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Diepeveen MH, Lathouwers D, José Santo R, Hoogeman MS, Habraken SJM. Two-dimensional oxygen-diffusion modelling for FLASH proton therapy with pencil beam scanning-Impact of diffusive tissue properties, dose, dose rate and scan patterns. Phys Med Biol 2024; 69:155020. [PMID: 38959905 DOI: 10.1088/1361-6560/ad5eee] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 07/03/2024] [Indexed: 07/05/2024]
Abstract
Objective.Oxygen depletion is generally believed to play an important role in the FLASH effect-a differential reduction of the radiosensitivity of healthy tissues, relative to that of the tumour under ultra-high dose-rate (UHDR) irradiation conditions. In proton therapy (PT) with pencil-beam scanning (PBS), the deposition of dose, and, hence, the degree of (radiolytic) oxygen depletion varies both spatially and temporally. Therefore, the resulting oxygen concentration and the healthy-tissue sparing effect through radiation-induced hypoxia varies both spatially and temporally as well.Approach.We propose and numerically solve a physical oxygen diffusion model to study these effects and their dependence on tissue parameters and the scan pattern in pencil-beam delivery. Since current clinical FLASH PT (FLASH-PT) is based on 250 MeV shoot-through (transmission) beams, for which dose and dose rate (DR) hardly vary with depth compared to the variation transverse to the beam axis, we focus on the two-dimensional case. We numerically integrate the model to obtain the oxygen concentration in each voxel as a function of time and extract voxel-based and spatially and temporarily integrated metrics for oxygen (FLASH) enhanced dose. Furthermore, we evaluate the impact on oxygen enhancement of standard pencil-beam delivery patterns and patterns that were optimised on dose-rate. Our model can contribute to the identification of tissue properties and pencil-beam delivery parameters that are critical for FLASH-PT and it may be used for the optimisation of FLASH-PT treatment plans and their delivery.Main results.(i) the diffusive properties of oxygen are critical for the steady state concentration and therefore the FLASH effect, even more so in two dimensions when compared to one dimension. (ii) The FLASH effect through oxygen depletion depends primarily on dose and less on other parameters. (iii) At a fixed fraction dose there is a slight dependence on DR. (iv) Scan patterns optimised on DR slightly increase the oxygen induced FLASH effect.Significance.To our best knowledge, this is the first study assessing the impact of scan-pattern optimization (SPO) in FLASH-PT with PBS on a biological FLASH model. While the observed impact of SPO is relatively small, a larger effect is expected for larger target volumes. A better understanding of the FLASH effect and the role of oxygen (depletion) therein is essential for the further development of FLASH-PT with PBS, and SPO.
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Affiliation(s)
- Maarten H Diepeveen
- Erasmus MC Cancer Institute, University Medical Center Rotterdam, Department of Radiotherapy, Rotterdam, The Netherlands
- Delft University of Technology, Department of Radiation Science and Technology, Delft, The Netherlands
| | - Danny Lathouwers
- Delft University of Technology, Department of Radiation Science and Technology, Delft, The Netherlands
- Holland Proton Therapy Center, Department of Medical Physics and Informatics, Delft, The Netherlands
| | - Rodrigo José Santo
- Erasmus MC Cancer Institute, University Medical Center Rotterdam, Department of Radiotherapy, Rotterdam, The Netherlands
- Holland Proton Therapy Center, Department of Medical Physics and Informatics, Delft, The Netherlands
| | - Mischa S Hoogeman
- Erasmus MC Cancer Institute, University Medical Center Rotterdam, Department of Radiotherapy, Rotterdam, The Netherlands
- Delft University of Technology, Department of Radiation Science and Technology, Delft, The Netherlands
- Holland Proton Therapy Center, Department of Medical Physics and Informatics, Delft, The Netherlands
| | - Steven J M Habraken
- Erasmus MC Cancer Institute, University Medical Center Rotterdam, Department of Radiotherapy, Rotterdam, The Netherlands
- Holland Proton Therapy Center, Department of Medical Physics and Informatics, Delft, The Netherlands
- Leiden University Medical Center, Department of Radiotherapy,Leiden, The Netherlands
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Waigh TA, Korabel N. Heterogeneous anomalous transport in cellular and molecular biology. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2023; 86:126601. [PMID: 37863075 DOI: 10.1088/1361-6633/ad058f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 10/20/2023] [Indexed: 10/22/2023]
Abstract
It is well established that a wide variety of phenomena in cellular and molecular biology involve anomalous transport e.g. the statistics for the motility of cells and molecules are fractional and do not conform to the archetypes of simple diffusion or ballistic transport. Recent research demonstrates that anomalous transport is in many cases heterogeneous in both time and space. Thus single anomalous exponents and single generalised diffusion coefficients are unable to satisfactorily describe many crucial phenomena in cellular and molecular biology. We consider advances in the field ofheterogeneous anomalous transport(HAT) highlighting: experimental techniques (single molecule methods, microscopy, image analysis, fluorescence correlation spectroscopy, inelastic neutron scattering, and nuclear magnetic resonance), theoretical tools for data analysis (robust statistical methods such as first passage probabilities, survival analysis, different varieties of mean square displacements, etc), analytic theory and generative theoretical models based on simulations. Special emphasis is made on high throughput analysis techniques based on machine learning and neural networks. Furthermore, we consider anomalous transport in the context of microrheology and the heterogeneous viscoelasticity of complex fluids. HAT in the wavefronts of reaction-diffusion systems is also considered since it plays an important role in morphogenesis and signalling. In addition, we present specific examples from cellular biology including embryonic cells, leucocytes, cancer cells, bacterial cells, bacterial biofilms, and eukaryotic microorganisms. Case studies from molecular biology include DNA, membranes, endosomal transport, endoplasmic reticula, mucins, globular proteins, and amyloids.
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Affiliation(s)
- Thomas Andrew Waigh
- Biological Physics, School of Physics and Astronomy, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Nickolay Korabel
- Department of Mathematics, The University of Manchester, Manchester M13 9PL, United Kingdom
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Gong X, Nguyen R, Chen Z, Wen Z, Zhang X, Mak M. Volumetric Compression Shifts Rho GTPase Balance and Induces Mechanobiological Cell State Transition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.08.561452. [PMID: 37873466 PMCID: PMC10592676 DOI: 10.1101/2023.10.08.561452] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
During development and disease progression, cells are subject to osmotic and mechanical stresses that modulate cell volume, which fundamentally influences cell homeostasis and has been linked to a variety of cellular functions. It is not well understood how the mechanobiological state of cells is programmed by the interplay of intracellular organization and complex extracellular mechanics when stimulated by cell volume modulation. Here, by controlling cell volume via osmotic pressure, we evaluate physical phenotypes (including cell shape, morphodynamics, traction force, and extracellular matrix (ECM) remodeling) and molecular signaling (YAP), and we uncover fundamental transitions in active biophysical states. We demonstrate that volumetric compression shifts the ratiometric balance of Rho GTPase activities, thereby altering mechanosensing and cytoskeletal organization in a reversible manner. Specifically, volumetric compression controls cell spreading, adhesion formation, and YAP nuclear translocation, while maintaining cell contractile activity. Furthermore, we show that on physiologically relevant fibrillar collagen I matrices, which are highly non-elastic, cells exhibit additional modes of cell volume-dependent mechanosensing that are not observable on elastic substrates. Notably, volumetric compression regulates the dynamics of cell-ECM interactions and irreversible ECM remodeling via Rac-directed protrusion dynamics, at both the single-cell level and the multicellular level. Our findings support that cell volume is a master biophysical regulator and reveal its roles in cell mechanical state transition, cell-ECM interactions, and biophysical tissue programming.
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Hu Y, Becker ML, Willits RK. Quantification of cell migration: metrics selection to model application. Front Cell Dev Biol 2023; 11:1155882. [PMID: 37255596 PMCID: PMC10225508 DOI: 10.3389/fcell.2023.1155882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/05/2023] [Indexed: 06/01/2023] Open
Abstract
Cell migration plays an essential role in physiological and pathological states, such as immune response, tissue generation and tumor development. This phenomenon can occur spontaneously or it can be triggered by an external stimuli, including biochemical, mechanical, or electrical cues that induce or direct cells to migrate. The migratory response to these cues is foundational to several fields including neuroscience, cancer and regenerative medicine. Various platforms are available to qualitatively and quantitatively measure cell migration, making the measurements of cell motility straight-forward. Migratory behavior must be analyzed by multiple metrics and then models to connect the measurements to physiological meaning. This review will focus on describing and quantifying cell movement for individual cell migration.
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Affiliation(s)
- Yang Hu
- Department of Chemical Engineering, College of Engineering, Northeastern University, Boston, MA, United States
| | - Matthew L. Becker
- Departments of Chemistry, Mechanical Engineering and Materials Science, Biomedical Engineering and Orthopedic Surgery, Duke University, Durham, NC, United States
| | - Rebecca Kuntz Willits
- Department of Chemical Engineering, College of Engineering, Northeastern University, Boston, MA, United States
- Department of Bioengineering, College of Engineering, Northeastern University, Boston, MA, United States
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5
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Buckwar E, Conte M, Meddah A. A stochastic hierarchical model for low grade glioma evolution. J Math Biol 2023; 86:89. [PMID: 37147527 PMCID: PMC10163130 DOI: 10.1007/s00285-023-01909-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 03/17/2023] [Accepted: 03/22/2023] [Indexed: 05/07/2023]
Abstract
A stochastic hierarchical model for the evolution of low grade gliomas is proposed. Starting with the description of cell motion using a piecewise diffusion Markov process (PDifMP) at the cellular level, we derive an equation for the density of the transition probability of this Markov process based on the generalised Fokker-Planck equation. Then, a macroscopic model is derived via parabolic limit and Hilbert expansions in the moment equations. After setting up the model, we perform several numerical tests to study the role of the local characteristics and the extended generator of the PDifMP in the process of tumour progression. The main aim focuses on understanding how the variations of the jump rate function of this process at the microscopic scale and the diffusion coefficient at the macroscopic scale are related to the diffusive behaviour of the glioma cells and to the onset of malignancy, i.e., the transition from low-grade to high-grade gliomas.
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Affiliation(s)
- Evelyn Buckwar
- Institute of Stochastics, Johannes Kepler University, Altenberger Straße 69, 4040, Linz, Austria
- Centre for Mathematical Sciences, Lund University, 221 00, Lund, Sweden
| | - Martina Conte
- Department of Mathematical Sciences "G. L. Lagrange", Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129, Torino, Italy
| | - Amira Meddah
- Institute of Stochastics, Johannes Kepler University, Altenberger Straße 69, 4040, Linz, Austria.
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Pérez-Rodríguez S, Borau C, García-Aznar JM, Gonzalo-Asensio J. A microfluidic-based analysis of 3D macrophage migration after stimulation by Mycobacterium, Salmonella and Escherichia. BMC Microbiol 2022; 22:211. [PMID: 36045335 PMCID: PMC9429415 DOI: 10.1186/s12866-022-02623-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/22/2022] [Indexed: 11/23/2022] Open
Abstract
Macrophages play an essential role in the process of recognition and containment of microbial infections. These immune cells are recruited to infectious sites to reach and phagocytose pathogens. Specifically, in this article, bacteria from the genus Mycobacterium, Salmonella and Escherichia, were selected to study the directional macrophage movement towards different bacterial fractions. We recreated a three-dimensional environment in a microfluidic device, using a collagen-based hydrogel that simulates the mechanical microarchitecture associated to the Extra Cellular Matrix (ECM). First, we showed that macrophage migration is affected by the collagen concentration of their environment, migrating greater distances at higher velocities with decreasing collagen concentrations. To recreate the infectious microenvironment, macrophages were exposed to lateral gradients of bacterial fractions obtained from the intracellular pathogens M. tuberculosis and S. typhimurium. Our results showed that macrophages migrated directionally, and in a concentration-dependent manner, towards the sites where bacterial fractions are located, suggesting the presence of attractants molecules in all the samples. We confirmed that purified M. tuberculosis antigens, as ESAT-6 and CFP-10, stimulated macrophage recruitment in our device. Finally, we also observed that macrophages migrate towards fractions from non-pathogenic bacteria, such as M. smegmatis and Escherichia coli. In conclusion, our microfluidic device is a useful tool which opens new perspectives to study the recognition of specific antigens by innate immune cells.
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Hohmann T, Hohmann U, Dahlmann M, Kobelt D, Stein U, Dehghani F. MACC1-Induced Collective Migration Is Promoted by Proliferation Rather Than Single Cell Biomechanics. Cancers (Basel) 2022; 14:cancers14122857. [PMID: 35740524 PMCID: PMC9221534 DOI: 10.3390/cancers14122857] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/25/2022] [Accepted: 06/07/2022] [Indexed: 02/05/2023] Open
Abstract
Metastasis-associated in colon cancer 1 (MACC1) is a marker for metastasis, tumor cell migration, and increased proliferation in colorectal cancer (CRC). Tumors with high MACC1 expression show a worse prognosis and higher invasion into neighboring structures. Yet, many facets of the pro-migratory effects are not fully understood. Atomic force microscopy and single cell live imaging were used to quantify biomechanical and migratory properties in low- and high-MACC1-expressing CRC cells. Furthermore, collective migration and expansion of small, cohesive cell colonies were analyzed using live cell imaging and particle image velocimetry. Lastly, the impact of proliferation on collective migration was determined by inhibition of proliferation using mitomycin. MACC1 did not affect elasticity, cortex tension, and single cell migration of CRC cells but promoted collective migration and colony expansion in vitro. Measurements of the local velocities in the dense cell layers revealed proliferation events as regions of high local speeds. Inhibition of proliferation via mitomycin abrogated the MACC1-associated effects on the collective migration speeds. A simple simulation revealed that the expansion of cell clusters without proliferation appeared to be determined mostly by single cell properties. MACC1 overexpression does not influence single cell biomechanics and migration but only collective migration in a proliferation-dependent manner. Thus, targeting proliferation in high-MACC1-expressing tumors may offer additional effects on cell migration.
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Affiliation(s)
- Tim Hohmann
- Department of Anatomy and Cell Biology, Martin Luther University Halle-Wittenberg, Grosse Steinstrasse 52, D-06108 Halle (Saale), Germany; (T.H.); (U.H.)
| | - Urszula Hohmann
- Department of Anatomy and Cell Biology, Martin Luther University Halle-Wittenberg, Grosse Steinstrasse 52, D-06108 Halle (Saale), Germany; (T.H.); (U.H.)
| | - Mathias Dahlmann
- Experimental and Clinical Research Center, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Charité—Universitätsmedizin Berlin, Robert-Rössle-Straße 10, D-13125 Berlin, Germany; (M.D.); (D.K.)
- German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany
| | - Dennis Kobelt
- Experimental and Clinical Research Center, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Charité—Universitätsmedizin Berlin, Robert-Rössle-Straße 10, D-13125 Berlin, Germany; (M.D.); (D.K.)
- German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany
| | - Ulrike Stein
- Experimental and Clinical Research Center, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Charité—Universitätsmedizin Berlin, Robert-Rössle-Straße 10, D-13125 Berlin, Germany; (M.D.); (D.K.)
- German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany
- Correspondence: (U.S.); (F.D.); Tel.: +49-9406-3432 (U.S.); +49-345-5571-944 (F.D.); Fax: +49-345-5571-700 (F.D.)
| | - Faramarz Dehghani
- Department of Anatomy and Cell Biology, Martin Luther University Halle-Wittenberg, Grosse Steinstrasse 52, D-06108 Halle (Saale), Germany; (T.H.); (U.H.)
- Correspondence: (U.S.); (F.D.); Tel.: +49-9406-3432 (U.S.); +49-345-5571-944 (F.D.); Fax: +49-345-5571-700 (F.D.)
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8
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Scott M, Żychaluk K, Bearon RN. A mathematical framework for modelling 3D cell motility: applications to glioblastoma cell migration. MATHEMATICAL MEDICINE AND BIOLOGY-A JOURNAL OF THE IMA 2021; 38:333-354. [PMID: 34189581 DOI: 10.1093/imammb/dqab009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 06/09/2021] [Accepted: 06/10/2021] [Indexed: 11/14/2022]
Abstract
The collection of 3D cell tracking data from live images of micro-tissues is a recent innovation made possible due to advances in imaging techniques. As such there is increased interest in studying cell motility in 3D in vitro model systems but a lack of rigorous methodology for analysing the resulting data sets. One such instance of the use of these in vitro models is in the study of cancerous tumours. Growing multicellular tumour spheroids in vitro allows for modelling of the tumour microenvironment and the study of tumour cell behaviours, such as migration, which improves understanding of these cells and in turn could potentially improve cancer treatments. In this paper, we present a workflow for the rigorous analysis of 3D cell tracking data, based on the persistent random walk model, but adaptable to other biologically informed mathematical models. We use statistical measures to assess the fit of the model to the motility data and to estimate model parameters and provide confidence intervals for those parameters, to allow for parametrization of the model taking correlation in the data into account. We use in silico simulations to validate the workflow in 3D before testing our method on cell tracking data taken from in vitro experiments on glioblastoma tumour cells, a brain cancer with a very poor prognosis. The presented approach is intended to be accessible to both modellers and experimentalists alike in that it provides tools for uncovering features of the data set that may suggest amendments to future experiments or modelling attempts.
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Affiliation(s)
- M Scott
- Department of Mathematical Sciences, University of Liverpool, Liverpool L69 7ZL, UK
| | - K Żychaluk
- Department of Mathematical Sciences, University of Liverpool, Liverpool L69 7ZL, UK
| | - R N Bearon
- Department of Mathematical Sciences, University of Liverpool, Liverpool L69 7ZL, UK
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9
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Koshkin V, De Oliveira MB, Peng C, Ailles LE, Liu G, Covens A, Krylov SN. Multi-drug-resistance efflux in cisplatin-naive and cisplatin-exposed A2780 ovarian cancer cells responds differently to cell culture dimensionality. Mol Clin Oncol 2021; 15:161. [PMID: 34295468 PMCID: PMC8273925 DOI: 10.3892/mco.2021.2323] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 06/02/2021] [Indexed: 01/20/2023] Open
Abstract
A primary reason for chemotherapy failure is chemoresistance, which is driven by various mechanisms. Multi-drug resistance (MDR) is one such mechanism that is responsible for drug extrusion from the intracellular space. MDR can be intrinsic and thus, may pre-exist the first application of chemotherapy. However, MDR may also be acquired during tumor exposure to chemotherapeutic agents. To understand whether cell clustering can influence intrinsic and acquired MDR, the present study assessed cultured monolayers (representing individual cells) and spheroids (representing clusters) formed by cisplatin-naïve (intrinsic MDR) and cisplatin-exposed (acquired MDR) lines of ovarian cancer A2780 cells by determining the cytometry of reaction rate constant (CRRC). MDR efflux was characterized using accurate and robust cell number vs. MDR efflux rate constant (kMDR) histograms. Both cisplatin-naïve and cisplatin-exposed monolayer cells presented unimodal histograms; the histogram of cisplatin-exposed cells was shifted towards a higher kMDR value suggesting greater MDR activity. Spheroids of cisplatin-naïve cells presented a bimodal histogram indicating the presence of two subpopulations with different MDR activity. In contrast, spheroids of cisplatin-exposed cells presented a unimodal histogram qualitatively similar to that of the monolayers of cisplatin-exposed cells but with a moderate shift towards greater MDR activity. A flow-cytometry assessment of multidrug resistance-associated protein 1 transporter levels in monolayers and dissociated spheroids revealed distributions similar to those of kMDR, thus, suggesting a plausible molecular mechanism for the observed differences in MDR activity. The observed greater effect of cell clustering on intrinsic rather than in acquired MDR can help guide the development of new therapeutic strategies targeting clusters of circulating tumor cells.
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Affiliation(s)
- Vasilij Koshkin
- Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | | | - Chun Peng
- Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Laurie E Ailles
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Geoffrey Liu
- Department of Medicine, Medical Oncology, Princess Margaret Cancer Centre, Toronto, Ontario M5G 2M9, Canada
| | - Allan Covens
- Sunnybrook Odette Cancer Centre, Toronto, Ontario M4N 3M5, Canada
| | - Sergey N Krylov
- Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
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10
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Scheda R, Vitali S, Giampieri E, Pagnini G, Zironi I. Study of Wound Healing Dynamics by Single Pseudo-Particle Tracking in Phase Contrast Images Acquired in Time-Lapse. ENTROPY 2021; 23:e23030284. [PMID: 33652826 PMCID: PMC7996888 DOI: 10.3390/e23030284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 02/11/2021] [Accepted: 02/23/2021] [Indexed: 11/16/2022]
Abstract
Cellular contacts modify the way cells migrate in a cohesive group with respect to a free single cell. The resulting motion is persistent and correlated, with cells’ velocities self-aligning in time. The presence of a dense agglomerate of cells makes the application of single particle tracking techniques to define cells dynamics difficult, especially in the case of phase contrast images. Here, we propose an original pipeline for the analysis of phase contrast images of the wound healing scratch assay acquired in time-lapse, with the aim of extracting single particle trajectories describing the dynamics of the wound closure. In such an approach, the membrane of the cells at the border of the wound is taken as a unicum, i.e., the wound edge, and the dynamics is described by the stochastic motion of an ensemble of points on such a membrane, i.e., pseudo-particles. For each single frame, the pipeline of analysis includes: first, a texture classification for separating the background from the cells and for identifying the wound edge; second, the computation of the coordinates of the ensemble of pseudo-particles, chosen to be uniformly distributed along the length of the wound edge. We show the results of this method applied to a glioma cell line (T98G) performing a wound healing scratch assay without external stimuli. We discuss the efficiency of the method to assess cell motility and possible applications to other experimental layouts, such as single cell motion. The pipeline is developed in the Python language and is available upon request.
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Affiliation(s)
- Riccardo Scheda
- DIFA-Physics and Astronomy Department, University of Bologna, Viale C. Berti Pichat 6/2, 40127 Bologna, Italy; (R.S.); (I.Z.)
| | - Silvia Vitali
- BCAM-Basque Center for Applied Mathematics, Alameda de Mazarredo 14, 48009 Bilbao, Spain;
- Correspondence:
| | - Enrico Giampieri
- eDIMESlab, Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Via Irnerio 49, 40126 Bologna, Italy;
| | - Gianni Pagnini
- BCAM-Basque Center for Applied Mathematics, Alameda de Mazarredo 14, 48009 Bilbao, Spain;
- Ikerbasque-Basque Foundation for Science, Plaza Euskadi 5, 48009 Bilbao, Spain
| | - Isabella Zironi
- DIFA-Physics and Astronomy Department, University of Bologna, Viale C. Berti Pichat 6/2, 40127 Bologna, Italy; (R.S.); (I.Z.)
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11
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Mitchell C, Caroff L, Solis-Lemus JA, Reyes-Aldasoro CC, Vigilante A, Warburton F, de Chaumont F, Dufour A, Dallongeville S, Olivo-Marin JC, Knight R. Cell Tracking Profiler - a user-driven analysis framework for evaluating 4D live-cell imaging data. J Cell Sci 2020; 133:jcs241422. [PMID: 33093241 PMCID: PMC7710012 DOI: 10.1242/jcs.241422] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 10/14/2020] [Indexed: 12/20/2022] Open
Abstract
Accurate measurements of cell morphology and behaviour are fundamentally important for understanding how disease, molecules and drugs affect cell function in vivo Here, by using muscle stem cell (muSC) responses to injury in zebrafish as our biological paradigm, we established a 'ground truth' for muSC behaviour. This revealed that segmentation and tracking algorithms from commonly used programs are error-prone, leading us to develop a fast semi-automated image analysis pipeline that allows user-defined parameters for segmentation and correction of cell tracking. Cell Tracking Profiler (CTP) is a package that runs two existing programs, HK Means and Phagosight within the Icy image analysis suite, to enable user-managed cell tracking from 3D time-lapse datasets to provide measures of cell shape and movement. We demonstrate how CTP can be used to reveal changes to cell behaviour of muSCs in response to manipulation of the cell cytoskeleton by small-molecule inhibitors. CTP and the associated tools we have developed for analysis of outputs thus provide a powerful framework for analysing complex cell behaviour in vivo from 4D datasets that are not amenable to straightforward analysis.
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Affiliation(s)
- Claire Mitchell
- Centre for Craniofacial and Regenerative Biology, King's College London, Guy's Hospital, London SE1 9RT, UK
| | - Lauryanne Caroff
- Centre for Craniofacial and Regenerative Biology, King's College London, Guy's Hospital, London SE1 9RT, UK
| | - Jose Alonso Solis-Lemus
- School of Mathematics, Computer Science and Engineering, City, University of London, Tait Building, Northampton Square, London EC1V 0HB, UK
| | - Constantino Carlos Reyes-Aldasoro
- School of Mathematics, Computer Science and Engineering, City, University of London, Tait Building, Northampton Square, London EC1V 0HB, UK
| | - Alessandra Vigilante
- Centre for Stem Cells and Regenerative Medicine, King's College London, Tower Wing, Guy's Hospital, London SE1 9RT, UK
| | - Fiona Warburton
- Centre for Oral, Clinical and Translational Sciences, King's College London, Guy's Hospital, London SE1 9RT, UK
| | | | - Alexandre Dufour
- Bioimage Analysis Unit, Institut Pasteur, Paris CEDEX 15, France
| | | | | | - Robert Knight
- Centre for Craniofacial and Regenerative Biology, King's College London, Guy's Hospital, London SE1 9RT, UK
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Baskaran JP, Weldy A, Guarin J, Munoz G, Shpilker PH, Kotlik M, Subbiah N, Wishart A, Peng Y, Miller MA, Cowen L, Oudin MJ. Cell shape, and not 2D migration, predicts extracellular matrix-driven 3D cell invasion in breast cancer. APL Bioeng 2020; 4:026105. [PMID: 32455252 PMCID: PMC7202897 DOI: 10.1063/1.5143779] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 04/14/2020] [Indexed: 12/13/2022] Open
Abstract
Metastasis, the leading cause of death in cancer patients, requires the invasion of tumor cells through the stroma in response to migratory cues, in part provided by the extracellular matrix (ECM). Recent advances in proteomics have led to the identification of hundreds of ECM proteins, which are more abundant in tumors relative to healthy tissue. Our goal was to develop a pipeline to easily predict which ECM proteins are more likely to have an effect on cancer invasion and metastasis. We evaluated the effect of four ECM proteins upregulated in breast tumor tissue in multiple human breast cancer cell lines in three assays. There was no linear relationship between cell adhesion to ECM proteins and ECM-driven 2D cell migration speed, persistence, or 3D invasion. We then used classifiers and partial-least squares regression analysis to identify which metrics best predicted ECM-driven 2D migration and 3D invasion responses. We find that ECM-driven 2D cell migration speed or persistence did not predict 3D invasion in response to the same cue. However, cell adhesion, and in particular cell elongation and shape irregularity, accurately predicted the magnitude of ECM-driven 2D migration and 3D invasion. Our models successfully predicted the effect of novel ECM proteins in a cell-line specific manner. Overall, our studies identify the cell morphological features that determine 3D invasion responses to individual ECM proteins. This platform will help provide insight into the functional role of ECM proteins abundant in tumor tissue and help prioritize strategies for targeting tumor-ECM interactions to treat metastasis.
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Affiliation(s)
- Janani P. Baskaran
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, USA
| | - Anna Weldy
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, USA
| | - Justinne Guarin
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, USA
| | - Gabrielle Munoz
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, USA
| | - Polina H. Shpilker
- Department of Computer Science, Tufts University, Medford, Massachusetts 02155, USA
| | - Michael Kotlik
- Department of Computer Science, Tufts University, Medford, Massachusetts 02155, USA
| | - Nandita Subbiah
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, USA
| | - Andrew Wishart
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, USA
| | - Yifan Peng
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, USA
| | - Miles A. Miller
- Center for Systems Biology, Massachusetts General Hospital Research Institute, Boston, Massachusetts 02114, USA
| | - Lenore Cowen
- Department of Computer Science, Tufts University, Medford, Massachusetts 02155, USA
| | - Madeleine J. Oudin
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, USA
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Galarza S, Kim H, Atay N, Peyton SR, Munson JM. 2D or 3D? How cell motility measurements are conserved across dimensions in vitro and translate in vivo. Bioeng Transl Med 2020; 5:e10148. [PMID: 31989037 PMCID: PMC6971446 DOI: 10.1002/btm2.10148] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 10/30/2019] [Accepted: 11/02/2019] [Indexed: 12/16/2022] Open
Abstract
Cell motility is a critical aspect of several processes, such as wound healing and immunity; however, it is dysregulated in cancer. Current limitations of imaging tools make it difficult to study cell migration in vivo. To overcome this, and to identify drivers from the microenvironment that regulate cell migration, bioengineers have developed 2D (two-dimensional) and 3D (three-dimensional) tissue model systems in which to study cell motility in vitro, with the aim of mimicking elements of the environments in which cells move in vivo. However, there has been no systematic study to explicitly relate and compare cell motility measurements between these geometries or systems. Here, we provide such analysis on our own data, as well as across data in existing literature to understand whether, and which, metrics are conserved across systems. To our surprise, only one metric of cell movement on 2D surfaces significantly and positively correlates with cell migration in 3D environments (percent migrating cells), and cell invasion in 3D has a weak, negative correlation with glioblastoma invasion in vivo. Finally, to compare across complex model systems, in vivo data, and data from different labs, we suggest that groups report an effect size, a statistical tool that is most translatable across experiments and labs, when conducting experiments that affect cellular motility.
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Affiliation(s)
- Sualyneth Galarza
- Department of Chemical EngineeringUniversity of Massachusetts AmherstAmherstMassachusetts
| | - Hyuna Kim
- Molecular and Cellular Biology ProgramUniversity of Massachusetts AmherstAmherstMassachusetts
| | - Naciye Atay
- Department of Biomedical Engineering and MechanicsVirginia Polytechnic Institute and State UniversityBlacksburgVirginia
| | - Shelly R. Peyton
- Department of Chemical EngineeringUniversity of Massachusetts AmherstAmherstMassachusetts
- Molecular and Cellular Biology ProgramUniversity of Massachusetts AmherstAmherstMassachusetts
| | - Jennifer M. Munson
- Department of Biomedical Engineering and MechanicsVirginia Polytechnic Institute and State UniversityBlacksburgVirginia
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