1
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Hilgendorf KI, Myers BR, Reiter JF. Emerging mechanistic understanding of cilia function in cellular signalling. Nat Rev Mol Cell Biol 2024; 25:555-573. [PMID: 38366037 PMCID: PMC11199107 DOI: 10.1038/s41580-023-00698-5] [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] [Accepted: 12/21/2023] [Indexed: 02/18/2024]
Abstract
Primary cilia are solitary, immotile sensory organelles present on most cells in the body that participate broadly in human health, physiology and disease. Cilia generate a unique environment for signal transduction with tight control of protein, lipid and second messenger concentrations within a relatively small compartment, enabling reception, transmission and integration of biological information. In this Review, we discuss how cilia function as signalling hubs in cell-cell communication using three signalling pathways as examples: ciliary G-protein-coupled receptors (GPCRs), the Hedgehog (Hh) pathway and polycystin ion channels. We review how defects in these ciliary signalling pathways lead to a heterogeneous group of conditions known as 'ciliopathies', including metabolic syndromes, birth defects and polycystic kidney disease. Emerging understanding of these pathways' transduction mechanisms reveals common themes between these cilia-based signalling pathways that may apply to other pathways as well. These mechanistic insights reveal how cilia orchestrate normal and pathophysiological signalling outputs broadly throughout human biology.
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Affiliation(s)
- Keren I Hilgendorf
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA.
| | - Benjamin R Myers
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA.
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA.
- Department of Bioengineering, University of Utah School of Medicine, Salt Lake City, UT, USA.
| | - Jeremy F Reiter
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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2
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Sagner A. Temporal patterning of the vertebrate developing neural tube. Curr Opin Genet Dev 2024; 86:102179. [PMID: 38490162 DOI: 10.1016/j.gde.2024.102179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/29/2023] [Accepted: 02/20/2024] [Indexed: 03/17/2024]
Abstract
The chronologically ordered generation of distinct cell types is essential for the establishment of neuronal diversity and the formation of neuronal circuits. Recently, single-cell transcriptomic analyses of various areas of the developing vertebrate nervous system have provided evidence for the existence of a shared temporal patterning program that partitions neurons based on the timing of neurogenesis. In this review, I summarize the findings that lead to the proposal of this shared temporal program before focusing on the developing spinal cord to discuss how temporal patterning in general and this program specifically contributes to the ordered formation of neuronal circuits.
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Affiliation(s)
- Andreas Sagner
- Institut für Biochemie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Fahrstraße 17, 91054 Erlangen, Germany.
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3
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Azzi C, Rayon T. Timing mechanisms: insights from comparative neural differentiation systems. Curr Opin Genet Dev 2024; 86:102197. [PMID: 38648722 DOI: 10.1016/j.gde.2024.102197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 03/27/2024] [Accepted: 04/04/2024] [Indexed: 04/25/2024]
Abstract
Temporal control is central to deploy and coordinate genetic programs during development. At present, there is limited understanding of the molecular mechanisms that govern the duration and speed of developmental processes. Timing mechanisms may run in parallel and/or interact with each other to integrate temporal signals throughout the organism. In this piece, we consider findings on the extrinsic control of developmental tempo and discuss the intrinsic roles of cell cycle, metabolic rates, protein turnover, and post-transcriptional mechanisms in the regulation of tempo during neural development.
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Affiliation(s)
- Chiara Azzi
- Epigenetics & Signalling Programmes, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK. https://twitter.com/@azziChiA
| | - Teresa Rayon
- Epigenetics & Signalling Programmes, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK.
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4
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Catela C, Assimacopoulos S, Chen Y, Tsioras K, Feng W, Kratsios P. The Iroquois ( Iro/Irx) homeobox genes are conserved Hox targets involved in motor neuron development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.30.596714. [PMID: 38853975 PMCID: PMC11160718 DOI: 10.1101/2024.05.30.596714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
The Iroquois (Iro/Irx) homeobox genes encode transcription factors with fundamental roles in animal development. Despite their link to various congenital conditions in humans, our understanding of Iro/Irx gene expression, function, and regulation remains incomplete. Here, we conducted a systematic expression analysis of all six mouse Irx genes in the embryonic spinal cord. We found five Irx genes (Irx1, Irx2, Irx3, Irx5, and Irx6) to be confined mostly to ventral spinal domains, offering new molecular markers for specific groups of post-mitotic motor neurons (MNs). Further, we engineered Irx2, Irx5, and Irx6 mouse mutants and uncovered essential but distinct roles for Irx2 and Irx6 in MN development. Last, we found that the highly conserved regulators of MN development across species, the HOX proteins, directly control Irx gene expression both in mouse and C. elegans MNs, critically expanding the repertoire of HOX target genes in the developing nervous system. Altogether, our study provides important insights into Iro/Irx expression and function in the developing spinal cord, and uncovers an ancient gene regulatory relationship between HOX and Iro/Irx genes.
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Affiliation(s)
- Catarina Catela
- Department of Neurobiology, University of Chicago, Chicago, IL, USA
- Neuroscience Institute, University of Chicago, Chicago, IL, USA
| | - Stavroula Assimacopoulos
- Department of Neurobiology, University of Chicago, Chicago, IL, USA
- Neuroscience Institute, University of Chicago, Chicago, IL, USA
| | - Yihan Chen
- Department of Neurobiology, University of Chicago, Chicago, IL, USA
- Neuroscience Institute, University of Chicago, Chicago, IL, USA
| | - Konstantinos Tsioras
- Department of Neurobiology, University of Chicago, Chicago, IL, USA
- Neuroscience Institute, University of Chicago, Chicago, IL, USA
| | - Weidong Feng
- Department of Neurobiology, University of Chicago, Chicago, IL, USA
- Neuroscience Institute, University of Chicago, Chicago, IL, USA
| | - Paschalis Kratsios
- Department of Neurobiology, University of Chicago, Chicago, IL, USA
- Neuroscience Institute, University of Chicago, Chicago, IL, USA
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5
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Masuda A, Nishida K, Ajima R, Saga Y, Bakhtan M, Klar A, Hirata T, Zhu Y. A global gene regulatory program and its region-specific regulator partition neurons into commissural and ipsilateral projection types. SCIENCE ADVANCES 2024; 10:eadk2149. [PMID: 38781326 PMCID: PMC11114196 DOI: 10.1126/sciadv.adk2149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 04/16/2024] [Indexed: 05/25/2024]
Abstract
Understanding the genetic programs that drive neuronal diversification into classes and subclasses is key to understand nervous system development. All neurons can be classified into two types: commissural and ipsilateral, based on whether their axons cross the midline or not. However, the gene regulatory program underlying this binary division is poorly understood. We identified a pair of basic helix-loop-helix transcription factors, Nhlh1 and Nhlh2, as a global transcriptional mechanism that controls the laterality of all floor plate-crossing commissural axons in mice. Mechanistically, Nhlh1/2 play an essential role in the expression of Robo3, the key guidance molecule for commissural axon projections. This genetic program appears to be evolutionarily conserved in chick. We further discovered that Isl1, primarily expressed in ipsilateral neurons within neural tubes, negatively regulates the Robo3 induction by Nhlh1/2. Our findings elucidate a gene regulatory strategy where a conserved global mechanism intersects with neuron class-specific regulators to control the partitioning of neurons based on axon laterality.
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Affiliation(s)
- Aki Masuda
- National Institute of Genetics, Graduate University for Advanced Studies, Sokendai, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Kazuhiko Nishida
- Department of Medical Chemistry, Kansai Medical University, Hirakata, Osaka 573-1010, Japan
| | - Rieko Ajima
- National Institute of Genetics, Graduate University for Advanced Studies, Sokendai, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Yumiko Saga
- National Institute of Genetics, Graduate University for Advanced Studies, Sokendai, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Marah Bakhtan
- Department of Medical Neurobiology, IMRIC, Hebrew University - Hadassah Medical School, Jerusalem, Israel
| | - Avihu Klar
- Department of Medical Neurobiology, IMRIC, Hebrew University - Hadassah Medical School, Jerusalem, Israel
| | - Tatsumi Hirata
- National Institute of Genetics, Graduate University for Advanced Studies, Sokendai, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Yan Zhu
- National Institute of Genetics, Graduate University for Advanced Studies, Sokendai, Yata 1111, Mishima, Shizuoka 411-8540, Japan
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6
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Krammer T, Stuart HT, Gromberg E, Ishihara K, Cislo D, Melchionda M, Becerril Perez F, Wang J, Costantini E, Lehr S, Arbanas L, Hörmann A, Neumüller RA, Elvassore N, Siggia E, Briscoe J, Kicheva A, Tanaka EM. Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition. Dev Cell 2024:S1534-5807(24)00297-1. [PMID: 38776925 DOI: 10.1016/j.devcel.2024.04.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 03/08/2024] [Accepted: 04/30/2024] [Indexed: 05/25/2024]
Abstract
During neural tube (NT) development, the notochord induces an organizer, the floorplate, which secretes Sonic Hedgehog (SHH) to pattern neural progenitors. Conversely, NT organoids (NTOs) from embryonic stem cells (ESCs) spontaneously form floorplates without the notochord, demonstrating that stem cells can self-organize without embryonic inducers. Here, we investigated floorplate self-organization in clonal mouse NTOs. Expression of the floorplate marker FOXA2 was initially spatially scattered before resolving into multiple clusters, which underwent competition and sorting, resulting in a stable "winning" floorplate. We identified that BMP signaling governed long-range cluster competition. FOXA2+ clusters expressed BMP4, suppressing FOXA2 in receiving cells while simultaneously expressing the BMP-inhibitor NOGGIN, promoting cluster persistence. Noggin mutation perturbed floorplate formation in NTOs and in the NT in vivo at mid/hindbrain regions, demonstrating how the floorplate can form autonomously without the notochord. Identifying the pathways governing organizer self-organization is critical for harnessing the developmental plasticity of stem cells in tissue engineering.
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Affiliation(s)
- Teresa Krammer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Hannah T Stuart
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria; The Francis Crick Institute, London, UK
| | - Elena Gromberg
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Keisuke Ishihara
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Dillon Cislo
- Center for Studies in Physics and Biology, The Rockefeller University, New York, NY, USA
| | | | - Fernando Becerril Perez
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Jingkui Wang
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Elena Costantini
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Stefanie Lehr
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Laura Arbanas
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | | | | | - Nicola Elvassore
- Department of Industrial Engineering, University of Padova & Veneto Institute of Molecular Medicine (VIMM), Padova, Italy
| | - Eric Siggia
- Center for Studies in Physics and Biology, The Rockefeller University, New York, NY, USA
| | | | - Anna Kicheva
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Elly M Tanaka
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria.
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7
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Maizels RJ, Snell DM, Briscoe J. Reconstructing developmental trajectories using latent dynamical systems and time-resolved transcriptomics. Cell Syst 2024; 15:411-424.e9. [PMID: 38754365 DOI: 10.1016/j.cels.2024.04.004] [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: 09/19/2023] [Revised: 02/01/2024] [Accepted: 04/17/2024] [Indexed: 05/18/2024]
Abstract
The snapshot nature of single-cell transcriptomics presents a challenge for studying the dynamics of cell fate decisions. Metabolic labeling and splicing can provide temporal information at single-cell level, but current methods have limitations. Here, we present a framework that overcomes these limitations: experimentally, we developed sci-FATE2, an optimized method for metabolic labeling with increased data quality, which we used to profile 45,000 embryonic stem (ES) cells differentiating into neural tube identities. Computationally, we developed a two-stage framework for dynamical modeling: VelvetVAE, a variational autoencoder (VAE) for velocity inference that outperforms all other tools tested, and VelvetSDE, a neural stochastic differential equation (nSDE) framework for simulating trajectory distributions. These recapitulate underlying dataset distributions and capture features such as decision boundaries between alternative fates and fate-specific gene expression. These methods recast single-cell analyses from descriptions of observed data to models of the dynamics that generated them, providing a framework for investigating developmental fate decisions.
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Affiliation(s)
- Rory J Maizels
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; University College, London, UK
| | - Daniel M Snell
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - James Briscoe
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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8
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González‐Llera L, Sobrido‐Cameán D, Quelle‐Regaldie A, Sánchez L, Barreiro‐Iglesias A. An in vivo drug screen in zebrafish reveals that cyclooxygenase 2-derived prostaglandin D 2 promotes spinal cord neurogenesis. Cell Prolif 2024; 57:e13594. [PMID: 38155412 PMCID: PMC11056714 DOI: 10.1111/cpr.13594] [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: 09/26/2023] [Revised: 11/27/2023] [Accepted: 12/18/2023] [Indexed: 12/30/2023] Open
Abstract
The study of neurogenesis is essential to understanding fundamental developmental processes and for the development of cell replacement therapies for central nervous system disorders. Here, we designed an in vivo drug screening protocol in developing zebrafish to find new molecules and signalling pathways regulating neurogenesis in the ventral spinal cord. This unbiased drug screen revealed that 4 cyclooxygenase (COX) inhibitors reduced the generation of serotonergic interneurons in the developing spinal cord. These results fitted very nicely with available single-cell RNAseq data revealing that floor plate cells show differential expression of 1 of the 2 COX2 zebrafish genes (ptgs2a). Indeed, several selective COX2 inhibitors and two different morpholinos against ptgs2a reduced the number of serotonergic neurons in the ventral spinal cord and led to locomotor deficits. Single-cell RNAseq data and different pharmacological manipulations further revealed that COX2-floor plate-derived prostaglandin D2 promotes neurogenesis in the developing spinal cord by promoting mitotic activity in progenitor cells. Rescue experiments using a phosphodiesterase-4 inhibitor suggest that intracellular changes in cAMP levels underlie the effects of COX inhibitors on neurogenesis and locomotion. Our study provides compelling in vivo evidence showing that prostaglandin signalling promotes neurogenesis in the ventral spinal cord.
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Affiliation(s)
- Laura González‐Llera
- Department of Functional Biology, CIBUS, Faculty of BiologyUniversidade de Santiago de CompostelaSantiago de CompostelaSpain
| | - Daniel Sobrido‐Cameán
- Department of Functional Biology, CIBUS, Faculty of BiologyUniversidade de Santiago de CompostelaSantiago de CompostelaSpain
- Present address:
Department of ZoologyUniversity of CambridgeCambridgeUK
| | - Ana Quelle‐Regaldie
- Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary ScienceUniversidade de Santiago de CompostelaLugoSpain
- Present address:
Translational Research for Neurological DiseasesInstitut Imagine, INSERM UMR 1163, Université Paris CitéParisFrance
| | - Laura Sánchez
- Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary ScienceUniversidade de Santiago de CompostelaLugoSpain
- Preclinical Animal Models GroupHealth Research Institute of Santiago de Compostela (IDIS)Santiago de CompostelaSpain
| | - Antón Barreiro‐Iglesias
- Department of Functional Biology, CIBUS, Faculty of BiologyUniversidade de Santiago de CompostelaSantiago de CompostelaSpain
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9
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Zhou G, Pang S, Li Y, Gao J. Progress in the generation of spinal cord organoids over the past decade and future perspectives. Neural Regen Res 2024; 19:1013-1019. [PMID: 37862203 PMCID: PMC10749595 DOI: 10.4103/1673-5374.385280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 06/25/2023] [Accepted: 08/01/2023] [Indexed: 10/22/2023] Open
Abstract
Spinal cord organoids are three-dimensional tissues derived from stem cells that recapitulate the primary morphological and functional characteristics of the spinal cord in vivo. As emerging bioengineering methods have led to the optimization of cell culture protocols, spinal cord organoids technology has made remarkable advancements in the past decade. Our literature search found that current spinal cord organoids do not only dynamically simulate neural tube formation but also exhibit diverse cytoarchitecture along the dorsal-ventral and rostral-caudal axes. Moreover, fused organoids that integrate motor neurons and other regionally specific organoids exhibit intricate neural circuits that allows for functional assessment. These qualities make spinal cord organoids valuable tools for disease modeling, drug screening, and tissue regeneration. By utilizing this emergent technology, researchers have made significant progress in investigating the pathogenesis and potential therapeutic targets of spinal cord diseases. However, at present, spinal cord organoid technology remains in its infancy and has not been widely applied in translational medicine. Establishment of the next generation of spinal cord organoids will depend on good manufacturing practice standards and needs to focus on diverse cell phenotypes and electrophysiological functionality evaluation.
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Affiliation(s)
- Gang Zhou
- Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Siyuan Pang
- Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yongning Li
- Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Department of International Medical Service, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jun Gao
- Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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10
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Maizels RJ. A dynamical perspective: moving towards mechanism in single-cell transcriptomics. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230049. [PMID: 38432314 PMCID: PMC10909508 DOI: 10.1098/rstb.2023.0049] [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: 07/10/2023] [Accepted: 10/31/2023] [Indexed: 03/05/2024] Open
Abstract
As the field of single-cell transcriptomics matures, research is shifting focus from phenomenological descriptions of cellular phenotypes to a mechanistic understanding of the gene regulation underneath. This perspective considers the value of capturing dynamical information at single-cell resolution for gaining mechanistic insight; reviews the available technologies for recording and inferring temporal information in single cells; and explores whether better dynamical resolution is sufficient to adequately capture the causal relationships driving complex biological systems. This article is part of a discussion meeting issue 'Causes and consequences of stochastic processes in development and disease'.
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Affiliation(s)
- Rory J. Maizels
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- University College London, London WC1E 6BT, UK
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11
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Xue X, Kim YS, Ponce-Arias AI, O'Laughlin R, Yan RZ, Kobayashi N, Tshuva RY, Tsai YH, Sun S, Zheng Y, Liu Y, Wong FCK, Surani A, Spence JR, Song H, Ming GL, Reiner O, Fu J. A patterned human neural tube model using microfluidic gradients. Nature 2024; 628:391-399. [PMID: 38408487 PMCID: PMC11006583 DOI: 10.1038/s41586-024-07204-7] [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: 01/26/2022] [Accepted: 02/16/2024] [Indexed: 02/28/2024]
Abstract
The human nervous system is a highly complex but organized organ. The foundation of its complexity and organization is laid down during regional patterning of the neural tube, the embryonic precursor to the human nervous system. Historically, studies of neural tube patterning have relied on animal models to uncover underlying principles. Recently, models of neurodevelopment based on human pluripotent stem cells, including neural organoids1-5 and bioengineered neural tube development models6-10, have emerged. However, such models fail to recapitulate neural patterning along both rostral-caudal and dorsal-ventral axes in a three-dimensional tubular geometry, a hallmark of neural tube development. Here we report a human pluripotent stem cell-based, microfluidic neural tube-like structure, the development of which recapitulates several crucial aspects of neural patterning in brain and spinal cord regions and along rostral-caudal and dorsal-ventral axes. This structure was utilized for studying neuronal lineage development, which revealed pre-patterning of axial identities of neural crest progenitors and functional roles of neuromesodermal progenitors and the caudal gene CDX2 in spinal cord and trunk neural crest development. We further developed dorsal-ventral patterned microfluidic forebrain-like structures with spatially segregated dorsal and ventral regions and layered apicobasal cellular organizations that mimic development of the human forebrain pallium and subpallium, respectively. Together, these microfluidics-based neurodevelopment models provide three-dimensional lumenal tissue architectures with in vivo-like spatiotemporal cell differentiation and organization, which will facilitate the study of human neurodevelopment and disease.
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Affiliation(s)
- Xufeng Xue
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Yung Su Kim
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Alfredo-Isaac Ponce-Arias
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Richard O'Laughlin
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Robin Zhexuan Yan
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Norio Kobayashi
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Rami Yair Tshuva
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Yu-Hwai Tsai
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Shiyu Sun
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Yi Zheng
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Yue Liu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Frederick C K Wong
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
| | - Azim Surani
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Jason R Spence
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI, USA
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Hongjun Song
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, USA
- The Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Guo-Li Ming
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Orly Reiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Jianping Fu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA.
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA.
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA.
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12
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Hsu HC, Hsu SP, Hsu FY, Chang M, Chen JA. LncRNA Litchi is a regulator for harmonizing maturity and resilient functionality in spinal motor neurons. iScience 2024; 27:109207. [PMID: 38433925 PMCID: PMC10906515 DOI: 10.1016/j.isci.2024.109207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/08/2023] [Accepted: 02/07/2024] [Indexed: 03/05/2024] Open
Abstract
Long noncoding RNAs (lncRNAs) play pivotal roles in modulating gene expression during development and disease. Despite their high expression in the central nervous system (CNS), understanding the precise physiological functions of CNS-associated lncRNAs has been challenging, largely due to the in vitro-centric nature of studies in this field. Here, utilizing mouse embryonic stem cell (ESC)-derived motor neurons (MNs), we identified an unexplored MN-specific lncRNA, Litchi (Long Intergenic RNAs in Chat Intron). By employing an "exon-only" deletion strategy in ESCs and a mouse model, we reveal that Litchi deletion profoundly impacts MN dendritic complexity, axonal growth, and altered action potential patterns. Mechanistically, voltage-gated channels and neurite growth-related genes exhibited heightened sensitivity to Litchi deletion. Our Litchi-knockout mouse model displayed compromised motor behaviors and reduced muscle strength, highlighting Litchi's critical role in motor function. This study unveils an underappreciated function of lncRNAs in orchestrating MN maturation and maintaining robust electrophysiological properties.
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Affiliation(s)
- Ho-Chiang Hsu
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
- Taiwan International Graduate Program in Interdisciplinary Neuroscience, National Cheng Kung University and Academia Sinica, Taipei, Taiwan
| | - Sheng-Ping Hsu
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Fang-Yu Hsu
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei 10617, Taiwan
| | - Mien Chang
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Jun-An Chen
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
- Taiwan International Graduate Program in Interdisciplinary Neuroscience, National Cheng Kung University and Academia Sinica, Taipei, Taiwan
- Neuroscience Program of Academia Sinica, Academia Sinica, Taipei, Taiwan
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei 10617, Taiwan
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13
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Manning E, Placzek M. Organizing activities of axial mesoderm. Curr Top Dev Biol 2024; 157:83-123. [PMID: 38556460 DOI: 10.1016/bs.ctdb.2024.02.007] [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: 04/02/2024]
Abstract
For almost a century, developmental biologists have appreciated that the ability of the embryonic organizer to induce and pattern the body plan is intertwined with its differentiation into axial mesoderm. Despite this, we still have a relatively poor understanding of the contribution of axial mesoderm to induction and patterning of different body regions, and the manner in which axial mesoderm-derived information is interpreted in tissues of changing competence. Here, with a particular focus on the nervous system, we review the evidence that axial mesoderm notochord and prechordal mesoderm/mesendoderm act as organizers, discuss how their influence extends through the different axes of the developing organism, and describe how the ability of axial mesoderm to direct morphogenesis impacts on its role as a local organizer.
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Affiliation(s)
- Elizabeth Manning
- School of Biosciences, University of Sheffield, Sheffield, United Kingdom; Bateson Centre, University of Sheffield, Sheffield, United Kingdom
| | - Marysia Placzek
- School of Biosciences, University of Sheffield, Sheffield, United Kingdom; Bateson Centre, University of Sheffield, Sheffield, United Kingdom; Neuroscience Institute, University of Sheffield, Sheffield, United Kingdom.
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14
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Mörsdorf D, Knabl P, Genikhovich G. Highly conserved and extremely evolvable: BMP signalling in secondary axis patterning of Cnidaria and Bilateria. Dev Genes Evol 2024:10.1007/s00427-024-00714-4. [PMID: 38472535 DOI: 10.1007/s00427-024-00714-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 03/06/2024] [Indexed: 03/14/2024]
Abstract
Bilateria encompass the vast majority of the animal phyla. As the name states, they are bilaterally symmetric, that is with a morphologically clear main body axis connecting their anterior and posterior ends, a second axis running between their dorsal and ventral surfaces, and with a left side being roughly a mirror image of their right side. Bone morphogenetic protein (BMP) signalling has widely conserved functions in the formation and patterning of the second, dorso-ventral (DV) body axis, albeit to different extents in different bilaterian species. Whilst initial findings in the fruit fly Drosophila and the frog Xenopus highlighted similarities amongst these evolutionarily very distant species, more recent analyses featuring other models revealed considerable diversity in the mechanisms underlying dorsoventral patterning. In fact, as phylogenetic sampling becomes broader, we find that this axis patterning system is so evolvable that even its core components can be deployed differently or lost in different model organisms. In this review, we will try to highlight the diversity of ways by which BMP signalling controls bilaterality in different animals, some of which do not belong to Bilateria. Future research combining functional analyses and modelling is bound to give us some understanding as to where the limits to the extent of the evolvability of BMP-dependent axial patterning may lie.
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Affiliation(s)
- David Mörsdorf
- Dept. Neurosciences and Developmental Biology, University of Vienna, UBB, Djerassiplatz 1, 1030, Vienna, Austria
| | - Paul Knabl
- Dept. Neurosciences and Developmental Biology, University of Vienna, UBB, Djerassiplatz 1, 1030, Vienna, Austria
- Vienna Doctoral School of Ecology and Evolution (VDSEE), University of Vienna, Vienna, Austria
| | - Grigory Genikhovich
- Dept. Neurosciences and Developmental Biology, University of Vienna, UBB, Djerassiplatz 1, 1030, Vienna, Austria.
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15
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Ang CE, Olmos VH, Vodehnal K, Zhou B, Lee QY, Sinha R, Narayanaswamy A, Mall M, Chesnov K, Dominicus CS, Südhof T, Wernig M. Generation of human excitatory forebrain neurons by cooperative binding of proneural NGN2 and homeobox factor EMX1. Proc Natl Acad Sci U S A 2024; 121:e2308401121. [PMID: 38446849 PMCID: PMC10945857 DOI: 10.1073/pnas.2308401121] [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: 05/24/2023] [Accepted: 01/24/2024] [Indexed: 03/08/2024] Open
Abstract
Generation of defined neuronal subtypes from human pluripotent stem cells remains a challenge. The proneural factor NGN2 has been shown to overcome experimental variability observed by morphogen-guided differentiation and directly converts pluripotent stem cells into neurons, but their cellular heterogeneity has not been investigated yet. Here, we found that NGN2 reproducibly produces three different kinds of excitatory neurons characterized by partial coactivation of other neurotransmitter programs. We explored two principle approaches to achieve more precise specification: prepatterning the chromatin landscape that NGN2 is exposed to and combining NGN2 with region-specific transcription factors. Unexpectedly, the chromatin context of regionalized neural progenitors only mildly altered genomic NGN2 binding and its transcriptional response and did not affect neurotransmitter specification. In contrast, coexpression of region-specific homeobox factors such as EMX1 resulted in drastic redistribution of NGN2 including recruitment to homeobox targets and resulted in glutamatergic neurons with silenced nonglutamatergic programs. These results provide the molecular basis for a blueprint for improved strategies for generating a plethora of defined neuronal subpopulations from pluripotent stem cells for therapeutic or disease-modeling purposes.
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Affiliation(s)
- Cheen Euong Ang
- Department of Bioengineering, Stanford University, Stanford, CA94305
- Department of Pathology, Stanford University, Stanford, CA94305
- Institute of Stem Cell and Regenerative Medicine, Stanford University, Stanford, CA94305
| | - Victor Hipolito Olmos
- Department of Pathology, Stanford University, Stanford, CA94305
- Institute of Stem Cell and Regenerative Medicine, Stanford University, Stanford, CA94305
| | - Kayla Vodehnal
- Department of Pathology, Stanford University, Stanford, CA94305
- Institute of Stem Cell and Regenerative Medicine, Stanford University, Stanford, CA94305
| | - Bo Zhou
- Department of Pathology, Stanford University, Stanford, CA94305
- Institute of Stem Cell and Regenerative Medicine, Stanford University, Stanford, CA94305
- HHMI, Stanford University, Stanford, CA94305
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA94305
| | - Qian Yi Lee
- Department of Bioengineering, Stanford University, Stanford, CA94305
- Department of Pathology, Stanford University, Stanford, CA94305
- Institute of Stem Cell and Regenerative Medicine, Stanford University, Stanford, CA94305
| | - Rahul Sinha
- Institute of Stem Cell and Regenerative Medicine, Stanford University, Stanford, CA94305
| | - Aadit Narayanaswamy
- Department of Pathology, Stanford University, Stanford, CA94305
- Institute of Stem Cell and Regenerative Medicine, Stanford University, Stanford, CA94305
| | - Moritz Mall
- Department of Pathology, Stanford University, Stanford, CA94305
- Institute of Stem Cell and Regenerative Medicine, Stanford University, Stanford, CA94305
| | - Kirill Chesnov
- Department of Pathology, Stanford University, Stanford, CA94305
- Institute of Stem Cell and Regenerative Medicine, Stanford University, Stanford, CA94305
| | - Caia S. Dominicus
- Wellcome Sanger Institute, Hinxton, CambridgeshireCB10 1SA, United Kingdom
- OpenTargets, Hinxton, CambridgeshireCB10 1SA, United Kingdom
| | - Thomas Südhof
- HHMI, Stanford University, Stanford, CA94305
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA94305
| | - Marius Wernig
- Department of Pathology, Stanford University, Stanford, CA94305
- Institute of Stem Cell and Regenerative Medicine, Stanford University, Stanford, CA94305
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16
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Nakamura K, Watanabe Y, Boitet C, Satake S, Iida H, Yoshihi K, Ishii Y, Kato K, Kondoh H. Wnt signal-dependent antero-posterior specification of early-stage CNS primordia modeled in EpiSC-derived neural stem cells. Front Cell Dev Biol 2024; 11:1260528. [PMID: 38405136 PMCID: PMC10884098 DOI: 10.3389/fcell.2023.1260528] [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: 07/18/2023] [Accepted: 11/30/2023] [Indexed: 02/27/2024] Open
Abstract
The specification of the embryonic central nervous system (CNS) into future brain (forebrain, midbrain, or hindbrain) and spinal cord (SC) regions is a critical step of CNS development. A previous chicken embryo study indicated that anterior epiblast cells marked by Sox2 N2 enhancer activity are specified to the respective brain regions during the transition phase of the epiblast to the neural plate-forming neural primordium. The present study showed that the SC precursors positioned posterior to the hindbrain precursors in the anterior epiblast migrated posteriorly in contrast to the anterior migration of brain precursors. The anteroposterior specification of the CNS precursors occurs at an analogous time (∼E7.5) in mouse embryos, in which an anterior-to-posterior incremental gradient of Wnt signal strength was observed. To examine the possible Wnt signal contribution to the anteroposterior CNS primordium specification, we utilized mouse epiblast stem cell (EpiSC)-derived neurogenesis in culture. EpiSCs maintained in an activin- and FGF2-containing medium start neural development after the removal of activin, following a day in a transitory state. We placed activin-free EpiSCs in EGF- and FGF2-containing medium to arrest neural development and expand the cells into neural stem cells (NSCs). Simultaneously, a Wnt antagonist or agonist was added to the culture, with the anticipation that different levels of Wnt signals would act on the transitory cells to specify CNS regionality; then, the Wnt-treated cells were expanded as NSCs. Gene expression profiles of six NSC lines were analyzed using microarrays and single-cell RNA-seq. The NSC lines demonstrated anteroposterior regional specification in response to increasing Wnt signal input levels: forebrain-midbrain-, hindbrain-, cervical SC-, and thoracic SC-like lines. The regional coverage of these NSC lines had a range; for instance, the XN1 line expressed Otx2 and En2, indicating midbrain characteristics, but additionally expressed the SC-characteristic Hoxa5. The ranges in the anteroposterior specification of neural primordia may be narrowed as neural development proceeds. The thoracic SC is presumably the posterior limit of the contribution by anterior epiblast-derived neural progenitors, as the characteristics of more posterior SC regions were not displayed.
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Affiliation(s)
- Kae Nakamura
- Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto, Japan
| | - Yusaku Watanabe
- Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto, Japan
| | - Claire Boitet
- Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto, Japan
- Université Joseph Fourier, Domaine Universitaire, Saint-Martin-d’Hères, France
| | - Sayaka Satake
- Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto, Japan
| | - Hideaki Iida
- Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto, Japan
| | - Koya Yoshihi
- Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto, Japan
| | - Yasuo Ishii
- Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto, Japan
- Department of Biology, School of Medicine, Tokyo Women’s Medical University, Tokyo, Japan
| | - Kagayaki Kato
- National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Hisato Kondoh
- Faculty of Life Sciences, Kyoto Sangyo University, Kita-ku, Kyoto, Japan
- Biohistory Research Hall, Takatsuki, Osaka, Japan
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17
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [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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18
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Cucun G, Köhler M, Pfitsch S, Rastegar S. Insights into the mechanisms of neuron generation and specification in the zebrafish ventral spinal cord. FEBS J 2024; 291:646-662. [PMID: 37498183 DOI: 10.1111/febs.16913] [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: 05/02/2023] [Revised: 06/20/2023] [Accepted: 07/25/2023] [Indexed: 07/28/2023]
Abstract
The vertebrate nervous system is composed of a wide range of neurons and complex synaptic connections, raising the intriguing question of how neuronal diversity is generated. The spinal cord provides an excellent model for exploring the mechanisms governing neuronal diversity due to its simple neural network and the conserved molecular processes involved in neuron formation and specification during evolution. This review specifically examines two distinct progenitor domains present in the zebrafish ventral spinal cord: the lateral floor plate (LFP) and the p2 progenitor domain. The LFP is responsible for the production of GABAergic Kolmer-Agduhr neurons (KA″), glutamatergic V3 neurons, and intraspinal serotonergic neurons, while the p2 domain generates V2 precursors that subsequently differentiate into three unique subpopulations of V2 neurons, namely glutamatergic V2a, GABAergic V2b, and glycinergic V2s. Based on recent findings, we will examine the fundamental signaling pathways and transcription factors that play a key role in the specification of these diverse neurons and neuronal subtypes derived from the LFP and p2 progenitor domains.
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Affiliation(s)
- Gokhan Cucun
- Institute for Biological and Chemical Systems - Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Melina Köhler
- Institute for Biological and Chemical Systems - Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Sabrina Pfitsch
- Institute for Biological and Chemical Systems - Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Sepand Rastegar
- Institute for Biological and Chemical Systems - Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
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19
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Filippopoulou K, Konstantinides N. Evolution of patterning. FEBS J 2024; 291:663-671. [PMID: 37943156 DOI: 10.1111/febs.16995] [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: 06/19/2023] [Revised: 09/28/2023] [Accepted: 11/07/2023] [Indexed: 11/10/2023]
Abstract
Developing tissues are patterned in space and time; this enables them to differentiate their cell types and form complex structures to support different body plans. Although space and time are two independent entities, there are many examples of spatial patterns that originate from temporal ones. The most prominent example is the expression of the genes hunchback, Krüppel, pdm, and castor, which are expressed temporally in the neural stem cells of the Drosophila ventral nerve cord and spatially along the anteroposterior axis of the blastoderm stage embryo. In this Viewpoint, we investigate the relationship between space and time in specific examples of spatial and temporal patterns with the aim of gaining insight into the evolutionary history of patterning.
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20
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Schilling K. Revisiting the development of cerebellar inhibitory interneurons in the light of single-cell genetic analyses. Histochem Cell Biol 2024; 161:5-27. [PMID: 37940705 PMCID: PMC10794478 DOI: 10.1007/s00418-023-02251-z] [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] [Accepted: 10/12/2023] [Indexed: 11/10/2023]
Abstract
The present review aims to provide a short update of our understanding of the inhibitory interneurons of the cerebellum. While these cells constitute but a minority of all cerebellar neurons, their functional significance is increasingly being recognized. For one, inhibitory interneurons of the cerebellar cortex are now known to constitute a clearly more diverse group than their traditional grouping as stellate, basket, and Golgi cells suggests, and this diversity is now substantiated by single-cell genetic data. The past decade or so has also provided important information about interneurons in cerebellar nuclei. Significantly, developmental studies have revealed that the specification and formation of cerebellar inhibitory interneurons fundamentally differ from, say, the cortical interneurons, and define a mode of diversification critically dependent on spatiotemporally patterned external signals. Last, but not least, in the past years, dysfunction of cerebellar inhibitory interneurons could also be linked with clinically defined deficits. I hope that this review, however fragmentary, may stimulate interest and help focus research towards understanding the cerebellum.
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Affiliation(s)
- Karl Schilling
- Anatomisches Institut - Anatomie und Zellbiologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Nussallee 10, 53115, Bonn, Germany.
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21
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Roman A, Huntemer-Silveira A, Waldron MA, Khalid Z, Blake J, Parr AM, Low WC. Cell Transplantation for Repair of the Spinal Cord and Prospects for Generating Region-Specific Exogenic Neuronal Cells. Cell Transplant 2024; 33:9636897241241998. [PMID: 38590295 PMCID: PMC11005494 DOI: 10.1177/09636897241241998] [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: 09/25/2023] [Revised: 03/05/2024] [Accepted: 03/11/2024] [Indexed: 04/10/2024] Open
Abstract
Spinal cord injury (SCI) is associated with currently irreversible consequences in several functional components of the central nervous system. Despite the severity of injury, there remains no approved treatment to restore function. However, with a growing number of preclinical studies and clinical trials, cell transplantation has gained significant potential as a treatment for SCI. Researchers have identified several cell types as potential candidates for transplantation. To optimize successful functional outcomes after transplantation, one key factor concerns generating neuronal cells with regional and subtype specificity, thus calling on the developmental transcriptome patterning of spinal cord cells. A potential source of spinal cord cells for transplantation is the generation of exogenic neuronal progenitor cells via the emerging technologies of gene editing and blastocyst complementation. This review highlights the use of cell transplantation to treat SCI in the context of relevant developmental gene expression patterns useful for producing regionally specific exogenic spinal cells via in vitro differentiation and blastocyst complementation.
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Affiliation(s)
- Alex Roman
- Department of Neuroscience, University of Minnesota, Minneapolis, MN, USA
- Graduate Program in Neuroscience, University of Minnesota, Minneapolis, MN, USA
- Department of Neurosurgery, Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
| | - Anne Huntemer-Silveira
- Department of Neuroscience, University of Minnesota, Minneapolis, MN, USA
- Graduate Program in Neuroscience, University of Minnesota, Minneapolis, MN, USA
| | - Madison A. Waldron
- Department of Neuroscience, University of Minnesota, Minneapolis, MN, USA
- Graduate Program in Neuroscience, University of Minnesota, Minneapolis, MN, USA
| | - Zainab Khalid
- Department of Neurosurgery, Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
| | - Jeffrey Blake
- Department of Neurosurgery, Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
| | - Ann M. Parr
- Graduate Program in Neuroscience, University of Minnesota, Minneapolis, MN, USA
- Department of Neurosurgery, Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
| | - Walter C. Low
- Graduate Program in Neuroscience, University of Minnesota, Minneapolis, MN, USA
- Department of Neurosurgery, Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
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22
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Mirdass C, Catala M, Bocel M, Nedelec S, Ribes V. Stem cell-derived models of spinal neurulation. Emerg Top Life Sci 2023; 7:423-437. [PMID: 38087891 DOI: 10.1042/etls20230087] [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: 09/21/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 12/19/2023]
Abstract
Neurulation is a critical step in early embryonic development, giving rise to the neural tube, the primordium of the central nervous system in amniotes. Understanding this complex, multi-scale, multi-tissue morphogenetic process is essential to provide insights into normal development and the etiology of neural tube defects. Innovations in tissue engineering have fostered the generation of pluripotent stem cell-based in vitro models, including organoids, that are emerging as unique tools for delving into neurulation mechanisms, especially in the context of human development. Each model captures specific aspects of neural tube morphogenesis, from epithelialization to neural tissue elongation, folding and cavitation. In particular, the recent models of human and mouse trunk morphogenesis, such as gastruloids, that form a spinal neural plate-like or neural tube-like structure are opening new avenues to study normal and pathological neurulation. Here, we review the morphogenetic events generating the neural tube in the mammalian embryo and questions that remain unanswered. We discuss the advantages and limitations of existing in vitro models of neurulation and possible future technical developments.
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Affiliation(s)
- Camil Mirdass
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
- Institut du Fer à Moulin, 75005 Paris, France
- Inserm, UMR-S 1270, 75005 Paris, France
- Sorbonne Université, Science and Engineering Faculty, 75005 Paris, France
| | - Martin Catala
- Institut de Biologie Paris Seine (IBPS) - Developmental Biology Laboratory, UMR7622 CNRS, INSERM ERL 1156, Sorbonne Université, 9 Quai Saint-Bernard, 75005 Paris, France
| | - Mikaëlle Bocel
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Stéphane Nedelec
- Institut du Fer à Moulin, 75005 Paris, France
- Inserm, UMR-S 1270, 75005 Paris, France
- Sorbonne Université, Science and Engineering Faculty, 75005 Paris, France
| | - Vanessa Ribes
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
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23
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Burda I, Martin AC, Roeder AHK, Collins MA. The dynamics and biophysics of shape formation: Common themes in plant and animal morphogenesis. Dev Cell 2023; 58:2850-2866. [PMID: 38113851 PMCID: PMC10752614 DOI: 10.1016/j.devcel.2023.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 09/19/2023] [Accepted: 11/10/2023] [Indexed: 12/21/2023]
Abstract
The emergence of tissue form in multicellular organisms results from the complex interplay between genetics and physics. In both plants and animals, cells must act in concert to pattern their behaviors. Our understanding of the factors sculpting multicellular form has increased dramatically in the past few decades. From this work, common themes have emerged that connect plant and animal morphogenesis-an exciting connection that solidifies our understanding of the developmental basis of multicellular life. In this review, we will discuss the themes and the underlying principles that connect plant and animal morphogenesis, including the coordination of gene expression, signaling, growth, contraction, and mechanical and geometric feedback.
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Affiliation(s)
- Isabella Burda
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA; Genetic Genomics and Development Program, Cornell University, Ithaca, NY 14853, USA
| | - Adam C Martin
- Biology Department, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Adrienne H K Roeder
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA; Genetic Genomics and Development Program, Cornell University, Ithaca, NY 14853, USA; School of Integrative Plant Sciences, Section of Plant Biology, Cornell University, Ithaca, NY 14850, USA.
| | - Mary Ann Collins
- Biology Department, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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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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25
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Worthy AE, Anderson JT, Lane AR, Gomez-Perez L, Wang AA, Griffith RW, Rivard AF, Bikoff JB, Alvarez FJ. SPINAL V1 INHIBITORY INTERNEURON CLADES DIFFER IN BIRTHDATE, PROJECTIONS TO MOTONEURONS AND HETEROGENEITY. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.29.569270. [PMID: 38076820 PMCID: PMC10705425 DOI: 10.1101/2023.11.29.569270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Spinal cord interneurons play a crucial role in shaping motor output, but their precise identity and circuit connectivity remain unclear. Focusing on the cardinal class of inhibitory V1 interneurons, we define the diversity of four major V1 subsets according to timing of neurogenesis, genetic lineage-tracing, synaptic output to motoneurons, and synaptic inputs from muscle afferents. Birthdating delineates two early-born (Renshaw and Pou6f2) and two late-born V1 clades (Foxp2 and Sp8) suggesting sequential neurogenesis gives rise to different V1 clades. Neurogenesis did not correlate with motoneuron targeting. Early-born Renshaw cells and late-born Foxp2-V1 interneurons both tightly coupled to motoneurons, while early-born Pou6f2-V1 and late-born Sp8-V1 interneurons did not. V1-clades also greatly differ in cell numbers and diversity. Lineage labeling of the Foxp2-V1 clade shows it contains over half of all V1 interneurons and provides the largest inhibitory input to motoneuron cell bodies. Foxp2-V1 subgroups differ in neurogenesis and proprioceptive input. Notably, one subgroup defined by Otp expression and located adjacent to the lateral motor column exhibits substantial input from proprioceptors, consistent with some Foxp2-V1 cells at this location forming part of reciprocal inhibitory pathways. This was confirmed with viral tracing methods for ankle flexors and extensors. The results validate the previous V1 clade classification as representing unique interneuron subtypes that differ in circuit placement with Foxp2-V1s forming the more complex subgroup. We discuss how V1 organizational diversity enables understanding of their roles in motor control, with implications for the ontogenetic and phylogenetic origins of their diversity. SIGNIFICANCE STATEMENT Spinal interneuron diversity and circuit organization represents a key challenge to understand the neural control of movement in normal adults and also during motor development and in disease. Inhibitory interneurons are a core element of these spinal circuits, acting on motoneurons either directly or via premotor networks. V1 interneurons comprise the largest group of inhibitory interneurons in the ventral horn and their organization remains unclear. Here we present a comprehensive examination of V1 subtypes according to neurogenesis, placement in spinal motor circuits and motoneuron synaptic targeting. V1 diversity increases during evolution from axial-swimming fishes to limb-based mammalian terrestrial locomotion and this is reflected in the size and heterogeneity of the Foxp2-V1 clade which is closely associated to limb motor pools. We show Foxp2-V1 interneurons establish the densest and more direct inhibitory synaptic input to motoneurons, especially on cell bodies. This is of further importance because deficits on motoneuron cell body inhibitory V1 synapses and on Foxp2-V1 interneurons themselves have recently been shown to be affected at early stages of pathology in motor neurodegenerative diseases like amyotrophic lateral sclerosis.
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Masak G, Davidson LA. Constructing the pharyngula: Connecting the primary axial tissues of the head with the posterior axial tissues of the tail. Cells Dev 2023; 176:203866. [PMID: 37394035 PMCID: PMC10756936 DOI: 10.1016/j.cdev.2023.203866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/04/2023] [Accepted: 06/29/2023] [Indexed: 07/04/2023]
Abstract
The pharyngula stage of vertebrate development is characterized by stereotypical arrangement of ectoderm, mesoderm, and neural tissues from the anterior spinal cord to the posterior, yet unformed tail. While early embryologists over-emphasized the similarity between vertebrate embryos at the pharyngula stage, there is clearly a common architecture upon which subsequent developmental programs generate diverse cranial structures and epithelial appendages such as fins, limbs, gills, and tails. The pharyngula stage is preceded by two morphogenetic events: gastrulation and neurulation, which establish common shared structures despite the occurrence of cellular processes that are distinct to each of the species. Even along the body axis of a singular organism, structures with seemingly uniform phenotypic characteristics at the pharyngula stage have been established by different processes. We focus our review on the processes underlying integration of posterior axial tissue formation with the primary axial tissues that creates the structures laid out in the pharyngula. Single cell sequencing and novel gene targeting technologies have provided us with new insights into the differences between the processes that form the anterior and posterior axis, but it is still unclear how these processes are integrated to create a seamless body. We suggest that the primary and posterior axial tissues in vertebrates form through distinct mechanisms and that the transition between these mechanisms occur at different locations along the anterior-posterior axis. Filling gaps that remain in our understanding of this transition could resolve ongoing problems in organoid culture and regeneration.
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Affiliation(s)
- Geneva Masak
- Integrative Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Lance A Davidson
- Integrative Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA; Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA 15260, USA; Department of Developmental Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA; Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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27
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England SJ, Rusnock AK, Mujcic A, Kowalchuk A, de Jager S, Hilinski WC, Juárez-Morales JL, Smith ME, Grieb G, Banerjee S, Lewis KE. Molecular analyses of zebrafish V0v spinal interneurons and identification of transcriptional regulators downstream of Evx1 and Evx2 in these cells. Neural Dev 2023; 18:8. [PMID: 38017520 PMCID: PMC10683209 DOI: 10.1186/s13064-023-00176-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 10/12/2023] [Indexed: 11/30/2023] Open
Abstract
BACKGROUND V0v spinal interneurons are highly conserved, glutamatergic, commissural neurons that function in locomotor circuits. We have previously shown that Evx1 and Evx2 are required to specify the neurotransmitter phenotype of these cells. However, we still know very little about the gene regulatory networks that act downstream of these transcription factors in V0v cells. METHODS To identify candidate members of V0v gene regulatory networks, we FAC-sorted wild-type and evx1;evx2 double mutant zebrafish V0v spinal interneurons and expression-profiled them using microarrays and single cell RNA-seq. We also used in situ hybridization to compare expression of a subset of candidate genes in evx1;evx2 double mutants and wild-type siblings. RESULTS Our data reveal two molecularly distinct subtypes of zebrafish V0v spinal interneurons at 48 h and suggest that, by this stage of development, evx1;evx2 double mutant cells transfate into either inhibitory spinal interneurons, or motoneurons. Our results also identify 25 transcriptional regulator genes that require Evx1/2 for their expression in V0v interneurons, plus a further 11 transcriptional regulator genes that are repressed in V0v interneurons by Evx1/2. Two of the latter genes are hmx2 and hmx3a. Intriguingly, we show that Hmx2/3a, repress dI2 interneuron expression of skor1a and nefma, two genes that require Evx1/2 for their expression in V0v interneurons. This suggests that Evx1/2 might regulate skor1a and nefma expression in V0v interneurons by repressing Hmx2/3a expression. CONCLUSIONS This study identifies two molecularly distinct subsets of zebrafish V0v spinal interneurons, as well as multiple transcriptional regulators that are strong candidates for acting downstream of Evx1/2 to specify the essential functional characteristics of these cells. Our data further suggest that in the absence of both Evx1 and Evx2, V0v spinal interneurons initially change their neurotransmitter phenotypes from excitatory to inhibitory and then, later, start to express markers of distinct types of inhibitory spinal interneurons, or motoneurons. Taken together, our findings significantly increase our knowledge of V0v and spinal development and move us closer towards the essential goal of identifying the complete gene regulatory networks that specify this crucial cell type.
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Affiliation(s)
| | | | - Amra Mujcic
- Biology Department, Syracuse University, Syracuse, NY, USA
| | | | - Sarah de Jager
- Physiology, Development and Neuroscience Department, Cambridge University, Cambridge, UK
| | | | - José L Juárez-Morales
- Biology Department, Syracuse University, Syracuse, NY, USA
- Programa de IxM-CONAHCYT, Centro de Investigaciones Biológicas del Noroeste, S.C. (CIBNOR), La Paz, Baja California Sur, México
| | | | - Ginny Grieb
- Biology Department, Syracuse University, Syracuse, NY, USA
| | - Santanu Banerjee
- Biological Sciences Department, SUNY-Cortland, Cortland, NY, USA
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28
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Huang X, Ren Q, Wang Y, Shimeld SM, Li G. Amphioxus Gli knockout disrupts the development of left-right asymmetry but has limited impact on neural patterning. MARINE LIFE SCIENCE & TECHNOLOGY 2023; 5:492-499. [PMID: 38045549 PMCID: PMC10689630 DOI: 10.1007/s42995-023-00195-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 09/18/2023] [Indexed: 12/05/2023]
Abstract
The Gli transcription factors are the primary mediators of Hedgehog (Hh) signaling. Vertebrate genomes contain multiple Gli paralogues with different functions downstream of Hh signal receipt, in part explaining the complexity of cellular responses to Hh that allow concentration-dependent target gene activation. Amphioxus is a chordate that split from the vertebrate lineage early in the evolution of chordates, before the genome duplications that occurred in early vertebrate evolution. It has a single Gli gene whose transcripts can be alternately spliced to yield two protein isoforms called GliS and GliL. We generated two knockout mutations in amphioxus Gli, one that affects the whole gene and a second that only affects GliL. Both knockouts showed major morphological and molecular defects in the development of left-right asymmetry, a phenotype that is similar but not identical to that previously found in Hh mutants. Hh signaling also patterns the amphioxus neural tube. Here, however, knockout of GliL showed no identifiable phenotype, while knockout of the full gene showed only small changes to the expression of one gene family, Olig. Other genes that were prominently affected by Hh knockout were not altered in expression in either knockout. Reasons for the differences between Hh and Gli knockouts in the pharynx and neural tube are discussed in the context of the likely different functions of amphioxus Gli isoforms. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-023-00195-w.
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Affiliation(s)
- Xin Huang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361005 China
| | - Qiongqiong Ren
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361005 China
| | - Yiquan Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361005 China
| | | | - Guang Li
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361005 China
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Wani AR, Chowdhury B, Luong J, Chaya GM, Patel K, Isaacman-Beck J, Shafer O, Kayser MS, Syed MH. Stem cell-specific ecdysone signaling regulates the development and function of a Drosophila sleep homeostat. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.29.560022. [PMID: 37873323 PMCID: PMC10592846 DOI: 10.1101/2023.09.29.560022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Complex behaviors arise from neural circuits that are assembled from diverse cell types. Sleep is a conserved and essential behavior, yet little is known regarding how the nervous system generates neuron types of the sleep-wake circuit. Here, we focus on the specification of Drosophila sleep-promoting neurons-long-field tangential input neurons that project to the dorsal layers of the fan-shaped body neuropil in the central complex (CX). We use lineage analysis and genetic birth dating to identify two bilateral Type II neural stem cells that generate these dorsal fan-shaped body (dFB) neurons. We show that adult dFB neurons express Ecdysone-induced protein E93, and loss of Ecdysone signaling or E93 in Type II NSCs results in the misspecification of the adult dFB neurons. Finally, we show that E93 knockdown in Type II NSCs affects adult sleep behavior. Our results provide insight into how extrinsic hormonal signaling acts on NSCs to generate neuronal diversity required for adult sleep behavior. These findings suggest that some adult sleep disorders might derive from defects in stem cell-specific temporal neurodevelopmental programs.
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Affiliation(s)
- Adil R Wani
- Neural Diversity Lab, Department of Biology, University of New Mexico, 219 Yale Blvd Ne, 87131 Albuquerque, NM, USA
| | - Budhaditya Chowdhury
- The Advanced Science Research Center, City University of New York, New York, NY 10031, USA
| | - Jenny Luong
- Department of Psychiatry, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gonzalo Morales Chaya
- Neural Diversity Lab, Department of Biology, University of New Mexico, 219 Yale Blvd Ne, 87131 Albuquerque, NM, USA
| | - Krishna Patel
- Neural Diversity Lab, Department of Biology, University of New Mexico, 219 Yale Blvd Ne, 87131 Albuquerque, NM, USA
| | | | - Orie Shafer
- The Advanced Science Research Center, City University of New York, New York, NY 10031, USA
| | - Matthew S. Kayser
- Department of Psychiatry, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Chronobiology Sleep Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mubarak Hussain Syed
- Neural Diversity Lab, Department of Biology, University of New Mexico, 219 Yale Blvd Ne, 87131 Albuquerque, NM, USA
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30
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Roome RB, Levine AJ. The organization of spinal neurons: Insights from single cell sequencing. Curr Opin Neurobiol 2023; 82:102762. [PMID: 37657185 PMCID: PMC10727478 DOI: 10.1016/j.conb.2023.102762] [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: 04/05/2023] [Revised: 06/16/2023] [Accepted: 07/22/2023] [Indexed: 09/03/2023]
Abstract
To understand how the spinal cord enacts complex sensorimotor functions, researchers have studied, classified, and functionally probed it's many neuronal populations for over a century. Recent developments in single-cell RNA-sequencing can characterize the gene expression signatures of the entire set of spinal neuron types and can simultaneously provide an unbiased view of their relationships to each other. This approach has revealed that the location of neurons predicts transcriptomic variability, as dorsal spinal neurons become highly distinct over development as ventral spinal neurons become less so. Temporal specification is also a major source of gene expression variation, subdividing many of the canonical embryonic lineage domains. Together, birthdate and cell body location are fundamental organizing features of spinal neuron diversity.
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Affiliation(s)
- R Brian Roome
- Spinal Circuits and Plasticity Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health; Bethesda, MD, USA. https://twitter.com/BrianRoome
| | - Ariel J Levine
- Spinal Circuits and Plasticity Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health; Bethesda, MD, USA.
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31
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Casas Gimeno G, Dvorianinova E, Lembke CS, Dijkstra ESC, Abbas H, Liu Y, Paridaen JTML. A quantitative characterization of early neuron generation in the developing zebrafish telencephalon. Dev Neurobiol 2023; 83:237-254. [PMID: 37679904 DOI: 10.1002/dneu.22926] [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: 05/05/2023] [Revised: 07/28/2023] [Accepted: 08/24/2023] [Indexed: 09/09/2023]
Abstract
The adult brain is made up of anatomically and functionally distinct regions with specific neuronal compositions. At the root of this neuronal diversity are neural stem and progenitor cells (NPCs) that produce many neurons throughout embryonic development. During development, NPCs switch from initial expanding divisions to neurogenic divisions, which marks the onset of neurogenesis. Here, we aimed to understand when NPCs switch division modes to generate the first neurons in the anterior-most part of the zebrafish brain, the telencephalon. To this end, we used the deep learning-based segmentation method Cellpose and clonal analysis of individual NPCs to assess the production of neurons by NPCs in the first 24 h of zebrafish telencephalon development. Our results provide a quantitative atlas detailing the production of telencephalic neurons and NPC division modes between 14 and 24 h postfertilization. We find that within this timeframe, the switch to neurogenesis is gradual, with considerable heterogeneity in individual NPC neurogenic potential and division rates. This quantitative characterization of initial neurogenesis in the zebrafish telencephalon establishes a basis for future studies aimed at illuminating the molecular mechanisms and regulators of early neurogenesis.
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Affiliation(s)
- Glòria Casas Gimeno
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen (UMCG), University of Groningen, Groningen, The Netherlands
| | - Ekaterina Dvorianinova
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen (UMCG), University of Groningen, Groningen, The Netherlands
| | - Carla-Sophie Lembke
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen (UMCG), University of Groningen, Groningen, The Netherlands
| | - Emma S C Dijkstra
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen (UMCG), University of Groningen, Groningen, The Netherlands
| | - Hussam Abbas
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen (UMCG), University of Groningen, Groningen, The Netherlands
| | - Yuanyuan Liu
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen (UMCG), University of Groningen, Groningen, The Netherlands
| | - Judith T M L Paridaen
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen (UMCG), University of Groningen, Groningen, The Netherlands
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32
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Nishida K, Matsumura S, Uchida H, Abe M, Sakimura K, Badea TC, Kobayashi T. Brn3a controls the soma localization and axonal extension patterns of developing spinal dorsal horn neurons. PLoS One 2023; 18:e0285295. [PMID: 37733805 PMCID: PMC10513334 DOI: 10.1371/journal.pone.0285295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 09/10/2023] [Indexed: 09/23/2023] Open
Abstract
The spinal dorsal horn comprises heterogeneous neuronal populations, that interconnect with one another to form neural circuits modulating various types of sensory information. Decades of evidence has revealed that transcription factors expressed in each neuronal progenitor subclass play pivotal roles in the cell fate specification of spinal dorsal horn neurons. However, the development of subtypes of these neurons is not fully understood in more detail as yet and warrants the investigation of additional transcription factors. In the present study, we examined the involvement of the POU domain-containing transcription factor Brn3a in the development of spinal dorsal horn neurons. Analyses of Brn3a expression in the developing spinal dorsal horn neurons in mice demonstrated that the majority of the Brn3a-lineage neurons ceased Brn3a expression during embryonic stages (Brn3a-transient neurons), whereas a limited population of them continued to express Brn3a at high levels after E18.5 (Brn3a-persistent neurons). Loss of Brn3a disrupted the localization pattern of Brn3a-persistent neurons, indicating a critical role of this transcription factor in the development of these neurons. In contrast, Brn3a overexpression in Brn3a-transient neurons directed their localization in a manner similar to that in Brn3a-persistent neurons. Moreover, Brn3a-overexpressing neurons exhibited increased axonal extension to the ventral and ventrolateral funiculi, where the axonal tracts of Brn3a-persistent neurons reside. These results suggest that Brn3a controls the soma localization and axonal extension patterns of Brn3a-persistent spinal dorsal horn neurons.
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Affiliation(s)
- Kazuhiko Nishida
- Department of Medical Chemistry, Kansai Medical University, Hirakata, Osaka, Japan
| | - Shinji Matsumura
- Department of Medical Chemistry, Kansai Medical University, Hirakata, Osaka, Japan
| | - Hitoshi Uchida
- Department of Cellular Neurobiology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Manabu Abe
- Department of Cellular Neurobiology, Brain Research Institute, Niigata University, Niigata, Japan
- Department of Animal Model Development, Brain Research Institute, Niigata University, Niigata, Japan
| | - Kenji Sakimura
- Department of Cellular Neurobiology, Brain Research Institute, Niigata University, Niigata, Japan
- Department of Animal Model Development, Brain Research Institute, Niigata University, Niigata, Japan
| | - Tudor Constantin Badea
- Research and Development Institute, Faculty of Medicine, Transylvania University of Brasov, Brasov, Romania
- National Brain Research Center, ICIA, Romanian Academy, Bucharest, Romania
| | - Takuya Kobayashi
- Department of Medical Chemistry, Kansai Medical University, Hirakata, Osaka, Japan
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Huntemer-Silveira A, Malone D, Frie A, Walsh P, Parr AM. Accelerated differentiation of human induced pluripotent stem cells into regionally specific dorsal and ventral spinal neural progenitor cells for application in spinal cord therapeutics. Front Neurosci 2023; 17:1251906. [PMID: 37781243 PMCID: PMC10540309 DOI: 10.3389/fnins.2023.1251906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 08/31/2023] [Indexed: 10/03/2023] Open
Abstract
Spinal cord injury can attenuate both motor and sensory function with minimal potential for full recovery. Research utilizing human induced pluripotent stem cell (hiPSC) -derived spinal cell types for in vivo remodeling and neuromodulation after spinal cord injury has grown substantially in recent years. However, the majority of protocols for the differentiation of spinal neurons are lengthy, lack the appropriate dorsoventral or rostrocaudal specification, and are not typically replicated in more than one cell line. Furthermore, most researchers currently utilize hiPSC-derived motor neurons for cell transplantation after injury, with very little exploration of spinal sensory neuron transplantation. The lack of studies that utilize sensory populations may be due in part to the relative scarcity of dorsal horn differentiation protocols. Building upon our previously published work that demonstrated the rapid establishment of a primitive ectoderm population from hiPSCs, we describe here the production of a diverse population of both ventral spinal and dorsal horn progenitor cells. Our work creates a novel system allowing dorsal and ventral spinal neurons to be differentiated from the same intermediate ectoderm population, making it possible to construct the dorsal and ventral domains of the spinal cord while decreasing variability. This technology can be used in tandem with biomaterials and pharmacology to improve cell transplantation for spinal cord injury, increasing the potential for neuroregeneration.
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Affiliation(s)
| | - Dane Malone
- Department of Neurosurgery, University of Minnesota, Minneapolis, MN, United States
| | - Anna Frie
- Department of Neuroscience, University of Minnesota, Minneapolis, MN, United States
| | - Patrick Walsh
- Anatomic Incorporated, Minneapolis, MN, United States
| | - Ann M. Parr
- Department of Neurosurgery, University of Minnesota, Minneapolis, MN, United States
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, United States
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Gribaudo S, Robert R, van Sambeek B, Mirdass C, Lyubimova A, Bouhali K, Ferent J, Morin X, van Oudenaarden A, Nedelec S. Self-organizing models of human trunk organogenesis recapitulate spinal cord and spine co-morphogenesis. Nat Biotechnol 2023:10.1038/s41587-023-01956-9. [PMID: 37709912 DOI: 10.1038/s41587-023-01956-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 08/18/2023] [Indexed: 09/16/2023]
Abstract
Integrated in vitro models of human organogenesis are needed to elucidate the multi-systemic events underlying development and disease. Here we report the generation of human trunk-like structures that model the co-morphogenesis, patterning and differentiation of the human spine and spinal cord. We identified differentiation conditions for human pluripotent stem cells favoring the formation of an embryo-like extending antero-posterior (AP) axis. Single-cell and spatial transcriptomics show that somitic and spinal cord differentiation trajectories organize along this axis and can self-assemble into a neural tube surrounded by somites upon extracellular matrix addition. Morphogenesis is coupled with AP patterning mechanisms, which results, at later stages of organogenesis, in in vivo-like arrays of neural subtypes along a neural tube surrounded by spine and muscle progenitors contacted by neuronal projections. This integrated system of trunk development indicates that in vivo-like multi-tissue co-morphogenesis and topographic organization of terminal cell types can be achieved in human organoids, opening windows for the development of more complex models of organogenesis.
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Affiliation(s)
- Simona Gribaudo
- Institut du Fer à Moulin, Paris, France
- Inserm, UMR-S 1270, Paris, France
- Sorbonne Université, Science and Engineering Faculty, Paris, France
| | - Rémi Robert
- Institut du Fer à Moulin, Paris, France
- Inserm, UMR-S 1270, Paris, France
- Sorbonne Université, Science and Engineering Faculty, Paris, France
| | - Björn van Sambeek
- Oncode Institute, Utrecht, The Netherlands
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Camil Mirdass
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, France
| | - Anna Lyubimova
- Oncode Institute, Utrecht, The Netherlands
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Kamal Bouhali
- Institut de Biologie de l'ENS (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Julien Ferent
- Institut du Fer à Moulin, Paris, France
- Inserm, UMR-S 1270, Paris, France
- Sorbonne Université, Science and Engineering Faculty, Paris, France
| | - Xavier Morin
- Institut de Biologie de l'ENS (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Alexander van Oudenaarden
- Oncode Institute, Utrecht, The Netherlands
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Stéphane Nedelec
- Institut du Fer à Moulin, Paris, France.
- Inserm, UMR-S 1270, Paris, France.
- Sorbonne Université, Science and Engineering Faculty, Paris, France.
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Yang M, Liu M, Sánchez YF, Avazzadeh S, Quinlan LR, Liu G, Lu Y, Yang G, O'Brien T, Henshall DC, Hardiman O, Shen S. A novel protocol to derive cervical motor neurons from induced pluripotent stem cells for amyotrophic lateral sclerosis. Stem Cell Reports 2023; 18:1870-1883. [PMID: 37595581 PMCID: PMC10545486 DOI: 10.1016/j.stemcr.2023.07.004] [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: 03/12/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 08/20/2023] Open
Abstract
Sporadic amyotrophic lateral sclerosis (sALS) is the majority of ALS, and the lack of appropriate disease models has hindered its research. Induced pluripotent stem cell (iPSC) technology now permits derivation of iPSCs from somatic cells of sALS patients to investigate disease phenotypes and mechanisms. Most existing differentiation protocols are time-consuming or low efficient in generating motor neurons (MNs). Here we report a rapid and simple protocol to differentiate MNs in monolayer culture using small molecules, which led to nearly pure neural stem cells in 6 days, robust OLIG2+ pMNs (73%-91%) in 12 days, enriched CHAT+ cervical spinal MNs (sMNs) (88%-97%) in 18 days, and functionally mature sMNs in 28 days. This simple and reproducible protocol permitted the identification of hyperexcitability phenotypes in our sALS iPSC-derived sMNs, and its application in neurodegenerative diseases should facilitate in vitro disease modeling, drug screening, and the development of cell therapy.
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Affiliation(s)
- Meimei Yang
- Regenerative Medicine Institute, School of Medicine, University of Galway, H91 W2TY Galway, Ireland; FutureNeuro SFI Research Centre for Chronic and Rare Neurological Diseases and Department of Physiology & Medical Physics, RCSI University of Medicine and Health Sciences, D02 YN77 Dublin, Ireland
| | - Min Liu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Yajaira Feller Sánchez
- Cellular Physiology Research Laboratory and CÚRAM SFI Centre for Research in Medical Devices, School of Medicine, University of Galway, H91 TK33 Galway, Ireland
| | - Sahar Avazzadeh
- Cellular Physiology Research Laboratory and CÚRAM SFI Centre for Research in Medical Devices, School of Medicine, University of Galway, H91 TK33 Galway, Ireland
| | - Leo R Quinlan
- Cellular Physiology Research Laboratory and CÚRAM SFI Centre for Research in Medical Devices, School of Medicine, University of Galway, H91 TK33 Galway, Ireland
| | - Gang Liu
- Department of Cardiology, The First Hospital of Hebei Medical University, Hebei Key Laboratory of Cardiac Injury Repair Mechanism Study, Hebei Key Laboratory of Heart and Metabolism, Hebei Engineering Research Center of Intelligent Medical Clinical Application, Hebei International Joint Research Center for Structural Heart Disease, Shijiazhuang, Hebei, China
| | - Yin Lu
- College of Pharmacy, Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine (TCM) Prevention and Treatment of Tumor, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China
| | - Guangming Yang
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China
| | - Timothy O'Brien
- Regenerative Medicine Institute, School of Medicine, University of Galway, H91 W2TY Galway, Ireland
| | - David C Henshall
- FutureNeuro SFI Research Centre for Chronic and Rare Neurological Diseases and Department of Physiology & Medical Physics, RCSI University of Medicine and Health Sciences, D02 YN77 Dublin, Ireland; Department of Physiology and Medical Physics, RCSI University of Medicine & Health Sciences, D02 YN77 Dublin, Ireland.
| | - Orla Hardiman
- FutureNeuro SFI Research Centre for Chronic and Rare Neurological Diseases and Department of Physiology & Medical Physics, RCSI University of Medicine and Health Sciences, D02 YN77 Dublin, Ireland; Academic Unit of Neurology, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland.
| | - Sanbing Shen
- Regenerative Medicine Institute, School of Medicine, University of Galway, H91 W2TY Galway, Ireland; FutureNeuro SFI Research Centre for Chronic and Rare Neurological Diseases and Department of Physiology & Medical Physics, RCSI University of Medicine and Health Sciences, D02 YN77 Dublin, Ireland.
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36
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England SJ, Woodard AK, Mujcic A, Kowalchuk A, de Jager S, Hilinski WC, Juárez-Morales JL, Smith ME, Grieb G, Banerjee S, Lewis KE. Molecular Analyses of V0v Spinal Interneurons and Identification of Transcriptional Regulators Downstream of Evx1 and Evx2 in these Cells. RESEARCH SQUARE 2023:rs.3.rs-3290462. [PMID: 37693471 PMCID: PMC10491344 DOI: 10.21203/rs.3.rs-3290462/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Background V0v spinal interneurons are highly conserved, glutamatergic, commissural neurons that function in locomotor circuits. We have previously shown that Evx1 and Evx2 are required to specify the neurotransmitter phenotype of these cells. However, we still know very little about the gene regulatory networks that act downstream of these transcription factors in V0v cells. Methods To identify candidate members of V0v gene regulatory networks, we FAC-sorted WT and evx1;evx2 double mutant zebrafish V0v spinal interneurons and expression-profiled them using microarrays and single cell RNA-seq. We also used in situ hybridization to compare expression of a subset of candidate genes in evx1;evx2 double mutants and wild-type siblings. Results Our data reveal two molecularly distinct subtypes of V0v spinal interneurons at 48 h and suggest that, by this stage of development, evx1;evx2 double mutant cells transfate into either inhibitory spinal interneurons, or motoneurons. Our results also identify 25 transcriptional regulator genes that require Evx1/2 for their expression in V0v interneurons, plus a further 11 transcriptional regulator genes that are repressed in V0v interneurons by Evx1/2. Two of the latter genes are hmx2 and hmx3a. Intriguingly, we show that Hmx2/3a, repress dI2 interneuronal expression of skor1a and nefma, two genes that require Evx1/2 for their expression in V0v interneurons. This suggests that Evx1/2 might regulate skor1a and nefma expression in V0v interneurons by repressing Hmx2/3a expression. Conclusions This study identifies two molecularly distinct subsets of V0v spinal interneurons, as well as multiple transcriptional regulators that are strong candidates for acting downstream of Evx1/2 to specify the essential functional characteristics of these cells. Our data further suggest that in the absence of both Evx1 and Evx2, V0v spinal interneurons initially change their neurotransmitter phenotypes from excitatory to inhibitory and then, later, start to express markers of distinct types of inhibitory spinal interneurons, or motoneurons. Taken together, our findings significantly increase our knowledge of V0v and spinal development and move us closer towards the essential goal of identifying the complete gene regulatory networks that specify this crucial cell type.
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Chen F, Köhler M, Cucun G, Takamiya M, Kizil C, Cosacak MI, Rastegar S. sox1a:eGFP transgenic line and single-cell transcriptomics reveal the origin of zebrafish intraspinal serotonergic neurons. iScience 2023; 26:107342. [PMID: 37529101 PMCID: PMC10387610 DOI: 10.1016/j.isci.2023.107342] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 06/03/2023] [Accepted: 07/06/2023] [Indexed: 08/03/2023] Open
Abstract
Sox transcription factors are crucial for vertebrate nervous system development. In zebrafish embryo, sox1 genes are expressed in neural progenitor cells and neurons of ventral spinal cord. Our recent study revealed that the loss of sox1a and sox1b function results in a significant decline of V2 subtype neurons (V2s). Using single-cell RNA sequencing, we analyzed the transcriptome of sox1a lineage progenitors and neurons in the zebrafish spinal cord at four time points during embryonic development, employing the Tg(sox1a:eGFP) line. In addition to previously characterized sox1a-expressing neurons, we discovered the expression of sox1a in late-developing intraspinal serotonergic neurons (ISNs). Developmental trajectory analysis suggests that ISNs arise from lateral floor plate (LFP) progenitor cells. Pharmacological inhibition of the Notch signaling pathway revealed its role in negatively regulating LFP progenitor cell differentiation into ISNs. Our findings highlight the zebrafish LFP as a progenitor domain for ISNs, alongside known Kolmer-Agduhr (KA) and V3 interneurons.
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Affiliation(s)
- Fushun Chen
- Institute of Biological and Chemical Systems-Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology (KIT), Campus North, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Melina Köhler
- Institute of Biological and Chemical Systems-Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology (KIT), Campus North, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Gokhan Cucun
- Institute of Biological and Chemical Systems-Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology (KIT), Campus North, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Masanari Takamiya
- Institute of Biological and Chemical Systems-Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology (KIT), Campus North, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Caghan Kizil
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Helmholtz Association, Tatzberg 41, 01307 Dresden, Germany
- Department of Neurology and the Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, 630 W 168th Street, New York, NY 10032, USA
| | - Mehmet Ilyas Cosacak
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Helmholtz Association, Tatzberg 41, 01307 Dresden, Germany
| | - Sepand Rastegar
- Institute of Biological and Chemical Systems-Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology (KIT), Campus North, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
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38
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O'Sullivan JDB, Blacker TS, Scott C, Chang W, Ahmed M, Yianni V, Mann ZF. Gradients of glucose metabolism regulate morphogen signalling required for specifying tonotopic organisation in the chicken cochlea. eLife 2023; 12:e86233. [PMID: 37539863 PMCID: PMC10425173 DOI: 10.7554/elife.86233] [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: 01/17/2023] [Accepted: 08/03/2023] [Indexed: 08/05/2023] Open
Abstract
In vertebrates with elongated auditory organs, mechanosensory hair cells (HCs) are organised such that complex sounds are broken down into their component frequencies along a proximal-to-distal long (tonotopic) axis. Acquisition of unique morphologies at the appropriate position along the chick cochlea, the basilar papilla, requires that nascent HCs determine their tonotopic positions during development. The complex signalling within the auditory organ between a developing HC and its local niche along the cochlea is poorly understood. Using a combination of live imaging and NAD(P)H fluorescence lifetime imaging microscopy, we reveal that there is a gradient in the cellular balance between glycolysis and the pentose phosphate pathway in developing HCs along the tonotopic axis. Perturbing this balance by inhibiting different branches of cytosolic glucose catabolism disrupts developmental morphogen signalling and abolishes the normal tonotopic gradient in HC morphology. These findings highlight a causal link between graded morphogen signalling and metabolic reprogramming in specifying the tonotopic identity of developing HCs.
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Affiliation(s)
- James DB O'Sullivan
- Centre for Craniofacial and Regenerative Biology, Faculty of Dentistry Oral and Craniofacial Sciences, King's College LondonLondonUnited Kingdom
| | - Thomas S Blacker
- Research Department of Structural and Molecular Biology, University College LondonLondonUnited Kingdom
| | - Claire Scott
- Centre for Craniofacial and Regenerative Biology, Faculty of Dentistry Oral and Craniofacial Sciences, King's College LondonLondonUnited Kingdom
| | - Weise Chang
- National Institute on Deafness and Other Communication Disorders, National Institutes of HealthBethesdaUnited States
| | - Mohi Ahmed
- Centre for Craniofacial and Regenerative Biology, Faculty of Dentistry Oral and Craniofacial Sciences, King's College LondonLondonUnited Kingdom
| | - Val Yianni
- Centre for Craniofacial and Regenerative Biology, Faculty of Dentistry Oral and Craniofacial Sciences, King's College LondonLondonUnited Kingdom
| | - Zoe F Mann
- Centre for Craniofacial and Regenerative Biology, Faculty of Dentistry Oral and Craniofacial Sciences, King's College LondonLondonUnited Kingdom
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39
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Deng Q, Wang S, Huang Z, Lan Q, Lai G, Xu J, Yuan Y, Liu C, Lin X, Feng W, Ma W, Cheng M, Hao S, Duan S, Zheng H, Chen X, Hou Y, Luo Y, Liu L, Liu C. Single-cell chromatin accessibility profiling of cell-state-specific gene regulatory programs during mouse organogenesis. Front Neurosci 2023; 17:1170355. [PMID: 37440917 PMCID: PMC10333525 DOI: 10.3389/fnins.2023.1170355] [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: 03/02/2023] [Accepted: 06/07/2023] [Indexed: 07/15/2023] Open
Abstract
In mammals, early organogenesis begins soon after gastrulation, accompanied by specification of various type of progenitor/precusor cells. In order to reveal dynamic chromatin landscape of precursor cells and decipher the underlying molecular mechanism driving early mouse organogenesis, we performed single-cell ATAC-seq of E8.5-E10.5 mouse embryos. We profiled a total of 101,599 single cells and identified 41 specific cell types at these stages. Besides, by performing integrated analysis of scATAC-seq and public scRNA-seq data, we identified the critical cis-regulatory elements and key transcription factors which drving development of spinal cord and somitogenesis. Furthermore, we intersected accessible peaks with human diseases/traits-related loci and found potential clinical associated single nucleotide variants (SNPs). Overall, our work provides a fundamental source for understanding cell fate determination and revealing the underlying mechanism during postimplantation embryonic development, and expand our knowledge of pathology for human developmental malformations.
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Affiliation(s)
- Qiuting Deng
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Hangzhou, Hangzhou, China
| | - Shengpeng Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Hangzhou, Hangzhou, China
| | - Zijie Huang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | | | | | | | | | | | - Xiumei Lin
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Hangzhou, Hangzhou, China
| | - Weimin Feng
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Hangzhou, Hangzhou, China
| | - Wen Ma
- BGI-Shenzhen, Shenzhen, China
| | | | - Shijie Hao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Hangzhou, Hangzhou, China
| | - Shanshan Duan
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Hangzhou, Hangzhou, China
| | | | | | - Yong Hou
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | | | - Longqi Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Hangzhou, Hangzhou, China
- BGI-Shenzhen, Shenzhen, China
- Shenzhen Bay Laboratory, Shenzhen, China
| | - Chuanyu Liu
- BGI-Shenzhen, Shenzhen, China
- Shenzhen Bay Laboratory, Shenzhen, China
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40
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Santos-França PL, David LA, Kassem F, Meng XQ, Cayouette M. Time to see: How temporal identity factors specify the developing mammalian retina. Semin Cell Dev Biol 2023; 142:36-42. [PMID: 35760728 DOI: 10.1016/j.semcdb.2022.06.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 06/08/2022] [Accepted: 06/09/2022] [Indexed: 11/30/2022]
Abstract
Understanding how retinal progenitor cells (RPCs) give rise to the variety of neural cell types of the retina has been a question of major interest over the last few decades. While environmental cues and transcription factor networks have been shown to control specific cell fate decisions, how RPCs alter fate output over time to control proper histogenesis remains poorly understood. In recent years, the identification of "temporal identity factors (TIFs)", which control RPC competence states to ensure that the right cell types are produced at the right time, has contributed to increasing our understanding of temporal patterning in the retina. Here, we review the different TIFs identified to date in the mammalian retina and discuss the underlying mechanisms by which they are thought to operate. We conclude by speculating on how identification of temporal patterning mechanisms might support the development of new therapeutic approaches against visual impairments.
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Affiliation(s)
- Pedro L Santos-França
- Cellular Neurobiology Research Unit, Institut de recherches cliniques de Montréal (IRCM), Montréal, QC, Canada; Molecular Biology Program, Université de Montréal, Montréal, QC, Canada
| | - Luke Ajay David
- Cellular Neurobiology Research Unit, Institut de recherches cliniques de Montréal (IRCM), Montréal, QC, Canada; Integrated Program in Neuroscience, Faculty of Medicine, McGill University, Montréal, QC, Canada
| | - Fatima Kassem
- Cellular Neurobiology Research Unit, Institut de recherches cliniques de Montréal (IRCM), Montréal, QC, Canada; Integrated Program in Neuroscience, Faculty of Medicine, McGill University, Montréal, QC, Canada
| | - Xiang Qi Meng
- Integrated Program in Neuroscience, Faculty of Medicine, McGill University, Montréal, QC, Canada
| | - Michel Cayouette
- Cellular Neurobiology Research Unit, Institut de recherches cliniques de Montréal (IRCM), Montréal, QC, Canada; Molecular Biology Program, Université de Montréal, Montréal, QC, Canada; Integrated Program in Neuroscience, Faculty of Medicine, McGill University, Montréal, QC, Canada; Department of Medicine, Université de Montréal, QC, Canada; Department of Anatomy and Cell Biology and Division of Experimental Medicine, McGill University, Montreal, QC, Canada.
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41
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Sen SQ. Generating neural diversity through spatial and temporal patterning. Semin Cell Dev Biol 2023; 142:54-66. [PMID: 35738966 DOI: 10.1016/j.semcdb.2022.06.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 06/08/2022] [Accepted: 06/08/2022] [Indexed: 11/19/2022]
Abstract
The nervous system consists of a vast diversity of neurons and glia that are accurately assembled into functional circuits. What are the mechanisms that generate these diverse cell types? During development, an epithelial sheet with neurogenic potential is initially regionalised into spatially restricted domains of gene expression. From this, pools of neural stem cells (NSCs) with distinct molecular profiles and the potential to generate different neuron types, are specified. These NSCs then divide asymmetrically to self-renew and generate post-mitotic neurons or glia. As NSCs age, they experience transitions in gene expression, which further allows them to generate different neurons or glia over time. Versions of this general template of spatial and temporal patterning operate during the development of different parts of different nervous systems. Here, I cover our current knowledge of Drosophila brain and optic lobe development as well as the development of the vertebrate cortex and spinal cord within the framework of this above template. I highlight where our knowledge is lacking, where mechanisms beyond these might operate, and how the emergence of new technologies might help address unanswered questions.
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Affiliation(s)
- Sonia Q Sen
- Tata Institute for Genetics and Society, UAS-GKVK Campus, Bellary Road, Bangalore, India.
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42
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Buchner F, Dokuzluoglu Z, Grass T, Rodriguez-Muela N. Spinal Cord Organoids to Study Motor Neuron Development and Disease. Life (Basel) 2023; 13:1254. [PMID: 37374039 DOI: 10.3390/life13061254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 05/18/2023] [Indexed: 06/29/2023] Open
Abstract
Motor neuron diseases (MNDs) are a heterogeneous group of disorders that affect the cranial and/or spinal motor neurons (spMNs), spinal sensory neurons and the muscular system. Although they have been investigated for decades, we still lack a comprehensive understanding of the underlying molecular mechanisms; and therefore, efficacious therapies are scarce. Model organisms and relatively simple two-dimensional cell culture systems have been instrumental in our current knowledge of neuromuscular disease pathology; however, in the recent years, human 3D in vitro models have transformed the disease-modeling landscape. While cerebral organoids have been pursued the most, interest in spinal cord organoids (SCOs) is now also increasing. Pluripotent stem cell (PSC)-based protocols to generate SpC-like structures, sometimes including the adjacent mesoderm and derived skeletal muscle, are constantly being refined and applied to study early human neuromuscular development and disease. In this review, we outline the evolution of human PSC-derived models for generating spMN and recapitulating SpC development. We also discuss how these models have been applied to exploring the basis of human neurodevelopmental and neurodegenerative diseases. Finally, we provide an overview of the main challenges to overcome in order to generate more physiologically relevant human SpC models and propose some exciting new perspectives.
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Affiliation(s)
- Felix Buchner
- German Center for Neurodegenerative Diseases, 01307 Dresden, Germany
| | | | - Tobias Grass
- German Center for Neurodegenerative Diseases, 01307 Dresden, Germany
| | - Natalia Rodriguez-Muela
- German Center for Neurodegenerative Diseases, 01307 Dresden, Germany
- Center for Regenerative Therapies Dresden, Technische Universität Dresden, 01307 Dresden, Germany
- Max Planck Institute for Molecular Cell Biology and Genetics, 01307 Dresden, Germany
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43
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Lefebvre-Omar C, Liu E, Dalle C, d'Incamps BL, Bigou S, Daube C, Karpf L, Davenne M, Robil N, Jost Mousseau C, Blanchard S, Tournaire G, Nicaise C, Salachas F, Lacomblez L, Seilhean D, Lobsiger CS, Millecamps S, Boillée S, Bohl D. Neurofilament accumulations in amyotrophic lateral sclerosis patients' motor neurons impair axonal initial segment integrity. Cell Mol Life Sci 2023; 80:150. [PMID: 37184603 DOI: 10.1007/s00018-023-04797-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 04/24/2023] [Accepted: 05/03/2023] [Indexed: 05/16/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is the most common motor neuron (MN) disease in adults with no curative treatment. Neurofilament (NF) level in patient' fluids have recently emerged as the prime biomarker of ALS disease progression, while NF accumulation in MNs of patients is the oldest and one of the best pathological hallmarks. However, the way NF accumulations could lead to MN degeneration remains unknown. To assess NF accumulations and study the impact on MNs, we compared MNs derived from induced pluripotent stem cells (iPSC) of patients carrying mutations in C9orf72, SOD1 and TARDBP genes, the three main ALS genetic causes. We show that in all mutant MNs, light NF (NF-L) chains rapidly accumulate in MN soma, while the phosphorylated heavy/medium NF (pNF-M/H) chains pile up in axonal proximal regions of only C9orf72 and SOD1 MNs. Excitability abnormalities were also only observed in these latter MNs. We demonstrate that the integrity of the MN axonal initial segment (AIS), the region of action potential initiation and responsible for maintaining axonal integrity, is impaired in the presence of pNF-M/H accumulations in C9orf72 and SOD1 MNs. We establish a strong correlation between these pNF-M/H accumulations, an AIS distal shift, increased axonal calibers and modified repartition of sodium channels. The results expand our understanding of how NF accumulation could dysregulate components of the axonal cytoskeleton and disrupt MN homeostasis. With recent cumulative evidence that AIS alterations are implicated in different brain diseases, preserving AIS integrity could have important therapeutic implications for ALS.
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Affiliation(s)
- Cynthia Lefebvre-Omar
- Sorbonne Université, Institut du Cerveau-Paris Brain Institute-ICM, Inserm, CNRS, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Elise Liu
- Sorbonne Université, Institut du Cerveau-Paris Brain Institute-ICM, Inserm, CNRS, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Carine Dalle
- Sorbonne Université, Institut du Cerveau-Paris Brain Institute-ICM, Inserm, CNRS, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Boris Lamotte d'Incamps
- Université Paris-Cité, CNRS, Saints-Pères Paris Institute for the Neurosciences, Paris, France
| | - Stéphanie Bigou
- Sorbonne Université, Institut du Cerveau-Paris Brain Institute-ICM, Inserm, CNRS, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Clément Daube
- Sorbonne Université, Institut du Cerveau-Paris Brain Institute-ICM, Inserm, CNRS, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Léa Karpf
- Sorbonne Université, Institut du Cerveau-Paris Brain Institute-ICM, Inserm, CNRS, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Marc Davenne
- Sorbonne Université, Institut du Cerveau-Paris Brain Institute-ICM, Inserm, CNRS, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, France
| | | | - Coline Jost Mousseau
- Sorbonne Université, Institut du Cerveau-Paris Brain Institute-ICM, Inserm, CNRS, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Stéphane Blanchard
- Institut Pasteur, INSERM U1115, Unité Biothérapies pour les Maladies Neurodégénératives, Paris, France
| | - Guillaume Tournaire
- Institut Pasteur, INSERM U1115, Unité Biothérapies pour les Maladies Neurodégénératives, Paris, France
| | | | - François Salachas
- Sorbonne Université, Institut du Cerveau-Paris Brain Institute-ICM, Inserm, CNRS, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, France
- Département de Neurologie, Assistance Publique Hôpitaux de Paris (APHP), Centre de Référence SLA Ile de France, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Lucette Lacomblez
- Département de Neurologie, Assistance Publique Hôpitaux de Paris (APHP), Centre de Référence SLA Ile de France, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Danielle Seilhean
- Sorbonne Université, Institut du Cerveau-Paris Brain Institute-ICM, Inserm, CNRS, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, France
- Département de Neuropathologie, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Christian S Lobsiger
- Sorbonne Université, Institut du Cerveau-Paris Brain Institute-ICM, Inserm, CNRS, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Stéphanie Millecamps
- Sorbonne Université, Institut du Cerveau-Paris Brain Institute-ICM, Inserm, CNRS, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Séverine Boillée
- Sorbonne Université, Institut du Cerveau-Paris Brain Institute-ICM, Inserm, CNRS, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Delphine Bohl
- Sorbonne Université, Institut du Cerveau-Paris Brain Institute-ICM, Inserm, CNRS, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, France.
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44
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Luxey M, Stieger G, Berki B, Tschopp P. Distinct patterning responses of wing and leg neuromuscular systems to different preaxial polydactylies. Front Cell Dev Biol 2023; 11:1154205. [PMID: 37215090 PMCID: PMC10192688 DOI: 10.3389/fcell.2023.1154205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 04/19/2023] [Indexed: 05/24/2023] Open
Abstract
The tetrapod limb has long served as a paradigm to study vertebrate pattern formation and evolutionary diversification. The distal part of the limb, the so-called autopod, is of particular interest in this regard, given the numerous modifications in both its morphology and behavioral motor output. While the underlying alterations in skeletal form have received considerable attention, much less is known about the accompanying changes in the neuromuscular system. However, modifications in the skeleton need to be properly integrated with both muscle and nerve patterns, to result in a fully functional limb. This task is further complicated by the distinct embryonic origins of the three main tissue types involved-skeleton, muscles and nerves-and, accordingly, how they are patterned and connected with one another during development. To evaluate the degree of regulative crosstalk in this complex limb patterning process, here we analyze the developing limb neuromuscular system of Silkie breed chicken. These animals display a preaxial polydactyly, due to a polymorphism in the limb regulatory region of the Sonic Hedgehog gene. Using lightsheet microscopy and 3D-reconstructions, we investigate the neuromuscular patterns of extra digits in Silkie wings and legs, and compare our results to Retinoic Acid-induced polydactylies. Contrary to previous findings, Silkie autopod muscle patterns do not adjust to alterations in the underlying skeletal topology, while nerves show partial responsiveness. We discuss the implications of tissue-specific sensitivities to global limb patterning cues for our understanding of the evolution of novel forms and functions in the distal tetrapod limb.
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Affiliation(s)
- Maëva Luxey
- *Correspondence: Maëva Luxey, ; Patrick Tschopp,
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45
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Andersen J, Thom N, Shadrach JL, Chen X, Onesto MM, Amin ND, Yoon SJ, Li L, Greenleaf WJ, Müller F, Pașca AM, Kaltschmidt JA, Pașca SP. Single-cell transcriptomic landscape of the developing human spinal cord. Nat Neurosci 2023; 26:902-914. [PMID: 37095394 DOI: 10.1038/s41593-023-01311-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 03/20/2023] [Indexed: 04/26/2023]
Abstract
Understanding spinal cord assembly is essential to elucidate how motor behavior is controlled and how disorders arise. The human spinal cord is exquisitely organized, and this complex organization contributes to the diversity and intricacy of motor behavior and sensory processing. But how this complexity arises at the cellular level in the human spinal cord remains unknown. Here we transcriptomically profiled the midgestation human spinal cord with single-cell resolution and discovered remarkable heterogeneity across and within cell types. Glia displayed diversity related to positional identity along the dorso-ventral and rostro-caudal axes, while astrocytes with specialized transcriptional programs mapped into white and gray matter subtypes. Motor neurons clustered at this stage into groups suggestive of alpha and gamma neurons. We also integrated our data with multiple existing datasets of the developing human spinal cord spanning 22 weeks of gestation to investigate the cell diversity over time. Together with mapping of disease-related genes, this transcriptomic mapping of the developing human spinal cord opens new avenues for interrogating the cellular basis of motor control in humans and guides human stem cell-based models of disease.
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Affiliation(s)
- Jimena Andersen
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Stanford Brain Organogenesis, Wu Tsai Neurosciences Institute, Stanford, CA, USA
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - Nicholas Thom
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Stanford Brain Organogenesis, Wu Tsai Neurosciences Institute, Stanford, CA, USA
| | | | - Xiaoyu Chen
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Stanford Brain Organogenesis, Wu Tsai Neurosciences Institute, Stanford, CA, USA
| | - Massimo Mario Onesto
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Stanford Brain Organogenesis, Wu Tsai Neurosciences Institute, Stanford, CA, USA
- Neurosciences Graduate Program, Stanford University, Stanford, CA, USA
| | - Neal D Amin
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Stanford Brain Organogenesis, Wu Tsai Neurosciences Institute, Stanford, CA, USA
| | - Se-Jin Yoon
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Stanford Brain Organogenesis, Wu Tsai Neurosciences Institute, Stanford, CA, USA
| | - Li Li
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Applied Physics, Stanford University, Stanford, CA, USA
| | - Fabian Müller
- Department of Genetics, Stanford University, Stanford, CA, USA
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Anca M Pașca
- Department of Pediatrics, Division of Neonatology, Stanford University, Stanford, CA, USA
| | | | - Sergiu P Pașca
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA.
- Stanford Brain Organogenesis, Wu Tsai Neurosciences Institute, Stanford, CA, USA.
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46
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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: 3.0] [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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47
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Zhang Y, Lowe S, Ding AZ, Li X. Notch-dependent binary fate choice regulates the Netrin pathway to control axon guidance of Drosophila visual projection neurons. Cell Rep 2023; 42:112143. [PMID: 36821442 PMCID: PMC10124989 DOI: 10.1016/j.celrep.2023.112143] [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: 01/13/2022] [Revised: 10/22/2022] [Accepted: 02/07/2023] [Indexed: 02/24/2023] Open
Abstract
Notch-dependent binary fate choice between sister neurons is one of the mechanisms to generate neural diversity. How these upstream neural fate specification programs regulate downstream effector genes to control axon targeting and neuropil assembly remains less well understood. Here, we report that Notch-dependent binary fate choice in Drosophila medulla neurons is required to regulate the Netrin axon guidance pathway, which controls targeting of transmedullary (Tm) neurons to lobula. In medulla neurons of Notch-on hemilineage composed of mostly lobula-targeting neurons, Notch signaling is required to activate the expression of Netrin-B and repress the expression of its repulsive receptor Unc-5. Turning off Unc-5 is necessary for Tm neurons to target lobula. Furthermore, Netrin-B provided by Notch-on medulla neurons is required for correct targeting of Tm axons from later-generated medulla columns. Thus, the coordinate regulation of Netrin pathway components by Notch signaling ensures correct targeting of Tm axons and contributes to the neuropil assembly.
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Affiliation(s)
- Yu Zhang
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Scott Lowe
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Andrew Z Ding
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Xin Li
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA.
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48
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Arcuschin CD, Pinkasz M, Schor IE. Mechanisms of robustness in gene regulatory networks involved in neural development. Front Mol Neurosci 2023; 16:1114015. [PMID: 36814969 PMCID: PMC9940843 DOI: 10.3389/fnmol.2023.1114015] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 01/16/2023] [Indexed: 02/08/2023] Open
Abstract
The functions of living organisms are affected by different kinds of perturbation, both internal and external, which in many cases have functional effects and phenotypic impact. The effects of these perturbations become particularly relevant for multicellular organisms with complex body patterns and cell type heterogeneity, where transcriptional programs controlled by gene regulatory networks determine, for example, the cell fate during embryonic development. Therefore, an essential aspect of development in these organisms is the ability to maintain the functionality of their genetic developmental programs even in the presence of genetic variation, changing environmental conditions and biochemical noise, a property commonly termed robustness. We discuss the implication of different molecular mechanisms of robustness involved in neurodevelopment, which is characterized by the interplay of many developmental programs at a molecular, cellular and systemic level. We specifically focus on processes affecting the function of gene regulatory networks, encompassing transcriptional regulatory elements and post-transcriptional processes such as miRNA-based regulation, but also higher order regulatory organization, such as gene network topology. We also present cases where impairment of robustness mechanisms can be associated with neurodevelopmental disorders, as well as reasons why understanding these mechanisms should represent an important part of the study of gene regulatory networks driving neural development.
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Affiliation(s)
- Camila D. Arcuschin
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Universidad de Buenos Aires—Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina,Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Marina Pinkasz
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Universidad de Buenos Aires—Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Ignacio E. Schor
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Universidad de Buenos Aires—Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina,Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina,*Correspondence: Ignacio E. Schor ✉
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49
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Yaman YI, Ramanathan S. Controlling human organoid symmetry breaking reveals signaling gradients drive segmentation clock waves. Cell 2023; 186:513-527.e19. [PMID: 36657441 PMCID: PMC10025047 DOI: 10.1016/j.cell.2022.12.042] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 09/29/2022] [Accepted: 12/21/2022] [Indexed: 01/19/2023]
Abstract
Axial development of mammals involves coordinated morphogenetic events, including axial elongation, somitogenesis, and neural tube formation. To gain insight into the signals controlling the dynamics of human axial morphogenesis, we generated axially elongating organoids by inducing anteroposterior symmetry breaking of spatially coupled epithelial cysts derived from human pluripotent stem cells. Each organoid was composed of a neural tube flanked by presomitic mesoderm sequentially segmented into somites. Periodic activation of the somite differentiation gene MESP2 coincided in space and time with anteriorly traveling segmentation clock waves in the presomitic mesoderm of the organoids, recapitulating critical aspects of somitogenesis. Timed perturbations demonstrated that FGF and WNT signaling play distinct roles in axial elongation and somitogenesis, and that FGF signaling gradients drive segmentation clock waves. By generating and perturbing organoids that robustly recapitulate the architecture of multiple axial tissues in human embryos, this work offers a means to dissect mechanisms underlying human embryogenesis.
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Affiliation(s)
- Yusuf Ilker Yaman
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Sharad Ramanathan
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
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50
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Wang Y, Zhang K, Guo J, Yang S, Shi X, Pan J, Sun Z, Zou J, Li Y, Li Y, Fan T, Song W, Cheng F, Zeng C, Li J, Zhang T, Sun ZS. Loss-of-Function of p21-Activated Kinase 2 Links BMP Signaling to Neural Tube Patterning Defects. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2204018. [PMID: 36504449 PMCID: PMC9896034 DOI: 10.1002/advs.202204018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 11/02/2022] [Indexed: 06/17/2023]
Abstract
Closure of the neural tube represents a highly complex and coordinated process, the failure of which constitutes common birth defects. The serine/threonine kinase p21-activated kinase 2 (PAK2) is a critical regulator of cytoskeleton dynamics; however, its role in the neurulation and pathogenesis of neural tube defects (NTDs) remains unclear. Here, the results show that Pak2-/- mouse embryos fail to develop dorsolateral hinge points (DLHPs) and exhibit craniorachischisis, a severe phenotype of NTDs. Pak2 knockout activates BMP signaling that involves in vertebrate bone formation. Single-cell transcriptomes reveal abnormal differentiation trajectories and transcriptional events in Pak2-/- mouse embryos during neural tube development. Two nonsynonymous and one recurrent splice-site mutations in the PAK2 gene are identified in five human NTD fetuses, which exhibit attenuated PAK2 expression and upregulated BMP signaling in the brain. Mechanistically, PAK2 regulates Smad9 phosphorylation to inhibit BMP signaling and ultimately induce DLHP formation. Depletion of pak2a in zebrafish induces defects in the neural tube, which are partially rescued by the overexpression of wild-type, but not mutant PAK2. The findings demonstrate the conserved role of PAK2 in neurulation in multiple vertebrate species, highlighting the molecular pathogenesis of PAK2 mutations in NTDs.
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Affiliation(s)
- Yan Wang
- Beijing Institutes of Life ScienceChinese Academy of SciencesBeijing100101China
- CAS Center for Excellence in Biotic InteractionsUniversity of Chinese Academy of SciencesBeijing100049China
| | - Kaifan Zhang
- Institute of Genomic MedicineWenzhou Medical UniversityWenzhouZhejiang325000China
| | - Jin Guo
- Beijing Municipal Key Laboratory of Child Development and NutriomicsCapital Institute of PediatricsBeijing100020China
| | - Shuyan Yang
- Beijing Municipal Key Laboratory of Child Development and NutriomicsCapital Institute of PediatricsBeijing100020China
| | - Xiaohui Shi
- Beijing Institutes of Life ScienceChinese Academy of SciencesBeijing100101China
- CAS Center for Excellence in Biotic InteractionsUniversity of Chinese Academy of SciencesBeijing100049China
| | - Jinrong Pan
- Beijing Institutes of Life ScienceChinese Academy of SciencesBeijing100101China
- CAS Center for Excellence in Biotic InteractionsUniversity of Chinese Academy of SciencesBeijing100049China
| | - Zheng Sun
- Beijing Institutes of Life ScienceChinese Academy of SciencesBeijing100101China
- CAS Center for Excellence in Biotic InteractionsUniversity of Chinese Academy of SciencesBeijing100049China
| | - Jizhen Zou
- Beijing Municipal Key Laboratory of Child Development and NutriomicsCapital Institute of PediatricsBeijing100020China
| | - Yi Li
- Institute of Genomic MedicineWenzhou Medical UniversityWenzhouZhejiang325000China
| | - Yuanyuan Li
- Beijing Institutes of Life ScienceChinese Academy of SciencesBeijing100101China
- CAS Center for Excellence in Biotic InteractionsUniversity of Chinese Academy of SciencesBeijing100049China
| | - Tianda Fan
- Institute of Genomic MedicineWenzhou Medical UniversityWenzhouZhejiang325000China
| | - Wei Song
- Beijing Institutes of Life ScienceChinese Academy of SciencesBeijing100101China
- CAS Center for Excellence in Biotic InteractionsUniversity of Chinese Academy of SciencesBeijing100049China
| | - Fang Cheng
- Institute of Genomic MedicineWenzhou Medical UniversityWenzhouZhejiang325000China
| | - Cheng Zeng
- Beijing Institutes of Life ScienceChinese Academy of SciencesBeijing100101China
- CAS Center for Excellence in Biotic InteractionsUniversity of Chinese Academy of SciencesBeijing100049China
| | - Jinchen Li
- Bioinformatics Center & National Clinical Research Center for Geriatric DisordersXiangya HospitalCentral South UniversityChangshaHunan410078China
| | - Ting Zhang
- Beijing Municipal Key Laboratory of Child Development and NutriomicsCapital Institute of PediatricsBeijing100020China
| | - Zhong Sheng Sun
- Beijing Institutes of Life ScienceChinese Academy of SciencesBeijing100101China
- CAS Center for Excellence in Biotic InteractionsUniversity of Chinese Academy of SciencesBeijing100049China
- Institute of Genomic MedicineWenzhou Medical UniversityWenzhouZhejiang325000China
- State Key Laboratory of Integrated Management of Pest Insects and RodentsChinese Academy of SciencesBeijing100101China
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