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
|
Kenny FN, Marcotti S, De Freitas DB, Drudi EM, Leech V, Bell RE, Easton J, Díaz-de-la-Loza MDC, Fleck R, Allison L, Philippeos C, Manhart A, Shaw TJ, Stramer BM. Autocrine IL-6 drives cell and extracellular matrix anisotropy in scar fibroblasts. Matrix Biol 2023; 123:1-16. [PMID: 37660739 PMCID: PMC10878985 DOI: 10.1016/j.matbio.2023.08.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/31/2023] [Accepted: 08/26/2023] [Indexed: 09/05/2023]
Abstract
Fibrosis is associated with dramatic changes in extracellular matrix (ECM) architecture of unknown etiology. Here we exploit keloid scars as a paradigm to understand fibrotic ECM organization. We reveal that keloid patient fibroblasts uniquely produce a globally aligned ECM network in 2-D culture as observed in scar tissue. ECM anisotropy develops after rapid initiation of a fibroblast supracellular actin network, suggesting that cell alignment initiates ECM patterning. Keloid fibroblasts produce elevated levels of IL-6, and autocrine IL-6 production is both necessary and sufficient to induce cell and ECM alignment, as evidenced by ligand stimulation of normal dermal fibroblasts and treatment of keloid fibroblasts with the function blocking IL-6 receptor monoclonal antibody, tocilizumab. Downstream of IL-6, supracellular organization of keloid fibroblasts is controlled by activation of cell-cell adhesion. Adhesion formation inhibits contact-induced cellular overlap leading to nematic organization of cells and an alignment of focal adhesions. Keloid fibroblasts placed on isotropic ECM align the pre-existing matrix, suggesting that focal adhesion alignment leads to active anisotropic remodeling. These results show that IL-6-induced fibroblast cooperativity can control the development of a nematic ECM, highlighting both IL-6 signaling and cell-cell adhesions as potential therapeutic targets to inhibit this common feature of fibrosis.
Collapse
Affiliation(s)
- Fiona N Kenny
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
| | - Stefania Marcotti
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
| | | | - Elena M Drudi
- Centre for Inflammation Biology & Cancer Immunology, Department of Inflammation Biology, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Vivienne Leech
- Department of Mathematics, University College London, UK
| | - Rachel E Bell
- Centre for Inflammation Biology & Cancer Immunology, Department of Inflammation Biology, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Jennifer Easton
- Centre for Inflammation Biology & Cancer Immunology, Department of Inflammation Biology, School of Immunology & Microbial Sciences, King's College London, London, UK
| | | | - Roland Fleck
- Centre for Ultrastructure Imaging, King's College London, UK
| | - Leanne Allison
- Centre for Ultrastructure Imaging, King's College London, UK
| | - Christina Philippeos
- Centre for Stem Cells and Regenerative Medicine, King's College London, London, UK
| | - Angelika Manhart
- Department of Mathematics, University College London, UK; Faculty of Mathematics, University of Vienna, Vienna, Austria
| | - Tanya J Shaw
- Centre for Inflammation Biology & Cancer Immunology, Department of Inflammation Biology, School of Immunology & Microbial Sciences, King's College London, London, UK.
| | - Brian M Stramer
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK.
| |
Collapse
|
3
|
Rafaeva M, Jensen ARD, Horton ER, Zornhagen KW, Strøbech JE, Fleischhauer L, Mayorca-Guiliani AE, Nielsen SR, Grønseth DS, Kuś F, Schoof EM, Arnes L, Koch M, Clausen-Schaumann H, Izzi V, Reuten R, Erler JT. Fibroblast-derived matrix models desmoplastic properties and forms a prognostic signature in cancer progression. Front Immunol 2023; 14:1154528. [PMID: 37539058 PMCID: PMC10395327 DOI: 10.3389/fimmu.2023.1154528] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/30/2023] [Indexed: 08/05/2023] Open
Abstract
The desmoplastic reaction observed in many cancers is a hallmark of disease progression and prognosis, particularly in breast and pancreatic cancer. Stromal-derived extracellular matrix (ECM) is significantly altered in desmoplasia, and as such plays a critical role in driving cancer progression. Using fibroblast-derived matrices (FDMs), we show that cancer cells have increased growth on cancer associated FDMs, when compared to FDMs derived from non-malignant tissue (normal) fibroblasts. We assess the changes in ECM characteristics from normal to cancer-associated stroma at the primary tumor site. Compositional, structural, and mechanical analyses reveal significant differences, with an increase in abundance of core ECM proteins, coupled with an increase in stiffness and density in cancer-associated FDMs. From compositional changes of FDM, we derived a 36-ECM protein signature, which we show matches in large part with the changes in pancreatic ductal adenocarcinoma (PDAC) tumor and metastases progression. Additionally, this signature also matches at the transcriptomic level in multiple cancer types in patients, prognostic of their survival. Together, our results show relevance of FDMs for cancer modelling and identification of desmoplastic ECM components for further mechanistic studies.
Collapse
Affiliation(s)
- Maria Rafaeva
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Adina R. D. Jensen
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Edward R. Horton
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Kamilla W. Zornhagen
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Jan E. Strøbech
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Lutz Fleischhauer
- Center for Applied Tissue Engineering and Regenerative Medicine-CANTER, Munich University of Applied Sciences, Munich, Germany
- Center for NanoScience – CsNS, Ludwig-Maximilians-University Munich, Munich, Germany
| | | | - Sebastian R. Nielsen
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Dina S. Grønseth
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Filip Kuś
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Erwin M. Schoof
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Centre for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Luis Arnes
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Manuel Koch
- Center for Biochemistry, Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Institute for Dental Research and Oral Musculoskeletal Biology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Hauke Clausen-Schaumann
- Center for Applied Tissue Engineering and Regenerative Medicine-CANTER, Munich University of Applied Sciences, Munich, Germany
- Center for NanoScience – CsNS, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Valerio Izzi
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
- Faculty of Medicine, University of Oulu, Oulu, Finland
- Foundation for the Finnish Cancer Institute, Helsinki, Finland
| | - Raphael Reuten
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
- Institute of Experimental and Clinical Pharmacology and Toxicology, Medical Faculty, University of Freiburg, Freiburg, Germany
- Department of Obstetrics and Gynecology, Medical Center, University of Freiburg, Freiburg, Germany
| | - Janine T. Erler
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
4
|
Deforet M. Long-range alteration of the physical environment mediates cooperation between Pseudomonas aeruginosa swarming colonies. Environ Microbiol 2023. [PMID: 36964975 DOI: 10.1111/1462-2920.16373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 03/15/2023] [Indexed: 03/27/2023]
Abstract
Pseudomonas aeruginosa makes and secretes massive amounts of rhamnolipid surfactants that enable swarming motility over biogel surfaces. But how these rhamnolipids interact with biogels to assist swarming remains unclear. Here, I use a combination of optical techniques across scales and genetically engineered strains to demonstrate that rhamnolipids can induce agar gel swelling over distances >10,000× the body size of an individual cell. The swelling front is on the micrometric scale and is easily visible using shadowgraphy. Rhamnolipid transport is not restricted to the surface of the gel but occurs through the whole thickness of the plate and, consequently, the spreading dynamics depend on the local thickness. Surprisingly, rhamnolipids can cross the whole gel and induce swelling on the opposite side of a two-face Petri dish. The swelling front delimits an area where the mechanical properties of the surface properties are modified: water wets the surface more easily, which increases the motility of individual bacteria and enables collective motility. A genetically engineered mutant unable to secrete rhamnolipids (ΔrhlA), and therefore unable to swarm, is rescued from afar with rhamnolipids produced by a remote colony. These results exemplify the remarkable capacity of bacteria to change the physical environment around them and its ecological consequences.
Collapse
Affiliation(s)
- Maxime Deforet
- Sorbonne Université, Centre National de la Recherche Scientifique, Laboratoire Jean Perrin, LJP, Paris, 75005, France
| |
Collapse
|
5
|
Sarkar T, Yashunsky V, Brézin L, Blanch Mercader C, Aryaksama T, Lacroix M, Risler T, Joanny JF, Silberzan P. Crisscross multilayering of cell sheets. PNAS NEXUS 2023; 2:pgad034. [PMID: 36938501 PMCID: PMC10019763 DOI: 10.1093/pnasnexus/pgad034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 12/19/2022] [Accepted: 01/04/2023] [Indexed: 02/05/2023]
Abstract
Hydrostatic skeletons such as the Hydra's consist of two stacked layers of muscle cells perpendicularly oriented. In vivo, these bilayers first assemble, and then the muscle fibers of both layers develop and organize with this crisscross orientation. In the present work, we identify an alternative mechanism of crisscross bilayering of myoblasts in vitro, which results from the prior local organization of these active cells in the initial monolayer. The myoblast sheet can be described as a contractile active nematic in which, as expected, most of the +1/2 topological defects associated with this nematic order self-propel. However, as a result of the production of extracellular matrix (ECM) by the cells, a subpopulation of these comet-like defects does not show any self-propulsion. Perpendicular bilayering occurs at these stationary defects. Cells located at the head of these defects converge toward their core where they accumulate until they start migrating on top of the tail of the first layer, while the tail cells migrate in the opposite direction under the head. Since the cells keep their initial orientations, the two stacked layers end up perpendicularly oriented. This concerted process leading to a crisscross bilayering is mediated by the secretion of ECM.
Collapse
Affiliation(s)
- Trinish Sarkar
- Laboratoire PhysicoChimie Curie UMR168, Institut Curie, Paris Sciences et Lettres, Centre National de la Recherche Scientifique, Sorbonne Université, 11 Rue Pierre et Marie Curie, 75248 Paris, France
| | - Victor Yashunsky
- Laboratoire PhysicoChimie Curie UMR168, Institut Curie, Paris Sciences et Lettres, Centre National de la Recherche Scientifique, Sorbonne Université, 11 Rue Pierre et Marie Curie, 75248 Paris, France
- Department of Solar Energy and Environmental Physics, The Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Negev, 84990, Israel
| | - Louis Brézin
- Laboratoire PhysicoChimie Curie UMR168, Institut Curie, Paris Sciences et Lettres, Centre National de la Recherche Scientifique, Sorbonne Université, 11 Rue Pierre et Marie Curie, 75248 Paris, France
- Collège de France, Paris Sciences et Lettres, 11 place Marcelin Berthelot, 75231 Paris, France
| | - Carles Blanch Mercader
- Laboratoire PhysicoChimie Curie UMR168, Institut Curie, Paris Sciences et Lettres, Centre National de la Recherche Scientifique, Sorbonne Université, 11 Rue Pierre et Marie Curie, 75248 Paris, France
| | - Thibault Aryaksama
- Laboratoire PhysicoChimie Curie UMR168, Institut Curie, Paris Sciences et Lettres, Centre National de la Recherche Scientifique, Sorbonne Université, 11 Rue Pierre et Marie Curie, 75248 Paris, France
| | - Mathilde Lacroix
- Laboratoire PhysicoChimie Curie UMR168, Institut Curie, Paris Sciences et Lettres, Centre National de la Recherche Scientifique, Sorbonne Université, 11 Rue Pierre et Marie Curie, 75248 Paris, France
| | - Thomas Risler
- Laboratoire PhysicoChimie Curie UMR168, Institut Curie, Paris Sciences et Lettres, Centre National de la Recherche Scientifique, Sorbonne Université, 11 Rue Pierre et Marie Curie, 75248 Paris, France
| | - Jean-François Joanny
- Laboratoire PhysicoChimie Curie UMR168, Institut Curie, Paris Sciences et Lettres, Centre National de la Recherche Scientifique, Sorbonne Université, 11 Rue Pierre et Marie Curie, 75248 Paris, France
- Collège de France, Paris Sciences et Lettres, 11 place Marcelin Berthelot, 75231 Paris, France
| | | |
Collapse
|
6
|
Erlich A, Étienne J, Fouchard J, Wyatt T. How dynamic prestress governs the shape of living systems, from the subcellular to tissue scale. Interface Focus 2022; 12:20220038. [PMID: 36330322 PMCID: PMC9560792 DOI: 10.1098/rsfs.2022.0038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 09/08/2022] [Indexed: 10/16/2023] Open
Abstract
Cells and tissues change shape both to carry out their function and during pathology. In most cases, these deformations are driven from within the systems themselves. This is permitted by a range of molecular actors, such as active crosslinkers and ion pumps, whose activity is biologically controlled in space and time. The resulting stresses are propagated within complex and dynamical architectures like networks or cell aggregates. From a mechanical point of view, these effects can be seen as the generation of prestress or prestrain, resulting from either a contractile or growth activity. In this review, we present this concept of prestress and the theoretical tools available to conceptualize the statics and dynamics of living systems. We then describe a range of phenomena where prestress controls shape changes in biopolymer networks (especially the actomyosin cytoskeleton and fibrous tissues) and cellularized tissues. Despite the diversity of scale and organization, we demonstrate that these phenomena stem from a limited number of spatial distributions of prestress, which can be categorized as heterogeneous, anisotropic or differential. We suggest that in addition to growth and contraction, a third type of prestress-topological prestress-can result from active processes altering the microstructure of tissue.
Collapse
Affiliation(s)
| | - Jocelyn Étienne
- Université Grenoble Alpes, CNRS, LIPHY, 38000 Grenoble, France
| | - Jonathan Fouchard
- Laboratoire de Biologie du Développement, Institut de Biologie Paris Seine (IBPS), Sorbonne Université, CNRS (UMR 7622), INSERM (URL 1156), 7 quai Saint Bernard, 75005 Paris, France
| | - Tom Wyatt
- Wellcome Trust–Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| |
Collapse
|
7
|
Combining experiments and in silico modeling to infer the role of adhesion and proliferation on the collective dynamics of cells. Sci Rep 2021; 11:19894. [PMID: 34615941 PMCID: PMC8494750 DOI: 10.1038/s41598-021-99390-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 09/23/2021] [Indexed: 02/06/2023] Open
Abstract
The collective dynamics of cells on surfaces and interfaces poses technological and theoretical challenges in the study of morphogenesis, tissue engineering, and cancer. Different mechanisms are at play, including, cell–cell adhesion, cell motility, and proliferation. However, the relative importance of each one is elusive. Here, experiments with a culture of glioblastoma multiforme cells on a substrate are combined with in silico modeling to infer the rate of each mechanism. By parametrizing these rates, the time-dependence of the spatial correlation observed experimentally is reproduced. The obtained results suggest a reduction in cell–cell adhesion with the density of cells. The reason for such reduction and possible implications for the collective dynamics of cancer cells are discussed.
Collapse
|
8
|
Yin J, Lin C, Jiang M, Tang X, Xie D, Chen J, Ke R. CENPL, ISG20L2, LSM4, MRPL3 are four novel hub genes and may serve as diagnostic and prognostic markers in breast cancer. Sci Rep 2021; 11:15610. [PMID: 34341433 PMCID: PMC8328991 DOI: 10.1038/s41598-021-95068-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 07/14/2021] [Indexed: 12/18/2022] Open
Abstract
As a highly prevalent disease among women worldwide, breast cancer remains in urgent need of further elucidation its molecular mechanisms to improve the patient outcomes. Identifying hub genes involved in the pathogenesis and progression of breast cancer can potentially help to unveil mechanism and also provide novel diagnostic and prognostic markers. In this study, we integrated multiple bioinformatic methods and RNA in situ detection technology to identify and validate hub genes. EZH2 was recognized as a key gene by PPI network analysis. CENPL, ISG20L2, LSM4, MRPL3 were identified as four novel hub genes through the WGCNA analysis and literate search. Among these, many studies on EZH2 in breast cancer have been reported, but no studies are related to the roles of CENPL, ISG20L2, MRPL3 and LSM4 in breast cancer. These four novel hub genes were up-regulated in tumor tissues and associated with cancer progression. The receiver operating characteristic analysis and Kaplan–Meier survival analysis indicated that these four hub genes are promising candidate genes that can serve as diagnostic and prognostic biomarkers for breast cancer. Moreover, these four newly identified hub genes as aberrant molecules in the maintenance of breast cancer development, their exact functional mechanisms deserve further in-depth study.
Collapse
Affiliation(s)
- Jinbao Yin
- School of Medicine, Huaqiao University, Quanzhou, 362021, Fujian, China.,Department of Pathology, Guangdong Medical University, Dongguan, 523808, Guangdong, China
| | - Chen Lin
- School of Medicine, Huaqiao University, Quanzhou, 362021, Fujian, China
| | - Meng Jiang
- School of Medicine, Huaqiao University, Quanzhou, 362021, Fujian, China
| | - Xinbin Tang
- School of Medicine, Huaqiao University, Quanzhou, 362021, Fujian, China
| | - Danlin Xie
- School of Medicine, Huaqiao University, Quanzhou, 362021, Fujian, China
| | - Jingwen Chen
- School of Medicine, Huaqiao University, Quanzhou, 362021, Fujian, China
| | - Rongqin Ke
- School of Medicine, Huaqiao University, Quanzhou, 362021, Fujian, China.
| |
Collapse
|
9
|
Wershof E, Park D, Barry DJ, Jenkins RP, Rullan A, Wilkins A, Schlegelmilch K, Roxanis I, Anderson KI, Bates PA, Sahai E. A FIJI macro for quantifying pattern in extracellular matrix. Life Sci Alliance 2021; 4:e202000880. [PMID: 33504622 PMCID: PMC7898596 DOI: 10.26508/lsa.202000880] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 01/07/2021] [Accepted: 01/08/2021] [Indexed: 11/24/2022] Open
Abstract
Diverse extracellular matrix patterns are observed in both normal and pathological tissue. However, most current tools for quantitative analysis focus on a single aspect of matrix patterning. Thus, an automated pipeline that simultaneously quantifies a broad range of metrics and enables a comprehensive description of varied matrix patterns is needed. To this end, we have developed an ImageJ plugin called TWOMBLI, which stands for The Workflow Of Matrix BioLogy Informatics. This pipeline includes metrics of matrix alignment, length, branching, end points, gaps, fractal dimension, curvature, and the distribution of fibre thickness. TWOMBLI is designed to be quick, versatile and easy-to-use particularly for non-computational scientists. TWOMBLI can be downloaded from https://github.com/wershofe/TWOMBLI together with detailed documentation and tutorial video. Although developed with the extracellular matrix in mind, TWOMBLI is versatile and can be applied to vascular and cytoskeletal networks. Here we present an overview of the pipeline together with examples from a wide range of contexts where matrix patterns are generated.
Collapse
Affiliation(s)
- Esther Wershof
- Biomolecular Modelling Laboratory, The Francis Crick Institute, London, UK
- Tumour Cell Biology Laboratory, The Francis Crick Institute, London, UK
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
| | - Danielle Park
- Developmental Signalling Laboratory, The Francis Crick Institute, London, UK
| | - David J Barry
- Advanced Light Microscopy Facility, The Francis Crick Institute, London, UK
| | - Robert P Jenkins
- Tumour Cell Biology Laboratory, The Francis Crick Institute, London, UK
| | - Antonio Rullan
- Tumour Cell Biology Laboratory, The Francis Crick Institute, London, UK
| | - Anna Wilkins
- Tumour Cell Biology Laboratory, The Francis Crick Institute, London, UK
| | | | - Ioannis Roxanis
- Breast Cancer Research Division, Toby Robins Breast Cancer Now Research Centre, The Institute of Cancer Research, London, UK
| | - Kurt I Anderson
- Advanced Light Microscopy Facility, The Francis Crick Institute, London, UK
| | - Paul A Bates
- Biomolecular Modelling Laboratory, The Francis Crick Institute, London, UK
| | - Erik Sahai
- Tumour Cell Biology Laboratory, The Francis Crick Institute, London, UK
| |
Collapse
|
10
|
Butler G, Keeton SJ, Johnson LJ, Dash PR. A phenotypic switch in the dispersal strategy of breast cancer cells selected for metastatic colonization. Proc Biol Sci 2020; 287:20202523. [PMID: 33259764 DOI: 10.1098/rspb.2020.2523] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
An important question in cancer evolution concerns which traits make a cell likely to successfully metastasize. Cell motility phenotypes, mediated by cell shape change, are strong candidates. We experimentally evolved breast cancer cells in vitro for metastatic capability, using selective regimes designed to simulate stages of metastasis, then quantified their motility behaviours using computer vision. All evolved lines showed changes to motility phenotypes, and we have identified a previously unknown density-dependent motility phenotype only seen in cells selected for colonization of decellularized lung tissue. These cells increase their rate of morphological change with an increase in migration speed when local cell density is high. However, when the local cell density is low, we find the opposite relationship: the rate of morphological change decreases with an increase in migration speed. Neither the ancestral population, nor cells selected for their ability to escape or invade extracellular matrix-like environments, displays this dynamic behavioural switch. Our results suggest that cells capable of distant-site colonization may be characterized by dynamic morphological phenotypes and the capacity to respond to the local social environment.
Collapse
Affiliation(s)
- George Butler
- School of Biological Sciences, University of Reading, Reading, UK
| | - Shirley J Keeton
- School of Biological Sciences, University of Reading, Reading, UK
| | - Louise J Johnson
- School of Biological Sciences, University of Reading, Reading, UK
| | - Philip R Dash
- School of Biological Sciences, University of Reading, Reading, UK
| |
Collapse
|