1
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Linneberg-Agerholm M, Sell AC, Redó-Riveiro A, Perera M, Proks M, Knudsen TE, Barral A, Manzanares M, Brickman JM. The primitive endoderm supports lineage plasticity to enable regulative development. Cell 2024:S0092-8674(24)00595-6. [PMID: 38917790 DOI: 10.1016/j.cell.2024.05.051] [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: 05/19/2023] [Revised: 02/27/2024] [Accepted: 05/28/2024] [Indexed: 06/27/2024]
Abstract
Mammalian blastocyst formation involves the specification of the trophectoderm followed by the differentiation of the inner cell mass into embryonic epiblast and extra-embryonic primitive endoderm (PrE). During this time, the embryo maintains a window of plasticity and can redirect its cellular fate when challenged experimentally. In this context, we found that the PrE alone was sufficient to regenerate a complete blastocyst and continue post-implantation development. We identify an in vitro population similar to the early PrE in vivo that exhibits the same embryonic and extra-embryonic potency and can form complete stem cell-based embryo models, termed blastoids. Commitment in the PrE is suppressed by JAK/STAT signaling, collaborating with OCT4 and the sustained expression of a subset of pluripotency-related transcription factors that safeguard an enhancer landscape permissive for multi-lineage differentiation. Our observations support the notion that transcription factor persistence underlies plasticity in regulative development and highlight the importance of the PrE in perturbed development.
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Affiliation(s)
- Madeleine Linneberg-Agerholm
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Annika Charlotte Sell
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Alba Redó-Riveiro
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Marta Perera
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Martin Proks
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Teresa E Knudsen
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Antonio Barral
- Centro de Biología Molecular Severo Ochoa (CBM), CSIC-UAM, 28049 Madrid, Spain
| | - Miguel Manzanares
- Centro de Biología Molecular Severo Ochoa (CBM), CSIC-UAM, 28049 Madrid, Spain
| | - Joshua M Brickman
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 2200 Copenhagen N, Denmark.
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2
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Simpson L, Strange A, Klisch D, Kraunsoe S, Azami T, Goszczynski D, Le Minh T, Planells B, Holmes N, Sang F, Henson S, Loose M, Nichols J, Alberio R. A single-cell atlas of pig gastrulation as a resource for comparative embryology. Nat Commun 2024; 15:5210. [PMID: 38890321 PMCID: PMC11189408 DOI: 10.1038/s41467-024-49407-6] [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: 08/21/2023] [Accepted: 06/04/2024] [Indexed: 06/20/2024] Open
Abstract
Cell-fate decisions during mammalian gastrulation are poorly understood outside of rodent embryos. The embryonic disc of pig embryos mirrors humans, making them a useful proxy for studying gastrulation. Here we present a single-cell transcriptomic atlas of pig gastrulation, revealing cell-fate emergence dynamics, as well as conserved and divergent gene programs governing early porcine, primate, and murine development. We highlight heterochronicity in extraembryonic cell-types, despite the broad conservation of cell-type-specific transcriptional programs. We apply these findings in combination with functional investigations, to outline conserved spatial, molecular, and temporal events during definitive endoderm specification. We find early FOXA2 + /TBXT- embryonic disc cells directly form definitive endoderm, contrasting later-emerging FOXA2/TBXT+ node/notochord progenitors. Unlike mesoderm, none of these progenitors undergo epithelial-to-mesenchymal transition. Endoderm/Node fate hinges on balanced WNT and hypoblast-derived NODAL, which is extinguished upon endodermal differentiation. These findings emphasise the interplay between temporal and topological signalling in fate determination during gastrulation.
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Affiliation(s)
- Luke Simpson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Nottingham, LE12 5RD, UK
| | - Andrew Strange
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Nottingham, LE12 5RD, UK
| | - Doris Klisch
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Nottingham, LE12 5RD, UK
| | - Sophie Kraunsoe
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Nottingham, LE12 5RD, UK
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Takuya Azami
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh, EH4 2XU, UK
| | - Daniel Goszczynski
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Nottingham, LE12 5RD, UK
| | - Triet Le Minh
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Nottingham, LE12 5RD, UK
| | - Benjamin Planells
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Nottingham, LE12 5RD, UK
| | - Nadine Holmes
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Fei Sang
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Sonal Henson
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Matthew Loose
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Jennifer Nichols
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh, EH4 2XU, UK
| | - Ramiro Alberio
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Nottingham, LE12 5RD, UK.
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3
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Yang X, Chen Y, Yang Y, Li S, Mi P, Jing N. The molecular and cellular choreography of early mammalian lung development. MEDICAL REVIEW (2021) 2024; 4:192-206. [PMID: 38919401 PMCID: PMC11195428 DOI: 10.1515/mr-2023-0064] [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: 12/04/2023] [Accepted: 03/08/2024] [Indexed: 06/27/2024]
Abstract
Mammalian lung development starts from a specific cluster of endodermal cells situated within the ventral foregut region. With the orchestrating of delicate choreography of transcription factors, signaling pathways, and cell-cell communications, the endodermal diverticulum extends into the surrounding mesenchyme, and builds the cellular and structural basis of the complex respiratory system. This review provides a comprehensive overview of the current molecular insights of mammalian lung development, with a particular focus on the early stage of lung cell fate differentiation and spatial patterning. Furthermore, we explore the implications of several congenital respiratory diseases and the relevance to early organogenesis. Finally, we summarize the unprecedented knowledge concerning lung cell compositions, regulatory networks as well as the promising prospect for gaining an unbiased understanding of lung development and lung malformations through state-of-the-art single-cell omics.
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Affiliation(s)
- Xianfa Yang
- Guangzhou National Laboratory, Guangzhou, Guangdong Province, China
| | - Yingying Chen
- Guangzhou National Laboratory, Guangzhou, Guangdong Province, China
| | - Yun Yang
- Guangzhou National Laboratory, Guangzhou, Guangdong Province, China
- Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Shiting Li
- Guangzhou National Laboratory, Guangzhou, Guangdong Province, China
- Institute of Biomedical Research, Yunnan University, Kunming, Yunnan Province, China
| | - Panpan Mi
- Guangzhou National Laboratory, Guangzhou, Guangdong Province, China
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong Province, China
| | - Naihe Jing
- Guangzhou National Laboratory, Guangzhou, Guangdong Province, China
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4
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Batki J, Hetzel S, Schifferl D, Bolondi A, Walther M, Wittler L, Grosswendt S, Herrmann BG, Meissner A. Extraembryonic gut endoderm cells undergo programmed cell death during development. Nat Cell Biol 2024; 26:868-877. [PMID: 38849542 PMCID: PMC11178501 DOI: 10.1038/s41556-024-01431-w] [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: 03/02/2023] [Accepted: 04/29/2024] [Indexed: 06/09/2024]
Abstract
Despite a distinct developmental origin, extraembryonic cells in mice contribute to gut endoderm and converge to transcriptionally resemble their embryonic counterparts. Notably, all extraembryonic progenitors share a non-canonical epigenome, raising several pertinent questions, including whether this landscape is reset to match the embryonic regulation and if extraembryonic cells persist into later development. Here we developed a two-colour lineage-tracing strategy to track and isolate extraembryonic cells over time. We find that extraembryonic gut cells display substantial memory of their developmental origin including retention of the original DNA methylation landscape and resulting transcriptional signatures. Furthermore, we show that extraembryonic gut cells undergo programmed cell death and neighbouring embryonic cells clear their remnants via non-professional phagocytosis. By midgestation, we no longer detect extraembryonic cells in the wild-type gut, whereas they persist and differentiate further in p53-mutant embryos. Our study provides key insights into the molecular and developmental fate of extraembryonic cells inside the embryo.
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Affiliation(s)
- Julia Batki
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Sara Hetzel
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Dennis Schifferl
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Adriano Bolondi
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Maria Walther
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Lars Wittler
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Stefanie Grosswendt
- Berlin Institute of Health (BIH), Charité - Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Bernhard G Herrmann
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Medical Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Alexander Meissner
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany.
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany.
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5
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Sadeghirad H, Yaghoubi Naei V, O'Byrne K, Warkiani ME, Kulasinghe A. In situ characterization of the tumor microenvironment. Curr Opin Biotechnol 2024; 86:103083. [PMID: 38382325 DOI: 10.1016/j.copbio.2024.103083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 12/07/2023] [Accepted: 01/30/2024] [Indexed: 02/23/2024]
Abstract
The development of new therapies for cancer is underpinned by an increasing need to comprehensively characterize the tumor microenvironment (TME). While traditional approaches have relied on bulk or single-cell approaches, these are limited in their ability to provide cellular context. Deconvolution of the complex TME is fundamental to understanding tumor dynamics and treatment resistance. Spatially resolved characterization of the TME is likely to provide greater insights into the cellular architecture, tumor-immune cell interactions, receptor-ligand interactions, and cell niches. In turn, these aid in dictating the optimal way in which to target each patient's individual cancer. In this review, we discuss a number of cutting-edge in situ spatial profiling methods giving us new insights into tumor biology.
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Affiliation(s)
- Habib Sadeghirad
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Vahid Yaghoubi Naei
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia; School of Biomedical Engineering, University of Technology Sydney, NSW, Australia
| | - Ken O'Byrne
- Princess Alexandra Hospital, Woolloongabba, QLD, Australia
| | - Majid E Warkiani
- School of Biomedical Engineering, University of Technology Sydney, NSW, Australia
| | - Arutha Kulasinghe
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia.
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6
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Perera M, Brickman JM. In vitro models of human hypoblast and mouse primitive endoderm. Curr Opin Genet Dev 2023; 83:102115. [PMID: 37783145 DOI: 10.1016/j.gde.2023.102115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 07/28/2023] [Accepted: 08/24/2023] [Indexed: 10/04/2023]
Abstract
The primitive endoderm (PrE, also named hypoblast), a predominantly extraembryonic epithelium that arises from the inner cell mass (ICM) of the mammalian pre-implantation blastocyst, plays a fundamental role in embryonic development, giving rise to the yolk sac, establishing the anterior-posterior axis and contributing to the gut. PrE is specified from the ICM at the same time as the epiblast (Epi) that will form the embryo proper. While in vitro cell lines resembling the pluripotent Epi have been derived from a variety of conditions, only one model system currently exists for the PrE, naïve extraembryonic endoderm (nEnd). As a result, considerably more is known about the gene regulatory networks and signalling requirements of pluripotent stem cells than nEnd. In this review, we describe the ontogeny and differentiation of the PrE or hypoblast in mouse and primate and then discuss in vitro cell culture models for different extraembryonic endodermal cell types.
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Affiliation(s)
- Marta Perera
- reNEW UCPH - The Novo Nordisk Foundation Center for Stem Cell Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark. https://twitter.com/@MartaPrera
| | - Joshua M Brickman
- reNEW UCPH - The Novo Nordisk Foundation Center for Stem Cell Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N, Denmark.
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7
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Knudsen TE, Hamilton WB, Proks M, Lykkegaard M, Linneberg-Agerholm M, Nielsen AV, Perera M, Malzard LL, Trusina A, Brickman JM. A bipartite function of ESRRB can integrate signaling over time to balance self-renewal and differentiation. Cell Syst 2023; 14:788-805.e8. [PMID: 37633265 DOI: 10.1016/j.cels.2023.07.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 03/22/2023] [Accepted: 07/28/2023] [Indexed: 08/28/2023]
Abstract
Cooperative DNA binding of transcription factors (TFs) integrates the cellular context to support cell specification during development. Naive mouse embryonic stem cells are derived from early development and can sustain their pluripotent identity indefinitely. Here, we ask whether TFs associated with pluripotency evolved to directly support this state or if the state emerges from their combinatorial action. NANOG and ESRRB are key pluripotency factors that co-bind DNA. We find that when both factors are expressed, ESRRB supports pluripotency. However, when NANOG is absent, ESRRB supports a bistable culture of cells with an embryo-like primitive endoderm identity ancillary to pluripotency. The stoichiometry between NANOG and ESRRB allows quantitative titration of this differentiation, and in silico modeling of bipartite ESRRB activity suggests it safeguards plasticity in differentiation. Thus, the concerted activity of cooperative TFs can transform their effect to sustain intermediate cell identities and allow ex vivo expansion of immortal stem cells. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Teresa E Knudsen
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
| | - William B Hamilton
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark.
| | - Martin Proks
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
| | - Maria Lykkegaard
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
| | - Madeleine Linneberg-Agerholm
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
| | | | - Marta Perera
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
| | | | - Ala Trusina
- Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - Joshua M Brickman
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark.
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8
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Suppinger S, Zinner M, Aizarani N, Lukonin I, Ortiz R, Azzi C, Stadler MB, Vianello S, Palla G, Kohler H, Mayran A, Lutolf MP, Liberali P. Multimodal characterization of murine gastruloid development. Cell Stem Cell 2023:S1934-5909(23)00170-4. [PMID: 37209681 DOI: 10.1016/j.stem.2023.04.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/16/2023] [Accepted: 04/25/2023] [Indexed: 05/22/2023]
Abstract
Gastruloids are 3D structures generated from pluripotent stem cells recapitulating fundamental principles of embryonic pattern formation. Using single-cell genomic analysis, we provide a resource mapping cell states and types during gastruloid development and compare them with the in vivo embryo. We developed a high-throughput handling and imaging pipeline to spatially monitor symmetry breaking during gastruloid development and report an early spatial variability in pluripotency determining a binary response to Wnt activation. Although cells in the gastruloid-core revert to pluripotency, peripheral cells become primitive streak-like. These two populations subsequently break radial symmetry and initiate axial elongation. By performing a compound screen, perturbing thousands of gastruloids, we derive a phenotypic landscape and infer networks of genetic interactions. Finally, using a dual Wnt modulation, we improve the formation of anterior structures in the existing gastruloid model. This work provides a resource to understand how gastruloids develop and generate complex patterns in vitro.
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Affiliation(s)
- Simon Suppinger
- Friedrich Miescher Institute for Biomedical Research (FMI), 4058 Basel, Switzerland; University of Basel, 4001 Basel, Switzerland
| | - Marietta Zinner
- Friedrich Miescher Institute for Biomedical Research (FMI), 4058 Basel, Switzerland
| | - Nadim Aizarani
- Friedrich Miescher Institute for Biomedical Research (FMI), 4058 Basel, Switzerland
| | - Ilya Lukonin
- Friedrich Miescher Institute for Biomedical Research (FMI), 4058 Basel, Switzerland; Roche Institute of Human Biology, 4058 Basel, Switzerland
| | - Raphael Ortiz
- Friedrich Miescher Institute for Biomedical Research (FMI), 4058 Basel, Switzerland
| | - Chiara Azzi
- Friedrich Miescher Institute for Biomedical Research (FMI), 4058 Basel, Switzerland; Babraham Institute, Cambridge CB22 3AT, UK
| | - Michael B Stadler
- Friedrich Miescher Institute for Biomedical Research (FMI), 4058 Basel, Switzerland; University of Basel, 4001 Basel, Switzerland; Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - Stefano Vianello
- School of Life Sciences, Federal Institute of Technology EPFL, 1015 Lausanne, Switzerland
| | - Giovanni Palla
- Institute of Computational Biology, Helmholtz Center Munich, 85764 Munich, Germany; TUM School of Life Sciences Weihenstephan, Technical University of Munich, 80333 Munich, Germany
| | - Hubertus Kohler
- Friedrich Miescher Institute for Biomedical Research (FMI), 4058 Basel, Switzerland
| | - Alexandre Mayran
- School of Life Sciences, Federal Institute of Technology EPFL, 1015 Lausanne, Switzerland
| | - Matthias P Lutolf
- Roche Institute of Human Biology, 4058 Basel, Switzerland; School of Life Sciences, Federal Institute of Technology EPFL, 1015 Lausanne, Switzerland
| | - Prisca Liberali
- Friedrich Miescher Institute for Biomedical Research (FMI), 4058 Basel, Switzerland; University of Basel, 4001 Basel, Switzerland.
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9
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Wong YF, Kumar Y, Proks M, Herrera JAR, Rothová MM, Monteiro RS, Pozzi S, Jennings RE, Hanley NA, Bickmore WA, Brickman JM. Expansion of ventral foregut is linked to changes in the enhancer landscape for organ-specific differentiation. Nat Cell Biol 2023; 25:481-492. [PMID: 36690849 PMCID: PMC10014581 DOI: 10.1038/s41556-022-01075-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 12/14/2022] [Indexed: 01/24/2023]
Abstract
Cell proliferation is fundamental for almost all stages of development and differentiation that require an increase in cell number. Although cell cycle phase has been associated with differentiation, the actual process of proliferation has not been considered as having a specific role. Here we exploit human embryonic stem cell-derived endodermal progenitors that we find are an in vitro model for the ventral foregut. These cells exhibit expansion-dependent increases in differentiation efficiency to pancreatic progenitors that are linked to organ-specific enhancer priming at the level of chromatin accessibility and the decommissioning of lineage-inappropriate enhancers. Our findings suggest that cell proliferation in embryonic development is about more than tissue expansion; it is required to ensure equilibration of gene regulatory networks allowing cells to become primed for future differentiation. Expansion of lineage-specific intermediates may therefore be an important step in achieving high-fidelity in vitro differentiation.
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Affiliation(s)
- Yan Fung Wong
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
| | - Yatendra Kumar
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Martin Proks
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
| | - Jose Alejandro Romero Herrera
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
- Center for Health Data Science, University of Copenhagen, Copenhagen, Denmark
| | - Michaela Mrugala Rothová
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
| | - Rita S Monteiro
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
| | - Sara Pozzi
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
| | - Rachel E Jennings
- Faculty of Biology, Medicine & Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Neil A Hanley
- Faculty of Biology, Medicine & Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
| | - Joshua M Brickman
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark.
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10
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Perera M, Nissen SB, Proks M, Pozzi S, Monteiro RS, Trusina A, Brickman JM. Transcriptional heterogeneity and cell cycle regulation as central determinants of primitive endoderm priming. eLife 2022; 11:78967. [PMID: 35969041 PMCID: PMC9417417 DOI: 10.7554/elife.78967] [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: 03/25/2022] [Accepted: 08/12/2022] [Indexed: 11/16/2022] Open
Abstract
During embryonic development cells acquire identity as they proliferate, implying that an intrinsic facet of cell fate choice requires coupling lineage decisions to cell division. How is the cell cycle regulated to promote or suppress heterogeneity and differentiation? We explore this question combining time lapse imaging with single-cell RNA-seq in the contexts of self-renewal, priming, and differentiation of mouse embryonic stem cells (ESCs) towards the Primitive Endoderm (PrE) lineage. Since ESCs are derived from the inner cell mass (ICM) of the mammalian blastocyst, ESCs in standard culture conditions are transcriptionally heterogeneous containing dynamically interconverting subfractions primed for either of the two ICM lineages, Epiblast and PrE. Here, we find that differential regulation of cell cycle can tip the balance between these primed populations, such that naïve ESC culture promotes Epiblast-like expansion and PrE differentiation stimulates the selective survival and proliferation of PrE-primed cells. In endoderm differentiation, this change is accompanied by a counter-intuitive increase in G1 length, also observed in vivo. While fibroblast growth factor/extracellular signal-regulated kinase (FGF/ERK) signalling is a key regulator of ESC differentiation and PrE specification, we find it is not just responsible for ESCs heterogeneity, but also the inheritance of similar cell cycles between sisters and cousins. Taken together, our results indicate a tight relationship between transcriptional heterogeneity and cell cycle regulation in lineage specification, with primed cell populations providing a pool of flexible cell types that can be expanded in a lineage-specific fashion while allowing plasticity during early determination.
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Affiliation(s)
- Marta Perera
- The Novo Nordisk Foundation Center for Stem Cell Medicine, University of Copenhagen, Copenhagen, Denmark
| | | | - Martin Proks
- The Novo Nordisk Foundation Center for Stem Cell Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Sara Pozzi
- The Novo Nordisk Foundation Center for Stem Cell Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Rita Soares Monteiro
- The Novo Nordisk Foundation Center for Stem Cell Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Ala Trusina
- Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - Joshua M Brickman
- The Novo Nordisk Foundation Center for Stem Cell Medicine, University of Copenhagen, Copenhagen, Denmark
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