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Sengupta K, Dillard P, Limozin L. Morphodynamics of T-lymphocytes: Scanning to spreading. Biophys J 2024:S0006-3495(24)00157-7. [PMID: 38425041 DOI: 10.1016/j.bpj.2024.02.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/29/2024] [Accepted: 02/26/2024] [Indexed: 03/02/2024] Open
Abstract
Binding of the T cell receptor complex to its ligand, the subsequent molecular rearrangement, and the concomitant cell-scale shape changes represent the very first steps of adaptive immune recognition. The first minutes of the interaction of T cells and antigen presenting cells have been extensively scrutinized; yet, gaps remain in our understanding of how the biophysical properties of the environment may impact the sequence of events. In particular, many pioneering experiments were done on immobilized ligands and gave major insights into the process of T cell activation, whereas later experiments have indicated that ligand mobility was of paramount importance, especially to enable the formation of T cell receptor clusters. Systematic experiments to compare and reconcile the two schools are still lacking. Furthermore, recent investigations using compliant substrates have elucidated other intriguing aspects of T cell mechanics. Here we review experiments on interaction of T cells with planar artificial antigen presenting cells to explore the impact of mechanics on adhesion and actin morphodynamics during the spreading process. We enumerate a sequence tracing first contact to final spread state that is consistent with current understanding. Finally, we interpret the presented experimental results in light of a mechanical model that captures all the different morphodynamic states.
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Affiliation(s)
- Kheya Sengupta
- Aix-Marseille Université, CNRS, CINAM, Turing Centre for Living Systems, Marseille, France.
| | - Pierre Dillard
- Aix-Marseille Université, CNRS, CINAM, Turing Centre for Living Systems, Marseille, France; Aix-Marseille Université, CNRS, INSERM, LAI, Turing Centre for Living Systems, Marseille, France
| | - Laurent Limozin
- Aix-Marseille Université, CNRS, INSERM, LAI, Turing Centre for Living Systems, Marseille, France.
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2
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Liu CSC, Mandal T, Biswas P, Hoque MA, Bandopadhyay P, Sinha BP, Sarif J, D'Rozario R, Sinha DK, Sinha B, Ganguly D. Piezo1 mechanosensing regulates integrin-dependent chemotactic migration in human T cells. eLife 2024; 12:RP91903. [PMID: 38393325 PMCID: PMC10942591 DOI: 10.7554/elife.91903] [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] [Indexed: 02/25/2024] Open
Abstract
T cells are crucial for efficient antigen-specific immune responses and thus their migration within the body, to inflamed tissues from circulating blood or to secondary lymphoid organs, plays a very critical role. T cell extravasation in inflamed tissues depends on chemotactic cues and interaction between endothelial adhesion molecules and cellular integrins. A migrating T cell is expected to sense diverse external and membrane-intrinsic mechano-physical cues, but molecular mechanisms of such mechanosensing in cell migration are not established. We explored if the professional mechanosensor Piezo1 plays any role during integrin-dependent chemotaxis of human T cells. We found that deficiency of Piezo1 in human T cells interfered with integrin-dependent cellular motility on ICAM-1-coated surface. Piezo1 recruitment at the leading edge of moving T cells is dependent on and follows focal adhesion formation at the leading edge and local increase in membrane tension upon chemokine receptor activation. Piezo1 recruitment and activation, followed by calcium influx and calpain activation, in turn, are crucial for the integrin LFA1 (CD11a/CD18) recruitment at the leading edge of the chemotactic human T cells. Thus, we find that Piezo1 activation in response to local mechanical cues constitutes a membrane-intrinsic component of the 'outside-in' signaling in human T cells, migrating in response to chemokines, that mediates integrin recruitment to the leading edge.
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Affiliation(s)
- Chinky Shiu Chen Liu
- IICB-Translational Research Unit of Excellence, CSIR-Indian Institute of Chemical BiologyKolkataIndia
| | - Tithi Mandal
- Department of Biological Sciences, Indian Institute of Science Education and ResearchKolkataIndia
| | - Parijat Biswas
- Department of Biological Sciences, Indian Association for Cultivation of ScienceKolkataIndia
| | - Md Asmaul Hoque
- IICB-Translational Research Unit of Excellence, CSIR-Indian Institute of Chemical BiologyKolkataIndia
- Academy of Scientific and Innovative ResearchGhaziabadIndia
| | - Purbita Bandopadhyay
- IICB-Translational Research Unit of Excellence, CSIR-Indian Institute of Chemical BiologyKolkataIndia
- Academy of Scientific and Innovative ResearchGhaziabadIndia
| | - Bishnu Prasad Sinha
- IICB-Translational Research Unit of Excellence, CSIR-Indian Institute of Chemical BiologyKolkataIndia
- Academy of Scientific and Innovative ResearchGhaziabadIndia
| | - Jafar Sarif
- IICB-Translational Research Unit of Excellence, CSIR-Indian Institute of Chemical BiologyKolkataIndia
- Academy of Scientific and Innovative ResearchGhaziabadIndia
| | - Ranit D'Rozario
- IICB-Translational Research Unit of Excellence, CSIR-Indian Institute of Chemical BiologyKolkataIndia
- Academy of Scientific and Innovative ResearchGhaziabadIndia
| | - Deepak Kumar Sinha
- Department of Biological Sciences, Indian Association for Cultivation of ScienceKolkataIndia
| | - Bidisha Sinha
- Department of Biological Sciences, Indian Institute of Science Education and ResearchKolkataIndia
| | - Dipyaman Ganguly
- IICB-Translational Research Unit of Excellence, CSIR-Indian Institute of Chemical BiologyKolkataIndia
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3
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Shannon MJ, Eisman SE, Lowe AR, Sloan T, Mace EM. cellPLATO: an unsupervised method for identifying cell behaviour in heterogeneous cell trajectory data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.28.564355. [PMID: 37961659 PMCID: PMC10634992 DOI: 10.1101/2023.10.28.564355] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Advances in imaging, cell segmentation, and cell tracking now routinely produce microscopy datasets of a size and complexity comparable to transcriptomics or proteomics. New tools are required to process this 'phenomics' type data. Cell PLasticity Analysis TOol (cellPLATO) is a Python-based analysis software designed for measurement and classification of diverse cell behaviours based on clustering of parameters of cell morphology and motility. cellPLATO is used after segmentation and tracking of cells from live cell microscopy data. The tool extracts morphological and motility metrics from each cell per timepoint, before being using them to segregate cells into behavioural subtypes with dimensionality reduction. Resultant cell tracks have a 'behavioural ID' for each cell per timepoint corresponding to their changing behaviour over time in a sequence. Similarity analysis allows the grouping of behavioural sequences into discrete trajectories with assigned IDs. Trajectories and underlying behaviours generate a phenotypic fingerprint for each experimental condition, and representative cells are mathematically identified and graphically displayed for human understanding of each subtype. Here, we use cellPLATO to investigate the role of IL-15 in modulating NK cell migration on ICAM-1 or VCAM-1. We find 8 behavioural subsets of NK cells based on their shape and migration dynamics, and 4 trajectories of behaviour. Therefore, using cellPLATO we show that IL-15 increases plasticity between cell migration behaviours and that different integrin ligands induce different forms of NK cell migration.
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Affiliation(s)
- Michael J Shannon
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York NY 10032
| | - Shira E Eisman
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York NY 10032
| | - Alan R Lowe
- Institute for the Physics of Living Systems, Institute for Structural and Molecular Biology and London Centre for Nanotechnology, University College London, London WC1H 0AH, United Kingdom
| | | | - Emily M Mace
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York NY 10032
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4
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Buffone A, Hammer DA, Kim SHJ, Anderson NR, Mochida A, Lee DH, Guin S. Not all (cells) who wander are lost: Upstream migration as a pervasive mode of amoeboid cell motility. Front Cell Dev Biol 2023; 11:1291201. [PMID: 38020916 PMCID: PMC10651737 DOI: 10.3389/fcell.2023.1291201] [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: 09/08/2023] [Accepted: 10/06/2023] [Indexed: 12/01/2023] Open
Abstract
Leukocytes possess the ability to migrate upstream-against the direction of flow-on surfaces of specific chemistry. Upstream migration was first characterized in vitro for T-cells on surfaces comprised of intracellular adhesion molecule-1 (ICAM-1). Upstream migration occurs when the integrin receptor αLβ2 (also known as lymphocyte function-associated antigen-1, or LFA-1) binds to ICAM-1. LFA-1/ICAM-1 interactions are ubiquitous and are widely found in leukocyte trafficking. Upstream migration would be employed after cells come to arrest on the apical surface of the endothelium and might confer an advantage for both trans-endothelial migration and tissue surveillance. It has now been shown that several other motile amoeboid cells which have the responsibility of trafficking from blood vessels into tissues, such as Marginal zone B cells, hematopoietic stem cells, and neutrophils (when macrophage-1 antigen, Mac-1, is blocked), can also migrate upstream on ICAM-1 surfaces. This review will summarize what is known about the basic mechanisms of upstream migration, which cells have displayed this phenomenon, and the possible role of upstream migration in physiology and tissue homeostasis.
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Affiliation(s)
- Alexander Buffone
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ, United States
- Chemical and Materials Engineering, New Jersey Institute of Technology, Newark, NJ, United States
| | - Daniel A. Hammer
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, United States
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA, United States
| | - Sarah Hyun Ji Kim
- Department of Medicine, University of California San Diego, La Jolla, CA, United States
| | | | - Ai Mochida
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, United States
| | - Dong-Hun Lee
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA, United States
| | - Subham Guin
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ, United States
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5
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Shi H, Shao B. LFA-1 Activation in T-Cell Migration and Immunological Synapse Formation. Cells 2023; 12:cells12081136. [PMID: 37190045 DOI: 10.3390/cells12081136] [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: 03/07/2023] [Revised: 04/02/2023] [Accepted: 04/06/2023] [Indexed: 05/17/2023] Open
Abstract
Integrin LFA-1 plays a critical role in T-cell migration and in the formation of immunological synapses. LFA-1 functions through interacting with its ligands with differing affinities: low, intermediate, and high. Most prior research has studied how LFA-1 in the high-affinity state regulates the trafficking and functions of T cells. LFA-1 is also presented in the intermediate-affinity state on T cells, however, the signaling to activate LFA-1 to the intermediate-affinity state and the role of LFA-1 in this affinity state both remain largely elusive. This review briefly summarizes the activation and roles of LFA-1 with varied ligand-binding affinities in the regulation of T-cell migration and immunological synapse formation.
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Affiliation(s)
- Huiping Shi
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Bojing Shao
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
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6
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Moon HR, Saha S, Mugler A, Han B. Cells function as a ternary logic gate to decide migration direction under integrated chemical and fluidic cues. LAB ON A CHIP 2023; 23:631-644. [PMID: 36524874 PMCID: PMC9926949 DOI: 10.1039/d2lc00807f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 11/22/2022] [Indexed: 06/17/2023]
Abstract
Cells sense various environmental cues and subsequently process intracellular signals to decide their migration direction in many physiological and pathological processes. Although several signaling molecules and networks have been identified in these directed migrations, it still remains ambiguous to predict the migration direction under multiple and integrated cues, specifically chemical and fluidic cues. Here, we investigated the cellular signal processing machinery by reverse-engineering directed cell migration under integrated chemical and fluidic cues. We imposed controlled chemical and fluidic cues to cells using a microfluidic platform and analyzed the extracellular coupling of the cues with respect to the cellular detection limit. Then, the cell's migratory behavior was reverse-engineered to build a cellular signal processing system as a logic gate, which is based on a "selection" gate. This framework is further discussed with a minimal intracellular signaling network of a shared pathway model. The proposed framework of the ternary logic gate suggests a systematic view to understand how cells decode multiple cues and make decisions about the migration direction.
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Affiliation(s)
- Hye-Ran Moon
- School of Mechanical Engineering, Purdue University, West Lafayette, IN, USA.
| | - Soutick Saha
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN, USA
| | - Andrew Mugler
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN, USA
- Purdue Center for Cancer Research, Purdue University, West Lafayette, IN, USA
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Bumsoo Han
- School of Mechanical Engineering, Purdue University, West Lafayette, IN, USA.
- Purdue Center for Cancer Research, Purdue University, West Lafayette, IN, USA
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
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7
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Yang H, Miao Y, Yu Z, Wei M, Jiao X. Cell adhesion molecules and immunotherapy in advanced non-small cell lung cancer: Current process and potential application. Front Oncol 2023; 13:1107631. [PMID: 36895477 PMCID: PMC9989313 DOI: 10.3389/fonc.2023.1107631] [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: 11/25/2022] [Accepted: 02/07/2023] [Indexed: 02/23/2023] Open
Abstract
Advanced non-small cell lung cancer (NSCLC) is a severe disease and still has high mortality rate after conventional treatment (e.g., surgical resection, chemotherapy, radiotherapy and targeted therapy). In NSCLC patients, cancer cells can induce immunosuppression, growth and metastasis by modulating cell adhesion molecules of both cancer cells and immune cells. Therefore, immunotherapy is increasingly concerned due to its promising anti-tumor effect and broader indication, which targets cell adhesion molecules to reverse the process. Among these therapies, immune checkpoint inhibitors (mainly anti-PD-(L)1 and anti-CTLA-4) are most successful and have been adapted as first or second line therapy in advanced NSCLC. However, drug resistance and immune-related adverse reactions restrict its further application. Further understanding of mechanism, adequate biomarkers and novel therapies are necessary to improve therapeutic effect and alleviate adverse effect.
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Affiliation(s)
- Hongjian Yang
- Innovative Institute, China Medical University, Shenyang, China
| | - Yuxi Miao
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China
| | - Zhaojin Yu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Shenyang, China
| | - Minjie Wei
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Liaoning Cancer Immune Peptide Drug Engineering Technology Research Centre, Shenyang, China
| | - Xue Jiao
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, China.,Shenyang Kangwei Medical Laboratory Analysis Co. LTD, Shenyang, China
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8
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Keratocytes migrate against flow with a roly-poly-like mechanism. Proc Natl Acad Sci U S A 2022; 119:e2210379119. [PMID: 36409912 PMCID: PMC9889884 DOI: 10.1073/pnas.2210379119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
While cell migration can be directed by various mechanical cues such as force, deformation, stiffness, or flow, the associated mechanisms and functions may remain elusive. Single cell migration against flow, repeatedly reported with leukocytes, is arguably considered as active and mediated by integrin mechanotransduction, or passive and determined by a mechanical bias. Here, we reveal a phenotype of flow mechanotaxis with fish epithelial keratocytes that orient upstream or downstream at shear stresses around tens of dyn cm-2. We show that each cell has an intrinsic orientation that results from the mechanical interaction of flow with its morphology. The bulbous trailing edge of a keratocyte generates a hydrodynamical torque under flow that stabilizes an upstream orientation, just as the heavy lower edge of a roly-poly toy generates a gravitational torque that stabilizes an upright position. In turn, the wide and flat leading edge of keratocytes destabilizes upstream orientation, allowing the existence of two distinct phenotypes. To formalize these observations, we propose a simple mechanical model that considers keratocyte morphology as a hemisphere preceded by a wide thin sheet. Our findings show that this model can recapitulate the phase diagram of single cell orientation under flow without adjustable parameters. From a larger perspective, this passive mechanism of keratocytes flow mechanotaxis implies a potential absence of physiological function and evolution-driven process.
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9
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Gahmberg CG, Grönholm M, Madhavan S. Regulation of Dynamic Cell Adhesion by Integrin-Integrin Crosstalk. Cells 2022; 11:cells11101685. [PMID: 35626722 PMCID: PMC9140058 DOI: 10.3390/cells11101685] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/11/2022] [Accepted: 05/17/2022] [Indexed: 02/07/2023] Open
Abstract
Most cells express several integrins. The integrins are able to respond to various cellular functions and needs by modifying their own activation state, but in addition by their ability to regulate each other by activation or inhibition. This crosstalk or transdominant regulation is strictly controlled. The mechanisms resulting in integrin crosstalk are incompletely understood, but they often involve intracellular signalling routes also used by other cell surface receptors. Several studies show that the integrin cytoplasmic tails bind to a number of cytoskeletal and adaptor molecules in a regulated manner. Recent work has shown that phosphorylations of integrins and key intracellular molecules are of pivotal importance in integrin-cytoplasmic interactions, and these in turn affect integrin activity and crosstalk. The integrin β-chains play a central role in regulating crosstalk. In addition to Integrin-integrin crosstalk, crosstalk may also occur between integrins and related receptors, including other adhesion receptors, growth factor and SARS-CoV-2 receptors.
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Affiliation(s)
- Carl G. Gahmberg
- Molecular and Integrative Biosciences Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9 C, 00014 Helsinki, Finland; (M.G.); (S.M.)
- Correspondence: ; Tel.: +358-50-539-9439
| | - Mikaela Grönholm
- Molecular and Integrative Biosciences Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9 C, 00014 Helsinki, Finland; (M.G.); (S.M.)
- Drug Research Program, Faculty of Pharmacy, University of Helsinki, Viikinkaari 9 C, 00014 Helsinki, Finland
| | - Sudarrshan Madhavan
- Molecular and Integrative Biosciences Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9 C, 00014 Helsinki, Finland; (M.G.); (S.M.)
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10
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White matter microglia heterogeneity in the CNS. Acta Neuropathol 2022; 143:125-141. [PMID: 34878590 DOI: 10.1007/s00401-021-02389-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 11/17/2021] [Accepted: 11/28/2021] [Indexed: 02/07/2023]
Abstract
Microglia, the resident myeloid cells in the central nervous system (CNS) play critical roles in shaping the brain during development, responding to invading pathogens, and clearing tissue debris or aberrant protein aggregations during ageing and neurodegeneration. The original concept that like macrophages, microglia are either damaging (pro-inflammatory) or regenerative (anti-inflammatory) has been updated to a kaleidoscope view of microglia phenotypes reflecting their wide-ranging roles in maintaining homeostasis in the CNS and, their contribution to CNS diseases, as well as aiding repair. The use of new technologies including single cell/nucleus RNA sequencing has led to the identification of many novel microglia states, allowing for a better understanding of their complexity and distinguishing regional variations in the CNS. This has also revealed differences between species and diseases, and between microglia and other myeloid cells in the CNS. However, most of the data on microglia heterogeneity have been generated on cells isolated from the cortex or whole brain, whereas white matter changes and differences between white and grey matter have been relatively understudied. Considering the importance of microglia in regulating white matter health, we provide a brief update on the current knowledge of microglia heterogeneity in the white matter, how microglia are important for the development of the CNS, and how microglial ageing affects CNS white matter homeostasis. We discuss how microglia are intricately linked to the classical white matter diseases such as multiple sclerosis and genetic white matter diseases, and their putative roles in neurodegenerative diseases in which white matter is also affected. Understanding the wide variety of microglial functions in the white matter may provide the basis for microglial targeted therapies for CNS diseases.
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11
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Avery L, Robertson TF, Wu CF, Roy NH, Chauvin SD, Perkey E, Vanderbeck A, Maillard I, Burkhardt JK. A Murine Model of X-Linked Moesin-Associated Immunodeficiency (X-MAID) Reveals Defects in T Cell Homeostasis and Migration. Front Immunol 2022; 12:726406. [PMID: 35069520 PMCID: PMC8770857 DOI: 10.3389/fimmu.2021.726406] [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: 06/16/2021] [Accepted: 12/13/2021] [Indexed: 11/25/2022] Open
Abstract
X-linked moesin associated immunodeficiency (X-MAID) is a primary immunodeficiency disease in which patients suffer from profound lymphopenia leading to recurrent infections. The disease is caused by a single point mutation leading to a R171W amino acid change in the protein moesin (moesinR171W). Moesin is a member of the ERM family of proteins, which reversibly link the cortical actin cytoskeleton to the plasma membrane. Here, we describe a novel mouse model with global expression of moesinR171W that recapitulates multiple facets of patient disease, including severe lymphopenia. Further analysis reveals that these mice have diminished numbers of thymocytes and bone marrow precursors. X-MAID mice also exhibit systemic inflammation that is ameliorated by elimination of mature lymphocytes through breeding to a Rag1-deficient background. The few T cells in the periphery of X-MAID mice are highly activated and have mostly lost moesinR171W expression. In contrast, single-positive (SP) thymocytes do not appear activated and retain high expression levels of moesinR171W. Analysis of ex vivo CD4 SP thymocytes reveals defects in chemotactic responses and reduced migration on integrin ligands. While chemokine signaling appears intact, CD4 SP thymocytes from X-MAID mice are unable to polarize and rearrange cytoskeletal elements. This mouse model will be a valuable tool for teasing apart the complexity of the immunodeficiency caused by moesinR171W, and will provide new insights into how the actin cortex regulates lymphocyte function.
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Affiliation(s)
- Lyndsay Avery
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia Research Institute, Philadelphia, PA, United States
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Tanner F. Robertson
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia Research Institute, Philadelphia, PA, United States
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Christine F. Wu
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia Research Institute, Philadelphia, PA, United States
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Nathan H. Roy
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia Research Institute, Philadelphia, PA, United States
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Samuel D. Chauvin
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia Research Institute, Philadelphia, PA, United States
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Eric Perkey
- Graduate Program in Cellular and Molecular Biology and Medical Scientist Training Program, University of Michigan, Ann Arbor, MI, United States
| | - Ashley Vanderbeck
- Division of Hematology/Oncology, Department of Medicine and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Ivan Maillard
- Division of Hematology/Oncology, Department of Medicine and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Janis K. Burkhardt
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia Research Institute, Philadelphia, PA, United States
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
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12
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Johansen KH. How CRISPR/Cas9 Gene Editing Is Revolutionizing T Cell Research. DNA Cell Biol 2021; 41:53-57. [PMID: 34939826 PMCID: PMC8787706 DOI: 10.1089/dna.2021.0579] [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] [Indexed: 11/12/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 allows for precise gene targeting in mammalian cells, including T cells, allowing scientists to disrupt or edit specific genes of interest. This has enabled immunologists to investigate T cell functions as well as opened the path for novel therapeutics involving gene editing of T cells ex vivo before transferring these back to patients to increase T cell efficacy. This review outlines how CRISPR/Cas9 has transformed T cell research allowing immunologists to rapidly probe the roles of genes in T cells thus paving the way for novel therapeutics. Furthermore, this review describes how these tools reduce the requirement for genetic mouse models, while increasing the translational potential of T cell research.
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Affiliation(s)
- Kristoffer Haurum Johansen
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
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13
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Thapa P, Guyer RS, Yang AY, Parks CA, Brusko TM, Brusko M, Connors TJ, Farber DL. Infant T cells are developmentally adapted for robust lung immune responses through enhanced T cell receptor signaling. Sci Immunol 2021; 6:eabj0789. [PMID: 34890254 PMCID: PMC8765725 DOI: 10.1126/sciimmunol.abj0789] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Infants require coordinated immune responses to prevent succumbing to multiple infectious challenges during early life, particularly in the respiratory tract. The mechanisms by which infant T cells are functionally adapted for these responses are not well understood. Here, we demonstrated using an in vivo mouse cotransfer model that infant T cells generated greater numbers of lung-homing effector cells in response to influenza infection compared with adult T cells in the same host, due to augmented T cell receptor (TCR)–mediated signaling. Mouse infant T cells showed increased sensitivity to low antigen doses, originating at the interface between T cells and antigen-bearing accessory cells—through actin-mediated mobilization of signaling molecules to the immune synapse. This enhanced signaling was also observed in human infant versus adult T cells. Our findings provide a mechanism for how infants control pathogen load and dissemination, which is important for designing developmentally targeted strategies for promoting immune responses at this vulnerable life stage.
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Affiliation(s)
- Puspa Thapa
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York NY 10032
| | - Rebecca S. Guyer
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York NY 10032
| | - Alexander Y. Yang
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York NY 10032
| | - Christopher A. Parks
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY 10032
- Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032
| | - Todd M. Brusko
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32611
| | - Maigan Brusko
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32611
| | - Thomas J. Connors
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032
| | - Donna L. Farber
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York NY 10032
- Department of Surgery, Columbia University Irving Medical Center, New York, NY 10032
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14
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Gahmberg CG, Grönholm M. How integrin phosphorylations regulate cell adhesion and signaling. Trends Biochem Sci 2021; 47:265-278. [PMID: 34872819 PMCID: PMC8642147 DOI: 10.1016/j.tibs.2021.11.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 11/08/2021] [Accepted: 11/08/2021] [Indexed: 12/13/2022]
Abstract
Cell adhesion is essential for the formation of organs, cellular migration, and interaction with target cells and the extracellular matrix. Integrins are large protein α/β-chain heterodimers and form a major family of cell adhesion molecules. Recent research has dramatically increased our knowledge of how integrin phosphorylations regulate integrin activity. Phosphorylations determine the signaling complexes formed on the cytoplasmic tails, regulating downstream signaling. α-Chain phosphorylation is necessary for inducing β-chain phosphorylation in LFA-1, and the crosstalk from one integrin to another activating or inactivating its function is in part mediated by phosphorylation of β-chains. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus receptor angiotensin-converting enzyme 2 (ACE2) and possible integrin coreceptors may crosstalk and induce a phosphorylation switch and autophagy.
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Affiliation(s)
- Carl G Gahmberg
- Molecular and Integrative Biosciences Research Programme, University of Helsinki, Viikinkaari 9 C, 00014 Helsinki, Finland.
| | - Mikaela Grönholm
- Molecular and Integrative Biosciences Research Programme, University of Helsinki, Viikinkaari 9 C, 00014 Helsinki, Finland; Faculty of Pharmacy, University of Helsinki, Viikinkaari 5E, 00014 Helsinki, Finland
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15
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Kim SHJ, Hammer DA. Integrin cross-talk modulates stiffness-independent motility of CD4+ T lymphocytes. Mol Biol Cell 2021; 32:1749-1757. [PMID: 34232700 PMCID: PMC8684734 DOI: 10.1091/mbc.e21-03-0131] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
To carry out their physiological responsibilities, CD4+ T lymphocytes interact with various tissues of different mechanical properties. Recent studies suggest that T cells migrate upstream on surfaces expressing intracellular adhesion molecule-1 (ICAM-1) through interaction with leukocyte function-associated antigen-1 (αLβ2) (LFA-1) integrins. LFA-1 likely behaves as a mechanosensor, and thus we hypothesized that substrate mechanics might affect the ability of LFA-1 to support upstream migration of T cells under flow. Here we measured motility of CD4+ T lymphocytes on polyacrylamide gels with predetermined stiffnesses containing ICAM-1, vascular cell adhesion molecule-1 (VCAM-1), or a 1:1 mixture of VCAM-1/ICAM-1. Under static conditions, we found that CD4+ T cells exhibit an increase in motility on ICAM-1, but not on VCAM-1 or VCAM-1/ICAM-1 mixed, surfaces as a function of matrix stiffness. The mechanosensitivity of T-cell motility on ICAM-1 is overcome when VLA-4 (very late antigen-4 [α4β1]) is ligated with soluble VCAM-1. Last, we observed that CD4+ T cells migrate upstream under flow on ICAM-1-functionalized hydrogels, independent of substrate stiffness. In summary, we show that CD4+ T cells under no flow respond to matrix stiffness through LFA-1, and that the cross-talk of VLA-4 and LFA-1 can compensate for deformable substrates. Interestingly, CD4+ T lymphocytes migrated upstream on ICAM-1 regardless of the substrate stiffness, suggesting that flow can compensate for substrate stiffness.
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Affiliation(s)
- Sarah Hyun Ji Kim
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104
| | - Daniel A Hammer
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104.,Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104
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16
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Robert P, Biarnes-Pelicot M, Garcia-Seyda N, Hatoum P, Touchard D, Brustlein S, Nicolas P, Malissen B, Valignat MP, Theodoly O. Functional Mapping of Adhesiveness on Live Cells Reveals How Guidance Phenotypes Can Emerge From Complex Spatiotemporal Integrin Regulation. Front Bioeng Biotechnol 2021; 9:625366. [PMID: 33898401 PMCID: PMC8058417 DOI: 10.3389/fbioe.2021.625366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 03/05/2021] [Indexed: 01/13/2023] Open
Abstract
Immune cells have the ubiquitous capability to migrate disregarding the adhesion properties of the environment, which requires a versatile adaptation of their adhesiveness mediated by integrins, a family of specialized adhesion proteins. Each subtype of integrins has several ligands and several affinity states controlled by internal and external stimuli. However, probing cell adhesion properties on live cells without perturbing cell motility is highly challenging, especially in vivo. Here, we developed a novel in vitro method using micron-size beads pulled by flow to functionally probe the local surface adhesiveness of live and motile cells. This method allowed a functional mapping of the adhesiveness mediated by VLA-4 and LFA-1 integrins on the trailing and leading edges of live human T lymphocytes. We show that cell polarization processes enhance integrin-mediated adhesiveness toward cell rear for VLA-4 and cell front for LFA-1. Furthermore, an inhibiting crosstalk of LFA-1 toward VLA-4 and an activating crosstalk of VLA-4 toward LFA-1 were found to modulate cell adhesiveness with a long-distance effect across the cell. These combined signaling processes directly support the bistable model that explains the emergence of the versatile guidance of lymphocyte under flow. Molecularly, Sharpin, an LFA-1 inhibitor in lymphocyte uropod, was found involved in the LFA-1 deadhesion of lymphocytes; however, both Sharpin and Myosin inhibition had a rather modest impact on adhesiveness. Quantitative 3D immunostaining identified high-affinity LFA-1 and VLA-4 densities at around 50 and 100 molecules/μm2 in basal adherent zones, respectively. Interestingly, a latent adhesiveness of dorsal zones was not grasped by immunostaining but assessed by direct functional assays with beads. The combination of live functional assays, molecular imaging, and genome editing is instrumental to characterizing the spatiotemporal regulation of integrin-mediated adhesiveness at molecular and cell scales, which opens a new perspective to decipher sophisticated phenotypes of motility and guidance.
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Affiliation(s)
- Philippe Robert
- LAI, Aix-Marseille University, CNRS, INSERM U1067 Adhésion Cellulaires et lnflammation, Turing Center for Living Systems, Marseille, France
| | - Martine Biarnes-Pelicot
- LAI, Aix-Marseille University, CNRS, INSERM U1067 Adhésion Cellulaires et lnflammation, Turing Center for Living Systems, Marseille, France
| | - Nicolas Garcia-Seyda
- LAI, Aix-Marseille University, CNRS, INSERM U1067 Adhésion Cellulaires et lnflammation, Turing Center for Living Systems, Marseille, France
| | - Petra Hatoum
- LAI, Aix-Marseille University, CNRS, INSERM U1067 Adhésion Cellulaires et lnflammation, Turing Center for Living Systems, Marseille, France
| | - Dominique Touchard
- LAI, Aix-Marseille University, CNRS, INSERM U1067 Adhésion Cellulaires et lnflammation, Turing Center for Living Systems, Marseille, France
| | - Sophie Brustlein
- LAI, Aix-Marseille University, CNRS, INSERM U1067 Adhésion Cellulaires et lnflammation, Turing Center for Living Systems, Marseille, France
| | - Philippe Nicolas
- Aix-Marseille University, CNRS, INSERM U1104 Centre d'immunologie de Marseille-Luminy, Marseille, France
| | - Bernard Malissen
- Aix-Marseille University, CNRS, INSERM U1104 Centre d'immunologie de Marseille-Luminy, Marseille, France
| | - Marie-Pierre Valignat
- LAI, Aix-Marseille University, CNRS, INSERM U1067 Adhésion Cellulaires et lnflammation, Turing Center for Living Systems, Marseille, France
| | - Olivier Theodoly
- LAI, Aix-Marseille University, CNRS, INSERM U1067 Adhésion Cellulaires et lnflammation, Turing Center for Living Systems, Marseille, France
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17
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Kawai K, Tomonou M, Machida Y, Karuo Y, Tarui A, Sato K, Ikeda Y, Kinashi T, Omote M. Effect of Learning Dataset for Identification of Active Molecules: A Case Study of Integrin αIIbβ3 Inhibitors. Mol Inform 2021; 40:e2060040. [PMID: 33738924 DOI: 10.1002/minf.202060040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 01/30/2021] [Indexed: 01/13/2023]
Abstract
Efficient in silico approaches are needed to identify strong integrin αIIbβ3 inhibitors through a small number of measurements. To address the challenge, we investigated the effect of learning dataset on the classification performance of machine learning models focusing on weak and inactive compounds. The structure and activity information of the compounds were obtained from ChEMBL, and pCHEMBL values were used to classify them as active, inactive, or weak. Datasets with various imbalance levels from active:inactive=1 : 1 to 1 : 1000 were used for the machine learning. The prediction scores of the weak samples were found to lie between the predictive values of active and inactive compounds. In addition, another dataset that consists of 149 actives and 6.9 million inactives was screened; the results indicated that the number of positive predictions decreased for models trained with a higher number of inactives. Although there is a trade-off between false positives and false negatives, for determination of compounds with strong activity using a reduced number of measurements, it is better to use a large number of inactives for learning and identifying compounds that score higher than the weak samples.
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Affiliation(s)
- Kentaro Kawai
- Faculty of Pharmaceutical Sciences, Setsunan University, 45-1, Nagaotoge-cho, Hirakata, Osaka, 573-0101, Japan
| | - Mami Tomonou
- Faculty of Pharmaceutical Sciences, Setsunan University, 45-1, Nagaotoge-cho, Hirakata, Osaka, 573-0101, Japan
| | - Yume Machida
- Faculty of Pharmaceutical Sciences, Setsunan University, 45-1, Nagaotoge-cho, Hirakata, Osaka, 573-0101, Japan
| | - Yukiko Karuo
- Faculty of Pharmaceutical Sciences, Setsunan University, 45-1, Nagaotoge-cho, Hirakata, Osaka, 573-0101, Japan
| | - Atsushi Tarui
- Faculty of Pharmaceutical Sciences, Setsunan University, 45-1, Nagaotoge-cho, Hirakata, Osaka, 573-0101, Japan
| | - Kazuyuki Sato
- Faculty of Pharmaceutical Sciences, Setsunan University, 45-1, Nagaotoge-cho, Hirakata, Osaka, 573-0101, Japan
| | - Yoshiki Ikeda
- Department of Molecular Genetics, Institute of Biomedical Science, Kansai Medical University, 2-5-1 Shin-machi, Hirakata, Osaka, 573-1010, Japan
| | - Tatsuo Kinashi
- Department of Molecular Genetics, Institute of Biomedical Science, Kansai Medical University, 2-5-1 Shin-machi, Hirakata, Osaka, 573-1010, Japan
| | - Masaaki Omote
- Faculty of Pharmaceutical Sciences, Setsunan University, 45-1, Nagaotoge-cho, Hirakata, Osaka, 573-0101, Japan
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18
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Shannon MJ, Mace EM. Natural Killer Cell Integrins and Their Functions in Tissue Residency. Front Immunol 2021; 12:647358. [PMID: 33777044 PMCID: PMC7987804 DOI: 10.3389/fimmu.2021.647358] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 02/16/2021] [Indexed: 12/12/2022] Open
Abstract
Integrins are transmembrane receptors associated with adhesion and migration and are often highly differentially expressed receptors amongst natural killer cell subsets in microenvironments. Tissue resident natural killer cells are frequently defined by their differential integrin expression compared to other NK cell subsets, and integrins can further localize tissue resident NK cells to tissue microenvironments. As such, integrins play important roles in both the phenotypic and functional identity of NK cell subsets. Here we review the expression of integrin subtypes on NK cells and NK cell subsets with the goal of better understanding how integrin selection can dictate tissue residency and mediate function from the nanoscale to the tissue environment.
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Affiliation(s)
| | - Emily M. Mace
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States
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19
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Histone deacetylase 1 controls CD4 + T cell trafficking in autoinflammatory diseases. J Autoimmun 2021; 119:102610. [PMID: 33621930 DOI: 10.1016/j.jaut.2021.102610] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 01/13/2023]
Abstract
CD4+ T cell trafficking is a fundamental property of adaptive immunity. In this study, we uncover a novel role for histone deacetylase 1 (HDAC1) in controlling effector CD4+ T cell migration, thereby providing mechanistic insight into why a T cell-specific deletion of HDAC1 protects against experimental autoimmune encephalomyelitis (EAE). HDAC1-deficient CD4+ T cells downregulated genes associated with leukocyte extravasation. In vitro, HDAC1-deficient CD4+ T cells displayed aberrant morphology and migration on surfaces coated with integrin LFA-1 ligand ICAM-1 and showed an impaired ability to arrest on and to migrate across a monolayer of primary mouse brain microvascular endothelial cells under physiological flow. Moreover, HDAC1 deficiency reduced homing of CD4+ T cells into the intestinal epithelium and lamina propria preventing weight-loss, crypt damage and intestinal inflammation in adoptive CD4+ T cell transfer colitis. This correlated with reduced expression levels of LFA-1 integrin chains CD11a and CD18 as well as of selectin ligands CD43, CD44 and CD162 on transferred circulating HDAC1-deficient CD4+ T cells. Our data reveal that HDAC1 controls T cell-mediated autoimmunity via the regulation of CD4+ T cell trafficking into the CNS and intestinal tissues.
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20
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Fazeli E, Roy NH, Follain G, Laine RF, von Chamier L, Hänninen PE, Eriksson JE, Tinevez JY, Jacquemet G. Automated cell tracking using StarDist and TrackMate. F1000Res 2020. [DOI: 10.12688/f1000research.27019.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The ability of cells to migrate is a fundamental physiological process involved in embryonic development, tissue homeostasis, immune surveillance, and wound healing. Therefore, the mechanisms governing cellular locomotion have been under intense scrutiny over the last 50 years. One of the main tools of this scrutiny is live-cell quantitative imaging, where researchers image cells over time to study their migration and quantitatively analyze their dynamics by tracking them using the recorded images. Despite the availability of computational tools, manual tracking remains widely used among researchers due to the difficulty setting up robust automated cell tracking and large-scale analysis. Here we provide a detailed analysis pipeline illustrating how the deep learning network StarDist can be combined with the popular tracking software TrackMate to perform 2D automated cell tracking and provide fully quantitative readouts. Our proposed protocol is compatible with both fluorescent and widefield images. It only requires freely available and open-source software (ZeroCostDL4Mic and Fiji), and does not require any coding knowledge from the users, making it a versatile and powerful tool for the field. We demonstrate this pipeline's usability by automatically tracking cancer cells and T cells using fluorescent and brightfield images. Importantly, we provide, as supplementary information, a detailed step-by-step protocol to allow researchers to implement it with their images.
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21
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Fazeli E, Roy NH, Follain G, Laine RF, von Chamier L, Hänninen PE, Eriksson JE, Tinevez JY, Jacquemet G. Automated cell tracking using StarDist and TrackMate. F1000Res 2020; 9:1279. [PMID: 33224481 PMCID: PMC7670479 DOI: 10.12688/f1000research.27019.1] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/21/2020] [Indexed: 12/30/2022] Open
Abstract
The ability of cells to migrate is a fundamental physiological process involved in embryonic development, tissue homeostasis, immune surveillance, and wound healing. Therefore, the mechanisms governing cellular locomotion have been under intense scrutiny over the last 50 years. One of the main tools of this scrutiny is live-cell quantitative imaging, where researchers image cells over time to study their migration and quantitatively analyze their dynamics by tracking them using the recorded images. Despite the availability of computational tools, manual tracking remains widely used among researchers due to the difficulty setting up robust automated cell tracking and large-scale analysis. Here we provide a detailed analysis pipeline illustrating how the deep learning network StarDist can be combined with the popular tracking software TrackMate to perform 2D automated cell tracking and provide fully quantitative readouts. Our proposed protocol is compatible with both fluorescent and widefield images. It only requires freely available and open-source software (ZeroCostDL4Mic and Fiji), and does not require any coding knowledge from the users, making it a versatile and powerful tool for the field. We demonstrate this pipeline's usability by automatically tracking cancer cells and T cells using fluorescent and brightfield images. Importantly, we provide, as supplementary information, a detailed step-by-step protocol to allow researchers to implement it with their images.
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Affiliation(s)
- Elnaz Fazeli
- Laboratory of Biophysics, Institute of Biomedicine, Faculty of Medicine, University of Turku, Turku, Finland
| | - Nathan H. Roy
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
| | - Gautier Follain
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- Cell Biology, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Romain F. Laine
- MRC-Laboratory for Molecular Cell Biology, University College London, London, UK
- The Francis Crick Institute, London, UK
| | - Lucas von Chamier
- MRC-Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Pekka E. Hänninen
- Laboratory of Biophysics, Institute of Biomedicine, Faculty of Medicine, University of Turku, Turku, Finland
| | - John E. Eriksson
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- Cell Biology, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | | | - Guillaume Jacquemet
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- Cell Biology, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
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22
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First person – Nathan Roy. J Cell Sci 2020. [DOI: 10.1242/jcs.253047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] 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 early-career researchers promote themselves alongside their papers. Nathan Roy is first author on ‘LFA-1 signals to promote actin polymerization and upstream migration in T cells’, published in JCS. Nathan is a postdoctoral fellow in the lab of Janis Burkhardt at the Children's Hospital of Philadelphia, Philadelphia, PA, investigating signaling events that drive immune cell migration in both normal and pathological conditions.
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