1
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Lu J, Veler A, Simonetti B, Raj T, Chou PH, Cross SJ, Phillips AM, Ruan X, Huynh L, Dowsey AW, Ye D, Murphy RF, Verkade P, Cullen PJ, Wülfing C. Five Inhibitory Receptors Display Distinct Vesicular Distributions in Murine T Cells. Cells 2023; 12:2558. [PMID: 37947636 PMCID: PMC10649679 DOI: 10.3390/cells12212558] [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: 07/21/2023] [Revised: 10/26/2023] [Accepted: 10/30/2023] [Indexed: 11/12/2023] Open
Abstract
T cells can express multiple inhibitory receptors. Upon induction of T cell exhaustion in response to a persistent antigen, prominently in the anti-tumor immune response, many are expressed simultaneously. Key inhibitory receptors are CTLA-4, PD-1, LAG3, TIM3, and TIGIT, as investigated here. These receptors are important as central therapeutic targets in cancer immunotherapy. Inhibitory receptors are not constitutively expressed on the cell surface, but substantial fractions reside in intracellular vesicular structures. It remains unresolved to which extent the subcellular localization of different inhibitory receptors is distinct. Using quantitative imaging of subcellular distributions and plasma membrane insertion as complemented by proximity proteomics and biochemical analysis of the association of the inhibitory receptors with trafficking adaptors, the subcellular distributions of the five inhibitory receptors were discrete. The distribution of CTLA-4 was most distinct, with preferential association with lysosomal-derived vesicles and the sorting nexin 1/2/5/6 transport machinery. With a lack of evidence for the existence of specific vesicle subtypes to explain divergent inhibitory receptor distributions, we suggest that such distributions are driven by divergent trafficking through an overlapping joint set of vesicular structures. This extensive characterization of the subcellular localization of five inhibitory receptors in relation to each other lays the foundation for the molecular investigation of their trafficking and its therapeutic exploitation.
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Affiliation(s)
- Jiahe Lu
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK; (J.L.); (A.V.); (T.R.); (P.H.C.); (L.H.)
- Department of Urology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai 200032, China;
| | - Alisa Veler
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK; (J.L.); (A.V.); (T.R.); (P.H.C.); (L.H.)
| | - Boris Simonetti
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK; (B.S.); (P.V.); (P.J.C.)
| | - Timsse Raj
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK; (J.L.); (A.V.); (T.R.); (P.H.C.); (L.H.)
| | - Po Han Chou
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK; (J.L.); (A.V.); (T.R.); (P.H.C.); (L.H.)
| | - Stephen J. Cross
- Wolfson Bioimaging Facility, University of Bristol, Bristol BS8 1TD, UK;
| | - Alexander M. Phillips
- Department of Electrical Engineering & Electronics and Computational Biology Facility, University of Liverpool, Liverpool L69 7ZX, UK;
| | - Xiongtao Ruan
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA; (X.R.); (R.F.M.)
| | - Lan Huynh
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK; (J.L.); (A.V.); (T.R.); (P.H.C.); (L.H.)
| | - Andrew W. Dowsey
- Bristol Veterinary School, University of Bristol, Bristol BS40 5DU, UK;
| | - Dingwei Ye
- Department of Urology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai 200032, China;
- Shanghai Genitourinary Cancer Institute, Shanghai 200032, China
| | - Robert F. Murphy
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA; (X.R.); (R.F.M.)
- Department of Biological Sciences, Biomedical Engineering and Machine Learning, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Paul Verkade
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK; (B.S.); (P.V.); (P.J.C.)
| | - Peter J. Cullen
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK; (B.S.); (P.V.); (P.J.C.)
| | - Christoph Wülfing
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK; (J.L.); (A.V.); (T.R.); (P.H.C.); (L.H.)
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2
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Jiang X, Isogai T, Chi J, Danuser G. Fine-grained, nonlinear registration of live cell movies reveals spatiotemporal organization of diffuse molecular processes. PLoS Comput Biol 2022; 18:e1009667. [PMID: 36584219 PMCID: PMC9870159 DOI: 10.1371/journal.pcbi.1009667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/23/2023] [Accepted: 11/28/2022] [Indexed: 01/01/2023] Open
Abstract
We present an application of nonlinear image registration to align in microscopy time lapse sequences for every frame the cell outline and interior with the outline and interior of the same cell in a reference frame. The registration relies on a subcellular fiducial marker, a cell motion mask, and a topological regularization that enforces diffeomorphism on the registration without significant loss of granularity. This allows spatiotemporal analysis of extremely noisy and diffuse molecular processes across the entire cell. We validate the registration method for different fiducial markers by measuring the intensity differences between predicted and original time lapse sequences of Actin cytoskeleton images and by uncovering zones of spatially organized GEF- and GTPase signaling dynamics visualized by FRET-based activity biosensors in MDA-MB-231 cells. We then demonstrate applications of the registration method in conjunction with stochastic time-series analysis. We describe distinct zones of locally coherent dynamics of the cytoplasmic protein Profilin in U2OS cells. Further analysis of the Profilin dynamics revealed strong relationships with Actin cytoskeleton reorganization during cell symmetry-breaking and polarization. This study thus provides a framework for extracting information to explore functional interactions between cell morphodynamics, protein distributions, and signaling in cells undergoing continuous shape changes. Matlab code implementing the proposed registration method is available at https://github.com/DanuserLab/Mask-Regularized-Diffeomorphic-Cell-Registration.
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Affiliation(s)
- Xuexia Jiang
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, Texas, United States of America
| | - Tadamoto Isogai
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, Texas, United States of America
| | - Joseph Chi
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, Texas, United States of America
| | - Gaudenz Danuser
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, Texas, United States of America
- * E-mail:
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3
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Yoon CW, Pan Y, Wang Y. The application of mechanobiotechnology for immuno-engineering and cancer immunotherapy. Front Cell Dev Biol 2022; 10:1064484. [PMID: 36483679 PMCID: PMC9725026 DOI: 10.3389/fcell.2022.1064484] [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: 10/08/2022] [Accepted: 11/08/2022] [Indexed: 11/24/2022] Open
Abstract
Immune-engineering is a rapidly emerging field in the past few years, as immunotherapy evolved from a paradigm-shifting therapeutic approach for cancer treatment to promising immuno-oncology models in clinical trials and commercial products. Linking the field of biomedical engineering with immunology, immuno-engineering applies engineering principles and utilizes synthetic biology tools to study and control the immune system for diseases treatments and interventions. Over the past decades, there has been a deeper understanding that mechanical forces play crucial roles in regulating immune cells at different stages from antigen recognition to actual killing, which suggests potential opportunities to design and tailor mechanobiology tools to novel immunotherapy. In this review, we first provide a brief introduction to recent technological and scientific advances in mechanobiology for immune cells. Different strategies for immuno-engineering are then discussed and evaluated. Furthermore, we describe the opportunities and challenges of applying mechanobiology and related technologies to study and engineer immune cells and ultimately modulate their function for immunotherapy. In summary, the synergetic integration of cutting-edge mechanical biology techniques into immune-engineering strategies can provide a powerful platform and allow new directions for the field of immunotherapy.
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4
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Case LB, De Pasquale M, Henry L, Rosen MK. Synergistic phase separation of two pathways promotes integrin clustering and nascent adhesion formation. eLife 2022; 11:e72588. [PMID: 35049497 PMCID: PMC8791637 DOI: 10.7554/elife.72588] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 01/10/2022] [Indexed: 12/14/2022] Open
Abstract
Integrin adhesion complexes (IACs) are integrin-based plasma-membrane-associated compartments where cells sense environmental cues. The physical mechanisms and molecular interactions that mediate initial IAC formation are unclear. We found that both p130Cas ('Cas') and Focal adhesion kinase ('FAK') undergo liquid-liquid phase separation in vitro under physiologic conditions. Cas- and FAK- driven phase separation is sufficient to reconstitute kindlin-dependent integrin clustering in vitro with recombinant mammalian proteins. In vitro condensates and IACs in mouse embryonic fibroblasts (MEFs) exhibit similar sensitivities to environmental perturbations including changes in temperature and pH. Furthermore, mutations that inhibit or enhance phase separation in vitro reduce or increase the number of IACs in MEFs, respectively. Finally, we find that the Cas and FAK pathways act synergistically to promote phase separation, integrin clustering, IAC formation and partitioning of key components in vitro and in cells. We propose that Cas- and FAK-driven phase separation provides an intracellular trigger for integrin clustering and nascent IAC formation.
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Affiliation(s)
- Lindsay B Case
- Department of Biophysics, Howard Hughes Medical Institute, The University of Texas Southwestern Medical CenterDallasUnited States
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Milagros De Pasquale
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Lisa Henry
- Department of Biophysics, Howard Hughes Medical Institute, The University of Texas Southwestern Medical CenterDallasUnited States
| | - Michael K Rosen
- Department of Biophysics, Howard Hughes Medical Institute, The University of Texas Southwestern Medical CenterDallasUnited States
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5
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Dupré L, Boztug K, Pfajfer L. Actin Dynamics at the T Cell Synapse as Revealed by Immune-Related Actinopathies. Front Cell Dev Biol 2021; 9:665519. [PMID: 34249918 PMCID: PMC8266300 DOI: 10.3389/fcell.2021.665519] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 04/06/2021] [Indexed: 01/21/2023] Open
Abstract
The actin cytoskeleton is composed of dynamic filament networks that build adaptable local architectures to sustain nearly all cellular activities in response to a myriad of stimuli. Although the function of numerous players that tune actin remodeling is known, the coordinated molecular orchestration of the actin cytoskeleton to guide cellular decisions is still ill defined. T lymphocytes provide a prototypical example of how a complex program of actin cytoskeleton remodeling sustains the spatio-temporal control of key cellular activities, namely antigen scanning and sensing, as well as polarized delivery of effector molecules, via the immunological synapse. We here review the unique knowledge on actin dynamics at the T lymphocyte synapse gained through the study of primary immunodeficiences caused by mutations in genes encoding actin regulatory proteins. Beyond the specific roles of individual actin remodelers, we further develop the view that these operate in a coordinated manner and are an integral part of multiple signaling pathways in T lymphocytes.
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Affiliation(s)
- Loïc Dupré
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases (LBI-RUD), Vienna, Austria.,Department of Dermatology, Medical University of Vienna, Vienna, Austria.,Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), INSERM, CNRS, Toulouse III Paul Sabatier University, Toulouse, France
| | - Kaan Boztug
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases (LBI-RUD), Vienna, Austria.,St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria.,CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria.,St. Anna Children's Hospital, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | - Laurène Pfajfer
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases (LBI-RUD), Vienna, Austria.,Department of Dermatology, Medical University of Vienna, Vienna, Austria.,Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), INSERM, CNRS, Toulouse III Paul Sabatier University, Toulouse, France.,St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
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6
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Li Y, Tunbridge HM, Britton GJ, Hill EV, Sinai P, Cirillo S, Thompson C, Fallah-Arani F, Dovedi SJ, Wraith DC, Wülfing C. A LAT-Based Signaling Complex in the Immunological Synapse as Determined with Live Cell Imaging Is Less Stable in T Cells with Regulatory Capability. Cells 2021; 10:418. [PMID: 33671236 PMCID: PMC7921939 DOI: 10.3390/cells10020418] [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: 12/02/2020] [Revised: 02/12/2021] [Accepted: 02/12/2021] [Indexed: 12/03/2022] Open
Abstract
Peripheral immune regulation is critical for the maintenance of self-tolerance. Here we have investigated signaling processes that distinguish T cells with regulatory capability from effector T cells. The murine Tg4 T cell receptor recognizes a peptide derived from the self-antigen myelin basic protein. T cells from Tg4 T cell receptor transgenic mice can be used to generate effector T cells and three types of T cells with regulatory capability, inducible regulatory T cells, T cells tolerized by repeated in vivo antigenic peptide exposure or T cells treated with the tolerogenic drug UCB9608 (a phosphatidylinositol 4 kinase IIIβ inhibitor). We comparatively studied signaling in all of these T cells by activating them with the same antigen presenting cells presenting the same myelin basic protein peptide. Supramolecular signaling structures, as efficiently detected by large-scale live cell imaging, are critical mediators of T cell activation. The formation of a supramolecular signaling complex anchored by the adaptor protein linker for activation of T cells (LAT) was consistently terminated more rapidly in Tg4 T cells with regulatory capability. Such termination could be partially reversed by blocking the inhibitory receptors CTLA-4 and PD-1. Our work suggests that attenuation of proximal signaling may favor regulatory over effector function in T cells.
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Affiliation(s)
- Yikui Li
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - Helen M Tunbridge
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - Graham J Britton
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Elaine V Hill
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - Parisa Sinai
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - Silvia Cirillo
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | | | | | - Simon J Dovedi
- R&D Oncology, AstraZeneca, Granta Park, Cambridge, CB21 6GH, UK
| | - David C Wraith
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK
| | - Christoph Wülfing
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
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7
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Ambler R, Edmunds GL, Tan SL, Cirillo S, Pernes JI, Ruan X, Huete-Carrasco J, Wong CCW, Lu J, Ward J, Toti G, Hedges AJ, Dovedi SJ, Murphy RF, Morgan DJ, Wülfing C. PD-1 suppresses the maintenance of cell couples between cytotoxic T cells and target tumor cells within the tumor. Sci Signal 2020; 13:13/649/eaau4518. [PMID: 32934075 DOI: 10.1126/scisignal.aau4518] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The killing of tumor cells by CD8+ T cells is suppressed by the tumor microenvironment, and increased expression of inhibitory receptors, including programmed cell death protein-1 (PD-1), is associated with tumor-mediated suppression of T cells. To find cellular defects triggered by tumor exposure and associated PD-1 signaling, we established an ex vivo imaging approach to investigate the response of antigen-specific, activated effector CD8+ tumor-infiltrating lymphocytes (TILs) after interaction with target tumor cells. Although TIL-tumor cell couples readily formed, couple stability deteriorated within minutes. This was associated with impaired F-actin clearing from the center of the cellular interface, reduced Ca2+ signaling, increased TIL locomotion, and impaired tumor cell killing. The interaction of CD8+ T lymphocytes with tumor cell spheroids in vitro induced a similar phenotype, supporting a critical role of direct T cell-tumor cell contact. Diminished engagement of PD-1 within the tumor, but not acute ex vivo blockade, partially restored cell couple maintenance and killing. PD-1 thus contributes to the suppression of TIL function by inducing a state of impaired subcellular organization.
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Affiliation(s)
- Rachel Ambler
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK
| | - Grace L Edmunds
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK
| | - Sin Lih Tan
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK
| | - Silvia Cirillo
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK
| | - Jane I Pernes
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK
| | - Xiongtao Ruan
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Jorge Huete-Carrasco
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK
| | - Carissa C W Wong
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK
| | - Jiahe Lu
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK
| | - Juma Ward
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK
| | - Giulia Toti
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK
| | - Alan J Hedges
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK
| | - Simon J Dovedi
- R&D Oncology, AstraZeneca, Granta Park, Cambridge CB21 6GH, UK
| | - Robert F Murphy
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.,Departments of Biological Sciences, Biomedical Engineering and Machine Learning, Carnegie Mellon University, Pittsburgh, PA 15213, USA.,Freiburg Institute for Advanced Studies and Faculty of Biology, Albert Ludwig University of Freiburg, 79104 Freiburg, Germany
| | - David J Morgan
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK.
| | - Christoph Wülfing
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK.
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8
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Ruan X, Murphy RF. Evaluation of methods for generative modeling of cell and nuclear shape. Bioinformatics 2020; 35:2475-2485. [PMID: 30535313 PMCID: PMC6612826 DOI: 10.1093/bioinformatics/bty983] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 10/30/2018] [Accepted: 12/06/2018] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Cell shape provides both geometry for, and a reflection of, cell function. Numerous methods for describing and modeling cell shape have been described, but previous evaluation of these methods in terms of the accuracy of generative models has been limited. RESULTS Here we compare traditional methods and deep autoencoders to build generative models for cell shapes in terms of the accuracy with which shapes can be reconstructed from models. We evaluated the methods on different collections of 2D and 3D cell images, and found that none of the methods gave accurate reconstructions using low dimensional encodings. As expected, much higher accuracies were observed using high dimensional encodings, with outline-based methods significantly outperforming image-based autoencoders. The latter tended to encode all cells as having smooth shapes, even for high dimensions. For complex 3D cell shapes, we developed a significant improvement of a method based on the spherical harmonic transform that performs significantly better than other methods. We obtained similar results for the joint modeling of cell and nuclear shape. Finally, we evaluated the modeling of shape dynamics by interpolation in the shape space. We found that our modified method provided lower deformation energies along linear interpolation paths than other methods. This allows practical shape evolution in high dimensional shape spaces. We conclude that our improved spherical harmonic based methods are preferable for cell and nuclear shape modeling, providing better representations, higher computational efficiency and requiring fewer training images than deep learning methods. AVAILABILITY AND IMPLEMENTATION All software and data is available at http://murphylab.cbd.cmu.edu/software. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Xiongtao Ruan
- Computational Biology Department, School of Computer Science
| | - Robert F Murphy
- Computational Biology Department, School of Computer Science.,Departments of Biological Sciences, Biomedical Engineering, and Machine Learning, Carnegie Mellon University, Pittsburgh, PA, USA
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9
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Thauland TJ, Khan HA, Butte MJ. The Actin-Capping Protein Alpha-Adducin Is Required for T-Cell Costimulation. Front Immunol 2019; 10:2706. [PMID: 31824498 PMCID: PMC6879651 DOI: 10.3389/fimmu.2019.02706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 11/04/2019] [Indexed: 11/13/2022] Open
Abstract
Alpha-adducin (Add1) is a critical component of the actin-spectrin network in erythrocytes, acting to cap the fast-growing, barbed ends of actin filaments, and recruiting spectrin to these junctions. Add1 is highly expressed in T cells, but its role in T-cell activation has not been examined. Using a conditional knockout model, we show that Add1 is necessary for complete activation of CD4+ T cells in response to low levels of antigen but is dispensable for CD8+ T cell activation and response to infection. Surprisingly, costimulatory signals through CD28 were completely abrogated in the absence of Add1. This study is the first to examine the role of actin-capping in T cells, and it reveals a previously unappreciated role for the actin cytoskeleton in regulating costimulation.
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Affiliation(s)
| | | | - Manish J. Butte
- Division of Immunology, Allergy, and Rheumatology, Department of Pediatrics, University of California, Los Angeles, Los Angeles, CA, United States
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10
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Clark DJ, McMillan LE, Tan SL, Bellomo G, Massoue C, Thompson H, Mykhaylechko L, Alibhai D, Ruan X, Singleton KL, Du M, Hedges A, Schwartzberg PL, Verkade P, Murphy RF, Wülfing C. Transient protein accumulation at the center of the T cell antigen-presenting cell interface drives efficient IL-2 secretion. eLife 2019; 8:45789. [PMID: 31663508 PMCID: PMC6821493 DOI: 10.7554/elife.45789] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 09/25/2019] [Indexed: 01/06/2023] Open
Abstract
Supramolecular signaling assemblies are of interest for their unique signaling properties. A µm scale signaling assembly, the central supramolecular signaling cluster (cSMAC), forms at the center of the interface of T cells activated by antigen-presenting cells. We have determined that it is composed of multiple complexes of a supramolecular volume of up to 0.5 µm3 and associated with extensive membrane undulations. To determine cSMAC function, we have systematically manipulated the localization of three adaptor proteins, LAT, SLP-76, and Grb2. cSMAC localization varied between the adaptors and was diminished upon blockade of the costimulatory receptor CD28 and deficiency of the signal amplifying kinase Itk. Reconstitution of cSMAC localization restored IL-2 secretion which is a key T cell effector function as dependent on reconstitution dynamics. Our data suggest that the cSMAC enhances early signaling by facilitating signaling interactions and attenuates signaling thereafter through sequestration of a more limited set of signaling intermediates. Cells receive dozens of signals at different times and in different places. Integrating incoming information and deciding how to respond is no easy task. Signaling molecules on the cell surface pass messages inwards using chemical messengers that interact in complicated networks within the cell. One way to unravel the complexity of these networks is to look at specific groups of signaling molecules in test tubes to see how they interact. But the interior of a living cell is a very different environment. Molecules inside cells are tightly packed and, under certain conditions, they interact with each other by the thousands. They form structures known as ‘supramolecular complexes’, which changes their behavior. One such supramolecular complex is the ‘central supramolecular activation cluster’, or cSMAC for short. It forms under the surface of immune cells called T cells when they are getting ready to fight an infection. Under the microscope, the cSMAC looks like the bullseye of a dartboard, forming a crowd of signaling molecules at the center of the interface between the T cell and another cell. Its exact role is not clear, but evidence suggests it helps to start and stop the signals that switch T cells on. The cSMAC contains two key protein adaptors called LAT and SLP-76 that help to hold the structure together. So, to find out what the cSMAC does, Clark et al. genetically modified these adaptors to gain control over when the cSMAC forms. Clark et al. examined mouse T cells using super-resolution microscopy and electron microscopy, watching as other immune cells delivered the signal to switch on. As the T cells started to activate, the composition of the cSMAC changed. In the first two minutes after the cells started activating, the cSMAC included a large number of different components. This made T cell activation more efficient, possibly because the supramolecular complex was helping the network of signals to interact. Later, the cSMAC started to lose many of these components. Separating components may have helped to stop the activation signals. Understanding how T cells activate could lead to the possibility of turning them on or off in immune-related diseases. But these findings are not just relevant to immune cells. Other cells also use supramolecular complexes to control their signaling. Investigating how these complexes change over time could help us to understand how other cell types make decisions.
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Affiliation(s)
- Danielle J Clark
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Laura E McMillan
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Sin Lih Tan
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Gaia Bellomo
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Clementine Massoue
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Harry Thompson
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Lidiya Mykhaylechko
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Dominic Alibhai
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Xiongtao Ruan
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, United States
| | - Kentner L Singleton
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Minna Du
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Alan Hedges
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Pamela L Schwartzberg
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, United States
| | - Paul Verkade
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Robert F Murphy
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, United States.,Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, United States.,Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, United States.,Department of Machine Learning, Carnegie Mellon University, Pittsburgh, United States.,Freiburg Institute for Advanced Studies, Albert Ludwig University of Freiburg, Freiburg, Germany.,Faculty of Biology, Albert Ludwig University of Freiburg, Freiburg, Germany
| | - Christoph Wülfing
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom.,Department of Immunology, University of Texas Southwestern Medical Center, Dallas, United States
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11
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Hammer JA, Wang JC, Saeed M, Pedrosa AT. Origin, Organization, Dynamics, and Function of Actin and Actomyosin Networks at the T Cell Immunological Synapse. Annu Rev Immunol 2019; 37:201-224. [PMID: 30576253 PMCID: PMC8343269 DOI: 10.1146/annurev-immunol-042718-041341] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The engagement of a T cell with an antigen-presenting cell (APC) or activating surface results in the formation within the T cell of several distinct actin and actomyosin networks. These networks reside largely within a narrow zone immediately under the T cell's plasma membrane at its site of contact with the APC or activating surface, i.e., at the immunological synapse. Here we review the origin, organization, dynamics, and function of these synapse-associated actin and actomyosin networks. Importantly, recent insights into the nature of these actin-based cytoskeletal structures were made possible in several cases by advances in light microscopy.
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Affiliation(s)
- John A Hammer
- Cell Biology and Physiology Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA;
| | - Jia C Wang
- Cell Biology and Physiology Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA;
| | - Mezida Saeed
- Cell Biology and Physiology Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA;
| | - Antonio T Pedrosa
- Cell Biology and Physiology Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA;
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Sawicka A, Babataheri A, Dogniaux S, Barakat AI, Gonzalez-Rodriguez D, Hivroz C, Husson J. Micropipette force probe to quantify single-cell force generation: application to T-cell activation. Mol Biol Cell 2017; 28:3229-3239. [PMID: 28931600 PMCID: PMC5687025 DOI: 10.1091/mbc.e17-06-0385] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 09/08/2017] [Accepted: 09/12/2017] [Indexed: 11/11/2022] Open
Abstract
We describe the micropipette force probe, a novel technique that uses a micropipette as a flexible cantilever that aspirates a coated microbead and brings it into contact with a cell. We apply the technique to quantify mechanical and morphological events occurring during T-cell activation. In response to engagement of surface molecules, cells generate active forces that regulate many cellular processes. Developing tools that permit gathering mechanical and morphological information on these forces is of the utmost importance. Here we describe a new technique, the micropipette force probe, that uses a micropipette as a flexible cantilever that can aspirate at its tip a bead that is coated with molecules of interest and is brought in contact with the cell. This technique simultaneously allows tracking the resulting changes in cell morphology and mechanics as well as measuring the forces generated by the cell. To illustrate the power of this technique, we applied it to the study of human primary T lymphocytes (T-cells). It allowed the fine monitoring of pushing and pulling forces generated by T-cells in response to various activating antibodies and bending stiffness of the micropipette. We further dissected the sequence of mechanical and morphological events occurring during T-cell activation to model force generation and to reveal heterogeneity in the cell population studied. We also report the first measurement of the changes in Young’s modulus of T-cells during their activation, showing that T-cells stiffen within the first minutes of the activation process.
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Affiliation(s)
- Anna Sawicka
- Laboratoire d'Hydrodynamique (LadHyX), Department of Mechanics, Ecole polytechnique-CNRS UMR7646, 91128 Palaiseau, France.,Institut Curie Section Recherche, INSERM U932 and PSL Research University, 75005 Paris, France
| | - Avin Babataheri
- Laboratoire d'Hydrodynamique (LadHyX), Department of Mechanics, Ecole polytechnique-CNRS UMR7646, 91128 Palaiseau, France
| | - Stéphanie Dogniaux
- Institut Curie Section Recherche, INSERM U932 and PSL Research University, 75005 Paris, France
| | - Abdul I Barakat
- Laboratoire d'Hydrodynamique (LadHyX), Department of Mechanics, Ecole polytechnique-CNRS UMR7646, 91128 Palaiseau, France
| | | | - Claire Hivroz
- Institut Curie Section Recherche, INSERM U932 and PSL Research University, 75005 Paris, France
| | - Julien Husson
- Laboratoire d'Hydrodynamique (LadHyX), Department of Mechanics, Ecole polytechnique-CNRS UMR7646, 91128 Palaiseau, France
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13
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Ruan X, Wülfing C, Murphy RF. Image-based spatiotemporal causality inference for protein signaling networks. Bioinformatics 2017; 33:i217-i224. [PMID: 28881992 PMCID: PMC5870542 DOI: 10.1093/bioinformatics/btx258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Motivation Efforts to model how signaling and regulatory networks work in cells have largely either not considered spatial organization or have used compartmental models with minimal spatial resolution. Fluorescence microscopy provides the ability to monitor the spatiotemporal distribution of many molecules during signaling events, but as of yet no methods have been described for large scale image analysis to learn a complex protein regulatory network. Here we present and evaluate methods for identifying how changes in concentration in one cell region influence concentration of other proteins in other regions. Results Using 3D confocal microscope movies of GFP-tagged T cells undergoing costimulation, we learned models containing putative causal relationships among 12 proteins involved in T cell signaling. The models included both relationships consistent with current knowledge and novel predictions deserving further exploration. Further, when these models were applied to the initial frames of movies of T cells that had been only partially stimulated, they predicted the localization of proteins at later times with statistically significant accuracy. The methods, consisting of spatiotemporal alignment, automated region identification, and causal inference, are anticipated to be applicable to a number of biological systems. Availability and implementation The source code and data are available as a Reproducible Research Archive at http://murphylab.cbd.cmu.edu/software/2017_TcellCausalModels/
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Affiliation(s)
- Xiongtao Ruan
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Christoph Wülfing
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS, UK
| | - Robert F Murphy
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA.,Departments of Biological Sciences, Biomedical Engineering, and Machine Learning, Carnegie Mellon University, Pittsburgh, PA, USA.,Freiburg Institute for Advanced Studies and Faculty of Biology, Albert Ludwig University of Freiburg, Freiburg im Breisgau, Baden-Württemberg, Germany
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14
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An Overview of data science uses in bioimage informatics. Methods 2017; 115:110-118. [DOI: 10.1016/j.ymeth.2016.12.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 12/09/2016] [Accepted: 12/30/2016] [Indexed: 01/17/2023] Open
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15
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Britton GJ, Ambler R, Clark DJ, Hill EV, Tunbridge HM, McNally KE, Burton BR, Butterweck P, Sabatos-Peyton C, Hampton-O'Neil LA, Verkade P, Wülfing C, Wraith DC. PKCθ links proximal T cell and Notch signaling through localized regulation of the actin cytoskeleton. eLife 2017; 6. [PMID: 28112644 PMCID: PMC5310840 DOI: 10.7554/elife.20003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Accepted: 01/22/2017] [Indexed: 11/16/2022] Open
Abstract
Notch is a critical regulator of T cell differentiation and is activated through proteolytic cleavage in response to ligand engagement. Using murine myelin-reactive CD4 T cells, we demonstrate that proximal T cell signaling modulates Notch activation by a spatiotemporally constrained mechanism. The protein kinase PKCθ is a critical mediator of signaling by the T cell antigen receptor and the principal costimulatory receptor CD28. PKCθ selectively inactivates the negative regulator of F-actin generation, Coronin 1A, at the center of the T cell interface with the antigen presenting cell (APC). This allows for effective generation of the large actin-based lamellum required for recruitment of the Notch-processing membrane metalloproteinase ADAM10. Such enhancement of Notch activation is critical for efficient T cell proliferation and Th17 differentiation. We reveal a novel mechanism that, through modulation of the cytoskeleton, controls Notch activation at the T cell:APC interface thereby linking T cell receptor and Notch signaling pathways. DOI:http://dx.doi.org/10.7554/eLife.20003.001 The body’s immune system recognizes and responds to foreign agents such as bacteria and viruses. Immune cells known as T cells recognize foreign substances through a protein on their surface called the T cell receptor. Specifically, the T cell receptor binds to fragments of foreign proteins displayed on the surface of other cells, which sets in motion a chain of events that leads to the T cell becoming activated. An activated T cell divides to form new cells that develop into “effector” T cells, which can mount an effective immune response. The T cell engages with the cell displaying the foreign proteins via an interface referred to as the immunological synapse. This zone of contact brings together the signaling machinery of the T cell. Like many other cells, T cells contain an internal skeleton-like structure made up of actin filaments. These filaments are crucial for the formation of the immunological synapse, in part because they help to transport the T cell receptor and other signaling proteins to the immunological synapse. Recent research suggests that a signaling protein called Notch plays an important role in instructing activated T cells to develop into effector cells. Notch is found on the surface of many cells, including T cells, and it becomes activated when it is cut by a specific enzyme. However, it was not entirely clear how T cell signaling drives the activation of the Notch protein. Britton et al. have now investigated the mechanism that leads to Notch activation in T cells from mice. The results show that a protein found inside the T cell, called PKCθ, is a major contributor to Notch activation when T cells become activated. So how does the PKCθ protein control the activation of Notch? Britton et al. observed that PKCθ inactivates a protein that normally inhibits actin filaments from forming, and does so specifically at the center of the immunological synapse. This inhibition promotes the generation of a large actin-rich structure known as the lamellal actin network. This structure is required to recruit the Notch-cutting enzyme to the immunological synapse. Further analysis revealed that Notch gets cut and activated during the first few minutes of T cell activation leading to cell division and the development of effector T cells. Following on from this work, the next challenge will be to explore if altering signaling from the T cell receptor – for example, using drugs or small molecules – can modify the activation of Notch. If so, it will be important to explore if the chemicals could potentially be used to treat diseases that develop when T cells go awry, such as rheumatoid arthritis, psoriasis and Crohn’s disease. DOI:http://dx.doi.org/10.7554/eLife.20003.002
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Affiliation(s)
- Graham J Britton
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Rachel Ambler
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Danielle J Clark
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Elaine V Hill
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Helen M Tunbridge
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Kerrie E McNally
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Bronwen R Burton
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Philomena Butterweck
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | | | - Lea A Hampton-O'Neil
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Paul Verkade
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Christoph Wülfing
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - David Cameron Wraith
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
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16
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Abstract
Three-dimensional live cell imaging of the interaction of T cells with antigen-presenting cells (APCs) visualizes the subcellular distributions of signaling intermediates during T cell activation at thousands of resolved positions within a cell. These information-rich maps of local protein concentrations are a valuable resource in understanding T cell signaling. Here, we describe a protocol for the efficient acquisition of such imaging data and their computational processing to create four-dimensional maps of local concentrations. This protocol allows quantitative analysis of T cell signaling as it occurs inside live cells with resolution in time and space across thousands of cells.
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Affiliation(s)
- Rachel Ambler
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - Xiangtao Ruan
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, 7723 Gates-Hillman Center, Pittsburgh, PA, 15213, USA
| | - Robert F Murphy
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, 7723 Gates-Hillman Center, Pittsburgh, PA, 15213, USA.
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.
- Department of Machine Learning, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.
| | - Christoph Wülfing
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK.
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17
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Huranova M, Stepanek O. Role of actin cytoskeleton at multiple levels of T cell activation. AIMS MOLECULAR SCIENCE 2016. [DOI: 10.3934/molsci.2016.4.585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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