1
|
Crossley RM, Johnson S, Tsingos E, Bell Z, Berardi M, Botticelli M, Braat QJS, Metzcar J, Ruscone M, Yin Y, Shuttleworth R. Modeling the extracellular matrix in cell migration and morphogenesis: a guide for the curious biologist. Front Cell Dev Biol 2024; 12:1354132. [PMID: 38495620 PMCID: PMC10940354 DOI: 10.3389/fcell.2024.1354132] [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: 12/11/2023] [Accepted: 02/12/2024] [Indexed: 03/19/2024] Open
Abstract
The extracellular matrix (ECM) is a highly complex structure through which biochemical and mechanical signals are transmitted. In processes of cell migration, the ECM also acts as a scaffold, providing structural support to cells as well as points of potential attachment. Although the ECM is a well-studied structure, its role in many biological processes remains difficult to investigate comprehensively due to its complexity and structural variation within an organism. In tandem with experiments, mathematical models are helpful in refining and testing hypotheses, generating predictions, and exploring conditions outside the scope of experiments. Such models can be combined and calibrated with in vivo and in vitro data to identify critical cell-ECM interactions that drive developmental and homeostatic processes, or the progression of diseases. In this review, we focus on mathematical and computational models of the ECM in processes such as cell migration including cancer metastasis, and in tissue structure and morphogenesis. By highlighting the predictive power of these models, we aim to help bridge the gap between experimental and computational approaches to studying the ECM and to provide guidance on selecting an appropriate model framework to complement corresponding experimental studies.
Collapse
Affiliation(s)
- Rebecca M. Crossley
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, United Kingdom
| | - Samuel Johnson
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, United Kingdom
| | - Erika Tsingos
- Computational Developmental Biology Group, Institute of Biodynamics and Biocomplexity, Utrecht University, Utrecht, Netherlands
| | - Zoe Bell
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Massimiliano Berardi
- LaserLab, Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- Optics11 life, Amsterdam, Netherlands
| | | | - Quirine J. S. Braat
- Department of Applied Physics and Science Education, Eindhoven University of Technology, Eindhoven, Netherlands
| | - John Metzcar
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, United States
- Department of Informatics, Indiana University, Bloomington, IN, United States
| | | | - Yuan Yin
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, United Kingdom
| | | |
Collapse
|
2
|
Subkhankulova T, Camargo Sosa K, Uroshlev LA, Nikaido M, Shriever N, Kasianov AS, Yang X, Rodrigues FSLM, Carney TJ, Bavister G, Schwetlick H, Dawes JHP, Rocco A, Makeev VJ, Kelsh RN. Zebrafish pigment cells develop directly from persistent highly multipotent progenitors. Nat Commun 2023; 14:1258. [PMID: 36878908 PMCID: PMC9988989 DOI: 10.1038/s41467-023-36876-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 02/17/2023] [Indexed: 03/08/2023] Open
Abstract
Neural crest cells are highly multipotent stem cells, but it remains unclear how their fate restriction to specific fates occurs. The direct fate restriction model hypothesises that migrating cells maintain full multipotency, whilst progressive fate restriction envisages fully multipotent cells transitioning to partially-restricted intermediates before committing to individual fates. Using zebrafish pigment cell development as a model, we show applying NanoString hybridization single cell transcriptional profiling and RNAscope in situ hybridization that neural crest cells retain broad multipotency throughout migration and even in post-migratory cells in vivo, with no evidence for partially-restricted intermediates. We find that leukocyte tyrosine kinase early expression marks a multipotent stage, with signalling driving iridophore differentiation through repression of fate-specific transcription factors for other fates. We reconcile the direct and progressive fate restriction models by proposing that pigment cell development occurs directly, but dynamically, from a highly multipotent state, consistent with our recently-proposed Cyclical Fate Restriction model.
Collapse
Affiliation(s)
| | - Karen Camargo Sosa
- Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Leonid A Uroshlev
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Ul. Gubkina 3, Moscow, 119991, Russia
| | - Masataka Nikaido
- Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK
- Graduate School of Science, University of Hyogo, Ako-gun, Hyogo Pref., 678-1297, Japan
| | - Noah Shriever
- Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Artem S Kasianov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Ul. Gubkina 3, Moscow, 119991, Russia
- Department of Medical and Biological Physics, Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, 141701, Russia
- A.A. Kharkevich Institute for Information Transmission Problems (IITP), Russian Academy of Sciences, Bolshoy Karetny per. 19, build.1, Moscow, 127051, Russia
| | - Xueyan Yang
- Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK
- The MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, PR China
| | | | - Thomas J Carney
- Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK
- Lee Kong Chian School of Medicine, Experimental Medicine Building, Yunnan Garden Campus, Nanyang Technological University, 59 Nanyang Drive, Yunnan Garden, 636921, Singapore
| | - Gemma Bavister
- Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Hartmut Schwetlick
- Department of Mathematical Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Jonathan H P Dawes
- Department of Mathematical Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Andrea Rocco
- Department of Microbial Sciences, FHMS, University of Surrey, GU2 7XH, Guildford, UK
- Department of Physics, FEPS, University of Surrey, GU2 7XH, Guildford, UK
| | - Vsevolod J Makeev
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Ul. Gubkina 3, Moscow, 119991, Russia
- Department of Medical and Biological Physics, Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region, 141701, Russia
- Laboratory 'Regulatory Genomics', Institute of Fundamental Medicine and Biology, Kazan Federal University, 18 Kremlyovskaya street, Kazan, 420008, Russia
| | - Robert N Kelsh
- Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
| |
Collapse
|