 10.1016/j.scr.2020.101931] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 07/19/2020] [Accepted: 07/22/2020] [Indexed: 01/10/2023] Open
Abstract
Reduced expression of Gtl2, Rian and Mirg in ES cells compromised survival of chimaeric fetuses. Reduced expression of Gtl2, Rian and Mirg was associated with hypermethylation. Compromised ES cells can be identified and eliminated from experiments to reduce animal use.
Mouse embryonic stem cells (ESCs) have played a crucial role in biomedical research where they can be used to elucidate gene function through the generation of genetically modified mice. A critical requirement for the success of this technology is the ability of ESCs to contribute to viable chimaeras with germ-line transmission of the genetically modified allele. We have identified several ESC clones that cause embryonic death of chimaeras at mid to late gestation stages. These clones had a normal karyotype, were pathogen free and their in vitro differentiation potential was not compromised. Chimaeric embryos developed normally up to E13.5 but showed a significant decrease in embryo survival by E17.5 with frequent haemorrhaging. We investigated the relationship between the ESCs transcriptional and epigenomic state and their ability to contribute to viable chimaeras. RNA sequencing identified four genes (Gtl2, Rian, Mirg and Rtl1as) located in the Dlk1-Dio3 imprinted locus that were expressed at lower levels in the compromised ESC clones and this was confirmed by qRT-PCR. Bisulphite sequencing analysis showed significant hypermethylation at the Dlk1-Dio3 imprinted locus with no consistent differences in methylation patterns at other imprinted loci. Treatment of the compromised ESCs with 5-azacytidine reactivated stable expression of Gtl2 and rescued the lethal phenotype but only gave low level chimaeras.
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Affiliation(s)
- Maria Schacker
- Reproductive Physiology Group, Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK
| | - Yi-Han Cheng
- Medimmune, Sir Aaron Klug Building, Granta Park, Cambridge CB21 6GH, UK
| | | | | | - William Henry Colledge
- Reproductive Physiology Group, Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK.
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Plausible Links Between Metabolic Networks, Stem Cells, and Longevity. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1201:355-388. [PMID: 31898793 DOI: 10.1007/978-3-030-31206-0_15] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Aging is an inevitable consequence of life, and all multicellular organisms undergo a decline in tissue and organ functions as they age. Several well-known risk factors, such as obesity, diabetes, and lack of physical activity that lead to the cardiovascular system, decline and impede the function of vital organs, ultimately limit overall life span. Over recent years, aging research has experienced an unparalleled growth, particularly with the discovery and recognition of genetic pathways and biochemical processes that control to some extent the rate of aging.In this chapter, we focus on several aspects of stem cell biology and aging, beginning with major cellular hallmarks of aging, endocrine regulation of aging and its impact on stem cell compartment, and mechanisms of increased longevity. We then discuss the role of epigenetic modifications associated with aging and provide an overview on a most recent search of antiaging modalities.
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Fattahi A, Latifi Z, Ghasemnejad T, Nejabati HR, Nouri M. Insights into in vitro spermatogenesis in mammals: Past, present, future. Mol Reprod Dev 2017; 84:560-575. [DOI: 10.1002/mrd.22819] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 04/03/2017] [Accepted: 04/17/2017] [Indexed: 12/23/2022]
Affiliation(s)
- Amir Fattahi
- Institute for Stem Cell and Regenerative Medicine; Tabriz University of Medical Sciences; Tabriz Iran
- Department of Reproductive Biology, Faculty of Advanced Medical Sciences; Tabriz University of Medical Sciences; Tabriz Iran
| | - Zeinab Latifi
- Department of Clinical Biochemistry, Faculty of Medicine; Tabriz University of Medical Sciences; Tabriz Iran
| | - Tohid Ghasemnejad
- Women's Reproductive Health Research Center; Tabriz University of Medical Sciences; Tabriz Iran
| | - Hamid Reza Nejabati
- Women's Reproductive Health Research Center; Tabriz University of Medical Sciences; Tabriz Iran
| | - Mohammad Nouri
- Department of Reproductive Biology, Faculty of Advanced Medical Sciences; Tabriz University of Medical Sciences; Tabriz Iran
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Sirt1 Regulates DNA Methylation and Differentiation Potential of Embryonic Stem Cells by Antagonizing Dnmt3l. Cell Rep 2017; 18:1930-1945. [DOI: 10.1016/j.celrep.2017.01.074] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Revised: 12/20/2016] [Accepted: 01/27/2017] [Indexed: 11/18/2022] Open
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5
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Marášek P, Dzijak R, Studenyak I, Fišerová J, Uličná L, Novák P, Hozák P. Paxillin-dependent regulation of IGF2 and H19 gene cluster expression. J Cell Sci 2015; 128:3106-16. [PMID: 26116569 PMCID: PMC4541046 DOI: 10.1242/jcs.170985] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 05/31/2015] [Indexed: 12/15/2022] Open
Abstract
Paxillin (PXN) is a focal adhesion protein that has been implicated in signal transduction from the extracellular matrix. Recently, it has been shown to shuttle between the cytoplasm and the nucleus. When inside the nucleus, paxillin promotes cell proliferation. Here, we introduce paxillin as a transcriptional regulator of IGF2 and H19 genes. It does not affect the allelic expression of the two genes; rather, it regulates long-range chromosomal interactions between the IGF2 or H19 promoter and a shared distal enhancer on an active allele. Specifically, paxillin stimulates the interaction between the enhancer and the IGF2 promoter, thus activating IGF2 gene transcription, whereas it restrains the interaction between the enhancer and the H19 promoter, downregulating the H19 gene. We found that paxillin interacts with cohesin and the mediator complex, which have been shown to mediate long-range chromosomal looping. We propose that these interactions occur at the IGF2 and H19 gene cluster and are involved in the formation of loops between the IGF2 and H19 promoters and the enhancer, and thus the expression of the corresponding genes. These observations contribute to a mechanistic explanation of the role of paxillin in proliferation and fetal development.
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Affiliation(s)
- Pavel Marášek
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics AS CR, Prague 142 20, Czech Republic Faculty of Science, Charles University in Prague, Prague 128 43, Czech Republic
| | - Rastislav Dzijak
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics AS CR, Prague 142 20, Czech Republic Department of Genome Integrity, Institute of Molecular Genetics AS CR, Prague 142 20, Czech Republic
| | - Irina Studenyak
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics AS CR, Prague 142 20, Czech Republic
| | - Jindřiška Fišerová
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics AS CR, Prague 142 20, Czech Republic
| | - Lívia Uličná
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics AS CR, Prague 142 20, Czech Republic
| | - Petr Novák
- Laboratory of Structural Biology and Cell Signaling, Institute of Microbiology AS CR, Prague 142 00, Czech Republic
| | - Pavel Hozák
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics AS CR, Prague 142 20, Czech Republic
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6
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Implications of epigenetics in tissue engineering. Tissue Eng Regen Med 2015. [DOI: 10.1007/s13770-014-0419-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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7
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Kimura Y, Oda M, Nakatani T, Sekita Y, Monfort A, Wutz A, Mochizuki H, Nakano T. CRISPR/Cas9-mediated reporter knock-in in mouse haploid embryonic stem cells. Sci Rep 2015; 5:10710. [PMID: 26039937 PMCID: PMC4454075 DOI: 10.1038/srep10710] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 04/29/2015] [Indexed: 12/26/2022] Open
Abstract
Mouse parthenogenetic haploid embryonic stem cells (ESCs) are pluripotent cells generated from chemically activated oocytes. Haploid ESCs provide an opportunity to study the effect of genetic alterations because of their hemizygotic characteristics. However, their further application for the selection of unique phenotypes remains limited since ideal reporters to monitor biological processes such as cell differentiation are missing. Here, we report the application of CRISPR/Cas9-mediated knock-in of a reporter cassette, which does not disrupt endogenous target genes in mouse haploid ESCs. We first validated the system by inserting the P2A-Venus reporter cassette into the housekeeping gene locus. In addition to the conventional strategy using the Cas9 nuclease, we employed the Cas9 nickase and truncated sgRNAs to reduce off-target mutagenesis. These strategies induce targeted insertions with an efficiency that correlated with sgRNA guiding activity. We also engineered the neural marker gene Sox1 locus and verified the precise insertion of the P2A-Venus reporter cassette and its functionality by monitoring neural differentiation. Our data demonstrate the successful application of the CRISPR/Cas9-mediated knock-in system for establishing haploid knock-in ESC lines carrying gene specific reporters. Genetically modified haploid ESCs have potential for applications in forward genetic screening of developmental pathways.
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Affiliation(s)
- Yasuyoshi Kimura
- Department of Pathology
- Department of Neurology, Graduate School of Medicine
| | - Masaaki Oda
- Department of Pathology
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | | | - Yoichi Sekita
- Department of Pathology
- Department of Biosciences, Kitasato University School of Science, Kanagawa, Japan
| | - Asun Monfort
- Institute of Molecular Health Sciences, Swiss Federal Institute of Technology, ETH Zürich, Hönggerberg, 8049 Zürich, Switzerland
| | - Anton Wutz
- Institute of Molecular Health Sciences, Swiss Federal Institute of Technology, ETH Zürich, Hönggerberg, 8049 Zürich, Switzerland
| | | | - Toru Nakano
- Department of Pathology
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
- JST, CREST.
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Xie P, Sun Y, Ouyang Q, Hu L, Tan Y, Zhou X, Xiong B, Zhang Q, Yuan D, Pan Y, Liu T, Liang P, Lu G, Lin G. Physiological oxygen prevents frequent silencing of the DLK1-DIO3 cluster during human embryonic stem cells culture. Stem Cells 2014; 32:391-401. [PMID: 24123616 DOI: 10.1002/stem.1558] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 07/28/2013] [Accepted: 08/25/2013] [Indexed: 12/18/2022]
Abstract
Genetic and epigenetic alterations are observed in long-term culture (>30 passages) of human embryonic stem cells (hESCs); however, little information is available in early cultures. Through a large-scale gene expression analysis between initial-passage hESCs (ihESCs, <10 passages) and early-passage hESCs (ehESCs, 20-30 passages) of 12 hESC lines, we found that the DLK1-DIO3 gene cluster was normally expressed and showed normal methylation pattern in ihESC, but was frequently silenced after 20 passages. Both the DLK1-DIO3 active status in ihESCs and the inactive status in ehESCs were inheritable during differentiation. Silencing of the DLK1-DIO3 cluster did not seem to compromise the multilineage differentiation ability of hESCs, but was associated with reduced DNA damage-induced apoptosis in ehESCs and their differentiated hepatocyte-like cell derivatives, possibly through attenuation of the expression and phosphorylation of p53. Furthermore, we demonstrated that 5% oxygen, instead of the commonly used 20% oxygen, is required for preserving the expression of the DLK1-DIO3 cluster. Overall, the data suggest that active expression of the DLK1-DIO3 cluster represents a new biomarker for epigenetic stability of hESCs and indicates the importance of using a proper physiological oxygen level during the derivation and culture of hESCs.
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Affiliation(s)
- Pingyuan Xie
- Institute of Reproductive & Stem Cell Engineering, Central South University, Changsha, China; Key Laboratory of Stem Cells and Reproductive Engineering, Ministry of Health, Changsha, China
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9
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Variable allelic expression of imprinted genes in human pluripotent stem cells during differentiation into specialized cell types in vitro. Biochem Biophys Res Commun 2014; 446:493-8. [DOI: 10.1016/j.bbrc.2014.02.141] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 02/28/2014] [Indexed: 12/27/2022]
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10
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Schneider G, Bowser MJ, Shin DM, Barr FG, Ratajczak MZ. The paternally imprinted DLK1-GTL2 locus is differentially methylated in embryonal and alveolar rhabdomyosarcomas. Int J Oncol 2013; 44:295-300. [PMID: 24173021 PMCID: PMC3867365 DOI: 10.3892/ijo.2013.2153] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 10/01/2013] [Indexed: 01/04/2023] Open
Abstract
Parental imprinting of differentially methylated regions (DMRs) contributes to appropriate expression of several developmentally important genes from paternally or maternally derived chromosomes. Rhabdomyosarcoma (RMS) is the most common soft-tissue sarcoma in children and is associated with altered expression of certain parentally imprinted genes. As previously reported, RMS cells display loss of imprinting (LOI) of the DMR at the IGF2-H19 locus, resulting in insulin-like growth factor 2 (IGF2) transcription from both paternally and maternally inherited chromosomes, and overall IGF2 overexpression. As the DLK1-GTL2 locus is structurally similar to the IGF2-H19 locus, the status of parental imprinting of the DLK1-GTL2 locus was studied in RMS. We observed that while both embryonal and alveolar rhabdomyosarcomas (ERMS and ARMS, respectively) show LOI of the DMR at the IGF2-H19 locus, imprinting of the DMR at the DLK1-GTL2 locus varies in association with the histological subtype of RMS. We found that, while ERMS tumors consistently show LOI of the DMR at the DLK1-GTL2 locus, ARMS tumors have erasure of imprinting (EOI) at this locus. These changes in imprinting status of the DLK1-GTL2 locus result in a higher GTL2/DLK1 mRNA ratio in ARMS as compared to ERMS. This difference in imprinting elucidates a novel genetic difference between these two RMS subtypes and may provide a potential diagnostic tool to distinguish between these subtypes.
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Affiliation(s)
- Gabriela Schneider
- Stem Cell Institute at the James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA
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11
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Muñoz M, Penarossa G, Caamaño JN, Díez C, Brevini TAL, Gómez E. Research with parthenogenetic stem cells will help decide whether a safer clinical use is possible. J Tissue Eng Regen Med 2013; 9:325-31. [PMID: 23798507 DOI: 10.1002/term.1779] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 04/08/2013] [Accepted: 04/22/2013] [Indexed: 01/07/2023]
Abstract
The derivation and use of parthenogenetic stem cells (pESCs) are envisaged as a reliable alternative to conventional embryonic stem cells. Similar to embryonic stem cells in their proliferation, expression of pluripotency markers and capacity to multilineage differentiation, pESCs are at a lower risk of immune rejection within stem cell-based therapeutics. Moreover, pESCs represent an important model system to study the effect of paternally imprinted genes on cell differentiation. However, currently available information about the genetic and epigenetic behaviour of pESCs is limited. Thus, a detailed look at the biology of parthenogenetic (PG) embryos and PG-derived cell lines would allow gaining insight into the full potential of pESC in biotechnology. In this commentary article we review some features related to the biology of PG embryos and pESCs. In addition, novel traits on bovine pESCs (bpESCs) are discussed.
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Affiliation(s)
- M Muñoz
- Centro de Biotecnología Animal - SERIDA, La Olla - Deva, Gijón, Asturias, Spain
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12
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Tralau T, Riebeling C, Pirow R, Oelgeschläger M, Seiler A, Liebsch M, Luch A. Wind of change challenges toxicological regulators. ENVIRONMENTAL HEALTH PERSPECTIVES 2012; 120:1489-94. [PMID: 22871563 PMCID: PMC3556610 DOI: 10.1289/ehp.1104782] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Accepted: 08/07/2012] [Indexed: 05/09/2023]
Abstract
BACKGROUND In biomedical research, the past two decades have seen the advent of in vitro model systems based on stem cells, humanized cell lines, and engineered organotypic tissues, as well as numerous cellular assays based on primarily established tumor-derived cell lines and their genetically modified derivatives. OBJECTIVE There are high hopes that these systems might replace the need for animal testing in regulatory toxicology. However, despite increasing pressure in recent years to reduce animal testing, regulators are still reluctant to adopt in vitro approaches on a large scale. It thus seems appropriate to consider how we could realistically perform regulatory toxicity testing using in vitro assays only. DISCUSSION AND CONCLUSION Here, we suggest an in vitro-only approach for regulatory testing that will benefit consumers, industry, and regulators alike.
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Affiliation(s)
- Tewes Tralau
- German Federal Institute for Risk Assessment (BfR), Center for Alternative Methods to Animal Experiments (ZEBET), Berlin, Germany
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13
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Harvey AJ, Mao S, Lalancette C, Krawetz SA, Brenner CA. Transcriptional differences between rhesus embryonic stem cells generated from in vitro and in vivo derived embryos. PLoS One 2012; 7:e43239. [PMID: 23028448 PMCID: PMC3445581 DOI: 10.1371/journal.pone.0043239] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Accepted: 07/18/2012] [Indexed: 01/16/2023] Open
Abstract
Numerous studies have focused on the transcriptional signatures that underlie the maintenance of embryonic stem cell (ESC) pluripotency. However, it remains unclear whether ESC retain transcriptional aberrations seen in in vitro cultured embryos. Here we report the first global transcriptional profile comparison between ESC generated from either in vitro cultured or in vivo derived primate embryos by microarray analysis. Genes involved in pluripotency, oxygen regulation and the cell cycle were downregulated in rhesus ESC generated from in vitro cultured embryos (in vitro ESC). Significantly, several gene differences are similarly downregulated in preimplantation embryos cultured in vitro, which have been associated with long term developmental consequences and disease predisposition. This data indicates that prior to derivation, embryo quality may influence the molecular signature of ESC lines, and may differentially impact the physiology of cells prior to or following differentiation.
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Affiliation(s)
- Alexandra J Harvey
- Department of Physiology, Wayne State University, Detroit, Michigan, United States of America.
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14
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Histone modifications and lamin A regulate chromatin protein dynamics in early embryonic stem cell differentiation. Nat Commun 2012; 3:910. [PMID: 22713752 DOI: 10.1038/ncomms1915] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Accepted: 05/18/2012] [Indexed: 12/20/2022] Open
Abstract
Embryonic stem cells are characterized by unique epigenetic features including decondensed chromatin and hyperdynamic association of chromatin proteins with chromatin. Here we investigate the potential mechanisms that regulate chromatin plasticity in embryonic stem cells. Using epigenetic drugs and mutant embryonic stem cells lacking various chromatin proteins, we find that histone acetylation, G9a-mediated histone H3 lysine 9 (H3K9) methylation and lamin A expression, all affect chromatin protein dynamics. Histone acetylation controls, almost exclusively, euchromatin protein dynamics; lamin A expression regulates heterochromatin protein dynamics, and G9a regulates both euchromatin and heterochromatin protein dynamics. In contrast, we find that DNA methylation and nucleosome repeat length have little or no effect on chromatin-binding protein dynamics in embryonic stem cells. Altered chromatin dynamics associates with perturbed embryonic stem cell differentiation. Together, these data provide mechanistic insights into the epigenetic pathways that are responsible for chromatin plasticity in embryonic stem cells, and indicate that the genome's epigenetic state modulates chromatin plasticity and differentiation potential of embryonic stem cells.
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15
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Sun B, Ito M, Mendjan S, Ito Y, Brons IGM, Murrell A, Vallier L, Ferguson-Smith AC, Pedersen RA. Status of genomic imprinting in epigenetically distinct pluripotent stem cells. Stem Cells 2012; 30:161-8. [PMID: 22109880 DOI: 10.1002/stem.793] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Mouse epiblast stem cells (EpiSCs) derived from postimplantation embryos are developmentally and functionally different from embryonic stem cells (ESCs) generated from blastocysts. EpiSCs require Activin A and FGF2 signaling for self-renewal, similar to human ESCs (hESCs), while mouse ESCs require LIF and BMP4. Unlike ESCs, EpiSCs have undergone X-inactivation, similar to the tendency of hESCs. The shared self-renewal and X-inactivation properties of EpiSCs and hESCs suggest that they have an epigenetic state distinct from ESCs. This hypothesis predicts that EpiSCs would have monoallelic expression of most imprinted genes, like that observed in hESCs. Here, we confirm this prediction. By contrast, we find that mouse induced pluripotent stem cells (iPSCs) tend to lose imprinting similar to mouse ESCs. These findings reveal that iPSCs have an epigenetic status associated with their pluripotent state rather than their developmental origin. Our results also reinforce the view that hESCs and EpiSCs are in vitro counterparts, sharing an epigenetic status distinct from ESCs and iPSCs.
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Affiliation(s)
- Bowen Sun
- The Anne McLaren Laboratory for Regenerative Medicine, Department of Surgery, University of Cambridge, Cambridge, United Kingdom
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Ratajczak MZ. Igf2-H19, an Imprinted Tandem Yin-Yanggene and its Emerging Role in Development, Proliferation of Pluripotent Stem Cells, Senescence and Cancerogenesis. ACTA ACUST UNITED AC 2012; 2. [PMID: 24380039 DOI: 10.4172/2157-7633.1000e108] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Mariusz Z Ratajczak
- Stem Cell Biology Program at the James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, USA
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17
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Affiliation(s)
- Denise P. Barlow
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria;
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18
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Lee S, Kim J, Park TJ, Shin Y, Lee SY, Han YM, Kang S, Park HS. The effects of the physical properties of culture substrates on the growth and differentiation of human embryonic stem cells. Biomaterials 2011; 32:8816-29. [DOI: 10.1016/j.biomaterials.2011.07.058] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Accepted: 07/16/2011] [Indexed: 12/19/2022]
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19
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Hochberg Z, Feil R, Constancia M, Fraga M, Junien C, Carel JC, Boileau P, Le Bouc Y, Deal CL, Lillycrop K, Scharfmann R, Sheppard A, Skinner M, Szyf M, Waterland RA, Waxman DJ, Whitelaw E, Ong K, Albertsson-Wikland K. Child health, developmental plasticity, and epigenetic programming. Endocr Rev 2011; 32:159-224. [PMID: 20971919 PMCID: PMC3365792 DOI: 10.1210/er.2009-0039] [Citation(s) in RCA: 401] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2009] [Accepted: 08/27/2010] [Indexed: 11/19/2022]
Abstract
Plasticity in developmental programming has evolved in order to provide the best chances of survival and reproductive success to the organism under changing environments. Environmental conditions that are experienced in early life can profoundly influence human biology and long-term health. Developmental origins of health and disease and life-history transitions are purported to use placental, nutritional, and endocrine cues for setting long-term biological, mental, and behavioral strategies in response to local ecological and/or social conditions. The window of developmental plasticity extends from preconception to early childhood and involves epigenetic responses to environmental changes, which exert their effects during life-history phase transitions. These epigenetic responses influence development, cell- and tissue-specific gene expression, and sexual dimorphism, and, in exceptional cases, could be transmitted transgenerationally. Translational epigenetic research in child health is a reiterative process that ranges from research in the basic sciences, preclinical research, and pediatric clinical research. Identifying the epigenetic consequences of fetal programming creates potential applications in clinical practice: the development of epigenetic biomarkers for early diagnosis of disease, the ability to identify susceptible individuals at risk for adult diseases, and the development of novel preventive and curative measures that are based on diet and/or novel epigenetic drugs.
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Affiliation(s)
- Z Hochberg
- Rambam Medical Center, Rappaport Faculty of Medicine and Research Institute, Technion–Israel Institute of Technology, Haifa, Israel.
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Abstract
ESCs (embryonic stem cells), derived from the blastocyst stage embryo, are characterized by an indefinite ability for self-renewal as well as pluripotency, enabling them to differentiate into all cell types of the three germ layers. In the undifferentiated state, ESCs display a global promiscuous transcriptional programme which is restricted gradually upon differentiation. Supporting transcriptional promiscuity, chromatin in pluripotent cells is more 'plastic' or 'open', with decondensed heterochromatin architecture, enrichment of active histone modifications, and a hyperdynamic association of chromatin proteins with chromatin. During ESC differentiation, nuclear architecture and chromatin undergo substantial changes. Heterochromatin foci appear smaller, more numerous and more condensed in the differentiated state, the nuclear lamina becomes more defined and chromatin protein dynamics becomes restricted. In the present chapter we discuss chromatin plasticity and epigenetics and the mechanisms that regulate the various chromatin states, which are currently a central theme in the studies of stem cell maintenance and differentiation, and which will no doubt assist in delineating the secrets of pluripotency and self-renewal.
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Xie X, Hiona A, Lee AS, Cao F, Huang M, Li Z, Cherry A, Pei X, Wu JC. Effects of long-term culture on human embryonic stem cell aging. Stem Cells Dev 2010; 20:127-38. [PMID: 20629482 DOI: 10.1089/scd.2009.0475] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In recent years, human embryonic stem (hES) cells have become a promising cell source for regenerative medicine. Although hES cells have the ability for unlimited self-renewal, potential adverse effects of long-term cell culture upon hES cells must be investigated before therapeutic applications of hES cells can be realized. Here we investigated changes in molecular profiles associated with young (<60 passages) and old (>120 passages) cells of the H9 hES cell line as well as young (<85 passages) and old (>120 passages) cells of the PKU1 hES cell line. Our results show that morphology, stem cell markers, and telomerase activity do not differ significantly between young and old passage cells. Cells from both age groups were also shown to differentiate into derivatives of all 3 germ layers upon spontaneous differentiation in vitro. Interestingly, mitochondrial dysfunction was found to occur with prolonged culture. Old passage cells of both the H9 and PKU1 lines were characterized by higher mitochondrial membrane potential, larger mitochondrial morphology, and higher reactive oxygen species content than their younger counterparts. Teratomas derived from higher passage cells were also found to have an uneven preference for differentiation compared with tumors derived from younger cells. These findings suggest that prolonged culture of hES cells may negatively impact mitochondrial function and possibly affect long-term pluripotency.
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Affiliation(s)
- Xiaoyan Xie
- Department of Medicine, Stanford University School of Medicine , Stanford, CA, USA
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22
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Mitjavila-Garcia MT, Bonnet ML, Yates F, Haddad R, Oudrhiri N, Féraud O, Magniez A, Makhlouf M, Vallot C, Rougeulle C, Bennaceur-Griscelli A, Turhan AG. Partial reversal of the methylation pattern of the X-linked gene HUMARA during hematopoietic differentiation of human embryonic stem cells. J Mol Cell Biol 2010; 2:291-8. [PMID: 20823083 DOI: 10.1093/jmcb/mjq026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Human embryonic stem cells (hESCs) can be induced to differentiate towards hematopoiesis with high efficiency. In this work, we analyzed the methylation status of the X-linked HUMARA (human androgen receptor) gene in hematopoietic cells derived from hESC line H9 before and after induction of hematopoietic differentiation. All passages of H9 and H9-derived hematopoietic cells displayed homogenous methylation pattern with disappearance of the same allele upon HpaII digestion. This pattern persisted in the great majority of different hematopoietic progenitors derived from H9, except in 11 of 86 individually plucked colonies in which an equal digestion of the HUMARA alleles has been found, suggesting that a methylation change occurring at this locus during differentiation. Interestingly, quantification of X inactive-specific transcript (XIST) RNA in undifferentiated H9 cell line and day 14 embryoid bodies (EB) by RT-PCR did not show any evidence of XIST expression either before or after differentiation. Thus, during self-renewal conditions and after induction of commitment towards the formation of EB, the methylation pattern of the HUMARA locus appears locked with the same unmethylated allele. However, hematopoietic differentiation seems to be permissive to the reversal of methylation status of HUMARA in some terminally differentiated progenitors. These data suggest that monitoring methylation of HUMARA gene during induced differentiation could be of use for studying hESC-derived hematopoiesis.
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23
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Shin DM, Zuba-Surma EK, Wu W, Ratajczak J, Wysoczynski M, Ratajczak MZ, Kucia M. Novel epigenetic mechanisms that control pluripotency and quiescence of adult bone marrow-derived Oct4(+) very small embryonic-like stem cells. Leukemia 2009; 23:2042-51. [PMID: 19641521 PMCID: PMC2783188 DOI: 10.1038/leu.2009.153] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2009] [Accepted: 06/22/2009] [Indexed: 01/05/2023]
Abstract
Recently, we identified in adult tissues a population of Oct4(+)SSEA-1(+)Sca-1(+)lin(-)CD45(-) very small embryonic-like stem cells (VSELs). First, to address recent controversies on Oct4 expression in cells isolated from adult organs, we show here evidence that Oct4 promoter in bone marrow (BM)-derived VSELs has an open chromatin structure and is actively transcribed. Next, to explain VSELs quiescence and lack of teratoma formation, we demonstrate a unique DNA methylation pattern at some developmentally crucial imprinted genes, showing hypomethylation/erasure of imprints in paternally methylated and hypermethylation of imprints in maternally methylated ones. These epigenetic characteristics leading to upregulation in VSELs of H19 and p57(KIP2) (also known as Cdkn1c) and repression of Igf2 and Rasgrf1 explain VSEL's quiescent status. Interestingly, this unique pattern in imprinted gene methylation is reverted in cocultures with a C2C12 supportive cell-line when VSELs are induced to form VSEL-derived spheres (VSEL-DSs) enriched for stem cells able to differentiate into all three germ layers. Therefore, we suggest that the proliferative/developmental potential of Oct4(+) VSELs is epigenetically regulated by expression of Oct4 and some imprinted genes, and postulate that restoring the proper methylation pattern of imprinted genes will be a crucial step for using these cells in regenerative medicine.
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Affiliation(s)
- Dong-Myung Shin
- Stem Cell Institute at the James Graham Brown Cancer Center, University of Louisville, KY, 40202, USA
| | - Ewa K. Zuba-Surma
- Stem Cell Institute at the James Graham Brown Cancer Center, University of Louisville, KY, 40202, USA
| | - Wan Wu
- Stem Cell Institute at the James Graham Brown Cancer Center, University of Louisville, KY, 40202, USA
| | - Janina Ratajczak
- Stem Cell Institute at the James Graham Brown Cancer Center, University of Louisville, KY, 40202, USA
| | - Marcin Wysoczynski
- Stem Cell Institute at the James Graham Brown Cancer Center, University of Louisville, KY, 40202, USA
| | - Mariusz Z. Ratajczak
- Stem Cell Institute at the James Graham Brown Cancer Center, University of Louisville, KY, 40202, USA
| | - Magda Kucia
- Stem Cell Institute at the James Graham Brown Cancer Center, University of Louisville, KY, 40202, USA
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24
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Carpenter MK, Frey-Vasconcells J, Rao MS. Developing safe therapies from human pluripotent stem cells. Nat Biotechnol 2009; 27:606-13. [PMID: 19587662 DOI: 10.1038/nbt0709-606] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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25
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Martín-Ibáñez R, Strömberg AM, Hovatta O, Canals JM. Cryopreservation of dissociated human embryonic stem cells in the presence of ROCK inhibitor. ACTA ACUST UNITED AC 2009; Chapter 1:Unit 1C.8. [PMID: 19585460 DOI: 10.1002/9780470151808.sc01c08s10] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Two different methods have been adopted for the cryopreservation of human embryonic stem cells (hESCs): vitrification and conventional slow freezing/rapid thawing. However, these methods present poor viability and high differentiation rates. Therefore, the development of an efficient cryopreservation protocol for hESCs is one of the major challenges for the application of these cells in clinical therapy and regenerative medicine. A novel method for the cryopreservation of dissociated hESCs in the presence of a selective Rho-associated kinase (ROCK) inhibitor that increases cell survival and the efficiency of colony formation of cryopreserved hESCs has been developed. Moreover, this protocol improves the existing methods presenting short recovery times and hardly any differentiation rates. Thus, an easy handling protocol that allows the cryopreservation of large amounts of hESCs is described.
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Affiliation(s)
- Raquel Martín-Ibáñez
- Departament de Biologia Cellular, Immunologia i Neurosciències, Facultad de Medicina, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Universitat de Barcelona and CIBERNED, Barcelona, Spain
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26
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Latos PA, Stricker SH, Steenpass L, Pauler FM, Huang R, Senergin BH, Regha K, Koerner MV, Warczok KE, Unger C, Barlow DP. An in vitro ES cell imprinting model shows that imprinted expression of the Igf2r gene arises from an allele-specific expression bias. Development 2009; 136:437-48. [PMID: 19141673 DOI: 10.1242/dev.032060] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Genomic imprinting is an epigenetic process that results in parental-specific gene expression. Advances in understanding the mechanism that regulates imprinted gene expression in mammals have largely depended on generating targeted manipulations in embryonic stem (ES) cells that are analysed in vivo in mice. However, genomic imprinting consists of distinct developmental steps, some of which occur in post-implantation embryos, indicating that they could be studied in vitro in ES cells. The mouse Igf2r gene shows imprinted expression only in post-implantation stages, when repression of the paternal allele has been shown to require cis-expression of the Airn non-coding (nc) RNA and to correlate with gain of DNA methylation and repressive histone modifications. Here we follow the gain of imprinted expression of Igf2r during in vitro ES cell differentiation and show that it coincides with the onset of paternal-specific expression of the Airn ncRNA. Notably, although Airn ncRNA expression leads, as predicted, to gain of repressive epigenetic marks on the paternal Igf2r promoter, we unexpectedly find that the paternal Igf2r promoter is expressed at similar low levels throughout ES cell differentiation. Our results further show that the maternal and paternal Igf2r promoters are expressed equally in undifferentiated ES cells, but during differentiation expression of the maternal Igf2r promoter increases up to 10-fold, while expression from the paternal Igf2r promoter remains constant. This indicates, contrary to expectation, that the Airn ncRNA induces imprinted Igf2r expression not by silencing the paternal Igf2r promoter, but by generating an expression bias between the two parental alleles.
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Affiliation(s)
- Paulina A Latos
- CeMM-Research Center for Molecular Medicine of the Austrian Academy of Sciences, Dr Bohr-Gasse 9/4, Vienna Biocenter, A-1030 Vienna, Austria
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27
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Henckel A, Feil R. [Differential epigenetic marking on imprinted genes and consequences in human diseases]. Med Sci (Paris) 2008; 24:747-52. [PMID: 18789223 DOI: 10.1051/medsci/20082489747] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
At the time of fertilisation, the parental genomes have a strikingly different organisation. Sperm DNA is packaged globally with protamines, whereas the oocyte's genome is wrapped around nucleosomes. The maternal and paternal genomes are functionally different as well, and are both required for normal uterine and postnatal development. The functional requirement of both parental genomes is a consequence of differential epigenetic marking by DNA methylation during oogenesis and spermatogenesis, on a group of genes called imprinted genes. After fertilisation, these parental marks persist throughout development and convey the allelic expression of imprinted genes. Pathological perturbation of methylation imprints, before fertilisation in the germ cells, or during development, gives rise to growth-related syndromes, and is frequently observed in cancer as well. Alteration of imprints is thought to occur early in carcinogenesis and shows similarities with the acquisition of aberrant DNA methylation at tumour suppressor genes. This suggests that similar underlying mechanisms could be involved.
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Affiliation(s)
- Amandine Henckel
- Institut de Génétique Moléculaire de Montpellier, CNRS et Université de Montpellier, 34293 Montpellier Cedex 5, France
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28
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Parthenogenesis as an approach to pluripotency: advantages and limitations involved. ACTA ACUST UNITED AC 2008; 4:127-35. [PMID: 18548354 DOI: 10.1007/s12015-008-9027-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/05/2008] [Indexed: 10/22/2022]
Abstract
Embryonic stem cells (ESCs) are invaluable cells derived from the inner cell mass of the mammalian blastocyst. They have nearly indefinite self-renewal, retain their developmental potential after prolonged periods in culture and display great plasticity that allow them to differentiate into all cell types of the body. They provide exciting opportunities to develop unique models for developmental research and hold great potential for cell and tissue replacement therapy. However, these unique cells cannot be obtained without destroying an embryo and, despite the potential therapeutic usefulness, their derivation in the human raises substantial ethical as well as legal and political concerns because it unavoidably involves the destruction of viable embryos. In the recent years a number of scientific proposals that do not require the generation and subsequent destruction of human embryos have been put forward in an attempt to fill the gap between ethical questions and potential scientific and medical benefits. In this review we briefly summarize data obtained from the literature related to these different alternative approaches and focus in more details on our experience in the derivation of parthenothes, as a possible alternative source for pluripotent cells, discussing the advantages as well as the limits of these cell lines.
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29
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Epigenetics and cancer, 2nd IARC meeting, Lyon, France, 6 and 7 December 2007. Mol Oncol 2008; 2:33-40. [PMID: 19383327 DOI: 10.1016/j.molonc.2008.03.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2008] [Revised: 03/14/2008] [Accepted: 03/17/2008] [Indexed: 12/28/2022] Open
Abstract
It is becoming widely accepted that epigenetic alterations are universally present in human malignancies and that cancer is as much a disease of abnormal epigenetics as it is a genetic disease. The potential utility of epigenetics and epigenomics in cancer research and cancer control is highlighted by the fact that many funding agencies put cancer epigenetics on the priority list. The goal of this meeting, held at the offices of the International Agency for Research on Cancer in Lyon, France, 6 and 7 December 2007, was to discuss recent conceptual and technological advances in cancer epigenetics and epigenomics, the future research needs in the field, and their implications for early detection, risk assessment and prevention of cancer. While epigenetics has been historically linked to phenomena that do not follow normal genetic principles of heritability, recent mechanistic advances have begun to change our understanding of complex diseases including cancer, traditionally viewed as genetic in origin. It is now known that epigenetic mechanisms play critical roles in regulation of many cellular functions and their deregulation may disrupt the control of fundamental processes leading to tumour formation. A flurry of screening and functional studies revealed that most key processes found in cancer cells, such as silencing of tumour suppressor genes, activation of oncogenes, aberrant cell cycle processes, defects in DNA repair, and deregulation of cell death, can be triggered by epigenetic deregulation. Two important features that distinguish epigenetic changes from genetic alterations are the gradual appearance and reversibility of epigenetic events. These features make epigenetic alterations an attractive target for therapeutic intervention and the development of preventive strategies. For example, aberrant patterns of DNA methylation and histone acetylation and methylation can be targeted by drugs aiming to re-activate epigenetically silenced genes. Until now, most studies on epigenetic changes in cancer were generally focused on specific genes. However, this meeting also stressed the need to take advantage of recent progress in epigenomics and emergence of powerful technologies for detection of epigenetic changes in high throughput and genome-wide settings. This may further advance our capacity to evaluate the contribution of epigenetic changes induced by environmental epimutagens to human cancer. This information may prove critical for the design of efficient strategies for early diagnosis, therapy, and prevention of cancer.
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