1
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Finnigan JP, Newman JH, Patskovsky Y, Patskovska L, Ishizuka AS, Lynn GM, Seder RA, Krogsgaard M, Bhardwaj N. Structural basis for self-discrimination by neoantigen-specific TCRs. Nat Commun 2024; 15:2140. [PMID: 38459027 PMCID: PMC10924104 DOI: 10.1038/s41467-024-46367-9] [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: 01/13/2023] [Accepted: 02/26/2024] [Indexed: 03/10/2024] Open
Abstract
T cell receptors (TCR) are pivotal in mediating tumour cell cytolysis via recognition of mutation-derived tumour neoantigens (neoAgs) presented by major histocompatibility class-I (MHC-I). Understanding the factors governing the emergence of neoAg from somatic mutations is a major focus of current research. However, the structural and cellular determinants controlling TCR recognition of neoAgs remain poorly understood. This study describes the multi-level analysis of a model neoAg from the B16F10 murine melanoma, H2-Db/Hsf2 p.K72N68-76, as well as its cognate TCR 47BE7. Through cellular, molecular and structural studies we demonstrate that the p.K72N mutation enhances H2-Db binding, thereby improving cell surface presentation and stabilizing the TCR 47BE7 epitope. Furthermore, TCR 47BE7 exhibited high functional avidity and selectivity, attributable to a broad, stringent, binding interface enabling recognition of native B16F10 despite low antigen density. Our findings provide insight into the generation of anchor-residue modified neoAg, and emphasize the value of molecular and structural investigations of neoAg in diverse MHC-I contexts for advancing the understanding of neoAg immunogenicity.
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Affiliation(s)
- John P Finnigan
- Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Pl., New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Ave., New York, NY, USA
- Department of Medicine, Division of Hematology and Medical Oncology, Mount Sinai Hospital, New York, NY, USA
- Department of Surgery, Division of Thoracic and Cardiac Surgery, Brigham and Women's Hospital, 75 Francis St., Boston, MA, USA
| | - Jenna H Newman
- Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Pl., New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Ave., New York, NY, USA
- Department of Medicine, Division of Hematology and Medical Oncology, Mount Sinai Hospital, New York, NY, USA
| | - Yury Patskovsky
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- Laura and Isaac Perlmutter Cancer Center at NYU Langone Health, New York, NY, USA
| | - Larysa Patskovska
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA
- Laura and Isaac Perlmutter Cancer Center at NYU Langone Health, New York, NY, USA
| | - Andrew S Ishizuka
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Barinthus Biotherapeutics, Germantown, MD, USA
| | - Geoffrey M Lynn
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Barinthus Biotherapeutics, Germantown, MD, USA
| | - Robert A Seder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Michelle Krogsgaard
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, USA.
- Laura and Isaac Perlmutter Cancer Center at NYU Langone Health, New York, NY, USA.
| | - Nina Bhardwaj
- Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Pl., New York, NY, USA.
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Ave., New York, NY, USA.
- Department of Medicine, Division of Hematology and Medical Oncology, Mount Sinai Hospital, New York, NY, USA.
- Parker Institute for Cancer Immunotherapy, Francisco, CA, USA.
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2
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Balasco N, Tagliamonte M, Buonaguro L, Vitagliano L, Paladino A. Structural and Dynamic-Based Characterization of the Recognition Patterns of E7 and TRP-2 Epitopes by MHC Class I Receptors through Computational Approaches. Int J Mol Sci 2024; 25:1384. [PMID: 38338663 PMCID: PMC10855917 DOI: 10.3390/ijms25031384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/16/2024] [Accepted: 01/19/2024] [Indexed: 02/12/2024] Open
Abstract
A detailed comprehension of MHC-epitope recognition is essential for the design and development of new antigens that could be effectively used in immunotherapy. Yet, the high variability of the peptide together with the large abundance of MHC variants binding makes the process highly specific and large-scale characterizations extremely challenging by standard experimental techniques. Taking advantage of the striking predictive accuracy of AlphaFold, we report a structural and dynamic-based strategy to gain insights into the molecular basis that drives the recognition and interaction of MHC class I in the immune response triggered by pathogens and/or tumor-derived peptides. Here, we investigated at the atomic level the recognition of E7 and TRP-2 epitopes to their known receptors, thus offering a structural explanation for the different binding preferences of the studied receptors for specific residues in certain positions of the antigen sequences. Moreover, our analysis provides clues on the determinants that dictate the affinity of the same epitope with different receptors. Collectively, the data here presented indicate the reliability of the approach that can be straightforwardly extended to a large number of related systems.
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Affiliation(s)
- Nicole Balasco
- Institute of Molecular Biology and Pathology IBPM-CNR c/o Department Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy;
| | - Maria Tagliamonte
- Immunological Models Lab, Istituto Nazionale Tumori—Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)—“Fond. G. Pascale”, Via Mariano Semmola 53, 80131 Napoli, Italy; (M.T.); (L.B.)
| | - Luigi Buonaguro
- Immunological Models Lab, Istituto Nazionale Tumori—Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)—“Fond. G. Pascale”, Via Mariano Semmola 53, 80131 Napoli, Italy; (M.T.); (L.B.)
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging IBB-CNR, Via Pietro Castellino 111, 80131 Napoli, Italy;
| | - Antonella Paladino
- Institute of Biostructures and Bioimaging IBB-CNR, Via Pietro Castellino 111, 80131 Napoli, Italy;
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3
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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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4
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Bloodworth N, Barbaro NR, Moretti R, Harrison DG, Meiler J. Rosetta FlexPepDock to predict peptide-MHC binding: An approach for non-canonical amino acids. PLoS One 2022; 17:e0275759. [PMID: 36512534 PMCID: PMC9746977 DOI: 10.1371/journal.pone.0275759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 09/22/2022] [Indexed: 12/15/2022] Open
Abstract
Computation methods that predict the binding of peptides to MHC-I are important tools for screening and identifying immunogenic antigens and have the potential to accelerate vaccine and drug development. However, most available tools are sequence-based and optimized only for peptides containing the twenty canonical amino acids. This omits a large number of peptides containing non-canonical amino acids (NCAA), or residues that undergo varied post-translational modifications such as glycosylation or phosphorylation. These modifications fundamentally alter peptide immunogenicity. Similarly, existing structure-based methods are biased towards canonical peptide backbone structures, which may or may not be preserved when NCAAs are present. Rosetta FlexPepDock ab-initio is a structure-based computational protocol able to evaluate peptide-receptor interaction where no prior information of the peptide backbone is known. We benchmarked FlexPepDock ab-initio for docking canonical peptides to MHC-I, and illustrate for the first time the method's ability to accurately model MHC-I bound epitopes containing NCAAs. FlexPepDock ab-initio protocol was able to recapitulate near-native structures (≤1.5Å) in the top lowest-energy models for 20 out of 25 cases in our initial benchmark. Using known experimental binding affinities of twenty peptides derived from an influenza-derived peptide, we showed that FlexPepDock protocol is able to predict relative binding affinity as Rosetta energies correlate well with experimental values (r = 0.59, p = 0.006). ROC analysis revealed 80% true positive and a 40% false positive rate, with a prediction power of 93%. Finally, we demonstrate the protocol's ability to accurately recapitulate HLA-A*02:01 bound phosphopeptide backbone structures and relative binding affinity changes, the theoretical structure of the lymphocytic choriomeningitis derived glycosylated peptide GP392 bound to MHC-I H-2Db, and isolevuglandin-adducted peptides. The ability to use non-canonical amino acids in the Rosetta FlexPepDock protocol may provide useful insight into critical amino acid positions where the post-translational modification modulates immunologic responses.
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Affiliation(s)
- Nathaniel Bloodworth
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Natália Ruggeri Barbaro
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Rocco Moretti
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - David G. Harrison
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Jens Meiler
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Institute for Drug Discovery, Leipzig University, Leipzig, Germany
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5
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Predicting immunogenic tumour mutations by combining mass spectrometry and exome sequencing. Nature 2015; 515:572-6. [PMID: 25428506 DOI: 10.1038/nature14001] [Citation(s) in RCA: 871] [Impact Index Per Article: 96.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 10/28/2014] [Indexed: 12/12/2022]
Abstract
Human tumours typically harbour a remarkable number of somatic mutations. If presented on major histocompatibility complex class I molecules (MHCI), peptides containing these mutations could potentially be immunogenic as they should be recognized as 'non-self' neo-antigens by the adaptive immune system. Recent work has confirmed that mutant peptides can serve as T-cell epitopes. However, few mutant epitopes have been described because their discovery required the laborious screening of patient tumour-infiltrating lymphocytes for their ability to recognize antigen libraries constructed following tumour exome sequencing. We sought to simplify the discovery of immunogenic mutant peptides by characterizing their general properties. We developed an approach that combines whole-exome and transcriptome sequencing analysis with mass spectrometry to identify neo-epitopes in two widely used murine tumour models. Of the >1,300 amino acid changes identified, ∼13% were predicted to bind MHCI, a small fraction of which were confirmed by mass spectrometry. The peptides were then structurally modelled bound to MHCI. Mutations that were solvent-exposed and therefore accessible to T-cell antigen receptors were predicted to be immunogenic. Vaccination of mice confirmed the approach, with each predicted immunogenic peptide yielding therapeutically active T-cell responses. The predictions also enabled the generation of peptide-MHCI dextramers that could be used to monitor the kinetics and distribution of the anti-tumour T-cell response before and after vaccination. These findings indicate that a suitable prediction algorithm may provide an approach for the pharmacodynamic monitoring of T-cell responses as well as for the development of personalized vaccines in cancer patients.
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6
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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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7
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Trost B, Kusalik A, Lucchese G, Kanduc D. Bacterial peptides are intensively present throughout the human proteome. SELF NONSELF 2014; 1:71-74. [PMID: 21559180 DOI: 10.4161/self.1.1.9588] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2009] [Revised: 07/16/2009] [Accepted: 07/22/2009] [Indexed: 11/19/2022]
Abstract
Forty bacterial proteomes-20 pathogens and 20 non-pathogens-were examined for amino acid sequence similarity to the human proteome. All bacterial proteomes, independent of their pathogenicity, share hundreds of nonamer sequences with the human proteome. This overlap is very widespread, with one third of human proteins sharing at least one nonapeptide with one of these bacteria. On the whole, the bacteria-versus-human nonamer overlap is numerically defined by 47,610 total perfect matches disseminated through 10,701 human proteins. These findings open new perspectives on the immune relationship between bacteria and host, and might help our understanding of fundamental phenomena such as self-nonself discrimination and tolerance versus auto-reactivity.
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Affiliation(s)
- Brett Trost
- Department of Computer Science; University of Saskatchewan; Saskatoon, SK CA
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8
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Birnbaum ME, Mendoza JL, Sethi DK, Dong S, Glanville J, Dobbins J, Özkan E, Davis MM, Wucherpfennig KW, Garcia KC. Deconstructing the peptide-MHC specificity of T cell recognition. Cell 2014; 157:1073-87. [PMID: 24855945 PMCID: PMC4071348 DOI: 10.1016/j.cell.2014.03.047] [Citation(s) in RCA: 399] [Impact Index Per Article: 39.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 02/17/2014] [Accepted: 03/14/2014] [Indexed: 01/07/2023]
Abstract
In order to survey a universe of major histocompatibility complex (MHC)-presented peptide antigens whose numbers greatly exceed the diversity of the T cell repertoire, T cell receptors (TCRs) are thought to be cross-reactive. However, the nature and extent of TCR cross-reactivity has not been conclusively measured experimentally. We developed a system to identify MHC-presented peptide ligands by combining TCR selection of highly diverse yeast-displayed peptide-MHC libraries with deep sequencing. Although we identified hundreds of peptides reactive with each of five different mouse and human TCRs, the selected peptides possessed TCR recognition motifs that bore a close resemblance to their known antigens. This structural conservation of the TCR interaction surface allowed us to exploit deep-sequencing information to computationally identify activating microbial and self-ligands for human autoimmune TCRs. The mechanistic basis of TCR cross-reactivity described here enables effective surveillance of diverse self and foreign antigens without necessitating degenerate recognition of nonhomologous peptides.
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Affiliation(s)
- Michael E. Birnbaum
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305,Program in Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305
| | - Juan L. Mendoza
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305
| | - Dhruv K. Sethi
- Department of Cancer Immunology & AIDS, Dana-Farber Cancer Institute, Boston, MA 02115
| | - Shen Dong
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305
| | - Jacob Glanville
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305,Program in Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305
| | - Jessica Dobbins
- Department of Cancer Immunology & AIDS, Dana-Farber Cancer Institute, Boston, MA 02115,Program in Immunology, Harvard Medical School, Boston, MA 02115
| | - Engin Özkan
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305,The Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305
| | - Mark M. Davis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305,Program in Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305,The Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305
| | - Kai W. Wucherpfennig
- Department of Cancer Immunology & AIDS, Dana-Farber Cancer Institute, Boston, MA 02115,Program in Immunology, Harvard Medical School, Boston, MA 02115
| | - K. Christopher Garcia
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305,Program in Immunology, Stanford University School of Medicine, Stanford University, Stanford, CA 94305,The Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305
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9
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Impact of multiple antigenic epitopes from ApoB100, hHSP60 and Chlamydophila pneumoniae on atherosclerotic lesion development in Apobtm2SgyLdlrtm1Her J mice. Atherosclerosis 2012; 225:56-68. [DOI: 10.1016/j.atherosclerosis.2012.07.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Revised: 06/06/2012] [Accepted: 07/13/2012] [Indexed: 11/18/2022]
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10
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Lu X, Xia M, Endresz V, Faludi I, Mundkur L, Gonczol E, Chen D, Kakkar VV. Immunization With a Combination of 2 Peptides Derived From the C5a Receptor Significantly Reduces Early Atherosclerotic Lesion in
Ldlr
tm1Her
Apob
tm2Sgy
J Mice. Arterioscler Thromb Vasc Biol 2012; 32:2358-71. [DOI: 10.1161/atvbaha.112.253179] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Objective—
The goal of this study was to assess whether immunization of
Ldlr
tm1Her
Apob
tm2Sgy
J mice with 2 peptides located at the N-terminus of the C5a receptor (C5aR), either alone or in combination, is effective in reducing atherosclerotic lesions.
Methods and Results—
Five- to 6-week-old female
Ldlr
tm1Her
Apob
tm2Sgy
J mice were immunized using a repetitive immunization multiple sites strategy with keyhole limpet hemocyanin-conjugated peptides derived from the C5aR, either alone (designated as C5aR-P1 [aa 1–21] and C5aR-P2 [aa 19–31]) or in combination (designated as C5aR-P1+C5aR-P2). Mice were fed a high-fat diet for 10 weeks. Lesions were evaluated histologically; local and systemic immune responses were analyzed by immunohistochemistry of aorta samples and cytokine measurements in plasma samples and splenocyte supernatants. Immunization of
Ldlr
tm1Her
Apob
tm2Sgy
J mice with these peptides elicited high concentrations of antibodies against each peptide. Immunization with the single peptide inhibited plaque development. Combined inoculation with C5aR-P1+C5aR-P2 had an additive effect on reducing the lesion in the aorta sinus and descending aortas when compared with controls. This effect correlated with cellular infiltration and cytokine/chemokine secretion in the serum or in stimulated spleen cells as well as specific cellular immune responses when compared with controls.
Conclusion—
Immunization of mice with C5aR-P1 and C5aR-P2, either alone or in combination, was effective in reducing early atherosclerotic lesion development. The combined peptide is more potential than either epitope alone to reduce atherosclerotic lesion formation through the induction of a specific Treg cell response as well as blockage of monocyte differentiation into macrophages.
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Affiliation(s)
- Xinjie Lu
- From the Mary and Garry Weston Molecular Immunology Laboratory, Thrombosis Research Institute, London, UK (X.L., M.X., D.C., V.V.K.); Department of Medical Microbiology and Immunobiology, University of Szeged, Szeged, Hungary (V.E., I.F.); Virology, National Center for Epidemiology, Budapest, Hungary (E.G.); MRC Centre for Transplantation, King’s College London, London, UK (D.C.); and the Thrombosis Research Institute, Bangalore, India (L.M., V.V.K.)
| | - Min Xia
- From the Mary and Garry Weston Molecular Immunology Laboratory, Thrombosis Research Institute, London, UK (X.L., M.X., D.C., V.V.K.); Department of Medical Microbiology and Immunobiology, University of Szeged, Szeged, Hungary (V.E., I.F.); Virology, National Center for Epidemiology, Budapest, Hungary (E.G.); MRC Centre for Transplantation, King’s College London, London, UK (D.C.); and the Thrombosis Research Institute, Bangalore, India (L.M., V.V.K.)
| | - Valeria Endresz
- From the Mary and Garry Weston Molecular Immunology Laboratory, Thrombosis Research Institute, London, UK (X.L., M.X., D.C., V.V.K.); Department of Medical Microbiology and Immunobiology, University of Szeged, Szeged, Hungary (V.E., I.F.); Virology, National Center for Epidemiology, Budapest, Hungary (E.G.); MRC Centre for Transplantation, King’s College London, London, UK (D.C.); and the Thrombosis Research Institute, Bangalore, India (L.M., V.V.K.)
| | - Ildiko Faludi
- From the Mary and Garry Weston Molecular Immunology Laboratory, Thrombosis Research Institute, London, UK (X.L., M.X., D.C., V.V.K.); Department of Medical Microbiology and Immunobiology, University of Szeged, Szeged, Hungary (V.E., I.F.); Virology, National Center for Epidemiology, Budapest, Hungary (E.G.); MRC Centre for Transplantation, King’s College London, London, UK (D.C.); and the Thrombosis Research Institute, Bangalore, India (L.M., V.V.K.)
| | - Lakshmi Mundkur
- From the Mary and Garry Weston Molecular Immunology Laboratory, Thrombosis Research Institute, London, UK (X.L., M.X., D.C., V.V.K.); Department of Medical Microbiology and Immunobiology, University of Szeged, Szeged, Hungary (V.E., I.F.); Virology, National Center for Epidemiology, Budapest, Hungary (E.G.); MRC Centre for Transplantation, King’s College London, London, UK (D.C.); and the Thrombosis Research Institute, Bangalore, India (L.M., V.V.K.)
| | - Eva Gonczol
- From the Mary and Garry Weston Molecular Immunology Laboratory, Thrombosis Research Institute, London, UK (X.L., M.X., D.C., V.V.K.); Department of Medical Microbiology and Immunobiology, University of Szeged, Szeged, Hungary (V.E., I.F.); Virology, National Center for Epidemiology, Budapest, Hungary (E.G.); MRC Centre for Transplantation, King’s College London, London, UK (D.C.); and the Thrombosis Research Institute, Bangalore, India (L.M., V.V.K.)
| | - Daxin Chen
- From the Mary and Garry Weston Molecular Immunology Laboratory, Thrombosis Research Institute, London, UK (X.L., M.X., D.C., V.V.K.); Department of Medical Microbiology and Immunobiology, University of Szeged, Szeged, Hungary (V.E., I.F.); Virology, National Center for Epidemiology, Budapest, Hungary (E.G.); MRC Centre for Transplantation, King’s College London, London, UK (D.C.); and the Thrombosis Research Institute, Bangalore, India (L.M., V.V.K.)
| | - Vijay V. Kakkar
- From the Mary and Garry Weston Molecular Immunology Laboratory, Thrombosis Research Institute, London, UK (X.L., M.X., D.C., V.V.K.); Department of Medical Microbiology and Immunobiology, University of Szeged, Szeged, Hungary (V.E., I.F.); Virology, National Center for Epidemiology, Budapest, Hungary (E.G.); MRC Centre for Transplantation, King’s College London, London, UK (D.C.); and the Thrombosis Research Institute, Bangalore, India (L.M., V.V.K.)
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11
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Gleimer M, Wahl AR, Hickman HD, Abi-Rached L, Norman PJ, Guethlein LA, Hammond JA, Draghi M, Adams EJ, Juo S, Jalili R, Gharizadeh B, Ronaghi M, Garcia KC, Hildebrand WH, Parham P. Although divergent in residues of the peptide binding site, conserved chimpanzee Patr-AL and polymorphic human HLA-A*02 have overlapping peptide-binding repertoires. THE JOURNAL OF IMMUNOLOGY 2011; 186:1575-88. [PMID: 21209280 DOI: 10.4049/jimmunol.1002990] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Patr-AL is an expressed, non-polymorphic MHC class I gene carried by ∼50% of chimpanzee MHC haplotypes. Comparing Patr-AL(+) and Patr-AL(-) haplotypes showed Patr-AL defines a unique 125-kb genomic block flanked by blocks containing classical Patr-A and pseudogene Patr-H. Orthologous to Patr-AL are polymorphic orangutan Popy-A and the 5' part of human pseudogene HLA-Y, carried by ∼10% of HLA haplotypes. Thus, the AL gene alternatively evolved in these closely related species to become classical, nonclassical, and nonfunctional. Although differing by 30 aa substitutions in the peptide-binding α(1) and α(2) domains, Patr-AL and HLA-A*0201 bind overlapping repertoires of peptides; the overlap being comparable with that between the A*0201 and A*0207 subtypes differing by one substitution. Patr-AL thus has the A02 supertypic peptide-binding specificity. Patr-AL and HLA-A*0201 have similar three-dimensional structures, binding peptides in similar conformation. Although comparable in size and shape, the B and F specificity pockets of Patr-AL and HLA-A*0201 differ in both their constituent residues and contacts with peptide anchors. Uniquely shared by Patr-AL, HLA-A*0201, and other members of the A02 supertype are the absence of serine at position 9 in the B pocket and the presence of tyrosine at position 116 in the F pocket. Distinguishing Patr-AL from HLA-A*02 is an unusually electropositive upper face on the α(2) helix. Stimulating PBMCs from Patr-AL(-) chimpanzees with B cells expressing Patr-AL produced potent alloreactive CD8 T cells with specificity for Patr-AL and no cross-reactivity toward other MHC class I molecules, including HLA-A*02. In contrast, PBMCs from Patr-AL(+) chimpanzees are tolerant of Patr-AL.
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Affiliation(s)
- Michael Gleimer
- Graduate Program in Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
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12
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Khitrov AN, Shogenov ZS, Tretyak EB, Ischenko AI, Matsuura E, Neuhaus O, Paltsev MA, Suchkov SV. Postinfectious immunodeficiency and autoimmunity: pathogenic and clinical values and implications. Expert Rev Clin Immunol 2010; 3:323-31. [PMID: 20477676 DOI: 10.1586/1744666x.3.3.323] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Autoimmunity is still a mystery of clinical immunology and medicine as a whole. The etiology and pathogenesis of autoimmune disorders remain unclear and, thus, are assessed as a balance between hereditary predisposition, triggering factors and the appearance of autoantibodies and/or self-reactive T cells. Among the immunological armamentarium, molecular mimicry, based on self-reactive T- and B-cell activation by cross-reactive epitopes of infectious agents, is of special value. Hypotheses regarding the possible involvement of molecular mimicry in the development of postinfectious autoimmunity are currently very intriguing. They provide new approaches for identifying etiological agents that are associated with postinfectious autoimmunity, paired microbial- and tissue-linked epitopes targeted for autoimmune reaction determination, postinfectious autoimmunity pathogenesis recognition and specific prevention, and therapy for autoimmune disorder development.
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Affiliation(s)
- Alexander N Khitrov
- IM Sechenov Moscow Medical Academy, Department of Pathology, Moscow, Russia.
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13
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Young EF, Hess PR, Arnold LW, Tisch R, Frelinger JA. Islet lymphocyte subsets in male and female NOD mice are qualitatively similar but quantitatively distinct. Autoimmunity 2010; 42:678-91. [PMID: 19886740 DOI: 10.3109/08916930903213993] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Islet-infiltrating lymphocytes of individual male and female non-obese diabetic (NOD) mice were examined with the purpose of determining the differences that lead to a predominance of diabetes in female versus males NOD mice. When normalized for the amount of islet lymphocytes recovered, the infiltrating lymphocytes of female NOD mice were indistinguishable from those of male NOD mice. The only observed difference was that islet inflammation progressed at an increased rate in female compared to male NOD mice. There was no difference in the composition of islet infiltrates in male and female NOD mice. Unexpectedly, the ratio of CD4(+):CD8(+) T cells was tightly controlled in the islets throughout diabetogenesis. The frequency of IL-4(+) CD4(+) T cells started high but quickly fell to 3% of the population that was maintained with increasing inflammation. A significant portion of the CD8(+) T cells were islet-specific glucose-6-phosphatase catalytic subunit-related protein specific in both male and female NOD mice and this population was antigen experienced and increased at high levels of islet inflammation. Surprisingly, a large pool of antigen inexperienced naïve T cells was detected in the islets. We conclude the underlying immunological processes in both male and female NOD mice are similar while the rates differ and the presence of naïve T cell in the islets may contribute to epitope spreading.
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Affiliation(s)
- Ellen F Young
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7290, USA.
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14
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Constraints within major histocompatibility complex class I restricted peptides: presentation and consequences for T-cell recognition. Proc Natl Acad Sci U S A 2010; 107:5534-9. [PMID: 20212169 DOI: 10.1073/pnas.1000032107] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Residues within processed protein fragments bound to major histocompatibility complex class I (MHC-I) glycoproteins have been considered to function as a series of "independent pegs" that either anchor the peptide (p) to the MHC-I and/or interact with the spectrum of alphabeta-T-cell receptors (TCRs) specific for the pMHC-I epitope in question. Mining of the extensive pMHC-I structural database established that many self- and viral peptides show extensive and direct interresidue interactions, an unexpected finding that has led us to the idea of "constrained" peptides. Mutational analysis of two constrained peptides (the HLA B44 restricted self-peptide (B44DPalpha-EEFGRAFSF) and an H2-D(b) restricted influenza peptide (D(b)PA, SSLENFRAYV) demonstrated that the conformation of the prominently exposed arginine in both peptides was governed by interactions with MHC-I-orientated flanking residues from the peptide itself. Using reverse genetics in a murine influenza model, we revealed that mutation of an MHC-I-orientated residue (SSLENFRAYV --> SSLENARAYV) within the constrained PA peptide resulted in a diminished cytotoxic T lymphocyte (CTL) response and the recruitment of a limited pMHC-I specific TCR repertoire. Interactions between individual peptide positions can thus impose fine control on the conformation of pMHC-I epitopes, whereas the perturbation of such constraints can lead to a previously unappreciated mechanism of viral escape.
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15
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Kumar P, Vahedi-Faridi A, Saenger W, Ziegler A, Uchanska-Ziegler B. Conformational changes within the HLA-A1:MAGE-A1 complex induced by binding of a recombinant antibody fragment with TCR-like specificity. Protein Sci 2009; 18:37-49. [PMID: 19177349 DOI: 10.1002/pro.4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Although there is X-ray crystallographic evidence that the interaction between major histocompatibility complex (MHC, in humans HLA) class I molecules and T cell receptors (TCR) or killer cell Ig-like receptors (KIR) may be accompanied by considerable changes in the conformation of selected residues or even entire loops within TCR or KIR, conformational changes between receptor-bound and -unbound MHC class I molecules of comparable magnitude have not been observed so far. We have previously determined the structure of the MHC class I molecule HLA-A1 bound to a melanoma antigen-encoding gene (MAGE)-A1-derived peptide in complex with a recombinant antibody fragment with TCR-like specificity, Fab-Hyb3. Here, we compare the X-ray structure of HLA-A1:MAGE-A1 with that complexed with Fab-Hyb3 to gain insight into structural changes of the MHC molecule that might be induced by the interaction with the antibody fragment. Apart from the expulsion of several water molecules from the interface, Fab-Hyb3 binding results in major rearrangements (up to 5.5 A) of heavy chain residues Arg65, Gln72, Arg145, and Lys146. Residue 65 is frequently and residues 72 and 146 are occasionally involved in TCR binding-induced conformational changes, as revealed by a comparison with MHC class I structures in TCR-liganded and -unliganded forms. On the other hand, residue 145 is subject to a reorientation following engagement of HLA-Cw4 and KIR2DL1. Therefore, conformational changes within the HLA-A1:MAGE-A1:Fab-Hyb3 complex include MHC residues that are also involved in reorientations in complexes with natural ligands, pointing to their central importance for the peptide-dependent recognition of MHC molecules.
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Affiliation(s)
- Pravin Kumar
- Institut für Immungenetik, Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, Freie Universität Berlin, Thielallee 73, Berlin 14195, Germany
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16
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Greene MT, Ercolini AM, DeGutes M, Miller SD. Differential induction of experimental autoimmune encephalomyelitis by myelin basic protein molecular mimics in mice humanized for HLA-DR2 and an MBP(85-99)-specific T cell receptor. J Autoimmun 2008; 31:399-407. [PMID: 19008075 DOI: 10.1016/j.jaut.2008.09.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2008] [Revised: 09/17/2008] [Accepted: 09/18/2008] [Indexed: 10/21/2022]
Abstract
Multiple sclerosis (MS) is a chronic autoimmune neurological disease characterized by infiltration of peripheral inflammatory cells to the central nervous system (CNS) and demyelination of CNS white matter. Epidemiological evidence suggests a possible infectious trigger. One potential mechanism by which an infectious agent may trigger MS is via molecular mimicry wherein T cells generated against foreign epitopes cross-react with self-myelin epitopes, such as myelin basic protein (MBP), with sufficient sequence similarity. It has been previously reported that an MBP(85-99)-reactive T cell clone derived from an MS patient cross-reacted with multiple bacterial-derived mimic peptides in vitro. We show that the same mimic peptides can induce clinical disease in two different strains of mice transgenic for both a human MBP(85-99)-specific TCR and HLA-DR2 (MHC II), albeit with different disease patterns - relapsing-remitting vs. monophasic. Interestingly, clinical disease correlates with CNS infiltration of CD4(+) T cells and F4/80(+) macrophages, but not with in vitro proliferative or cytokine responses of splenocytes in response to either MBP(85-99) or its mimics.
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Affiliation(s)
- Maria T Greene
- Department of Microbiology-Immunology and Interdepartmental Immunobiology Center, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, United States
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17
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Tian S, Maile R, Collins EJ, Frelinger JA. CD8+ T cell activation is governed by TCR-peptide/MHC affinity, not dissociation rate. THE JOURNAL OF IMMUNOLOGY 2007; 179:2952-60. [PMID: 17709510 DOI: 10.4049/jimmunol.179.5.2952] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Binding of peptide/MHC (pMHC) complexes by TCR initiates T cell activation. Despite long interest, the exact relationship between the biochemistry of TCR/pMHC interaction (particularly TCR affinity or ligand off-rate) and T cell responses remains unresolved, because the number of complexes examined in each independent system has been too small to draw a definitive conclusion. To test the current models of T cell activation, we have analyzed the interactions between the mouse P14 TCR and a set of altered peptides based on the lymphocytic choriomeningitis virus epitope gp33-41 sequence bound to mouse class I MHC D(b). pMHC binding, TCR-binding characteristics, CD8+ T cell cytotoxicity, and IFN-gamma production were measured for the peptides. We found affinity correlated well with both cytotoxicity and IFN-gamma production. In contrast, no correlation was observed between any kinetic parameter of TCR-pMHC interaction and cytotoxicity or IFN-gamma production. This study strongly argues for an affinity threshold model of T cell activation.
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Affiliation(s)
- Shaomin Tian
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599, USA
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18
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Borbulevych OY, Insaidoo FK, Baxter TK, Powell DJ, Johnson LA, Restifo NP, Baker BM. Structures of MART-126/27-35 Peptide/HLA-A2 complexes reveal a remarkable disconnect between antigen structural homology and T cell recognition. J Mol Biol 2007; 372:1123-36. [PMID: 17719062 PMCID: PMC2134917 DOI: 10.1016/j.jmb.2007.07.025] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2007] [Revised: 07/07/2007] [Accepted: 07/10/2007] [Indexed: 11/24/2022]
Abstract
Small structural changes in peptides presented by major histocompatibility complex (MHC) molecules often result in large changes in immunogenicity, supporting the notion that T cell receptors are exquisitely sensitive to antigen structure. Yet there are striking examples of TCR recognition of structurally dissimilar ligands. The resulting unpredictability of how T cells will respond to different or modified antigens impacts both our understanding of the physical bases for TCR specificity as well as efforts to engineer peptides for immunomodulation. In cancer immunotherapy, epitopes and variants derived from the MART-1/Melan-A protein are widely used as clinical vaccines. Two overlapping epitopes spanning amino acid residues 26 through 35 are of particular interest: numerous clinical studies have been performed using variants of the MART-1 26-35 decamer, although only the 27-35 nonamer has been found on the surface of targeted melanoma cells. Here, we show that the 26-35 and 27-35 peptides adopt strikingly different conformations when bound to HLA-A2. Nevertheless, clonally distinct MART-1(26/27-35)-reactive T cells show broad cross-reactivity towards these ligands. Simultaneously, however, many of the cross-reactive T cells remain unable to recognize anchor-modified variants with very subtle structural differences. These dichotomous observations challenge our thinking about how structural information on unligated peptide/MHC complexes should be best used when addressing questions of TCR specificity. Our findings also indicate that caution is warranted in the design of immunotherapeutics based on the MART-1 26/27-35 epitopes, as neither cross-reactivity nor selectivity is predictable based on the analysis of the structures alone.
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Affiliation(s)
- Oleg Y. Borbulevych
- Department of Chemistry and Biochemistry, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame IN 46556, USA
- Walther Cancer Research Center, 251 Nieuwland Science Hall, University of Notre Dame Notre Dame, IN 46530, USA
| | - Francis K. Insaidoo
- Department of Chemistry and Biochemistry, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame IN 46556, USA
| | - Tiffany K. Baxter
- Department of Chemistry and Biochemistry, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame IN 46556, USA
| | - Daniel J. Powell
- National Cancer Institute, National Institutes of Health Bethesda, MD 20892, USA
| | - Laura A. Johnson
- National Cancer Institute, National Institutes of Health Bethesda, MD 20892, USA
| | - Nicholas P. Restifo
- National Cancer Institute, National Institutes of Health Bethesda, MD 20892, USA
| | - Brian M. Baker
- Department of Chemistry and Biochemistry, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame IN 46556, USA
- Walther Cancer Research Center, 251 Nieuwland Science Hall, University of Notre Dame Notre Dame, IN 46530, USA
- *E-mail address of the corresponding author:
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19
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Zhang ZX, Ma Y, Wang H, Arp J, Jiang J, Huang X, He KM, Garcia B, Madrenas J, Zhong R. Double-Negative T Cells, Activated by Xenoantigen, Lyse Autologous B and T Cells Using a Perforin/Granzyme-Dependent, Fas-Fas Ligand-Independent Pathway. THE JOURNAL OF IMMUNOLOGY 2006; 177:6920-9. [PMID: 17082607 DOI: 10.4049/jimmunol.177.10.6920] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The ability to control the response of B cells is of particular interest in xenotransplantation as Ab-mediated hyperacute and acute xenograft rejection are major obstacles in achieving long-term graft survival. Regulatory T cells have been proven to play a very important role in the regulation of immune responses to self or non-self Ags. Previous studies have shown that TCRalphabeta+CD3+CD4-CD8- (double-negative (DN)) T cells possess an immune regulatory function, capable of controlling antidonor T cell responses in allo- and xenotransplantation through Fas-Fas ligand interaction. In this study, we investigated the possibility that xenoreactive DNT cells suppress B cells. We found that DNT cells generated from wild-type C57BL/6 mice expressed B220 and CD25 after rat Ag stimulation. These xenoreactive B220+CD25+ DNT cells lysed activated, but not naive, B and T cells. This killing, which took place through cell-cell contact, required participation of adhesion molecules. Our results indicate that Fas ligand, TGF-beta, TNF-alpha, and TCR-MHC recognition was not involved in DNT cell-mediated syngenic cell killing, but instead this killing was mediated by perforin and granzymes. The xenoreactive DNT cells expressed high levels of granzymes in comparison to allo- or xenoreactive CD8+ T cells. Adoptive transfer of DNT cells in combination with early immune suppression by immunosuppressive analog of 15-deoxyspergualin, LF15-0195, significantly prolonged rat heart graft survival to 62.1 +/- 13.9 days in mice recipients. In conclusion, this study suggests that xenoreactive DNT cells can control B and T cell responses in perforin/granzyme-dependent mechanisms. DNT cells may be valuable in controlling B and T cell responses in xenotransplantation.
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Affiliation(s)
- Zhu-Xu Zhang
- Department of Surgery, University of Western Ontario, London, Ontario, Canada.
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20
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Gagnon SJ, Borbulevych OY, Davis-Harrison RL, Turner RV, Damirjian M, Wojnarowicz A, Biddison WE, Baker BM. T cell receptor recognition via cooperative conformational plasticity. J Mol Biol 2006; 363:228-43. [PMID: 16962135 DOI: 10.1016/j.jmb.2006.08.045] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2006] [Revised: 08/15/2006] [Accepted: 08/16/2006] [Indexed: 11/25/2022]
Abstract
Although T cell receptor cross-reactivity is a fundamental property of the immune system and is implicated in numerous autoimmune pathologies, the molecular mechanisms by which T cell receptors can recognize and respond to diverse ligands are incompletely understood. In the current study we examined the response of the human T cell lymphotropic virus-1 (HTLV-1) Tax-specific T cell receptor (TCR) A6 to a panel of structurally distinct haptens coupled to the Tax 11-19 peptide with a lysine substitution at position 5 (Tax5K, LLFG[K-hapten]PVYV). The A6 TCR could cross-reactively recognize one of these haptenated peptides, Tax-5K-4-(3-Indolyl)-butyric acid (IBA), presented by HLA-A*0201. The crystal structures of Tax5K-IBA/HLA-A2 free and in complex with A6 reveal that binding is mediated by a mechanism of cooperative conformational plasticity involving conformational changes on both sides of the protein-protein interface, including the TCR complementarity determining region (CDR) loops, Valpha/Vbeta domain orientation, and the hapten-modified peptide. Our findings illustrate the complex role that protein dynamics can play in TCR cross-reactivity and highlight that T cell receptor recognition of ligand can be achieved through diverse and complex molecular mechanisms that can occur simultaneously in the interface, not limited to molecular mimicry and CDR loop shifts.
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Affiliation(s)
- Susan J Gagnon
- Molecular Immunology Section, Neuroimmunology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
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21
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Bordner AJ, Abagyan R. Ab initio prediction of peptide-MHC binding geometry for diverse class I MHC allotypes. Proteins 2006; 63:512-26. [PMID: 16470819 DOI: 10.1002/prot.20831] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Since determining the crystallographic structure of all peptide-MHC complexes is infeasible, an accurate prediction of the conformation is a critical computational problem. These models can be useful for determining binding energetics, predicting the structures of specific ternary complexes with T-cell receptors, and designing new molecules interacting with these complexes. The main difficulties are (1) adequate sampling of the large number of conformational degrees of freedom for the flexible peptide, (2) predicting subtle changes in the MHC interface geometry upon binding, and (3) building models for numerous MHC allotypes without known structures. Whereas previous studies have approached the sampling problem by dividing the conformational variables into different sets and predicting them separately, we have refined the Biased-Probability Monte Carlo docking protocol in internal coordinates to optimize a physical energy function for all peptide variables simultaneously. We also imitated the induced fit by docking into a more permissive smooth grid representation of the MHC followed by refinement and reranking using an all-atom MHC model. Our method was tested by a comparison of the results of cross-docking 14 peptides into HLA-A*0201 and 9 peptides into H-2K(b) as well as docking peptides into homology models for five different HLA allotypes with a comprehensive set of experimental structures. The surprisingly accurate prediction (0.75 A backbone RMSD) for cross-docking of a highly flexible decapeptide, dissimilar to the original bound peptide, as well as docking predictions using homology models for two allotypes with low average backbone RMSDs of less than 1.0 A illustrate the method's effectiveness. Finally, energy terms calculated using the predicted structures were combined with supervised learning on a large data set to classify peptides as either HLA-A*0201 binders or nonbinders. In contrast with sequence-based prediction methods, this model was also able to predict the binding affinity for peptides to a different MHC allotype (H-2K(b)), not used for training, with comparable prediction accuracy.
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Affiliation(s)
- Andrew J Bordner
- Department of Molecular Biology, The Scripps Research Institute, San Diego, California, USA.
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22
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Bui HH, Schiewe AJ, von Grafenstein H, Haworth IS. Structural prediction of peptides binding to MHC class I molecules. Proteins 2006; 63:43-52. [PMID: 16447245 DOI: 10.1002/prot.20870] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Peptide binding to class I major histocompatibility complex (MHCI) molecules is a key step in the immune response and the structural details of this interaction are of importance in the design of peptide vaccines. Algorithms based on primary sequence have had success in predicting potential antigenic peptides for MHCI, but such algorithms have limited accuracy and provide no structural information. Here, we present an algorithm, PePSSI (peptide-MHC prediction of structure through solvated interfaces), for the prediction of peptide structure when bound to the MHCI molecule, HLA-A2. The algorithm combines sampling of peptide backbone conformations and flexible movement of MHC side chains and is unique among other prediction algorithms in its incorporation of explicit water molecules at the peptide-MHC interface. In an initial test of the algorithm, PePSSI was used to predict the conformation of eight peptides bound to HLA-A2, for which X-ray data are available. Comparison of the predicted and X-ray conformations of these peptides gave RMSD values between 1.301 and 2.475 A. Binding conformations of 266 peptides with known binding affinities for HLA-A2 were then predicted using PePSSI. Structural analyses of these peptide-HLA-A2 conformations showed that peptide binding affinity is positively correlated with the number of peptide-MHC contacts and negatively correlated with the number of interfacial water molecules. These results are consistent with the relatively hydrophobic binding nature of the HLA-A2 peptide binding interface. In summary, PePSSI is capable of rapid and accurate prediction of peptide-MHC binding conformations, which may in turn allow estimation of MHCI-peptide binding affinity.
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Affiliation(s)
- Huynh-Hoa Bui
- Department of Pharmaceutical Sciences, University of Southern California, Los Angeles, California 90089, USA
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23
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Martinez-Hackert E, Anikeeva N, Kalams SA, Walker BD, Hendrickson WA, Sykulev Y. Structural basis for degenerate recognition of natural HIV peptide variants by cytotoxic lymphocytes. J Biol Chem 2006; 281:20205-12. [PMID: 16702212 DOI: 10.1074/jbc.m601934200] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
It is well established that even small changes in amino acid side chains of antigenic peptide bound to major histocompatibility complex (MHC) protein may completely abrogate recognition of the peptide-MHC (pMHC) complex by the T cell receptor (TCR). Often, however, several nonconservative substitutions in the peptide antigen are accommodated and do not impair its recognition by TCR. For example, a preponderance of natural sequence variants of the human immunodeficiency virus p17 Gag-derived peptide SLYNTVATL (SL9) are recognized by cytotoxic T lymphocytes, which implies that interactions with SL9 variants are degenerate both with respect to the class I MHC molecule and with respect to TCR. Here we study the molecular basis for this degenerate recognition of SL9 variants. We show that several SL9 variants bind comparably well to soluble HLA-A2 and to a particular soluble TCR and that these variants are active in the cognate cytotoxicity assay. Natural SL9 variation is restricted by its context in the HIV p17 matrix protein. High resolution crystal structures of seven selected SL9 variants bound to HLA-A2 all have remarkably similar peptide conformations and side-chain dispositions outside sites of substitution. This preservation of the peptide conformation despite epitope variations suggests a mechanism for the observed degeneracy in pMHC recognition by TCR and may contribute to the persistence of SL9-mediated immune responses in chronically infected individuals.
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Affiliation(s)
- Erik Martinez-Hackert
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
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24
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Roden MM, Brims DR, Fedorov AA, DiLorenzo TP, Almo SC, Nathenson SG. Structural analysis of H2-Db class I molecules containing two different allelic forms of the type 1 diabetes susceptibility factor beta-2 microglobulin: Implications for the mechanism underlying variations in antigen presentation. Mol Immunol 2006; 43:1370-8. [PMID: 16229893 DOI: 10.1016/j.molimm.2005.08.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2005] [Accepted: 08/23/2005] [Indexed: 11/21/2022]
Abstract
Beta-2 microglobulin (beta2m) is a member of the immunoglobulin-like domain superfamily that is an essential structural subunit of the MHC class I (MHC-I) molecule. beta2m was previously identified as a susceptibility factor for the development of type 1 diabetes (T1D) in NOD mice, whereby transgenic expression of the beta2ma variant, but not the beta2mb variant, restored diabetes susceptibility to normally resistant NOD.beta2mnull mice. Here we report the crystal structures and thermodynamic stabilities of the NOD MHC-I molecule H2-Db containing these two variants. Our results reveal subtle differences in the structures of the beta2m variants, namely in minor loop shifts and in variations in the hydrogen bonding networks at the interfaces between the components of the ternary complex. We also demonstrate that the thermodynamic stabilities of the beta2m variants in isolation differ. However, the conformation of the peptide in the MHC cleft is unchanged in beta2m allelic Db complexes, as are the TCR recognition surfaces. Thus, despite modest structural differences between allelic complexes, the evidence indicates that Db peptide presentation of the representative peptide is unchanged in the context of either beta2m allelic variant. These data suggest that other mechanisms, such as differential association of MHC-I in multiprotein complexes, are likely responsible for the effect of beta2m on T1D development.
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Affiliation(s)
- Matthew M Roden
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
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25
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Gagnon SJ, Turner RV, Shiue MG, Damirjian M, Biddison WE. Extensive T cell receptor cross-reactivity on structurally diverse haptenated peptides presented by HLA-A2. Mol Immunol 2006; 43:346-56. [PMID: 16310048 DOI: 10.1016/j.molimm.2005.02.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2005] [Accepted: 02/15/2005] [Indexed: 11/23/2022]
Abstract
Previous studies have shown that individual TCRs are able to effectively recognize multiple peptide/MHC complexes that have varying degrees of structural diversity. These TCR cross-reactivities have usually been demonstrated by using peptides that have different amino acid sequences. To further examine the extent to which TCRs can accommodate structurally diverse ligands, we analyzed human TCR cross-reactivity to eight structurally distinct haptens that are coupled to the HLA-A2-binding Tax peptide with a lysine substitution at position 5 (Tax-5K, LLFG[K-hapten]PVYV). The results demonstrate that 71% percent of the haptenated-peptide-induced CTL lines could cross-react on at least one other hapten. We compared the effects of HLA-A2 mutants with substitutions at known TCR contact sites for recognition by hapten-cross-reactive CTL. Recognition of the A2 mutants was remarkably similar whether they were presenting the immunizing or the cross-reactive peptide, indicating that similar amino acid contacts are made by the TCR during recognition of both complexes. Thus, hapten cross-reactivity is apparently accomplished without major adjustments to the interaction between the TCR and the surface of the HLA-A2 molecule. Collectively, these results suggest that TCRs possess the molecular flexibility to accommodate very structurally diverse ligands while retaining conserved interactions with the surface of the MHC molecule.
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Affiliation(s)
- Susan J Gagnon
- Molecular Immunology Section, Neuroimmunology Branch, National Institute of Neurological Diseases and Stroke, National Institutes of Health, Building 10, Room 5B-16, Bethesda, MD 20892, USA.
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26
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Thilo C, Berglund P, Applequist SE, Yewdell JW, Ljunggren HG, Achour A. Dissection of the interaction of the human cytomegalovirus-derived US2 protein with major histocompatibility complex class I molecules: prominent role of a single arginine residue in human leukocyte antigen-A2. J Biol Chem 2006; 281:8950-7. [PMID: 16452487 DOI: 10.1074/jbc.m507121200] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human cytomegalovirus encodes several proteins that interfere with expression of major histocompatibility complex (MHC) class I molecules on the surface of infected cells. The unique short protein 2 (US2) binds to many MHC class I allomorphs in the endoplasmic reticulum, preventing cell surface expression of the class I molecule in question. The molecular interactions underlying US2 binding to MHC class I molecules and its allele specificity have not been fully clarified. In the present study, we first compared the sequences and the structures of US2 retained versus non-retained human leukocyte antigen (HLA) class I allomorphs to identify MHC residues of potential importance for US2 binding. On the basis of this analysis, 18 individual HLA-A2 mutants were generated and the ability of full-length US2 to bind wild-type and mutated HLA-A2 complexes was assessed. We demonstrate that Arg181 plays a critical role in US2-mediated inhibition of HLA-A2 cell surface expression. The structural comparison of all known crystal structures of HLA-A2 either alone, or in complex with T cell receptor or the CD8 co-receptor, indicates that binding of US2 to HLA-A2 results in a unique, large conformational change of the side chain of Arg181. However, although the presence of Arg181 seems to be a prerequisite for US2 binding to HLA-A2, it is not sufficient for binding to all MHC class I alleles.
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Affiliation(s)
- Claudia Thilo
- Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, S-141 86 Stockholm, Sweden
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Hattotuwagama CK, Doytchinova IA, Flower DR. In silico prediction of peptide binding affinity to class I mouse major histocompatibility complexes: a comparative molecular similarity index analysis (CoMSIA) study. J Chem Inf Model 2005; 45:1415-23. [PMID: 16180918 DOI: 10.1021/ci049667l] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Current methods for the in silico identification of T cell epitopes (which form the basis of many vaccines, diagnostics, and reagents) rely on the accurate prediction of peptide-major histocompatibility complex (MHC) affinity. A three-dimensional quantitative structure-activity relationship (3D-QSAR) for the prediction of peptide binding to class I MHC molecules was established using the comparative molecular similarity index analysis (CoMSIA) method. Three MHC alleles were studied: H2-D(b), H2-K(b), and H2-K(k). Models were produced for each allele. Each model consisted of five physicochemical descriptors-steric bulk, electrostatic potentials, hydrophobic interactions, and hydrogen-bond donor and hydrogen-bond acceptor abilities. The models have an acceptable level of predictivity: cross-validation leave-one-out statistical terms q2 and SEP (standard error of prediction) ranged between 0.490 and 0.679 and between 0.525 and 0.889, respectively. The non-cross-validated statistical terms r2 and SEE (standard error of estimate) ranged between 0.913 and 0.979 and between 0.167 and 0.248, respectively. The use of coefficient contour maps, which indicate favored and disfavored areas for each position of the MHC-bound peptides, allowed the binding specificity of each allele to be identified, visualized, and understood. The present study demonstrates the effectiveness of CoMSIA as a method for studying peptide-MHC interactions. The peptides used in this study are available on the Internet (http://www.jenner.ac.uk/AntiJen). The partial least-squares method is available commercially in the SYBYL molecular modeling software package.
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28
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Fagerberg T, Cerottini JC, Michielin O. Structural prediction of peptides bound to MHC class I. J Mol Biol 2005; 356:521-46. [PMID: 16368108 DOI: 10.1016/j.jmb.2005.11.059] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2005] [Revised: 11/16/2005] [Accepted: 11/17/2005] [Indexed: 11/29/2022]
Abstract
An ab initio structure prediction approach adapted to the peptide-major histocompatibility complex (MHC) class I system is presented. Based on structure comparisons of a large set of peptide-MHC class I complexes, a molecular dynamics protocol is proposed using simulated annealing (SA) cycles to sample the conformational space of the peptide in its fixed MHC environment. A set of 14 peptide-human leukocyte antigen (HLA) A0201 and 27 peptide-non-HLA A0201 complexes for which X-ray structures are available is used to test the accuracy of the prediction method. For each complex, 1000 peptide conformers are obtained from the SA sampling. A graph theory clustering algorithm based on heavy atom root-mean-square deviation (RMSD) values is applied to the sampled conformers. The clusters are ranked using cluster size, mean effective or conformational free energies, with solvation free energies computed using Generalized Born MV 2 (GB-MV2) and Poisson-Boltzmann (PB) continuum models. The final conformation is chosen as the center of the best-ranked cluster. With conformational free energies, the overall prediction success is 83% using a 1.00 Angstroms crystal RMSD criterion for main-chain atoms, and 76% using a 1.50 Angstroms RMSD criterion for heavy atoms. The prediction success is even higher for the set of 14 peptide-HLA A0201 complexes: 100% of the peptides have main-chain RMSD values < or =1.00 Angstroms and 93% of the peptides have heavy atom RMSD values < or =1.50 Angstroms. This structure prediction method can be applied to complexes of natural or modified antigenic peptides in their MHC environment with the aim to perform rational structure-based optimizations of tumor vaccines.
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Affiliation(s)
- Theres Fagerberg
- Ludwig Institute for Cancer Research, University of Lausanne, Epalinges, Switzerland
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29
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Prat E, Tomaru U, Sabater L, Park DM, Granger R, Kruse N, Ohayon JM, Bettinotti MP, Martin R. HLA-DRB5*0101 and -DRB1*1501 expression in the multiple sclerosis-associated HLA-DR15 haplotype. J Neuroimmunol 2005; 167:108-19. [PMID: 16111772 DOI: 10.1016/j.jneuroim.2005.04.027] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2004] [Revised: 04/13/2005] [Accepted: 04/22/2005] [Indexed: 10/25/2022]
Abstract
The HLA region, and particularly the DR15 haplotype (containing the two DRB* genes DRB1*1501 and DRB5*0101 and the tightly linked DQ alleles DQA*0102 and DQB1*0602, which together form the DQw6 molecule) in Caucasians, shows the strongest genetic association with multiple sclerosis (MS). In the DR15 haplotype, two beta-chains HLA-DRB1*1501 and -DRB5*0101 are co-expressed resulting in two different surface HLA-DR alphabeta heterodimers, DR2b and DR2a. Most previous studies focused on DRB1*1501, however, both DR2a and DR2b may contribute to MS pathogenesis via antigen presentation to myelin-specific T lymphocytes. We therefore analyzed the expression of the two DR15 genes in various antigen presenting cells (APCs), central nervous system and thymic tissues. Transcript levels were higher for DRB5*0101 in all cell types and tissues. Both HLA-DR heterodimers were expressed at significant levels on the cell surface, where they showed a differential expression pattern in different APCs. They were similarly regulated after stimulation with interferon-gamma and interleukin-4. Finally, immunohistochemistry experiments indicated that both molecules were expressed in thymic tissue. Our results encourage future research to investigate the potential functional relevance of both genes for the pathogenesis of MS.
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Affiliation(s)
- Elisabetta Prat
- Neuroimmunology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Building 10, Room 5B16, 10 Center DR, Bethesda, MD 20892-1400, USA
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30
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Kellenberger C, Roussel A, Malissen B. The H-2KkMHC Peptide-Binding Groove Anchors the Backbone of an Octameric Antigenic Peptide in an Unprecedented Mode. THE JOURNAL OF IMMUNOLOGY 2005; 175:3819-25. [PMID: 16148128 DOI: 10.4049/jimmunol.175.6.3819] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
A wealth of data has accumulated on the structure of mouse MHC class I (MHCI) molecules encoded by the H-2(b) and H-2(d) haplotypes. In contrast, there is a dearth of structural data regarding H-2(k)-encoded molecules. Therefore, the structures of H-2K(k) complexed to an octameric peptide from influenza A virus (HA(259-266)) and to a nonameric peptide from SV40 (SV40(560-568)) have been determined by x-ray crystallography at 2.5 and 3.0 A resolutions, respectively. The structure of the H-2K(k)-HA(259-266) complex reveals that residues located on the floor of the peptide-binding groove contact directly the backbone of the octameric peptide and force it to lie deep within the H-2K(k) groove. This unprecedented mode of peptide binding occurs despite the presence of bulky residues in the middle of the floor of the H-2K(k) peptide-binding groove. As a result, the Calpha atoms of peptide residues P5 and P6 are more buried than the corresponding residues of H-2K(b)-bound octapeptides, making them even less accessible to TCR contact. When bound to H-2K(k), the backbone of the SV40(560-568) nonapeptide bulges out of the peptide-binding groove and adopts a conformation reminiscent of that observed for peptides bound to H-2L(d). This structural convergence occurs despite the totally different architectures of the H-2L(d) and H-2K(k) peptide-binding grooves. Therefore, these two H-2K(k)-peptide complexes provide insights into the mechanisms through which MHC polymorphism outside primary peptide pockets influences the conformation of the bound peptides and have implications for TCR recognition and vaccine design.
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Affiliation(s)
- Christine Kellenberger
- Centre d'Immunologie de Marseille-Luminy, Institut National de la Santé et de la Recherche Médicale-Centre National Recherche de la Scientifique-Université de la Méditerranée, Parc Scientifique de Luminy, Marseille, France.
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31
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Rohrlich PS, Fazilleau N, Ginhoux F, Firat H, Michel F, Cochet M, Laham N, Roth MP, Pascolo S, Nato F, Coppin H, Charneau P, Danos O, Acuto O, Ehrlich R, Kanellopoulos J, Lemonnier FA. Direct recognition by alphabeta cytolytic T cells of Hfe, a MHC class Ib molecule without antigen-presenting function. Proc Natl Acad Sci U S A 2005; 102:12855-60. [PMID: 16123136 PMCID: PMC1200262 DOI: 10.1073/pnas.0502309102] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2005] [Indexed: 12/17/2022] Open
Abstract
Crystallographic analysis of human Hfe has documented an overall structure similar to classical (class Ia) MHC molecules with a peptide binding groove deprived of ligand. Thus, to address the question of whether alphabeta T cells could recognize MHC molecules independently of bound ligands, we studied human and mouse Hfe interactions with T lymphocytes. We provide formal evidence of direct cytolytic recognition of human Hfe by mouse alphabeta T cell receptors (TCR) in HLA-A*0201 transgenic mice and that this interaction results in ZAP-70 phosphorylation. Furthermore, direct recognition of mouse Hfe molecules by cytotoxic T lymphocytes (CTLs) was demonstrated in DBA/2 Hfe knockout mice. These CTLs express predominantly two T cell antigen receptor alpha variable gene segments (AV6.1 and AV6.6). Interestingly, in wild-type mice we identified a subset of CD8+ T cells positively selected by Hfe that expresses the AV6.1/AV6.6 gene segments. T cell antigen receptor recognition of MHC molecules independently of bound ligand has potential general implications in alloreactivity and identifies in the Hfe case a cognitive link supporting the concept that the immune system could be involved in the control of iron metabolism.
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Affiliation(s)
- Pierre S Rohrlich
- Unité d'Immunité Cellulaire Antivirale, Département d'Immunologie, Institut Pasteur, 75724 Paris, France
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32
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Olson R, Huey-Tubman KE, Dulac C, Bjorkman PJ. Structure of a pheromone receptor-associated MHC molecule with an open and empty groove. PLoS Biol 2005; 3:e257. [PMID: 16089503 PMCID: PMC1174912 DOI: 10.1371/journal.pbio.0030257] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2005] [Accepted: 05/18/2005] [Indexed: 11/24/2022] Open
Abstract
Neurons in the murine vomeronasal organ (VNO) express a family of class Ib major histocompatibility complex (MHC) proteins (M10s) that interact with the V2R class of VNO receptors. This interaction may play a direct role in the detection of pheromonal cues that initiate reproductive and territorial behaviors. The crystal structure of M10.5, an M10 family member, is similar to that of classical MHC molecules. However, the M10.5 counterpart of the MHC peptide-binding groove is open and unoccupied, revealing the first structure of an empty class I MHC molecule. Similar to empty MHC molecules, but unlike peptide-filled MHC proteins and non-peptide–binding MHC homologs, M10.5 is thermally unstable, suggesting that its groove is normally occupied. However, M10.5 does not bind endogenous peptides when expressed in mammalian cells or when offered a mixture of class I–binding peptides. The F pocket side of the M10.5 groove is open, suggesting that ligands larger than 8–10-mer class I–binding peptides could fit by extending out of the groove. Moreover, variable residues point up from the groove helices, rather than toward the groove as in classical MHC structures. These data suggest that M10s are unlikely to provide specific recognition of class I MHC–binding peptides, but are consistent with binding to other ligands, including proteins such as the V2Rs. MHC-like protein M10.5 is expressed in the vomeronasal organ. The structure does not bind endogenous class I-binding peptides, but is thought to interact with a larger V2R pheromone receptor.
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Affiliation(s)
- Rich Olson
- 1 Division of Biology, California Institute of Technology, Pasadena, California, United States of America
| | - Kathryn E Huey-Tubman
- 1 Division of Biology, California Institute of Technology, Pasadena, California, United States of America
- 2 Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California, United States of America
| | - Catherine Dulac
- 3 Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts, United States of America
| | - Pamela J Bjorkman
- 1 Division of Biology, California Institute of Technology, Pasadena, California, United States of America
- 2 Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California, United States of America
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33
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Borbulevych OY, Baxter TK, Yu Z, Restifo NP, Baker BM. Increased immunogenicity of an anchor-modified tumor-associated antigen is due to the enhanced stability of the peptide/MHC complex: implications for vaccine design. THE JOURNAL OF IMMUNOLOGY 2005; 174:4812-20. [PMID: 15814707 PMCID: PMC2241749 DOI: 10.4049/jimmunol.174.8.4812] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The use of "anchor-fixed" altered peptide ligands is of considerable interest in the development of therapeutic vaccines for cancer and infectious diseases, but the mechanism by which successful altered peptide ligands elicit enhanced immunity is unclear. In this study, we have determined the crystallographic structure of a major tumor rejection Ag, gp100(209-217), in complex with the HLA-A*0201 (HLA-A2) molecule, as well as the structure of a modified version of the peptide which substitutes methionine for threonine at position 2 (T2M; gp100(209-2M)). The T2M-modified peptide, which is more immunogenic in vitro and in vivo, binds HLA-A2 with a approximately 9-fold greater affinity and has a approximately 7-fold slower dissociation rate at physiological temperature. Within the limit of the crystallographic data, the T2M substitution does not alter the structure of the peptide/HLA-A2 complex. Consistent with this finding, in peripheral blood from 95 human subjects, we were unable to identify higher frequencies of T cells specific for either the native or modified peptide. These data strongly support the conclusion that the greater immunogenicity of the gp100(209-2M) peptide is due to the enhanced stability of the peptide/MHC complex, validating the anchor-fixing approach for generating therapeutic vaccine candidates. Thermodynamic data suggest that the enhanced stability of the T2M-modified peptide/HLA-A2 complex is attributable to the increased hydrophobicity of the modified peptide, but the gain due to hydrophobicity is offset considerably by the loss of a hydrogen bond made by the native peptide to the HLA-A2 molecule. Our findings have broad implications for the optimization of current vaccine-design strategies.
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Affiliation(s)
- Oleg Y Borbulevych
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
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34
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Turner SJ, Kedzierska K, Komodromou H, La Gruta NL, Dunstone MA, Webb AI, Webby R, Walden H, Xie W, McCluskey J, Purcell AW, Rossjohn J, Doherty PC. Lack of prominent peptide-major histocompatibility complex features limits repertoire diversity in virus-specific CD8+ T cell populations. Nat Immunol 2005; 6:382-9. [PMID: 15735650 DOI: 10.1038/ni1175] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2004] [Accepted: 01/31/2005] [Indexed: 11/08/2022]
Abstract
Using both 'reverse genetics' and structural analysis, we have examined the in vivo relationship between antigenicity and T cell receptor (TCR) repertoire diversity. Influenza A virus infection of C57BL/6 mice induces profoundly different TCR repertoires specific for the nucleoprotein peptide of amino acids 366-374 (NP366) and the acid polymerase peptide of amino acids 224-233 (PA224) presented by H-2D(b). Here we show the H-2D(b)-NP366 complex with a 'featureless' structure selected a limited TCR repertoire characterized by 'public' TCR usage. In contrast, the prominent H-2D(b)-PA224 complex selected diverse, individually 'private' TCR repertoires. Substitution of the arginine at position 7 of PA224 with an alanine reduced the accessible side chains of the epitope. Infection with an engineered virus containing a mutation at the site encoding the exposed arginine at position 7 of PA224 selected a restricted TCR repertoire similar in diversity to that of the H-2D(b)-NP366-specific response. Thus, the lack of prominent features in an antigenic complex of peptide and major histocompatibility complex class I is associated with a diminished spectrum of TCR usage.
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Affiliation(s)
- Stephen J Turner
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, Victoria 3010, Australia
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35
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Baxter TK, Gagnon SJ, Davis-Harrison RL, Beck JC, Binz AK, Turner RV, Biddison WE, Baker BM. Strategic Mutations in the Class I Major Histocompatibility Complex HLA-A2 Independently Affect Both Peptide Binding and T Cell Receptor Recognition. J Biol Chem 2004; 279:29175-84. [PMID: 15131131 DOI: 10.1074/jbc.m403372200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mutational studies of T cell receptor (TCR) contact residues on the surface of the human class I major histocompatibility complex (MHC) molecule HLA-A2 have identified a "functional hot spot" that comprises Arg(65) and Lys(66) and is involved in recognition by most peptide-specific HLA-A2-restricted TCRs. Although there is a significant amount of functional data on the effects of mutations at these positions, there is comparatively little biochemical information that could illuminate their mode of action. Here, we have used a combination of fluorescence anisotropy, functional assays, and Biacore binding experiments to examine the effects of mutations at these positions on the peptide-MHC interaction and TCR recognition. The results indicate that mutations at both position 65 and position 66 influence peptide binding by HLA-A2 to various extents. In particular, mutations at position 66 result in significantly increased peptide dissociation rates. However, these effects are independent of their effects on TCR recognition, and the Arg(65)-Lys(66) region thus represents a true "hot spot" for TCR recognition. We also made the observation that in vitro T cell reactivity does not scale with the half-life of the peptide-MHC complex, as is often assumed. Finally, position 66 is implicated in the "dual recognition" of both peptide and TCR, emphasizing the multiple roles of the class I MHC peptide-binding domain.
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Affiliation(s)
- Tiffany K Baxter
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
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36
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Zhao B, Mathura VS, Rajaseger G, Moochhala S, Sakharkar MK, Kangueane P. A novel MHCp binding prediction model. Hum Immunol 2003; 64:1123-43. [PMID: 14630395 DOI: 10.1016/j.humimm.2003.08.343] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Many statistical and molecular mechanics models have been developed and tested for major histocompatibility complex peptide (MHCp) binding predictions during the last decade. The statistical model prediction using pooled peptide sequence data and three-dimensional modeling prediction by molecular mechanics calculations have been assessed for efficiency and human leukocyte antigen diversity coverage. We describe a novel predictive model using information gleaned from 29 human MHCp crystal structures. The validation for the new model is performed using four different sets of data: (1) MHCp crystal structures, (2) peptides with known IC(50) binding values, (3) peptides tested positive by tetramer staining, (4) peptides with known binding information at the MHCBN database. The model produces high prediction efficiencies (average 60 %) with good sensitivity (approximately 50%-73%) and specificity (52%-58%) values. The average positive predictive value of the model is 89%, while the average negative predictive value is only 18%. The efficiency is very high in predicting binders and very low in predicting nonbinders. This model is superior to many existing methods because of its potential application to any given MHC allele whose sequence is clearly defined.
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Affiliation(s)
- Bing Zhao
- School of Mechanical and Production Engineering, Nanyang Centre for Supercomputing and Visualization, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639 798, Republic of Singapore
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37
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Buslepp J, Wang H, Biddison WE, Appella E, Collins EJ. A Correlation between TCR Vα Docking on MHC and CD8 Dependence. Immunity 2003; 19:595-606. [PMID: 14563323 DOI: 10.1016/s1074-7613(03)00269-3] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
T cell receptors (TCR) adopt a similar orientation when binding with major histocompatibility complex (MHC) molecules, yet the biological mechanism that generates this similar TCR orientation remains obscure. We show here the cocrystallographic structure of a mouse TCR bound to a human MHC molecule not seen by the TCR during thymic development. The orientation of this xenoreactive murine TCR atop human MHC deviates from the typical orientation more than any previously determined TCR/MHC structure. This unique orientation is solely due to the placement of the TCR Valpha domain on the MHC. In light of new information provided by this structure, we have reanalyzed the existing TCR/MHC cocrystal structures and discovered unique features of TCR Valpha domain position on class I MHC that correlate with CD8 dependence. Finally, we propose that the orientation seen in TCR recognition of MHC is a consequence of selection during T cell development.
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Affiliation(s)
- Jennifer Buslepp
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA
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38
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Cunto-Amesty G, Monzavi-Karbassi B, Luo P, Jousheghany F, Kieber-Emmons T. Strategies in cancer vaccines development. Int J Parasitol 2003; 33:597-613. [PMID: 12782058 DOI: 10.1016/s0020-7519(03)00054-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The recent definition of tumour-specific immunity in cancer patients and the identification of tumour-associated antigens have generated renewed enthusiasm for the application of immune-based therapies for the treatment of malignancies. Recent developments in cancer vaccines have also been based on an improved understanding of the cellular interactions required to induce a specific anti-tumour immune response. Consequently, a number of cancer vaccines have entered clinical trials. Targeting broad-spectrum tumour-associated antigens has emerged as a strategy to lower the risk of tumour escape due to the loss of specific nominal antigen. Amongst the most challenging of tumour-associated antigens to which to target in active specific immunotherapy applications are carbohydrate antigens. As carbohydrates are intrinsically T-cell-independent antigens, more novel approaches are perhaps needed to drive specific-T-cell-dependent immune responses to carbohydrate antigens. In this context peptide mimetics of core structures of tumour-associated carbohydrate antigens might be developed to augment immune responses to these broad-spectrum antigens.
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Affiliation(s)
- Gina Cunto-Amesty
- Department of Pathology, University of Pennsylvania, Philadelphia, PA 19104, USA
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39
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Kohm AP, Fuller KG, Miller SD. Mimicking the way to autoimmunity: an evolving theory of sequence and structural homology. Trends Microbiol 2003; 11:101-5. [PMID: 12648936 DOI: 10.1016/s0966-842x(03)00006-4] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although the etiology of autoimmune diseases remains largely unknown, a prevailing theory concerns the infection-induced activation of self-reactive lymphocytes via the process of molecular mimicry. Here, we discuss the theory of molecular mimicry and its continued evolution from the initial basic considerations of sequence similarity to the current theories of structural homology. Such findings serve to further our understanding of T-cell receptor degeneracy and might one day provide a direct link between infection and autoimmune disease.
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Affiliation(s)
- Adam P Kohm
- Department of Microbiology-Immunology and Interdepartmental Immunobiology Center, Northwestern University Medical School, 303 E. Chicago Avenue, Chicago, IL 60611, USA
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40
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Buslepp J, Kerry SE, Loftus D, Frelinger JA, Appella E, Collins EJ. High affinity xenoreactive TCR:MHC interaction recruits CD8 in absence of binding to MHC. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2003; 170:373-83. [PMID: 12496422 DOI: 10.4049/jimmunol.170.1.373] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The TCR from a xenoreactive murine cytotoxic T lymphocyte clone, AHIII 12.2, recognizes murine H-2D(b) complexed with peptide p1058 (FAPGFFPYL) as well as human HLA-A2.1 complexed with human self-peptide p1049 (ALWGFFPVL). To understand more about T cell biology and cross-reactivity, the ectodomains of the AHIII 12.2 TCR have been produced in E. coli as inclusion bodies and the protein folded to its native conformation. Flow cytometric and surface plasmon resonance analyses indicate that human p1049/A2 has a significantly greater affinity for the murine AHIII 12.2 TCR than does murine p1058/D(b). Yet, T cell binding and cytolytic activity are independent of CD8 when stimulated with human p1049/A2 as demonstrated with anti-CD8 Abs that block CD8 association with MHC. Even in the absence of direct CD8 binding, stimulation of AHIII 12.2 T cells with "CD8-independent" p1049/A2 produces p56(lck) activation and calcium flux. Confocal fluorescence microscopy and fluorescence resonance energy transfer flow cytometry demonstrate CD8 is recruited to the site of TCR:peptide MHC binding. Taken together, these results indicate that there exists another mechanism for recruitment of CD8 during high affinity TCR:peptide MHC engagement.
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MESH Headings
- Animals
- Antigen Presentation/genetics
- Antigens, Heterophile/metabolism
- CD8 Antigens/metabolism
- CD8 Antigens/physiology
- CHO Cells
- Cell Line
- Clone Cells
- Cricetinae
- Cytotoxicity, Immunologic/genetics
- H-2 Antigens/genetics
- H-2 Antigens/metabolism
- HLA-A2 Antigen/genetics
- HLA-A2 Antigen/metabolism
- Histocompatibility Antigen H-2D
- Humans
- Lymphocyte Activation/genetics
- Mice
- Mice, Inbred C57BL
- Oligopeptides/immunology
- Oligopeptides/metabolism
- Protein Binding/genetics
- Protein Binding/immunology
- Receptors, Antigen, T-Cell/biosynthesis
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/metabolism
- Recombinant Proteins/biosynthesis
- Recombinant Proteins/metabolism
- Signal Transduction/genetics
- Signal Transduction/immunology
- Surface Plasmon Resonance
- T-Lymphocytes, Cytotoxic/immunology
- T-Lymphocytes, Cytotoxic/metabolism
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Affiliation(s)
- Jennifer Buslepp
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA
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41
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Wang B, Sharma A, Maile R, Saad M, Collins EJ, Frelinger JA. Peptidic termini play a significant role in TCR recognition. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2002; 169:3137-45. [PMID: 12218131 DOI: 10.4049/jimmunol.169.6.3137] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
TCR recognition of class I MHC is dependent on the composition of the antigenic peptide and the MHC. Single amino acid substitutions in either the MHC or the peptide may dramatically alter recognition. While the major interactions between TCR and the peptide/MHC complex appear to be focused on the complementarity-determining region (CDR)3, it is also clear from the cocrystal structure of class I MHC and TCR that the amino and carboxyl ends of the peptide may play a role through interactions with the CDR1. In this work we show that gp33 variants substituted at the peptidic termini at the putative CDR1 contact regions show improved recognition in B6 mice. The rank order of recognition is different using the P14 transgenic T cells, suggesting that one reason for improved recognition is a change in the TCR repertoire that recognizes the peptide. However, the affinity of the TCR by some of the peptide/MHC complex with increased recognition is improved, as shown by increased tetramer binding to P14 T cells. These substitutions at the termini of the peptide-binding cleft cause localized conformational changes as seen by changes in mAb binding and crystallographic structures. The different peptide structures also show different conformations in the center of the peptide, but these are shown to be energetically similar and thus most likely have no significance with respect to TCR recognition. Therefore, small conformational changes, localized to the CDR1 contact regions, may play a significant role in TCR recognition.
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MESH Headings
- Amino Acid Substitution/genetics
- Amino Acid Substitution/immunology
- Animals
- Antigens, Viral/immunology
- Antigens, Viral/metabolism
- CD8-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/metabolism
- Cells, Cultured
- Cytotoxicity Tests, Immunologic
- Glycoproteins/immunology
- Glycoproteins/metabolism
- H-2 Antigens/immunology
- H-2 Antigens/metabolism
- Histocompatibility Antigen H-2D
- Lymphocytic choriomeningitis virus/immunology
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Mice, Transgenic
- Oligopeptides/immunology
- Oligopeptides/metabolism
- Oligopeptides/physiology
- Peptide Fragments/immunology
- Peptide Fragments/metabolism
- Protein Binding/immunology
- Protein Conformation
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/metabolism
- Viral Proteins/immunology
- Viral Proteins/metabolism
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Affiliation(s)
- Bo Wang
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599, USA
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42
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Lang HLE, Jacobsen H, Ikemizu S, Andersson C, Harlos K, Madsen L, Hjorth P, Sondergaard L, Svejgaard A, Wucherpfennig K, Stuart DI, Bell JI, Jones EY, Fugger L. A functional and structural basis for TCR cross-reactivity in multiple sclerosis. Nat Immunol 2002; 3:940-3. [PMID: 12244309 DOI: 10.1038/ni835] [Citation(s) in RCA: 377] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2002] [Accepted: 08/05/2002] [Indexed: 02/08/2023]
Abstract
The multiple sclerosis (MS)-associated HLA major histocompatibility complex (MHC) class II alleles DRB1*1501, DRB5*0101 and DQB1*0602 are in strong linkage disequilibrium, making it difficult to determine which is the principal MS risk gene. Here we show that together the DRB1 and DRB5 loci may influence susceptibility to MS. We demonstrate that a T cell receptor (TCR) from an MS patient recognized both a DRB1*1501-restricted myelin basic protein (MBP) and DRB5*0101-restricted Epstein-Barr virus (EBV) peptide. Crystal structure determination of the DRB5*0101-EBV peptide complex revealed a marked degree of structural equivalence to the DRB1*1501-MBP peptide complex at the surface presented for TCR recognition. This provides structural evidence for molecular mimicry involving HLA molecules. The structural details suggest an explanation for the preponderance of MHC class II associations in HLA-associated diseases.
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MESH Headings
- Animals
- B-Lymphocytes/cytology
- B-Lymphocytes/immunology
- Cell Line
- Cross Reactions
- Crystallography, X-Ray
- HLA-DR Antigens/chemistry
- HLA-DR Antigens/immunology
- HLA-DRB1 Chains
- HLA-DRB5 Chains
- Herpesvirus 4, Human/immunology
- Humans
- Mice
- Mice, Transgenic
- Models, Molecular
- Multiple Sclerosis/immunology
- Myelin Basic Protein/chemistry
- Myelin Basic Protein/immunology
- Protein Structure, Tertiary
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
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Affiliation(s)
- Heather L E Lang
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
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43
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Adrian PEH, Rajaseger G, Mathura VS, Sakharkar MK, Kangueane P. Types of inter-atomic interactions at the MHC-peptide interface: identifying commonality from accumulated data. BMC STRUCTURAL BIOLOGY 2002; 2:2. [PMID: 12010576 PMCID: PMC113755 DOI: 10.1186/1472-6807-2-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2001] [Accepted: 05/13/2002] [Indexed: 11/10/2022]
Abstract
BACKGROUND Quantitative information on the types of inter-atomic interactions at the MHC-peptide interface will provide insights to backbone/sidechain atom preference during binding. Qualitative descriptions of such interactions in each complex have been documented by protein crystallographers. However, no comprehensive report is available to account for the common types of inter-atomic interactions in a set of MHC-peptide complexes characterized by variation in MHC allele and peptide sequence. The available x-ray crystallography data for these complexes in the Protein Databank (PDB) provides an opportunity to identify the prevalent types of such interactions at the binding interface. RESULTS We calculated the percentage distributions of four types of interactions at varying inter-atomic distances. The mean percentage distribution for these interactions and their standard deviation about the mean distribution is presented. The prevalence of SS and SB interactions at the MHC-peptide interface is shown in this study. SB is clearly dominant at an inter-atomic distance of 3A. CONCLUSION The prevalently dominant SB interactions at the interface suggest the importance of peptide backbone conformation during MHC-peptide binding. Currently, available algorithms are developed for protein sidechain prediction upon fixed backbone template. This study shows the preference of backbone atoms in MHC-peptide binding and hence emphasizes the need for accurate peptide backbone prediction in quantitative MHC-peptide binding calculations.
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Affiliation(s)
- Png Eak Hock Adrian
- National University of Singapore, Department of Microbiology, Medical Drive, Singapore.
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44
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Felix NJ, de Serres S, Meyer AA, Ting JPY. Comparison of Abeta(b-/-), H2-DM(-), and CIITA(-/-) in second-set skin allograft rejection. J Surg Res 2002; 102:185-92. [PMID: 11796017 DOI: 10.1006/jsre.2001.6311] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
BACKGROUND Responses against donor MHC antigens are the major contributor to allograft rejection. Currently, it is unclear whether both direct and indirect recognition pathways are necessary and/or sufficient for allograft rejection. Previously, we found donor MHC class II and H2-DM to have dramatic effects on cardiac allograft survival. METHODS Here, we used H2-DM(-) mice, which express CLIP-MHC class II complexes, and CIITA(-/-) mice, which lack all class II proteins, to examine the role of direct and indirect recognition on skin allograft rejection. Recipients were primed with donor cultured keratinocytes and later tested for accelerated memory response by challenge with full-thickness tail skin grafts. RESULTS As previously reported, Abeta(b-/-) grafts survived longer than wild-type grafts, while H2-DM(-) grafts were rejected as rapidly as wild-type grafts. Skin grafts deficient for both beta2m and H2-DM survived longer than grafts lacking only H2-DM, but not as long as Abeta(b-/-) grafts. Additionally, CIITA(-/-) grafts survived as long as Abeta(b-/-) grafts. CONCLUSIONS The delayed rejection of Abeta(b-/-) compared to H2-DM(-) suggests that indirect recognition of surface-expressed donor MHC class II is sufficient to mediate rapid skin allograft rejection. The equivalent survival of CIITA(-/-) and Abeta(b-/-) grafts suggests that indirect presentation of donor class II molecules (Aalpha or Ebeta) present in Abeta(b-/-) but not CIITA(-/-) mice does not contribute to graft rejection. These results reveal a modest role for surface-expressed donor class II in primed keratinocyte rejection, but also reveal a dramatic contrast to the cardiac allograft system and indicate tissue/organ-specific mechanisms of rejection.
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MESH Headings
- Animals
- Antigens, Differentiation, B-Lymphocyte/genetics
- Antigens, Differentiation, B-Lymphocyte/immunology
- Cells, Cultured
- Dermatologic Surgical Procedures
- Female
- Gene Expression/immunology
- Graft Rejection/genetics
- Graft Rejection/immunology
- H-2 Antigens/genetics
- H-2 Antigens/immunology
- Histocompatibility Antigens Class II/genetics
- Histocompatibility Antigens Class II/immunology
- Immunologic Memory
- Keratinocytes/cytology
- Keratinocytes/transplantation
- Male
- Mice
- Mice, Inbred BALB C
- Mice, Inbred C57BL
- Mice, Inbred DBA
- Mice, Knockout
- Nuclear Proteins
- Skin/immunology
- T-Lymphocytes, Cytotoxic/immunology
- Trans-Activators/genetics
- Trans-Activators/immunology
- Transplantation, Homologous
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Affiliation(s)
- Nathan J Felix
- Lineberger Comprehensive Cancer Center, Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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45
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Ostrov DA, Roden MM, Shi W, Palmieri E, Christianson GJ, Mendoza L, Villaflor G, Tilley D, Shastri N, Grey H, Almo SC, Roopenian D, Nathenson SG. How H13 histocompatibility peptides differing by a single methyl group and lacking conventional MHC binding anchor motifs determine self-nonself discrimination. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2002; 168:283-9. [PMID: 11751972 DOI: 10.4049/jimmunol.168.1.283] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The mouse H13 minor histocompatibility (H) Ag, originally detected as a barrier to allograft transplants, is remarkable in that rejection is a consequence of an extremely subtle interchange, P4(Val/Ile), in a nonamer H2-D(b)-bound peptide. Moreover, H13 peptides lack the canonical P5(Asn) central anchor residue normally considered important for forming a peptide/MHC complex. To understand how these noncanonical peptide pMHC complexes form physiologically active TCR ligands, crystal structures of allelic H13 pD(b) complexes and a P5(Asn) anchored pD(b) analog were solved to high resolution. The structures show that the basis of TCRs to distinguish self from nonself H13 peptides is their ability to distinguish a single solvent-exposed methyl group. In addition, the structures demonstrate that there is no need for H13 peptides to derive any stabilization from interactions within the central C pocket to generate fully functional pMHC complexes. These results provide a structural explanation for a classical non-MHC-encoded H Ag, and they call into question the requirement for contact between anchor residues and the major MHC binding pockets in vaccine design.
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Affiliation(s)
- David A Ostrov
- Department of Biochemistry, Albert Einstein College of Medicine, 1600 Morris Boulevard, Bronx, NY 10461, USA
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46
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Buslepp J, Zhao R, Donnini D, Loftus D, Saad M, Appella E, Collins EJ. T cell activity correlates with oligomeric peptide-major histocompatibility complex binding on T cell surface. J Biol Chem 2001; 276:47320-8. [PMID: 11584024 DOI: 10.1074/jbc.m109231200] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Recognition of virally infected cells by CD8+ T cells requires differentiation between self and nonself peptide-class I major histocompatibility complexes (pMHC). Recognition of foreign pMHC by host T cells is a major factor in the rejection of transplanted organs from the same species (allotransplant) or different species (xenotransplant). AHIII12.2 is a murine T cell clone that recognizes the xenogeneic (human) class I MHC HLA-A2.1 molecule (A2) and the syngeneic murine class I MHC H-2 D(b) molecule (D(b)). Recognition of both A2 and D(b) are peptide-dependent, and the sequences of the peptides recognized have been determined. Alterations in the antigenic peptides bound to A2 cause large changes in AHIII12.2 T cell responsiveness. Crystal structures of three representative peptides (agonist, null, and antagonist) bound to A2 partially explain the changes in AHIII12.2 responsiveness. Using class I pMHC octamers, a strong correlation is seen between T cell activity and the affinity of pMHC complexes for the T cell receptor. However, contrary to previous studies, we see similar half-lives for the pMHC multimers bound to the AHIII12.2 cell surface.
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Affiliation(s)
- J Buslepp
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599, USA
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47
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Ciatto C, Tissot AC, Tschopp M, Capitani G, Pecorari F, Plückthun A, Grütter MG. Zooming in on the hydrophobic ridge of H-2D(b): implications for the conformational variability of bound peptides. J Mol Biol 2001; 312:1059-71. [PMID: 11580250 DOI: 10.1006/jmbi.2001.5016] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Class I major histocompatibility complex (MHC) molecules, which display intracellularly processed peptides on the cell surface for scanning by T-cell receptors (TCRs), are extraordinarily polymorphic. MHC polymorphism is believed to result from natural selection, since individuals heterozygous at the corresponding loci can cope with a larger number of pathogens. Here, we present the crystal structures of the murine MHC molecule H-2D(b) in complex with the peptides gp276 and np396 from the lymphocytic choriomeningitis virus (LCMV), solved at 2.18 A and 2.20 A resolution, respectively. The most prominent feature of H-2D(b) is a hydrophobic ridge that cuts across its antigen-binding site, which is conserved in the L(d)-like family of class I MHC molecules. The comparison with previously solved crystal structures of peptide/H-2D(b) complexes shows that the hydrophobic ridge focuses the conformational variability of the bound peptides in a "hot-spot", which could allow optimal TCR interaction and discrimination. This finding suggests a functional reason for the conservation of this structural element.
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MESH Headings
- Amino Acid Sequence
- Animals
- Antigens, Viral/chemistry
- Antigens, Viral/immunology
- Binding Sites
- Crystallography, X-Ray
- Epitopes/chemistry
- Epitopes/immunology
- Evolution, Molecular
- H-2 Antigens/chemistry
- H-2 Antigens/immunology
- Histocompatibility Antigen H-2D
- Hydrogen Bonding
- Lymphocytic choriomeningitis virus/chemistry
- Lymphocytic choriomeningitis virus/immunology
- Mice
- Models, Molecular
- Peptides/chemistry
- Peptides/immunology
- Protein Structure, Secondary
- Receptors, Antigen, T-Cell/chemistry
- Receptors, Antigen, T-Cell/immunology
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Affiliation(s)
- C Ciatto
- Biochemisches Insitut, der Universität Zürich, Winterthurerstrasse 190, Zürich, CH-8057, Switzerland
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48
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Sebille F, Gagne K, Guillet M, Degauque N, Pallier A, Brouard S, Vanhove B, Delsuc MA, Soulillou JP. Direct recognition of foreign MHC determinants by naive T cells mobilizes specific Vbeta families without skewing of the complementarity-determining region 3 length distribution. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2001; 167:3082-8. [PMID: 11544292 DOI: 10.4049/jimmunol.167.6.3082] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The capacity of T cells to interact with nonself-APC, also referred to as direct allorecognition, is an essential feature of the cellular response involved in graft rejection. However, there is no study on TCR repertoire biases associated with direct restricted T cell activation. In this paper, we have addressed the impact of direct recognition on the whole naive T cell repertoire, using a new approach that provides, for the first time, an integrated depiction of the quantitative and qualitative alterations in the TCR Vbeta transcriptome. This method can differentiate resting patterns from polyclonally activated ones, as evidenced by superantigen usage. According to this new readout, we show that direct recognition of nonself-MHC molecules triggers mRNA accumulation of several TCR Vbeta families, specific to the combination studied. Moreover, in marked contrast to the situation that prevails in indirect allorecognition, T cell activation through the direct presentation pathway was not associated with skewing of the complementarity determining region (CDR) 3 length distribution. Altogether, these data argue for the significance of TCR contacts with the MHC framework in direct allorecognition. In addition, the TCR diversity mobilized by this interaction and the massive TCRbeta mRNA accumulation observed after a few days of culture suggest that a significant proportion of naive T cells receive a signal leading to TCRbeta transcriptional activation even though only a few of them engage in mitosis.
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MESH Headings
- Animals
- Antigen Presentation/immunology
- Antigens, Heterophile/immunology
- Bacterial Toxins
- Cells, Cultured
- Cricetinae
- Dendritic Cells/immunology
- Enterotoxins/immunology
- Gene Expression Profiling
- Gene Rearrangement, beta-Chain T-Cell Antigen Receptor
- Genes, Immunoglobulin
- Histocompatibility Antigens/immunology
- Humans
- Immunization
- Immunoglobulin Variable Region/genetics
- Isoantigens/immunology
- Lymphocyte Activation
- Mesocricetus
- Peptide Fragments/analysis
- RNA, Messenger/biosynthesis
- RNA, Messenger/genetics
- Rats
- Rats, Inbred Lew
- Receptors, Antigen, T-Cell, alpha-beta/biosynthesis
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Self Tolerance/immunology
- Species Specificity
- Superantigens
- T-Lymphocyte Subsets/immunology
- Transcription, Genetic
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Affiliation(s)
- F Sebille
- Institut National de la Santé et de la Recherche Medicale, Unité 437, "Immunointervention dans les Allo et Xenotransplantations" and Institut de Transplantation et de Recherche en Transplantation, Nantes, France
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49
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Hillig RC, Coulie PG, Stroobant V, Saenger W, Ziegler A, Hülsmeyer M. High-resolution structure of HLA-A*0201 in complex with a tumour-specific antigenic peptide encoded by the MAGE-A4 gene. J Mol Biol 2001; 310:1167-76. [PMID: 11502003 DOI: 10.1006/jmbi.2001.4816] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The heterotrimeric complex of the human major histocompatibity complex (MHC) molecule HLA-A*0201, beta2-microglobulin and the decameric peptide GVYDGREHTV derived from the melanoma antigen (MAGE-A4 protein has been determined by X-ray crystallography at 1.4 A resolution. MAGE-A4 belongs to a family of genes that are specifically expressed in a variety of tumours. MAGE-A4-derived peptides are presented by MHC molecules at the cell surface to cytotoxic T-lymphocytes. As the HLA-A*0201:MAGE-A4 complex occurs only on tumour cells, it is considered to be an appropriate target for immunotherapy. The structure presented here reveals potential epitopes specific to the complex and indicates which peptide residues could be recognised by T-cell receptors. In addition, as the structure could be refined anisotropically, it was possible to describe the movements of the bound peptide in more detail.
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MESH Headings
- Amino Acid Sequence
- Antigens, Neoplasm/chemistry
- Antigens, Neoplasm/genetics
- Antigens, Neoplasm/immunology
- Antigens, Neoplasm/metabolism
- Binding Sites
- Circular Dichroism
- Crystallography, X-Ray
- Epitopes, T-Lymphocyte/chemistry
- Epitopes, T-Lymphocyte/immunology
- HLA-A Antigens/chemistry
- HLA-A Antigens/immunology
- HLA-A Antigens/metabolism
- Humans
- Immunotherapy
- Ligands
- Models, Molecular
- Neoplasm Proteins/chemistry
- Neoplasm Proteins/genetics
- Neoplasm Proteins/immunology
- Neoplasm Proteins/metabolism
- Peptide Fragments/chemistry
- Peptide Fragments/immunology
- Peptide Fragments/metabolism
- Polyethylene Glycols/chemistry
- Polyethylene Glycols/metabolism
- Protein Binding
- Protein Conformation
- Protein Denaturation
- Receptors, Antigen, T-Cell/immunology
- Temperature
- Thermodynamics
- beta 2-Microglobulin/chemistry
- beta 2-Microglobulin/metabolism
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Affiliation(s)
- R C Hillig
- Institut für Immungenetik, Universitätsklinikum Charité, Humboldt-Universität zu Berlin, Germany
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50
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Messaoudi I, LeMaoult J, Metzner BM, Miley MJ, Fremont DH, Nikolich-Zugich J. Functional evidence that conserved TCR CDR alpha 3 loop docking governs the cross-recognition of closely related peptide:class I complexes. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2001; 167:836-43. [PMID: 11441090 DOI: 10.4049/jimmunol.167.2.836] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The TCR recognizes its peptide:MHC (pMHC) ligand by assuming a diagonal orientation relative to the MHC helices, but it is unclear whether and to what degree individual TCRs exhibit docking variations when contacting similar pMHC complexes. We analyzed monospecific and cross-reactive recognition by diverse TCRs of an immunodominant HVH-1 glycoprotein B epitope (HSV-8p) bound to two closely related MHC class I molecules, H-2K(b) and H-2K(bm8). Previous studies indicated that the pMHC portion likely to vary in conformation between the two complexes resided at the N-terminal part of the complex, adjacent to peptide residues 2-4 and the neighboring MHC side chains. We found that CTL clones sharing TCR beta-chains exhibited disparate recognition patterns, whereas those with drastically different TCRbeta-chains but sharing identical TCRalpha CDR3 loops displayed identical functional specificity. This suggested that the CDRalpha3 loop determines the TCR specificity in our model, the conclusion supported by modeling of the TCR over the actual HSV-8:K(b) crystal structure. Importantly, these results indicate a remarkable conservation in CDRalpha3 positioning, and, therefore, in docking of diverse TCRalphabeta heterodimers onto variant peptide:class I complexes, implying a high degree of determinism in thymic selection and T cell activation.
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MESH Headings
- Amino Acid Sequence
- Animals
- Cell Line
- Clone Cells
- Conserved Sequence/genetics
- Conserved Sequence/immunology
- Crystallization
- Crystallography, X-Ray
- Epitopes, T-Lymphocyte/genetics
- Epitopes, T-Lymphocyte/metabolism
- H-2 Antigens/genetics
- H-2 Antigens/metabolism
- Herpesvirus 1, Human/immunology
- Immunodominant Epitopes/genetics
- Immunodominant Epitopes/metabolism
- Lymphocyte Activation/genetics
- Mice
- Mice, Inbred C57BL
- Models, Molecular
- Molecular Sequence Data
- Peptide Fragments/genetics
- Peptide Fragments/immunology
- Peptide Fragments/metabolism
- Protein Structure, Secondary/genetics
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/metabolism
- T-Lymphocytes, Cytotoxic/immunology
- T-Lymphocytes, Cytotoxic/metabolism
- Viral Envelope Proteins/immunology
- Viral Envelope Proteins/metabolism
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Affiliation(s)
- I Messaoudi
- Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA
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