1
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Wu Y, Wang C, Fan X, Ma Y, Liu Z, Ye X, Shen C, Wu C. The impact of induced pluripotent stem cells in animal conservation. Vet Res Commun 2024; 48:649-663. [PMID: 38228922 DOI: 10.1007/s11259-024-10294-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 01/04/2024] [Indexed: 01/18/2024]
Abstract
It is widely acknowledged that we are currently facing a critical tipping point with regards to global extinction, with human activities driving us perilously close to the brink of a devastating sixth mass extinction. As a promising option for safeguarding endangered species, induced pluripotent stem cells (iPSCs) hold great potential to aid in the preservation of threatened animal populations. For endangered species, such as the northern white rhinoceros (Ceratotherium simum cottoni), supply of embryos is often limited. After the death of the last male in 2019, only two females remained in the world. IPSC technology offers novel approaches and techniques for obtaining pluripotent stem cells (PSCs) from rare and endangered animal species. Successful generation of iPSCs circumvents several bottlenecks that impede the development of PSCs, including the challenges associated with establishing embryonic stem cells, limited embryo sources and immune rejection following embryo transfer. To provide more opportunities and room for growth in our work on animal welfare, in this paper we will focus on the progress made with iPSC lines derived from endangered and extinct species, exploring their potential applications and limitations in animal welfare research.
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Affiliation(s)
- Yurou Wu
- School of Pharmacy/School of Modem Chinese Medicine Industry, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, People's Republic of China
| | - Chengwei Wang
- School of Pharmacy/School of Modem Chinese Medicine Industry, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, People's Republic of China
| | - Xinyun Fan
- School of Pharmacy/School of Modem Chinese Medicine Industry, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, People's Republic of China
| | - Yuxiao Ma
- Department of Biology, New York University, New York, NY, USA
| | - Zibo Liu
- School of Pharmacy/School of Modem Chinese Medicine Industry, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, People's Republic of China
| | - Xun Ye
- School of Pharmacy/School of Modem Chinese Medicine Industry, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, People's Republic of China
| | - Chongyang Shen
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, People's Republic of China.
| | - Chunjie Wu
- Innovative Institute of Chinese Medicine and Pharmacy/Academy for Interdiscipline, Chengdu Univesity of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, People's Republic of China.
- Sichuan Engineering Research Center for Endangered Medicinal Animals, Chengdu, China.
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2
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Dejosez M, Dall'Agnese A, Ramamoorthy M, Platt J, Yin X, Hogan M, Brosh R, Weintraub AS, Hnisz D, Abraham BJ, Young RA, Zwaka TP. Regulatory architecture of housekeeping genes is driven by promoter assemblies. Cell Rep 2023; 42:112505. [PMID: 37182209 PMCID: PMC10329844 DOI: 10.1016/j.celrep.2023.112505] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 01/22/2023] [Accepted: 04/28/2023] [Indexed: 05/16/2023] Open
Abstract
Genes that are key to cell identity are generally regulated by cell-type-specific enhancer elements bound by transcription factors, some of which facilitate looping to distant gene promoters. In contrast, genes that encode housekeeping functions, whose regulation is essential for normal cell metabolism and growth, generally lack interactions with distal enhancers. We find that Ronin (Thap11) assembles multiple promoters of housekeeping and metabolic genes to regulate gene expression. This behavior is analogous to how enhancers are brought together with promoters to regulate cell identity genes. Thus, Ronin-dependent promoter assemblies provide a mechanism to explain why housekeeping genes can forgo distal enhancer elements and why Ronin is important for cellular metabolism and growth control. We propose that clustering of regulatory elements is a mechanism common to cell identity and housekeeping genes but is accomplished by different factors binding distinct control elements to establish enhancer-promoter or promoter-promoter interactions, respectively.
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Affiliation(s)
- Marion Dejosez
- Black Family Stem Cell Institute, Huffington Center for Cell-based Research in Parkinson's Disease, Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA
| | - Alessandra Dall'Agnese
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Mahesh Ramamoorthy
- Black Family Stem Cell Institute, Huffington Center for Cell-based Research in Parkinson's Disease, Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA
| | - Jesse Platt
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Xing Yin
- Black Family Stem Cell Institute, Huffington Center for Cell-based Research in Parkinson's Disease, Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA
| | - Megan Hogan
- Black Family Stem Cell Institute, Huffington Center for Cell-based Research in Parkinson's Disease, Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA
| | - Ran Brosh
- Black Family Stem Cell Institute, Huffington Center for Cell-based Research in Parkinson's Disease, Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA
| | - Abraham S Weintraub
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Denes Hnisz
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Brian J Abraham
- St. Jude Research Children's Hospital, Memphis, TN 38105, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
| | - Thomas P Zwaka
- Black Family Stem Cell Institute, Huffington Center for Cell-based Research in Parkinson's Disease, Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10502, USA.
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3
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Mendoza G, González-Pastor R, Sánchez JM, Arce-Cerezo A, Quintanilla M, Moreno-Bueno G, Pujol A, Belmar-López C, de Martino A, Riu E, Rodriguez TA, Martin-Duque P. The E1a Adenoviral Gene Upregulates the Yamanaka Factors to Induce Partial Cellular Reprogramming. Cells 2023; 12:cells12091338. [PMID: 37174738 PMCID: PMC10177049 DOI: 10.3390/cells12091338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 04/29/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023] Open
Abstract
The induction of pluripotency by enforced expression of different sets of genes in somatic cells has been achieved with reprogramming technologies first described by Yamanaka's group. Methodologies for generating induced pluripotent stem cells are as varied as the combinations of genes used. It has previously been reported that the adenoviral E1a gene can induce the expression of two of the Yamanaka factors (c-Myc and Oct-4) and epigenetic changes. Here, we demonstrate that the E1a-12S over-expression is sufficient to induce pluripotent-like characteristics closely to epiblast stem cells in mouse embryonic fibroblasts through the activation of the pluripotency gene regulatory network. These findings provide not only empirical evidence that the expression of one single factor is sufficient for partial reprogramming but also a potential mechanistic explanation for how viral infection could lead to neoplasia if they are surrounded by the appropriate environment or the right medium, as happens with the tumorogenic niche.
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Affiliation(s)
- Gracia Mendoza
- Instituto Aragonés de Ciencias de la Salud (IACS), 50009 Zaragoza, Spain
- Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain
| | - Rebeca González-Pastor
- Instituto Aragonés de Ciencias de la Salud (IACS), 50009 Zaragoza, Spain
- Centro de Investigación Biomédica (CENBIO), Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito 170527, Ecuador
| | - Juan Miguel Sánchez
- National Heart and Lung Institute, Imperial College London, London W12 ONN, UK
| | - Altamira Arce-Cerezo
- Centro de Biotecnología Animal y de Terapia Génica (CBATEG), Universidad Autónoma de Barcelona, 08193 Bellaterra, Spain
| | - Miguel Quintanilla
- Departamento de Bioquímica, Instituto de Investigaciones Biomédicas 'Alberto Sols', Universidad Autónoma de Madrid (UAM), (UAM-CSIC), 28029 Madrid, Spain
| | - Gema Moreno-Bueno
- Departamento de Bioquímica, Instituto de Investigaciones Biomédicas 'Alberto Sols', Universidad Autónoma de Madrid (UAM), (UAM-CSIC), 28029 Madrid, Spain
- Fundación MD Anderson Internacional, 28033 Madrid, Spain
- Centro de Investigación Biomédica en Red, Instituto de Salud Carlos III, Red de Cáncer (CIBERONC) and Red de Nanomedicina y Nanomateriales (CIBER-BBN), 28029 Madrid, Spain
| | - Anna Pujol
- Centro de Biotecnología Animal y de Terapia Génica (CBATEG), Universidad Autónoma de Barcelona, 08193 Bellaterra, Spain
| | - Carolina Belmar-López
- Instituto Aragonés de Ciencias de la Salud (IACS), 50009 Zaragoza, Spain
- OncoGenomics Lab, Universidad Privada San Juan Bautista, Lima 15038, Peru
| | - Alba de Martino
- Instituto Aragonés de Ciencias de la Salud (IACS), 50009 Zaragoza, Spain
| | - Efrén Riu
- Centro de Biotecnología Animal y de Terapia Génica (CBATEG), Universidad Autónoma de Barcelona, 08193 Bellaterra, Spain
| | - Tristan A Rodriguez
- National Heart and Lung Institute, Imperial College London, London W12 ONN, UK
| | - Pilar Martin-Duque
- Instituto Aragonés de Ciencias de la Salud (IACS), 50009 Zaragoza, Spain
- Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red, Instituto de Salud Carlos III, Red de Cáncer (CIBERONC) and Red de Nanomedicina y Nanomateriales (CIBER-BBN), 28029 Madrid, Spain
- Fundación Araid, 50018 Zaragoza, Spain
- Departamento de Cirugía, Facultad de Medicina, Universidad de Zaragoza, 50009 Zaragoza, Spain
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4
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Wang J, Fang J, Feng M, Li L, Ma L, Zhao X, Dai Y. Inhibition of EED activity enhances cell survival of female germline stem cell and improves the oocytes production during oogenesis in vitro. Open Biol 2023; 13:220211. [PMID: 36695089 PMCID: PMC9874982 DOI: 10.1098/rsob.220211] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Ovarian organoids, based on female germline stem cells (FGSCs), are nowadays widely applied for reproductive medicine screening and exploring the potential mechanisms during mammalian oogenesis. However, there are still key issues that urgently need to be resolved in ovarian organoid technology, one of which is to establish a culture system that effectively expands FGSCs in vitro, as well as maintaining the unipotentcy of FGSCs to differentiate into oocytes. Here, FGSCs were EED226 treated and processed for examination of proliferation and differentiation in vitro. According to the results, EED226 specifically increased FGSC survival by decreasing the enrichment of H3K27me3 on Oct4 promoter and exon, as well as enhancing OCT4 expression and inhibiting P53 and P63 expression. Notably, we also found that FGSCs with EED226 treatment differentiated into more oocytes during oogenesis in vitro, and the resultant oocytes maintained a low level of P63 versus control at early stage development. These results demonstrated that inhibition of EED activity appeared to promote the survival of FGSCs and markedly inhibited their apoptosis during in vitro differentiation. As a result of our study, we propose an effective culture strategy to culture FGSCs and obtain oocytes in vitro, which provides a new vision for oogenesis in vitro.
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Affiliation(s)
- Jiapeng Wang
- College of Life Sciences, Inner Mongolia University, Xilingol South Road No. 49, Hohhot 010020, People's Republic of China
| | - Junxian Fang
- College of Life Sciences, Inner Mongolia University, Xilingol South Road No. 49, Hohhot 010020, People's Republic of China
| | - Mingqian Feng
- College of Life Sciences, Inner Mongolia University, Xilingol South Road No. 49, Hohhot 010020, People's Republic of China
| | - Liping Li
- College of Life Sciences, Inner Mongolia University, Xilingol South Road No. 49, Hohhot 010020, People's Republic of China
| | - Lixin Ma
- College of Life Sciences, Inner Mongolia University, Xilingol South Road No. 49, Hohhot 010020, People's Republic of China
| | - Xiaorong Zhao
- College of Life Sciences, Inner Mongolia University, Xilingol South Road No. 49, Hohhot 010020, People's Republic of China
| | - Yanfeng Dai
- College of Life Sciences, Inner Mongolia University, Xilingol South Road No. 49, Hohhot 010020, People's Republic of China
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5
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Salewskij K, Gross-Thebing T, Ing-Simmons E, Duethorn B, Rieger B, Fan R, Chen R, Govindasamy N, Brinkmann H, Kremer L, Kuempel-Rink N, Mildner K, Zeuschner D, Stehling M, Dejosez M, Zwaka TP, Schöler HR, Busch KB, Vaquerizas JM, Bedzhov I. Ronin governs the metabolic capacity of the embryonic lineage for post-implantation development. EMBO Rep 2021; 22:e53048. [PMID: 34515391 PMCID: PMC8567215 DOI: 10.15252/embr.202153048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 08/23/2021] [Accepted: 08/26/2021] [Indexed: 12/02/2022] Open
Abstract
During implantation, the murine embryo transitions from a “quiet” into an active metabolic/proliferative state, which kick‐starts the growth and morphogenesis of the post‐implantation conceptus. Such transition is also required for embryonic stem cells to be established from mouse blastocysts, but the factors regulating this process are poorly understood. Here, we show that Ronin plays a critical role in the process by enabling active energy production, and the loss of Ronin results in the establishment of a reversible quiescent state in which naïve pluripotency is promoted. In addition, Ronin fine‐tunes the expression of genes that encode ribosomal proteins and is required for proper tissue‐scale organisation of the pluripotent lineage during the transition from blastocyst to egg cylinder stage. Thus, Ronin function is essential for governing the metabolic capacity so that it can support the pluripotent lineage’s high‐energy demands for cell proliferation and morphogenesis.
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Affiliation(s)
- Kirill Salewskij
- Embryonic Self-Organization Research Group, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Theresa Gross-Thebing
- Embryonic Self-Organization Research Group, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Elizabeth Ing-Simmons
- Regulatory Genomics Group, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Binyamin Duethorn
- Embryonic Self-Organization Research Group, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Bettina Rieger
- Institut für Integrative Zellbiologie und Physiologie, University of Münster, Münster, Germany
| | - Rui Fan
- Embryonic Self-Organization Research Group, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Rui Chen
- Embryonic Self-Organization Research Group, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Niraimathi Govindasamy
- Embryonic Self-Organization Research Group, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Heike Brinkmann
- Embryonic Self-Organization Research Group, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Ludmila Kremer
- Transgenic Facility, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Nannette Kuempel-Rink
- Transgenic Facility, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Karina Mildner
- Electron Microscopy Facility, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Dagmar Zeuschner
- Electron Microscopy Facility, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Martin Stehling
- Flow Cytometry Unit, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Marion Dejosez
- Department for Cell, Regenerative and Developmental Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, Huffington Foundation Center for Cell-based Research in Parkinson's Disease, New York, NY, USA
| | - Thomas P Zwaka
- Department for Cell, Regenerative and Developmental Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, Huffington Foundation Center for Cell-based Research in Parkinson's Disease, New York, NY, USA
| | - Hans R Schöler
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Karin B Busch
- Institut für Integrative Zellbiologie und Physiologie, University of Münster, Münster, Germany
| | - Juan M Vaquerizas
- Regulatory Genomics Group, Max Planck Institute for Molecular Biomedicine, Münster, Germany.,MRC London Institute of Medical Sciences, London, UK.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, UK
| | - Ivan Bedzhov
- Embryonic Self-Organization Research Group, Max Planck Institute for Molecular Biomedicine, Münster, Germany
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6
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Rodrigues AS, Pereira SL, Ramalho-Santos J. Stem metabolism: Insights from oncometabolism and vice versa. Biochim Biophys Acta Mol Basis Dis 2020; 1866:165760. [PMID: 32151634 DOI: 10.1016/j.bbadis.2020.165760] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 02/16/2020] [Accepted: 03/04/2020] [Indexed: 02/06/2023]
Abstract
Metabolism, is a transversal hot research topic in different areas, resulting in the integration of cellular needs with external cues, involving a highly coordinated set of activities in which nutrients are converted into building blocks for macromolecules, energy currencies and biomass. Importantly, cells can adjust different metabolic pathways defining its cellular identity. Both cancer cell and embryonic stem cells share the common hallmark of high proliferative ability but while the first represent a huge social-economic burden the second symbolize a huge promise. Importantly, research on both fields points out that stem cells share common metabolic strategies with cancer cells to maintain their identity as well as proliferative capability and, vice versa cancer cells also share common strategies regarding pluripotent markers. Moreover, the Warburg effect can be found in highly proliferative non-cancer stem cells as well as in embryonic stem cells that are primed towards differentiation, while a bivalent metabolism is characteristic of embryonic stem cells that are in a true naïve pluripotent state and cancer stem cells can also range from glycolysis to oxidative phosphorylation. Therefore, this review aims to highlight major metabolic similarities between cancer cells and embryonic stem cells demonstrating that they have similar strategies in both signaling pathways regulation as well as metabolic profiles while focusing on key metabolites.
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Affiliation(s)
- Ana Sofia Rodrigues
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Rua Larga, Faculty of Medicine, Pólo I, 3004-504 Coimbra, Portugal.
| | - Sandro L Pereira
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg.
| | - João Ramalho-Santos
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Rua Larga, Faculty of Medicine, Pólo I, 3004-504 Coimbra, Portugal; Department of Life Sciences, University of Coimbra, Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal.
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7
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Yang P, Humphrey SJ, Cinghu S, Pathania R, Oldfield AJ, Kumar D, Perera D, Yang JYH, James DE, Mann M, Jothi R. Multi-omic Profiling Reveals Dynamics of the Phased Progression of Pluripotency. Cell Syst 2019; 8:427-445.e10. [PMID: 31078527 DOI: 10.1016/j.cels.2019.03.012] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 02/12/2019] [Accepted: 03/19/2019] [Indexed: 12/28/2022]
Abstract
Pluripotency is highly dynamic and progresses through a continuum of pluripotent stem cell states. The two states that bookend the pluripotency continuum, naive and primed, are well characterized, but our understanding of the intermediate states and transitions between them remains incomplete. Here, we dissect the dynamics of pluripotent state transitions underlying pre- to post-implantation epiblast differentiation. Through comprehensive mapping of the proteome, phosphoproteome, transcriptome, and epigenome of embryonic stem cells transitioning from naive to primed pluripotency, we find that rapid, acute, and widespread changes to the phosphoproteome precede ordered changes to the epigenome, transcriptome, and proteome. Reconstruction of the kinase-substrate networks reveals signaling cascades, dynamics, and crosstalk. Distinct waves of global proteomic changes mark discrete phases of pluripotency, with cell-state-specific surface markers tracking pluripotent state transitions. Our data provide new insights into multi-layered control of the phased progression of pluripotency and a foundation for modeling mechanisms regulating pluripotent state transitions (www.stemcellatlas.org).
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Affiliation(s)
- Pengyi Yang
- Epigenetics & Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA; Charles Perkins Centre, School of Mathematics and Statistics, University of Sydney, Sydney, NSW 2006, Australia.
| | - Sean J Humphrey
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany; Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia.
| | - Senthilkumar Cinghu
- Epigenetics & Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Rajneesh Pathania
- Epigenetics & Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Andrew J Oldfield
- Epigenetics & Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Dhirendra Kumar
- Epigenetics & Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Dinuka Perera
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Jean Y H Yang
- Charles Perkins Centre, School of Mathematics and Statistics, University of Sydney, Sydney, NSW 2006, Australia
| | - David E James
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Raja Jothi
- Epigenetics & Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA.
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8
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Perestrelo T, Correia M, Ramalho-Santos J, Wirtz D. Metabolic and Mechanical Cues Regulating Pluripotent Stem Cell Fate. Trends Cell Biol 2018; 28:1014-1029. [DOI: 10.1016/j.tcb.2018.09.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 08/30/2018] [Accepted: 09/25/2018] [Indexed: 02/07/2023]
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9
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Abstract
Abundant cell death marks early embryonic development. New work reported in Developmental Cell from Diaz-Diaz and colleagues (2017) proposes that this death results from cell competition arising from differences in cellular differentiation status, thus providing a physiological mechanism for controlling the make-up of the pluripotent stem cell population.
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Affiliation(s)
- Thomas P Zwaka
- Black Family Stem Cell Institute, Huffington Foundation Center for Cell-Based Research in Parkinson's Disease, Department of Cell, Developmental & Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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10
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11
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Seifert BA, Dejosez M, Zwaka TP. Ronin influences the DNA damage response in pluripotent stem cells. Stem Cell Res 2017; 23:98-104. [PMID: 28715716 DOI: 10.1016/j.scr.2017.06.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Revised: 06/20/2017] [Accepted: 06/29/2017] [Indexed: 12/12/2022] Open
Abstract
Early mammalian embryonic cells must maintain a particularly robust DNA repair system, as mutations at this developmental point have detrimental consequences for the organism. How the repair system can be tuned to fulfill such elevated requirements is largely unknown, but it may involve transcriptional regulation. Ronin (Thap11) is a transcriptional regulator responsible for vital programs in pluripotent cells. Here, we report that this protein also modulates the DNA damage response of such cells. We show that conditional Ronin knockout sensitizes embryonic stem cells (ESCs) to UV-C-induced DNA damage in association with Atr pathway activation and G2/M arrest. Ronin binds to and regulates the genes encoding several DNA repair factors, including Gtf2h4 and Rad18, providing a potential mechanism for this phenotype. Our results suggest that the unique DNA repair requirements of the early embryo are not met by a static system, but rather via highly regulated processes.
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Affiliation(s)
- Bryce A Seifert
- Graduate Program in Molecular and Human Genetics at Baylor College of Medicine, Houston, TX 77030, USA.
| | - Marion Dejosez
- Huffington Center for Cell-Based Research in Parkinson's Disease, Black Family Stem Cell Institute, Department of Cell, Developmental & Regenerative Biology, Graduate School of Biomedical Sciences, New York, NY 10029, USA.
| | - Thomas P Zwaka
- Huffington Center for Cell-Based Research in Parkinson's Disease, Black Family Stem Cell Institute, Department of Cell, Developmental & Regenerative Biology, Graduate School of Biomedical Sciences, New York, NY 10029, USA.
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12
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Chen Q, Hu G. Post-transcriptional regulation of the pluripotent state. Curr Opin Genet Dev 2017; 46:15-23. [PMID: 28654825 DOI: 10.1016/j.gde.2017.06.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 04/17/2017] [Accepted: 06/08/2017] [Indexed: 12/20/2022]
Abstract
Pluripotency describes the developmental capacity to give rise to all cell types in the adult body. A comprehensive understanding of the molecular mechanisms that regulate pluripotency is important for both basic and translational research. While earlier studies mostly focused on signaling pathways, transcriptional regulation, and epigenetic modifications, recent investigations showed that RNA binding proteins, RNA processing machineries, and regulatory RNA molecules also play essential roles. Here, we provide a concise review on the latest findings and developments in post-transcriptional regulation of the pluripotent state.
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Affiliation(s)
- Qing Chen
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, RTP, NC, United States.
| | - Guang Hu
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, RTP, NC, United States.
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13
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Sun H, Cao J, Zhao L, Zhu S, Chen S, Li Y, Zhao B, Zhao T. PIM2 regulates stemness through phosphorylation of 4E-BP1. Sci Bull (Beijing) 2017; 62:679-685. [PMID: 36659438 DOI: 10.1016/j.scib.2017.04.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 04/12/2017] [Accepted: 04/12/2017] [Indexed: 01/21/2023]
Abstract
Embryonic stem cells (ESCs) can undergo unlimited self-renewal and maintain pluripotency to differentiate into any cell type of the three germ layers. Extensive studies have shown ESC identity is regulated by transcription factors, epigenetic regulators and multiple signal transduction pathways. However, the kinase regulation of pluripotency is not well understood. Here we show that the serine/threonine kinase PIM2, which is highly expressed in ESCs but not in somatic cells, functions as a crucial stemness regulator in ESCs. Knockout of Pim2 inhibits the self-renewal and differentiation capability of ESCs. Mechanistic studies identified that PIM2 can directly phosphorylate 4E-BP1, leading to release of eIF4E which facilitates the translation of pluripotent genes in ESCs. Our study highlights a novel kinase cascade pathway for ESC identity maintenance.
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Affiliation(s)
- Hongyan Sun
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Graduate University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiani Cao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Lin Zhao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Chinese Medicine Hospital in Linyi City, Linyi 276600, China
| | - Shaohua Zhu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shenghui Chen
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Graduate University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaqiong Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Graduate University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bin Zhao
- Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Tongbiao Zhao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Graduate University of Chinese Academy of Sciences, Beijing 100049, China.
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14
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Sudhir PR, Kumari MP, Hsu WT, Chen CH, Kuo HC, Chen CH. Integrative omics connects N-glycoproteome-wide alterations with pathways and regulatory events in induced pluripotent stem cells. Sci Rep 2016; 6:36109. [PMID: 27808266 PMCID: PMC5093713 DOI: 10.1038/srep36109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 10/05/2016] [Indexed: 12/27/2022] Open
Abstract
Molecular-level differences ranging from genomes to proteomes, but not N-glycoproteomes, between human induced pluripotent stem cells (hiPSCs) and embryonic stem cells (hESCs) have been assessed to gain insights into cell reprogramming and induced pluripotency. Our multiplexed quantitative N-glycoproteomics study identified altered N-glycoproteins that significantly regulate cell adhesion processes in hiPSCs compared to hESCs. The integrative proteomics and functional network analyses of the altered N-glycoproteins revealed their significant interactions with known PluriNet (pluripotency-associated network) proteins. We found that these interactions potentially regulate various signaling pathways including focal adhesion, PI3K-Akt signaling, regulation of actin cytoskeleton, and spliceosome. Furthermore, the integrative transcriptomics analysis revealed that imperfectly reprogrammed subunits of the oligosaccharyltransferase (OST) and dolichol-phosphate-mannose synthase (DPM) complexes were potential candidate regulatory events for the altered N-glycoprotein levels. Together, the results of our study suggest that imperfect reprogramming of the protein complexes linked with the N-glycosylation process may result in N-glycoprotein alterations that affect induced pluripotency through their functional protein interactions.
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Affiliation(s)
| | | | - Wei-Ting Hsu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Chein-Hung Chen
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Hung-Chih Kuo
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan.,Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
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15
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CNOT3-Dependent mRNA Deadenylation Safeguards the Pluripotent State. Stem Cell Reports 2016; 7:897-910. [PMID: 27746116 PMCID: PMC5106518 DOI: 10.1016/j.stemcr.2016.09.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 09/14/2016] [Accepted: 09/15/2016] [Indexed: 01/07/2023] Open
Abstract
Poly(A) tail length and mRNA deadenylation play important roles in gene regulation. However, how they regulate embryonic development and pluripotent cell fate is not fully understood. Here we present evidence that CNOT3-dependent mRNA deadenylation governs the pluripotent state. We show that CNOT3, a component of the Ccr4-Not deadenylase complex, is required for mouse epiblast maintenance. It is highly expressed in blastocysts and its deletion leads to peri-implantation lethality. The epiblast cells in Cnot3 deletion embryos are quickly lost during diapause and fail to outgrow in culture. Mechanistically, CNOT3 C terminus is required for its interaction with the complex and its function in embryonic stem cells (ESCs). Furthermore, Cnot3 deletion results in increases in the poly(A) tail lengths, half-lives, and steady-state levels of differentiation gene mRNAs. The half-lives of CNOT3 target mRNAs are shorter in ESCs and become longer during normal differentiation. Together, we propose that CNOT3 maintains the pluripotent state by promoting differentiation gene mRNA deadenylation and degradation, and we identify poly(A) tail-length regulation as a post-transcriptional mechanism that controls pluripotency. CNOT3 is required for mouse epiblast maintenance during early development CNOT3 C-terminal domain is necessary for the maintenance of the pluripotent state CNOT3 promotes differentiation gene mRNA deadenylation and degradation mRNA poly(A) tail regulation plays a critical role in pluripotency
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16
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Sudhir PR, Chen CH. Proteomics-Based Analysis of Protein Complexes in Pluripotent Stem Cells and Cancer Biology. Int J Mol Sci 2016; 17:432. [PMID: 27011181 PMCID: PMC4813282 DOI: 10.3390/ijms17030432] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 03/08/2016] [Accepted: 03/16/2016] [Indexed: 12/24/2022] Open
Abstract
A protein complex consists of two or more proteins that are linked together through protein-protein interactions. The proteins show stable/transient and direct/indirect interactions within the protein complex or between the protein complexes. Protein complexes are involved in regulation of most of the cellular processes and molecular functions. The delineation of protein complexes is important to expand our knowledge on proteins functional roles in physiological and pathological conditions. The genetic yeast-2-hybrid method has been extensively used to characterize protein-protein interactions. Alternatively, a biochemical-based affinity purification coupled with mass spectrometry (AP-MS) approach has been widely used to characterize the protein complexes. In the AP-MS method, a protein complex of a target protein of interest is purified using a specific antibody or an affinity tag (e.g., DYKDDDDK peptide (FLAG) and polyhistidine (His)) and is subsequently analyzed by means of MS. Tandem affinity purification, a two-step purification system, coupled with MS has been widely used mainly to reduce the contaminants. We review here a general principle for AP-MS-based characterization of protein complexes and we explore several protein complexes identified in pluripotent stem cell biology and cancer biology as examples.
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Affiliation(s)
| | - Chung-Hsuan Chen
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan.
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17
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Huan Y, Wang H, Wu Z, Zhang J, Zhu J, Liu Z, He H. Epigenetic Modification of Cloned Embryos Improves Nanog Reprogramming in Pigs. Cell Reprogram 2015; 17:191-8. [PMID: 26053519 PMCID: PMC4487246 DOI: 10.1089/cell.2014.0103] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Incomplete reprogramming of pluripotent genes in cloned embryos is associated with low cloning efficiency. Epigenetic modification agents have been shown to enhance the developmental competence of cloned embryos; however, the effect of the epigenetic modification agents on pluripotent gene reprogramming remains unclear. Here, we investigated Nanog reprogramming and the expression patterns of pluripotent transcription factors during early embryo development in pigs. We found that compared with fertilized embryos, cloned embryos displayed higher methylation in the promoter and 5'-untranslated region and lower methylation in the first exon of Nanog. When 5-aza-2'-deoxycytidine (5-aza-dC) or trichostatin A (TSA) enhanced the development of porcine cloned embryos, Nanog methylation reprogramming was also improved, similar to that detected in fertilized counterparts. Furthermore, our results showed that the epigenetic modification agents improved the expression levels of Oct4 and Sox2 and effectively promoted Nanog transcription in cloned embryos. In conclusion, our results demonstrated that the epigenetic modification agent 5-aza-dC or TSA improved Nanog methylation reprogramming and the expression patterns of pluripotent transcription factors, thereby resulting in the enhanced expression of Nanog and high development of porcine cloned embryos. This work has important implications in the improvement of cloning efficiency.
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Affiliation(s)
- Yanjun Huan
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong Province, 250010, China
- College of Life Science, Northeast Agricultural University, Haerbin, Heilongjiang Province, 150030, China
| | - Hongmei Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong Province, 250010, China
| | - Zhanfeng Wu
- Shouguang City Hospital of Chinese medicine, Weifang, Shandong Province, 262700, China
| | - Jiguang Zhang
- Shouguang City Hospital of Chinese medicine, Weifang, Shandong Province, 262700, China
| | - Jiang Zhu
- College of Life Science, Northeast Agricultural University, Haerbin, Heilongjiang Province, 150030, China
| | - Zhonghua Liu
- College of Life Science, Northeast Agricultural University, Haerbin, Heilongjiang Province, 150030, China
| | - Hongbin He
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, Shandong Province, 250010, China
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18
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Chen Q, Gao S, He W, Kou X, Zhao Y, Wang H, Gao S. Xist repression shows time-dependent effects on the reprogramming of female somatic cells to induced pluripotent stem cells. Stem Cells 2015; 32:2642-56. [PMID: 24965076 DOI: 10.1002/stem.1775] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Revised: 05/17/2014] [Accepted: 05/23/2014] [Indexed: 11/10/2022]
Abstract
Although the reactivation of silenced X chromosomes has been observed as part of the process of reprogramming female somatic cells into induced pluripotent stem cells (iPSCs), it remains unknown whether repression of the X-inactive specific transcript (Xist) can greatly enhance female iPSC induction similar to that observed in somatic cell nuclear transfer studies. In this study, we discovered that the repression of Xist plays opposite roles in the early and late phases of female iPSCs induction. Our results demonstrate that the downregulation of Xist by an isopropyl β-d-1-thiogalactopyranoside (IPTG)-inducible short hairpin RNA (shRNA) system can greatly impair the mesenchymal-to-epithelial transition (MET) in the early phase of iPSC induction but can significantly promote the transition of pre-iPSCs to iPSCs in the late phase. Furthermore, we demonstrate that although the knockdown of Xist did not affect the H3K27me3 modification on the X chromosome, macroH2A was released from the inactivated X chromosome (Xi). This enables the X chromosome silencing to be a reversible event. Moreover, we demonstrate that the supplementation of vitamin C (Vc) can augment and stabilize the reversible X chromosome by preventing the relocalization of macroH2A to the Xi. Therefore, our study reveals an opposite role of Xist repression in the early and late stages of reprogramming female somatic cells to pluripotency and demonstrates that the release of macroH2A by Xist repression enables the transition from pre-iPSCs to iPSCs.
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Affiliation(s)
- Qi Chen
- School of Life Sciences, Beijing Normal University, Beijing, China; National Institute of Biological Sciences (NIBS), Beijing, China
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19
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Glycolysis-mediated changes in acetyl-CoA and histone acetylation control the early differentiation of embryonic stem cells. Cell Metab 2015; 21:392-402. [PMID: 25738455 DOI: 10.1016/j.cmet.2015.02.002] [Citation(s) in RCA: 460] [Impact Index Per Article: 51.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 11/16/2014] [Accepted: 02/06/2015] [Indexed: 02/07/2023]
Abstract
Loss of pluripotency is a gradual event whose initiating factors are largely unknown. Here we report the earliest metabolic changes induced during the first hours of differentiation. High-resolution NMR identified 44 metabolites and a distinct metabolic transition occurring during early differentiation. Metabolic and transcriptional analyses showed that pluripotent cells produced acetyl-CoA through glycolysis and rapidly lost this function during differentiation. Importantly, modulation of glycolysis blocked histone deacetylation and differentiation in human and mouse embryonic stem cells. Acetate, a precursor of acetyl-CoA, delayed differentiation and blocked early histone deacetylation in a dose-dependent manner. Inhibitors upstream of acetyl-CoA caused differentiation of pluripotent cells, while those downstream delayed differentiation. Our results show a metabolic switch causing a loss of histone acetylation and pluripotent state during the first hours of differentiation. Our data highlight the important role metabolism plays in pluripotency and suggest that a glycolytic switch controlling histone acetylation can release stem cells from pluripotency.
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20
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Wang L, Du Y, Ward JM, Shimbo T, Lackford B, Zheng X, Miao YL, Zhou B, Han L, Fargo DC, Jothi R, Williams CJ, Wade PA, Hu G. INO80 facilitates pluripotency gene activation in embryonic stem cell self-renewal, reprogramming, and blastocyst development. Cell Stem Cell 2014; 14:575-91. [PMID: 24792115 DOI: 10.1016/j.stem.2014.02.013] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 12/17/2013] [Accepted: 02/21/2014] [Indexed: 11/17/2022]
Abstract
The master transcription factors play integral roles in the pluripotency transcription circuitry of embryonic stem cells (ESCs). How they selectively activate expression of the pluripotency network while simultaneously repressing genes involved in differentiation is not fully understood. Here, we define a requirement for the INO80 complex, a SWI/SNF family chromatin remodeler, in ESC self-renewal, somatic cell reprogramming, and blastocyst development. We show that Ino80, the chromatin remodeling ATPase, co-occupies pluripotency gene promoters with the master transcription factors, and its occupancy is dependent on OCT4 and WDR5. At the pluripotency genes, Ino80 maintains an open chromatin architecture and licenses recruitment of Mediator and RNA polymerase II for gene activation. Our data reveal an essential role for INO80 in the expression of the pluripotency network and illustrate the coordination among chromatin remodeler, transcription factor, and histone-modifying enzyme in the regulation of the pluripotent state.
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Affiliation(s)
- Li Wang
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Ying Du
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - James M Ward
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Takashi Shimbo
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Brad Lackford
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Xiaofeng Zheng
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Yi-liang Miao
- Laboratory of Reproductive and Developmental Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Bingying Zhou
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Leng Han
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, The University of Texas, Houston, TX 77030, USA
| | - David C Fargo
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Raja Jothi
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Carmen J Williams
- Laboratory of Reproductive and Developmental Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Paul A Wade
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA.
| | - Guang Hu
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA.
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21
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Wang L, Miao YL, Zheng X, Lackford B, Zhou B, Han L, Yao C, Ward JM, Burkholder A, Lipchina I, Fargo DC, Hochedlinger K, Shi Y, Williams CJ, Hu G. The THO complex regulates pluripotency gene mRNA export and controls embryonic stem cell self-renewal and somatic cell reprogramming. Cell Stem Cell 2014; 13:676-90. [PMID: 24315442 DOI: 10.1016/j.stem.2013.10.008] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 09/14/2013] [Accepted: 10/16/2013] [Indexed: 12/20/2022]
Abstract
Embryonic stem cell (ESC) self-renewal and differentiation are governed by a broad-ranging regulatory network. Although the transcriptional regulatory mechanisms involved have been investigated extensively, posttranscriptional regulation is still poorly understood. Here we describe a critical role of the THO complex in ESC self-renewal and differentiation. We show that THO preferentially interacts with pluripotency gene transcripts through Thoc5 and is required for self-renewal at least in part by regulating their export and expression. During differentiation, THO loses its interaction with those transcripts due to reduced Thoc5 expression, leading to decreased expression of pluripotency proteins that facilitates exit from self-renewal. THO is also important for the establishment of pluripotency, because its depletion inhibits somatic cell reprogramming and blastocyst development. Together, our data indicate that THO regulates pluripotency gene mRNA export to control ESC self-renewal and differentiation, and therefore uncover a role for this aspect of posttranscriptional regulation in stem cell fate specification.
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Affiliation(s)
- Li Wang
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
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22
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Tan X, Xu X, Elkenani M, Smorag L, Zechner U, Nolte J, Engel W, Pantakani DK. Zfp819, a novel KRAB-zinc finger protein, interacts with KAP1 and functions in genomic integrity maintenance of mouse embryonic stem cells. Stem Cell Res 2013; 11:1045-59. [DOI: 10.1016/j.scr.2013.07.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Revised: 07/09/2013] [Accepted: 07/22/2013] [Indexed: 01/12/2023] Open
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23
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Wierstra I. The transcription factor FOXM1 (Forkhead box M1): proliferation-specific expression, transcription factor function, target genes, mouse models, and normal biological roles. Adv Cancer Res 2013; 118:97-398. [PMID: 23768511 DOI: 10.1016/b978-0-12-407173-5.00004-2] [Citation(s) in RCA: 125] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
FOXM1 (Forkhead box M1) is a typical proliferation-associated transcription factor, which stimulates cell proliferation and exhibits a proliferation-specific expression pattern. Accordingly, both the expression and the transcriptional activity of FOXM1 are increased by proliferation signals, but decreased by antiproliferation signals, including the positive and negative regulation by protooncoproteins or tumor suppressors, respectively. FOXM1 stimulates cell cycle progression by promoting the entry into S-phase and M-phase. Moreover, FOXM1 is required for proper execution of mitosis. Accordingly, FOXM1 regulates the expression of genes, whose products control G1/S-transition, S-phase progression, G2/M-transition, and M-phase progression. Additionally, FOXM1 target genes encode proteins with functions in the execution of DNA replication and mitosis. FOXM1 is a transcriptional activator with a forkhead domain as DNA binding domain and with a very strong acidic transactivation domain. However, wild-type FOXM1 is (almost) inactive because the transactivation domain is repressed by three inhibitory domains. Inactive FOXM1 can be converted into a very potent transactivator by activating signals, which release the transactivation domain from its inhibition by the inhibitory domains. FOXM1 is essential for embryonic development and the foxm1 knockout is embryonically lethal. In adults, FOXM1 is important for tissue repair after injury. FOXM1 prevents premature senescence and interferes with contact inhibition. FOXM1 plays a role for maintenance of stem cell pluripotency and for self-renewal capacity of stem cells. The functions of FOXM1 in prevention of polyploidy and aneuploidy and in homologous recombination repair of DNA-double-strand breaks suggest an importance of FOXM1 for the maintenance of genomic stability and chromosomal integrity.
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24
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Tabrizi GA, Böse K, Reimann Y, Kessel M. Geminin is required for the maintenance of pluripotency. PLoS One 2013; 8:e73826. [PMID: 24069236 PMCID: PMC3777968 DOI: 10.1371/journal.pone.0073826] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 07/23/2013] [Indexed: 12/28/2022] Open
Abstract
Pluripotency requires the expression of the three core transcriptions factors Oct4, Sox2 and Nanog, as well as further, complementary proteins. The geminin protein is part of this network, and was shown to play a role in the regulation of DNA replication, the control of the cell cycle, and the acquisition of neural fate. It is highly expressed in the early embryo, in particular the epiblast and the early neural ectoderm, and also in pluripotent embryonic stem cells. The genetic inactivation of geminin resulted in lethality after the first few cell divisions, and thus prohibited the outgrowth of pluripotent cells. We established embryonic stem cells allowing the deletion of the geminin gene by induction of of Cre-recombinase with tamoxifen. Here, we show that geminin deficiency quickly leads to a loss of pluripotency, and to differentiation into the mesendodermal direction with high Oct4/low Sox2 levels. Simultaneous loss of geminin and induction of the neural lineage resulted in immediate apoptosis. These results suggested that in early development geminin functions via the co-expressed Sox2 gene. We found that the stem cell enhancer SRR2 of Sox2 is occupied by the activating esBAF complex in the presence of geminin, but becomes epigenetically repressed in its absence by the Polycomb repressive complex PRC2. The importance of geminin for Sox2 expression also explains the absolute requirement for geminin during the induction of pluripotency by OSKM viruses. In summary, geminin is required for Sox2 expression, and thus for the maintenance of totipotency, pluripotency and the early neural lineage.
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Affiliation(s)
| | - Kerstin Böse
- Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Yvonne Reimann
- Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Michael Kessel
- Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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25
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Jiang K, Ren C, Nair VD. MicroRNA-137 represses Klf4 and Tbx3 during differentiation of mouse embryonic stem cells. Stem Cell Res 2013; 11:1299-313. [PMID: 24084696 DOI: 10.1016/j.scr.2013.09.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 09/05/2013] [Accepted: 09/05/2013] [Indexed: 02/01/2023] Open
Abstract
MicroRNA-137 (miR-137) has been shown to play an important role in the differentiation of neural stem cells. Embryonic stem (ES) cells have the potential to differentiate into different cell types including neurons; however, the contribution of miR-137 in the maintenance and differentiation of ES cells remains unknown. Here, we show that miR-137 is mainly expressed in ES cells at the mitotic phase of the cell cycle and highly upregulated during differentiation. We identify that ES cell transcription factors, Klf4 and Tbx3, are downstream targets of miR-137, and we show that endogenous miR-137 represses the 3' untranslated regions of Klf4 and Tbx3. Transfection of ES cells with mature miR-137 RNA duplexes led to a significant reduction in cell proliferation and the expression of Klf4, Tbx3, and other self-renewal genes. Furthermore, we demonstrate that increased miR-137 expression accelerates differentiation of ES cells in vitro. Loss of miR-137 during ES cell differentiation significantly impeded neuronal gene expression and morphogenesis. Taken together, our results suggest that miR-137 regulates ES cell proliferation and differentiation by repressing the expression of downstream targets, including Klf4 and Tbx3.
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Affiliation(s)
- Ke Jiang
- Department of Neurology, Mount Sinai School of Medicine, New York, NY 10029, USA
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26
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Rosselló RA, Chen CC, Dai R, Howard JT, Hochgeschwender U, Jarvis ED. Mammalian genes induce partially reprogrammed pluripotent stem cells in non-mammalian vertebrate and invertebrate species. eLife 2013; 2:e00036. [PMID: 24015354 PMCID: PMC3762186 DOI: 10.7554/elife.00036] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 07/27/2013] [Indexed: 12/21/2022] Open
Abstract
Cells are fundamental units of life, but little is known about evolution of cell states. Induced pluripotent stem cells (iPSCs) are once differentiated cells that have been re-programmed to an embryonic stem cell-like state, providing a powerful platform for biology and medicine. However, they have been limited to a few mammalian species. Here we found that a set of four mammalian transcription factor genes used to generate iPSCs in mouse and humans can induce a partially reprogrammed pluripotent stem cell (PRPSCs) state in vertebrate and invertebrate model organisms, in mammals, birds, fish, and fly, which span 550 million years from a common ancestor. These findings are one of the first to show cross-lineage stem cell-like induction, and to generate pluripotent-like cells for several of these species with in vivo chimeras. We suggest that the stem-cell state may be highly conserved across a wide phylogenetic range. DOI:http://dx.doi.org/10.7554/eLife.00036.001 Stem cells are ‘pluripotent’—in other words, they have the potential to become many other cell types. This ability makes them extremely valuable for research. They also hold substantial promise for medical applications, since they can be used to replace cells lost or damaged by disease or injury. Embryos represent a rich source of stem cells; however, obtaining these cells from human embryos raises obvious ethical and practical concerns, and they have also been difficult to isolate from many species. A recent discovery circumvented these issues for humans and several mammalian species commonly studied in the laboratory. This technique can turn cells from adult mammals into ‘induced pluripotent stem cells’, or iPSCs, by switching on four genes. Nevertheless, no analogous method has yet been established to create similar cell populations in non-mammalian organisms, which are also important models for human development and disease. Now, Rosselló et al. have shown that cells from both invertebrate and non-mammalian vertebrate species—including birds, fish and insects—can be reprogrammed into cells that closely resemble iPSCs. Intriguingly, these cells were created by switching on the same four genes that generate iPSCs in mammals, even though vertebrates and invertebrates are separated by around 550 million years of evolution. Rosselló et al. used a viral vector that carries the four stem-cell genes (from the mouse) into target cells from the different species. The genetically altered cells developed into iPSC-like cells with many of the characteristics of natural mammalian and bird stem cells. To confirm that the cells were pluripotent, Rossello et al. first showed that the cells could develop into primitive early embryos called embryoid bodies. For the vertebrate species tested, the embryoid bodies contained cells from each of the three main vertebrate embryo cell types. Secondly, iPSC-like cells from two organisms—chicks and zebrafish—formed various mature cell types when injected into developing chick or zebrafish embryos. These results have two important implications. They suggest that the genetic mechanisms by which cells can be reprogrammed into a stem-like state have been conserved through 550 million years of evolution; additionally, they demonstrate that stem-like cells can be generated from important experimental organisms, and provide an important tool for both biological and biomedical research. DOI:http://dx.doi.org/10.7554/eLife.00036.002
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Affiliation(s)
- Ricardo Antonio Rosselló
- Department of Biochemistry , University of Puerto Rico Medical Sciences Campus , San Juan , Puerto Rico ; Department of Neurobiology , Duke University Medical Center , Durham , United States ; Howard Hughes Medical Institute, Duke University Medical Center , Durham , United States
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Sinha A, Khadilkar RJ, S VK, Roychowdhury Sinha A, Inamdar MS. Conserved regulation of the Jak/STAT pathway by the endosomal protein asrij maintains stem cell potency. Cell Rep 2013; 4:649-58. [PMID: 23972987 PMCID: PMC4673900 DOI: 10.1016/j.celrep.2013.07.029] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2012] [Revised: 05/18/2013] [Accepted: 07/18/2013] [Indexed: 11/17/2022] Open
Abstract
Asrij/OCIAD1 is an endosomal protein expressed in stem cells and cardiovascular lineages and aberrantly expressed in several cancers. We show that dose-dependent modulation of cytokine-dependent JAK/STAT signaling by Asrij regulates mouse embryonic stem cell pluripotency as well as Drosophila hematopoietic stem cell maintenance. Furthermore, mouse asrij can substitute for Drosophila asrij, indicating that they are true homologs. We identify a conserved region of Asrij that is necessary and sufficient for vesicular localization and function. We also show that Asrij and STAT3 colocalize in endosomes and interact biochemically. We propose that Asrij provides an endosomal scaffold for STAT3 interaction and activation, and may similarly control other circuits that maintain stemness. Thus, Asrij provides a key point of control for spatial and kinetic regulation of stem cell signals.
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Affiliation(s)
- Abhishek Sinha
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
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28
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Abstract
Stem cells are a unique population that lies at the summit of any, or at least most, biological systems. They can differentiate in a variety of mature cell types, but they also have the ability to self-renew, that is, the capacity to divide and retain all the features of the mother cell. The regulation of self-renewal has been studied for many years, but several aspects of this regulation are still vague. The combined decision to divide and self-renew or differentiate suggests that the mechanisms that regulate self-renewal and cell cycle activity are intermingled. While inactivation of many cell cycle regulators impacts the physiological and pathological biology of stem cells, the exact mechanisms that link the decision to enter the cell cycle and the choice of the cellular fate are poorly understood. The multiplicity of signals and pathways regulating self-renewal add to the complexity of the phenomenon. Here, I will review the described links between the cell cycle and self-renewal and discuss the role of the niche in the regulation of both mechanisms.
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Affiliation(s)
- Patrick Viatour
- Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, PA, USA ; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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Wierstra I. FOXM1 (Forkhead box M1) in tumorigenesis: overexpression in human cancer, implication in tumorigenesis, oncogenic functions, tumor-suppressive properties, and target of anticancer therapy. Adv Cancer Res 2013; 119:191-419. [PMID: 23870513 DOI: 10.1016/b978-0-12-407190-2.00016-2] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
FOXM1 (Forkhead box M1) is a typical proliferation-associated transcription factor and is also intimately involved in tumorigenesis. FOXM1 stimulates cell proliferation and cell cycle progression by promoting the entry into S-phase and M-phase. Additionally, FOXM1 is required for proper execution of mitosis. In accordance with its role in stimulation of cell proliferation, FOXM1 exhibits a proliferation-specific expression pattern and its expression is regulated by proliferation and anti-proliferation signals as well as by proto-oncoproteins and tumor suppressors. Since these factors are often mutated, overexpressed, or lost in human cancer, the normal control of the foxm1 expression by them provides the basis for deregulated FOXM1 expression in tumors. Accordingly, FOXM1 is overexpressed in many types of human cancer. FOXM1 is intimately involved in tumorigenesis, because it contributes to oncogenic transformation and participates in tumor initiation, growth, and progression, including positive effects on angiogenesis, migration, invasion, epithelial-mesenchymal transition, metastasis, recruitment of tumor-associated macrophages, tumor-associated lung inflammation, self-renewal capacity of cancer cells, prevention of premature cellular senescence, and chemotherapeutic drug resistance. However, in the context of urethane-induced lung tumorigenesis, FOXM1 has an unexpected tumor suppressor role in endothelial cells because it limits pulmonary inflammation and canonical Wnt signaling in epithelial lung cells, thereby restricting carcinogenesis. Accordingly, FOXM1 plays a role in homologous recombination repair of DNA double-strand breaks and maintenance of genomic stability, that is, prevention of polyploidy and aneuploidy. The implication of FOXM1 in tumorigenesis makes it an attractive target for anticancer therapy, and several antitumor drugs have been reported to decrease FOXM1 expression.
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Zwaka T. Pluripotency Network in Embryonic Stem Cells: Maybe Leibniz Was Right All Along. Cell Stem Cell 2012; 11:441-2. [DOI: 10.1016/j.stem.2012.09.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Ion channels in hematopoietic and mesenchymal stem cells. Stem Cells Int 2012; 2012:217910. [PMID: 22919401 PMCID: PMC3420091 DOI: 10.1155/2012/217910] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Accepted: 07/05/2012] [Indexed: 12/19/2022] Open
Abstract
Hematopoietic stem cells (HSCs) reside in bone marrow niches and give rise to hematopoietic precursor cells (HPCs). These have more restricted lineage potential and eventually differentiate into specific blood cell types. Bone marrow also contains mesenchymal stromal cells (MSCs), which present multilineage differentiation potential toward mesodermal cell types. In bone marrow niches, stem cell interaction with the extracellular matrix is mediated by integrin receptors. Ion channels regulate cell proliferation and differentiation by controlling intracellular Ca(2+), cell volume, release of growth factors, and so forth. Although little evidence is available about the ion channel roles in true HSCs, increasing information is available about HPCs and MSCs, which present a complex pattern of K(+) channel expression. K(+) channels cooperate with Ca(2+) and Cl(-) channels in regulating calcium entry and cell volume during mitosis. Other K(+) channels modulate the integrin-dependent interaction between leukemic progenitor cells and the niche stroma. These channels can also regulate leukemia cell interaction with MSCs, which also involves integrin receptors and affects the MSC-mediated protection from chemotherapy. Ligand-gated channels are also implicated in these processes. Nicotinic acetylcholine receptors regulate cell proliferation and migration in HSCs and MSCs and may be implicated in the harmful effects of smoking.
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