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Pymm P, Saunders PM, Anand S, MacLachlan BJ, Faoro C, Hitchen C, Rossjohn J, Brooks AG, Vivian JP. The Structural Basis for Recognition of Human Leukocyte Antigen Class I Molecules by the Pan-HLA Antibody W6/32. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 213:876-885. [PMID: 39093013 DOI: 10.4049/jimmunol.2400328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Accepted: 07/09/2024] [Indexed: 08/04/2024]
Abstract
The central immunological role of HLA class I (HLA-I) in presenting peptide Ags to cellular components of the immune system has been the focus of intense study for >60 y. A confounding factor in the study of HLA-I has been the extreme polymorphism of these molecules. The mAb W6/32 has been a fundamental reagent bypassing the issue of polymorphism by recognizing an epitope that is conserved across diverse HLA-I allotypes. However, despite the widespread use of W6/32, the epitope of this Ab has not been definitively mapped. In this study, we present the crystal structure of the Fab fragment of W6/32 in complex with peptide-HLA-B*27:05. W6/32 bound to HLA-B*27:05 beneath the Ag-binding groove, recognizing a discontinuous epitope comprised of the α1, α2, and α3 domains of HLA-I and β2-microglobulin. The epitope comprises a region of low polymorphism reflecting the pan-HLA-I nature of the binding. Notably, the W6/32 epitope neither overlaps the HLA-I binding sites of either T cell Ag receptors or killer cell Ig-like receptors. However, it does coincide with the binding sites for leukocyte Ig-like receptors and CD8 coreceptors. Consistent with this, the use of W6/32 to block the interaction of NK cells with HLA-I only weakly impaired inhibition mediated by KIR3DL1, but impacted HLA-LILR recognition.
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Affiliation(s)
- Phillip Pymm
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Philippa M Saunders
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria, Australia
| | - Sushma Anand
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Bruce J MacLachlan
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Camilla Faoro
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Corinne Hitchen
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
- Institute of Infection and Immunity, Cardiff University, School of Medicine, Heath Park, Cardiff
| | - Andrew G Brooks
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria, Australia
| | - Julian P Vivian
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
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Maso L, Rajak E, Bang I, Koide A, Hattori T, Neel BG, Koide S. Molecular basis for antibody recognition of multiple drug-peptide/MHC complexes. Proc Natl Acad Sci U S A 2024; 121:e2319029121. [PMID: 38781214 PMCID: PMC11145297 DOI: 10.1073/pnas.2319029121] [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: 10/30/2023] [Accepted: 02/14/2024] [Indexed: 05/25/2024] Open
Abstract
The HapImmuneTM platform exploits covalent inhibitors as haptens for creating major histocompatibility complex (MHC)-presented tumor-specific neoantigens by design, combining targeted therapies with immunotherapy for the treatment of drug-resistant cancers. A HapImmune antibody, R023, recognizes multiple sotorasib-conjugated KRAS(G12C) peptides presented by different human leukocyte antigens (HLAs). This high specificity to sotorasib, coupled with broad HLA-binding capability, enables such antibodies, when reformatted as T cell engagers, to potently and selectively kill sotorasib-resistant KRAS(G12C) cancer cells expressing different HLAs upon sotorasib treatment. The loosening of HLA restriction could increase the patient population that can benefit from this therapeutic approach. To understand the molecular basis for its unconventional binding capability, we used single-particle cryogenic electron microscopy to determine the structures of R023 bound to multiple sotorasib-peptide conjugates presented by different HLAs. R023 forms a pocket for sotorasib between the VH and VL domains, binds HLAs in an unconventional, angled way, with VL making most contacts with them, and makes few contacts with the peptide moieties. This binding mode enables the antibody to accommodate different hapten-peptide conjugates and to adjust its conformation to different HLAs presenting hapten-peptides. Deep mutational scanning validated the structures and revealed distinct levels of mutation tolerance by sotorasib- and HLA-binding residues. Together, our structural information and sequence landscape analysis reveal key features for achieving MHC-restricted recognition of multiple hapten-peptide antigens, which will inform the development of next-generation therapeutic antibodies.
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Affiliation(s)
- Lorenzo Maso
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY10016
| | - Epsa Rajak
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY10016
| | - Injin Bang
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY10016
| | - Akiko Koide
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY10016
- Department of Medicine, New York University School of Medicine, New York, NY10016
| | - Takamitsu Hattori
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY10016
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY10016
| | - Benjamin G. Neel
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY10016
- Department of Medicine, New York University School of Medicine, New York, NY10016
| | - Shohei Koide
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY10016
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY10016
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3
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Ostmeyer J, Park JY, von Itzstein MS, Hsiehchen D, Fattah F, Gwin M, Catalan R, Khan S, Raj P, Wakeland EK, Xie Y, Gerber DE. T-cell tolerant fraction as a predictor of immune-related adverse events. J Immunother Cancer 2023; 11:e006437. [PMID: 37580069 PMCID: PMC10432621 DOI: 10.1136/jitc-2022-006437] [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] [Accepted: 06/28/2023] [Indexed: 08/16/2023] Open
Abstract
BACKGROUND Immune checkpoint inhibitor (ICI) therapies may cause unpredictable and potentially severe autoimmune toxicities termed immune-related adverse events (irAEs). Because T cells mediate ICI effects, T cell profiling may provide insight into the risk of irAEs. Here we evaluate a novel metric-the T-cell tolerant fraction-as a predictor of future irAEs. METHODS We examined T-cell receptor beta (TRB) locus sequencing from baseline pretreatment samples from an institutional registry and previously published studies. For each patient, we used TRB sequences to calculate the T-cell tolerant fraction, which was then assessed as a predictor of future irAEs (classified as Common Terminology Criteria for Adverse Event grade 0-1 vs grade ≥2). We then compared the tolerant fraction to TRB clonality and diversity. Finally, the tolerant fraction was assessed on (1) T cells enriched against napsin A, a potential autoantigen of irAEs; (2) thymic versus peripheral blood T cells; and (3) TRBs specific for various infections and autoimmune diseases. RESULTS A total of 77 patients with cancer (22 from an institutional registry and 55 from published studies) receiving ICI therapy (43 CTLA4, 19 PD1/PDL1, 15 combination CTLA4+PD1/PDL1) were included in the study. The tolerant fraction was significantly lower in cases with clinically significant irAEs (p<0.001) and had an area under the receiver operating curve (AUC) of 0.79. The tolerant fraction was lower for each ICI treatment category, reaching statistical significance for CTLA4 (p<0.001) and demonstrating non-significant trends for PD1/PDL1 (p=0.21) and combination ICI (p=0.18). The tolerant fraction for T cells enriched against napsin A was lower than other samples. The tolerant fraction was also lower in thymic versus peripheral blood samples, and lower in some (multiple sclerosis) but not other (type 1 diabetes) autoimmune diseases. In our study cohort, TRB clonality had an AUC of 0.62, and TRB diversity had an AUC of 0.60 for predicting irAEs. CONCLUSIONS Among patients receiving ICI, the baseline T-cell tolerant fraction may serve as a predictor of clinically significant irAEs.
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Affiliation(s)
- Jared Ostmeyer
- Peter O'Donnell School of Public Health, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Jason Y Park
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Mitchell S von Itzstein
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - David Hsiehchen
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Harold C Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Farjana Fattah
- Harold C Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Mary Gwin
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Rodrigo Catalan
- Harold C Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Shaheen Khan
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Prithvi Raj
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Edward K Wakeland
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Yang Xie
- Peter O'Donnell School of Public Health, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Harold C Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - David E Gerber
- Peter O'Donnell School of Public Health, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Harold C Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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4
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Morita D, Asa M, Sugita M. Engagement with the TCR induces plasticity in antigenic ligands bound to MHC class I and CD1 molecules. Int Immunol 2023; 35:7-17. [PMID: 36053252 DOI: 10.1093/intimm/dxac046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 08/31/2022] [Indexed: 01/25/2023] Open
Abstract
Complementarity-determining regions (CDRs) of αβ T-cell receptors (TCRs) sense peptide-bound MHC (pMHC) complexes via chemical interactions, thereby mediating antigen specificity and MHC restriction. Flexible finger-like movement of CDR loops contributes to the establishment of optimal interactions with pMHCs. In contrast, peptide ligands captured in MHC molecules are considered more static because of the rigid hydrogen-bond network that stabilizes peptide ligands in the antigen-binding groove of MHC molecules. An array of crystal structures delineating pMHC complexes in TCR-docked and TCR-undocked forms is now available, which enables us to assess TCR engagement-induced conformational changes in peptide ligands. In this short review, we overview conformational changes in MHC class I-bound peptide ligands upon TCR docking, followed by those for CD1-bound glycolipid ligands. Finally, we analyze the co-crystal structure of the TCR:lipopeptide-bound MHC class I complex that we recently reported. We argue that TCR engagement-induced conformational changes markedly occur in lipopeptide ligands, which are essential for exposure of a primary T-cell epitope to TCRs. These conformational changes are affected by amino acid residues, such as glycine, that do not interact directly with TCRs. Thus, ligand recognition by specific TCRs involves not only T-cell epitopes but also non-epitopic amino acid residues. In light of their critical function, we propose to refer to these residues as non-epitopic residues affecting ligand plasticity and antigenicity (NR-PA).
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Affiliation(s)
- Daisuke Morita
- Laboratory of Cell Regulation, Institute for Life and Medical Sciences, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan.,Laboratory of Cell Regulation and Molecular Network, Graduate School of Biostudies, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Minori Asa
- Laboratory of Cell Regulation, Institute for Life and Medical Sciences, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan.,Laboratory of Cell Regulation and Molecular Network, Graduate School of Biostudies, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Masahiko Sugita
- Laboratory of Cell Regulation, Institute for Life and Medical Sciences, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan.,Laboratory of Cell Regulation and Molecular Network, Graduate School of Biostudies, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
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5
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Finton KAK, Rupert PB, Friend DJ, Dinca A, Lovelace ES, Buerger M, Rusnac DV, Foote-McNabb U, Chour W, Heath JR, Campbell JS, Pierce RH, Strong RK. Effects of HLA single chain trimer design on peptide presentation and stability. Front Immunol 2023; 14:1170462. [PMID: 37207206 PMCID: PMC10189100 DOI: 10.3389/fimmu.2023.1170462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 04/21/2023] [Indexed: 05/21/2023] Open
Abstract
MHC class I "single-chain trimer" molecules, coupling MHC heavy chain, β2-microglobulin, and a specific peptide into a single polypeptide chain, are widely used in research. To more fully understand caveats associated with this design that may affect its use for basic and translational studies, we evaluated a set of engineered single-chain trimers with combinations of stabilizing mutations across eight different classical and non-classical human class I alleles with 44 different peptides, including a novel human/murine chimeric design. While, overall, single-chain trimers accurately recapitulate native molecules, care was needed in selecting designs for studying peptides longer or shorter than 9-mers, as single-chain trimer design could affect peptide conformation. In the process, we observed that predictions of peptide binding were often discordant with experiment and that yields and stabilities varied widely with construct design. We also developed novel reagents to improve the crystallizability of these proteins and confirmed novel modes of peptide presentation.
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Affiliation(s)
- Kathryn A. K. Finton
- Division of Basic Science, Fred Hutchinson Cancer Research Center (FHCC), Seattle, WA, United States
| | - Peter B. Rupert
- Division of Basic Science, Fred Hutchinson Cancer Research Center (FHCC), Seattle, WA, United States
| | - Della J. Friend
- Division of Basic Science, Fred Hutchinson Cancer Research Center (FHCC), Seattle, WA, United States
| | - Ana Dinca
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Erica S. Lovelace
- Division of Basic Science, Fred Hutchinson Cancer Research Center (FHCC), Seattle, WA, United States
| | - Matthew Buerger
- Division of Basic Science, Fred Hutchinson Cancer Research Center (FHCC), Seattle, WA, United States
| | - Domnita V. Rusnac
- Division of Basic Science, Fred Hutchinson Cancer Research Center (FHCC), Seattle, WA, United States
| | - Ulysses Foote-McNabb
- Division of Basic Science, Fred Hutchinson Cancer Research Center (FHCC), Seattle, WA, United States
| | - William Chour
- Institute for Systems Biology, Seattle, WA, United States
| | - James R. Heath
- Institute for Systems Biology, Seattle, WA, United States
| | - Jean S. Campbell
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Robert H. Pierce
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Roland K. Strong
- Division of Basic Science, Fred Hutchinson Cancer Research Center (FHCC), Seattle, WA, United States
- *Correspondence: Roland K. Strong,
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6
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Meeuwsen MH, Wouters AK, Hagedoorn RS, Kester MGD, Remst DFG, van der Steen DM, de Ru A, van Veelen PA, Rossjohn J, Gras S, Falkenburg JHF, Heemskerk MHM. Cutting Edge: Unconventional CD8 + T Cell Recognition of a Naturally Occurring HLA-A*02:01-Restricted 20mer Epitope. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:1851-1856. [PMID: 35379743 DOI: 10.4049/jimmunol.2101208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
Unconventional HLA class I-restricted CD8+ T cell epitopes, longer than 10 aa, have been implicated to play a role in human immunity against viruses and cancer. T cell recognition of long peptides, centrally bulging from the HLA cleft, has been described previously. Alternatively, long peptides can contain a linear HLA-bound core peptide, with a N- or C-terminal peptide "tail" extending from the HLA peptide binding groove. The role of such a peptide "tail" in CD8+ T cell recognition remains unclear. In this study, we identified a 20mer peptide (FLPTPEELGLLGPPRPQVLA [FLP]) derived from the IL-27R subunit α gene restricted to HLA-A*02:01, for which we solved the crystal structure and demonstrated a long C-terminal "tail" extension. FLP-specific T cell clones demonstrated various recognition modes, some T cells recognized the FLP core peptide, while for other T cells the peptide tail was essential for recognition. These results demonstrate a crucial role for a C-terminal peptide tail in immunogenicity.
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Affiliation(s)
- Miranda H Meeuwsen
- Department of Hematology, Leiden University Medical Center, Leiden, the Netherlands;
| | - Anne K Wouters
- Department of Hematology, Leiden University Medical Center, Leiden, the Netherlands
| | - Renate S Hagedoorn
- Department of Hematology, Leiden University Medical Center, Leiden, the Netherlands
| | - Michel G D Kester
- Department of Hematology, Leiden University Medical Center, Leiden, the Netherlands
| | - Dennis F G Remst
- Department of Hematology, Leiden University Medical Center, Leiden, the Netherlands
| | - Dirk M van der Steen
- Department of Hematology, Leiden University Medical Center, Leiden, the Netherlands
| | - Arnoud de Ru
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Peter A van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Jamie Rossjohn
- Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia; and
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Stephanie Gras
- Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia; and
| | | | - Mirjam H M Heemskerk
- Department of Hematology, Leiden University Medical Center, Leiden, the Netherlands;
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7
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Lu T, Zhang Z, Zhu J, Wang Y, Jiang P, Xiao X, Bernatchez C, Heymach JV, Gibbons DL, Wang J, Xu L, Reuben A, Wang T. Deep learning-based prediction of the T cell receptor-antigen binding specificity. NAT MACH INTELL 2021; 3:864-875. [PMID: 36003885 PMCID: PMC9396750 DOI: 10.1038/s42256-021-00383-2] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 07/01/2021] [Indexed: 02/05/2023]
Abstract
Neoantigens play a key role in the recognition of tumor cells by T cells. However, only a small proportion of neoantigens truly elicit T cell responses, and fewer clues exist as to which neoantigens are recognized by which T cell receptors (TCRs). We built a transfer learning-based model, named pMHC-TCR binding prediction network (pMTnet), to predict TCR-binding specificities of neoantigens, and T cell antigens in general, presented by class I major histocompatibility complexes (pMHCs). pMTnet was comprehensively validated by a series of analyses, and showed advance over previous work by a large margin. By applying pMTnet in human tumor genomics data, we discovered that neoantigens were generally more immunogenic than self-antigens, but HERV-E, a special type of self-antigen that is re-activated in kidney cancer, is more immunogenic than neoantigens. We further discovered that patients with more clonally expanded T cells exhibiting better affinity against truncal, rather than subclonal, neoantigens, had more favorable prognosis and treatment response to immunotherapy, in melanoma and lung cancer but not in kidney cancer. Predicting TCR-neoantigen/antigen pairs is one of the most daunting challenges in modern immunology. However, we achieved an accurate prediction of the pairing only using the TCR sequence (CDR3β), antigen sequence, and class I MHC allele, and our work revealed unique insights into the interactions of TCRs and pMHCs in human tumors using pMTnet as a discovery tool.
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Affiliation(s)
- Tianshi Lu
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA, 75390
| | - Ze Zhang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA, 75390
| | - James Zhu
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA, 75390
| | - Yunguan Wang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA, 75390
| | - Peixin Jiang
- Department of Thoracic/Head & Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX USA, 77030
| | - Xue Xiao
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA, 75390
| | - Chantale Bernatchez
- Department of Melanoma Medical Oncology, MD Anderson Cancer Center, Houston, TX USA, 77030
| | - John V. Heymach
- Department of Thoracic/Head & Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX USA, 77030
| | - Don L. Gibbons
- Department of Thoracic/Head & Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX USA, 77030
| | - Jun Wang
- Department of Pathology, New York University Grossman School of Medicine, New York, NY 10016
| | - Lin Xu
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA, 75390
| | - Alexandre Reuben
- Department of Thoracic/Head & Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX USA, 77030
| | - Tao Wang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA, 75390
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA, 75390
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8
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Milighetti M, Shawe-Taylor J, Chain B. Predicting T Cell Receptor Antigen Specificity From Structural Features Derived From Homology Models of Receptor-Peptide-Major Histocompatibility Complexes. Front Physiol 2021; 12:730908. [PMID: 34566692 PMCID: PMC8456106 DOI: 10.3389/fphys.2021.730908] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/02/2021] [Indexed: 11/13/2022] Open
Abstract
The physical interaction between the T cell receptor (TCR) and its cognate antigen causes T cells to activate and participate in the immune response. Understanding this physical interaction is important in predicting TCR binding to a target epitope, as well as potential cross-reactivity. Here, we propose a way of collecting informative features of the binding interface from homology models of T cell receptor-peptide-major histocompatibility complex (TCR-pMHC) complexes. The information collected from these structures is sufficient to discriminate binding from non-binding TCR-pMHC pairs in multiple independent datasets. The classifier is limited by the number of crystal structures available for the homology modelling and by the size of the training set. However, the classifier shows comparable performance to sequence-based classifiers requiring much larger training sets.
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Affiliation(s)
- Martina Milighetti
- Division of Infection and Immunity, University College London, London, United Kingdom
- Cancer Institute, University College London, London, United Kingdom
| | - John Shawe-Taylor
- Department of Computer Science, University College London, London, United Kingdom
| | - Benny Chain
- Division of Infection and Immunity, University College London, London, United Kingdom
- Department of Computer Science, University College London, London, United Kingdom
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9
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Genetic Bias, Diversity Indices, Physiochemical Properties and CDR3 Motifs Divide Auto-Reactive from Allo-Reactive T-Cell Repertoires. Int J Mol Sci 2021; 22:ijms22041625. [PMID: 33562731 PMCID: PMC7915266 DOI: 10.3390/ijms22041625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/30/2021] [Accepted: 01/31/2021] [Indexed: 12/26/2022] Open
Abstract
The distinct properties of allo-reactive T-cell repertoires are not well understood. To investigate whether auto-reactive and allo-reactive T-cell repertoires encoded distinct properties, we used dextramer enumeration, enrichment, single-cell T-cell receptor (TCR) sequencing and multiparameter analysis. We found auto-reactive and allo-reactive T-cells differed in mean ex vivo frequency which was antigen dependent. Allo-reactive T-cells showed clear differences in TCR architecture, with enriched usage of specific T-cell receptor variable (TRBJ) genes and broader use of T-cell receptor variable joining (TRBJ) genes. Auto-reactive T-cell repertoires exhibited complementary determining regions three (CDR3) lengths using a Gaussian distribution whereas allo-reactive T-cell repertoires exhibited distorted patterns in CDR3 length. CDR3 loops from allo-reactive T-cells showed distinct physical-chemical properties, tending to encode loops that were more acidic in charge. Allo-reactive T-cell repertoires differed in diversity metrics, tending to show increased overall diversity and increased homogeneity between repertoires. Motif analysis of CDR3 loops showed allo-reactive T-cell repertoires differed in motif preference which included broader motif use. Collectively, these data conclude that allo-reactive T-cell repertoires are indeed different to auto-reactive repertoires and provide tangible metrics for further investigations and validation. Given that the antigens studied here are overexpressed on multiple cancers and that allo-reactive TCRs often show increased ligand affinity, this new TCR bank also has translational potential for adoptive cell therapy, soluble TCR-based therapy and rational TCR design.
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10
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TCR Recognition of Peptide-MHC-I: Rule Makers and Breakers. Int J Mol Sci 2020; 22:ijms22010068. [PMID: 33374673 PMCID: PMC7793522 DOI: 10.3390/ijms22010068] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/16/2020] [Accepted: 12/21/2020] [Indexed: 12/15/2022] Open
Abstract
T cells are a critical part of the adaptive immune system that are able to distinguish between healthy and unhealthy cells. Upon recognition of protein fragments (peptides), activated T cells will contribute to the immune response and help clear infection. The major histocompatibility complex (MHC) molecules, or human leukocyte antigens (HLA) in humans, bind these peptides to present them to T cells that recognise them with their surface T cell receptors (TCR). This recognition event is the first step that leads to T cell activation, and in turn can dictate disease outcomes. The visualisation of TCR interaction with pMHC using structural biology has been crucial in understanding this key event, unravelling the parameters that drive this interaction and their impact on the immune response. The last five years has been the most productive within the field, wherein half of current unique TCR-pMHC-I structures to date were determined within this time. Here, we review the new insights learned from these recent TCR-pMHC-I structures and their impact on T cell activation.
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11
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Watkins TS, Miles JJ. The human T-cell receptor repertoire in health and disease and potential for omics integration. Immunol Cell Biol 2020; 99:135-145. [PMID: 32677130 DOI: 10.1111/imcb.12377] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 07/07/2020] [Accepted: 07/12/2020] [Indexed: 12/11/2022]
Abstract
The adaptive immune system arose 600 million years ago in a cold-blooded fish. Over countless generations, our antecedents tuned the function of the T-cell receptor (TCR). The TCR system is arguably the most complex known to science. The TCR evolved hypervariability to fight the hypervariability of pathogens and cancers that look to consume our resources. This review describes the genetics and architecture of the human TCR and highlights surprising new discoveries over the past years that have disproved very old dogmas. The standardization of TCR sequencing data is discussed in preparation for big data bioinformatics and predictive analysis. We next catalogue new signatures and phenomenon discovered by TCR next generation sequencing (NGS) in health and disease and work that remain to be done in this space. Finally, we discuss how TCR NGS can add to immunodiagnostics and integrate with other omics platforms for both a deeper understanding of TCR biology and its use in the clinical setting.
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Affiliation(s)
- Thomas S Watkins
- The Australian Institute of Tropical Health and Medicine (AITHM), James Cook University, Cairns, QLD, Australia.,Centre for Molecular Therapeutics, James Cook University, Cairns, QLD, Australia.,Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Cairns, QLD, Australia
| | - John J Miles
- The Australian Institute of Tropical Health and Medicine (AITHM), James Cook University, Cairns, QLD, Australia.,Centre for Molecular Therapeutics, James Cook University, Cairns, QLD, Australia.,Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Cairns, QLD, Australia
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12
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Coles CH, Mulvaney RM, Malla S, Walker A, Smith KJ, Lloyd A, Lowe KL, McCully ML, Martinez Hague R, Aleksic M, Harper J, Paston SJ, Donnellan Z, Chester F, Wiederhold K, Robinson RA, Knox A, Stacey AR, Dukes J, Baston E, Griffin S, Jakobsen BK, Vuidepot A, Harper S. TCRs with Distinct Specificity Profiles Use Different Binding Modes to Engage an Identical Peptide-HLA Complex. THE JOURNAL OF IMMUNOLOGY 2020; 204:1943-1953. [PMID: 32102902 DOI: 10.4049/jimmunol.1900915] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 12/29/2019] [Indexed: 12/18/2022]
Abstract
The molecular rules driving TCR cross-reactivity are poorly understood and, consequently, it is unclear the extent to which TCRs targeting the same Ag recognize the same off-target peptides. We determined TCR-peptide-HLA crystal structures and, using a single-chain peptide-HLA phage library, we generated peptide specificity profiles for three newly identified human TCRs specific for the cancer testis Ag NY-ESO-1157-165-HLA-A2. Two TCRs engaged the same central peptide feature, although were more permissive at peripheral peptide positions and, accordingly, possessed partially overlapping peptide specificity profiles. The third TCR engaged a flipped peptide conformation, leading to the recognition of off-target peptides sharing little similarity with the cognate peptide. These data show that TCRs specific for a cognate peptide recognize discrete peptide repertoires and reconciles how an individual's limited TCR repertoire following negative selection in the thymus is able to recognize a vastly larger antigenic pool.
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Affiliation(s)
- Charlotte H Coles
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Rachel M Mulvaney
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Sunir Malla
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Andrew Walker
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Kathrine J Smith
- GlaxoSmithKline, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Angharad Lloyd
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Kate L Lowe
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | | | | | - Milos Aleksic
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Jane Harper
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Samantha J Paston
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Zoe Donnellan
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Fiona Chester
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Katrin Wiederhold
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Ross A Robinson
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Andrew Knox
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Andrea R Stacey
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Joseph Dukes
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Emma Baston
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Sue Griffin
- GlaxoSmithKline, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Bent K Jakobsen
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Annelise Vuidepot
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Stephen Harper
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
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13
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Targeting the MHC Ligandome by Use of TCR-Like Antibodies. Antibodies (Basel) 2019; 8:antib8020032. [PMID: 31544838 PMCID: PMC6640717 DOI: 10.3390/antib8020032] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/06/2019] [Accepted: 05/07/2019] [Indexed: 12/11/2022] Open
Abstract
Monoclonal antibodies (mAbs) are valuable as research reagents, in diagnosis and in therapy. Their high specificity, the ease in production, favorable biophysical properties and the opportunity to engineer different properties make mAbs a versatile class of biologics. mAbs targeting peptide–major histocompatibility molecule (pMHC) complexes are often referred to as “TCR-like” mAbs, as pMHC complexes are generally recognized by T-cell receptors (TCRs). Presentation of self- and non-self-derived peptide fragments on MHC molecules and subsequent activation of T cells dictate immune responses in health and disease. This includes responses to infectious agents or cancer but also aberrant responses against harmless self-peptides in autoimmune diseases. The ability of TCR-like mAbs to target specific peptides presented on MHC allows for their use to study peptide presentation or for diagnosis and therapy. This extends the scope of conventional mAbs, which are generally limited to cell-surface or soluble antigens. Herein, we review the strategies used to generate TCR-like mAbs and provide a structural comparison with the analogous TCR in pMHC binding. We further discuss their applications as research tools and therapeutic reagents in preclinical models as well as challenges and limitations associated with their use.
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14
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Pump WC, Kraemer T, Huyton T, Hò GGT, Blasczyk R, Bade-Doeding C. Between Innate and Adaptive Immune Responses: NKG2A, NKG2C, and CD8⁺ T Cell Recognition of HLA-E Restricted Self-Peptides Acquired in the Absence of HLA-Ia. Int J Mol Sci 2019; 20:E1454. [PMID: 30909402 PMCID: PMC6471057 DOI: 10.3390/ijms20061454] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 03/15/2019] [Accepted: 03/19/2019] [Indexed: 12/18/2022] Open
Abstract
On healthy cells the non-classical HLA class Ib molecule HLA-E displays the cognate ligand for the NK cell receptor NKG2A/CD94 when bound to HLA class I signal peptide sequences. In a pathogenic situation when HLA class I is absent, HLA-E is bound to a diverse set of peptides and enables the stimulatory NKG2C/CD94 receptor to bind. The activation of CD8⁺ T cells by certain p:HLA-E complexes illustrates the dual role of this low polymorphic HLA molecule in innate and adaptive immunity. Recent studies revealed a shift in the HLA-E peptide repertoire in cells with defects in the peptide loading complex machinery. We recently showed that HLA-E presents a highly diverse set of peptides in the absence of HLA class Ia and revealed a non-protective feature against NK cell cytotoxicity mediated by these peptides. In the present study we have evaluated the molecular basis for the impaired NK cell inhibition by these peptides and determined the cell surface stability of individual p:HLA-E complexes and their binding efficiency to soluble NKG2A/CD94 or NKG2C/CD94 receptors. Additionally, we analyzed the recognition of these p:HLA-E epitopes by CD8⁺ T cells. We show that non-canonical peptides provide stable cell surface expression of HLA-E, and these p:HLA-E complexes still bind to NKG2/CD94 receptors in a peptide-restricted fashion. Furthermore, individual p:HLA-E complexes elicit activation of CD8⁺ T cells with an effector memory phenotype. These novel HLA-E epitopes provide new implications for therapies targeting cells with abnormal HLA class I expression.
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Affiliation(s)
- Wiebke C Pump
- Institute for Transfusion Medicine, Hannover Medical School, Medical Park, Feodor-Lynen-Str. 5, 30625 Hannover, Germany.
| | - Thomas Kraemer
- Institute for Transfusion Medicine, Hannover Medical School, Medical Park, Feodor-Lynen-Str. 5, 30625 Hannover, Germany.
| | - Trevor Huyton
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
| | - Gia-Gia T Hò
- Institute for Transfusion Medicine, Hannover Medical School, Medical Park, Feodor-Lynen-Str. 5, 30625 Hannover, Germany.
| | - Rainer Blasczyk
- Institute for Transfusion Medicine, Hannover Medical School, Medical Park, Feodor-Lynen-Str. 5, 30625 Hannover, Germany.
| | - Christina Bade-Doeding
- Institute for Transfusion Medicine, Hannover Medical School, Medical Park, Feodor-Lynen-Str. 5, 30625 Hannover, Germany.
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15
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Bradley P, Thomas PG. Using T Cell Receptor Repertoires to Understand the Principles of Adaptive Immune Recognition. Annu Rev Immunol 2019; 37:547-570. [PMID: 30699000 DOI: 10.1146/annurev-immunol-042718-041757] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Adaptive immune recognition is mediated by antigen receptors on B and T cells generated by somatic recombination during lineage development. The high level of diversity resulting from this process posed technical limitations that previously limited the comprehensive analysis of adaptive immune recognition. Advances over the last ten years have produced data and approaches allowing insights into how T cells develop, evolutionary signatures of recombination and selection, and the features of T cell receptors that mediate epitope-specific binding and T cell activation. The size and complexity of these data have necessitated the generation of novel computational and analytical approaches, which are transforming how T cell immunology is conducted. Here we review the development and application of novel biological, theoretical, and computational methods for understanding T cell recognition and discuss the potential for improved models of receptor:antigen interactions.
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Affiliation(s)
- Philip Bradley
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA; .,Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA;
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16
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Abstract
Human leukocyte antigen (HLA)-I molecules generally bind short peptides (8–10 amino acids), although extended HLA-I restricted peptides (>10 amino acids) can be presented to T cells. However, the function of such extended HLA-I epitopes in tumour immunity, and how they would be recognised by T-cell receptors (TCR) remains unclear. Here we show that the structures of two distinct TCRs (TRAV4+TRAJ21+-TRBV28+TRBJ2-3+ and TRAV4+TRAJ8+-TRBV9+TRBJ2-1+), originating from a polyclonal T-cell repertoire, bind to HLA-B*07:02, presenting a 13-amino-acid-long tumour-associated peptide, NY-ESO-160–72. Comparison of the structures reveals that the two TCRs differentially binds NY-ESO-160–72–HLA-B*07:02 complex, and induces differing extent of conformational change of the NY-ESO-160–72 epitope. Accordingly, polyclonal TCR usage towards an extended HLA-I restricted tumour epitope translates to differing TCR recognition modes, whereby extensive flexibility at the TCR–pHLA-I interface engenders recognition. Human leukocyte antigen (HLA) presents peptides to activate T cells, but many aspects in the T cell receptor (TCR)/HLA interaction remain unclear. Here the authors show, via structural data, that two TCRs differentially recognize the same tumour peptide/HLA complex and induce contrasting conformation changes of the peptide.
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17
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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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18
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Yang X, Chen G, Weng NP, Mariuzza RA. Structural basis for clonal diversity of the human T-cell response to a dominant influenza virus epitope. J Biol Chem 2017; 292:18618-18627. [PMID: 28931605 DOI: 10.1074/jbc.m117.810382] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 09/08/2017] [Indexed: 12/20/2022] Open
Abstract
Influenza A virus (IAV) causes an acute infection in humans that is normally eliminated by CD8+ cytotoxic T lymphocytes. Individuals expressing the MHC class I molecule HLA-A2 produce cytotoxic T lymphocytes bearing T-cell receptors (TCRs) that recognize the immunodominant IAV epitope GILGFVFTL (GIL). Most GIL-specific TCRs utilize α/β chain pairs encoded by the TRAV27/TRBV19 gene combination to recognize this relatively featureless peptide epitope (canonical TCRs). However, ∼40% of GIL-specific TCRs express a wide variety of other TRAV/TRBV combinations (non-canonical TCRs). To investigate the structural underpinnings of this remarkable diversity, we determined the crystal structure of a non-canonical GIL-specific TCR (F50) expressing the TRAV13-1/TRBV27 gene combination bound to GIL-HLA-A2 to 1.7 Å resolution. Comparison of the F50-GIL-HLA-A2 complex with the previously published complex formed by a canonical TCR (JM22) revealed that F50 and JM22 engage GIL-HLA-A2 in markedly different orientations. These orientations are distinguished by crossing angles of TCR to peptide-MHC of 29° for F50 versus 69° for JM22 and by a focus by F50 on the C terminus rather than the center of the MHC α1 helix for JM22. In addition, F50, unlike JM22, uses a tryptophan instead of an arginine to fill a critical notch between GIL and the HLA-A2 α2 helix. The F50-GIL-HLA-A2 complex shows that there are multiple structurally distinct solutions to recognizing an identical peptide-MHC ligand with sufficient affinity to elicit a broad anti-IAV response that protects against viral escape and T-cell clonal loss.
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Affiliation(s)
- Xinbo Yang
- From the University of Maryland Institute for Bioscience and Biotechnology Research, W. M. Keck Laboratory for Structural Biology, Rockville, Maryland 20850.,the Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742, and
| | - Guobing Chen
- the Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224
| | - Nan-Ping Weng
- the Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224
| | - Roy A Mariuzza
- From the University of Maryland Institute for Bioscience and Biotechnology Research, W. M. Keck Laboratory for Structural Biology, Rockville, Maryland 20850, .,the Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742, and
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19
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Josephs TM, Grant EJ, Gras S. Molecular challenges imposed by MHC-I restricted long epitopes on T cell immunity. Biol Chem 2017; 398:1027-1036. [PMID: 28141543 DOI: 10.1515/hsz-2016-0305] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 01/25/2017] [Indexed: 11/15/2022]
Abstract
It has widely been accepted that major histocompatibility complex class I molecules (MHC-I) are limited to binding small peptides of 8-10 residues in length. However, this consensus has recently been challenged with the identification of longer peptides (≥11 residues) that can also elicit cytotoxic CD8+ T cell responses. Indeed, a growing number of studies demonstrate that these non-canonical epitopes are important targets for the immune system. As long epitopes represent up to 10% of the peptide repertoire bound to MHC-I molecules, here we review their impact on antigen presentation by MHC-I, TCR recognition, and T cell immunity.
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20
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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: 62] [Impact Index Per Article: 8.9] [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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21
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Deciphering the clinical relevance of allo-human leukocyte antigen cross-reactivity in mediating alloimmunity following transplantation. Curr Opin Organ Transplant 2016; 21:29-39. [PMID: 26575852 DOI: 10.1097/mot.0000000000000264] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
PURPOSE OF REVIEW Despite a growing awareness regarding the potential of cross-reactive virus-specific memory T cells to mediate alloimmunity, there has been limited clinical evaluation on allograft immunopathology. This review will explore published models of human T-cell cross-reactivity and discuss criteria required to drive this mechanism as a contributing cause of allograft dysfunction in transplantation. RECENT FINDINGS Published models of human allogeneic (allo)-human leukocyte antigen (HLA) cross-reactivity have enabled dissection of the cross-reactive T cell receptor/peptide/major histocompatibility complex (TCR/peptide/MHC) interaction. In many of the models, the cross-reactive T cells express a unique TCR, although the relevance of a public cross-reactive TCR repertoire has yet to be determined. Equally, allopeptide identity, a vital component driving cross-recognition, remains unknown in the majority of models thereby prompting further characterization utilizing novel technologies. Although clinical studies examining the presence and impact of specific cross-reactive virus-specific T cells have been minimally explored, the existing data suggest that there may be a marginal set of requirements that need to be satisfied before the potentially damaging effects of allo-HLA cross-reactivity can be realized. SUMMARY Our understanding of allo-HLA cross-reactivity continues to evolve as improved technology and novel strategies allow us to better question the contribution of allo-HLA cross-reactivity in clinically relevant allograft dysfunction.
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22
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How structural adaptability exists alongside HLA-A2 bias in the human αβ TCR repertoire. Proc Natl Acad Sci U S A 2016; 113:E1276-85. [PMID: 26884163 DOI: 10.1073/pnas.1522069113] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
How T-cell receptors (TCRs) can be intrinsically biased toward MHC proteins while simultaneously display the structural adaptability required to engage diverse ligands remains a controversial puzzle. We addressed this by examining αβ TCR sequences and structures for evidence of physicochemical compatibility with MHC proteins. We found that human TCRs are enriched in the capacity to engage a polymorphic, positively charged "hot-spot" region that is almost exclusive to the α1-helix of the common human class I MHC protein, HLA-A*0201 (HLA-A2). TCR binding necessitates hot-spot burial, yielding high energetic penalties that must be offset via complementary electrostatic interactions. Enrichment of negative charges in TCR binding loops, particularly the germ-line loops encoded by the TCR Vα and Vβ genes, provides this capacity and is correlated with restricted positioning of TCRs over HLA-A2. Notably, this enrichment is absent from antibody genes. The data suggest a built-in TCR compatibility with HLA-A2 that biases receptors toward, but does not compel, particular binding modes. Our findings provide an instructional example for how structurally pliant MHC biases can be encoded within TCRs.
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23
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Structural interplay between germline interactions and adaptive recognition determines the bandwidth of TCR-peptide-MHC cross-reactivity. Nat Immunol 2016; 17:87-94. [PMID: 26523866 PMCID: PMC4684756 DOI: 10.1038/ni.3310] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Accepted: 09/29/2015] [Indexed: 01/07/2023]
Abstract
The T cell antigen receptor (TCR)-peptide-major histocompatibility complex (MHC) interface is composed of conserved and diverse regions, yet the relative contribution of each in shaping recognition by T cells remains unclear. Here we isolated cross-reactive peptides with limited homology, which allowed us to compare the structural properties of nine peptides for a single TCR-MHC pair. The TCR's cross-reactivity was rooted in highly similar recognition of an apical 'hot-spot' position in the peptide with tolerance of sequence variation at ancillary positions. Furthermore, we found a striking structural convergence onto a germline-mediated interaction between the TCR CDR1α region and the MHC α2 helix in twelve TCR-peptide-MHC complexes. Our studies suggest that TCR-MHC germline-mediated constraints, together with a focus on a small peptide hot spot, might place limits on peptide antigen cross-reactivity.
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24
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Textoris-Taube K, Keller C, Liepe J, Henklein P, Sidney J, Sette A, Kloetzel PM, Mishto M. The T210M Substitution in the HLA-a*02:01 gp100 Epitope Strongly Affects Overall Proteasomal Cleavage Site Usage and Antigen Processing. J Biol Chem 2015; 290:30417-28. [PMID: 26507656 DOI: 10.1074/jbc.m115.695189] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Indexed: 01/01/2023] Open
Abstract
MHC class I-restricted epitopes, which carry a tumor-specific mutation resulting in improved MHC binding affinity, are preferred T cell receptor targets in innovative adoptive T cell therapies. However, T cell therapy requires efficient generation of the selected epitope. How such mutations may affect proteasome-mediated antigen processing has so far not been studied. Therefore, we analyzed by in vitro experiments the effect on antigen processing and recognition of a T210M exchange, which previously had been introduced into the melanoma gp100209-217 tumor epitope to improve the HLA-A*02:01 binding and its immunogenicity. A quantitative analysis of the main steps of antigen processing shows that the T210M exchange affects proteasomal cleavage site usage within the mutgp100201-230 polypeptide, leading to the generation of an unique set of cleavage products. The T210M substitution qualitatively affects the proteasome-catalyzed generation of spliced and non-spliced peptides predicted to bind HLA-A or -B complexes. The T210M substitution also induces an enhanced production of the mutgp100209-217 epitope and its N-terminally extended peptides. The T210M exchange revealed no effect on ERAP1-mediated N-terminal trimming of the precursor peptides. However, mutant N-terminally extended peptides exhibited significantly increased HLA-A*02:01 binding affinity and elicited CD8(+) T cell stimulation in vitro similar to the wtgp100209-217 epitope. Thus, our experiments demonstrate that amino acid exchanges within an epitope can result in the generation of an altered peptide pool with new antigenic peptides and in a wider CD8(+) T cell response also towards N-terminally extended versions of the minimal epitope.
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Affiliation(s)
- Kathrin Textoris-Taube
- From the Institut für Biochemie, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Christin Keller
- From the Institut für Biochemie, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Juliane Liepe
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, SW7 2AZ, United Kingdom, and
| | - Petra Henklein
- From the Institut für Biochemie, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California 92037
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California 92037
| | - Peter M Kloetzel
- From the Institut für Biochemie, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany,
| | - Michele Mishto
- From the Institut für Biochemie, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany,
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25
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Yang X, Gao M, Chen G, Pierce BG, Lu J, Weng NP, Mariuzza RA. Structural Basis for Clonal Diversity of the Public T Cell Response to a Dominant Human Cytomegalovirus Epitope. J Biol Chem 2015; 290:29106-19. [PMID: 26429912 DOI: 10.1074/jbc.m115.691311] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Indexed: 11/06/2022] Open
Abstract
Cytomegalovirus (CMV) is a ubiquitous and persistent human pathogen that is kept in check by CD8(+) cytotoxic T lymphocytes. Individuals expressing the major histocompatibility complex (MHC) class I molecule HLA-A2 produce cytotoxic T lymphocytes bearing T cell receptors (TCRs) that recognize the immunodominant CMV epitope NLVPMVATV (NLV). The NLV-specific T cell repertoire is characterized by a high prevalence of TCRs that are frequently observed in multiple unrelated individuals. These public TCRs feature identical, or nearly identical, complementarity-determining region 3α (CDR3α) and/or CDR3β sequences. The TCRs may express public CDR3α motifs alone, public CDR3β motifs alone, or dual public CDR3αβ motifs. In addition, the same public CDR3α motif may pair with different CDR3β motifs (and the reverse), giving rise to highly diverse NLV-specific TCR repertoires. To investigate the structural underpinnings of this clonal diversity, we determined crystal structures of two public TCRs (C7 and C25) in complex with NLV·HLA-A2. These TCRs utilize completely different CDR3α and CDR3β motifs that, in addition, can associate with multiple variable α and variable β regions in NLV-specific T cell repertoires. The C7·NLV·HLA-A2 and C25·NLV·HLA-A2 complexes exhibit divergent TCR footprints on peptide-MHC such that C25 is more focused on the central portion of the NLV peptide than is C7. These structures combined with molecular modeling show how the public CDR3α motif of C25 may associate with different variable α regions and how the public CDR3α motif of C7 may pair with different CDR3β motifs. This interchangeability of TCR V regions and CDR3 motifs permits multiple structural solutions to binding an identical peptide-MHC ligand and thereby the generation of a clonally diverse public T cell response to CMV.
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Affiliation(s)
- Xinbo Yang
- From the University of Maryland Institute for Bioscience and Biotechnology Research, W. M. Keck Laboratory for Structural Biology, Rockville, Maryland 20850, Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742
| | - Mingming Gao
- From the University of Maryland Institute for Bioscience and Biotechnology Research, W. M. Keck Laboratory for Structural Biology, Rockville, Maryland 20850, Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742
| | - Guobing Chen
- Lymphocyte Differentiation Section, Laboratory of Molecular Biology and Immunology, NIA, National Institutes of Health, Baltimore, Maryland 21224, and
| | - Brian G Pierce
- From the University of Maryland Institute for Bioscience and Biotechnology Research, W. M. Keck Laboratory for Structural Biology, Rockville, Maryland 20850
| | - Jinghua Lu
- Structural Immunology Section, Laboratory of Immunogenetics, NIAID, National Institutes of Health, Rockville, Maryland 20852
| | - Nan-Ping Weng
- Lymphocyte Differentiation Section, Laboratory of Molecular Biology and Immunology, NIA, National Institutes of Health, Baltimore, Maryland 21224, and
| | - Roy A Mariuzza
- From the University of Maryland Institute for Bioscience and Biotechnology Research, W. M. Keck Laboratory for Structural Biology, Rockville, Maryland 20850, Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742,
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26
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Rödström KEJ, Regenthal P, Lindkvist-Petersson K. Structure of Staphylococcal Enterotoxin E in Complex with TCR Defines the Role of TCR Loop Positioning in Superantigen Recognition. PLoS One 2015; 10:e0131988. [PMID: 26147596 PMCID: PMC4492778 DOI: 10.1371/journal.pone.0131988] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 06/09/2015] [Indexed: 11/18/2022] Open
Abstract
T cells are crucial players in cell-mediated immunity. The specificity of their receptor, the T cell receptor (TCR), is central for the immune system to distinguish foreign from host antigens. Superantigens are bacterial toxins capable of inducing a toxic immune response by cross-linking the TCR and the major histocompatibility complex (MHC) class II and circumventing the antigen specificity. Here, we present the structure of staphylococcal enterotoxin E (SEE) in complex with a human T cell receptor, as well as the unligated T cell receptor structure. There are clear structural changes in the TCR loops upon superantigen binding. In particular, the HV4 loop moves to circumvent steric clashes upon complex formation. In addition, a predicted ternary model of SEE in complex with both TCR and MHC class II displays intermolecular contacts between the TCR α-chain and the MHC, suggesting that the TCR α-chain is of importance for complex formation.
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Affiliation(s)
- Karin E. J. Rödström
- Department of Experimental Medical Science, Lund University, BMC C13, 22 184, Lund, Sweden
| | - Paulina Regenthal
- Department of Experimental Medical Science, Lund University, BMC C13, 22 184, Lund, Sweden
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27
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Miles JJ, McCluskey J, Rossjohn J, Gras S. Understanding the complexity and malleability of T-cell recognition. Immunol Cell Biol 2015; 93:433-41. [PMID: 25582337 DOI: 10.1038/icb.2014.112] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 11/21/2014] [Accepted: 11/23/2014] [Indexed: 12/15/2022]
Abstract
T cells are the master regulators of immune system function, continually walking the biological tightrope between adequate host defence and accidental host pathology. Tolerance is maintained or broken through an intricate structural interplay between the T-cell receptor (TCR) and major histocompatibility complex (MHC) molecule cradling peptide antigens (p). Recent advances in structural biology have shown that the TCR/pMHC interface is surprising precise and extraordinarily malleable. We have seen that seemingly minor changes in the TCR/pMHC interface can abrogate function, as well as substantial conformational changes before and after TCR docking. Our understanding of T-cell biology has also been altered with the knowledge that MHC molecules can bind not only peptides, but also an array of natural and synthetic compounds. Here, we review some examples of the precision and flexibility intrinsic to the TCR/p/MHCI axis.
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Affiliation(s)
- John J Miles
- 1] QIMR Berghofer Medical Research Institute and QIMR Berghofer Centre for Immunotherapy and Vaccine Development, Brisbane, Queensland, Australia [2] School of Medicine, The University of Queensland, Brisbane, Queensland, Australia [3] Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, Wales, UK
| | - James McCluskey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia
| | - Jamie Rossjohn
- 1] Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, Wales, UK [2] Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria, Australia [3] ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | - Stephanie Gras
- 1] Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria, Australia [2] ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
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28
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Hassan C, Chabrol E, Jahn L, Kester MGD, de Ru AH, Drijfhout JW, Rossjohn J, Falkenburg JHF, Heemskerk MHM, Gras S, van Veelen PA. Naturally processed non-canonical HLA-A*02:01 presented peptides. J Biol Chem 2014; 290:2593-603. [PMID: 25505266 DOI: 10.1074/jbc.m114.607028] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Human leukocyte antigen (HLA) class I molecules generally present peptides (p) of 8 to 11 amino acids (aa) in length. Although an increasing number of examples with lengthy (>11 aa) peptides, presented mostly by HLA-B alleles, have been reported. Here we characterize HLA-A*02:01 restricted, in addition to the HLA-B*0702 and HLA-B*4402 restricted, lengthy peptides (>11 aa) arising from the B-cell ligandome. We analyzed a number of 15-mer peptides presented by HLA-A*02:01, and confirmed pHLA-I formation by HLA folding and thermal stability assays. Surprisingly the binding affinity and stability of the 15-mer epitopes in complex with HLA-A*02:01 were comparable with the values observed for canonical length (8 to 11 aa) HLA-A*02:01-restricted peptides. We solved the structures of two 15-mer epitopes in complex with HLA-A*02:01, within which the peptides adopted distinct super-bulged conformations. Moreover, we demonstrate that T-cells can recognize the 15-mer peptides in the context of HLA-A*02:01, indicating that these 15-mer peptides represent immunogenic ligands. Collectively, our data expand our understanding of longer epitopes in the context of HLA-I, highlighting that they are not limited to the HLA-B family, but can bind the ubiquitous HLA-A*02:01 molecule, and play an important role in T-cell immunity.
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Affiliation(s)
- Chopie Hassan
- From the Departments of Immunohematology and Blood Transfusion and
| | - Eric Chabrol
- the Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton 3800, Australia
| | - Lorenz Jahn
- Hematology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Michel G D Kester
- Hematology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Arnoud H de Ru
- From the Departments of Immunohematology and Blood Transfusion and
| | - Jan W Drijfhout
- From the Departments of Immunohematology and Blood Transfusion and
| | - Jamie Rossjohn
- the Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton 3800, Australia, the ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton 3800, Australia, and the Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, Wales, United Kingdom
| | | | | | - Stephanie Gras
- the Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton 3800, Australia, the ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton 3800, Australia, and
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29
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Rossjohn J, Gras S, Miles JJ, Turner SJ, Godfrey DI, McCluskey J. T cell antigen receptor recognition of antigen-presenting molecules. Annu Rev Immunol 2014; 33:169-200. [PMID: 25493333 DOI: 10.1146/annurev-immunol-032414-112334] [Citation(s) in RCA: 508] [Impact Index Per Article: 50.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The Major Histocompatibility Complex (MHC) locus encodes classical MHC class I and MHC class II molecules and nonclassical MHC-I molecules. The architecture of these molecules is ideally suited to capture and present an array of peptide antigens (Ags). In addition, the CD1 family members and MR1 are MHC class I-like molecules that bind lipid-based Ags and vitamin B precursors, respectively. These Ag-bound molecules are subsequently recognized by T cell antigen receptors (TCRs) expressed on the surface of T lymphocytes. Structural and associated functional studies have been highly informative in providing insight into these interactions, which are crucial to immunity, and how they can lead to aberrant T cell reactivity. Investigators have determined over thirty unique TCR-peptide-MHC-I complex structures and twenty unique TCR-peptide-MHC-II complex structures. These investigations have shown a broad consensus in docking geometry and provided insight into MHC restriction. Structural studies on TCR-mediated recognition of lipid and metabolite Ags have been mostly confined to TCRs from innate-like natural killer T cells and mucosal-associated invariant T cells, respectively. These studies revealed clear differences between TCR-lipid-CD1, TCR-metabolite-MR1, and TCR-peptide-MHC recognition. Accordingly, TCRs show remarkable structural and biological versatility in engaging different classes of Ag that are presented by polymorphic and monomorphic Ag-presenting molecules of the immune system.
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Affiliation(s)
- Jamie Rossjohn
- 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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Reiser JB, Legoux F, Gras S, Trudel E, Chouquet A, Léger A, Le Gorrec M, Machillot P, Bonneville M, Saulquin X, Housset D. Analysis of relationships between peptide/MHC structural features and naive T cell frequency in humans. THE JOURNAL OF IMMUNOLOGY 2014; 193:5816-26. [PMID: 25392532 DOI: 10.4049/jimmunol.1303084] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The structural rules governing peptide/MHC (pMHC) recognition by T cells remain unclear. To address this question, we performed a structural characterization of several HLA-A2/peptide complexes and assessed in parallel their antigenicity, by analyzing the frequency of the corresponding Ag-specific naive T cells in A2(+) and A2(-) individuals, as well as within CD4(+) and CD8(+) subsets. We were able to find a correlation between specific naive T cell frequency and peptide solvent accessibility and/or mobility for a subset of moderately prominent peptides. However, one single structural parameter of the pMHC complexes could not be identified to explain each peptide antigenicity. Enhanced pMHC antigenicity was associated with both highly biased TRAV usage, possibly reflecting favored interaction between particular pMHC complexes and germline TRAV loops, and peptide structural features allowing interactions with a broad range of permissive CDR3 loops. In this context of constrained TCR docking mode, an optimal peptide solvent exposed surface leading to an optimal complementarity with TCR interface may constitute one of the key features leading to high frequency of specific T cells. Altogether our results suggest that frequency of specific T cells depends on the fine-tuning of several parameters, the structural determinants governing TCR-pMHC interaction being just one of them.
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Affiliation(s)
- Jean-Baptiste Reiser
- Université de Grenoble Alpes, Institut de Biologie Structurale, F-38044 Grenoble, France; Commissariat à l'énergie atomique et aux énergies alternatives, Direction des sciences du vivant, Institut de Biologie Structurale, F-38044 Grenoble, France; Centre national de la recherche scientifique, Institut de Biologie Structurale, F-38044 Grenoble, France
| | - François Legoux
- Institut national de la santé et de la recherche médicale, Unité mixte de recherche 892, Centre de Recherche en Cancérologie Nantes Angers, F-44000 Nantes, France; and
| | - Stéphanie Gras
- Université de Grenoble Alpes, Institut de Biologie Structurale, F-38044 Grenoble, France; Commissariat à l'énergie atomique et aux énergies alternatives, Direction des sciences du vivant, Institut de Biologie Structurale, F-38044 Grenoble, France; Centre national de la recherche scientifique, Institut de Biologie Structurale, F-38044 Grenoble, France
| | - Eric Trudel
- Université de Grenoble Alpes, Institut de Biologie Structurale, F-38044 Grenoble, France; Commissariat à l'énergie atomique et aux énergies alternatives, Direction des sciences du vivant, Institut de Biologie Structurale, F-38044 Grenoble, France; Centre national de la recherche scientifique, Institut de Biologie Structurale, F-38044 Grenoble, France
| | - Anne Chouquet
- Université de Grenoble Alpes, Institut de Biologie Structurale, F-38044 Grenoble, France; Commissariat à l'énergie atomique et aux énergies alternatives, Direction des sciences du vivant, Institut de Biologie Structurale, F-38044 Grenoble, France; Centre national de la recherche scientifique, Institut de Biologie Structurale, F-38044 Grenoble, France
| | - Alexandra Léger
- Institut national de la santé et de la recherche médicale, Unité mixte de recherche 892, Centre de Recherche en Cancérologie Nantes Angers, F-44000 Nantes, France; and
| | - Madalen Le Gorrec
- Université de Grenoble Alpes, Institut de Biologie Structurale, F-38044 Grenoble, France; Commissariat à l'énergie atomique et aux énergies alternatives, Direction des sciences du vivant, Institut de Biologie Structurale, F-38044 Grenoble, France; Centre national de la recherche scientifique, Institut de Biologie Structurale, F-38044 Grenoble, France
| | - Paul Machillot
- Université de Grenoble Alpes, Institut de Biologie Structurale, F-38044 Grenoble, France; Commissariat à l'énergie atomique et aux énergies alternatives, Direction des sciences du vivant, Institut de Biologie Structurale, F-38044 Grenoble, France; Centre national de la recherche scientifique, Institut de Biologie Structurale, F-38044 Grenoble, France
| | - Marc Bonneville
- Institut national de la santé et de la recherche médicale, Unité mixte de recherche 892, Centre de Recherche en Cancérologie Nantes Angers, F-44000 Nantes, France; and
| | - Xavier Saulquin
- Institut national de la santé et de la recherche médicale, Unité mixte de recherche 892, Centre de Recherche en Cancérologie Nantes Angers, F-44000 Nantes, France; and Université de Nantes, F-44000 Nantes, France
| | - Dominique Housset
- Université de Grenoble Alpes, Institut de Biologie Structurale, F-38044 Grenoble, France; Commissariat à l'énergie atomique et aux énergies alternatives, Direction des sciences du vivant, Institut de Biologie Structurale, F-38044 Grenoble, France; Centre national de la recherche scientifique, Institut de Biologie Structurale, F-38044 Grenoble, France;
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31
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Rangarajan S, Mariuzza RA. T cell receptor bias for MHC: co-evolution or co-receptors? Cell Mol Life Sci 2014; 71:3059-68. [PMID: 24633202 PMCID: PMC11113676 DOI: 10.1007/s00018-014-1600-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 02/06/2014] [Accepted: 02/28/2014] [Indexed: 10/25/2022]
Abstract
In contrast to antibodies, which recognize antigens in native form, αβ T cell receptors (TCRs) only recognize antigens as peptide fragments bound to MHC molecules, a feature known as MHC restriction. The mechanism by which MHC restriction is imposed on the TCR repertoire is an unsolved problem that has generated considerable debate. Two principal models have been advanced to explain TCR bias for MHC. According to the germline model, MHC restriction is intrinsic to TCR structure because TCR and MHC molecules have co-evolved to conserve germline-encoded TCR sequences with the ability to bind MHC, while eliminating TCR sequences lacking MHC reactivity. According to the selection model, MHC restriction is not intrinsic to TCR structure, but is imposed by the CD4 and CD8 co-receptors that promote signaling by delivering the Src tyrosine kinase Lck to TCR-MHC complexes through co-receptor binding to MHC during positive selection. Here, we review the evidence for and against each model and conclude that both contribute to determining TCR specificity, although their relative contributions remain to be defined. Thus, TCR bias for MHC reflects not only germline-encoded TCR-MHC interactions but also the requirement to form a ternary complex with the CD4 or CD8 co-receptor that is geometrically competent to deliver a maturation signal to double-positive thymocytes during T cell selection.
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Affiliation(s)
- Sneha Rangarajan
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850 USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742 USA
| | - Roy A. Mariuzza
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850 USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742 USA
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32
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Stadinski BD, Trenh P, Duke B, Huseby PG, Li G, Stern LJ, Huseby ES. Effect of CDR3 sequences and distal V gene residues in regulating TCR-MHC contacts and ligand specificity. THE JOURNAL OF IMMUNOLOGY 2014; 192:6071-82. [PMID: 24813203 DOI: 10.4049/jimmunol.1303209] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The mature T cell repertoire has the ability to orchestrate immunity to a wide range of potential pathogen challenges. This ability stems from thymic development producing individual T cell clonotypes that express TCRs with unique patterns of Ag reactivity. The Ag specificity of TCRs is created from the combinatorial pairing of one of a set of germline encoded TCR Vα and Vβ gene segments with randomly created CDR3 sequences. How the amalgamation of germline encoded and randomly created TCR sequences results in Ag receptors with unique patterns of ligand specificity is not fully understood. Using cellular, biophysical, and structural analyses, we show that CDR3α residues can modulate the geometry in which TCRs bind peptide-MHC (pMHC), governing whether and how germline encoded TCR Vα and Vβ residues interact with MHC. In addition, a CDR1α residue that is positioned distal to the TCR-pMHC binding interface is shown to contribute to the peptide specificity of T cells. These findings demonstrate that the specificity of individual T cell clonotypes arises not only from TCR residues that create direct contacts with the pMHC, but also from a collection of indirect effects that modulate how TCR residues are used to bind pMHC.
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Affiliation(s)
- Brian D Stadinski
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01655; and
| | - Peter Trenh
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01655; and
| | - Brian Duke
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01655; and
| | - Priya G Huseby
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01655; and
| | - Guoqi Li
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01655; and
| | - Lawrence J Stern
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01655; and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655
| | - Eric S Huseby
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01655; and
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33
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Predisposed αβ T cell antigen receptor recognition of MHC and MHC-I like molecules? Curr Opin Immunol 2013; 25:653-9. [PMID: 23993410 DOI: 10.1016/j.coi.2013.07.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 07/28/2013] [Accepted: 07/30/2013] [Indexed: 12/11/2022]
Abstract
The diverse αβ T cell receptor (TCR) repertoire exhibits versatility in its ability to generate antigen (Ag) receptors capable of interacting with polymorphic Major Histocompatibility Complex (MHC) molecules and monomorphic MHC-I like molecules, including the CD1 and MR1 families. Collectively, these evolutionarily related Ag-presenting molecules present peptides, lipids and vitamin B metabolites for T cell surveillance. Interestingly, whilst common TCR gene usage can underpin recognition of these distinct classes of Ags, it is unclear whether the 'rules' that govern αβTCR-Ag MHC interactions are shared. We highlight recent observations in the context of TCR biases towards MHC and MHC-I like molecules.
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34
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Burrows SR, Miles JJ. Immune parameters to consider when choosing T-cell receptors for therapy. Front Immunol 2013; 4:229. [PMID: 23935599 PMCID: PMC3733007 DOI: 10.3389/fimmu.2013.00229] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Accepted: 07/22/2013] [Indexed: 11/13/2022] Open
Abstract
T-cell receptor (TCR) therapy has arrived as a realistic treatment option for many human diseases. TCR gene therapy allows for the mass redirection of T-cells against a defined antigen while high affinity TCR engineering allows for the creation of a new class of soluble drugs. However, deciding which TCR blueprint to take forward for gene therapy or engineering is difficult. More than one quintillion TCR combinations can be generated by somatic recombination and we are only now beginning to appreciate that not all are functionally equal. TCRs can exhibit high or low degrees of HLA-restricted cross-reactivity and alloreact against one or a combination of HLA alleles. Identifying TCR candidates with high specificity and minimal cross-reactivity/alloreactivity footprints before engineering is obviously highly desirable. Here we will summarize what we currently know about TCR biology with regard to immunoengineering.
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Affiliation(s)
- Scott R Burrows
- Human Immunity Laboratory and Cellular Immunology Laboratory, Queensland Institute of Medical Research , Brisbane, QLD , Australia ; School of Medicine, The University of Queensland , Brisbane, QLD , Australia
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35
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Venturi V, Rudd BD, Davenport MP. Specificity, promiscuity, and precursor frequency in immunoreceptors. Curr Opin Immunol 2013; 25:639-45. [PMID: 23880376 DOI: 10.1016/j.coi.2013.07.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Revised: 07/01/2013] [Accepted: 07/01/2013] [Indexed: 10/26/2022]
Abstract
The immune system is comprised of various immune cell populations that utilize a spectrum of immunoreceptors characterized by different levels of specificity, diversity, and prevalence within a host and across a population. These range from the universal receptors employed by both innate cells and innate-like cells, such as NKT and MAIT cells, through to receptors expressed on T cells with sporadic incidence. Here we review recent advances in understanding the molecular mechanisms that drive the observed spectra of T cell receptors in vivo.
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Affiliation(s)
- Vanessa Venturi
- Computational Biology Group, Centre for Vascular Research, University of New South Wales, Kensington, New South Wales 2052, Australia.
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