1
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Chowdhury MM, Zimmerman S, Leeson H, Nefzger CM, Mar JC, Laslett A, Polo JM, Wolvetang E, Cooper-White JJ. Superior Induced Pluripotent Stem Cell Generation through Phactr3-Driven Mechanomodulation of Both Early and Late Phases of Cell Reprogramming. Biomater Res 2024; 28:0025. [PMID: 38774128 PMCID: PMC11106629 DOI: 10.34133/bmr.0025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 03/25/2024] [Indexed: 05/24/2024] Open
Abstract
Human cell reprogramming traditionally involves time-intensive, multistage, costly tissue culture polystyrene-based cell culture practices that ultimately produce low numbers of reprogrammed cells of variable quality. Previous studies have shown that very soft 2- and 3-dimensional hydrogel substrates/matrices (of stiffnesses ≤ 1 kPa) can drive ~2× improvements in human cell reprogramming outcomes. Unfortunately, these similarly complex multistage protocols lack intrinsic scalability, and, furthermore, the associated underlying molecular mechanisms remain to be fully elucidated, limiting the potential to further maximize reprogramming outcomes. In screening the largest range of polyacrylamide (pAAm) hydrogels of varying stiffness to date (1 kPa to 1.3 MPa), we have found that a medium stiffness gel (~100 kPa) increased the overall number of reprogrammed cells by up to 10-fold (10×), accelerated reprogramming kinetics, improved both early and late phases of reprogramming, and produced induced pluripotent stem cells (iPSCs) having more naïve characteristics and lower remnant transgene expression, compared to the gold standard tissue culture polystyrene practice. Functionalization of these pAAm hydrogels with poly-l-dopamine enabled, for the first-time, continuous, single-step reprogramming of fibroblasts to iPSCs on hydrogel substrates (noting that even the tissue culture polystyrene practice is a 2-stage process). Comparative RNA sequencing analyses coupled with experimental validation revealed that a novel reprogramming regulator, protein phosphatase and actin regulator 3, up-regulated under the gel condition at a very early time point, was responsible for the observed enhanced reprogramming outcomes. This study provides a novel culture protocol and substrate for continuous hydrogel-based cell reprogramming and previously unattained clarity of the underlying mechanisms via which substrate stiffness modulates reprogramming kinetics and iPSC quality outcomes.
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Affiliation(s)
- Mohammad Mahfuz Chowdhury
- Australian Institute of Bioengineering and Nanotechnology (AIBN),
The University of Queensland, St. Lucia, QLD 4072, Australia
| | | | - Hannah Leeson
- Australian Institute of Bioengineering and Nanotechnology (AIBN),
The University of Queensland, St. Lucia, QLD 4072, Australia
| | | | - Jessica Cara Mar
- Australian Institute of Bioengineering and Nanotechnology (AIBN),
The University of Queensland, St. Lucia, QLD 4072, Australia
- Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Andrew Laslett
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Jose Maria Polo
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute and the Australian Regenerative Medicine Institute,
Monash University, Clayton, VIC 3800, Australia
- Adelaide Centre for Epigenetics and the South Australian Immunogenomics Cancer Institute, Faculty of Health and Medical Sciences,
The University of Adelaide, Adelaide, SA 5005, Australia
| | - Ernst Wolvetang
- Australian Institute of Bioengineering and Nanotechnology (AIBN),
The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Justin John Cooper-White
- Australian Institute of Bioengineering and Nanotechnology (AIBN),
The University of Queensland, St. Lucia, QLD 4072, Australia
- School of Chemical Engineering, Andrew N. Liveris Building,
The University of Queensland, St. Lucia, QLD 4072, Australia
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2
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Lando D, Ma X, Cao Y, Jartseva A, Stevens TJ, Boucher W, Reynolds N, Montibus B, Hall D, Lackner A, Ragheb R, Leeb M, Hendrich BD, Laue ED. Enhancer-promoter interactions are reconfigured through the formation of long-range multiway hubs as mouse ES cells exit pluripotency. Mol Cell 2024; 84:1406-1421.e8. [PMID: 38490199 PMCID: PMC7616059 DOI: 10.1016/j.molcel.2024.02.015] [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: 02/02/2023] [Revised: 12/19/2023] [Accepted: 02/14/2024] [Indexed: 03/17/2024]
Abstract
Enhancers bind transcription factors, chromatin regulators, and non-coding transcripts to modulate the expression of target genes. Here, we report 3D genome structures of single mouse ES cells as they are induced to exit pluripotency and transition through a formative stage prior to undergoing neuroectodermal differentiation. We find that there is a remarkable reorganization of 3D genome structure where inter-chromosomal intermingling increases dramatically in the formative state. This intermingling is associated with the formation of a large number of multiway hubs that bring together enhancers and promoters with similar chromatin states from typically 5-8 distant chromosomal sites that are often separated by many Mb from each other. In the formative state, genes important for pluripotency exit establish contacts with emerging enhancers within these multiway hubs, suggesting that the structural changes we have observed may play an important role in modulating transcription and establishing new cell identities.
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Affiliation(s)
- David Lando
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Xiaoyan Ma
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Yang Cao
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | | | - Tim J Stevens
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Wayne Boucher
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Nicola Reynolds
- Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge CB2 0AW, UK
| | - Bertille Montibus
- Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge CB2 0AW, UK
| | - Dominic Hall
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK; Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge CB2 0AW, UK
| | - Andreas Lackner
- Max Perutz Laboratories Vienna, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Ramy Ragheb
- Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge CB2 0AW, UK
| | - Martin Leeb
- Max Perutz Laboratories Vienna, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Brian D Hendrich
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK; Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge CB2 0AW, UK.
| | - Ernest D Laue
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK; Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge CB2 0AW, UK.
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3
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Carvalho S, Zea-Redondo L, Tang TCC, Stachel-Braum P, Miller D, Caldas P, Kukalev A, Diecke S, Grosswendt S, Grosso AR, Pombo A. SRRM2 splicing factor modulates cell fate in early development. Biol Open 2024; 13:bio060415. [PMID: 38656788 PMCID: PMC11070786 DOI: 10.1242/bio.060415] [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: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/26/2024] Open
Abstract
Embryo development is an orchestrated process that relies on tight regulation of gene expression to guide cell differentiation and fate decisions. The Srrm2 splicing factor has recently been implicated in developmental disorders and diseases, but its role in early mammalian development remains unexplored. Here, we show that Srrm2 dosage is critical for maintaining embryonic stem cell pluripotency and cell identity. Srrm2 heterozygosity promotes loss of stemness, characterised by the coexistence of cells expressing naive and formative pluripotency markers, together with extensive changes in gene expression, including genes regulated by serum-response transcription factor (SRF) and differentiation-related genes. Depletion of Srrm2 by RNA interference in embryonic stem cells shows that the earliest effects of Srrm2 heterozygosity are specific alternative splicing events on a small number of genes, followed by expression changes in metabolism and differentiation-related genes. Our findings unveil molecular and cellular roles of Srrm2 in stemness and lineage commitment, shedding light on the roles of splicing regulators in early embryogenesis, developmental diseases and tumorigenesis.
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Affiliation(s)
- Silvia Carvalho
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Structure Group, 10115 Berlin, Germany
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO – Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, 4050-313 Porto, Portugal
- Graduate Program in Areas of Basic and Applied Biology (GABBA), ICBAS, University of Porto, 4050-313 Porto, Portugal
| | - Luna Zea-Redondo
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Structure Group, 10115 Berlin, Germany
- Humboldt-Universität zu Berlin, Institute of Biology, 10115 Berlin, Germany
| | - Tsz Ching Chloe Tang
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Structure Group, 10115 Berlin, Germany
| | - Philipp Stachel-Braum
- Humboldt-Universität zu Berlin, Institute of Biology, 10115 Berlin, Germany
- Berlin Institute of Health (BIH) at Charité – Universitätsmedizin Berlin, Exploratory Diagnostic Sciences (EDS) 10178 Berlin, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), From Cell State to Function Group, 10115 Berlin, Germany
| | - Duncan Miller
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Pluripotent Stem Cells Platform, 13125 Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, 10785 Berlin, Germany
| | - Paulo Caldas
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO – Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Alexander Kukalev
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Structure Group, 10115 Berlin, Germany
| | - Sebastian Diecke
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Pluripotent Stem Cells Platform, 13125 Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, 10785 Berlin, Germany
| | - Stefanie Grosswendt
- Berlin Institute of Health (BIH) at Charité – Universitätsmedizin Berlin, Exploratory Diagnostic Sciences (EDS) 10178 Berlin, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), From Cell State to Function Group, 10115 Berlin, Germany
| | - Ana Rita Grosso
- Associate Laboratory i4HB – Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO – Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Ana Pombo
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Epigenetic Regulation and Chromatin Structure Group, 10115 Berlin, Germany
- Humboldt-Universität zu Berlin, Institute of Biology, 10115 Berlin, Germany
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4
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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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5
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Terzi Cizmecioglu N. Roles and Regulation of H3K4 Methylation During Mammalian Early Embryogenesis and Embryonic Stem Cell Differentiation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024. [PMID: 38231346 DOI: 10.1007/5584_2023_794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
From generation of germ cells, fertilization, and throughout early mammalian embryonic development, the chromatin undergoes significant alterations to enable precise regulation of gene expression and genome use. Methylation of histone 3 lysine 4 (H3K4) correlates with active regions of the genome, and it has emerged as a dynamic mark throughout this timeline. The pattern and the level of H3K4 methylation are regulated by methyltransferases and demethylases. These enzymes, as well as their protein partners, play important roles in early embryonic development and show phenotypes in embryonic stem cell self-renewal and differentiation. The various roles of H3K4 methylation are interpreted by dedicated chromatin reader proteins, linking this modification to broader molecular and cellular phenotypes. In this review, we discuss the regulation of different levels of H3K4 methylation, their distinct accumulation pattern, and downstream molecular roles with an early embryogenesis perspective.
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6
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Terzi Çizmecioğlu N. ARID4B loss leads to activated STAT1-dependent interferon pathway in mouse embryonic stem cells and during meso/endodermal differentiation. J Turk Ger Gynecol Assoc 2023; 24:187-196. [PMID: 37675520 PMCID: PMC10493817 DOI: 10.4274/jtgga.galenos.2023.2023-7-5] [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: 07/11/2023] [Accepted: 07/26/2023] [Indexed: 09/08/2023] Open
Abstract
Objective Proper deactivation of the pluripotency network and activation of a lineage-specific gene expression program are critical for mouse embryonic stem cell (mESC) differentiation. This is achieved by the coordinated action of transcription and chromatin factors. Our previous work identified ARID4B as a critical chromatin factor for mesoderm and endoderm differentiation. As part of a histone deacetylase complex, ARID4B plays a role in transcriptional suppression of its direct targets. Here, we investigated the mechanism of ARID4B function in mESC differentiation by focusing on genes and pathways that are upregulated in its absence. Material and Methods We analyzed transcriptomic results of wild-type and arid4bΔ endoderm or mesoderm differentiated cells through integrative genomics viewer and ingenuity pathway analysis. We performed real-time quantitative polymerase chain reaction for selected genes. To understand pathway activation, we performed Western blot for candidate proteins during the time-course of differentiation. We also analyzed H3K4me3, H3K27me3 and H3K27Ac ChIP-seq results to understand changes in the chromatin environment. Results Interferon-related genes were activated in arid4bΔ mESCs and endoderm or mesoderm directed cells. Consistent with this, higher phosphorylated STAT1 levels were found in arid4bΔ mESCs while a related phosphorylated STAT3 was unchanged. Finally, we observed a significant increase in H3K4me3 around interferon-related distal gene regulatory regions with a combination of either upregulation of H3K27Ac level or downregulation of H3K27me3 level. Conclusion These results provide evidence that ARID4B is involved in the suppression of interferon-related genes in mESCs and during meso/endoderm differentiation through modulation, mainly of H3K4me3. This regulation might be important for successful mESC differentiation.
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Affiliation(s)
- Nihal Terzi Çizmecioğlu
- Department of Biological Sciences, Middle East Technical University, Faculty of Arts and Sciences, Ankara, Turkey
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7
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Wu J, Shi Y, Yang S, Tang Z, Li Z, Li Z, Zuo J, Ji W, Niu Y. Current state of stem cell research in non-human primates: an overview. MEDICAL REVIEW (2021) 2023; 3:277-304. [PMID: 38235400 PMCID: PMC10790211 DOI: 10.1515/mr-2023-0035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/04/2023] [Indexed: 01/19/2024]
Abstract
The remarkable similarity between non-human primates (NHPs) and humans establishes them as essential models for understanding human biology and diseases, as well as for developing novel therapeutic strategies, thereby providing more comprehensive reference data for clinical treatment. Pluripotent stem cells such as embryonic stem cells and induced pluripotent stem cells provide unprecedented opportunities for cell therapies against intractable diseases and injuries. As continue to harness the potential of these biotechnological therapies, NHPs are increasingly being employed in preclinical trials, serving as a pivotal tool to evaluate the safety and efficacy of these interventions. Here, we review the recent advancements in the fundamental research of stem cells and the progress made in studies involving NHPs.
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Affiliation(s)
- Junmo Wu
- Kunming University of Science and Technology, Kunming, Yunnan Province, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan Province, China
| | - Yuxi Shi
- Kunming University of Science and Technology, Kunming, Yunnan Province, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan Province, China
| | - Shanshan Yang
- Kunming University of Science and Technology, Kunming, Yunnan Province, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan Province, China
| | - Zengli Tang
- Kunming University of Science and Technology, Kunming, Yunnan Province, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan Province, China
| | - Zifan Li
- Kunming University of Science and Technology, Kunming, Yunnan Province, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan Province, China
| | - Zhuoyao Li
- Kunming University of Science and Technology, Kunming, Yunnan Province, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan Province, China
| | - Jiawei Zuo
- Kunming University of Science and Technology, Kunming, Yunnan Province, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan Province, China
| | - Weizhi Ji
- Kunming University of Science and Technology, Kunming, Yunnan Province, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan Province, China
| | - Yuyu Niu
- Kunming University of Science and Technology, Kunming, Yunnan Province, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan Province, China
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8
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Ruden X, Singh A, Marben T, Tang W, Awonuga A, Ruden DM, Puscheck E, Feng H, Rappolee D. A single cell transcriptomic fingerprint of stressed premature, imbalanced differentiation of embryonic stem cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.23.541952. [PMID: 37292812 PMCID: PMC10245821 DOI: 10.1101/2023.05.23.541952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Cultured naïve pluripotent ESC differentiate into first lineage, XEN or second lineage, formative pluripotency. Hyperosmotic stress (sorbitol), like retinoic acid, decreases naive pluripotency and increases XEN in two ESC lines, as reported by bulk and scRNAseq, analyzed by UMAP. Sorbitol overrides pluripotency in two ESC lines as reported by bulk and scRNAseq, analyzed by UMAP. UMAP analyzed the effects of 5 stimuli - three stressed (200-300mM sorbitol with leukemia inhibitory factor +LIF) and two unstressed (+LIF, normal stemness-NS and -LIF, normal differentiation-ND). Sorbitol and RA decrease naive pluripotency and increase subpopulations of 2-cell embryo-like and XEN sub-lineages; primitive, parietal, and visceral endoderm (VE). Between the naïve pluripotency and primitive endoderm clusters is a stress-induced cluster with transient intermediate cells with higher LIF receptor signaling, with increased Stat3, Klf4, and Tbx3 expression. Sorbitol, like RA, also suppresses formative pluripotency, increasing lineage imbalance. Although bulk RNAseq and gene ontology group analyses suggest that stress induces head organizer and placental markers, scRNAseq reveals few cells. But VE and placental markers/cells were in adjacent clusters, like recent reports. UMAPs show that dose-dependent stress overrides stemness to force premature lineage imbalance. Hyperosmotic stress induces lineage imbalance, and other toxicological stresses, like drugs with RA, may cause lineage imbalance, resulting in miscarriages or birth defects.
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9
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Aydin S, Pham DT, Zhang T, Keele GR, Skelly DA, Paulo JA, Pankratz M, Choi T, Gygi SP, Reinholdt LG, Baker CL, Churchill GA, Munger SC. Genetic dissection of the pluripotent proteome through multi-omics data integration. CELL GENOMICS 2023; 3:100283. [PMID: 37082146 PMCID: PMC10112288 DOI: 10.1016/j.xgen.2023.100283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 09/12/2022] [Accepted: 02/27/2023] [Indexed: 04/22/2023]
Abstract
Genetic background drives phenotypic variability in pluripotent stem cells (PSCs). Most studies to date have used transcript abundance as the primary molecular readout of cell state in PSCs. We performed a comprehensive proteogenomics analysis of 190 genetically diverse mouse embryonic stem cell (mESC) lines. The quantitative proteome is highly variable across lines, and we identified pluripotency-associated pathways that were differentially activated in the proteomics data that were not evident in transcriptome data from the same lines. Integration of protein abundance to transcript levels and chromatin accessibility revealed broad co-variation across molecular layers as well as shared and unique drivers of quantitative variation in pluripotency-associated pathways. Quantitative trait locus (QTL) mapping localized the drivers of these multi-omic signatures to genomic hotspots. This study reveals post-transcriptional mechanisms and genetic interactions that underlie quantitative variability in the pluripotent proteome and provides a regulatory map for mESCs that can provide a basis for future mechanistic studies.
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Affiliation(s)
- Selcan Aydin
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Duy T. Pham
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Tian Zhang
- Harvard Medical School, Boston, MA 02115, USA
| | | | | | | | | | - Ted Choi
- Predictive Biology, Inc., Carlsbad, CA 92010, USA
| | | | - Laura G. Reinholdt
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
- Graduate School of Biomedical Sciences, Tufts University, Boston, MA 02111, USA
| | - Christopher L. Baker
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
- Graduate School of Biomedical Sciences, Tufts University, Boston, MA 02111, USA
| | - Gary A. Churchill
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
- Graduate School of Biomedical Sciences, Tufts University, Boston, MA 02111, USA
| | - Steven C. Munger
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
- Graduate School of Biomedical Sciences, Tufts University, Boston, MA 02111, USA
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10
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Han D, Liu G, Oh Y, Oh S, Yang S, Mandjikian L, Rani N, Almeida MC, Kosik KS, Jang J. ZBTB12 is a molecular barrier to dedifferentiation in human pluripotent stem cells. Nat Commun 2023; 14:632. [PMID: 36759523 PMCID: PMC9911396 DOI: 10.1038/s41467-023-36178-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 01/18/2023] [Indexed: 02/11/2023] Open
Abstract
Development is generally viewed as one-way traffic of cell state transition from primitive to developmentally advanced states. However, molecular mechanisms that ensure the unidirectional transition of cell fates remain largely unknown. Through exact transcription start site mapping, we report an evolutionarily conserved BTB domain-containing zinc finger protein, ZBTB12, as a molecular barrier for dedifferentiation of human pluripotent stem cells (hPSCs). Single-cell RNA sequencing reveals that ZBTB12 is essential for three germ layer differentiation by blocking hPSC dedifferentiation. Mechanistically, ZBTB12 fine-tunes the expression of human endogenous retrovirus H (HERVH), a primate-specific retrotransposon, and targets specific transcripts that utilize HERVH as a regulatory element. In particular, the downregulation of HERVH-overlapping long non-coding RNAs (lncRNAs) by ZBTB12 is necessary for a successful exit from a pluripotent state and lineage derivation. Overall, we identify ZBTB12 as a molecular barrier that safeguards the unidirectional transition of metastable stem cell fates toward developmentally advanced states.
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Affiliation(s)
- Dasol Han
- Neuroscience Research Institute, Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Guojing Liu
- Neuroscience Research Institute, Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA.,Novogene Co., Ltd, Beijing, China
| | - Yujeong Oh
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Korea
| | - Seyoun Oh
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Korea
| | - Seungbok Yang
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Korea
| | - Lori Mandjikian
- Neuroscience Research Institute, Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Neha Rani
- Neuroscience Research Institute, Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA.,Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur, India
| | - Maria C Almeida
- Neuroscience Research Institute, Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA.,Federal University of ABC, Center for Natural and Human Sciences São Bernardo do Campo, Santo André, Brazil
| | - Kenneth S Kosik
- Neuroscience Research Institute, Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA.
| | - Jiwon Jang
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Korea.
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11
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Furlan G, Huyghe A, Combémorel N, Lavial F. Molecular versatility during pluripotency progression. Nat Commun 2023; 14:68. [PMID: 36604434 PMCID: PMC9814743 DOI: 10.1038/s41467-022-35775-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 12/22/2022] [Indexed: 01/07/2023] Open
Abstract
A challenge during development is to ensure lineage segregation while preserving plasticity. Using pluripotency progression as a paradigm, we review how developmental transitions are coordinated by redeployments, rather than global resettings, of cellular components. We highlight how changes in response to extrinsic cues (FGF, WNT, Activin/Nodal, Netrin-1), context- and stoichiometry-dependent action of transcription factors (Oct4, Nanog) and reconfigurations of epigenetic regulators (enhancers, promoters, TrxG, PRC) may confer robustness to naïve to primed pluripotency transition. We propose the notion of Molecular Versatility to regroup mechanisms by which molecules are repurposed to exert different, sometimes opposite, functions in close stem cell configurations.
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Affiliation(s)
- Giacomo Furlan
- Cellular reprogramming, stem cells and oncogenesis laboratory - Equipe labellisée La Ligue Contre le Cancer - LabEx Dev2Can - Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, 69008, France.,Lunenfeld-Tanenbaum Research Institute, University of Toronto, Toronto, ON, Canada
| | - Aurélia Huyghe
- Cellular reprogramming, stem cells and oncogenesis laboratory - Equipe labellisée La Ligue Contre le Cancer - LabEx Dev2Can - Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, 69008, France
| | - Noémie Combémorel
- Cellular reprogramming, stem cells and oncogenesis laboratory - Equipe labellisée La Ligue Contre le Cancer - LabEx Dev2Can - Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, 69008, France
| | - Fabrice Lavial
- Cellular reprogramming, stem cells and oncogenesis laboratory - Equipe labellisée La Ligue Contre le Cancer - LabEx Dev2Can - Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, 69008, France.
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12
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Pfeffer PL. Alternative mammalian strategies leading towards gastrulation: losing polar trophoblast (Rauber's layer) or gaining an epiblast cavity. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210254. [PMID: 36252216 PMCID: PMC9574635 DOI: 10.1098/rstb.2021.0254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Using embryological data from 14 mammalian orders, the hypothesis is presented that in placental mammals, epiblast cavitation and polar trophoblast loss are alternative developmental solutions to shield the central epiblast from extraembryonic signalling. It is argued that such reciprocal signalling between the edge of the epiblast and the adjoining polar trophoblast or edge of the mural trophoblast or with the amniotic ectoderm is necessary for the induction of gastrulation. This article is part of the theme issue 'Extraembryonic tissues: exploring concepts, definitions and functions across the animal kingdom'.
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Affiliation(s)
- Peter L. Pfeffer
- School of Biological Sciences, Victoria University of Wellington, Kelburn Parade, Wellington 6010, New Zealand
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13
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Wang X, Wu Q. The Divergent Pluripotent States in Mouse and Human Cells. Genes (Basel) 2022; 13:genes13081459. [PMID: 36011370 PMCID: PMC9408542 DOI: 10.3390/genes13081459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/12/2022] [Accepted: 06/16/2022] [Indexed: 11/17/2022] Open
Abstract
Pluripotent stem cells (PSCs), which can self-renew and give rise to all cell types in all three germ layers, have great potential in regenerative medicine. Recent studies have shown that PSCs can have three distinct but interrelated pluripotent states: naive, formative, and primed. The PSCs of each state are derived from different stages of the early developing embryo and can be maintained in culture by different molecular mechanisms. In this review, we summarize the current understanding on features of the three pluripotent states and review the underlying molecular mechanisms of maintaining their identities. Lastly, we discuss the interrelation and transition among these pluripotency states. We believe that comprehending the divergence of pluripotent states is essential to fully harness the great potential of stem cells in regenerative medicine.
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Affiliation(s)
| | - Qiang Wu
- Correspondence: ; Tel.: +853-8897-2708
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14
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Epigenetics as "conductor" in "orchestra" of pluripotent states. Cell Tissue Res 2022; 390:141-172. [PMID: 35838826 DOI: 10.1007/s00441-022-03667-0] [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: 12/30/2021] [Accepted: 07/01/2022] [Indexed: 11/02/2022]
Abstract
Pluripotent character is described as the potency of cells to differentiate into all three germ layers. The best example to reinstate the term lies in the context of embryonic stem cells (ESCs). Pluripotent ESC describes the in vitro status of those cells that originate during the complex process of embryogenesis. Pre-implantation to post-implantation development of embryo embrace cells with different levels of stemness. Currently, four states of pluripotency have been recognized, in the progressing order of "naïve," "poised," "formative," and "primed." Epigenetics act as the "conductor" in this "orchestra" of transition in pluripotent states. With a distinguishable gene expression profile, these four states associate with different epigenetic signatures, sometimes distinct while otherwise overlapping. The present review focuses on how epigenetic factors, including DNA methylation, bivalent chromatin, chromatin remodelers, chromatin/nuclear architecture, and microRNA, could dictate pluripotent states and their transition among themselves.
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15
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Aloisio FM, Barber DL. Arp2/3 complex activity is necessary for mouse ESC differentiation, times formative pluripotency, and enables lineage specification. Stem Cell Reports 2022; 17:1318-1333. [PMID: 35658973 PMCID: PMC9214060 DOI: 10.1016/j.stemcr.2022.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 05/04/2022] [Accepted: 05/05/2022] [Indexed: 11/28/2022] Open
Abstract
Mouse embryonic stem cells (mESCs), a model for differentiation into primed epiblast-like cells (EpiLCs), have revealed transcriptional and epigenetic control of early embryonic development. The control and significance of morphological changes, however, remain less defined. We show marked changes in morphology and actin architectures during differentiation that depend on Arp2/3 complex but not formin activity. Inhibiting Arp2/3 complex activity pharmacologically or genetically does not block exit from naive pluripotency, but attenuates increases in EpiLC markers. We find that inhibiting Arp2/3 complex activity delays formative pluripotency and causes globally defective lineage specification as indicated by RNA sequencing, with significant effects on TBX3-depedendent transcriptional programs. We also identify two previously unreported indicators of mESC differentiation, namely, MRTF and FHL2, which have inverse Arp2/3 complex-dependent nuclear translocation. Our findings on Arp2/3 complex activity in differentiation and the established role of formins in EMT indicate that these two actin nucleators regulate distinct modes of epithelial plasticity.
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Affiliation(s)
- Francesca M Aloisio
- Department of Cell & Tissue Biology, University of California San Francisco, Box 0512, 513 Parnassus Ave., San Francisco, CA 94143, USA
| | - Diane L Barber
- Department of Cell & Tissue Biology, University of California San Francisco, Box 0512, 513 Parnassus Ave., San Francisco, CA 94143, USA.
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16
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Romayor I, Herrera L, Burón M, Martin-Inaraja M, Prieto L, Etxaniz J, Inglés-Ferrándiz M, Pineda JR, Eguizabal C. A Comparative Study of Cell Culture Conditions during Conversion from Primed to Naive Human Pluripotent Stem Cells. Biomedicines 2022; 10:biomedicines10061358. [PMID: 35740381 PMCID: PMC9219795 DOI: 10.3390/biomedicines10061358] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/01/2022] [Accepted: 06/03/2022] [Indexed: 11/16/2022] Open
Abstract
The successful reprogramming of human somatic cells into induced pluripotent stem cells (hiPSCs) represented a turning point in the stem cell research field, owing to their ability to differentiate into any cell type with fewer ethical issues than human embryonic stem cells (hESCs). In mice, PSCs are thought to exist in a naive state, the cell culture equivalent of the immature pre-implantation embryo, whereas in humans, PSCs are in a primed state, which is a more committed pluripotent state than a naive state. Recent studies have focused on capturing a similar cell stage in human cells. Given their earlier developmental stage and therefore lack of cell-of-origin epigenetic memory, these cells would be better candidates for further re-differentiation, use in disease modeling, regenerative medicine and drug discovery. In this study, we used primed hiPSCs and hESCs to evaluate the successful establishment and maintenance of a naive cell stage using three different naive-conversion media, both in the feeder and feeder-free cells conditions. In addition, we compared the directed differentiation capacity of primed and naive cells into the three germ layers and characterized these different cell stages with commonly used pluripotent and lineage-specific markers. Our results show that, in general, naive culture NHSM medium (in both feeder and feeder-free systems) confers greater hiPSCs and hESCs viability and the highest naive pluripotency markers expression. This medium also allows better cell differentiation cells toward endoderm and mesoderm.
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Affiliation(s)
- Irene Romayor
- Cell Therapy, Stem Cells and Tissues Group, Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain; (I.R.); (L.H.); (M.B.); (M.M.-I.); (L.P.); (J.E.); (M.I.-F.)
- Research Unit, Basque Centre for Blood Transfusion and Human Tissues, 48960 Galdakao, Spain
- Cell Biology and Histology Department, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain;
| | - Lara Herrera
- Cell Therapy, Stem Cells and Tissues Group, Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain; (I.R.); (L.H.); (M.B.); (M.M.-I.); (L.P.); (J.E.); (M.I.-F.)
- Research Unit, Basque Centre for Blood Transfusion and Human Tissues, 48960 Galdakao, Spain
| | - Maria Burón
- Cell Therapy, Stem Cells and Tissues Group, Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain; (I.R.); (L.H.); (M.B.); (M.M.-I.); (L.P.); (J.E.); (M.I.-F.)
- Research Unit, Basque Centre for Blood Transfusion and Human Tissues, 48960 Galdakao, Spain
| | - Myriam Martin-Inaraja
- Cell Therapy, Stem Cells and Tissues Group, Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain; (I.R.); (L.H.); (M.B.); (M.M.-I.); (L.P.); (J.E.); (M.I.-F.)
- Research Unit, Basque Centre for Blood Transfusion and Human Tissues, 48960 Galdakao, Spain
| | - Laura Prieto
- Cell Therapy, Stem Cells and Tissues Group, Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain; (I.R.); (L.H.); (M.B.); (M.M.-I.); (L.P.); (J.E.); (M.I.-F.)
- Research Unit, Basque Centre for Blood Transfusion and Human Tissues, 48960 Galdakao, Spain
| | - Jone Etxaniz
- Cell Therapy, Stem Cells and Tissues Group, Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain; (I.R.); (L.H.); (M.B.); (M.M.-I.); (L.P.); (J.E.); (M.I.-F.)
- Research Unit, Basque Centre for Blood Transfusion and Human Tissues, 48960 Galdakao, Spain
| | - Marta Inglés-Ferrándiz
- Cell Therapy, Stem Cells and Tissues Group, Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain; (I.R.); (L.H.); (M.B.); (M.M.-I.); (L.P.); (J.E.); (M.I.-F.)
- Research Unit, Basque Centre for Blood Transfusion and Human Tissues, 48960 Galdakao, Spain
| | - Jose Ramon Pineda
- Cell Biology and Histology Department, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain;
- Achucarro Basque Center for Neuroscience, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
| | - Cristina Eguizabal
- Cell Therapy, Stem Cells and Tissues Group, Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain; (I.R.); (L.H.); (M.B.); (M.M.-I.); (L.P.); (J.E.); (M.I.-F.)
- Research Unit, Basque Centre for Blood Transfusion and Human Tissues, 48960 Galdakao, Spain
- Correspondence: ; Tel.: +34-944-007-151
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17
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Wang Y, Jia L, Wang C, Du Z, Zhang S, Zhou L, Wen X, Li H, Chen H, Nie Y, Li D, Liu S, Figueroa DS, Ay F, Xu W, Zhang S, Li W, Cui J, Hoffman AR, Guo H, Hu JF. Pluripotency exit is guided by the Peln1-mediated disruption of intrachromosomal architecture. J Cell Biol 2022; 221:213009. [PMID: 35171230 PMCID: PMC8855478 DOI: 10.1083/jcb.202009134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 12/01/2021] [Accepted: 01/19/2022] [Indexed: 11/22/2022] Open
Abstract
The molecular circuitry that causes stem cells to exit from pluripotency remains largely uncharacterized. Using chromatin RNA in situ reverse transcription sequencing, we identified Peln1 as a novel chromatin RNA component in the promoter complex of Oct4, a stem cell master transcription factor gene. Peln1 was negatively associated with pluripotent status during somatic reprogramming. Peln1 overexpression caused E14 cells to exit from pluripotency, while Peln1 downregulation induced robust reprogramming. Mechanistically, we discovered that Peln1 interacted with the Oct4 promoter and recruited the DNA methyltransferase DNMT3A. By de novo altering the epigenotype in the Oct4 promoter, Peln1 dismantled the intrachromosomal loop that is required for the maintenance of pluripotency. Using RNA reverse transcription-associated trap sequencing, we showed that Peln1 targets multiple pathway genes that are associated with stem cell self-renewal. These findings demonstrate that Peln1 can act as a new epigenetic player and use a trans mechanism to induce an exit from the pluripotent state in stem cells.
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Affiliation(s)
- Yichen Wang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China.,Department of Endocrinology, First Hospital of Jilin University, Changchun, Jilin, China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA
| | - Lin Jia
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA
| | - Cong Wang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA
| | - Zhonghua Du
- Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA
| | - Shilin Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA
| | - Lei Zhou
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA
| | - Xue Wen
- Department of Endocrinology, First Hospital of Jilin University, Changchun, Jilin, China
| | - Hui Li
- Department of Endocrinology, First Hospital of Jilin University, Changchun, Jilin, China
| | - Huiling Chen
- Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA
| | - Yuanyuan Nie
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA
| | - Dan Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China
| | - Shanshan Liu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA
| | | | - Ferhat Ay
- La Jolla Institute for Allergy and Immunology, La Jolla, CA
| | - Wei Xu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China
| | - Songling Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China
| | - Wei Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China
| | - Jiuwei Cui
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China
| | - Andrew R Hoffman
- Department of Endocrinology, First Hospital of Jilin University, Changchun, Jilin, China
| | - Hui Guo
- Department of Endocrinology, First Hospital of Jilin University, Changchun, Jilin, China
| | - Ji-Fan Hu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA
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18
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Carter T, Singh M, Dumbovic G, Chobirko JD, Rinn JL, Feschotte C. Mosaic cis-regulatory evolution drives transcriptional partitioning of HERVH endogenous retrovirus in the human embryo. eLife 2022; 11:76257. [PMID: 35179489 PMCID: PMC8912925 DOI: 10.7554/elife.76257] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 02/17/2022] [Indexed: 12/05/2022] Open
Abstract
The human endogenous retrovirus type-H (HERVH) family is expressed in the preimplantation embryo. A subset of these elements are specifically transcribed in pluripotent stem cells where they appear to exert regulatory activities promoting self-renewal and pluripotency. How HERVH elements achieve such transcriptional specificity remains poorly understood. To uncover the sequence features underlying HERVH transcriptional activity, we performed a phyloregulatory analysis of the long terminal repeats (LTR7) of the HERVH family, which harbor its promoter, using a wealth of regulatory genomics data. We found that the family includes at least eight previously unrecognized subfamilies that have been active at different timepoints in primate evolution and display distinct expression patterns during human embryonic development. Notably, nearly all HERVH elements transcribed in ESCs belong to one of the youngest subfamilies we dubbed LTR7up. LTR7 sequence evolution was driven by a mixture of mutational processes, including point mutations, duplications, and multiple recombination events between subfamilies, that led to transcription factor binding motif modules characteristic of each subfamily. Using a reporter assay, we show that one such motif, a predicted SOX2/3 binding site unique to LTR7up, is essential for robust promoter activity in induced pluripotent stem cells. Together these findings illuminate the mechanisms by which HERVH diversified its expression pattern during evolution to colonize distinct cellular niches within the human embryo.
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Affiliation(s)
- Thomas Carter
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, United States [US]
| | - Manvendra Singh
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, United States
| | - Gabrijela Dumbovic
- Department of Biochemistry, University of Colorado Boulder, Boulder, United States
| | - Jason D Chobirko
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, United States
| | - John L Rinn
- Department of Biochemistry, University of Colorado Boulder, Boulder, United States
| | - Cédric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, United States
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19
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von Meyenn F. Profiling DNA Methylation in Human Naïve Pluripotent Stem Cells. Methods Mol Biol 2022; 2416:157-180. [PMID: 34870836 DOI: 10.1007/978-1-0716-1908-7_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
DNA methylation represents one of the best characterized epigenetic modifications. In particular, global demethylation is a common feature of epigenetic reprogramming to naïve pluripotency in human and mouse pluripotent stem cells. In parallel to the global changes, several locus-specific changes to the DNA methylation landscape occur and also loss of imprinting has been observed in naïve human pluripotent stem cells. The current gold standard to assess and quantitively map DNA methylation is bisulfite sequencing. Various protocols are available for genome-wide bisulfite sequencing and here I describe an optimized method based on Post Bisulfite Adapter Tagging (PBAT) for low amounts of DNA or cells, with as little as 50 cells as minimum requirement, and with the possibility to process a large number of samples in parallel. I outline the basic bioinformatic steps needed to process raw Illumina sequencing data and then describe the inital steps of the analysis of DNA methylation datasets, including an assessment of imprint control regions.
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Affiliation(s)
- Ferdinand von Meyenn
- Laboratory of Nutrition and Metabolic Epigenetics, Institute of Food, Nutrition and Health, ETH Zurich, Schwerzenbach, Switzerland. .,Department of Medical & Molecular Genetics, King's College London, London, UK.
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20
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Pui HP, Deng Q. In Vitro Differentiation of Murine Embryonic Stem Cells (ESCs) into Primordial Germ Cell-like Cells (PGCLCs). Methods Mol Biol 2022; 2490:213-233. [PMID: 35486249 DOI: 10.1007/978-1-0716-2281-0_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The ability to generate primordial germ cell-like cells (PGCLCs) from murine embryonic stem cells (ESCs) has enabled in vitro investigation of the molecular mechanisms regulating this process without the use of a mouse model. Here we describe the procedures from the culture of ESCs to the detection of PGCLCs in the embryoid bodies (spheroids).
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Affiliation(s)
- Han-Pin Pui
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Qiaolin Deng
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.
- Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden.
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21
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N6-methyladenosine (m 6A) depletion regulates pluripotency exit by activating signaling pathways in embryonic stem cells. Proc Natl Acad Sci U S A 2021; 118:2105192118. [PMID: 34921114 PMCID: PMC8713808 DOI: 10.1073/pnas.2105192118] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2021] [Indexed: 12/12/2022] Open
Abstract
Dynamic deposition of the N6-methyladenosine (m6A) modification on
messenger RNA (mRNA) regulates pluripotency in embryonic stem cells. Reports
show that depletion of m6A abundances increases the mRNA stability of
pluripotency and lineage transcription factors (TFs) alike. If the mRNAs of
these two TF groups become stabilized, it remains unclear how the pluripotency
or lineage commitment decision is implemented. Quantification of pluripotency
TFs live at single-cell resolution over generations shows long-term preservation
of both pluripotency and priming. m6A depletion activates key
signaling pathways involved in pluripotency versus commitment decisions. This
occurs independently of m6A control over TF mRNA transcript
stability. m6A deposition regulates TF protein expression levels by
activating pErk and pAkt signaling to enact cell-fate determination in
pluripotent stem cells. N6-methyladenosine (m6A) deposition on messenger RNA (mRNA) controls
embryonic stem cell (ESC) fate by regulating the mRNA stabilities of
pluripotency and lineage transcription factors (TFs) [P. J. Batista
et al., Cell Stem Cell 15, 707–719 (2014); Y.
Wang et al., Nat. Cell Biol. 16, 191–198 (2014);
and S. Geula et al., Science 347, 1002–1006
(2015)]. If the mRNAs of these two TF groups become stabilized, it remains
unclear how the pluripotency or lineage commitment decision is implemented. We
performed noninvasive quantification of Nanog and Oct4 TF protein levels in
reporter ESCs to define cell-state dynamics at single-cell resolution. Long-term
single-cell tracking shows that immediate m6A depletion by Mettl3
knock-down in serum/leukemia inhibitory factor supports both pluripotency
maintenance and its departure. This is mediated by differential and opposing
signaling pathways. Increased FGF5 mRNA stability activates pErk, leading to
Nanog down-regulation. FGF5-mediated coactivation of pAkt reenforces Nanog
expression. In formative stem cells poised toward differentiation,
m6A depletion activates both pErk and pAkt, increasing the propensity
for mesendodermal lineage induction. Stable m6A depletion by Mettl3
knock-out also promotes pErk activation. Higher pErk counteracts the
pluripotency exit delay exhibited by stably m6A-depleted cells upon
differentiation. At single-cell resolution, we illustrate that decreasing
m6A abundances activates pErk and pAkt-signaling, regulating
pluripotency departure.
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22
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Rafiee MR, Zagalak JA, Sidorov S, Steinhauser S, Davey K, Ule J, Luscombe NM. Chromatin-contact atlas reveals disorder-mediated protein interactions and moonlighting chromatin-associated RBPs. Nucleic Acids Res 2021; 49:13092-13107. [PMID: 34871434 PMCID: PMC8682780 DOI: 10.1093/nar/gkab1180] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/05/2021] [Accepted: 11/12/2021] [Indexed: 11/13/2022] Open
Abstract
RNA-binding proteins (RBPs) play diverse roles in regulating co-transcriptional RNA-processing and chromatin functions, but our knowledge of the repertoire of chromatin-associated RBPs (caRBPs) and their interactions with chromatin remains limited. Here, we developed SPACE (Silica Particle Assisted Chromatin Enrichment) to isolate global and regional chromatin components with high specificity and sensitivity, and SPACEmap to identify the chromatin-contact regions in proteins. Applied to mouse embryonic stem cells, SPACE identified 1459 chromatin-associated proteins, ∼48% of which are annotated as RBPs, indicating their dual roles in chromatin and RNA-binding. Additionally, SPACEmap stringently verified chromatin-binding of 403 RBPs and identified their chromatin-contact regions. Notably, SPACEmap showed that about 40% of the caRBPs bind chromatin by intrinsically disordered regions (IDRs). Studying SPACE and total proteome dynamics from mES cells grown in 2iL and serum medium indicates significant correlation (R = 0.62). One of the most dynamic caRBPs is Dazl, which we find co-localized with PRC2 at transcription start sites of genes that are distinct from Dazl mRNA binding. Dazl and other PRC2-colocalised caRBPs are rich in intrinsically disordered regions (IDRs), which could contribute to the formation and regulation of phase-separated PRC condensates. Together, our approach provides an unprecedented insight into IDR-mediated interactions and caRBPs with moonlighting functions in native chromatin.
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Affiliation(s)
| | - Julian A Zagalak
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.,Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | | | | | - Karen Davey
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Jernej Ule
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.,Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK.,National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
| | - Nicholas M Luscombe
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.,Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK.,UCL Genetics Institute, University College London, Gower Street, London WC1E 6BT, UK.,Okinawa Institute of Science & Technology Graduate University, Okinawa 904-0495, Japan
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23
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Pera MF, Rossant J. The exploration of pluripotency space: Charting cell state transitions in peri-implantation development. Cell Stem Cell 2021; 28:1896-1906. [PMID: 34672948 DOI: 10.1016/j.stem.2021.10.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 09/06/2021] [Accepted: 10/04/2021] [Indexed: 11/16/2022]
Abstract
Pluripotent cells in the mammalian embryo undergo state transitions marked by changes in patterns of gene expression and developmental potential as they progress from pre-implantation through post-implantation stages of development. Recent studies of cultured mouse and human pluripotent stem cells (hPSCs) have identified cells representative of an intermediate stage (referred to as the formative state) between naive pluripotency (equivalent to pre-implantation epiblast) and primed pluripotency (equivalent to late post-implantation epiblast). We examine these recent findings in light of our knowledge of peri-implantation mouse and human development, and we consider the implications of this work for deriving human embryo models from pluripotent cells.
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Affiliation(s)
| | - Janet Rossant
- The Hospital for Sick Children and the Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; The Gairdner Foundation, Toronto, ON, Canada.
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24
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Qin W, Ugur E, Mulholland CB, Bultmann S, Solovei I, Modic M, Smets M, Wierer M, Forné I, Imhof A, Cardoso MC, Leonhardt H. Phosphorylation of the HP1β hinge region sequesters KAP1 in heterochromatin and promotes the exit from naïve pluripotency. Nucleic Acids Res 2021; 49:7406-7423. [PMID: 34214177 PMCID: PMC8287961 DOI: 10.1093/nar/gkab548] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/31/2021] [Accepted: 06/11/2021] [Indexed: 12/26/2022] Open
Abstract
Heterochromatin binding protein HP1β plays an important role in chromatin organization and cell differentiation, however the underlying mechanisms remain unclear. Here, we generated HP1β−/− embryonic stem cells and observed reduced heterochromatin clustering and impaired differentiation. We found that during stem cell differentiation, HP1β is phosphorylated at serine 89 by CK2, which creates a binding site for the pluripotency regulator KAP1. This phosphorylation dependent sequestration of KAP1 in heterochromatin compartments causes a downregulation of pluripotency factors and triggers pluripotency exit. Accordingly, HP1β−/− and phospho-mutant cells exhibited impaired differentiation, while ubiquitination-deficient KAP1−/− cells had the opposite phenotype with enhanced differentiation. These results suggest that KAP1 regulates pluripotency via its ubiquitination activity. We propose that the formation of subnuclear membraneless heterochromatin compartments may serve as a dynamic reservoir to trap or release cellular factors. The sequestration of essential regulators defines a novel and active role of heterochromatin in gene regulation and represents a dynamic mode of remote control to regulate cellular processes like cell fate decisions.
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Affiliation(s)
- Weihua Qin
- Faculty of Biology, Ludwig-Maximilians-Universität München, Butenandtstraße 1, D-81377 Munich, Germany
| | - Enes Ugur
- Faculty of Biology, Ludwig-Maximilians-Universität München, Butenandtstraße 1, D-81377 Munich, Germany.,Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Christopher B Mulholland
- Faculty of Biology, Ludwig-Maximilians-Universität München, Butenandtstraße 1, D-81377 Munich, Germany
| | - Sebastian Bultmann
- Faculty of Biology, Ludwig-Maximilians-Universität München, Butenandtstraße 1, D-81377 Munich, Germany
| | - Irina Solovei
- Faculty of Biology, Ludwig-Maximilians-Universität München, Butenandtstraße 1, D-81377 Munich, Germany
| | - Miha Modic
- The Francis Crick Institute and UCL Queen Square Institute of Neurology, London NW1 1AT, United Kingdom
| | - Martha Smets
- Faculty of Biology, Ludwig-Maximilians-Universität München, Butenandtstraße 1, D-81377 Munich, Germany
| | - Michael Wierer
- Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Ignasi Forné
- Biomedical Center Munich, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, 82152 Planegg-Martinsried, Germany
| | - Axel Imhof
- Biomedical Center Munich, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, 82152 Planegg-Martinsried, Germany
| | - M Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - Heinrich Leonhardt
- Faculty of Biology, Ludwig-Maximilians-Universität München, Butenandtstraße 1, D-81377 Munich, Germany
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25
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Liu Y, Yamane J, Tanaka A, Fujibuchi W, Yamashita JK. AMPK activation reverts mouse epiblast stem cells to naive state. iScience 2021; 24:102783. [PMID: 34308289 PMCID: PMC8283141 DOI: 10.1016/j.isci.2021.102783] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 05/01/2021] [Accepted: 06/23/2021] [Indexed: 12/25/2022] Open
Abstract
Despite increasing knowledge on primed and naive pluripotency, the cell signaling that regulates the pluripotency type in stem cells remains not fully understood. Here we show that AMP kinase (AMPK) activators can induce the reversion of primed mouse epiblast stem cells (mEpiSCs) to the naive pluripotent state. The addition of AMPK activators alone or together with leukemia inhibitory factor to primed mEpiSCs induced the appearance of naive-like cells. After passaging in naive culture conditions, the colony morphology, protein expression, and global gene expression profiles indicated the naive state, as did germline transmission ability. Loss-of-function and gain-of-function studies suggested that p38 is a critical downstream target in AMPK activation. Finally, single-cell RNA sequencing analysis revealed that the reversion process through AMPK signaling passes an intermediate naive-like population. In conclusion, the AMPK pathway is a critical driving force in the reversion of primed to naive pluripotency.
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Affiliation(s)
- Yajing Liu
- The Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Junko Yamane
- The Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Akito Tanaka
- The Department of Animal Research Facility, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Wataru Fujibuchi
- The Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Jun K. Yamashita
- The Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
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26
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Zablon HA, Ko CI, Puga A. Converging Roles of the Aryl Hydrocarbon Receptor in Early Embryonic Development, Maintenance of Stemness, and Tissue Repair. Toxicol Sci 2021; 182:1-9. [PMID: 34009372 PMCID: PMC8285021 DOI: 10.1093/toxsci/kfab050] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor well-known for its adaptive role as a sensor of environmental toxicants and mediator of the metabolic detoxification of xenobiotic ligands. In addition, a growing body of experimental data has provided indisputable evidence that the AHR regulates critical functions of cell physiology and embryonic development. Recent studies have shown that the naïve AHR-that is, unliganded to xenobiotics but activated endogenously-has a crucial role in maintenance of embryonic stem cell pluripotency, tissue repair, and regulation of cancer stem cell stemness. Depending on the cellular context, AHR silences the expression of pluripotency genes Oct4 and Nanog and potentiates differentiation, whereas curtailing cellular plasticity and stemness. In these processes, AHR-mediated contextual responses and outcomes are dictated by changes of interacting partners in signaling pathways, gene networks, and cell-type-specific genomic structures. In this review, we focus on AHR-mediated changes of genomic architecture as an emerging mechanism for the AHR to regulate gene expression at the transcriptional level. Collective evidence places this receptor as a physiological hub connecting multiple biological processes whose disruption impacts on embryonic development, tissue repair, and maintenance or loss of stemness.
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Affiliation(s)
| | | | - Alvaro Puga
- Department of Environmental and Public Health Sciences, Center for Environmental Genetics, University of Cincinnati College of Medicine, Cincinnati, Ohio 45267, USA
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27
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Olivieri D, Paramanathan S, Bardet AF, Hess D, Smallwood SA, Elling U, Betschinger J. The BTB-domain transcription factor ZBTB2 recruits chromatin remodelers and a histone chaperone during the exit from pluripotency. J Biol Chem 2021; 297:100947. [PMID: 34270961 PMCID: PMC8350017 DOI: 10.1016/j.jbc.2021.100947] [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: 01/05/2021] [Revised: 06/21/2021] [Accepted: 07/08/2021] [Indexed: 12/12/2022] Open
Abstract
Transcription factors (TFs) harboring broad-complex, tramtrack, and bric-a-brac (BTB) domains play important roles in development and disease. These BTB domains are thought to recruit transcriptional modulators to target DNA regions. However, a systematic molecular understanding of the mechanism of action of this TF family is lacking. Here, we identify the zinc finger BTB-TF Zbtb2 from a genetic screen for regulators of exit from pluripotency and demonstrate that its absence perturbs embryonic stem cell differentiation and the gene expression dynamics underlying peri-implantation development. We show that ZBTB2 binds the chromatin remodeler Ep400 to mediate downstream transcription. Independently, the BTB domain directly interacts with nucleosome remodeling and deacetylase and histone chaperone histone regulator A. Nucleosome remodeling and deacetylase recruitment is a common feature of BTB TFs, and based on phylogenetic analysis, we propose that this is a conserved evolutionary property. Binding to UBN2, in contrast, is specific to ZBTB2 and requires a C-terminal extension of the BTB domain. Taken together, this study identifies a BTB-domain TF that recruits chromatin modifiers and a histone chaperone during a developmental cell state transition and defines unique and shared molecular functions of the BTB-domain TF family.
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Affiliation(s)
- Daniel Olivieri
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
| | | | - Anaïs F Bardet
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; CNRS, University of Strasbourg, UMR7242 Biotechnology and Cell Signaling, Illkirch, France
| | - Daniel Hess
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | | | - Ulrich Elling
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Joerg Betschinger
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
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28
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Dierolf JG, Watson AJ, Betts DH. Differential localization patterns of pyruvate kinase isoforms in murine naïve, formative, and primed pluripotent states. Exp Cell Res 2021; 405:112714. [PMID: 34181938 DOI: 10.1016/j.yexcr.2021.112714] [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: 10/26/2020] [Revised: 05/17/2021] [Accepted: 06/22/2021] [Indexed: 12/28/2022]
Abstract
Mouse embryonic stem cells (mESCs) and mouse epiblast stem cells (mEpiSCs) represent opposite ends of the pluripotency continuum, referred to as naïve and primed pluripotent states, respectively. These divergent pluripotent states differ in several ways, including growth factor requirements, transcription factor expression, DNA methylation patterns, and metabolic profiles. Naïve cells employ both glycolysis and oxidative phosphorylation (OXPHOS), whereas primed cells preferentially utilize aerobic glycolysis, a trait shared with cancer cells referred to as the Warburg Effect. Until recently, metabolism has been regarded as a by-product of cell fate, however, evidence now supports metabolism as being a driver of stem cell state and fate decisions. Pyruvate kinase muscle isoforms (PKM1 and PKM2) are important for generating and maintaining pluripotent stem cells (PSCs) and mediating the Warburg Effect. Both isoforms catalyze the final, rate limiting step of glycolysis, generating adenosine triphosphate and pyruvate, however, the precise role(s) of PKM1/2 in naïve and primed pluripotency is not well understood. The primary objective of this study was to characterize the cellular expression and localization patterns of PKM1 and PKM2 in mESCs, chemically transitioned epiblast-like cells (mEpiLCs) representing formative pluripotency, and mEpiSCs using immunoblotting and confocal microscopy. The results indicate that PKM1 and PKM2 are not only localized to the cytoplasm, but also accumulate in differential subnuclear regions of mESC, mEpiLCs, and mEpiSCs as determined by a quantitative confocal microscopy employing orthogonal projections and airyscan processing. Importantly, we discovered that the subnuclear localization of PKM1/2 changes during the transition from mESCs, mEpiLCs, and mEpiSCs. Finally, we have comprehensively validated the appropriateness and power of the Pearson's correlation coefficient and Manders's overlap coefficient for assessing nuclear and cytoplasmic protein colocalization in PSCs by immunofluorescence confocal microscopy. We propose that nuclear PKM1/2 may assist with distinct pluripotency state maintenance and lineage priming by non-canonical mechanisms. These results advance our understanding of the overall mechanisms controlling naïve, formative, and primed pluripotency.
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Affiliation(s)
- Joshua G Dierolf
- Department of Physiology and Pharmacology, Schulich School of Medicine & Dentistry, The University of Western Ontario, London, Canada
| | - Andrew J Watson
- Department of Physiology and Pharmacology, Schulich School of Medicine & Dentistry, The University of Western Ontario, London, Canada; Department of Obstetrics and Gynecology, Schulich School of Medicine & Dentistry, The University of Western Ontario, London, Canada; The Children's Health Research Institute (CHRI), Lawson Health Research Institute, London, Canada
| | - Dean H Betts
- Department of Physiology and Pharmacology, Schulich School of Medicine & Dentistry, The University of Western Ontario, London, Canada; Department of Obstetrics and Gynecology, Schulich School of Medicine & Dentistry, The University of Western Ontario, London, Canada; The Children's Health Research Institute (CHRI), Lawson Health Research Institute, London, Canada.
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29
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Molè MA, Coorens THH, Shahbazi MN, Weberling A, Weatherbee BAT, Gantner CW, Sancho-Serra C, Richardson L, Drinkwater A, Syed N, Engley S, Snell P, Christie L, Elder K, Campbell A, Fishel S, Behjati S, Vento-Tormo R, Zernicka-Goetz M. A single cell characterisation of human embryogenesis identifies pluripotency transitions and putative anterior hypoblast centre. Nat Commun 2021; 12:3679. [PMID: 34140473 PMCID: PMC8211662 DOI: 10.1038/s41467-021-23758-w] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 05/11/2021] [Indexed: 01/02/2023] Open
Abstract
Following implantation, the human embryo undergoes major morphogenetic transformations that establish the future body plan. While the molecular events underpinning this process are established in mice, they remain unknown in humans. Here we characterise key events of human embryo morphogenesis, in the period between implantation and gastrulation, using single-cell analyses and functional studies. First, the embryonic epiblast cells transition through different pluripotent states and act as a source of FGF signals that ensure proliferation of both embryonic and extra-embryonic tissues. In a subset of embryos, we identify a group of asymmetrically positioned extra-embryonic hypoblast cells expressing inhibitors of BMP, NODAL and WNT signalling pathways. We suggest that this group of cells can act as the anterior singalling centre to pattern the epiblast. These results provide insights into pluripotency state transitions, the role of FGF signalling and the specification of anterior-posterior axis during human embryo development. Single cell analysis of early human embryos identifies key changes in pluripotency, the requirement of FGF signalling for embryo survival, and defines a putative anterior-like region of hypoblast cells, providing insights into how early human development is regulated.
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Affiliation(s)
- Matteo A Molè
- Department of Physiology, Development and Neuroscience, Mammalian Embryo and Stem Cell Group, University of Cambridge, Cambridge, UK.,Babraham Institute, Babraham Research Campus, Cambridge, UK
| | | | - Marta N Shahbazi
- Department of Physiology, Development and Neuroscience, Mammalian Embryo and Stem Cell Group, University of Cambridge, Cambridge, UK.,MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Antonia Weberling
- Department of Physiology, Development and Neuroscience, Mammalian Embryo and Stem Cell Group, University of Cambridge, Cambridge, UK
| | - Bailey A T Weatherbee
- Department of Physiology, Development and Neuroscience, Mammalian Embryo and Stem Cell Group, University of Cambridge, Cambridge, UK
| | - Carlos W Gantner
- Department of Physiology, Development and Neuroscience, Mammalian Embryo and Stem Cell Group, University of Cambridge, Cambridge, UK
| | | | - Lucy Richardson
- Herts & Essex Fertility Centre, Bishops College, Cheshunt, Herts, UK
| | - Abbie Drinkwater
- Herts & Essex Fertility Centre, Bishops College, Cheshunt, Herts, UK
| | - Najma Syed
- Herts & Essex Fertility Centre, Bishops College, Cheshunt, Herts, UK
| | - Stephanie Engley
- Herts & Essex Fertility Centre, Bishops College, Cheshunt, Herts, UK
| | | | | | | | | | - Simon Fishel
- CARE Fertility Group, Nottingham, UK.,School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool, UK
| | - Sam Behjati
- Wellcome Sanger Institute, Hinxton, UK. .,Cambridge University Hospital, NHS Foundation Trust, Cambridge, UK. .,Department of Paediatrics, University of Cambridge, Cambridge, UK.
| | | | - Magdalena Zernicka-Goetz
- Department of Physiology, Development and Neuroscience, Mammalian Embryo and Stem Cell Group, University of Cambridge, Cambridge, UK. .,Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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30
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Shyh-Chang N, Li L. Stabilizing Formative Pluripotent States with Germ Cell Competency. Cell Stem Cell 2021; 28:361-363. [PMID: 33667353 DOI: 10.1016/j.stem.2021.02.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Previous work demonstrating the existence of intermediate pluripotency states in post-implantation embryos had ignited a debate on whether "formative" pluripotency can be stabilized in pluripotent stem cell (PSC) lines. In this issue of Cell Stem Cell, two papers show that polarized epithelial and germ cell-competent formative PSCs can be maintained in modified activin-dependent conditions.
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Affiliation(s)
- Ng Shyh-Chang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District 100101, Beijing, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Chaoyang District 100101, Beijing, China; Beijing Institute of Stem Cell and Regenerative Medicine, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 101408, China.
| | - Lei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District 100101, Beijing, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Chaoyang District 100101, Beijing, China; Beijing Institute of Stem Cell and Regenerative Medicine, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 101408, China.
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31
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Wang X, Ruan Y, Zhang J, Tian Y, Liu L, Wang J, Liu G, Cheng Y, Xu Y, Yang Y, Yu M, Zhao B, Zhang Y, Wang J, Wang J, Wu W, He P, Xiao L, Xiong J, Jian R. Expression levels and activation status of Yap splicing isoforms determine self-renewal and differentiation potential of embryonic stem cells. STEM CELLS (DAYTON, OHIO) 2021; 39:1178-1191. [PMID: 33938099 DOI: 10.1002/stem.3389] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 03/30/2021] [Indexed: 11/10/2022]
Abstract
Yap is the key effector of Hippo signaling; however, its role in embryonic stem cells (ESCs) remains controversial. Here, we identify two Yap splicing isoforms (Yap472 and Yap488), which show equal expression levels but heterogeneous distribution in ESCs. Knockout (KO) of both isoforms reduces ESC self-renewal, accelerates pluripotency exit, but arrests terminal differentiation, while overexpression of each isoform leads to the reverse phenotype. The effect of both Yap isoforms on self-renewal is Teads-dependent and mediated by c-Myc. Nonetheless, different isoforms are found to affect overlapping yet distinct genes, and confer different developmental potential to Yap-KO cells, with Yap472 exerting a more pronounced biological effect and being more essential for neuroectoderm differentiation. Constitutive activation of Yaps, particularly Yap472, dramatically upregulates p53 and Cdx2, inducing trophectoderm trans-differentiation even under self-renewal conditions. These findings reveal the combined roles of different Yap splicing isoforms and mechanisms in regulating self-renewal efficiency and differentiation potential of ESCs.
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Affiliation(s)
- Xueyue Wang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Army Medical University, Chongqing, People's Republic of China.,Department of Paediatrics, The General Hospital of PLA Tibet Military Area Command, Lhasa, People's Republic of China
| | - Yan Ruan
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Army Medical University, Chongqing, People's Republic of China
| | - Junlei Zhang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Army Medical University, Chongqing, People's Republic of China
| | - Yanping Tian
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Army Medical University, Chongqing, People's Republic of China
| | - Lianlian Liu
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Army Medical University, Chongqing, People's Republic of China
| | - JiaLi Wang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Army Medical University, Chongqing, People's Republic of China
| | - Gaoke Liu
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Army Medical University, Chongqing, People's Republic of China
| | - Yuda Cheng
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Army Medical University, Chongqing, People's Republic of China
| | - Yixiao Xu
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Army Medical University, Chongqing, People's Republic of China.,Southwest Hospital/Southwest Eye Hospital, The First Hospital Affiliated to Army Medical University, Chongqing, People's Republic of China
| | - Yi Yang
- Experimental Center of Basic Medicine, College of Basic Medical Sciences, Army Medical University, Chongqing, People's Republic of China
| | - Meng Yu
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Army Medical University, Chongqing, People's Republic of China
| | - Binyu Zhao
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Army Medical University, Chongqing, People's Republic of China
| | - Yue Zhang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Army Medical University, Chongqing, People's Republic of China.,Southwest Hospital/Southwest Eye Hospital, The First Hospital Affiliated to Army Medical University, Chongqing, People's Republic of China
| | - Jiaqi Wang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Army Medical University, Chongqing, People's Republic of China
| | - Jiangjun Wang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Army Medical University, Chongqing, People's Republic of China
| | - Wei Wu
- Thoracic Surgery Department, Southwest Hospital, The First Hospital Affiliated to Army Medical University, Chongqing, People's Republic of China
| | - Ping He
- Cardiac Surgery Department, Southwest Hospital, The First Hospital Affiliated to Army Medical University, Chongqing, People's Republic of China
| | - Lan Xiao
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Army Medical University, Chongqing, People's Republic of China
| | - Jiaxiang Xiong
- Experimental Center of Basic Medicine, College of Basic Medical Sciences, Army Medical University, Chongqing, People's Republic of China
| | - Rui Jian
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Army Medical University, Chongqing, People's Republic of China
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32
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Bertels S, Jaggy M, Richter B, Keppler S, Weber K, Genthner E, Fischer AC, Thiel M, Wegener M, Greiner AM, Autenrieth TJ, Bastmeyer M. Geometrically defined environments direct cell division rate and subcellular YAP localization in single mouse embryonic stem cells. Sci Rep 2021; 11:9269. [PMID: 33927254 PMCID: PMC8084931 DOI: 10.1038/s41598-021-88336-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 04/01/2021] [Indexed: 01/09/2023] Open
Abstract
Mechanotransduction via yes-associated protein (YAP) is a central mechanism for decision-making in mouse embryonic stem cells (mESCs). Nuclear localization of YAP is tightly connected to pluripotency and increases the cell division rate (CDR). How the geometry of the extracellular environment influences mechanotransduction, thereby YAP localization, and decision-making of single isolated mESCs is largely unknown. To investigate this relation, we produced well-defined 2D and 2.5D microenvironments and monitored CDR and subcellular YAP localization in single mESCs hence excluding cell–cell interactions. By systematically varying size and shape of the 2D and 2.5D substrates we observed that the geometry of the growth environment affects the CDR. Whereas CDR increases with increasing adhesive area in 2D, CDR is highest in small 2.5D micro-wells. Here, mESCs attach to all four walls and exhibit a cross-shaped cell and nuclear morphology. This observation indicates that changes in cell shape are linked to a high CDR. Inhibition of actomyosin activity abrogate these effects. Correspondingly, nuclear YAP localization decreases in inhibitor treated cells, suggesting a relation between cell shape, intracellular forces, and cell division rate. The simplicity of our system guarantees high standardization and reproducibility for monitoring stem cell reactions and allows addressing a variety of fundamental biological questions on a single cell level.
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Affiliation(s)
- Sarah Bertels
- Zoological Institute, Cell- and Neurobiology, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany.,Institute of Functional Interfaces, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany.,3DMM2O - Cluster of Excellence (EXC-2082/1 - 390761711), Karlsruhe, Germany
| | - Mona Jaggy
- Zoological Institute, Cell- and Neurobiology, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany.,Institute of Functional Interfaces, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Benjamin Richter
- Zoological Institute, Cell- and Neurobiology, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany
| | - Stephan Keppler
- Zoological Institute, Cell- and Neurobiology, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany.,3DMM2O - Cluster of Excellence (EXC-2082/1 - 390761711), Karlsruhe, Germany
| | - Kerstin Weber
- Zoological Institute, Cell- and Neurobiology, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany
| | - Elisa Genthner
- Zoological Institute, Cell- and Neurobiology, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany.,3DMM2O - Cluster of Excellence (EXC-2082/1 - 390761711), Karlsruhe, Germany
| | - Andrea C Fischer
- Zoological Institute, Cell- and Neurobiology, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany.,Institute of Applied Physics, Karlsruhe Institute of Technology, Wolfgang-Gaede-Straße 1, 76131, Karlsruhe, Germany
| | - Michael Thiel
- Nanoscribe GmbH, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Martin Wegener
- Institute of Applied Physics, Karlsruhe Institute of Technology, Wolfgang-Gaede-Straße 1, 76131, Karlsruhe, Germany.,Institute of Nanotechnology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany.,3DMM2O - Cluster of Excellence (EXC-2082/1 - 390761711), Karlsruhe, Germany
| | - Alexandra M Greiner
- Zoological Institute, Cell- and Neurobiology, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany
| | - Tatjana J Autenrieth
- Zoological Institute, Cell- and Neurobiology, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany.,Institute of Functional Interfaces, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Martin Bastmeyer
- Zoological Institute, Cell- and Neurobiology, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany. .,Institute of Functional Interfaces, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany. .,3DMM2O - Cluster of Excellence (EXC-2082/1 - 390761711), Karlsruhe, Germany. .,Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany.
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Molè MA, Weberling A, Fässler R, Campbell A, Fishel S, Zernicka-Goetz M. Integrin β1 coordinates survival and morphogenesis of the embryonic lineage upon implantation and pluripotency transition. Cell Rep 2021; 34:108834. [PMID: 33691117 PMCID: PMC7966855 DOI: 10.1016/j.celrep.2021.108834] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 11/30/2020] [Accepted: 02/17/2021] [Indexed: 12/13/2022] Open
Abstract
At implantation, the embryo establishes contacts with the maternal endometrium. This stage is associated with a high incidence of preclinical pregnancy losses. While the maternal factors underlying uterine receptivity have been investigated, the signals required by the embryo for successful peri-implantation development remain elusive. To explore these, we studied integrin β1 signaling, as embryos deficient for this receptor degenerate at implantation. We demonstrate that the coordinated action of pro-survival signals and localized actomyosin suppression via integrin β1 permits the development of the embryo beyond implantation. Failure of either process leads to developmental arrest and apoptosis. Pharmacological stimulation through fibroblast growth factor 2 (FGF2) and insulin-like growth factor 1 (IGF1), coupled with ROCK-mediated actomyosin inhibition, rescues the deficiency of integrin β1, promoting progression to post-implantation stages. Mutual exclusion between integrin β1 and actomyosin seems to be conserved in the human embryo, suggesting the possibility that these mechanisms could also underlie the transition of the human epiblast from pre- to post-implantation.
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Affiliation(s)
- Matteo Amitaba Molè
- Mammalian Embryo and Stem Cell Group, Department of Physiology, Development, and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK
| | - Antonia Weberling
- Mammalian Embryo and Stem Cell Group, Department of Physiology, Development, and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK
| | - Reinhard Fässler
- Department of Molecular Medicine, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Alison Campbell
- CARE Fertility Group, John Webster House, 6 Lawrence Drive, Nottingham Business Park, Nottingham NG8 6PZ, UK
| | - Simon Fishel
- CARE Fertility Group, John Webster House, 6 Lawrence Drive, Nottingham Business Park, Nottingham NG8 6PZ, UK; School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK
| | - Magdalena Zernicka-Goetz
- Mammalian Embryo and Stem Cell Group, Department of Physiology, Development, and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK; Plasticity and Self-Organization Group, Division of Biology and Biological Engineering, California Institute of Technology (Caltech), Pasadena, CA 91125, USA.
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34
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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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35
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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: 119] [Impact Index Per Article: 39.7] [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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36
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Semi K, Takashima Y. Pluripotent stem cells for the study of early human embryology. Dev Growth Differ 2021; 63:104-115. [PMID: 33570781 PMCID: PMC8251740 DOI: 10.1111/dgd.12715] [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: 11/21/2020] [Revised: 02/02/2021] [Accepted: 02/08/2021] [Indexed: 02/06/2023]
Abstract
Forty years have passed since the first pluripotent stem cells (PSCs), mouse embryonic stem cells (ESCs), were established. Since then, several PSCs have been reported, including human ESCs in 1998, mouse epiblast stem cells (EpiSCs) in 2007, induced PSCs (iPSCs) in 2006 and 2007, and naïve human PSCs in 2014. Naïve PSCs are thought to correspond to pre-implantation epiblast cells, whereas conventional (or primed) human PSCs correspond to post-implantation epiblast cells. Thus, naïve and primed PSCs are classified by their developmental stages and have stage-specific characteristics, despite sharing the common feature of pluripotency. In this review, we discuss the current status of PSCs and their use to model human peri-implantation development.
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Affiliation(s)
- Katsunori Semi
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Yasuhiro Takashima
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
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37
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Abstract
In the past several decades, the establishment of in vitro models of pluripotency has ushered in a golden era for developmental and stem cell biology. Research in this arena has led to profound insights into the regulatory features that shape early embryonic development. Nevertheless, an integrative theory of the epigenetic principles that govern the pluripotent nucleus remains elusive. Here, we summarize the epigenetic characteristics that define the pluripotent state. We cover what is currently known about the epigenome of pluripotent stem cells and reflect on the use of embryonic stem cells as an experimental system. In addition, we highlight insights from super-resolution microscopy, which have advanced our understanding of the form and function of chromatin, particularly its role in establishing the characteristically "open chromatin" of pluripotent nuclei. Further, we discuss the rapid improvements in 3C-based methods, which have given us a means to investigate the 3D spatial organization of the pluripotent genome. This has aided the adaptation of prior notions of a "pluripotent molecular circuitry" into a more holistic model, where hotspots of co-interacting domains correspond with the accumulation of pluripotency-associated factors. Finally, we relate these earlier hypotheses to an emerging model of phase separation, which posits that a biophysical mechanism may presuppose the formation of a pluripotent-state-defining transcriptional program.
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Affiliation(s)
| | - Eran Meshorer
- Department of Genetics, the Institute of Life Sciences
- Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Jerusalem, Israel 9190400
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38
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Hayashi K, Galli C, Diecke S, Hildebrandt TB. Artificially produced gametes in mice, humans and other species. Reprod Fertil Dev 2021; 33:91-101. [PMID: 38769675 DOI: 10.1071/rd20265] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024] Open
Abstract
The production of gametes from pluripotent stem cells in culture, also known as invitro gametogenesis, will make an important contribution to reproductive biology and regenerative medicine, both as a unique tool for understanding germ cell development and as an alternative source of gametes for reproduction. Invitro gametogenesis was developed using mouse pluripotent stem cells but is increasingly being applied in other mammalian species, including humans. In principle, the entire process of germ cell development is nearly reconstitutable in culture using mouse pluripotent stem cells, although the fidelity of differentiation processes and the quality of resultant gametes remain to be refined. The methodology in the mouse system is only partially applicable to other species, and thus it must be optimised for each species. In this review, we update the current status of invitro gametogenesis in mice, humans and other animals, and discuss challenges for further development of this technology.
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Affiliation(s)
- Katsuhiko Hayashi
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-0054, Japan; and Corresponding author
| | - Cesare Galli
- Avantea, Laboratory of Reproductive Technologies, 26100 Cremona, Italy; and Fondazione Avantea, 26100 Cremona, Italy
| | - Sebastian Diecke
- Max-Delbrueck-Center for Molecular Medicine, 13092 Berlin, Germany
| | - Thomas B Hildebrandt
- Leibniz Institute for Zoo and Wildlife Research, D-10315 Berlin, Germany; and Freie Universität Berlin, D-14195 Berlin, Germany
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39
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Lezmi E, Weissbein U, Golan-Lev T, Nissim-Rafinia M, Meshorer E, Benvenisty N. The Chromatin Regulator ZMYM2 Restricts Human Pluripotent Stem Cell Growth and Is Essential for Teratoma Formation. Stem Cell Reports 2020; 15:1275-1286. [PMID: 32559458 PMCID: PMC7724477 DOI: 10.1016/j.stemcr.2020.05.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 05/19/2020] [Accepted: 05/19/2020] [Indexed: 01/13/2023] Open
Abstract
Chromatin regulators play fundamental roles in controlling pluripotency and differentiation. We examined the effect of mutations in 703 genes from nearly 70 chromatin-modifying complexes on human embryonic stem cell (ESC) growth. While the vast majority of chromatin-associated complexes are essential for ESC growth, the only complexes that conferred growth advantage upon mutation of their members, were the repressive complexes LSD-CoREST and BHC. Both complexes include the most potent growth-restricting chromatin-related protein, ZMYM2. Interestingly, while ZMYM2 expression is rather low in human blastocysts, its expression peaks in primed ESCs and is again downregulated upon differentiation. ZMYM2-null ESCs overexpress pluripotency genes and show genome-wide promotor-localized histone H3 hyper-acetylation. These mutant cells were also refractory to differentiate in vitro and failed to produce teratomas upon injection into immunodeficient mice. Our results suggest a central role for ZMYM2 in the transcriptional regulation of the undifferentiated state and in the exit-from-pluripotency of human ESCs.
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Affiliation(s)
- Elyad Lezmi
- The Azrieli Center for Stem Cells and Genetic Research, The Hebrew University, Jerusalem, Israel
| | - Uri Weissbein
- The Azrieli Center for Stem Cells and Genetic Research, The Hebrew University, Jerusalem, Israel
| | - Tamar Golan-Lev
- The Azrieli Center for Stem Cells and Genetic Research, The Hebrew University, Jerusalem, Israel; Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Malka Nissim-Rafinia
- Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel; Edmond and Lily Center for Brain Sciences (ELSC), The Hebrew University, Jerusalem, Israel
| | - Eran Meshorer
- Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel; Edmond and Lily Center for Brain Sciences (ELSC), The Hebrew University, Jerusalem, Israel.
| | - Nissim Benvenisty
- The Azrieli Center for Stem Cells and Genetic Research, The Hebrew University, Jerusalem, Israel; Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel.
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40
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Optimized Approaches for the Induction of Putative Canine Induced Pluripotent Stem Cells from Old Fibroblasts Using Synthetic RNAs. Animals (Basel) 2020; 10:ani10101848. [PMID: 33050577 PMCID: PMC7601034 DOI: 10.3390/ani10101848] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/02/2020] [Accepted: 10/07/2020] [Indexed: 12/16/2022] Open
Abstract
Simple Summary A non-integrating and self-replicating Venezuelan equine encephalitis RNA replicon system can potentially make a great contribution to the generation of clinically applicable canine induced pluripotent stem cells. Our study shows a new method to utilize the synthetic RNA-based approach for canine somatic cell reprogramming regarding transfection and reprogramming efficiency. Abstract Canine induced pluripotent stem cells (ciPSCs) can provide great potential for regenerative veterinary medicine. Several reports have described the generation of canine somatic cell-derived iPSCs; however, none have described the canine somatic cell reprogramming using a non-integrating and self-replicating RNA transfection method. The purpose of this study was to investigate the optimal strategy using this approach and characterize the transition stage of ciPSCs. In this study, fibroblasts obtained from a 13-year-old dog were reprogrammed using a non-integrating Venezuelan equine encephalitis (VEE) RNA virus replicon, which has four reprogramming factors (collectively referred to as T7-VEE-OKS-iG and comprised of hOct4, hKlf4, hSox2, and hGlis1) and co-transfected with the T7-VEE-OKS-iG RNA and B18R mRNA for 4 h. One day after the final transfection, the cells were selected with puromycin (0.5 µg/mL) until day 10. After about 25 days, putative ciPSC colonies were identified showing TRA-1-60 expression and alkaline phosphatase activity. To determine the optimal culture conditions, the basic fibroblast growth factor in the culture medium was replaced with a modified medium supplemented with murine leukemia inhibitory factor (mLIF) and two kinase inhibitors (2i), PD0325901(MEK1/2 inhibitor) and CHIR99021 (GSK3β inhibitor). The derived colonies showed resemblance to naïve iPSCs in their morphology (dome-shaped) and are dependent on mLIF and 2i condition to maintain an undifferentiated phenotype. The expression of endogenous pluripotency markers such as Oct4, Nanog, and Rex1 transcripts were confirmed, suggesting that induced ciPSCs were in the late intermediate stage of reprogramming. In conclusion, the non-integrating and self-replicating VEE RNA replicon system can potentially make a great contribution to the generation of clinically applicable ciPSCs, and the findings of this study suggest a new method to utilize the VEE RNA approach for canine somatic cell reprogramming.
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41
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Navarro M, Soto DA, Pinzon CA, Wu J, Ross PJ. Livestock pluripotency is finally captured in vitro. Reprod Fertil Dev 2020; 32:11-39. [PMID: 32188555 DOI: 10.1071/rd19272] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Pluripotent stem cells (PSCs) have demonstrated great utility in improving our understanding of mammalian development and continue to revolutionise regenerative medicine. Thanks to the improved understanding of pluripotency in mice and humans, it has recently become feasible to generate stable livestock PSCs. Although it is unlikely that livestock PSCs will be used for similar applications as their murine and human counterparts, new exciting applications that could greatly advance animal agriculture are being developed, including the use of PSCs for complex genome editing, cellular agriculture, gamete generation and invitro breeding schemes.
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Affiliation(s)
- Micaela Navarro
- Department of Animal Science, University of California, 450 Bioletti Way, Davis, CA 95616, USA
| | - Delia A Soto
- Department of Animal Science, University of California, 450 Bioletti Way, Davis, CA 95616, USA
| | - Carlos A Pinzon
- Department of Molecular Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Jun Wu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA; and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Pablo J Ross
- Department of Animal Science, University of California, 450 Bioletti Way, Davis, CA 95616, USA; and Corresponding author.
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42
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ZIC3 Controls the Transition from Naive to Primed Pluripotency. Cell Rep 2020; 27:3215-3227.e6. [PMID: 31189106 PMCID: PMC6581693 DOI: 10.1016/j.celrep.2019.05.026] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 03/14/2019] [Accepted: 05/06/2019] [Indexed: 01/06/2023] Open
Abstract
Embryonic stem cells (ESCs) must transition through a series of intermediate cell states before becoming terminally differentiated. Here, we investigated the early events in this transition by determining the changes in the open chromatin landscape as naive mouse ESCs transition to epiblast-like cells (EpiLCs). Motif enrichment analysis of the newly opening regions coupled with expression analysis identified ZIC3 as a potential regulator of this cell fate transition. Chromatin binding and genome-wide transcriptional profiling following Zic3 depletion confirmed ZIC3 as an important regulatory transcription factor, and among its targets are genes encoding a number of transcription factors. Among these is GRHL2, which acts through enhancer switching to maintain the expression of a subset of genes from the ESC state. Our data therefore place ZIC3 upstream of a set of pro-differentiation transcriptional regulators and provide an important advance in our understanding of the regulatory factors governing the early steps in ESC differentiation. Transcription factor ZIC3 regulates gene expression during the ESC to EpiLC transition Extensive changes occur in the open chromatin landscape as ESCs progress to EpiLCs ZIC3 activates the expression of a network of transcription factors ZIC3-activated genes in EpiLCs are upregulated in the post-implantation epiblast
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43
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Abstract
Gene regulatory networks and tissue morphogenetic events drive the emergence of shape and function: the pillars of embryo development. Although model systems offer a window into the molecular biology of cell fate and tissue shape, mechanistic studies of our own development have so far been technically and ethically challenging. However, recent technical developments provide the tools to describe, manipulate and mimic human embryos in a dish, thus opening a new avenue to exploring human development. Here, I discuss the evidence that supports a role for the crosstalk between cell fate and tissue shape during early human embryogenesis. This is a critical developmental period, when the body plan is laid out and many pregnancies fail. Dissecting the basic mechanisms that coordinate cell fate and tissue shape will generate an integrated understanding of early embryogenesis and new strategies for therapeutic intervention in early pregnancy loss.
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Affiliation(s)
- Marta N Shahbazi
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
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44
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Mulas C, Hodgson AC, Kohler TN, Agley CC, Humphreys P, Kleine-Brüggeney H, Hollfelder F, Smith A, Chalut KJ. Microfluidic platform for 3D cell culture with live imaging and clone retrieval. LAB ON A CHIP 2020; 20:2580-2591. [PMID: 32573646 DOI: 10.1039/d0lc00165a] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Combining live imaging with the ability to retrieve individual cells of interest remains a technical challenge. Combining imaging with precise cell retrieval is of particular interest when studying highly dynamic or transient, asynchronous, or heterogeneous cell biological and developmental processes. Here, we present a method to encapsulate live cells in a 3D hydrogel matrix, via hydrogel bead compartmentalisation. Using a small-scale screen, we optimised matrix conditions for the culture and multilineage differentiation of mouse embryonic stem cells. Moreover, we designed a custom microfluidic platform that is compatible with live imaging. With this platform we can long-term culture and subsequently extract individual cells-in-beads by media flow only, obviating the need for enzymatic cell removal from the platform. Specific beads may be extracted from the platform in isolation, without disrupting the adjacent beads. We show that we can differentiate mouse embryonic stem cells, monitor reporter expression by live imaging, and retrieve individual beads for functional assays, correlating reporter expression with functional response. Overall, we present a highly flexible 3D cell encapsulation and microfluidic platform that enables both monitoring of cellular dynamics and retrieval for molecular and functional assays.
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Affiliation(s)
- Carla Mulas
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK.
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45
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Cheng L, Zhang X, Wang Y, Gan H, Xu X, Lv X, Hua X, Que J, Ordog T, Zhang Z. Chromatin Assembly Factor 1 (CAF-1) facilitates the establishment of facultative heterochromatin during pluripotency exit. Nucleic Acids Res 2020; 47:11114-11131. [PMID: 31586391 PMCID: PMC6868363 DOI: 10.1093/nar/gkz858] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 08/29/2019] [Accepted: 10/01/2019] [Indexed: 11/24/2022] Open
Abstract
Establishment and subsequent maintenance of distinct chromatin domains during embryonic stem cell (ESC) differentiation are crucial for lineage specification and cell fate determination. Here we show that the histone chaperone Chromatin Assembly Factor 1 (CAF-1), which is recruited to DNA replication forks through its interaction with proliferating cell nuclear antigen (PCNA) for nucleosome assembly, participates in the establishment of H3K27me3-mediated silencing during differentiation. Deletion of CAF-1 p150 subunit impairs the silencing of many genes including Oct4, Sox2 and Nanog as well as the establishment of H3K27me3 at these gene promoters during ESC differentiation. Mutations of PCNA residues involved in recruiting CAF-1 to the chromatin also result in defects in differentiation in vitro and impair early embryonic development as p150 deletion. Together, these results reveal that the CAF-1-PCNA nucleosome assembly pathway plays an important role in the establishment of H3K27me3-mediated silencing during cell fate determination.
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Affiliation(s)
- Liang Cheng
- Biochemistry and Molecular Biology Track, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN 55902, USA.,Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.,Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA
| | - Xu Zhang
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA.,Department of Pediatrics, Columbia University, New York, NY 10032, USA.,Department of Genetics and Development, Columbia University, New York, NY 10032, USA
| | - Yan Wang
- Biochemistry and Molecular Biology Track, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN 55902, USA.,Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Haiyun Gan
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA.,Department of Pediatrics, Columbia University, New York, NY 10032, USA.,Department of Genetics and Development, Columbia University, New York, NY 10032, USA
| | - Xiaowei Xu
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA.,Department of Pediatrics, Columbia University, New York, NY 10032, USA.,Department of Genetics and Development, Columbia University, New York, NY 10032, USA
| | - Xiangdong Lv
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA.,Department of Pediatrics, Columbia University, New York, NY 10032, USA.,Department of Genetics and Development, Columbia University, New York, NY 10032, USA
| | - Xu Hua
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA.,Department of Genetics and Development, Columbia University, New York, NY 10032, USA
| | - Jianwen Que
- Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Tamas Ordog
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA.,Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA.,Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Zhiguo Zhang
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA.,Department of Pediatrics, Columbia University, New York, NY 10032, USA.,Department of Genetics and Development, Columbia University, New York, NY 10032, USA
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46
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White MD, Plachta N. Specification of the First Mammalian Cell Lineages In Vivo and In Vitro. Cold Spring Harb Perspect Biol 2020; 12:cshperspect.a035634. [PMID: 31615786 DOI: 10.1101/cshperspect.a035634] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Our understanding of how the first mammalian cell lineages arise has been shaped largely by studies of the preimplantation mouse embryo. Painstaking work over many decades has begun to reveal how a single totipotent cell is transformed into a multilayered structure representing the foundations of the body plan. Here, we review how the first lineage decision is initiated by epigenetic regulation but consolidated by the integration of morphological features and transcription factor activity. The establishment of pluripotent and multipotent stem cell lines has enabled deeper analysis of molecular and epigenetic regulation of cell fate decisions. The capability to assemble these stem cells into artificial embryos is an exciting new avenue of research that offers a long-awaited window into cell fate specification in the human embryo. Together, these approaches are poised to profoundly increase our understanding of how the first lineage decisions are made during mammalian embryonic development.
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Affiliation(s)
- Melanie D White
- Institute of Molecular and Cell Biology, A*STAR, Singapore 138673
| | - Nicolas Plachta
- Institute of Molecular and Cell Biology, A*STAR, Singapore 138673
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47
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Kim HJ, Osteil P, Humphrey SJ, Cinghu S, Oldfield AJ, Patrick E, Wilkie EE, Peng G, Suo S, Jothi R, Tam PPL, Yang P. Transcriptional network dynamics during the progression of pluripotency revealed by integrative statistical learning. Nucleic Acids Res 2020; 48:1828-1842. [PMID: 31853542 PMCID: PMC7038952 DOI: 10.1093/nar/gkz1179] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 12/02/2019] [Accepted: 12/09/2019] [Indexed: 12/12/2022] Open
Abstract
The developmental potential of cells, termed pluripotency, is highly dynamic and progresses through a continuum of naive, formative and primed states. Pluripotency progression of mouse embryonic stem cells (ESCs) from naive to formative and primed state is governed by transcription factors (TFs) and their target genes. Genomic techniques have uncovered a multitude of TF binding sites in ESCs, yet a major challenge lies in identifying target genes from functional binding sites and reconstructing dynamic transcriptional networks underlying pluripotency progression. Here, we integrated time-resolved ‘trans-omic’ datasets together with TF binding profiles and chromatin conformation data to identify target genes of a panel of TFs. Our analyses revealed that naive TF target genes are more likely to be TFs themselves than those of formative TFs, suggesting denser hierarchies among naive TFs. We also discovered that formative TF target genes are marked by permissive epigenomic signatures in the naive state, indicating that they are poised for expression prior to the initiation of pluripotency transition to the formative state. Finally, our reconstructed transcriptional networks pinpointed the precise timing from naive to formative pluripotency progression and enabled the spatiotemporal mapping of differentiating ESCs to their in vivo counterparts in developing embryos.
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Affiliation(s)
- Hani Jieun Kim
- Charles Perkins Centre, School of Mathematics and Statistics, University of Sydney, Sydney, NSW 2006, Australia.,Computational Systems Biology Group, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia.,School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, NSW 2006, Australia
| | - Pierre Osteil
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, NSW 2006, Australia.,Embryology Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Sean J Humphrey
- Charles Perkins Centre, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Senthilkumar Cinghu
- Epigenetics & Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Andrew J Oldfield
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France
| | - Ellis Patrick
- Charles Perkins Centre, School of Mathematics and Statistics, University of Sydney, Sydney, NSW 2006, Australia.,School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, NSW 2006, Australia.,Westmead Institute for Medical Research, University of Sydney, Westmead, NSW 2145, Australia
| | - Emilie E Wilkie
- Embryology Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Guangdun Peng
- CAS 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, Guangzhou 510530, China, and Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), Guangzhou 510005, China
| | - Shengbao Suo
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA
| | - Raja Jothi
- Epigenetics & Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Patrick P L Tam
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, NSW 2006, Australia.,Embryology Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Pengyi Yang
- Charles Perkins Centre, School of Mathematics and Statistics, University of Sydney, Sydney, NSW 2006, Australia.,Computational Systems Biology Group, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia.,School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, NSW 2006, Australia
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48
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Pluripotency on Lockdown after Deletion of Three Transcription Regulators. Cell Stem Cell 2020; 24:681-683. [PMID: 31051130 DOI: 10.1016/j.stem.2019.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Exit from the naive pluripotent state occurs through a series of changes in the gene regulatory circuitry, allowing cells to become primed for lineage commitment. In this issue of Cell Stem Cell, Kalkan et al. (2019) show that three transcription regulators are required for naive mouse embryonic stem cells (ESCs) to exit the pluripotent state.
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49
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Prajapati RS, Hintze M, Streit A. PRDM1 controls the sequential activation of neural, neural crest and sensory progenitor determinants. Development 2019; 146:dev.181107. [PMID: 31806661 DOI: 10.1242/dev.181107] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Accepted: 11/27/2019] [Indexed: 12/25/2022]
Abstract
During early embryogenesis, the ectoderm is rapidly subdivided into neural, neural crest and sensory progenitors. How the onset of lineage determinants and the loss of pluripotency markers are temporally and spatially coordinated in vivo is still debated. Here, we identify a crucial role for the transcription factor PRDM1 in the orderly transition from epiblast to defined neural lineages in chick. PRDM1 is initially expressed broadly in the entire epiblast, but becomes gradually restricted as cell fates are specified. We find that PRDM1 is required for the loss of some pluripotency markers and the onset of neural, neural crest and sensory progenitor specifier genes. PRDM1 directly activates their expression by binding to their promoter regions and recruiting the histone demethylase Kdm4a to remove repressive histone marks. However, once neural lineage determinants become expressed, they in turn repress PRDM1, whereas prolonged PRDM1 expression inhibits neural, neural crest and sensory progenitor genes, suggesting that its downregulation is necessary for cells to maintain their identity. Therefore, PRDM1 plays multiple roles during ectodermal cell fate allocation.
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Affiliation(s)
- Ravindra S Prajapati
- Centre for Craniofacial & Regenerative Biology, Faculty of Dental, Oral and Craniofacial Sciences, King's College London, London SE1 9RT, UK
| | - Mark Hintze
- Centre for Craniofacial & Regenerative Biology, Faculty of Dental, Oral and Craniofacial Sciences, King's College London, London SE1 9RT, UK
| | - Andrea Streit
- Centre for Craniofacial & Regenerative Biology, Faculty of Dental, Oral and Craniofacial Sciences, King's College London, London SE1 9RT, UK
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50
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Kang Y, Ai Z, Duan K, Si C, Wang Y, Zheng Y, He J, Yin Y, Zhao S, Niu B, Zhu X, Liu L, Xiang L, Zhang L, Niu Y, Ji W, Li T. Improving Cell Survival in Injected Embryos Allows Primed Pluripotent Stem Cells to Generate Chimeric Cynomolgus Monkeys. Cell Rep 2019; 25:2563-2576.e9. [PMID: 30485820 DOI: 10.1016/j.celrep.2018.11.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 09/11/2018] [Accepted: 10/30/2018] [Indexed: 12/17/2022] Open
Abstract
Monkeys are an optimal model species for developing stem cell therapies. We previously reported generating chimeric cynomolgus monkey fetuses using dome-shaped embryonic stem cells (dESCs). However, conventional primed pluripotent stem cells (pPSCs) lack chimera competency. Here, by altering the media in which injected morulae are cultured, we observed increased survival of cynomolgus monkey primed ESCs, induced PSCs, and somatic cell nuclear transfer-derived ESCs, thereby enabling chimeric contributions with 0.1%-4.5% chimerism into the embryonic and placental tissues, including germ cell progenitors in chimeric monkeys. Mechanically, dESCs and pPSCs belong to different cell types and similarly express epiblast ontogenic genes. The host embryonic microenvironment could reprogram injected PSCs to embryonic-like cells. However, the reprogramming level and chimerism were associated with the cell state of injected PSCs. Our findings provide a method to understand pluripotency and broaden the use of embryonic chimeras for basic developmental biology research and regenerative medicine.
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Affiliation(s)
- Yu Kang
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Provincial Academy of Science and Technology, Kunming, Yunnan 650500, China
| | - Zongyong Ai
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Provincial Academy of Science and Technology, Kunming, Yunnan 650500, China; Kunming Enovate Institute of Bioscience, Kunming, Yunnan 650500, China
| | - Kui Duan
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Provincial Academy of Science and Technology, Kunming, Yunnan 650500, China
| | - Chenyang Si
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Provincial Academy of Science and Technology, Kunming, Yunnan 650500, China
| | - Yong Wang
- Department of Laboratory Animal Science, College of Basic Medical Sciences, Third Military Medical University, Chongqing 400038, China
| | - Yun Zheng
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Provincial Academy of Science and Technology, Kunming, Yunnan 650500, China
| | - Jingjing He
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Provincial Academy of Science and Technology, Kunming, Yunnan 650500, China
| | - Yu Yin
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Provincial Academy of Science and Technology, Kunming, Yunnan 650500, China
| | - Shumei Zhao
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Provincial Academy of Science and Technology, Kunming, Yunnan 650500, China
| | - Baohua Niu
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Provincial Academy of Science and Technology, Kunming, Yunnan 650500, China
| | - Xiaoqing Zhu
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Provincial Academy of Science and Technology, Kunming, Yunnan 650500, China; Kunming Enovate Institute of Bioscience, Kunming, Yunnan 650500, China
| | - Li Liu
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Provincial Academy of Science and Technology, Kunming, Yunnan 650500, China
| | - Lifeng Xiang
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Provincial Academy of Science and Technology, Kunming, Yunnan 650500, China
| | - Linming Zhang
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Yuyu Niu
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Provincial Academy of Science and Technology, Kunming, Yunnan 650500, China; Kunming Enovate Institute of Bioscience, Kunming, Yunnan 650500, China
| | - Weizhi Ji
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Provincial Academy of Science and Technology, Kunming, Yunnan 650500, China; Kunming Enovate Institute of Bioscience, Kunming, Yunnan 650500, China
| | - Tianqing Li
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Provincial Academy of Science and Technology, Kunming, Yunnan 650500, China; Kunming Enovate Institute of Bioscience, Kunming, Yunnan 650500, China.
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