1
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Toscano E, Cimmino E, Pennacchio FA, Riccio P, Poli A, Liu YJ, Maiuri P, Sepe L, Paolella G. Methods and computational tools to study eukaryotic cell migration in vitro. Front Cell Dev Biol 2024; 12:1385991. [PMID: 38887515 PMCID: PMC11180820 DOI: 10.3389/fcell.2024.1385991] [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: 02/14/2024] [Accepted: 05/13/2024] [Indexed: 06/20/2024] Open
Abstract
Cellular movement is essential for many vital biological functions where it plays a pivotal role both at the single cell level, such as during division or differentiation, and at the macroscopic level within tissues, where coordinated migration is crucial for proper morphogenesis. It also has an impact on various pathological processes, one for all, cancer spreading. Cell migration is a complex phenomenon and diverse experimental methods have been developed aimed at dissecting and analysing its distinct facets independently. In parallel, corresponding analytical procedures and tools have been devised to gain deep insight and interpret experimental results. Here we review established experimental techniques designed to investigate specific aspects of cell migration and present a broad collection of historical as well as cutting-edge computational tools used in quantitative analysis of cell motion.
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Affiliation(s)
- Elvira Toscano
- Department of Molecular Medicine and Medical Biotechnology, Università Degli Studi di Napoli “Federico II”, Naples, Italy
- CEINGE Biotecnologie Avanzate Franco Salvatore, Naples, Italy
| | - Elena Cimmino
- Department of Molecular Medicine and Medical Biotechnology, Università Degli Studi di Napoli “Federico II”, Naples, Italy
| | - Fabrizio A. Pennacchio
- Laboratory of Applied Mechanobiology, Department of Health Sciences and Technology, Zurich, Switzerland
| | - Patrizia Riccio
- Department of Molecular Medicine and Medical Biotechnology, Università Degli Studi di Napoli “Federico II”, Naples, Italy
| | | | - Yan-Jun Liu
- Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Paolo Maiuri
- Department of Molecular Medicine and Medical Biotechnology, Università Degli Studi di Napoli “Federico II”, Naples, Italy
| | - Leandra Sepe
- Department of Molecular Medicine and Medical Biotechnology, Università Degli Studi di Napoli “Federico II”, Naples, Italy
| | - Giovanni Paolella
- Department of Molecular Medicine and Medical Biotechnology, Università Degli Studi di Napoli “Federico II”, Naples, Italy
- CEINGE Biotecnologie Avanzate Franco Salvatore, Naples, Italy
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2
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Seo B, Lee D, Jeon H, Ha J, Suh S. MotGen: a closed-loop bacterial motility control framework using generative adversarial networks. Bioinformatics 2024; 40:btae170. [PMID: 38552318 PMCID: PMC11031359 DOI: 10.1093/bioinformatics/btae170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 03/02/2024] [Accepted: 03/27/2024] [Indexed: 04/21/2024] Open
Abstract
MOTIVATION Many organisms' survival and behavior hinge on their responses to environmental signals. While research on bacteria-directed therapeutic agents has increased, systematic exploration of real-time modulation of bacterial motility remains limited. Current studies often focus on permanent motility changes through genetic alterations, restricting the ability to modulate bacterial motility dynamically on a large scale. To address this gap, we propose a novel real-time control framework for systematically modulating bacterial motility dynamics. RESULTS We introduce MotGen, a deep learning approach leveraging Generative Adversarial Networks to analyze swimming performance statistics of motile bacteria based on live cell imaging data. By tracking objects and optimizing cell trajectory mapping under environmentally altered conditions, we trained MotGen on a comprehensive statistical dataset derived from real image data. Our experimental results demonstrate MotGen's ability to capture motility dynamics from real bacterial populations with low mean absolute error in both simulated and real datasets. MotGen allows us to approach optimal swimming conditions for desired motility statistics in real-time. MotGen's potential extends to practical biomedical applications, including immune response prediction, by providing imputation of bacterial motility patterns based on external environmental conditions. Our short-term, in-situ interventions for controlling motility behavior offer a promising foundation for the development of bacteria-based biomedical applications. AVAILABILITY AND IMPLEMENTATION MotGen is presented as a combination of Matlab image analysis code and a machine learning workflow in Python. Codes are available at https://github.com/bgmseo/MotGen, for cell tracking and implementation of trained models to generate bacterial motility statistics.
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Affiliation(s)
- BoGeum Seo
- Department of Mechanical Engineering, Seoul National University, 08826 Seoul, Republic of Korea
| | - DoHee Lee
- Center for Healthcare Robotics, Korea Institute of Science & Technology, 02792 Seoul, Republic of Korea
| | - Heungjin Jeon
- Infection Control Convergence Research Center, Chungnam National University, 34134 Daejeon, Republic of Korea
| | - Junhyoung Ha
- Center for Healthcare Robotics, Korea Institute of Science & Technology, 02792 Seoul, Republic of Korea
| | - SeungBeum Suh
- Center for Healthcare Robotics, Korea Institute of Science & Technology, 02792 Seoul, Republic of Korea
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3
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Joshi AS, Madhusudanan M, Mijakovic I. 3D printed inserts for reproducible high throughput screening of cell migration. Front Cell Dev Biol 2023; 11:1256250. [PMID: 37711850 PMCID: PMC10498783 DOI: 10.3389/fcell.2023.1256250] [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: 07/10/2023] [Accepted: 08/07/2023] [Indexed: 09/16/2023] Open
Abstract
Cell migration is a fundamental and complex phenomenon that occurs in normal physiology and in diseases like cancer. Hence, understanding cell migration is very important in the fields of developmental biology and biomedical sciences. Cell migration occurs in 3 dimensions (3D) and involves an interplay of migrating cell(s), neighboring cells, extracellular matrix, and signaling molecules. To understand this phenomenon, most of the currently available techniques still rely on 2-dimensional (2D) cell migration assay, also known as the scratch assay or the wound healing assay. These methods suffer from limited reproducibility in creating a cell-free region (a scratch or a wound). Mechanical/heat related stress to cells is another issue which hampers the applicability of these methods. To tackle these problems, we developed an alternative method based on 3D printed biocompatible cell inserts, for quantifying cell migration in 24-well plates. The inserts were successfully validated via a high throughput assay for following migration of lung cancer cell line (A549 cell line) in the presence of standard cell migration promoters and inhibitors. We also developed an accompanying image analysis pipeline which demonstrated that our method outperforms the state-of-the-art methodologies for assessing the cell migration in terms of reproducibility and simplicity.
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Affiliation(s)
- Abhayraj S. Joshi
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Mukil Madhusudanan
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ivan Mijakovic
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
- Department of Biology and Biological Engineering, Division of Systems and Synthetic Biology, Chalmers University of Technology, Gothenburg, Sweden
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4
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Kołodziej T, Mielnicka A, Dziob D, Chojnacka AK, Rawski M, Mazurkiewicz J, Rajfur Z. Morphomigrational description as a new approach connecting cell's migration with its morphology. Sci Rep 2023; 13:11006. [PMID: 37419901 PMCID: PMC10328925 DOI: 10.1038/s41598-023-35827-9] [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: 08/03/2022] [Accepted: 05/24/2023] [Indexed: 07/09/2023] Open
Abstract
The examination of morphology and migration of cells plays substantial role in understanding the cellular behaviour, being described by plethora of quantitative parameters and models. These descriptions, however, treat cell migration and morphology as independent properties of temporal cell state, while not taking into account their strong interdependence in adherent cells. Here we present the new and simple mathematical parameter called signed morphomigrational angle (sMM angle) that links cell geometry with translocation of cell centroid, considering them as one morphomigrational behaviour. The sMM angle combined with pre-existing quantitative parameters enabled us to build a new tool called morphomigrational description, used to assign the numerical values to several cellular behaviours. Thus, the cellular activities that until now were characterized using verbal description or by complex mathematical models, are described here by a set of numbers. Our tool can be further used in automatic analysis of cell populations as well as in studies focused on cellular response to environmental directional signals.
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Affiliation(s)
- Tomasz Kołodziej
- Department of Pharmaceutical Biophysics, Faculty of Pharmacy, Jagiellonian University Medical College, ul. Medyczna 9, 30-688, Kraków, Poland.
- Department of Molecular and Interfacial Biophysics, Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, ul. Lojasiewicza 11, 30-348, Kraków, Poland.
| | - Aleksandra Mielnicka
- Department of Molecular and Interfacial Biophysics, Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, ul. Lojasiewicza 11, 30-348, Kraków, Poland
- BRAINCITY, Laboratory of Neurobiology, The Nencki Institute of Experimental Biology, PAS, ul. Ludwika Pasteura 3, 02-093, Warsaw, Poland
| | - Daniel Dziob
- Department of Pharmaceutical Biophysics, Faculty of Pharmacy, Jagiellonian University Medical College, ul. Medyczna 9, 30-688, Kraków, Poland
| | - Anna Katarzyna Chojnacka
- Department of Molecular and Interfacial Biophysics, Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, ul. Lojasiewicza 11, 30-348, Kraków, Poland
- Cellular Signalling and Cytoskeletal Function Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, United Kingdom
| | - Mateusz Rawski
- Laboratory of Inland Fisheries and Aquaculture, Department of Zoology, Faculty of Veterinary Medicine and Animal Science, Poznań University of Life Sciences, ul. Wojska Polskiego 71C, 60-625, Poznań, Poland
| | - Jan Mazurkiewicz
- Laboratory of Inland Fisheries and Aquaculture, Department of Zoology, Faculty of Veterinary Medicine and Animal Science, Poznań University of Life Sciences, ul. Wojska Polskiego 71C, 60-625, Poznań, Poland
| | - Zenon Rajfur
- Department of Molecular and Interfacial Biophysics, Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, ul. Lojasiewicza 11, 30-348, Kraków, Poland.
- Jagiellonian Center of Biomedical Imaging, Jagiellonian University, 30-348, Kraków, Poland.
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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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Hohmann T, Hohmann U, Dehghani F. MACC1-induced migration in tumors: Current state and perspective. Front Oncol 2023; 13:1165676. [PMID: 37051546 PMCID: PMC10084939 DOI: 10.3389/fonc.2023.1165676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 03/14/2023] [Indexed: 03/29/2023] Open
Abstract
Malignant tumors are still a global, heavy health burden. Many tumor types cannot be treated curatively, underlining the need for new treatment targets. In recent years, metastasis associated in colon cancer 1 (MACC1) was identified as a promising biomarker and drug target, as it is promoting tumor migration, initiation, proliferation, and others in a multitude of solid cancers. Here, we will summarize the current knowledge about MACC1-induced tumor cell migration with a special focus on the cytoskeletal and adhesive systems. In addition, a brief overview of several in vitro models used for the analysis of cell migration is given. In this context, we will point to issues with the currently most prevalent models used to study MACC1-dependent migration. Lastly, open questions about MACC1-dependent effects on tumor cell migration will be addressed.
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7
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Toscano E, Sepe L, del Giudice G, Tufano R, Paolella G. A three component model for superdiffusive motion effectively describes migration of eukaryotic cells moving freely or under a directional stimulus. PLoS One 2022; 17:e0272259. [PMID: 35917375 PMCID: PMC9345344 DOI: 10.1371/journal.pone.0272259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 07/15/2022] [Indexed: 11/25/2022] Open
Abstract
Although the simple diffusion model can effectively describe the movement of eukaryotic cells on a culture surface observed at relatively low sampling frequency, at higher sampling rates more complex models are often necessary to better fit the experimental data. Currently available models can describe motion paths by involving additional parameters, such as linearity or directional persistence in time. However sometimes difficulties arise as it is not easy to effectively evaluate persistence in presence of a directional bias. Here we present a procedure which helps solve this problem, based on a model which describes displacement as the vectorial sum of three components: diffusion, persistence and directional bias. The described model has been tested by analysing the migratory behaviour of simulated cell populations and used to analyse a collection of experimental datasets, obtained by observing cell cultures in time lapse microscopy. Overall, the method produces a good description of migration behaviour as it appears to capture the expected increase in the directional bias in presence of wound without a large concomitant increase in the persistence module, allowing it to remain as a physically meaningful quantity in the presence of a directional stimulus.
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Affiliation(s)
- Elvira Toscano
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli studi di Napoli “Federico II”, Napoli, Italy
- Ceinge Biotecnologie Avanzate, Napoli, Italy
| | - Leandra Sepe
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli studi di Napoli “Federico II”, Napoli, Italy
- Ceinge Biotecnologie Avanzate, Napoli, Italy
| | - Giusy del Giudice
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli studi di Napoli “Federico II”, Napoli, Italy
| | | | - Giovanni Paolella
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli studi di Napoli “Federico II”, Napoli, Italy
- Ceinge Biotecnologie Avanzate, Napoli, Italy
- * E-mail:
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8
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Shaji N, Nunes F, Ines Rocha M, Gomes EF, Castro H. MigraR: An open-source, R-based application for analysis and quantification of cell migration parameters. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2022; 213:106529. [PMID: 34839272 DOI: 10.1016/j.cmpb.2021.106529] [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: 03/07/2021] [Revised: 10/20/2021] [Accepted: 11/09/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND AND OBJECTIVE Cell migration is essential for many biological phenomena with direct impact on human health and disease. One conventional approach to study cell migration involves the quantitative analysis of individual cell trajectories recorded by time-lapse video microscopy. Dedicated software tools exist to assist the automated or semi-automated tracking of cells and translate these into coordinate positions along time. However, cell biologists usually bump into the difficulty of plotting and computing these data sets into biologically meaningful figures and metrics. METHODS This report describes MigraR, an intuitive graphical user interface executed from the RStudioTM (via the R package Shiny), which greatly simplifies the task of translating coordinate positions of moving cells into measurable parameters of cell migration (velocity, straightness, and direction of movement), as well as of plotting cell trajectories and migration metrics. One innovative function of this interface is that it allows users to refine their data sets by setting limits based on time, velocity and straightness. RESULTS MigraR was tested on different data to assess its applicability. Intended users of MigraR are cell biologists with no prior knowledge of data analysis, seeking to accelerate the quantification and visualization of cell migration data sets delivered in the format of Excel files by available cell-tracking software. CONCLUSIONS Through the graphics it provides, MigraR is an useful tool for the analysis of migration parameters and cellular trajectories. Since its source code is open, it can be subject of refinement by expert users to best suit the needs of other researchers. It is available at GitHub and can be easily reproduced.
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Affiliation(s)
- Nirbhaya Shaji
- FCUP - Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre s/n, Porto 4169-007, Portugal; INESC-TEC - Instituto de Engenharia de Sistemas e Computadores, Tecnologia e Ciência, Campus da Faculdade de Engenharia da Universidade do Porto, Rua Dr. Roberto Frias, Porto 4200-465, Portugal
| | - Florbela Nunes
- ISEP - Instituto Superior de Engenharia do Porto, Politécnico do Porto, Rua Dr. Antnio Bernardino de Almeida 431, Porto 4249-015, Portugal; i3S - Instituto de Investigação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, Porto 4200-135, Portugal
| | - M Ines Rocha
- i3S - Instituto de Investigação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, Porto 4200-135, Portugal
| | - Elsa Ferreira Gomes
- ISEP - Instituto Superior de Engenharia do Porto, Politécnico do Porto, Rua Dr. Antnio Bernardino de Almeida 431, Porto 4249-015, Portugal; INESC-TEC - Instituto de Engenharia de Sistemas e Computadores, Tecnologia e Ciência, Campus da Faculdade de Engenharia da Universidade do Porto, Rua Dr. Roberto Frias, Porto 4200-465, Portugal.
| | - Helena Castro
- i3S - Instituto de Investigação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, Porto 4200-135, Portugal
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Schienstock D, Mueller SN. Moving beyond velocity: Opportunities and challenges to quantify immune cell behavior. Immunol Rev 2021; 306:123-136. [PMID: 34786722 DOI: 10.1111/imr.13038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 10/20/2021] [Accepted: 11/02/2021] [Indexed: 12/22/2022]
Abstract
The analysis of cellular behavior using intravital multi-photon microscopy has contributed substantially to our understanding of the priming and effector phases of immune responses. Yet, many questions remain unanswered and unexplored. Though advancements in intravital imaging techniques and animal models continue to drive new discoveries, continued improvements in analysis methods are needed to extract detailed information about cellular behavior. Focusing on dendritic cell (DC) and T cell interactions as an exemplar, here we discuss key limitations for intravital imaging studies and review and explore alternative approaches to quantify immune cell behavior. We touch upon current developments in deep learning models, as well as established methods from unrelated fields such as ecology to detect and track objects over time. As developments in open-source software make it possible to process and interactively view larger datasets, the challenge for the field will be to determine how best to combine intravital imaging with multi-parameter imaging of larger tissue regions to discover new facets of leukocyte dynamics and how these contribute to immune responses.
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Affiliation(s)
- Dominik Schienstock
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Vic, Australia
| | - Scott N Mueller
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Vic, Australia
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10
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Tsai NC, Hsu TS, Kuo SC, Kao CT, Hung TH, Lin DG, Yeh CS, Chu CC, Lin JS, Lin HH, Ko CY, Chang TH, Su JC, Lin YCJ. Large-scale data analysis for robotic yeast one-hybrid platforms and multi-disciplinary studies using GateMultiplex. BMC Biol 2021; 19:214. [PMID: 34560855 PMCID: PMC8461970 DOI: 10.1186/s12915-021-01140-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 09/03/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Yeast one-hybrid (Y1H) is a common technique for identifying DNA-protein interactions, and robotic platforms have been developed for high-throughput analyses to unravel the gene regulatory networks in many organisms. Use of these high-throughput techniques has led to the generation of increasingly large datasets, and several software packages have been developed to analyze such data. We previously established the currently most efficient Y1H system, meiosis-directed Y1H; however, the available software tools were not designed for processing the additional parameters suggested by meiosis-directed Y1H to avoid false positives and required programming skills for operation. RESULTS We developed a new tool named GateMultiplex with high computing performance using C++. GateMultiplex incorporated a graphical user interface (GUI), which allows the operation without any programming skills. Flexible parameter options were designed for multiple experimental purposes to enable the application of GateMultiplex even beyond Y1H platforms. We further demonstrated the data analysis from other three fields using GateMultiplex, the identification of lead compounds in preclinical cancer drug discovery, the crop line selection in precision agriculture, and the ocean pollution detection from deep-sea fishery. CONCLUSIONS The user-friendly GUI, fast C++ computing speed, flexible parameter setting, and applicability of GateMultiplex facilitate the feasibility of large-scale data analysis in life science fields.
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Affiliation(s)
- Ni-Chiao Tsai
- Department of Life Science and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Tzu-Shu Hsu
- Department of Pharmacy, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan
| | - Shang-Che Kuo
- Department of Pharmacy, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, 10617, Taiwan
| | - Chung-Ting Kao
- Department of Life Science and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Tzu-Huan Hung
- Biotechnology Division, Taiwan Agricultural Research Institute, Taichung, 41362, Taiwan
| | - Da-Gin Lin
- Biotechnology Division, Taiwan Agricultural Research Institute, Taichung, 41362, Taiwan
| | - Chung-Shu Yeh
- Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Chia-Chen Chu
- Department of Life Science and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Jeng-Shane Lin
- Department of Life Sciences, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Hsin-Hung Lin
- Department of Horticulture and Biotechnology, Chinese Culture University, Taipei, 11114, Taiwan
| | - Chia-Ying Ko
- Department of Life Sciences and Institute of Fisheries Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Tien-Hsien Chang
- Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan.
| | - Jung-Chen Su
- Department of Pharmacy, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan.
| | - Ying-Chung Jimmy Lin
- Department of Life Science and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, 10617, Taiwan.
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, 10617, Taiwan.
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11
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Belyaev I, Praetorius JP, Medyukhina A, Figge MT. Enhanced segmentation of label-free cells for automated migration and interaction tracking. Cytometry A 2021; 99:1218-1229. [PMID: 34060210 DOI: 10.1002/cyto.a.24466] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 05/25/2021] [Indexed: 02/01/2023]
Abstract
In biomedical research, the migration behavior of cells and interactions between various cell types are frequently studied subjects. An automated and quantitative analysis of time-lapse microscopy data is an essential component of these studies, especially when characteristic migration patterns need to be identified. Plenty of software tools have been developed to serve this need. However, the majority of algorithms is designed for fluorescently labeled cells, even though it is well-known that fluorescent labels can substantially interfere with the physiological behavior of interacting cells. We here present a fully revised version of our algorithm for migration and interaction tracking (AMIT), which includes a novel segmentation approach. This approach allows segmenting label-free cells with high accuracy and also enables detecting almost all cells within the field of view. With regard to cell tracking, we designed and implemented a new method for cluster detection and splitting. This method does not rely on any geometrical characteristics of individual objects inside a cluster but relies on monitoring the events of cell-cell fusion from and cluster fission into single cells forward and backward in time. We demonstrate that focusing on these events provides accurate splitting of transient clusters. Furthermore, the substantially improved quantitative analysis of cell migration by the revised version of AMIT is more than two orders of magnitude faster than the previous implementation, which makes it feasible to process video data at higher spatial and temporal resolutions.
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Affiliation(s)
- Ivan Belyaev
- Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Jena, Germany.,Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany
| | - Jan-Philipp Praetorius
- Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Jena, Germany.,Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany
| | - Anna Medyukhina
- Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Jena, Germany.,Center for Bioimage Informatics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Marc Thilo Figge
- Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Jena, Germany.,Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany
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12
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Qin J, Lovelace MD, Mitchell AJ, de Koning-Ward T, Grau GE, Pai S. Perivascular macrophages create an intravascular niche for CD8 + T cell localisation prior to the onset of fatal experimental cerebral malaria. Clin Transl Immunology 2021; 10:e1273. [PMID: 33854773 PMCID: PMC8026342 DOI: 10.1002/cti2.1273] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 02/03/2021] [Accepted: 03/14/2021] [Indexed: 12/12/2022] Open
Abstract
Objectives The immunologic events that build up to the fatal neurological stage of experimental cerebral malaria (ECM) are incompletely understood. Here, we dissect immune cell behaviour occurring in the central nervous system (CNS) when Plasmodium berghei ANKA (PbA)‐infected mice show only minor clinical signs. Methods A 2‐photon intravital microscopy (2P‐IVM) brain imaging model was used to study the spatiotemporal context of early immunological events in situ during ECM. Results Early in the disease course, antigen‐specific CD8+ T cells came in contact and arrested on the endothelium of post‐capillary venules. CD8+ T cells typically adhered adjacent to, or were in the near vicinity of, perivascular macrophages (PVMs) that line post‐capillary venules. Closer examination revealed that CD8+ T cells crawled along the inner vessel wall towards PVMs that lay on the abluminal side of large post‐capillary venules. ‘Activity hotspots’ in large post‐capillary venules were characterised by T‐cell localisation, activated morphology and clustering of PVM, increased abutting of post‐capillary venules by PVM and augmented monocyte accumulation. In the later stages of infection, when mice exhibited neurological signs, intravascular CD8+ T cells increased in number and changed their behaviour, actively crawling along the endothelium and displaying frequent, short‐term interactions with the inner vessel wall at hotspots. Conclusion Our study suggests an active interaction between PVM and CD8+ T cells occurs across the blood–brain barrier (BBB) in early ECM, which may be the initiating event in the inflammatory cascade leading to BBB alteration and neuropathology.
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Affiliation(s)
| | - Michael D Lovelace
- Applied Neurosciences Program Peter Duncan Neurosciences Research Unit St Vincent's Centre for Applied Medical Research Sydney NSW Australia.,UNSW St Vincent's Clinical School Faculty of Medicine UNSW Sydney Sydney NSW Australia
| | - Andrew J Mitchell
- Materials Characterisation and Fabrication Platform Department of Chemical Engineering University of Melbourne Parkville VIC Australia
| | | | - Georges Er Grau
- Vascular Immunology Unit Discipline of Pathology School of Medical Sciences University of Sydney Camperdown NSW Australia
| | - Saparna Pai
- Centre for Molecular Therapeutics Australian Institute of Tropical Health and Medicine James Cook University Cairns QLD Australia.,Faculty of Medicine and Health University of Sydney Sydney NSW Australia
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13
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Barua A, Nava-Sedeño JM, Meyer-Hermann M, Hatzikirou H. A least microenvironmental uncertainty principle (LEUP) as a generative model of collective cell migration mechanisms. Sci Rep 2020; 10:22371. [PMID: 33353977 PMCID: PMC7755925 DOI: 10.1038/s41598-020-79119-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 11/27/2020] [Indexed: 11/09/2022] Open
Abstract
Collective migration is commonly observed in groups of migrating cells, in the form of swarms or aggregates. Mechanistic models have proven very useful in understanding collective cell migration. Such models, either explicitly consider the forces involved in the interaction and movement of individuals or phenomenologically define rules which mimic the observed behavior of cells. However, mechanisms leading to collective migration are varied and specific to the type of cells involved. Additionally, the precise and complete dynamics of many important chemomechanical factors influencing cell movement, from signalling pathways to substrate sensing, are typically either too complex or largely unknown. The question is how to make quantitative/qualitative predictions of collective behavior without exact mechanistic knowledge. Here we propose the least microenvironmental uncertainty principle (LEUP) that may serve as a generative model of collective migration without precise incorporation of full mechanistic details. Using statistical physics tools, we show that the famous Vicsek model is a special case of LEUP. Finally, to test the biological applicability of our theory, we apply LEUP to construct a model of the collective behavior of spherical Serratia marcescens bacteria, where the underlying migration mechanisms remain elusive.
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Affiliation(s)
- Arnab Barua
- Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, Rebenring 56, 38106, Braunschweig, Germany
- Center for Information Services and High Performance Computing, Technische Univesität Dresden, Nöthnitzer Straße 46, 01062, Dresden, Germany
| | - Josue M Nava-Sedeño
- Center for Information Services and High Performance Computing, Technische Univesität Dresden, Nöthnitzer Straße 46, 01062, Dresden, Germany
- Universidad Nacional Autónoma de México, Faculty of Sciences, Department of Mathematics, Circuito Exterior, Ciudad Universitaria, 04510, Mexico City, Mexico
| | - Michael Meyer-Hermann
- Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, Rebenring 56, 38106, Braunschweig, Germany
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Haralampos Hatzikirou
- Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, Rebenring 56, 38106, Braunschweig, Germany.
- Center for Information Services and High Performance Computing, Technische Univesität Dresden, Nöthnitzer Straße 46, 01062, Dresden, Germany.
- Mathematics Department, Khalifa University, P.O. Box 127788, Abu Dhabi, UAE.
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14
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Gonzalez-Beltran AN, Masuzzo P, Ampe C, Bakker GJ, Besson S, Eibl RH, Friedl P, Gunzer M, Kittisopikul M, Dévédec SEL, Leo S, Moore J, Paran Y, Prilusky J, Rocca-Serra P, Roudot P, Schuster M, Sergeant G, Strömblad S, Swedlow JR, van Erp M, Van Troys M, Zaritsky A, Sansone SA, Martens L. Community standards for open cell migration data. Gigascience 2020; 9:giaa041. [PMID: 32396199 PMCID: PMC7317087 DOI: 10.1093/gigascience/giaa041] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 04/02/2020] [Accepted: 04/02/2020] [Indexed: 01/08/2023] Open
Abstract
Cell migration research has become a high-content field. However, the quantitative information encapsulated in these complex and high-dimensional datasets is not fully exploited owing to the diversity of experimental protocols and non-standardized output formats. In addition, typically the datasets are not open for reuse. Making the data open and Findable, Accessible, Interoperable, and Reusable (FAIR) will enable meta-analysis, data integration, and data mining. Standardized data formats and controlled vocabularies are essential for building a suitable infrastructure for that purpose but are not available in the cell migration domain. We here present standardization efforts by the Cell Migration Standardisation Organisation (CMSO), an open community-driven organization to facilitate the development of standards for cell migration data. This work will foster the development of improved algorithms and tools and enable secondary analysis of public datasets, ultimately unlocking new knowledge of the complex biological process of cell migration.
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Affiliation(s)
- Alejandra N Gonzalez-Beltran
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, Oxford OX1 3QG, Oxford, UK
| | - Paola Masuzzo
- VIB-UGent Center for Medical Biotechnology, VIB, A. Baertsoenkaai 3, B-9000, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, A. Baertsoenkaai 3, B-9000, Ghent, Belgium
- Institute for Globally Distributed Open Research and Education (IGDORE), Kabupaten Gianyar, Bali 80571, Indonesia
| | - Christophe Ampe
- Department of Biomolecular Medicine, Ghent University, A. Baertsoenkaai 3, B-9000, Ghent, Belgium
| | - Gert-Jan Bakker
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Geert Grooteplein 28 6525 GA Nijmegen, The Netherlands
| | - Sébastien Besson
- Centre for Gene Regulation & Expression & Division of Computational Biology, University of Dundee, School of Life Sciences, Dow St Dundee DD1 5EH, Scotland, UK
| | - Robert H Eibl
- German Cancer Research Center, DKFZ Alumni Association, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Peter Friedl
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Geert Grooteplein 28 6525 GA Nijmegen, The Netherlands
- David H. Koch Center for Applied Genitourinary Medicine, UT MD Anderson Cancer Center, 6767 Bertner Ave, Mitchell Basic Science Research Building, 77030 Houston, TX, USA
- Cancer Genomics Center, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands
| | - Matthias Gunzer
- Institute for Experimental Immunology and Imaging, University Hospital, University Duisburg-Essen, Universitätsstr. 2, 45141 Essen, Germany
- Leibniz Institute for Analytical Sciences, ISAS, Bunsen-Kirchhoff-Straße 11, 44139 Dortmund, Germany
| | - Mark Kittisopikul
- Department of Biophysics, UT Southwestern Medical Center, 5323 Harry Hines Blvd. Dallas, TX 75390, USA
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, 303 E. Chicago Ave, Chicago, IL 60611, USA
| | - Sylvia E Le Dévédec
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, PO box 9502 2300 RA Leiden, The Netherlands
| | - Simone Leo
- Centre for Gene Regulation & Expression & Division of Computational Biology, University of Dundee, School of Life Sciences, Dow St Dundee DD1 5EH, Scotland, UK
- Center for Advanced Studies, Research, and Development in Sardinia (CRS4), Loc. Piscina Manna, Edificio 1, 09050 Pula (CA) , Italy
| | - Josh Moore
- Centre for Gene Regulation & Expression & Division of Computational Biology, University of Dundee, School of Life Sciences, Dow St Dundee DD1 5EH, Scotland, UK
| | - Yael Paran
- IDEA Bio-Medical Ltd, 2 Prof. Bergman St., Rehovot 76705, Israel
| | - Jaime Prilusky
- Life Science Core Facilities, Weizmann Institute of Science, P.O. Box 26 Rehovot 76100, Israel
| | - Philippe Rocca-Serra
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, Oxford OX1 3QG, Oxford, UK
| | - Philippe Roudot
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, 5323 Harry Hines Blvd. Dallas, TX 75390, USA
| | - Marc Schuster
- Institute for Experimental Immunology and Imaging, University Hospital, University Duisburg-Essen, Universitätsstr. 2, 45141 Essen, Germany
| | - Gwendolien Sergeant
- Department of Biomolecular Medicine, Ghent University, A. Baertsoenkaai 3, B-9000, Ghent, Belgium
| | - Staffan Strömblad
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, SE-141 83 Huddinge, Sweden
| | - Jason R Swedlow
- Centre for Gene Regulation & Expression & Division of Computational Biology, University of Dundee, School of Life Sciences, Dow St Dundee DD1 5EH, Scotland, UK
| | - Merijn van Erp
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Geert Grooteplein 28 6525 GA Nijmegen, The Netherlands
| | - Marleen Van Troys
- Department of Biomolecular Medicine, Ghent University, A. Baertsoenkaai 3, B-9000, Ghent, Belgium
| | - Assaf Zaritsky
- Department of Software and Information Systems Engineering, Ben-Gurion University of the Negev, P.O.B. 653, 8410501 Beer-Sheva, Israel
| | - Susanna-Assunta Sansone
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, Oxford OX1 3QG, Oxford, UK
| | - Lennart Martens
- VIB-UGent Center for Medical Biotechnology, VIB, A. Baertsoenkaai 3, B-9000, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, A. Baertsoenkaai 3, B-9000, Ghent, Belgium
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15
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Makowiecka A, Malek N, Mazurkiewicz E, Mrówczyńska E, Nowak D, Mazur AJ. Thymosin β4 Regulates Focal Adhesion Formation in Human Melanoma Cells and Affects Their Migration and Invasion. Front Cell Dev Biol 2019; 7:304. [PMID: 31921836 PMCID: PMC6935720 DOI: 10.3389/fcell.2019.00304] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 11/11/2019] [Indexed: 12/17/2022] Open
Abstract
Thymosin β4 (Tβ4), a multifunctional 44-amino acid polypeptide and a member of actin-binding proteins (ABPs), plays an important role in developmental processes and wound healing. In recent years an increasing number of data has been published suggesting Tβ4's involvement in tumorigenesis. However, Tβ4's role in melanoma tumor development still remains to be elucidated. In our study we demonstrate that Tβ4 is crucial for melanoma adhesion and invasion. For the purpose of our research we tested melanoma cell lines differing in invasive potential. Moreover, we applied shRNAs to silence TMSB4X (gene encoding Tβ4) expression in a cell line with high TMSB4X expression. We found out that Tβ4 is not only a component of focal adhesions (FAs) and interacts with several FAs components but also regulates FAs formation. We demonstrate that Tβ4 level has an impact on FAs' number and morphology. Moreover, manipulation with TMSB4X expression resulted in changes in cells' motility on non-coated and MatrigelTM (resembling basement membrane composition)-coated surfaces and drastically decreased invasion abilities of the cells. Additionally, a correlation between Tβ4 expression level and exhibition of mesenchymal-like [epithelial-mesenchymal transition (EMT)] features was discovered. Cells with lowered TMSB4X expression were less EMT-progressed than control cells. Summarizing, obtained results show that Tβ4 by regulating melanoma cells' adhesion has an impact on motility features and EMT. Our study not only contributes to a better understanding of the processes underlying melanoma cells' capacity to create metastases but also highlights Tβ4 as a potential target for melanoma management therapy.
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Affiliation(s)
- Aleksandra Makowiecka
- Department of Cell Pathology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Natalia Malek
- Department of Cell Pathology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Ewa Mazurkiewicz
- Department of Cell Pathology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Ewa Mrówczyńska
- Department of Cell Pathology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Dorota Nowak
- Department of Cell Pathology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Antonina Joanna Mazur
- Department of Cell Pathology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
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16
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Modeling and analysis of melanoblast motion. J Math Biol 2019; 79:2111-2132. [PMID: 31515603 DOI: 10.1007/s00285-019-01422-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 07/05/2019] [Indexed: 10/26/2022]
Abstract
Melanoblast migration is important for embryogenesis and is a key feature of melanoma metastasis. Many studies have characterized melanoblast movement, focusing on statistical properties and have highlighted basic mechanisms of melanoblast motility. We took a slightly different and complementary approach: we previously developed a mathematical model of melanoblast motion that enables the testing of biological assumptions about the displacement of melanoblasts and we created tests to analyze the geometric features of cell trajectories and the specific issue of trajectory interactions. Within this model, we performed simulations and compared the results with experimental data using geometric tests. In this paper, we developed the associated mathematical model and the main focus is to study the crossings between trajectories with new theoretical results about the variation of number of intersection points with respect to the crossing times. Using these results it is possible to study the random nature of displacements and the interactions between trajectories. This analysis has raised new questions, leading to the generation of strong arguments in favor of a trail left behind each moving melanoblast.
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17
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Hofmann A, Preston S, Cross M, Herath HMPD, Simon A, Gasser RB. DRfit: a Java tool for the analysis of discrete data from multi-well plate assays. BMC Bioinformatics 2019; 20:262. [PMID: 31113359 PMCID: PMC6528253 DOI: 10.1186/s12859-019-2891-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 05/10/2019] [Indexed: 12/14/2022] Open
Abstract
Background Analyses of replicates in sets of discrete data, typically acquired in multi-well plate formats, is a recurring task in many contemporary areas in the Life Sciences. The availability of accessible cross-platform data analysis tools for such fundamental tasks in varied projects and environments is an important prerequisite to ensuring a reliable and timely turnaround as well as to provide practical analytical tools for student training. Results We have developed an easy-to-use, interactive software tool for the analysis of multiple data sets comprising replicates of discrete bivariate data points. For each dataset, the software identifies the replicate data points from a defined matrix layout and calculates their means and standard errors. The averaged values are then automatically fitted using either a linear or a logistic dose response function. Conclusions DRfit is a practical and convenient tool for the analysis of one or multiple sets of discrete data points acquired as replicates from multi-well plate assays. The design of the graphical user interface and the built-in analysis features make it a flexible and useful tool for a wide range of different assays. Electronic supplementary material The online version of this article (10.1186/s12859-019-2891-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andreas Hofmann
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland, 4111, Australia. .,Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, 3010, Australia.
| | - Sarah Preston
- Faculty of Science and Technology, Federation University, Ballarat, Victoria, 3350, Australia
| | - Megan Cross
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland, 4111, Australia
| | - H M P Dilrukshi Herath
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Anne Simon
- Université Claude Bernard Lyon 1, Bâtiment Curien, Villeurbanne and Laboratoire Chimie et Biologie des Membranes et des Nanoobjets, Université de Bordeaux, Pessac, France
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, 3010, Australia
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18
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Interplay Between the Persistent Random Walk and the Contact Inhibition of Locomotion Leads to Collective Cell Behaviors. Bull Math Biol 2019; 81:3301-3321. [PMID: 30788690 DOI: 10.1007/s11538-019-00585-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 02/12/2019] [Indexed: 01/23/2023]
Abstract
Cell migration plays an important role in physiology and pathophysiology. It was observed in the experiments that cells, such as fibroblast, leukocytes, and cancer cells, exhibit a wide variety of migratory behaviors, such as persistent random walk, contact inhibition of locomotion, and ordered behaviors. To identify biophysical mechanisms for these cellular behaviors, we developed a rigorous computational model of cell migration on a two-dimensional non-deformable substrate. Cells in the model undergo motion driven by mechanical interactions between cellular protrusions and the substrate via the balance of tensile forces. Properties of dynamic formation of lamellipodia induced the persistent random walk behavior of a migrating cell. When multiple cells are included in the simulation, the model recapitulated the contact inhibition of locomotion between cells at low density without any phenomenological assumptions or momentum transfer. Instead, the model showed that contact inhibition of locomotion can emerge via indirect interactions between the cells through their interactions with the underlying substrate. At high density, contact inhibition of locomotion between numerous cells gave rise to confined motions or ordered behaviors, depending on cell density and how likely lamellipodia turn over due to contact with other cells. Results in our study suggest that various collective migratory behaviors may emerge without more restrictive assumptions or direct cell-to-cell biomechanical interactions.
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19
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Sergeant G, Martens L, Van Troys M, Masuzzo P. DoRes within CellMissy: dose-response analysis on cell migration and related data. Bioinformatics 2019; 35:696-697. [PMID: 30052834 PMCID: PMC6378935 DOI: 10.1093/bioinformatics/bty634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 07/10/2018] [Accepted: 07/24/2018] [Indexed: 11/16/2022] Open
Abstract
Summary In cancer research, cell-based assays are used to assess cell migration and invasion. The major bottleneck is the lack of automated tools to visualize and analyse the large amounts of biological dose-response data produced. To address this challenge, we have developed an automated and free software package for dose-response analyses, DoRes, which is released as an add-on of the freely available and open-source tool CellMissy, dedicated to the management and analysis of cell migration data. DoRes implements non-linear curve fitting functionality into a robust, user-friendly and flexible software package with the possibility of importing a tabular file or starting from a cell migration experiment. We demonstrate the ability of the software by analysing public dose-response data and a typical cell migration experiment, and show that the extracted dose-response parameters and the calculated statistical values are consistently comparable to those of the widely used, commercial software GraphPad Prism. Availability and implementation The software here presented is a new module in CellMissy, an open-source and cross-platform package dedicated to the management, storage and analysis of cell migration data. The new module is written in Java, and inherits the cross-platform support from CellMissy. Source code and binaries are freely available under the Apache2 open-source licence at https://github.com/compomics/cellmissy/. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Gwendolien Sergeant
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium.,Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Lennart Martens
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium.,Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Marleen Van Troys
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Paola Masuzzo
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium.,Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
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20
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Abstract
In vitro tests of cancer cell invasion are the "first line" tools of preclinical researchers for screening the multitude of chemical compounds or cell perturbations that may aid in halting or treating cancer malignancy. In order to have predictive value or to contribute to designing personalized treatment regimes, these tests need to take into account the cancer cell environment and measure effects on invasion in sufficient detail. The in vitro invasion assays presented here are a trade-off between feasibility in a multisample format and mimicking the complexity of the tumor microenvironment. They allow testing multiple samples and conditions in parallel using 3D-matrix-embedded cells and deal with the heterogeneous behavior of an invading cell population in time. We describe the steps to take, the technical problems to tackle and useful software tools for the entire workflow: from the experimental setup to the quantification of the invasive capacity of the cells. The protocol is intended to guide researchers to standardize experimental set-ups and to annotate their invasion experiments in sufficient detail. In addition, it provides options for image processing and a solution for storage, visualization, quantitative analysis, and multisample comparison of acquired cell invasion data.
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21
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Svensson CM, Medyukhina A, Belyaev I, Al-Zaben N, Figge MT. Untangling cell tracks: Quantifying cell migration by time lapse image data analysis. Cytometry A 2017; 93:357-370. [DOI: 10.1002/cyto.a.23249] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Carl-Magnus Svensson
- Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI); Jena Germany
| | - Anna Medyukhina
- Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI); Jena Germany
| | - Ivan Belyaev
- Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI); Jena Germany
- Friedrich Schiller University; Jena Germany
| | - Naim Al-Zaben
- Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI); Jena Germany
- Friedrich Schiller University; Jena Germany
| | - Marc Thilo Figge
- Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI); Jena Germany
- Friedrich Schiller University; Jena Germany
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