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Modic M, Kuret K, Steinhauser S, Faraway R, van Genderen E, Ruiz de Los Mozos I, Novljan J, Vičič Ž, Lee FCY, Ten Berge D, Luscombe NM, Ule J. Poised PABP-RNA hubs implement signal-dependent mRNA decay in development. Nat Struct Mol Biol 2024; 31:1439-1447. [PMID: 39054355 PMCID: PMC11402784 DOI: 10.1038/s41594-024-01363-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 06/28/2024] [Indexed: 07/27/2024]
Abstract
Signaling pathways drive cell fate transitions largely by changing gene expression. However, the mechanisms for rapid and selective transcriptome rewiring in response to signaling cues remain elusive. Here we use deep learning to deconvolve both the sequence determinants and the trans-acting regulators that trigger extracellular signal-regulated kinase (ERK)-mitogen-activated protein kinase kinase (MEK)-induced decay of the naive pluripotency mRNAs. Timing of decay is coupled to embryo implantation through ERK-MEK phosphorylation of LIN28A, which repositions pLIN28A to the highly A+U-rich 3' untranslated region (3'UTR) termini of naive pluripotency mRNAs. Interestingly, these A+U-rich 3'UTR termini serve as poly(A)-binding protein (PABP)-binding hubs, poised for signal-induced convergence with LIN28A. The multivalency of AUU motifs determines the efficacy of pLIN28A-PABP convergence, which enhances PABP 3'UTR binding, decreases the protection of poly(A) tails and activates mRNA decay to enable progression toward primed pluripotency. Thus, the signal-induced convergence of LIN28A with PABP-RNA hubs drives the rapid selection of naive mRNAs for decay, enabling the transcriptome remodeling that ensures swift developmental progression.
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Affiliation(s)
- Miha Modic
- The Francis Crick Institute, London, UK.
- UK Dementia Research Institute at King's College London, London, UK.
- National Institute of Chemistry, Ljubljana, Slovenia.
| | - Klara Kuret
- The Francis Crick Institute, London, UK
- National Institute of Chemistry, Ljubljana, Slovenia
- Jozef Stefan International Postgraduate School, Ljubljana, Slovenia
| | | | - Rupert Faraway
- The Francis Crick Institute, London, UK
- UK Dementia Research Institute at King's College London, London, UK
| | - Emiel van Genderen
- Department of Cell Biology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Igor Ruiz de Los Mozos
- The Francis Crick Institute, London, UK
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, Spain
| | - Jona Novljan
- National Institute of Chemistry, Ljubljana, Slovenia
| | - Žiga Vičič
- National Institute of Chemistry, Ljubljana, Slovenia
| | - Flora C Y Lee
- The Francis Crick Institute, London, UK
- UK Dementia Research Institute at King's College London, London, UK
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Derk Ten Berge
- Department of Cell Biology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Nicholas M Luscombe
- The Francis Crick Institute, London, UK
- Okinawa Institute of Science and Technology, Okinawa, Japan
| | - Jernej Ule
- The Francis Crick Institute, London, UK.
- UK Dementia Research Institute at King's College London, London, UK.
- National Institute of Chemistry, Ljubljana, Slovenia.
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2
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Massafret O, Barragán M, Álvarez-González L, Aran B, Martín-Mur B, Esteve-Codina A, Ruiz-Herrera A, Ibáñez E, Santaló J. The pluripotency state of human embryonic stem cells derived from single blastomeres of eight-cell embryos. Cells Dev 2024; 179:203935. [PMID: 38914137 DOI: 10.1016/j.cdev.2024.203935] [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: 04/26/2024] [Revised: 06/17/2024] [Accepted: 06/20/2024] [Indexed: 06/26/2024]
Abstract
Human embryonic stem cells (hESCs) derived from blastocyst stage embryos present a primed state of pluripotency, whereas mouse ESCs (mESCs) display naïve pluripotency. Their unique characteristics make naïve hESCs more suitable for particular applications in biomedical research. This work aimed to derive hESCs from single blastomeres and determine their pluripotency state, which is currently unclear. We derived hESC lines from single blastomeres of 8-cell embryos and from whole blastocysts, and analysed several naïve pluripotency indicators, their transcriptomic profile and their trilineage differentiation potential. No significant differences were observed between blastomere-derived hESCs (bm-hESCs) and blastocyst-derived hESCs (bc-hESCs) for most naïve pluripotency indicators, including TFE3 localization, mitochondrial activity, and global DNA methylation and hydroxymethylation, nor for their trilineage differentiation potential. Nevertheless, bm-hESCs showed an increased single-cell clonogenicity and a higher expression of naïve pluripotency markers at early passages than bc-hESCs. Furthermore, RNA-seq revealed that bc-hESCs overexpressed a set of genes related to the post-implantational epiblast. Altogether, these results suggest that bm-hESCs, although displaying primed pluripotency, would be slightly closer to the naïve end of the pluripotency continuum than bc-hESCs.
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Affiliation(s)
- Ot Massafret
- Genome Integrity and Reproductive Biology Group, Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; Bioengineering in Reproductive Health, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - Montserrat Barragán
- Basic Research Laboratory, Eugin Group, Parc Científic de Barcelona, 08028 Barcelona, Spain
| | - Lucía Álvarez-González
- Genome Integrity and Reproductive Biology Group, Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Begoña Aran
- Stem Cell Bank, Regenerative Medicine Program, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), 08908 L'Hospitalet de Llobregat, Spain
| | - Beatriz Martín-Mur
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Anna Esteve-Codina
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08028 Barcelona, Spain.; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Aurora Ruiz-Herrera
- Genome Integrity and Reproductive Biology Group, Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Elena Ibáñez
- Genome Integrity and Reproductive Biology Group, Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
| | - Josep Santaló
- Genome Integrity and Reproductive Biology Group, Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
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3
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Lebek T, Malaguti M, Boezio GL, Zoupi L, Briscoe J, Elfick A, Lowell S. PUFFFIN: an ultra-bright, customisable, single-plasmid system for labelling cell neighbourhoods. EMBO J 2024; 43:4110-4135. [PMID: 38997504 PMCID: PMC11405414 DOI: 10.1038/s44318-024-00154-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: 10/28/2023] [Revised: 06/05/2024] [Accepted: 06/10/2024] [Indexed: 07/14/2024] Open
Abstract
Cell communication coordinates developmental processes, maintains homeostasis, and contributes to disease. Therefore, understanding the relationship between cells in a shared environment is crucial. Here we introduce Positive Ultra-bright Fluorescent Fusion For Identifying Neighbours (PUFFFIN), a cell neighbour-labelling system based upon secretion and uptake of positively supercharged fluorescent protein s36GFP. We fused s36GFP to mNeonGreen or to a HaloTag, facilitating ultra-bright, sensitive, colour-of-choice labelling. Secretor cells transfer PUFFFIN to neighbours while retaining nuclear mCherry, making identification, isolation, and investigation of live neighbours straightforward. PUFFFIN can be delivered to cells, tissues, or embryos on a customisable single-plasmid construct composed of interchangeable components with the option to incorporate any transgene. This versatility enables the manipulation of cell properties, while simultaneously labelling surrounding cells, in cell culture or in vivo. We use PUFFFIN to ask whether pluripotent cells adjust the pace of differentiation to synchronise with their neighbours during exit from naïve pluripotency. PUFFFIN offers a simple, sensitive, customisable approach to profile non-cell-autonomous responses to natural or induced changes in cell identity or behaviour.
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Affiliation(s)
- Tamina Lebek
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, School of Biological Sciences, The University of Edinburgh, Edinburgh, EH16 4UU, UK
| | - Mattias Malaguti
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, School of Biological Sciences, The University of Edinburgh, Edinburgh, EH16 4UU, UK
- Centre for Engineering Biology, Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, The University of Edinburgh, Edinburgh, EH9 3FF, UK
| | | | - Lida Zoupi
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, EH8 9XD, UK
- Simons Initiative for the Developing Brain, The University of Edinburgh, Edinburgh, EH8 9XD, UK
| | | | - Alistair Elfick
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh, EH8 3DW, UK
- UK Centre for Mammalian Synthetic Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Sally Lowell
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, School of Biological Sciences, The University of Edinburgh, Edinburgh, EH16 4UU, UK.
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Smith A. Propagating pluripotency - The conundrum of self-renewal. Bioessays 2024:e2400108. [PMID: 39180242 DOI: 10.1002/bies.202400108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 07/29/2024] [Accepted: 08/06/2024] [Indexed: 08/26/2024]
Abstract
The discovery of mouse embryonic stem cells in 1981 transformed research in mammalian developmental biology and functional genomics. The subsequent generation of human pluripotent stem cells (PSCs) and the development of molecular reprogramming have opened unheralded avenues for drug discovery and cell replacement therapy. Here, I review the history of PSCs from the perspective that long-term self-renewal is a product of the in vitro signaling environment, rather than an intrinsic feature of embryos. I discuss the relationship between pluripotent states captured in vitro to stages of epiblast in the embryo and suggest key considerations for evaluation of PSCs. A remaining fundamental challenge is to determine whether naïve pluripotency can be propagated from the broad range of mammals by exploiting common principles in gene regulatory architecture.
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Affiliation(s)
- Austin Smith
- Living Systems Institute, University of Exeter, Exeter, UK
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5
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Neira JA, Conrad JV, Rusteika M, Chu LF. The progress of induced pluripotent stem cells derived from pigs: a mini review of recent advances. Front Cell Dev Biol 2024; 12:1371240. [PMID: 38979033 PMCID: PMC11228285 DOI: 10.3389/fcell.2024.1371240] [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: 01/16/2024] [Accepted: 04/10/2024] [Indexed: 07/10/2024] Open
Abstract
Pigs (Sus scrofa) are widely acknowledged as an important large mammalian animal model due to their similarity to human physiology, genetics, and immunology. Leveraging the full potential of this model presents significant opportunities for major advancements in the fields of comparative biology, disease modeling, and regenerative medicine. Thus, the derivation of pluripotent stem cells from this species can offer new tools for disease modeling and serve as a stepping stone to test future autologous or allogeneic cell-based therapies. Over the past few decades, great progress has been made in establishing porcine pluripotent stem cells (pPSCs), including embryonic stem cells (pESCs) derived from pre- and peri-implantation embryos, and porcine induced pluripotent stem cells (piPSCs) using a variety of cellular reprogramming strategies. However, the stabilization of pPSCs was not as straightforward as directly applying the culture conditions developed and optimized for murine or primate PSCs. Therefore, it has historically been challenging to establish stable pPSC lines that could pass stringent pluripotency tests. Here, we review recent advances in the establishment of stable porcine PSCs. We focus on the evolving derivation methods that eventually led to the establishment of pESCs and transgene-free piPSCs, as well as current challenges and opportunities in this rapidly advancing field.
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Affiliation(s)
- Jaime A Neira
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
- Reproductive Biology and Regenerative Medicine Research Group, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, Calgary, AB, Canada
| | - J Vanessa Conrad
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
- Reproductive Biology and Regenerative Medicine Research Group, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, Calgary, AB, Canada
| | - Margaret Rusteika
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
- Reproductive Biology and Regenerative Medicine Research Group, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, Calgary, AB, Canada
- Biomedical Engineering Graduate Program, University of Calgary, Calgary, AB, Canada
| | - Li-Fang Chu
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
- Reproductive Biology and Regenerative Medicine Research Group, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, Calgary, AB, Canada
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6
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Taylor MA, Kandyba E, Halliwill K, Delrosario R, Khoroshkin M, Goodarzi H, Quigley D, Li YR, Wu D, Bollam SR, Mirzoeva OK, Akhurst RJ, Balmain A. Stem-cell states converge in multistage cutaneous squamous cell carcinoma development. Science 2024; 384:eadi7453. [PMID: 38815020 DOI: 10.1126/science.adi7453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 04/05/2024] [Indexed: 06/01/2024]
Abstract
Stem cells play a critical role in cancer development by contributing to cell heterogeneity, lineage plasticity, and drug resistance. We created gene expression networks from hundreds of mouse tissue samples (both normal and tumor) and integrated these with lineage tracing and single-cell RNA-seq, to identify convergence of cell states in premalignant tumor cells expressing markers of lineage plasticity and drug resistance. Two of these cell states representing multilineage plasticity or proliferation were inversely correlated, suggesting a mutually exclusive relationship. Treatment of carcinomas in vivo with chemotherapy repressed the proliferative state and activated multilineage plasticity whereas inhibition of differentiation repressed plasticity and potentiated responses to cell cycle inhibitors. Manipulation of this cell state transition point may provide a source of potential combinatorial targets for cancer therapy.
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Affiliation(s)
- Mark A Taylor
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
- Clinical Research Centre, Medical University of Bialystok, Bialystok 15-089, Poland
| | - Eve Kandyba
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
| | - Kyle Halliwill
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
- AbbVie, South San Francisco, CA 94080, USA
| | - Reyno Delrosario
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
| | - Matvei Khoroshkin
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
| | - Hani Goodarzi
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94518, USA
- Department of Urology, University of California San Francisco, San Francisco, CA 94518, USA
- Arc Institute, Palo Alto, CA 94304, USA
| | - David Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
- Department of Urology, University of California San Francisco, San Francisco, CA 94518, USA
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA 94518, USA
| | - Yun Rose Li
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
- Department of Radiation Oncology, City of Hope National Medical Center, Duarte, CA 91010, USA
- Department of Cancer Genetics & Epigenetics, City of Hope National Medical Center, Duarte, CA 91010, USA
- Division of Quantitative Medicine & Systems Biology, Translational Genomics Research Institute, Phoenix, CA 85004, USA
| | - Di Wu
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
| | - Saumya R Bollam
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA 94518, USA
| | - Olga K Mirzoeva
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
| | - Rosemary J Akhurst
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94518, USA
| | - Allan Balmain
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94518, USA
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Du P, Wu J. Hallmarks of totipotent and pluripotent stem cell states. Cell Stem Cell 2024; 31:312-333. [PMID: 38382531 PMCID: PMC10939785 DOI: 10.1016/j.stem.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/18/2024] [Accepted: 01/26/2024] [Indexed: 02/23/2024]
Abstract
Though totipotency and pluripotency are transient during early embryogenesis, they establish the foundation for the development of all mammals. Studying these in vivo has been challenging due to limited access and ethical constraints, particularly in humans. Recent progress has led to diverse culture adaptations of epiblast cells in vitro in the form of totipotent and pluripotent stem cells, which not only deepen our understanding of embryonic development but also serve as invaluable resources for animal reproduction and regenerative medicine. This review delves into the hallmarks of totipotent and pluripotent stem cells, shedding light on their key molecular and functional features.
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Affiliation(s)
- Peng Du
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China.
| | - Jun Wu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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8
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Liu Y, Li X, Ma X, Du Q, Wang J, Yu H. MiR-290 Family Maintains Pluripotency and Self-Renewal by Regulating MAPK Signaling Pathway in Intermediate Pluripotent Stem Cells. Int J Mol Sci 2024; 25:2681. [PMID: 38473927 DOI: 10.3390/ijms25052681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/21/2023] [Accepted: 11/23/2023] [Indexed: 03/14/2024] Open
Abstract
Mouse embryonic stem cells (ESCs) and epiblast stem cells (EpiSCs) are derived from pre- and post-implantation embryos, representing the initial "naïve" and final "primed" states of pluripotency, respectively. In this study, novel reprogrammed pluripotent stem cells (rPSCs) were induced from mouse EpiSCs using a chemically defined medium containing mouse LIF, BMP4, CHIR99021, XAV939, and SB203580. The rPSCs exhibited domed clones and expressed key pluripotency genes, with both X chromosomes active in female cells. Furthermore, rPSCs differentiated into cells of all three germ layers in vivo through teratoma formation. Regarding epigenetic modifications, the DNA methylation of Oct4, Sox2, and Nanog promoter regions and the mRNA levels of Dnmt3a, Dnmt3b, and Dnmt1 were reduced in rPSCs compared with EpiSCs. However, the miR-290 family was significantly upregulated in rPSCs. After removing SB203580, an inhibitor of the p38 MAPK pathway, the cell colonies changed from domed to flat, with a significant decrease in the expression of pluripotency genes and the miR-290 family. Conversely, overexpression of pri-miR-290 reversed these changes. In addition, Map2k6 was identified as a direct target gene of miR-291b-3p, indicating that the miR-290 family maintains pluripotency and self-renewal in rPSCs by regulating the MAPK signaling pathway.
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Affiliation(s)
- Yueshi Liu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (RRBGL), Inner Mongolia University, Hohhot 010070, China
| | - Xiangnan Li
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (RRBGL), Inner Mongolia University, Hohhot 010070, China
| | - Xiaozhuang Ma
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (RRBGL), Inner Mongolia University, Hohhot 010070, China
| | - Qiankun Du
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (RRBGL), Inner Mongolia University, Hohhot 010070, China
| | - Jiemin Wang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (RRBGL), Inner Mongolia University, Hohhot 010070, China
| | - Haiquan Yu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (RRBGL), Inner Mongolia University, Hohhot 010070, China
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Shankar V, van Blitterswijk C, Vrij E, Giselbrecht S. Automated, High-Throughput Phenotypic Screening and Analysis Platform to Study Pre- and Post-Implantation Morphogenesis in Stem Cell-Derived Embryo-Like Structures. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2304987. [PMID: 37991133 PMCID: PMC10811479 DOI: 10.1002/advs.202304987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 10/11/2023] [Indexed: 11/23/2023]
Abstract
Combining high-throughput generation and high-content imaging of embryo models will enable large-scale screening assays in the fields of (embryo) toxicity, drug development, embryogenesis, and reproductive medicine. This study shows the continuous culture and in situ (i.e., in microwell) imaging-based readout of a 3D stem cell-based model of peri-implantation epiblast (Epi)/extraembryonic endoderm (XEn) development with an expanded pro-amniotic cavity (PAC) (E3.5 E5.5), namely XEn/EPiCs. Automated image analysis and supervised machine learning permit the identification of embryonic morphogenesis, tissue compartmentalization, cell differentiation, and consecutive classification. Screens with signaling pathway modulators at different time windows provide spatiotemporal information on their phenotypic effect on developmental processes leading to the formation of XEn/EPiCs. Exposure of the biological model in the microwell platform to pathway modulators at two time windows, namely 0-72 h and 48-120 h, show that Wnt and Fgf/MAPK pathway modulators affect Epi differentiation and its polarization, while modulation of BMP and Tgfβ/Nodal pathway affects XEn specification and epithelialization. Further, their collective role is identified in the timing of the formation and expansion of PAC. The newly developed, scalable culture and analysis platform, thereby, provides a unique opportunity to quantitatively and systematically study effects of pathway modulators on early embryonic development.
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Affiliation(s)
- Vinidhra Shankar
- MERLN Institute for Technology‐Inspired Regenerative MedicineDepartment for Instructive Biomaterials Engineering (IBE)Maastricht UniversityMaastricht6229ETThe Netherlands
| | - Clemens van Blitterswijk
- MERLN Institute for Technology‐Inspired Regenerative MedicineDepartment for Instructive Biomaterials Engineering (IBE)Maastricht UniversityMaastricht6229ETThe Netherlands
| | - Erik Vrij
- MERLN Institute for Technology‐Inspired Regenerative MedicineDepartment for Instructive Biomaterials Engineering (IBE)Maastricht UniversityMaastricht6229ETThe Netherlands
| | - Stefan Giselbrecht
- MERLN Institute for Technology‐Inspired Regenerative MedicineDepartment for Instructive Biomaterials Engineering (IBE)Maastricht UniversityMaastricht6229ETThe Netherlands
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Hornung BVH, Azmani Z, den Dekker AT, Oole E, Ozgur Z, Brouwer RWW, van den Hout MCGN, van IJcken WFJ. Comparison of Single Cell Transcriptome Sequencing Methods: Of Mice and Men. Genes (Basel) 2023; 14:2226. [PMID: 38137048 PMCID: PMC10743076 DOI: 10.3390/genes14122226] [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: 10/31/2023] [Revised: 12/04/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
Single cell RNAseq has been a big leap in many areas of biology. Rather than investigating gene expression on a whole organism level, this technology enables scientists to get a detailed look at rare single cells or within their cell population of interest. The field is growing, and many new methods appear each year. We compared methods utilized in our core facility: Smart-seq3, PlexWell, FLASH-seq, VASA-seq, SORT-seq, 10X, Evercode, and HIVE. We characterized the equipment requirements for each method. We evaluated the performances of these methods based on detected features, transcriptome diversity, mitochondrial RNA abundance and multiplets, among others and benchmarked them against bulk RNA sequencing. Here, we show that bulk transcriptome detects more unique transcripts than any single cell method. While most methods are comparable in many regards, FLASH-seq and VASA-seq yielded the best metrics, e.g., in number of features. If no equipment for automation is available or many cells are desired, then HIVE or 10X yield good results. In general, more recently developed methods perform better. This also leads to the conclusion that older methods should be phased out, and that the development of single cell RNAseq methods is still progressing considerably.
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Affiliation(s)
- Bastian V. H. Hornung
- Department of Cell Biology, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands; (B.V.H.H.); (M.C.G.N.v.d.H.)
- Genomics Core Facility, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands
| | - Zakia Azmani
- Department of Cell Biology, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands; (B.V.H.H.); (M.C.G.N.v.d.H.)
- Genomics Core Facility, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands
| | - Alexander T. den Dekker
- Department of Cell Biology, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands; (B.V.H.H.); (M.C.G.N.v.d.H.)
- Genomics Core Facility, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands
| | - Edwin Oole
- Department of Cell Biology, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands; (B.V.H.H.); (M.C.G.N.v.d.H.)
- Genomics Core Facility, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands
| | - Zeliha Ozgur
- Department of Cell Biology, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands; (B.V.H.H.); (M.C.G.N.v.d.H.)
- Genomics Core Facility, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands
| | - Rutger W. W. Brouwer
- Department of Cell Biology, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands; (B.V.H.H.); (M.C.G.N.v.d.H.)
- Genomics Core Facility, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands
| | - Mirjam C. G. N. van den Hout
- Department of Cell Biology, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands; (B.V.H.H.); (M.C.G.N.v.d.H.)
- Genomics Core Facility, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands
| | - Wilfred F. J. van IJcken
- Department of Cell Biology, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands; (B.V.H.H.); (M.C.G.N.v.d.H.)
- Genomics Core Facility, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands
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11
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Teague S, Yao L, Heemskerk I. The many dimensions of germline competence. Curr Opin Cell Biol 2023; 85:102259. [PMID: 37852152 PMCID: PMC11123554 DOI: 10.1016/j.ceb.2023.102259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/15/2023] [Accepted: 09/17/2023] [Indexed: 10/20/2023]
Abstract
Primordial germ cell (PGC) specification is the first step in the development of the germline. Recent work has elucidated human-mouse differences in PGC differentiation and identified cell states with enhanced competency for PGC-like cell (PGCLC) differentiation in vitro in both species. However, it remains a subject of debate how different PGC competent states in vitro relate to each other, to embryonic development, and to the origin of PGCs in vivo. Here we review recent literature on human PGCLC differentiation in the context of mouse and non-human primate models. In contrast to what was previously thought, recent work suggests human pluripotent stem cells (hPSCs) are highly germline competent. We argue that paradoxical observations regarding the origin and signaling requirements of hPGCLCs may be due to local cell interactions. These confound assays of competence by generating endogenous signaling gradients and spatially modulating the ability to receive exogenous inductive signals. Furthermore, combinatorial signaling suggests that there is no unique germline competent state: rather than a one-dimensional spectrum of developmental progression, competence should be considered in a higher dimensional landscape of cell states.
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Affiliation(s)
- Seth Teague
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - LiAng Yao
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Idse Heemskerk
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA; Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA; Center for Cell Plasticity and Organ Design, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Physics, University of Michigan, Ann Arbor, MI, USA.
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12
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Zhu P, Zhang B, Sun R, Wang J, Liu Z, Liu X, Yan M, Cui Y, Sha J, Yuan Y. Derivation of new pluripotent stem cells from human extended pluripotent stem cells with formative features and trophectoderm potential. Cell Prolif 2023; 56:e13480. [PMID: 37052060 PMCID: PMC10623941 DOI: 10.1111/cpr.13480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 03/28/2023] [Accepted: 04/04/2023] [Indexed: 04/14/2023] Open
Abstract
Previous studies have demonstrated the existence of intermediate stem cells, which have been successfully obtained from human naive pluripotent stem cells (PSCs) and peri-implantation embryos. However, it is not known whether human extended pluripotent stem cells (hEPSCs) can be directly induced into intermediate stem cells. Moreover, the ability of extra-embryonic lineage differentiation in intermediate stem cells has not been verified. In this issue, we transformed hEPSCs into a kind of novel intermediate pluripotent stem cell resembling embryonic days 8-9 (E8-E9) epiblasts and proved its feature of formative epiblasts. We engineered hEPSCs from primed hPSCs under N2B27-LCDM (N2B27 plus Lif, CHIR, DiH and MiH) conditions. Then, we added Activin A, FGF and XAV939 to modulate signalling pathways related to early humans' embryogenesis. We performed RNA-seq and CUT&Tag analysis to compare with AF9-hPSCs from different pluripotency stages of hPSCs. Trophectoderm (TE), primordial germ cells-like cells (PGCLC) and endoderm, mesoderm, and neural ectoderm induction were conducted by specific small molecules and proteins. AF9-hPSCs transcription resembled that of E8-E9 peri-implantation epiblasts. Signalling pathway responsiveness and histone methylation further revealed their formative pluripotency. Additionally, AF9-hPSCs responded directly to primordial germ cells (PGCs) specification and three germ layer differentiation signals in vitro. Moreover, AF9-hPSCs could differentiate into the TE lineage. Therefore, AF9-hPSCs represented an E8-E9 formative pluripotency state between naïve and primed pluripotency, opening new avenues for studying human pluripotency development during embryogenesis.
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Affiliation(s)
- Pinmou Zhu
- State Key Laboratory of Reproductive MedicineNanjing Medical UniversityNanjingChina
| | - Bohang Zhang
- State Key Laboratory of Reproductive MedicineNanjing Medical UniversityNanjingChina
| | - Ruiqi Sun
- State Key Laboratory of Reproductive MedicineNanjing Medical UniversityNanjingChina
| | - Jiachen Wang
- State Key Laboratory of Reproductive MedicineNanjing Medical UniversityNanjingChina
| | - Zhaode Liu
- State Key Laboratory of Reproductive MedicineNanjing Medical UniversityNanjingChina
| | - Xiaorui Liu
- State Key Laboratory of Reproductive MedicineNanjing Medical UniversityNanjingChina
| | - Min Yan
- State Key Laboratory of Reproductive MedicineNanjing Medical UniversityNanjingChina
| | - Yiqiang Cui
- State Key Laboratory of Reproductive MedicineNanjing Medical UniversityNanjingChina
| | - Jiahao Sha
- State Key Laboratory of Reproductive MedicineWomen's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical UniversityNanjingChina
| | - Yan Yuan
- State Key Laboratory of Reproductive MedicineNanjing Medical UniversityNanjingChina
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13
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van Loo B, Ten Den SA, Araújo-Gomes N, de Jong V, Snabel RR, Schot M, Rivera-Arbeláez JM, Veenstra GJC, Passier R, Kamperman T, Leijten J. Mass production of lumenogenic human embryoid bodies and functional cardiospheres using in-air-generated microcapsules. Nat Commun 2023; 14:6685. [PMID: 37865642 PMCID: PMC10590445 DOI: 10.1038/s41467-023-42297-0] [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: 08/17/2022] [Accepted: 10/05/2023] [Indexed: 10/23/2023] Open
Abstract
Organoids are engineered 3D miniature tissues that are defined by their organ-like structures, which drive a fundamental understanding of human development. However, current organoid generation methods are associated with low production throughputs and poor control over size and function including due to organoid merging, which limits their clinical and industrial translation. Here, we present a microfluidic platform for the mass production of lumenogenic embryoid bodies and functional cardiospheres. Specifically, we apply triple-jet in-air microfluidics for the ultra-high-throughput generation of hollow, thin-shelled, hydrogel microcapsules that can act as spheroid-forming bioreactors in a cytocompatible, oil-free, surfactant-free, and size-controlled manner. Uniquely, we show that microcapsules generated by in-air microfluidics provide a lumenogenic microenvironment with near 100% efficient cavitation of spheroids. We demonstrate that upon chemical stimulation, human pluripotent stem cell-derived spheroids undergo cardiomyogenic differentiation, effectively resulting in the mass production of homogeneous and functional cardiospheres that are responsive to external electrical stimulation. These findings drive clinical and industrial adaption of stem cell technology in tissue engineering and drug testing.
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Affiliation(s)
- Bas van Loo
- University of Twente, TechMed Centre, Department of Developmental BioEngineering, Enschede, The Netherlands
| | - Simone A Ten Den
- University of Twente, TechMed Centre, Department of Applied Stem Cell Technology, Enschede, The Netherlands
| | - Nuno Araújo-Gomes
- University of Twente, TechMed Centre, Department of Developmental BioEngineering, Enschede, The Netherlands
| | - Vincent de Jong
- University of Twente, TechMed Centre, Department of Developmental BioEngineering, Enschede, The Netherlands
| | - Rebecca R Snabel
- Radboud University, Radboud Institute for Molecular Life Sciences, Faculty of Science, Department of Molecular Developmental Biology, Nijmegen, The Netherlands
| | - Maik Schot
- University of Twente, TechMed Centre, Department of Developmental BioEngineering, Enschede, The Netherlands
| | - José M Rivera-Arbeláez
- University of Twente, TechMed Centre, Department of Applied Stem Cell Technology, Enschede, The Netherlands
- University of Twente, TechMed Centre, Max Planck Center for Complex Fluid Dynamics, BIOS Lab-on-a-Chip Group, Enschede, The Netherlands
| | - Gert Jan C Veenstra
- Radboud University, Radboud Institute for Molecular Life Sciences, Faculty of Science, Department of Molecular Developmental Biology, Nijmegen, The Netherlands
| | - Robert Passier
- University of Twente, TechMed Centre, Department of Applied Stem Cell Technology, Enschede, The Netherlands
- Leiden University Medical Centre, Department of Anatomy and Embryology, Leiden, Netherlands
| | - Tom Kamperman
- University of Twente, TechMed Centre, Department of Developmental BioEngineering, Enschede, The Netherlands
- IamFluidics B.V., De Veldmaat 17, 7522NM, Enschede, The Netherlands
| | - Jeroen Leijten
- University of Twente, TechMed Centre, Department of Developmental BioEngineering, Enschede, The Netherlands.
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14
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Li Y, Zheng C, Liu Y, He J, Zhang Q, Zhang Y, Kou X, Zhao Y, Liu K, Bai D, Jia Y, Han X, Sheng Y, Yin J, Wang H, Gao S, Liu W, Gao S. Inhibition of Wnt activity improves peri-implantation development of somatic cell nuclear transfer embryos. Natl Sci Rev 2023; 10:nwad173. [PMID: 37593113 PMCID: PMC10430793 DOI: 10.1093/nsr/nwad173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 06/02/2023] [Indexed: 08/19/2023] Open
Abstract
Somatic cell nuclear transfer (SCNT) can reprogram differentiated somatic cells into totipotency. Although pre-implantation development of SCNT embryos has greatly improved, most SCNT blastocysts are still arrested at the peri-implantation stage, and the underlying mechanism remains elusive. Here, we develop a 3D in vitro culture system for SCNT peri-implantation embryos and discover that persistent Wnt signals block the naïve-to-primed pluripotency transition of epiblasts with aberrant H3K27me3 occupancy, which in turn leads to defects in epiblast transformation events and subsequent implantation failure. Strikingly, manipulating Wnt signals can attenuate the pluripotency transition and H3K27me3 deposition defects in epiblasts and achieve up to a 9-fold increase in cloning efficiency. Finally, single-cell RNA-seq analysis reveals that Wnt inhibition markedly enhances the lineage developmental trajectories of SCNT blastocysts during peri-implantation development. Overall, these findings reveal diminished potentials of SCNT blastocysts for lineage specification and validate a critical peri-implantation barrier for SCNT embryos.
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Affiliation(s)
- Yanhe Li
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Caihong Zheng
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Yingdong Liu
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Jincan He
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Qiang Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the MARA, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yalin Zhang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Xiaochen Kou
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yanhong Zhao
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Kuisheng Liu
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Dandan Bai
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yanping Jia
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Xiaoxiao Han
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yifan Sheng
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Jiqing Yin
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Hong Wang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Shuai Gao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the MARA, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Wenqiang Liu
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Shaorong Gao
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
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15
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Cao S, Gao X, Liu F, Chen Y, Na Q, Meng Q, Shao P, Chen C, Song Y, Wu B, Li X, Bao S. Derivation and characteristics of induced pluripotent stem cells from a patient with acute myelitis. Front Cell Dev Biol 2023; 11:1172385. [PMID: 37519296 PMCID: PMC10375497 DOI: 10.3389/fcell.2023.1172385] [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: 02/23/2023] [Accepted: 07/03/2023] [Indexed: 08/01/2023] Open
Abstract
The emergence and development of induced pluripotent stem cells (iPSCs) provides an approach to understand the regulatory mechanisms of cell pluripotency and demonstrates the great potential of iPSCs in disease modeling. Acute myelitis defines a group of inflammatory diseases that cause acute nerve damage in the spinal cord; however, its pathophysiology remains to be elusive. In this study, we derived skin fibroblasts from a patient with acute myelitis (P-HAF) and then reprogrammed P-HAF cells to iPSCs using eight exogenous factors (namely, OCT4, SOX2, c-MYC, KLF4, NANOG, LIN28, RARG, and LRH1). We performed transcriptomic analysis of the P-HAF and compared the biological characteristics of the iPSCs derived from the patient (P-iPSCs) with those derived from normal individuals in terms of pluripotency, transcriptomic characteristics, and differentiation ability toward the ectoderm. Compared to the control iPSCs, the P-iPSCs displayed similar features of pluripotency and comparable capability of ectoderm differentiation in the specified culture. However, when tested in the common medium, the P-iPSCs showed attenuated potential for ectoderm differentiation. The transcriptomic analysis revealed that pathways enriched in P-iPSCs included those involved in Wnt signaling. To this end, we treated iPSCs and P-iPSCs with the Wnt signaling pathway inhibitor IWR1 during the differentiation process and found that the expression of the ectoderm marker Sox1 was increased significantly in P-iPSCs. This study provides a novel approach to investigating the pathogenesis of acute myelitis.
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Affiliation(s)
- Shuo Cao
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, China
- Research Center for Animal Genetic Resources of Mongolia Plateau, College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Xinyue Gao
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, China
- Research Center for Animal Genetic Resources of Mongolia Plateau, College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Fangyuan Liu
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, China
- Research Center for Animal Genetic Resources of Mongolia Plateau, College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Yanglin Chen
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, China
- Research Center for Animal Genetic Resources of Mongolia Plateau, College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Qin Na
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, China
- Research Center for Animal Genetic Resources of Mongolia Plateau, College of Life Sciences, Inner Mongolia University, Hohhot, China
- College of Basic Medicine, Inner Mongolia Medical University, Hohhot, China
| | - Qiaoqiao Meng
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, China
- Research Center for Animal Genetic Resources of Mongolia Plateau, College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Peng Shao
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, China
- Research Center for Animal Genetic Resources of Mongolia Plateau, College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Chen Chen
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, China
- Research Center for Animal Genetic Resources of Mongolia Plateau, College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Yongli Song
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, China
- Research Center for Animal Genetic Resources of Mongolia Plateau, College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Baojiang Wu
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, China
- Research Center for Animal Genetic Resources of Mongolia Plateau, College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Xihe Li
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, China
- Research Center for Animal Genetic Resources of Mongolia Plateau, College of Life Sciences, Inner Mongolia University, Hohhot, China
- Inner Mongolia Saikexing Institute of Breeding and Reproductive Biotechnology in Domestic Animal, Hohhot, China
| | - Siqin Bao
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, China
- Research Center for Animal Genetic Resources of Mongolia Plateau, College of Life Sciences, Inner Mongolia University, Hohhot, China
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16
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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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17
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Shi Y, Kopparapu N, Ohler L, Dickinson DJ. Efficient and rapid fluorescent protein knock-in with universal donors in mouse embryonic stem cells. Development 2023; 150:dev201367. [PMID: 37129004 PMCID: PMC10233722 DOI: 10.1242/dev.201367] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 04/18/2023] [Indexed: 05/03/2023]
Abstract
Fluorescent protein (FP) tagging is a key method for observing protein distribution, dynamics and interaction with other proteins in living cells. However, the typical approach using overexpression of tagged proteins can perturb cell behavior and introduce localization artifacts. To preserve native expression, fluorescent proteins can be inserted directly into endogenous genes. This approach has been widely used in yeast for decades, and more recently in invertebrate model organisms with the advent of CRISPR/Cas9. However, endogenous FP tagging has not been widely used in mammalian cells due to inefficient homology-directed repair. Recently, the CRISPaint system used non-homologous end joining for efficient integration of FP tags into native loci, but it only allows C-terminal knock-ins. Here, we have enhanced the CRISPaint system by introducing new universal donors for N-terminal insertion and for multi-color tagging with orthogonal selection markers. We adapted the procedure for mouse embryonic stem cells, which can be differentiated into diverse cell types. Our protocol is rapid and efficient, enabling live imaging in less than 2 weeks post-transfection. These improvements increase the versatility and applicability of FP knock-in in mammalian cells.
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Affiliation(s)
- Yu Shi
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Nitya Kopparapu
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Lauren Ohler
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Daniel J. Dickinson
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
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18
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Carbognin E, Carlini V, Panariello F, Chieregato M, Guerzoni E, Benvegnù D, Perrera V, Malucelli C, Cesana M, Grimaldi A, Mutarelli M, Carissimo A, Tannenbaum E, Kugler H, Hackett JA, Cacchiarelli D, Martello G. Esrrb guides naive pluripotent cells through the formative transcriptional programme. Nat Cell Biol 2023; 25:643-657. [PMID: 37106060 PMCID: PMC7614557 DOI: 10.1038/s41556-023-01131-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 03/15/2023] [Indexed: 04/29/2023]
Abstract
During embryonic development, naive pluripotent epiblast cells transit to a formative state. The formative epiblast cells form a polarized epithelium, exhibit distinct transcriptional and epigenetic profiles and acquire competence to differentiate into all somatic and germline lineages. However, we have limited understanding of how the transition to a formative state is molecularly controlled. Here we used murine embryonic stem cell models to show that ESRRB is both required and sufficient to activate formative genes. Genetic inactivation of Esrrb leads to illegitimate expression of mesendoderm and extra-embryonic markers, impaired formative expression and failure to self-organize in 3D. Functionally, this results in impaired ability to generate formative stem cells and primordial germ cells in the absence of Esrrb. Computational modelling and genomic analyses revealed that ESRRB occupies key formative genes in naive cells and throughout the formative state. In so doing, ESRRB kickstarts the formative transition, leading to timely and unbiased capacity for multi-lineage differentiation.
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Affiliation(s)
- Elena Carbognin
- Department of Molecular Medicine, Medical School, University of Padua, Padua, Italy
- Department of Biology, University of Padua, Padua, Italy
| | - Valentina Carlini
- Epigenetics & Neurobiology Unit, European Molecular Biology Laboratory (EMBL)-Rome, Adriano Buzzati-Traverso Campus, Rome, Italy
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Francesco Panariello
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
| | | | - Elena Guerzoni
- Department of Biology, University of Padua, Padua, Italy
| | | | - Valentina Perrera
- Department of Molecular Medicine, Medical School, University of Padua, Padua, Italy
| | - Cristina Malucelli
- Department of Molecular Medicine, Medical School, University of Padua, Padua, Italy
| | - Marcella Cesana
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
- Department of Advanced Biomedical Sciences, University of Naples 'Federico II', Naples, Italy
| | - Antonio Grimaldi
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
| | - Margherita Mutarelli
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
- Istituto di Scienze Applicate e Sistemi Intelligenti 'Eduardo Caianiello', Consiglio Nazionale delle Ricerche, Pozzuoli, Italy
| | - Annamaria Carissimo
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy
- Istituto per le Applicazioni del Calcolo 'Mauro Picone,' Consiglio Nazionale delle Ricerche, Naples, Italy
| | - Eitan Tannenbaum
- The Faculty of Engineering, Bar-Ilan University, Ramat Gan, Israel
| | - Hillel Kugler
- The Faculty of Engineering, Bar-Ilan University, Ramat Gan, Israel
| | - Jamie A Hackett
- Epigenetics & Neurobiology Unit, European Molecular Biology Laboratory (EMBL)-Rome, Adriano Buzzati-Traverso Campus, Rome, Italy.
| | - Davide Cacchiarelli
- Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics, Pozzuoli, Italy.
- Department of Translational Medicine, University of Naples 'Federico II', Naples, Italy.
- School for Advanced Studies, Genomics and Experimental Medicine Program, University of Naples 'Federico II', Naples, Italy.
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19
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Kuzma-Hunt AG, Shah V, DiMarco S, Koch TG, Russell KA, Betts DH. Opening the 'black box' underlying barriers to the use of canine induced pluripotent stem cells: a narrative review. Stem Cells Dev 2023. [PMID: 36884307 DOI: 10.1089/scd.2022.0300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023] Open
Abstract
Induced pluripotent stem cells (iPSCs) are produced by resetting the epigenetic and transcriptional landscapes of somatic cells to express the endogenous pluripotency network and revert them back to an undifferentiated state. The reduced ethical concerns associated with iPSCs, their capacity for extensive self-renewal and differentiation capabilities, make them an unparalleled resource for drug discovery, disease modelling and novel therapies. Canines (c) share many human diseases and environmental exposures, making them a superior translational model for drug screening and investigating human pathologies compared to other mammals. However, well-defined protocols for legitimate ciPSC production are lacking. Problems during canine somatic cell reprogramming (SCR) yield putative ciPSCs with incomplete pluripotency, at very low efficiencies. Despite the value of ciPSCs, the molecular mechanisms underlying their unsuccessful production and how these may be addressed have not been fully elucidated. Factors including cost, species differences, safety and feasibility may also limit the widespread clinical adoption of ciPSCs for treating canine disease. The purpose of this narrative review is to identify barriers to canine SCR on molecular and cellular levels, using comparative research to inform potential solutions to their use in both research and clinical contexts. Current research is opening new doors for the application of ciPSCs in regenerative medicine for the mutual benefit of veterinary and human medicine.
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Affiliation(s)
- Alexander George Kuzma-Hunt
- University of Guelph, 3653, Biomedical Sciences, 50 Stone Rd East, Guelph, Guelph, Ontario, Canada, N1G 2W1.,Canada;
| | - Vipra Shah
- University of Guelph, 3653, Biomedical Sciences, Guelph, Ontario, Canada;
| | - Sierra DiMarco
- University of Guelph Ontario Veterinary College Department of Biomedical Sciences, 538728, Guelph, Ontario, Canada, N1G 2W1;
| | - Thomas G Koch
- University of Guelph, 3653, Biomedical Sciences, Guelph, Ontario, Canada, N1G 2W1;
| | - Keith A Russell
- University of Guelph, 3653, Biomedical Sciences, Guelph, Ontario, Canada;
| | - Dean Harvey Betts
- The University of Western Ontario, Physiology and Pharmacology, Schulich School of Medicine & Dentistry, Dental Sciences Building, rm 2022, London, Ontario, Canada, N6A 5C1.,LAB: 519-661-2111; x80971;
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20
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Athanasouli P, Balli M, De Jaime-Soguero A, Boel A, Papanikolaou S, van der Veer BK, Janiszewski A, Vanhessche T, Francis A, El Laithy Y, Nigro AL, Aulicino F, Koh KP, Pasque V, Cosma MP, Verfaillie C, Zwijsen A, Heindryckx B, Nikolaou C, Lluis F. The Wnt/TCF7L1 transcriptional repressor axis drives primitive endoderm formation by antagonizing naive and formative pluripotency. Nat Commun 2023; 14:1210. [PMID: 36869101 PMCID: PMC9984534 DOI: 10.1038/s41467-023-36914-1] [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: 11/19/2021] [Accepted: 02/23/2023] [Indexed: 03/05/2023] Open
Abstract
Early during preimplantation development and in heterogeneous mouse embryonic stem cells (mESC) culture, pluripotent cells are specified towards either the primed epiblast or the primitive endoderm (PE) lineage. Canonical Wnt signaling is crucial for safeguarding naive pluripotency and embryo implantation, yet the role and relevance of canonical Wnt inhibition during early mammalian development remains unknown. Here, we demonstrate that transcriptional repression exerted by Wnt/TCF7L1 promotes PE differentiation of mESCs and in preimplantation inner cell mass. Time-series RNA sequencing and promoter occupancy data reveal that TCF7L1 binds and represses genes encoding essential naive pluripotency factors and indispensable regulators of the formative pluripotency program, including Otx2 and Lef1. Consequently, TCF7L1 promotes pluripotency exit and suppresses epiblast lineage formation, thereby driving cells into PE specification. Conversely, TCF7L1 is required for PE specification as deletion of Tcf7l1 abrogates PE differentiation without restraining epiblast priming. Taken together, our study underscores the importance of transcriptional Wnt inhibition in regulating lineage specification in ESCs and preimplantation embryo development as well as identifies TCF7L1 as key regulator of this process.
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Affiliation(s)
- Paraskevi Athanasouli
- KU Leuven, Department of Development and Regeneration, Stem Cell Institute, B-3000, Leuven, Belgium
| | - Martina Balli
- KU Leuven, Department of Development and Regeneration, Stem Cell Institute, B-3000, Leuven, Belgium
| | - Anchel De Jaime-Soguero
- KU Leuven, Department of Development and Regeneration, Stem Cell Institute, B-3000, Leuven, Belgium.
| | - Annekatrien Boel
- Ghent-Fertility And Stem cell Team (G-FaST), Department for Reproductive Medicine, Department for Human Structure and Repair, Ghent University Hospital, 9000, Ghent, Belgium
| | - Sofia Papanikolaou
- Department of Rheumatology, Clinical Immunology, Medical School, University of Crete, 70013, Heraklion, Greece.,Computational Genomics Group, Institute of Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming", 16672, Athens, Greece
| | - Bernard K van der Veer
- KU Leuven, Department of Development and Regeneration, Stem Cell Institute, B-3000, Leuven, Belgium
| | - Adrian Janiszewski
- KU Leuven, Department of Development and Regeneration, Stem Cell Institute, B-3000, Leuven, Belgium
| | - Tijs Vanhessche
- KU Leuven, Department of Development and Regeneration, Stem Cell Institute, B-3000, Leuven, Belgium
| | - Annick Francis
- Department of Cardiovascular Sciences, KU Leuven, 3000, Leuven, Belgium
| | - Youssef El Laithy
- KU Leuven, Department of Development and Regeneration, Stem Cell Institute, B-3000, Leuven, Belgium
| | - Antonio Lo Nigro
- KU Leuven, Department of Development and Regeneration, Stem Cell Institute, B-3000, Leuven, Belgium
| | - Francesco Aulicino
- Centre for Genomic Regulation (CRG), Dr Aiguader 88, 08003, Barcelona, Spain
| | - Kian Peng Koh
- KU Leuven, Department of Development and Regeneration, Stem Cell Institute, B-3000, Leuven, Belgium
| | - Vincent Pasque
- KU Leuven, Department of Development and Regeneration, Stem Cell Institute, B-3000, Leuven, Belgium.,KU Leuven Institute for Single-Cell Omics (LISCO), 3000, Leuven, Belgium
| | - Maria Pia Cosma
- Centre for Genomic Regulation (CRG), Dr Aiguader 88, 08003, Barcelona, Spain.,ICREA, Pg. Lluis Companys 23, Barcelona, 08010, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Catherine Verfaillie
- KU Leuven, Department of Development and Regeneration, Stem Cell Institute, B-3000, Leuven, Belgium
| | - An Zwijsen
- Department of Cardiovascular Sciences, KU Leuven, 3000, Leuven, Belgium
| | - Björn Heindryckx
- Ghent-Fertility And Stem cell Team (G-FaST), Department for Reproductive Medicine, Department for Human Structure and Repair, Ghent University Hospital, 9000, Ghent, Belgium
| | - Christoforos Nikolaou
- Computational Genomics Group, Institute of Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming", 16672, Athens, Greece
| | - Frederic Lluis
- KU Leuven, Department of Development and Regeneration, Stem Cell Institute, B-3000, Leuven, Belgium.
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21
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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: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [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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22
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Wnt signaling and the regulation of pluripotency. Curr Top Dev Biol 2023; 153:95-119. [PMID: 36967203 DOI: 10.1016/bs.ctdb.2023.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
The role of Wnt signaling in stem cells has been mired in seemingly contradictory findings. On one hand, Wnt has been heralded as a self-renewal factor. On the other hand, Wnt's association with differentiation and lineage commitment is indisputable. This apparent contradiction is particularly evident in pluripotent stem cells, where Wnt promotes self-renewal as well as differentiation. To resolve this discrepancy one must delve into fundamental principles of pluripotency and gain an appreciation for the concept of pluripotency states, which exist in a continuum with intermediate metastable states, some of which have been stabilized in vitro. Wnt signaling is a critical regulator of transitions between pluripotent states. Here, we will discuss Wnt's roles in maintaining pluripotency, promoting differentiation, as well as stimulating reprogramming of somatic cells to an induced pluripotent state.
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23
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Schnirman RE, Kuo SJ, Kelly RC, Yamaguchi TP. The role of Wnt signaling in the development of the epiblast and axial progenitors. Curr Top Dev Biol 2023; 153:145-180. [PMID: 36967193 DOI: 10.1016/bs.ctdb.2023.01.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Understanding how the body plan is established during embryogenesis remains a fundamental biological question. The Wnt/β-catenin signaling pathway plays a crucial and highly conserved role in body plan formation, functioning to polarize the primary anterior-posterior (AP) or head-to-tail body axis in most metazoans. In this chapter, we focus on the roles that the mammalian Wnt/β-catenin pathway plays to prepare the pluripotent epiblast for gastrulation, and to elicit the emergence of multipotent axial progenitors from the caudal epiblast. Interactions between Wnt and retinoic acid (RA), another powerful family of developmental signaling molecules, in axial progenitors will also be discussed. Gastrulation movements and somitogenesis result in the anterior displacement of the RA source (the rostral somites and lateral plate mesoderm (LPM)), from the posterior Wnt source (the primitive streak (PS)), leading to the establishment of antiparallel gradients of RA and Wnt that control the self-renewal and successive differentiation of neck, trunk and tail progenitors.
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Affiliation(s)
| | - Samuel J Kuo
- NCI-Frederick, NIH, Frederick, MD, United States
| | - Ryan C Kelly
- NCI-Frederick, NIH, Frederick, MD, United States
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24
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Byers C, Spruce C, Fortin HJ, Hartig EI, Czechanski A, Munger SC, Reinholdt LG, Skelly DA, Baker CL. Genetic control of the pluripotency epigenome determines differentiation bias in mouse embryonic stem cells. EMBO J 2022; 41:e109445. [PMID: 34931323 PMCID: PMC8762565 DOI: 10.15252/embj.2021109445] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/01/2021] [Accepted: 11/16/2021] [Indexed: 02/03/2023] Open
Abstract
Genetically diverse pluripotent stem cells display varied, heritable responses to differentiation cues. Here, we harnessed these disparities through derivation of mouse embryonic stem cells from the BXD genetic reference panel, along with C57BL/6J (B6) and DBA/2J (D2) parental strains, to identify loci regulating cell state transitions. Upon transition to formative pluripotency, B6 stem cells quickly dissolved naïve networks adopting gene expression modules indicative of neuroectoderm lineages, whereas D2 retained aspects of naïve pluripotency. Spontaneous formation of embryoid bodies identified divergent differentiation where B6 showed a propensity toward neuroectoderm and D2 toward definitive endoderm. Genetic mapping identified major trans-acting loci co-regulating chromatin accessibility and gene expression in both naïve and formative pluripotency. These loci distally modulated occupancy of pluripotency factors at hundreds of regulatory elements. One trans-acting locus on Chr 12 primarily impacted chromatin accessibility in embryonic stem cells, while in epiblast-like cells, the same locus subsequently influenced expression of genes enriched for neurogenesis, suggesting early chromatin priming. These results demonstrate genetically determined biases in lineage commitment and identify major regulators of the pluripotency epigenome.
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Affiliation(s)
- Candice Byers
- The Jackson LaboratoryBar HarborMEUSA
- Graduate School of Biomedical SciencesTufts UniversityBostonMAUSA
| | | | - Haley J Fortin
- The Jackson LaboratoryBar HarborMEUSA
- Graduate School of Biomedical SciencesTufts UniversityBostonMAUSA
| | - Ellen I Hartig
- The Jackson LaboratoryBar HarborMEUSA
- Graduate School of Biomedical SciencesTufts UniversityBostonMAUSA
| | | | - Steven C Munger
- The Jackson LaboratoryBar HarborMEUSA
- Graduate School of Biomedical SciencesTufts UniversityBostonMAUSA
| | | | | | - Christopher L Baker
- The Jackson LaboratoryBar HarborMEUSA
- Graduate School of Biomedical SciencesTufts UniversityBostonMAUSA
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25
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Bi J, Wang W, Zhang M, Zhang B, Liu M, Su G, Chen F, Chen B, Shi T, Zheng Y, Zhao X, Zhao Z, Shi J, Li P, Zhang L, Lu W. KLF4 inhibits early neural differentiation of ESCs by coordinating specific 3D chromatin structure. Nucleic Acids Res 2022; 50:12235-12250. [PMID: 36477888 PMCID: PMC9757050 DOI: 10.1093/nar/gkac1118] [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: 04/20/2022] [Revised: 10/27/2022] [Accepted: 11/08/2022] [Indexed: 12/12/2022] Open
Abstract
Neural differentiation of embryonic stem cells (ESCs) requires precisely orchestrated gene regulation, a process governed in part by changes in 3D chromatin structure. How these changes regulate gene expression in this context remains unclear. In this study, we observed enrichment of the transcription factor KLF4 at some poised or closed enhancers at TSS-linked regions of genes associated with neural differentiation. Combination analysis of ChIP, HiChIP and RNA-seq data indicated that KLF4 loss in ESCs induced changes in 3D chromatin structure, including increased chromatin interaction loops between neural differentiation-associated genes and active enhancers, leading to upregulated expression of neural differentiation-associated genes and therefore early neural differentiation. This study suggests KLF4 inhibits early neural differentiation by regulation of 3D chromatin structure, which is a new mechanism of early neural differentiation.
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Affiliation(s)
| | | | - Meng Zhang
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, 300071 Tianjin, China
| | - Baoying Zhang
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, 300071 Tianjin, China
| | - Man Liu
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, 300071 Tianjin, China
| | - Guangsong Su
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, 300071 Tianjin, China
| | - Fuquan Chen
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, 300071 Tianjin, China
| | - Bohan Chen
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, 300071 Tianjin, China
| | - Tengfei Shi
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, 300071 Tianjin, China
| | - Yaoqiang Zheng
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, 300071 Tianjin, China
| | - Xueyuan Zhao
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, 300071 Tianjin, China
| | - Zhongfang Zhao
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, 300071 Tianjin, China
| | - Jiandang Shi
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, 300071 Tianjin, China
| | - Peng Li
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, 300071 Tianjin, China
| | - Lei Zhang
- Correspondence may also be addressed to Lei Zhang. Tel: +86 22 23503617; Fax: +86 22 23503617;
| | - Wange Lu
- To whom correspondence should be addressed. Tel: +86 22 23503617; Fax: +86 22 23503617;
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26
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Hu S, Metcalf E, Mahat DB, Chan L, Sohal N, Chakraborty M, Hamilton M, Singh A, Singh A, Lees JA, Sharp PA, Garg S. Transcription factor antagonism regulates heterogeneity in embryonic stem cell states. Mol Cell 2022; 82:4410-4427.e12. [PMID: 36356583 PMCID: PMC9722640 DOI: 10.1016/j.molcel.2022.10.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/19/2022] [Accepted: 10/20/2022] [Indexed: 11/10/2022]
Abstract
Gene expression heterogeneity underlies cell states and contributes to developmental robustness. While heterogeneity can arise from stochastic transcriptional processes, the extent to which it is regulated is unclear. Here, we characterize the regulatory program underlying heterogeneity in murine embryonic stem cell (mESC) states. We identify differentially active and transcribed enhancers (DATEs) across states. DATEs regulate differentially expressed genes and are distinguished by co-binding of transcription factors Klf4 and Zfp281. In contrast to other factors that interact in a positive feedback network stabilizing mESC cell-type identity, Klf4 and Zfp281 drive opposing transcriptional and chromatin programs. Abrogation of factor binding to DATEs dampens variation in gene expression, and factor loss alters kinetics of switching between states. These results show antagonism between factors at enhancers results in gene expression heterogeneity and formation of cell states, with implications for the generation of diverse cell types during development.
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Affiliation(s)
- Sofia Hu
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA
| | - Emily Metcalf
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Dig Bijay Mahat
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Lynette Chan
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Noor Sohal
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Meenakshi Chakraborty
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Maxwell Hamilton
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Arundeep Singh
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Abhyudai Singh
- Department of Electrical and Computer Engineering, University of Delaware, Newark, DE 19716, USA
| | - Jacqueline A Lees
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Phillip A Sharp
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Salil Garg
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Laboratory Medicine, Yale Stem Cell Center and Center for RNA Science and Medicine, Yale School of Medicine, New Haven, CT 06510, USA.
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27
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Carleton AE, Duncan MC, Taniguchi K. Human epiblast lumenogenesis: From a cell aggregate to a lumenal cyst. Semin Cell Dev Biol 2022; 131:117-123. [PMID: 35637065 PMCID: PMC9529837 DOI: 10.1016/j.semcdb.2022.05.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/13/2022] [Accepted: 05/13/2022] [Indexed: 12/14/2022]
Abstract
The formation of a central lumen in the human epiblast is a critical step for development. However, because the lumen forms in the epiblast coincident with implantation, the molecular and cellular events of this early lumenogenesis process cannot be studied in vivo. Recent developments using new model systems have revealed insight into the underpinnings of epiblast formation. To provide an up-to-date comprehensive review of human epiblast lumenogenesis, we highlight recent findings from human and mouse models with an emphasis on new molecular understanding of a newly described apicosome compartment, a novel 'formative' state of pluripotency that coordinates with epiblast polarization, and new evidence about the physical and polarized trafficking mechanisms contributing to lumenogenesis.
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Affiliation(s)
- Amber E. Carleton
- Departments of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin USA
| | - Mara C. Duncan
- Departments of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan USA,Co-corresponding authors
| | - Kenichiro Taniguchi
- Departments of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin USA,Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin USA,Co-corresponding authors
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28
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López-Anguita N, Gassaloglu SI, Stötzel M, Bolondi A, Conkar D, Typou M, Buschow R, Veenvliet JV, Bulut-Karslioglu A. Hypoxia induces an early primitive streak signature, enhancing spontaneous elongation and lineage representation in gastruloids. Development 2022; 149:dev200679. [PMID: 36102628 PMCID: PMC9578691 DOI: 10.1242/dev.200679] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 08/03/2022] [Indexed: 11/20/2022]
Abstract
The cellular microenvironment, together with intrinsic regulators, shapes stem cell identity and differentiation capacity. Mammalian early embryos are exposed to hypoxia in vivo and appear to benefit from hypoxic culture in vitro. Yet, how hypoxia influences stem cell transcriptional networks and lineage choices remain poorly understood. Here, we investigated the molecular effects of acute and prolonged hypoxia on embryonic and extra-embryonic stem cells as well as the functional impact on differentiation potential. We find a temporal and cell type-specific transcriptional response including an early primitive streak signature in hypoxic embryonic stem cells mediated by HIF1α. Using a 3D gastruloid differentiation model, we show that hypoxia-induced T expression enables symmetry breaking and axial elongation in the absence of exogenous WNT activation. When combined with exogenous WNT activation, hypoxia enhances lineage representation in gastruloids, as demonstrated by highly enriched signatures of gut endoderm, notochord, neuromesodermal progenitors and somites. Our findings directly link the microenvironment to stem cell function and provide a rationale supportive of applying physiological conditions in models of embryo development.
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Affiliation(s)
- Natalia López-Anguita
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
- Institute of Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany
| | - Seher Ipek Gassaloglu
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
- Stembryogenesis Lab, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Maximilian Stötzel
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
- Institute of Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany
| | - Adriano Bolondi
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
- Institute of Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany
| | - Deniz Conkar
- Stembryogenesis Lab, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Marina Typou
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
- Medical School, Democritus University of Thrace, 681 00 Alexandroupoli, Greece
- Department of Biomedical Sciences, International Hellenic University, 570 01, Thessaloniki, Greece
| | - René Buschow
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Jesse V. Veenvliet
- Stembryogenesis Lab, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Cluster of Excellence Physics of Life, Technische Universität Dresden, 01307 Dresden, Germany
| | - Aydan Bulut-Karslioglu
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
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Vrij EJ, Scholte op Reimer YS, Fuentes LR, Guerreiro IM, Holzmann V, Aldeguer JF, Sestini G, Koo BK, Kind J, van Blitterswijk CA, Rivron NC. A pendulum of induction between the epiblast and extra-embryonic endoderm supports post-implantation progression. Development 2022; 149:dev192310. [PMID: 35993866 PMCID: PMC9534490 DOI: 10.1242/dev.192310] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 06/23/2022] [Indexed: 08/17/2023]
Abstract
Embryogenesis is supported by dynamic loops of cellular interactions. Here, we create a partial mouse embryo model to elucidate the principles of epiblast (Epi) and extra-embryonic endoderm co-development (XEn). We trigger naive mouse embryonic stem cells to form a blastocyst-stage niche of Epi-like cells and XEn-like cells (3D, hydrogel free and serum free). Once established, these two lineages autonomously progress in minimal medium to form an inner pro-amniotic-like cavity surrounded by polarized Epi-like cells covered with visceral endoderm (VE)-like cells. The progression occurs through reciprocal inductions by which the Epi supports the primitive endoderm (PrE) to produce a basal lamina that subsequently regulates Epi polarization and/or cavitation, which, in return, channels the transcriptomic progression to VE. This VE then contributes to Epi bifurcation into anterior- and posterior-like states. Similarly, boosting the formation of PrE-like cells within blastoids supports developmental progression. We argue that self-organization can arise from lineage bifurcation followed by a pendulum of induction that propagates over time.
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Affiliation(s)
- Erik J. Vrij
- MERLN Institute for Technology-inspired Regenerative Medicine, Maastricht University, Universiteitssingel 40, 6229 ER Maastricht, Netherlands
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Yvonne S. Scholte op Reimer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Laury Roa Fuentes
- MERLN Institute for Technology-inspired Regenerative Medicine, Maastricht University, Universiteitssingel 40, 6229 ER Maastricht, Netherlands
| | - Isabel Misteli Guerreiro
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, UtrechtUppsalalaan 8, 3584 CT Utrecht, Netherlands
| | - Viktoria Holzmann
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Javier Frias Aldeguer
- MERLN Institute for Technology-inspired Regenerative Medicine, Maastricht University, Universiteitssingel 40, 6229 ER Maastricht, Netherlands
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, UtrechtUppsalalaan 8, 3584 CT Utrecht, Netherlands
| | - Giovanni Sestini
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Bon-Kyoung Koo
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Jop Kind
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, UtrechtUppsalalaan 8, 3584 CT Utrecht, Netherlands
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, Netherlands
| | - Clemens A. van Blitterswijk
- MERLN Institute for Technology-inspired Regenerative Medicine, Maastricht University, Universiteitssingel 40, 6229 ER Maastricht, Netherlands
| | - Nicolas C. Rivron
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
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30
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Sukparangsi W, Morganti E, Lowndes M, Mayeur H, Weisser M, Hammachi F, Peradziryi H, Roske F, Hölzenspies J, Livigni A, Godard BG, Sugahara F, Kuratani S, Montoya G, Frankenberg SR, Mazan S, Brickman JM. Evolutionary origin of vertebrate OCT4/POU5 functions in supporting pluripotency. Nat Commun 2022; 13:5537. [PMID: 36130934 PMCID: PMC9492771 DOI: 10.1038/s41467-022-32481-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 07/30/2022] [Indexed: 12/31/2022] Open
Abstract
The support of pluripotent cells over time is an essential feature of development. In eutherian embryos, pluripotency is maintained from naïve states in peri-implantation to primed pluripotency at gastrulation. To understand how these states emerged, we reconstruct the evolutionary trajectory of the Pou5 gene family, which contains the central pluripotency factor OCT4. By coupling evolutionary sequence analysis with functional studies in mouse embryonic stem cells, we find that the ability of POU5 proteins to support pluripotency originated in the gnathostome lineage, prior to the generation of two paralogues, Pou5f1 and Pou5f3 via gene duplication. In osteichthyans, retaining both genes, the paralogues differ in their support of naïve and primed pluripotency. The specialization of these duplicates enables the diversification of function in self-renewal and differentiation. By integrating sequence evolution, cell phenotypes, developmental contexts and structural modelling, we pinpoint OCT4 regions sufficient for naïve pluripotency and describe their adaptation over evolutionary time.
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Affiliation(s)
- Woranop Sukparangsi
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 3B Blegdamsvej, 2200, Copenhagen, Denmark.,Department of Biology, Faculty of Science, Burapha University, Chon Buri, Thailand
| | - Elena Morganti
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 3B Blegdamsvej, 2200, Copenhagen, Denmark
| | - Molly Lowndes
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 3B Blegdamsvej, 2200, Copenhagen, Denmark
| | - Hélène Mayeur
- CNRS, Sorbonne Université, Biologie Intégrative des Organismes Marins, UMR7232, F-66650, Banyuls sur Mer, France
| | - Melanie Weisser
- Structural Molecular Biology Group, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 3B Blegdamsvej, 2200, Copenhagen, Denmark
| | - Fella Hammachi
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, 5 Little France Drive, University of Edinburgh, Edinburgh, EH16 4UU, UK
| | - Hanna Peradziryi
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 3B Blegdamsvej, 2200, Copenhagen, Denmark
| | - Fabian Roske
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 3B Blegdamsvej, 2200, Copenhagen, Denmark
| | - Jurriaan Hölzenspies
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 3B Blegdamsvej, 2200, Copenhagen, Denmark
| | - Alessandra Livigni
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, 5 Little France Drive, University of Edinburgh, Edinburgh, EH16 4UU, UK
| | - Benoit Gilbert Godard
- CNRS, Sorbonne Université, UPMC Univ Paris 06, FR2424, Development and Evolution of Vertebrates Group, Station Biologique, F-29688, Roscoff, France.,CNRS, Sorbonne Université, Laboratoire de Biologie du Développement de Villefranche, UMR7009, F-06234, Villefranche sur Mer, France
| | - Fumiaki Sugahara
- Division of Biology, Hyogo College of Medicine, Nishinomiya, Hyogo, Japan
| | - Shigeru Kuratani
- Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
| | - Guillermo Montoya
- Structural Molecular Biology Group, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 3B Blegdamsvej, 2200, Copenhagen, Denmark
| | | | - Sylvie Mazan
- CNRS, Sorbonne Université, Biologie Intégrative des Organismes Marins, UMR7232, F-66650, Banyuls sur Mer, France.
| | - Joshua M Brickman
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, 3B Blegdamsvej, 2200, Copenhagen, Denmark.
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31
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Endoh M, Niwa H. Stepwise pluripotency transitions in mouse stem cells. EMBO Rep 2022; 23:e55010. [PMID: 35903955 PMCID: PMC9442314 DOI: 10.15252/embr.202255010] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 05/13/2022] [Accepted: 07/01/2022] [Indexed: 07/31/2023] Open
Abstract
Pluripotent cells in mouse embryos, which first emerge in the inner cell mass of the blastocyst, undergo gradual transition marked by changes in gene expression, developmental potential, polarity, and morphology as they develop from the pre-implantation until post-implantation gastrula stage. Recent studies of cultured mouse pluripotent stem cells (PSCs) have clarified the presence of intermediate pluripotent stages between the naïve pluripotent state represented by embryonic stem cells (ESCs-equivalent to the pre-implantation epiblast) and the primed pluripotent state represented by epiblast stem cells (EpiSCs-equivalent to the late post-implantation gastrula epiblast). In this review, we discuss these recent findings in light of our knowledge on peri-implantation mouse development and consider the implications of these new PSCs to understand their temporal sequence and the feasibility of using them as model system for pluripotency.
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Affiliation(s)
- Mitsuhiro Endoh
- Department of Pluripotent Stem Cell Biology, Institute of Molecular Embryology and Genetics (IMEG)Kumamoto UniversityKumamotoJapan
| | - Hitoshi Niwa
- Department of Pluripotent Stem Cell Biology, Institute of Molecular Embryology and Genetics (IMEG)Kumamoto UniversityKumamotoJapan
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32
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H3K27me3 at pericentromeric heterochromatin is a defining feature of the early mouse blastocyst. Sci Rep 2022; 12:13908. [PMID: 35974030 PMCID: PMC9381757 DOI: 10.1038/s41598-022-17730-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 07/29/2022] [Indexed: 11/09/2022] Open
Abstract
Early mouse development is characterized by structural and epigenetic changes while cells progress towards differentiation. At blastocyst stage, the segregation of the three primordial lineages is accompanied by establishment of differential patterns of DNA methylation and post-translational modifications of histones, such as H3K27me3. Here, we analysed the dynamics of H3K27me3 at pericentromeric heterochromatin (PCH) during early development. We also followed the localization of EZH2 and BEND3, previously shown in ESCs to drive PRC2 to hypomethylated PCH. We show that the location of H3K27me3 at PCH, in addition to H3K9me3, is a defining feature of embryonic cells in vivo. Moreover, it may play an important role in structuring PCH and preserving genomic integrity at a time of globally relaxed chromatin. At peri-implantation stages, while DNA methylation is still low, EZH2 and then H3K27me3, leave PCH in epiblast progenitors at the time of their spatial segregation from primitive endoderm cells, while BEND3 remains there up to implantation. The comparison with stem cells (ESCs and TSCs) reveals that the epigenetic marks (i.e. H3K9me3 and H3K27me3) of PCH are reset during in vitro derivation and only partially restored thereafter. This highlights possible divergences between in vitro and "in embryo" epigenetic regulation regarding constitutive heterochromatin.
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33
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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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34
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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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35
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Ávila-González D, Portillo W, Barragán-Álvarez CP, Hernandez-Montes G, Flores-Garza E, Molina-Hernández A, Diaz-Martinez NE, Diaz NF. The human amniotic epithelium confers a bias to differentiate toward the neuroectoderm lineage in human embryonic stem cells. eLife 2022; 11:68035. [PMID: 35815953 PMCID: PMC9313526 DOI: 10.7554/elife.68035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 07/08/2022] [Indexed: 11/28/2022] Open
Abstract
Human embryonic stem cells (hESCs) derive from the epiblast and have pluripotent potential. To maintain the conventional conditions of the pluripotent potential in an undifferentiated state, inactivated mouse embryonic fibroblast (iMEF) is used as a feeder layer. However, it has been suggested that hESC under this conventional condition (hESC-iMEF) is an artifact that does not correspond to the in vitro counterpart of the human epiblast. Our previous studies demonstrated the use of an alternative feeder layer of human amniotic epithelial cells (hAECs) to derive and maintain hESC. We wondered if the hESC-hAEC culture could represent a different pluripotent stage than that of naïve or primed conventional conditions, simulating the stage in which the amniotic epithelium derives from the epiblast during peri-implantation. Like the conventional primed hESC-iMEF, hESC-hAEC has the same levels of expression as the ‘pluripotency core’ and does not express markers of naïve pluripotency. However, it presents a downregulation of HOX genes and genes associated with the endoderm and mesoderm, and it exhibits an increase in the expression of ectoderm lineage genes, specifically in the anterior neuroectoderm. Transcriptome analysis showed in hESC-hAEC an upregulated signature of genes coding for transcription factors involved in neural induction and forebrain development, and the ability to differentiate into a neural lineage was superior in comparison with conventional hESC-iMEF. We propose that the interaction of hESC with hAEC confers hESC a biased potential that resembles the anteriorized epiblast, which is predisposed to form the neural ectoderm.
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Affiliation(s)
- Daniela Ávila-González
- Fisiología y Desarrollo Celular, Instituto Nacional de Perinatología Isidro Espinosa de los Reyes, Mexico City, Mexico
| | - Wendy Portillo
- Behavioral and Cognitive Neurobiology, Universidad Nacional Autónoma de México, Querétaro, Mexico
| | - Carla P Barragán-Álvarez
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, Guadalajara, Mexico
| | | | - Eliezer Flores-Garza
- Departamento de Biología Molecular y Biotecnología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Anayansi Molina-Hernández
- Fisiología y Desarrollo Celular, Instituto Nacional de Perinatología Isidro Espinosa de los Reyes, Mexico City, Mexico
| | | | - Nestor F Diaz
- Fisiología y Desarrollo Celular, Instituto Nacional de Perinatología Isidro Espinosa de los Reyes, Mexico City, Mexico
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36
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Minchiotti G, D’Aniello C, Fico A, De Cesare D, Patriarca EJ. Capturing Transitional Pluripotency through Proline Metabolism. Cells 2022; 11:cells11142125. [PMID: 35883568 PMCID: PMC9323356 DOI: 10.3390/cells11142125] [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: 06/10/2022] [Revised: 07/01/2022] [Accepted: 07/04/2022] [Indexed: 12/03/2022] Open
Abstract
In this paper, we summarize the current knowledge of the role of proline metabolism in the control of the identity of Embryonic Stem Cells (ESCs). An imbalance in proline metabolism shifts mouse ESCs toward a stable naïve-to-primed intermediate state of pluripotency. Proline-induced cells (PiCs), also named primitive ectoderm-like cells (EPLs), are phenotypically metastable, a trait linked to a rapid and reversible relocalization of E-cadherin from the plasma membrane to intracellular membrane compartments. The ESC-to-PiC transition relies on the activation of Erk and Tgfβ/Activin signaling pathways and is associated with extensive remodeling of the transcriptome, metabolome and epigenome. PiCs maintain several properties of naïve pluripotency (teratoma formation, blastocyst colonization and 3D gastruloid development) and acquire a few traits of primed cells (flat-shaped colony morphology, aerobic glycolysis metabolism and competence for primordial germ cell fate). Overall, the molecular and phenotypic features of PiCs resemble those of an early-primed state of pluripotency, providing a robust model to study the role of metabolic perturbations in pluripotency and cell fate decisions.
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37
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Quan Y, Wang M, Xu C, Wang X, Wu Y, Qin D, Lin Y, Lu X, Lu F, Li L. Cnot8 eliminates naïve regulation networks and is essential for naïve-to-formative pluripotency transition. Nucleic Acids Res 2022; 50:4414-4435. [PMID: 35390160 PMCID: PMC9071485 DOI: 10.1093/nar/gkac236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 03/11/2022] [Accepted: 03/26/2022] [Indexed: 11/14/2022] Open
Abstract
Mammalian early epiblasts at different phases are characterized by naïve, formative, and primed pluripotency states, involving extensive transcriptome changes. Here, we report that deadenylase Cnot8 of Ccr4-Not complex plays essential roles during the transition from naïve to formative state. Knock out (KO) Cnot8 resulted in early embryonic lethality in mice, but Cnot8 KO embryonic stem cells (ESCs) could be established. Compared with the cells differentiated from normal ESCs, Cnot8 KO cells highly expressed a great many genes during their differentiation into the formative state, including several hundred naïve-like genes enriched in lipid metabolic process and gene expression regulation that may form the naïve regulation networks. Knockdown expression of the selected genes of naïve regulation networks partially rescued the differentiation defects of Cnot8 KO ESCs. Cnot8 depletion led to the deadenylation defects of its targets, increasing their poly(A) tail lengths and half-life, eventually elevating their expression levels. We further found that Cnot8 was involved in the clearance of targets through its deadenylase activity and the binding of Ccr4-Not complex, as well as the interacting with Tob1 and Pabpc1. Our results suggest that Cnot8 eliminates naïve regulation networks through mRNA clearance, and is essential for naïve-to-formative pluripotency transition.
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Affiliation(s)
- Yujun Quan
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meijiao Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Chengpeng Xu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoxiao Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yu Wu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dandan Qin
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuxuan Lin
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xukun Lu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Falong Lu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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38
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Quan Y, Wang X, Li L. In vitro investigation of mammalian peri-implantation embryogenesis†. Biol Reprod 2022; 107:205-211. [PMID: 35294001 DOI: 10.1093/biolre/ioac055] [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: 12/29/2021] [Revised: 03/02/2022] [Accepted: 03/03/2022] [Indexed: 11/14/2022] Open
Abstract
The embryos attach and invade into the uterus and establish the connection with their mother in peri-implantation development. During this period, the pluripotent epiblast cells of embryo undergo symmetry breaking, cell lineage allocation, and morphogenetic remodeling, accompanying with the dramatic changes of transcriptome, epigenome, and signal pathways, to prepare a state for their differentiation and gastrulation. The progresses in mouse genetics and stem cell biology have largely advanced the knowledge of these transformations which are largely hindered by the hard accessibility of natural embryos. To gain insight into mammalian peri-implantation development, great efforts have been made in the field. Recently, the advances in the prolonged in vitro culture of blastocysts, the derivation of multiple pluripotent stem cells, as well as the construction of stem cell-based embryo-like models have opened novel avenues to investigate peri-implantation development in mammals, especially for the humans. Combining with other emerging new technologies, these new models will substantially promote the comprehension of mammalian peri-implantation development, accelerating the progress of reproductive and regenerative medicine.
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Affiliation(s)
- Yujun Quan
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoxiao Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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39
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Luijkx D, Shankar V, van Blitterswijk C, Giselbrecht S, Vrij E. From Mice to Men: Generation of Human Blastocyst-Like Structures In Vitro. Front Cell Dev Biol 2022; 10:838356. [PMID: 35359453 PMCID: PMC8963787 DOI: 10.3389/fcell.2022.838356] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/26/2022] [Indexed: 01/04/2023] Open
Abstract
Advances in the field of stem cell-based models have in recent years lead to the development of blastocyst-like structures termed blastoids. Blastoids can be used to study key events in mammalian pre-implantation development, as they mimic the blastocyst morphologically and transcriptionally, can progress to the post-implantation stage and can be generated in large numbers. Blastoids were originally developed using mouse pluripotent stem cells, and since several groups have successfully generated blastocyst models of the human system. Here we provide a comparison of the mouse and human protocols with the aim of deriving the core requirements for blastoid formation, discuss the models’ current ability to mimic blastocysts and give an outlook on potential future applications.
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Affiliation(s)
| | | | | | | | - Erik Vrij
- *Correspondence: Erik Vrij, ; Stefan Giselbrecht,
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40
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Gordeev MN, Bakhmet EI, Tomilin AN. Pluripotency Dynamics during Embryogenesis and in Cell Culture. Russ J Dev Biol 2021. [DOI: 10.1134/s1062360421060059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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41
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Induction of Rosette-to-Lumen stage embryoids using reprogramming paradigms in ESCs. Nat Commun 2021; 12:7322. [PMID: 34916498 PMCID: PMC8677818 DOI: 10.1038/s41467-021-27586-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 11/19/2021] [Indexed: 01/01/2023] Open
Abstract
Blastocyst-derived stem cell lines were shown to self-organize into embryo-like structures in 3D cell culture environments. Here, we provide evidence that embryo-like structures can be generated solely based on transcription factor-mediated reprogramming of embryonic stem cells in a simple 3D co-culture system. Embryonic stem cells in these cultures self-organize into elongated, compartmentalized embryo-like structures reflecting aspects of the inner regions of the early post-implantation embryo. Single-cell RNA-sequencing reveals transcriptional profiles resembling epiblast, primitive-/visceral endoderm, and extraembryonic ectoderm of early murine embryos around E4.5-E5.5. In this stem cell-based embryo model, progression from rosette formation to lumenogenesis accompanied by progression from naïve- to primed pluripotency was observed within Epi-like cells. Additionally, lineage specification of primordial germ cells and distal/anterior visceral endoderm-like cells was observed in epiblast- or visceral endoderm-like compartments, respectively. The system presented in this study allows for fast and reproducible generation of embryo-like structures, providing an additional tool to study aspects of early embryogenesis.
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42
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Loh CH, van Genesen S, Perino M, Bark MR, Veenstra GJC. Loss of PRC2 subunits primes lineage choice during exit of pluripotency. Nat Commun 2021; 12:6985. [PMID: 34848733 PMCID: PMC8632979 DOI: 10.1038/s41467-021-27314-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 11/09/2021] [Indexed: 12/11/2022] Open
Abstract
Polycomb Repressive Complex 2 (PRC2) is crucial for the coordinated expression of genes during early embryonic development, catalyzing histone H3 lysine 27 trimethylation. Two distinct PRC2 complexes, PRC2.1 and PRC2.2, contain respectively MTF2 and JARID2 in embryonic stem cells (ESCs). In this study, we explored their roles in lineage specification and commitment, using single-cell transcriptomics and mouse embryoid bodies derived from Mtf2 and Jarid2 null ESCs. We observe that the loss of Mtf2 results in enhanced and faster differentiation towards cell fates from all germ layers, while the Jarid2 null cells are predominantly directed towards early differentiating precursors, with reduced efficiency towards mesendodermal lineages. These effects are caused by derepression of developmental regulators that are poised for activation in pluripotent cells and gain H3K4me3 at their promoters in the absence of PRC2 repression. Upon lineage commitment, the differentiation trajectories are relatively similar to those of wild-type cells. Together, our results uncover a major role for MTF2-containing PRC2.1 in balancing poised lineage-specific gene activation, whereas the contribution of JARID2-containing PRC2 is more selective in nature compared to MTF2. These data explain how PRC2 imposes thresholds for lineage choice during the exit of pluripotency.
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Affiliation(s)
- Chet H. Loh
- grid.5590.90000000122931605Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - Siebe van Genesen
- grid.5590.90000000122931605Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - Matteo Perino
- grid.5590.90000000122931605Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands ,grid.4709.a0000 0004 0495 846XPresent Address: Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Magnus R. Bark
- grid.5590.90000000122931605Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - Gert Jan C. Veenstra
- grid.5590.90000000122931605Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
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43
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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: 39] [Impact Index Per Article: 13.0] [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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44
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Vega-Sendino M, Olbrich T, Tillo D, Tran AD, Domingo CN, Franco M, FitzGerald PC, Kruhlak MJ, Ruiz S. The ETS transcription factor ERF controls the exit from the naïve pluripotent state in a MAPK-dependent manner. SCIENCE ADVANCES 2021; 7:eabg8306. [PMID: 34597136 DOI: 10.1126/sciadv.abg8306] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The naïve epiblast transitions to a pluripotent primed state during embryo implantation. Despite the relevance of the FGF pathway during this period, little is known about the downstream effectors regulating this signaling. Here, we examined the molecular mechanisms coordinating the naïve to primed transition by using inducible ESC to genetically eliminate all RAS proteins. We show that differentiated RASKO ESC remain trapped in an intermediate state of pluripotency with naïve-associated features. Elimination of the transcription factor ERF overcomes the developmental blockage of RAS-deficient cells by naïve enhancer decommissioning. Mechanistically, ERF regulates NANOG expression and ensures naïve pluripotency by strengthening naïve transcription factor binding at ESC enhancers. Moreover, ERF negatively regulates the expression of the methyltransferase DNMT3B, which participates in the extinction of the naïve transcriptional program. Collectively, we demonstrated an essential role for ERF controlling the exit from naïve pluripotency in a MAPK-dependent manner during the progression to primed pluripotency.
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Affiliation(s)
- Maria Vega-Sendino
- Laboratory of Genome Integrity, CCR, NCI, National Institutes of Health, Bethesda, MD, USA
| | - Teresa Olbrich
- Laboratory of Genome Integrity, CCR, NCI, National Institutes of Health, Bethesda, MD, USA
| | - Desiree Tillo
- Genetics Branch, CCR, NCI, National Institutes of Health, National Institutes of Health, Bethesda, MD, USA
| | - Andy D Tran
- Laboratory of Cancer Biology and Genetics, CCR, NCI, National Institutes of Health, Bethesda, MD, USA
| | - Catherine N Domingo
- Laboratory of Genome Integrity, CCR, NCI, National Institutes of Health, Bethesda, MD, USA
| | - Mariajose Franco
- Laboratory of Genome Integrity, CCR, NCI, National Institutes of Health, Bethesda, MD, USA
| | - Peter C FitzGerald
- Genome Analysis Unit, CCR, NCI, National Institutes of Health, Bethesda, MD, USA
| | - Michael J Kruhlak
- Laboratory of Cancer Biology and Genetics, CCR, NCI, National Institutes of Health, Bethesda, MD, USA
| | - Sergio Ruiz
- Laboratory of Genome Integrity, CCR, NCI, National Institutes of Health, Bethesda, MD, USA
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45
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Saba JA, Liakath-Ali K, Green R, Watt FM. Translational control of stem cell function. Nat Rev Mol Cell Biol 2021; 22:671-690. [PMID: 34272502 DOI: 10.1038/s41580-021-00386-2] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/27/2021] [Indexed: 12/22/2022]
Abstract
Stem cells are characterized by their ability to self-renew and differentiate into many different cell types. Research has focused primarily on how these processes are regulated at a transcriptional level. However, recent studies have indicated that stem cell behaviour is strongly coupled to the regulation of protein synthesis by the ribosome. In this Review, we discuss how different translation mechanisms control the function of adult and embryonic stem cells. Stem cells are characterized by low global translation rates despite high levels of ribosome biogenesis. The maintenance of pluripotency, the commitment to a specific cell fate and the switch to cell differentiation depend on the tight regulation of protein synthesis and ribosome biogenesis. Translation regulatory mechanisms that impact on stem cell function include mTOR signalling, ribosome levels, and mRNA and tRNA features and amounts. Understanding these mechanisms important for stem cell self-renewal and differentiation may also guide our understanding of cancer grade and metastasis.
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Affiliation(s)
- James A Saba
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kifayathullah Liakath-Ali
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Rachel Green
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Fiona M Watt
- King's College London Centre for Stem Cells and Regenerative Medicine, Guy's Hospital, London, UK.
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46
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Junyent S, Reeves J, Habib SJ. Assessing the Wnt-reactivity of cytonemes of mouse embryonic stem cells using a bioengineering approach. STAR Protoc 2021; 2:100813. [PMID: 34568840 PMCID: PMC8449058 DOI: 10.1016/j.xpro.2021.100813] [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] [Indexed: 11/02/2022] Open
Abstract
These protocols investigate the interaction of cytonemes with localized Wnt. Cell-niche signaling between naive or primed mouse embryonic stem cells (ESCs) and either Wnt-secreting trophoblast stem cells (TSCs) or Wnt signals tethered to microbeads can be scrutinized in vitro. This approach analyzes cytoneme reactivity during Wnt-interaction initiation, Ca2+ transients at Wnt-contacting cytonemes, and subsequent pairing between ESCs and Wnt-sources. This pairing interaction is crucial to synthetic embryogenesis; hence this protocol is effective for in vitro studies of developmental biology. For complete details on the use and execution of this protocol, please refer to Junyent et al. (2020, 2021a, 2021b).
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Affiliation(s)
- Sergi Junyent
- Centre for Stem Cells and Regenerative Medicine, King’s College London, London SE1 9RT, UK
| | - Joshua Reeves
- Centre for Stem Cells and Regenerative Medicine, King’s College London, London SE1 9RT, UK
| | - Shukry J. Habib
- Centre for Stem Cells and Regenerative Medicine, King’s College London, London SE1 9RT, UK
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47
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Wei M, Chen Y, Zhao C, Zheng L, Wu B, Chen C, Li X, Bao S. Establishment of Mouse Primed Stem Cells by Combination of Activin and LIF Signaling. Front Cell Dev Biol 2021; 9:713503. [PMID: 34422831 PMCID: PMC8375391 DOI: 10.3389/fcell.2021.713503] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 07/09/2021] [Indexed: 01/09/2023] Open
Abstract
In mice, embryonic stem cells (ESCs) and epiblast stem cells (EpiSCs) are established from pre- and post-implantation embryos and represent the naive and primed state, respectively. Herein we used mouse leukemia inhibitory factor (LIF), which supports ESCs self-renewal and Activin A (Act A), which is the main factor in maintaining EpiSCs in post-implantation epiblast cultures, to derive a primed stem cell line named ALSCs. Like EpiSCs, ALSCs express key pluripotent genes Oct4, Sox2, and Nanog; one X chromosome was inactivated; and the cells failed to contribute to chimera formation in vivo. Notably, compared to EpiSCs, ALSCs efficiently reversed to ESCs (rESCs) on activation of Wnt signaling. Moreover, we also discovered that culturing EpiSCs in AL medium for several passages favored Wnt signaling-driven naive pluripotency. Our results show that ALSCs is a primed state stem cell and represents a simple model to study the control of pluripotency fate and conversion from the primed to the naive state.
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Affiliation(s)
- Mengyi Wei
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, China.,Institute of Animal Genetic Research of Mongolia Plateau, College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Yanglin Chen
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, China.,Institute of Animal Genetic Research of Mongolia Plateau, College of Life Sciences, Inner Mongolia University, Hohhot, China.,School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Chaoyue Zhao
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, China.,Institute of Animal Genetic Research of Mongolia Plateau, College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Li Zheng
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, China.,Institute of Animal Genetic Research of Mongolia Plateau, College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Baojiang Wu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, China.,Institute of Animal Genetic Research of Mongolia Plateau, College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Chen Chen
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, China.,Institute of Animal Genetic Research of Mongolia Plateau, College of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Xihe Li
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, China.,Institute of Animal Genetic Research of Mongolia Plateau, College of Life Sciences, Inner Mongolia University, Hohhot, China.,Inner Mongolia Saikexing Institute of Breeding and Reproductive Biotechnology in Domestic Animal, Hohhot, China
| | - Siqin Bao
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, China.,Institute of Animal Genetic Research of Mongolia Plateau, College of Life Sciences, Inner Mongolia University, Hohhot, China
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48
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Udomlumleart T, Hu S, Garg S. Lineages of embryonic stem cells show non-Markovian state transitions. iScience 2021; 24:102879. [PMID: 34401663 PMCID: PMC8353490 DOI: 10.1016/j.isci.2021.102879] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 06/13/2021] [Accepted: 07/15/2021] [Indexed: 11/24/2022] Open
Abstract
Pluripotent embryonic stem cells (ESCs) constitute the cell types of the adult vertebrate through a series of developmental state transitions. These states can be defined by expression levels of marker genes, such as Nanog and Sox2. In culture, ESCs reversibly transition between states. However, whether ESCs retain memory of their previous states or transition in a memoryless (Markovian) process remains relatively unknown. Here, we show some highly dynamic lineages of ESCs do not exhibit the Markovian property: their previous states and kin relations influence future choices. Unexpectedly, the distribution of lineages across their composition between states is constant over time, contrasting with the predictions of a Markov model. Additionally, highly dynamic ESC lineages show skewed cell fate distributions after retinoic acid differentiation. Together, these data suggest ESC lineage is an important variable governing future cell states, with implications for stem cell function and development.
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Affiliation(s)
- Tee Udomlumleart
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Sofia Hu
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Harvard-MIT MD PhD Program, Harvard Medical School, Boston, MA 02115, USA
| | - Salil Garg
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
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49
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Building Pluripotency Identity in the Early Embryo and Derived Stem Cells. Cells 2021; 10:cells10082049. [PMID: 34440818 PMCID: PMC8391114 DOI: 10.3390/cells10082049] [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: 12/11/2020] [Revised: 07/27/2021] [Accepted: 08/06/2021] [Indexed: 12/13/2022] Open
Abstract
The fusion of two highly differentiated cells, an oocyte with a spermatozoon, gives rise to the zygote, a single totipotent cell, which has the capability to develop into a complete, fully functional organism. Then, as development proceeds, a series of programmed cell divisions occur whereby the arising cells progressively acquire their own cellular and molecular identity, and totipotency narrows until when pluripotency is achieved. The path towards pluripotency involves transcriptome modulation, remodeling of the chromatin epigenetic landscape to which external modulators contribute. Both human and mouse embryos are a source of different types of pluripotent stem cells whose characteristics can be captured and maintained in vitro. The main aim of this review is to address the cellular properties and the molecular signature of the emerging cells during mouse and human early development, highlighting similarities and differences between the two species and between the embryos and their cognate stem cells.
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50
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Wu J, Barbaric I. Fitness selection in human pluripotent stem cells and interspecies chimeras: Implications for human development and regenerative medicine. Dev Biol 2021; 476:209-217. [PMID: 33891964 PMCID: PMC8209287 DOI: 10.1016/j.ydbio.2021.03.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/25/2021] [Accepted: 03/30/2021] [Indexed: 12/12/2022]
Abstract
A small number of pluripotent cells within early embryo gives rise to all cells in the adult body, including germ cells. Hence, any mutations occurring in the pluripotent cell population are at risk of being propagated to their daughter cells and could lead to congenital defects or embryonic lethality and pose a risk of being transmitted to future generations. The observation that genetic errors are relatively common in preimplantation embryos, but their levels reduce as development progresses, suggests the existence of mechanisms for clearance of aberrant, unfit or damaged cells. Although early human embryogenesis is largely experimentally inaccessible, pluripotent stem cell (PSC) lines can be derived either from the inner cell mass (ICM) of a blastocyst or by reprogramming somatic cells into an embryonic stem cell-like state. PSCs retain the ability to differentiate into any cell type in vitro and, hence, they represent a unique and powerful tool for studying otherwise intractable stages of human development. The advent of PSCs has also opened up a possibility of developing regenerative medicine therapies, either through PSC differentiation in vitro or by creating interspecies chimeras for organ replacement. Here, we discuss the emerging evidence of cell selection in human PSC populations in vivo and in vitro and we highlight the implications of understanding this phenomenon for human development and regenerative medicine.
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Affiliation(s)
- Jun Wu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
| | - Ivana Barbaric
- Centre for Stem Cell Biology, Department of Biomedical Science, The University of Sheffield, Western Bank, Sheffield, S10 2TN, United Kingdom; Neuroscience Institute, The University of Sheffield, Western Bank, Sheffield, S10 2TN, United Kingdom.
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