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Schardt S, Fischer SC. Adjusting the range of cell-cell communication enables fine-tuning of cell fate patterns from checkerboard to engulfing. J Math Biol 2023; 87:54. [PMID: 37679573 PMCID: PMC10485129 DOI: 10.1007/s00285-023-01959-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 06/20/2023] [Accepted: 06/25/2023] [Indexed: 09/09/2023]
Abstract
During development, spatio-temporal patterns ranging from checkerboard to engulfing occur with precise proportions of the respective cell fates. Key developmental regulators are intracellular transcriptional interactions and intercellular signaling. We present an analytically tractable mathematical model based on signaling that reliably generates different cell type patterns with specified proportions. Employing statistical mechanics, We derived a cell fate decision model for two cell types. A detailed steady state analysis on the resulting dynamical system yielded necessary conditions to generate spatially heterogeneous patterns. This allows the cell type proportions to be controlled by a single model parameter. Cell-cell communication is realized by local and global signaling mechanisms. These result in different cell type patterns. A nearest neighbor signal yields checkerboard patterns. Increasing the signal dispersion, cell fate clusters and an engulfing pattern can be generated. Altogether, the presented model allows us to reliably generate heterogeneous cell type patterns of different kinds as well as desired proportions.
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Affiliation(s)
- Simon Schardt
- Center for Computational and Theoretical Biology, University of Würzburg, Würzburg, Germany
| | - Sabine C. Fischer
- Center for Computational and Theoretical Biology, University of Würzburg, Würzburg, Germany
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2
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Echlin M, Aguilar B, Shmulevich I. Characterizing the Impact of Communication on Cellular and Collective Behavior Using a Three-Dimensional Multiscale Cellular Model. Entropy (Basel) 2023; 25:319. [PMID: 36832685 PMCID: PMC9955575 DOI: 10.3390/e25020319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/29/2023] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
Communication between cells enables the coordination that drives structural and functional complexity in biological systems. Both single and multicellular organisms have evolved diverse communication systems for a range of purposes, including synchronization of behavior, division of labor, and spatial organization. Synthetic systems are also increasingly being engineered to utilize cell-cell communication. While research has elucidated the form and function of cell-cell communication in many biological systems, our knowledge is still limited by the confounding effects of other biological phenomena at play and the bias of the evolutionary background. In this work, our goal is to push forward the context-free understanding of what impact cell-cell communication can have on cellular and population behavior to more fully understand the extent to which cell-cell communication systems can be utilized, modified, and engineered. We use an in silico model of 3D multiscale cellular populations, with dynamic intracellular networks interacting via diffusible signals. We focus on two key communication parameters: the effective interaction distance at which cells are able to interact and the receptor activation threshold. We found that cell-cell communication can be divided into six different forms along the parameter axes, three asocial and three social. We also show that cellular behavior, tissue composition, and tissue diversity are all highly sensitive to both the general form and specific parameters of communication even when the cellular network has not been biased towards that behavior.
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Affiliation(s)
- Moriah Echlin
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University, FI-33014 Tampere, Finland
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Boris Aguilar
- Institute for Systems Biology, Seattle, WA 98109, USA
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3
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Gordeeva O, Gordeev A, Erokhov P. Archetypal Architecture Construction, Patterning, and Scaling Invariance in a 3D Embryoid Body Differentiation Model. Front Cell Dev Biol 2022; 10:852071. [PMID: 35573693 PMCID: PMC9091174 DOI: 10.3389/fcell.2022.852071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 04/11/2022] [Indexed: 11/13/2022] Open
Abstract
Self-organized patterning and architecture construction studying is a priority goal for fundamental developmental and stem cell biology. To study the spatiotemporal patterning of pluripotent stem cells of different origins, we developed a three-dimensional embryoid body (EB) differentiation model quantifying volumetric parameters and investigated how the EB architecture formation, patterning, and scaling depend on the proliferation, cavitation, and differentiation dynamics, external environmental factors, and cell numbers. We identified three similar spatiotemporal patterns in the EB architectures, regardless of cell origin, which constitute the EB archetype and mimick the pre-gastrulation embryonic patterns. We found that the EB patterning depends strongly on cellular positional information, culture media factor/morphogen content, and free diffusion from the external environment and between EB cell layers. However, the EB archetype formation is independent of the EB size and initial cell numbers forming EBs; therefore, it is capable of scaling invariance and patterning regulation. Our findings indicate that the underlying principles of reaction-diffusion and positional information concepts can serve as the basis for EB architecture construction, patterning, and scaling. Thus, the 3D EB differentiation model represents a highly reproducible and reliable platform for experimental and theoretical research on developmental and stem cell biology issues.
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Affiliation(s)
- Olga Gordeeva
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia
- *Correspondence: Olga Gordeeva,
| | - Andrey Gordeev
- National Institutes of Health’s National Library of Medicine, Bethesda, MD, United States
| | - Pavel Erokhov
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia
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Yanagida A, Corujo-Simon E, Revell CK, Sahu P, Stirparo GG, Aspalter IM, Winkel AK, Peters R, De Belly H, Cassani DAD, Achouri S, Blumenfeld R, Franze K, Hannezo E, Paluch EK, Nichols J, Chalut KJ. Cell surface fluctuations regulate early embryonic lineage sorting. Cell 2022; 185:777-793.e20. [PMID: 35196500 PMCID: PMC8896887 DOI: 10.1016/j.cell.2022.01.022] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 10/22/2021] [Accepted: 01/26/2022] [Indexed: 01/24/2023]
Abstract
In development, lineage segregation is coordinated in time and space. An important example is the mammalian inner cell mass, in which the primitive endoderm (PrE, founder of the yolk sac) physically segregates from the epiblast (EPI, founder of the fetus). While the molecular requirements have been well studied, the physical mechanisms determining spatial segregation between EPI and PrE remain elusive. Here, we investigate the mechanical basis of EPI and PrE sorting. We find that rather than the differences in static cell surface mechanical parameters as in classical sorting models, it is the differences in surface fluctuations that robustly ensure physical lineage sorting. These differential surface fluctuations systematically correlate with differential cellular fluidity, which we propose together constitute a non-equilibrium sorting mechanism for EPI and PrE lineages. By combining experiments and modeling, we identify cell surface dynamics as a key factor orchestrating the correct spatial segregation of the founder embryonic lineages.
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Affiliation(s)
- Ayaka Yanagida
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK; Centre for Trophoblast Research, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK; Living Systems Institute, University of Exeter, Exeter EX4 4QD, UK
| | - Elena Corujo-Simon
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Christopher K Revell
- Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Ave, Cambridge CB3 0HE, UK
| | - Preeti Sahu
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg 3400, Austria
| | - Giuliano G Stirparo
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Irene M Aspalter
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Alex K Winkel
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Ruby Peters
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Henry De Belly
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK; MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Davide A D Cassani
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Sarra Achouri
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK; Centre for Trophoblast Research, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK
| | - Raphael Blumenfeld
- Gonville & Caius College, University of Cambridge, Trinity St., Cambridge CB2 1TA, UK
| | - Kristian Franze
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Edouard Hannezo
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg 3400, Austria
| | - Ewa K Paluch
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK.
| | - Jennifer Nichols
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK; Centre for Trophoblast Research, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK.
| | - Kevin J Chalut
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK.
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Dokmegang J. Modeling Epiblast Shape in Implanting Mammalian Embryos. Methods Mol Biol 2022; 2490:281-296. [PMID: 35486253 DOI: 10.1007/978-1-0716-2281-0_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
An indispensable prerequisite of mammalian development is successful morphogenesis in the epiblast, the embryonic tissue that gives rise to all differentiated cells of the adult mammal. The right control of both epiblast morphogenesis and the events that regulate its shape in particular during implantation is henceforth of tremendous importance. However, monitoring the process of development in implanting human embryos is ethically and technically challenging, making it difficult to troubleshoot when things go wrong, as it is unfortunately the case with over 30% of pregnancy failures. Although modern in vitro techniques have proven very insightful lately, more tools are needed in the quest to elucidate mammalian and human development. Mathematical and computational modeling position themselves as helpful complementary tools in the biologist's toolbox, enabling the exploration of the living in silico, beyond the boundaries set by ethical concerns and the potential limitations of wet lab techniques. Here, we show how mathematical modeling and computer simulations can be used to emulate and investigate mechanisms driving epiblast shape changes in mouse and human embryos during implantation.
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Affiliation(s)
- Joel Dokmegang
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL, USA.
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.
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Gómez-Gálvez P, Anbari S, Escudero LM, Buceta J. Mechanics and self-organization in tissue development. Semin Cell Dev Biol 2021; 120:147-159. [PMID: 34417092 DOI: 10.1016/j.semcdb.2021.07.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/25/2021] [Accepted: 07/01/2021] [Indexed: 01/01/2023]
Abstract
Self-organization is an all-important feature of living systems that provides the means to achieve specialization and functionality at distinct spatio-temporal scales. Herein, we review this concept by addressing the packing organization of cells, the sorting/compartmentalization phenomenon of cell populations, and the propagation of organizing cues at the tissue level through traveling waves. We elaborate on how different theoretical models and tools from Topology, Physics, and Dynamical Systems have improved the understanding of self-organization by shedding light on the role played by mechanics as a driver of morphogenesis. Altogether, by providing a historical perspective, we show how ideas and hypotheses in the field have been revisited, developed, and/or rejected and what are the open questions that need to be tackled by future research.
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Affiliation(s)
- Pedro Gómez-Gálvez
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocio/CSIC/Universidad de Sevilla and Departamento de Biologia Celular, Universidad de Sevilla, 41013 Seville, Spain; Biomedical Network Research Centre on Neurodegenerative Diseases (CIBERNED), 28031 Madrid, Spain
| | - Samira Anbari
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Luis M Escudero
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocio/CSIC/Universidad de Sevilla and Departamento de Biologia Celular, Universidad de Sevilla, 41013 Seville, Spain; Biomedical Network Research Centre on Neurodegenerative Diseases (CIBERNED), 28031 Madrid, Spain
| | - Javier Buceta
- Institute for Integrative Systems Biology (I2SysBio), CSIC-UV, Paterna, 46980 Valencia, Spain.
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Abstract
Morphogenesis is one of the most remarkable examples of biological pattern formation. Despite substantial progress in the field, we still do not understand the organizational principles responsible for the robust convergence of the morphogenesis process across scales to form viable organisms under variable conditions. Achieving large-scale coordination requires feedback between mechanical and biochemical processes, spanning all levels of organization and relating the emerging patterns with the mechanisms driving their formation. In this review, we highlight the role of mechanics in the patterning process, emphasizing the active and synergistic manner in which mechanical processes participate in developmental patterning rather than merely following a program set by biochemical signals. We discuss the value of applying a coarse-grained approach toward understanding this complex interplay, which considers the large-scale dynamics and feedback as well as complementing the reductionist approach focused on molecular detail. A central challenge in this approach is identifying relevant coarse-grained variables and developing effective theories that can serve as a basis for an integrated framework for understanding this remarkable pattern-formation process. Expected final online publication date for the Annual Review of Cell and Developmental Biology, Volume 37 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Yonit Maroudas-Sacks
- Department of Physics, Technion-Israel Institute of Technology, Haifa 32000, Israel;
| | - Kinneret Keren
- Department of Physics, Technion-Israel Institute of Technology, Haifa 32000, Israel; .,Network Biology Research Laboratories and The Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology, Haifa 32000, Israel
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