1
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Brunnberg J, Barends M, Frühschulz S, Winter C, Battin C, de Wet B, Cole DK, Steinberger P, Tampé R. Dual role of the peptide-loading complex as proofreader and limiter of MHC-I presentation. Proc Natl Acad Sci U S A 2024; 121:e2321600121. [PMID: 38771881 PMCID: PMC11145271 DOI: 10.1073/pnas.2321600121] [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: 12/08/2023] [Accepted: 04/17/2024] [Indexed: 05/23/2024] Open
Abstract
Antigen presentation via major histocompatibility complex class I (MHC-I) molecules is essential for surveillance by the adaptive immune system. Central to this process is the peptide-loading complex (PLC), which translocates peptides from the cytosol to the endoplasmic reticulum and catalyzes peptide loading and proofreading of peptide-MHC-I (pMHC-I) complexes. Despite its importance, the impact of individual PLC components on the presented pMHC-I complexes is still insufficiently understood. Here, we used stoichiometrically defined antibody-nanobody complexes and engineered soluble T cell receptors (sTCRs) to quantify different MHC-I allomorphs and defined pMHC-I complexes, respectively. Thereby, we uncovered distinct effects of individual PLC components on the pMHC-I surface pool. Knockouts of components of the PLC editing modules, namely tapasin, ERp57, or calreticulin, changed the MHC-I surface composition to a reduced proportion of HLA-A*02:01 presentation compensated by a higher ratio of HLA-B*40:01 molecules. Intriguingly, these knockouts not only increased the presentation of suboptimally loaded HLA-A*02:01 complexes but also elevated the presentation of high-affinity peptides overexpressed in the cytosol. Our findings suggest that the components of the PLC editing module serve a dual role, acting not only as peptide proofreaders but also as limiters for abundant peptides. This dual function ensures the presentation of a broad spectrum of antigenic peptides.
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Affiliation(s)
- Jamina Brunnberg
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt am Main60438, Germany
| | - Martina Barends
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt am Main60438, Germany
| | - Stefan Frühschulz
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt am Main60438, Germany
| | - Christian Winter
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt am Main60438, Germany
| | - Claire Battin
- Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna1090, Austria
| | - Ben de Wet
- Immunocore Ltd., AbingdonOX14 4RY, United Kingdom
| | | | - Peter Steinberger
- Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna1090, Austria
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt am Main60438, Germany
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2
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Zhang M, Xu W, Luo L, Guan F, Wang X, Zhu P, Zhang J, Zhou X, Wang F, Ye S. Identification and affinity enhancement of T-cell receptor targeting a KRAS G12V cancer neoantigen. Commun Biol 2024; 7:512. [PMID: 38684865 PMCID: PMC11058820 DOI: 10.1038/s42003-024-06209-2] [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: 10/31/2023] [Accepted: 04/17/2024] [Indexed: 05/02/2024] Open
Abstract
Neoantigens derived from somatic mutations in Kirsten Rat Sarcoma Viral Oncogene Homolog (KRAS), the most frequently mutated oncogene, represent promising targets for cancer immunotherapy. Recent research highlights the potential role of human leukocyte antigen (HLA) allele A*11:01 in presenting these altered KRAS variants to the immune system. In this study, we successfully generate and identify murine T-cell receptors (TCRs) that specifically recognize KRAS8-16G12V from three predicted high affinity peptides. By determining the structure of the tumor-specific 4TCR2 bound to KRASG12V-HLA-A*11:01, we conduct structure-based design to create and evaluate TCR variants with markedly enhanced affinity, up to 15.8-fold. This high-affinity TCR mutant, which involved only two amino acid substitutions, display minimal conformational alterations while maintaining a high degree of specificity for the KRASG12V peptide. Our research unveils the molecular mechanisms governing TCR recognition towards KRASG12V neoantigen and yields a range of affinity-enhanced TCR mutants with significant potential for immunotherapy strategies targeting tumors harboring the KRASG12V mutation.
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Affiliation(s)
- Mengyu Zhang
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, 92 Weijin Road, Nankai District, Tianjin, 300072, China
| | - Wei Xu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- Department of Savaid Medical School, University of Chinese Academy of Sciences (CAS), Beijing, 100049, China
| | - Lingjie Luo
- School of Medicine, Shanghai University, Shanghai, 200444, China
| | - Fenghui Guan
- The Cancer Hospital of the University of Chinese Academy of Sciences, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Xiangyao Wang
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, 92 Weijin Road, Nankai District, Tianjin, 300072, China
| | - Pei Zhu
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, 92 Weijin Road, Nankai District, Tianjin, 300072, China
| | - Jianhua Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- Department of Savaid Medical School, University of Chinese Academy of Sciences (CAS), Beijing, 100049, China
| | - Xuyu Zhou
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, 100101, China.
- Department of Savaid Medical School, University of Chinese Academy of Sciences (CAS), Beijing, 100049, China.
| | - Feng Wang
- State Key Laboratory of Oncogenes and Related Genes, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Sheng Ye
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, 92 Weijin Road, Nankai District, Tianjin, 300072, China.
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3
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Therapeutic high affinity T cell receptor targeting a KRASG12D cancer neoantigen. Nat Commun 2022; 13:5333. [PMID: 36088370 PMCID: PMC9464187 DOI: 10.1038/s41467-022-32811-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 08/16/2022] [Indexed: 11/09/2022] Open
Abstract
Neoantigens derived from somatic mutations are specific to cancer cells and are ideal targets for cancer immunotherapy. KRAS is the most frequently mutated oncogene and drives the pathogenesis of several cancers. Here we show the identification and development of an affinity-enhanced T cell receptor (TCR) that recognizes a peptide derived from the most common KRAS mutant, KRASG12D, presented in the context of HLA-A*11:01. The affinity of the engineered TCR is increased by over one million-fold yet fully able to distinguish KRASG12D over KRASWT. While crystal structures reveal few discernible differences in TCR interactions with KRASWT versus KRASG12D, thermodynamic analysis and molecular dynamics simulations reveal that TCR specificity is driven by differences in indirect electrostatic interactions. The affinity enhanced TCR, fused to a humanized anti-CD3 scFv, enables selective killing of cancer cells expressing KRASG12D. Our work thus reveals a molecular mechanism that drives TCR selectivity and describes a soluble bispecific molecule with therapeutic potential against cancers harboring a common shared neoantigen. Cancers often harbor mutations in genes encoding important regulatory proteins, but therapeutic targeting of these molecules proves difficult due to their high structural similarity to their non-mutated counterpart. Here authors show the engineering of T cell engaging bispecific protein able to selectively target cancer cells with a high-frequency mutation in the KRAS oncogene.
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4
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Crean RM, Pudney CR, Cole DK, van der Kamp MW. Reliable In Silico Ranking of Engineered Therapeutic TCR Binding Affinities with MMPB/GBSA. J Chem Inf Model 2022; 62:577-590. [PMID: 35049312 PMCID: PMC9097153 DOI: 10.1021/acs.jcim.1c00765] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
Accurate
and efficient in silico ranking of protein–protein
binding affinities is useful for protein design with applications
in biological therapeutics. One popular approach to rank binding affinities
is to apply the molecular mechanics Poisson–Boltzmann/generalized
Born surface area (MMPB/GBSA) method to molecular dynamics (MD) trajectories.
Here, we identify protocols that enable the reliable evaluation of
T-cell receptor (TCR) variants binding to their target, peptide-human
leukocyte antigens (pHLAs). We suggest different protocols for variant
sets with a few (≤4) or many mutations, with entropy corrections
important for the latter. We demonstrate how potential outliers could
be identified in advance and that just 5–10 replicas of short
(4 ns) MD simulations may be sufficient for the reproducible and accurate
ranking of TCR variants. The protocols developed here can be applied
toward in silico screening during the optimization
of therapeutic TCRs, potentially reducing both the cost and time taken
for biologic development.
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Affiliation(s)
| | | | - David K. Cole
- Immunocore Ltd., Milton Park, Abingdon OX14 4RY, U.K
- Division of Infection & Immunity, Cardiff University, Cardiff CF14 4XN, U.K
| | - Marc W. van der Kamp
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, Bristol BS8 1TD, U.K
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5
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Abstract
Grouping TCRs on the similarity of CDR3 sequences could effectively cluster them by specificity. Three versions of the GLIPH algorithm are described briefly here, with instructions to use GLIPH algorithms to cluster TCRs by specificity.
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Affiliation(s)
- Chunlin Wang
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA.
| | - Huang Huang
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Mark M Davis
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- The Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
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6
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McDaid WJ, Lissin N, Pollheimer E, Greene M, Leach A, Smyth P, Bossi G, Longley D, Cole DK, Scott CJ. Enhanced target-specific delivery of docetaxel-loaded nanoparticles using engineered T cell receptors. NANOSCALE 2021; 13:15010-15020. [PMID: 34533174 PMCID: PMC8447836 DOI: 10.1039/d1nr04001d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 08/18/2021] [Indexed: 06/13/2023]
Abstract
For effective targeted therapy of cancer with chemotherapy-loaded nanoparticles (NPs), antigens that are selective for cancer cells should be targeted to minimise off-tumour toxicity. Human leukocyte antigens (HLAs) are attractive cancer targets as they can present peptides from tumour-selective proteins on the cell surface, which can be recognised by T cells via T cell receptors (TCRs). In this study, docetaxel-loaded polymeric NPs were conjugated to recombinant affinity-enhanced TCRs to target breast cancer cells presenting a tumour-selective peptide-HLA complex. The TCR-conjugated nanoparticles enabled enhanced delivery of docetaxel and induced cell death through tumour-specific peptide-HLA targeting. These in vitro data demonstrate the potential of targeting tumour-restricted peptide-HLA epitopes using high affinity TCR-conjugated nanoparticles, representing a novel treatment strategy to deliver therapeutic drugs specifically to cancer cells.
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Affiliation(s)
- William J McDaid
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK, BT9 7AE.
- Cancer Research UK Manchester Institute, Alderley Park, Congleton Rd, Alderley Edge, Macclesfield, UK, SK10 4TG
| | - Nikolai Lissin
- Immunocore Ltd, 101 Park Dr, Milton, Abingdon, United Kingdom OX14 4RY
| | - Ellen Pollheimer
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK, BT9 7AE.
| | - Michelle Greene
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK, BT9 7AE.
| | - Adam Leach
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK, BT9 7AE.
- Institute of Cancer Research, 15 Cotswold Rd, Sutton, London, SM2 5NG, UK
| | - Peter Smyth
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK, BT9 7AE.
| | - Giovanna Bossi
- Immunocore Ltd, 101 Park Dr, Milton, Abingdon, United Kingdom OX14 4RY
| | - Daniel Longley
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK, BT9 7AE.
| | - David K Cole
- Immunocore Ltd, 101 Park Dr, Milton, Abingdon, United Kingdom OX14 4RY
| | - Christopher J Scott
- The Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK, BT9 7AE.
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7
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Zhu Y, Huang C, Su M, Ge Z, Gao L, Shi Y, Wang X, Chen J. Characterization of amino acid residues of T-cell receptors interacting with HLA-A*02-restricted antigen peptides. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:495. [PMID: 33850892 PMCID: PMC8039679 DOI: 10.21037/atm-21-835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Background The present study aimed to explore residues’ properties interacting with HLA-A*02-restricted peptides on T-cell receptors (TCRs) and their effects on bond types of interaction and binding free energy. Methods We searched the crystal structures of HLA-A*02-restricted peptide-TCR complexes from the Protein Data Bank (PDB) database and subsequently collected relevant parameters. We then employed Schrodinger to analyze the bond types of interaction and Gromacs 2019 to evaluate the TCR-antigen peptide complex’s molecular dynamics simulation. Finally, we compared the changes of bond types of interaction and binding free energy before and after residue substitution to ensure consistency of the conditions before and after residue substitution. Results The main sites on the antigen peptides that formed the intermolecular interaction [hydrogen bond (HB) and pi stack] with TCRs were P4, P8, P2, and P6. The hydrophobicity of the amino acids inside or outside the disulfide bond of TCRs may be related to the intermolecular interaction and binding free energy between TCRs and peptides. Residues located outside the disulfide bond of TCR α or β chains and forming pi stack force played favorable roles in the complex intermolecular interaction and binding free energy. The residues of the TCR α or β chains that interacted with peptides were replaced by alanine (Ala) or glycine (Gly), and their intermolecular binding free energy of the complex had been improved. However, it had nothing to do with the formation of HB. Conclusions The findings of this study suggest that the hydrophobic nature of the amino acids inside or outside the disulfide bonds on the TCR may be associated with the intermolecular interaction and binding between the TCR and polypeptide. The residues located outside the TCR α or β single-chain disulfide bond and forming the pi-stack force showed a beneficial effect on the intermolecular interaction and binding of the complex. In addition, the part of the residues on the TCR α or β single chain that produced bond types of interaction with the polypeptide after being replaced by Ala or Gly, the intermolecular binding free energy of the complex was increased, regardless of whether HB was formed.
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Affiliation(s)
- Ying Zhu
- Department of Oncology, First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Changxin Huang
- Department of Oncology, Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
| | - Meng Su
- Master Class, Zhejiang Chinese Medical University, Fourth School of Clinical Medicine, Hangzhou, China
| | - Zuanmin Ge
- Master Class, Hangzhou Normal University, School of Medicine, Hangzhou, China
| | - Lanlan Gao
- Master Class, Hangzhou Normal University, School of Medicine, Hangzhou, China
| | - Yanfei Shi
- Master Class, Hangzhou Normal University, School of Medicine, Hangzhou, China
| | - Xuechun Wang
- Master Class, Zhejiang Chinese Medical University, Fourth School of Clinical Medicine, Hangzhou, China
| | - Jianfeng Chen
- Department of Proctology, Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
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8
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Holland CJ, Crean RM, Pentier JM, de Wet B, Lloyd A, Srikannathasan V, Lissin N, Lloyd KA, Blicher TH, Conroy PJ, Hock M, Pengelly RJ, Spinner TE, Cameron B, Potter EA, Jeyanthan A, Molloy PE, Sami M, Aleksic M, Liddy N, Robinson RA, Harper S, Lepore M, Pudney CR, van der Kamp MW, Rizkallah PJ, Jakobsen BK, Vuidepot A, Cole DK. Specificity of bispecific T cell receptors and antibodies targeting peptide-HLA. J Clin Invest 2021; 130:2673-2688. [PMID: 32310221 DOI: 10.1172/jci130562] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 02/11/2020] [Indexed: 01/09/2023] Open
Abstract
Tumor-associated peptide-human leukocyte antigen complexes (pHLAs) represent the largest pool of cell surface-expressed cancer-specific epitopes, making them attractive targets for cancer therapies. Soluble bispecific molecules that incorporate an anti-CD3 effector function are being developed to redirect T cells against these targets using 2 different approaches. The first achieves pHLA recognition via affinity-enhanced versions of natural TCRs (e.g., immune-mobilizing monoclonal T cell receptors against cancer [ImmTAC] molecules), whereas the second harnesses an antibody-based format (TCR-mimic antibodies). For both classes of reagent, target specificity is vital, considering the vast universe of potential pHLA molecules that can be presented on healthy cells. Here, we made use of structural, biochemical, and computational approaches to investigate the molecular rules underpinning the reactivity patterns of pHLA-targeting bispecifics. We demonstrate that affinity-enhanced TCRs engage pHLA using a comparatively broad and balanced energetic footprint, with interactions distributed over several HLA and peptide side chains. As ImmTAC molecules, these TCRs also retained a greater degree of pHLA selectivity, with less off-target activity in cellular assays. Conversely, TCR-mimic antibodies tended to exhibit binding modes focused more toward hot spots on the HLA surface and exhibited a greater degree of crossreactivity. Our findings extend our understanding of the basic principles that underpin pHLA selectivity and exemplify a number of molecular approaches that can be used to probe the specificity of pHLA-targeting molecules, aiding the development of future reagents.
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Affiliation(s)
| | - Rory M Crean
- Department of Biology and Biochemistry and.,Doctoral Training Centre in Sustainable Chemical Technologies, University of Bath, Bath, United Kingdom
| | | | - Ben de Wet
- Immunocore Ltd., Milton Park, Abingdon, United Kingdom
| | | | | | | | - Katy A Lloyd
- Immunocore Ltd., Milton Park, Abingdon, United Kingdom
| | | | - Paul J Conroy
- Immunocore Ltd., Milton Park, Abingdon, United Kingdom
| | - Miriam Hock
- Immunocore Ltd., Milton Park, Abingdon, United Kingdom
| | | | | | - Brian Cameron
- Immunocore Ltd., Milton Park, Abingdon, United Kingdom
| | | | | | | | - Malkit Sami
- Immunocore Ltd., Milton Park, Abingdon, United Kingdom
| | - Milos Aleksic
- Immunocore Ltd., Milton Park, Abingdon, United Kingdom
| | | | | | | | - Marco Lepore
- Immunocore Ltd., Milton Park, Abingdon, United Kingdom
| | | | | | - Pierre J Rizkallah
- Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
| | | | | | - David K Cole
- Immunocore Ltd., Milton Park, Abingdon, United Kingdom.,Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
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9
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Crean RM, MacLachlan BJ, Madura F, Whalley T, Rizkallah PJ, Holland CJ, McMurran C, Harper S, Godkin A, Sewell AK, Pudney CR, van der Kamp MW, Cole DK. Molecular Rules Underpinning Enhanced Affinity Binding of Human T Cell Receptors Engineered for Immunotherapy. Mol Ther Oncolytics 2020; 18:443-456. [PMID: 32913893 PMCID: PMC7452143 DOI: 10.1016/j.omto.2020.07.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 07/27/2020] [Indexed: 10/25/2022] Open
Abstract
Immuno-oncology approaches that utilize T cell receptors (TCRs) are becoming highly attractive because of their potential to target virtually all cellular proteins, including cancer-specific epitopes, via the recognition of peptide-human leukocyte antigen (pHLA) complexes presented at the cell surface. However, because natural TCRs generally recognize cancer-derived pHLAs with very weak affinities, efforts have been made to enhance their binding strength, in some cases by several million-fold. In this study, we investigated the mechanisms underpinning human TCR affinity enhancement by comparing the crystal structures of engineered enhanced affinity TCRs with those of their wild-type progenitors. Additionally, we performed molecular dynamics simulations to better understand the energetic mechanisms driving the affinity enhancements. These data demonstrate that supra-physiological binding affinities can be achieved without altering native TCR-pHLA binding modes via relatively subtle modifications to the interface contacts, often driven through the addition of buried hydrophobic residues. Individual energetic components of the TCR-pHLA interaction governing affinity enhancements were distinct and highly variable for each TCR, often resulting from additive, or knock-on, effects beyond the mutated residues. This comprehensive analysis of affinity-enhanced TCRs has important implications for the future rational design of engineered TCRs as efficacious and safe drugs for cancer treatment.
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Affiliation(s)
- Rory M. Crean
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
- Doctoral Training Centre in Sustainable Chemical Technologies, University of Bath, Bath, BA2 7AY, UK
| | | | - Florian Madura
- Division of Infection & Immunity, Cardiff University, Cardiff, CF14 4XN, UK
| | - Thomas Whalley
- Division of Infection & Immunity, Cardiff University, Cardiff, CF14 4XN, UK
| | | | | | | | | | - Andrew Godkin
- Division of Infection & Immunity, Cardiff University, Cardiff, CF14 4XN, UK
| | - Andrew K. Sewell
- Division of Infection & Immunity, Cardiff University, Cardiff, CF14 4XN, UK
| | - Christopher R. Pudney
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
- Centre for Therapeutic Innovation, University of Bath, Bath, BA2 7AY, UK
| | - Marc W. van der Kamp
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol, BS8 1TD, UK
| | - David K. Cole
- Division of Infection & Immunity, Cardiff University, Cardiff, CF14 4XN, UK
- Immunocore, Ltd., Abingdon, OX14 4RY, UK
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10
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Fischer DS, Wu Y, Schubert B, Theis FJ. Predicting antigen specificity of single T cells based on TCR CDR3 regions. Mol Syst Biol 2020; 16:e9416. [PMID: 32779888 PMCID: PMC7418512 DOI: 10.15252/msb.20199416] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 07/13/2020] [Accepted: 07/22/2020] [Indexed: 11/12/2022] Open
Abstract
It has recently become possible to simultaneously assay T-cell specificity with respect to large sets of antigens and the T-cell receptor sequence in high-throughput single-cell experiments. Leveraging this new type of data, we propose and benchmark a collection of deep learning architectures to model T-cell specificity in single cells. In agreement with previous results, we found that models that treat antigens as categorical outcome variables outperform those that model the TCR and antigen sequence jointly. Moreover, we show that variability in single-cell immune repertoire screens can be mitigated by modeling cell-specific covariates. Lastly, we demonstrate that the number of bound pMHC complexes can be predicted in a continuous fashion providing a gateway to disentangle cell-to-dextramer binding strength and receptor-to-pMHC affinity. We provide these models in the Python package TcellMatch to allow imputation of antigen specificities in single-cell RNA-seq studies on T cells without the need for MHC staining.
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Affiliation(s)
- David S Fischer
- Institute of Computational BiologyHelmholtz Zentrum MünchenNeuherbergGermany
- TUM School of Life Sciences WeihenstephanTechnical University of MunichFreisingGermany
| | - Yihan Wu
- Institute of Computational BiologyHelmholtz Zentrum MünchenNeuherbergGermany
| | - Benjamin Schubert
- Institute of Computational BiologyHelmholtz Zentrum MünchenNeuherbergGermany
- Department of MathematicsTechnical University of MunichGarching bei MünchenGermany
| | - Fabian J Theis
- Institute of Computational BiologyHelmholtz Zentrum MünchenNeuherbergGermany
- TUM School of Life Sciences WeihenstephanTechnical University of MunichFreisingGermany
- Department of MathematicsTechnical University of MunichGarching bei MünchenGermany
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11
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Coles CH, McMurran C, Lloyd A, Hock M, Hibbert L, Raman MCC, Hayes C, Lupardus P, Cole DK, Harper S. T cell receptor interactions with human leukocyte antigen govern indirect peptide selectivity for the cancer testis antigen MAGE-A4. J Biol Chem 2020; 295:11486-11494. [PMID: 32532817 PMCID: PMC7450119 DOI: 10.1074/jbc.ra120.014016] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/11/2020] [Indexed: 12/18/2022] Open
Abstract
T cell-mediated immunity is governed primarily by T cell receptor (TCR) recognition of peptide-human leukocyte antigen (pHLA) complexes and is essential for immunosurveillance and disease control. This interaction is generally stabilized by interactions between the HLA surface and TCR germline-encoded complementarity-determining region (CDR) loops 1 and 2, whereas peptide selectivity is guided by direct interactions with the TCR CDR3 loops. Here, we solved the structure of a newly identified TCR in complex with a clinically relevant peptide derived from the cancer testis antigen melanoma antigen-A4 (MAGE-A4). The TCR bound pHLA in a position shifted toward the peptide's N terminus. This enabled the TCR to achieve peptide selectivity via an indirect mechanism, whereby the TCR sensed the first residue of the peptide through HLA residue Trp-167, which acted as a tunable gateway. Amino acid substitutions at peptide position 1 predicted to alter the HLA Trp-167 side-chain conformation abrogated TCR binding, indicating that this indirect binding mechanism is essential for peptide recognition. These findings extend our understanding of the molecular rules that underpin antigen recognition by TCRs and have important implications for the development of TCR-based therapies.
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Affiliation(s)
| | | | | | | | | | | | | | | | - David K Cole
- Immunocore Ltd., Abingdon, United Kingdom .,Cardiff University School of Medicine, Cardiff, United Kingdom
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12
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Madura F, Rizkallah PJ, Legut M, Holland CJ, Fuller A, Bulek A, Schauenburg AJ, Trimby A, Hopkins JR, Wells SA, Godkin A, Miles JJ, Sami M, Li Y, Liddy N, Jakobsen BK, Loveridge EJ, Cole DK, Sewell AK. TCR-induced alteration of primary MHC peptide anchor residue. Eur J Immunol 2019; 49:1052-1066. [PMID: 31091334 PMCID: PMC6618058 DOI: 10.1002/eji.201948085] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 03/21/2019] [Accepted: 05/14/2019] [Indexed: 12/12/2022]
Abstract
The HLA-A*02:01-restricted decapeptide EAAGIGILTV, derived from melanoma antigen recognized by T-cells-1 (MART-1) protein, represents one of the best-studied tumor associated T-cell epitopes, but clinical results targeting this peptide have been disappointing. This limitation may reflect the dominance of the nonapeptide, AAGIGILTV, at the melanoma cell surface. The decapeptide and nonapeptide are presented in distinct conformations by HLA-A*02:01 and TCRs from clinically relevant T-cell clones recognize the nonapeptide poorly. Here, we studied the MEL5 TCR that potently recognizes the nonapeptide. The structure of the MEL5-HLA-A*02:01-AAGIGILTV complex revealed an induced fit mechanism of antigen recognition involving altered peptide-MHC anchoring. This "flexing" at the TCR-peptide-MHC interface to accommodate the peptide antigen explains previously observed incongruences in this well-studied system and has important implications for future therapeutic approaches. Finally, this study expands upon the mechanisms by which molecular plasticity can influence antigen recognition by T cells.
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Affiliation(s)
| | | | | | | | - Anna Fuller
- School of MedicineCardiff UniversityCardiffUK
| | - Anna Bulek
- School of MedicineCardiff UniversityCardiffUK
| | | | | | | | | | | | - John J. Miles
- School of MedicineCardiff UniversityCardiffUK
- Centre for Biodiscovery and Molecular Development of TherapeuticsAustralian Institute of Tropical Health and MedicineJames Cook UniversityCairnsQueenslandAustralia
| | | | - Yi Li
- Immunocore Ltd.AbingdonUK
| | | | | | - E. Joel Loveridge
- School of ChemistryCardiff UniversityCardiffUK
- Department of ChemistrySwansea UniversitySwanseaUK
| | - David K. Cole
- School of MedicineCardiff UniversityCardiffUK
- Immunocore Ltd.AbingdonUK
| | - Andrew K. Sewell
- School of MedicineCardiff UniversityCardiffUK
- Systems Immunity Research InstituteCardiff UniversityCardiffUK
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13
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Riley TP, Baker BM. The intersection of affinity and specificity in the development and optimization of T cell receptor based therapeutics. Semin Cell Dev Biol 2018; 84:30-41. [DOI: 10.1016/j.semcdb.2017.10.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 10/07/2017] [Accepted: 10/17/2017] [Indexed: 12/29/2022]
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14
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Crooks JE, Boughter CT, Scott LR, Adams EJ. The Hypervariable Loops of Free TCRs Sample Multiple Distinct Metastable Conformations in Solution. Front Mol Biosci 2018; 5:95. [PMID: 30483515 PMCID: PMC6243104 DOI: 10.3389/fmolb.2018.00095] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 10/22/2018] [Indexed: 01/12/2023] Open
Abstract
CD4+ and CD8+ αβ T cell antigen recognition is determined by the interaction between the TCR Complementarity Determining Region (CDR) loops and the peptide-presenting MHC complex. These T cells are known for their ability to recognize multiple pMHC complexes, and for a necessary promiscuity that is required for their selection and function in the periphery. Crystallographic studies have previously elucidated the role of structural interactions in TCR engagement, but our understanding of the dynamic process that occurs during TCR binding is limited. To better understand the dynamic states that exist for TCR CDR loops in solution, and how this relates to their states when in complex with pMHC, we simulated the 2C T cell receptor in solution using all-atom molecular dynamics in explicit water and constructed a Markov State Model for each of the CDR3α and CDR3β loops. These models reveal multiple metastable states for the CDR3 loops in solution. Simulation data and metastable states reproduce known CDR3β crystal conformations, and reveal several novel conformations suggesting that CDR3β bound states are the result of search processes from nearby pre-existing equilibrium conformational states. Similar simulations of the invariant, Type I Natural Killer T cell receptor NKT15, which engages the monomorphic, MHC-like CD1d ligand, demonstrate that iNKT TCRs also have distinct states, but comparatively restricted degrees of motion.
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Affiliation(s)
- James E Crooks
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL, United States
| | - Christopher T Boughter
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL, United States
| | - L Ridgway Scott
- Department of Computer Science, University of Chicago, Chicago, IL, United States
| | - Erin J Adams
- Committee on Immunology University of Chicago, Chicago, IL, United States
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15
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Singh NK, Riley TP, Baker SCB, Borrman T, Weng Z, Baker BM. Emerging Concepts in TCR Specificity: Rationalizing and (Maybe) Predicting Outcomes. THE JOURNAL OF IMMUNOLOGY 2017; 199:2203-2213. [PMID: 28923982 DOI: 10.4049/jimmunol.1700744] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 07/10/2017] [Indexed: 12/14/2022]
Abstract
T cell specificity emerges from a myriad of processes, ranging from the biological pathways that control T cell signaling to the structural and physical mechanisms that influence how TCRs bind peptides and MHC proteins. Of these processes, the binding specificity of the TCR is a key component. However, TCR specificity is enigmatic: TCRs are at once specific but also cross-reactive. Although long appreciated, this duality continues to puzzle immunologists and has implications for the development of TCR-based therapeutics. In this review, we discuss TCR specificity, emphasizing results that have emerged from structural and physical studies of TCR binding. We show how the TCR specificity/cross-reactivity duality can be rationalized from structural and biophysical principles. There is excellent agreement between predictions from these principles and classic predictions about the scope of TCR cross-reactivity. We demonstrate how these same principles can also explain amino acid preferences in immunogenic epitopes and highlight opportunities for structural considerations in predictive immunology.
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Affiliation(s)
- Nishant K Singh
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556.,Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556; and
| | - Timothy P Riley
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556.,Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556; and
| | - Sarah Catherine B Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556.,Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556; and
| | - Tyler Borrman
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Brian M Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556; .,Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556; and
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16
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Broad TCR repertoire and diverse structural solutions for recognition of an immunodominant CD8 + T cell epitope. Nat Struct Mol Biol 2017; 24:395-406. [PMID: 28250417 PMCID: PMC5383516 DOI: 10.1038/nsmb.3383] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 01/30/2017] [Indexed: 12/16/2022]
Abstract
A keystone of antiviral immunity is CD8 T-cell recognition of viral peptides bound to MHC-I proteins. The recognition mode of individual T cell receptors (TCRs) has been studied in some detail, but how TCR variation functions in providing a robust response to viral antigen is unclear. The influenza M1 epitope is an immunodominant target of CD8 T cells helping to control influenza in HLA-A2+ individuals. Here, we show that many distinct TCRs are used by CD8 T cells to recognize HLA-A2/M1, encoding different structural solutions to the problem of specifically recognizing a relatively featureless peptide antigen. The vast majority of responding TCRs target small clefts between peptide and MHC. These broad repertoires lead to plasticity in antigen recognition and protection against T cell clonal loss and viral escape.
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17
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MacLachlan BJ, Greenshields-Watson A, Mason GH, Schauenburg AJ, Bianchi V, Rizkallah PJ, Sewell AK, Fuller A, Cole DK. Using X-ray Crystallography, Biophysics, and Functional Assays to Determine the Mechanisms Governing T-cell Receptor Recognition of Cancer Antigens. J Vis Exp 2017:54991. [PMID: 28287509 PMCID: PMC5408581 DOI: 10.3791/54991] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Human CD8+ cytotoxic T lymphocytes (CTLs) are known to play an important role in tumor control. In order to carry out this function, the cell surface-expressed T-cell receptor (TCR) must functionally recognize human leukocyte antigen (HLA)-restricted tumor-derived peptides (pHLA). However, we and others have shown that most TCRs bind sub-optimally to tumor antigens. Uncovering the molecular mechanisms that define this poor recognition could aid in the development of new targeted therapies that circumnavigate these shortcomings. Indeed, present therapies that lack this molecular understanding have not been universally effective. Here, we describe methods that we commonly employ in the laboratory to determine how the nature of the interaction between TCRs and pHLA governs T-cell functionality. These methods include the generation of soluble TCRs and pHLA and the use of these reagents for X-ray crystallography, biophysical analysis, and antigen-specific T-cell staining with pHLA multimers. Using these approaches and guided by structural analysis, it is possible to modify the interaction between TCRs and pHLA and to then test how these modifications impact T-cell antigen recognition. These findings have already helped to clarify the mechanism of T-cell recognition of a number of cancer antigens and could direct the development of altered peptides and modified TCRs for new cancer therapies.
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Affiliation(s)
- Bruce J MacLachlan
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University
| | | | - Georgina H Mason
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University
| | - Andrea J Schauenburg
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University
| | - Valentina Bianchi
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University; Department of Oncology, University Hospital of Lausanne (CHUV); Ludwig Insitutue for Cancer Research, Lausanne Branch, University of Lausanne
| | - Pierre J Rizkallah
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University
| | - Andrew K Sewell
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University
| | - Anna Fuller
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University
| | - David K Cole
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University;
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18
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Cole DK, van den Berg HA, Lloyd A, Crowther MD, Beck K, Ekeruche-Makinde J, Miles JJ, Bulek AM, Dolton G, Schauenburg AJ, Wall A, Fuller A, Clement M, Laugel B, Rizkallah PJ, Wooldridge L, Sewell AK. Structural Mechanism Underpinning Cross-reactivity of a CD8+ T-cell Clone That Recognizes a Peptide Derived from Human Telomerase Reverse Transcriptase. J Biol Chem 2016; 292:802-813. [PMID: 27903649 PMCID: PMC5247654 DOI: 10.1074/jbc.m116.741603] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 11/18/2016] [Indexed: 01/20/2023] Open
Abstract
T-cell cross-reactivity is essential for effective immune surveillance but has also been implicated as a pathway to autoimmunity. Previous studies have demonstrated that T-cell receptors (TCRs) that focus on a minimal motif within the peptide are able to facilitate a high level of T-cell cross-reactivity. However, the structural database shows that most TCRs exhibit less focused antigen binding involving contact with more peptide residues. To further explore the structural features that allow the clonally expressed TCR to functionally engage with multiple peptide-major histocompatibility complexes (pMHCs), we examined the ILA1 CD8+ T-cell clone that responds to a peptide sequence derived from human telomerase reverse transcriptase. The ILA1 TCR contacted its pMHC with a broad peptide binding footprint encompassing spatially distant peptide residues. Despite the lack of focused TCR-peptide binding, the ILA1 T-cell clone was still cross-reactive. Overall, the TCR-peptide contacts apparent in the structure correlated well with the level of degeneracy at different peptide positions. Thus, the ILA1 TCR was less tolerant of changes at peptide residues that were at, or adjacent to, key contact sites. This study provides new insights into the molecular mechanisms that control T-cell cross-reactivity with important implications for pathogen surveillance, autoimmunity, and transplant rejection.
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Affiliation(s)
- David K Cole
- From the Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom,
| | - Hugo A van den Berg
- the Mathematics Institute, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Angharad Lloyd
- From the Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Michael D Crowther
- From the Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Konrad Beck
- the Cardiff University School of Dentistry, Heath Park, Cardiff CF14 4XY, United Kingdom
| | - Julia Ekeruche-Makinde
- From the Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - John J Miles
- From the Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom.,the Queensland Institute of Medical Research Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia.,James Cook University, Cairns, Queensland 4870, Australia, and
| | - Anna M Bulek
- From the Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Garry Dolton
- From the Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Andrea J Schauenburg
- From the Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Aaron Wall
- From the Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Anna Fuller
- From the Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Mathew Clement
- From the Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Bruno Laugel
- From the Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Pierre J Rizkallah
- From the Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Linda Wooldridge
- the Faculty of Health Sciences, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Andrew K Sewell
- From the Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom,
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19
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Raman MCC, Rizkallah PJ, Simmons R, Donnellan Z, Dukes J, Bossi G, Le Provost GS, Todorov P, Baston E, Hickman E, Mahon T, Hassan N, Vuidepot A, Sami M, Cole DK, Jakobsen BK. Direct molecular mimicry enables off-target cardiovascular toxicity by an enhanced affinity TCR designed for cancer immunotherapy. Sci Rep 2016; 6:18851. [PMID: 26758806 PMCID: PMC4725365 DOI: 10.1038/srep18851] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 11/27/2015] [Indexed: 12/11/2022] Open
Abstract
Natural T-cell responses generally lack the potency to eradicate cancer. Enhanced affinity T-cell receptors (TCRs) provide an ideal approach to target cancer cells, with emerging clinical data showing significant promise. Nevertheless, the risk of off target reactivity remains a key concern, as exemplified in a recent clinical report describing fatal cardiac toxicity, following administration of MAGE-A3 specific TCR-engineered T-cells, mediated through cross-reactivity with an unrelated epitope from the Titin protein presented on cardiac tissue. Here, we investigated the structural mechanism enabling TCR cross-recognition of MAGE-A3 and Titin, and applied the resulting data to rationally design mutants with improved antigen discrimination, providing a proof-of-concept strategy for altering the fine specificity of a TCR towards an intended target antigen. This study represents the first example of direct molecular mimicry leading to clinically relevant fatal toxicity, mediated by a modified enhanced affinity TCR designed for cancer immunotherapy. Furthermore, these data demonstrate that self-antigens that are expressed at high levels on healthy tissue should be treated with extreme caution when designing immuno-therapeutics.
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Affiliation(s)
- Marine C C Raman
- Immunocore Limited, 101 Park Drive, Milton Park, Abingdon, Oxon, OX14 4RX, United Kingdom
| | - Pierre J Rizkallah
- Division of Infection and Immunity, Cardiff University School of Medicine, Henry Wellcome building, Heath Park, Cardiff, CF14 4XN, United Kingdom
| | - Ruth Simmons
- Immunocore Limited, 101 Park Drive, Milton Park, Abingdon, Oxon, OX14 4RX, United Kingdom
| | - Zoe Donnellan
- Immunocore Limited, 101 Park Drive, Milton Park, Abingdon, Oxon, OX14 4RX, United Kingdom
| | - Joseph Dukes
- Immunocore Limited, 101 Park Drive, Milton Park, Abingdon, Oxon, OX14 4RX, United Kingdom
| | - Giovanna Bossi
- Immunocore Limited, 101 Park Drive, Milton Park, Abingdon, Oxon, OX14 4RX, United Kingdom
| | - Gabrielle S Le Provost
- Immunocore Limited, 101 Park Drive, Milton Park, Abingdon, Oxon, OX14 4RX, United Kingdom
| | - Penio Todorov
- Immunocore Limited, 101 Park Drive, Milton Park, Abingdon, Oxon, OX14 4RX, United Kingdom
| | - Emma Baston
- Immunocore Limited, 101 Park Drive, Milton Park, Abingdon, Oxon, OX14 4RX, United Kingdom
| | - Emma Hickman
- Immunocore Limited, 101 Park Drive, Milton Park, Abingdon, Oxon, OX14 4RX, United Kingdom
| | - Tara Mahon
- Immunocore Limited, 101 Park Drive, Milton Park, Abingdon, Oxon, OX14 4RX, United Kingdom
| | - Namir Hassan
- Immunocore Limited, 101 Park Drive, Milton Park, Abingdon, Oxon, OX14 4RX, United Kingdom
| | - Annelise Vuidepot
- Immunocore Limited, 101 Park Drive, Milton Park, Abingdon, Oxon, OX14 4RX, United Kingdom
| | - Malkit Sami
- Immunocore Limited, 101 Park Drive, Milton Park, Abingdon, Oxon, OX14 4RX, United Kingdom
| | - David K Cole
- Division of Infection and Immunity, Cardiff University School of Medicine, Henry Wellcome building, Heath Park, Cardiff, CF14 4XN, United Kingdom
| | - Bent K Jakobsen
- Immunocore Limited, 101 Park Drive, Milton Park, Abingdon, Oxon, OX14 4RX, United Kingdom
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20
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Holland CJ, Dolton G, Scurr M, Ladell K, Schauenburg AJ, Miners K, Madura F, Sewell AK, Price DA, Cole DK, Godkin AJ. Enhanced Detection of Antigen-Specific CD4+ T Cells Using Altered Peptide Flanking Residue Peptide-MHC Class II Multimers. THE JOURNAL OF IMMUNOLOGY 2015; 195:5827-36. [PMID: 26553072 PMCID: PMC4671089 DOI: 10.4049/jimmunol.1402787] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 10/08/2015] [Indexed: 11/22/2022]
Abstract
Fluorochrome-conjugated peptide–MHC (pMHC) class I multimers are staple components of the immunologist’s toolbox, enabling reliable quantification and analysis of Ag-specific CD8+ T cells irrespective of functional outputs. In contrast, widespread use of the equivalent pMHC class II (pMHC-II) reagents has been hindered by intrinsically weaker TCR affinities for pMHC-II, a lack of cooperative binding between the TCR and CD4 coreceptor, and a low frequency of Ag-specific CD4+ T cell populations in the peripheral blood. In this study, we show that peptide flanking regions, extending beyond the central nonamer core of MHC-II–bound peptides, can enhance TCR–pMHC-II binding and T cell activation without loss of specificity. Consistent with these findings, pMHC-II multimers incorporating peptide flanking residue modifications proved superior for the ex vivo detection, characterization, and manipulation of Ag-specific CD4+ T cells, highlighting an unappreciated feature of TCR–pMHC-II interactions.
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Affiliation(s)
- Christopher J Holland
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, Wales, United Kingdom; and
| | - Garry Dolton
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, Wales, United Kingdom; and
| | - Martin Scurr
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, Wales, United Kingdom; and
| | - Kristin Ladell
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, Wales, United Kingdom; and
| | - Andrea J Schauenburg
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, Wales, United Kingdom; and
| | - Kelly Miners
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, Wales, United Kingdom; and
| | - Florian Madura
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, Wales, United Kingdom; and
| | - Andrew K Sewell
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, Wales, United Kingdom; and
| | - David A Price
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, Wales, United Kingdom; and
| | - David K Cole
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, Wales, United Kingdom; and
| | - Andrew J Godkin
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, Wales, United Kingdom; and Department of Integrated Medicine, University Hospital of Wales, Cardiff CF14 4XW, Wales, United Kingdom
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21
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Motozono C, Pearson JA, De Leenheer E, Rizkallah PJ, Beck K, Trimby A, Sewell AK, Wong FS, Cole DK. Distortion of the Major Histocompatibility Complex Class I Binding Groove to Accommodate an Insulin-derived 10-Mer Peptide. J Biol Chem 2015; 290:18924-33. [PMID: 26085090 PMCID: PMC4521012 DOI: 10.1074/jbc.m114.622522] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Indexed: 01/23/2023] Open
Abstract
The non-obese diabetic mouse model of type 1 diabetes continues to be an important tool for delineating the role of T-cell-mediated destruction of pancreatic β-cells. However, little is known about the molecular mechanisms that enable this disease pathway. We show that insulin reactivity by a CD8+ T-cell clone, known to induce type 1 diabetes, is characterized by weak T-cell antigen receptor binding to a relatively unstable peptide-MHC. The structure of the native 9- and 10-mer insulin epitopes demonstrated that peptide residues 7 and 8 form a prominent solvent-exposed bulge that could potentially be the main focus of T-cell receptor binding. The C terminus of the peptide governed peptide-MHC stability. Unexpectedly, we further demonstrate a novel mode of flexible peptide presentation in which the MHC peptide-binding groove is able to “open the back door” to accommodate extra C-terminal peptide residues.
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Affiliation(s)
- Chihiro Motozono
- From the Division of Infection and Immunity and the Department of Immunology, Kinki University School of Medicine, Osaka 589-8511, Japan, and
| | - James A Pearson
- the Institute of Molecular and Experimental Medicine, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Evy De Leenheer
- the Institute of Molecular and Experimental Medicine, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
| | | | - Konrad Beck
- the Cardiff University School of Dentistry, Heath Park, Cardiff CF14 4XY, United Kingdom
| | | | | | - F Susan Wong
- the Institute of Molecular and Experimental Medicine, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom,
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22
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Gilham DE, Anderson J, Bridgeman JS, Hawkins RE, Exley MA, Stauss H, Maher J, Pule M, Sewell AK, Bendle G, Lee S, Qasim W, Thrasher A, Morris E. Adoptive T-cell therapy for cancer in the United kingdom: a review of activity for the British Society of Gene and Cell Therapy annual meeting 2015. Hum Gene Ther 2015; 26:276-85. [PMID: 25860661 PMCID: PMC4442586 DOI: 10.1089/hum.2015.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 03/31/2015] [Indexed: 12/25/2022] Open
Abstract
Adoptive T-cell therapy is delivering objective clinical responses across a number of cancer indications in the early phase clinical setting. Much of this clinical activity is taking place at major clinical academic centers across the United States. This review focuses upon cancer-focused cell therapy activity within the United Kingdom as a contribution to the 2015 British Society of Gene and Cell Therapy annual general meeting. This overview reflects the diversity and expansion of clinical and preclinical studies within the United Kingdom while considering the background context of this work against new infrastructural developments and the requirements of nationalized healthcare delivery within the UK National Health Service.
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Affiliation(s)
- David Edward Gilham
- Clinical and Experimental Immunotherapy Group, Institute of Cancer Sciences, The University of Manchester, Manchester M20 4BX, United Kingdom
| | - John Anderson
- UCL Institute of Child Health, London WC1N 1EH, United Kingdom
| | | | - Robert Edward Hawkins
- Clinical and Experimental Immunotherapy Group, Institute of Cancer Sciences, The University of Manchester, Manchester M20 4BX, United Kingdom
- Cellular Therapeutics Ltd., UMIC Bio-incubator, Manchester M13 9XX, United Kingdom
| | - Mark Adrian Exley
- MCCIR, Faculty of Medicine, The University of Manchester, Manchester M13 9NT, United Kingdom
| | - Hans Stauss
- Department of Immunology, University College London, Royal Free Hospital, London NW3 2PF, United Kingdom
| | - John Maher
- Department of Research Oncology, Bermondsey Wing, Guy's Hospital, London SE1 9RT, United Kingdom
| | - Martin Pule
- Research Department of Haematology, UCL Cancer Institute, London WC1E 6DD, United Kingdom
| | - Andrew Kelvin Sewell
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital, Cardiff CF14 4XN, United Kingdom
| | - Gavin Bendle
- School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Steven Lee
- School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Waseem Qasim
- Molecular and Cellular Immunology Institute, Institute of Child Health, London WC1N 1EH, United Kingdom
| | - Adrian Thrasher
- Molecular and Cellular Immunology Institute, Institute of Child Health, London WC1N 1EH, United Kingdom
| | - Emma Morris
- Department of Immunology, University College London, Royal Free Hospital, London NW3 2PF, United Kingdom
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23
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Nakatsugawa M, Yamashita Y, Ochi T, Tanaka S, Chamoto K, Guo T, Butler MO, Hirano N. Specific roles of each TCR hemichain in generating functional chain-centric TCR. THE JOURNAL OF IMMUNOLOGY 2015; 194:3487-500. [PMID: 25710913 DOI: 10.4049/jimmunol.1401717] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
TCRα- and β-chains cooperatively recognize peptide-MHC complexes. It has been shown that a "chain-centric" TCR hemichain can, by itself, dictate MHC-restricted Ag specificity without requiring major contributions from the paired TCR counterchain. Little is known, however, regarding the relative contributions and roles of chain-centric and its counter, non-chain-centric, hemichains in determining T cell avidity. We comprehensively analyzed a thymically unselected T cell repertoire generated by transducing the α-chain-centric HLA-A*02:01(A2)/MART127-35 TCRα, clone SIG35α, into A2-matched and unmatched postthymic T cells. Regardless of their HLA-A2 positivity, a substantial subset of peripheral T cells transduced with SIG35α gained reactivity for A2/MART127-35. Although the generated A2/MART127-35-specific T cells used various TRBV genes, TRBV27 predominated with >10(2) highly diverse and unique clonotypic CDR3β sequences. T cells individually reconstituted with various A2/MART127-35 TRBV27 TCRβ genes along with SIG35α possessed a wide range (>2 log orders) of avidity. Approximately half possessed avidity higher than T cells expressing clone DMF5, a naturally occurring A2/MART127-35 TCR with one of the highest affinities. Importantly, similar findings were recapitulated with other self-Ags. Our results indicate that, although a chain-centric TCR hemichain determines Ag specificity, the paired counterchain can regulate avidity over a broad range (>2 log orders) without compromising Ag specificity. TCR chain centricity can be exploited to generate a thymically unselected Ag-specific T cell repertoire, which can be used to isolate high-avidity antitumor T cells and their uniquely encoded TCRs rarely found in the periphery because of tolerance.
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Affiliation(s)
- Munehide Nakatsugawa
- Immune Therapy Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada; Campbell Family Institute for Breast Cancer Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada; Campbell Family Cancer Research Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada
| | - Yuki Yamashita
- Immune Therapy Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada; Campbell Family Institute for Breast Cancer Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada; Campbell Family Cancer Research Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada
| | - Toshiki Ochi
- Immune Therapy Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada; Campbell Family Institute for Breast Cancer Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada; Campbell Family Cancer Research Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada
| | - Shinya Tanaka
- Immune Therapy Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada; Campbell Family Institute for Breast Cancer Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada; Campbell Family Cancer Research Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada; Takara Bio, Inc., Otsu, Shiga 520-2193, Japan
| | - Kenji Chamoto
- Immune Therapy Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada; Campbell Family Institute for Breast Cancer Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada; Campbell Family Cancer Research Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada
| | - Tingxi Guo
- Immune Therapy Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada; Campbell Family Institute for Breast Cancer Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada; Campbell Family Cancer Research Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada; Department of Immunology, University of Toronto, Toronto, Ontario M5S 1A8, Canada; and
| | - Marcus O Butler
- Immune Therapy Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada; Campbell Family Institute for Breast Cancer Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada; Campbell Family Cancer Research Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada; Department of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Naoto Hirano
- Immune Therapy Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada; Campbell Family Institute for Breast Cancer Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada; Campbell Family Cancer Research Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada; Department of Immunology, University of Toronto, Toronto, Ontario M5S 1A8, Canada; and
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24
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Løset GÅ, Berntzen G, Frigstad T, Pollmann S, Gunnarsen KS, Sandlie I. Phage Display Engineered T Cell Receptors as Tools for the Study of Tumor Peptide-MHC Interactions. Front Oncol 2015; 4:378. [PMID: 25629004 PMCID: PMC4290511 DOI: 10.3389/fonc.2014.00378] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 12/17/2014] [Indexed: 11/13/2022] Open
Abstract
Cancer immunotherapy has finally come of age, demonstrated by recent progress in strategies that engage the endogenous adaptive immune response in tumor killing. Occasionally, significant and durable tumor regression has been achieved. A giant leap forward was the demonstration that the pre-existing polyclonal T cell repertoire could be re-directed by use of cloned T cell receptors (TCRs), to obtain a defined tumor-specific pool of T cells. However, the procedure must be performed with caution to avoid deleterious cross-reactivity. Here, the use of engineered soluble TCRs may represent a safer, yet powerful, alternative. There is also a need for deeper understanding of the processes that underlie antigen presentation in disease and homeostasis, how tumor-specific peptides are generated, and how epitope spreading evolves during tumor development. Due to its plasticity, the pivotal interaction where a TCR engages a peptide/MHC (pMHC) also requires closer attention. For this purpose, phage display as a tool to evolve cloned TCRs represents an attractive avenue to generate suitable reagents allowing the study of defined pMHC presentation, TCR engagement, as well as for the discovery of novel therapeutic leads. Here, we highlight important aspects of the current status in this field.
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Affiliation(s)
- Geir Åge Løset
- Nextera AS , Oslo , Norway ; Centre for Immune Regulation, Oslo University Hospital, University of Oslo , Oslo , Norway ; Department of Biosciences, University of Oslo , Oslo , Norway
| | | | | | | | - Kristin S Gunnarsen
- Centre for Immune Regulation, Oslo University Hospital, University of Oslo , Oslo , Norway
| | - Inger Sandlie
- Centre for Immune Regulation, Oslo University Hospital, University of Oslo , Oslo , Norway ; Department of Biosciences, University of Oslo , Oslo , Norway
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25
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Madura F, Rizkallah PJ, Holland CJ, Fuller A, Bulek A, Godkin AJ, Schauenburg AJ, Cole DK, Sewell AK. Structural basis for ineffective T-cell responses to MHC anchor residue-improved "heteroclitic" peptides. Eur J Immunol 2014; 45:584-91. [PMID: 25471691 PMCID: PMC4357396 DOI: 10.1002/eji.201445114] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2014] [Revised: 10/03/2014] [Accepted: 11/26/2014] [Indexed: 12/11/2022]
Abstract
MHC anchor residue-modified “heteroclitic” peptides have been used in many cancer vaccine trials and often induce greater immune responses than the wild-type peptide. The best-studied system to date is the decamer MART-1/Melan-A26–35 peptide, EAAGIGILTV, where the natural alanine at position 2 has been modified to leucine to improve human leukocyte antigen (HLA)-A*0201 anchoring. The resulting ELAGIGILTV peptide has been used in many studies. We recently showed that T cells primed with the ELAGIGILTV peptide can fail to recognize the natural tumor-expressed peptide efficiently, thereby providing a potential molecular reason for why clinical trials of this peptide have been unsuccessful. Here, we solved the structure of a TCR in complex with HLA-A*0201-EAAGIGILTV peptide and compared it with its heteroclitic counterpart, HLA-A*0201-ELAGIGILTV. The data demonstrate that a suboptimal anchor residue at position 2 enables the TCR to “pull” the peptide away from the MHC binding groove, facilitating extra contacts with both the peptide and MHC surface. These data explain how a TCR can distinguish between two epitopes that differ by only a single MHC anchor residue and demonstrate how weak MHC anchoring can enable an induced-fit interaction with the TCR. Our findings constitute a novel demonstration of the extreme sensitivity of the TCR to minor alterations in peptide conformation.
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MESH Headings
- Alanine/chemistry
- Alanine/genetics
- Amino Acid Sequence
- Amino Acid Substitution
- Crystallography, X-Ray
- Epitopes, T-Lymphocyte/genetics
- Epitopes, T-Lymphocyte/immunology
- Epitopes, T-Lymphocyte/metabolism
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Gene Expression
- HLA-A2 Antigen/chemistry
- HLA-A2 Antigen/genetics
- HLA-A2 Antigen/immunology
- Humans
- Leucine/chemistry
- Leucine/genetics
- MART-1 Antigen/chemistry
- MART-1 Antigen/genetics
- MART-1 Antigen/immunology
- Models, Molecular
- Molecular Sequence Data
- Peptides/chemistry
- Peptides/genetics
- Peptides/immunology
- Protein Binding
- Protein Interaction Domains and Motifs
- Receptors, Antigen, T-Cell, alpha-beta/chemistry
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/immunology
- T-Lymphocytes, Cytotoxic/cytology
- T-Lymphocytes, Cytotoxic/immunology
- T-Lymphocytes, Cytotoxic/metabolism
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Affiliation(s)
- Florian Madura
- Division of Infection and Immunity, Cardiff University School of MedicineHeath Park, Cardiff, UK
| | - Pierre J Rizkallah
- Division of Infection and Immunity, Cardiff University School of MedicineHeath Park, Cardiff, UK
| | - Christopher J Holland
- Division of Infection and Immunity, Cardiff University School of MedicineHeath Park, Cardiff, UK
| | - Anna Fuller
- Division of Infection and Immunity, Cardiff University School of MedicineHeath Park, Cardiff, UK
| | - Anna Bulek
- Division of Infection and Immunity, Cardiff University School of MedicineHeath Park, Cardiff, UK
| | - Andrew J Godkin
- Division of Infection and Immunity, Cardiff University School of MedicineHeath Park, Cardiff, UK
| | - Andrea J Schauenburg
- Division of Infection and Immunity, Cardiff University School of MedicineHeath Park, Cardiff, UK
| | - David K Cole
- Division of Infection and Immunity, Cardiff University School of MedicineHeath Park, Cardiff, UK
- Additional correspondence: Dr. David Cole, Cardiff University School of Medicine, Heath Park, Cardiff, UK., e-mail:
| | - Andrew K Sewell
- Division of Infection and Immunity, Cardiff University School of MedicineHeath Park, Cardiff, UK
- Full correspondence: Professor Andrew Sewell; Cardiff University School of Medicine, Heath Park, Cardiff, UK, e-mail:
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26
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Smith SN, Wang Y, Baylon JL, Singh NK, Baker BM, Tajkhorshid E, Kranz DM. Changing the peptide specificity of a human T-cell receptor by directed evolution. Nat Commun 2014; 5:5223. [PMID: 25376839 PMCID: PMC4225554 DOI: 10.1038/ncomms6223] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 09/10/2014] [Indexed: 11/09/2022] Open
Abstract
Binding of a T-cell receptor (TCR) to a peptide/major histocompatibility complex is the key interaction involved in antigen specificity of T cells. The recognition involves up to six complementarity determining regions (CDR) of the TCR. Efforts to examine the structural basis of these interactions and to exploit them in adoptive T-cell therapies has required the isolation of specific T-cell clones and their clonotypic TCRs. Here we describe a strategy using in vitro-directed evolution of a single TCR to change its peptide specificity, thereby avoiding the need to isolate T-cell clones. The human TCR A6, which recognizes the viral peptide Tax/HLA-A2, was converted to TCR variants that recognized the cancer peptide MART1/HLA-A2. Mutational studies and molecular dynamics simulations identified CDR residues that were predicted to be important in the specificity switch. Thus, in vitro engineering strategies alone can be used to discover TCRs with desired specificities.
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Affiliation(s)
- Sheena N. Smith
- Department of Biochemistry, University of Illinois, 600 S. Matthews Ave., Urbana, IL 61801, USA
| | - Yuhang Wang
- Center for Biophysics and Computational Biology, University of Illinois, Urbana, IL 61802, USA
| | - Javier L. Baylon
- Center for Biophysics and Computational Biology, University of Illinois, Urbana, IL 61802, USA
| | - Nishant K. Singh
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, 1234 Notre Dame Avenue, South Bend, IN 46557, USA
| | - Brian M. Baker
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, 1234 Notre Dame Avenue, South Bend, IN 46557, USA
| | - Emad Tajkhorshid
- Department of Biochemistry, University of Illinois, 600 S. Matthews Ave., Urbana, IL 61801, USA
- Center for Biophysics and Computational Biology, University of Illinois, Urbana, IL 61802, USA
| | - David M. Kranz
- Department of Biochemistry, University of Illinois, 600 S. Matthews Ave., Urbana, IL 61801, USA
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27
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Large scale characterization of the LC13 TCR and HLA-B8 structural landscape in reaction to 172 altered peptide ligands: a molecular dynamics simulation study. PLoS Comput Biol 2014; 10:e1003748. [PMID: 25101830 PMCID: PMC4125040 DOI: 10.1371/journal.pcbi.1003748] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 05/28/2014] [Indexed: 12/29/2022] Open
Abstract
The interplay between T cell receptors (TCRs) and peptides bound by major histocompatibility complexes (MHCs) is one of the most important interactions in the adaptive immune system. Several previous studies have computationally investigated their structural dynamics. On the basis of these simulations several structural and dynamical properties have been proposed as effectors of the immunogenicity. Here we present the results of a large scale Molecular Dynamics simulation study consisting of 100 ns simulations of 172 different complexes. These complexes consisted of all possible point mutations of the Epstein Barr Virus peptide FLRGRAYGL bound by HLA-B*08:01 and presented to the LC13 TCR. We compare the results of these 172 structural simulations with experimental immunogenicity data. We found that simulations with more immunogenic peptides and those with less immunogenic peptides are in fact highly similar and on average only minor differences in the hydrogen binding footprints, interface distances, and the relative orientation between the TCR chains are present. Thus our large scale data analysis shows that many previously suggested dynamical and structural properties of the TCR/peptide/MHC interface are unlikely to be conserved causal factors for peptide immunogenicity.
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28
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Pierce BG, Hellman LM, Hossain M, Singh NK, Vander Kooi CW, Weng Z, Baker BM. Computational design of the affinity and specificity of a therapeutic T cell receptor. PLoS Comput Biol 2014; 10:e1003478. [PMID: 24550723 PMCID: PMC3923660 DOI: 10.1371/journal.pcbi.1003478] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 01/02/2014] [Indexed: 01/15/2023] Open
Abstract
T cell receptors (TCRs) are key to antigen-specific immunity and are increasingly being explored as therapeutics, most visibly in cancer immunotherapy. As TCRs typically possess only low-to-moderate affinity for their peptide/MHC (pMHC) ligands, there is a recognized need to develop affinity-enhanced TCR variants. Previous in vitro engineering efforts have yielded remarkable improvements in TCR affinity, yet concerns exist about the maintenance of peptide specificity and the biological impacts of ultra-high affinity. As opposed to in vitro engineering, computational design can directly address these issues, in theory permitting the rational control of peptide specificity together with relatively controlled increments in affinity. Here we explored the efficacy of computational design with the clinically relevant TCR DMF5, which recognizes nonameric and decameric epitopes from the melanoma-associated Melan-A/MART-1 protein presented by the class I MHC HLA-A2. We tested multiple mutations selected by flexible and rigid modeling protocols, assessed impacts on affinity and specificity, and utilized the data to examine and improve algorithmic performance. We identified multiple mutations that improved binding affinity, and characterized the structure, affinity, and binding kinetics of a previously reported double mutant that exhibits an impressive 400-fold affinity improvement for the decameric pMHC ligand without detectable binding to non-cognate ligands. The structure of this high affinity mutant indicated very little conformational consequences and emphasized the high fidelity of our modeling procedure. Overall, our work showcases the capability of computational design to generate TCRs with improved pMHC affinities while explicitly accounting for peptide specificity, as well as its potential for generating TCRs with customized antigen targeting capabilities.
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Affiliation(s)
- Brian G. Pierce
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Lance M. Hellman
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Moushumi Hossain
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Nishant K. Singh
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Craig W. Vander Kooi
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Brian M. Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, United States of America
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana, United States of America
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29
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Bhati M, Cole DK, McCluskey J, Sewell AK, Rossjohn J. The versatility of the αβ T-cell antigen receptor. Protein Sci 2014; 23:260-72. [PMID: 24375592 DOI: 10.1002/pro.2412] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Revised: 12/20/2013] [Accepted: 12/20/2013] [Indexed: 02/06/2023]
Abstract
The T-cell antigen receptor is a heterodimeric αβ protein (TCR) expressed on the surface of T-lymphocytes, with each chain of the TCR comprising three complementarity-determining regions (CDRs) that collectively form the antigen-binding site. Unlike antibodies, which are closely related proteins that recognize intact protein antigens, TCRs classically bind, via their CDR loops, to peptides (p) that are presented by molecules of the major histocompatibility complex (MHC). This TCR-pMHC interaction is crucially important in cell-mediated immunity, with the specificity in the cellular immune response being attributable to MHC polymorphism, an extensive TCR repertoire and a variable peptide cargo. The ensuing structural and biophysical studies within the TCR-pMHC axis have been highly informative in understanding the fundamental events that underpin protective immunity and dysfunctional T-cell responses that occur during autoimmunity. In addition, TCRs can recognize the CD1 family, a family of MHC-related molecules that instead of presenting peptides are ideally suited to bind lipid-based antigens. Structural studies within the CD1-lipid antigen system are beginning to inform us how lipid antigens are specifically presented by CD1, and how such CD1-lipid antigen complexes are recognized by the TCR. Moreover, it has recently been shown that certain TCRs can bind to vitamin B based metabolites that are bound to an MHC-like molecule termed MR1. Thus, TCRs can recognize peptides, lipids, and small molecule metabolites, and here we review the basic principles underpinning this versatile and fascinating receptor recognition system that is vital to a host's survival.
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Affiliation(s)
- Mugdha Bhati
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria, 3800, Australia
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30
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Backbone flexibility of CDR3 and immune recognition of antigens. J Mol Biol 2013; 426:1583-99. [PMID: 24380763 DOI: 10.1016/j.jmb.2013.12.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 12/03/2013] [Accepted: 12/19/2013] [Indexed: 11/22/2022]
Abstract
Conformational entropy is an important component of protein-protein interactions; however, there is no reliable method for computing this parameter. We have developed a statistical measure of residual backbone entropy in folded proteins by using the ϕ-ψ distributions of the 20 amino acids in common secondary structures. The backbone entropy patterns of amino acids within helix, sheet or coil form clusters that recapitulate the branching and hydrogen bonding properties of the side chains in the secondary structure type. The same types of residues in coil and sheet have identical backbone entropies, while helix residues have much smaller conformational entropies. We estimated the backbone entropy change for immunoglobulin complementarity-determining regions (CDRs) from the crystal structures of 34 low-affinity T-cell receptors and 40 high-affinity Fabs as a result of the formation of protein complexes. Surprisingly, we discovered that the computed backbone entropy loss of only the CDR3, but not all CDRs, correlated significantly with the kinetic and affinity constants of the 74 selected complexes. Consequently, we propose a simple algorithm to introduce proline mutations that restrict the conformational flexibility of CDRs and enhance the kinetics and affinity of immunoglobulin interactions. Combining the proline mutations with rationally designed mutants from a previous study led to 2400-fold increase in the affinity of the A6 T-cell receptor for Tax-HLAA2. However, this mutational scheme failed to induce significant binding changes in the already-high-affinity C225-Fab/huEGFR interface. Our results will serve as a roadmap to formulate more effective target functions to design immune complexes with improved biological functions.
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31
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Cole DK, Miles KM, Madura F, Holland CJ, Schauenburg AJA, Godkin AJ, Bulek AM, Fuller A, Akpovwa HJE, Pymm PG, Liddy N, Sami M, Li Y, Rizkallah PJ, Jakobsen BK, Sewell AK. T-cell receptor (TCR)-peptide specificity overrides affinity-enhancing TCR-major histocompatibility complex interactions. J Biol Chem 2013; 289:628-38. [PMID: 24196962 PMCID: PMC3887192 DOI: 10.1074/jbc.m113.522110] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
αβ T-cell receptors (TCRs) engage antigens using complementarity-determining region (CDR) loops that are either germ line-encoded (CDR1 and CDR2) or somatically rearranged (CDR3). TCR ligands compose a presentation platform (major histocompatibility complex (MHC)) and a variable antigenic component consisting of a short “foreign” peptide. The sequence of events when the TCR engages its peptide-MHC (pMHC) ligand remains unclear. Some studies suggest that the germ line elements of the TCR engage the MHC prior to peptide scanning, but this order of binding is difficult to reconcile with some TCR-pMHC structures. Here, we used TCRs that exhibited enhanced pMHC binding as a result of mutations in either CDR2 and/or CDR3 loops, that bound to the MHC or peptide, respectively, to dissect the roles of these loops in stabilizing TCR-pMHC interactions. Our data show that TCR-peptide interactions play a strongly dominant energetic role providing a binding mode that is both temporally and energetically complementary with a system requiring positive selection by self-pMHC in the thymus and rapid recognition of non-self-pMHC in the periphery.
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Affiliation(s)
- David K Cole
- From Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN
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32
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Cole DK, Sami M, Scott DR, Rizkallah PJ, Borbulevych OY, Todorov PT, Moysey RK, Jakobsen BK, Boulter JM, Baker BM, Yi Li. Increased Peptide Contacts Govern High Affinity Binding of a Modified TCR Whilst Maintaining a Native pMHC Docking Mode. Front Immunol 2013; 4:168. [PMID: 23805144 PMCID: PMC3693486 DOI: 10.3389/fimmu.2013.00168] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 06/12/2013] [Indexed: 12/15/2022] Open
Abstract
Natural T cell receptors (TCRs) generally bind to their cognate pMHC molecules with weak affinity and fast kinetics, limiting their use as therapeutic agents. Using phage display, we have engineered a high affinity version of the A6 wild-type TCR (A6wt), specific for the human leukocyte antigen (HLA-A∗0201) complexed with human T cell lymphotropic virus type 111–19 peptide (A2-Tax). Mutations in just 4 residues in the CDR3β loop region of the A6wt TCR were selected that improved binding to A2-Tax by nearly 1000-fold. Biophysical measurements of this mutant TCR (A6c134) demonstrated that the enhanced binding was derived through favorable enthalpy and a slower off-rate. The structure of the free A6c134 TCR and the A6c134/A2-Tax complex revealed a native binding mode, similar to the A6wt/A2-Tax complex. However, concordant with the more favorable binding enthalpy, the A6c134 TCR made increased contacts with the Tax peptide compared with the A6wt/A2-Tax complex, demonstrating a peptide-focused mechanism for the enhanced affinity that directly involved the mutated residues in the A6c134 TCR CDR3β loop. This peptide-focused enhanced TCR binding may represent an important approach for developing antigen specific high affinity TCR reagents for use in T cell based therapies.
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Affiliation(s)
- David K Cole
- Cardiff University School of Medicine, Heath Park , Cardiff , UK
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