1
|
Nguyen NM, Farge E. Mechanical induction in metazoan development and evolution: from earliest multi-cellular organisms to modern animal embryos. Nat Commun 2024; 15:10695. [PMID: 39702750 DOI: 10.1038/s41467-024-55100-5] [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: 12/07/2023] [Accepted: 11/27/2024] [Indexed: 12/21/2024] Open
Abstract
The development and origin of animal body forms have long been intensely explored, from the analysis of morphological traits during antiquity to Newtonian mechanical conceptions of morphogenesis. Advent of molecular biology then focused most interests on the biochemical patterning and genetic regulation of embryonic development. Today, a view is arising of development of multicellular living forms as a phenomenon emerging from non-hierarchical, reciprocal mechanical and mechanotransductive interactions between biochemical patterning and biomechanical morphogenesis. Here we discuss the nature of these processes and put forward findings on how early biochemical and biomechanical patterning of metazoans may have emerged from a primitive behavioural mechanotransducive feeding response to marine environment which might have initiated the development of first animal multicellular organisms.
Collapse
Affiliation(s)
- Ngoc Minh Nguyen
- Mechanics and Genetics of Embryonic Development group, Institut Curie, Centre OCAV PSL Research University, Sorbonne University, CNRS UMR168 Physics of Cells and Cancer, Inserm, 11 rue Pierre et Marie Curie, 75005, Paris, France
| | - Emmanuel Farge
- Mechanics and Genetics of Embryonic Development group, Institut Curie, Centre OCAV PSL Research University, Sorbonne University, CNRS UMR168 Physics of Cells and Cancer, Inserm, 11 rue Pierre et Marie Curie, 75005, Paris, France.
| |
Collapse
|
2
|
Refahi Y, Zoghlami A, Viné T, Terryn C, Paës G. Plant cell wall enzymatic deconstruction: Bridging the gap between micro and nano scales. BIORESOURCE TECHNOLOGY 2024; 414:131551. [PMID: 39370009 DOI: 10.1016/j.biortech.2024.131551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2024] [Revised: 09/27/2024] [Accepted: 09/29/2024] [Indexed: 10/08/2024]
Abstract
Understanding lignocellulosic biomass resistance to enzymatic deconstruction is crucial for its sustainable conversion into bioproducts. Despite scientific advances, quantitative morphological analysis of plant deconstruction at cell and tissue scales remains under-explored. In this study, an original pipeline is devised, involving four-dimensional (space + time) fluorescence confocal imaging, and a novel computational tool, to track and quantify deconstruction at cell and tissue scales. By applying this pipeline to poplar wood, dynamics of cellular parameters was computed and cellulose conversion during enzymatic deconstruction was measured. Results showed that enzymatic deconstruction predominantly impacts cell wall volume rather than surface area. Additionally, a negative correlation was observed between pre-hydrolysis compactness measures and volumetric cell wall deconstruction rate, whose strength was modulated by enzymatic activity. Results also revealed a strong positive correlation between average volumetric cell wall deconstruction rate and cellulose conversion rate. These findings link key deconstruction parameters across nano and micro scales.
Collapse
Affiliation(s)
- Yassin Refahi
- Université de Reims-Champagne-Ardenne, INRAE, FARE, UMR A 614, Reims 51100, France
| | - Aya Zoghlami
- Université de Reims-Champagne-Ardenne, INRAE, FARE, UMR A 614, Reims 51100, France
| | - Thibaut Viné
- Université de Reims-Champagne-Ardenne, INRAE, FARE, UMR A 614, Reims 51100, France
| | - Christine Terryn
- Platform of Cellular and Tissular Imaging (PICT), Université de Reims Champagne Ardenne, 51100 Reims, France
| | - Gabriel Paës
- Université de Reims-Champagne-Ardenne, INRAE, FARE, UMR A 614, Reims 51100, France
| |
Collapse
|
3
|
Lange M, Granados A, VijayKumar S, Bragantini J, Ancheta S, Kim YJ, Santhosh S, Borja M, Kobayashi H, McGeever E, Solak AC, Yang B, Zhao X, Liu Y, Detweiler AM, Paul S, Theodoro I, Mekonen H, Charlton C, Lao T, Banks R, Xiao S, Jacobo A, Balla K, Awayan K, D'Souza S, Haase R, Dizeux A, Pourquie O, Gómez-Sjöberg R, Huber G, Serra M, Neff N, Pisco AO, Royer LA. A multimodal zebrafish developmental atlas reveals the state-transition dynamics of late-vertebrate pluripotent axial progenitors. Cell 2024; 187:6742-6759.e17. [PMID: 39454574 DOI: 10.1016/j.cell.2024.09.047] [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: 06/20/2023] [Revised: 05/02/2024] [Accepted: 09/27/2024] [Indexed: 10/28/2024]
Abstract
Elucidating organismal developmental processes requires a comprehensive understanding of cellular lineages in the spatial, temporal, and molecular domains. In this study, we introduce Zebrahub, a dynamic atlas of zebrafish embryonic development that integrates single-cell sequencing time course data with lineage reconstructions facilitated by light-sheet microscopy. This atlas offers high-resolution and in-depth molecular insights into zebrafish development, achieved through the sequencing of individual embryos across ten developmental stages, complemented by reconstructions of cellular trajectories. Zebrahub also incorporates an interactive tool to navigate the complex cellular flows and lineages derived from light-sheet microscopy data, enabling in silico fate-mapping experiments. To demonstrate the versatility of our multimodal resource, we utilize Zebrahub to provide fresh insights into the pluripotency of neuro-mesodermal progenitors (NMPs) and the origins of a joint kidney-hemangioblast progenitor population.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Bin Yang
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Xiang Zhao
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Yang Liu
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | - Sheryl Paul
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | | | | | - Tiger Lao
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | - Sheng Xiao
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | - Keir Balla
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Kyle Awayan
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | - Robert Haase
- Cluster of Excellence "Physics of Life," TU Dresden, Dresden, Germany
| | - Alexandre Dizeux
- Institute of Physics for Medicine Paris, ESPCI Paris-PSL, Paris, France
| | | | | | - Greg Huber
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Mattia Serra
- University of California, San Diego, San Diego, CA, USA
| | - Norma Neff
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | | |
Collapse
|
4
|
Fabrèges D, Corominas-Murtra B, Moghe P, Kickuth A, Ichikawa T, Iwatani C, Tsukiyama T, Daniel N, Gering J, Stokkermans A, Wolny A, Kreshuk A, Duranthon V, Uhlmann V, Hannezo E, Hiiragi T. Temporal variability and cell mechanics control robustness in mammalian embryogenesis. Science 2024; 386:eadh1145. [PMID: 39388574 DOI: 10.1126/science.adh1145] [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: 02/14/2023] [Revised: 10/02/2023] [Accepted: 08/20/2024] [Indexed: 10/12/2024]
Abstract
How living systems achieve precision in form and function despite their intrinsic stochasticity is a fundamental yet ongoing question in biology. We generated morphomaps of preimplantation embryogenesis in mouse, rabbit, and monkey embryos, and these morphomaps revealed that although blastomere divisions desynchronized passively, 8-cell embryos converged toward robust three-dimensional shapes. Using topological analysis and genetic perturbations, we found that embryos progressively changed their cellular connectivity to a preferred topology, which could be predicted by a physical model in which actomyosin contractility and noise facilitate topological transitions, lowering surface energy. This mechanism favored regular embryo packing and promoted a higher number of inner cells in the 16-cell embryo. Synchronized division reduced embryo packing and generated substantially more misallocated cells and fewer inner-cell-mass cells. These findings suggest that stochasticity in division timing contributes to robust patterning.
Collapse
Affiliation(s)
- Dimitri Fabrèges
- Hubrecht Institute, Utrecht, Netherlands
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Prachiti Moghe
- Hubrecht Institute, Utrecht, Netherlands
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Alison Kickuth
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Takafumi Ichikawa
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
- Department of Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Chizuru Iwatani
- Research Center for Animal Life Science, Shiga University of Medical Science, Shiga, Japan
| | - Tomoyuki Tsukiyama
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
- Research Center for Animal Life Science, Shiga University of Medical Science, Shiga, Japan
| | - Nathalie Daniel
- UVSQ, INRAE, BREED, Paris-Saclay University, Jouy-en-Josas, France
| | | | | | - Adrian Wolny
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Anna Kreshuk
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Véronique Duranthon
- UVSQ, INRAE, BREED, Paris-Saclay University, Jouy-en-Josas, France
- École Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort, France
| | | | - Edouard Hannezo
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Takashi Hiiragi
- Hubrecht Institute, Utrecht, Netherlands
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
- Department of Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| |
Collapse
|
5
|
Skinner DJ, Lemaire P, Mani M. Physical modeling of embryonic transcriptomes identifies collective modes of gene expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.26.605398. [PMID: 39131269 PMCID: PMC11312445 DOI: 10.1101/2024.07.26.605398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Starting from one totipotent cell, complex multicellular organisms form through a series of differentiation and morphogenetic events, culminating in a multitude of cell types arranged in a functional and intricate spatial pattern. To do so, cells coordinate with each other, resulting in dynamics which follow a precise developmental trajectory, constraining the space of possible embryo-to-embryo variation. Using recent single-cell sequencing data of early ascidian embryos, we leverage natural variation together with modeling and inference techniques from statistical physics to investigate development at the level of a complete interconnected embryo - an embryonic transcriptome. After developing a robust and biophysically motivated approach to identifying distinct transcriptomic states or cell types, a statistical analysis reveals correlations within embryos and across cell types demonstrating the presence of collective variation. From these intra-embryo correlations, we infer minimal networks of cell-cell interactions, which reveal the collective modes of gene expression. Our work demonstrates how the existence and nature of spatial interactions along with the collective modes of expression that they give rise to can be inferred from single-cell gene expression measurements, opening up a wider range of biological questions that can be addressed using sequencing-based modalities.
Collapse
Affiliation(s)
- Dominic J. Skinner
- Center for Computational Biology, Flatiron Institute, 162 5th Ave, New York, NY 10010, USA
- NSF-Simons Center for Quantitative Biology, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA
| | - Patrick Lemaire
- CRBM, Université de Montpellier, CNRS, 34293 Montpellier, France
| | - Madhav Mani
- NSF-Simons Center for Quantitative Biology, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL 60208, USA
| |
Collapse
|
6
|
Bernadskaya YY, Kuan A, Tjärnberg A, Brandenburg J, Zheng P, Wiechecki K, Kaplan N, Failla M, Bikou M, Madilian O, Wang W, Christiaen L. Cell cycle-driven transcriptome maturation confers multilineage competence to cardiopharyngeal progenitors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.23.604718. [PMID: 39091743 PMCID: PMC11291048 DOI: 10.1101/2024.07.23.604718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
During development, stem and progenitor cells divide and transition through germ layer- and lineage-specific multipotent states to generate the diverse cell types that compose an animal. Defined changes in biomolecular composition underlie the progressive loss of potency and acquisition of lineage-specific characteristics. For example, multipotent cardiopharyngeal progenitors display multilineage transcriptional priming, whereby both the cardiac and pharyngeal muscle programs are partially active and coexist in the same progenitor cells, while their daughter cells engage in a cardiac or pharyngeal muscle differentiation path only after cell division. Here, using the tunicate Ciona, we studied the acquisition of multilineage competence and the coupling between fate decisions and cell cycle progression. We showed that multipotent cardiopharyngeal progenitors acquire the competence to produce distinct Tbx1/10(+) and (-) daughter cells shortly before mitosis, which is necessary for Tbx1/10 activation. By combining transgene-based sample barcoding with single cell RNA-seq (scRNA-seq), we uncovered transcriptome-wide dynamics in migrating cardiopharyngeal progenitors as cells progress through G1, S and G2 phases. We termed this process "transcriptome maturation", and identified candidate "mature genes", including the Rho GAP-coding gene Depdc1, which peak in late G2. Functional assays indicated that transcriptome maturation fosters cardiopharyngeal competence, in part through multilineage priming and proper oriented and asymmetric division that influences subsequent fate decisions, illustrating the concept of "behavioral competence". Both classic feedforward circuits and coupling with cell cycle progression drive transcriptome maturation, uncovering distinct levels of coupling between cell cycle progression and fateful molecular transitions. We propose that coupling competence and fate decision with the G2 and G1 phases, respectively, ensures the timely deployment of lineage-specific programs.
Collapse
Affiliation(s)
| | - Ariel Kuan
- Department of Biology, New York University, New York, NY, USA
| | | | | | - Ping Zheng
- Fang Centre, Ocean University of China, Qingdao, China
| | - Keira Wiechecki
- Department of Biology, New York University, New York, NY, USA
| | - Nicole Kaplan
- Department of Biology, New York University, New York, NY, USA
| | - Margaux Failla
- Michael Sars Centre, University of Bergen, Bergen, Norway
- Department of Biology, New York University, New York, NY, USA
| | - Maria Bikou
- Department of Biology, New York University, New York, NY, USA
| | - Oliver Madilian
- Department of Biology, New York University, New York, NY, USA
| | - Wei Wang
- Department of Biology, New York University, New York, NY, USA
- Fang Centre, Ocean University of China, Qingdao, China
| | - Lionel Christiaen
- Michael Sars Centre, University of Bergen, Bergen, Norway
- Department of Biology, New York University, New York, NY, USA
| |
Collapse
|
7
|
Gigante ED, Piekarz KM, Gurgis A, Cohen L, Razy-Krajka F, Popsuj S, Johnson CJ, Ali HS, Mohana Sundaram S, Stolfi A. Specification and survival of post-metamorphic branchiomeric neurons in a non-vertebrate chordate. Development 2024; 151:dev202719. [PMID: 38895900 PMCID: PMC11273300 DOI: 10.1242/dev.202719] [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: 01/22/2024] [Accepted: 06/10/2024] [Indexed: 06/21/2024]
Abstract
Tunicates are the sister group to the vertebrates, yet most species have a life cycle split between swimming larva and sedentary adult phases. During metamorphosis, larval neurons are replaced by adult-specific ones. The regulatory mechanisms underlying this replacement remain largely unknown. Using tissue-specific CRISPR/Cas9-mediated mutagenesis in the tunicate Ciona, we show that orthologs of conserved hindbrain and branchiomeric neuron regulatory factors Pax2/5/8 and Phox2 are required to specify the 'neck', a cellular compartment set aside in the larva to give rise to cranial motor neuron-like neurons post-metamorphosis. Using bulk and single-cell RNA-sequencing analyses, we characterize the transcriptome of the neck downstream of Pax2/5/8. We present evidence that neck-derived adult ciliomotor neurons begin to differentiate in the larva and persist through metamorphosis, contrary to the assumption that the adult nervous system is formed after settlement and the death of larval neurons during metamorphosis. Finally, we show that FGF signaling during the larval phase alters the patterning of the neck and its derivatives. Suppression of FGF converts neck cells into larval neurons that fail to survive metamorphosis, whereas prolonged FGF signaling promotes an adult neural stem cell-like fate.
Collapse
Affiliation(s)
- Eduardo D. Gigante
- School of Biological Sciences, College of Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Katarzyna M. Piekarz
- School of Biological Sciences, College of Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Alexandra Gurgis
- School of Biological Sciences, College of Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Department of Biology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Leslie Cohen
- School of Biological Sciences, College of Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Florian Razy-Krajka
- School of Biological Sciences, College of Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Sydney Popsuj
- School of Biological Sciences, College of Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Christopher J. Johnson
- School of Biological Sciences, College of Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Hussan S. Ali
- School of Biological Sciences, College of Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Shruthi Mohana Sundaram
- School of Biological Sciences, College of Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Alberto Stolfi
- School of Biological Sciences, College of Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| |
Collapse
|
8
|
Bolondi A, Law BK, Kretzmer H, Gassaloglu SI, Buschow R, Riemenschneider C, Yang D, Walther M, Veenvliet JV, Meissner A, Smith ZD, Chan MM. Reconstructing axial progenitor field dynamics in mouse stem cell-derived embryoids. Dev Cell 2024; 59:1489-1505.e14. [PMID: 38579718 PMCID: PMC11187653 DOI: 10.1016/j.devcel.2024.03.024] [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: 08/15/2023] [Revised: 12/13/2023] [Accepted: 03/12/2024] [Indexed: 04/07/2024]
Abstract
Embryogenesis requires substantial coordination to translate genetic programs to the collective behavior of differentiating cells, but understanding how cellular decisions control tissue morphology remains conceptually and technically challenging. Here, we combine continuous Cas9-based molecular recording with a mouse embryonic stem cell-based model of the embryonic trunk to build single-cell phylogenies that describe the behavior of transient, multipotent neuro-mesodermal progenitors (NMPs) as they commit into neural and somitic cell types. We find that NMPs show subtle transcriptional signatures related to their recent differentiation and contribute to downstream lineages through a surprisingly broad distribution of individual fate outcomes. Although decision-making can be heavily influenced by environmental cues to induce morphological phenotypes, axial progenitors intrinsically mature over developmental time to favor the neural lineage. Using these data, we present an experimental and analytical framework for exploring the non-homeostatic dynamics of transient progenitor populations as they shape complex tissues during critical developmental windows.
Collapse
Affiliation(s)
- Adriano Bolondi
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Benjamin K Law
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Helene Kretzmer
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Seher Ipek Gassaloglu
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - René Buschow
- Microscopy Core Facility, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | | | - Dian Yang
- Department of Molecular Pharmacology and Therapeutics & Systems Biology, Columbia University, New York, NY 10032, USA
| | - Maria Walther
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Jesse V Veenvliet
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany; Cluster of Excellence Physics of Life, Technische Universität Dresden, 01307 Dresden, Germany; Center for Systems Biology Dresden, 01307 Dresden, Germany
| | - Alexander Meissner
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany.
| | - Zachary D Smith
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06519, USA.
| | - Michelle M Chan
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
| |
Collapse
|
9
|
Guan G, Chen Y, Wang H, Ouyang Q, Tang C. Characterizing Cellular Physiological States with Three-Dimensional Shape Descriptors for Cell Membranes. MEMBRANES 2024; 14:137. [PMID: 38921504 PMCID: PMC11205511 DOI: 10.3390/membranes14060137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 06/03/2024] [Accepted: 06/06/2024] [Indexed: 06/27/2024]
Abstract
The shape of a cell as defined by its membrane can be closely associated with its physiological state. For example, the irregular shapes of cancerous cells and elongated shapes of neuron cells often reflect specific functions, such as cell motility and cell communication. However, it remains unclear whether and which cell shape descriptors can characterize different cellular physiological states. In this study, 12 geometric shape descriptors for a three-dimensional (3D) object were collected from the previous literature and tested with a public dataset of ~400,000 independent 3D cell regions segmented based on fluorescent labeling of the cell membranes in Caenorhabditis elegans embryos. It is revealed that those shape descriptors can faithfully characterize cellular physiological states, including (1) cell division (cytokinesis), along with an abrupt increase in the elongation ratio; (2) a negative correlation of cell migration speed with cell sphericity; (3) cell lineage specification with symmetrically patterned cell shape changes; and (4) cell fate specification with differential gene expression and differential cell shapes. The descriptors established may be used to identify and predict the diverse physiological states in numerous cells, which could be used for not only studying developmental morphogenesis but also diagnosing human disease (e.g., the rapid detection of abnormal cells).
Collapse
Affiliation(s)
- Guoye Guan
- Center for Quantitative Biology, Peking University, Beijing 100871, China; (G.G.); (Q.O.)
| | - Yixuan Chen
- School of Physics, Peking University, Beijing 100871, China;
| | - Hongli Wang
- Center for Quantitative Biology, Peking University, Beijing 100871, China; (G.G.); (Q.O.)
- School of Physics, Peking University, Beijing 100871, China;
| | - Qi Ouyang
- Center for Quantitative Biology, Peking University, Beijing 100871, China; (G.G.); (Q.O.)
- School of Physics, Peking University, Beijing 100871, China;
- School of Physics, Zhejiang University, Hangzhou 310027, China
| | - Chao Tang
- Center for Quantitative Biology, Peking University, Beijing 100871, China; (G.G.); (Q.O.)
- School of Physics, Peking University, Beijing 100871, China;
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| |
Collapse
|
10
|
Katoh TA, Fukai YT, Ishibashi T. Optical microscopic imaging, manipulation, and analysis methods for morphogenesis research. Microscopy (Oxf) 2024; 73:226-242. [PMID: 38102756 PMCID: PMC11154147 DOI: 10.1093/jmicro/dfad059] [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: 06/30/2023] [Revised: 11/20/2023] [Accepted: 03/22/2024] [Indexed: 12/17/2023] Open
Abstract
Morphogenesis is a developmental process of organisms being shaped through complex and cooperative cellular movements. To understand the interplay between genetic programs and the resulting multicellular morphogenesis, it is essential to characterize the morphologies and dynamics at the single-cell level and to understand how physical forces serve as both signaling components and driving forces of tissue deformations. In recent years, advances in microscopy techniques have led to improvements in imaging speed, resolution and depth. Concurrently, the development of various software packages has supported large-scale, analyses of challenging images at the single-cell resolution. While these tools have enhanced our ability to examine dynamics of cells and mechanical processes during morphogenesis, their effective integration requires specialized expertise. With this background, this review provides a practical overview of those techniques. First, we introduce microscopic techniques for multicellular imaging and image analysis software tools with a focus on cell segmentation and tracking. Second, we provide an overview of cutting-edge techniques for mechanical manipulation of cells and tissues. Finally, we introduce recent findings on morphogenetic mechanisms and mechanosensations that have been achieved by effectively combining microscopy, image analysis tools and mechanical manipulation techniques.
Collapse
Affiliation(s)
- Takanobu A Katoh
- Department of Cell Biology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yohsuke T Fukai
- Nonequilibrium Physics of Living Matter RIKEN Hakubi Research Team, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Tomoki Ishibashi
- Laboratory for Physical Biology, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| |
Collapse
|
11
|
Merle M, Friedman L, Chureau C, Shoushtarizadeh A, Gregor T. Precise and scalable self-organization in mammalian pseudo-embryos. Nat Struct Mol Biol 2024; 31:896-902. [PMID: 38491138 DOI: 10.1038/s41594-024-01251-4] [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: 06/11/2023] [Accepted: 02/08/2024] [Indexed: 03/18/2024]
Abstract
Gene expression is inherently noisy, posing a challenge to understanding how precise and reproducible patterns of gene expression emerge in mammals. Here we investigate this phenomenon using gastruloids, a three-dimensional in vitro model for early mammalian development. Our study reveals intrinsic reproducibility in the self-organization of gastruloids, encompassing growth dynamics and gene expression patterns. We observe a remarkable degree of control over gene expression along the main body axis, with pattern boundaries positioned with single-cell precision. Furthermore, as gastruloids grow, both their physical proportions and gene expression patterns scale proportionally with system size. Notably, these properties emerge spontaneously in self-organizing cell aggregates, distinct from many in vivo systems constrained by fixed boundary conditions. Our findings shed light on the intricacies of developmental precision, reproducibility and size scaling within a mammalian system, suggesting that these phenomena might constitute fundamental features of multicellularity.
Collapse
Affiliation(s)
- Mélody Merle
- Department of Developmental and Stem Cell Biology, CNRS UMR3738 Paris Cité, Institut Pasteur, Paris, France
| | - Leah Friedman
- Department of Developmental and Stem Cell Biology, CNRS UMR3738 Paris Cité, Institut Pasteur, Paris, France
| | - Corinne Chureau
- Department of Developmental and Stem Cell Biology, CNRS UMR3738 Paris Cité, Institut Pasteur, Paris, France
| | - Armin Shoushtarizadeh
- Department of Developmental and Stem Cell Biology, CNRS UMR3738 Paris Cité, Institut Pasteur, Paris, France
| | - Thomas Gregor
- Department of Developmental and Stem Cell Biology, CNRS UMR3738 Paris Cité, Institut Pasteur, Paris, France.
- Joseph Henry Laboratories of Physics & Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
| |
Collapse
|
12
|
Zhang L, Xue G, Zhou X, Huang J, Li Z. A mathematical framework for understanding the spontaneous emergence of complexity applicable to growing multicellular systems. PLoS Comput Biol 2024; 20:e1011882. [PMID: 38838038 PMCID: PMC11182560 DOI: 10.1371/journal.pcbi.1011882] [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: 02/02/2024] [Revised: 06/17/2024] [Accepted: 05/20/2024] [Indexed: 06/07/2024] Open
Abstract
In embryonic development and organogenesis, cells sharing identical genetic codes acquire diverse gene expression states in a highly reproducible spatial distribution, crucial for multicellular formation and quantifiable through positional information. To understand the spontaneous growth of complexity, we constructed a one-dimensional division-decision model, simulating the growth of cells with identical genetic networks from a single cell. Our findings highlight the pivotal role of cell division in providing positional cues, escorting the system toward states rich in information. Moreover, we pinpointed lateral inhibition as a critical mechanism translating spatial contacts into gene expression. Our model demonstrates that the spatial arrangement resulting from cell division, combined with cell lineages, imparts positional information, specifying multiple cell states with increased complexity-illustrated through examples in C.elegans. This study constitutes a foundational step in comprehending developmental intricacies, paving the way for future quantitative formulations to construct synthetic multicellular patterns.
Collapse
Affiliation(s)
- Lu Zhang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Gang Xue
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Xiaolin Zhou
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Jiandong Huang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Chinese Academy of Sciences (CAS) Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Zhiyuan Li
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| |
Collapse
|
13
|
Piekarz KM, Stolfi A. Development and circuitry of the tunicate larval Motor Ganglion, a putative hindbrain/spinal cord homolog. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2024; 342:200-211. [PMID: 37675754 PMCID: PMC10918034 DOI: 10.1002/jez.b.23221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/13/2023] [Accepted: 08/22/2023] [Indexed: 09/08/2023]
Abstract
The Motor Ganglion (MG) is a small collection of neurons that control the swimming movements of the tunicate tadpole larva. Situated at the base of the tail, molecular and functional comparisons suggest that may be a homolog of the spinal cord and/or hindbrain ("rhombospinal" region) of vertebrates. Here we review the most current knowledge of the development, connectivity, functions, and unique identities of the neurons that comprise the MG, drawn mostly from studies in Ciona spp. The simple cell lineages, minimal cellular composition, and comprehensively mapped "connectome" of the Ciona MG all make this an excellent model for studying the development and physiology of motor control in aquatic larvae.
Collapse
Affiliation(s)
| | - Alberto Stolfi
- School of Biological Sciences, Georgia Institute of Technology
| |
Collapse
|
14
|
Campàs O, Noordstra I, Yap AS. Adherens junctions as molecular regulators of emergent tissue mechanics. Nat Rev Mol Cell Biol 2024; 25:252-269. [PMID: 38093099 DOI: 10.1038/s41580-023-00688-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/08/2023] [Indexed: 03/28/2024]
Abstract
Tissue and organ development during embryogenesis relies on the collective and coordinated action of many cells. Recent studies have revealed that tissue material properties, including transitions between fluid and solid tissue states, are controlled in space and time to shape embryonic structures and regulate cell behaviours. Although the collective cellular flows that sculpt tissues are guided by tissue-level physical changes, these ultimately emerge from cellular-level and subcellular-level molecular mechanisms. Adherens junctions are key subcellular structures, built from clusters of classical cadherin receptors. They mediate physical interactions between cells and connect biochemical signalling to the physical characteristics of cell contacts, hence playing a fundamental role in tissue morphogenesis. In this Review, we take advantage of the results of recent, quantitative measurements of tissue mechanics to relate the molecular and cellular characteristics of adherens junctions, including adhesion strength, tension and dynamics, to the emergent physical state of embryonic tissues. We focus on systems in which cell-cell interactions are the primary contributor to morphogenesis, without significant contribution from cell-matrix interactions. We suggest that emergent tissue mechanics is an important direction for future research, bridging cell biology, developmental biology and mechanobiology to provide a holistic understanding of morphogenesis in health and disease.
Collapse
Affiliation(s)
- Otger Campàs
- Cluster of Excellence Physics of Life, TU Dresden, Dresden, Germany.
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
- Center for Systems Biology Dresden, Dresden, Germany.
| | - Ivar Noordstra
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
| | - Alpha S Yap
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia.
| |
Collapse
|
15
|
Gauquelin E, Kuromiya K, Namba T, Ikawa K, Fujita Y, Ishihara S, Sugimura K. Mechanical convergence in mixed populations of mammalian epithelial cells. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2024; 47:21. [PMID: 38538808 PMCID: PMC10973031 DOI: 10.1140/epje/s10189-024-00415-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 03/05/2024] [Indexed: 04/09/2024]
Abstract
Tissues consist of cells with different molecular and/or mechanical properties. Measuring the forces and stresses in mixed-cell populations is essential for understanding the mechanisms by which tissue development, homeostasis, and disease emerge from the cooperation of distinct cell types. However, many previous studies have primarily focused their mechanical measurements on dissociated cells or aggregates of a single-cell type, leaving the mechanics of mixed-cell populations largely unexplored. In the present study, we aimed to elucidate the influence of interactions between different cell types on cell mechanics by conducting in situ mechanical measurements on a monolayer of mammalian epithelial cells. Our findings revealed that while individual cell types displayed varying magnitudes of traction and intercellular stress before mixing, these mechanical values shifted in the mixed monolayer, becoming nearly indistinguishable between the cell types. Moreover, by analyzing a mixed-phase model of active tissues, we identified physical conditions under which such mechanical convergence is induced. Overall, the present study underscores the importance of in situ mechanical measurements in mixed-cell populations to deepen our understanding of the mechanics of multicellular systems.
Collapse
Affiliation(s)
- Estelle Gauquelin
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Keisuke Kuromiya
- Department of Molecular Oncology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan
| | - Toshinori Namba
- Universal Biology Institute, The University of Tokyo, Tokyo, 113-0033, Japan
- Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, 153-0041, Japan
| | - Keisuke Ikawa
- Division of Biological Science, Graduate School of Science, Nagoya University, Aichi, 464-8602, Japan
| | - Yasuyuki Fujita
- Department of Molecular Oncology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan
| | - Shuji Ishihara
- Universal Biology Institute, The University of Tokyo, Tokyo, 113-0033, Japan.
- Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, 153-0041, Japan.
| | - Kaoru Sugimura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0032, Japan.
- Universal Biology Institute, The University of Tokyo, Tokyo, 113-0033, Japan.
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8561, Japan.
| |
Collapse
|
16
|
Wei J, Zhang W, Jiang A, Peng H, Zhang Q, Li Y, Bi J, Wang L, Liu P, Wang J, Ge Y, Zhang L, Yu H, Li L, Wang S, Leng L, Chen K, Dong B. Temporospatial hierarchy and allele-specific expression of zygotic genome activation revealed by distant interspecific urochordate hybrids. Nat Commun 2024; 15:2395. [PMID: 38493164 PMCID: PMC10944513 DOI: 10.1038/s41467-024-46780-0] [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: 01/27/2023] [Accepted: 03/06/2024] [Indexed: 03/18/2024] Open
Abstract
Zygotic genome activation (ZGA) is a universal process in early embryogenesis of metazoan, when the quiescent zygotic nucleus initiates global transcription. However, the mechanisms related to massive genome activation and allele-specific expression (ASE) remain not well understood. Here, we develop hybrids from two deeply diverged (120 Mya) ascidian species to symmetrically document the dynamics of ZGA. We identify two coordinated ZGA waves represent early developmental and housekeeping gene reactivation, respectively. Single-cell RNA sequencing reveals that the major expression wave exhibits spatial heterogeneity and significantly correlates with cell fate. Moreover, allele-specific expression occurs in a species- rather than parent-related manner, demonstrating the divergence of cis-regulatory elements between the two species. These findings provide insights into ZGA in chordates.
Collapse
Affiliation(s)
- Jiankai Wei
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266237, China
- MoE Key Laboratory of Evolution and Marine Biodiversity, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Wei Zhang
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - An Jiang
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Hongzhe Peng
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Quanyong Zhang
- State Key Laboratory of Primate Biomedical Research and Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China
| | - Yuting Li
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Jianqing Bi
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Linting Wang
- National Center of Mathematics and Interdisciplinary Sciences, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China
| | - Penghui Liu
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Jing Wang
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Yonghang Ge
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Liya Zhang
- State Key Laboratory of Primate Biomedical Research and Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China
| | - Haiyan Yu
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Lei Li
- National Center of Mathematics and Interdisciplinary Sciences, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China
| | - Shi Wang
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266237, China
| | - Liang Leng
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
| | - Kai Chen
- State Key Laboratory of Primate Biomedical Research and Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No. 1119 Haibin Rd, Nansha Dist., Guangzhou, 511458, China.
| | - Bo Dong
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266237, China.
- MoE Key Laboratory of Evolution and Marine Biodiversity, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
| |
Collapse
|
17
|
Schindler-Johnson M, Petridou NI. Collective effects of cell cleavage dynamics. Front Cell Dev Biol 2024; 12:1358971. [PMID: 38559810 PMCID: PMC10978805 DOI: 10.3389/fcell.2024.1358971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 03/05/2024] [Indexed: 04/04/2024] Open
Abstract
A conserved process of early embryonic development in metazoans is the reductive cell divisions following oocyte fertilization, termed cell cleavages. Cell cleavage cycles usually start synchronously, lengthen differentially between the embryonic cells becoming asynchronous, and cease before major morphogenetic events, such as germ layer formation and gastrulation. Despite exhibiting species-specific characteristics, the regulation of cell cleavage dynamics comes down to common controllers acting mostly at the single cell/nucleus level, such as nucleus-to-cytoplasmic ratio and zygotic genome activation. Remarkably, recent work has linked cell cleavage dynamics to the emergence of collective behavior during embryogenesis, including pattern formation and changes in embryo-scale mechanics, raising the question how single-cell controllers coordinate embryo-scale processes. In this review, we summarize studies across species where an association between cell cleavages and collective behavior was made, discuss the underlying mechanisms, and propose that cell-to-cell variability in cell cleavage dynamics can serve as a mechanism of long-range coordination in developing embryos.
Collapse
Affiliation(s)
- Magdalena Schindler-Johnson
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Nicoletta I. Petridou
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| |
Collapse
|
18
|
Popkova A, Andrenšek U, Pagnotta S, Ziherl P, Krajnc M, Rauzi M. A mechanical wave travels along a genetic guide to drive the formation of an epithelial furrow during Drosophila gastrulation. Dev Cell 2024; 59:400-414.e5. [PMID: 38228140 DOI: 10.1016/j.devcel.2023.12.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/08/2023] [Accepted: 12/21/2023] [Indexed: 01/18/2024]
Abstract
Epithelial furrowing is a fundamental morphogenetic process during gastrulation, neurulation, and body shaping. A furrow often results from a fold that propagates along a line. How fold formation and propagation are controlled and driven is poorly understood. To shed light on this, we study the formation of the cephalic furrow, a fold that runs along the embryo dorsal-ventral axis during Drosophila gastrulation and the developmental role of which is still unknown. We provide evidence of its function and show that epithelial furrowing is initiated by a group of cells. This cellular cluster works as a pacemaker, triggering a bidirectional morphogenetic wave powered by actomyosin contractions and sustained by de novo medial apex-to-apex cell adhesion. The pacemaker's Cartesian position is under the crossed control of the anterior-posterior and dorsal-ventral gene patterning systems. Thus, furrow formation is driven by a mechanical trigger wave that travels under the control of a multidimensional genetic guide.
Collapse
Affiliation(s)
- Anna Popkova
- Université Côte d'Azur, CNRS, Inserm, iBV, Nice, France.
| | - Urška Andrenšek
- Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, 1000 Ljubljana, Slovenia; Jožef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
| | - Sophie Pagnotta
- Université Côte d'Azur, Centre Commun de Microscopie Appliquée, Nice, France
| | - Primož Ziherl
- Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, 1000 Ljubljana, Slovenia; Jožef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
| | - Matej Krajnc
- Jožef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
| | - Matteo Rauzi
- Université Côte d'Azur, CNRS, Inserm, iBV, Nice, France.
| |
Collapse
|
19
|
Schwayer C, Brückner DB. Connecting theory and experiment in cell and tissue mechanics. J Cell Sci 2023; 136:jcs261515. [PMID: 38149871 DOI: 10.1242/jcs.261515] [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] [Indexed: 12/28/2023] Open
Abstract
Understanding complex living systems, which are fundamentally constrained by physical phenomena, requires combining experimental data with theoretical physical and mathematical models. To develop such models, collaborations between experimental cell biologists and theoreticians are increasingly important but these two groups often face challenges achieving mutual understanding. To help navigate these challenges, this Perspective discusses different modelling approaches, including bottom-up hypothesis-driven and top-down data-driven models, and highlights their strengths and applications. Using cell mechanics as an example, we explore the integration of specific physical models with experimental data from the molecular, cellular and tissue level up to multiscale input. We also emphasize the importance of constraining model complexity and outline strategies for crosstalk between experimental design and model development. Furthermore, we highlight how physical models can provide conceptual insights and produce unifying and generalizable frameworks for biological phenomena. Overall, this Perspective aims to promote fruitful collaborations that advance our understanding of complex biological systems.
Collapse
Affiliation(s)
- Cornelia Schwayer
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - David B Brückner
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| |
Collapse
|
20
|
Ichbiah S, Delbary F, McDougall A, Dumollard R, Turlier H. Embryo mechanics cartography: inference of 3D force atlases from fluorescence microscopy. Nat Methods 2023; 20:1989-1999. [PMID: 38057527 PMCID: PMC10703677 DOI: 10.1038/s41592-023-02084-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 10/12/2023] [Indexed: 12/08/2023]
Abstract
Tissue morphogenesis results from a tight interplay between gene expression, biochemical signaling and mechanics. Although sequencing methods allow the generation of cell-resolved spatiotemporal maps of gene expression, creating similar maps of cell mechanics in three-dimensional (3D) developing tissues has remained a real challenge. Exploiting the foam-like arrangement of cells, we propose a robust end-to-end computational method called 'foambryo' to infer spatiotemporal atlases of cellular forces from fluorescence microscopy images of cell membranes. Our method generates precise 3D meshes of cells' geometry and successively predicts relative cell surface tensions and pressures. We validate it with 3D foam simulations, study its noise sensitivity and prove its biological relevance in mouse, ascidian and worm embryos. 3D force inference allows us to recover mechanical features identified previously, but also predicts new ones, unveiling potential new insights on the spatiotemporal regulation of cell mechanics in developing embryos. Our code is freely available and paves the way for unraveling the unknown mechanochemical feedbacks that control embryo and tissue morphogenesis.
Collapse
Affiliation(s)
- Sacha Ichbiah
- Center for Interdisciplinary Research in Biology, College of France, CNRS, INSERM, University of PSL, Paris, France
| | - Fabrice Delbary
- Center for Interdisciplinary Research in Biology, College of France, CNRS, INSERM, University of PSL, Paris, France
| | - Alex McDougall
- Laboratory of Developmental Biology of the Villefranche-sur-Mer, Institute of Villefranche-sur-Mer, Sorbonne University, CNRS, Villefranche-sur-Mer, France
| | - Rémi Dumollard
- Laboratory of Developmental Biology of the Villefranche-sur-Mer, Institute of Villefranche-sur-Mer, Sorbonne University, CNRS, Villefranche-sur-Mer, France
| | - Hervé Turlier
- Center for Interdisciplinary Research in Biology, College of France, CNRS, INSERM, University of PSL, Paris, France.
| |
Collapse
|
21
|
Crozet F, Levayer R. Emerging roles and mechanisms of ERK pathway mechanosensing. Cell Mol Life Sci 2023; 80:355. [PMID: 37947896 PMCID: PMC10638131 DOI: 10.1007/s00018-023-05007-z] [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: 08/31/2023] [Revised: 10/11/2023] [Accepted: 10/16/2023] [Indexed: 11/12/2023]
Abstract
The coupling between mechanical forces and modulation of cell signalling pathways is essential for tissue plasticity and their adaptation to changing environments. Whilst the number of physiological and pathological relevant roles of mechanotransduction has been rapidly expanding over the last decade, studies have been mostly focussing on a limited number of mechanosensitive pathways, which include for instance Hippo/YAP/TAZ pathway, Wnt/β-catenin or the stretch-activated channel Piezo. However, the recent development and spreading of new live sensors has provided new insights into the contribution of ERK pathway in mechanosensing in various systems, which emerges now as a fast and modular mechanosensitive pathway. In this review, we will document key in vivo and in vitro examples that have established a clear link between cell deformation, mechanical stress and modulation of ERK signalling, comparing the relevant timescale and mechanical stress. We will then discuss different molecular mechanisms that have been proposed so far, focussing on the epistatic link between mechanics and ERK and discussing the relevant cellular parameters affecting ERK signalling. We will finish by discussing the physiological and the pathological consequences of the link between ERK and mechanics, outlining how this interplay is instrumental for self-organisation and long-range cell-cell coordination.
Collapse
Affiliation(s)
- Flora Crozet
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université de Paris Cité, CNRS UMR 3738, 25 Rue du Dr. Roux, 75015, Paris, France
| | - Romain Levayer
- Department of Developmental and Stem Cell Biology, Institut Pasteur, Université de Paris Cité, CNRS UMR 3738, 25 Rue du Dr. Roux, 75015, Paris, France.
| |
Collapse
|
22
|
Lin B, Shi W, Lu Q, Shito TT, Yu H, Dong B. Establishment of a developmental atlas and transgenetic tools in the ascidian Styela clava. MARINE LIFE SCIENCE & TECHNOLOGY 2023; 5:435-454. [PMID: 38045543 PMCID: PMC10689645 DOI: 10.1007/s42995-023-00200-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 09/28/2023] [Indexed: 12/05/2023]
Abstract
The ascidian Styela clava is an ecologically important species that is distributed along coastal regions worldwide. It has a long history as a model animal for evolutionary and developmental biology research owing to its phylogenetic position between vertebrates and invertebrates, and its classical mosaic expression patterns. However, the standard developmental atlas and protocols and tools for molecular manipulation of this organism are inadequate. In this study, we established a standard developmental table and provided a web-based digital image resource for S. clava embryogenesis at each developmental stage from fertilized eggs to hatching larvae by utilizing confocal laser microscopy and 3D reconstruction images. It takes around 10 h for fertilized eggs to develop into swimming larvae and 20-30 min to complete the tail regression processes at the metamorphic stage. We observed that the notochord cells in S. clava embryos did not produce an extracellular lumen like Ciona robusta, but showed polarized elongation behaviors, providing us an ideal comparative model to study tissue morphogenesis. In addition, we established a chemical-washing procedure to remove the chorion easily from the fertilized eggs. Based on the dechorionation technique, we further realized transgenic manipulation by electroporation and successfully applied tissue-specific fluorescent labeling in S. clava embryos. Our work provides a standard imaging atlas and powerful genetic tools for investigating embryogenesis and evolution using S. clava as a model organism. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-023-00200-2.
Collapse
Affiliation(s)
- Boyan Lin
- Fang Zongxi Center, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
| | - Wenjie Shi
- Fang Zongxi Center, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
| | - Qiongxuan Lu
- Fang Zongxi Center, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
| | - Takumi T. Shito
- Department of Bioscience and Informatics, Faculty of Science and Technology, Keio University, Yokohama, 223-8522 Japan
| | - Haiyan Yu
- Fang Zongxi Center, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
| | - Bo Dong
- Fang Zongxi Center, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
- Laoshan Laboratory, Qingdao, 266237 China
- MoE Key Laboratory of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| |
Collapse
|
23
|
Ramos AP, Szalapak A, Ferme LC, Modes CD. From cells to form: A roadmap to study shape emergence in vivo. Biophys J 2023; 122:3587-3599. [PMID: 37243338 PMCID: PMC10541488 DOI: 10.1016/j.bpj.2023.05.015] [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: 02/19/2023] [Revised: 04/25/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023] Open
Abstract
Organogenesis arises from the collective arrangement of cells into progressively 3D-shaped tissue. The acquisition of a correctly shaped organ is then the result of a complex interplay between molecular cues, responsible for differentiation and patterning, and the mechanical properties of the system, which generate the necessary forces that drive correct shape emergence. Nowadays, technological advances in the fields of microscopy, molecular biology, and computer science are making it possible to see and record such complex interactions in incredible, unforeseen detail within the global context of the developing embryo. A quantitative and interdisciplinary perspective of developmental biology becomes then necessary for a comprehensive understanding of morphogenesis. Here, we provide a roadmap to quantify the events that lead to morphogenesis from imaging to image analysis, quantification, and modeling, focusing on the discrete cellular and tissue shape changes, as well as their mechanical properties.
Collapse
Affiliation(s)
| | - Alicja Szalapak
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany; Center for Systems Biology Dresden, Dresden, Germany
| | | | - Carl D Modes
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany; Center for Systems Biology Dresden, Dresden, Germany; Cluster of Excellence Physics of Life, TU Dresden, Dresden, Germany
| |
Collapse
|
24
|
Skinner DJ, Jeckel H, Martin AC, Drescher K, Dunkel J. Topological packing statistics of living and nonliving matter. SCIENCE ADVANCES 2023; 9:eadg1261. [PMID: 37672580 PMCID: PMC10482333 DOI: 10.1126/sciadv.adg1261] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 07/27/2023] [Indexed: 09/08/2023]
Abstract
Complex disordered matter is of central importance to a wide range of disciplines, from bacterial colonies and embryonic tissues in biology to foams and granular media in materials science to stellar configurations in astrophysics. Because of the vast differences in composition and scale, comparing structural features across such disparate systems remains challenging. Here, by using the statistical properties of Delaunay tessellations, we introduce a mathematical framework for measuring topological distances between general three-dimensional point clouds. The resulting system-agnostic metric reveals subtle structural differences between bacterial biofilms as well as between zebrafish brain regions, and it recovers temporal ordering of embryonic development. We apply the metric to construct a universal topological atlas encompassing bacterial biofilms, snowflake yeast, plant shoots, zebrafish brain matter, organoids, and embryonic tissues as well as foams, colloidal packings, glassy materials, and stellar configurations. Living systems localize within a bounded island-like region of the atlas, reflecting that biological growth mechanisms result in characteristic topological properties.
Collapse
Affiliation(s)
- Dominic J Skinner
- Department of Mathematics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- NSF-Simons Center for Quantitative Biology, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA
| | - Hannah Jeckel
- Department of Physics, Philipps-Universität Marburg, Renthof 6, 35032 Marburg, Germany
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Adam C Martin
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA
| | - Knut Drescher
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Jörn Dunkel
- Department of Mathematics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| |
Collapse
|
25
|
Gigante ED, Piekarz KM, Gurgis A, Cohen L, Razy-Krajka F, Popsuj S, Ali HS, Sundaram SM, Stolfi A. Specification and survival of post-metamorphic branchiomeric neurons in the hindbrain of a non-vertebrate chordate. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.16.545305. [PMID: 37645866 PMCID: PMC10461979 DOI: 10.1101/2023.06.16.545305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Tunicates are the sister group to the vertebrates, yet most species have a life cycle split between swimming larva and sedentary adult phases. During metamorphosis, larval neurons are largely replaced by adult-specific ones. Yet the regulatory mechanisms underlying this neural replacement remain largely unknown. Using tissue-specific CRISPR/Cas9-mediated mutagenesis in the tunicate Ciona, we show that orthologs of conserved hindbrain and branchiomeric neuron regulatory factors Pax2/5/8 and Phox2 are required to specify the "Neck", a compartment of cells set aside in the larva to give rise to cranial motor neuron-like neurons in the adult. Using bulk and single-cell RNAseq analyses, we also characterize the transcriptome of the Neck downstream of Pax2/5/8. Surprisingly, we find that Neck-derived adult ciliomotor neurons begin to differentiate in the larva, contrary to the long-held assumption that the adult nervous system is formed only after settlement and the death of larval neurons during metamorphosis. Finally, we show that manipulating FGF signaling during the larval phase alters the patterning of the Neck and its derivatives. Suppression of FGF converts Neck cells into larval neurons that fail to survive metamorphosis, while prolonged FGF signaling promotes an adult neural stem cell-like fate instead.
Collapse
Affiliation(s)
- Eduardo D Gigante
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332; USA
| | - Katarzyna M Piekarz
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332; USA
| | - Alexandra Gurgis
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332; USA
- Department of Biology, Case Western Reserve University, Cleveland, OH, 44106; USA
| | - Leslie Cohen
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332; USA
| | - Florian Razy-Krajka
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332; USA
| | - Sydney Popsuj
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332; USA
| | - Hussan S Ali
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332; USA
| | | | - Alberto Stolfi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332; USA
| |
Collapse
|
26
|
Wei H, Du S, Parksong J, Pasolli HA, Matte-Martone C, Regot S, Gonzalez LE, Xin T, Greco V. Organ function is preserved despite reorganization of niche architecture in the hair follicle. Cell Stem Cell 2023; 30:962-972.e6. [PMID: 37419106 PMCID: PMC10362479 DOI: 10.1016/j.stem.2023.06.003] [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: 06/24/2022] [Revised: 05/01/2023] [Accepted: 06/07/2023] [Indexed: 07/09/2023]
Abstract
The ability of stem cells to build and replenish tissues depends on support from their niche. Although niche architecture varies across organs, its functional importance is unclear. During hair follicle growth, multipotent epithelial progenitors build hair via crosstalk with their remodeling fibroblast niche, the dermal papilla, providing a powerful model to functionally interrogate niche architecture. Through mouse intravital imaging, we show that dermal papilla fibroblasts remodel individually and collectively to form a morphologically polarized, structurally robust niche. Asymmetric TGF-β signaling precedes morphological niche polarity, and loss of TGF-β signaling in dermal papilla fibroblasts leads them to progressively lose their stereotypic architecture, instead surrounding the epithelium. The reorganized niche induces the redistribution of multipotent progenitors but nevertheless supports their proliferation and differentiation. However, the differentiated lineages and hairs produced by progenitors are shorter. Overall, our results reveal that niche architecture optimizes organ efficiency but is not absolutely essential for organ function.
Collapse
Affiliation(s)
- Haoyang Wei
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Shuangshuang Du
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Jeeun Parksong
- Departments of Cell Biology and Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - H Amalia Pasolli
- Electron Microscopy Resource Center, The Rockefeller University, New York, NY 10065, USA
| | | | - Sergi Regot
- Department of Molecular Biology and Genetics, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Lauren E Gonzalez
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Tianchi Xin
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA.
| | - Valentina Greco
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA; Departments of Cell Biology and Dermatology, Yale Stem Cell Center, Yale Cancer Center, Yale School of Medicine, New Haven, CT 06510, USA.
| |
Collapse
|
27
|
Mapping and exploring the organoid state space using synthetic biology. Semin Cell Dev Biol 2023; 141:23-32. [PMID: 35466054 DOI: 10.1016/j.semcdb.2022.04.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/13/2022] [Indexed: 12/12/2022]
Abstract
The functional relevance of an organoid is dependent on the differentiation, morphology, cell arrangement and biophysical properties, which collectively define the state of an organoid. For an organoid culture, an individual organoid or the cells that compose it, these state variables can be characterised, most easily by transcriptomics and by high-content image analysis. Their states can be compared to their in vivo counterparts. Current evidence suggests that organoids explore a wider state space than organs in vivo due to the lack of niche signalling and the variability of boundary conditions in vitro. Using data-driven state inference and in silico modelling, phase diagrams can be constructed to systematically sort organoids along biochemical or biophysical axes. These phase diagrams allow us to identify control strategies to modulate organoid state. To do so, the biochemical and biophysical environment, as well as the cells that seed organoids, can be manipulated.
Collapse
|
28
|
Smith MB, Sparks H, Almagro J, Chaigne A, Behrens A, Dunsby C, Salbreux G. Active mesh and neural network pipeline for cell aggregate segmentation. Biophys J 2023; 122:1586-1599. [PMID: 37002604 PMCID: PMC10183373 DOI: 10.1016/j.bpj.2023.03.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 02/16/2023] [Accepted: 03/24/2023] [Indexed: 04/03/2023] Open
Abstract
Segmenting cells within cellular aggregates in 3D is a growing challenge in cell biology due to improvements in capacity and accuracy of microscopy techniques. Here, we describe a pipeline to segment images of cell aggregates in 3D. The pipeline combines neural network segmentations with active meshes. We apply our segmentation method to cultured mouse mammary gland organoids imaged over 24 h with oblique plane microscopy, a high-throughput light-sheet fluorescence microscopy technique. We show that our method can also be applied to images of mouse embryonic stem cells imaged with a spinning disc microscope. We segment individual cells based on nuclei and cell membrane fluorescent markers, and track cells over time. We describe metrics to quantify the quality of the automated segmentation. Our segmentation pipeline involves a Fiji plugin that implements active mesh deformation and allows a user to create training data, automatically obtain segmentation meshes from original image data or neural network prediction, and manually curate segmentation data to identify and correct mistakes. Our active meshes-based approach facilitates segmentation postprocessing, correction, and integration with neural network prediction.
Collapse
Affiliation(s)
| | - Hugh Sparks
- Photonics Group, Department of Physics, Imperial College London, London, United Kingdom
| | | | - Agathe Chaigne
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Axel Behrens
- Cancer Stem Cell Team, The Institute of Cancer Research, London, United Kingdom
| | - Chris Dunsby
- Photonics Group, Department of Physics, Imperial College London, London, United Kingdom
| | - Guillaume Salbreux
- The Francis Crick Institute, London, United Kingdom; Department of Genetics and Evolution, Geneva, Switzerland.
| |
Collapse
|
29
|
Nishida HY, Hamada K, Koshita M, Ohta Y, Nishida H. Ascidian gastrulation and blebbing activity of isolated endoderm blastomeres. Dev Biol 2023; 496:24-35. [PMID: 36702215 DOI: 10.1016/j.ydbio.2023.01.007] [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] [Received: 05/27/2022] [Revised: 01/16/2023] [Accepted: 01/20/2023] [Indexed: 01/24/2023]
Abstract
Gastrulation is the first dynamic cell movement during embryogenesis. Endoderm and mesoderm cells are internalized into embryos during this process. Ascidian embryos provide a simple system for studying gastrulation in chordates. Gastrulation starts in spherical late 64-cell embryos with 10 endoderm blastomeres. The mechanisms of gastrulation in ascidians have been investigated, and a two-step model has been proposed. The first step involves apical constriction of endoderm cells, followed by apicobasal shortening in the second step. In this study, isolated ascidian endoderm progenitor cells displayed dynamic blebbing activity at the gastrula stage, although such a dynamic cell-shape change was not recognized in toto. Blebbing is often observed in migrating animal cells. In ascidians, endoderm cells displayed blebbing activity, while mesoderm and ectoderm cells did not. The timing of blebbing of isolated endoderm cells coincided with that of cell invagination. The constriction rate of apical surfaces correlated with the intensity of blebbing activity in each endoderm-lineage cell. Fibroblast growth factor (FGF) signaling was both necessary and sufficient for inducing blebbing activity, independent of cell fate specification. In contrast, the timing of initiation of blebbing and intensity of blebbing response to FGF signaling were controlled by intrinsic cellular factors. It is likely that the difference in intensity of blebbing activity between the anterior A-line and posterior B-line cells could account for the anteroposterior difference in the steepness of the archenteron wall. Inhibition of zygotic transcription, FGF signaling, and Rho kinase, all of which suppressed blebbing activity, resulted in incomplete apical constriction and failure of the eventual formation of cup-shaped gastrulae. Blebbing activity was involved in the progression and maintenance of apical constriction, but not in apicobasal shortening in whole embryos. Apical constriction is mediated by distinct blebbing-dependent and blebbing-independent mechanisms. Surface tension and consequent membrane contraction may not be the sole mechanical force for apical constriction and formation of cup-shaped gastrulae. The present study reveals the hidden cellular potential of endodermal cells during gastrulation and discusses the possible roles of blebbing in the invagination process.
Collapse
Affiliation(s)
- Haruka Y Nishida
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
| | - Kaho Hamada
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
| | - Mika Koshita
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
| | - Yuki Ohta
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
| | - Hiroki Nishida
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan.
| |
Collapse
|
30
|
Gires PY, Thampi M, Krauss SW, Weiss M. Exploring generic principles of compartmentalization in a developmental in vitro model. Development 2023; 150:286676. [PMID: 36647820 DOI: 10.1242/dev.200851] [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: 04/14/2022] [Accepted: 01/03/2023] [Indexed: 01/18/2023]
Abstract
Self-organization of cells into higher-order structures is key for multicellular organisms, for example via repetitive replication of template-like founder cells or syncytial energids. Yet, very similar spatial arrangements of cell-like compartments ('protocells') are also seen in a minimal model system of Xenopus egg extracts in the absence of template structures and chromatin, with dynamic microtubule assemblies driving the self-organization process. Quantifying geometrical features over time, we show here that protocell patterns are highly organized with a spatial arrangement and coarsening dynamics similar to that of two-dimensional foams but without the long-range ordering expected for hexagonal patterns. These features remain invariant when enforcing smaller protocells by adding taxol, i.e. patterns are dominated by a single, microtubule-derived length scale. Comparing our data to generic models, we conclude that protocell patterns emerge by simultaneous formation of randomly assembling protocells that grow at a uniform rate towards a frustrated arrangement before fusion of adjacent protocells eventually drives coarsening. The similarity of protocell patterns to arrays of energids and cells in developing organisms, but also to epithelial monolayers, suggests generic mechanical cues to drive self-organized space compartmentalization.
Collapse
Affiliation(s)
- Pierre-Yves Gires
- Experimental Physics I, University of Bayreuth, Universitätsstrasse 30, D-95447 Bayreuth, Germany
| | - Mithun Thampi
- Experimental Physics I, University of Bayreuth, Universitätsstrasse 30, D-95447 Bayreuth, Germany
| | - Sebastian W Krauss
- Experimental Physics I, University of Bayreuth, Universitätsstrasse 30, D-95447 Bayreuth, Germany
| | - Matthias Weiss
- Experimental Physics I, University of Bayreuth, Universitätsstrasse 30, D-95447 Bayreuth, Germany
| |
Collapse
|
31
|
Bettoni R, Hudson C, Williaume G, Sirour C, Yasuo H, de Buyl S, Dupont G. Model of neural induction in the ascidian embryo. PLoS Comput Biol 2023; 19:e1010335. [PMID: 36735746 PMCID: PMC9931142 DOI: 10.1371/journal.pcbi.1010335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 02/15/2023] [Accepted: 01/17/2023] [Indexed: 02/04/2023] Open
Abstract
How cell specification can be controlled in a reproducible manner is a fundamental question in developmental biology. In ascidians, a group of invertebrate chordates, geometry plays a key role in achieving this control. Here, we use mathematical modeling to demonstrate that geometry dictates the neural-epidermal cell fate choice in the 32-cell stage ascidian embryo by a two-step process involving first the modulation of ERK signaling and second, the expression of the neural marker gene, Otx. The model describes signal transduction by the ERK pathway that is stimulated by FGF and attenuated by ephrin, and ERK-mediated control of Otx gene expression, which involves both an activator and a repressor of ETS-family transcription factors. Considering the measured area of cell surface contacts with FGF- or ephrin-expressing cells as inputs, the solutions of the model reproduce the experimental observations about ERK activation and Otx expression in the different cells under normal and perturbed conditions. Sensitivity analyses and computations of Hill coefficients allow us to quantify the robustness of the specification mechanism controlled by cell surface area and to identify the respective role played by each signaling input. Simulations also predict in which conditions the dual control of gene expression by an activator and a repressor that are both under the control of ERK can induce a robust ON/OFF control of neural fate induction.
Collapse
Affiliation(s)
- Rossana Bettoni
- Unité de Chronobiologie Théorique, Faculté des Sciences, CP231, Université Libre de Bruxelles (ULB), Boulevard du Triomphe, Brussels, Belgium
- Applied Physics Research Group, Vrije Universiteit Brussel, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, La Plaine Campus, Brussels, Belgium
| | - Clare Hudson
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche-sur-Mer, Sorbonne Université, CNRS, Villefranche-sur-Mer, France
| | - Géraldine Williaume
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche-sur-Mer, Sorbonne Université, CNRS, Villefranche-sur-Mer, France
| | - Cathy Sirour
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche-sur-Mer, Sorbonne Université, CNRS, Villefranche-sur-Mer, France
| | - Hitoyoshi Yasuo
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche-sur-Mer, Sorbonne Université, CNRS, Villefranche-sur-Mer, France
| | - Sophie de Buyl
- Applied Physics Research Group, Vrije Universiteit Brussel, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, La Plaine Campus, Brussels, Belgium
| | - Geneviève Dupont
- Unité de Chronobiologie Théorique, Faculté des Sciences, CP231, Université Libre de Bruxelles (ULB), Boulevard du Triomphe, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, La Plaine Campus, Brussels, Belgium
| |
Collapse
|
32
|
Treen N, Chavarria E, Weaver CJ, Brangwynne CP, Levine M. An FGF timer for zygotic genome activation. Genes Dev 2023; 37:80-85. [PMID: 36801820 PMCID: PMC10069452 DOI: 10.1101/gad.350164.122] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 01/19/2023] [Indexed: 02/19/2023]
Abstract
Zygotic genome activation has been extensively studied in a variety of systems including flies, frogs, and mammals. However, there is comparatively little known about the precise timing of gene induction during the earliest phases of embryogenesis. Here we used high-resolution in situ detection methods, along with genetic and experimental manipulations, to study the timing of zygotic activation in the simple model chordate Ciona with minute-scale temporal precision. We found that two Prdm1 homologs in Ciona are the earliest genes that respond to FGF signaling. We present evidence for a FGF timing mechanism that is driven by ERK-mediated derepression of the ERF repressor. Depletion of ERF results in ectopic activation of FGF target genes throughout the embryo. A highlight of this timer is the sharp transition in FGF responsiveness between the eight- and 16-cell stages of development. We propose that this timer is an innovation of chordates that is also used by vertebrates.
Collapse
Affiliation(s)
- Nicholas Treen
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA;
| | - Emily Chavarria
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - Claire J Weaver
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - Clifford P Brangwynne
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Michael Levine
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| |
Collapse
|
33
|
Azuma Y, Okada H, Onami S. Systematic analysis of cell morphodynamics in C. elegans early embryogenesis. FRONTIERS IN BIOINFORMATICS 2023; 3:1082531. [PMID: 37026092 PMCID: PMC10070942 DOI: 10.3389/fbinf.2023.1082531] [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: 10/28/2022] [Accepted: 03/07/2023] [Indexed: 04/08/2023] Open
Abstract
The invariant cell lineage of Caenorhabditis elegans allows unambiguous assignment of the identity for each cell, which offers a unique opportunity to study developmental dynamics such as the timing of cell division, dynamics of gene expression, and cell fate decisions at single-cell resolution. However, little is known about cell morphodynamics, including the extent to which they are variable between individuals, mainly due to the lack of sufficient amount and quality of quantified data. In this study, we systematically quantified the cell morphodynamics in 52 C. elegans embryos from the two-cell stage to mid-gastrulation at the high spatiotemporal resolution, 0.5 μm thickness of optical sections, and 30-second intervals of recordings. Our data allowed systematic analyses of the morphological features. We analyzed sphericity dynamics and found a significant increase at the end of metaphase in every cell, indicating the universality of the mitotic cell rounding. Concomitant with the rounding, the volume also increased in most but not all cells, suggesting less universality of the mitotic swelling. Combining all features showed that cell morphodynamics was unique for each cell type. The cells before the onset of gastrulation could be distinguished from all the other cell types. Quantification of reproducibility in cell-cell contact revealed that variability in division timings and cell arrangements produced variability in contacts between the embryos. However, the area of such contacts occupied less than 5% of the total area, suggesting the high reproducibility of spatial occupancies and adjacency relationships of the cells. By comparing the morphodynamics of identical cells between the embryos, we observed diversity in the variability between cells and found it was determined by multiple factors, including cell lineage, cell generation, and cell-cell contact. We compared the variabilities of cell morphodynamics and cell-cell contacts with those in ascidian Phallusia mammillata embryos. The variabilities were larger in C. elegans, despite smaller differences in embryo size and number of cells at each developmental stage.
Collapse
|
34
|
Laruelle E, Belcram K, Trubuil A, Palauqui JC, Andrey P. Large-scale analysis and computer modeling reveal hidden regularities behind variability of cell division patterns in Arabidopsis thaliana embryogenesis. eLife 2022; 11:79224. [DOI: 10.7554/elife.79224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 11/07/2022] [Indexed: 11/30/2022] Open
Abstract
Noise plays a major role in cellular processes and in the development of tissues and organs. Several studies have examined the origin, the integration or the accommodation of noise in gene expression, cell growth and elaboration of organ shape. By contrast, much less is known about variability in cell division plane positioning, its origin and links with cell geometry, and its impact on tissue organization. Taking advantage of the first-stereotyped-then-variable division patterns in the embryo of the model plant Arabidopsis thaliana, we combined 3D imaging and quantitative cell shape and cell lineage analysis together with mathematical and computer modeling to perform a large-scale, systematic analysis of variability in division plane orientation. Our results reveal that, paradoxically, variability in cell division patterns of Arabidopsis embryos is accompanied by a progressive reduction of heterogeneity in cell shape topology. The paradox is solved by showing that variability operates within a reduced repertoire of possible division plane orientations that is related to cell geometry. We show that in several domains of the embryo, a recently proposed geometrical division rule recapitulates observed variable patterns, suggesting that variable patterns emerge from deterministic principles operating in a variable geometrical context. Our work highlights the importance of emerging patterns in the plant embryo under iterated division principles, but also reveal domains where deviations between rule predictions and experimental observations point to additional regulatory mechanisms.
Collapse
Affiliation(s)
- Elise Laruelle
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin
- Université Paris-Saclay, INRAE, MaIAGE
| | - Katia Belcram
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin
| | | | | | - Philippe Andrey
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin
| |
Collapse
|
35
|
Pentinmikko N, Lozano R, Scharaw S, Andersson S, Englund JI, Castillo-Azofeifa D, Gallagher A, Broberg M, Song KY, Sola Carvajal A, Speidel AT, Sundstrom M, Allbritton N, Stevens MM, Klein OD, Teixeira A, Katajisto P. Cellular shape reinforces niche to stem cell signaling in the small intestine. SCIENCE ADVANCES 2022; 8:eabm1847. [PMID: 36240269 PMCID: PMC9565803 DOI: 10.1126/sciadv.abm1847] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 08/30/2022] [Indexed: 06/06/2023]
Abstract
Niche-derived factors regulate tissue stem cells, but apart from the mechanosensory pathways, the effect of niche geometry is not well understood. We used organoids and bioengineered tissue culture platforms to demonstrate that the conical shape of Lgr5+ small intestinal stem cells (ISCs) facilitate their self-renewal and function. Inhibition of non-muscle myosin II (NM II)-driven apical constriction altered ISC shape and reduced niche curvature and stem cell capacity. Niche curvature is decreased in aged mice, suggesting that suboptimal interactions between old ISCs and their niche develop with age. We show that activation of NM IIC or physical restriction to young topology improves in vitro regeneration by old epithelium. We propose that the increase in lateral surface area of ISCs induced by apical constriction promotes interactions between neighboring cells, and the curved topology of the intestinal niche has evolved to maximize signaling between ISCs and neighboring cells.
Collapse
Affiliation(s)
- Nalle Pentinmikko
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Rodrigo Lozano
- Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Stockholm, Sweden
- Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet, and Karolinska University Hospital, Stockholm, Sweden
| | - Sandra Scharaw
- Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Stockholm, Sweden
| | - Simon Andersson
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Johanna I. Englund
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - David Castillo-Azofeifa
- Department of Orofacial Sciences and Program in Craniofacial Biology, University of California, San Francisco, San Francisco, CA, USA
- Immunology Discovery, Genentech Inc., South San Francisco, CA, USA
| | - Aaron Gallagher
- Department of Orofacial Sciences and Program in Craniofacial Biology, University of California, San Francisco, San Francisco, CA, USA
| | - Martin Broberg
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Ki-Young Song
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Agustín Sola Carvajal
- Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Stockholm, Sweden
| | - Alessondra T. Speidel
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Michael Sundstrom
- Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet, and Karolinska University Hospital, Stockholm, Sweden
| | - Nancy Allbritton
- University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Molly M. Stevens
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Department of Materials and Department of Bioengineering, Imperial College London, UK
| | - Ophir D. Klein
- Department of Orofacial Sciences and Program in Craniofacial Biology, University of California, San Francisco, San Francisco, CA, USA
- Department of Pediatrics and Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ana Teixeira
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Pekka Katajisto
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
- Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Stockholm, Sweden
- Molecular and Integrative Bioscience Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| |
Collapse
|
36
|
Barone V, Lyons DC. Live imaging of echinoderm embryos to illuminate evo-devo. Front Cell Dev Biol 2022; 10:1007775. [PMID: 36187474 PMCID: PMC9521734 DOI: 10.3389/fcell.2022.1007775] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022] Open
Abstract
Echinoderm embryos have been model systems for cell and developmental biology for over 150 years, in good part because of their optical clarity. Discoveries that shaped our understanding of fertilization, cell division and cell differentiation were only possible because of the transparency of sea urchin eggs and embryos, which allowed direct observations of intracellular structures. More recently, live imaging of sea urchin embryos, coupled with fluorescence microscopy, has proven pivotal to uncovering mechanisms of epithelial to mesenchymal transition, cell migration and gastrulation. However, live imaging has mainly been performed on sea urchin embryos, while echinoderms include numerous experimentally tractable species that present interesting variation in key aspects of morphogenesis, including differences in embryo compaction and mechanisms of blastula formation. The study of such variation would allow us not only to understand how tissues are formed in echinoderms, but also to identify which changes in cell shape, cell-matrix and cell-cell contact formation are more likely to result in evolution of new embryonic shapes. Here we argue that adapting live imaging techniques to more echinoderm species will be fundamental to exploit such an evolutionary approach to the study of morphogenesis, as it will allow measuring differences in dynamic cellular behaviors - such as changes in cell shape and cell adhesion - between species. We briefly review existing methods for live imaging of echinoderm embryos and describe in detail how we adapted those methods to allow long-term live imaging of several species, namely the sea urchin Lytechinus pictus and the sea stars Patiria miniata and Patiriella regularis. We outline procedures to successfully label, mount and image early embryos for 10-16 h, from cleavage stages to early blastula. We show that data obtained with these methods allows 3D segmentation and tracking of individual cells over time, the first step to analyze how cell shape and cell contact differ among species. The methods presented here can be easily adopted by most cell and developmental biology laboratories and adapted to successfully image early embryos of additional species, therefore broadening our understanding of the evolution of morphogenesis.
Collapse
Affiliation(s)
- Vanessa Barone
- Center for Marine Biotechnology and Biomedicine, University of California, San Diego, La Jolla, CA, United States
| | - Deirdre C. Lyons
- Center for Marine Biotechnology and Biomedicine, University of California, San Diego, La Jolla, CA, United States
| |
Collapse
|
37
|
Guan G, Zhao Z, Tang C. Delineating the mechanisms and design principles of Caenorhabditis elegans embryogenesis using in toto high-resolution imaging data and computational modeling. Comput Struct Biotechnol J 2022; 20:5500-5515. [PMID: 36284714 PMCID: PMC9562942 DOI: 10.1016/j.csbj.2022.08.024] [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: 04/26/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 11/19/2022] Open
Abstract
The nematode (roundworm) Caenorhabditis elegans is one of the most popular animal models for the study of developmental biology, as its invariant development and transparent body enable in toto cellular-resolution fluorescence microscopy imaging of developmental processes at 1-min intervals. This has led to the development of various computational tools for the systematic and automated analysis of imaging data to delineate the molecular and cellular processes throughout the embryogenesis of C. elegans, such as those associated with cell lineage, cell migration, cell morphology, and gene activity. In this review, we first introduce C. elegans embryogenesis and the development of techniques for tracking cell lineage and reconstructing cell morphology during this process. We then contrast the developmental modes of C. elegans and the customized technologies used for studying them with the ones of other animal models, highlighting its advantage for studying embryogenesis with exceptional spatial and temporal resolution. This is followed by an examination of the physical models that have been devised-based on accurate determinations of developmental processes afforded by analyses of imaging data-to interpret the early embryonic development of C. elegans from subcellular to intercellular levels of multiple cells, which focus on two key processes: cell polarization and morphogenesis. We subsequently discuss how quantitative data-based theoretical modeling has improved our understanding of the mechanisms of C. elegans embryogenesis. We conclude by summarizing the challenges associated with the acquisition of C. elegans embryogenesis data, the construction of algorithms to analyze them, and the theoretical interpretation.
Collapse
Affiliation(s)
- Guoye Guan
- Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Zhongying Zhao
- Department of Biology, Hong Kong Baptist University, Hong Kong 999077, China
- State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong 999077, China
| | - Chao Tang
- Center for Quantitative Biology, Peking University, Beijing 100871, China
- Peking–Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- School of Physics, Peking University, Beijing 100871, China
| |
Collapse
|
38
|
Gómez-Gálvez P, Vicente-Munuera P, Anbari S, Tagua A, Gordillo-Vázquez C, Andrés-San Román JA, Franco-Barranco D, Palacios AM, Velasco A, Capitán-Agudo C, Grima C, Annese V, Arganda-Carreras I, Robles R, Márquez A, Buceta J, Escudero LM. A quantitative biophysical principle to explain the 3D cellular connectivity in curved epithelia. Cell Syst 2022; 13:631-643.e8. [PMID: 35835108 DOI: 10.1016/j.cels.2022.06.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 02/15/2022] [Accepted: 06/15/2022] [Indexed: 01/26/2023]
Abstract
Epithelial cell organization and the mechanical stability of tissues are closely related. In this context, it has been recently shown that packing optimization in bended or folded epithelia is achieved by an energy minimization mechanism that leads to a complex cellular shape: the "scutoid". Here, we focus on the relationship between this shape and the connectivity between cells. We use a combination of computational, experimental, and biophysical approaches to examine how energy drivers affect the three-dimensional (3D) packing of tubular epithelia. We propose an energy-based stochastic model that explains the 3D cellular connectivity. Then, we challenge it by experimentally reducing the cell adhesion. As a result, we observed an increment in the appearance of scutoids that correlated with a decrease in the energy barrier necessary to connect with new cells. We conclude that tubular epithelia satisfy a quantitative biophysical principle that links tissue geometry and energetics with the average cellular connectivity.
Collapse
Affiliation(s)
- Pedro Gómez-Gálvez
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Universidad de Sevilla, 41013 Seville, Spain; Biomedical Network Research Centre on Neurodegenerative Diseases (CIBERNED), Madrid, Spain.
| | - Pablo Vicente-Munuera
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Universidad de Sevilla, 41013 Seville, Spain; Biomedical Network Research Centre on Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Samira Anbari
- Chemical and Biomolecular Engineering Department, Lehigh University, Bethlehem, PA 18018, USA
| | - Antonio Tagua
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Universidad de Sevilla, 41013 Seville, Spain; Biomedical Network Research Centre on Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Carmen Gordillo-Vázquez
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Universidad de Sevilla, 41013 Seville, Spain; Biomedical Network Research Centre on Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Jesús A Andrés-San Román
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Universidad de Sevilla, 41013 Seville, Spain; Biomedical Network Research Centre on Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Daniel Franco-Barranco
- Department of Computer Science and Artificial Intelligence, University of the Basque Country (UPV/EHU), San Sebastian, Spain; Donostia International Physics Center (DIPC), San Sebastian, Spain
| | - Ana M Palacios
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Universidad de Sevilla, 41013 Seville, Spain; Biomedical Network Research Centre on Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Antonio Velasco
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Universidad de Sevilla, 41013 Seville, Spain
| | - Carlos Capitán-Agudo
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Universidad de Sevilla, 41013 Seville, Spain
| | - Clara Grima
- Departamento de Matemática Aplicada I, Universidad de Sevilla, Seville 41012, Spain
| | - Valentina Annese
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Universidad de Sevilla, 41013 Seville, Spain; Biomedical Network Research Centre on Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Ignacio Arganda-Carreras
- Department of Computer Science and Artificial Intelligence, University of the Basque Country (UPV/EHU), San Sebastian, Spain; Donostia International Physics Center (DIPC), San Sebastian, Spain; Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Rafael Robles
- Departamento de Matemática Aplicada I, Universidad de Sevilla, Seville 41012, Spain
| | - Alberto Márquez
- Departamento de Matemática Aplicada I, Universidad de Sevilla, Seville 41012, Spain
| | - Javier Buceta
- Institute for Integrative Systems Biology (I2SysBio), CSIC-UV, Paterna 46980, Spain.
| | - Luis M Escudero
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Universidad de Sevilla, 41013 Seville, Spain; Biomedical Network Research Centre on Neurodegenerative Diseases (CIBERNED), Madrid, Spain.
| |
Collapse
|
39
|
Fierling J, John A, Delorme B, Torzynski A, Blanchard GB, Lye CM, Popkova A, Malandain G, Sanson B, Étienne J, Marmottant P, Quilliet C, Rauzi M. Embryo-scale epithelial buckling forms a propagating furrow that initiates gastrulation. Nat Commun 2022; 13:3348. [PMID: 35688832 PMCID: PMC9187723 DOI: 10.1038/s41467-022-30493-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 05/04/2022] [Indexed: 11/26/2022] Open
Abstract
Cell apical constriction driven by actomyosin contraction forces is a conserved mechanism during tissue folding in embryo development. While much is now understood of the molecular mechanism responsible for apical constriction and of the tissue-scale integration of the ensuing in-plane deformations, it is still not clear if apical actomyosin contraction forces are necessary or sufficient per se to drive tissue folding. To tackle this question, we use the Drosophila embryo model system that forms a furrow on the ventral side, initiating mesoderm internalization. Past computational models support the idea that cell apical contraction forces may not be sufficient and that active or passive cell apico-basal forces may be necessary to drive cell wedging leading to tissue furrowing. By using 3D computational modelling and in toto embryo image analysis and manipulation, we now challenge this idea and show that embryo-scale force balance at the tissue surface, rather than cell-autonomous shape changes, is necessary and sufficient to drive a buckling of the epithelial surface forming a furrow which propagates and initiates embryo gastrulation. Drosophila mesoderm invagination begins with the formation of a furrow. Here they show that a long-range mechanism, powered by actomyosin contraction between the embryo polar caps, works like a ‘cheese-cutter wire’ indenting the tissue surface and folding it into a propagating furrow.
Collapse
Affiliation(s)
| | - Alphy John
- Université Côte d'Azur, CNRS, Inserm, iBV, Nice, France
| | | | | | - Guy B Blanchard
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, Great-Britain, England
| | - Claire M Lye
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, Great-Britain, England
| | - Anna Popkova
- Université Côte d'Azur, CNRS, Inserm, iBV, Nice, France
| | | | - Bénédicte Sanson
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, Great-Britain, England
| | | | | | | | - Matteo Rauzi
- Université Côte d'Azur, CNRS, Inserm, iBV, Nice, France.
| |
Collapse
|
40
|
Reddy GA, Katira P. Differences in cell death and division rules can alter tissue rigidity and fluidization. SOFT MATTER 2022; 18:3713-3724. [PMID: 35502875 DOI: 10.1039/d2sm00174h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Tissue mechanical properties such as rigidity and fluidity, and changes in these properties driven by jamming-unjamming transitions (UJT), have come under recent highlight as mechanical markers of health and disease in various biological processes including cancer. However, most analyses of these mechanical properties and UJT have sidestepped the effect of cellular death and division in these systems. Cellular apoptosis (programmed cell death) and mitosis (cell division) can drive significant changes in tissue properties. The balance between the two is crucial in maintaining tissue function, and an imbalance between the two is seen in situations such as cancer progression, wound healing and necrosis. In this work we investigate the impact of cell death and division on tissue mechanical properties, by incorporating specific mechanosensitive triggers of cell death and division based on the size and geometry of the cell within in silico models of tissue dynamics. Specifically, we look at cell migration, tissue response to external stress, tissue extrusion propensity and self-organization of different cell types within the tissue, as a function of cell death and division and the rules that trigger these events. We find that not only do cell death and division events significantly alter tissue mechanics when compared to systems without these events, but that the choice of triggers driving these cell death and division events also alters the predicted tissue mechanics and overall system behavior.
Collapse
Affiliation(s)
- Gudur Ashrith Reddy
- Mechanical Engineering Department, San Diego State University, San Diego, CA, USA.
- Department of Bioengineering, University of California - San Diego, San Diego, CA, USA
| | - Parag Katira
- Mechanical Engineering Department, San Diego State University, San Diego, CA, USA.
- Computational Science Research Center, San Diego State University, San Diego, CA, USA
| |
Collapse
|
41
|
Fulton T, Verd B, Steventon B. The unappreciated generative role of cell movements in pattern formation. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211293. [PMID: 35601454 PMCID: PMC9043703 DOI: 10.1098/rsos.211293] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 04/05/2022] [Indexed: 06/15/2023]
Abstract
The mechanisms underpinning the formation of patterned cellular landscapes has been the subject of extensive study as a fundamental problem of developmental biology. In most cases, attention has been given to situations in which cell movements are negligible, allowing researchers to focus on the cell-extrinsic signalling mechanisms, and intrinsic gene regulatory interactions that lead to pattern emergence at the tissue level. However, in many scenarios during development, cells rapidly change their neighbour relationships in order to drive tissue morphogenesis, while also undergoing patterning. To draw attention to the ubiquity of this problem and propose methodologies that will accommodate morphogenesis into the study of pattern formation, we review the current approaches to studying pattern formation in both static and motile cellular environments. We then consider how the cell movements themselves may contribute to the generation of pattern, rather than hinder it, with both a species specific and evolutionary viewpoint.
Collapse
Affiliation(s)
- Timothy Fulton
- Department of Genetics, University of Cambridge, Cambridge, UK
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Berta Verd
- Department of Genetics, University of Cambridge, Cambridge, UK
- Department of Zoology, University of Oxford, Oxford, UK
| | | |
Collapse
|
42
|
Kar A, Petit M, Refahi Y, Cerutti G, Godin C, Traas J. Benchmarking of deep learning algorithms for 3D instance segmentation of confocal image datasets. PLoS Comput Biol 2022; 18:e1009879. [PMID: 35421081 PMCID: PMC9009699 DOI: 10.1371/journal.pcbi.1009879] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Segmenting three-dimensional (3D) microscopy images is essential for understanding phenomena like morphogenesis, cell division, cellular growth, and genetic expression patterns. Recently, deep learning (DL) pipelines have been developed, which claim to provide high accuracy segmentation of cellular images and are increasingly considered as the state of the art for image segmentation problems. However, it remains difficult to define their relative performances as the concurrent diversity and lack of uniform evaluation strategies makes it difficult to know how their results compare. In this paper, we first made an inventory of the available DL methods for 3D cell segmentation. We next implemented and quantitatively compared a number of representative DL pipelines, alongside a highly efficient non-DL method named MARS. The DL methods were trained on a common dataset of 3D cellular confocal microscopy images. Their segmentation accuracies were also tested in the presence of different image artifacts. A specific method for segmentation quality evaluation was adopted, which isolates segmentation errors due to under- or oversegmentation. This is complemented with a 3D visualization strategy for interactive exploration of segmentation quality. Our analysis shows that the DL pipelines have different levels of accuracy. Two of them, which are end-to-end 3D and were originally designed for cell boundary detection, show high performance and offer clear advantages in terms of adaptability to new data.
Collapse
Affiliation(s)
- Anuradha Kar
- Laboratoire RDP, Université de Lyon 1, ENS-Lyon INRAE, INRIA, CNRS, UCBL, Lyon, France
- Institut du Cerveau–Paris Brain Institute, Paris, France
| | - Manuel Petit
- Laboratoire RDP, Université de Lyon 1, ENS-Lyon INRAE, INRIA, CNRS, UCBL, Lyon, France
| | - Yassin Refahi
- Université de Reims Champagne Ardenne, INRAE, FARE, UMR A 614, Reims, France
| | - Guillaume Cerutti
- Laboratoire RDP, Université de Lyon 1, ENS-Lyon INRAE, INRIA, CNRS, UCBL, Lyon, France
| | - Christophe Godin
- Laboratoire RDP, Université de Lyon 1, ENS-Lyon INRAE, INRIA, CNRS, UCBL, Lyon, France
| | - Jan Traas
- Laboratoire RDP, Université de Lyon 1, ENS-Lyon INRAE, INRIA, CNRS, UCBL, Lyon, France
| |
Collapse
|
43
|
Flom H, Adamska M, Lami R, Gazave E, D'Aniello S, Schierwater B, Boutet A. Digital Marine: An online platform for blended learning in a marine experimental biology module, the Schmid Training Course. Bioessays 2022; 44:e2100264. [DOI: 10.1002/bies.202100264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 02/25/2022] [Accepted: 03/02/2022] [Indexed: 11/12/2022]
Affiliation(s)
- Haley Flom
- Sorbonne Université (SU) Centre National de la Recherche Scientifique (CNRS) Fédération de Recherche FR3724 Observatoire Océanologique de Banyuls‐sur‐Mer (OOB) France
| | - Maja Adamska
- Research School of Biology Australian National University (ANU) Canberra Australia
| | - Raphaël Lami
- Sorbonne Université CNRS Laboratoire de Biodiversité et Biotechnologies Microbiennes USR3579 Observatoire Océanologique de Banyuls‐sur‐Mer (OOB) France
| | - Eve Gazave
- Université de Paris CNRS Institut Jacques Monod Paris France
| | - Salvatore D'Aniello
- Department of Biology and Evolution of Marine Organisms (BEOM) Stazione Zoologica Anton Dohrn Napoli Italy
| | | | - Agnès Boutet
- SU, CNRS Integrative Biology of Marine Models (LBI2M) France
| |
Collapse
|
44
|
ERK signaling dissolves ERF repression condensates in living embryos. Proc Natl Acad Sci U S A 2022; 119:2119187119. [PMID: 35217620 PMCID: PMC8892517 DOI: 10.1073/pnas.2119187119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2022] [Indexed: 12/23/2022] Open
Abstract
Phase separation underlies the organization of the nucleus, including the biogenesis of nucleoli and the packaging of heterochromatin. Here we explore the regulation of transcription factor condensates involved in gene repression by ERK signaling in gastrulating embryos of a simple proto-vertebrate (Ciona). ERK signaling induces nuclear export of the transcriptional repressor Ets-2 repressive factor (ERF), which has been linked to various human developmental disorders. Using high-resolution imaging, we show that ERF is localized within discrete nuclear condensates that dissolve upon ERK activation. Interestingly, we observe dynamic pulses of assembly and dissociation during interphase, providing visualization of a nuclear phase separation process regulated by cell signaling. We discuss the implications of these observations for producing sharp on/off switches in gene activity and suppressing noise in cell-cell signaling events.
Collapse
|
45
|
Fiúza UM, Lemaire P. Methods for the Study of Apical Constriction During Ascidian Gastrulation. Methods Mol Biol 2022; 2438:377-413. [PMID: 35147954 DOI: 10.1007/978-1-0716-2035-9_23] [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: 06/14/2023]
Abstract
Gastrulation is the first major morphogenetic event during ascidian embryogenesis. Ascidian gastrulation begins with the invagination of the endodermal progenitors, a two-step process driven by individual cell shape changes of endoderm cells. During the first step, endoderm cells constrict apically, thereby flattening the vegetal side of the embryo. During the second step, endoderm cells shorten along their apicobasal axis and tissue invagination ensues. Individual cell shape changes are mediated by localized actomyosin contractile activity. Here, we describe methods used during ascidian endoderm apical constriction to study myosin activity and cellular morphodynamics with confocal and light sheet microscopy and followed by quantitative image analysis.
Collapse
Affiliation(s)
- Ulla-Maj Fiúza
- Systems Bioengineering, DCEXS Universidad Pompeu Fabra, Barcelona, Spain.
| | | |
Collapse
|
46
|
Dissecting the Complexity of Early Heart Progenitor Cells. J Cardiovasc Dev Dis 2021; 9:jcdd9010005. [PMID: 35050215 PMCID: PMC8779398 DOI: 10.3390/jcdd9010005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/17/2021] [Accepted: 12/22/2021] [Indexed: 12/23/2022] Open
Abstract
Early heart development depends on the coordinated participation of heterogeneous cell sources. As pioneer work from Adriana C. Gittenberger-de Groot demonstrated, characterizing these distinct cell sources helps us to understand congenital heart defects. Despite decades of research on the segregation of lineages that form the primitive heart tube, we are far from understanding its full complexity. Currently, single-cell approaches are providing an unprecedented level of detail on cellular heterogeneity, offering new opportunities to decipher its functional role. In this review, we will focus on three key aspects of early heart morphogenesis: First, the segregation of myocardial and endocardial lineages, which yields an early lineage diversification in cardiac development; second, the signaling cues driving differentiation in these progenitor cells; and third, the transcriptional heterogeneity of cardiomyocyte progenitors of the primitive heart tube. Finally, we discuss how single-cell transcriptomics and epigenomics, together with live imaging and functional analyses, will likely transform the way we delve into the complexity of cardiac development and its links with congenital defects.
Collapse
|
47
|
Funakoshi HM, Shito TT, Oka K, Hotta K. Developmental Table and Three-Dimensional Embryological Image Resource of the Ascidian Ascidiella aspersa. Front Cell Dev Biol 2021; 9:789046. [PMID: 34977032 PMCID: PMC8718802 DOI: 10.3389/fcell.2021.789046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 11/29/2021] [Indexed: 11/13/2022] Open
Abstract
Ascidiella aspersa is an ascidian in the class of chordates—the closest relatives of vertebrates. A. aspersa is a potential model organism for bio-imaging studies due to its extremely transparent embryos as well as is a globally distributed cosmopolitan species. However, there is no standard developmental table for this organism. Here, as a first step to establish A. aspersa as a model organism, we report a standard developmental table as a web-based digital image resource. This resource used confocal laser scanning microscopy to scan more than 3,000 cross-sectional images and 3D-reconstructed images of A. aspersa embryos during embryogenesis. With reference to the standardized developmental table of Ciona intestinalis type A, 26 different developmental stages (Stages 1–26) from fertilized eggs to hatched larvae were redefined for A. aspersa. Cell lineages up to the cleavage period were annotated: The cleavage patterns, the embryonic morphology, and the developmental time were then compared with Ciona. We found that the cleavage patterns and developmental time up to the neurula period in A. aspersa were extremely conserved versus. Ciona. The ratio of the trunk and tail length in the tailbud period were smaller than Ciona indicating a relatively short tail. In addition, the timing of the bending of the tail is earlier than Ciona. This A. aspersa standard 3D digital resource is essential for connecting different omics data to different spatiotemporal hierarchies and is useful for a system-level understanding of chordate development and evolution.
Collapse
Affiliation(s)
- Haruka M. Funakoshi
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Japan
| | - Takumi T. Shito
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Japan
| | - Kotaro Oka
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Japan
- Waseda Research Institute for Science and Engineering, Waseda University, Shinjuku, Japan
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung City, Taiwan
| | - Kohji Hotta
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, Yokohama, Japan
- *Correspondence: Kohji Hotta,
| |
Collapse
|
48
|
Tan S, Huan P, Liu B. Molluscan dorsal-ventral patterning relying on BMP2/4 and Chordin provides insights into spiralian development and evolution. Mol Biol Evol 2021; 39:6424002. [PMID: 34751376 PMCID: PMC8789067 DOI: 10.1093/molbev/msab322] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although a conserved mechanism relying on BMP2/4 and Chordin is suggested for animal dorsal–ventral (DV) patterning, this mechanism has not been reported in spiralians, one of the three major clades of bilaterians. Studies on limited spiralian representatives have suggested markedly diverse DV patterning mechanisms, a considerable number of which no longer deploy BMP signaling. Here, we showed that BMP2/4 and Chordin regulate DV patterning in the mollusk Lottia goshimai, which was predicted in spiralians but not previously reported. In the context of the diverse reports in spiralians, it conversely represents a relatively unusual case. We showed that BMP2/4 and Chordin coordinate to mediate signaling from the D-quadrant organizer to induce the DV axis, and Chordin relays the symmetry-breaking information from the organizer. Further investigations on L. goshimai embryos with impaired DV patterning suggested roles of BMP signaling in regulating the behavior of the blastopore and the organization of the nervous system. These findings provide insights into the evolution of animal DV patterning and the unique development mode of spiralians driven by the D-quadrant organizer.
Collapse
Affiliation(s)
- Sujian Tan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266000, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Pin Huan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266000, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Baozhong Liu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266000, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| |
Collapse
|
49
|
Williaume G, de Buyl S, Sirour C, Haupaix N, Bettoni R, Imai KS, Satou Y, Dupont G, Hudson C, Yasuo H. Cell geometry, signal dampening, and a bimodal transcriptional response underlie the spatial precision of an ERK-mediated embryonic induction. Dev Cell 2021; 56:2966-2979.e10. [PMID: 34672970 DOI: 10.1016/j.devcel.2021.09.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 07/16/2021] [Accepted: 09/24/2021] [Indexed: 12/13/2022]
Abstract
Precise control of lineage segregation is critical for the development of multicellular organisms, but our quantitative understanding of how variable signaling inputs are integrated to activate lineage-specific gene programs remains limited. Here, we show how precisely two out of eight ectoderm cells adopt neural fates in response to ephrin and FGF signals during ascidian neural induction. In each ectoderm cell, FGF signals activate ERK to a level that mirrors its cell contact surface with FGF-expressing mesendoderm cells. This gradual interpretation of FGF inputs is followed by a bimodal transcriptional response of the immediate early gene, Otx, resulting in its activation specifically in the neural precursors. At low levels of ERK, Otx is repressed by an ETS family transcriptional repressor, ERF2. Ephrin signals are critical for dampening ERK activation levels across ectoderm cells so that only neural precursors exhibit above-threshold levels, evade ERF repression, and "switch on" Otx transcription.
Collapse
Affiliation(s)
- Géraldine Williaume
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche-sur-Mer, Sorbonne Université, CNRS, 06230 Villefranche-sur-Mer, France
| | - Sophie de Buyl
- Applied Physics Research Group, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, La Plaine Campus, 1050 Brussels, Belgium
| | - Cathy Sirour
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche-sur-Mer, Sorbonne Université, CNRS, 06230 Villefranche-sur-Mer, France
| | - Nicolas Haupaix
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche-sur-Mer, Sorbonne Université, CNRS, 06230 Villefranche-sur-Mer, France
| | - Rossana Bettoni
- Applied Physics Research Group, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, La Plaine Campus, 1050 Brussels, Belgium; Unité de Chronobiologie Théorique, Faculté des Sciences, CP231, Université Libre de Bruxelles (ULB), Boulevard du Triomphe, 1050 Brussels, Belgium
| | - Kaoru S Imai
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Yutaka Satou
- Department of Zoology, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Geneviève Dupont
- Unité de Chronobiologie Théorique, Faculté des Sciences, CP231, Université Libre de Bruxelles (ULB), Boulevard du Triomphe, 1050 Brussels, Belgium.
| | - Clare Hudson
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche-sur-Mer, Sorbonne Université, CNRS, 06230 Villefranche-sur-Mer, France.
| | - Hitoyoshi Yasuo
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche-sur-Mer, Sorbonne Université, CNRS, 06230 Villefranche-sur-Mer, France.
| |
Collapse
|
50
|
Özpolat BD, Randel N, Williams EA, Bezares-Calderón LA, Andreatta G, Balavoine G, Bertucci PY, Ferrier DEK, Gambi MC, Gazave E, Handberg-Thorsager M, Hardege J, Hird C, Hsieh YW, Hui J, Mutemi KN, Schneider SQ, Simakov O, Vergara HM, Vervoort M, Jékely G, Tessmar-Raible K, Raible F, Arendt D. The Nereid on the rise: Platynereis as a model system. EvoDevo 2021; 12:10. [PMID: 34579780 PMCID: PMC8477482 DOI: 10.1186/s13227-021-00180-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 08/20/2021] [Indexed: 01/02/2023] Open
Abstract
The Nereid Platynereis dumerilii (Audouin and Milne Edwards (Annales des Sciences Naturelles 1:195-269, 1833) is a marine annelid that belongs to the Nereididae, a family of errant polychaete worms. The Nereid shows a pelago-benthic life cycle: as a general characteristic for the superphylum of Lophotrochozoa/Spiralia, it has spirally cleaving embryos developing into swimming trochophore larvae. The larvae then metamorphose into benthic worms living in self-spun tubes on macroalgae. Platynereis is used as a model for genetics, regeneration, reproduction biology, development, evolution, chronobiology, neurobiology, ecology, ecotoxicology, and most recently also for connectomics and single-cell genomics. Research on the Nereid started with studies on eye development and spiralian embryogenesis in the nineteenth and early twentieth centuries. Transitioning into the molecular era, Platynereis research focused on posterior growth and regeneration, neuroendocrinology, circadian and lunar cycles, fertilization, and oocyte maturation. Other work covered segmentation, photoreceptors and other sensory cells, nephridia, and population dynamics. Most recently, the unique advantages of the Nereid young worm for whole-body volume electron microscopy and single-cell sequencing became apparent, enabling the tracing of all neurons in its rope-ladder-like central nervous system, and the construction of multimodal cellular atlases. Here, we provide an overview of current topics and methodologies for P. dumerilii, with the aim of stimulating further interest into our unique model and expanding the active and vibrant Platynereis community.
Collapse
Affiliation(s)
- B. Duygu Özpolat
- Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA 02543 USA
| | - Nadine Randel
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ UK
| | - Elizabeth A. Williams
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | | | - Gabriele Andreatta
- Max Perutz Labs, University of Vienna, Dr. Bohr-Gasse 9/4, 1030 Vienna, Austria
| | - Guillaume Balavoine
- Institut Jacques Monod, University of Paris/CNRS, 15 rue Hélène Brion, 75013 Paris, France
| | - Paola Y. Bertucci
- European Molecular Biology Laboratory, Developmental Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - David E. K. Ferrier
- Gatty Marine Laboratory, The Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife, KY16 8LB UK
| | | | - Eve Gazave
- Institut Jacques Monod, University of Paris/CNRS, 15 rue Hélène Brion, 75013 Paris, France
| | - Mette Handberg-Thorsager
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany
| | - Jörg Hardege
- Department of Biological & Marine Sciences, Hull University, Cottingham Road, Hull, HU67RX UK
| | - Cameron Hird
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, UK
| | - Yu-Wen Hsieh
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany
| | - Jerome Hui
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Kevin Nzumbi Mutemi
- European Molecular Biology Laboratory, Developmental Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Stephan Q. Schneider
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Sec. 2, Academia Road, Nankang, Taipei, 11529 Taiwan
| | - Oleg Simakov
- Department for Neurosciences and Developmental Biology, University of Vienna, Vienna, Austria
| | - Hernando M. Vergara
- Sainsbury Wellcome Centre for Neural Circuits and Behaviour, Howland Street 25, London, W1T 4JG UK
| | - Michel Vervoort
- Institut Jacques Monod, University of Paris/CNRS, 15 rue Hélène Brion, 75013 Paris, France
| | - Gáspár Jékely
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, UK
| | | | - Florian Raible
- Max Perutz Labs, University of Vienna, Dr. Bohr-Gasse 9/4, 1030 Vienna, Austria
| | - Detlev Arendt
- European Molecular Biology Laboratory, Developmental Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Centre for Organismal Studies (COS), University of Heidelberg, 69120 Heidelberg, Germany
| |
Collapse
|