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Xu X, Wang W, Liu Y, Bäckemo J, Heuchel M, Wang W, Nie Y, Iqbal I, Kratz K, Lendlein A, Ma N. Substrates mimicking the blastocyst geometry revert pluripotent stem cell to naivety. NATURE MATERIALS 2024:10.1038/s41563-024-01971-4. [PMID: 39134648 DOI: 10.1038/s41563-024-01971-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 07/11/2024] [Indexed: 09/22/2024]
Abstract
Naive pluripotent stem cells have the highest developmental potential but their in vivo existence in the blastocyst is transient. Here we report a blastocyst motif substrate for the in vitro reversion of mouse and human pluripotent stem cells to a naive state. The substrate features randomly varied microstructures, which we call motifs, mimicking the geometry of the blastocyst. Motifs representing mouse-blastocyst-scaled curvature ranging between 15 and 62 mm-1 were the most efficient in promoting reversion to naivety, as determined by time-resolved correlative analysis. In these substrates, apical constriction enhances E-cadherin/RAC1 signalling and activates the mechanosensitive nuclear transducer YAP, promoting the histone modification of pluripotency genes. This results in enhanced levels of pluripotency transcription factor NANOG, which persist even after cells are removed from the substrate. Pluripotent stem cells cultured in blastocyst motif substrates display a higher development potential in generating embryoid bodies and teratomas. These findings shed light on naivety-promoting substrate design and their large-scale implementation.
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Affiliation(s)
- Xun Xu
- Institute of Active Polymers and Berlin-Brandenburg Center for Regenerative Therapies, Helmholtz-Zentrum Hereon, Teltow, Germany
| | - Weiwei Wang
- Institute of Active Polymers and Berlin-Brandenburg Center for Regenerative Therapies, Helmholtz-Zentrum Hereon, Teltow, Germany
| | - Yue Liu
- Institute of Active Polymers and Berlin-Brandenburg Center for Regenerative Therapies, Helmholtz-Zentrum Hereon, Teltow, Germany
| | - Johan Bäckemo
- Institute of Active Polymers and Berlin-Brandenburg Center for Regenerative Therapies, Helmholtz-Zentrum Hereon, Teltow, Germany
- Institute of Chemistry, University of Potsdam, Potsdam, Germany
| | - Matthias Heuchel
- Institute of Active Polymers and Berlin-Brandenburg Center for Regenerative Therapies, Helmholtz-Zentrum Hereon, Teltow, Germany
| | - Wei Wang
- Institute of Active Polymers and Berlin-Brandenburg Center for Regenerative Therapies, Helmholtz-Zentrum Hereon, Teltow, Germany
| | - Yan Nie
- Institute of Active Polymers and Berlin-Brandenburg Center for Regenerative Therapies, Helmholtz-Zentrum Hereon, Teltow, Germany
| | - Imran Iqbal
- Institute of Active Polymers and Berlin-Brandenburg Center for Regenerative Therapies, Helmholtz-Zentrum Hereon, Teltow, Germany
| | - Karl Kratz
- Institute of Active Polymers and Berlin-Brandenburg Center for Regenerative Therapies, Helmholtz-Zentrum Hereon, Teltow, Germany
- Helmholtz Virtual Institute-Multifunctional Biomaterials for Medicine, Berlin and Teltow, Teltow, Germany
| | - Andreas Lendlein
- Institute of Active Polymers and Berlin-Brandenburg Center for Regenerative Therapies, Helmholtz-Zentrum Hereon, Teltow, Germany.
- Institute of Chemistry, University of Potsdam, Potsdam, Germany.
- Helmholtz Virtual Institute-Multifunctional Biomaterials for Medicine, Berlin and Teltow, Teltow, Germany.
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany.
| | - Nan Ma
- Institute of Active Polymers and Berlin-Brandenburg Center for Regenerative Therapies, Helmholtz-Zentrum Hereon, Teltow, Germany.
- Helmholtz Virtual Institute-Multifunctional Biomaterials for Medicine, Berlin and Teltow, Teltow, Germany.
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany.
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2
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Simon CS, Garg V, Kuo YY, Niakan KK, Hadjantonakis AK. ETV4 and ETV5 Orchestrate FGF-Mediated Lineage Specification and Epiblast Maturation during Early Mouse Development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.24.604964. [PMID: 39091858 PMCID: PMC11291132 DOI: 10.1101/2024.07.24.604964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Cell fate decisions in early mammalian embryos are tightly regulated processes crucial for proper development. While FGF signaling plays key roles in early embryo patterning, its downstream effectors remain poorly understood. Our study demonstrates that the transcription factors Etv4 and Etv5 are critical mediators of FGF signaling in cell lineage specification and maturation in mouse embryos. We show that loss of Etv5 compromises primitive endoderm formation at pre-implantation stages. Furthermore, Etv4/5 deficiency delays naïve pluripotency exit and epiblast maturation, leading to elevated NANOG and reduced OTX2 expression within the blastocyst epiblast. As a consequence of delayed pluripotency progression, Etv4/5 deficient embryos exhibit anterior visceral endoderm migration defects post-implantation, a process essential for coordinated embryonic patterning and gastrulation initiation. Our results demonstrate the successive roles of these FGF signaling effectors in early lineage specification and embryonic body plan establishment, providing new insights into the molecular control of mammalian development.
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Affiliation(s)
- Claire S. Simon
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Human Embryo and Stem Cell Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- The Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
| | - Vidur Garg
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ying-Yi Kuo
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Kathy K. Niakan
- Human Embryo and Stem Cell Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- The Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
- Wellcome Trust – Medical Research Council Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge CB2 0AW, UK
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Anna-Katerina Hadjantonakis
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
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3
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Zhao H, Li D, Xiao X, Liu C, Chen G, Su X, Yan Z, Gu S, Wang Y, Li G, Feng J, Li W, Chen P, Yang J, Li Q. Pluripotency state transition of embryonic stem cells requires the turnover of histone chaperone FACT on chromatin. iScience 2024; 27:108537. [PMID: 38213626 PMCID: PMC10783625 DOI: 10.1016/j.isci.2023.108537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 10/06/2023] [Accepted: 11/20/2023] [Indexed: 01/13/2024] Open
Abstract
The differentiation of embryonic stem cells (ESCs) begins with the transition from the naive to the primed state. The formative state was recently established as a critical intermediate between the two states. Here, we demonstrate the role of the histone chaperone FACT in regulating the naive-to-formative transition. We found that the Q265K mutation in the FACT subunit SSRP1 increased the binding of FACT to histone H3-H4, impaired nucleosome disassembly in vitro, and reduced the turnover of FACT on chromatin in vivo. Strikingly, mouse ESCs harboring this mutation showed elevated naive-to-formative transition. Mechanistically, the SSRP1-Q265K mutation enriched FACT at the enhancers of formative-specific genes to increase targeted gene expression. Together, these findings suggest that the turnover of FACT on chromatin is crucial for regulating the enhancers of formative-specific genes, thereby mediating the naive-to-formative transition. This study highlights the significance of FACT in fine-tuning cell fate transition during early development.
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Affiliation(s)
- Hang Zhao
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Di Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Xue Xiao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Cuifang Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Guifang Chen
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, China
| | - Xiaoyu Su
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Zhenxin Yan
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Shijia Gu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Yizhou Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Guohong Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianxun Feng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Wei Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Ping Chen
- Department of Immunology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Jiayi Yang
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, China
| | - Qing Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
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4
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Saha D, Hailu S, Hada A, Lee J, Luo J, Ranish JA, Lin YC, Feola K, Persinger J, Jain A, Liu B, Lu Y, Sen P, Bartholomew B. The AT-hook is an evolutionarily conserved auto-regulatory domain of SWI/SNF required for cell lineage priming. Nat Commun 2023; 14:4682. [PMID: 37542049 PMCID: PMC10403523 DOI: 10.1038/s41467-023-40386-8] [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: 12/30/2022] [Accepted: 07/26/2023] [Indexed: 08/06/2023] Open
Abstract
The SWI/SNF ATP-dependent chromatin remodeler is a master regulator of the epigenome, controlling pluripotency and differentiation. Towards the C-terminus of the catalytic subunit of SWI/SNF is a motif called the AT-hook that is evolutionary conserved. The AT-hook is present in many chromatin modifiers and generally thought to help anchor them to DNA. We observe however that the AT-hook regulates the intrinsic DNA-stimulated ATPase activity aside from promoting SWI/SNF recruitment to DNA or nucleosomes by increasing the reaction velocity a factor of 13 with no accompanying change in substrate affinity (KM). The changes in ATP hydrolysis causes an equivalent change in nucleosome movement, confirming they are tightly coupled. The catalytic subunit's AT-hook is required in vivo for SWI/SNF remodeling activity in yeast and mouse embryonic stem cells. The AT-hook in SWI/SNF is required for transcription regulation and activation of stage-specific enhancers critical in cell lineage priming. Similarly, growth assays suggest the AT-hook is required in yeast SWI/SNF for activation of genes involved in amino acid biosynthesis and metabolizing ethanol. Our findings highlight the importance of studying SWI/SNF attenuation versus eliminating the catalytic subunit or completely shutting down its enzymatic activity.
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Affiliation(s)
- Dhurjhoti Saha
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA
- University of Texas MD Anderson Cancer Center, Center for Cancer Epigenetics, Houston, TX, 77230, USA
| | - Solomon Hailu
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA
- University of Texas MD Anderson Cancer Center, Center for Cancer Epigenetics, Houston, TX, 77230, USA
- Illumina, 5200 Illumina Way, San Diego, CA, 92122, USA
| | - Arjan Hada
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA
- University of Texas MD Anderson Cancer Center, Center for Cancer Epigenetics, Houston, TX, 77230, USA
| | - Junwoo Lee
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA
- University of Texas MD Anderson Cancer Center, Center for Cancer Epigenetics, Houston, TX, 77230, USA
| | - Jie Luo
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | - Jeff A Ranish
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | - Yuan-Chi Lin
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA
- University of Texas MD Anderson Cancer Center, Center for Cancer Epigenetics, Houston, TX, 77230, USA
- BioAgilytix, Durham, NC, 27713, USA
| | - Kyle Feola
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA
- Department of Internal Medicine (Nephrology) and Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Jim Persinger
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA
- University of Texas MD Anderson Cancer Center, Center for Cancer Epigenetics, Houston, TX, 77230, USA
| | - Abhinav Jain
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA
- University of Texas MD Anderson Cancer Center, Center for Cancer Epigenetics, Houston, TX, 77230, USA
| | - Bin Liu
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA
| | - Yue Lu
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA
| | - Payel Sen
- Laboratory of Genetics and Genomics, National Institute on Aging, Baltimore, MD, 21224, USA
| | - Blaine Bartholomew
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA.
- University of Texas MD Anderson Cancer Center, Center for Cancer Epigenetics, Houston, TX, 77230, USA.
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5
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Kohler TN, De Jonghe J, Ellermann AL, Yanagida A, Herger M, Slatery EM, Weberling A, Munger C, Fischer K, Mulas C, Winkel A, Ross C, Bergmann S, Franze K, Chalut K, Nichols J, Boroviak TE, Hollfelder F. Plakoglobin is a mechanoresponsive regulator of naive pluripotency. Nat Commun 2023; 14:4022. [PMID: 37419903 PMCID: PMC10329048 DOI: 10.1038/s41467-023-39515-0] [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: 03/14/2022] [Accepted: 06/09/2023] [Indexed: 07/09/2023] Open
Abstract
Biomechanical cues are instrumental in guiding embryonic development and cell differentiation. Understanding how these physical stimuli translate into transcriptional programs will provide insight into mechanisms underlying mammalian pre-implantation development. Here, we explore this type of regulation by exerting microenvironmental control over mouse embryonic stem cells. Microfluidic encapsulation of mouse embryonic stem cells in agarose microgels stabilizes the naive pluripotency network and specifically induces expression of Plakoglobin (Jup), a vertebrate homolog of β-catenin. Overexpression of Plakoglobin is sufficient to fully re-establish the naive pluripotency gene regulatory network under metastable pluripotency conditions, as confirmed by single-cell transcriptome profiling. Finally, we find that, in the epiblast, Plakoglobin was exclusively expressed at the blastocyst stage in human and mouse embryos - further strengthening the link between Plakoglobin and naive pluripotency in vivo. Our work reveals Plakoglobin as a mechanosensitive regulator of naive pluripotency and provides a paradigm to interrogate the effects of volumetric confinement on cell-fate transitions.
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Affiliation(s)
- Timo N Kohler
- Department of Biochemistry, University of Cambridge, Hopkins Building, Tennis Court Road, Cambridge, CB2 1QW, UK
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - Joachim De Jonghe
- Department of Biochemistry, University of Cambridge, Hopkins Building, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Anna L Ellermann
- Department of Biochemistry, University of Cambridge, Hopkins Building, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Ayaka Yanagida
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK
- Department of Veterinary Anatomy, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan
- Stem Cell Therapy Laboratory, Advanced Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Michael Herger
- Department of Biochemistry, University of Cambridge, Hopkins Building, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Erin M Slatery
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3DY, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, CB2 3EG, UK
| | - Antonia Weberling
- Department of Biochemistry, University of Cambridge, Hopkins Building, Tennis Court Road, Cambridge, CB2 1QW, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3DY, UK
| | - Clara Munger
- Department of Biochemistry, University of Cambridge, Hopkins Building, Tennis Court Road, Cambridge, CB2 1QW, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3DY, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, CB2 3EG, UK
| | - Katrin Fischer
- Department of Biochemistry, University of Cambridge, Hopkins Building, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Carla Mulas
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, SE1 1UL, UK
- Altos Labs, Cambridge Institute of Science, Cambridge, UK
| | - Alex Winkel
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3DY, UK
| | - Connor Ross
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3DY, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Sophie Bergmann
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3DY, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, CB2 3EG, UK
| | - Kristian Franze
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3DY, UK
- Institute of Medical Physics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Henkestr. 91, 91052, Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, 91054, Erlangen, Germany
| | - Kevin Chalut
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK
- Altos Labs, Cambridge Institute of Science, Cambridge, UK
| | - Jennifer Nichols
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3DY, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Thorsten E Boroviak
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK.
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3DY, UK.
- Centre for Trophoblast Research, University of Cambridge, Cambridge, CB2 3EG, UK.
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, Hopkins Building, Tennis Court Road, Cambridge, CB2 1QW, UK.
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6
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Carbognin E, Carlini V, Panariello F, Chieregato M, Guerzoni E, Benvegnù D, Perrera V, Malucelli C, Cesana M, Grimaldi A, Mutarelli M, Carissimo A, Tannenbaum E, Kugler H, Hackett JA, Cacchiarelli D, Martello G. Esrrb guides naive pluripotent cells through the formative transcriptional programme. Nat Cell Biol 2023; 25:643-657. [PMID: 37106060 PMCID: PMC7614557 DOI: 10.1038/s41556-023-01131-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 03/15/2023] [Indexed: 04/29/2023]
Abstract
During embryonic development, naive pluripotent epiblast cells transit to a formative state. The formative epiblast cells form a polarized epithelium, exhibit distinct transcriptional and epigenetic profiles and acquire competence to differentiate into all somatic and germline lineages. However, we have limited understanding of how the transition to a formative state is molecularly controlled. Here we used murine embryonic stem cell models to show that ESRRB is both required and sufficient to activate formative genes. Genetic inactivation of Esrrb leads to illegitimate expression of mesendoderm and extra-embryonic markers, impaired formative expression and failure to self-organize in 3D. Functionally, this results in impaired ability to generate formative stem cells and primordial germ cells in the absence of Esrrb. Computational modelling and genomic analyses revealed that ESRRB occupies key formative genes in naive cells and throughout the formative state. In so doing, ESRRB kickstarts the formative transition, leading to timely and unbiased capacity for multi-lineage differentiation.
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Affiliation(s)
- Elena Carbognin
- Department of Molecular Medicine, Medical School, University of Padua, Padua, Italy
- Department of Biology, University of Padua, Padua, Italy
| | - Valentina Carlini
- Epigenetics & Neurobiology Unit, European Molecular Biology Laboratory (EMBL)-Rome, Adriano Buzzati-Traverso Campus, Rome, Italy
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Francesco Panariello
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
| | | | - Elena Guerzoni
- Department of Biology, University of Padua, Padua, Italy
| | | | - Valentina Perrera
- Department of Molecular Medicine, Medical School, University of Padua, Padua, Italy
| | - Cristina Malucelli
- Department of Molecular Medicine, Medical School, University of Padua, Padua, Italy
| | - Marcella Cesana
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
- Department of Advanced Biomedical Sciences, University of Naples 'Federico II', Naples, Italy
| | - Antonio Grimaldi
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
| | - Margherita Mutarelli
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
- Istituto di Scienze Applicate e Sistemi Intelligenti 'Eduardo Caianiello', Consiglio Nazionale delle Ricerche, Pozzuoli, Italy
| | - Annamaria Carissimo
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
- Istituto per le Applicazioni del Calcolo 'Mauro Picone,' Consiglio Nazionale delle Ricerche, Naples, Italy
| | - Eitan Tannenbaum
- The Faculty of Engineering, Bar-Ilan University, Ramat Gan, Israel
| | - Hillel Kugler
- The Faculty of Engineering, Bar-Ilan University, Ramat Gan, Israel
| | - Jamie A Hackett
- Epigenetics & Neurobiology Unit, European Molecular Biology Laboratory (EMBL)-Rome, Adriano Buzzati-Traverso Campus, Rome, Italy.
| | - Davide Cacchiarelli
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy.
- Department of Translational Medicine, University of Naples 'Federico II', Naples, Italy.
- School for Advanced Studies, Genomics and Experimental Medicine Program, University of Naples 'Federico II', Naples, Italy.
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7
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Gaudreau-Lapierre A, Klonisch T, Nicolas H, Thanasupawat T, Trinkle-Mulcahy L, Hombach-Klonisch S. Nuclear High Mobility Group A2 (HMGA2) Interactome Revealed by Biotin Proximity Labeling. Int J Mol Sci 2023; 24:ijms24044246. [PMID: 36835656 PMCID: PMC9966875 DOI: 10.3390/ijms24044246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 02/23/2023] Open
Abstract
The non-histone chromatin binding protein High Mobility Group AT-hook protein 2 (HMGA2) has important functions in chromatin remodeling, and genome maintenance and protection. Expression of HMGA2 is highest in embryonic stem cells, declines during cell differentiation and cell aging, but it is re-expressed in some cancers, where high HMGA2 expression frequently coincides with a poor prognosis. The nuclear functions of HMGA2 cannot be explained by binding to chromatin alone but involve complex interactions with other proteins that are incompletely understood. The present study used biotin proximity labeling, followed by proteomic analysis, to identify the nuclear interaction partners of HMGA2. We tested two different biotin ligase HMGA2 constructs (BioID2 and miniTurbo) with similar results, and identified known and new HMGA2 interaction partners, with functionalities mainly in chromatin biology. These HMGA2 biotin ligase fusion constructs offer exciting new possibilities for interactome discovery research, enabling the monitoring of nuclear HMGA2 interactomes during drug treatments.
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Affiliation(s)
- Antoine Gaudreau-Lapierre
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Thomas Klonisch
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, College of Medicine, University of Manitoba, CancerCare Manitoba, Winnipeg, MB R3T 2N2, Canada
- Department of Pathology, Rady Faculty of Health Sciences, College of Medicine, University of Manitoba, CancerCare Manitoba, Winnipeg, MB R3T 2N2, Canada
- Department of Medical Microbiology & Infectious Diseases, Rady Faculty of Health Sciences, College of Medicine, University of Manitoba, CancerCare Manitoba, Winnipeg, MB R3T 2N2, Canada
- Research Institute in Oncology and Hematology (RIOH), CancerCare Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Hannah Nicolas
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Thatchawan Thanasupawat
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, College of Medicine, University of Manitoba, CancerCare Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Laura Trinkle-Mulcahy
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Sabine Hombach-Klonisch
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, College of Medicine, University of Manitoba, CancerCare Manitoba, Winnipeg, MB R3T 2N2, Canada
- Department of Pathology, Rady Faculty of Health Sciences, College of Medicine, University of Manitoba, CancerCare Manitoba, Winnipeg, MB R3T 2N2, Canada
- Correspondence: ; Tel.: +1-204-789-3982; Fax: +1-204-789-3920
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8
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Schnirman RE, Kuo SJ, Kelly RC, Yamaguchi TP. The role of Wnt signaling in the development of the epiblast and axial progenitors. Curr Top Dev Biol 2023; 153:145-180. [PMID: 36967193 DOI: 10.1016/bs.ctdb.2023.01.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Understanding how the body plan is established during embryogenesis remains a fundamental biological question. The Wnt/β-catenin signaling pathway plays a crucial and highly conserved role in body plan formation, functioning to polarize the primary anterior-posterior (AP) or head-to-tail body axis in most metazoans. In this chapter, we focus on the roles that the mammalian Wnt/β-catenin pathway plays to prepare the pluripotent epiblast for gastrulation, and to elicit the emergence of multipotent axial progenitors from the caudal epiblast. Interactions between Wnt and retinoic acid (RA), another powerful family of developmental signaling molecules, in axial progenitors will also be discussed. Gastrulation movements and somitogenesis result in the anterior displacement of the RA source (the rostral somites and lateral plate mesoderm (LPM)), from the posterior Wnt source (the primitive streak (PS)), leading to the establishment of antiparallel gradients of RA and Wnt that control the self-renewal and successive differentiation of neck, trunk and tail progenitors.
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Affiliation(s)
| | - Samuel J Kuo
- NCI-Frederick, NIH, Frederick, MD, United States
| | - Ryan C Kelly
- NCI-Frederick, NIH, Frederick, MD, United States
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9
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Hu S, Metcalf E, Mahat DB, Chan L, Sohal N, Chakraborty M, Hamilton M, Singh A, Singh A, Lees JA, Sharp PA, Garg S. Transcription factor antagonism regulates heterogeneity in embryonic stem cell states. Mol Cell 2022; 82:4410-4427.e12. [PMID: 36356583 PMCID: PMC9722640 DOI: 10.1016/j.molcel.2022.10.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/19/2022] [Accepted: 10/20/2022] [Indexed: 11/10/2022]
Abstract
Gene expression heterogeneity underlies cell states and contributes to developmental robustness. While heterogeneity can arise from stochastic transcriptional processes, the extent to which it is regulated is unclear. Here, we characterize the regulatory program underlying heterogeneity in murine embryonic stem cell (mESC) states. We identify differentially active and transcribed enhancers (DATEs) across states. DATEs regulate differentially expressed genes and are distinguished by co-binding of transcription factors Klf4 and Zfp281. In contrast to other factors that interact in a positive feedback network stabilizing mESC cell-type identity, Klf4 and Zfp281 drive opposing transcriptional and chromatin programs. Abrogation of factor binding to DATEs dampens variation in gene expression, and factor loss alters kinetics of switching between states. These results show antagonism between factors at enhancers results in gene expression heterogeneity and formation of cell states, with implications for the generation of diverse cell types during development.
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Affiliation(s)
- Sofia Hu
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA
| | - Emily Metcalf
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Dig Bijay Mahat
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Lynette Chan
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Noor Sohal
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Meenakshi Chakraborty
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Maxwell Hamilton
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Arundeep Singh
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Abhyudai Singh
- Department of Electrical and Computer Engineering, University of Delaware, Newark, DE 19716, USA
| | - Jacqueline A Lees
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Phillip A Sharp
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Salil Garg
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Laboratory Medicine, Yale Stem Cell Center and Center for RNA Science and Medicine, Yale School of Medicine, New Haven, CT 06510, USA.
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10
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Botigelli RC, Pieri NCG, Bessi BW, Machado LS, Bridi A, de Souza AF, Recchia K, Neto PF, Ross PJ, Bressan FF, Nogueira MFG. Acquisition and maintenance of pluripotency are influenced by fibroblast growth factor, leukemia inhibitory factor, and 2i in bovine-induced pluripotent stem cells. Front Cell Dev Biol 2022; 10:938709. [PMID: 36187479 PMCID: PMC9515551 DOI: 10.3389/fcell.2022.938709] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 08/11/2022] [Indexed: 12/03/2022] Open
Abstract
Several opportunities for embryo development, stem cell maintenance, cell fate, and differentiation have emerged using induced pluripotent stem cells (iPSCs). However, the difficulty in comparing bovine iPSCs (biPSCs) with embryonic stem cells (ESCs) was a challenge for many years. Here, we reprogrammed fetal fibroblasts by transient expression of the four transcription factors (Oct4, Sox2, Klf4, and c-Myc, collectively termed “OSKM” factors) and cultured in iPSC medium, supplemented with bFGF, bFGF2i, leukemia inhibitory factor (LIF), or LIF2i, and then compared these biPSC lines with bESC to evaluate the pluripotent state. biPSC lines were generated in all experimental groups. Particularly, reprogrammed cells treated with bFGF were more efficient in promoting the acquisition of pluripotency. However, LIF2i treatment did not promote continuous self-renewal. biPSCs (line 2) labeled with GFP were injected into early embryos (day 4.5) to assess the potential to contribute to chimeric blastocysts. The biPSC lines show a pluripotency state and are differentiated into three embryonic layers. Moreover, biPSCs and bESCs labeled with GFP were able to contribute to chimeric blastocysts. Additionally, biPSCs have shown promising potential for contributing to chimeric blastocysts and for future studies.
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Affiliation(s)
- Ramon Cesar Botigelli
- Multiuser Facility (FitoFarmaTec), Department of Pharmacology, Biosciences Institute (IBB), São Paulo State University (UNESP), Botucatu, Brazil
- Laboratory of Molecular Morphophysiology and Development (LMMD), Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering (FZEA), University of São Paulo (USP), Pirassununga, Brazil
- Correspondence: Ramon Cesar Botigelli, ; Marcelo Fábio Gouveia Nogueira,
| | - Naira Carolina Godoy Pieri
- Laboratory of Molecular Morphophysiology and Development (LMMD), Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering (FZEA), University of São Paulo (USP), Pirassununga, Brazil
| | - Brendon William Bessi
- Laboratory of Molecular Morphophysiology and Development (LMMD), Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering (FZEA), University of São Paulo (USP), Pirassununga, Brazil
| | - Lucas Simões Machado
- Laboratory of Molecular Morphophysiology and Development (LMMD), Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering (FZEA), University of São Paulo (USP), Pirassununga, Brazil
- Paulista School of Medicine (EPM), Laboratory of Neurobiology, Department of Biochemistry, Federal University of São Paulo (UNIFESP), São Paulo, Brazil
| | - Alessandra Bridi
- Laboratory of Molecular Morphophysiology and Development (LMMD), Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering (FZEA), University of São Paulo (USP), Pirassununga, Brazil
| | - Aline Fernanda de Souza
- Laboratory Biomedical Science, Department of Biomedical Science, Ontario Veterinary College (OVC), University of Guelph, Guelph, ON, Canada
| | - Kaiana Recchia
- Laboratory of Molecular Morphophysiology and Development (LMMD), Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering (FZEA), University of São Paulo (USP), Pirassununga, Brazil
| | - Paulo Fantinato Neto
- Laboratory of Molecular Morphophysiology and Development (LMMD), Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering (FZEA), University of São Paulo (USP), Pirassununga, Brazil
| | - Pablo Juan Ross
- Laboratory Department of Animal Science, University of California, Davis, Davis, CA, United States
| | - Fabiana Fernandes Bressan
- Laboratory of Molecular Morphophysiology and Development (LMMD), Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering (FZEA), University of São Paulo (USP), Pirassununga, Brazil
| | - Marcelo Fábio Gouveia Nogueira
- Multiuser Facility (FitoFarmaTec), Department of Pharmacology, Biosciences Institute (IBB), São Paulo State University (UNESP), Botucatu, Brazil
- School of Sciences and Languages, Laboratory of Embryonic Micromanipulation, Department of Biological Sciences, São Paulo State University (UNESP), Assis, Brazil
- Correspondence: Ramon Cesar Botigelli, ; Marcelo Fábio Gouveia Nogueira,
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11
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Endoh M, Niwa H. Stepwise pluripotency transitions in mouse stem cells. EMBO Rep 2022; 23:e55010. [PMID: 35903955 PMCID: PMC9442314 DOI: 10.15252/embr.202255010] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 05/13/2022] [Accepted: 07/01/2022] [Indexed: 07/31/2023] Open
Abstract
Pluripotent cells in mouse embryos, which first emerge in the inner cell mass of the blastocyst, undergo gradual transition marked by changes in gene expression, developmental potential, polarity, and morphology as they develop from the pre-implantation until post-implantation gastrula stage. Recent studies of cultured mouse pluripotent stem cells (PSCs) have clarified the presence of intermediate pluripotent stages between the naïve pluripotent state represented by embryonic stem cells (ESCs-equivalent to the pre-implantation epiblast) and the primed pluripotent state represented by epiblast stem cells (EpiSCs-equivalent to the late post-implantation gastrula epiblast). In this review, we discuss these recent findings in light of our knowledge on peri-implantation mouse development and consider the implications of these new PSCs to understand their temporal sequence and the feasibility of using them as model system for pluripotency.
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Affiliation(s)
- Mitsuhiro Endoh
- Department of Pluripotent Stem Cell Biology, Institute of Molecular Embryology and Genetics (IMEG)Kumamoto UniversityKumamotoJapan
| | - Hitoshi Niwa
- Department of Pluripotent Stem Cell Biology, Institute of Molecular Embryology and Genetics (IMEG)Kumamoto UniversityKumamotoJapan
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12
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Khateb M, Perovanovic J, Ko KD, Jiang K, Feng X, Acevedo-Luna N, Chal J, Ciuffoli V, Genzor P, Simone J, Haase AD, Pourquié O, Dell'Orso S, Sartorelli V. Transcriptomics, regulatory syntax, and enhancer identification in mesoderm-induced ESCs at single-cell resolution. Cell Rep 2022; 40:111219. [PMID: 35977485 DOI: 10.1016/j.celrep.2022.111219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/11/2022] [Accepted: 07/25/2022] [Indexed: 11/03/2022] Open
Abstract
Embryonic stem cells (ESCs) can adopt lineage-specific gene-expression programs by stepwise exposure to defined factors, resulting in the generation of functional cell types. Bulk and single-cell-based assays were employed to catalog gene expression, histone modifications, chromatin conformation, and accessibility transitions in ESC populations and individual cells acquiring a presomitic mesoderm fate and undergoing further specification toward myogenic and neurogenic lineages. These assays identified cis-regulatory regions and transcription factors presiding over gene-expression programs occurring at defined ESC transitions and revealed the presence of heterogeneous cell populations within discrete ESC developmental stages. The datasets were employed to identify previously unappreciated genomic elements directing the initial activation of Pax7 and myogenic and neurogenic gene-expression programs. This study provides a resource for the discovery of genomic and transcriptional features of pluripotent, mesoderm-induced ESCs and ESC-derived cell lineages.
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Affiliation(s)
- Mamduh Khateb
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD, USA
| | - Jelena Perovanovic
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD, USA
| | - Kyung Dae Ko
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD, USA
| | - Kan Jiang
- Biodata Mining and Discovery Section, NIAMS, NIH, Bethesda, MD, USA
| | - Xuesong Feng
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD, USA
| | - Natalia Acevedo-Luna
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD, USA
| | - Jérome Chal
- Department of Genetics, Harvard Medical School, Boston, MA, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA; Harvard Stem Cell Institute, Boston, MA, USA
| | - Veronica Ciuffoli
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD, USA
| | - Pavol Genzor
- National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD, USA
| | - James Simone
- FlowCytometry Section, NIAMS, NIH, Bethesda, MD, USA
| | - Astrid D Haase
- National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD, USA
| | - Olivier Pourquié
- Department of Genetics, Harvard Medical School, Boston, MA, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA; Harvard Stem Cell Institute, Boston, MA, USA
| | | | - Vittorio Sartorelli
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD, USA.
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13
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Tsume-Kajioka M, Kimura-Yoshida C, Mochida K, Ueda Y, Matsuo I. BET proteins are essential for the specification and maintenance of the epiblast lineage in mouse preimplantation embryos. BMC Biol 2022; 20:64. [PMID: 35264162 PMCID: PMC8905768 DOI: 10.1186/s12915-022-01251-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 02/09/2022] [Indexed: 11/23/2022] Open
Abstract
Background During mammalian preimplantation development, as the fertilized egg develops and differentiates, three cell lineages become specified: trophectoderm (TE), epiblast, and primitive endoderm (PrE). Through two steps of cell fate decisions, 16-cell blastomeres develop into TE and an inner cell mass (ICM), and thereafter, the latter differentiates into pluripotent epiblast and PrE. Although bromodomain and extra-terminal domain (BET) proteins, such as BRD4, are necessary for the transcriptional activation of genes involved in the maintenance of mouse embryonic stem cells by occupying their enhancers, their roles in the development of mouse preimplantation are unknown. Results To evaluate the effect of BET protein deficiency on cell lineage formation, we cultured preimplantation embryos in the presence of JQ1, which blocks the binding of BET bromodomains to acetylated-histones. We found BET inhibition blocked the transcriptional activation of genes, such as Nanog, Otx2, and Sox2, important for the formation of the epiblast lineage in blastocysts. Expression studies with lineage-specific markers in morulae and blastocysts revealed BET proteins were essential for the specification and maintenance of the epiblast lineage but were dispensable for the formation of primarily extraembryonic TE and PrE lineages. Additional Ingenuity Pathway Analysis and expression studies with a transcriptionally active form of signal transducer and activator of the transcription 3 (STAT3) suggested BET-dependent activation was partly associated with the STAT3-dependent pathway to maintain the epiblast lineage. To identify BET proteins involved in the formation of the epiblast lineage, we analyzed mutant embryos deficient in Brd4, Brd2, and double mutants. Abolishment of NANOG-positive epiblast cells was only evident in Brd4/Brd2 double-deficient morulae. Thus, the phenotype of JQ1-treated embryos is reproduced not by a Brd4- or Brd2-single deficiency, but only Brd4/Brd2-double deficiency, demonstrating the redundant roles of BRD2 and BRD4 in the specification of the epiblast lineage. Conclusions BET proteins are essential to the specification and maintenance of the epiblast lineage by activating lineage-specific core transcription factors during mouse preimplantation development. Among BET proteins, BRD4 plays a central role and BRD2 a complementary role in the specification and maintenance of epiblast lineages. Additionally, BET-dependent maintenance of the epiblast lineage may be partly associated with the STAT3-dependent pathway. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01251-0.
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Affiliation(s)
- Mami Tsume-Kajioka
- Department of Molecular Embryology, Research Institute, Osaka Women's and Children's Hospital, Osaka Prefectural Hospital Organization, 840, Murodo-cho, Izumi, Osaka, 594-1101, Japan
| | - Chiharu Kimura-Yoshida
- Department of Molecular Embryology, Research Institute, Osaka Women's and Children's Hospital, Osaka Prefectural Hospital Organization, 840, Murodo-cho, Izumi, Osaka, 594-1101, Japan
| | - Kyoko Mochida
- Department of Molecular Embryology, Research Institute, Osaka Women's and Children's Hospital, Osaka Prefectural Hospital Organization, 840, Murodo-cho, Izumi, Osaka, 594-1101, Japan
| | - Yoko Ueda
- Department of Molecular Embryology, Research Institute, Osaka Women's and Children's Hospital, Osaka Prefectural Hospital Organization, 840, Murodo-cho, Izumi, Osaka, 594-1101, Japan
| | - Isao Matsuo
- Department of Molecular Embryology, Research Institute, Osaka Women's and Children's Hospital, Osaka Prefectural Hospital Organization, 840, Murodo-cho, Izumi, Osaka, 594-1101, Japan. .,Department of Pediatric and Neonatal-Perinatal Research, Osaka Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan.
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14
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NMD is required for timely cell fate transitions by fine-tuning gene expression and regulating translation. Genes Dev 2022; 36:348-367. [PMID: 35241478 PMCID: PMC8973849 DOI: 10.1101/gad.347690.120] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/11/2022] [Indexed: 11/25/2022]
Abstract
Here, Huth et al. investigated the role of components of the nonsense-mediated mRNA decay (NMD) pathway in regulating embryonic stem cell (ESC) differentiation, and show that NMD controls expression levels of the translation initiation factor Eif4a2 and its premature termination codon-encoding isoform (Eif4a2PTC). Their findings expose an intricate link between mRNA homeostasis and mTORC1 activity that must be maintained for normal dynamics of cell state transitions. Cell fate transitions depend on balanced rewiring of transcription and translation programs to mediate ordered developmental progression. Components of the nonsense-mediated mRNA decay (NMD) pathway have been implicated in regulating embryonic stem cell (ESC) differentiation, but the exact mechanism is unclear. Here we show that NMD controls expression levels of the translation initiation factor Eif4a2 and its premature termination codon-encoding isoform (Eif4a2PTC). NMD deficiency leads to translation of the truncated eIF4A2PTC protein. eIF4A2PTC elicits increased mTORC1 activity and translation rates and causes differentiation delays. This establishes a previously unknown feedback loop between NMD and translation initiation. Furthermore, our results show a clear hierarchy in the severity of target deregulation and differentiation phenotypes between NMD effector KOs (Smg5 KO > Smg6 KO > Smg7 KO), which highlights heterodimer-independent functions for SMG5 and SMG7. Together, our findings expose an intricate link between mRNA homeostasis and mTORC1 activity that must be maintained for normal dynamics of cell state transitions.
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15
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Yeh CY, Huang WH, Chen HC, Meir YJJ. Capturing Pluripotency and Beyond. Cells 2021; 10:cells10123558. [PMID: 34944066 PMCID: PMC8700150 DOI: 10.3390/cells10123558] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 11/16/2022] Open
Abstract
During the development of a multicellular organism, the specification of different cell lineages originates in a small group of pluripotent cells, the epiblasts, formed in the preimplantation embryo. The pluripotent epiblast is protected from premature differentiation until exposure to inductive cues in strictly controlled spatially and temporally organized patterns guiding fetus formation. Epiblasts cultured in vitro are embryonic stem cells (ESCs), which recapitulate the self-renewal and lineage specification properties of their endogenous counterparts. The characteristics of totipotency, although less understood than pluripotency, are becoming clearer. Recent studies have shown that a minor ESC subpopulation exhibits expanded developmental potential beyond pluripotency, displaying a characteristic reminiscent of two-cell embryo blastomeres (2CLCs). In addition, reprogramming both mouse and human ESCs in defined media can produce expanded/extended pluripotent stem cells (EPSCs) similar to but different from 2CLCs. Further, the molecular roadmaps driving the transition of various potency states have been clarified. These recent key findings will allow us to understand eutherian mammalian development by comparing the underlying differences between potency network components during development. Using the mouse as a paradigm and recent progress in human PSCs, we review the epiblast's identity acquisition during embryogenesis and their ESC counterparts regarding their pluripotent fates and beyond.
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Affiliation(s)
- Chih-Yu Yeh
- Department of Medicine, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (C.-Y.Y.); (W.-H.H.)
| | - Wei-Han Huang
- Department of Medicine, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (C.-Y.Y.); (W.-H.H.)
| | - Hung-Chi Chen
- Department of Medicine, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (C.-Y.Y.); (W.-H.H.)
- Limbal Stem Cell Laboratory, Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou 333, Taiwan
- Correspondence: (H.-C.C.); (Y.-J.J.M.)
| | - Yaa-Jyuhn James Meir
- Limbal Stem Cell Laboratory, Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou 333, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
- Correspondence: (H.-C.C.); (Y.-J.J.M.)
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16
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Zhang J, Pang J, Bai Y, Lin Z, Huang J, Songyang Z, Shi G. Global molecular features in transcription and chromatin accessibility in human extended pluripotent stem cells. Biochem Biophys Res Commun 2021; 574:63-69. [PMID: 34438348 DOI: 10.1016/j.bbrc.2021.08.047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 08/18/2021] [Indexed: 11/15/2022]
Abstract
Human extended pluripotent stem (hEPS) cell is a newly established human embryonic stem cell (hESC) line with the capacity of chimerizing both embryonic and extraembryonic tissues compared with primed hESCs which are inefficient to contribute to the inner cell mass (ICM). The molecular mechanism underlying the pluripotency of hEPS cells is still not clear. We conducted RNA-seq and ATAC-seq analysis to investigate the differential expression profiling and genomic chromatin accessibility features. According to our data, more than 2000 genes were specially up-regulated in hEPS cells. Furthermore, the open chromatin regions in these two human embryonic stem cell lines were quite different. In hEPS cells, transcriptional factors binding motifs associated with pluripotency maintenance were enriched in chromatin accessible regions. Integrating the results from ATAC-seq and RNA-seq, we identified new regulatory features which were important for pluripotency maintenance and cell development in hEPS cells. Together, these results provided a new perspective on the understanding of molecular features of hESCs in different pluripotent states and a novel resource for further studies on regenerative medicine by using hEPS cells.
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Affiliation(s)
- Jingran Zhang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Junjie Pang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yaofu Bai
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Zhancheng Lin
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Junjiu Huang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Zhou Songyang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Guang Shi
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
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17
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Planques A, Oliveira Moreira V, Benacom D, Bernard C, Jourdren L, Blugeon C, Dingli F, Masson V, Loew D, Prochiantz A, Di Nardo AA. OTX2 Homeoprotein Functions in Adult Choroid Plexus. Int J Mol Sci 2021; 22:8951. [PMID: 34445655 PMCID: PMC8396604 DOI: 10.3390/ijms22168951] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/12/2021] [Accepted: 08/17/2021] [Indexed: 01/18/2023] Open
Abstract
The choroid plexus is an important blood barrier that secretes cerebrospinal fluid, which essential for embryonic brain development and adult brain homeostasis. The OTX2 homeoprotein is a transcription factor that is critical for choroid plexus development and remains highly expressed in adult choroid plexus. Through RNA sequencing analyses of constitutive and conditional knockdown adult mouse models, we reveal putative functional roles for OTX2 in adult choroid plexus function, including cell signaling and adhesion, and show that OTX2 regulates the expression of factors that are secreted into the cerebrospinal fluid, notably transthyretin. We also show that Otx2 expression impacts choroid plexus immune and stress responses, and affects splicing, leading to changes in the mRNA isoforms of proteins that are implicated in the oxidative stress response and DNA repair. Through mass spectrometry analysis of OTX2 protein partners in the choroid plexus, and in known non-cell-autonomous target regions, such as the visual cortex and subventricular zone, we identify putative targets that are involved in cell adhesion, chromatin structure, and RNA processing. Thus, OTX2 retains important roles for regulating choroid plexus function and brain homeostasis throughout life.
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Affiliation(s)
- Anabelle Planques
- Centre for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR7241, INSERM U1050, Labex MemoLife, PSL University, 75005 Paris, France; (A.P.); (V.O.M.); (D.B.); (C.B.); (A.P.)
| | - Vanessa Oliveira Moreira
- Centre for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR7241, INSERM U1050, Labex MemoLife, PSL University, 75005 Paris, France; (A.P.); (V.O.M.); (D.B.); (C.B.); (A.P.)
| | - David Benacom
- Centre for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR7241, INSERM U1050, Labex MemoLife, PSL University, 75005 Paris, France; (A.P.); (V.O.M.); (D.B.); (C.B.); (A.P.)
| | - Clémence Bernard
- Centre for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR7241, INSERM U1050, Labex MemoLife, PSL University, 75005 Paris, France; (A.P.); (V.O.M.); (D.B.); (C.B.); (A.P.)
| | - Laurent Jourdren
- Genomics Core Facility, Institut de Biologie de l’ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, PSL University, 75005 Paris, France; (L.J.); (C.B.)
| | - Corinne Blugeon
- Genomics Core Facility, Institut de Biologie de l’ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, PSL University, 75005 Paris, France; (L.J.); (C.B.)
| | - Florent Dingli
- Laboratoire de Spectrométrie de Masse Protéomique, Centre de Recherche, Institut Curie, CEDEX 05, 75248 Paris, France; (F.D.); (V.M.); (D.L.)
| | - Vanessa Masson
- Laboratoire de Spectrométrie de Masse Protéomique, Centre de Recherche, Institut Curie, CEDEX 05, 75248 Paris, France; (F.D.); (V.M.); (D.L.)
| | - Damarys Loew
- Laboratoire de Spectrométrie de Masse Protéomique, Centre de Recherche, Institut Curie, CEDEX 05, 75248 Paris, France; (F.D.); (V.M.); (D.L.)
| | - Alain Prochiantz
- Centre for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR7241, INSERM U1050, Labex MemoLife, PSL University, 75005 Paris, France; (A.P.); (V.O.M.); (D.B.); (C.B.); (A.P.)
- Institute of Neurosciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Ariel A. Di Nardo
- Centre for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR7241, INSERM U1050, Labex MemoLife, PSL University, 75005 Paris, France; (A.P.); (V.O.M.); (D.B.); (C.B.); (A.P.)
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18
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Antonio Urrutia G, Ramachandran H, Cauchy P, Boo K, Ramamoorthy S, Boller S, Dogan E, Clapes T, Trompouki E, Torres-Padilla ME, Palvimo JJ, Pichler A, Grosschedl R. ZFP451-mediated SUMOylation of SATB2 drives embryonic stem cell differentiation. Genes Dev 2021; 35:1142-1160. [PMID: 34244292 PMCID: PMC8336893 DOI: 10.1101/gad.345843.120] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 06/08/2021] [Indexed: 12/15/2022]
Abstract
Here, Urrutia et al. set out to study the mechanism that regulates the choice between pluripotency and differentiation in embryonic stem cells (ESCs). Using biochemical and genomic analyses, the authors identify SUMO2 modification of Satb2 by the E3 ligase Zfp451 as a driver of ESC differentiation. The establishment of cell fates involves alterations of transcription factor repertoires and repurposing of transcription factors by post-translational modifications. In embryonic stem cells (ESCs), the chromatin organizers SATB2 and SATB1 balance pluripotency and differentiation by activating and repressing pluripotency genes, respectively. Here, we show that conditional Satb2 gene inactivation weakens ESC pluripotency, and we identify SUMO2 modification of SATB2 by the E3 ligase ZFP451 as a potential driver of ESC differentiation. Mutations of two SUMO-acceptor lysines of Satb2 (Satb2K →R) or knockout of Zfp451 impair the ability of ESCs to silence pluripotency genes and activate differentiation-associated genes in response to retinoic acid (RA) treatment. Notably, the forced expression of a SUMO2-SATB2 fusion protein in either Satb2K →R or Zfp451−/− ESCs rescues, in part, their impaired differentiation potential and enhances the down-regulation of Nanog. The differentiation defect of Satb2K →R ESCs correlates with altered higher-order chromatin interactions relative to Satb2wt ESCs. Upon RA treatment of Satb2wt ESCs, SATB2 interacts with ZFP451 and the LSD1/CoREST complex and gains binding at differentiation genes, which is not observed in RA-treated Satb2K →R cells. Thus, SATB2 SUMOylation may contribute to the rewiring of transcriptional networks and the chromatin interactome of ESCs in the transition of pluripotency to differentiation.
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Affiliation(s)
- Gustavo Antonio Urrutia
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Haribaskar Ramachandran
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Pierre Cauchy
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Kyungjin Boo
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Senthilkumar Ramamoorthy
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Soeren Boller
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Esen Dogan
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Thomas Clapes
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Eirini Trompouki
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | | | - Jorma J Palvimo
- Institute of Biomedicine, University of Eastern Finland, 70210 Kuopio, Finland
| | - Andrea Pichler
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Rudolf Grosschedl
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
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19
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Guo SM, Mei NH, Yang J, Zhou LQ. Transcription factor OTX2 silences the expression of cleavage embryo genes and transposable elements. J Reprod Dev 2021; 67:223-228. [PMID: 33896883 PMCID: PMC8238675 DOI: 10.1262/jrd.2021-007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 03/28/2021] [Indexed: 11/20/2022] Open
Abstract
Upon mammalian fertilization, zygotic genome activation (ZGA) and activation of transposable elements (TEs) occur in early embryos to establish totipotency and support embryogenesis. However, the molecular mechanisms controlling the expression of these genes in mammals remain poorly understood. The 2-cell-like population of mouse embryonic stem cells (mESCs) mimics cleavage-stage embryos with transient Dux activation. In this study, we demonstrated that deficiency of the transcription factor OTX2 stimulates the expression of ZGA genes in mESCs. Further analysis revealed that OTX2 is incorporated at the Dux locus with corepressors for transcriptional inhibition. We also found that OTX2 associates with TEs and silences the subtypes of TEs. Therefore, OTX2 protein plays an important role in ZGA and TE expression in mESCs to orchestrate the transcriptional network.
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Affiliation(s)
- Shi-Meng Guo
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Hubei 430030, China
| | - Ning-Hua Mei
- Reproductive Medical Center, Renmin Hospital of Wuhan University & Hubei Clinic Research Center for Assisted Reproductive Technology and Embryonic Development, Wuhan, China
| | - Jing Yang
- Reproductive Medical Center, Renmin Hospital of Wuhan University & Hubei Clinic Research Center for Assisted Reproductive Technology and Embryonic Development, Wuhan, China
| | - Li-Quan Zhou
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Hubei 430030, China
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20
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Biological importance of OCT transcription factors in reprogramming and development. Exp Mol Med 2021; 53:1018-1028. [PMID: 34117345 PMCID: PMC8257633 DOI: 10.1038/s12276-021-00637-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 03/22/2021] [Accepted: 03/24/2021] [Indexed: 02/07/2023] Open
Abstract
Ectopic expression of Oct4, Sox2, Klf4 and c-Myc can reprogram somatic cells into induced pluripotent stem cells (iPSCs). Attempts to identify genes or chemicals that can functionally replace each of these four reprogramming factors have revealed that exogenous Oct4 is not necessary for reprogramming under certain conditions or in the presence of alternative factors that can regulate endogenous Oct4 expression. For example, polycistronic expression of Sox2, Klf4 and c-Myc can elicit reprogramming by activating endogenous Oct4 expression indirectly. Experiments in which the reprogramming competence of all other Oct family members tested and also in different species have led to the decisive conclusion that Oct proteins display different reprogramming competences and species-dependent reprogramming activity despite their profound sequence conservation. We discuss the roles of the structural components of Oct proteins in reprogramming and how donor cell epigenomes endow Oct proteins with different reprogramming competences. Cells can be reprogrammed into induced pluripotent stem cells (iPSCs), embryonic-like stem cells that can turn into any cell type and have extensive potential medical uses, without adding the transcription factor OCT4. Although other nearly identical OCT family members had been tried, only OCT4 could induce reprogramming and was previously thought to be indispensable. However, it now appears that the reprogramming can be induced by multiple pathways, as detailed in a review by Hans Schöler, Max Planck Institute for Biomolecular Medicine, Münster, and Johnny Kim, Max Planck Institute for Heart and Lung Research, Bad Nauheim, in Germany. They report that any factors that trigger cells to activate endogeous OCT4 can produce iPSCs without exogeously admistration of OCT4. The mechanisms for producing iPSCs can differ between species. These results illuminate the complex mechanisms of reprogramming.
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21
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Meistermann D, Bruneau A, Loubersac S, Reignier A, Firmin J, François-Campion V, Kilens S, Lelièvre Y, Lammers J, Feyeux M, Hulin P, Nedellec S, Bretin B, Castel G, Allègre N, Covin S, Bihouée A, Soumillon M, Mikkelsen T, Barrière P, Chazaud C, Chappell J, Pasque V, Bourdon J, Fréour T, David L. Integrated pseudotime analysis of human pre-implantation embryo single-cell transcriptomes reveals the dynamics of lineage specification. Cell Stem Cell 2021; 28:1625-1640.e6. [PMID: 34004179 DOI: 10.1016/j.stem.2021.04.027] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 07/16/2020] [Accepted: 04/22/2021] [Indexed: 12/22/2022]
Abstract
Understanding lineage specification during human pre-implantation development is a gateway to improving assisted reproductive technologies and stem cell research. Here we employ pseudotime analysis of single-cell RNA sequencing (scRNA-seq) data to reconstruct early mouse and human embryo development. Using time-lapse imaging of annotated embryos, we provide an integrated, ordered, and continuous analysis of transcriptomics changes throughout human development. We reveal that human trophectoderm/inner cell mass transcriptomes diverge at the transition from the B2 to the B3 blastocyst stage, just before blastocyst expansion. We explore the dynamics of the fate markers IFI16 and GATA4 and show that they gradually become mutually exclusive upon establishment of epiblast and primitive endoderm fates, respectively. We also provide evidence that NR2F2 marks trophectoderm maturation, initiating from the polar side, and subsequently spreads to all cells after implantation. Our study pinpoints the precise timing of lineage specification events in the human embryo and identifies transcriptomics hallmarks and cell fate markers.
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Affiliation(s)
- Dimitri Meistermann
- Université de Nantes, CHU Nantes, INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, 44000 Nantes, France; LS2N, UNIV Nantes, CNRS, Nantes, France
| | - Alexandre Bruneau
- Université de Nantes, CHU Nantes, INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, 44000 Nantes, France
| | - Sophie Loubersac
- Université de Nantes, CHU Nantes, INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, 44000 Nantes, France; CHU Nantes, Université de Nantes, Service de Biologie de la Reproduction, 44000 Nantes, France
| | - Arnaud Reignier
- Université de Nantes, CHU Nantes, INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, 44000 Nantes, France; CHU Nantes, Université de Nantes, Service de Biologie de la Reproduction, 44000 Nantes, France
| | - Julie Firmin
- Université de Nantes, CHU Nantes, INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, 44000 Nantes, France; CHU Nantes, Université de Nantes, Service de Biologie de la Reproduction, 44000 Nantes, France
| | - Valentin François-Campion
- Université de Nantes, CHU Nantes, INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, 44000 Nantes, France
| | - Stéphanie Kilens
- Université de Nantes, CHU Nantes, INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, 44000 Nantes, France
| | | | - Jenna Lammers
- CHU Nantes, Université de Nantes, Service de Biologie de la Reproduction, 44000 Nantes, France
| | - Magalie Feyeux
- Université de Nantes, CHU Nantes, INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, 44000 Nantes, France; Université de Nantes, CHU Nantes, INSERM, CNRS, SFR Santé, FED 4203, INSERM UMS 016, CNRS UMS 3556, Nantes, France
| | - Phillipe Hulin
- Université de Nantes, CHU Nantes, INSERM, CNRS, SFR Santé, FED 4203, INSERM UMS 016, CNRS UMS 3556, Nantes, France
| | - Steven Nedellec
- Université de Nantes, CHU Nantes, INSERM, CNRS, SFR Santé, FED 4203, INSERM UMS 016, CNRS UMS 3556, Nantes, France
| | - Betty Bretin
- Université de Nantes, CHU Nantes, INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, 44000 Nantes, France
| | - Gaël Castel
- Université de Nantes, CHU Nantes, INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, 44000 Nantes, France
| | - Nicolas Allègre
- GReD Laboratory, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, CRBC, 63000 Clermont-Ferrand, France
| | - Simon Covin
- Université de Nantes, CHU Nantes, INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, 44000 Nantes, France
| | - Audrey Bihouée
- Université de Nantes, CHU Nantes, INSERM, CNRS, SFR Santé, FED 4203, INSERM UMS 016, CNRS UMS 3556, Nantes, France; Institut du Thorax, UNIV Nantes, INSERM, CNRS, Nantes, France
| | - Magali Soumillon
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute, Cambridge, MA 02142, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Tarjei Mikkelsen
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute, Cambridge, MA 02142, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Paul Barrière
- Université de Nantes, CHU Nantes, INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, 44000 Nantes, France; CHU Nantes, Université de Nantes, Service de Biologie de la Reproduction, 44000 Nantes, France
| | - Claire Chazaud
- GReD Laboratory, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, CRBC, 63000 Clermont-Ferrand, France
| | - Joel Chappell
- KU Leuven - University of Leuven, Department of Development and Regeneration, Institute for Single Cell Omics, Leuven Stem Cell Institute, Herestraat 49, 3000 Leuven, Belgium
| | - Vincent Pasque
- KU Leuven - University of Leuven, Department of Development and Regeneration, Institute for Single Cell Omics, Leuven Stem Cell Institute, Herestraat 49, 3000 Leuven, Belgium
| | | | - Thomas Fréour
- Université de Nantes, CHU Nantes, INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, 44000 Nantes, France; CHU Nantes, Université de Nantes, Service de Biologie de la Reproduction, 44000 Nantes, France.
| | - Laurent David
- Université de Nantes, CHU Nantes, INSERM, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, 44000 Nantes, France; Université de Nantes, CHU Nantes, INSERM, CNRS, SFR Santé, FED 4203, INSERM UMS 016, CNRS UMS 3556, Nantes, France.
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22
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Di Giovannantonio LG, Acampora D, Omodei D, Nigro V, Barba P, Barbieri E, Chambers I, Simeone A. Direct repression of Nanog and Oct4 by OTX2 modulates the contribution of epiblast-derived cells to germline and somatic lineage. Development 2021; 148:263923. [PMID: 33999993 DOI: 10.1242/dev.199166] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 04/12/2021] [Indexed: 11/20/2022]
Abstract
In mammals, the pre-gastrula proximal epiblast gives rise to primordial germ cells (PGCs) or somatic precursors in response to BMP4 and WNT signaling. Entry into the germline requires activation of a naïve-like pluripotency gene regulatory network (GRN). Recent work has shown that suppression of OTX2 expression in the epiblast by BMP4 allows cells to develop a PGC fate in a precise temporal window. However, the mechanisms by which OTX2 suppresses PGC fate are unknown. Here, we show that, in mice, OTX2 prevents epiblast cells from activating the pluripotency GRN by direct repression of Oct4 and Nanog. Loss of this control during PGC differentiation in vitro causes widespread activation of the pluripotency GRN and a deregulated response to LIF, BMP4 and WNT signaling. These abnormalities, in specific cell culture conditions, result in massive germline entry at the expense of somatic mesoderm differentiation. Increased generation of PGCs also occurs in mutant embryos. We propose that the OTX2-mediated repressive control of Oct4 and Nanog is the basis of the mechanism that determines epiblast contribution to germline and somatic lineage.
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Affiliation(s)
| | - Dario Acampora
- Institute of Genetics and Biophysics 'Adriano Buzzati-Traverso', CNR, Via P. Castellino, 111, 80131 Naples, Italy
| | - Daniela Omodei
- Institute of Genetics and Biophysics 'Adriano Buzzati-Traverso', CNR, Via P. Castellino, 111, 80131 Naples, Italy.,Institute of Biostructures and Bioimaging, CNR, Via Tommaso De Amicis, 95, 80145 Naples, Italy
| | - Vincenzo Nigro
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania 'Luigi Vanvitelli', Via L. De Crecchio, 7, 80138 Naples, Italy.,Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei, 34, 80087 Pozzuoli (NA), Italy
| | - Pasquale Barba
- Institute of Genetics and Biophysics 'Adriano Buzzati-Traverso', CNR, Via P. Castellino, 111, 80131 Naples, Italy
| | - Elisa Barbieri
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK.,Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, UK
| | - Ian Chambers
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK.,Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, UK
| | - Antonio Simeone
- Institute of Genetics and Biophysics 'Adriano Buzzati-Traverso', CNR, Via P. Castellino, 111, 80131 Naples, Italy
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23
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Lackner A, Sehlke R, Garmhausen M, Giuseppe Stirparo G, Huth M, Titz-Teixeira F, van der Lelij P, Ramesmayer J, Thomas HF, Ralser M, Santini L, Galimberti E, Sarov M, Stewart AF, Smith A, Beyer A, Leeb M. Cooperative genetic networks drive embryonic stem cell transition from naïve to formative pluripotency. EMBO J 2021; 40:e105776. [PMID: 33687089 PMCID: PMC8047444 DOI: 10.15252/embj.2020105776] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 12/11/2022] Open
Abstract
In the mammalian embryo, epiblast cells must exit the naïve state and acquire formative pluripotency. This cell state transition is recapitulated by mouse embryonic stem cells (ESCs), which undergo pluripotency progression in defined conditions in vitro. However, our understanding of the molecular cascades and gene networks involved in the exit from naïve pluripotency remains fragmentary. Here, we employed a combination of genetic screens in haploid ESCs, CRISPR/Cas9 gene disruption, large‐scale transcriptomics and computational systems biology to delineate the regulatory circuits governing naïve state exit. Transcriptome profiles for 73 ESC lines deficient for regulators of the exit from naïve pluripotency predominantly manifest delays on the trajectory from naïve to formative epiblast. We find that gene networks operative in ESCs are also active during transition from pre‐ to post‐implantation epiblast in utero. We identified 496 naïve state‐associated genes tightly connected to the in vivo epiblast state transition and largely conserved in primate embryos. Integrated analysis of mutant transcriptomes revealed funnelling of multiple gene activities into discrete regulatory modules. Finally, we delineate how intersections with signalling pathways direct this pivotal mammalian cell state transition.
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Affiliation(s)
- Andreas Lackner
- Max Perutz Laboratories Vienna, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Robert Sehlke
- Cologne Excellence Cluster Cellular Stress Response in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Marius Garmhausen
- Cologne Excellence Cluster Cellular Stress Response in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Giuliano Giuseppe Stirparo
- Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.,Living Systems Institute, University of Exeter, Exeter, UK
| | - Michelle Huth
- Max Perutz Laboratories Vienna, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Fabian Titz-Teixeira
- Cologne Excellence Cluster Cellular Stress Response in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Petra van der Lelij
- Max Perutz Laboratories Vienna, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Julia Ramesmayer
- Max Perutz Laboratories Vienna, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Henry F Thomas
- Max Perutz Laboratories Vienna, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Meryem Ralser
- Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Laura Santini
- Max Perutz Laboratories Vienna, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Elena Galimberti
- Max Perutz Laboratories Vienna, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Mihail Sarov
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - A Francis Stewart
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - Austin Smith
- Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.,Living Systems Institute, University of Exeter, Exeter, UK
| | - Andreas Beyer
- Cologne Excellence Cluster Cellular Stress Response in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany
| | - Martin Leeb
- Max Perutz Laboratories Vienna, University of Vienna, Vienna Biocenter, Vienna, Austria
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24
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Kinoshita M, Barber M, Mansfield W, Cui Y, Spindlow D, Stirparo GG, Dietmann S, Nichols J, Smith A. Capture of Mouse and Human Stem Cells with Features of Formative Pluripotency. Cell Stem Cell 2021; 28:453-471.e8. [PMID: 33271069 PMCID: PMC7939546 DOI: 10.1016/j.stem.2020.11.005] [Citation(s) in RCA: 129] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 09/03/2020] [Accepted: 11/09/2020] [Indexed: 02/06/2023]
Abstract
Pluripotent cells emerge as a naive founder population in the blastocyst, acquire capacity for germline and soma formation, and then undergo lineage priming. Mouse embryonic stem cells (ESCs) and epiblast-derived stem cells (EpiSCs) represent the initial naive and final primed phases of pluripotency, respectively. Here, we investigate the intermediate formative stage. Using minimal exposure to specification cues, we derive stem cells from formative mouse epiblast. Unlike ESCs or EpiSCs, formative stem (FS) cells respond directly to germ cell induction. They colonize somatic tissues and germline in chimeras. Whole-transcriptome analyses show similarity to pre-gastrulation formative epiblast. Signal responsiveness and chromatin accessibility features reflect lineage capacitation. Furthermore, FS cells show distinct transcription factor dependencies, relying critically on Otx2. Finally, FS cell culture conditions applied to human naive cells or embryos support expansion of similar stem cells, consistent with a conserved staging post on the trajectory of mammalian pluripotency.
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Affiliation(s)
- Masaki Kinoshita
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK.
| | - Michael Barber
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK
| | - William Mansfield
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK
| | - Yingzhi Cui
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Daniel Spindlow
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Living Systems Institute, University of Exeter, Exeter EX4 4QD, UK
| | - Giuliano Giuseppe Stirparo
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Living Systems Institute, University of Exeter, Exeter EX4 4QD, UK
| | - Sabine Dietmann
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK
| | - Jennifer Nichols
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
| | - Austin Smith
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK; Living Systems Institute, University of Exeter, Exeter EX4 4QD, UK.
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25
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Agarwal S, Bonefas KM, Garay PM, Brookes E, Murata-Nakamura Y, Porter RS, Macfarlan TS, Ren B, Iwase S. KDM1A maintains genome-wide homeostasis of transcriptional enhancers. Genome Res 2021; 31:186-197. [PMID: 33414108 PMCID: PMC7849409 DOI: 10.1101/gr.234559.118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 12/07/2020] [Indexed: 12/27/2022]
Abstract
Transcriptional enhancers enable exquisite spatiotemporal control of gene expression in metazoans. Enrichment of monomethylation of histone H3 lysine 4 (H3K4me1) is a major chromatin signature of transcriptional enhancers. Lysine (K)-specific demethylase 1A (KDM1A, also known as LSD1), an H3K4me2/me1 demethylase, inactivates stem-cell enhancers during the differentiation of mouse embryonic stem cells (mESCs). However, its role in undifferentiated mESCs remains obscure. Here, we show that KDM1A actively maintains the optimal enhancer status in both undifferentiated and lineage-committed cells. KDM1A occupies a majority of enhancers in undifferentiated mESCs. KDM1A levels at enhancers exhibit clear positive correlations with its substrate H3K4me2, H3K27ac, and transcription at enhancers. In Kdm1a-deficient mESCs, a large fraction of these enhancers gains additional H3K4 methylation, which is accompanied by increases in H3K27 acetylation and increased expression of both enhancer RNAs (eRNAs) and target genes. In postmitotic neurons, loss of KDM1A leads to premature activation of neuronal activity-dependent enhancers and genes. Taken together, these results suggest that KDM1A is a versatile regulator of enhancers and acts as a rheostat to maintain optimal enhancer activity by counterbalancing H3K4 methylation at enhancers.
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Affiliation(s)
- Saurabh Agarwal
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, California 92093-0653, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Katherine M Bonefas
- Neuroscience Graduate Program, The University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Patricia M Garay
- Neuroscience Graduate Program, The University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Emily Brookes
- Division of Newborn Medicine, Boston Children's Hospital, and Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Yumie Murata-Nakamura
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Robert S Porter
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Todd S Macfarlan
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, California 92093-0653, USA
| | - Shigeki Iwase
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
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26
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Weberling A, Zernicka-Goetz M. Trophectoderm mechanics direct epiblast shape upon embryo implantation. Cell Rep 2021; 34:108655. [PMID: 33472064 PMCID: PMC7816124 DOI: 10.1016/j.celrep.2020.108655] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 10/12/2020] [Accepted: 12/22/2020] [Indexed: 12/18/2022] Open
Abstract
Implantation is a hallmark of mammalian embryogenesis during which embryos establish their contacts with the maternal endometrium, remodel, and undertake growth and differentiation. The mechanisms and sequence of events through which embryos change their shape during this transition are largely unexplored. Here, we show that the first extraembryonic lineage, the polar trophectoderm, is the key regulator for remodeling the embryonic epiblast. Loss of its function after immuno-surgery or inhibitor treatments prevents the epiblast shape transitions. In the mouse, the polar trophectoderm exerts physical force upon the epiblast, causing it to transform from an oval into a cup shape. In human embryos, the polar trophectoderm behaves in the opposite manner, exerting a stretching force. By mimicking this stretching behavior in mouse embryogenesis, we could direct the epiblast to adopt the disc-like shape characteristic of human embryos at this stage. Thus, the polar trophectoderm acts as a conserved regulator of epiblast shape. Mouse epiblast remodeling from blastocyst to egg cylinder is achieved in five stages Epiblast remodeling upon implantation is not inherent to the embryonic lineage The polar trophectoderm mediates epiblast shape acquisition Epiblast shape regulation by the polar trophectoderm appears conserved in evolution
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Affiliation(s)
- Antonia Weberling
- Mammalian Embryo and Stem Cell Group, University of Cambridge, Department of Physiology, Development and Neuroscience, Downing Street, Cambridge CB2 3DY, UK
| | - Magdalena Zernicka-Goetz
- Mammalian Embryo and Stem Cell Group, University of Cambridge, Department of Physiology, Development and Neuroscience, Downing Street, Cambridge CB2 3DY, UK; Plasticity and Self-Organization Group, California Institute of Technology, Division of Biology and Biological Engineering, 1200 E. California Boulevard, Pasadena, CA 91125, USA.
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27
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Vila-Cejudo M, Alonso-Alonso S, Pujol A, Santaló J, Ibáñez E. Wnt pathway modulation generates blastomere-derived mouse embryonic stem cells with different pluripotency features. J Assist Reprod Genet 2020; 37:2967-2979. [PMID: 33047186 DOI: 10.1007/s10815-020-01964-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 10/04/2020] [Indexed: 11/30/2022] Open
Abstract
PURPOSE This study aimed to determine the role of Wnt pathway in mouse embryonic stem cell (mESC) derivation from single blastomeres isolated from eight-cell embryos and in the pluripotency features of the mESC established. METHODS Wnt activator CHIR99021, Wnt inhibitor IWR-1-endo, and MEK inhibitor PD0325901 were used alone or in combination during ESC derivation and maintenance from single blastomeres biopsied from eight-cell embryos. Alkaline phosphatase activity, FGF5 levels, expression of key pluripotency genes, and chimera formation were assessed to determine the pluripotency state of the mESC lines. RESULTS Derivation efficiencies were highest when combining pairs of inhibitors (15-24.7%) than when using single inhibitors or none (1.4-10.1%). Full naïve pluripotency was only achieved in CHIR- and 2i-treated mESC lines, whereas IWR and PD treatments or the absence of treatment resulted in co-existence of naïve-like and primed-like pluripotency features. IWR + CHIR- and IWR + PD-treated mESC displayed features of primed pluripotency, but IWR + CHIR-treated lines were able to generate germline-competent chimeric mice, resembling the predicted properties of formative pluripotency. CONCLUSION Wnt and MAPK pathways have a key role in the successful derivation and pluripotency features of mESC from single precompaction blastomeres. Modulation of these pathways results in mESC lines with various degrees of naïve-like and primed-like pluripotency features.
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Affiliation(s)
- Marta Vila-Cejudo
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.,Tissue Engineering Unit, Centre for Genomic Regulation, Carrer del Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Sandra Alonso-Alonso
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Anna Pujol
- Department of Biochemistry and Molecular Biology, School of Veterinary Medicine and Center of Animal Biotechnology and Gene Therapy, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Josep Santaló
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Elena Ibáñez
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.
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28
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Kim KP, Wu Y, Yoon J, Adachi K, Wu G, Velychko S, MacCarthy CM, Shin B, Röpke A, Arauzo-Bravo MJ, Stehling M, Han DW, Gao Y, Kim J, Gao S, Schöler HR. Reprogramming competence of OCT factors is determined by transactivation domains. SCIENCE ADVANCES 2020; 6:6/36/eaaz7364. [PMID: 32917606 PMCID: PMC7467702 DOI: 10.1126/sciadv.aaz7364] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 07/20/2020] [Indexed: 06/11/2023]
Abstract
OCT4 (also known as POU5F1) plays an essential role in reprogramming. It is the only member of the POU (Pit-Oct-Unc) family of transcription factors that can induce pluripotency despite sharing high structural similarities to all other members. Here, we discover that OCT6 (also known as POU3F1) can elicit reprogramming specifically in human cells. OCT6-based reprogramming does not alter the mesenchymal-epithelial transition but is attenuated through the delayed activation of the pluripotency network in comparison with OCT4-based reprogramming. Creating a series of reciprocal domain-swapped chimeras and mutants across all OCT factors, we clearly delineate essential elements of OCT4/OCT6-dependent reprogramming and, conversely, identify the features that prevent induction of pluripotency by other OCT factors. With this strategy, we further discover various chimeric proteins that are superior to OCT4 in reprogramming. Our findings clarify how reprogramming competences of OCT factors are conferred through their structural components.
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Affiliation(s)
- Kee-Pyo Kim
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, Münster 48149, Germany
| | - You Wu
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Juyong Yoon
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, Münster 48149, Germany
| | - Kenjiro Adachi
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, Münster 48149, Germany
| | - Guangming Wu
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, Münster 48149, Germany
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kai Yuan Avenue, Science Park, Guangzhou 510530, China
| | - Sergiy Velychko
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, Münster 48149, Germany
| | - Caitlin M MacCarthy
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, Münster 48149, Germany
| | - Borami Shin
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, Münster 48149, Germany
| | - Albrecht Röpke
- Institute of Human Genetics, University of Münster, Vesaliusweg 12-14, Münster 48149, Germany
| | - Marcos J Arauzo-Bravo
- Group of Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, San Sebastian 20014, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao 48011, Spain
| | - Martin Stehling
- Flow Cytometry Unit, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, Münster 48149, Germany
| | - Dong Wook Han
- School of Biotechnology and Healthcare, Wuyi University, Jiangmen 529020, China
| | - Yawei Gao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Johnny Kim
- Department of Cardiac Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim 61231, Germany
| | - Shaorong Gao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Hans R Schöler
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, Münster 48149, Germany.
- University of Münster, Medical Faculty, Domagkstrasse 3, Münster 48149, Germany
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29
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Shanak S, Helms V. DNA methylation and the core pluripotency network. Dev Biol 2020; 464:145-160. [PMID: 32562758 DOI: 10.1016/j.ydbio.2020.06.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 05/01/2020] [Accepted: 06/04/2020] [Indexed: 01/06/2023]
Abstract
From the onset of fertilization, the genome undergoes cell division and differentiation. All of these developmental transitions and differentiation processes include cell-specific signatures and gradual changes of the epigenome. Understanding what keeps stem cells in the pluripotent state and what leads to differentiation are fascinating and biomedically highly important issues. Numerous studies have identified genes, proteins, microRNAs and small molecules that exert essential effects. Notably, there exists a core pluripotency network that consists of several transcription factors and accessory proteins. Three eminent transcription factors, OCT4, SOX2 and NANOG, serve as hubs in this core pluripotency network. They bind to the enhancer regions of their target genes and modulate, among others, the expression levels of genes that are associated with Gene Ontology terms related to differentiation and self-renewal. Also, much has been learned about the epigenetic rewiring processes during these changes of cell fate. For example, DNA methylation dynamics is pivotal during embryonic development. The main goal of this review is to highlight an intricate interplay of (a) DNA methyltransferases controlling the expression levels of core pluripotency factors by modulation of the DNA methylation levels in their enhancer regions, and of (b) the core pluripotency factors controlling the transcriptional regulation of DNA methyltransferases. We discuss these processes both at the global level and in atomistic detail based on information from structural studies and from computer simulations.
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Affiliation(s)
- Siba Shanak
- Faculty of Science, Arab-American University, Jenin, Palestine; Center for Bioinformatics, Saarland University, Saarbruecken, Germany
| | - Volkhard Helms
- Center for Bioinformatics, Saarland University, Saarbruecken, Germany.
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30
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Gao J, Petraki S, Sun X, Brooks LA, Lynch TJ, Hsieh CL, Elteriefi R, Lorenzana Z, Punj V, Engelhardt JF, Parekh KR, Ryan AL. Derivation of induced pluripotent stem cells from ferret somatic cells. Am J Physiol Lung Cell Mol Physiol 2020; 318:L671-L683. [PMID: 32073882 DOI: 10.1152/ajplung.00456.2019] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Ferrets are an attractive mammalian model for several diseases, especially those affecting the lungs, liver, brain, and kidneys. Many chronic human diseases have been difficult to model in rodents due to differences in size and cellular anatomy. This is particularly the case for the lung, where ferrets provide an attractive mammalian model of both acute and chronic lung diseases, such as influenza, cystic fibrosis, A1A emphysema, and obliterative bronchiolitis, closely recapitulating disease pathogenesis, as it occurs in humans. As such, ferrets have the potential to be a valuable preclinical model for the evaluation of cell-based therapies for lung regeneration and, likely, for other tissues. Induced pluripotent stem cells (iPSCs) provide a great option for provision of enough autologous cells to make patient-specific cell therapies a reality. Unfortunately, they have not been successfully created from ferrets. In this study, we demonstrate the generation of ferret iPSCs that reflect the primed pluripotent state of human iPSCs. Ferret fetal fibroblasts were reprogrammed and acquired core features of pluripotency, having the capacity for self-renewal, multilineage differentiation, and a high-level expression of the core pluripotency genes and pathways at both the transcriptional and protein level. In conclusion, we have generated ferret pluripotent stem cells that provide an opportunity for advancing our capacity to evaluate autologous cell engraftment in ferrets.
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Affiliation(s)
- Jinghui Gao
- Hastings Center for Pulmonary Research, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Southern California, Los Angeles, California
| | - Sophia Petraki
- Hastings Center for Pulmonary Research, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Southern California, Los Angeles, California
| | - Xingshen Sun
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, Iowa
| | - Leonard A Brooks
- Division of Cardiothoracic Surgery, University of Iowa, Iowa City, Iowa
| | - Thomas J Lynch
- Division of Cardiothoracic Surgery, University of Iowa, Iowa City, Iowa
| | - Chih-Lin Hsieh
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - Reem Elteriefi
- Hastings Center for Pulmonary Research, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Southern California, Los Angeles, California
| | - Zareeb Lorenzana
- Hastings Center for Pulmonary Research, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Southern California, Los Angeles, California
| | - Vasu Punj
- Hastings Center for Pulmonary Research, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Southern California, Los Angeles, California
| | - John F Engelhardt
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, Iowa
| | - Kalpaj R Parekh
- Division of Cardiothoracic Surgery, University of Iowa, Iowa City, Iowa
| | - Amy L Ryan
- Hastings Center for Pulmonary Research, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Southern California, Los Angeles, California.,Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, California
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31
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Yang L, Zhu Y, Yu H, Cheng X, Chen S, Chu Y, Huang H, Zhang J, Li W. scMAGeCK links genotypes with multiple phenotypes in single-cell CRISPR screens. Genome Biol 2020; 21:19. [PMID: 31980032 PMCID: PMC6979386 DOI: 10.1186/s13059-020-1928-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Accepted: 01/07/2020] [Indexed: 02/06/2023] Open
Abstract
We present scMAGeCK, a computational framework to identify genomic elements associated with multiple expression-based phenotypes in CRISPR/Cas9 functional screening that uses single-cell RNA-seq as readout. scMAGeCK outperforms existing methods, identifies genes and enhancers with known and novel functions in cell proliferation, and enables an unbiased construction of genotype-phenotype network. Single-cell CRISPR screening on mouse embryonic stem cells identifies key genes associated with different pluripotency states. Applying scMAGeCK on multiple datasets, we identify key factors that improve the power of single-cell CRISPR screening. Collectively, scMAGeCK is a novel tool to study genotype-phenotype relationships at a single-cell level.
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Affiliation(s)
- Lin Yang
- Center for Genetic Medicine Research, Children's National Hospital, 111 Michigan Ave NW, Washington, DC, 20010, USA.,Department of Genomics and Precision Medicine, George Washington University, 111 Michigan Ave NW, Washington, DC, 20010, USA.,Department of Biochemistry & Molecular Medicine, George Washington University, 2300 Eye St., NW, Washington, DC, 20037, USA
| | - Yuqing Zhu
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang, China.,Institute of Hematology, Zhejiang University, Hangzhou, 310058, Zhejiang, China.,Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Haining, 314400, Zhejiang, China
| | - Hua Yu
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang, China.,Institute of Hematology, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Xiaolong Cheng
- Center for Genetic Medicine Research, Children's National Hospital, 111 Michigan Ave NW, Washington, DC, 20010, USA.,Department of Genomics and Precision Medicine, George Washington University, 111 Michigan Ave NW, Washington, DC, 20010, USA
| | - Sitong Chen
- Center for Genetic Medicine Research, Children's National Hospital, 111 Michigan Ave NW, Washington, DC, 20010, USA.,Department of Genomics and Precision Medicine, George Washington University, 111 Michigan Ave NW, Washington, DC, 20010, USA.,Department of Biochemistry & Molecular Medicine, George Washington University, 2300 Eye St., NW, Washington, DC, 20037, USA
| | - Yulan Chu
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang, China.,Institute of Hematology, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - He Huang
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang, China.,Institute of Hematology, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Jin Zhang
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang, China. .,Institute of Hematology, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
| | - Wei Li
- Center for Genetic Medicine Research, Children's National Hospital, 111 Michigan Ave NW, Washington, DC, 20010, USA. .,Department of Genomics and Precision Medicine, George Washington University, 111 Michigan Ave NW, Washington, DC, 20010, USA.
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32
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Oxygen Regulates Human Pluripotent Stem Cell Metabolic Flux. Stem Cells Int 2019; 2019:8195614. [PMID: 31236115 PMCID: PMC6545818 DOI: 10.1155/2019/8195614] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 02/27/2019] [Indexed: 02/07/2023] Open
Abstract
Metabolism has been shown to alter cell fate in human pluripotent stem cells (hPSC). However, current understanding is almost exclusively based on work performed at 20% oxygen (air), with very few studies reporting on hPSC at physiological oxygen (5%). In this study, we integrated metabolic, transcriptomic, and epigenetic data to elucidate the impact of oxygen on hPSC. Using 13C-glucose labeling, we show that 5% oxygen increased the intracellular levels of glycolytic intermediates, glycogen, and the antioxidant response in hPSC. In contrast, 20% oxygen increased metabolite flux through the TCA cycle, activity of mitochondria, and ATP production. Acetylation of H3K9 and H3K27 was elevated at 5% oxygen while H3K27 trimethylation was decreased, conforming to a more open chromatin structure. RNA-seq analysis of 5% oxygen hPSC also indicated increases in glycolysis, lysine demethylases, and glucose-derived carbon metabolism, while increased methyltransferase and cell cycle activity was indicated at 20% oxygen. Our findings show that oxygen drives metabolite flux and specifies carbon fate in hPSC and, although the mechanism remains to be elucidated, oxygen was shown to alter methyltransferase and demethylase activity and the global epigenetic landscape.
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33
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OTX2 Signals from the Choroid Plexus to Regulate Adult Neurogenesis. eNeuro 2019; 6:ENEURO.0262-18.2019. [PMID: 31064838 PMCID: PMC6506823 DOI: 10.1523/eneuro.0262-18.2019] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 02/12/2019] [Accepted: 02/16/2019] [Indexed: 01/09/2023] Open
Abstract
Proliferation and migration during adult neurogenesis are regulated by a microenvironment of signaling molecules originating from local vasculature, from CSF produced by the choroid plexus, and from local supporting cells including astrocytes. Here, we focus on the function of OTX2 homeoprotein transcription factor in the mouse adult ventricular-subventricular zone (V-SVZ), which generates olfactory bulb neurons. We find that OTX2 secreted by choroid plexus is transferred to the supporting cells of the V-SVZ and rostral migratory stream. Deletion of Otx2 in choroid plexus affects neuroblast migration and reduces the number of olfactory bulb newborn neurons. Adult neurogenesis was also decreased by expressing secreted single-chain antibodies to sequester OTX2 in the CSF, demonstrating the importance of non-cell-autonomous OTX2. We show that OTX2 activity modifies extracellular matrix components and signaling molecules produced by supporting astrocytes. Thus, we reveal a multilevel and non-cell-autonomous role of a homeoprotein and reinforce the choroid plexus and astrocytes as key niche compartments affecting adult neurogenesis.
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34
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Rostovskaya M, Stirparo GG, Smith A. Capacitation of human naïve pluripotent stem cells for multi-lineage differentiation. Development 2019; 146:dev172916. [PMID: 30944104 PMCID: PMC6467473 DOI: 10.1242/dev.172916] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 02/22/2019] [Indexed: 12/14/2022]
Abstract
Human naïve pluripotent stem cells (PSCs) share features with the pre-implantation epiblast. They therefore provide an unmatched opportunity for characterising the developmental programme of pluripotency in Homo sapiens Here, we confirm that naïve PSCs do not respond directly to germ layer induction, but must first acquire competence. Capacitation for multi-lineage differentiation occurs without exogenous growth factor stimulation and is facilitated by inhibition of Wnt signalling. Whole-transcriptome profiling during this formative transition highlights dynamic changes in gene expression, which affect many cellular properties including metabolism and epithelial features. Notably, naïve pluripotency factors are exchanged for postimplantation factors, but competent cells remain devoid of lineage-specific transcription. The gradual pace of transition for human naïve PSCs is consistent with the timespan of primate development from blastocyst to gastrulation. Transcriptome trajectory during in vitro capacitation of human naïve cells tracks the progression of the epiblast during embryogenesis in Macaca fascicularis, but shows greater divergence from mouse development. Thus, the formative transition of naïve PSCs in a simple culture system may recapitulate essential and specific features of pluripotency dynamics during an inaccessible period of human embryogenesis.
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Affiliation(s)
- Maria Rostovskaya
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge CB2 1QR, United Kingdom
| | - Giuliano G Stirparo
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge CB2 1QR, United Kingdom
| | - Austin Smith
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge CB2 1QR, United Kingdom
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35
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Xie Y, Cao H, Zhang Z, Zhang S, Wang H. Molecular network of miR-1343 regulates the pluripotency of porcine pluripotent stem cells via repressing OTX2 expression. RNA Biol 2018; 16:82-92. [PMID: 30567463 DOI: 10.1080/15476286.2018.1559688] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
Porcine OTX2 was found to be highly activated in porcine iPS cells (piPSCs) that were reported by different laboratories worldwide. To reveal the regulatory function of OTX2 in porcine reprogrammed cells, we screened porcine miRNA-seq databases and found two miRNAs, miR-1343 and miR-545, that could specifically bind to 3'UTR of OTX2 and suppress endogenous OTX2 expression in piPSCs. Knockdown of OTX2 by miR-1343 and miR-545 could significantly increase the expression of SOX2 and ESRRB, but did not alter the expressions of OCT4 and KLF4, and improve the pluripotency of piPSCs. The promoter-based assays showed that OTX2 potentially bound to the promoter region of SOX2 and ESRRB and suppressed their expression. On the other hand, SOX2 could interact with OTX2 promoter. Ectopic expression of SOX2 could significantly decrease OTX2 promoter activity, showing that there is a negative feedback loop between SOX2 and OTX2. Additionally, SOX2 and ESRRB significantly stimulated miR-1343 expression in piPSCs, but OTX2 down regulated the expression of miR-1343 in either direct or indirect manners. In summary, this study demonstrates that there is a regulatory network mediated by miR-1343, in which downregulation of OTX2 by miR-1343 can elevate the expression of pluripotent genes that were then sustain the pluripotency of piPSCs.
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Affiliation(s)
- Youlong Xie
- a Department of Animal Biotechnology , College of Veterinary Medicine, Northwest A&F University , Yangling , Shaanxi , China
| | - Hongxia Cao
- a Department of Animal Biotechnology , College of Veterinary Medicine, Northwest A&F University , Yangling , Shaanxi , China
| | - Zhiyi Zhang
- a Department of Animal Biotechnology , College of Veterinary Medicine, Northwest A&F University , Yangling , Shaanxi , China
| | - Shiqiang Zhang
- a Department of Animal Biotechnology , College of Veterinary Medicine, Northwest A&F University , Yangling , Shaanxi , China
| | - Huayan Wang
- a Department of Animal Biotechnology , College of Veterinary Medicine, Northwest A&F University , Yangling , Shaanxi , China
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36
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Dunn SJ, Li MA, Carbognin E, Smith A, Martello G. A common molecular logic determines embryonic stem cell self-renewal and reprogramming. EMBO J 2018; 38:embj.2018100003. [PMID: 30482756 PMCID: PMC6316172 DOI: 10.15252/embj.2018100003] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 10/03/2018] [Accepted: 10/04/2018] [Indexed: 11/18/2022] Open
Abstract
During differentiation and reprogramming, new cell identities are generated by reconfiguration of gene regulatory networks. Here, we combined automated formal reasoning with experimentation to expose the logic of network activation during induction of naïve pluripotency. We find that a Boolean network architecture defined for maintenance of naïve state embryonic stem cells (ESC) also explains transcription factor behaviour and potency during resetting from primed pluripotency. Computationally identified gene activation trajectories were experimentally substantiated at single‐cell resolution by RT–qPCR. Contingency of factor availability explains the counterintuitive observation that Klf2, which is dispensable for ESC maintenance, is required during resetting. We tested 124 predictions formulated by the dynamic network, finding a predictive accuracy of 77.4%. Finally, we show that this network explains and predicts experimental observations of somatic cell reprogramming. We conclude that a common deterministic program of gene regulation is sufficient to govern maintenance and induction of naïve pluripotency. The tools exemplified here could be broadly applied to delineate dynamic networks underlying cell fate transitions.
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Affiliation(s)
- Sara-Jane Dunn
- Microsoft Research, Cambridge, UK.,Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Meng Amy Li
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Elena Carbognin
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Austin Smith
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK .,Department of Biochemistry, University of Cambridge, Cambridge, UK
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37
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Boroviak T, Stirparo GG, Dietmann S, Hernando-Herraez I, Mohammed H, Reik W, Smith A, Sasaki E, Nichols J, Bertone P. Single cell transcriptome analysis of human, marmoset and mouse embryos reveals common and divergent features of preimplantation development. Development 2018; 145:145/21/dev167833. [PMID: 30413530 PMCID: PMC6240320 DOI: 10.1242/dev.167833] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Accepted: 10/04/2018] [Indexed: 12/12/2022]
Abstract
The mouse embryo is the canonical model for mammalian preimplantation development. Recent advances in single cell profiling allow detailed analysis of embryogenesis in other eutherian species, including human, to distinguish conserved from divergent regulatory programs and signalling pathways in the rodent paradigm. Here, we identify and compare transcriptional features of human, marmoset and mouse embryos by single cell RNA-seq. Zygotic genome activation correlates with the presence of polycomb repressive complexes in all three species, while ribosome biogenesis emerges as a predominant attribute in primate embryos, supporting prolonged translation of maternally deposited RNAs. We find that transposable element expression signatures are species, stage and lineage specific. The pluripotency network in the primate epiblast lacks certain regulators that are operative in mouse, but encompasses WNT components and genes associated with trophoblast specification. Sequential activation of GATA6, SOX17 and GATA4 markers of primitive endoderm identity is conserved in primates. Unexpectedly, OTX2 is also associated with primitive endoderm specification in human and non-human primate blastocysts. Our cross-species analysis demarcates both conserved and primate-specific features of preimplantation development, and underscores the molecular adaptability of early mammalian embryogenesis. Highlighted Article: Analysis of stage-matched, single-cell gene expression data from three mammalian species reveals conserved and primate-specific regulation of early embryogenesis and lineage specification.
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Affiliation(s)
- Thorsten Boroviak
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK.,Department of Physiology, Development and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge CB2 3EG, UK
| | - Giuliano G Stirparo
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Sabine Dietmann
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | | | - Hisham Mohammed
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Wolf Reik
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Austin Smith
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK.,Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| | - Erika Sasaki
- Central Institute for Experimental Animals, Department of Applied Developmental Biology, 3-25-12 Tonomachi, Kawasaki-ku, Kawasaki 210-0821, Japan
| | - Jennifer Nichols
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK.,Department of Physiology, Development and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge CB2 3EG, UK
| | - Paul Bertone
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
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38
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Nett IR, Mulas C, Gatto L, Lilley KS, Smith A. Negative feedback via RSK modulates Erk-dependent progression from naïve pluripotency. EMBO Rep 2018; 19:e45642. [PMID: 29895711 PMCID: PMC6073214 DOI: 10.15252/embr.201745642] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 05/16/2018] [Accepted: 05/18/2018] [Indexed: 01/08/2023] Open
Abstract
Mitogen-activated protein kinase (MAPK)/extracellular signal-regulated kinase (ERK) signalling is implicated in initiation of embryonic stem (ES) cell differentiation. The pathway is subject to complex feedback regulation. Here, we examined the ERK-responsive phosphoproteome in ES cells and identified the negative regulator RSK1 as a prominent target. We used CRISPR/Cas9 to create combinatorial mutations in RSK family genes. Genotypes that included homozygous null mutations in Rps6ka1, encoding RSK1, resulted in elevated ERK phosphorylation. These RSK-depleted ES cells exhibit altered kinetics of transition into differentiation, with accelerated downregulation of naïve pluripotency factors, precocious expression of transitional epiblast markers and early onset of lineage specification. We further show that chemical inhibition of RSK increases ERK phosphorylation and expedites ES cell transition without compromising multilineage potential. These findings demonstrate that the ERK activation profile influences the dynamics of pluripotency progression and highlight the role of signalling feedback in temporal control of cell state transitions.
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Affiliation(s)
- Isabelle Re Nett
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Carla Mulas
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Laurent Gatto
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK
- Computational Proteomics Unit, Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK
| | - Kathryn S Lilley
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Austin Smith
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Biochemistry, University of Cambridge, Cambridge, UK
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39
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Su Z, Zhang Y, Liao B, Zhong X, Chen X, Wang H, Guo Y, Shan Y, Wang L, Pan G. Antagonism between the transcription factors NANOG and OTX2 specifies rostral or caudal cell fate during neural patterning transition. J Biol Chem 2018; 293:4445-4455. [PMID: 29386354 DOI: 10.1074/jbc.m117.815449] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Revised: 01/29/2018] [Indexed: 01/08/2023] Open
Abstract
During neurogenesis, neural patterning is a critical step during which neural progenitor cells differentiate into neurons with distinct functions. However, the molecular determinants that regulate neural patterning remain poorly understood. Here we optimized the "dual SMAD inhibition" method to specifically promote differentiation of human pluripotent stem cells (hPSCs) into forebrain and hindbrain neural progenitor cells along the rostral-caudal axis. We report that neural patterning determination occurs at the very early stage in this differentiation. Undifferentiated hPSCs expressed basal levels of the transcription factor orthodenticle homeobox 2 (OTX2) that dominantly drove hPSCs into the "default" rostral fate at the beginning of differentiation. Inhibition of glycogen synthase kinase 3β (GSK3β) through CHIR99021 application sustained transient expression of the transcription factor NANOG at early differentiation stages through Wnt signaling. Wnt signaling and NANOG antagonized OTX2 and, in the later stages of differentiation, switched the default rostral cell fate to the caudal one. Our findings have uncovered a mutual antagonism between NANOG and OTX2 underlying cell fate decisions during neural patterning, critical for the regulation of early neural development in humans.
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Affiliation(s)
- Zhenghui Su
- From the School of Life Sciences, University of Science and Technology of China, 230027 Hefei, China.,the Chinese Academy of Sciences Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530 Guangzhou, China.,the Hefei Institute of Stem Cell and Regenerative Medicine, 230088 Hefei, China
| | - Yanqi Zhang
- the Chinese Academy of Sciences Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530 Guangzhou, China
| | - Baojian Liao
- the Chinese Academy of Sciences Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530 Guangzhou, China.,the Hefei Institute of Stem Cell and Regenerative Medicine, 230088 Hefei, China
| | - Xiaofen Zhong
- the Chinese Academy of Sciences Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530 Guangzhou, China
| | - Xin Chen
- the School of Automation, Guangdong University of Technology, 510006 Guangzhou, China, and
| | - Haitao Wang
- From the School of Life Sciences, University of Science and Technology of China, 230027 Hefei, China
| | - Yiping Guo
- the Chinese Academy of Sciences Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530 Guangzhou, China
| | - Yongli Shan
- the Chinese Academy of Sciences Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530 Guangzhou, China
| | - Lihui Wang
- the Department of Pathology, Medical College, Jinan University, 510632 Guangzhou, China
| | - Guangjin Pan
- the Chinese Academy of Sciences Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530 Guangzhou, China, .,the Hefei Institute of Stem Cell and Regenerative Medicine, 230088 Hefei, China
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40
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Ying QL, Smith A. The Art of Capturing Pluripotency: Creating the Right Culture. Stem Cell Reports 2018; 8:1457-1464. [PMID: 28591647 PMCID: PMC5470336 DOI: 10.1016/j.stemcr.2017.05.020] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 05/17/2017] [Accepted: 05/17/2017] [Indexed: 12/14/2022] Open
Abstract
Embryonic stem cells (ESCs) are a unique tool for genetic perturbation of mammalian cellular and organismal processes additionally in humans offer unprecedented opportunities for disease modeling and cell therapy. Furthermore, ESCs are a powerful system for exploring the fundamental biology of pluripotency. Indeed understanding the control of self-renewal and differentiation is key to realizing the potential of ESCs. Building on previous observations, we found that mouse ESCs can be derived and maintained with high efficiency through insulation from differentiation cues combined with consolidation of an innate cell proliferation program. This finding of a pluripotent ground state has led to conceptual and practical advances, including the establishment of germline-competent ESCs from recalcitrant mouse strains and for the first time from the rat. Here, we summarize historical and recent progress in defining the signaling environment that supports self-renewal. We compare the contrasting requirements of two types of pluripotent stem cell, naive ESCs and primed post-implantation epiblast stem cells (EpiSCs), and consider the outstanding challenge of generating naive pluripotent stem cells from different mammals.
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Affiliation(s)
- Qi-Long Ying
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research at USC, Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.
| | - Austin Smith
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK; Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK.
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41
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Kinoshita M, Smith A. Pluripotency Deconstructed. Dev Growth Differ 2018; 60:44-52. [PMID: 29359419 DOI: 10.1111/dgd.12419] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 12/02/2017] [Indexed: 12/14/2022]
Abstract
Pluripotency denotes the flexible capacity of single cells to give rise to all somatic lineages and typically also the germline. Mouse ES cells and post-implantation epiblast-derived stem cells (EpiSC) are widely used pluripotent cell culture systems. These two in vitro stem cell types have divergent characteristics. They are considered as representative of distinct developmental stages, distinguished by using the terms "naïve" and "primed". A binary description is an over-simplification, however. Here, we discuss an intermediate stage of pluripotency that we term "formative". Formative pluripotency features a gene regulatory network switch from the naïve state and comprises capacitation of enhancers, signaling pathways and epigenetic machinery in order to install competence for lineage specification.
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Affiliation(s)
- Masaki Kinoshita
- Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, UK
| | - Austin Smith
- Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, UK.,Department of Biochemistry, University of Cambridge, Cambridge, UK
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42
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Acampora D, Di Giovannantonio LG, Garofalo A, Nigro V, Omodei D, Lombardi A, Zhang J, Chambers I, Simeone A. Functional Antagonism between OTX2 and NANOG Specifies a Spectrum of Heterogeneous Identities in Embryonic Stem Cells. Stem Cell Reports 2017; 9:1642-1659. [PMID: 29056334 PMCID: PMC5935799 DOI: 10.1016/j.stemcr.2017.09.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 09/22/2017] [Accepted: 09/25/2017] [Indexed: 01/12/2023] Open
Abstract
Embryonic stem cells (ESCs) cultured in leukemia inhibitory factor (LIF) plus fetal bovine serum (FBS) exhibit heterogeneity in the expression of naive and primed transcription factors. This heterogeneity reflects the dynamic condition of ESCs and their versatility to promptly respond to signaling effectors promoting naive or primed pluripotency. Here, we report that ESCs lacking Nanog or overexpressing Otx2 exhibit an early primed identity in LIF + FBS and fail to convert into 2i-induced naive state. Conversely, Otx2-null ESCs possess naive identity features in LIF + FBS similar to Nanog-overexpressing ESCs and convert poorly into FGF-induced early primed state. When both Nanog and Otx2 are inactivated, ESCs cultured in LIF + FBS exhibit primed identity and weakened ability to convert into naive state. These data suggest that, through mutual antagonism, NANOG and OTX2 specify the heterogeneous identity of ESCs cultured in LIF + FBS and individually predispose them for optimal response to naive or primed inducing factors.
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Affiliation(s)
- Dario Acampora
- Institute of Genetics and Biophysics "Adriano Buzzati-Traverso", CNR, Via P. Castellino,111, 80131 Naples, Italy; IRCCS Neuromed, 86077 Pozzilli, IS, Italy
| | | | - Arcomaria Garofalo
- Dipartimento di Biochimica, Biofisica e Patologia Generale, Università della Campania "Luigi Vanvitelli", Via L. De Crecchio, 7, 80138 Naples, Italy; Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei, 34, 80087 Pozzuoli, NA, Italy
| | - Vincenzo Nigro
- Dipartimento di Biochimica, Biofisica e Patologia Generale, Università della Campania "Luigi Vanvitelli", Via L. De Crecchio, 7, 80138 Naples, Italy; Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei, 34, 80087 Pozzuoli, NA, Italy
| | - Daniela Omodei
- Institute of Genetics and Biophysics "Adriano Buzzati-Traverso", CNR, Via P. Castellino,111, 80131 Naples, Italy
| | | | - Jingchao Zhang
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Ian Chambers
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Antonio Simeone
- Institute of Genetics and Biophysics "Adriano Buzzati-Traverso", CNR, Via P. Castellino,111, 80131 Naples, Italy; IRCCS Neuromed, 86077 Pozzilli, IS, Italy.
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43
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Piliszek A, Madeja ZE, Plusa B. Suppression of ERK signalling abolishes primitive endoderm formation but does not promote pluripotency in rabbit embryo. Development 2017; 144:3719-3730. [PMID: 28935706 PMCID: PMC5675450 DOI: 10.1242/dev.156406] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 09/04/2017] [Indexed: 12/13/2022]
Abstract
Formation of epiblast (EPI) – the founder line of all embryonic lineages – and extra-embryonic supportive tissues is one of the key events in mammalian development. The prevailing model of early mammalian development is based almost exclusively on the mouse. Here, we provide a comprehensive, stage-by-stage analysis of EPI and extra-embryonic primitive endoderm (PrE) formation during preimplantation development of the rabbit. Although we observed that rabbit embryos have several features in common with mouse embryos, including a stage-related initiation of lineage specification, our results demonstrate the existence of some key differences in lineage specification among mammals. Contrary to the current view, our data suggest that reciprocal repression of GATA6 and NANOG is not fundamental for the initial stages of PrE versus EPI specification in mammals. Furthermore, our results provide insight into the observed discrepancies relating to the role of FGF/ERK signalling in PrE versus EPI specification between mouse and other mammals. Highlighted Article: A comprehensive analysis of rabbit preimplantation development reveals key differences between rabbit and mouse, with some aspects of lineage specification in rabbit more closely resembling that of human and primate embryos.
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Affiliation(s)
- Anna Piliszek
- Department of Experimental Embryology, Institute of Genetics and Animal Breeding, Polish Academy of Sciences, Postępu 36a, 05-552 Jastrzębiec, Poland
| | - Zofia E Madeja
- Department of Genetics and Animal Breeding, Faculty of Veterinary Medicine and Animal Sciences, Poznan University of Life Sciences, Wołyńska 33, 60-637 Poznań, Poland
| | - Berenika Plusa
- Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester M13 9PT, UK
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44
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Smith A. Formative pluripotency: the executive phase in a developmental continuum. Development 2017; 144:365-373. [PMID: 28143843 PMCID: PMC5430734 DOI: 10.1242/dev.142679] [Citation(s) in RCA: 292] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The regulative capability of single cells to give rise to all primary embryonic lineages is termed pluripotency. Observations of fluctuating gene expression and phenotypic heterogeneity in vitro have fostered a conception of pluripotency as an intrinsically metastable and precarious state. However, in the embryo and in defined culture environments the properties of pluripotent cells change in an orderly sequence. Two phases of pluripotency, called naïve and primed, have previously been described. In this Hypothesis article, a third phase, called formative pluripotency, is proposed to exist as part of a developmental continuum between the naïve and primed phases. The formative phase is hypothesised to be enabling for the execution of pluripotency, entailing remodelling of transcriptional, epigenetic, signalling and metabolic networks to constitute multi-lineage competence and responsiveness to specification cues. Summary: This Hypothesis article poses that a third state of pluripotency, called formative pluripotency, exists between the naïve and primed states, and is enabling for the execution of pluripotency.
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Affiliation(s)
- Austin Smith
- Wellcome Trust-Medical Research Council Stem Cell Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
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45
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Li MA, Amaral PP, Cheung P, Bergmann JH, Kinoshita M, Kalkan T, Ralser M, Robson S, von Meyenn F, Paramor M, Yang F, Chen C, Nichols J, Spector DL, Kouzarides T, He L, Smith A. A lncRNA fine tunes the dynamics of a cell state transition involving Lin28, let-7 and de novo DNA methylation. eLife 2017; 6:e23468. [PMID: 28820723 PMCID: PMC5562443 DOI: 10.7554/elife.23468] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Accepted: 07/24/2017] [Indexed: 12/24/2022] Open
Abstract
Execution of pluripotency requires progression from the naïve status represented by mouse embryonic stem cells (ESCs) to a state capacitated for lineage specification. This transition is coordinated at multiple levels. Non-coding RNAs may contribute to this regulatory orchestra. We identified a rodent-specific long non-coding RNA (lncRNA) linc1281, hereafter Ephemeron (Eprn), that modulates the dynamics of exit from naïve pluripotency. Eprn deletion delays the extinction of ESC identity, an effect associated with perduring Nanog expression. In the absence of Eprn, Lin28a expression is reduced which results in persistence of let-7 microRNAs, and the up-regulation of de novo methyltransferases Dnmt3a/b is delayed. Dnmt3a/b deletion retards ES cell transition, correlating with delayed Nanog promoter methylation and phenocopying loss of Eprn or Lin28a. The connection from lncRNA to miRNA and DNA methylation facilitates the acute extinction of naïve pluripotency, a pre-requisite for rapid progression from preimplantation epiblast to gastrulation in rodents. Eprn illustrates how lncRNAs may introduce species-specific network modulations.
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Affiliation(s)
- Meng Amy Li
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
- Division of Cellular and Developmental Biology, Department of Molecular and Cellular Biology, University of California Berkeley, Berkeley, United States
| | - Paulo P Amaral
- The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - Priscilla Cheung
- Division of Cellular and Developmental Biology, Department of Molecular and Cellular Biology, University of California Berkeley, Berkeley, United States
| | - Jan H Bergmann
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
| | - Masaki Kinoshita
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Tüzer Kalkan
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Meryem Ralser
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Sam Robson
- The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | | | - Maike Paramor
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Fengtang Yang
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Caifu Chen
- Integrated DNA Technologies, Redwood, United States
| | - Jennifer Nichols
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - David L Spector
- Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
| | - Tony Kouzarides
- The Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - Lin He
- Division of Cellular and Developmental Biology, Department of Molecular and Cellular Biology, University of California Berkeley, Berkeley, United States
| | - Austin Smith
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
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46
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Kalkan T, Olova N, Roode M, Mulas C, Lee HJ, Nett I, Marks H, Walker R, Stunnenberg HG, Lilley KS, Nichols J, Reik W, Bertone P, Smith A. Tracking the embryonic stem cell transition from ground state pluripotency. Development 2017; 144:1221-1234. [PMID: 28174249 PMCID: PMC5399622 DOI: 10.1242/dev.142711] [Citation(s) in RCA: 158] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 01/25/2017] [Indexed: 12/14/2022]
Abstract
Mouse embryonic stem (ES) cells are locked into self-renewal by shielding from inductive cues. Release from this ground state in minimal conditions offers a system for delineating developmental progression from naïve pluripotency. Here, we examine the initial transition process. The ES cell population behaves asynchronously. We therefore exploited a short-half-life Rex1::GFP reporter to isolate cells either side of exit from naïve status. Extinction of ES cell identity in single cells is acute. It occurs only after near-complete elimination of naïve pluripotency factors, but precedes appearance of lineage specification markers. Cells newly departed from the ES cell state display features of early post-implantation epiblast and are distinct from primed epiblast. They also exhibit a genome-wide increase in DNA methylation, intermediate between early and late epiblast. These findings are consistent with the proposition that naïve cells transition to a distinct formative phase of pluripotency preparatory to lineage priming.
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Affiliation(s)
- Tüzer Kalkan
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Cambridge CB2 1QR, UK
| | | | - Mila Roode
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Cambridge CB2 1QR, UK
| | - Carla Mulas
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Cambridge CB2 1QR, UK
| | - Heather J Lee
- Babraham Institute, Cambridge CB22 3AT, UK.,Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Isabelle Nett
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Cambridge CB2 1QR, UK
| | - Hendrik Marks
- Radboud University, Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Nijmegen 6500HB, The Netherlands
| | - Rachael Walker
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Cambridge CB2 1QR, UK.,Babraham Institute, Cambridge CB22 3AT, UK
| | - Hendrik G Stunnenberg
- Radboud University, Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Nijmegen 6500HB, The Netherlands
| | - Kathryn S Lilley
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK.,The Cambridge Centre for Proteomics, Cambridge System Biology Centre, University of Cambridge, Cambridge CB2 1QR, UK
| | - Jennifer Nichols
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Cambridge CB2 1QR, UK.,Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 4BG, UK
| | - Wolf Reik
- Babraham Institute, Cambridge CB22 3AT, UK.,Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK.,Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK
| | - Paul Bertone
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Cambridge CB2 1QR, UK
| | - Austin Smith
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Cambridge CB2 1QR, UK .,Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
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Parisi S, Passaro F, Russo L, Musto A, Navarra A, Romano S, Petrosino G, Russo T. Lin28 is induced in primed embryonic stem cells and regulates let-7-independent events. FASEB J 2016; 31:1046-1058. [PMID: 27920151 DOI: 10.1096/fj.201600848r] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 11/22/2016] [Indexed: 12/22/2022]
Abstract
Lin28 RNA-binding proteins play important roles in pluripotent stem cells, but the regulation of their expression and the mechanisms underlying their functions are still not definitively understood. Here we address the above-mentioned issues in the first steps of mouse embryonic stem cell (ESC) differentiation. We observed that the expression of Lin28 genes is transiently induced soon after the exit of ESCs from the naive ground state and that this induction is due to the Hmga2-dependent engagement of Otx2 with enhancers present at both Lin28 gene loci. These mechanisms are crucial for Lin28 regulation, as demonstrated by the abolishment of the Lin28 accumulation in Otx2- or Hmga2-knockout cells compared to the control cells. We have also found that Lin28 controls Hmga2 expression levels during ESC differentiation through a let-7-independent mechanism. Indeed, we found that Lin28 proteins bind a highly conserved element in the 3' UTR of Hmga2 mRNA, and this provokes a down-regulation of its translation. This mechanism prevents the inappropriate accumulation of Hmga2 that would modify the proliferation and physiological apoptosis of differentiating ESCs. In summary, we demonstrated that during ESC differentiation, Lin28 transient induction is dependent on Otx2 and Hmga2 and prevents an inappropriate excessive rise of Hmga2 levels.-Parisi, S., Passaro, F., Russo, L., Musto, A., Navarra, A., Romano, S., Petrosino, G., Russo, T. Lin28 is induced in primed embryonic stem cells and regulates let-7-independent events.
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Affiliation(s)
- Silvia Parisi
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Naples, Italy; and
| | - Fabiana Passaro
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Naples, Italy; and
| | - Luigi Russo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Naples, Italy; and
| | - Anna Musto
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Naples, Italy; and
| | - Angelica Navarra
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Naples, Italy; and
| | - Simona Romano
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Naples, Italy; and
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