Systems approach to the analysis of T cell receptor signal transduction
Lead Research Organisation:
University of Oxford
Department Name: Sir William Dunn Sch of Pathology
Abstract
T cells are white blood cells that continuously patrol the body in search of evidence of infection or cancer. Recognition by T cells occurs when receptors on the T cell surface directly bind to fragments or 'antigens' derived from infectious organisms or cancer cells. This recognition is particularly important because T cells, in addition to themselves killing infected or cancerous cells, also coordinate and control other elements of the immune response that are required to remove these threats. T cell antigen recognition is the key to understanding appropriate and helpful immune responses to dangerous antigens (e.g. from harmful bacteria) as well as inappropriate, unhelpful responses to innocuous or self-antigens, which results in allergic and autoimmune diseases, respectively. Although the T cell antigen receptor (TCR) is clearly very important it is still unclear how binding of the TCR to antigen leads to the activation of the T cell and how the TCR detects the rare dangerous antigens amongst the far more numerous harmless antigens. This study aims to address these questions using a systems medicine based approach combining mathematical modelling and range of experimental techniques. An improved understanding of T cell antigen recognition will enhance our ability to manipulate the immune response in order to improve vaccines, treat autoimmune and allergic diseases, and prevent rejection of organ transplants.
Technical Summary
Antigen recognition by T cells is mediated by the multisubunit T cell antigen receptor (TCR) complex. Extensive research into signal transduction through the TCR has highlighted the complexity of this receptor. Subunits in the TCR complex involved in signal transduction contain 10 immuno-tyrosine based activation motifs (ITAMs), which are sequentially phosphorylated by the kinase Lck and dephosphorylated by phosphatases such as CD45. Phosphorylated ITAMs serve as docking sites for the cytosolic kinase ZAP-70, which has been shown to bind these ITAMs with differing affinities. Despite this extensive research, the purpose of multiple ITAMs, their sequential phosphorylation by Lck, and the differential affinity of ZAP-70 are unknown.
The aim of this project is to use a detailed systems medicine approach to integrate these known TCR properties into a mathematical model. Predictions from the model will be tested experimentally and the model will subsequently be revised. A preliminary mathematical model that includes these TCR properties has suggested that the combination of these features (e.g. ITAM multiplicity, sequential phosphorylation, and differential ZAP-70 affinity) may be important for conferring sensitivity and discriminatory ability to the process of antigen recognition. In order to test these predictions, the TCR ITAMs will be systematically mutated and rearranged, and proximal and distal readouts of TCR signal transduction analysed. Based on these experiments, the mathematical model will be revised and calibrated so that it can be used to make further predictions. In addition, we will investigate the role of basic-residue-rich motifs that have been recently implicated in controlling ITAM phosphorylation in the underlying mechanism of sequential ITAM phosphorylation.
Collectively, this combined mathematical and experimental work will enhance our understanding of the mechanisms and properties of T cell antigen recognition.
The aim of this project is to use a detailed systems medicine approach to integrate these known TCR properties into a mathematical model. Predictions from the model will be tested experimentally and the model will subsequently be revised. A preliminary mathematical model that includes these TCR properties has suggested that the combination of these features (e.g. ITAM multiplicity, sequential phosphorylation, and differential ZAP-70 affinity) may be important for conferring sensitivity and discriminatory ability to the process of antigen recognition. In order to test these predictions, the TCR ITAMs will be systematically mutated and rearranged, and proximal and distal readouts of TCR signal transduction analysed. Based on these experiments, the mathematical model will be revised and calibrated so that it can be used to make further predictions. In addition, we will investigate the role of basic-residue-rich motifs that have been recently implicated in controlling ITAM phosphorylation in the underlying mechanism of sequential ITAM phosphorylation.
Collectively, this combined mathematical and experimental work will enhance our understanding of the mechanisms and properties of T cell antigen recognition.
Planned Impact
Our proposed research utilizes a systems medicine approach to relate molecular events proximal to the T cell receptor to the expected cellular response. We expect that our experimentally validated systems model will benefit translational research in both academia and industry.
Specialized impact. There are many scientists around the world who study the T cell receptor in the hope that a deeper understanding antigen induced TCR signalling can be exploited for the benefit of human health. We expect that these scientists will directly benefit from our work as it will provide a unifying quantitative framework for understanding multiple events associated with antigen induced TCR signalling.
Interdisciplinary impact. There are a growing number of projects aimed at translational research. In particular, a number of researchers are attempting to modulate immune responses by adoptively transferring modified T cells into animal models of various diseases. These modified T cells often have a chimeric antigen receptor (CAR), which contains engineered signalling chains to increase the potency of the receptor. A key output from the proposed project will be a calibrated mathematical model which can be used for in silico predictions of various T cell receptor and chimeric antigen receptor modifications. For example, the mathematical model has uncovered mechanisms by which the potency of the receptor can be enhanced and this information, once confirmed in experiments, can be used to generate novel therapies. We expect that this basic research leg work will set the stage for testing in animal models and will inform on the rational design of translational research projects.
Public impact. Many companies around the world are focused on developing novel immune based therapies to treat cancers, viral infections, autoimmune diseases, and allergies. The United Kingdom is home to world-leading companies in T cell receptor based immunotherapy, such as Immunocore and Adaptimmune. A collaboration has been initiated with these companies so that their reagents will facilitate our research and our findings and mathematical model can inform their own work. In this way, the company can maintain their competitive edge and potentially increase the rate at which such therapies enter the public domain.
Training. This project involves both experimental and mathematical components and will bring together scientists with diverse backgrounds. A specific goal of the project is to train experimentalists to use mathematical modeling and data fitting, which are tools essential for modern biomedical research. The applicants will run a workshop detailing the procedure of data analysis and fitting for biomedical scientists that will be open to all researchers.
Specialized impact. There are many scientists around the world who study the T cell receptor in the hope that a deeper understanding antigen induced TCR signalling can be exploited for the benefit of human health. We expect that these scientists will directly benefit from our work as it will provide a unifying quantitative framework for understanding multiple events associated with antigen induced TCR signalling.
Interdisciplinary impact. There are a growing number of projects aimed at translational research. In particular, a number of researchers are attempting to modulate immune responses by adoptively transferring modified T cells into animal models of various diseases. These modified T cells often have a chimeric antigen receptor (CAR), which contains engineered signalling chains to increase the potency of the receptor. A key output from the proposed project will be a calibrated mathematical model which can be used for in silico predictions of various T cell receptor and chimeric antigen receptor modifications. For example, the mathematical model has uncovered mechanisms by which the potency of the receptor can be enhanced and this information, once confirmed in experiments, can be used to generate novel therapies. We expect that this basic research leg work will set the stage for testing in animal models and will inform on the rational design of translational research projects.
Public impact. Many companies around the world are focused on developing novel immune based therapies to treat cancers, viral infections, autoimmune diseases, and allergies. The United Kingdom is home to world-leading companies in T cell receptor based immunotherapy, such as Immunocore and Adaptimmune. A collaboration has been initiated with these companies so that their reagents will facilitate our research and our findings and mathematical model can inform their own work. In this way, the company can maintain their competitive edge and potentially increase the rate at which such therapies enter the public domain.
Training. This project involves both experimental and mathematical components and will bring together scientists with diverse backgrounds. A specific goal of the project is to train experimentalists to use mathematical modeling and data fitting, which are tools essential for modern biomedical research. The applicants will run a workshop detailing the procedure of data analysis and fitting for biomedical scientists that will be open to all researchers.
Publications
Banerji S
(2016)
Homodimerization of the Lymph Vessel Endothelial Receptor LYVE-1 through a Redox-labile Disulfide Is Critical for Hyaluronan Binding in Lymphatic Endothelium.
in The Journal of biological chemistry
Brodovitch A
(2015)
T lymphocytes need less than 3 min to discriminate between peptide MHCs with similar TCR-binding parameters.
in European journal of immunology
Dushek O
(2012)
Non-catalytic tyrosine-phosphorylated receptors.
in Immunological reviews
Dushek O
(2014)
An induced rebinding model of antigen discrimination.
in Trends in immunology
Goyette J
(2022)
Dephosphorylation accelerates the dissociation of ZAP70 from the T cell receptor.
in Proceedings of the National Academy of Sciences of the United States of America
Illingworth J
(2012)
Dissecting T-cell activation with high-resolution live-cell microscopy
in Immunology
Knapp B
(2019)
MHC binding affects the dynamics of different T-cell receptors in different ways.
in PLoS computational biology
Knapp B
(2018)
pyHVis3D: visualising molecular simulation deduced H-bond networks in 3D: application to T-cell receptor interactions.
in Bioinformatics (Oxford, England)
Lever M
(2014)
Phenotypic models of T cell activation.
in Nature reviews. Immunology
Lever M
(2016)
Architecture of a minimal signaling pathway explains the T-cell response to a 1 million-fold variation in antigen affinity and dose.
in Proceedings of the National Academy of Sciences of the United States of America
Limozin L
(2019)
TCR-pMHC kinetics under force in a cell-free system show no intrinsic catch bond, but a minimal encounter duration before binding.
in Proceedings of the National Academy of Sciences of the United States of America
Mukhopadhyay H
(2016)
Multisite Phosphorylation Modulates the T Cell Receptor ?-Chain Potency but not the Switchlike Response.
in Biophysical journal
Mukhopadhyay H
(2013)
Systems model of T cell receptor proximal signaling reveals emergent ultrasensitivity.
in PLoS computational biology
Robert P
(2021)
CD8 Co-Receptor Enhances T-Cell Activation without Any Effect on Initial Attachment.
in Cells
Stewart-Jones GB
(2012)
Structural features underlying T-cell receptor sensitivity to concealed MHC class I micropolymorphisms.
in Proceedings of the National Academy of Sciences of the United States of America
Van Der Merwe PA
(2012)
Why do some T cell receptor cytoplasmic domains associate with the plasma membrane?
in Frontiers in immunology
Zhang H
(2016)
The contribution of major histocompatibility complex contacts to the affinity and kinetics of T cell receptor binding.
in Scientific reports
Title | Surface plasmon resonance facility |
Description | We have established a Facility for studying molecular interactions using surface plasmon resonance. |
Type Of Material | Improvements to research infrastructure |
Provided To Others? | Yes |
Impact | Many publications have resulted from data obtained using this facility |
Description | Measuring the 2D binding and mechanical properties of TCR/pMHC interaction |
Organisation | National Institute of Health and Medical Research (INSERM) |
Department | U600 |
Country | France |
Sector | Public |
PI Contribution | We initiated the projects, provided reagents, and designed experiments, which were performed in their laboratory using their bead flow system |
Collaborator Contribution | They provided the equipment and specific expertise |
Impact | Publication in press Philippe Robert et al (2011) |
Start Year | 2007 |
Description | Systems biology of T cel antigen recognition |
Organisation | Immunocore Ltd |
Country | United Kingdom |
Sector | Private |
PI Contribution | We have generated a range of pMHC variant for the 1G4 and related TCRs and characterised the binding properties by SPR. We are now studying the functional effects of these pMHC on T cell. |
Collaborator Contribution | They have contribute reagents and expertise with respect to transducing high affinity TCRs into lymphocytes. |
Impact | Non yet |
Start Year | 2011 |
Description | High School visit |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Type Of Presentation | Keynote/Invited Speaker |
Geographic Reach | Local |
Primary Audience | Schools |
Results and Impact | ~100 sixth form children attended the talk which was followed by a substantial discussion Contact with school continues. I advice the sixth form students on special project that they all do if they wish to work in my area. |
Year(s) Of Engagement Activity | 2012 |