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Gómez-de-Mariscal E, Grobe H, Pylvänäinen JW, Xénard L, Henriques R, Tinevez JY, Jacquemet G. CellTracksColab is a platform that enables compilation, analysis, and exploration of cell tracking data. PLoS Biol 2024; 22:e3002740. [PMID: 39116189 DOI: 10.1371/journal.pbio.3002740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 07/08/2024] [Indexed: 08/10/2024] Open
Abstract
In life sciences, tracking objects from movies enables researchers to quantify the behavior of single particles, organelles, bacteria, cells, and even whole animals. While numerous tools now allow automated tracking from video, a significant challenge persists in compiling, analyzing, and exploring the large datasets generated by these approaches. Here, we introduce CellTracksColab, a platform tailored to simplify the exploration and analysis of cell tracking data. CellTracksColab facilitates the compiling and analysis of results across multiple fields of view, conditions, and repeats, ensuring a holistic dataset overview. CellTracksColab also harnesses the power of high-dimensional data reduction and clustering, enabling researchers to identify distinct behavioral patterns and trends without bias. Finally, CellTracksColab also includes specialized analysis modules enabling spatial analyses (clustering, proximity to specific regions of interest). We demonstrate CellTracksColab capabilities with 3 use cases, including T cells and cancer cell migration, as well as filopodia dynamics. CellTracksColab is available for the broader scientific community at https://github.com/CellMigrationLab/CellTracksColab.
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Affiliation(s)
| | - Hanna Grobe
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland
| | - Joanna W Pylvänäinen
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku and Åbo Akademi University, Turku, Finland
| | - Laura Xénard
- Institut Pasteur, Université Paris Cité, Image Analysis Hub, Paris, France
- Institut Pasteur, Université Paris Cité, INSERM UMR1225, Pathogenesis of Vascular Infections, Paris, France
| | - Ricardo Henriques
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- UCL Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Jean-Yves Tinevez
- Institut Pasteur, Université Paris Cité, Image Analysis Hub, Paris, France
| | - Guillaume Jacquemet
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku and Åbo Akademi University, Turku, Finland
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- Turku Bioimaging, University of Turku and Åbo Akademi University, Turku, Finland
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Fox S, Gaudreau-LaPierre A, Reshke R, Podinic I, Gibbings DJ, Trinkle-Mulcahy L, Copeland JW. Identification of an FMNL2 Interactome by Quantitative Mass Spectrometry. Int J Mol Sci 2024; 25:5686. [PMID: 38891874 PMCID: PMC11171801 DOI: 10.3390/ijms25115686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/14/2024] [Accepted: 05/16/2024] [Indexed: 06/21/2024] Open
Abstract
Formin Homology Proteins (Formins) are a highly conserved family of cytoskeletal regulatory proteins that participate in a diverse range of cellular processes. FMNL2 is a member of the Diaphanous-Related Formin sub-group, and previous reports suggest FMNL2's role in filopodia assembly, force generation at lamellipodia, subcellular trafficking, cell-cell junction assembly, and focal adhesion formation. How FMNL2 is recruited to these sites of action is not well understood. To shed light on how FMNL2 activity is partitioned between subcellular locations, we used biotin proximity labeling and proteomic analysis to identify an FMNL2 interactome. The interactome identified known and new FMNL2 interacting proteins with functions related to previously described FMNL2 activities. In addition, our interactome predicts a novel connection between FMNL2 and extracellular vesicle assembly. We show directly that FMNL2 protein is present in exosomes.
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Affiliation(s)
| | | | | | | | | | | | - John W. Copeland
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (S.F.)
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Fitz GN, Tyska MJ. Molecular counting of myosin force generators in growing filopodia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.14.593924. [PMID: 38798618 PMCID: PMC11118519 DOI: 10.1101/2024.05.14.593924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Animal cells build actin-based surface protrusions to enable biological activities ranging from cell motility to mechanosensation to solute uptake. Long-standing models of protrusion growth suggest that actin filament polymerization provides the primary mechanical force for "pushing" the plasma membrane outward at the distal tip. Expanding on these actin-centric models, our recent studies used a chemically inducible system to establish that plasma membrane-bound myosin motors, which are abundant in protrusions and accumulate at the distal tips, can also power robust filopodial growth. How protrusion resident myosins coordinate with actin polymerization to drive elongation remains unclear, in part because the number of force generators and thus, the scale of their mechanical contributions remain undefined. To address this gap, we leveraged the SunTag system to count membrane-bound myosin motors in actively growing filopodia. Using this approach, we found that the number of myosins is log-normally distributed with a mean of 12.0 ± 2.5 motors [GeoMean ± GeoSD] per filopodium. Together with unitary force values and duty ratio estimates derived from biophysical studies for the motor used in these experiments, we calculate that a distal tip population of myosins could generate a time averaged force of ∼tens of pN to elongate filopodia. This range is comparable to the expected force production of actin polymerization in this system, a point that necessitates revision of popular physical models for protrusion growth. SIGNIFICANCE STATEMENT This study describes the results of in-cell molecular counting experiments to define the number of myosin motors that are mechanically active in growing filopodia. This data should be used to constrain future physical models of the formation of actin-based protrusions.
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First person – Ana Popović. J Cell Sci 2023. [DOI: 10.1242/jcs.261054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023] Open
Abstract
ABSTRACT
First Person is a series of interviews with the first authors of a selection of papers published in Journal of Cell Science, helping researchers promote themselves alongside their papers. Ana Popović is first author on ‘ Myosin-X recruits lamellipodin to filopodia tips’, published in JCS. Ana is a PhD student in the lab of Guillaume Jacquemet at Åbo Akademi University, Turku, Finland, investigating cell migration with a focus on cellular protrusions called filopodia.
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Pylvänäinen JW, Laine RF, Saraiva BMS, Ghimire S, Follain G, Henriques R, Jacquemet G. Fast4DReg - fast registration of 4D microscopy datasets. J Cell Sci 2023; 136:287682. [PMID: 36727532 PMCID: PMC10022679 DOI: 10.1242/jcs.260728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 01/25/2023] [Indexed: 02/03/2023] Open
Abstract
Unwanted sample drift is a common issue that plagues microscopy experiments, preventing accurate temporal visualization and quantification of biological processes. Although multiple methods and tools exist to correct images post acquisition, performing drift correction of three-dimensional (3D) videos using open-source solutions remains challenging and time consuming. Here, we present a new tool developed for ImageJ or Fiji called Fast4DReg that can quickly correct axial and lateral drift in 3D video-microscopy datasets. Fast4DReg works by creating intensity projections along multiple axes and estimating the drift between frames using two-dimensional cross-correlations. Using synthetic and acquired datasets, we demonstrate that Fast4DReg can perform better than other state-of-the-art open-source drift-correction tools and significantly outperforms them in speed. We also demonstrate that Fast4DReg can be used to register misaligned channels in 3D using either calibration slides or misaligned images directly. Altogether, Fast4DReg provides a quick and easy-to-use method to correct 3D imaging data before further visualization and analysis.
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Affiliation(s)
- Joanna W. Pylvänäinen
- Åbo Akademi University, Faculty of Science and Engineering, Biosciences, Turku 20520, Finland
- Turku Bioimaging, University of Turku and Åbo Akademi University, Turku 20520, Finland
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
| | - Romain F. Laine
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
- The Francis Crick Institute, London NW1 1AT, UK
| | | | - Sujan Ghimire
- Åbo Akademi University, Faculty of Science and Engineering, Biosciences, Turku 20520, Finland
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
| | - Gautier Follain
- Åbo Akademi University, Faculty of Science and Engineering, Biosciences, Turku 20520, Finland
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
| | | | - Guillaume Jacquemet
- Åbo Akademi University, Faculty of Science and Engineering, Biosciences, Turku 20520, Finland
- Turku Bioimaging, University of Turku and Åbo Akademi University, Turku 20520, Finland
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
- InFLAMES Research Flagship Center, Åbo Akademi University, Turku 20520, Finland
- Author for correspondence ()
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