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Barone V, Tagua A, Román JÁAS, Hamdoun A, Garrido-García J, Lyons DC, Escudero LM. Local and global changes in cell density induce reorganisation of 3D packing in a proliferating epithelium. Development 2024; 151:dev202362. [PMID: 38619327 DOI: 10.1242/dev.202362] [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: 09/15/2023] [Accepted: 03/28/2024] [Indexed: 04/16/2024]
Abstract
Tissue morphogenesis is intimately linked to the changes in shape and organisation of individual cells. In curved epithelia, cells can intercalate along their own apicobasal axes, adopting a shape named 'scutoid' that allows energy minimization in the tissue. Although several geometric and biophysical factors have been associated with this 3D reorganisation, the dynamic changes underlying scutoid formation in 3D epithelial packing remain poorly understood. Here, we use live imaging of the sea star embryo coupled with deep learning-based segmentation to dissect the relative contributions of cell density, tissue compaction and cell proliferation on epithelial architecture. We find that tissue compaction, which naturally occurs in the embryo, is necessary for the appearance of scutoids. Physical compression experiments identify cell density as the factor promoting scutoid formation at a global level. Finally, the comparison of the developing embryo with computational models indicates that the increase in the proportion of scutoids is directly associated with cell divisions. Our results suggest that apico-basal intercalations appearing immediately after mitosis may help accommodate the new cells within the tissue. We propose that proliferation in a compact epithelium induces 3D cell rearrangements during development.
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Affiliation(s)
- Vanessa Barone
- Center for Marine Biotechnology and Biomedicine, University of California San Diego, La Jolla, CA 92093, USA
- Hopkins Marine Station, Department of Biology, Stanford University, Pacific Grove, CA 93950, USA
| | - Antonio Tagua
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, 41013 Seville, Spain
| | - Jesus Á Andrés-San Román
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, 41013 Seville, Spain
| | - Amro Hamdoun
- Center for Marine Biotechnology and Biomedicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Juan Garrido-García
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, 41013 Seville, Spain
| | - Deirdre C Lyons
- Center for Marine Biotechnology and Biomedicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Luis M Escudero
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, 41013 Seville, Spain
- Biomedical Network Research Centre on Neurodegenerative Diseases (CIBERNED), 28029 Madrid, Spain
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2
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Barone V, Tagua A, Andrés-San Román JÁ, Hamdoun A, Garrido-García J, Lyons DC, Escudero LM. Local and global changes in cell density induce reorganisation of 3D packing in a proliferating epithelium. bioRxiv 2024:2024.02.08.579268. [PMID: 38370815 PMCID: PMC10871321 DOI: 10.1101/2024.02.08.579268] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Tissue morphogenesis is intimately linked to the changes in shape and organisation of individual cells. In curved epithelia, cells can intercalate along their own apicobasal axes adopting a shape named "scutoid" that allows energy minimization in the tissue. Although several geometric and biophysical factors have been associated with this 3D reorganisation, the dynamic changes underlying scutoid formation in 3D epithelial packing remain poorly understood. Here we use live-imaging of the sea star embryo coupled with deep learning-based segmentation, to dissect the relative contributions of cell density, tissue compaction, and cell proliferation on epithelial architecture. We find that tissue compaction, which naturally occurs in the embryo, is necessary for the appearance of scutoids. Physical compression experiments identify cell density as the factor promoting scutoid formation at a global level. Finally, the comparison of the developing embryo with computational models indicates that the increase in the proportion of scutoids is directly associated with cell divisions. Our results suggest that apico-basal intercalations appearing just after mitosis may help accommodate the new cells within the tissue. We propose that proliferation in a compact epithelium induces 3D cell rearrangements during development.
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Affiliation(s)
- Vanessa Barone
- Center for Marine Biotechnology and Biomedicine, University of California San Diego, La Jolla, CA, 92093, USA
- Hopkins Marine Station, Department of Biology, Stanford University, Pacific Grove, CA, 93950, USA
| | - Antonio Tagua
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla. 41013 Seville, Spain
| | - Jesus Á Andrés-San Román
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla. 41013 Seville, Spain
| | - Amro Hamdoun
- Center for Marine Biotechnology and Biomedicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Juan Garrido-García
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla. 41013 Seville, Spain
| | - Deirdre C Lyons
- Center for Marine Biotechnology and Biomedicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Luis M Escudero
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla. 41013 Seville, Spain
- Biomedical Network Research Centre on Neurodegenerative Diseases (CIBERNED), 28029 Madrid, Spain
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3
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Andrés-San Román JA, Gordillo-Vázquez C, Franco-Barranco D, Morato L, Fernández-Espartero CH, Baonza G, Tagua A, Vicente-Munuera P, Palacios AM, Gavilán MP, Martín-Belmonte F, Annese V, Gómez-Gálvez P, Arganda-Carreras I, Escudero LM. CartoCell, a high-content pipeline for 3D image analysis, unveils cell morphology patterns in epithelia. Cell Rep Methods 2023; 3:100597. [PMID: 37751739 PMCID: PMC10626192 DOI: 10.1016/j.crmeth.2023.100597] [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] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 07/19/2023] [Accepted: 08/31/2023] [Indexed: 09/28/2023]
Abstract
Decades of research have not yet fully explained the mechanisms of epithelial self-organization and 3D packing. Single-cell analysis of large 3D epithelial libraries is crucial for understanding the assembly and function of whole tissues. Combining 3D epithelial imaging with advanced deep-learning segmentation methods is essential for enabling this high-content analysis. We introduce CartoCell, a deep-learning-based pipeline that uses small datasets to generate accurate labels for hundreds of whole 3D epithelial cysts. Our method detects the realistic morphology of epithelial cells and their contacts in the 3D structure of the tissue. CartoCell enables the quantification of geometric and packing features at the cellular level. Our single-cell cartography approach then maps the distribution of these features on 2D plots and 3D surface maps, revealing cell morphology patterns in epithelial cysts. Additionally, we show that CartoCell can be adapted to other types of epithelial tissues.
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Affiliation(s)
- 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, Facultad de Biología, Universidad de Sevilla, 41013 Seville, Spain
| | - Carmen Gordillo-Vázquez
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, 41013 Seville, Spain
| | - Daniel Franco-Barranco
- Department of Computer Science and Artificial Intelligence, University of the Basque Country (UPV/EHU), 20018 San Sebastian, Spain; Donostia International Physics Center (DIPC), 20018 San Sebastian, Spain
| | - Laura Morato
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, 41013 Seville, Spain
| | - Cecilia H Fernández-Espartero
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, 41013 Seville, Spain
| | - Gabriel Baonza
- Program of Tissue and Organ Homeostasis, Centro de Biología Molecular Severo Ochoa, CSIC-UAM and Ramón & Cajal Health Research Institute (IRYCIS), Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain
| | - Antonio Tagua
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, 41013 Seville, Spain
| | | | - Ana M Palacios
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, 41013 Seville, Spain
| | - María P Gavilán
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), JA/CSIC/Universidad de Sevilla/Universidad Pablo de Olavide and Departamento de Citología e Histología Normal y Patológica, Facultad de Medicina, Universidad de Sevilla, 41009 Seville, Spain
| | - Fernando Martín-Belmonte
- Program of Tissue and Organ Homeostasis, Centro de Biología Molecular Severo Ochoa, CSIC-UAM and Ramón & Cajal Health Research Institute (IRYCIS), Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain
| | - Valentina Annese
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, 41013 Seville, Spain
| | - Pedro Gómez-Gálvez
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, 41013 Seville, Spain; MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Trumpington, Cambridge CB2 0QH, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK.
| | - Ignacio Arganda-Carreras
- Department of Computer Science and Artificial Intelligence, University of the Basque Country (UPV/EHU), 20018 San Sebastian, Spain; Donostia International Physics Center (DIPC), 20018 San Sebastian, Spain; Ikerbasque, Basque Foundation for Science, 48009 Bilbao, Spain; Biofisika Institute, 48940 Leioa, Spain.
| | - Luis M Escudero
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, 41013 Seville, Spain; Biomedical Network Research Centre on Neurodegenerative Diseases (CIBERNED), 28029 Madrid, Spain.
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4
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Schamberger B, Ziege R, Anselme K, Ben Amar M, Bykowski M, Castro APG, Cipitria A, Coles RA, Dimova R, Eder M, Ehrig S, Escudero LM, Evans ME, Fernandes PR, Fratzl P, Geris L, Gierlinger N, Hannezo E, Iglič A, Kirkensgaard JJK, Kollmannsberger P, Kowalewska Ł, Kurniawan NA, Papantoniou I, Pieuchot L, Pires THV, Renner LD, Sageman-Furnas AO, Schröder-Turk GE, Sengupta A, Sharma VR, Tagua A, Tomba C, Trepat X, Waters SL, Yeo EF, Roschger A, Bidan CM, Dunlop JWC. Curvature in Biological Systems: Its Quantification, Emergence, and Implications across the Scales. Adv Mater 2023; 35:e2206110. [PMID: 36461812 DOI: 10.1002/adma.202206110] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 11/22/2022] [Indexed: 06/17/2023]
Abstract
Surface curvature both emerges from, and influences the behavior of, living objects at length scales ranging from cell membranes to single cells to tissues and organs. The relevance of surface curvature in biology is supported by numerous experimental and theoretical investigations in recent years. In this review, first, a brief introduction to the key ideas of surface curvature in the context of biological systems is given and the challenges that arise when measuring surface curvature are discussed. Giving an overview of the emergence of curvature in biological systems, its significance at different length scales becomes apparent. On the other hand, summarizing current findings also shows that both single cells and entire cell sheets, tissues or organisms respond to curvature by modulating their shape and their migration behavior. Finally, the interplay between the distribution of morphogens or micro-organisms and the emergence of curvature across length scales is addressed with examples demonstrating these key mechanistic principles of morphogenesis. Overall, this review highlights that curved interfaces are not merely a passive by-product of the chemical, biological, and mechanical processes but that curvature acts also as a signal that co-determines these processes.
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Affiliation(s)
- Barbara Schamberger
- Department of the Chemistry and Physics of Materials, Paris-Lodron University of Salzburg, 5020, Salzburg, Austria
| | - Ricardo Ziege
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, 14476, Potsdam, Germany
| | - Karine Anselme
- IS2M (CNRS - UMR 7361), Université de Haute-Alsace, F-68100, Mulhouse, France
- Université de Strasbourg, F-67081, Strasbourg, France
| | - Martine Ben Amar
- Department of Physics, Laboratoire de Physique de l'Ecole Normale Supérieure, 24 rue Lhomond, 75005, Paris, France
| | - Michał Bykowski
- Department of Plant Anatomy and Cytology, Faculty of Biology, University of Warsaw, 02-096, Warsaw, Poland
| | - André P G Castro
- IDMEC, Instituto Superior Técnico, Universidade de Lisboa, 1049-001, Lisboa, Portugal
- ESTS, Instituto Politécnico de Setúbal, 2914-761, Setúbal, Portugal
| | - Amaia Cipitria
- IS2M (CNRS - UMR 7361), Université de Haute-Alsace, F-68100, Mulhouse, France
- Group of Bioengineering in Regeneration and Cancer, Biodonostia Health Research Institute, 20014, San Sebastian, Spain
- IKERBASQUE, Basque Foundation for Science, 48009, Bilbao, Spain
| | - Rhoslyn A Coles
- Cluster of Excellence, Matters of Activity, Humboldt-Universität zu Berlin, 10178, Berlin, Germany
| | - Rumiana Dimova
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, 14476, Potsdam, Germany
| | - Michaela Eder
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, 14476, Potsdam, Germany
| | - Sebastian Ehrig
- Max Delbrück Center for Molecular Medicine, 13125, Berlin, Germany
- Berlin Institute for Medical Systems Biology, 10115, Berlin, Germany
| | - 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), 28031, Madrid, Spain
| | - Myfanwy E Evans
- Institute for Mathematics, University of Potsdam, 14476, Potsdam, Germany
| | - Paulo R Fernandes
- IDMEC, Instituto Superior Técnico, Universidade de Lisboa, 1049-001, Lisboa, Portugal
| | - Peter Fratzl
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, 14476, Potsdam, Germany
| | - Liesbet Geris
- Biomechanics Research Unit, GIGA In Silico Medicine, University of Liège, 4000, Liège, Belgium
| | - Notburga Gierlinger
- Institute of Biophysics, Department of Nanobiotechnology, University of Natural Resources and Life Sciences Vienna (Boku), 1190, Vienna, Austria
| | - Edouard Hannezo
- Institute of Science and Technology Austria, 3400, Klosterneuburg, Austria
| | - Aleš Iglič
- Laboratory of Physics, Faculty of Electrical engineering, University of Ljubljana, Tržaška 25, SI-1000, Ljubljana, Slovenia
| | - Jacob J K Kirkensgaard
- Condensed Matter Physics, Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, 2100, København Ø, Denmark
- Ingredients and Dairy Technology, Department of Food Science, University of Copenhagen, Rolighedsvej 26, 1958, Frederiksberg, Denmark
| | - Philip Kollmannsberger
- Center for Computational and Theoretical Biology, University of Würzburg, 97074, Würzburg, Germany
| | - Łucja Kowalewska
- Department of Plant Anatomy and Cytology, Faculty of Biology, University of Warsaw, 02-096, Warsaw, Poland
| | - Nicholas A Kurniawan
- Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, 5600 MB, Eindhoven, The Netherlands
| | - Ioannis Papantoniou
- Prometheus Division of Skeletal Tissue Engineering, KU Leuven, O&N1, Herestraat 49, PB 813, 3000, Leuven, Belgium
- Skeletal Biology and Engineering Research Center, Department of Development and Regeneration, KU Leuven, O&N1, Herestraat 49, PB 813, 3000, Leuven, Belgium
- Institute of Chemical Engineering Sciences, Foundation for Research and Technology (FORTH), Stadiou Str., 26504, Patras, Greece
| | - Laurent Pieuchot
- IS2M (CNRS - UMR 7361), Université de Haute-Alsace, F-68100, Mulhouse, France
- Université de Strasbourg, F-67081, Strasbourg, France
| | - Tiago H V Pires
- IDMEC, Instituto Superior Técnico, Universidade de Lisboa, 1049-001, Lisboa, Portugal
| | - Lars D Renner
- Leibniz Institute of Polymer Research and the Max Bergmann Center of Biomaterials, 01069, Dresden, Germany
| | | | - Gerd E Schröder-Turk
- School of Physics, Chemistry and Mathematics, Murdoch University, 90 South St, Murdoch, WA, 6150, Australia
- Department of Materials Physics, Research School of Physics, The Australian National University, Canberra, ACT, 2600, Australia
| | - Anupam Sengupta
- Physics of Living Matter, Department of Physics and Materials Science, University of Luxembourg, L-1511, Luxembourg City, Grand Duchy of Luxembourg
| | - Vikas R Sharma
- Department of the Chemistry and Physics of Materials, Paris-Lodron University of Salzburg, 5020, Salzburg, Austria
| | - 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), 28031, Madrid, Spain
| | - Caterina Tomba
- Univ Lyon, CNRS, INSA Lyon, Ecole Centrale de Lyon, Université Claude Bernard Lyon 1, CPE Lyon, INL, UMR5270, 69622, Villeurbanne, France
| | - Xavier Trepat
- ICREA at the Institute for Bioengineering of Catalonia, The Barcelona Institute for Science and Technology, 08028, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), 08028, Barcelona, Spain
| | - Sarah L Waters
- Mathematical Institute, University of Oxford, OX2 6GG, Oxford, UK
| | - Edwina F Yeo
- Mathematical Institute, University of Oxford, OX2 6GG, Oxford, UK
| | - Andreas Roschger
- Department of the Chemistry and Physics of Materials, Paris-Lodron University of Salzburg, 5020, Salzburg, Austria
| | - Cécile M Bidan
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, 14476, Potsdam, Germany
| | - John W C Dunlop
- Department of the Chemistry and Physics of Materials, Paris-Lodron University of Salzburg, 5020, Salzburg, Austria
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5
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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: 2] [Impact Index Per Article: 1.0] [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: 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.
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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.
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6
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Vicente-Munuera P, Gómez-Gálvez P, Tetley RJ, Forja C, Tagua A, Letrán M, Tozluoglu M, Mao Y, Escudero LM. EpiGraph: an open-source platform to quantify epithelial organization. Bioinformatics 2020; 36:1314-1316. [PMID: 31544932 PMCID: PMC7703762 DOI: 10.1093/bioinformatics/btz683] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 08/21/2019] [Accepted: 08/29/2019] [Indexed: 01/09/2023] Open
Abstract
Summary Here we present EpiGraph, an image analysis tool that quantifies epithelial organization. Our method combines computational geometry and graph theory to measure the degree of order of any packed tissue. EpiGraph goes beyond the traditional polygon distribution analysis, capturing other organizational traits that improve the characterization of epithelia. EpiGraph can objectively compare the rearrangements of epithelial cells during development and homeostasis to quantify how the global ensemble is affected. Importantly, it has been implemented in the open-access platform Fiji. This makes EpiGraph very user friendly, with no programming skills required. Availability and implementation EpiGraph is available at https://imagej.net/EpiGraph and the code is accessible (https://github.com/ComplexOrganizationOfLivingMatter/Epigraph) under GPLv3 license. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- 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, Seville 41013, Spain.,Biomedical Network Research Centre on Neurodegenerative Diseases (CIBERNED), Madrid 28031, Spain
| | - 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, Seville 41013, Spain.,Biomedical Network Research Centre on Neurodegenerative Diseases (CIBERNED), Madrid 28031, Spain
| | - Robert J Tetley
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Cristina Forja
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Universidad de Sevilla, Seville 41013, Spain
| | - 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, Seville 41013, Spain.,Biomedical Network Research Centre on Neurodegenerative Diseases (CIBERNED), Madrid 28031, Spain
| | - Marta Letrán
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla and Departamento de Biología Celular, Universidad de Sevilla, Seville 41013, Spain
| | - Melda Tozluoglu
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Yanlan Mao
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK.,College of Information and Control, Nanjing University of Information Science and Technology, Nanjing, Jiangsu 210044, China
| | - 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, Seville 41013, Spain.,Biomedical Network Research Centre on Neurodegenerative Diseases (CIBERNED), Madrid 28031, Spain
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Gómez-Gálvez P, Vicente-Munuera P, Tagua A, Forja C, Castro AM, Letrán M, Valencia-Expósito A, Grima C, Bermúdez-Gallardo M, Serrano-Pérez-Higueras Ó, Cavodeassi F, Sotillos S, Martín-Bermudo MD, Márquez A, Buceta J, Escudero LM. Author Correction: Scutoids are a geometrical solution to three-dimensional packing of epithelia. Nat Commun 2018; 9:4210. [PMID: 30297704 PMCID: PMC6175858 DOI: 10.1038/s41467-018-06671-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Affiliation(s)
- Pedro Gómez-Gálvez
- Departamento de Biología Celular, Universidad de Sevilla and Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41013, Seville, Spain
| | - Pablo Vicente-Munuera
- Departamento de Biología Celular, Universidad de Sevilla and Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41013, Seville, Spain
| | - Antonio Tagua
- Departamento de Biología Celular, Universidad de Sevilla and Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41013, Seville, Spain
| | - Cristina Forja
- Departamento de Biología Celular, Universidad de Sevilla and Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41013, Seville, Spain
| | - Ana M Castro
- Departamento de Biología Celular, Universidad de Sevilla and Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41013, Seville, Spain
| | - Marta Letrán
- Departamento de Biología Celular, Universidad de Sevilla and Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41013, Seville, Spain
| | | | - Clara Grima
- Departamento de Matemática Aplicada I, Universidad de Sevilla, 41012, Seville, Spain
| | - Marina Bermúdez-Gallardo
- Departamento de Biología Celular, Universidad de Sevilla and Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41013, Seville, Spain
| | - Óscar Serrano-Pérez-Higueras
- Departamento de Biología Celular, Universidad de Sevilla and Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41013, Seville, Spain
| | - Florencia Cavodeassi
- Centro de Biología Molecular Severo Ochoa and CIBER de Enfermedades Raras, C/ Nicolás Cabrera 1, 28049, Madrid, Spain.,St. George's, University of London, Cranmer Terrace, London, SW17 0RE, UK
| | - Sol Sotillos
- CABD, CSIC/JA/UPO, Campus Universidad Pablo de Olavide, 41013, Seville, Spain
| | | | - Alberto Márquez
- Departamento de Matemática Aplicada I, Universidad de Sevilla, 41012, Seville, Spain
| | - Javier Buceta
- Bioengineering Department, Lehigh University, Bethlehem, PA, 18018, USA. .,Chemical and Biomolecular Engineering Department, Lehigh University, Bethlehem, PA, 18018, USA.
| | - Luis M Escudero
- Departamento de Biología Celular, Universidad de Sevilla and Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41013, Seville, Spain.
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8
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Gómez-Gálvez P, Vicente-Munuera P, Tagua A, Forja C, Castro AM, Letrán M, Valencia-Expósito A, Grima C, Bermúdez-Gallardo M, Serrano-Pérez-Higueras Ó, Cavodeassi F, Sotillos S, Martín-Bermudo MD, Márquez A, Buceta J, Escudero LM. Scutoids are a geometrical solution to three-dimensional packing of epithelia. Nat Commun 2018; 9:2960. [PMID: 30054479 PMCID: PMC6063940 DOI: 10.1038/s41467-018-05376-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Accepted: 06/11/2018] [Indexed: 02/08/2023] Open
Abstract
As animals develop, tissue bending contributes to shape the organs into complex three-dimensional structures. However, the architecture and packing of curved epithelia remains largely unknown. Here we show by means of mathematical modelling that cells in bent epithelia can undergo intercalations along the apico-basal axis. This phenomenon forces cells to have different neighbours in their basal and apical surfaces. As a consequence, epithelial cells adopt a novel shape that we term "scutoid". The detailed analysis of diverse tissues confirms that generation of apico-basal intercalations between cells is a common feature during morphogenesis. Using biophysical arguments, we propose that scutoids make possible the minimization of the tissue energy and stabilize three-dimensional packing. Hence, we conclude that scutoids are one of nature's solutions to achieve epithelial bending. Our findings pave the way to understand the three-dimensional organization of epithelial organs.
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Affiliation(s)
- Pedro Gómez-Gálvez
- Departamento de Biología Celular, Universidad de Sevilla and Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41013, Seville, Spain
| | - Pablo Vicente-Munuera
- Departamento de Biología Celular, Universidad de Sevilla and Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41013, Seville, Spain
| | - Antonio Tagua
- Departamento de Biología Celular, Universidad de Sevilla and Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41013, Seville, Spain
| | - Cristina Forja
- Departamento de Biología Celular, Universidad de Sevilla and Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41013, Seville, Spain
| | - Ana M Castro
- Departamento de Biología Celular, Universidad de Sevilla and Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41013, Seville, Spain
| | - Marta Letrán
- Departamento de Biología Celular, Universidad de Sevilla and Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41013, Seville, Spain
| | | | - Clara Grima
- Departamento de Matemática Aplicada I, Universidad de Sevilla, 41012, Seville, Spain
| | - Marina Bermúdez-Gallardo
- Departamento de Biología Celular, Universidad de Sevilla and Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41013, Seville, Spain
| | - Óscar Serrano-Pérez-Higueras
- Departamento de Biología Celular, Universidad de Sevilla and Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41013, Seville, Spain
| | - Florencia Cavodeassi
- Centro de Biología Molecular Severo Ochoa and CIBER de Enfermedades Raras. C/ Nicolás Cabrera 1, 28049, Madrid, Spain
- St. George's, University of London, Cranmer Terrace, SW17 0RE, London, UK
| | - Sol Sotillos
- CABD, CSIC/JA/UPO, Campus Universidad Pablo de Olavide, 41013, Seville, Spain
| | | | - Alberto Márquez
- Departamento de Matemática Aplicada I, Universidad de Sevilla, 41012, Seville, Spain
| | - Javier Buceta
- Bioengineering Department, Lehigh University, Bethlehem, PA, 18018, USA.
- Chemical and Biomolecular Engineering Department, Lehigh University, Bethlehem, PA, 18018, USA.
| | - Luis M Escudero
- Departamento de Biología Celular, Universidad de Sevilla and Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41013, Seville, Spain.
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