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Balit N, Cermakian N, Khadra A. The influence of circadian rhythms on CD8 + T cell activation upon vaccination: A mathematical modeling perspective. J Theor Biol 2024; 590:111852. [PMID: 38796098 DOI: 10.1016/j.jtbi.2024.111852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 03/30/2024] [Accepted: 05/14/2024] [Indexed: 05/28/2024]
Abstract
Circadian rhythms have been implicated in the modulation of many physiological processes, including those associated with the immune system. For example, these rhythms influence CD8+ T cell responses within the adaptive immune system. The mechanism underlying this immune-circadian interaction, however, remains unclear, particularly in the context of vaccination. Here, we devise a molecularly-explicit gene regulatory network model of early signaling in the naïve CD8+ T cell activation pathway, comprised of three axes (or subsystems) labeled ZAP70, LAT and CD28, to elucidate the molecular details of this immune-circadian mechanism and its relation to vaccination. This is done by coupling the model to a periodic forcing function to identify the molecular players targeted by circadian rhythms, and analyzing how these rhythms subsequently affect CD8+ T cell activation under differing levels of T cell receptor (TCR) phosphorylation, which we designate as vaccine load. By performing both bifurcation and parameter sensitivity analyses on the model at the single cell and ensemble levels, we find that applying periodic forcing on molecular targets within the ZAP70 axis is sufficient to create a day-night discrepancy in CD8+ T cell activation in a manner that is dependent on the bistable switch inherent in CD8+ T cell early signaling. We also demonstrate that the resulting CD8+ T cell activation is dependent on the strength of the periodic coupling as well as on the level of TCR phosphorylation. Our results show that this day-night discrepancy is not transmitted to certain downstream molecules within the LAT subsystem, such as mTORC1, suggesting a secondary, independent circadian regulation on that protein complex. We also corroborate experimental results by showing that the circadian regulation of CD8+ T cell primarily acts at a baseline, pre-vaccination state, playing a facilitating role in priming CD8+ T cells to vaccine inputs according to the time of day. By applying an ensemble level analysis using bifurcation theory and by including several hypothesized molecular targets of this circadian rhythm, we further demonstrate an increased variability between CD8+ T cells (due to heterogeneity) induced by its circadian regulation, which may allow an ensemble of CD8+ T cells to activate at a lower vaccine load, improving its sensitivity. This modeling study thus provides insights into the immune targets of the circadian clock, and proposes an interaction between vaccine load and the influence of circadian rhythms on CD8+ T cell activation.
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Affiliation(s)
- Nasri Balit
- Department of Physiology, McGill University, Montreal, Quebec, Canada.
| | - Nicolas Cermakian
- Douglas Research Center, Department of Psychiatry, McGill University, Montreal, Quebec, Canada.
| | - Anmar Khadra
- Department of Physiology, McGill University, Montreal, Quebec, Canada.
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2
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Mukherjee R, Sengar A, Cabello-García J, Ouldridge TE. Kinetic Proofreading Can Enhance Specificity in a Nonenzymatic DNA Strand Displacement Network. J Am Chem Soc 2024; 146:18916-18926. [PMID: 38951503 PMCID: PMC11258683 DOI: 10.1021/jacs.3c14673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 06/22/2024] [Accepted: 06/24/2024] [Indexed: 07/03/2024]
Abstract
Kinetic proofreading is used throughout natural systems to enhance the specificity of molecular recognition. At its most basic level, kinetic proofreading uses a supply of chemical fuel to drive a recognition interaction out of equilibrium, allowing a single free-energy difference between correct and incorrect targets to be exploited two or more times. Despite its importance in biology, there has been little effort to incorporate kinetic proofreading into synthetic systems in which molecular recognition is important, such as nucleic acid nanotechnology. In this article, we introduce a DNA strand displacement-based kinetic proofreading motif, showing that the consumption of a DNA-based fuel can be used to enhance molecular recognition during a templated dimerization reaction. We then show that kinetic proofreading can enhance the specificity with which a probe discriminates single nucleotide mutations, both in terms of the initial rate with which the probe reacts and the long-time behavior.
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Affiliation(s)
- Rakesh Mukherjee
- Department
of Bioengineering, Imperial College London, London SW7 2AZ, U.K.
| | - Aditya Sengar
- Department
of Bioengineering, Imperial College London, London SW7 2AZ, U.K.
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3
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Pathni A, Wagh K, Rey-Suarez I, Upadhyaya A. Mechanical regulation of lymphocyte activation and function. J Cell Sci 2024; 137:jcs219030. [PMID: 38995113 DOI: 10.1242/jcs.219030] [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: 07/13/2024] Open
Abstract
Mechanosensing, or how cells sense and respond to the physical environment, is crucial for many aspects of biological function, ranging from cell movement during development to cancer metastasis, the immune response and gene expression driving cell fate determination. Relevant physical stimuli include the stiffness of the extracellular matrix, contractile forces, shear flows in blood vessels, complex topography of the cellular microenvironment and membrane protein mobility. Although mechanosensing has been more widely studied in non-immune cells, it has become increasingly clear that physical cues profoundly affect the signaling function of cells of the immune system. In this Review, we summarize recent studies on mechanical regulation of immune cells, specifically lymphocytes, and explore how the force-generating cytoskeletal machinery might mediate mechanosensing. We discuss general principles governing mechanical regulation of lymphocyte function, spanning from the molecular scale of receptor activation to cellular responses to mechanical stimuli.
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Affiliation(s)
- Aashli Pathni
- Biological Sciences Graduate Program, University of Maryland, College Park, MD 20742, USA
| | - Kaustubh Wagh
- Department of Physics, University of Maryland, College Park, MD 20742, USA
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ivan Rey-Suarez
- Insitute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
- Microcore, Universidad de Los Andes, Bogota, DC 111711, USA
| | - Arpita Upadhyaya
- Biological Sciences Graduate Program, University of Maryland, College Park, MD 20742, USA
- Department of Physics, University of Maryland, College Park, MD 20742, USA
- Insitute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
- Biophysics Program, University of Maryland, College Park, MD 20742, USA
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4
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Ha G, Dieterle P, Shen H, Amir A, Needleman DJ. Measuring and modeling the dynamics of mitotic error correction. Proc Natl Acad Sci U S A 2024; 121:e2323009121. [PMID: 38875144 PMCID: PMC11194551 DOI: 10.1073/pnas.2323009121] [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: 01/23/2024] [Accepted: 05/11/2024] [Indexed: 06/16/2024] Open
Abstract
Error correction is central to many biological systems and is critical for protein function and cell health. During mitosis, error correction is required for the faithful inheritance of genetic material. When functioning properly, the mitotic spindle segregates an equal number of chromosomes to daughter cells with high fidelity. Over the course of spindle assembly, many initially erroneous attachments between kinetochores and microtubules are fixed through the process of error correction. Despite the importance of chromosome segregation errors in cancer and other diseases, there is a lack of methods to characterize the dynamics of error correction and how it can go wrong. Here, we present an experimental method and analysis framework to quantify chromosome segregation error correction in human tissue culture cells with live cell confocal imaging, timed premature anaphase, and automated counting of kinetochores after cell division. We find that errors decrease exponentially over time during spindle assembly. A coarse-grained model, in which errors are corrected in a chromosome-autonomous manner at a constant rate, can quantitatively explain both the measured error correction dynamics and the distribution of anaphase onset times. We further validated our model using perturbations that destabilized microtubules and changed the initial configuration of chromosomal attachments. Taken together, this work provides a quantitative framework for understanding the dynamics of mitotic error correction.
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Affiliation(s)
- Gloria Ha
- Department of Systems Biology, Harvard Medical School, Boston, MA02115
| | - Paul Dieterle
- Department of Physics, Harvard University, Cambridge, MA02138
| | - Hao Shen
- Reverie Labs, Cambridge, MA02139
| | - Ariel Amir
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA02138
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot7610001, Israel
| | - Daniel J. Needleman
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA02138
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA02138
- Center for Computational Biology, Flatiron Institute, New York, NY10010
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5
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Terui R, Berger SE, Sambel LA, Song D, Chistol G. Single-molecule imaging reveals the mechanism of bidirectional replication initiation in metazoa. Cell 2024:S0092-8674(24)00533-6. [PMID: 38866019 DOI: 10.1016/j.cell.2024.05.024] [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: 10/19/2023] [Revised: 03/28/2024] [Accepted: 05/13/2024] [Indexed: 06/14/2024]
Abstract
Metazoan genomes are copied bidirectionally from thousands of replication origins. Replication initiation entails the assembly and activation of two CMG helicases (Cdc45⋅Mcm2-7⋅GINS) at each origin. This requires several replication firing factors (including TopBP1, RecQL4, and DONSON) whose exact roles are still under debate. How two helicases are correctly assembled and activated at each origin is a long-standing question. By visualizing the recruitment of GINS, Cdc45, TopBP1, RecQL4, and DONSON in real time, we uncovered that replication initiation is surprisingly dynamic. First, TopBP1 transiently binds to the origin and dissociates before the start of DNA synthesis. Second, two Cdc45 are recruited together, even though Cdc45 alone cannot dimerize. Next, two copies of DONSON and two GINS simultaneously arrive at the origin, completing the assembly of two CMG helicases. Finally, RecQL4 is recruited to the CMG⋅DONSON⋅DONSON⋅CMG complex and promotes DONSON dissociation and CMG activation via its ATPase activity.
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Affiliation(s)
- Riki Terui
- Chemical and Systems Biology Department, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Scott E Berger
- Biophysics Program, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Larissa A Sambel
- Chemical and Systems Biology Department, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Dan Song
- Chemical and Systems Biology Department, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Gheorghe Chistol
- Chemical and Systems Biology Department, Stanford School of Medicine, Stanford, CA 94305, USA; Biophysics Program, Stanford School of Medicine, Stanford, CA 94305, USA; Cancer Biology Program, Stanford School of Medicine, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA 94305, USA; BioX Interdisciplinary Institute, Stanford School of Medicine, Stanford, CA 94305, USA.
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6
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Li X, Chou T. Reliable ligand discrimination in stochastic multistep kinetic proofreading: First passage time vs. product counting strategies. PLoS Comput Biol 2024; 20:e1012183. [PMID: 38857304 PMCID: PMC11192422 DOI: 10.1371/journal.pcbi.1012183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 06/21/2024] [Accepted: 05/20/2024] [Indexed: 06/12/2024] Open
Abstract
Cellular signaling, crucial for biological processes like immune response and homeostasis, relies on specificity and fidelity in signal transduction to accurately respond to stimuli amidst biological noise. Kinetic proofreading (KPR) is a key mechanism enhancing signaling specificity through time-delayed steps, although its effectiveness is debated due to intrinsic noise potentially reducing signal fidelity. In this study, we reformulate the theory of kinetic proofreading (KPR) by convolving multiple intermediate states into a single state and then define an overall "processing" time required to traverse these states. This simplification allows us to succinctly describe kinetic proofreading in terms of a single waiting time parameter, facilitating a more direct evaluation and comparison of KPR performance across different biological contexts such as DNA replication and T cell receptor (TCR) signaling. We find that loss of fidelity for longer proofreading steps relies on the specific strategy of information extraction and show that in the first-passage time (FPT) discrimination strategy, longer proofreading steps can exponentially improve the accuracy of KPR at the cost of speed. Thus, KPR can still be an effective discrimination mechanism in the high noise regime. However, in a product concentration-based discrimination strategy, longer proofreading steps do not necessarily lead to an increase in performance. However, by introducing activation thresholds on product concentrations, can we decompose the product-based strategy into a series of FPT-based strategies to better resolve the subtleties of KPR-mediated product discrimination. Our findings underscore the importance of understanding KPR in the context of how information is extracted and processed in the cell.
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Affiliation(s)
- Xiangting Li
- Department of Computational Medicine, University of California, Los Angeles, California, United States of America
| | - Tom Chou
- Department of Computational Medicine, University of California, Los Angeles, California, United States of America
- Department of Mathematics, University of California, Los Angeles, California, United States of America
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7
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Rogers J, Bajur AT, Salaita K, Spillane KM. Mechanical control of antigen detection and discrimination by T and B cell receptors. Biophys J 2024:S0006-3495(24)00347-3. [PMID: 38794795 DOI: 10.1016/j.bpj.2024.05.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 05/10/2024] [Accepted: 05/21/2024] [Indexed: 05/26/2024] Open
Abstract
The adaptive immune response is orchestrated by just two cell types, T cells and B cells. Both cells possess the remarkable ability to recognize virtually any antigen through their respective antigen receptors-the T cell receptor (TCR) and B cell receptor (BCR). Despite extensive investigations into the biochemical signaling events triggered by antigen recognition in these cells, our ability to predict or control the outcome of T and B cell activation remains elusive. This challenge is compounded by the sensitivity of T and B cells to the biophysical properties of antigens and the cells presenting them-a phenomenon we are just beginning to understand. Recent insights underscore the central role of mechanical forces in this process, governing the conformation, signaling activity, and spatial organization of TCRs and BCRs within the cell membrane, ultimately eliciting distinct cellular responses. Traditionally, T cells and B cells have been studied independently, with researchers working in parallel to decipher the mechanisms of activation. While these investigations have unveiled many overlaps in how these cell types sense and respond to antigens, notable differences exist. To fully grasp their biology and harness it for therapeutic purposes, these distinctions must be considered. This review compares and contrasts the TCR and BCR, placing emphasis on the role of mechanical force in regulating the activity of both receptors to shape cellular and humoral adaptive immune responses.
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Affiliation(s)
- Jhordan Rogers
- Department of Chemistry, Emory University, Atlanta, Georgia
| | - Anna T Bajur
- Department of Physics, King's College London, London, United Kingdom; Randall Centre for Cell and Molecular Biophysics, King's College London, London, United Kingdom
| | - Khalid Salaita
- Department of Chemistry, Emory University, Atlanta, Georgia; Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia.
| | - Katelyn M Spillane
- Department of Physics, King's College London, London, United Kingdom; Randall Centre for Cell and Molecular Biophysics, King's College London, London, United Kingdom; Department of Life Sciences, Imperial College London, London, United Kingdom.
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8
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Moon S, Zhao F, Uddin MN, Tucker CJ, Karmaus PWF, Fessler MB. Flotillin-2 dampens T cell antigen-sensitivity and functionality. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.26.591344. [PMID: 38746431 PMCID: PMC11092481 DOI: 10.1101/2024.04.26.591344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
T cell receptor (TCR) engagement triggers T cell responses, yet how TCR-mediated activation is regulated at the plasma membrane remains unclear. Here, we report that deleting the membrane scaffolding protein Flotillin-2 (Flot2) increases T cell antigen sensitivity, resulting in enhanced TCR signaling and effector function to weak TCR stimulation. T cell-specific Flot2-deficient mice exhibited reduced tumor growth and enhanced immunity to infection. Flot2-null CD4 + T cells exhibited increased T helper 1 polarization, proliferation, Nur77 induction, and phosphorylation of ZAP70 and LCK upon weak TCR stimulation, indicating a sensitized TCR-triggering threshold. Single cell-RNA sequencing suggested that Flot2 - null CD4 + T cells follow a similar route of activation as wild-type CD4 + T cells but exhibit higher occupancy of a discrete activation state under weak TCR stimulation. Given prior reports that TCR clustering influences sensitivity of T cells to stimuli, we evaluated TCR distribution with super-resolution microscopy. Flot2 ablation increased the number of surface TCR nanoclusters on naïve CD4 + T cells. Collectively, we posit that Flot2 modulates T cell functionality to weak TCR stimulation, at least in part, by regulating surface TCR clustering. Our findings have implications for improving T cell reactivity in diseases with poor antigenicity, such as cancer and chronic infections.
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9
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Wilhelm KB, Vissa A, Groves JT. Differential Roles of Kinetic On- and Off-Rates in T-Cell Receptor Signal Integration Revealed with a Modified Fab'-DNA Ligand. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.01.587588. [PMID: 38617215 PMCID: PMC11014569 DOI: 10.1101/2024.04.01.587588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Antibody-derived T-cell receptor (TCR) agonists are commonly used to activate T cells. While antibodies can trigger TCRs regardless of clonotype, they bypass native T cell signal integration mechanisms that rely on monovalent, membrane-associated, and relatively weakly-binding ligand in the context of cellular adhesion. Commonly used antibodies and their derivatives bind much more strongly than native peptide-MHC (pMHC) ligands bind their cognate TCRs. Because ligand dwell time is a critical parameter that tightly correlates with physiological function of the TCR signaling system, there is a general need, both in research and therapeutics, for universal TCR ligands with controlled kinetic binding parameters. To this end, we have introduced point mutations into recombinantly expressed α-TCRβ H57 Fab to modulate the dwell time of monovalent Fab binding to TCR. When tethered to a supported lipid bilayer via DNA complementation, these monovalent Fab'-DNA ligands activate T cells with potencies well-correlated with their TCR binding dwell time. Single-molecule tracking studies in live T cells reveal that individual binding events between Fab'-DNA ligands and TCRs elicit local signaling responses closely resembling native pMHC. The unique combination of high on- and off-rate of the H57 R97L mutant enables direct observations of cooperative interplay between ligand binding and TCR-proximal condensation of the linker for activation of T cells (LAT), which is not readily visualized with pMHC. This work provides insights into how T cells integrate kinetic information from synthetic ligands and introduces a method to develop affinity panels for polyclonal T cells, such as cells from a human patient.
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Affiliation(s)
- Kiera B Wilhelm
- Department of Chemistry, University of California-Berkeley, Berkeley, CA, 93720
| | - Anand Vissa
- Department of Chemistry, University of California-Berkeley, Berkeley, CA, 93720
| | - Jay T Groves
- Department of Chemistry, University of California-Berkeley, Berkeley, CA, 93720
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10
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Terui R, Berger S, Sambel L, Song D, Chistol G. Single-Molecule Imaging Reveals the Mechanism of Bidirectional Replication Initiation in Metazoa. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.28.587265. [PMID: 38585807 PMCID: PMC10996697 DOI: 10.1101/2024.03.28.587265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Metazoan genomes are copied bidirectionally from thousands of replication origins. Replication initiation entails the assembly and activation of two CMG (Cdc45•Mcm2-7•GINS) helicases at each origin. This requires several firing factors (including TopBP1, RecQL4, DONSON) whose exact roles remain unclear. How two helicases are correctly assembled and activated at every single origin is a long-standing question. By visualizing the recruitment of GINS, Cdc45, TopBP1, RecQL4, and DONSON in real time, we uncovered a surprisingly dynamic picture of initiation. Firing factors transiently bind origins but do not travel with replisomes. Two Cdc45 simultaneously arrive at each origin and two GINS are recruited together, even though neither protein can dimerize. The synchronized delivery of two GINS is mediated by DONSON, which acts as a dimerization scaffold. We show that RecQL4 promotes DONSON dissociation and facilitates helicase activation. The high fidelity of bidirectional origin firing can be explained by a Hopfield-style kinetic proofreading mechanism.
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Affiliation(s)
- Riki Terui
- Chemical and Systems Biology, Stanford School of Medicine, Stanford CA94305
| | - Scott Berger
- Biophysics Program, Stanford School of Medicine, Stanford CA94305
| | - Larissa Sambel
- Chemical and Systems Biology, Stanford School of Medicine, Stanford CA94305
| | - Dan Song
- Current Address: Eikon Therapeutics Inc
| | - Gheorghe Chistol
- Chemical and Systems Biology, Stanford School of Medicine, Stanford CA94305
- Biophysics Program, Stanford School of Medicine, Stanford CA94305
- Cancer Biology Program, Stanford School of Medicine, Stanford CA94305
- Stanford Cancer Institute, Stanford School of Medicine, Stanford CA94305
- BioX Interdisciplinary Institute, Stanford School of Medicine, Stanford CA94305
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11
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Rosenberg AM, Ayres CM, Medina-Cucurella AV, Whitehead TA, Baker BM. Enhanced T cell receptor specificity through framework engineering. Front Immunol 2024; 15:1345368. [PMID: 38545094 PMCID: PMC10967027 DOI: 10.3389/fimmu.2024.1345368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 02/15/2024] [Indexed: 04/12/2024] Open
Abstract
Development of T cell receptors (TCRs) as immunotherapeutics is hindered by inherent TCR cross-reactivity. Engineering more specific TCRs has proven challenging, as unlike antibodies, improving TCR affinity does not usually improve specificity. Although various protein design approaches have been explored to surmount this, mutations in TCR binding interfaces risk broadening specificity or introducing new reactivities. Here we explored if TCR specificity could alternatively be tuned through framework mutations distant from the interface. Studying the 868 TCR specific for the HIV SL9 epitope presented by HLA-A2, we used deep mutational scanning to identify a framework mutation above the mobile CDR3β loop. This glycine to proline mutation had no discernable impact on binding affinity or functional avidity towards the SL9 epitope but weakened recognition of SL9 escape variants and led to fewer responses in a SL9-derived positional scanning library. In contrast, an interfacial mutation near the tip of CDR3α that also did not impact affinity or functional avidity towards SL9 weakened specificity. Simulations indicated that the specificity-enhancing mutation functions by reducing the range of loop motions, limiting the ability of the TCR to adjust to different ligands. Although our results are likely to be TCR dependent, using framework engineering to control TCR loop motions may be a viable strategy for improving the specificity of TCR-based immunotherapies.
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Affiliation(s)
- Aaron M. Rosenberg
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, United States
| | - Cory M. Ayres
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, United States
| | | | - Timothy A. Whitehead
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, United States
| | - Brian M. Baker
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, United States
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12
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Jeffreys N, Brockman JM, Zhai Y, Ingber DE, Mooney DJ. Mechanical forces amplify TCR mechanotransduction in T cell activation and function. APPLIED PHYSICS REVIEWS 2024; 11:011304. [PMID: 38434676 PMCID: PMC10848667 DOI: 10.1063/5.0166848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 12/08/2023] [Indexed: 03/05/2024]
Abstract
Adoptive T cell immunotherapies, including engineered T cell receptor (eTCR) and chimeric antigen receptor (CAR) T cell immunotherapies, have shown efficacy in treating a subset of hematologic malignancies, exhibit promise in solid tumors, and have many other potential applications, such as in fibrosis, autoimmunity, and regenerative medicine. While immunoengineering has focused on designing biomaterials to present biochemical cues to manipulate T cells ex vivo and in vivo, mechanical cues that regulate their biology have been largely underappreciated. This review highlights the contributions of mechanical force to several receptor-ligand interactions critical to T cell function, with central focus on the TCR-peptide-loaded major histocompatibility complex (pMHC). We then emphasize the role of mechanical forces in (i) allosteric strengthening of the TCR-pMHC interaction in amplifying ligand discrimination during T cell antigen recognition prior to activation and (ii) T cell interactions with the extracellular matrix. We then describe approaches to design eTCRs, CARs, and biomaterials to exploit TCR mechanosensitivity in order to potentiate T cell manufacturing and function in adoptive T cell immunotherapy.
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Affiliation(s)
| | | | - Yunhao Zhai
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts 02115, USA
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13
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Acuto O. T-cell virtuosity in ''knowing thyself". Front Immunol 2024; 15:1343575. [PMID: 38415261 PMCID: PMC10896960 DOI: 10.3389/fimmu.2024.1343575] [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: 11/23/2023] [Accepted: 01/17/2024] [Indexed: 02/29/2024] Open
Abstract
Major Histocompatibility Complex (MHC) I and II and the αβ T-cell antigen receptor (TCRαβ) govern fundamental traits of adaptive immunity. They form a membrane-borne ligand-receptor system weighing host proteome integrity to detect contamination by nonself proteins. MHC-I and -II exhibit the "MHC-fold", which is able to bind a large assortment of short peptides as proxies for self and nonself proteins. The ensuing varying surfaces are mandatory ligands for Ig-like TCRαβ highly mutable binding sites. Conserved molecular signatures guide TCRαβ ligand binding sites to focus on the MHC-fold (MHC-restriction) while leaving many opportunities for its most hypervariable determinants to contact the peptide. This riveting molecular strategy affords many options for binding energy compatible with specific recognition and signalling aimed to eradicated microbial pathogens and cancer cells. While the molecular foundations of αβ T-cell adaptive immunity are largely understood, uncertainty persists on how peptide-MHC binding induces the TCRαβ signals that instruct cell-fate decisions. Solving this mystery is another milestone for understanding αβ T-cells' self/nonself discrimination. Recent developments revealing the innermost links between TCRαβ structural dynamics and signalling modality should help dissipate this long-sought-after enigma.
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Affiliation(s)
- Oreste Acuto
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
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14
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Robertson IB, Mulvaney R, Dieckmann N, Vantellini A, Canestraro M, Amicarella F, O'Dwyer R, Cole DK, Harper S, Dushek O, Kirk P. Tuning the potency and selectivity of ImmTAC molecules by affinity modulation. Clin Exp Immunol 2024; 215:105-119. [PMID: 37930865 PMCID: PMC10847821 DOI: 10.1093/cei/uxad120] [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: 06/01/2023] [Revised: 09/08/2023] [Accepted: 10/31/2023] [Indexed: 11/08/2023] Open
Abstract
T-cell-engaging bispecifics have great clinical potential for the treatment of cancer and infectious diseases. The binding affinity and kinetics of a bispecific molecule for both target and T-cell CD3 have substantial effects on potency and specificity, but the rules governing these relationships are not fully understood. Using immune mobilizing monoclonal TCRs against cancer (ImmTAC) molecules as a model, we explored the impact of altering affinity for target and CD3 on the potency and specificity of the redirected T-cell response. This class of bispecifics binds specific target peptides presented by human leukocyte antigen on the cell surface via an affinity-enhanced T-cell receptor and can redirect T-cell activation with an anti-CD3 effector moiety. The data reveal that combining a strong affinity TCR with an intermediate affinity anti-CD3 results in optimal T-cell activation, while strong affinity of both targeting and effector domains significantly reduces maximum cytokine release. Moreover, by optimizing the affinity of both parts of the molecule, it is possible to improve the selectivity. These results could be effectively modelled based on kinetic proofreading with limited signalling. This model explained the experimental observation that strong binding at both ends of the molecules leads to reduced activity, through very stable target-bispecific-effector complexes leading to CD3 entering a non-signalling dark state. These findings have important implications for the design of anti-CD3-based bispecifics with optimal biophysical parameters for both activity and specificity.
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Affiliation(s)
- Ian B Robertson
- Immunocore Limited, Drug Discovery and Protein Engineering, Abingdon, Oxon, UK
| | - Rachel Mulvaney
- Immunocore Limited, Drug Discovery and Protein Engineering, Abingdon, Oxon, UK
| | - Nele Dieckmann
- Immunocore Limited, Drug Discovery and Protein Engineering, Abingdon, Oxon, UK
| | - Alessio Vantellini
- Immunocore Limited, Drug Discovery and Protein Engineering, Abingdon, Oxon, UK
| | - Martina Canestraro
- Immunocore Limited, Drug Discovery and Protein Engineering, Abingdon, Oxon, UK
| | | | - Ronan O'Dwyer
- Immunocore Limited, Drug Discovery and Protein Engineering, Abingdon, Oxon, UK
| | - David K Cole
- Immunocore Limited, Drug Discovery and Protein Engineering, Abingdon, Oxon, UK
| | - Stephen Harper
- Immunocore Limited, Drug Discovery and Protein Engineering, Abingdon, Oxon, UK
| | - Omer Dushek
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Peter Kirk
- Immunocore Limited, Drug Discovery and Protein Engineering, Abingdon, Oxon, UK
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15
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Yanaka S, Watanabe H, Yogo R, Kongsema M, Kondo S, Yagi H, Uchihashi T, Kato K. Quantitative Analysis of Therapeutic Antibody Interactions with Fcγ Receptors Using High-Speed Atomic Force Microscopy. Biol Pharm Bull 2024; 47:334-338. [PMID: 38143078 DOI: 10.1248/bpb.b23-00751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2023]
Abstract
This study employed high-speed atomic force microscopy to quantitatively analyze the interactions between therapeutic antibodies and Fcγ receptors (FcγRs). Antibodies are essential components of the immune system and are integral to biopharmaceuticals. The focus of this study was on immunoglobulin G molecules, which are crucial for antigen binding via the Fab segments and cytotoxic functions through their Fc portions. We conducted real-time, label-free observations of the interactions of rituximab and mogamulizumab with the recombinant FcγRIIIa and FcγRIIa. The dwell times of FcγR binding were measured at the single-molecule level, which revealed an extended interaction duration of mogamulizumab with FcγRIIIa compared with that of rituximab. This is linked to enhanced antibody-dependent cellular cytotoxicity that is attributed to the absence of the core fucosylation of Fc-linked N-glycan. This study also emphasizes the crucial role of the Fab segments in the interaction with FcγRIIa as well as that with FcγRIIIa. This approach provided quantitative insight into therapeutic antibody interactions and exemplified kinetic proofreading, where cellular discrimination relies on ligand residence times. Observing the dwell times of antibodies on the effector molecules has emerged as a robust indicator of therapeutic antibody efficacy. Ultimately, these findings pave the way for the development of refined therapeutic antibodies with tailored interactions with specific FcγRs. This research contributes to the advancement of biopharmaceutical antibody design and optimizing antibody-based treatments for enhanced efficacy and precision.
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Affiliation(s)
- Saeko Yanaka
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences
- Institute for Molecular Science (IMS), National Institutes of Natural Sciences
- Graduate School of Pharmaceutical Sciences, Nagoya City University
- Graduate School of Pharmaceutical Sciences, Kyushu University
| | - Hiroki Watanabe
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences
| | - Rina Yogo
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences
- Institute for Molecular Science (IMS), National Institutes of Natural Sciences
- Graduate School of Pharmaceutical Sciences, Nagoya City University
| | | | - Sachiko Kondo
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences
- Graduate School of Pharmaceutical Sciences, Nagoya City University
| | - Hirokazu Yagi
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences
- Graduate School of Pharmaceutical Sciences, Nagoya City University
| | - Takayuki Uchihashi
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences
- Department of Physics and Institute for Glyco-core Research (iGCORE), Nagoya University
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences
- Institute for Molecular Science (IMS), National Institutes of Natural Sciences
- Graduate School of Pharmaceutical Sciences, Nagoya City University
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16
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de Groen PC. A new, all-encompassing aetiology of type 1 diabetes. Immunology 2024; 171:77-91. [PMID: 37772700 DOI: 10.1111/imm.13700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 09/10/2023] [Indexed: 09/30/2023] Open
Abstract
The aetiology of type 1 diabetes (T1D) is considered multifactorial with the contribution of the MHC on chromosome 6 being most important. Multiple factors also contribute to the aetiology of colorectal neoplasia, but the final event causing the change from normal mucosa to polyp and from polyp to cancer is due to a single somatic mutation event. Repeated formation of colorectal neoplasia within an at-risk population results in a predictable, tapering, exponential neoplasia distribution. Critical mutations driving colorectal neoplasia formation occur in mutation-prone DNA. These observations led to three hypotheses related to T1D. First, a single somatic mutation within the MHC of antigen presenting cells results in a change in phenotype from normal to T1D. Second, the distribution of additional autoimmune diseases (AAIDs) among persons with T1D adheres to a predictable, tapering, exponential distribution. And third, critical mutations driving development of T1D occur in mutation-prone DNA. To address the hypotheses in an orderly fashion, a new analytical method called genome-wide aetiology analysis (GWEA) consisting of nine steps is presented. All data required for GWEA of T1D are obtained from peer-reviewed publications or publicly available genome and proteome databases. Critical GWEA steps include AAID distribution among persons with T1D, analysis of at-risk HLA loci for mutation-prone DNA, determination of the role of non-MHC genes on GWAS, and verification of human data by cell culture or animal experiments. GWEA results show that distribution of AAID among persons with T1D adheres to a predictable, tapering, exponential distribution. A single, critical, somatic mutation within the epitope-binding groove of at-risk HLA loci alters HLA-insulin-peptide-T-cell-receptor (TCR) complex binding affinity and creates a new pathway that leads to loss of self-tolerance. The at-risk HLA loci, in particular binding pockets P1, P4 and P9, are encoded by mutation-prone DNA: GC-rich DNA sequence and somatic hypermutation hotspots. All other genes on GWAS can but do not have to amplify the new autoimmune pathway by facilitating DNA mutations, changing peptide binding affinity, reducing signal inhibition or augmenting signal intensity. Animal experiments agree with human studies. In conclusion, T1D is caused by a somatic mutation within the epitope-binding groove of an at-risk HLA gene that affects HLA-insulin-peptide-TCR complex binding affinity and initiates an autoimmune pathway. The nature of the peptide that binds to a mutated epitope-binding groove of an at-risk HLA gene determines the type of autoimmune disease that develops, that is, one at-risk HLA locus, multiple autoimmune diseases. Thus, T1D and AAIDs, and therefore common autoimmune diseases, share a similar somatic mutation-based aetiology.
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Affiliation(s)
- Piet C de Groen
- Division of Gastroenterology, Hepatology & Nutrition, University of Minnesota, Minneapolis, Minnesota, USA
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17
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Wither MJ, White WL, Pendyala S, Leanza PJ, Fowler DM, Kueh HY. Antigen perception in T cells by long-term Erk and NFAT signaling dynamics. Proc Natl Acad Sci U S A 2023; 120:e2308366120. [PMID: 38113261 PMCID: PMC10756264 DOI: 10.1073/pnas.2308366120] [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: 05/29/2023] [Accepted: 10/20/2023] [Indexed: 12/21/2023] Open
Abstract
Immune system threat detection hinges on T cells' ability to perceive varying peptide-major histocompatibility complex (pMHC) antigens. As the Erk and NFAT pathways link T cell receptor engagement to gene regulation, their signaling dynamics may convey information about pMHC inputs. To test this idea, we developed a dual reporter mouse strain and a quantitative imaging assay that, together, enable simultaneous monitoring of Erk and NFAT dynamics in live T cells over day-long timescales as they respond to varying pMHC inputs. Both pathways initially activate uniformly across various pMHC inputs but diverge only over longer (9+ h) timescales, enabling independent encoding of pMHC affinity and dose. These late signaling dynamics are decoded via multiple temporal and combinatorial mechanisms to generate pMHC-specific transcriptional responses. Our findings underscore the importance of long timescale signaling dynamics in antigen perception and establish a framework for understanding T cell responses under diverse contexts.
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Affiliation(s)
- Matthew J. Wither
- University of Washington, Department of Bioengineering, Seattle, WA98195
| | - William L. White
- University of Washington, Department of Bioengineering, Seattle, WA98195
| | - Sriram Pendyala
- University of Washington, Department of Genome Sciences, Seattle, WA98195
| | - Paul J. Leanza
- University of Washington, Department of Bioengineering, Seattle, WA98195
| | - Douglas M. Fowler
- University of Washington, Department of Genome Sciences, Seattle, WA98195
| | - Hao Yuan Kueh
- University of Washington, Department of Bioengineering, Seattle, WA98195
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA98109
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18
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McDonald B, Chick BY, Hargreaves DC, Kaech SM. Early Chromatin Remodeling Events in Acutely Stimulated CD8 + T Cells. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2023; 96:467-473. [PMID: 38161581 PMCID: PMC10751865 DOI: 10.59249/axgu7370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
T cells undergo extensive chromatin remodeling over several days following stimulation through the T cell receptor. However, the kinetics and gene loci targeted by early remodeling events within the first 24 hours of T cell priming to orchestrate effector differentiation have not been well described. We identified that chromatin accessibility is rapidly and extensively remodeled within 1 hour of stimulation of naïve CD8+ T cells, leading to increased global chromatin accessibility at many effector T cell-associated genes that are enriched for AP-1, early growth response (EGR), and nuclear factor of activated T cells (NFAT) binding sites, but this short duration of stimulation is insufficient for commitment to clonal expansion in vivo. Sustained 24-hour stimulation led to further chromatin remodeling and was sufficient to enable clonal expansion. These data suggest that the duration of antigen receptor signaling is intimately coupled to chromatin remodeling and activation of genes involved in effector cell differentiation and highlight a potential mechanism that helps CD8+ T cells discriminate between foreign- and self-antigens.
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Affiliation(s)
- Bryan McDonald
- NOMIS Center for Immunobiology and Microbial
Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA, USA
- Biomedical Sciences Graduate Program, University of
California San Diego, La Jolla, CA, USA
| | - Brent Y. Chick
- Molecular and Cell Biology Laboratory, Salk Institute
for Biological Studies, La Jolla, CA, USA
- Biological Sciences Graduate Program, University of
California at San Diego, La Jolla, California, USA
| | - Diana C. Hargreaves
- Molecular and Cell Biology Laboratory, Salk Institute
for Biological Studies, La Jolla, CA, USA
| | - Susan M. Kaech
- NOMIS Center for Immunobiology and Microbial
Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA, USA
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19
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Sun Y, Florio TJ, Gupta S, Young MC, Marshall QF, Garfinkle SE, Papadaki GF, Truong HV, Mycek E, Li P, Farrel A, Church NL, Jabar S, Beasley MD, Kiefel BR, Yarmarkovich M, Mallik L, Maris JM, Sgourakis NG. Structural principles of peptide-centric chimeric antigen receptor recognition guide therapeutic expansion. Sci Immunol 2023; 8:eadj5792. [PMID: 38039376 PMCID: PMC10782944 DOI: 10.1126/sciimmunol.adj5792] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 11/08/2023] [Indexed: 12/03/2023]
Abstract
Peptide-centric chimeric antigen receptors (PC-CARs) recognize oncoprotein epitopes displayed by cell-surface human leukocyte antigens (HLAs) and offer a promising strategy for targeted cancer therapy. We have previously developed a PC-CAR targeting a neuroblastoma-associated PHOX2B peptide, leading to robust tumor cell lysis restricted by two common HLA allotypes. Here, we determine the 2.1-angstrom crystal structure of the PC-CAR-PHOX2B-HLA-A*24:02-β2m complex, which reveals the basis for antigen-specific recognition through interactions with CAR complementarity-determining regions (CDRs). This PC-CAR adopts a diagonal docking mode, where interactions with both conserved and polymorphic HLA framework residues permit recognition of multiple HLA allotypes from the A9 serological cross-reactive group, covering a combined global population frequency of up to 46.7%. Biochemical binding assays, molecular dynamics simulations, and structural and functional analyses demonstrate that high-affinity PC-CAR recognition of cross-reactive pHLAs necessitates the presentation of a specific peptide backbone, where subtle structural adaptations of the peptide are critical for high-affinity complex formation, and CAR T cell killing. Our results provide a molecular blueprint for engineering CARs with optimal recognition of tumor-associated antigens in the context of different HLAs, while minimizing cross-reactivity with self-epitopes.
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Affiliation(s)
- Yi Sun
- Center for Computational and Genomic Medicine and Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Tyler J. Florio
- Center for Computational and Genomic Medicine and Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Sagar Gupta
- Center for Computational and Genomic Medicine and Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Michael C. Young
- Center for Computational and Genomic Medicine and Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Quinlen F. Marshall
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Samuel E. Garfinkle
- Center for Computational and Genomic Medicine and Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Georgia F. Papadaki
- Center for Computational and Genomic Medicine and Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Hau V. Truong
- Center for Computational and Genomic Medicine and Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Emily Mycek
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Peiyao Li
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Alvin Farrel
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | | | | | | | | | - Mark Yarmarkovich
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Perlmutter Cancer Center, New York University Grossman School of Medicine, New York, NY, USA
| | - Leena Mallik
- Center for Computational and Genomic Medicine and Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - John M. Maris
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Nikolaos G. Sgourakis
- Center for Computational and Genomic Medicine and Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
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20
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Forsdyke DR. Aggregation-prone peptides from within a non-self-protein homoaggregate are preferred for MHC association: Historical overview. Scand J Immunol 2023; 98:e13306. [PMID: 38441340 DOI: 10.1111/sji.13306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 06/02/2023] [Accepted: 06/12/2023] [Indexed: 03/07/2024]
Abstract
New technologies assist re-evaluation of hypotheses on generation of immune cell repertoires and distinctions of self from non-self. Findings include positive correlations between peptide propensities to aggregate and their binding to major histocompatibility complex (MHC) proteins. This recalls the hypothesis that foreign proteins may homoaggregate in host cytosols prior to releasing their peptides (p) to form pMHC complexes. Clues to this included aggregation-related phenomena associated with infections (rouleaux formation, pyrexia, certain brain diseases). By virtue of 'promiscuous' gene expression by thymic presenting cells - perhaps adapted from earlier evolving gonadal mechanisms - developing T cells monitor surface pMHC clusterings. This evaluates intracellular concentrations of the corresponding proteins, and hence, following Burnet's two signal principle, degrees of self-reactivity. After positive selection in the thymic cortex for reactivity with 'near-self', high-level pMHC clustering suffices in the medulla for negatively selection. Following Burnet's principle, in the periphery low-level clustering suffices for T cell stimulation and high-level clustering again provokes negative selection (immunological tolerance). For evolving intracellular pathogens, fine-tuned polymorphisms of their host species have limited to 'near-self' some mimicking adaptations. It is proposed that while entire pathogen proteins may have evolved to minimize their aggregability, the greater aggregability of their peptides remains partially hidden within. Two-step proofreading mechanisms in prospective hosts select proteins containing aggregable peptide for the generation of pMHC clusters at the surface of presenting cells. Through mutations, some proteins of pathogens and cancer cells tend to converge towards the host 'near-self' that its T cells have auditioned to address.
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Affiliation(s)
- Donald R Forsdyke
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
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21
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Rajakaruna H, Desai M, Das J. PASCAR: a multiscale framework to explore the design space of constitutive and inducible CAR T cells. Life Sci Alliance 2023; 6:e202302171. [PMID: 37507138 PMCID: PMC10387492 DOI: 10.26508/lsa.202302171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/08/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
CAR T cells are engineered to bind and destroy tumor cells by targeting overexpressed surface antigens. However, healthy cells expressing lower abundances of these antigens can also be lysed by CAR T cells. Various CAR T cell designs increase tumor cell elimination, whereas reducing damage to healthy cells. However, these efforts are costly and labor-intensive, constraining systematic exploration of potential hypotheses. We develop a protein abundance structured population dynamic model for CAR T cells (PASCAR), a framework that combines multiscale population dynamic models and multi-objective optimization approaches with data from cytometry and cytotoxicity assays to systematically explore the design space of constitutive and tunable CAR T cells. PASCAR can quantitatively describe in vitro and in vivo results for constitutive and inducible CAR T cells and can successfully predict experiments outside the training data. Our exploration of the CAR design space reveals that optimal CAR affinities in the intermediate range of dissociation constants effectively reduce healthy cell lysis, whereas maintaining high tumor cell-killing rates. Furthermore, our modeling offers guidance for optimizing CAR expressions in synthetic notch CAR T cells. PASCAR can be extended to other CAR immune cells.
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Affiliation(s)
- Harshana Rajakaruna
- The Steve and Cindy Rasmussen Institute for Genomics, The Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, USA
| | - Milie Desai
- Department of Biology, Indian Institute of Science Education and Research, Pune, India
| | - Jayajit Das
- The Steve and Cindy Rasmussen Institute for Genomics, The Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics and Pelotonia Institute for Immuno-Oncology, College of Medicine, Columbus, OH, USA
- Biophysics Program, The Ohio State University, Columbus, OH, USA
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22
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Wu J, Stewart WCL, Jayaprakash C, Das J. BioNetGMMFit: estimating parameters of a BioNetGen model from time-stamped snapshots of single cells. NPJ Syst Biol Appl 2023; 9:46. [PMID: 37736766 PMCID: PMC10516955 DOI: 10.1038/s41540-023-00299-0] [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: 01/28/2023] [Accepted: 07/31/2023] [Indexed: 09/23/2023] Open
Abstract
Mechanistic models are commonly employed to describe signaling and gene regulatory kinetics in single cells and cell populations. Recent advances in single-cell technologies have produced multidimensional datasets where snapshots of copy numbers (or abundances) of a large number of proteins and mRNA are measured across time in single cells. The availability of such datasets presents an attractive scenario where mechanistic models are validated against experiments, and estimated model parameters enable quantitative predictions of signaling or gene regulatory kinetics. To empower the systems biology community to easily estimate parameters accurately from multidimensional single-cell data, we have merged a widely used rule-based modeling software package BioNetGen, which provides a user-friendly way to code for mechanistic models describing biochemical reactions, and the recently introduced CyGMM, that uses cell-to-cell differences to improve parameter estimation for such networks, into a single software package: BioNetGMMFit. BioNetGMMFit provides parameter estimates of the model, supplied by the user in the BioNetGen markup language (BNGL), which yield the best fit for the observed single-cell, time-stamped data of cellular components. Furthermore, for more precise estimates, our software generates confidence intervals around each model parameter. BioNetGMMFit is capable of fitting datasets of increasing cell population sizes for any mechanistic model specified in the BioNetGen markup language. By streamlining the process of developing mechanistic models for large single-cell datasets, BioNetGMMFit provides an easily-accessible modeling framework designed for scale and the broader biochemical signaling community.
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Affiliation(s)
- John Wu
- Department of Computer Science, The Ohio State University, 281 W Lane Ave, Columbus, OH, 43210, USA.
- Steve and Cindy Rasmussen Institute for Genomics, The Abigail Wexner Research Institute, Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH, 43205, USA.
| | | | - Ciriyam Jayaprakash
- Department of Physics, The Ohio State University, 191 W Woodruff Ave, Columbus, OH, 43210, USA
| | - Jayajit Das
- Steve and Cindy Rasmussen Institute for Genomics, The Abigail Wexner Research Institute, Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH, 43205, USA.
- Departments of Pediatrics, Biomedical Informatics, Pelotonia Institute of Immuno-Oncology, College of Medicine, and Biophysics Program, The Ohio State University, 370 W 9th Ave, Columbus, OH, 43210, USA.
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23
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Ghoreyshi ZS, George JT. Quantitative approaches for decoding the specificity of the human T cell repertoire. Front Immunol 2023; 14:1228873. [PMID: 37781387 PMCID: PMC10539903 DOI: 10.3389/fimmu.2023.1228873] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 08/17/2023] [Indexed: 10/03/2023] Open
Abstract
T cell receptor (TCR)-peptide-major histocompatibility complex (pMHC) interactions play a vital role in initiating immune responses against pathogens, and the specificity of TCRpMHC interactions is crucial for developing optimized therapeutic strategies. The advent of high-throughput immunological and structural evaluation of TCR and pMHC has provided an abundance of data for computational approaches that aim to predict favorable TCR-pMHC interactions. Current models are constructed using information on protein sequence, structures, or a combination of both, and utilize a variety of statistical learning-based approaches for identifying the rules governing specificity. This review examines the current theoretical, computational, and deep learning approaches for identifying TCR-pMHC recognition pairs, placing emphasis on each method's mathematical approach, predictive performance, and limitations.
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Affiliation(s)
- Zahra S. Ghoreyshi
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, United States
| | - Jason T. George
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, United States
- Engineering Medicine Program, Texas A&M University, Houston, TX, United States
- Center for Theoretical Biological Physics, Rice University, Houston, TX, United States
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24
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Fernández-Aguilar LM, Vico-Barranco I, Arbulo-Echevarria MM, Aguado E. A Story of Kinases and Adaptors: The Role of Lck, ZAP-70 and LAT in Switch Panel Governing T-Cell Development and Activation. BIOLOGY 2023; 12:1163. [PMID: 37759563 PMCID: PMC10525366 DOI: 10.3390/biology12091163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/18/2023] [Accepted: 08/20/2023] [Indexed: 09/29/2023]
Abstract
Specific antigen recognition is one of the immune system's features that allows it to mount intense yet controlled responses to an infinity of potential threats. T cells play a relevant role in the host defense and the clearance of pathogens by means of the specific recognition of peptide antigens presented by antigen-presenting cells (APCs), and, to do so, they are equipped with a clonally distributed antigen receptor called the T-cell receptor (TCR). Upon the specific engagement of the TCR, multiple intracellular signals are triggered, which lead to the activation, proliferation and differentiation of T lymphocytes into effector cells. In addition, this signaling cascade also operates during T-cell development, allowing for the generation of cells that can be helpful in the defense against threats, as well as preventing the generation of autoreactive cells. Early TCR signals include phosphorylation events in which the tyrosine kinases Lck and ZAP70 are involved. The sequential activation of these kinases leads to the phosphorylation of the transmembrane adaptor LAT, which constitutes a signaling hub for the generation of a signalosome, finally resulting in T-cell activation. These early signals play a relevant role in triggering the development, activation, proliferation and apoptosis of T cells, and the negative regulation of these signals is key to avoid aberrant processes that could generate inappropriate cellular responses and disease. In this review, we will examine and discuss the roles of the tyrosine kinases Lck and ZAP70 and the membrane adaptor LAT in these cellular processes.
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Grants
- PY20_01297 Consejería de Transformación Económica, Industria, Conocimiento y Universidades, Junta de Andalucía, Spain
- PID2020-113943RB-I00 Agencia Estatal de Investigación, Ministerio de Ciencia e Innovación, Spain
- PR2022-037 University of Cádiz
- PAIDI2020/DOC_01433 Consejería de Transformación Económica, Industria, Conocimiento y Universidades, Junta de Andalucía, Spain
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Affiliation(s)
- Luis M. Fernández-Aguilar
- Institute for Biomedical Research of Cadiz (INIBICA), 11009 Cadiz, Spain; (L.M.F.-A.); (I.V.-B.); (M.M.A.-E.)
- Department of Biomedicine, Biotechnology and Public Health (Immunology), University of Cadiz, 11002 Cadiz, Spain
| | - Inmaculada Vico-Barranco
- Institute for Biomedical Research of Cadiz (INIBICA), 11009 Cadiz, Spain; (L.M.F.-A.); (I.V.-B.); (M.M.A.-E.)
- Department of Biomedicine, Biotechnology and Public Health (Immunology), University of Cadiz, 11002 Cadiz, Spain
| | - Mikel M. Arbulo-Echevarria
- Institute for Biomedical Research of Cadiz (INIBICA), 11009 Cadiz, Spain; (L.M.F.-A.); (I.V.-B.); (M.M.A.-E.)
- Department of Biomedicine, Biotechnology and Public Health (Immunology), University of Cadiz, 11002 Cadiz, Spain
| | - Enrique Aguado
- Institute for Biomedical Research of Cadiz (INIBICA), 11009 Cadiz, Spain; (L.M.F.-A.); (I.V.-B.); (M.M.A.-E.)
- Department of Biomedicine, Biotechnology and Public Health (Immunology), University of Cadiz, 11002 Cadiz, Spain
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25
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Leblanc JA, Sugiyama MG, Antonescu CN, Brown AI. Quantitative modeling of EGF receptor ligand discrimination via internalization proofreading. Phys Biol 2023; 20:056008. [PMID: 37557183 DOI: 10.1088/1478-3975/aceecd] [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: 05/11/2023] [Accepted: 08/09/2023] [Indexed: 08/11/2023]
Abstract
The epidermal growth factor receptor (EGFR) is a central regulator of cell physiology that is stimulated by multiple distinct ligands. Although ligands bind to EGFR while the receptor is exposed on the plasma membrane, EGFR incorporation into endosomes following receptor internalization is an important aspect of EGFR signaling, with EGFR internalization behavior dependent upon the type of ligand bound. We develop quantitative modeling for EGFR recruitment to and internalization from clathrin domains, focusing on how internalization competes with ligand unbinding from EGFR. We develop two model versions: a kinetic model with EGFR behavior described as transitions between discrete states and a spatial model with EGFR diffusion to circular clathrin domains. We find that a combination of spatial and kinetic proofreading leads to enhanced EGFR internalization ratios in comparison to unbinding differences between ligand types. Various stages of the EGFR internalization process, including recruitment to and internalization from clathrin domains, modulate the internalization differences between receptors bound to different ligands. Our results indicate that following ligand binding, EGFR may encounter multiple clathrin domains before successful recruitment and internalization. The quantitative modeling we have developed describes competition between EGFR internalization and ligand unbinding and the resulting proofreading.
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Affiliation(s)
- Jaleesa A Leblanc
- Department of Physics, Toronto Metropolitan University, Toronto, Ontario, Canada
| | - Michael G Sugiyama
- Department of Chemistry and Biology, Toronto Metropolitan University, Toronto, Ontario, Canada
| | - Costin N Antonescu
- Department of Chemistry and Biology, Toronto Metropolitan University, Toronto, Ontario, Canada
| | - Aidan I Brown
- Department of Physics, Toronto Metropolitan University, Toronto, Ontario, Canada
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26
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Ayres CM, Corcelli SA, Baker BM. The Energetic Landscape of Catch Bonds in TCR Interfaces. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 211:325-332. [PMID: 37459192 PMCID: PMC10361606 DOI: 10.4049/jimmunol.2300121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 04/14/2023] [Indexed: 07/20/2023]
Abstract
Recognition of peptide/MHC complexes by αβ TCRs has traditionally been viewed through the lens of conventional receptor-ligand theory. Recent work, however, has shown that TCR recognition and T cell signaling can be profoundly influenced and tuned by mechanical forces. One outcome of applied force is the catch bond, where TCR dissociation rates decrease (half-lives increase) when limited force is applied. Although catch bond behavior is believed to be widespread in biology, its counterintuitive nature coupled with the difficulties of describing mechanisms at the structural level have resulted in considerable mystique. In this review, we demonstrate that viewing catch bonds through the lens of energy landscapes, barriers, and the ensuing reaction rates can help demystify catch bonding and provide a foundation on which atomic-level TCR catch bond mechanisms can be built.
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Affiliation(s)
- Cory M Ayres
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN
- The Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN
| | - Steve A Corcelli
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN
| | - Brian M Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN
- The Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN
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27
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Morgan J, Lindsay AE. Modulation of antigen discrimination by duration of immune contacts in a kinetic proofreading model of T cell activation with extreme statistics. PLoS Comput Biol 2023; 19:e1011216. [PMID: 37647345 PMCID: PMC10497171 DOI: 10.1371/journal.pcbi.1011216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 09/12/2023] [Accepted: 08/05/2023] [Indexed: 09/01/2023] Open
Abstract
T cells form transient cell-to-cell contacts with antigen presenting cells (APCs) to facilitate surface interrogation by membrane bound T cell receptors (TCRs). Upon recognition of molecular signatures (antigen) of pathogen, T cells may initiate an adaptive immune response. The duration of the T cell/APC contact is observed to vary widely, yet it is unclear what constructive role, if any, such variations might play in immune signaling. Modeling efforts describing antigen discrimination often focus on steady-state approximations and do not account for the transient nature of cellular contacts. Within the framework of a kinetic proofreading (KP) mechanism, we develop a stochastic First Receptor Activation Model (FRAM) describing the likelihood that a productive immune signal is produced before the expiry of the contact. Through the use of extreme statistics, we characterize the probability that the first TCR triggering is induced by a rare agonist antigen and not by that of an abundant self-antigen. We show that defining positive immune outcomes as resilience to extreme statistics and sensitivity to rare events mitigates classic tradeoffs associated with KP. By choosing a sufficient number of KP steps, our model is able to yield single agonist sensitivity whilst remaining non-reactive to large populations of self antigen, even when self and agonist antigen are similar in dissociation rate to the TCR but differ largely in expression. Additionally, our model achieves high levels of accuracy even when agonist positive APCs encounters are rare. Finally, we discuss potential biological costs associated with high classification accuracy, particularly in challenging T cell environments.
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Affiliation(s)
- Jonathan Morgan
- Department of Applied and Computational Mathematics and Statistics, University of Notre Dame, South Bend, Indiana, United States of America
- Biophysics Graduate Program, University of Notre Dame, South Bend, Indiana, United States of America
| | - Alan E. Lindsay
- Department of Applied and Computational Mathematics and Statistics, University of Notre Dame, South Bend, Indiana, United States of America
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28
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Hu Y, Duan Y, Salaita K. DNA Nanotechnology for Investigating Mechanical Signaling in the Immune System. Angew Chem Int Ed Engl 2023; 62:e202302967. [PMID: 37186502 DOI: 10.1002/anie.202302967] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Indexed: 05/17/2023]
Abstract
Immune recognition occurs at specialized cell-cell junctions when immune cells and target cells physically touch. In this junction, groups of receptor-ligand complexes assemble and experience molecular forces that are ultimately generated by the cellular cytoskeleton. These forces are in the range of piconewton (pN) but play crucial roles in immune cell activation and subsequent effector responses. In this minireview, we will review the development of DNA based molecular tension sensors and their applications in mapping and quantifying mechanical forces experienced by immunoreceptors including T-cell receptor (TCR), Lymphocyte function-associated antigen (LFA-1), and the B-cell receptor (BCR) among others. In addition, we will highlight the use of DNA as a mechanical gate to manipulate mechanotransduction and decipher how mechanical forces regulate antigen discrimination and receptor signaling.
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Affiliation(s)
- Yuesong Hu
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Yuxin Duan
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Khalid Salaita
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
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29
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Sun L, Shen F, Qu Y, Liu Z. Functional DNA as a Molecular Tool in Regulating Immunoreceptor-Ligand Interactions. JACS AU 2023; 3:1820-1834. [PMID: 37502159 PMCID: PMC10369416 DOI: 10.1021/jacsau.3c00291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 06/24/2023] [Accepted: 06/27/2023] [Indexed: 07/29/2023]
Abstract
During immune responses, activating ligands would trigger dynamic spatiotemporal organization of immunoreceptors at the cell interface, governing the fate and effector functions of immune cells. To understand the biophysical mechanisms of immunoreceptor signaling, diverse tools, including DNA technologies, have been developed to manipulate receptor-ligand interactions during the immune activation process. With great capability in the controllable assembly of biomolecules, functional DNA-based precise arrangement of immune molecules at cell interfaces has provided a powerful means in revealing the principles of immunoreceptor triggering, even at the single-molecule level. In addition, precisely regulating immunoreceptor-ligand interactions with functional DNA has been applied in immunotherapies of major diseases. This Perspective will focus on the recent advances in exploring immunoreceptor signaling with functional DNA as the molecular tool as well as the applications of functional DNA mediated regulation of immunoreceptor activation. We also outline the challenges and opportunities of applying functional DNA in immune modulation and immunotherapy.
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Affiliation(s)
- Lele Sun
- Institute
of Materiobiology, Department of Chemistry, College of Science, Shanghai University, Shanghai 200444, China
| | - Fengyun Shen
- School
of Chemistry and Chemical Engineering, Shanghai
Jiao Tong University, Shanghai 201240, China
| | - Yanfei Qu
- Institute
of Materiobiology, Department of Chemistry, College of Science, Shanghai University, Shanghai 200444, China
| | - Zhuang Liu
- Institute
of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Lab
Carbon Based Functional Materials and Devices, Soochow University, Suzhou, Jiangsu 215123, China
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30
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Du Y, Lyu Y, Lin J, Ma C, Zhang Q, Zhang Y, Qiu L, Tan W. Membrane-anchored DNA nanojunctions enable closer antigen-presenting cell-T-cell contact in elevated T-cell receptor triggering. NATURE NANOTECHNOLOGY 2023; 18:818-827. [PMID: 36894782 DOI: 10.1038/s41565-023-01333-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
How the engagement of a T-cell receptor to antigenic peptide-loaded major histocompatibility complex on antigen-presenting cells (APCs) initiates intracellular signalling cascades in T cells is not well understood. In particular, the dimension of the cellular contact zone is regarded as a determinant, but its influence remains controversial. This is due to the need for appropriate strategies for manipulating intermembrane spacing between the APC-T-cell interfaces without involving protein modification. Here we describe a membrane-anchored DNA nanojunction with distinct sizes to extend, maintain and shorten the APC-T-cell interface down to 10 nm. Our results suggest that the axial distance of the contact zone is critical in T-cell activation, presumably by modulating protein reorganization and mechanical force. Notably, we observe the promotion of T-cell signalling by shortening the intermembrane distance.
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Affiliation(s)
- Yulin Du
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, China
| | - Yifan Lyu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, China
| | - Jie Lin
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, China
| | - Chunran Ma
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, China
| | - Qiang Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, China
| | - Yutong Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, China
| | - Liping Qiu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, China.
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, China.
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, China.
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, China.
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, China.
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31
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Wither MJ, White WL, Pendyala S, Leanza PJ, Fowler D, Kueh HY. Antigen perception in T cells by long-term Erk and NFAT signaling dynamics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.01.543260. [PMID: 37333368 PMCID: PMC10274683 DOI: 10.1101/2023.06.01.543260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Immune system threat detection hinges on T cells' ability to perceive varying peptide major-histocompatibility complex (pMHC) antigens. As the Erk and NFAT pathways link T cell receptor engagement to gene regulation, their signaling dynamics may convey information about pMHC inputs. To test this idea, we developed a dual reporter mouse strain and a quantitative imaging assay that, together, enable simultaneous monitoring of Erk and NFAT dynamics in live T cells over day-long timescales as they respond to varying pMHC inputs. Both pathways initially activate uniformly across various pMHC inputs, but diverge only over longer (9+ hrs) timescales, enabling independent encoding of pMHC affinity and dose. These late signaling dynamics are decoded via multiple temporal and combinatorial mechanisms to generate pMHC-specific transcriptional responses. Our findings underscore the importance of long timescale signaling dynamics in antigen perception, and establish a framework for understanding T cell responses under diverse contexts. SIGNIFICANCE STATEMENT To counter diverse pathogens, T cells mount distinct responses to varying peptide-major histocompatibility complex ligands (pMHCs). They perceive the affinity of pMHCs for the T cell receptor (TCR), which reflects its foreignness, as well as pMHC abundance. By tracking signaling responses in single living cells to different pMHCs, we find that T cells can independently perceive pMHC affinity vs dose, and encode this information through the dynamics of Erk and NFAT signaling pathways downstream of the TCR. These dynamics are jointly decoded by gene regulatory mechanisms to produce pMHC-specific activation responses. Our work reveals how T cells can elicit tailored functional responses to diverse threats and how dysregulation of these responses may lead to immune pathologies.
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32
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Zeng Q, Li R, Wang J. Improvement of Error Correction in Nonequilibrium Information Dynamics. ENTROPY (BASEL, SWITZERLAND) 2023; 25:881. [PMID: 37372225 DOI: 10.3390/e25060881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 05/22/2023] [Accepted: 05/22/2023] [Indexed: 06/29/2023]
Abstract
Errors are inevitable in information processing and transfer. While error correction is widely studied in engineering, the underlying physics is not fully understood. Due to the complexity and energy exchange involved, information transmission should be considered as a nonequilibrium process. In this study, we investigate the effects of nonequilibrium dynamics on error correction using a memoryless channel model. Our findings suggest that error correction improves as nonequilibrium increases, and the thermodynamic cost can be utilized to improve the correction quality. Our results inspire new approaches to error correction that incorporate nonequilibrium dynamics and thermodynamics, and highlight the importance of the nonequilibrium effects in error correction design, particularly in biological systems.
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Affiliation(s)
- Qian Zeng
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Changchun 130022, China
| | - Ran Li
- Center for Theoretical Interdisciplinary Sciences, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325001, China
| | - Jin Wang
- Department of Chemistry and Physics, State University of New York, Stony Brook, NY 11794, USA
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33
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Sun Y, Florio TJ, Gupta S, Young MC, Marshall QF, Garfinkle SE, Papadaki GF, Truong HV, Mycek E, Li P, Farrel A, Church NL, Jabar S, Beasley MD, Kiefel BR, Yarmarkovich M, Mallik L, Maris JM, Sgourakis NG. Structural principles of peptide-centric Chimeric Antigen Receptor recognition guide therapeutic expansion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.24.542108. [PMID: 37292750 PMCID: PMC10245919 DOI: 10.1101/2023.05.24.542108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Peptide-Centric Chimeric Antigen Receptors (PC-CARs), which recognize oncoprotein epitopes displayed by human leukocyte antigens (HLAs) on the cell surface, offer a promising strategy for targeted cancer therapy 1 . We have previously developed a PC-CAR targeting a neuroblastoma- associated PHOX2B peptide, leading to robust tumor cell lysis restricted by two common HLA allotypes 2 . Here, we determine the 2.1 Å structure of the PC-CAR:PHOX2B/HLA-A*24:02/β2m complex, which reveals the basis for antigen-specific recognition through interactions with CAR complementarity-determining regions (CDRs). The PC-CAR adopts a diagonal docking mode, where interactions with both conserved and polymorphic HLA framework residues permit recognition of multiple HLA allotypes from the A9 serological cross-reactivity group, covering a combined American population frequency of up to 25.2%. Comprehensive characterization using biochemical binding assays, molecular dynamics simulations, and structural and functional analyses demonstrate that high-affinity PC-CAR recognition of cross-reactive pHLAs necessitates the presentation of a specific peptide backbone, where subtle structural adaptations of the peptide are critical for high-affinity complex formation and CAR-T cell killing. Our results provide a molecular blueprint for engineering CARs with optimal recognition of tumor-associated antigens in the context of different HLAs, while minimizing cross-reactivity with self-epitopes.
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34
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Kirby D, Zilman A. Proofreading does not result in more reliable ligand discrimination in receptor signaling due to its inherent stochasticity. Proc Natl Acad Sci U S A 2023; 120:e2212795120. [PMID: 37192165 PMCID: PMC10214210 DOI: 10.1073/pnas.2212795120] [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: 07/25/2022] [Accepted: 04/05/2023] [Indexed: 05/18/2023] Open
Abstract
Kinetic proofreading (KPR) has been used as a paradigmatic explanation for the high specificity of ligand discrimination by cellular receptors. KPR enhances the difference in the mean receptor occupancy between different ligands compared to a nonproofread receptor, thus potentially enabling better discrimination. On the other hand, proofreading also attenuates the signal and introduces additional stochastic receptor transitions relative to a nonproofreading receptor. This increases the relative magnitude of noise in the downstream signal, which can interfere with reliable ligand discrimination. To understand the effect of noise on ligand discrimination beyond the comparison of the mean signals, we formulate the task of ligand discrimination as a problem of statistical estimation of the receptor affinity of ligands based on the molecular signaling output. Our analysis reveals that proofreading typically worsens ligand resolution compared to a nonproofread receptor. Furthermore, the resolution decreases further with more proofreading steps under most commonly biologically considered conditions. This contrasts with the usual notion that KPR universally improves ligand discrimination with additional proofreading steps. Our results are consistent across a variety of different proofreading schemes and metrics of performance, suggesting that they are inherent to the KPR mechanism itself rather than any particular model of molecular noise. Based on our results, we suggest alternative roles for KPR schemes such as multiplexing and combinatorial encoding in multi-ligand/multi-output pathways.
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Affiliation(s)
- Duncan Kirby
- Department of Physics, University of Toronto, 60 St George St, Toronto, ONM5S 1A7, Canada
| | - Anton Zilman
- Department of Physics, University of Toronto, 60 St George St, Toronto, ONM5S 1A7, Canada
- Institute for Biomedical Engineering, University of Toronto, 164 college St, Toronto, ONM5S 1A7, Canada
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35
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Choi HK, Cong P, Ge C, Natarajan A, Liu B, Zhang Y, Li K, Rushdi MN, Chen W, Lou J, Krogsgaard M, Zhu C. Catch bond models may explain how force amplifies TCR signaling and antigen discrimination. Nat Commun 2023; 14:2616. [PMID: 37147290 PMCID: PMC10163261 DOI: 10.1038/s41467-023-38267-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 04/24/2023] [Indexed: 05/07/2023] Open
Abstract
The TCR integrates forces in its triggering process upon interaction with pMHC. Force elicits TCR catch-slip bonds with strong pMHCs but slip-only bonds with weak pMHCs. We develop two models and apply them to analyze 55 datasets, demonstrating the models' ability to quantitatively integrate and classify a broad range of bond behaviors and biological activities. Comparing to a generic two-state model, our models can distinguish class I from class II MHCs and correlate their structural parameters with the TCR/pMHC's potency to trigger T cell activation. The models are tested by mutagenesis using an MHC and a TCR mutated to alter conformation changes. The extensive comparisons between theory and experiment provide model validation and testable hypothesis regarding specific conformational changes that control bond profiles, thereby suggesting structural mechanisms for the inner workings of the TCR mechanosensing machinery and plausible explanations of why and how force may amplify TCR signaling and antigen discrimination.
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Affiliation(s)
- Hyun-Kyu Choi
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, USA
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Peiwen Cong
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, USA
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Chenghao Ge
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, USA
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- Amgen Inc., One Amgen Center Dr., Thousand Oaks, CA, 91320, USA
| | - Aswin Natarajan
- Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Baoyu Liu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, USA
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA
| | - Yong Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Kaitao Li
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, USA
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Muaz Nik Rushdi
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, USA
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
- Medtronic CO., Minneapolis, MN, 55432, USA
| | - Wei Chen
- Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Jizhong Lou
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Michelle Krogsgaard
- Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, New York, NY, 10016, USA
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Cheng Zhu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, USA.
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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36
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McFarlane A, Pohler E, Moraga I. Molecular and cellular factors determining the functional pleiotropy of cytokines. FEBS J 2023; 290:2525-2552. [PMID: 35246947 PMCID: PMC10952290 DOI: 10.1111/febs.16420] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/26/2022] [Accepted: 03/03/2022] [Indexed: 11/30/2022]
Abstract
Cytokines are soluble factors vital for mammalian physiology. Cytokines elicit highly pleiotropic activities, characterized by their ability to induce a wide spectrum of functional responses in a diverse range of cell subsets, which makes their study very challenging. Cytokines activate signalling via receptor dimerization/oligomerization, triggering activation of the JAK (Janus kinase)/STAT (signal transducer and activator of transcription) signalling pathway. Given the strong crosstalk and shared usage of key components of cytokine signalling pathways, a long-standing question in the field pertains to how functional diversity is achieved by cytokines. Here, we discuss how biophysical - for example, ligand-receptor binding affinity and topology - and cellular - for example, receptor, JAK and STAT protein levels, endosomal compartment - parameters contribute to the modulation and diversification of cytokine responses. We review how these parameters ultimately converge into a common mechanism to fine-tune cytokine signalling that involves the control of the number of Tyr residues phosphorylated in the receptor intracellular domain upon cytokine stimulation. This results in different kinetics of STAT activation, and induction of specific gene expression programs, ensuring the generation of functional diversity by cytokines using a limited set of signalling intermediaries. We describe how these first principles of cytokine signalling have been exploited using protein engineering to design cytokine variants with more specific and less toxic responses for immunotherapy.
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Affiliation(s)
- Alison McFarlane
- Division of Cell Signalling and ImmunologySchool of Life SciencesUniversity of DundeeUK
| | - Elizabeth Pohler
- Division of Cell Signalling and ImmunologySchool of Life SciencesUniversity of DundeeUK
| | - Ignacio Moraga
- Division of Cell Signalling and ImmunologySchool of Life SciencesUniversity of DundeeUK
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Mahdavi S, Salmon GL, Daghlian P, Garcia HG, Phillips R. Flexibility and sensitivity in gene regulation out of equilibrium. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.11.536490. [PMID: 37090612 PMCID: PMC10120662 DOI: 10.1101/2023.04.11.536490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Cells adapt to environments and tune gene expression by controlling the concentrations of proteins and their kinetics in regulatory networks. In both eukaryotes and prokaryotes, experiments and theory increasingly attest that these networks can and do consume bio-chemical energy. How does this dissipation enable cellular behaviors unobtainable in equilibrium? This open question demands quantitative models that transcend thermodynamic equilibrium. Here we study the control of a simple, ubiquitous gene regulatory motif to explore the consequences of departing equilibrium in kinetic cycles. Employing graph theory, we find that dissipation unlocks nonmonotonicity and enhanced sensitivity of gene expression with respect to a transcription factor's concentration. These features allow a single transcription factor to act as both a repressor and activator at different levels or achieve outputs with multiple concentration regions of locally-enhanced sensitivity. We systematically dissect how energetically-driving individual transitions within regulatory networks, or pairs of transitions, generates more adjustable and sensitive phenotypic responses. Our findings quantify necessary conditions and detectable consequences of energy expenditure. These richer mathematical behaviors-feasibly accessed using biological energy budgets and rates-may empower cells to accomplish sophisticated regulation with simpler architectures than those required at equilibrium. Significance Statement Growing theoretical and experimental evidence demonstrates that cells can (and do) spend biochemical energy while regulating their genes. Here we explore the impact of departing from equilibrium in simple regulatory cycles, and learn that beyond increasing sensitivity, dissipation can unlock more flexible input-output behaviors that are otherwise forbidden without spending energy. These more complex behaviors could enable cells to perform more sophisticated functions using simpler systems than those needed at equilibrium.
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Huppa JB, Schütz GJ. T-cell antigen recognition: catch-as-catch-can or catch-22? EMBO J 2023; 42:e113507. [PMID: 36808636 PMCID: PMC10068317 DOI: 10.15252/embj.2023113507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 02/08/2023] [Indexed: 02/22/2023] Open
Abstract
T-cell antigen recognition is invariably affected by tensile forces as they are exerted on T-cell antigen receptors (TCRs) transiently binding antigenic peptide/MHC complexes. In this issue of The EMBO Journal, Pettmann and colleagues promote the concept that forces reduce the lifetime of more stable stimulatory TCR-pMHC interactions to a larger extent than that of less stable non-stimulatory TCR-pMHC interactions. The authors argue that forces impede rather than boost T-cell antigen discrimination, which is promoted by force-shielding within the immunological synapse through cell adhesion via CD2/CD58 and LFA-1/ICAM-1.
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Affiliation(s)
- Johannes B Huppa
- Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology, ImmunologyMedical University of ViennaViennaAustria
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39
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Lo WL, Kuhlmann M, Rizzuto G, Ekiz HA, Kolawole EM, Revelo MP, Andargachew R, Li Z, Tsai YL, Marson A, Evavold BD, Zehn D, Weiss A. A single-amino acid substitution in the adaptor LAT accelerates TCR proofreading kinetics and alters T-cell selection, maintenance and function. Nat Immunol 2023; 24:676-689. [PMID: 36914891 PMCID: PMC10063449 DOI: 10.1038/s41590-023-01444-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 01/25/2023] [Indexed: 03/14/2023]
Abstract
Mature T cells must discriminate between brief interactions with self-peptides and prolonged binding to agonists. The kinetic proofreading model posits that certain T-cell antigen receptor signaling nodes serve as molecular timers to facilitate such discrimination. However, the physiological significance of this regulatory mechanism and the pathological consequences of disrupting it are unknown. Here we report that accelerating the normally slow phosphorylation of the linker for activation of T cells (LAT) residue Y136 by introducing an adjacent Gly135Asp alteration (LATG135D) disrupts ligand discrimination in vivo. The enhanced self-reactivity of LATG135D T cells triggers excessive thymic negative selection and promotes T-cell anergy. During Listeria infection, LATG135D T cells expand more than wild-type counterparts in response to very weak stimuli but display an imbalance between effector and memory responses. Moreover, despite their enhanced engagement of central and peripheral tolerance mechanisms, mice bearing LATG135D show features associated with autoimmunity and immunopathology. Our data reveal the importance of kinetic proofreading in balancing tolerance and immunity.
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Affiliation(s)
- Wan-Lin Lo
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA.
| | - Miriam Kuhlmann
- Division of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Gabrielle Rizzuto
- Human Oncology and Pathogenesis Program, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - H Atakan Ekiz
- Department of Molecular Biology and Genetics, Izmir Institute of Technology, Gulbahce, Turkey
| | - Elizabeth M Kolawole
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Monica P Revelo
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Rakieb Andargachew
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Zhongmei Li
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Yuan-Li Tsai
- Division of Rheumatology, Rosalind Russell and Ephraim P. Engleman Arthritis Research Center, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Alexander Marson
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Brian D Evavold
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Dietmar Zehn
- Division of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Freising, Germany.
| | - Arthur Weiss
- Division of Rheumatology, Rosalind Russell and Ephraim P. Engleman Arthritis Research Center, Department of Medicine, University of California San Francisco, San Francisco, CA, USA.
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40
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Pineros-Rodriguez M, Richez L, Khadra A. Theoretical quantification of the polyvalent binding of nanoparticles coated with peptide-major histocompatibility complex to T cell receptor-nanoclusters. Math Biosci 2023; 358:108995. [PMID: 36924879 DOI: 10.1016/j.mbs.2023.108995] [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: 09/30/2022] [Revised: 03/06/2023] [Accepted: 03/08/2023] [Indexed: 03/17/2023]
Abstract
Nanoparticles (NPs) coated with peptide-major histocompatibility complexes (pMHCs) can be used as a therapy to treat autoimmune diseases. They do so by inducing the differentiation and expansion of disease-suppressing T regulatory type 1 (Tr1) cells by binding to their T cell receptors (TCRs) expressed as TCR-nanoclusters (TCRnc). Their efficacy can be controlled by adjusting NP size and number of pMHCs coated on them (referred to as valence). The binding of these NPs to TCRnc on T cells is thus polyvalent and occurs at three levels: the TCR-pMHC, NP-TCRnc and T cell levels. In this study, we explore how this polyvalent interaction is manifested and examine if it can facilitate T cell activation downstream. This is done by developing a multiscale biophysical model that takes into account the three levels of interactions and the geometrical complexity of the binding. Using the model, we quantify several key parameters associated with this interaction analytically and numerically, including the insertion probability that specifies the number of remaining pMHC binding sites in the contact area between T cells and NPs, the dwell time of interaction between NPs and TCRnc, carrying capacity of TCRnc, the distribution of covered and bound TCRs, and cooperativity in the binding of pMHCs within the contact area. The model was fit to previously published dose-response curves of interferon-γ obtained experimentally by stimulating a population of T cells with increasing concentrations of NPs at various valences and NP sizes. Exploring the parameter space of the model revealed that for an appropriate choice of the contact area angle, the model can produce moderate jumps between dose-response curves at low valences. This suggests that the geometry and kinetics of NP binding to TCRnc can act in synergy to facilitate T cell activation.
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Affiliation(s)
| | - Louis Richez
- Quantitative Life Sciences Program, McGill University, Montreal, Canada
| | - Anmar Khadra
- Department of Physiology, McGill University, Montreal, Canada.
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41
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Watanabe M, Motooka D, Yamasaki S. The kinetics of signaling through the common FcRγ chain determine cytokine profiles in dendritic cells. Sci Signal 2023; 16:eabn9909. [PMID: 36881655 DOI: 10.1126/scisignal.abn9909] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
The common Fc receptor γ (FcRγ) chain is a signaling subunit common to several immune receptors, but cellular responses induced by FcRγ-coupled receptors are diverse. We investigated the mechanisms by which FcRγ generates divergent signals when coupled to Dectin-2 and Mincle, structurally similar C-type lectin receptors that induce the release of different cytokines from dendritic cells. Chronological tracing of transcriptomic and epigenetic changes upon stimulation revealed that Dectin-2 induced early and strong signaling, whereas Mincle-mediated signaling was delayed, which reflects their expression patterns. Generation of early and strong FcRγ-Syk signaling by engineered chimeric receptors was sufficient to recapitulate a Dectin-2-like gene expression profile. Early Syk signaling selectively stimulated the activity of the calcium ion-activated transcription factor NFAT, which rapidly altered the chromatin status and transcription of the Il2 gene. In contrast, proinflammatory cytokines, such as TNF, were induced regardless of FcRγ signaling kinetics. These results suggest that the strength and timing of FcRγ-Syk signaling can alter the quality of cellular responses through kinetics-sensing signaling machineries.
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Affiliation(s)
- Miyuki Watanabe
- Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan.,Laboratory of Molecular Immunology, Immunology Frontier Research Center (IFReC), Osaka University, Osaka 565-0871, Japan
| | - Daisuke Motooka
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan.,Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Osaka 565-0871, Japan
| | - Sho Yamasaki
- Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan.,Laboratory of Molecular Immunology, Immunology Frontier Research Center (IFReC), Osaka University, Osaka 565-0871, Japan.,Center for Infectious Disease Education and Research (CiDER), Osaka University, Osaka 565-0871, Japan.,Division of Molecular Design, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan.,Division of Molecular Immunology, Medical Mycology Research Center, Chiba University, Chiba 260-8673, Japan
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42
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Understanding How Cells Probe the World: A Preliminary Step towards Modeling Cell Behavior? Int J Mol Sci 2023; 24:ijms24032266. [PMID: 36768586 PMCID: PMC9916635 DOI: 10.3390/ijms24032266] [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: 12/19/2022] [Revised: 01/16/2023] [Accepted: 01/20/2023] [Indexed: 01/26/2023] Open
Abstract
Cell biologists have long aimed at quantitatively modeling cell function. Recently, the outstanding progress of high-throughput measurement methods and data processing tools has made this a realistic goal. The aim of this paper is twofold: First, to suggest that, while much progress has been done in modeling cell states and transitions, current accounts of environmental cues driving these transitions remain insufficient. There is a need to provide an integrated view of the biochemical, topographical and mechanical information processed by cells to take decisions. It might be rewarding in the near future to try to connect cell environmental cues to physiologically relevant outcomes rather than modeling relationships between these cues and internal signaling networks. The second aim of this paper is to review exogenous signals that are sensed by living cells and significantly influence fate decisions. Indeed, in addition to the composition of the surrounding medium, cells are highly sensitive to the properties of neighboring surfaces, including the spatial organization of anchored molecules and substrate mechanical and topographical properties. These properties should thus be included in models of cell behavior. It is also suggested that attempts at cell modeling could strongly benefit from two research lines: (i) trying to decipher the way cells encode the information they retrieve from environment analysis, and (ii) developing more standardized means of assessing the quality of proposed models, as was done in other research domains such as protein structure prediction.
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43
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Qin R, An C, Chen W. Physical-Chemical Regulation of Membrane Receptors Dynamics in Viral Invasion and Immune Defense. J Mol Biol 2023; 435:167800. [PMID: 36007627 PMCID: PMC9394170 DOI: 10.1016/j.jmb.2022.167800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/13/2022] [Accepted: 08/18/2022] [Indexed: 02/04/2023]
Abstract
Mechanical cues dynamically regulate membrane receptors functions to trigger various physiological and pathological processes from viral invasion to immune defense. These cues mainly include various types of dynamic mechanical forces and the spatial confinement of plasma membrane. However, the molecular mechanisms of how they couple with biochemical cues in regulating membrane receptors functions still remain mysterious. Here, we review recent advances in methodologies of single-molecule biomechanical techniques and in novel biomechanical regulatory mechanisms of critical ligand recognition of viral and immune receptors including SARS-CoV-2 spike protein, T cell receptor (TCR) and other co-stimulatory immune receptors. Furthermore, we provide our perspectives of the general principle of how force-dependent kinetics determine the dynamic functions of membrane receptors and of biomechanical-mechanism-driven SARS-CoV-2 neutralizing antibody design and TCR engineering for T-cell-based therapies.
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Affiliation(s)
- Rui Qin
- Department of Cell Biology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Chenyi An
- Department of Cell Biology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China; School of Biology and Engineering, Guizhou Medical University, Guiyang, China
| | - Wei Chen
- Department of Cell Biology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China; Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the MOE Frontier Science Center for Brain Science & Brain-Machine Integration, State Key Laboratory for Modern Optical Instrumentation Key Laboratory for Biomedical Engineering of the Ministry of Education, College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou 310058, Zhejiang, China.
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44
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McAffee DB, O'Dair MK, Lin JJ, Low-Nam ST, Wilhelm KB, Kim S, Morita S, Groves JT. Discrete LAT condensates encode antigen information from single pMHC:TCR binding events. Nat Commun 2022; 13:7446. [PMID: 36460640 PMCID: PMC9718779 DOI: 10.1038/s41467-022-35093-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 11/17/2022] [Indexed: 12/05/2022] Open
Abstract
LAT assembly into a two-dimensional protein condensate is a prominent feature of antigen discrimination by T cells. Here, we use single-molecule imaging techniques to resolve the spatial position and temporal duration of each pMHC:TCR molecular binding event while simultaneously monitoring LAT condensation at the membrane. An individual binding event is sufficient to trigger a LAT condensate, which is self-limiting, and neither its size nor lifetime is correlated with the duration of the originating pMHC:TCR binding event. Only the probability of the LAT condensate forming is related to the pMHC:TCR binding dwell time. LAT condenses abruptly, but after an extended delay from the originating binding event. A LAT mutation that facilitates phosphorylation at the PLC-γ1 recruitment site shortens the delay time to LAT condensation and alters T cell antigen specificity. These results identify a function for the LAT protein condensation phase transition in setting antigen discrimination thresholds in T cells.
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Affiliation(s)
- Darren B McAffee
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Mark K O'Dair
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Jenny J Lin
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Shalini T Low-Nam
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Kiera B Wilhelm
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Sungi Kim
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Shumpei Morita
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Jay T Groves
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720, USA.
- Institute for Digital Molecular Analytics and Science, Nanyang Technological University, 59 Nanyang Drive, Singapore, 636921, Singapore.
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45
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Shevyrev DV, Tereshchenko VP, Sennikov SV. The Enigmatic Nature of the TCR-pMHC Interaction: Implications for CAR-T and TCR-T Engineering. Int J Mol Sci 2022; 23:ijms232314728. [PMID: 36499057 PMCID: PMC9740949 DOI: 10.3390/ijms232314728] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/11/2022] [Accepted: 11/21/2022] [Indexed: 11/29/2022] Open
Abstract
The interaction of the T-cell receptor (TCR) with a peptide in the major histocompatibility complex (pMHC) plays a central role in the adaptive immunity of higher chordates. Due to the high specificity and sensitivity of this process, the immune system quickly recognizes and efficiently responds to the appearance of foreign and altered self-antigens. This is important for ensuring anti-infectious and antitumor immunity, in addition to maintaining self-tolerance. The most common parameter used for assessing the specificity of TCR-pMHC interaction is affinity. This thermodynamic characteristic is widely used not only in various theoretical aspects, but also in practice, for example, in the engineering of various T-cell products with a chimeric (CAR-T) or artificial (TCR-engineered T-cell) antigen receptor. However, increasing data reveal the fact that, in addition to the thermodynamic component, the specificity of antigen recognition is based on the kinetics and mechanics of the process, having even greater influence on the selectivity of the process and T lymphocyte activation than affinity. Therefore, the kinetic and mechanical aspects of antigen recognition should be taken into account when designing artificial antigen receptors, especially those that recognize antigens in the MHC complex. This review describes the current understanding of the nature of the TCR-pMHC interaction, in addition to the thermodynamic, kinetic, and mechanical principles underlying the specificity and high sensitivity of this interaction.
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Affiliation(s)
- D. V. Shevyrev
- Laboratory of molecular Immunology, Research Institute for Fundamental and Clinical Immunology, 630099 Novosibirsk, Russia
- Center for Cell Technology and Immunology, Sirius University of Science and Technology, 354340 Sochi, Russia
- Correspondence: ; Tel.: +7-9231345505
| | - V. P. Tereshchenko
- Laboratory of molecular Immunology, Research Institute for Fundamental and Clinical Immunology, 630099 Novosibirsk, Russia
- Center for Cell Technology and Immunology, Sirius University of Science and Technology, 354340 Sochi, Russia
| | - S. V. Sennikov
- Laboratory of molecular Immunology, Research Institute for Fundamental and Clinical Immunology, 630099 Novosibirsk, Russia
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46
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Morgan J, Pettmann J, Dushek O, Lindsay AE. T cell microvilli simulations show operation near packing limit and impact on antigen recognition. Biophys J 2022; 121:4128-4136. [PMID: 36181267 PMCID: PMC9675027 DOI: 10.1016/j.bpj.2022.09.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 07/11/2022] [Accepted: 09/26/2022] [Indexed: 11/02/2022] Open
Abstract
T cells are immune cells that continuously scan for foreign-derived antigens on the surfaces of nearly all cells, termed antigen-presenting cells (APCs). They do this by dynamically extending numerous protrusions called microvilli (MVs) that contain T cell receptors toward the APC surface in order to scan for antigens. The number, size, and dynamics of these MVs, and the complex multiscale topography that results, play a yet unknown role in antigen recognition. We develop an anatomically informed model that confines antigen recognition to small areas representing MVs that can dynamically form and dissolve and use the model to study how MV dynamics impact antigen sensitivity and discrimination. We find that MV surveillance reduces antigen sensitivity compared with a completely flat interface, unless MV are stabilized in an antigen-dependent manner, and observe that MVs have only a modest impact on antigen discrimination. The model highlights that MV contacts optimize the competing demands of fast scanning speeds of the APC surface with antigen sensitivity. Our model predicts an interface packing fraction that corresponds closely to those observed experimentally, indicating that T cells operate their MVs near the limits imposed by anatomical and geometric constraints. Finally, we find that observed MV contact lifetimes can be largely influenced by conditions in the T cell/APC interface, with these lifetimes often being longer than the simulation or experimental observation period. This work highlights the role of MVs in antigen recognition.
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Affiliation(s)
- Jonathan Morgan
- Department of Applied and Computational Mathematics and Statistics, University of Notre Dame, Notre Dame, Indiana; Biophysics Graduate Program, University of Notre Dame, Notre Dame, Indiana
| | - Johannes Pettmann
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Omer Dushek
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Alan E Lindsay
- Department of Applied and Computational Mathematics and Statistics, University of Notre Dame, Notre Dame, Indiana.
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47
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Britain DM, Town JP, Weiner OD. Progressive enhancement of kinetic proofreading in T cell antigen discrimination from receptor activation to DAG generation. eLife 2022; 11:e75263. [PMID: 36125261 PMCID: PMC9536835 DOI: 10.7554/elife.75263] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 09/18/2022] [Indexed: 11/16/2022] Open
Abstract
T cells use kinetic proofreading to discriminate antigens by converting small changes in antigen-binding lifetime into large differences in cell activation, but where in the signaling cascade this computation is performed is unknown. Previously, we developed a light-gated immune receptor to probe the role of ligand kinetics in T cell antigen signaling. We found significant kinetic proofreading at the level of the signaling lipid diacylglycerol (DAG) but lacked the ability to determine where the multiple signaling steps required for kinetic discrimination originate in the upstream signaling cascade (Tiseher and Weiner, 2019). Here, we uncover where kinetic proofreading is executed by adapting our optogenetic system for robust activation of early signaling events. We find the strength of kinetic proofreading progressively increases from Zap70 recruitment to LAT clustering to downstream DAG generation. Leveraging the ability of our system to rapidly disengage ligand binding, we also measure slower reset rates for downstream signaling events. These data suggest a distributed kinetic proofreading mechanism, with proofreading steps both at the receptor and at slower resetting downstream signaling complexes that could help balance antigen sensitivity and discrimination.
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Affiliation(s)
- Derek M Britain
- Cardiovascular Research Institute and Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Jason P Town
- Cardiovascular Research Institute and Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Orion David Weiner
- Cardiovascular Research Institute and Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
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48
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Wu Y, Biswas D, Swanton C. Impact of cancer evolution on immune surveillance and checkpoint inhibitor response. Semin Cancer Biol 2022; 84:89-102. [PMID: 33631295 PMCID: PMC9253787 DOI: 10.1016/j.semcancer.2021.02.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 02/18/2021] [Accepted: 02/19/2021] [Indexed: 12/21/2022]
Abstract
Intratumour heterogeneity (ITH) is pervasive across all cancers studied and may provide the evolving tumour multiple routes to escape immune surveillance. Immune checkpoint inhibitors (CPIs) are rapidly becoming standard of care for many cancers. Here, we discuss recent work investigating the influence of ITH on patient response to immune checkpoint inhibitor (CPI) therapy. At its simplest, ITH may confound the diagnostic accuracy of predictive biomarkers used to stratify patients for CPI therapy. Furthermore, ITH is fuelled by mechanisms of genetic instability that can both engage immune surveillance and drive immune evasion. A greater appreciation of the interplay between ITH and the immune system may hold the key to increasing the proportion of patients experiencing durable responses from CPI therapy.
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Affiliation(s)
- Yin Wu
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, NW1 1AT, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, Paul O'Gorman Building, London, WC1E 6DD, UK; Peter Gorer Department of Immunobiology, School of Immunology & Microbial Sciences, King's College London, London, SE1 9RT, UK
| | - Dhruva Biswas
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, NW1 1AT, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, Paul O'Gorman Building, London, WC1E 6DD, UK; Bill Lyons Informatics Centre, University College London Cancer Institute, Paul O'Gorman Building, London, WC1E 6DD, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, NW1 1AT, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, Paul O'Gorman Building, London, WC1E 6DD, UK.
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49
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Swamy M. ZAP70 holds the key to kinetic proofreading for TCR ligand discrimination. Nat Immunol 2022; 23:1293-1294. [PMID: 36045188 DOI: 10.1038/s41590-022-01297-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Mahima Swamy
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK.
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50
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Voisinne G, Locard-Paulet M, Froment C, Maturin E, Menoita MG, Girard L, Mellado V, Burlet-Schiltz O, Malissen B, Gonzalez de Peredo A, Roncagalli R. Kinetic proofreading through the multi-step activation of the ZAP70 kinase underlies early T cell ligand discrimination. Nat Immunol 2022; 23:1355-1364. [PMID: 36045187 PMCID: PMC9477740 DOI: 10.1038/s41590-022-01288-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 07/15/2022] [Indexed: 12/18/2022]
Abstract
T cells recognize a few high-affinity antigens among a vast array of lower affinity antigens. According to the kinetic proofreading model, antigen discrimination properties could be explained by the gradual amplification of small differences in binding affinities as the signal is transduced downstream of the T cell receptor. Which early molecular events are affected by ligand affinity, and how, has not been fully resolved. Here, we used time-resolved high-throughput proteomic analyses to identify and quantify the phosphorylation events and protein-protein interactions encoding T cell ligand discrimination in antigen-experienced T cells. Although low-affinity ligands induced phosphorylation of the Cd3 chains of the T cell receptor and the interaction of Cd3 with the Zap70 kinase as strongly as high-affinity ligands, they failed to activate Zap70 to the same extent. As a result, formation of the signalosome of the Lat adaptor was severely impaired with low- compared with high-affinity ligands, whereas formation of the signalosome of the Cd6 receptor was affected only partially. Overall, this study provides a comprehensive map of molecular events associated with T cell ligand discrimination.
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Affiliation(s)
- Guillaume Voisinne
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, Marseille, France
| | - Marie Locard-Paulet
- Département Biologie Structural Biophysique, Institut de Pharmacologie et de Biologie Structurale, Protéomique Génopole Toulouse Midi Pyrénées CNRS UMR, Toulouse, France.,Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Carine Froment
- Département Biologie Structural Biophysique, Institut de Pharmacologie et de Biologie Structurale, Protéomique Génopole Toulouse Midi Pyrénées CNRS UMR, Toulouse, France
| | - Emilie Maturin
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, Marseille, France
| | - Marisa Goncalves Menoita
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, Marseille, France
| | - Laura Girard
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, Marseille, France.,Centre d'Immunophénomique, Aix Marseille Université, INSERM, CNRS, Marseille, France
| | - Valentin Mellado
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, Marseille, France
| | - Odile Burlet-Schiltz
- Département Biologie Structural Biophysique, Institut de Pharmacologie et de Biologie Structurale, Protéomique Génopole Toulouse Midi Pyrénées CNRS UMR, Toulouse, France
| | - Bernard Malissen
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, Marseille, France. .,Centre d'Immunophénomique, Aix Marseille Université, INSERM, CNRS, Marseille, France.
| | - Anne Gonzalez de Peredo
- Département Biologie Structural Biophysique, Institut de Pharmacologie et de Biologie Structurale, Protéomique Génopole Toulouse Midi Pyrénées CNRS UMR, Toulouse, France.
| | - Romain Roncagalli
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, Marseille, France.
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