1
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Strauss ME, Ton MLN, Mason S, Bagri J, Harland LT, Imaz-Rosshandler I, Wilson NK, Nichols J, Tyser RC, Göttgens B, Marioni JC, Guibentif C. A single-cell and tissue-scale analysis suite resolves Mixl1's role in heart development. iScience 2025; 28:112397. [PMID: 40330894 PMCID: PMC12051648 DOI: 10.1016/j.isci.2025.112397] [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: 12/14/2023] [Revised: 12/10/2024] [Accepted: 04/07/2025] [Indexed: 05/08/2025] Open
Abstract
Perturbation studies using gene knockouts have become a key tool for understanding the roles of regulatory genes in development. However, large-scale studies dissecting the molecular role of development master regulators in every cell type throughout the embryo are technically challenging and scarce. Here, we systematically characterize the knockout effects of the key developmental regulators T/Brachyury and Mixl1 in gastrulation and early organogenesis using single-cell profiling of chimeric mouse embryos. For the analysis of these experimental data, we present COSICC, an effective suite of statistical tools to characterize perturbation effects in complex developing cell populations. We gain insights into T's role in lateral plate mesoderm, limb development, and posterior intermediate mesoderm specification. Furthermore, we generate Mixl1 -/- embryonic chimeras and reveal the role of this key transcription factor in discrete mesoderm lineages, in particular concerning developmental dysregulation of the recently identified juxta-cardiac field.
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Affiliation(s)
- Magdalena E. Strauss
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK
- Department of Mathematics and Statistics, University of Exeter, Exeter EX4 4PY, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Mai-Linh Nu Ton
- Department of Haematology, University of Cambridge, Cambridge CB2 0AW, UK
- Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Samantha Mason
- Department of Haematology, University of Cambridge, Cambridge CB2 0AW, UK
- Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Jaana Bagri
- Department of Haematology, University of Cambridge, Cambridge CB2 0AW, UK
- Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Luke T.G. Harland
- Department of Haematology, University of Cambridge, Cambridge CB2 0AW, UK
- Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | | | - Nicola K. Wilson
- Department of Haematology, University of Cambridge, Cambridge CB2 0AW, UK
- Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Jennifer Nichols
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Richard C.V. Tyser
- Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Berthold Göttgens
- Department of Haematology, University of Cambridge, Cambridge CB2 0AW, UK
- Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - John C. Marioni
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK
| | - Carolina Guibentif
- Institute Biomedicine, Department of Microbiology and Immunology, Sahlgrenska Center for Cancer Research, University of Gothenburg, 413 90 Gothenburg, Sweden
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2
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Chen B, Khan H, Yu Z, Yao L, Freeburne E, Jo K, Johnson C, Heemskerk I. Extended culture of 2D gastruloids to model human mesoderm development. Nat Methods 2025:10.1038/s41592-025-02669-4. [PMID: 40335707 DOI: 10.1038/s41592-025-02669-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 03/18/2025] [Indexed: 05/09/2025]
Abstract
Micropatterned human pluripotent stem cells treated with BMP4 (two-dimensional (2D) gastruloids) are among the most widely used stem cell models for human gastrulation. Due to its simplicity and reproducibility, this system is ideal for high-throughput quantitative studies of tissue patterning and has led to many insights into the mechanisms of mammalian gastrulation. However, 2D gastruloids have been studied only up to about 2 days owing to a loss of organization beyond this time with earlier protocols. Here we report an extended 2D gastruloid model to up to 10 days. We discovered a phase of highly reproducible morphogenesis between 2 and 4 days during which directed migration from the primitive streak-like region gives rise to a mesodermal layer beneath an epiblast-like layer. Multiple types of mesoderm arise with striking spatial organization including lateral plate mesoderm-like cells on the colony border and paraxial mesoderm-like cells further inside the colony. Single-cell transcriptomics showed strong similarity of these cells to mesoderm in human and nonhuman primate embryos. Our results illustrate that extended culture of 2D gastruloids provides a powerful model for human mesoderm differentiation and morphogenesis.
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Affiliation(s)
- Bohan Chen
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Hina Khan
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Zhiyuan Yu
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - LiAng Yao
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Emily Freeburne
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Kyoung Jo
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Craig Johnson
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Idse Heemskerk
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA.
- Department of Cell and Developmental Biology, 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 Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA.
- Department of Physics, University of Michigan, Ann Arbor, MI, USA.
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3
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Azami T, Theeuwes B, Nu Ton ML, Mansfield W, Harland L, Kinoshita M, Gottgens B, Nichols J. STAT3 signaling enhances tissue expansion during postimplantation mouse development. Cell Rep 2025; 44:115506. [PMID: 40188437 DOI: 10.1016/j.celrep.2025.115506] [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: 03/03/2024] [Revised: 01/10/2025] [Accepted: 03/12/2025] [Indexed: 04/08/2025] Open
Abstract
Signal transducer and activator of transcription (STAT)3 signaling has been studied extensively using mouse embryonic stem cells. Zygotic deletion of Stat3 enables embryo implantation, but thereafter, mutants resemble non-affected littermates from the previous day until around mid-gestation. This probably results from the loss of serine-phosphorylated STAT3, the predominant form in early postimplantation embryonic tissues associated with mitochondrial activity. Bulk RNA sequencing of isolated mouse epiblasts confirmed developmental delay transcriptionally. Single-cell RNA sequencing revealed the exclusion of derivatives of Stat3 null embryonic stem cells exclusively from the erythroid lineage of mid-gestation chimeras. We show that Stat3 null embryonic stem cells can differentiate into erythroid and hematopoietic lineages in vitro but become outcompeted when mixed with wild-type cells. Our results implicate a role for STAT3 in the temporal control of embryonic progression, particularly in tissues requiring rapid cell division, such as postimplantation epiblast and hematopoietic lineages. Interestingly, mutations in STAT3 are associated with short stature in humans.
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Affiliation(s)
- Takuya Azami
- Cambridge Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge CB2 0AW, UK.
| | - Bart Theeuwes
- Cambridge Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Mai-Linh Nu Ton
- Cambridge Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge CB2 0AW, UK
| | - William Mansfield
- Cambridge Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Luke Harland
- Cambridge Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Masaki Kinoshita
- Cambridge Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Berthold Gottgens
- Cambridge Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Jennifer Nichols
- Cambridge Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge CB2 0AW, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge CB2 3EG, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge, UK.
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4
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Jin H, Liu Z, Mou J, Tang M, Huang X, Liu K, Zhang Q, Lui KO, Zhou B. Dual genetic tracing demonstrates the heterogeneous differentiation and function of neuromesodermal progenitors in vivo. Proc Natl Acad Sci U S A 2025; 122:e2402305122. [PMID: 40178900 PMCID: PMC12002027 DOI: 10.1073/pnas.2402305122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 03/04/2025] [Indexed: 04/05/2025] Open
Abstract
In recent decades, the traditional paradigm of three distinct germ layers formed during gastrulation has been revised with the identification of neuromesodermal progenitors (NMPs). These progenitors emerge during gastrulation and contribute to both the neural ectoderm, particularly the spinal cord, and the adjacent paraxial mesoderm [D. Henrique et al., Development 142, 2864-2875 (2015); R. J. Garriock et al., Development 142, 1628-1638 (2015); E. Tzouanacou et al., Dev. Cell 17, 365-376 (2009)]. However, effective genetic tools for lineage tracing and functional assessments of NMPs in vivo are currently lacking. Here, we developed a dual recombinase-mediated genetic system to specifically trace and ablate Brachyury+Sox2+ NMPs. Our genetic tracing and single-cell RNA sequencing analyses revealed that NMPs consist of three distinct unipotent and bipotent progenitor populations that progressively differentiate into neural and mesodermal fates. Genetic depletion of NMPs demonstrated their critical role in trunk and tail formation. This study provides in vivo genetic evidence supporting the heterogeneity of NMPs in terms of cell fate determination and their functional roles in the developing embryo.
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Affiliation(s)
- Hengwei Jin
- Chinese Academy of Sciences Center for Excellence in Molecuar Cell Science-Chinese University of Hong kong (CAS CEMCS-CUHK) Joint Laboratories, New Cornerstone Science Laboratory, State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai200031, China
| | - Zixin Liu
- Chinese Academy of Sciences Center for Excellence in Molecuar Cell Science-Chinese University of Hong kong (CAS CEMCS-CUHK) Joint Laboratories, New Cornerstone Science Laboratory, State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai200031, China
| | - Jialing Mou
- Chinese Academy of Sciences Center for Excellence in Molecuar Cell Science-Chinese University of Hong kong (CAS CEMCS-CUHK) Joint Laboratories, New Cornerstone Science Laboratory, State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai200031, China
| | - Muxue Tang
- Chinese Academy of Sciences Center for Excellence in Molecuar Cell Science-Chinese University of Hong kong (CAS CEMCS-CUHK) Joint Laboratories, New Cornerstone Science Laboratory, State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai200031, China
| | - Xiuzhen Huang
- Chinese Academy of Sciences Center for Excellence in Molecuar Cell Science-Chinese University of Hong kong (CAS CEMCS-CUHK) Joint Laboratories, New Cornerstone Science Laboratory, State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai200031, China
| | - Kuo Liu
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou310024, China
| | - Qianyu Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai201210, China
| | - Kathy O. Lui
- CAS CEMCS-CUHK Joint Laboratories, Department of Chemical Pathology, and Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong999077, China
| | - Bin Zhou
- Chinese Academy of Sciences Center for Excellence in Molecuar Cell Science-Chinese University of Hong kong (CAS CEMCS-CUHK) Joint Laboratories, New Cornerstone Science Laboratory, State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai200031, China
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou310024, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai201210, China
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5
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Isomura A, Kageyama R. Progress in understanding the vertebrate segmentation clock. Nat Rev Genet 2025:10.1038/s41576-025-00813-6. [PMID: 40038453 DOI: 10.1038/s41576-025-00813-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/02/2025] [Indexed: 03/06/2025]
Abstract
The segmentation clock is a molecular oscillator that regulates the periodic formation of somites from the presomitic mesoderm during vertebrate embryogenesis. Synchronous oscillatory expression of a Hairy homologue or Hairy-related basic helix-loop-helix (bHLH) transcriptional repressor in presomitic mesoderm cells regulates periodic expression of downstream factors that control somite segmentation with a periodicity that varies across species. Although many of the key components of the clock have been identified and characterized, less is known about how the clock is synchronized across cells and how species-specific periodicity is achieved. Advances in live imaging, stem cell and organoid technologies, and synthetic approaches have started to uncover the detailed mechanisms underlying these aspects of somitogenesis, providing insight into how morphogenesis is coordinated in space and time during embryonic development.
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Affiliation(s)
- Akihiro Isomura
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.
- Institute for Integrated Cell-Material Sciences (KUIAS-iCeMS), Kyoto University, Kyoto, Japan.
- Japan Science and Technology Agency, PRESTO, Saitama, Japan.
- RIKEN Center for Brain Science, Wako, Japan.
| | - Ryoichiro Kageyama
- Institute for Integrated Cell-Material Sciences (KUIAS-iCeMS), Kyoto University, Kyoto, Japan.
- RIKEN Center for Brain Science, Wako, Japan.
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6
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Pop NS, Dolt KS, Hohenstein P. Understanding developing kidneys and Wilms tumors one cell at a time. Curr Top Dev Biol 2025; 163:129-167. [PMID: 40254343 DOI: 10.1016/bs.ctdb.2024.11.005] [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] [Indexed: 04/22/2025]
Abstract
Single-cell sequencing-based techniques are revolutionizing all fields of biomedical sciences, including normal kidney development and how this is disturbed in the development of Wilms tumor. The many different techniques and the differences between them can obscure which technique is best used to answer which question. In this review we summarize the techniques currently available, discuss which have been used in kidney development or Wilms tumor context, and which techniques can or should be combined to maximize the increase in biological understanding we can get from them.
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Affiliation(s)
- Nine Solee Pop
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Karamjit Singh Dolt
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Peter Hohenstein
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands.
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7
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Morabito RD, Tatarakis D, Swick R, Stettnisch S, Schilling TF, Horsfield JA, Martin BL. The ratio of Wnt signaling activity to Sox2 transcription factor levels predicts neuromesodermal fate potential. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.16.633481. [PMID: 39868081 PMCID: PMC11761523 DOI: 10.1101/2025.01.16.633481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/28/2025]
Abstract
Neuromesodermal progenitors (NMPs) are a vertebrate cell type that contribute descendants to both the spinal cord and the mesoderm. The undifferentiated bipotential NMP state is maintained when both Wnt signaling is active and Sox2 is present. We used transgenic reporter lines to live-image both Wnt activity and Sox2 levels in NMPs and observed a unique cellular ratio in NMPs compared to NMP-derived mesoderm or neural tissue. We used this unique signature to identify the previously unknown anatomical position of a progenitor population that gives rise to the midline tissues of the floor plate of the spinal cord and the mesodermal notochord. Thus, quantification of the active Wnt signaling to Sox2 ratio can be used to predict and identify cells with neuromesodermal potential. We also developed the auxin inducible degron 2 system for use in zebrafish to test the temporal role that Sox2 plays during midline formation. We found ectopic Sox2 in the presence of Wnt activity holds cells in the undifferentiated floor plate/notochord progenitor state, and that degradation of the ectopic Sox2 is required for cells to adopt a notochord fate.
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Affiliation(s)
- Robert D. Morabito
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11733, USA
| | - David Tatarakis
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA
| | - Ryan Swick
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11733, USA
| | - Samantha Stettnisch
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11733, USA
| | - Thomas F. Schilling
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA
| | - Julia A. Horsfield
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
- The Maurice Wilkins Centre for Biodiscovery, The University of Auckland, Auckland, New Zealand
- Genetics Otago Research Centre, University of Otago, Dunedin, New Zealand
| | - Benjamin L. Martin
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11733, USA
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8
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Anlaş K, Gritti N, Nakaki F, Salamó Palau L, Tlili SL, Oriola D, Arató K, Le Lim J, Sharpe J, Trivedi V. Early autonomous patterning of the anteroposterior axis in gastruloids. Development 2024; 151:dev202171. [PMID: 39552366 DOI: 10.1242/dev.202171] [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: 07/11/2023] [Accepted: 06/17/2024] [Indexed: 11/19/2024]
Abstract
Minimal in vitro systems composed of embryonic stem cells (ESCs) have been shown to recapitulate the establishment of the anteroposterior (AP) axis. In contrast to the native embryo, ESC aggregates - such as gastruloids - can break symmetry, which is demarcated by polarization of the mesodermal marker T, autonomously without any localized external cues. However, associated earliest patterning events, such as the spatial restriction of cell fates and concomitant transcriptional changes, remain poorly understood. Here, we dissect the dynamics of AP axis establishment in mouse gastruloids, particularly before external Wnt stimulation. Through single-cell RNA sequencing, we identify key cell state transitions and the molecular signatures of T+ and T- populations underpinning AP polarization. We also show that this process is robust to modifications of aggregate size. Finally, transcriptomic comparison with the mouse embryo indicates that gastruloids develop similar mesendodermal cell types, despite initial differences in their primed pluripotent populations, which adopt a more mesenchymal state in lieu of an epiblast-like transcriptome. Hence, our findings suggest the possibility of alternate ESC states in vivo and in vitro that can converge onto similar cell fates.
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Affiliation(s)
| | | | | | | | - Sham Leilah Tlili
- Aix-Marseille Univ., CNRS, UMR 7288, IBDM, Turing Center for Living Systems, 13288 Marseille, France
| | | | | | | | - James Sharpe
- EMBL Barcelona, 08003 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain
| | - Vikas Trivedi
- EMBL Barcelona, 08003 Barcelona, Spain
- EMBL Heidelberg, Developmental Biology Unit, 69117 Heidelberg, Germany
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9
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Lange M, Piran Z, Klein M, Spanjaard B, Klein D, Junker JP, Theis FJ, Nitzan M. Mapping lineage-traced cells across time points with moslin. Genome Biol 2024; 25:277. [PMID: 39434128 PMCID: PMC11492637 DOI: 10.1186/s13059-024-03422-4] [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: 02/29/2024] [Accepted: 10/10/2024] [Indexed: 10/23/2024] Open
Abstract
Simultaneous profiling of single-cell gene expression and lineage history holds enormous potential for studying cellular decision-making. Recent computational approaches combine both modalities into cellular trajectories; however, they cannot make use of all available lineage information in destructive time-series experiments. Here, we present moslin, a Gromov-Wasserstein-based model to couple cellular profiles across time points based on lineage and gene expression information. We validate our approach in simulations and demonstrate on Caenorhabditis elegans embryonic development how moslin predicts fate probabilities and putative decision driver genes. Finally, we use moslin to delineate lineage relationships among transiently activated fibroblast states during zebrafish heart regeneration.
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Affiliation(s)
- Marius Lange
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Department of Mathematics, Technical University of Munich, Munich, Germany
- Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
| | - Zoe Piran
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | | | - Bastiaan Spanjaard
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Department of Paediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Dominik Klein
- Department of Mathematics, Technical University of Munich, Munich, Germany
- Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany
| | - Jan Philipp Junker
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Charité-Universitätsmedizin Berlin, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
| | - Fabian J Theis
- Department of Mathematics, Technical University of Munich, Munich, Germany.
- Institute of Computational Biology, Helmholtz Center Munich, Munich, Germany.
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany.
| | - Mor Nitzan
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel.
- Racah Institute of Physics, The Hebrew University of Jerusalem, Jerusalem, Israel.
- Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.
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10
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Kim SK, Seo S, Stein-O'Brien G, Jaishankar A, Ogawa K, Micali N, Luria V, Karger A, Wang Y, Kim H, Hyde TM, Kleinman JE, Voss T, Fertig EJ, Shin JH, Bürli R, Cross AJ, Brandon NJ, Weinberger DR, Chenoweth JG, Hoeppner DJ, Sestan N, Colantuoni C, McKay RD. Individual variation in the emergence of anterior-to-posterior neural fates from human pluripotent stem cells. Stem Cell Reports 2024; 19:1336-1350. [PMID: 39151428 PMCID: PMC11411333 DOI: 10.1016/j.stemcr.2024.07.004] [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: 09/18/2023] [Revised: 07/16/2024] [Accepted: 07/16/2024] [Indexed: 08/19/2024] Open
Abstract
Variability between human pluripotent stem cell (hPSC) lines remains a challenge and opportunity in biomedicine. In this study, hPSC lines from multiple donors were differentiated toward neuroectoderm and mesendoderm lineages. We revealed dynamic transcriptomic patterns that delineate the emergence of these lineages, which were conserved across lines, along with individual line-specific transcriptional signatures that were invariant throughout differentiation. These transcriptomic signatures predicted an antagonism between SOX21-driven forebrain fates and retinoic acid-induced hindbrain fates. Replicate lines and paired adult tissue demonstrated the stability of these line-specific transcriptomic traits. We show that this transcriptomic variation in lineage bias had both genetic and epigenetic origins, aligned with the anterior-to-posterior structure of early mammalian development, and was present across a large collection of hPSC lines. These findings contribute to developing systematic analyses of PSCs to define the origin and consequences of variation in the early events orchestrating individual human development.
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Affiliation(s)
- Suel-Kee Kim
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA; Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Seungmae Seo
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA
| | | | - Amritha Jaishankar
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA
| | - Kazuya Ogawa
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA
| | - Nicola Micali
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA; Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Victor Luria
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Amir Karger
- IT-Research Computing, Harvard Medical School, Boston, MA 02115, USA
| | - Yanhong Wang
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA
| | - Hyojin Kim
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Thomas M Hyde
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA; Departments of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; Departments of Psychiatry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Joel E Kleinman
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA; Departments of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Ty Voss
- Division of Preclinical Innovation, Nation Center for Advancing Translational Science, NIH, Bethesda, MD 20892, USA
| | - Elana J Fertig
- Departments of Oncology, Biomedical Engineering, and Applied Mathematics and Statistics, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Joo-Heon Shin
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA
| | - Roland Bürli
- Astra-Zeneca Neuroscience iMED., 141 Portland Street, Cambridge, MA 01239, USA
| | - Alan J Cross
- Astra-Zeneca Neuroscience iMED., 141 Portland Street, Cambridge, MA 01239, USA
| | - Nicholas J Brandon
- Astra-Zeneca Neuroscience iMED., 141 Portland Street, Cambridge, MA 01239, USA
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA; Departments of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; Departments of Psychiatry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; Departments of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Joshua G Chenoweth
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA
| | - Daniel J Hoeppner
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA
| | - Nenad Sestan
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA; Departments of Genetics, Psychiatry, and Comparative Medicine, Kavli Institute for Neuroscience, Program in Cellular Neuroscience, Neurodegeneration and Repair, Child Study Center, Yale School of Medicine, New Haven, CT 06510, USA.
| | - Carlo Colantuoni
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA; Departments of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; Departments of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
| | - Ronald D McKay
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA; Departments of Cell Biology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.
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11
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Stassen SV, Kobashi M, Lam EY, Huang Y, Ho JWK, Tsia KK. StaVia: spatially and temporally aware cartography with higher-order random walks for cell atlases. Genome Biol 2024; 25:224. [PMID: 39152459 PMCID: PMC11328412 DOI: 10.1186/s13059-024-03347-y] [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: 10/24/2023] [Accepted: 07/23/2024] [Indexed: 08/19/2024] Open
Abstract
Single-cell atlases pose daunting computational challenges pertaining to the integration of spatial and temporal information and the visualization of trajectories across large atlases. We introduce StaVia, a computational framework that synergizes multi-faceted single-cell data with higher-order random walks that leverage the memory of cells' past states, fused with a cartographic Atlas View that offers intuitive graph visualization. This spatially aware cartography captures relationships between cell populations based on their spatial location as well as their gene expression and developmental stage. We demonstrate this using zebrafish gastrulation data, underscoring its potential to dissect complex biological landscapes in both spatial and temporal contexts.
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Affiliation(s)
- Shobana V Stassen
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam, Hong Kong, Hong Kong.
| | - Minato Kobashi
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Edmund Y Lam
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam, Hong Kong, Hong Kong
- AI Chip Center for Emerging Smart Systems, Hong Kong Science Park, Shatin, New Territories, Hong Kong
| | - Yuanhua Huang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
- Department of Statistics and Actuarial Science, The University of Hong Kong, Pokfulam, Hong Kong
| | - Joshua W K Ho
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
- Laboratory of Data Discovery for Health, Hong Kong Science Park, Shatin, New Territories, Hong Kong
| | - Kevin K Tsia
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam, Hong Kong, Hong Kong.
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong.
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12
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Guillot C, Djeffal Y, Serra M, Pourquié O. Control of epiblast cell fate by mechanical cues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.24.600402. [PMID: 38979228 PMCID: PMC11230242 DOI: 10.1101/2024.06.24.600402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
In amniotes, embryonic tissues originate from multipotent epiblast cells, arranged in a mosaic of presumptive territories. How these domains fated to specific lineages become segregated during body formation remains poorly understood. Using single cell RNA sequencing analysis and lineage tracing in the chicken embryo, we identify epiblast cells contributing descendants to the neural tube, somites and lateral plate after completion of gastrulation. We show that intercalation after cell division generates important movements of epiblast cells which lead to their relocation to different presumptive territories, explaining this broad spectrum of fates. This tissue remodeling phase is transient, being soon followed by the establishment of boundaries restricting cell movements therefore defining the presumptive territories of the epiblast. Finally, we find that the epiblast faces distinct mechanical constraints along the antero-posterior axis, leading to cell fate alterations when challenged. Together, we demonstrate the critical role of mechanical cues in epiblast fate determination.
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13
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Simpson L, Strange A, Klisch D, Kraunsoe S, Azami T, Goszczynski D, Le Minh T, Planells B, Holmes N, Sang F, Henson S, Loose M, Nichols J, Alberio R. A single-cell atlas of pig gastrulation as a resource for comparative embryology. Nat Commun 2024; 15:5210. [PMID: 38890321 PMCID: PMC11189408 DOI: 10.1038/s41467-024-49407-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 06/04/2024] [Indexed: 06/20/2024] Open
Abstract
Cell-fate decisions during mammalian gastrulation are poorly understood outside of rodent embryos. The embryonic disc of pig embryos mirrors humans, making them a useful proxy for studying gastrulation. Here we present a single-cell transcriptomic atlas of pig gastrulation, revealing cell-fate emergence dynamics, as well as conserved and divergent gene programs governing early porcine, primate, and murine development. We highlight heterochronicity in extraembryonic cell-types, despite the broad conservation of cell-type-specific transcriptional programs. We apply these findings in combination with functional investigations, to outline conserved spatial, molecular, and temporal events during definitive endoderm specification. We find early FOXA2 + /TBXT- embryonic disc cells directly form definitive endoderm, contrasting later-emerging FOXA2/TBXT+ node/notochord progenitors. Unlike mesoderm, none of these progenitors undergo epithelial-to-mesenchymal transition. Endoderm/Node fate hinges on balanced WNT and hypoblast-derived NODAL, which is extinguished upon endodermal differentiation. These findings emphasise the interplay between temporal and topological signalling in fate determination during gastrulation.
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Affiliation(s)
- Luke Simpson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Nottingham, LE12 5RD, UK
| | - Andrew Strange
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Nottingham, LE12 5RD, UK
| | - Doris Klisch
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Nottingham, LE12 5RD, UK
| | - Sophie Kraunsoe
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Nottingham, LE12 5RD, UK
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Takuya Azami
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh, EH4 2XU, UK
| | - Daniel Goszczynski
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Nottingham, LE12 5RD, UK
| | - Triet Le Minh
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Nottingham, LE12 5RD, UK
| | - Benjamin Planells
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Nottingham, LE12 5RD, UK
| | - Nadine Holmes
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Fei Sang
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Sonal Henson
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Matthew Loose
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Jennifer Nichols
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh, EH4 2XU, UK
| | - Ramiro Alberio
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Nottingham, LE12 5RD, UK.
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14
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Dingare C, Cao D, Yang JJ, Sozen B, Steventon B. Mannose controls mesoderm specification and symmetry breaking in mouse gastruloids. Dev Cell 2024; 59:1523-1537.e6. [PMID: 38636516 DOI: 10.1016/j.devcel.2024.03.031] [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: 07/03/2023] [Revised: 01/29/2024] [Accepted: 03/21/2024] [Indexed: 04/20/2024]
Abstract
Patterning and growth are fundamental features of embryonic development that must be tightly coordinated. To understand how metabolism impacts early mesoderm development, we used mouse embryonic stem-cell-derived gastruloids, that co-expressed glucose transporters with the mesodermal marker T/Bra. We found that the glucose mimic, 2-deoxy-D-glucose (2-DG), blocked T/Bra expression and abolished axial elongation in gastruloids. However, glucose removal did not phenocopy 2-DG treatment despite a decline in glycolytic intermediates. As 2-DG can also act as a competitive inhibitor of mannose in protein glycosylation, we added mannose together with 2-DG and found that it could rescue the mesoderm specification both in vivo and in vitro. We further showed that blocking production and intracellular recycling of mannose abrogated mesoderm specification. Proteomics analysis demonstrated that mannose reversed glycosylation of the Wnt pathway regulator, secreted frizzled receptor Frzb. Our study showed how mannose controls mesoderm specification in mouse gastruloids.
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Affiliation(s)
- Chaitanya Dingare
- Deptartment of Genetics, University of Cambridge, Downing Site, Cambridge CB2 3EH, UK.
| | - Dominica Cao
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Jenny Jingni Yang
- Deptartment of Genetics, University of Cambridge, Downing Site, Cambridge CB2 3EH, UK
| | - Berna Sozen
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT, USA; Yale Stem Cell Centre, Yale University, New Haven, CT, USA; Department of Obstetrics, Gynaecology and Reproductive Sciences, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Benjamin Steventon
- Deptartment of Genetics, University of Cambridge, Downing Site, Cambridge CB2 3EH, UK.
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15
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Su H, Zhi D, Song Y, Yang Y, Wang D, Li X, Cao G. Exploring the formation mechanism of short-tailed phenotypes in animals using mutant mice with the TBXT gene c.G334T developed by CRISPR/Cas9. Gene 2024; 910:148310. [PMID: 38401832 DOI: 10.1016/j.gene.2024.148310] [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: 09/03/2023] [Revised: 02/01/2024] [Accepted: 02/21/2024] [Indexed: 02/26/2024]
Abstract
With the change in diet structure, individuals prefer to consume mutton with less fat. However, sheep tail has a lot of fat. We identified a breed of low-fat short-tailed sheep (i.e., Hulunbuir short-tailed sheep). It is necessary to develop an animal model that can promote research on the potential mechanisms of the short-tail phenotype in sheep, which results from the TBXT gene c.G334T mutation. To create animal models, we selected mice as experimental animals. Mouse embryos lacking the TBXT protein, which crucially regulates mouse embryonic development, cannot develop normally. We utilized CRISPR/Cas9 gene editing technology to generate site-specific mutation (c.G334T) in the TBXT gene of mice, and found that the mouse TBXT mutation (c.G334T) leads to a short-tail phenotype. Furthermore, we investigated the interaction between TBXT and Wnt signaling pathways. The expressions of TBXT, Axin2, Dkk1, Wnt3, Wnt3a, and Wnt5a were discovered to be significantly different between mutant embryos and wild embryos by obtaining mouse embryos at various developmental stages and examining the expression relationship between the TBXT and Wnt signaling pathway-related components in all of these embryos. Therefore, as a transcription factor, TBXT regulates the expression of the aforementioned Wnt signaling pathway components by forming a regulatory network for the normal development of mouse embryos. This study enriches the research on the functional role of the TBXT in the development of mouse embryos and the mechanism by which the short-tailed phenotype in sheep develops.
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Affiliation(s)
- Hong Su
- College of Veterinary Medicine, Inner Mongolia Agricultural University, China; Animal Embryo and Developmental Engineering Key Laboratory of Higher Education, Institutions of Inner Mongolia Autonomous Region, China; Inner Mongolia Autonomous Region Key Laboratory of Basic Veterinary Medicine, China.
| | - Dafu Zhi
- College of Veterinary Medicine, Inner Mongolia Agricultural University, China; Animal Embryo and Developmental Engineering Key Laboratory of Higher Education, Institutions of Inner Mongolia Autonomous Region, China; Inner Mongolia Autonomous Region Key Laboratory of Basic Veterinary Medicine, China.
| | - Yongli Song
- College of Life Sciences, Inner Mongolia University, China.
| | - Yanyan Yang
- Inner Mongolia Academy of Agriculture and Animal Husbandry, China.
| | - Daqing Wang
- College of Veterinary Medicine, Inner Mongolia Agricultural University, China; Animal Embryo and Developmental Engineering Key Laboratory of Higher Education, Institutions of Inner Mongolia Autonomous Region, China; Inner Mongolia Autonomous Region Key Laboratory of Basic Veterinary Medicine, China; Inner Mongolia Academy of Agriculture and Animal Husbandry, China.
| | - Xiunan Li
- College of Veterinary Medicine, Inner Mongolia Agricultural University, China; Animal Embryo and Developmental Engineering Key Laboratory of Higher Education, Institutions of Inner Mongolia Autonomous Region, China; Inner Mongolia Autonomous Region Key Laboratory of Basic Veterinary Medicine, China; Inner Mongolia Academy of Agriculture and Animal Husbandry, China.
| | - Guifang Cao
- College of Veterinary Medicine, Inner Mongolia Agricultural University, China; Animal Embryo and Developmental Engineering Key Laboratory of Higher Education, Institutions of Inner Mongolia Autonomous Region, China; Inner Mongolia Autonomous Region Key Laboratory of Basic Veterinary Medicine, China.
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16
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Chea S, Kreger J, Lopez-Burks ME, MacLean AL, Lander AD, Calof AL. Gastrulation-stage gene expression in Nipbl+/- mouse embryos foreshadows the development of syndromic birth defects. SCIENCE ADVANCES 2024; 10:eadl4239. [PMID: 38507484 PMCID: PMC10954218 DOI: 10.1126/sciadv.adl4239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 02/15/2024] [Indexed: 03/22/2024]
Abstract
In animal models, Nipbl deficiency phenocopies gene expression changes and birth defects seen in Cornelia de Lange syndrome, the most common cause of which is Nipbl haploinsufficiency. Previous studies in Nipbl+/- mice suggested that heart development is abnormal as soon as cardiogenic tissue is formed. To investigate this, we performed single-cell RNA sequencing on wild-type and Nipbl+/- mouse embryos at gastrulation and early cardiac crescent stages. Nipbl+/- embryos had fewer mesoderm cells than wild-type and altered proportions of mesodermal cell subpopulations. These findings were associated with underexpression of genes implicated in driving specific mesodermal lineages. In addition, Nanog was found to be overexpressed in all germ layers, and many gene expression changes observed in Nipbl+/- embryos could be attributed to Nanog overexpression. These findings establish a link between Nipbl deficiency, Nanog overexpression, and gene expression dysregulation/lineage misallocation, which ultimately manifest as birth defects in Nipbl+/- animals and Cornelia de Lange syndrome.
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Affiliation(s)
- Stephenson Chea
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California Irvine, Irvine, CA 92697, USA
- Center for Complex Biological Systems, University of California Irvine, Irvine, CA 92697, USA
| | - Jesse Kreger
- Department of Quantitative and Computational Biology, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Martha E. Lopez-Burks
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California Irvine, Irvine, CA 92697, USA
- Center for Complex Biological Systems, University of California Irvine, Irvine, CA 92697, USA
| | - Adam L. MacLean
- Department of Quantitative and Computational Biology, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Arthur D. Lander
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California Irvine, Irvine, CA 92697, USA
- Center for Complex Biological Systems, University of California Irvine, Irvine, CA 92697, USA
| | - Anne L. Calof
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California Irvine, Irvine, CA 92697, USA
- Center for Complex Biological Systems, University of California Irvine, Irvine, CA 92697, USA
- Department of Anatomy and Neurobiology, School of Medicine, University of California Irvine, Irvine, CA 92697, USA
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17
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Kondoh H, Takemoto T. The Origin and Regulation of Neuromesodermal Progenitors (NMPs) in Embryos. Cells 2024; 13:549. [PMID: 38534393 PMCID: PMC10968745 DOI: 10.3390/cells13060549] [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: 01/29/2024] [Revised: 03/04/2024] [Accepted: 03/18/2024] [Indexed: 03/28/2024] Open
Abstract
Neuromesodermal progenitors (NMPs), serving as the common origin of neural and paraxial mesodermal development in a large part of the trunk, have recently gained significant attention because of their critical importance in the understanding of embryonic organogenesis and the design of in vitro models of organogenesis. However, the nature of NMPs at many essential points remains only vaguely understood or even incorrectly assumed. Here, we discuss the nature of NMPs, focusing on their dynamic migratory behavior during embryogenesis and the mechanisms underlying their neural vs. mesodermal fate choice. The discussion points include the following: (1) How the sinus rhomboidals is organized; the tissue where the neural or mesodermal fate choice of NMPs occurs. (2) NMPs originating from the broad posterior epiblast are associated with Sox2 N1 enhancer activity. (3) Tbx6-dependent Sox2 repression occurs during NMP-derived paraxial mesoderm development. (4) The nephric mesenchyme, a component of the intermediate mesoderm, was newly identified as an NMP derivative. (5) The transition of embryonic tissue development from tissue-specific progenitors in the anterior part to that from NMPs occurs at the forelimb bud axial level. (6) The coexpression of Sox2 and Bra in NMPs is conditional and is not a hallmark of NMPs. (7) The ability of the NMP pool to sustain axial embryo growth depends on Wnt3a signaling in the NMP population. Current in vitro models of NMPs are also critically reviewed.
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Affiliation(s)
- Hisato Kondoh
- Biohistory Research Hall, Takatsuki 569-1125, Japan
- Osaka University, Suita 565-0871, Japan
| | - Tatsuya Takemoto
- Laboratory for Embryology, Institute for Advanced Medical Sciences, Tokushima University, Tokushima 770-8503, Japan
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18
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Martins-Costa C, Wilson V, Binagui-Casas A. Neuromesodermal specification during head-to-tail body axis formation. Curr Top Dev Biol 2024; 159:232-271. [PMID: 38729677 DOI: 10.1016/bs.ctdb.2024.02.012] [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] [Indexed: 05/12/2024]
Abstract
The anterior-to-posterior (head-to-tail) body axis is extraordinarily diverse among vertebrates but conserved within species. Body axis development requires a population of axial progenitors that resides at the posterior of the embryo to sustain elongation and is then eliminated once axis extension is complete. These progenitors occupy distinct domains in the posterior (tail-end) of the embryo and contribute to various lineages along the body axis. The subset of axial progenitors with neuromesodermal competency will generate both the neural tube (the precursor of the spinal cord), and the trunk and tail somites (producing the musculoskeleton) during embryo development. These axial progenitors are called Neuromesodermal Competent cells (NMCs) and Neuromesodermal Progenitors (NMPs). NMCs/NMPs have recently attracted interest beyond the field of developmental biology due to their clinical potential. In the mouse, the maintenance of neuromesodermal competency relies on a fine balance between a trio of known signals: Wnt/β-catenin, FGF signalling activity and suppression of retinoic acid signalling. These signals regulate the relative expression levels of the mesodermal transcription factor Brachyury and the neural transcription factor Sox2, permitting the maintenance of progenitor identity when co-expressed, and either mesoderm or neural lineage commitment when the balance is tilted towards either Brachyury or Sox2, respectively. Despite important advances in understanding key genes and cellular behaviours involved in these fate decisions, how the balance between mesodermal and neural fates is achieved remains largely unknown. In this chapter, we provide an overview of signalling and gene regulatory networks in NMCs/NMPs. We discuss mutant phenotypes associated with axial defects, hinting at the potential significant role of lesser studied proteins in the maintenance and differentiation of the progenitors that fuel axial elongation.
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Affiliation(s)
- C Martins-Costa
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - V Wilson
- Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom.
| | - A Binagui-Casas
- Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom.
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19
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Chea S, Kreger J, Lopez-Burks ME, MacLean AL, Lander AD, Calof AL. Gastrulation-stage gene expression in Nipbl +/- mouse embryos foreshadows the development of syndromic birth defects. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.16.558465. [PMID: 37905011 PMCID: PMC10614802 DOI: 10.1101/2023.10.16.558465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
In animal models, Nipbl-deficiency phenocopies gene expression changes and birth defects seen in Cornelia de Lange Syndrome (CdLS), the most common cause of which is Nipbl-haploinsufficiency. Previous studies in Nipbl+/- mice suggested that heart development is abnormal as soon as cardiogenic tissue is formed. To investigate this, we performed single-cell RNA-sequencing on wildtype (WT) and Nipbl+/- mouse embryos at gastrulation and early cardiac crescent stages. Nipbl+/- embryos had fewer mesoderm cells than WT and altered proportions of mesodermal cell subpopulations. These findings were associated with underexpression of genes implicated in driving specific mesodermal lineages. In addition, Nanog was found to be overexpressed in all germ layers, and many gene expression changes observed in Nipbl+/- embryos could be attributed to Nanog overexpression. These findings establish a link between Nipbl-deficiency, Nanog overexpression, and gene expression dysregulation/lineage misallocation, which ultimately manifest as birth defects in Nipbl+/- animals and CdLS. Teaser Gene expression changes during gastrulation of Nipbl-deficient mice shed light on early origins of structural birth defects.
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20
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Cooper F, Souilhol C, Haston S, Gray S, Boswell K, Gogolou A, Frith TJR, Stavish D, James BM, Bose D, Kim Dale J, Tsakiridis A. Notch signalling influences cell fate decisions and HOX gene induction in axial progenitors. Development 2024; 151:dev202098. [PMID: 38223992 PMCID: PMC10911136 DOI: 10.1242/dev.202098] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 12/20/2023] [Indexed: 01/16/2024]
Abstract
The generation of the post-cranial embryonic body relies on the coordinated production of spinal cord neurectoderm and presomitic mesoderm cells from neuromesodermal progenitors (NMPs). This process is orchestrated by pro-neural and pro-mesodermal transcription factors that are co-expressed in NMPs together with Hox genes, which are essential for axial allocation of NMP derivatives. NMPs reside in a posterior growth region, which is marked by the expression of Wnt, FGF and Notch signalling components. Although the importance of Wnt and FGF in influencing the induction and differentiation of NMPs is well established, the precise role of Notch remains unclear. Here, we show that the Wnt/FGF-driven induction of NMPs from human embryonic stem cells (hESCs) relies on Notch signalling. Using hESC-derived NMPs and chick embryo grafting, we demonstrate that Notch directs a pro-mesodermal character at the expense of neural fate. We show that Notch also contributes to activation of HOX gene expression in human NMPs, partly in a non-cell-autonomous manner. Finally, we provide evidence that Notch exerts its effects via the establishment of a negative-feedback loop with FGF signalling.
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Affiliation(s)
- Fay Cooper
- School of Biosciences, The University of Sheffield, Sheffield S10 2TN, UK
- Neuroscience Institute, The University of Sheffield, Sheffield S10 2TN, UK
| | - Celine Souilhol
- School of Biosciences, The University of Sheffield, Sheffield S10 2TN, UK
- Neuroscience Institute, The University of Sheffield, Sheffield S10 2TN, UK
- Biomolecular Sciences Research Centre, Department of Biosciences and Chemistry, Sheffield Hallam University, Sheffield S1 1WB, UK
| | - Scott Haston
- Developmental Biology and Cancer, Birth Defects Research Centre, UCL GOS Institute of Child Health, London WC1N 1EH, UK
- Division of Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 4HN, UK
| | - Shona Gray
- Division of Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 4HN, UK
| | - Katy Boswell
- School of Biosciences, The University of Sheffield, Sheffield S10 2TN, UK
- Neuroscience Institute, The University of Sheffield, Sheffield S10 2TN, UK
| | - Antigoni Gogolou
- School of Biosciences, The University of Sheffield, Sheffield S10 2TN, UK
- Neuroscience Institute, The University of Sheffield, Sheffield S10 2TN, UK
| | - Thomas J. R. Frith
- School of Biosciences, The University of Sheffield, Sheffield S10 2TN, UK
- Neuroscience Institute, The University of Sheffield, Sheffield S10 2TN, UK
| | - Dylan Stavish
- School of Biosciences, The University of Sheffield, Sheffield S10 2TN, UK
- Neuroscience Institute, The University of Sheffield, Sheffield S10 2TN, UK
| | - Bethany M. James
- School of Biosciences, The University of Sheffield, Sheffield S10 2TN, UK
- Neuroscience Institute, The University of Sheffield, Sheffield S10 2TN, UK
| | - Daniel Bose
- School of Biosciences, The University of Sheffield, Sheffield S10 2TN, UK
- Neuroscience Institute, The University of Sheffield, Sheffield S10 2TN, UK
| | - Jacqueline Kim Dale
- Division of Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 4HN, UK
| | - Anestis Tsakiridis
- School of Biosciences, The University of Sheffield, Sheffield S10 2TN, UK
- Neuroscience Institute, The University of Sheffield, Sheffield S10 2TN, UK
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21
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Qiu C, Martin BK, Welsh IC, Daza RM, Le TM, Huang X, Nichols EK, Taylor ML, Fulton O, O'Day DR, Gomes AR, Ilcisin S, Srivatsan S, Deng X, Disteche CM, Noble WS, Hamazaki N, Moens CB, Kimelman D, Cao J, Schier AF, Spielmann M, Murray SA, Trapnell C, Shendure J. A single-cell time-lapse of mouse prenatal development from gastrula to birth. Nature 2024; 626:1084-1093. [PMID: 38355799 PMCID: PMC10901739 DOI: 10.1038/s41586-024-07069-w] [Citation(s) in RCA: 57] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 01/15/2024] [Indexed: 02/16/2024]
Abstract
The house mouse (Mus musculus) is an exceptional model system, combining genetic tractability with close evolutionary affinity to humans1,2. Mouse gestation lasts only 3 weeks, during which the genome orchestrates the astonishing transformation of a single-cell zygote into a free-living pup composed of more than 500 million cells. Here, to establish a global framework for exploring mammalian development, we applied optimized single-cell combinatorial indexing3 to profile the transcriptional states of 12.4 million nuclei from 83 embryos, precisely staged at 2- to 6-hour intervals spanning late gastrulation (embryonic day 8) to birth (postnatal day 0). From these data, we annotate hundreds of cell types and explore the ontogenesis of the posterior embryo during somitogenesis and of kidney, mesenchyme, retina and early neurons. We leverage the temporal resolution and sampling depth of these whole-embryo snapshots, together with published data4-8 from earlier timepoints, to construct a rooted tree of cell-type relationships that spans the entirety of prenatal development, from zygote to birth. Throughout this tree, we systematically nominate genes encoding transcription factors and other proteins as candidate drivers of the in vivo differentiation of hundreds of cell types. Remarkably, the most marked temporal shifts in cell states are observed within one hour of birth and presumably underlie the massive physiological adaptations that must accompany the successful transition of a mammalian fetus to life outside the womb.
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Affiliation(s)
- Chengxiang Qiu
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | - Beth K Martin
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Riza M Daza
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Truc-Mai Le
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Xingfan Huang
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - Eva K Nichols
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Megan L Taylor
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Olivia Fulton
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Diana R O'Day
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | | | - Saskia Ilcisin
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Sanjay Srivatsan
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Xinxian Deng
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Christine M Disteche
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - William Stafford Noble
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - Nobuhiko Hamazaki
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| | - Cecilia B Moens
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - David Kimelman
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Junyue Cao
- Laboratory of Single-Cell Genomics and Population dynamics, The Rockefeller University, New York, NY, USA
| | - Alexander F Schier
- Biozentrum, University of Basel, Basel, Switzerland
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
| | - Malte Spielmann
- Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute of Human Genetics, University Hospitals Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Kiel, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg, Lübeck, Kiel, Lübeck, Germany
| | | | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
- Seattle Hub for Synthetic Biology, Seattle, WA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
- Howard Hughes Medical Institute, Seattle, WA, USA.
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA.
- Seattle Hub for Synthetic Biology, Seattle, WA, USA.
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22
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Ghazanfar S, Guibentif C, Marioni JC. Stabilized mosaic single-cell data integration using unshared features. Nat Biotechnol 2024; 42:284-292. [PMID: 37231260 PMCID: PMC10869270 DOI: 10.1038/s41587-023-01766-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 03/28/2023] [Indexed: 05/27/2023]
Abstract
Currently available single-cell omics technologies capture many unique features with different biological information content. Data integration aims to place cells, captured with different technologies, onto a common embedding to facilitate downstream analytical tasks. Current horizontal data integration techniques use a set of common features, thereby ignoring non-overlapping features and losing information. Here we introduce StabMap, a mosaic data integration technique that stabilizes mapping of single-cell data by exploiting the non-overlapping features. StabMap first infers a mosaic data topology based on shared features, then projects all cells onto supervised or unsupervised reference coordinates by traversing shortest paths along the topology. We show that StabMap performs well in various simulation contexts, facilitates 'multi-hop' mosaic data integration where some datasets do not share any features and enables the use of spatial gene expression features for mapping dissociated single-cell data onto a spatial transcriptomic reference.
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Affiliation(s)
- Shila Ghazanfar
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK.
- School of Mathematics and Statistics, The University of Sydney, Camperdown, New South Wales, Australia.
- Charles Perkins Centre, The University of Sydney, Camperdown, New South Wales, Australia.
| | - Carolina Guibentif
- Sahlgrenska Center for Cancer Research, Inst. Biomedicine, Dept. Microbiology and Immunology, University of Gothenburg, Gothenburg, Sweden
| | - John C Marioni
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK.
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
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23
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Imaz-Rosshandler I, Rode C, Guibentif C, Harland LTG, Ton MLN, Dhapola P, Keitley D, Argelaguet R, Calero-Nieto FJ, Nichols J, Marioni JC, de Bruijn MFTR, Göttgens B. Tracking early mammalian organogenesis - prediction and validation of differentiation trajectories at whole organism scale. Development 2024; 151:dev201867. [PMID: 37982461 PMCID: PMC10906099 DOI: 10.1242/dev.201867] [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: 04/12/2023] [Accepted: 10/30/2023] [Indexed: 11/21/2023]
Abstract
Early organogenesis represents a key step in animal development, during which pluripotent cells diversify to initiate organ formation. Here, we sampled 300,000 single-cell transcriptomes from mouse embryos between E8.5 and E9.5 in 6-h intervals and combined this new dataset with our previous atlas (E6.5-E8.5) to produce a densely sampled timecourse of >400,000 cells from early gastrulation to organogenesis. Computational lineage reconstruction identified complex waves of blood and endothelial development, including a new programme for somite-derived endothelium. We also dissected the E7.5 primitive streak into four adjacent regions, performed scRNA-seq and predicted cell fates computationally. Finally, we defined developmental state/fate relationships by combining orthotopic grafting, microscopic analysis and scRNA-seq to transcriptionally determine cell fates of grafted primitive streak regions after 24 h of in vitro embryo culture. Experimentally determined fate outcomes were in good agreement with computationally predicted fates, demonstrating how classical grafting experiments can be revisited to establish high-resolution cell state/fate relationships. Such interdisciplinary approaches will benefit future studies in developmental biology and guide the in vitro production of cells for organ regeneration and repair.
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Affiliation(s)
- Ivan Imaz-Rosshandler
- Department of Haematology, University of Cambridge, Cambridge CB2 0RE, UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Christina Rode
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Carolina Guibentif
- Department of Microbiology and Immunology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Luke T. G. Harland
- Department of Haematology, University of Cambridge, Cambridge CB2 0RE, UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Mai-Linh N. Ton
- Department of Haematology, University of Cambridge, Cambridge CB2 0RE, UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Parashar Dhapola
- Division of Molecular Hematology, Lund Stem Cell Center, Lund University, 221 00 Lund, Sweden
| | - Daniel Keitley
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Ricard Argelaguet
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
- Altos Labs Cambridge Institute, Granta Park, Cambridge CB21 6GP, UK
| | - Fernando J. Calero-Nieto
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Jennifer Nichols
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - John C. Marioni
- Wellcome Sanger Institute, Wellcome Genome Campus, Saffron Walden CB10 1SA, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Saffron Walden CB10 1SA, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Marella F. T. R. de Bruijn
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Berthold Göttgens
- Department of Haematology, University of Cambridge, Cambridge CB2 0RE, UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
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24
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Kondoh H. Gastrulation: Its Principles and Variations. Results Probl Cell Differ 2024; 72:27-60. [PMID: 38509251 DOI: 10.1007/978-3-031-39027-2_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
As epiblast cells initiate development into various somatic cells, they undergo a large-scale reorganization, called gastrulation. The gastrulation of the epiblast cells produces three groups of cells: the endoderm layer, the collection of miscellaneous mesodermal tissues, and the ectodermal layer, which includes the neural, epidermal, and associated tissues. Most studies of gastrulation have focused on the formation of the tissues that provide the primary route for cell reorganization, that is, the primitive streak, in the chicken and mouse. In contrast, how gastrulation alters epiblast-derived cells has remained underinvestigated. This chapter highlights the regulation of cell and tissue fate via the gastrulation process. The roles and regulatory functions of neuromesodermal progenitors (NMPs) in the gastrulation process, elucidated in the last decade, are discussed in depth to resolve points of confusion. Chicken and mouse embryos, which form a primitive streak as the site of mesoderm precursor ingression, have been investigated extensively. However, primitive streak formation is an exception, even among amniotes. The roles of gastrulation processes in generating various somatic tissues will be discussed broadly.
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Affiliation(s)
- Hisato Kondoh
- Osaka University, Suita, Osaka, Japan
- Biohistory Research Hall, Takatsuki, Osaka, Japan
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25
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Frith TJR, Briscoe J, Boezio GLM. From signalling to form: the coordination of neural tube patterning. Curr Top Dev Biol 2023; 159:168-231. [PMID: 38729676 DOI: 10.1016/bs.ctdb.2023.11.004] [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] [Indexed: 05/12/2024]
Abstract
The development of the vertebrate spinal cord involves the formation of the neural tube and the generation of multiple distinct cell types. The process starts during gastrulation, combining axial elongation with specification of neural cells and the formation of the neuroepithelium. Tissue movements produce the neural tube which is then exposed to signals that provide patterning information to neural progenitors. The intracellular response to these signals, via a gene regulatory network, governs the spatial and temporal differentiation of progenitors into specific cell types, facilitating the assembly of functional neuronal circuits. The interplay between the gene regulatory network, cell movement, and tissue mechanics generates the conserved neural tube pattern observed across species. In this review we offer an overview of the molecular and cellular processes governing the formation and patterning of the neural tube, highlighting how the remarkable complexity and precision of vertebrate nervous system arises. We argue that a multidisciplinary and multiscale understanding of the neural tube development, paired with the study of species-specific strategies, will be crucial to tackle the open questions.
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Affiliation(s)
| | - James Briscoe
- The Francis Crick Institute, London, United Kingdom.
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26
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Lozovska A, Korovesi AG, Duarte P, Casaca A, Assunção T, Mallo M. The control of transitions along the main body axis. Curr Top Dev Biol 2023; 159:272-308. [PMID: 38729678 DOI: 10.1016/bs.ctdb.2023.11.002] [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] [Indexed: 05/12/2024]
Abstract
Although vertebrates display a large variety of forms and sizes, the mechanisms controlling the layout of the basic body plan are substantially conserved throughout the clade. Following gastrulation, head, trunk, and tail are sequentially generated through the continuous addition of tissue at the caudal embryonic end. Development of each of these major embryonic regions is regulated by a distinct genetic network. The transitions from head-to-trunk and from trunk-to-tail development thus involve major changes in regulatory mechanisms, requiring proper coordination to guarantee smooth progression of embryonic development. In this review, we will discuss the key cellular and embryological events associated with those transitions giving particular attention to their regulation, aiming to provide a cohesive outlook of this important component of vertebrate development.
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Affiliation(s)
| | | | - Patricia Duarte
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, Oeiras, Portugal
| | - Ana Casaca
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, Oeiras, Portugal
| | - Tereza Assunção
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, Oeiras, Portugal
| | - Moises Mallo
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, Oeiras, Portugal.
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27
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Steinhart MR, van der Valk WH, Osorio D, Serdy SA, Zhang J, Nist-Lund C, Kim J, Moncada-Reid C, Sun L, Lee J, Koehler KR. Mapping oto-pharyngeal development in a human inner ear organoid model. Development 2023; 150:dev201871. [PMID: 37796037 PMCID: PMC10698753 DOI: 10.1242/dev.201871] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 09/08/2023] [Indexed: 10/06/2023]
Abstract
Inner ear development requires the coordination of cell types from distinct epithelial, mesenchymal and neuronal lineages. Although we have learned much from animal models, many details about human inner ear development remain elusive. We recently developed an in vitro model of human inner ear organogenesis using pluripotent stem cells in a 3D culture, fostering the growth of a sensorineural circuit, including hair cells and neurons. Despite previously characterizing some cell types, many remain undefined. This study aimed to chart the in vitro development timeline of the inner ear organoid to understand the mechanisms at play. Using single-cell RNA sequencing at ten stages during the first 36 days of differentiation, we tracked the evolution from pluripotency to various ear cell types after exposure to specific signaling modulators. Our findings showcase gene expression that influences differentiation, identifying a plethora of ectodermal and mesenchymal cell types. We also discern aspects of the organoid model consistent with in vivo development, while highlighting potential discrepancies. Our study establishes the Inner Ear Organoid Developmental Atlas (IODA), offering deeper insights into human biology and improving inner ear tissue differentiation.
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Affiliation(s)
- Matthew R. Steinhart
- Department of Otolaryngology, Boston Children's Hospital, Boston, MA 02115, USA
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Otolaryngology-Head and Neck Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Medical Neuroscience Graduate Program, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Wouter H. van der Valk
- Department of Otolaryngology, Boston Children's Hospital, Boston, MA 02115, USA
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Otolaryngology-Head and Neck Surgery, Harvard Medical School, Boston, MA 02115, USA
- OtoBiology Leiden, Department of Otorhinolaryngology and Head & Neck Surgery; Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW); Leiden University Medical Center, Leiden, 2333 ZA, the Netherlands
| | - Daniel Osorio
- Research Computing, Department of Information Technology; Boston Children's Hospital, Boston, MA 02115, USA
| | - Sara A. Serdy
- Department of Otolaryngology, Boston Children's Hospital, Boston, MA 02115, USA
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA
| | - Jingyuan Zhang
- Department of Otolaryngology, Boston Children's Hospital, Boston, MA 02115, USA
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Otolaryngology-Head and Neck Surgery, Harvard Medical School, Boston, MA 02115, USA
| | - Carl Nist-Lund
- Department of Otolaryngology, Boston Children's Hospital, Boston, MA 02115, USA
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA
- Program in Neuroscience, Harvard Medical School, Boston, MA 02115, USA
| | - Jin Kim
- Department of Otolaryngology, Boston Children's Hospital, Boston, MA 02115, USA
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Otolaryngology-Head and Neck Surgery, Harvard Medical School, Boston, MA 02115, USA
- Department of Plastic and Oral Surgery, Boston Children's Hospital, Boston, MA 02115, USA
| | - Cynthia Moncada-Reid
- Speech and Hearing Bioscience and Technology (SHBT) Graduate Program, Harvard Medical School, Boston, MA 02115, USA
| | - Liang Sun
- Research Computing, Department of Information Technology; Boston Children's Hospital, Boston, MA 02115, USA
| | - Jiyoon Lee
- Department of Otolaryngology, Boston Children's Hospital, Boston, MA 02115, USA
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Otolaryngology-Head and Neck Surgery, Harvard Medical School, Boston, MA 02115, USA
- Department of Plastic and Oral Surgery, Boston Children's Hospital, Boston, MA 02115, USA
| | - Karl R. Koehler
- Department of Otolaryngology, Boston Children's Hospital, Boston, MA 02115, USA
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Otolaryngology-Head and Neck Surgery, Harvard Medical School, Boston, MA 02115, USA
- Department of Plastic and Oral Surgery, Boston Children's Hospital, Boston, MA 02115, USA
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28
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Schüle KM, Weckerle J, Probst S, Wehmeyer AE, Zissel L, Schröder CM, Tekman M, Kim GJ, Schlägl IM, Sagar, Arnold SJ. Eomes restricts Brachyury functions at the onset of mouse gastrulation. Dev Cell 2023; 58:1627-1642.e7. [PMID: 37633271 DOI: 10.1016/j.devcel.2023.07.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 06/12/2023] [Accepted: 07/31/2023] [Indexed: 08/28/2023]
Abstract
Mammalian specification of mesoderm and definitive endoderm (DE) is instructed by the two related Tbx transcription factors (TFs) Eomesodermin (Eomes) and Brachyury sharing partially redundant functions. Gross differences in mutant embryonic phenotypes suggest specific functions of each TF. To date, the molecular details of separated lineage-specific gene regulation by Eomes and Brachyury remain poorly understood. Here, we combine mouse embryonic and stem-cell-based analyses to delineate the non-overlapping, lineage-specific transcriptional activities. On a genome-wide scale, binding of both TFs overlaps at promoters of target genes but shows specificity for distal enhancer regions that is conferred by differences in Tbx DNA-binding motifs. The unique binding to enhancer sites instructs the specification of anterior mesoderm (AM) and DE by Eomes and caudal mesoderm by Brachyury. Remarkably, EOMES antagonizes BRACHYURY gene regulatory functions in coexpressing cells during early gastrulation to ensure the proper sequence of early AM and DE lineage specification followed by posterior mesoderm derivatives.
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Affiliation(s)
- Katrin M Schüle
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Albertstrasse 25, 79104 Freiburg, Germany.
| | - Jelena Weckerle
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Albertstrasse 25, 79104 Freiburg, Germany
| | - Simone Probst
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Albertstrasse 25, 79104 Freiburg, Germany
| | - Alexandra E Wehmeyer
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Albertstrasse 25, 79104 Freiburg, Germany
| | - Lea Zissel
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Albertstrasse 25, 79104 Freiburg, Germany; Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Chiara M Schröder
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Albertstrasse 25, 79104 Freiburg, Germany; Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstrasse 19a, 79104 Freiburg, Germany; Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany; Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Schänzlestrasse18, 79104 Freiburg, Germany
| | - Mehmet Tekman
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Albertstrasse 25, 79104 Freiburg, Germany
| | - Gwang-Jin Kim
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Albertstrasse 25, 79104 Freiburg, Germany
| | - Inga-Marie Schlägl
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Albertstrasse 25, 79104 Freiburg, Germany
| | - Sagar
- Department of Medicine II, Medical Center University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Sebastian J Arnold
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Albertstrasse 25, 79104 Freiburg, Germany; Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Schänzlestrasse18, 79104 Freiburg, Germany.
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29
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Cisar C, Keener N, Ruffalo M, Paten B. A unified pipeline for FISH spatial transcriptomics. CELL GENOMICS 2023; 3:100384. [PMID: 37719153 PMCID: PMC10504669 DOI: 10.1016/j.xgen.2023.100384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 06/23/2023] [Accepted: 07/24/2023] [Indexed: 09/19/2023]
Abstract
High-throughput spatial transcriptomics has emerged as a powerful tool for investigating the spatial distribution of mRNA expression and its effects on cellular function. There is a lack of standardized tools for analyzing spatial transcriptomics data, leading many groups to write their own in-house tools that are often poorly documented and not generalizable. To address this, we have expanded and improved the starfish library and used those tools to create PIPEFISH, a semi-automated and generalizable pipeline that performs transcript annotation for fluorescence in situ hybridization (FISH)-based spatial transcriptomics. We used this pipeline to annotate transcript locations from three real datasets from three different common types of FISH image-based experiments, MERFISH, seqFISH, and targeted in situ sequencing (ISS), and verified that the results were high quality using the internal quality metrics of the pipeline and also a comparison with an orthogonal method of measuring RNA expression. PIPEFISH is a publicly available and open-source tool.
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Affiliation(s)
- Cecilia Cisar
- Department of Biomolecular Engineering, School of Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Nicholas Keener
- Department of Biomolecular Engineering, School of Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Mathew Ruffalo
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Benedict Paten
- Department of Biomolecular Engineering, School of Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
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30
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Perovanovic J, Wu Y, Abewe H, Shen Z, Hughes EP, Gertz J, Chandrasekharan MB, Tantin D. Oct1 cooperates with the Smad family of transcription factors to promote mesodermal lineage specification. Sci Signal 2023; 16:eadd5750. [PMID: 37071732 PMCID: PMC10360295 DOI: 10.1126/scisignal.add5750] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 03/14/2023] [Indexed: 04/20/2023]
Abstract
The transition between pluripotent and tissue-specific states is a key aspect of development. Understanding the pathways driving these transitions will facilitate the engineering of properly differentiated cells for experimental and therapeutic uses. Here, we showed that during mesoderm differentiation, the transcription factor Oct1 activated developmental lineage-appropriate genes that were silent in pluripotent cells. Using mouse embryonic stem cells (ESCs) with an inducible knockout of Oct1, we showed that Oct1 deficiency resulted in poor induction of mesoderm-specific genes, leading to impaired mesodermal and terminal muscle differentiation. Oct1-deficient cells exhibited poor temporal coordination of the induction of lineage-specific genes and showed inappropriate developmental lineage branching, resulting in poorly differentiated cell states retaining epithelial characteristics. In ESCs, Oct1 localized with the pluripotency factor Oct4 at mesoderm-associated genes and remained bound to those loci during differentiation after the dissociation of Oct4. Binding events for Oct1 overlapped with those for the histone lysine demethylase Utx, and an interaction between Oct1 and Utx suggested that these two proteins cooperate to activate gene expression. The specificity of the ubiquitous Oct1 for the induction of mesodermal genes could be partially explained by the frequent coexistence of Smad and Oct binding sites at mesoderm-specific genes and the cooperative stimulation of mesodermal gene transcription by Oct1 and Smad3. Together, these results identify Oct1 as a key mediator of mesoderm lineage-specific gene induction.
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Affiliation(s)
- Jelena Perovanovic
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Yifan Wu
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Hosiana Abewe
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Zuolian Shen
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Erik P. Hughes
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Jason Gertz
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Mahesh B. Chandrasekharan
- Department of Radiation Oncology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Dean Tantin
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
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31
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Qiu C, Martin BK, Welsh IC, Daza RM, Le TM, Huang X, Nichols EK, Taylor ML, Fulton O, O’Day DR, Gomes AR, Ilcisin S, Srivatsan S, Deng X, Disteche CM, Noble WS, Hamazaki N, Moens CB, Kimelman D, Cao J, Schier AF, Spielmann M, Murray SA, Trapnell C, Shendure J. A single-cell transcriptional timelapse of mouse embryonic development, from gastrula to pup. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.05.535726. [PMID: 37066300 PMCID: PMC10104014 DOI: 10.1101/2023.04.05.535726] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
The house mouse, Mus musculus, is an exceptional model system, combining genetic tractability with close homology to human biology. Gestation in mouse development lasts just under three weeks, a period during which its genome orchestrates the astonishing transformation of a single cell zygote into a free-living pup composed of >500 million cells. Towards a global framework for exploring mammalian development, we applied single cell combinatorial indexing (sci-*) to profile the transcriptional states of 12.4 million nuclei from 83 precisely staged embryos spanning late gastrulation (embryonic day 8 or E8) to birth (postnatal day 0 or P0), with 2-hr temporal resolution during somitogenesis, 6-hr resolution through to birth, and 20-min resolution during the immediate postpartum period. From these data (E8 to P0), we annotate dozens of trajectories and hundreds of cell types and perform deeper analyses of the unfolding of the posterior embryo during somitogenesis as well as the ontogenesis of the kidney, mesenchyme, retina, and early neurons. Finally, we leverage the depth and temporal resolution of these whole embryo snapshots, together with other published data, to construct and curate a rooted tree of cell type relationships that spans mouse development from zygote to pup. Throughout this tree, we systematically nominate sets of transcription factors (TFs) and other genes as candidate drivers of the in vivo differentiation of hundreds of mammalian cell types. Remarkably, the most dramatic shifts in transcriptional state are observed in a restricted set of cell types in the hours immediately following birth, and presumably underlie the massive changes in physiology that must accompany the successful transition of a placental mammal to extrauterine life.
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Affiliation(s)
- Chengxiang Qiu
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Beth K. Martin
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Riza M. Daza
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Truc-Mai Le
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Xingfan Huang
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA
| | - Eva K. Nichols
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Megan L. Taylor
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Olivia Fulton
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Diana R. O’Day
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | | | - Saskia Ilcisin
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Sanjay Srivatsan
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Xinxian Deng
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Christine M. Disteche
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - William Stafford Noble
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA
| | - Nobuhiko Hamazaki
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| | - Cecilia B. Moens
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - David Kimelman
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Junyue Cao
- Laboratory of Single-cell genomics and Population dynamics, The Rockefeller University, New York, NY, USA
| | - Alexander F. Schier
- Biozentrum, University of Basel, Basel, Switzerland
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
| | - Malte Spielmann
- Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute of Human Genetics, University Hospitals Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Kiel, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Hamburg, Lübeck, Kiel, Lübeck, Germany
| | | | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
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32
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Eve A. An interview with Valerie Wilson. Development 2022; 149:dev201442. [PMID: 36515643 DOI: 10.1242/dev.201442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Valerie Wilson is Professor of Early Embryo Development and a group leader at the Centre for Regenerative Medicine at the University of Edinburgh, UK. Val's lab works on the development of the vertebrate head-to-tail axis, focusing on the differentiation potential of axial progenitors. In 2022, she was awarded the British Society for Developmental Biology's (BSDB) Waddington Medal, which recognises outstanding individuals who have made major contributions to UK developmental biology. After her award lecture, we spoke to Val about her career and heard her thoughts on the past, present and future of the field.
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Busby L, Saunders D, Serrano Nájera G, Steventon B. Quantitative Experimental Embryology: A Modern Classical Approach. J Dev Biol 2022; 10:44. [PMID: 36278549 PMCID: PMC9624316 DOI: 10.3390/jdb10040044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/04/2022] [Accepted: 10/11/2022] [Indexed: 11/17/2022] Open
Abstract
Experimental Embryology is often referred to as a classical approach of developmental biology that has been to some extent replaced by the introduction of molecular biology and genetic techniques to the field. Inspired by the combination of this approach with advanced techniques to uncover core principles of neural crest development by the laboratory of Roberto Mayor, we review key quantitative examples of experimental embryology from recent work in a broad range of developmental biology questions. We propose that quantitative experimental embryology offers essential ways to explore the reaction of cells and tissues to targeted cell addition, removal, and confinement. In doing so, it is an essential methodology to uncover principles of development that remain elusive such as pattern regulation, scaling, and self-organisation.
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Clark SJ, Argelaguet R, Lohoff T, Krueger F, Drage D, Göttgens B, Marioni JC, Nichols J, Reik W. Single-cell multi-omics profiling links dynamic DNA methylation to cell fate decisions during mouse early organogenesis. Genome Biol 2022; 23:202. [PMID: 36163261 PMCID: PMC9511790 DOI: 10.1186/s13059-022-02762-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 08/31/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Perturbation of DNA methyltransferases (DNMTs) and of the active DNA demethylation pathway via ten-eleven translocation (TET) methylcytosine dioxygenases results in severe developmental defects and embryonic lethality. Dynamic control of DNA methylation is therefore vital for embryogenesis, yet the underlying mechanisms remain poorly understood. RESULTS Here we report a single-cell transcriptomic atlas from Dnmt and Tet mutant mouse embryos during early organogenesis. We show that both the maintenance and de novo methyltransferase enzymes are dispensable for the formation of all major cell types at E8.5. However, DNA methyltransferases are required for silencing of prior or alternative cell fates such as pluripotency and extraembryonic programmes. Deletion of all three TET enzymes produces substantial lineage biases, in particular, a failure to generate primitive erythrocytes. Single-cell multi-omics profiling moreover reveals that this is linked to a failure to demethylate distal regulatory elements in Tet triple-knockout embryos. CONCLUSIONS This study provides a detailed analysis of the effects of perturbing DNA methylation on mouse organogenesis at a whole organism scale and affords new insights into the regulatory mechanisms of cell fate decisions.
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Affiliation(s)
- Stephen J Clark
- Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT, UK.
- Altos Labs Cambridge Institute of Science, Granta Park, Cambridge, UK.
| | - Ricard Argelaguet
- Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT, UK.
- Altos Labs Cambridge Institute of Science, Granta Park, Cambridge, UK.
| | - Tim Lohoff
- Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT, UK
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - Felix Krueger
- Altos Labs Cambridge Institute of Science, Granta Park, Cambridge, UK
- Bioinformatics Group, Babraham Institute, Cambridge, CB22 3AT, UK
| | - Deborah Drage
- Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT, UK
- Altos Labs Cambridge Institute of Science, Granta Park, Cambridge, UK
| | - Berthold Göttgens
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - John C Marioni
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Jennifer Nichols
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge, CB2 3EG, UK
- Current address: MRC Human Genetics Unit, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Wolf Reik
- Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT, UK.
- Altos Labs Cambridge Institute of Science, Granta Park, Cambridge, UK.
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, CB2 0AW, UK.
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK.
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Ho VW, Grainger DE, Chagraoui H, Porcher C. Specification of the haematopoietic stem cell lineage: From blood-fated mesodermal angioblasts to haemogenic endothelium. Semin Cell Dev Biol 2022; 127:59-67. [PMID: 35125239 DOI: 10.1016/j.semcdb.2022.01.008] [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: 11/06/2021] [Revised: 01/20/2022] [Accepted: 01/24/2022] [Indexed: 11/19/2022]
Abstract
Haematopoietic stem and progenitor cells emerge from specialized haemogenic endothelial cells in select vascular beds during embryonic development. Specification and commitment to the blood lineage, however, occur before endothelial cells are endowed with haemogenic competence, at the time of mesoderm patterning and production of endothelial cell progenitors (angioblasts). Whilst early blood cell fate specification has long been recognized, very little is known about the mechanisms that induce endothelial cell diversification and progressive acquisition of a blood identity by a subset of these cells. Here, we review the endothelial origin of the haematopoietic system and the complex developmental journey of blood-fated angioblasts. We discuss how recent technological advances will be instrumental to examine the diversity of the embryonic anatomical niches, signaling pathways and downstream epigenetic and transcriptional processes controlling endothelial cell heterogeneity and blood cell fate specification. Ultimately, this will give essential insights into the ontogeny of the cells giving rise to haematopoietic stem cells, that may aid in the development of novel strategies for their in vitro production for clinical purposes.
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Affiliation(s)
- Vivien W Ho
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - David E Grainger
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Hedia Chagraoui
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Catherine Porcher
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK.
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36
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Mesp1 controls the chromatin and enhancer landscapes essential for spatiotemporal patterning of early cardiovascular progenitors. Nat Cell Biol 2022; 24:1114-1128. [PMID: 35817961 PMCID: PMC7613098 DOI: 10.1038/s41556-022-00947-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 05/25/2022] [Indexed: 01/13/2023]
Abstract
The mammalian heart arises from various populations of Mesp1-expressing cardiovascular progenitors (CPs) that are specified during the early stages of gastrulation. Mesp1 is a transcription factor that acts as a master regulator of CP specification and differentiation. However, how Mesp1 regulates the chromatin landscape of nascent mesodermal cells to define the temporal and spatial patterning of the distinct populations of CPs remains unknown. Here, by combining ChIP-seq, RNA-seq and ATAC-seq during mouse pluripotent stem cell differentiation, we defined the dynamic remodelling of the chromatin landscape mediated by Mesp1. We identified different enhancers that are temporally regulated to erase the pluripotent state and specify the pools of CPs that mediate heart development. We identified Zic2 and Zic3 as essential cofactors that act with Mesp1 to regulate its transcription-factor activity at key mesodermal enhancers, thereby regulating the chromatin remodelling and gene expression associated with the specification of the different populations of CPs in vivo. Our study identifies the dynamics of the chromatin landscape and enhancer remodelling associated with temporal patterning of early mesodermal cells into the distinct populations of CPs that mediate heart development.
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37
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Martin BL. Mesoderm induction and patterning: Insights from neuromesodermal progenitors. Semin Cell Dev Biol 2022; 127:37-45. [PMID: 34840081 PMCID: PMC9130346 DOI: 10.1016/j.semcdb.2021.11.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/02/2021] [Accepted: 11/10/2021] [Indexed: 12/23/2022]
Abstract
The discovery of mesoderm inducing signals helped usher in the era of molecular developmental biology, and today the mechanisms of mesoderm induction and patterning are still intensely studied. Mesoderm induction begins during gastrulation, but recent evidence in vertebrates shows that this process continues after gastrulation in a group of posteriorly localized cells called neuromesodermal progenitors (NMPs). NMPs reside within the post-gastrulation embryonic structure called the tailbud, where they make a lineage decision between ectoderm (spinal cord) and mesoderm. The majority of NMP-derived mesoderm generates somites, but also contributes to lateral mesoderm fates such as endothelium. The discovery of NMPs provides a new paradigm in which to study vertebrate mesoderm induction. This review will discuss mechanisms of mesoderm induction within NMPs, and how they have informed our understanding of mesoderm induction more broadly within vertebrates as well as animal species outside of the vertebrate lineage. Special focus will be given to the signaling networks underlying NMP-derived mesoderm induction and patterning, as well as emerging work on the significance of partial epithelial-mesenchymal states in coordinating cell fate and morphogenesis.
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Affiliation(s)
- Benjamin L Martin
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA.
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38
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Lee J, van der Valk WH, Serdy SA, Deakin C, Kim J, Le AP, Koehler KR. Generation and characterization of hair-bearing skin organoids from human pluripotent stem cells. Nat Protoc 2022; 17:1266-1305. [PMID: 35322210 PMCID: PMC10461778 DOI: 10.1038/s41596-022-00681-y] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 01/04/2022] [Indexed: 12/28/2022]
Abstract
Human skin uses millions of hairs and glands distributed across the body surface to function as an external barrier, thermoregulator and stimuli sensor. The large-scale generation of human skin with these appendages would be beneficial, but is challenging. Here, we describe a detailed protocol for generating hair-bearing skin tissue entirely from a homogeneous population of human pluripotent stem cells in a three-dimensional in vitro culture system. Defined culture conditions are used over a 2-week period to induce differentiation of pluripotent stem cells to surface ectoderm and cranial neural crest cells, which give rise to the epidermis and dermis, respectively, in each organoid unit. After 60 d of incubation, the skin organoids produce hair follicles. By day ~130, the skin organoids reach full complexity and contain stratified skin layers, pigmented hair follicles, sebaceous glands, Merkel cells and sensory neurons, recapitulating the cell composition and architecture of fetal skin tissue at week 18 of gestation. Skin organoids can be maintained in culture using this protocol for up to 150 d, enabling the organoids to be used to investigate basic skin biology, model disease and, further, reconstruct or regenerate skin tissue.
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Affiliation(s)
- Jiyoon Lee
- Department of Otolaryngology, Boston Children's Hospital, Boston, MA, USA.
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA.
- Department of Plastic and Oral Surgery, Boston Children's Hospital, Boston, MA, USA.
- Department of Surgery, Harvard Medical School, Boston, MA, USA.
- Department of Otolaryngology-Head and Neck Surgery, Harvard Medical School, Boston, MA, USA.
| | - Wouter H van der Valk
- Department of Otolaryngology, Boston Children's Hospital, Boston, MA, USA
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
- Department of Otolaryngology-Head and Neck Surgery, Harvard Medical School, Boston, MA, USA
- Department of Otorhinolaryngology and Head & Neck Surgery, Leiden University Medical Center, Leiden, the Netherlands
| | - Sara A Serdy
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
| | - CiCi Deakin
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
- Department of Biological Engineering, Wentworth Institute of Technology, Boston, MA, USA
| | - Jin Kim
- Department of Otolaryngology, Boston Children's Hospital, Boston, MA, USA
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
- Department of Plastic and Oral Surgery, Boston Children's Hospital, Boston, MA, USA
- Department of Otolaryngology-Head and Neck Surgery, Harvard Medical School, Boston, MA, USA
| | - Anh Phuong Le
- Department of Otolaryngology, Boston Children's Hospital, Boston, MA, USA
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA
- Department of Plastic and Oral Surgery, Boston Children's Hospital, Boston, MA, USA
- Department of Otolaryngology-Head and Neck Surgery, Harvard Medical School, Boston, MA, USA
| | - Karl R Koehler
- Department of Otolaryngology, Boston Children's Hospital, Boston, MA, USA.
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA, USA.
- Department of Plastic and Oral Surgery, Boston Children's Hospital, Boston, MA, USA.
- Department of Otolaryngology-Head and Neck Surgery, Harvard Medical School, Boston, MA, USA.
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Li R, Wang TY, Xu X, Emery OM, Yi M, Wu SP, DeMayo FJ. Spatial transcriptomic profiles of mouse uterine microenvironments at pregnancy day 7.5†. Biol Reprod 2022; 107:529-545. [PMID: 35357464 PMCID: PMC9382390 DOI: 10.1093/biolre/ioac061] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 02/03/2022] [Accepted: 03/30/2022] [Indexed: 01/17/2023] Open
Abstract
Uterine dysfunctions lead to fertility disorders and pregnancy complications. Normal uterine functions at pregnancy depend on crosstalk among multiple cell types in uterine microenvironments. Here, we performed the spatial transcriptomics and single-cell RNA-seq assays to determine local gene expression profiles at the embryo implantation site of the mouse uterus on pregnancy day 7.5 (D7.5). The spatial transcriptomic annotation identified 11 domains of distinct gene signatures, including a mesometrial myometrium, an anti-mesometrial myometrium, a mesometrial decidua enriched with natural killer cells, a vascular sinus zone for maternal vessel remodeling, a fetal-maternal interface, a primary decidual zone, a transition decidual zone, a secondary decidual zone, undifferentiated stroma, uterine glands, and the embryo. The scRNA-Seq identified 12 types of cells in the D7.5 uterus including three types of stromal fibroblasts with differentiated and undifferentiated markers, one cluster of epithelium including luminal and glandular epithelium, mesothelium, endothelia, pericytes, myelomonocytic cell, natural killer cells, and lymphocyte B. These single-cell RNA signatures were then utilized to deconvolute the cell-type compositions of each individual uterine microenvironment. Functional annotation assays on spatial transcriptomic data revealed uterine microenvironments with distinguished metabolic preferences, immune responses, and various cellular behaviors that are regulated by region-specific endocrine and paracrine signals. Global interactome among regions is also projected based on the spatial transcriptomic data. This study provides high-resolution transcriptome profiles with locality information at the embryo implantation site to facilitate further investigations on molecular mechanisms for normal pregnancy progression.
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Affiliation(s)
- Rong Li
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Tian-yuan Wang
- Integrative Bioinformatics Supportive Group, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Xin Xu
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Olivia M Emery
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - MyeongJin Yi
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - San-Pin Wu
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Francesco J DeMayo
- Correspondence: Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, 111 T. W. Alexander Dr., Research Triangle Park, NC 27709, USA. Tel: +9842873987; E-mail:
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40
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Huang M, Wang X, Banerjee M, Mukherji ST, Kutz LC, Zhao A, Sepanski M, Fan CM, Zhu GZ, Tian J, Wang DZ, Zhu H, Xie ZJ, Pierre SV, Cai L. Regulation of Myogenesis by a Na/K-ATPase α1 Caveolin-Binding Motif. Stem Cells 2022; 40:133-148. [PMID: 35257186 PMCID: PMC8943859 DOI: 10.1093/stmcls/sxab012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 09/25/2021] [Indexed: 01/12/2024]
Abstract
The N-terminal caveolin-binding motif (CBM) in Na/K-ATPase (NKA) α1 subunit is essential for cell signaling and somitogenesis in animals. To further investigate the molecular mechanism, we have generated CBM mutant human-induced pluripotent stem cells (iPSCs) through CRISPR/Cas9 genome editing and examined their ability to differentiate into skeletal muscle (Skm) cells. Compared with the parental wild-type human iPSCs, the CBM mutant cells lost their ability of Skm differentiation, which was evidenced by the absence of spontaneous cell contraction, marker gene expression, and subcellular myofiber banding structures in the final differentiated induced Skm cells. Another NKA functional mutant, A420P, which lacks NKA/Src signaling function, did not produce a similar defect. Indeed, A420P mutant iPSCs retained intact pluripotency and ability of Skm differentiation. Mechanistically, the myogenic transcription factor MYOD was greatly suppressed by the CBM mutation. Overexpression of a mouse Myod cDNA through lentiviral delivery restored the CBM mutant cells' ability to differentiate into Skm. Upstream of MYOD, Wnt signaling was demonstrated from the TOPFlash assay to have a similar inhibition. This effect on Wnt activity was further confirmed functionally by defective induction of the presomitic mesoderm marker genes BRACHYURY (T) and MESOGENIN1 (MSGN1) by Wnt3a ligand or the GSK3 inhibitor/Wnt pathway activator CHIR. Further investigation through immunofluorescence imaging and cell fractionation revealed a shifted membrane localization of β-catenin in CBM mutant iPSCs, revealing a novel molecular component of NKA-Wnt regulation. This study sheds light on a genetic regulation of myogenesis through the CBM of NKA and control of Wnt/β-catenin signaling.
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Affiliation(s)
- Minqi Huang
- Marshall Institute for Interdisciplinary Research (MIIR) at Marshall University, Huntington, WV 25703, USA
| | - Xiaoliang Wang
- Marshall Institute for Interdisciplinary Research (MIIR) at Marshall University, Huntington, WV 25703, USA
- Joan C. Edwards School of Medicine at Marshall University, Huntington, WV 25703, USA
| | - Moumita Banerjee
- Marshall Institute for Interdisciplinary Research (MIIR) at Marshall University, Huntington, WV 25703, USA
| | - Shreya T Mukherji
- Marshall Institute for Interdisciplinary Research (MIIR) at Marshall University, Huntington, WV 25703, USA
| | - Laura C Kutz
- Marshall Institute for Interdisciplinary Research (MIIR) at Marshall University, Huntington, WV 25703, USA
| | - Aijie Zhao
- Marshall Institute for Interdisciplinary Research (MIIR) at Marshall University, Huntington, WV 25703, USA
| | - Michael Sepanski
- Department of Embryology, Carnegie Institution for Science, 3520 San Martin Drive, Baltimore, MD 21218, USA
| | - Chen-Ming Fan
- Department of Embryology, Carnegie Institution for Science, 3520 San Martin Drive, Baltimore, MD 21218, USA
| | - Guo-Zhang Zhu
- Department of Biological Sciences, Marshall University, Huntington, WV 25703, USA
| | - Jiang Tian
- Marshall Institute for Interdisciplinary Research (MIIR) at Marshall University, Huntington, WV 25703, USA
- Joan C. Edwards School of Medicine at Marshall University, Huntington, WV 25703, USA
| | - Da-Zhi Wang
- University of South Florida Health Heart Institute, Morsani College of Medicine, University of South Florida, 560 Channelside Drive, Tampa, FL 33602, USA
| | - Hua Zhu
- Department of Surgery, The Ohio State University, 396 Biomedical Research Tower, 460 W. 12th Avenue, Columbus, OH 43210, USA
| | - Zi-Jian Xie
- Marshall Institute for Interdisciplinary Research (MIIR) at Marshall University, Huntington, WV 25703, USA
| | - Sandrine V Pierre
- Marshall Institute for Interdisciplinary Research (MIIR) at Marshall University, Huntington, WV 25703, USA
| | - Liquan Cai
- Marshall Institute for Interdisciplinary Research (MIIR) at Marshall University, Huntington, WV 25703, USA
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41
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de Lemos L, Dias A, Nóvoa A, Mallo M. Epha1 is a cell-surface marker for the neuromesodermal competent population. Development 2022; 149:274735. [DOI: 10.1242/dev.198812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 02/02/2022] [Indexed: 11/20/2022]
Abstract
ABSTRACT
The vertebrate body is built during embryonic development by the sequential addition of new tissue as the embryo grows at its caudal end. During this process, progenitor cells within the neuromesodermal competent (NMC) region generate the postcranial neural tube and paraxial mesoderm. Here, we have applied a genetic strategy to recover the NMC cell population from mouse embryonic tissues and have searched their transcriptome for cell-surface markers that would give access to these cells without previous genetic modifications. We found that Epha1 expression is restricted to the axial progenitor-containing areas of the mouse embryo. Epha1-positive cells isolated from the mouse tailbud generate neural and mesodermal derivatives when cultured in vitro. This observation, together with their enrichment in the Sox2+/Tbxt+ molecular phenotype, indicates a direct association between Epha1 and the NMC population. Additional analyses suggest that tailbud cells expressing low Epha1 levels might also contain notochord progenitors, and that high Epha1 expression might be associated with progenitors entering paraxial mesoderm differentiation. Epha1 could thus be a valuable cell-surface marker for labeling and recovering physiologically active axial progenitors from embryonic tissues.
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Affiliation(s)
- Luisa de Lemos
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal
| | - André Dias
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal
| | - Ana Nóvoa
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal
| | - Moisés Mallo
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal
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42
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Needham J, Metzis V. Heads or tails: Making the spinal cord. Dev Biol 2022; 485:80-92. [DOI: 10.1016/j.ydbio.2022.03.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 12/15/2021] [Accepted: 03/02/2022] [Indexed: 12/14/2022]
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43
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Lohoff T, Ghazanfar S, Missarova A, Koulena N, Pierson N, Griffiths JA, Bardot ES, Eng CHL, Tyser RCV, Argelaguet R, Guibentif C, Srinivas S, Briscoe J, Simons BD, Hadjantonakis AK, Göttgens B, Reik W, Nichols J, Cai L, Marioni JC. Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis. Nat Biotechnol 2022; 40:74-85. [PMID: 34489600 PMCID: PMC8763645 DOI: 10.1038/s41587-021-01006-2] [Citation(s) in RCA: 177] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 07/07/2021] [Indexed: 02/07/2023]
Abstract
Molecular profiling of single cells has advanced our knowledge of the molecular basis of development. However, current approaches mostly rely on dissociating cells from tissues, thereby losing the crucial spatial context of regulatory processes. Here, we apply an image-based single-cell transcriptomics method, sequential fluorescence in situ hybridization (seqFISH), to detect mRNAs for 387 target genes in tissue sections of mouse embryos at the 8-12 somite stage. By integrating spatial context and multiplexed transcriptional measurements with two single-cell transcriptome atlases, we characterize cell types across the embryo and demonstrate that spatially resolved expression of genes not profiled by seqFISH can be imputed. We use this high-resolution spatial map to characterize fundamental steps in the patterning of the midbrain-hindbrain boundary (MHB) and the developing gut tube. We uncover axes of cell differentiation that are not apparent from single-cell RNA-sequencing (scRNA-seq) data, such as early dorsal-ventral separation of esophageal and tracheal progenitor populations in the gut tube. Our method provides an approach for studying cell fate decisions in complex tissues and development.
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Affiliation(s)
- T Lohoff
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
- Epigenetics Programme, Babraham Institute, Cambridge, UK
| | - S Ghazanfar
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - A Missarova
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - N Koulena
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - N Pierson
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - J A Griffiths
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Genomics Plc, Cambridge, UK
| | - E S Bardot
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - C-H L Eng
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - R C V Tyser
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - R Argelaguet
- Epigenetics Programme, Babraham Institute, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - C Guibentif
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Sahlgrenska Center for Cancer Research, Department of Microbiology and Immunology, University of Gothenburg, Gothenburg, Sweden
| | - S Srinivas
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - J Briscoe
- The Francis Crick Institute, London, UK
| | - B D Simons
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- The Wellcome/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Cambridge, UK
| | - A-K Hadjantonakis
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - B Göttgens
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - W Reik
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
- Epigenetics Programme, Babraham Institute, Cambridge, UK.
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK.
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
| | - J Nichols
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK.
| | - L Cai
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
| | - J C Marioni
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK.
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
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44
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Junion G, Jagla K. Diversification of muscle types in Drosophila embryos. Exp Cell Res 2022; 410:112950. [PMID: 34838813 DOI: 10.1016/j.yexcr.2021.112950] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 11/22/2021] [Accepted: 11/24/2021] [Indexed: 12/31/2022]
Abstract
Drosophila embryonic somatic muscles represent a simple and tractable model system to study the gene regulatory networks that control diversification of cell types. Somatic myogenesis in Drosophila is initiated by intrinsic action of the mesodermal master gene twist, which activates a cascade of transcriptional outputs including myogenic differentiation factor Mef2, which triggers all aspects of the myogenic differentiation program. In parallel, the expression of a combinatorial code of identity transcription factors (iTFs) defines discrete particular features of each muscle fiber, such as number of fusion events, and specific attachment to tendon cells or innervation, thus ensuring diversification of muscle types. Here, we take the example of a subset of lateral transverse (LT) muscles and discuss how the iTF code and downstream effector genes progressively define individual LT properties such as fusion program, attachment and innervation. We discuss new challenges in the field including the contribution of posttranscriptional and epitranscriptomic regulation of gene expression in the diversification of cell types.
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Affiliation(s)
- Guillaume Junion
- Genetics Reproduction and Development Institute (iGReD), CNRS UMR6293, INSERM U1103, University of Clermont Auvergne, Clermont-Ferrand, France
| | - Krzysztof Jagla
- Genetics Reproduction and Development Institute (iGReD), CNRS UMR6293, INSERM U1103, University of Clermont Auvergne, Clermont-Ferrand, France.
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45
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Binagui-Casas A, Dias A, Guillot C, Metzis V, Saunders D. Building consensus in neuromesodermal research: Current advances and future biomedical perspectives. Curr Opin Cell Biol 2021; 73:133-140. [PMID: 34717142 DOI: 10.1016/j.ceb.2021.08.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 08/12/2021] [Accepted: 08/31/2021] [Indexed: 10/20/2022]
Abstract
The development of the vertebrate body axis relies on the activity of different populations of axial progenitors, including neuromesodermal progenitors. Currently, the term 'Neuromesodermal progenitors' is associated with various definitions. Here, we use distinct terminologies to highlight advances in our understanding of this cell type at both the single-cell and population levels. We discuss how these recent insights prompt new opportunities to address a range of biomedical questions spanning cancer metastasis, congenital disorders, cellular metabolism, regenerative medicine, and evolution. Finally, we outline some of the major unanswered questions and propose future directions at the forefront of neuromesodermal research.
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Affiliation(s)
- Anahí Binagui-Casas
- Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh, EH16 4UU, UK
| | - André Dias
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal.
| | - Charlène Guillot
- Department of Pathology, Brigham and Women's Hospital & Department of Genetics, Harvard Medical School, 60 Fenwood Road, Boston, MA, USA; Institute of Genetics, Reproduction and Development, Medical school, University of Clermont Auvergne, 28, Place Henri Dunant, 63001 Clermont-Ferrand, France
| | - Vicki Metzis
- Institute of Clinical Sciences, Imperial College London, London, W12 0NN, UK
| | - Dillan Saunders
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
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46
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Weldon SA, Münsterberg AE. Somite development and regionalisation of the vertebral axial skeleton. Semin Cell Dev Biol 2021; 127:10-16. [PMID: 34690064 DOI: 10.1016/j.semcdb.2021.10.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/27/2021] [Accepted: 10/06/2021] [Indexed: 11/25/2022]
Abstract
A critical stage in the development of all vertebrate embryos is the generation of the body plan and its subsequent patterning and regionalisation along the main anterior-posterior axis. This includes the formation of the vertebral axial skeleton. Its organisation begins during early embryonic development with the periodic formation of paired blocks of mesoderm tissue called somites. Here, we review axial patterning of somites, with a focus on studies using amniote model systems - avian and mouse. We summarise the molecular and cellular mechanisms that generate paraxial mesoderm and review how the different anatomical regions of the vertebral column acquire their specific identity and thus shape the body plan. We also discuss the generation of organoids and embryo-like structures from embryonic stem cells, which provide insights regarding axis formation and promise to be useful for disease modelling.
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Affiliation(s)
- Shannon A Weldon
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
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47
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Romanos M, Allio G, Roussigné M, Combres L, Escalas N, Soula C, Médevielle F, Steventon B, Trescases A, Bénazéraf B. Cell-to-cell heterogeneity in Sox2 and Bra expression guides progenitor motility and destiny. eLife 2021; 10:e66588. [PMID: 34607629 PMCID: PMC8492064 DOI: 10.7554/elife.66588] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 09/13/2021] [Indexed: 12/13/2022] Open
Abstract
Although cell-to-cell heterogeneity in gene and protein expression within cell populations has been widely documented, we know little about its biological functions. By studying progenitors of the posterior region of bird embryos, we found that expression levels of transcription factors Sox2 and Bra, respectively involved in neural tube (NT) and mesoderm specification, display a high degree of cell-to-cell heterogeneity. By combining forced expression and downregulation approaches with time-lapse imaging, we demonstrate that Sox2-to-Bra ratio guides progenitor's motility and their ability to stay in or exit the progenitor zone to integrate neural or mesodermal tissues. Indeed, high Bra levels confer high motility that pushes cells to join the paraxial mesoderm, while high levels of Sox2 tend to inhibit cell movement forcing cells to integrate the NT. Mathematical modeling captures the importance of cell motility regulation in this process and further suggests that randomness in Sox2/Bra cell-to-cell distribution favors cell rearrangements and tissue shape conservation.
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Affiliation(s)
- Michèle Romanos
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPSToulouseFrance
- Institut de Mathématiques de Toulouse UMR 5219, Université de ToulouseToulouseFrance
| | - Guillaume Allio
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPSToulouseFrance
| | - Myriam Roussigné
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPSToulouseFrance
| | - Léa Combres
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPSToulouseFrance
| | - Nathalie Escalas
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPSToulouseFrance
| | - Cathy Soula
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPSToulouseFrance
| | - François Médevielle
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPSToulouseFrance
| | | | - Ariane Trescases
- Institut de Mathématiques de Toulouse UMR 5219, Université de ToulouseToulouseFrance
| | - Bertrand Bénazéraf
- Molecular, Cellular and Developmental biology department (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPSToulouseFrance
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48
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Guillot C, Djeffal Y, Michaut A, Rabe B, Pourquié O. Dynamics of primitive streak regression controls the fate of neuromesodermal progenitors in the chicken embryo. eLife 2021; 10:64819. [PMID: 34227938 PMCID: PMC8260230 DOI: 10.7554/elife.64819] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 06/23/2021] [Indexed: 12/20/2022] Open
Abstract
In classical descriptions of vertebrate development, the segregation of the three embryonic germ layers completes by the end of gastrulation. Body formation then proceeds in a head to tail fashion by progressive deposition of lineage-committed progenitors during regression of the primitive streak (PS) and tail bud (TB). The identification by retrospective clonal analysis of a population of neuromesodermal progenitors (NMPs) contributing to both musculoskeletal precursors (paraxial mesoderm) and spinal cord during axis formation challenged these notions. However, classical fate mapping studies of the PS region in amniotes have so far failed to provide direct evidence for such bipotential cells at the single-cell level. Here, using lineage tracing and single-cell RNA sequencing in the chicken embryo, we identify a resident cell population of the anterior PS epiblast, which contributes to neural and mesodermal lineages in trunk and tail. These cells initially behave as monopotent progenitors as classically described and only acquire a bipotential fate later, in more posterior regions. We show that NMPs exhibit a conserved transcriptomic signature during axis elongation but lose their epithelial characteristicsin the TB. Posterior to anterior gradients of convergence speed and ingression along the PS lead to asymmetric exhaustion of PS mesodermal precursor territories. Through limited ingression and increased proliferation, NMPs are maintained and amplified as a cell population which constitute the main progenitors in the TB. Together, our studies provide a novel understanding of the PS and TB contribution through the NMPs to the formation of the body of amniote embryos.
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Affiliation(s)
- Charlene Guillot
- Department of Pathology, Brigham and Women's Hospital, Boston, United States.,Department of Genetics, Harvard Medical School, Boston, United States.,Harvard Stem Cell Institute, Boston, United States
| | - Yannis Djeffal
- Department of Pathology, Brigham and Women's Hospital, Boston, United States.,Department of Genetics, Harvard Medical School, Boston, United States.,Harvard Stem Cell Institute, Boston, United States
| | - Arthur Michaut
- Department of Pathology, Brigham and Women's Hospital, Boston, United States.,Department of Genetics, Harvard Medical School, Boston, United States.,Harvard Stem Cell Institute, Boston, United States
| | - Brian Rabe
- Department of Genetics, Harvard Medical School, Boston, United States.,Howard Hughes Medical Institute, Boston, United States
| | - Olivier Pourquié
- Department of Pathology, Brigham and Women's Hospital, Boston, United States.,Department of Genetics, Harvard Medical School, Boston, United States.,Harvard Stem Cell Institute, Boston, United States
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49
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Barile M, Imaz-Rosshandler I, Inzani I, Ghazanfar S, Nichols J, Marioni JC, Guibentif C, Göttgens B. Coordinated changes in gene expression kinetics underlie both mouse and human erythroid maturation. Genome Biol 2021; 22:197. [PMID: 34225769 PMCID: PMC8258993 DOI: 10.1186/s13059-021-02414-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/21/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Single-cell technologies are transforming biomedical research, including the recent demonstration that unspliced pre-mRNA present in single-cell RNA-Seq permits prediction of future expression states. Here we apply this RNA velocity concept to an extended timecourse dataset covering mouse gastrulation and early organogenesis. RESULTS Intriguingly, RNA velocity correctly identifies epiblast cells as the starting point, but several trajectory predictions at later stages are inconsistent with both real-time ordering and existing knowledge. The most striking discrepancy concerns red blood cell maturation, with velocity-inferred trajectories opposing the true differentiation path. Investigating the underlying causes reveals a group of genes with a coordinated step-change in transcription, thus violating the assumptions behind current velocity analysis suites, which do not accommodate time-dependent changes in expression dynamics. Using scRNA-Seq analysis of chimeric mouse embryos lacking the major erythroid regulator Gata1, we show that genes with the step-changes in expression dynamics during erythroid differentiation fail to be upregulated in the mutant cells, thus underscoring the coordination of modulating transcription rate along a differentiation trajectory. In addition to the expected block in erythroid maturation, the Gata1-chimera dataset reveals induction of PU.1 and expansion of megakaryocyte progenitors. Finally, we show that erythropoiesis in human fetal liver is similarly characterized by a coordinated step-change in gene expression. CONCLUSIONS By identifying a limitation of the current velocity framework coupled with in vivo analysis of mutant cells, we reveal a coordinated step-change in gene expression kinetics during erythropoiesis, with likely implications for many other differentiation processes.
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Affiliation(s)
- Melania Barile
- Department of Haematology, University of Cambridge, Cambridge, CB2 0AW UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0AW UK
| | - Ivan Imaz-Rosshandler
- Department of Haematology, University of Cambridge, Cambridge, CB2 0AW UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0AW UK
| | - Isabella Inzani
- University of Cambridge Metabolic Research Laboratories and MRC Metabolic Diseases Unit, Cambridge, CB2 0QQ UK
| | - Shila Ghazanfar
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE UK
| | - Jennifer Nichols
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0AW UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3DY UK
| | - John C. Marioni
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, CB10 1SD UK
| | - Carolina Guibentif
- Department of Haematology, University of Cambridge, Cambridge, CB2 0AW UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0AW UK
- Sahlgrenska Center for Cancer Research, Department of Microbiology and Immunology, University of Gothenburg, 413 90 Gothenburg, Sweden
| | - Berthold Göttgens
- Department of Haematology, University of Cambridge, Cambridge, CB2 0AW UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0AW UK
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50
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Libby ARG, Joy DA, Elder NH, Bulger EA, Krakora MZ, Gaylord EA, Mendoza-Camacho F, Butts JC, McDevitt TC. Axial elongation of caudalized human organoids mimics aspects of neural tube development. Development 2021; 148:269182. [PMID: 34142711 DOI: 10.1242/dev.198275] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 05/07/2021] [Indexed: 12/12/2022]
Abstract
Axial elongation of the neural tube is crucial during mammalian embryogenesis for anterior-posterior body axis establishment and subsequent spinal cord development, but these processes cannot be interrogated directly in humans as they occur post-implantation. Here, we report an organoid model of neural tube extension derived from human pluripotent stem cell (hPSC) aggregates that have been caudalized with Wnt agonism, enabling them to recapitulate aspects of the morphological and temporal gene expression patterns of neural tube development. Elongating organoids consist largely of neuroepithelial compartments and contain TBXT+SOX2+ neuro-mesodermal progenitors in addition to PAX6+NES+ neural progenitors. A critical threshold of Wnt agonism stimulated singular axial extensions while maintaining multiple cell lineages, such that organoids displayed regionalized anterior-to-posterior HOX gene expression with hindbrain (HOXB1) regions spatially distinct from brachial (HOXC6) and thoracic (HOXB9) regions. CRISPR interference-mediated silencing of TBXT, a Wnt pathway target, increased neuroepithelial compartmentalization, abrogated HOX expression and disrupted uniaxial elongation. Together, these results demonstrate the potent capacity of caudalized hPSC organoids to undergo axial elongation in a manner that can be used to dissect the cellular organization and patterning decisions that dictate early human nervous system development.
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Affiliation(s)
- Ashley R G Libby
- Developmental and Stem Cell Biology PhD Program, University of California, San Francisco, CA 94143, USA.,Gladstone Institutes, San Francisco, CA 94158, USA
| | - David A Joy
- Gladstone Institutes, San Francisco, CA 94158, USA.,UC Berkeley-UC San Francisco Graduate Program in Bioengineering, San Francisco, CA 94158, USA
| | - Nicholas H Elder
- Developmental and Stem Cell Biology PhD Program, University of California, San Francisco, CA 94143, USA.,Gladstone Institutes, San Francisco, CA 94158, USA
| | - Emily A Bulger
- Developmental and Stem Cell Biology PhD Program, University of California, San Francisco, CA 94143, USA.,Gladstone Institutes, San Francisco, CA 94158, USA
| | | | - Eliza A Gaylord
- Developmental and Stem Cell Biology PhD Program, University of California, San Francisco, CA 94143, USA
| | - Frederico Mendoza-Camacho
- Developmental and Stem Cell Biology PhD Program, University of California, San Francisco, CA 94143, USA
| | | | - Todd C McDevitt
- Gladstone Institutes, San Francisco, CA 94158, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
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