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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] [Grants] [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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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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3
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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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Egan JR, Abu-Shah E, Dushek O, Elliott T, MacArthur BD. Fluctuations in T cell receptor and pMHC interactions regulate T cell activation. J R Soc Interface 2022; 19:20210589. [PMID: 35135295 PMCID: PMC8833104 DOI: 10.1098/rsif.2021.0589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Adaptive immune responses depend on interactions between T cell receptors (TCRs) and peptide major histocompatibility complex (pMHC) ligands located on the surface of T cells and antigen presenting cells (APCs), respectively. As TCRs and pMHCs are often only present at low copy numbers their interactions are inherently stochastic, yet the role of stochastic fluctuations on T cell function is unclear. Here, we introduce a minimal stochastic model of T cell activation that accounts for serial TCR-pMHC engagement, reversible TCR conformational change and TCR aggregation. Analysis of this model indicates that it is not the strength of binding between the T cell and the APC cell per se that elicits an immune response, but rather the information imparted to the T cell from the encounter, as assessed by the entropy rate of the TCR-pMHC binding dynamics. This view provides an information-theoretic interpretation of T cell activation that explains a range of experimental observations. Based on this analysis, we propose that effective T cell therapeutics may be enhanced by optimizing the inherent stochasticity of TCR-pMHC binding dynamics.
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Affiliation(s)
- Joseph R Egan
- Mathematical Sciences, Stem Cells and Regeneration, University of Southampton, Southampton SO17 1BJ, UK.,Institute for Life Sciences, Stem Cells and Regeneration, University of Southampton, Southampton SO17 1BJ, UK.,Centre for Cancer Immunology, University Hospital Southampton, Southampton SO16 6YD, UK.,Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Enas Abu-Shah
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK.,Kennedy Institute of Rheumatology, University of Oxford, Oxford OX3 7FY, UK
| | - Omer Dushek
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Tim Elliott
- Institute for Life Sciences, Stem Cells and Regeneration, University of Southampton, Southampton SO17 1BJ, UK.,Centre for Cancer Immunology, University Hospital Southampton, Southampton SO16 6YD, UK.,Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Ben D MacArthur
- Mathematical Sciences, Stem Cells and Regeneration, University of Southampton, Southampton SO17 1BJ, UK.,Institute for Life Sciences, Stem Cells and Regeneration, University of Southampton, Southampton SO17 1BJ, UK.,Centre for Human Development, Stem Cells and Regeneration, University of Southampton, Southampton SO17 1BJ, UK.,Alan Turing Institute, London NW1 2DB, UK
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Gálvez J, Gálvez JJ, García-Peñarrubia P. Is TCR/pMHC Affinity a Good Estimate of the T-cell Response? An Answer Based on Predictions From 12 Phenotypic Models. Front Immunol 2019; 10:349. [PMID: 30886616 PMCID: PMC6410681 DOI: 10.3389/fimmu.2019.00349] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 02/11/2019] [Indexed: 11/13/2022] Open
Abstract
On the T-cell surface the TCR is the only molecule that senses antigen, and the engagement of TCR with its specific antigenic peptide (agonist)/MHC complex (pMHC) is determined by the biochemical parameters of the TCR-pMHC interaction. This interaction is the keystone of the adaptive immune response by triggering intracellular signaling pathways that induce the expression of genes required for T cell-mediated effector functions, such as T cell proliferation, cytokine secretion and cytotoxicity. To study the TCR-pMHC interaction one of its properties most extensively analyzed has been TCR-pMHC affinity. However, and despite of intensive experimental research, the results obtained are far from conclusive. Here, to determine if TCR-pMHC affinity is a reliable parameter to characterize T-cell responses, a systematic study has been performed based on the predictions of 12 phenotypic models. This approach has the advantage that allow us to study the response of a given system as a function of only those parameters in which we are interested while other system parameters remain constant. A little surprising, only the simple occupancy model predicts a direct relationship between affinity and response so that an increase in affinity always leads to larger responses. Conversely, in the others more elaborate models this clear situation does not occur, i.e., that a general positive correlation between affinity and immune response does not exist. This is mainly because affinity values are given by the quotient k on/k off where k on and k off are the rate constants of the binding process (i.e., affinity is in fact the quotient of two parameters), so that different sets of these rate constants can give the same value of affinity. However, except in the occupancy model, the predicted T-cell responses depend on the individual values of k on and k off rather than on their quotient k on/k off. This allows: a) that systems with the same affinity can show quite different responses; and b) that systems with low affinity may exhibit larger responses than systems with higher affinities. This would make affinity a poor estimate of T-cell responses and, as a result, data correlations between affinity and immune response should be interpreted and used with caution.
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Affiliation(s)
- Jesús Gálvez
- Department of Physical Chemistry, Faculty of Chemistry, University of Murcia, Murcia, Spain
| | - Juan J Gálvez
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Pilar García-Peñarrubia
- Department of Biochemistry and Molecular Biology B and Immunology, School of Medicine, University of Murcia, Murcia, Spain
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WEDAGEDERA JANAKR, BURROUGHS NJ. COMPARISON OF A DUAL STRATEGY FOR T-CELL ACTIVATION UNDER INHIBITION OF THE CD4 RECEPTOR. J BIOL SYST 2018. [DOI: 10.1142/s0218339018500158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
We consider a stochastic model for T-cell activation proposed in Refs. [1] and [2] to compare the specificity and sensitivity of two different strategies for T-cell activation that utilize the history of phosphorylation of T-cell receptor (TCR). We compare these two strategies when the temporal signals/events that are essential for progressive T-cell activation are suppressed by blockade of CD4 receptor that may have caused by disease or therapeutic effects.3–6 We show that under these conditions, a threshold-strategy which is capable of maintaining a threshold (for total number of phosphorylated TCRs by time [Formula: see text]) for a further duration [Formula: see text] performs better in discriminating agonist peptides than a single-threshold strategy (reached by time [Formula: see text]) leading to T-cell activation using the Wentzell-Friedlin theory for large deviations for stochastic processes.7,8
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Affiliation(s)
- JANAK R. WEDAGEDERA
- Certara UK Limited, Simcyp Division, Level 2-Acero, 1 Concourse Way, Sheffield S1 2BJ, United Kingdom
| | - N. J. BURROUGHS
- Mathematics Institute and Warwick Systems, Biology Centre, University of Warwick, Coventry CV4 7AL, United Kingdom
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Ashouri JF, Weiss A. Endogenous Nur77 Is a Specific Indicator of Antigen Receptor Signaling in Human T and B Cells. THE JOURNAL OF IMMUNOLOGY 2016; 198:657-668. [PMID: 27940659 DOI: 10.4049/jimmunol.1601301] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 11/14/2016] [Indexed: 12/20/2022]
Abstract
Distinguishing true Ag-stimulated lymphocytes from bystanders activated by the inflammatory milieu has been difficult. Nur77 is an immediate early gene whose expression is rapidly upregulated by TCR signaling in murine T cells and human thymocytes. Nur77-GFP transgenes serve as specific TCR and BCR signaling reporters in murine transgenic models. In this study, we demonstrate that endogenous Nur77 protein expression can serve as a reporter of TCR and BCR specific signaling in human PBMCs. Nur77 protein amounts were assessed by immunofluorescence and flow cytometry in T and B cells isolated from human PBMCs obtained from healthy donors that had been stimulated by their respective Ag receptors. We demonstrate that endogenous Nur77 is a more specific reporter of Ag-specific signaling events than the commonly used CD69 activation marker in both human T and B cells. This is reflective of the disparity in signaling pathways that regulate the expression of Nur77 and CD69. Assessing endogenous Nur77 protein expression has great potential to identify Ag-activated lymphocytes in human disease.
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Affiliation(s)
- Judith F Ashouri
- The Rosalind Russell and Ephraim P. Engleman Rheumatology Research Center, Division of Rheumatology, Department of Medicine, and the Howard Hughes Medical Institute at the University of California, San Francisco, San Francisco, CA 94143
| | - Arthur Weiss
- The Rosalind Russell and Ephraim P. Engleman Rheumatology Research Center, Division of Rheumatology, Department of Medicine, and the Howard Hughes Medical Institute at the University of California, San Francisco, San Francisco, CA 94143
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Lever M, Lim HS, Kruger P, Nguyen J, Trendel N, Abu-Shah E, Maini PK, van der Merwe PA, Dushek O. Architecture of a minimal signaling pathway explains the T-cell response to a 1 million-fold variation in antigen affinity and dose. Proc Natl Acad Sci U S A 2016; 113:E6630-E6638. [PMID: 27702900 PMCID: PMC5087047 DOI: 10.1073/pnas.1608820113] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
T cells must respond differently to antigens of varying affinity presented at different doses. Previous attempts to map peptide MHC (pMHC) affinity onto T-cell responses have produced inconsistent patterns of responses, preventing formulations of canonical models of T-cell signaling. Here, a systematic analysis of T-cell responses to 1 million-fold variations in both pMHC affinity and dose produced bell-shaped dose-response curves and different optimal pMHC affinities at different pMHC doses. Using sequential model rejection/identification algorithms, we identified a unique, minimal model of cellular signaling incorporating kinetic proofreading with limited signaling coupled to an incoherent feed-forward loop (KPL-IFF) that reproduces these observations. We show that the KPL-IFF model correctly predicts the T-cell response to antigen copresentation. Our work offers a general approach for studying cellular signaling that does not require full details of biochemical pathways.
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Affiliation(s)
- Melissa Lever
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Hong-Sheng Lim
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Philipp Kruger
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - John Nguyen
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Nicola Trendel
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Enas Abu-Shah
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Philip Kumar Maini
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford OX2 6GG, United Kingdom
| | | | - Omer Dushek
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom; Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford OX2 6GG, United Kingdom
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Cai LL, Liu GY, Tzeng CM. Genome-wide DNA methylation profiling and its involved molecular pathways from one individual with thyroid malignant/benign tumor and hyperplasia: A case report. Medicine (Baltimore) 2016; 95:e4695. [PMID: 27583899 PMCID: PMC5008583 DOI: 10.1097/md.0000000000004695] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND During development, methylation permanently changes gene activity, while aberrant gene methylation is key to human tumorigenesis. Gene methylation is an epigenetic event leading to gene silencing and some tumor suppressor genes that are aberrantly methylated in both thyroid cancer and benign thyroid tumor, suggesting a role for methylation in early thyroid tumorigenesis. Specific gene methylation occurs in certain types of thyroid cancer and depends on particular signaling pathways. Most reports rely on data from varied samples that vary tremendously with respect to methylation. RESULTS We observed that hyperplastic/malignant (H/M) thyroid tissue and benign/manligant (B/M) tissue had the most profoundly methylated loci compared to hyperplastic/benign (H/B) tissue. These loci are mapped to 863 genes (|Δβ value| > 0.15) in B/M and 1082 genes (|Δβ value| > 0.15) in H/M. After bioinformatic analysis, these genes were found to be involved in T-cell receptor signaling pathway (B/M) and Jak-Stat signaling pathways (H/M). CONCLUSION Our study offers the most comprehensive DNA methylation data for thyroid disease to date, using 1 patient with 3 tissue types and high-resolution 450K arrays. Our data may lay the foundation for future identification of novel epigenetic targets or diagnosis of thyroid cancer.
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Affiliation(s)
- Liang-Liang Cai
- Translational Medicine Research Center, School of Pharmaceutical Sciences
| | - Guo-Yan Liu
- Department of Gastrointestinal Surgery, Zhongshan Hospital, Xiamen University
| | - Chi-Meng Tzeng
- Translational Medicine Research Center, School of Pharmaceutical Sciences
- Key Laboratory for Cancer T-Cell Theranostics and Clinical Translation
- INNOVA Cell: TDx Clinics and TRANSLATE Health Group, Xiamen University, China
- Correspondence: Chi-Meng Tzeng, School of Pharmaceutical Sciences, Xiamen University, China (e-mail: )
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Lou J, Rossy J, Deng Q, Pageon SV, Gaus K. New Insights into How Trafficking Regulates T Cell Receptor Signaling. Front Cell Dev Biol 2016; 4:77. [PMID: 27508206 PMCID: PMC4960267 DOI: 10.3389/fcell.2016.00077] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 07/11/2016] [Indexed: 02/04/2023] Open
Abstract
There is emerging evidence that exocytosis plays an important role in regulating T cell receptor (TCR) signaling. The trafficking molecules involved in lytic granule (LG) secretion in cytotoxic T lymphocytes (CTL) have been well-studied due to the immune disorder known as familial hemophagocytic lymphohistiocytosis (FHLH). However, the knowledge of trafficking machineries regulating the exocytosis of receptors and signaling molecules remains quite limited. In this review, we summarize the reported trafficking molecules involved in the transport of the TCR and downstream signaling molecules to the cell surface. By combining this information with the known knowledge of LG exocytosis and general exocytic trafficking machinery, we attempt to draw a more complete picture of how the TCR signaling network and exocytic trafficking matrix are interconnected to facilitate T cell activation. This also highlights how membrane compartmentalization facilitates the spatiotemporal organization of cellular responses that are essential for immune functions.
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Affiliation(s)
- Jieqiong Lou
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, University of New South WalesSydney, NSW, Australia; ARC Centre of Excellence in Advanced Molecular Imaging, University of New South WalesSydney, NSW, Australia
| | - Jérémie Rossy
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, University of New South WalesSydney, NSW, Australia; ARC Centre of Excellence in Advanced Molecular Imaging, University of New South WalesSydney, NSW, Australia
| | - Qiji Deng
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, University of New South WalesSydney, NSW, Australia; ARC Centre of Excellence in Advanced Molecular Imaging, University of New South WalesSydney, NSW, Australia
| | - Sophie V Pageon
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, University of New South WalesSydney, NSW, Australia; ARC Centre of Excellence in Advanced Molecular Imaging, University of New South WalesSydney, NSW, Australia
| | - Katharina Gaus
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, University of New South WalesSydney, NSW, Australia; ARC Centre of Excellence in Advanced Molecular Imaging, University of New South WalesSydney, NSW, Australia
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Vásquez-Montoya GA, Danobeitia JS, Fernández LA, Hernández-Ortiz JP. Computational immuno-biology for organ transplantation and regenerative medicine. Transplant Rev (Orlando) 2016; 30:235-46. [PMID: 27296889 DOI: 10.1016/j.trre.2016.05.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 05/20/2016] [Accepted: 05/22/2016] [Indexed: 10/21/2022]
Abstract
Organ transplantation and regenerative medicine are adopted platforms that provide replacement tissues and organs from natural or engineered sources. Acceptance, tolerance and rejection depend greatly on the proper control of the immune response against graft antigens, motivating the development of immunological and genetical therapies that prevent organ failure. They rely on a complete, or partial, understanding of the immune system. Ultimately, they are innovative technologies that ensure permanent graft tolerance and indefinite graft survival through the modulation of the immune system. Computational immunology has arisen as a tool towards a mechanistic understanding of the biological and physicochemical processes surrounding an immune response. It comprehends theoretical and computational frameworks that simulate immuno-biological systems. The challenge is centered on the multi-scale character of the immune system that spans from atomistic scales, during peptide-epitope and protein interactions, to macroscopic scales, for lymph transport and organ-organ reactions. In this paper, we discuss, from an engineering perspective, the biological processes that are involved during the immune response of organ transplantation. Previous computational efforts, including their characteristics and visible limitations, are described. Finally, future perspectives and challenges are listed to motivate further developments.
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Affiliation(s)
- Gustavo A Vásquez-Montoya
- Departamento de Materiales y Minerales, Universidad Nacional de Colombia, Sede Medellín, Medellín, Colombia
| | - Juan S Danobeitia
- Department of Surgery, Division of Organ Transplantation, University of Wisconsin-Madison, Madison, WI, USA
| | - Luis A Fernández
- Department of Surgery, Division of Organ Transplantation, University of Wisconsin-Madison, Madison, WI, USA
| | - Juan P Hernández-Ortiz
- Departamento de Materiales y Minerales, Universidad Nacional de Colombia, Sede Medellín, Medellín, Colombia; Institute for Molecular Engineering, University of Chicago, Chicago, IL, USA; Laboratory for Molecular and Computational Genomics, UW Biotechnology Center, University of Wisconsin-Madison, Madison, WI 53706, USA.
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Abstract
Mathematical and statistical methods enable multidisciplinary approaches that catalyse discovery. Together with experimental methods, they identify key hypotheses, define measurable observables and reconcile disparate results. We collect a representative sample of studies in T-cell biology that illustrate the benefits of modelling–experimental collaborations and that have proven valuable or even groundbreaking. We conclude that it is possible to find excellent examples of synergy between mathematical modelling and experiment in immunology, which have brought significant insight that would not be available without these collaborations, but that much remains to be discovered.
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Affiliation(s)
- Mario Castro
- Universidad Pontificia Comillas , E28015 Madrid , Spain
| | - Grant Lythe
- Department of Applied Mathematics, School of Mathematics , University of Leeds , Leeds LS2 9JT , UK
| | - Carmen Molina-París
- Department of Applied Mathematics, School of Mathematics , University of Leeds , Leeds LS2 9JT , UK
| | - Ruy M Ribeiro
- Los Alamos National Laboratory , Theoretical Biology and Biophysics , Los Alamos, NM 87545 , USA
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13
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Insights into the initiation of TCR signaling. Nat Immunol 2014; 15:798-807. [PMID: 25137454 DOI: 10.1038/ni.2940] [Citation(s) in RCA: 257] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Accepted: 06/10/2014] [Indexed: 12/13/2022]
Abstract
The initiation of T cell antigen receptor signaling is a key step that can result in T cell activation and the orchestration of an adaptive immune response. Early events in T cell receptor signaling can distinguish between agonist and endogenous ligands with exquisite selectivity, and show extraordinary sensitivity to minute numbers of agonists in a sea of endogenous ligands. We review our current knowledge of models and crucial molecules that aim to provide a mechanistic explanation for these observations. Building on current understanding and a discussion of unresolved issues, we propose a molecular model for initiation of T cell receptor signaling that may serve as a useful guide for future studies.
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14
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Resolving Early Signaling Events in T-Cell Activation Leading to IL-2 and FOXP3 Transcription. Processes (Basel) 2014. [DOI: 10.3390/pr2040867] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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16
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Castro M, van Santen HM, Férez M, Alarcón B, Lythe G, Molina-París C. Receptor Pre-Clustering and T cell Responses: Insights into Molecular Mechanisms. Front Immunol 2014; 5:132. [PMID: 24817867 PMCID: PMC4012210 DOI: 10.3389/fimmu.2014.00132] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 03/15/2014] [Indexed: 11/13/2022] Open
Abstract
T cell activation, initiated by T cell receptor (TCR) mediated recognition of pathogen-derived peptides presented by major histocompatibility complex class I or II molecules (pMHC), shows exquisite specificity and sensitivity, even though the TCR-pMHC binding interaction is of low affinity. Recent experimental work suggests that TCR pre-clustering may be a mechanism via which T cells can achieve such high sensitivity. The unresolved stoichiometry of the TCR makes TCR-pMHC binding and TCR triggering, an open question. We formulate a mathematical model to characterize the pre-clustering of T cell receptors (TCRs) on the surface of T cells, motivated by the experimentally observed distribution of TCR clusters on the surface of naive and memory T cells. We extend a recently introduced stochastic criterion to compute the timescales of T cell responses, assuming that ligand-induced cross-linked TCR is the minimum signaling unit. We derive an approximate formula for the mean time to signal initiation. Our results show that pre-clustering reduces the mean activation time. However, additional mechanisms favoring the existence of clusters are required to explain the difference between naive and memory T cell responses. We discuss the biological implications of our results, and both the compatibility and complementarity of our approach with other existing mathematical models.
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Affiliation(s)
- Mario Castro
- Grupo de Dinámica No-Lineal and Grupo Interdisciplinar de Sistemas Complejos (GISC), Escuela Técnica Superior de Ingeniería (ICAI), Universidad Pontificia Comillas , Madrid , Spain
| | - Hisse M van Santen
- Departamento de Biología Celular e Inmunología, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid , Madrid , Spain
| | - María Férez
- Departamento de Biología Celular e Inmunología, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid , Madrid , Spain
| | - Balbino Alarcón
- Departamento de Biología Celular e Inmunología, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid , Madrid , Spain
| | - Grant Lythe
- Department of Applied Mathematics, School of Mathematics, University of Leeds , Leeds , UK
| | - Carmen Molina-París
- Department of Applied Mathematics, School of Mathematics, University of Leeds , Leeds , UK
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17
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Cheng X, Merchan L, Tchernookov M, Nemenman I. A large number of receptors may reduce cellular response time variation. Phys Biol 2013; 10:035008. [PMID: 23735700 DOI: 10.1088/1478-3975/10/3/035008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cells often have tens of thousands of receptors, even though only a few activated receptors can trigger full cellular responses. Reasons for the overabundance of receptors remain unclear. We suggest that, under certain conditions, the large number of receptors can result in a competition among receptors to be the first to activate the cell. The competition decreases the variability of the time to cellular activation, and hence results in a more synchronous activation of cells. We argue that, in simple models, this variability reduction does not necessarily interfere with the receptor specificity to ligands achieved by the kinetic proofreading mechanism. Thus cells can be activated accurately in time and specifically to certain signals. We predict the minimum number of receptors needed to reduce the coefficient of variation for the time to activation following binding of a specific ligand. Furthermore, we predict the maximum number of receptors so that the kinetic proofreading mechanism still can improve the specificity of the activation. These predictions fall in line with experimentally reported receptor numbers for multiple systems.
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Affiliation(s)
- Xiang Cheng
- Department of Physics, Emory University, Atlanta, GA 30322, USA.
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18
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Modulation of tumor immunity by soluble and membrane-bound molecules at the immunological synapse. Clin Dev Immunol 2013; 2013:450291. [PMID: 23533456 PMCID: PMC3606757 DOI: 10.1155/2013/450291] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 01/15/2013] [Indexed: 12/31/2022]
Abstract
To circumvent pathology caused by infectious microbes and tumor growth, the host immune system must constantly clear harmful microorganisms and potentially malignant transformed cells. This task is accomplished in part by T-cells, which can directly kill infected or tumorigenic cells. A crucial event determining the recognition and elimination of detrimental cells is antigen recognition by the T cell receptor (TCR) expressed on the surface of T cells. Upon binding of the TCR to cognate peptide-MHC complexes presented on the surface of antigen presenting cells (APCs), a specialized supramolecular structure known as the immunological synapse (IS) assembles at the T cell-APC interface. Such a structure involves massive redistribution of membrane proteins, including TCR/pMHC complexes, modulatory receptor pairs, and adhesion molecules. Furthermore, assembly of the immunological synapse leads to intracellular events that modulate and define the magnitude and characteristics of the T cell response. Here, we discuss recent literature on the regulation and assembly of IS and the mechanisms evolved by tumors to modulate its function to escape T cell cytotoxicity, as well as novel strategies targeting the IS for therapy.
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19
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Curado S, Kumari S, Dustin ML. "Cell biology meets physiology: functional organization of vertebrate plasma membranes"--the immunological synapse. CURRENT TOPICS IN MEMBRANES 2013; 72:313-46. [PMID: 24210434 PMCID: PMC4878826 DOI: 10.1016/b978-0-12-417027-8.00009-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The immunological synapse (IS) is an excellent example of cell-cell communication, where signals are exchanged between two cells, resulting in a well-structured line of defense during adaptive immune response. This process has been the focus of several studies that aimed at understanding its formation and subsequent events and has led to the realization that it relies on a well-orchestrated molecular program that only occurs when specific requirements are met. The development of more precise and controllable T cell activation systems has led to new insights including the role of mechanotransduction in the process of formation of the IS and T cell activation. Continuous advances in our understanding of the IS formation, particularly in the context of T cell activation and differentiation, as well the development of new T cell activation systems are being applied to the establishment and improvement of immune therapeutical approaches.
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Affiliation(s)
- Silvia Curado
- Skirball Institute of Biomolecular Medicine, and Department of Pathology, New York University School of Medicine, 540 First Ave, New York, NY 10016, USA and Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Roosevelt Drive, Headington, Oxfordshire, OX3 7FY, UK
| | - Sudha Kumari
- Skirball Institute of Biomolecular Medicine, and Department of Pathology, New York University School of Medicine, 540 First Ave, New York, NY 10016, USA and Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Roosevelt Drive, Headington, Oxfordshire, OX3 7FY, UK
| | - Michael L. Dustin
- Skirball Institute of Biomolecular Medicine, and Department of Pathology, New York University School of Medicine, 540 First Ave, New York, NY 10016, USA and Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Roosevelt Drive, Headington, Oxfordshire, OX3 7FY, UK
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20
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Rossy J, Williamson DJ, Benzing C, Gaus K. The integration of signaling and the spatial organization of the T cell synapse. Front Immunol 2012. [PMID: 23189081 PMCID: PMC3504718 DOI: 10.3389/fimmu.2012.00352] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Engagement of the T cell antigen receptor (TCR) triggers signaling pathways that lead to T cell selection, differentiation and clonal expansion. Superimposed onto the biochemical network is a spatial organization that describes individual receptor molecules, dimers, oligomers and higher order structures. Here we discuss recent findings and new concepts that may regulate TCR organization in naïve and memory T cells. A key question that has emerged is how antigen-TCR interactions encode spatial information to direct T cell activation and differentiation. Single molecule super-resolution microscopy may become an important tool in decoding receptor organization at the molecular level.
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Affiliation(s)
- Jérémie Rossy
- Centre for Vascular Research and Australian Centre for Nanomedicine, University of New South Wales Sydney, NSW, Australia
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21
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Abstract
Leukocytes play a critical role in recognizing and responding to infection and cancer. Central to this function is an array of cell-surface receptors that lack sequence homology. Many of these receptors have in common the fact that their signaling involves phosphorylation of cytoplasmic domains by extrinsic tyrosine kinases. These non-catalytic tyrosine-phosphorylated receptors (NTRs) share a number of other features, including small size and optimal stimulation by surface-associated ligands. We argue here that NTRs are also likely to share the same kinetic-segregation triggering mechanism, which involves segregation of the engaged NTR from receptor tyrosine phosphatases with large ectodomains such as CD45 and CD148. NTRs signal through tyrosine-containing cytoplasmic motifs, which recruit distinct cytoplasmic signaling proteins when phosphorylated, transducing activatory or inhibitory signals. They have two features that make them uniquely well suited to their role in immune recognition of infection and cancer. Their modular structure enables the coupling of many rapidly evolving receptors with diverse ligand specificities to the same conserved signaling machinery. Their similarity in size and shared signaling machinery enables them to colocalize at cell-cell interfaces when they engage ligands, facilitating the integration of activatory and inhibitory signals from multiple receptors at the cell surface.
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Affiliation(s)
- Omer Dushek
- Sir William Dunn School of Pathology, University of Oxford, UK
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22
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Valitutti S. The Serial Engagement Model 17 Years After: From TCR Triggering to Immunotherapy. Front Immunol 2012; 3:272. [PMID: 22973273 PMCID: PMC3428561 DOI: 10.3389/fimmu.2012.00272] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2012] [Accepted: 08/08/2012] [Indexed: 12/27/2022] Open
Abstract
More than 15 years ago the serial engagement model was proposed as an attempt to solve the low affinity/high sensitivity paradox of TCR antigen recognition. Since then, the model has undergone ups and downs marked by the technical and conceptual advancements made in the field of T lymphocyte activation. Here, I describe the development of the model and survey recent literature providing evidence either for or against the idea that serial TCR/pMHC engagement might contribute to T lymphocyte activation. I also discuss how the concept of serial TCR engagement might be useful in the design of immunotherapeutic approaches aimed at potentiating T lymphocyte responses in vivo.
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Affiliation(s)
- Salvatore Valitutti
- INSERM, UMR 1043, Section Dynamique Moléculaire des Interactions Lymphocytaires, Centre de Physiopathologie de Toulouse Purpan Toulouse, France
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23
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Riquelme SA, Bueno SM, Kalergis AM. IgG keeps virulent Salmonella from evading dendritic cell uptake. Immunology 2012; 136:291-305. [PMID: 22352313 DOI: 10.1111/j.1365-2567.2012.03578.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Dendritic cells (DCs) are phagocytic professional antigen-presenting cells that can prime naive T cells and initiate anti-bacterial immunity. However, several pathogenic bacteria have developed virulence mechanisms to impair DC function. For instance, Salmonella enterica serovar Typhimurium can prevent DCs from activating antigen-specific T cells. In addition, it has been described that the Salmonella Pathogenicity Island 1 (SPI-1), which promotes phagocytosis of bacteria in non-phagocytic cells, can suppress this process in DCs in a phosphatidylinositol 3-kinase (PI3K) -dependent manner. Both mechanisms allow Salmonella to evade host adaptive immunity. Recent studies have shown that IgG-opsonization of Salmonella can restore the capacity of DCs to present antigenic peptide-MHC complexes and prime T cells. Interestingly, T-cell activation requires Fcγ receptor III (FcγRIII) expression over the DC surface, suggesting that this receptor could counteract both antigen presentation and phagocytosis evasion by bacteria. We show that, despite IgG-coated Salmonella retaining its capacity to secrete anti-capture proteins, DCs are efficiently capable of engulfing a large number of IgG-coated bacteria. These results suggest that DCs employ another mechanism to engulf IgG-coated Salmonella, different from that used for free bacteria. In this context, we noted that DCs do not employ PI3K, actin cytoskeleton or dynamin to capture IgG-coated bacteria. Likewise, we observed that the capture is an FcγR-independent mechanism. Interestingly, these internalized bacteria were rapidly targeted for degradation within lysosomal compartments. Hence, our results suggest a novel mechanism in DCs that does not employ PI3K/actin cytoskeleton/dynamin/FcγRs to engulf IgG-coated Salmonella, is not affected by anti-capture SPI-1-derived effectors and enhances DC immunogenicity, bacterial degradation and antigen presentation.
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Affiliation(s)
- Sebastián A Riquelme
- Millennium Institute of Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile Departamento de Reumatología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
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24
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Zarnitsyna V, Zhu C. T cell triggering: insights from 2D kinetics analysis of molecular interactions. Phys Biol 2012; 9:045005. [PMID: 22871794 DOI: 10.1088/1478-3975/9/4/045005] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Interaction of the T cell receptor (TCR) with pathogen-derived peptide presented by the major histocompatibility complex (pMHC) molecule is central to adaptive immunity as it initiates intracellular signaling to trigger T cell response to infection. Kinetic parameters of this interaction have been under intensive investigation for more than two decades using soluble pMHCs and/or TCRs with at least one of them in the solution (three-dimensional (3D) methods). Recently, several techniques have been developed to enable kinetic analysis on live T cells with pMHCs presented by surrogate antigen presenting cells (APCs) or supported planar lipid bilayers (two-dimensional (2D) methods). Comparison of 2D versus 3D parameters reveals drastic differences with broader ranges of 2D affinities and on-rates and orders of magnitude faster 2D off-rates for functionally distinct pMHCs. Here we review new 2D data and discuss how it may impact previously developed models of T cell discrimination between pMHCs of different potencies.
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Affiliation(s)
- Veronika Zarnitsyna
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA.
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25
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Currie J, Castro M, Lythe G, Palmer E, Molina-París C. A stochastic T cell response criterion. J R Soc Interface 2012; 9:2856-70. [PMID: 22745227 PMCID: PMC3479899 DOI: 10.1098/rsif.2012.0205] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The adaptive immune system relies on different cell types to provide fast and coordinated responses, characterized by recognition of pathogenic challenge, extensive cellular proliferation and differentiation, as well as death. T cells are a subset of the adaptive immune cellular pool that recognize immunogenic peptides expressed on the surface of antigen-presenting cells by means of specialized receptors on their membrane. T cell receptor binding to ligand determines T cell responses at different times and locations during the life of a T cell. Current experimental evidence provides support to the following: (i) sufficiently long receptor–ligand engagements are required to initiate the T cell signalling cascade that results in productive signal transduction and (ii) counting devices are at work in T cells to allow signal accumulation, decoding and translation into biological responses. In the light of these results, we explore, with mathematical models, the timescales associated with T cell responses. We consider two different criteria: a stochastic one (the mean time it takes to have had N receptor–ligand complexes bound for at least a dwell time, τ, each) and one based on equilibrium (the time to reach a threshold number N of receptor–ligand complexes). We have applied mathematical models to previous experiments in the context of thymic negative selection and to recent two-dimensional experiments. Our results indicate that the stochastic criterion provides support to the thymic affinity threshold hypothesis, whereas the equilibrium one does not, and agrees with the ligand hierarchy experimentally established for thymic negative selection.
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Affiliation(s)
- James Currie
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds LS2 9JT, UK
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26
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Bridgeman JS, Sewell AK, Miles JJ, Price DA, Cole DK. Structural and biophysical determinants of αβ T-cell antigen recognition. Immunology 2012; 135:9-18. [PMID: 22044041 DOI: 10.1111/j.1365-2567.2011.03515.x] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The molecular rules that govern MHC restriction, and allow T-cells to differentiate between peptides derived from healthy cells and those from diseased cells, remain poorly understood. Here we provide an overview of the structural constraints that enable the T-cell receptor (TCR) to discriminate between self and non-self peptides, and summarize studies that have attempted to correlate the biophysical parameters of TCR/peptide-major histocompatibility complex (pMHC) binding with T-cell activation. We further review how the antigenic origin of peptide epitopes affects TCR binding parameters and the 'quality' of a T-cell response. Understanding the principles that govern pMHC recognition by T-cells will unlock pathways to the rational development of immunotherapeutic approaches for the treatment of infectious disease, cancer and autoimmunity.
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Affiliation(s)
- John S Bridgeman
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, UK
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27
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Tsourkas PK, Liu W, Das SC, Pierce SK, Raychaudhuri S. Discrimination of membrane antigen affinity by B cells requires dominance of kinetic proofreading over serial engagement. Cell Mol Immunol 2012; 9:62-74. [PMID: 21909127 PMCID: PMC3756518 DOI: 10.1038/cmi.2011.29] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Revised: 07/06/2011] [Accepted: 07/07/2011] [Indexed: 02/02/2023] Open
Abstract
B-cell receptor signaling in response to membrane-bound antigen increases with antigen affinity, a process known as affinity discrimination. We use computational modeling to show that B-cell affinity discrimination requires that kinetic proofreading predominate over serial engagement. We find that if B-cell receptors become signaling-capable immediately upon antigen binding, which results in decreasing serial engagement as affinity increases, then increasing affinity can lead to weaker signaling. Rather, antigen must stay bound to B-cell receptors for a threshold time of several seconds before becoming signaling-capable, a process similar to kinetic proofreading. This process overcomes the loss in serial engagement due to increasing antigen affinity, and replicates the monotonic increase in B-cell signaling with increasing affinity that has been observed in B-cell activation experiments. This finding matches well with the experimentally observed time (∼20 s) required for the B-cell receptor signaling domains to undergo antigen and lipid raft-mediated conformational changes that lead to Src-family kinase recruitment. We hypothesize that the physical basis for a threshold time of antigen binding might lie in the formation timescale of B-cell receptor dimers. The time required for dimer formation decreases with increasing antigen affinity, thereby resulting in shorter threshold antigen binding times as affinity increases. Such an affinity-dependent kinetic proofreading requirement results in affinity discrimination very similar to that observed in biological experiments. B-cell affinity discrimination is critical to the process of affinity maturation and the production of high-affinity antibodies, and thus our results have important implications in applications such as vaccine design.
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Affiliation(s)
- Philippos K Tsourkas
- Department of Biomedical Engineering, University of California-Davis, One Shields Ave., Davis, CA 95616, USA
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28
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Systems biology approaches for understanding cellular mechanisms of immunity in lymph nodes during infection. J Theor Biol 2011; 287:160-70. [PMID: 21798267 DOI: 10.1016/j.jtbi.2011.06.037] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Revised: 06/30/2011] [Accepted: 06/30/2011] [Indexed: 12/20/2022]
Abstract
Adaptive immunity is initiated in secondary lymphoid tissues when naive T cells recognize foreign antigen presented as MHC-bound peptide on the surface of dendritic cells. Only a small fraction of T cells in the naive repertoire will express T cell receptors specific for a given epitope, but antigen recognition triggers T cell activation and proliferation, thus greatly expanding antigen-specific clones. Expanded T cells can serve a helper function for B cell responses or traffic to sites of infection to secrete cytokines or kill infected cells. Over the past decade, two-photon microscopy of lymphoid tissues has shed important light on T cell development, antigen recognition, cell trafficking and effector functions. These data have enabled the development of sophisticated quantitative and computational models that, in turn, have been used to test hypotheses in silico that would otherwise be impossible or difficult to explore experimentally. Here, we review these models and their principal findings and highlight remaining questions where modeling approaches are poised to advance our understanding of complex immunological systems.
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29
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Carreño LJ, González PA, Bueno SM, Riedel CA, Kalergis AM. Modulation of the dendritic cell-T-cell synapse to promote pathogen immunity and prevent autoimmunity. Immunotherapy 2011; 3:6-11. [PMID: 21524159 DOI: 10.2217/imt.11.38] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The molecular interactions occurring at the interface between dendritic cells (DCs) and T cells play an important role in the immune surveillance against infectious agents, as well as in autoimmune pathogenesis. Therefore, regulation of this interaction arises as an important tool for the prevention and treatment of immune disorders and to improve the protection against pathogens without causing detrimental inflammation. Some of the molecular interactions defining the outcome of the DC-T cell interaction are: T-cell receptor (TCR) binding to the pMHC on the DC surface, which is responsible for the antigenic specificity; and the ratio of activating/inhibitory receptor pairs on the surface of DCs and T cells, which modulate DC immunogenicity and T-cell function, respectively. An alteration in the proper function of these molecules could lead to unbalanced DC-T-cell synapses that either cause a failure to control infections or exacerbated inflammation. Furthermore, some pathogens have developed molecular strategies to impair the function of the synapse to evade adaptive immunity. In this article, we will discuss recent work relative to the molecular mechanisms controlling DC-T-cell synapse and their implications on immunoregulation to control autoimmunity and potentiate pathogen immunity.
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Affiliation(s)
- Leandro J Carreño
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Alameda 340, Casilla 114-D, Santiago, Chile
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30
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Germain RN, Meier-Schellersheim M, Nita-Lazar A, Fraser IDC. Systems biology in immunology: a computational modeling perspective. Annu Rev Immunol 2011; 29:527-85. [PMID: 21219182 DOI: 10.1146/annurev-immunol-030409-101317] [Citation(s) in RCA: 140] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Systems biology is an emerging discipline that combines high-content, multiplexed measurements with informatic and computational modeling methods to better understand biological function at various scales. Here we present a detailed review of the methods used to create computational models and to conduct simulations of immune function. We provide descriptions of the key data-gathering techniques employed to generate the quantitative and qualitative data required for such modeling and simulation and summarize the progress to date in applying these tools and techniques to questions of immunological interest, including infectious disease. We include comments on what insights modeling can provide that complement information obtained from the more familiar experimental discovery methods used by most investigators and the reasons why quantitative methods are needed to eventually produce a better understanding of immune system operation in health and disease.
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Affiliation(s)
- Ronald N Germain
- Program in Systems Immunology and Infectious Disease Modeling, National Institute of Allergy and Infectious Disease, Laboratory of Immunology, National Institutes of Health, Bethesda, Maryland 20892, USA.
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31
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Dushek O, Aleksic M, Wheeler RJ, Zhang H, Cordoba SP, Peng YC, Chen JL, Cerundolo V, Dong T, Coombs D, van der Merwe PA. Antigen potency and maximal efficacy reveal a mechanism of efficient T cell activation. Sci Signal 2011; 4:ra39. [PMID: 21653229 PMCID: PMC4143974 DOI: 10.1126/scisignal.2001430] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
T cell activation, a critical event in adaptive immune responses, depends on productive interactions between T cell receptors (TCRs) and antigens presented as peptide-bound major histocompatibility complexes (pMHCs). Activated T cells lyse infected cells, secrete cytokines, and perform other effector functions with various efficiencies, which depend on the binding parameters of the TCR-pMHC complex. The mechanism through which binding parameters are translated to the efficiency of T cell activation, however, remains controversial. The "affinity model" suggests that the dissociation constant (KD) of the TCR-pMHC complex determines the response, whereas the "productive hit rate model" suggests that the off-rate (koff) is critical. Here, we used mathematical modeling to show that antigen potency, as determined by the EC50 (half-maximal effective concentration), which is used to support KD-based models, could not discriminate between the affinity and the productive hit rate models. Both models predicted a correlation between EC50 and KD, but only the productive hit rate model predicted a correlation between maximal efficacy (Emax), the maximal T cell response induced by pMHC, and koff. We confirmed the predictions made by the productive hit rate model in experiments with cytotoxic T cell clones and a panel of pMHC variants. Thus, we propose that the activity of an antigen is determined by both its potency (EC50) and maximal efficacy (Emax).
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Affiliation(s)
- Omer Dushek
- Sir William Dunn School of Pathology, University of Oxford, OX1 3RE, UK
- Centre for Mathematical Biology, University of Oxford, OX1 3LB, UK
| | - Milos Aleksic
- Sir William Dunn School of Pathology, University of Oxford, OX1 3RE, UK
| | | | - Hao Zhang
- Sir William Dunn School of Pathology, University of Oxford, OX1 3RE, UK
| | | | - Yan-Chun Peng
- Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS, UK
| | - Ji-Li Chen
- Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS, UK
| | - Vincenzo Cerundolo
- Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS, UK
| | - Tao Dong
- Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS, UK
| | - Daniel Coombs
- Department of Mathematics and Institute of Applied Mathematics, University of British Columbia, V6T 1Z2, Canada
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32
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de la Cruz J, Kruger T, Parks CA, Silge RL, van Oers NSC, Luescher IF, Schrum AG, Gil D. Basal and antigen-induced exposure of the proline-rich sequence in CD3ε. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2011; 186:2282-90. [PMID: 21228347 PMCID: PMC3810001 DOI: 10.4049/jimmunol.1003225] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The CD3ε cytoplasmic tail contains a conserved proline-rich sequence (PRS) that influences TCR-CD3 expression and signaling. Although the PRS can bind the SH3.1 domain of the cytosolic adapter Nck, whether the PRS is constitutively available for Nck binding or instead represents a cryptic motif that is exposed via conformational change upon TCR-CD3 engagement (CD3Δc) is currently unresolved. Furthermore, the extent to which a cis-acting CD3ε basic amino acid-rich stretch (BRS), with its unique phosphoinositide-binding capability, might impact PRS accessibility is not clear. In this study, we found that freshly harvested primary thymocytes expressed low to moderate basal levels of Nck-accessible PRS ("open-CD3"), although most TCR-CD3 complexes were inaccessible to Nck ("closed-CD3"). Ag presentation in vivo induced open-CD3, accounting for half of the basal level found in thymocytes from MHC(+) mice. Additional stimulation with either anti-CD3 Abs or peptide-MHC ligands further elevated open-CD3 above basal levels, consistent with a model wherein antigenic engagement induces maximum PRS exposure. We also found that the open-CD3 conformation induced by APCs outlasted the time of ligand occupancy, marking receptors that had been engaged. Finally, CD3ε BRS-phosphoinositide interactions played no role in either adoption of the initial closed-CD3 conformation or induction of open-CD3 by Ab stimulation. Thus, a basal level of open-CD3 is succeeded by a higher, induced level upon TCR-CD3 engagement, involving CD3Δc and prolonged accessibility of the CD3ε PRS to Nck.
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MESH Headings
- Amino Acid Motifs/immunology
- Animals
- Antigen-Presenting Cells/immunology
- Antigen-Presenting Cells/metabolism
- CD3 Complex/genetics
- CD3 Complex/immunology
- CD3 Complex/metabolism
- Cell Line, Tumor
- Epitopes, T-Lymphocyte/physiology
- Hybridomas
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Mice, Transgenic
- Peptide Fragments/genetics
- Peptide Fragments/immunology
- Peptide Fragments/metabolism
- Proline/immunology
- Proline/metabolism
- Receptor-CD3 Complex, Antigen, T-Cell/genetics
- Receptor-CD3 Complex, Antigen, T-Cell/immunology
- Receptor-CD3 Complex, Antigen, T-Cell/metabolism
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
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Affiliation(s)
- Javier de la Cruz
- Department of Immunology, College of Medicine, Mayo Clinic, Rochester, MN 55905
- Initiative to Maximize Student Diversity and Post Baccalaureate Research Education Program, College of Medicine, Mayo Clinic, Rochester, MN 55905
| | - Travis Kruger
- Department of Immunology, College of Medicine, Mayo Clinic, Rochester, MN 55905
- Summer Undergraduate Research Fellowship Program, College of Medicine, Mayo Clinic, Rochester, MN 55905
| | - Christopher A. Parks
- Department of Immunology, College of Medicine, Mayo Clinic, Rochester, MN 55905
- Summer Undergraduate Research Fellowship Program, College of Medicine, Mayo Clinic, Rochester, MN 55905
| | - Robert L. Silge
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Nicolai S. C. van Oers
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Immanuel F. Luescher
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne, 1066 Epalinges, Switzerland
| | - Adam G. Schrum
- Department of Immunology, College of Medicine, Mayo Clinic, Rochester, MN 55905
| | - Diana Gil
- Department of Immunology, College of Medicine, Mayo Clinic, Rochester, MN 55905
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33
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Jansson A. A mathematical framework for analyzing T cell receptor scanning of peptides. Biophys J 2011; 99:2717-25. [PMID: 21044568 DOI: 10.1016/j.bpj.2010.08.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Revised: 08/09/2010] [Accepted: 08/16/2010] [Indexed: 10/18/2022] Open
Abstract
T cells continuously search for antigenic peptides presented on major histocompatibility complexes expressed on nearly all nucleated cells. Because only a few antigenic peptides are presented in a sea of thousands of self-peptides, the T cells have a critical task in discriminating between self- and nonself-peptides. This search process for antigens must be performed with sufficient speed in order to induce a fast response against invading pathogens. This study presents a mathematical framework for analyzing the scanning process of peptides. The framework includes analytic expressions for calculating the sampling rate as well as continuous-systems- and stochastic-agent-based models. The results show that the scanning of self-peptides is a very fast process due to fast off-rates. The simulations also predict the existence of an optimal sampling rate for a certain range of on-rates based on the recently proposed confinement time model. Calculations reveal that most of the self-peptides located within a microdomain are scanned within just a few seconds, and that the T cell receptors have kinetics for self-peptides, facilitating fast scanning. The derived mathematical expressions within this study provide conceptual calculations for further investigations of how the T cell discriminates between self- and nonself-peptides.
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Affiliation(s)
- Andreas Jansson
- Infofusion, Systems Biology Research Centre, School of Life Sciences, University of Skövde, Skövde, Sweden.
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34
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Jansson A. Kinetic proofreading and the search for nonself-peptides. SELF NONSELF 2011; 2:1-3. [PMID: 21776328 DOI: 10.4161/self.2.1.15362] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Revised: 03/03/2011] [Accepted: 03/03/2011] [Indexed: 11/19/2022]
Abstract
The T cells scan the surface of antigen-presenting cells with their T cell receptors (TCR) in order to find and respond to specific peptide-major histocompatibility complexes (pMHC). Since mainly self-peptides are expressed on antigen-presenting cells, the T cells must utilize sensitive mechanisms in order to quickly discriminate between self and nonself-peptides. A range of different models have been proposed to account for this process. Due to the experimental inconsistency of how T cells respond to altered peptides it has been difficult to validate the competing models. Recent models, based on the kinetic proofreading model, propose that a short life-time of the TCR/pMHC complexes may be compensated by fast rebinding of the individual molecules. Hence, both the on- and off-rate involved in the interaction between pMHCs and TCRs will determine the fate of the T cell discrimination. I here briefly review some of the proposed models on T cell discrimination and scanning, and discuss the significance of determining self-peptide kinetics to validate the different models.
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Affiliation(s)
- Andreas Jansson
- Systems Biology Research Centre; School of Life Sciences; University of Skövde; Skövde, Sweden
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35
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Strome M, Lott DG. Anti-αβ-T-cell receptor antibodies in the setting of laryngeal transplantation. Immunotherapy 2010; 2:835-45. [PMID: 21091115 DOI: 10.2217/imt.10.72] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Inhibiting T-cell activation is critically important to the induction of transplantation tolerance. Monoclonal antibodies directed against the αβ-T-cell receptor have been shown to cause selective immunodepletion of this T-cell population and can provide long-term allograft acceptance. This article discusses the role of this promising immunosuppressive agent in scientific research and clinical utilization. Specifically, the article focuses on its efficacy and mechanism of tolerance induction in solid tissue and composite tissue allograft transplantation with a particular focus on laryngeal transplantation.
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36
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Choudhuri K, Dustin ML. Signaling microdomains in T cells. FEBS Lett 2010; 584:4823-31. [PMID: 20965175 DOI: 10.1016/j.febslet.2010.10.015] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2010] [Revised: 10/12/2010] [Accepted: 10/13/2010] [Indexed: 01/22/2023]
Abstract
Sub-micron scale signaling domains induced in the plasma membrane of cells are thought to play important roles in signal transduction. In T cells, agonist MHC-peptide complexes induce small diffraction-limited domains enriched in T cell receptor (TCR) and signaling molecules. These microclusters serve as transient platforms for signal initiation and are required for sustained signaling in T cells, although each microcluster functions for only a couple of minutes. How they are formed, and what mechanisms promote and regulate signaling within TCR microclusters is largely unknown, although it is clear that TCR engagement and dynamic reorganization of cortical actin are involved. Here, we review current understanding of signaling within microclusters in T cells, and speculate on how these structures may form, initiate biochemical signals, and serve as sites of both signal integration and amplification, while also facilitating appropriate termination of TCR and related signaling.
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Affiliation(s)
- Kaushik Choudhuri
- Helen L and Martin S Kimmel Center for Biology and Medicine of the Skirball Institute of Biomolecular Medicine, New York, NY 10016, USA
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37
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Valitutti S, Coombs D, Dupré L. The space and time frames of T cell activation at the immunological synapse. FEBS Lett 2010; 584:4851-7. [PMID: 20940018 DOI: 10.1016/j.febslet.2010.10.010] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2010] [Revised: 10/06/2010] [Accepted: 10/06/2010] [Indexed: 01/17/2023]
Abstract
The selective recognition of antigenic peptides by T cells requires the spatio/temporal integration of a panoply of molecular triggers. The space frame of T cell antigen receptors (TCR) interaction with peptide/MHC complexes (pMHC) displayed by antigen presenting cells is delineated by the micrometer-scale area of the immunological synapse. The time frame of T cell stimulation is governed by a series of short TCR-pMHC interactions that are integrated into sustained signaling leading to productive activation. We discuss here how approaching antigen recognition from the time and space angles is key to the comprehension of the puzzling process of T cell activation.
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Affiliation(s)
- Salvatore Valitutti
- INSERM, U563, Centre de Physiopathologie de Toulouse Purpan, Toulouse, France.
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38
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Nag A, Monine MI, Blinov ML, Goldstein B. A detailed mathematical model predicts that serial engagement of IgE-Fc epsilon RI complexes can enhance Syk activation in mast cells. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2010; 185:3268-76. [PMID: 20733205 PMCID: PMC3102320 DOI: 10.4049/jimmunol.1000326] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The term serial engagement was introduced to describe the ability of a single peptide, bound to a MHC molecule, to sequentially interact with TCRs within the contact region between a T cell and an APC. In addition to ligands on surfaces, soluble multivalent ligands can serially engage cell surface receptors with sites on the ligand, binding and dissociating from receptors many times before all ligand sites become free and the ligand leaves the surface. To evaluate the role of serial engagement in Syk activation, we use a detailed mathematical model of the initial signaling cascade that is triggered when FcepsilonRI is aggregated on mast cells by multivalent Ags. Although serial engagement is not required for mast cell signaling, it can influence the recruitment of Syk to the receptor and subsequent Syk phosphorylation. Simulating the response of mast cells to ligands that serially engage receptors at different rates shows that increasing the rate of serial engagement by increasing the rate of dissociation of the ligand-receptor bond decreases Syk phosphorylation. Increasing serial engagement by increasing the rate at which receptors are cross-linked (for example by increasing the forward rate constant for cross-linking or increasing the valence of the ligand) increases Syk phosphorylation. When serial engagement enhances Syk phosphorylation, it does so by partially reversing the effects of kinetic proofreading. Serial engagement rapidly returns receptors that have dissociated from aggregates to new aggregates before the receptors have fully returned to their basal state.
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MESH Headings
- Animals
- Binding Sites, Antibody/genetics
- Cell Line, Tumor
- Enzyme Activation/genetics
- Enzyme Activation/immunology
- Immunoglobulin E/chemistry
- Immunoglobulin E/metabolism
- Immunoglobulin E/physiology
- Immunoglobulin Fragments/chemistry
- Immunoglobulin Fragments/metabolism
- Immunoglobulin Fragments/physiology
- Intracellular Signaling Peptides and Proteins/metabolism
- Leukemia, Basophilic, Acute/enzymology
- Leukemia, Basophilic, Acute/immunology
- Ligands
- Lymphocyte Activation/genetics
- Lymphocyte Activation/immunology
- Mast Cells/enzymology
- Mast Cells/immunology
- Mast Cells/metabolism
- Models, Immunological
- Predictive Value of Tests
- Protein Transport/genetics
- Protein Transport/immunology
- Protein-Tyrosine Kinases/metabolism
- Rats
- Receptors, IgE/chemistry
- Receptors, IgE/metabolism
- Receptors, IgE/physiology
- Signal Transduction/genetics
- Signal Transduction/immunology
- Syk Kinase
- Up-Regulation/genetics
- Up-Regulation/immunology
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Affiliation(s)
- Ambarish Nag
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Michael I. Monine
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Michael L. Blinov
- Center for Cell Analysis and Modeling, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT 06032-1507
| | - Byron Goldstein
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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39
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Beemiller P, Krummel MF. Mediation of T-cell activation by actin meshworks. Cold Spring Harb Perspect Biol 2010; 2:a002444. [PMID: 20702599 DOI: 10.1101/cshperspect.a002444] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Although the actin cytoskeleton and T-cell receptor (TCR) signaling complexes are seemingly distinct molecular structures, they are tightly integrated in T cells. The signaling pathways initiated by TCRs binding to peptide MHC complexes are extensively influenced by the actin cytoskeletal activities of the motile phase before TCR signaling, the signalosome scaffolding function of the cytoskeleton, and the translocation of signaling clusters that precedes the termination of signaling at these complexes. As these three successive phases constitute essentially all the steps consequent to immune synapse formation, it has become clear that the substantial physical forces and signaling interactions generated by the actin cytoskeleton dominate the signaling life cycle of TCR signalosomes. We discuss the contributions of the actin cytoskeleton to TCR signaling phases and model some remaining questions about how specific cytoskeletal factors regulate TCR signaling outcomes.
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Affiliation(s)
- Peter Beemiller
- Department of Pathology, University of California, San Francisco, San Francisco, California 94143-0511, USA
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40
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Abstract
Higher organisms, such as humans, have an adaptive immune system that usually enables them to successfully combat diverse (and evolving) microbial pathogens. The adaptive immune system is not preprogrammed to respond to prescribed pathogens. Yet it mounts pathogen-specific responses against diverse microbes and establishes memory of past infections (the basis of vaccination). Although major advances have been made in understanding pertinent molecular and cellular phenomena, the mechanistic principles that govern many aspects of an immune response are not known. We illustrate how complementary approaches from the physical and life sciences can help confront this challenge. Specifically, we describe work that brings together statistical mechanics and cell biology to shed light on how key molecular/cellular components of the adaptive immune system are selected to enable pathogen-specific responses. We hope these examples encourage physical chemists to work at this crossroad of disciplines where fundamental discoveries with implications for human health might be made.
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Affiliation(s)
- Arup K Chakraborty
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
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41
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James SE, Greenberg PD, Jensen MC, Lin Y, Wang J, Budde LE, Till BG, Raubitschek AA, Forman SJ, Press OW. Mathematical modeling of chimeric TCR triggering predicts the magnitude of target lysis and its impairment by TCR downmodulation. THE JOURNAL OF IMMUNOLOGY 2010; 184:4284-94. [PMID: 20220093 DOI: 10.4049/jimmunol.0903701] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
We investigated relationships among chimeric TCR (cTCR) expression density, target Ag density, and cTCR triggering to predict lysis of target cells by cTCR(+) CD8(+) T human cells as a function of Ag density. Triggering of cTCR and canonical TCR by Ag could be quantified by the same mathematical equation, but cTCR represented a special case in which serial triggering was abrogated. The magnitude of target lysis could be predicted as a function of cTCR triggering, and the predicted minimum cTCR density required for maximal target lysis by CD20-specific cTCR was experimentally tested. cTCR density below approximately 20,000 cTCR/cell impaired target lysis, but increasing cTCR expression above this density did not improve target lysis or Ag sensitivity. cTCR downmodulation to densities below this critical minimum by interaction with Ag-expressing targets limited the sequential lysis of targets in a manner that could be predicted based on the number of cTCRs remaining. In contrast, acute inhibition of lysis of primary, intended targets (e.g., leukemic B cells) due to the presence of an excess of secondary targets (e.g., normal B cells) was dependent on the Ag density of the secondary target but occurred at Ag densities insufficient to promote significant cTCR downmodulation, suggesting a role for functional exhaustion rather than insufficient cTCR density. This suggests increasing cTCR density above a critical threshold may enhance sequential lysis of intended targets in isolation, but will not overcome the functional exhaustion of cTCR(+) T cells encountered in the presence of secondary targets with high Ag density.
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Affiliation(s)
- Scott E James
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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42
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Carreño LJ, Riquelme EM, González PA, Espagnolle N, Riedel CA, Valitutti S, Kalergis AM. T-cell antagonism by short half-life pMHC ligands can be mediated by an efficient trapping of T-cell polarization toward the APC. Proc Natl Acad Sci U S A 2010; 107:210-5. [PMID: 20075022 PMCID: PMC2806700 DOI: 10.1073/pnas.0911258107] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
T-cell activation results from productive T-cell receptor (TCR) engagement by a cognate peptide-MHC (pMHC) complex on the antigen presenting cell (APC) surface, a process leading to the polarization of the T-cell secretory machinery toward the APC interface. We have previously shown that the half-life of the TCR/pMHC interaction and the density of pMHC on the APC are two parameters determining T-cell activation. However, whether the half-life of the TCR/pMHC interaction can modulate the efficiency of T-cell secretory machinery polarization toward an APC still remains unclear. Here, by using altered peptide ligands conferring different half-lives to the TCR/pMHC interaction, we have tested how this parameter can control T-cell polarization. We observed that only TCR/pMHC interactions with intermediate half-lives can promote the assembly of synapses that lead to T-cell activation. Strikingly, intermediate half-life interactions can be competed out by short half-life interactions, which can efficiently promote T-cell polarization and antagonize T-cell activation that was induced by activating intermediate half-life interactions. However, short TCR/pMHC interactions fail at promoting phosphorylation of signaling molecules at the T-cell-APC contact interface, which are needed for T-cell activation. Our data suggest that although intermediate half-life pMHC ligands promote assembly of activating synapses, this process can be inhibited by short half-life antagonistic pMHC ligands, which promote the assembly of non activating synapses.
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Affiliation(s)
- Leandro J. Carreño
- Millennium Nucleus on Immunology and Immunotherapy, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331010, Chile
| | - Erick M. Riquelme
- Millennium Nucleus on Immunology and Immunotherapy, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331010, Chile
| | - Pablo A. González
- Millennium Nucleus on Immunology and Immunotherapy, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331010, Chile
| | | | - Claudia A. Riedel
- Millennium Nucleus on Immunology and Immunotherapy, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331010, Chile
- Facultad de Ciencias Biológicas and
- Facultad de Medicina, Universidad Andrés Bello, Santiago 8370146, Chile; and
| | | | - Alexis M. Kalergis
- Millennium Nucleus on Immunology and Immunotherapy, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331010, Chile
- Facultad de Medicina. Pontificia Universidad Católica de Chile, Santiago 8331010, Chile
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43
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Chakraborty AK, Das J. Pairing computation with experimentation: a powerful coupling for understanding T cell signalling. Nat Rev Immunol 2010; 10:59-71. [DOI: 10.1038/nri2688] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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44
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Walker LJ, Sewell AK, Klenerman P. T cell sensitivity and the outcome of viral infection. Clin Exp Immunol 2009; 159:245-55. [PMID: 19968665 DOI: 10.1111/j.1365-2249.2009.04047.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The importance of CD8(+) T cells in the control of viral infections is well established. However, what differentiates CD8(+) T cell responses in individuals who control infection and those who do not is not well understood. 'Functional sensitivity' describes an important quality of the T cell response and is determined in part by the affinity of the T cell receptor for antigen. A more sensitive T cell response is generally believed to be more efficient and associated with better control of viral infection, yet may also drive viral mutation and immune escape. Various in vitro techniques have been used to measure T cell sensitivity; however, rapid ex vivo analysis of this has been made possible by the application of the 'magic' tetramer technology. Such tools have potentially important applications in the design and evaluation of vaccines.
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Affiliation(s)
- L J Walker
- Nuffield Department of Medicine and NIHR Biomedical Research Centre Programme, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
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45
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Dushek O, Das R, Coombs D. A role for rebinding in rapid and reliable T cell responses to antigen. PLoS Comput Biol 2009; 5:e1000578. [PMID: 19956745 PMCID: PMC2775163 DOI: 10.1371/journal.pcbi.1000578] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2009] [Accepted: 10/23/2009] [Indexed: 01/13/2023] Open
Abstract
Experimental work has shown that T cells of the immune system rapidly and specifically respond to antigenic molecules presented on the surface of antigen-presenting-cells and are able to discriminate between potential stimuli based on the kinetic parameters of the T cell receptor-antigen bond. These antigenic molecules are presented among thousands of chemically similar endogenous peptides, raising the question of how T cells can reliably make a decision to respond to certain antigens but not others within minutes of encountering an antigen presenting cell. In this theoretical study, we investigate the role of localized rebinding between a T cell receptor and an antigen. We show that by allowing the signaling state of individual receptors to persist during brief unbinding events, T cells are able to discriminate antigens based on both their unbinding and rebinding rates. We demonstrate that T cell receptor coreceptors, but not receptor clustering, are important in promoting localized rebinding, and show that requiring rebinding for productive signaling reduces signals from a high concentration of endogenous pMHC. In developing our main results, we use a relatively simple model based on kinetic proofreading. However, we additionally show that all our results are recapitulated when we use a detailed T cell receptor signaling model. We discuss our results in the context of existing models and recent experimental work and propose new experiments to test our findings.
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Affiliation(s)
- Omer Dushek
- Department of Mathematics, University of British Columbia, Vancouver, British Columbia, Canada
- Institute of Applied Mathematics, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
| | - Raibatak Das
- Department of Mathematics, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Daniel Coombs
- Department of Mathematics, University of British Columbia, Vancouver, British Columbia, Canada
- Institute of Applied Mathematics, University of British Columbia, Vancouver, British Columbia, Canada
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46
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Penaloza-MacMaster P, Masopust D, Ahmed R. T-cell reconstitution without T-cell immunopathology in two models of T-cell-mediated tissue destruction. Immunology 2009; 128:164-71. [PMID: 19740373 PMCID: PMC2767306 DOI: 10.1111/j.1365-2567.2009.03080.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2008] [Revised: 01/21/2009] [Accepted: 02/04/2009] [Indexed: 11/30/2022] Open
Abstract
Antigen-specific T cells play a pivotal role in adaptive immune responses. However, they also contribute to the progression of a variety of diseases including autoimmune disorders, graft rejection and graft-versus-host disease (GVHD). Non-specific immune-ablation treatments compromise the ability of the host to respond to infection, whereas the selective removal of epitope-specific T cells could theoretically ameliorate T-cell-mediated pathology while preserving the rest of the host immune function. In this study we investigated whether it is possible to destroy specific unwanted antigen-specific T cells by incubating polyclonal T-cell populations with major histocompatibility complex (MHC) tetramers that are conjugated to the ribosomal-inactivating toxin, saporin. This strategy resulted in a dramatic reduction in the number of targeted antigen (Ag)-specific CD8 T cells with no observable bystander toxicity in vitro. Moreover, in a model of transferable T-cell-dependent neurological disease induced by intracerebral (i.c.) lymphocytic choriomeningitis virus (LCMV) infection, the targeted killing of LCMV-specific CD8 T cells extended the survival of mice or fully prevented their death, depending on the dose of cells transferred. In addition, the tetramer- saporin conjugate also reduced liver damage in a model of donor T-cell-mediated hepatic destruction. These data provide a proof of principle that MHC tetramers could be exploited for the elimination or clinical manipulation of T-cell responses by linking effector molecules (a toxin in this case) to MHC tetramers. Also, the results suggest that it may be feasible to remodel T-cell responses, especially in immunocompromised hosts who receive adoptive cell transfers with many potential alloreactive cells.
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Affiliation(s)
- Pablo Penaloza-MacMaster
- Emory Vaccine Center and Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA.
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47
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Riquelme E, Carreño LJ, González PA, Kalergis AM. The duration of TCR/pMHC interactions regulates CTL effector function and tumor-killing capacity. Eur J Immunol 2009; 39:2259-69. [PMID: 19637198 DOI: 10.1002/eji.200939341] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Effector CTL contribute to tumoral immunity by killing tumor cells through secretion of cytotoxic granules and cytokines. Activation of CTL requires specific recognition of cognate peptide-MHC-I (pMHC) complexes on the tumor cell surface by the CTL TCR. It has been suggested that the half-life (t(1/2)) of the TCR/pMHC interaction modulates the activation of naïve CD8(+) T cells; however, it remains unknown whether CTL effector function can also be regulated by the TCR/pMHC t(1/2). Here, we have studied CTL activity in response to tumor cells loaded with pMHC that bind the TCR with different t(1/2). We observed that the TCR/pMHC t(1/2) can differentially regulate CTL effector function during the interaction with tumor cells and defines the nature of anti-tumoral CTL responses in vivo. Although prolonged TCR/pMHC t(1/2) promoted only partial expression of cytotoxic molecules, short t(1/2) induced partial polarization of lytic machinery toward target cells. In contrast, intermediate TCR/pMHC t(1/2) induced strong expression of cytotoxic molecules, efficient polarization of lytic machinery and subsequent release of toxic granules by CTL that killed tumor cells. Consistently, efficient in vivo CTL-mediated tumor clearance was only observed for tumors expressing intermediate t(1/2) pMHC ligands. These data suggest that there is an optimal TCR/pMHC t(1/2) for efficient CTL activity.
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MESH Headings
- Animals
- CD4-Positive T-Lymphocytes/cytology
- CD4-Positive T-Lymphocytes/immunology
- CD4-Positive T-Lymphocytes/metabolism
- CD8-Positive T-Lymphocytes/cytology
- CD8-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/metabolism
- Cell Line, Tumor
- Coculture Techniques
- Cytotoxicity, Immunologic/immunology
- Flow Cytometry
- Histocompatibility Antigens Class I/metabolism
- Immunotherapy, Adoptive
- Interferon-gamma/metabolism
- Lymphocyte Activation/immunology
- Lysosomal Membrane Proteins/immunology
- Lysosomal Membrane Proteins/metabolism
- Melanoma, Experimental/immunology
- Melanoma, Experimental/pathology
- Melanoma, Experimental/therapy
- Mice
- Mice, Inbred C57BL
- Mice, Transgenic
- Protein Binding
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/metabolism
- T-Lymphocytes, Cytotoxic/cytology
- T-Lymphocytes, Cytotoxic/immunology
- T-Lymphocytes, Cytotoxic/metabolism
- Time Factors
- Tumor Burden/immunology
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Affiliation(s)
- Erick Riquelme
- Millennium Nucleus on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
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48
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Goldstein B, Coombs D, Faeder JR, Hlavacek WS. Kinetic proofreading model. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2008; 640:82-94. [PMID: 19065786 DOI: 10.1007/978-0-387-09789-3_8] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Kinetic proofreading is an intrinsic property of the cell signaling process. It arises as a consequence of the multiple interactions that occur after a ligand triggers a receptor to initiate a ignaling cascade and it ensures that false signals do not propagate to completion. In order for an active signaling complex to form after a ligand binds to a cell surface receptor, a sequence of binding and phosphorylation events must occur that are rapidly reversed if the ligand dissociates from the receptor. This gives rise to a mechanism by which cells can discriminate among ligands that bind to the same receptor but form ligand-receptor complexes with different lifetimes. We review experiments designed to test for kinetic proofreading and models that exhibit kinetic proofreading.
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Affiliation(s)
- Byron Goldstein
- Theoretical Biology and Biophysics Group, T-10 MS K710, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 875435, USA.
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49
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Rudd BD, Brien JD, Davenport MP, Nikolich-Zugich J. Cutting edge: TLR ligands increase TCR triggering by slowing peptide-MHC class I decay rates. THE JOURNAL OF IMMUNOLOGY 2008; 181:5199-203. [PMID: 18832671 DOI: 10.4049/jimmunol.181.8.5199] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
TLR ligands are among the key stimuli driving the optimal dendritic cell (DC) maturation critical for strong and efficacious T cell priming. In this study, we show that part of this effect occurs via increased TCR triggering. Pretreatment of DCs with TLR ligands resulted in the triggering of many more TCRs in responding CD8(+) T cells. Importantly, even when DCs expressed the same amount of cognate peptide-MHC (pMHC) molecules, TLR ligand treatment resulted in down-regulation of larger numbers of TCR molecules. This was independent of the up-regulation of costimulatory, adhesion or cytokine molecules or the amount of noncognate pMHCs. Rather, DCs pretreated with TLR ligands exhibited increased stability of cognate pMHCs, enabling extended TCR triggering. These findings are of potential importance to T cell vaccination.
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Affiliation(s)
- Brian D Rudd
- Department of Immunobiology and the Arizona Center on Aging, University of Arizona College of Medicine, Tucson, AZ 85718, USA
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50
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Zint N, Baake E, den Hollander F. How T-cells use large deviations to recognize foreign antigens. J Math Biol 2008; 57:841-61. [DOI: 10.1007/s00285-008-0191-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2006] [Revised: 01/28/2008] [Indexed: 11/24/2022]
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