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Cole DK, Fuller A, Dolton G, Zervoudi E, Legut M, Miles K, Blanchfield L, Madura F, Holland CJ, Bulek AM, Bridgeman JS, Miles JJ, Schauenburg AJA, Beck K, Evavold BD, Rizkallah PJ, Sewell AK. Dual Molecular Mechanisms Govern Escape at Immunodominant HLA A2-Restricted HIV Epitope. Front Immunol 2017; 8:1503. [PMID: 29209312 PMCID: PMC5701626 DOI: 10.3389/fimmu.2017.01503] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 10/25/2017] [Indexed: 12/05/2022] Open
Abstract
Serial accumulation of mutations to fixation in the SLYNTVATL (SL9) immunodominant, HIV p17 Gag-derived, HLA A2-restricted cytotoxic T lymphocyte epitope produce the SLFNTIAVL triple mutant “ultimate” escape variant. These mutations in solvent-exposed residues are believed to interfere with TCR recognition, although confirmation has awaited structural verification. Here, we solved a TCR co-complex structure with SL9 and the triple escape mutant to determine the mechanism of immune escape in this eminent system. We show that, in contrast to prevailing hypotheses, the main TCR contact residue is 4N and the dominant mechanism of escape is not via lack of TCR engagement. Instead, mutation of solvent-exposed residues in the peptide destabilise the peptide–HLA and reduce peptide density at the cell surface. These results highlight the extraordinary lengths that HIV employs to evade detection by high-affinity TCRs with a broad peptide-binding footprint and necessitate re-evaluation of this exemplar model of HIV TCR escape.
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Affiliation(s)
- David K Cole
- Cardiff University School of Medicine, University Hospital, Heath Park, Cardiff, United Kingdom
| | - Anna Fuller
- Cardiff University School of Medicine, University Hospital, Heath Park, Cardiff, United Kingdom
| | - Garry Dolton
- Cardiff University School of Medicine, University Hospital, Heath Park, Cardiff, United Kingdom
| | - Efthalia Zervoudi
- Cardiff University School of Medicine, University Hospital, Heath Park, Cardiff, United Kingdom
| | - Mateusz Legut
- Cardiff University School of Medicine, University Hospital, Heath Park, Cardiff, United Kingdom
| | - Kim Miles
- Cardiff University School of Medicine, University Hospital, Heath Park, Cardiff, United Kingdom
| | - Lori Blanchfield
- Department of Microbiology and Immunology, Emory University, Atlanta, GA, United States
| | - Florian Madura
- Cardiff University School of Medicine, University Hospital, Heath Park, Cardiff, United Kingdom
| | - Christopher J Holland
- Cardiff University School of Medicine, University Hospital, Heath Park, Cardiff, United Kingdom
| | - Anna M Bulek
- Cardiff University School of Medicine, University Hospital, Heath Park, Cardiff, United Kingdom
| | - John S Bridgeman
- Cardiff University School of Medicine, University Hospital, Heath Park, Cardiff, United Kingdom
| | - John J Miles
- Cardiff University School of Medicine, University Hospital, Heath Park, Cardiff, United Kingdom.,James Cook University, Cairns, QLD, Australia
| | - Andrea J A Schauenburg
- Cardiff University School of Medicine, University Hospital, Heath Park, Cardiff, United Kingdom
| | - Konrad Beck
- Cardiff University School of Dentistry, University Hospital, Heath Park, Cardiff, United Kingdom
| | - Brian D Evavold
- Department of Microbiology and Immunology, Emory University, Atlanta, GA, United States
| | - Pierre J Rizkallah
- Cardiff University School of Medicine, University Hospital, Heath Park, Cardiff, United Kingdom
| | - Andrew K Sewell
- Cardiff University School of Medicine, University Hospital, Heath Park, Cardiff, United Kingdom
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Neller MA, Ladell K, McLaren JE, Matthews KK, Gostick E, Pentier JM, Dolton G, Schauenburg AJA, Koning D, Fontaine Costa AICA, Watkins TS, Venturi V, Smith C, Khanna R, Miners K, Clement M, Wooldridge L, Cole DK, van Baarle D, Sewell AK, Burrows SR, Price DA, Miles JJ. Naive CD8⁺ T-cell precursors display structured TCR repertoires and composite antigen-driven selection dynamics. Immunol Cell Biol 2015; 93:625-33. [PMID: 25801351 PMCID: PMC4533101 DOI: 10.1038/icb.2015.17] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 01/04/2015] [Accepted: 01/22/2015] [Indexed: 02/07/2023]
Abstract
Basic parameters of the naive antigen (Ag)-specific T-cell repertoire in humans remain poorly defined. Systematic characterization of this ‘ground state' immunity in comparison with memory will allow a better understanding of clonal selection during immune challenge. Here, we used high-definition cell isolation from umbilical cord blood samples to establish the baseline frequency, phenotype and T-cell antigen receptor (TCR) repertoire of CD8+ T-cell precursor populations specific for a range of viral and self-derived Ags. Across the board, these precursor populations were phenotypically naive and occurred with hierarchical frequencies clustered by Ag specificity. The corresponding patterns of TCR architecture were highly ordered and displayed partial overlap with adult memory, indicating biased structuring of the T-cell repertoire during Ag-driven selection. Collectively, these results provide new insights into the complex nature and dynamics of the naive T-cell compartment.
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Affiliation(s)
- Michelle A Neller
- Human Immunity Laboratory, Cellular Immunology Laboratory and Tumour Immunology Laboratory, Queensland Institute of Medical Research, Brisbane, QLD, Australia
| | - Kristin Ladell
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - James E McLaren
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Katherine K Matthews
- Human Immunity Laboratory, Cellular Immunology Laboratory and Tumour Immunology Laboratory, Queensland Institute of Medical Research, Brisbane, QLD, Australia
| | - Emma Gostick
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Johanne M Pentier
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Garry Dolton
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Andrea J A Schauenburg
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Dan Koning
- Department of Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Thomas S Watkins
- Human Immunity Laboratory, Cellular Immunology Laboratory and Tumour Immunology Laboratory, Queensland Institute of Medical Research, Brisbane, QLD, Australia
| | - Vanessa Venturi
- Computational Biology Unit, Centre for Vascular Research, University of New South Wales, Kensington, NSW, Australia
| | - Corey Smith
- Human Immunity Laboratory, Cellular Immunology Laboratory and Tumour Immunology Laboratory, Queensland Institute of Medical Research, Brisbane, QLD, Australia
| | - Rajiv Khanna
- Human Immunity Laboratory, Cellular Immunology Laboratory and Tumour Immunology Laboratory, Queensland Institute of Medical Research, Brisbane, QLD, Australia
| | - Kelly Miners
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Mathew Clement
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Linda Wooldridge
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - David K Cole
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Debbie van Baarle
- Department of Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Andrew K Sewell
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Scott R Burrows
- 1] Human Immunity Laboratory, Cellular Immunology Laboratory and Tumour Immunology Laboratory, Queensland Institute of Medical Research, Brisbane, QLD, Australia [2] School of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - David A Price
- 1] Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK [2] Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - John J Miles
- 1] Human Immunity Laboratory, Cellular Immunology Laboratory and Tumour Immunology Laboratory, Queensland Institute of Medical Research, Brisbane, QLD, Australia [2] Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK [3] School of Medicine, The University of Queensland, Brisbane, QLD, Australia
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Cole DK, Miles KM, Madura F, Holland CJ, Schauenburg AJA, Godkin AJ, Bulek AM, Fuller A, Akpovwa HJE, Pymm PG, Liddy N, Sami M, Li Y, Rizkallah PJ, Jakobsen BK, Sewell AK. T-cell receptor (TCR)-peptide specificity overrides affinity-enhancing TCR-major histocompatibility complex interactions. J Biol Chem 2013; 289:628-38. [PMID: 24196962 PMCID: PMC3887192 DOI: 10.1074/jbc.m113.522110] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
αβ T-cell receptors (TCRs) engage antigens using complementarity-determining region (CDR) loops that are either germ line-encoded (CDR1 and CDR2) or somatically rearranged (CDR3). TCR ligands compose a presentation platform (major histocompatibility complex (MHC)) and a variable antigenic component consisting of a short “foreign” peptide. The sequence of events when the TCR engages its peptide-MHC (pMHC) ligand remains unclear. Some studies suggest that the germ line elements of the TCR engage the MHC prior to peptide scanning, but this order of binding is difficult to reconcile with some TCR-pMHC structures. Here, we used TCRs that exhibited enhanced pMHC binding as a result of mutations in either CDR2 and/or CDR3 loops, that bound to the MHC or peptide, respectively, to dissect the roles of these loops in stabilizing TCR-pMHC interactions. Our data show that TCR-peptide interactions play a strongly dominant energetic role providing a binding mode that is both temporally and energetically complementary with a system requiring positive selection by self-pMHC in the thymus and rapid recognition of non-self-pMHC in the periphery.
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Affiliation(s)
- David K Cole
- From Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN
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Madura F, Rizkallah PJ, Miles KM, Holland CJ, Bulek AM, Fuller A, Schauenburg AJA, Miles JJ, Liddy N, Sami M, Li Y, Hossain M, Baker BM, Jakobsen BK, Sewell AK, Cole DK. T-cell receptor specificity maintained by altered thermodynamics. J Biol Chem 2013; 288:18766-75. [PMID: 23698002 PMCID: PMC3696650 DOI: 10.1074/jbc.m113.464560] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The T-cell receptor (TCR) recognizes peptides bound to major histocompatibility molecules (MHC) and allows T-cells to interrogate the cellular proteome for internal anomalies from the cell surface. The TCR contacts both MHC and peptide in an interaction characterized by weak affinity (KD = 100 nM to 270 μM). We used phage-display to produce a melanoma-specific TCR (α24β17) with a 30,000-fold enhanced binding affinity (KD = 0.6 nM) to aid our exploration of the molecular mechanisms utilized to maintain peptide specificity. Remarkably, although the enhanced affinity was mediated primarily through new TCR-MHC contacts, α24β17 remained acutely sensitive to modifications at every position along the peptide backbone, mimicking the specificity of the wild type TCR. Thermodynamic analyses revealed an important role for solvation in directing peptide specificity. These findings advance our understanding of the molecular mechanisms that can govern the exquisite peptide specificity characteristic of TCR recognition.
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Affiliation(s)
- Florian Madura
- Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
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Clement M, Ladell K, Ekeruche-Makinde J, Miles JJ, Edwards ESJ, Dolton G, Williams T, Schauenburg AJA, Cole DK, Lauder SN, Gallimore AM, Godkin AJ, Burrows SR, Price DA, Sewell AK, Wooldridge L. Anti-CD8 antibodies can trigger CD8+ T cell effector function in the absence of TCR engagement and improve peptide-MHCI tetramer staining. J Immunol 2011; 187:654-63. [PMID: 21677135 PMCID: PMC3145095 DOI: 10.4049/jimmunol.1003941] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
CD8(+) T cells recognize immunogenic peptides presented at the cell surface bound to MHCI molecules. Ag recognition involves the binding of both TCR and CD8 coreceptor to the same peptide-MHCI (pMHCI) ligand. Specificity is determined by the TCR, whereas CD8 mediates effects on Ag sensitivity. Anti-CD8 Abs have been used extensively to examine the role of CD8 in CD8(+) T cell activation. However, as previous studies have yielded conflicting results, it is unclear from the literature whether anti-CD8 Abs per se are capable of inducing effector function. In this article, we report on the ability of seven monoclonal anti-human CD8 Abs to activate six human CD8(+) T cell clones with a total of five different specificities. Six of seven anti-human CD8 Abs tested did not activate CD8(+) T cells. In contrast, one anti-human CD8 Ab, OKT8, induced effector function in all CD8(+) T cells examined. Moreover, OKT8 was found to enhance TCR/pMHCI on-rates and, as a consequence, could be used to improve pMHCI tetramer staining and the visualization of Ag-specific CD8(+) T cells. The anti-mouse CD8 Abs, CT-CD8a and CT-CD8b, also activated CD8(+) T cells despite opposing effects on pMHCI tetramer staining. The observed heterogeneity in the ability of anti-CD8 Abs to trigger T cell effector function provides an explanation for the apparent incongruity observed in previous studies and should be taken into consideration when interpreting results generated with these reagents. Furthermore, the ability of Ab-mediated CD8 engagement to deliver an activation signal underscores the importance of CD8 in CD8(+) T cell signaling.
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Affiliation(s)
- Mathew Clement
- Department of Infection, Immunity and Biochemisty, Henry Wellcome Building, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Kristin Ladell
- Department of Infection, Immunity and Biochemisty, Henry Wellcome Building, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Julia Ekeruche-Makinde
- Department of Infection, Immunity and Biochemisty, Henry Wellcome Building, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - John J. Miles
- Department of Infection, Immunity and Biochemisty, Henry Wellcome Building, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Emily S. J. Edwards
- Department of Infection, Immunity and Biochemisty, Henry Wellcome Building, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Garry Dolton
- Department of Infection, Immunity and Biochemisty, Henry Wellcome Building, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Tamsin Williams
- Department of Infection, Immunity and Biochemisty, Henry Wellcome Building, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Andrea J. A. Schauenburg
- Department of Infection, Immunity and Biochemisty, Henry Wellcome Building, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - David K. Cole
- Department of Infection, Immunity and Biochemisty, Henry Wellcome Building, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Sarah N. Lauder
- Department of Infection, Immunity and Biochemisty, Henry Wellcome Building, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Awen M. Gallimore
- Department of Infection, Immunity and Biochemisty, Henry Wellcome Building, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Andrew J. Godkin
- Department of Infection, Immunity and Biochemisty, Henry Wellcome Building, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Scott R. Burrows
- Cellular Immunology Laboratory, Department of Infectious Disease and Immunology, Queensland Institute of Medical Research, Brisbane 4029, Australia
| | - David A. Price
- Department of Infection, Immunity and Biochemisty, Henry Wellcome Building, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Andrew K. Sewell
- Department of Infection, Immunity and Biochemisty, Henry Wellcome Building, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Linda Wooldridge
- Department of Infection, Immunity and Biochemisty, Henry Wellcome Building, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
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Miles JJ, Bulek AM, Cole DK, Gostick E, Schauenburg AJA, Dolton G, Venturi V, Davenport MP, Tan MP, Burrows SR, Wooldridge L, Price DA, Rizkallah PJ, Sewell AK. Genetic and structural basis for selection of a ubiquitous T cell receptor deployed in Epstein-Barr virus infection. PLoS Pathog 2010; 6:e1001198. [PMID: 21124993 PMCID: PMC2987824 DOI: 10.1371/journal.ppat.1001198] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2010] [Accepted: 10/15/2010] [Indexed: 12/02/2022] Open
Abstract
Despite the ∼10(18) αβ T cell receptor (TCR) structures that can be randomly manufactured by the human thymus, some surface more frequently than others. The pinnacles of this distortion are public TCRs, which exhibit amino acid-identical structures across different individuals. Public TCRs are thought to result from both recombinatorial bias and antigen-driven selection, but the mechanisms that underlie inter-individual TCR sharing are still largely theoretical. To examine this phenomenon at the atomic level, we solved the co-complex structure of one of the most widespread and numerically frequent public TCRs in the human population. The archetypal AS01 public TCR recognizes an immunodominant BMLF1 peptide, derived from the ubiquitous Epstein-Barr virus, bound to HLA-A*0201. The AS01 TCR was observed to dock in a diagonal fashion, grasping the solvent exposed peptide crest with two sets of complementarity-determining region (CDR) loops, and was fastened to the peptide and HLA-A*0201 platform with residue sets found only within TCR genes biased in the public response. Computer simulations of a random V(D)J recombination process demonstrated that both TCRα and TCRβ amino acid sequences could be manufactured easily, thereby explaining the prevalence of this receptor across different individuals. Interestingly, the AS01 TCR was encoded largely by germline DNA, indicating that the TCR loci already comprise gene segments that specifically recognize this ancient pathogen. Such pattern recognition receptor-like traits within the αβ TCR system further blur the boundaries between the adaptive and innate immune systems.
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MESH Headings
- Amino Acid Sequence
- Antigens, Viral/immunology
- CD8-Positive T-Lymphocytes
- Computer Simulation
- Crystallization
- Crystallography, X-Ray
- Cytotoxicity, Immunologic
- HLA-A Antigens/immunology
- HLA-A2 Antigen
- Herpesviridae Infections/immunology
- Herpesviridae Infections/metabolism
- Herpesviridae Infections/virology
- Herpesvirus 4, Human/immunology
- Humans
- Immune Tolerance
- Molecular Sequence Data
- Protein Conformation
- Receptors, Antigen, T-Cell, alpha-beta/chemistry
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Recombination, Genetic
- Sequence Homology, Amino Acid
- Surface Plasmon Resonance
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Affiliation(s)
- John J Miles
- Department of Infection, Cardiff University School of Medicine, Heath Park, Cardiff, UK.
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