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; 187:4010-4029.e16. [PMID: 38917790 PMCID: PMC11290322 DOI: 10.1016/j.cell.2024.05.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [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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Reprogramming of fibroblast cells to totipotent state by DNA demethylation. Sci Rep 2023; 13:1154. [PMID: 36670207 PMCID: PMC9859804 DOI: 10.1038/s41598-023-28457-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 01/18/2023] [Indexed: 01/22/2023] Open
Abstract
Many attempts have been made to induce high-quality embryonic stem cells such as pluripotent stem cells and totipotent stem cells, but challenges remain to be overcome such as appropriate methods and sources. Demethylation of the genome after fertilization is an important step to initiate zygote gene activation, which can lead to the development of new embryos. Here, we tried to induce totipotent stem cells by mimicking DNA demethylation patterns of the embryo. Our data showed, after induction of DNA demethylation via chemicals or knockdown of Dnmts, cells positive for Nanog, and Cdx2 emerged. These cells could differentiate into the pluripotent and trophoblast lineage cells in-vitro. After transferring these cells to the uterus, they can implant and form embryo-like structures. Our study showed the importance of DNA demethylation roles in totipotent stem cell induction and a new and easy way to induce this cell type.
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3
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Comparative Analyses of Single-Cell Transcriptomic Profiles between In Vitro Totipotent Blastomere-like Cells and In Vivo Early Mouse Embryonic Cells. Cells 2021; 10:cells10113111. [PMID: 34831338 PMCID: PMC8621967 DOI: 10.3390/cells10113111] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/25/2021] [Accepted: 11/06/2021] [Indexed: 01/23/2023] Open
Abstract
The developmental potential within pluripotent cells in the canonical model is restricted to embryonic tissues, whereas totipotent cells can differentiate into both embryonic and extraembryonic tissues. Currently, the ability to culture in vitro totipotent cells possessing molecular and functional features like those of an early embryo in vivo has been a challenge. Recently, it was reported that treatment with a single spliceosome inhibitor, pladienolide B (plaB), can successfully reprogram mouse pluripotent stem cells into totipotent blastomere-like cells (TBLCs) in vitro. The TBLCs exhibited totipotency transcriptionally and acquired expanded developmental potential with the ability to yield various embryonic and extraembryonic tissues that may be employed as novel mouse developmental cell models. However, it is disputed whether TBLCs are ‘true’ totipotent stem cells equivalent to in vivo two-cell stage embryos. To address this question, single-cell RNA sequencing was applied to TBLCs and cells from early mouse embryonic developmental stages and the data were integrated using canonical correlation analyses. Differential expression analyses were performed between TBLCs and multi-embryonic cell stages to identify differentially expressed genes. Remarkably, a subpopulation within the TBLCs population expressed a high level of the totipotent-related genes Zscan4s and displayed transcriptomic features similar to mouse two-cell stage embryonic cells. This study underscores the subtle differences between in vitro derived TBLCs and in vivo mouse early developmental cell stages at the single-cell transcriptomic level. Our study has identified a new experimental model for stem cell biology, namely ‘cluster 3’, as a subpopulation of TBLCs that can be molecularly defined as near totipotent cells.
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4
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Prenatal and postnatal MRI imaging findings of intracranial parasitic fetus: a case report. Childs Nerv Syst 2021; 37:1803-1806. [PMID: 32968878 DOI: 10.1007/s00381-020-04891-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 09/16/2020] [Indexed: 12/16/2022]
Abstract
Fetus in fetu (FIF) is an extremely rare anomaly. It is predominantly seen retroperitoneally in 80% of cases but can present at atypical sites like the skull, sacrum, scrotum and the mouth. We reported a rare case of intracranial parasitic fetus. We described the prenatal and postnatal MRI findings of the case. There was no obvious spinal signal on the imaging findings at 35 weeks of gestation. However, the postnatal MRI revealed spinal column signal at 5 months and 11 days.
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5
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Dirks RAM, Thomas PC, Wu H, Jones RC, Stunnenberg HG, Marks H. A plug and play microfluidic platform for standardized sensitive low-input chromatin immunoprecipitation. Genome Res 2021; 31:919-933. [PMID: 33707229 PMCID: PMC8092002 DOI: 10.1101/gr.260745.120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 02/22/2021] [Indexed: 11/24/2022]
Abstract
Epigenetic profiling by chromatin immunoprecipitation followed by sequencing (ChIP-seq) has become a powerful tool for genome-wide identification of regulatory elements, for defining transcriptional regulatory networks, and for screening for biomarkers. However, the ChIP-seq protocol for low-input samples is laborious and time-consuming and suffers from experimental variation, resulting in poor reproducibility and low throughput. Although prototypic microfluidic ChIP-seq platforms have been developed, these are poorly transferable as they require sophisticated custom-made equipment and in-depth microfluidic and ChIP expertise, while lacking parallelization. To enable standardized, automated ChIP-seq profiling of low-input samples, we constructed microfluidic PDMS-based plates capable of performing 24 sensitive ChIP reactions within 30 min of hands-on time and 4.5 h of machine-running time. These disposable plates can be conveniently loaded into a widely available controller for pneumatics and thermocycling. In light of the plug and play (PnP) ChIP plates and workflow, we named our procedure PnP-ChIP-seq. We show high-quality ChIP-seq on hundreds to a few thousand of cells for all six post-translational histone modifications that are included in the International Human Epigenome Consortium set of reference epigenomes. PnP-ChIP-seq robustly detects epigenetic differences on promoters and enhancers between naive and more primed mouse embryonic stem cells (mESCs). Furthermore, we used our platform to generate epigenetic profiles of rare subpopulations of mESCs that resemble the two-cell stage of embryonic development. PnP-ChIP-seq allows nonexpert laboratories worldwide to conveniently run robust, standardized ChIP-seq, whereas its high throughput, consistency, and sensitivity pave the way toward large-scale profiling of precious sample types such as rare subpopulations of cells or biopsies.
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Affiliation(s)
- René A M Dirks
- Department of Molecular Biology, Faculty of Science, Radboud University, Radboud Institute for Molecular Life Sciences (RIMLS), 6525GA Nijmegen, the Netherlands
| | - Peter C Thomas
- Fluidigm Corporation, South San Francisco, California 94080, USA
| | - Haoyu Wu
- Department of Molecular Biology, Faculty of Science, Radboud University, Radboud Institute for Molecular Life Sciences (RIMLS), 6525GA Nijmegen, the Netherlands
| | - Robert C Jones
- Fluidigm Corporation, South San Francisco, California 94080, USA
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Faculty of Science, Radboud University, Radboud Institute for Molecular Life Sciences (RIMLS), 6525GA Nijmegen, the Netherlands
| | - Hendrik Marks
- Department of Molecular Biology, Faculty of Science, Radboud University, Radboud Institute for Molecular Life Sciences (RIMLS), 6525GA Nijmegen, the Netherlands
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6
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Riveiro AR, Brickman JM. From pluripotency to totipotency: an experimentalist's guide to cellular potency. Development 2020; 147:147/16/dev189845. [PMID: 32847824 DOI: 10.1242/dev.189845] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 07/16/2020] [Indexed: 12/12/2022]
Abstract
Embryonic stem cells (ESCs) are derived from the pre-implantation mammalian blastocyst. At this point in time, the newly formed embryo is concerned with the generation and expansion of both the embryonic lineages required to build the embryo and the extra-embryonic lineages that support development. When used in grafting experiments, embryonic cells from early developmental stages can contribute to both embryonic and extra-embryonic lineages, but it is generally accepted that ESCs can give rise to only embryonic lineages. As a result, they are referred to as pluripotent, rather than totipotent. Here, we consider the experimental potential of various ESC populations and a number of recently identified in vitro culture systems producing states beyond pluripotency and reminiscent of those observed during pre-implantation development. We also consider the nature of totipotency and the extent to which cell populations in these culture systems exhibit this property.
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Affiliation(s)
- Alba Redó Riveiro
- Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen N, Denmark
| | - Joshua Mark Brickman
- Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen N, Denmark
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7
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Genet M, Torres-Padilla ME. The molecular and cellular features of 2-cell-like cells: a reference guide. Development 2020; 147:147/16/dev189688. [PMID: 32847823 DOI: 10.1242/dev.189688] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Currently, two main cell culture models predominate pluripotent stem cell research: embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs). Thanks to their ability to contribute to and form all tissues within the body, ESCs and iPSCs have proven invaluable in understanding pluripotent states, early embryonic development and cell differentiation, as well as in devising strategies for regenerative medicine. Comparatively little is known about totipotency - a cellular state with greater developmental potential. In mice, only the zygote and the blastomeres of the 2-cell-stage embryo are truly totipotent, as they alone can develop to form the embryo and all of its supportive extra-embryonic tissues. However, the discovery of a rare subpopulation of cells in murine ESC cultures, possessing features of 2-cell embryo blastomeres and expanded cell fate potential, has provided a biochemically tractable model to enable the in vitro study of totipotency. Here, we summarize current known features of these 2-cell-like cells (2CLCs) in an effort to provide a reference for the community, and to clarify what we know about their identity so far.
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Affiliation(s)
- Marion Genet
- Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum München, D-81377, Germany
| | - Maria-Elena Torres-Padilla
- Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum München, D-81377, Germany .,Faculty of Biology, Ludwig-Maximilians Universität, 82152 Martinsried, Germany
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8
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Hu K. On Mammalian Totipotency: What Is the Molecular Underpinning for the Totipotency of Zygote? Stem Cells Dev 2020; 28:897-906. [PMID: 31122174 PMCID: PMC6648208 DOI: 10.1089/scd.2019.0057] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The mammalian zygote is described as a totipotent cell in the literature, but this characterization is elusive ignoring the molecular underpinnings. Totipotency can connote genetic totipotency, epigenetic totipotency, or the reprogramming capacity of a cell to epigenetic totipotency. Here, the implications of these concepts are discussed in the context of the properties of the zygote. Although genetically totipotent as any diploid somatic cell is, a zygote seems not totipotent transcriptionally, epigenetically, or functionally. Yet, a zygote may retain most of the key factors from its parental oocyte to reprogram an implanted differentiated genome or the zygote genome toward totipotency. This totipotent reprogramming process may extend to blastomeres in the two-cell-stage embryo. Thus, a revised alternative model of mammalian cellular totipotency is proposed, in which an epigenetically totipotent cell exists after the major embryonic genome activation and before the separation of the first two embryonic lineages.
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Affiliation(s)
- Kejin Hu
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama
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9
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Rothman J, Jarriault S. Developmental Plasticity and Cellular Reprogramming in Caenorhabditis elegans. Genetics 2019; 213:723-757. [PMID: 31685551 PMCID: PMC6827377 DOI: 10.1534/genetics.119.302333] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 07/25/2019] [Indexed: 12/28/2022] Open
Abstract
While Caenorhabditis elegans was originally regarded as a model for investigating determinate developmental programs, landmark studies have subsequently shown that the largely invariant pattern of development in the animal does not reflect irreversibility in rigidly fixed cell fates. Rather, cells at all stages of development, in both the soma and germline, have been shown to be capable of changing their fates through mutation or forced expression of fate-determining factors, as well as during the normal course of development. In this chapter, we review the basis for natural and induced cellular plasticity in C. elegans We describe the events that progressively restrict cellular differentiation during embryogenesis, starting with the multipotency-to-commitment transition (MCT) and subsequently through postembryonic development of the animal, and consider the range of molecular processes, including transcriptional and translational control systems, that contribute to cellular plasticity. These findings in the worm are discussed in the context of both classical and recent studies of cellular plasticity in vertebrate systems.
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Affiliation(s)
- Joel Rothman
- Department of MCD Biology and Neuroscience Research Institute, University of California, Santa Barbara, California 93111, and
| | - Sophie Jarriault
- IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), Department of Development and Stem Cells, CNRS UMR7104, Inserm U1258, Université de Strasbourg, 67404 Illkirch CU Strasbourg, France
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10
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Piechowski J. Plausibility of trophoblastic-like regulation of cancer tissue. Cancer Manag Res 2019; 11:5033-5046. [PMID: 31213916 PMCID: PMC6549421 DOI: 10.2147/cmar.s190932] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 04/30/2019] [Indexed: 01/15/2023] Open
Abstract
Background: Thus far, a well-established logical pattern of malignancy does not exist. The current approach to cancer properties is primarily descriptive with usually, for each of them, extensive analyses of the underlying associated biomolecular mechanisms. However, this remains a catalog and it would be valuable to determine the organizational chart that could account for their implementation, hierarchical links and input into tumor regulation. Hypothesis: Striking phenotypic similarities exist between trophoblast (invasive and expanding early placenta) and cancer regarding cell functions, logistics of development, means of protection and capacity to hold sway over the host organism. The concept of cancer cell trophoblastic-like transdifferentiation appears to be a rational proposal in an attempt to explain this analogy and provide a consistent insight into how cancer cells are functioning. Should this concept be validated, it could pave the way to promising research and therapeutic perspectives given that the trophoblastic properties are vital for the tumor while they are permanently epigenetically turned off in normal cells. Specifically targeting expression of the trophoblastic master genes could thereby be envisaged to jeopardize the tumor and its metastases without, in principle, inducing adverse side effects in the healthy tissues. Conclusion: A wide set of functional features of cancer tissue regulation, including some apparently paradoxical facts, was reviewed. Cancer cell misuse of physiological trophoblastic functions can clearly account for them, which identifies trophoblastic-like transdifferentiation as a likely key component of malignancy and makes it a potential relevant anticancer target.
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11
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Suman S, Domingues A, Ratajczak J, Ratajczak MZ. Potential Clinical Applications of Stem Cells in Regenerative Medicine. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1201:1-22. [PMID: 31898779 DOI: 10.1007/978-3-030-31206-0_1] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The field of regenerative medicine is looking for a pluripotent/multipotent stem cell able to differentiate across germ layers and be safely employed in therapy. Unfortunately, with the exception of hematopoietic stem/progenitor cells (HSPCs) for hematological applications, the current clinical results with stem cells are somewhat disappointing. The potential clinical applications of the more primitive embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) have so far been discouraging, as both have exhibited several problems, including genomic instability, a risk of teratoma formation, and the possibility of rejection. Therefore, the only safe stem cells that have so far been employed in regenerative medicine are monopotent stem cells, such as the abovementioned HSPCs or mesenchymal stem cells (MSCs) isolated from postnatal tissues. However, their monopotency, and therefore limited differentiation potential, is a barrier to their broader application in the clinic. Interestingly, results have accumulated indicating that adult tissues contain rare, early-development stem cells known as very small embryonic-like stem cells (VSELs), which can differentiate into cells from more than one germ layer. This chapter addresses different sources of stem cells for potential clinical application and their advantages and problems to be solved.
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Affiliation(s)
- Suman Suman
- Stem Cell Institute at James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA
| | - Alison Domingues
- Stem Cell Institute at James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA
| | - Janina Ratajczak
- Stem Cell Institute at James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA
| | - Mariusz Z Ratajczak
- Stem Cell Institute at James Graham Brown Cancer Center, University of Louisville, Louisville, KY, USA. .,Department of Regenerative Medicine, Center for Preclinical Research and Technology, Warsaw Medical University, Warsaw, Poland.
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12
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Rothová M, Hölzenspies JJ, Livigni A, Villegas SN, Brickman JM. Differentiation of Mouse Embryonic Stem Cells into Ventral Foregut Precursors. ACTA ACUST UNITED AC 2018; 36:1G.3.1-1G.3.12. [DOI: 10.1002/9780470151808.sc01g03s36] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
| | | | - Alessandra Livigni
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, University of Edinburgh Edinburgh United Kingdom
| | - Santiago Nahuel Villegas
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, University of Edinburgh Edinburgh United Kingdom
- Instituto de Neurociencias, Consejo Superior de Investigaciones Cientificas, Universidad Miguel Hernandez de Elche Alicante Spain
| | - Joshua M. Brickman
- Centre (DanStem), University of Copenhagen Copenhagen Denmark
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, University of Edinburgh Edinburgh United Kingdom
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13
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Dynamics of lineage commitment revealed by single-cell transcriptomics of differentiating embryonic stem cells. Nat Commun 2017; 8:1096. [PMID: 29061959 PMCID: PMC5653659 DOI: 10.1038/s41467-017-01076-4] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 08/15/2017] [Indexed: 01/01/2023] Open
Abstract
Gene expression heterogeneity in the pluripotent state of mouse
embryonic stem cells (mESCs) has been increasingly well-characterized. In contrast,
exit from pluripotency and lineage commitment have not been studied systematically
at the single-cell level. Here we measure the gene expression dynamics of retinoic
acid driven mESC differentiation from pluripotency to lineage commitment, using an
unbiased single-cell transcriptomics approach. We find that the exit from
pluripotency marks the start of a lineage transition as well as a transient phase of
increased susceptibility to lineage specifying signals. Our study reveals several
transcriptional signatures of this phase, including a sharp increase of gene
expression variability and sequential expression of two classes of transcriptional
regulators. In summary, we provide a comprehensive analysis of the exit from
pluripotency and lineage commitment at the single cell level, a potential stepping
stone to improved lineage manipulation through timing of differentiation
cues. Commitment to different fates by differentiating pluripotent cells
depends upon integration of external and internal signals. Here the authors analyse
the entry of mouse embryonic stem cells into retinoic acid-mediated differentiation
using single cell transcriptomics with high temporal resolution.
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14
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Anderson KGV, Hamilton WB, Roske FV, Azad A, Knudsen TE, Canham M, Forrester LM, Brickman JM. Insulin fine-tunes self-renewal pathways governing naive pluripotency and extra-embryonic endoderm. Nat Cell Biol 2017; 19:1164-1177. [DOI: 10.1038/ncb3617] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 08/17/2017] [Indexed: 12/16/2022]
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15
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Hendrickson PG, Doráis JA, Grow EJ, Whiddon JL, Lim JW, Wike CL, Weaver BD, Pflueger C, Emery BR, Wilcox AL, Nix DA, Peterson CM, Tapscott SJ, Carrell DT, Cairns BR. Conserved roles of mouse DUX and human DUX4 in activating cleavage-stage genes and MERVL/HERVL retrotransposons. Nat Genet 2017; 49:925-934. [PMID: 28459457 PMCID: PMC5703070 DOI: 10.1038/ng.3844] [Citation(s) in RCA: 473] [Impact Index Per Article: 67.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 03/21/2017] [Indexed: 12/13/2022]
Abstract
To better understand transcriptional regulation during human oogenesis and pre-implantation development, we defined stage-specific transcription, which revealed the cleavage stage as highly distinctive. Here, we present multiple lines of evidence that a eutherian-specific, multi-copy retrogene, DUX4, encodes a transcription factor which activates hundreds of endogenous genes (e.g. ZSCAN4, ZFP352, KDM4E) and retroviral elements (MERVL/HERVL-family) that defines the cleavage-specific transcriptional programs in mouse and human. Remarkably, mouse Dux expression is both necessary and sufficient to convert mouse embryonic stem cells into two-cell embryo-like (‘2C-like’) cells, measured here by the reactivation of ‘2C’ genes and repeat elements, the loss of POU5F1 protein and chromocenters, and by the conversion of the chromatin landscape (assessed by ATAC-seq) to a state strongly resembling mouse two-cell embryos. Taken together, we propose mouse DUX and human DUX4 as major drivers of the cleavage/‘2C’ state.
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Affiliation(s)
- Peter G Hendrickson
- Department of Oncological Sciences, Huntsman Cancer Institute and Howard Hughes Medical Institute, Salt Lake City, Utah, USA
| | - Jessie A Doráis
- Department of Oncological Sciences, Huntsman Cancer Institute and Howard Hughes Medical Institute, Salt Lake City, Utah, USA.,Departments of Obstetrics and Gynecology, and Surgery, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Edward J Grow
- Department of Oncological Sciences, Huntsman Cancer Institute and Howard Hughes Medical Institute, Salt Lake City, Utah, USA
| | - Jennifer L Whiddon
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Jong-Won Lim
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Candice L Wike
- Department of Oncological Sciences, Huntsman Cancer Institute and Howard Hughes Medical Institute, Salt Lake City, Utah, USA
| | - Bradley D Weaver
- Department of Oncological Sciences, Huntsman Cancer Institute and Howard Hughes Medical Institute, Salt Lake City, Utah, USA
| | - Christian Pflueger
- Department of Oncological Sciences, Huntsman Cancer Institute and Howard Hughes Medical Institute, Salt Lake City, Utah, USA
| | - Benjamin R Emery
- Departments of Obstetrics and Gynecology, and Surgery, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Aaron L Wilcox
- Departments of Obstetrics and Gynecology, and Surgery, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - David A Nix
- Department of Oncological Sciences, Huntsman Cancer Institute and Howard Hughes Medical Institute, Salt Lake City, Utah, USA
| | - C Matthew Peterson
- Departments of Obstetrics and Gynecology, and Surgery, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Stephen J Tapscott
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Douglas T Carrell
- Departments of Obstetrics and Gynecology, and Surgery, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Bradley R Cairns
- Department of Oncological Sciences, Huntsman Cancer Institute and Howard Hughes Medical Institute, Salt Lake City, Utah, USA
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16
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Hagiwara-Chatani N, Shirai K, Kido T, Horigome T, Yasue A, Adachi N, Hirai Y. Membrane translocation of t-SNARE protein syntaxin-4 abrogates ground-state pluripotency in mouse embryonic stem cells. Sci Rep 2017; 7:39868. [PMID: 28057922 PMCID: PMC5216394 DOI: 10.1038/srep39868] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 11/28/2016] [Indexed: 02/08/2023] Open
Abstract
Embryonic stem (ES) and induced pluripotent stem (iPS) cells are attractive tools for regenerative medicine therapies. However, aberrant cell populations that display flattened morphology and lose ground-state pluripotency often appear spontaneously, unless glycogen synthase kinase 3β (GSK3β) and mitogen-activated protein kinase kinase (MEK1/2) are inactivated. Here, we show that membrane translocation of the t-SNARE protein syntaxin-4 possibly is involved in this phenomenon. We found that mouse ES cells cultured without GSK3β/MEK1/2 inhibitors (2i) spontaneously extrude syntaxin-4 at the cell surface and that artificial expression of cell surface syntaxin-4 induces appreciable morphological changes and mesodermal differentiation through dephosphorylation of Akt. Transcriptome analyses revealed several candidate elements responsible for this, specifically, an E-to P-cadherin switch and a marked downregulation of Zscan4 proteins, which are DNA-binding proteins essential for ES cell pluripotency. Embryonic carcinoma cell lines F9 and P19CL6, which maintain undifferentiated states independently of Zscan4 proteins, exhibited similar cellular behaviors upon stimulation with cell surface syntaxin-4. The functional ablation of E-cadherin and overexpression of P-cadherin reproduced syntaxin-4-induced cell morphology, demonstrating that the E- to P-cadherin switch executes morphological signals from cell surface syntaxin-4. Thus, spontaneous membrane translocation of syntaxin-4 emerged as a critical element for maintenance of the stem-cell niche.
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Affiliation(s)
- Natsumi Hagiwara-Chatani
- Department of Biomedical Chemistry, Graduate School of Science and Technology, Kwansei Gakuin University, Sanda, Japan
| | - Kota Shirai
- Department of Biomedical Chemistry, Graduate School of Science and Technology, Kwansei Gakuin University, Sanda, Japan
| | - Takumi Kido
- Department of Biomedical Chemistry, Graduate School of Science and Technology, Kwansei Gakuin University, Sanda, Japan
| | - Tomoatsu Horigome
- Department of Biomedical Chemistry, Graduate School of Science and Technology, Kwansei Gakuin University, Sanda, Japan
| | - Akihiro Yasue
- Department of Orthodontics and Dentofacial Orthopedics, Institute of Health Biosciences, The University of Tokushima, Tokushima, Japan
| | - Naoki Adachi
- Department of Biomedical Chemistry, Graduate School of Science and Technology, Kwansei Gakuin University, Sanda, Japan
| | - Yohei Hirai
- Department of Biomedical Chemistry, Graduate School of Science and Technology, Kwansei Gakuin University, Sanda, Japan
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17
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Davis TL, Rebay I. Master regulators in development: Views from the Drosophila retinal determination and mammalian pluripotency gene networks. Dev Biol 2016; 421:93-107. [PMID: 27979656 DOI: 10.1016/j.ydbio.2016.12.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 12/03/2016] [Accepted: 12/03/2016] [Indexed: 02/07/2023]
Abstract
Among the mechanisms that steer cells to their correct fate during development, master regulatory networks are unique in their sufficiency to trigger a developmental program outside of its normal context. In this review we discuss the key features that underlie master regulatory potency during normal and ectopic development, focusing on two examples, the retinal determination gene network (RDGN) that directs eye development in the fruit fly and the pluripotency gene network (PGN) that maintains cell fate competency in the early mammalian embryo. In addition to the hierarchical transcriptional activation, extensive positive transcriptional feedback, and cooperative protein-protein interactions that enable master regulators to override competing cellular programs, recent evidence suggests that network topology must also be dynamic, with extensive rewiring of the interactions and feedback loops required to navigate the correct sequence of developmental transitions to reach a final fate. By synthesizing the in vivo evidence provided by the RDGN with the extensive mechanistic insight gleaned from the PGN, we highlight the unique regulatory capabilities that continual reorganization into new hierarchies confers on master control networks. We suggest that deeper understanding of such dynamics should be a priority, as accurate spatiotemporal remodeling of network topology will undoubtedly be essential for successful stem cell based therapeutic efforts.
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Affiliation(s)
- Trevor L Davis
- Committee on Development, Regeneration, and Stem Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - Ilaria Rebay
- Committee on Development, Regeneration, and Stem Cell Biology, University of Chicago, Chicago, IL 60637, USA; Ben May Department for Cancer Research, University of Chicago, Chicago, IL 60637, USA.
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18
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Maeso I, Dunwell TL, Wyatt CDR, Marlétaz F, Vető B, Bernal JA, Quah S, Irimia M, Holland PWH. Evolutionary origin and functional divergence of totipotent cell homeobox genes in eutherian mammals. BMC Biol 2016; 14:45. [PMID: 27296695 PMCID: PMC4904359 DOI: 10.1186/s12915-016-0267-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Accepted: 05/27/2016] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND A central goal of evolutionary biology is to link genomic change to phenotypic evolution. The origin of new transcription factors is a special case of genomic evolution since it brings opportunities for novel regulatory interactions and potentially the emergence of new biological properties. RESULTS We demonstrate that a group of four homeobox gene families (Argfx, Leutx, Dprx, Tprx), plus a gene newly described here (Pargfx), arose by tandem gene duplication from the retinal-expressed Crx gene, followed by asymmetric sequence evolution. We show these genes arose as part of repeated gene gain and loss events on a dynamic chromosomal region in the stem lineage of placental mammals, on the forerunner of human chromosome 19. The human orthologues of these genes are expressed specifically in early embryo totipotent cells, peaking from 8-cell to morula, prior to cell fate restrictions; cow orthologues have similar expression. To examine biological roles, we used ectopic gene expression in cultured human cells followed by high-throughput RNA-seq and uncovered extensive transcriptional remodelling driven by three of the genes. Comparison to transcriptional profiles of early human embryos suggest roles in activating and repressing a set of developmentally-important genes that spike at 8-cell to morula, rather than a general role in genome activation. CONCLUSIONS We conclude that a dynamic chromosome region spawned a set of evolutionarily new homeobox genes, the ETCHbox genes, specifically in eutherian mammals. After these genes diverged from the parental Crx gene, we argue they were recruited for roles in the preimplantation embryo including activation of genes at the 8-cell stage and repression after morula. We propose these new homeobox gene roles permitted fine-tuning of cell fate decisions necessary for specification and function of embryonic and extra-embryonic tissues utilised in mammalian development and pregnancy.
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Affiliation(s)
- Ignacio Maeso
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, 41013, Sevilla, Spain
| | - Thomas L Dunwell
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - Chris D R Wyatt
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Ferdinand Marlétaz
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - Borbála Vető
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Juan A Bernal
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Shan Quah
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - Manuel Irimia
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Peter W H Holland
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK.
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Nicolescu MI. Regenerative Perspective in Modern Dentistry. Dent J (Basel) 2016; 4:dj4020010. [PMID: 29563452 PMCID: PMC5851266 DOI: 10.3390/dj4020010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 04/16/2016] [Accepted: 04/21/2016] [Indexed: 12/02/2022] Open
Abstract
This review aims to trace the contour lines of regenerative dentistry, to offer an introductory overview on this emerging field to both dental students and practitioners. The crystallized depiction of the concept is a translational approach, connecting dental academics to scientific research and clinical utility. Therefore, this review begins by presenting the general features of regenerative medicine, and then gradually introduces the specific aspects of major dental subdomains, highlighting the progress achieved during the last years by scientific research and, in some cases, which has already been translated into clinical results. The distinct characteristics of stem cells and their microenvironment, together with their diversity in the oral cavity, are put into the context of research and clinical use. Examples of regenerative studies regarding endodontic and periodontal compartments, as well as hard (alveolar bone) and soft (salivary glands) related tissues, are presented to make the reader further acquainted with the topic. Instead of providing a conclusion, we will emphasize the importance for all dental community members, from young students to experienced dentists, of an early awareness rising regarding biomedical research progress in general and regenerative dentistry in particular.
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Affiliation(s)
- Mihnea Ioan Nicolescu
- Carol Davila University of Medicine and Pharmacy, Faculty of Dental Medicine, Histology and Cytology Division, Bucharest, 8 Eroilor Sanitari Blvd., RO-050474, Romania.
- Victor Babeș National Institute of Pathology, Radiobiology Laboratory, Bucharest, Romania.
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Semrau S, van Oudenaarden A. Studying Lineage Decision-Making In Vitro: Emerging Concepts and Novel Tools. Annu Rev Cell Dev Biol 2015; 31:317-45. [DOI: 10.1146/annurev-cellbio-100814-125300] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Alexander van Oudenaarden
- Hubrecht Institute, 3584 CT Utrecht, The Netherlands;
- University Medical Center Utrecht, Cancer Genomics Netherlands, 3584 CG Utrecht, The Netherlands
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Abstract
This review deals with the latest advances in the study of embryonic stem cells (ESC) and induced pluripotent stem cells (iPSC) from domesticated species, with a focus on pigs, cattle, sheep, goats, horses, cats, and dogs. Whereas the derivation of fully pluripotent ESC from these species has proved slow, reprogramming of somatic cells to iPSC has been more straightforward. However, most of these iPSC depend on the continued expression of the introduced transgenes, a major drawback to their utility. The persistent failure in generating ESC and the dependency of iPSC on ectopic genes probably stem from an inability to maintain the stability of the endogenous gene networks necessary to maintain pluripotency. Based on work in humans and rodents, achievement of full pluripotency will likely require fine adjustments in the growth factors and signaling inhibitors provided to the cells. Finally, we discuss the future utility of these cells for biomedical and agricultural purposes.
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Affiliation(s)
- Toshihiko Ezashi
- Division of Animal Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211; , ,
| | - Ye Yuan
- Division of Animal Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211; , ,
| | - R Michael Roberts
- Division of Animal Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211; , ,
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22
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Akiyama T, Xin L, Oda M, Sharov AA, Amano M, Piao Y, Cadet JS, Dudekula DB, Qian Y, Wang W, Ko SBH, Ko MSH. Transient bursts of Zscan4 expression are accompanied by the rapid derepression of heterochromatin in mouse embryonic stem cells. DNA Res 2015; 22:307-18. [PMID: 26324425 PMCID: PMC4596397 DOI: 10.1093/dnares/dsv013] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 06/24/2015] [Indexed: 01/06/2023] Open
Abstract
Mouse embryonic stem cells (mESCs) have a remarkable capacity to maintain normal genome stability and karyotype in culture. We previously showed that infrequent bursts of Zscan4 expression (Z4 events) are important for the maintenance of telomere length and genome stability in mESCs. However, the molecular details of Z4 events remain unclear. Here we show that Z4 events involve unexpected transcriptional derepression in heterochromatin regions that usually remain silent. During a Z4 event, we see rapid derepression and rerepression of heterochromatin leading to a burst of transcription that coincides with transient histone hyperacetylation and DNA demethylation, clustering of pericentromeric heterochromatin around the nucleolus, and accumulation of activating and repressive chromatin remodelling complexes. This heterochromatin-based transcriptional activity suggests that mESCs may maintain their extraordinary genome stability at least in part by transiently resetting their heterochromatin.
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Affiliation(s)
- Tomohiko Akiyama
- Department of Systems Medicine, Keio University School of Medicine, Tokyo 160, Japan Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Li Xin
- Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Mayumi Oda
- Department of Systems Medicine, Keio University School of Medicine, Tokyo 160, Japan
| | - Alexei A Sharov
- Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Misa Amano
- Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Yulan Piao
- Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - J Scotty Cadet
- Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Dawood B Dudekula
- Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Yong Qian
- Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Weidong Wang
- Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Shigeru B H Ko
- Department of Systems Medicine, Keio University School of Medicine, Tokyo 160, Japan
| | - Minoru S H Ko
- Department of Systems Medicine, Keio University School of Medicine, Tokyo 160, Japan Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
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23
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Zernicka-Goetz M, Hadjantonakis AK. From pluripotency to differentiation: laying foundations for the body pattern in the mouse embryo. Philos Trans R Soc Lond B Biol Sci 2015; 369:rstb.2013.0535. [PMID: 25349444 DOI: 10.1098/rstb.2013.0535] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Magdalena Zernicka-Goetz
- Department of Physiology, Development and Neuroscience, Gurdon Institute, University of Cambridge, Downing St., Cambridge CB2 3DY, UK
| | - Anna-Katerina Hadjantonakis
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
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24
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Morgani SM, Brickman JM. LIF supports primitive endoderm expansion during pre-implantation development. Development 2015; 142:3488-99. [DOI: 10.1242/dev.125021] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 08/19/2015] [Indexed: 01/31/2023]
Abstract
Embryonic stem cells (ESCs) are pluripotent cell lines that can be maintained indefinitely in an early developmental state. ESC culture conditions almost all require the cytokine LIF to maintain self-renewal. As ESCs are not homogeneous, but contain multiple populations reminiscent of the blastocyst, identifying the target cells of LIF is necessary to understand the propagation of pluripotency. We recently found that LIF acts under self-renewing conditions to stimulate the fraction of ESCs that express extraembryonic markers, but has little impact on pluripotent gene expression. Here we report that LIF has two distinct roles. It blocks early epiblast differentiation and supports the expansion of primitive endoderm (PrE) primed ESCs and PrE in vivo. We find that activation of JAK/STAT signalling downstream of LIF occurs initially throughout the pre-implantation embryo, but later marks the PrE. Moreover, the addition of LIF to cultured embryos increases the GATA6+ PrE population while inhibition of JAK/STAT reduces both NANOG+ epiblast (Epi) and GATA6+ PrE. The reduction of the NANOG+ Epi may be explained by its precocious differentiation to later Epi derivatives, while the increase in PrE is mediated both by an increase in proliferation and inhibition of PrE apoptosis that is normally triggered in embryos with an excess of GATA6+ cells. Thus, it appears that the relative size of the PrE is determined by the number of LIF-producing cells in the embryo. This suggests a mechanism by which the embryo adjusts the relative ratio of the primary lineages in response to experimental manipulation.
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Affiliation(s)
- Sophie M. Morgani
- The Danish Stem Cell Centre - DanStem, University of Copenhagen, 3B Blegdamsvej, DK-2200 Copenhagen N, Denmark
| | - Joshua M. Brickman
- The Danish Stem Cell Centre - DanStem, University of Copenhagen, 3B Blegdamsvej, DK-2200 Copenhagen N, Denmark
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25
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Ledford H. Questions linger over stress-induced stem cells. Nature 2014. [DOI: 10.1038/nature.2014.16648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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