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Zimmermann C, Watson GM, Bauersfeld L, Berry R, Ciblis B, Lan H, Gerke C, Oberhardt V, Fuchs J, Hofmann M, Freund C, Rossjohn J, Momburg F, Hengel H, Halenius A. Diverse cytomegalovirus US11 antagonism and MHC-A evasion strategies reveal a tit-for-tat coevolutionary arms race in hominids. Proc Natl Acad Sci U S A 2024; 121:e2315985121. [PMID: 38377192 PMCID: PMC10907249 DOI: 10.1073/pnas.2315985121] [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: 09/14/2023] [Accepted: 01/10/2024] [Indexed: 02/22/2024] Open
Abstract
Recurrent, ancient arms races between viruses and hosts have shaped both host immunological defense strategies as well as viral countermeasures. One such battle is waged by the glycoprotein US11 encoded by the persisting human cytomegalovirus. US11 mediates degradation of major histocompatibility class I (MHC-I) molecules to prevent CD8+ T-cell activation. Here, we studied the consequences of the arms race between US11 and primate MHC-A proteins, leading us to uncover a tit-for-tat coevolution and its impact on MHC-A diversification. We found that US11 spurred MHC-A adaptation to evade viral antagonism: In an ancestor of great apes, the MHC-A A2 lineage acquired a Pro184Ala mutation, which confers resistance against the ancestral US11 targeting strategy. In response, US11 deployed a unique low-complexity region (LCR), which exploits the MHC-I peptide loading complex to target the MHC-A2 peptide-binding groove. In addition, the global spread of the human HLA-A*02 allelic family prompted US11 to employ a superior LCR strategy with an optimally fitting peptide mimetic that specifically antagonizes HLA-A*02. Thus, despite cytomegaloviruses low pathogenic potential, the increasing commitment of US11 to MHC-A has significantly promoted diversification of MHC-A in hominids.
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Affiliation(s)
- Cosima Zimmermann
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, 79104Freiburg, Germany
| | - Gabrielle M. Watson
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC3800, Australia
| | - Liane Bauersfeld
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, 79104Freiburg, Germany
| | - Richard Berry
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC3800, Australia
| | - Barbara Ciblis
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, 79104Freiburg, Germany
| | - Huan Lan
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, 14195Berlin, Germany
| | - Carolin Gerke
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, 79104Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg, 79104Freiburg, Germany
| | - Valerie Oberhardt
- Department of Medicine II, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, 79104Freiburg, Germany
| | - Jonas Fuchs
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, 79104Freiburg, Germany
| | - Maike Hofmann
- Department of Medicine II, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, 79104Freiburg, Germany
| | - Christian Freund
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, 14195Berlin, Germany
| | - Jamie Rossjohn
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC3800, Australia
- Systems Immunity Research Institute, Cardiff University School of Medicine, University Hospital of Wales, Cardiff CF14 4XN, United Kingdom
| | - Frank Momburg
- Antigen Presentation and T/NK Cell Activation Group, German Cancer Research Center, Clinical Cooperation Unit Applied Tumor Immunity, German Cancer Research Center, 69120Heidelberg, Germany
| | - Hartmut Hengel
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, 79104Freiburg, Germany
| | - Anne Halenius
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, 79104Freiburg, Germany
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2
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Anand S, Littler DR, Mobbs JI, Braun A, Baker DG, Tennant L, Purcell AW, Vivian JP, Rossjohn J. Complimentary electrostatics dominate T Cell Receptor binding to a psoriasis-associated-peptide-antigen presented by Human Leukocyte Antigen (HLA) C*06:02. J Biol Chem 2023:104930. [PMID: 37330172 PMCID: PMC10371836 DOI: 10.1016/j.jbc.2023.104930] [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: 04/20/2023] [Revised: 06/05/2023] [Accepted: 06/13/2023] [Indexed: 06/19/2023] Open
Abstract
Psoriasis is a chronic skin disease characterised by hyperproliferative epidermal lesions infiltrated by autoreactive T cells. Individuals expressing the Human Leukocyte antigen (HLA) C*06:02 allele are at highest risk for developing psoriasis. An autoreactive T cell clone (termed Vα3S1/Vβ13S1) isolated from psoriatic plaques is selective for HLA-C*06:02-presenting a peptide derived from the melanocyte-specific auto-antigen ADAMTSL5 (VRSRRCLRL). Here we determine the crystal structure of this psoriatic TCR-HLA-C*06:02- ADAMTSL5 complex with a stabilised peptide. Docking of the TCR involves an extensive complementary charge network formed between negatively charged TCR residues interleaving with exposed arginine residues from the self-peptide and the HLA-C*06:02 α1 helix. We probed these interactions through mutagenesis and activation assays. The charged interface spans the polymorphic region of the C1/C2 HLA group. Notably the peptide binding groove of HLA C*06:02 appears exquisitely suited for presenting highly charged Arg-rich epitopes recognised by this acidic psoriatic TCR. Overall, we provide a structural basis for understanding engagement of melanocyte antigen-presenting cells by a TCR implicated in psoriasis, while simultaneously expanding our knowledge of how TCRs engage HLA-C.
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Affiliation(s)
- Sushma Anand
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton Victoria, Australia
| | - Dene R Littler
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton Victoria, Australia
| | - Jesse I Mobbs
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton Victoria, Australia
| | - Asolina Braun
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton Victoria, Australia
| | - Daniel G Baker
- Janssen Research & Development, LLC, Horsham, Philadelphia, Pennsylvania, USA
| | - Luke Tennant
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton Victoria, Australia
| | - Anthony W Purcell
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton Victoria, Australia
| | - Julian P Vivian
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton Victoria, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton Victoria, Australia; Institute of Infection and Immunity, Cardiff University, School of Medicine, Cardiff, UK.
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3
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Hopkins JR, MacLachlan BJ, Harper S, Sewell AK, Cole DK. Unconventional modes of peptide-HLA-I presentation change the rules of TCR engagement. DISCOVERY IMMUNOLOGY 2022; 1:kyac001. [PMID: 38566908 PMCID: PMC10917088 DOI: 10.1093/discim/kyac001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 03/18/2022] [Accepted: 04/06/2022] [Indexed: 04/04/2024]
Abstract
The intracellular proteome of virtually every nucleated cell in the body is continuously presented at the cell surface via the human leukocyte antigen class I (HLA-I) antigen processing pathway. This pathway classically involves proteasomal degradation of intracellular proteins into short peptides that can be presented by HLA-I molecules for interrogation by T-cell receptors (TCRs) expressed on the surface of CD8+ T cells. During the initiation of a T-cell immune response, the TCR acts as the T cell's primary sensor, using flexible loops to mould around the surface of the pHLA-I molecule to identify foreign or dysregulated antigens. Recent findings demonstrate that pHLA-I molecules can also be highly flexible and dynamic, altering their shape according to minor polymorphisms between different HLA-I alleles, or interactions with different peptides. These flexible presentation modes have important biological consequences that can, for example, explain why some HLA-I alleles offer greater protection against HIV, or why some cancer vaccine approaches have been ineffective. This review explores how these recent findings redefine the rules for peptide presentation by HLA-I molecules and extend our understanding of the molecular mechanisms that govern TCR-mediated antigen discrimination.
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Affiliation(s)
- Jade R Hopkins
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Bruce J MacLachlan
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | | | - Andrew K Sewell
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - David K Cole
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, UK
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4
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Le Gall C, Cammarata A, de Haas L, Ramos-Tomillero I, Cuenca-Escalona J, Schouren K, Wijfjes Z, Becker AMD, Bödder J, Dölen Y, de Vries IJM, Figdor CG, Flórez-Grau G, Verdoes M. Efficient targeting of NY-ESO-1 tumor antigen to human cDC1s by lymphotactin results in cross-presentation and antigen-specific T cell expansion. J Immunother Cancer 2022; 10:jitc-2021-004309. [PMID: 35428705 PMCID: PMC9014073 DOI: 10.1136/jitc-2021-004309] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/15/2022] [Indexed: 12/20/2022] Open
Abstract
Background Type 1 conventional dendritic cells (cDC1s) are characterized by their ability to induce potent CD8+ T cell responses. In efforts to generate novel vaccination strategies, notably against cancer, human cDC1s emerge as an ideal target to deliver antigens. cDC1s uniquely express XCR1, a seven transmembrane G protein-coupled receptor. Due to its restricted expression and endocytic nature, XCR1 represents an attractive receptor to mediate antigen-delivery to human cDC1s. Methods To explore tumor antigen delivery to human cDC1s, we used an engineered version of XCR1-binding lymphotactin (XCL1), XCL1(CC3). Site-specific sortase-mediated transpeptidation was performed to conjugate XCL1(CC3) to an analog of the HLA-A*02:01 epitope of the cancer testis antigen New York Esophageal Squamous Cell Carcinoma-1 (NY-ESO-1). While poor epitope solubility prevented isolation of stable XCL1-antigen conjugates, incorporation of a single polyethylene glycol (PEG) chain upstream of the epitope-containing peptide enabled generation of soluble XCL1(CC3)-antigen fusion constructs. Binding and chemotactic characteristics of the XCL1-antigen conjugate, as well as its ability to induce antigen-specific CD8+ T cell activation by cDC1s, was assessed. Results PEGylated XCL1(CC3)-antigen conjugates retained binding to XCR1, and induced cDC1 chemoattraction in vitro. The model epitope was efficiently cross-presented by human cDC1s to activate NY-ESO-1-specific CD8+ T cells. Importantly, vaccine activity was increased by targeting XCR1 at the surface of cDC1s. Conclusion Our results present a novel strategy for the generation of targeted vaccines fused to insoluble antigens. Moreover, our data emphasize the potential of targeting XCR1 at the surface of primary human cDC1s to induce potent CD8+ T cell responses.
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Affiliation(s)
- Camille Le Gall
- Department of Tumor Immunology, Radboudumc Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
- Department of Tumor Immunology, Oncode Institute, Nijmegen, The Netherlands
| | - Anna Cammarata
- Department of Tumor Immunology, Radboudumc Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Lukas de Haas
- Department of Tumor Immunology, Radboudumc Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Iván Ramos-Tomillero
- Department of Tumor Immunology, Radboudumc Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
- Institute for Chemical Immunology, Nijmegen, The Netherlands
| | - Jorge Cuenca-Escalona
- Department of Tumor Immunology, Radboudumc Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Kayleigh Schouren
- Department of Tumor Immunology, Radboudumc Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Zacharias Wijfjes
- Department of Tumor Immunology, Radboudumc Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
- Institute for Chemical Immunology, Nijmegen, The Netherlands
| | - Anouk M D Becker
- Department of Tumor Immunology, Radboudumc Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Johanna Bödder
- Department of Tumor Immunology, Radboudumc Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Yusuf Dölen
- Department of Tumor Immunology, Radboudumc Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
- Department of Tumor Immunology, Oncode Institute, Nijmegen, The Netherlands
| | - I Jolanda M de Vries
- Department of Tumor Immunology, Radboudumc Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Carl G Figdor
- Department of Tumor Immunology, Radboudumc Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
- Department of Tumor Immunology, Oncode Institute, Nijmegen, The Netherlands
| | - Georgina Flórez-Grau
- Department of Tumor Immunology, Radboudumc Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Martijn Verdoes
- Department of Tumor Immunology, Radboudumc Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
- Institute for Chemical Immunology, Nijmegen, The Netherlands
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Bhatt P, Sharma M, Sharma S. Prediction and identification of T cell epitopes of COVID-19 with balanced cytokine response for the development of peptide based vaccines. In Silico Pharmacol 2021; 9:40. [PMID: 34221846 PMCID: PMC8237047 DOI: 10.1007/s40203-021-00098-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 06/05/2021] [Indexed: 12/27/2022] Open
Abstract
Recent outbreak of 2019 novel Corona virus poses serious challenge for the global health system. In lieu of paucity of experimental data, tools and the very basic understanding of host immune responses against SARS-CoV-2, well thought effective measures are needed to control COVID-19 pandemic. We have identified specific overlapping antigenic peptide epitopes (OAPE) within the 4 structural proteins of SARS-CoV-2 predictive of triggering robust CD4 and CD8 T cell responses in host using bio-informatics tools (NetMHC4.0, IEDB, and Vaxijen2.0). We speculate an early release of pro-inflammatory cytokines for protection and later release of anti-inflammatory cytokines for prevention of immunopathology in designing a vaccine for Covid-19. Therefore, the selected immunogenic OAPE were subjected to in silico tools (IL-6-Pred, IFNepitope and PIP-EL) for analyzing their pro-inflammatory response. The OAPEs found to be pro-inflammatory in nature were further subjected to prediction servers (IL-4-Pred, IL-10-Pred, Pre-AIP) to characterize them as inducers of anti-inflammatory response as well. We finally filtered out 12 OAPE which had affinity for both CD4 and CD8 T cells as well as were inducers of pro-inflammatory and anti-inflammatory cytokines. On confirmation of OAPE binding affinity for respective T cell specific MHC allele using docking studies (pepATTRACT, Hex8.0 and Discovery studio) they were found to be have more immunogenic potential than the 3 negative control peptides (NCPs) included in the study. Additionally, we constructed CTxB-adjuvanated multi-epitopic vaccine inclusive of the 12 OAPEs which was non-toxic, non-allergenic and capable of inducing both pro-inflammatory and anti-inflammatory cytokines. A successful in silico cloning and docking of modeled subunit vaccine construct with toll like receptor-2 (TLR-2) confirmed the high efficacy of our multi-epitopic vaccine which can through a balanced interplay of cytokines help in creating a steady-state immune equilibrium. In silico immune simulation studies with the vaccine using C-ImmSim server also showed higher percentage of T cells along with production of pro-inflammatory as well as some anti-inflammatory cytokines. Experimental validation of this prediction based study on Peripheral Blood Mononuclear Cells (PBMCs) of un-infected individuals, patients and recovered individuals will facilitate production of high priority effective SARS -CoV-2 vaccine candidate. Supplementary Information The online version contains supplementary material available at 10.1007/s40203-021-00098-7.
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Affiliation(s)
- Parul Bhatt
- DS Kothari Central Facility for Interdisciplinary Research, Miranda House, University of Delhi, Delhi, 110007 India
- Department of Zoology, Miranda House, University of Delhi, Delhi, 110007 India
| | - Monika Sharma
- DS Kothari Central Facility for Interdisciplinary Research, Miranda House, University of Delhi, Delhi, 110007 India
- Department of Zoology, Miranda House, University of Delhi, Delhi, 110007 India
| | - Sadhna Sharma
- DS Kothari Central Facility for Interdisciplinary Research, Miranda House, University of Delhi, Delhi, 110007 India
- Department of Zoology, Miranda House, University of Delhi, Delhi, 110007 India
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6
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Madan R, Pandit K, Bhati L, Kumar H, Kumari N, Singh S. Mining the Mycobacterium tuberculosis proteome for identification of potential T-cell epitope based vaccine candidates. Microb Pathog 2021; 157:104996. [PMID: 34044044 DOI: 10.1016/j.micpath.2021.104996] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 05/07/2021] [Accepted: 05/10/2021] [Indexed: 12/22/2022]
Abstract
Identification of protective antigens for designing a high-efficacy tuberculosis vaccine is the need of the hour. Till date only 7% of the Mycobacterium tuberculosis proteome has been explored for discovering antigens capable of activating T-cell responses. Therefore, it becomes crucial to screen the remaining Mycobacterium tuberculosis proteome for more immunodominant T-cell epitopes. An extensive knowledge of the epitopes recognized by our immune system can aid this process of finding potential T cell antigens for development of a better TB vaccine. In the present in-silico study, 237 proteins belonging to the 'virulence, detoxification, and adaptation' category of Mycobacterium tuberculosis proteome were targeted for T-cell epitope screening. 50825 MHC Class I and 49357 MHC Class II epitopes were generated using NetMHC3.4 and IEDB servers respectively and tested for their antigenicity and cytokine stimulation. The highest antigenic epitopes were analyzed for their world population coverage and epitope conservancy. Molecular docking and molecular dynamics simulation studies were performed to corroborate the binding affinities and structural stability of the peptide-MHC complexes. We predicted a total of 3 MHC Class I (ILLKMCWPA, FAVGMNVYV, and SLAGNSAKV) and 7 MHC Class II (DLTIGFFLHIPFPPV, RPDLTIGFFLHIPFP, LTIGFFLHIPFPPVE, VLVFALVVALVYLQF, LVFALVVALVYLQFR, PNLVAARFIQLTPVY, and LVLVFALVVALVYLQ) epitopes that can be promising vaccine candidates. These predicted epitopes belong to 6 distinct proteins: Rv0169 (mce1a), Rv3490 (ostA), Rv3496 (mce4D), Rv1085c, Rv0563 (HtpX), Rv3497c (mce4C). All these proteins are expressed at different stages in the life cycle of Mycobacterium tuberculosis and thus, the predicted epitopes could be employed as candidates for designing a multistage-multiepitopic vaccine.
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Affiliation(s)
- Riya Madan
- Department of Zoology, Hansraj College, University of Delhi, India.
| | - Kushankur Pandit
- Department of Zoology, Hansraj College, University of Delhi, India.
| | - Lavi Bhati
- Department of Zoology, Hansraj College, University of Delhi, India.
| | - Hindesh Kumar
- Department of Zoology, Hansraj College, University of Delhi, India.
| | - Neha Kumari
- Department of Zoology, Hansraj College, University of Delhi, India.
| | - Swati Singh
- Department of Zoology, Hansraj College, University of Delhi, India.
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7
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Alonso JA, Smith AR, Baker BM. Tumor rejection properties of gp100 209-specific T cells correlate with T cell receptor binding affinity towards the wild type rather than anchor-modified antigen. Mol Immunol 2021; 135:365-372. [PMID: 33990005 DOI: 10.1016/j.molimm.2021.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/03/2021] [Accepted: 05/03/2021] [Indexed: 10/21/2022]
Abstract
Although there are exceptions and outliers, T cell functional responses generally correlate with the affinity of a TCR for a peptide/MHC complex. In one recently described outlier case, the most promising clinical candidate in a series of TCRs specific for the gp100209 melanoma antigen bound with the weakest solution affinity and produced the least amount of cytokine in vitro. Hypotheses for this outlier behavior included unusual cytokine expression patterns arising from an atypical TCR binding geometry. Studying this instance in more detail, we found here that outlier behavior is attributable not to unusual cytokine patterns or TCR binding, but the use of a position 2 anchor-modified peptide variant in in vitro experiments instead of the wild type antigen that is present in vivo. Although the anchor-modified variant has been widely used in basic and clinical immunology as a surrogate for the wild type peptide, prior work has shown that TCRs can clearly distinguish between the two. We show that when this differential recognition is accounted for, the functional properties of gp100209-specific TCRs track with their affinity towards the peptide/MHC complex. Beyond demonstrating the correlates with T cell function for a clinically relevant TCR, our results provide important considerations for selection of TCRs for immunotherapy and the use of modified peptides in immunology.
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Affiliation(s)
- Jesus A Alonso
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Angela R Smith
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Brian M Baker
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA.
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8
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Gibadullin R, Randall CJ, Sidney J, Sette A, Gellman SH. Backbone Modifications of HLA-A2-Restricted Antigens Induce Diverse Binding and T Cell Activation Outcomes. J Am Chem Soc 2021; 143:6470-6481. [PMID: 33881854 DOI: 10.1021/jacs.1c00016] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
CD8+ T cells express T cell receptors (TCRs) that recognize short peptide antigens in the context of major histocompatibility class I (MHC I) molecules. This recognition process produces an array of cytokine-mediated signals that help to govern immunological responses. Design of biostable MHC I peptide vaccines containing unnatural subunits is desirable, and synthetic antigens in which a native α-amino acid residue is replaced by a homologous β-amino acid residue (native side chain but extended backbone) might be useful in this regard. We have evaluated the impact of α-to-β backbone modification at a single site on T cell-mediated recognition of six clinically important viral and tumor-associated antigens bound to an MHC I. Effects of this modification on MHC I affinity and T cell activation were measured. Many of these modifications diminish or prevent T cell response. However, a number of α/β-peptide antigens were found to mimic the activity of natural antigens or to enhance maximal T cell response, as measured by interferon-γ release. Results from this broad exploratory study advance our understanding of immunological responses to antigens bearing unnatural modifications and suggest that α/β-peptides could be a source of potent and proteolytically stable variants of native antigens.
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Affiliation(s)
- Ruslan Gibadullin
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Caleb J Randall
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, California 92037, United States
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, California 92037, United States.,Department of Medicine, University of California, San Diego, California 92093, United States
| | - Samuel H Gellman
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
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9
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Hsiue EHC, Wright KM, Douglass J, Hwang MS, Mog BJ, Pearlman AH, Paul S, DiNapoli SR, Konig MF, Wang Q, Schaefer A, Miller MS, Skora AD, Azurmendi PA, Murphy MB, Liu Q, Watson E, Li Y, Pardoll DM, Bettegowda C, Papadopoulos N, Kinzler KW, Vogelstein B, Gabelli SB, Zhou S. Targeting a neoantigen derived from a common TP53 mutation. Science 2021; 371:eabc8697. [PMID: 33649166 PMCID: PMC8208645 DOI: 10.1126/science.abc8697] [Citation(s) in RCA: 182] [Impact Index Per Article: 60.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 11/30/2020] [Accepted: 02/05/2021] [Indexed: 12/12/2022]
Abstract
TP53 (tumor protein p53) is the most commonly mutated cancer driver gene, but drugs that target mutant tumor suppressor genes, such as TP53, are not yet available. Here, we describe the identification of an antibody highly specific to the most common TP53 mutation (R175H, in which arginine at position 175 is replaced with histidine) in complex with a common human leukocyte antigen-A (HLA-A) allele on the cell surface. We describe the structural basis of this specificity and its conversion into an immunotherapeutic agent: a bispecific single-chain diabody. Despite the extremely low p53 peptide-HLA complex density on the cancer cell surface, the bispecific antibody effectively activated T cells to lyse cancer cells that presented the neoantigen in vitro and in mice. This approach could in theory be used to target cancers containing mutations that are difficult to target in conventional ways.
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Affiliation(s)
- Emily Han-Chung Hsiue
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Katharine M Wright
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287, USA
| | - Jacqueline Douglass
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Michael S Hwang
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Brian J Mog
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Alexander H Pearlman
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Suman Paul
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Sarah R DiNapoli
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Maximilian F Konig
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Division of Rheumatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21224, USA
| | - Qing Wang
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Complete Omics, Baltimore, MD 21227, USA
| | - Annika Schaefer
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Michelle S Miller
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287, USA
| | - Andrew D Skora
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - P Aitana Azurmendi
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287, USA
| | | | - Qiang Liu
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Evangeline Watson
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Yana Li
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Drew M Pardoll
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Chetan Bettegowda
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Neurosurgery, Johns Hopkins University School of Medicine, MD 21205, USA
| | - Nickolas Papadopoulos
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Kenneth W Kinzler
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287, USA
| | - Bert Vogelstein
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Sandra B Gabelli
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Shibin Zhou
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287, USA
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10
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Smith AR, Alonso JA, Ayres CM, Singh NK, Hellman LM, Baker BM. Structurally silent peptide anchor modifications allosterically modulate T cell recognition in a receptor-dependent manner. Proc Natl Acad Sci U S A 2021; 118:e2018125118. [PMID: 33468649 PMCID: PMC7848747 DOI: 10.1073/pnas.2018125118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Presentation of peptides by class I MHC proteins underlies T cell immune responses to pathogens and cancer. The association between peptide binding affinity and immunogenicity has led to the engineering of modified peptides with improved MHC binding, with the hope that these peptides would be useful for eliciting cross-reactive immune responses directed toward their weak binding, unmodified counterparts. Increasing evidence, however, indicates that T cell receptors (TCRs) can perceive such anchor-modified peptides differently than wild-type (WT) peptides, although the scope of discrimination is unclear. We show here that even modifications at primary anchors that have no discernible structural impact can lead to substantially stronger or weaker T cell recognition depending on the TCR. Surprisingly, the effect of peptide anchor modification can be sensed by a TCR at regions distant from the site of modification, indicating a through-protein mechanism in which the anchor residue serves as an allosteric modulator for TCR binding. Our findings emphasize caution in the use and interpretation of results from anchor-modified peptides and have implications for how anchor modifications are accounted for in other circumstances, such as predicting the immunogenicity of tumor neoantigens. Our data also highlight an important need to better understand the highly tunable dynamic nature of class I MHC proteins and the impact this has on various forms of immune recognition.
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MESH Headings
- Allosteric Regulation
- Binding Sites
- Cloning, Molecular
- Crystallography, X-Ray
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Gene Expression
- Genetic Vectors/chemistry
- Genetic Vectors/metabolism
- HLA-A2 Antigen/chemistry
- HLA-A2 Antigen/genetics
- HLA-A2 Antigen/immunology
- Humans
- Jurkat Cells
- Kinetics
- Models, Molecular
- Peptides/chemistry
- Peptides/genetics
- Peptides/immunology
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Engineering
- Protein Interaction Domains and Motifs
- Receptors, Antigen, T-Cell, alpha-beta/chemistry
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/immunology
- Th2 Cells/cytology
- Th2 Cells/immunology
- Thermodynamics
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Affiliation(s)
- Angela R Smith
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556
| | - Jesus A Alonso
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556
| | - Cory M Ayres
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556
| | - Nishant K Singh
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556
| | - Lance M Hellman
- Department of Physical and Life Sciences, Nevada State College, Henderson, NV 89002
| | - Brian M Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556;
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556
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11
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Duru AD, Sun R, Allerbring EB, Chadderton J, Kadri N, Han X, Peqini K, Uchtenhagen H, Madhurantakam C, Pellegrino S, Sandalova T, Nygren PÅ, Turner SJ, Achour A. Tuning antiviral CD8 T-cell response via proline-altered peptide ligand vaccination. PLoS Pathog 2020; 16:e1008244. [PMID: 32365082 PMCID: PMC7224568 DOI: 10.1371/journal.ppat.1008244] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 05/14/2020] [Accepted: 04/11/2020] [Indexed: 12/16/2022] Open
Abstract
Viral escape from CD8+ cytotoxic T lymphocyte responses correlates with disease progression and represents a significant challenge for vaccination. Here, we demonstrate that CD8+ T cell recognition of the naturally occurring MHC-I-restricted LCMV-associated immune escape variant Y4F is restored following vaccination with a proline-altered peptide ligand (APL). The APL increases MHC/peptide (pMHC) complex stability, rigidifies the peptide and facilitates T cell receptor (TCR) recognition through reduced entropy costs. Structural analyses of pMHC complexes before and after TCR binding, combined with biophysical analyses, revealed that although the TCR binds similarly to all complexes, the p3P modification alters the conformations of a very limited amount of specific MHC and peptide residues, facilitating efficient TCR recognition. This approach can be easily introduced in peptides restricted to other MHC alleles, and can be combined with currently available and future vaccination protocols in order to prevent viral immune escape.
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Affiliation(s)
- Adil Doganay Duru
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Solna, Stockholm, Sweden
- NSU Cell Therapy Institute & Dr. Kiran C. Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, Florida, United States of America
| | - Renhua Sun
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Solna, Stockholm, Sweden
| | - Eva B. Allerbring
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Solna, Stockholm, Sweden
| | - Jesseka Chadderton
- Department of Microbiology, Biomedical Discovery Institute, Monash University, Clayton, Australia
| | - Nadir Kadri
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Solna, Stockholm, Sweden
| | - Xiao Han
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Solna, Stockholm, Sweden
| | - Kaliroi Peqini
- DISFARM, Dipartimento di Scienze Farmaceutiche, Sezinone Chimica Generale e Organica, Università degli Studi, Milano, Italy
| | - Hannes Uchtenhagen
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Solna, Stockholm, Sweden
| | - Chaithanya Madhurantakam
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Solna, Stockholm, Sweden
- Structural and Molecular Biology Laboratory, Department of Biotechnology, TERI, School of Advanced Studies, New Delhi, India
| | - Sara Pellegrino
- DISFARM, Dipartimento di Scienze Farmaceutiche, Sezinone Chimica Generale e Organica, Università degli Studi, Milano, Italy
| | - Tatyana Sandalova
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Solna, Stockholm, Sweden
| | - Per-Åke Nygren
- Division of Protein Engineering, Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, AlbaNova University Center, Royal Institute of Technology, Stockholm, Sweden
| | - Stephen J. Turner
- Department of Microbiology, Biomedical Discovery Institute, Monash University, Clayton, Australia
| | - Adnane Achour
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, Solna, Stockholm, Sweden
- * E-mail:
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12
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Coles CH, Mulvaney RM, Malla S, Walker A, Smith KJ, Lloyd A, Lowe KL, McCully ML, Martinez Hague R, Aleksic M, Harper J, Paston SJ, Donnellan Z, Chester F, Wiederhold K, Robinson RA, Knox A, Stacey AR, Dukes J, Baston E, Griffin S, Jakobsen BK, Vuidepot A, Harper S. TCRs with Distinct Specificity Profiles Use Different Binding Modes to Engage an Identical Peptide-HLA Complex. THE JOURNAL OF IMMUNOLOGY 2020; 204:1943-1953. [PMID: 32102902 DOI: 10.4049/jimmunol.1900915] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 12/29/2019] [Indexed: 12/18/2022]
Abstract
The molecular rules driving TCR cross-reactivity are poorly understood and, consequently, it is unclear the extent to which TCRs targeting the same Ag recognize the same off-target peptides. We determined TCR-peptide-HLA crystal structures and, using a single-chain peptide-HLA phage library, we generated peptide specificity profiles for three newly identified human TCRs specific for the cancer testis Ag NY-ESO-1157-165-HLA-A2. Two TCRs engaged the same central peptide feature, although were more permissive at peripheral peptide positions and, accordingly, possessed partially overlapping peptide specificity profiles. The third TCR engaged a flipped peptide conformation, leading to the recognition of off-target peptides sharing little similarity with the cognate peptide. These data show that TCRs specific for a cognate peptide recognize discrete peptide repertoires and reconciles how an individual's limited TCR repertoire following negative selection in the thymus is able to recognize a vastly larger antigenic pool.
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Affiliation(s)
- Charlotte H Coles
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Rachel M Mulvaney
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Sunir Malla
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Andrew Walker
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Kathrine J Smith
- GlaxoSmithKline, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Angharad Lloyd
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Kate L Lowe
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | | | | | - Milos Aleksic
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Jane Harper
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Samantha J Paston
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Zoe Donnellan
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Fiona Chester
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Katrin Wiederhold
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Ross A Robinson
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Andrew Knox
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Andrea R Stacey
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Joseph Dukes
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Emma Baston
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Sue Griffin
- GlaxoSmithKline, Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Bent K Jakobsen
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Annelise Vuidepot
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
| | - Stephen Harper
- Immunocore, Ltd., Abingdon, Oxfordshire OX14 4RY, United Kingdom; and
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13
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Abstract
T cells recognize and respond to self antigens in both cancer and autoimmunity. One strategy to influence this response is to incorporate amino acid substitutions into these T cell-specific epitopes. This strategy is being reconsidered now with the goal of increasing time to regression with checkpoint blockade therapies in cancer and antigen-specific immunotherapies in autoimmunity. We discuss how these amino acid substitutions change the interactions with the MHC class I or II molecule and the responding T cell repertoire. Amino acid substitutions in epitopes that are the most effective in therapies bind more strongly to T cell receptor and/or MHC molecules and cross-react with the same repertoire of T cells as the natural antigen.
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Affiliation(s)
- Jill E Slansky
- Department of Immunology and Microbiology, University of Colorado School of Medicine, 12800 E. 19thAvenue, Aurora, CO 80045, USA.
| | - Maki Nakayama
- Department of Immunology and Microbiology, University of Colorado School of Medicine, 12800 E. 19thAvenue, Aurora, CO 80045, USA; Barbara Davis Center for Childhood Diabetes, University of Colorado School of Medicine, 1775 Aurora Court, Aurora, CO 80045, USA
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14
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Madura F, Rizkallah PJ, Legut M, Holland CJ, Fuller A, Bulek A, Schauenburg AJ, Trimby A, Hopkins JR, Wells SA, Godkin A, Miles JJ, Sami M, Li Y, Liddy N, Jakobsen BK, Loveridge EJ, Cole DK, Sewell AK. TCR-induced alteration of primary MHC peptide anchor residue. Eur J Immunol 2019; 49:1052-1066. [PMID: 31091334 PMCID: PMC6618058 DOI: 10.1002/eji.201948085] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 03/21/2019] [Accepted: 05/14/2019] [Indexed: 12/12/2022]
Abstract
The HLA-A*02:01-restricted decapeptide EAAGIGILTV, derived from melanoma antigen recognized by T-cells-1 (MART-1) protein, represents one of the best-studied tumor associated T-cell epitopes, but clinical results targeting this peptide have been disappointing. This limitation may reflect the dominance of the nonapeptide, AAGIGILTV, at the melanoma cell surface. The decapeptide and nonapeptide are presented in distinct conformations by HLA-A*02:01 and TCRs from clinically relevant T-cell clones recognize the nonapeptide poorly. Here, we studied the MEL5 TCR that potently recognizes the nonapeptide. The structure of the MEL5-HLA-A*02:01-AAGIGILTV complex revealed an induced fit mechanism of antigen recognition involving altered peptide-MHC anchoring. This "flexing" at the TCR-peptide-MHC interface to accommodate the peptide antigen explains previously observed incongruences in this well-studied system and has important implications for future therapeutic approaches. Finally, this study expands upon the mechanisms by which molecular plasticity can influence antigen recognition by T cells.
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Affiliation(s)
| | | | | | | | - Anna Fuller
- School of MedicineCardiff UniversityCardiffUK
| | - Anna Bulek
- School of MedicineCardiff UniversityCardiffUK
| | | | | | | | | | | | - John J. Miles
- School of MedicineCardiff UniversityCardiffUK
- Centre for Biodiscovery and Molecular Development of TherapeuticsAustralian Institute of Tropical Health and MedicineJames Cook UniversityCairnsQueenslandAustralia
| | | | - Yi Li
- Immunocore Ltd.AbingdonUK
| | | | | | - E. Joel Loveridge
- School of ChemistryCardiff UniversityCardiffUK
- Department of ChemistrySwansea UniversitySwanseaUK
| | - David K. Cole
- School of MedicineCardiff UniversityCardiffUK
- Immunocore Ltd.AbingdonUK
| | - Andrew K. Sewell
- School of MedicineCardiff UniversityCardiffUK
- Systems Immunity Research InstituteCardiff UniversityCardiffUK
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15
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Mullan KA, Anderson A, Illing PT, Kwan P, Purcell AW, Mifsud NA. HLA-associated antiepileptic drug-induced cutaneous adverse reactions. HLA 2019; 93:417-435. [PMID: 30895730 DOI: 10.1111/tan.13530] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 02/20/2019] [Accepted: 03/18/2019] [Indexed: 12/31/2022]
Abstract
Adverse drug reactions (ADRs) are a common cause of hospital admissions (up to 19%), with the majority of cases due to off-target predictable drug effects (type A reactions). However, idiosyncratic drug-induced immune activated (type B) reactions contribute to a range of hypersensitivity reactions, with T-cell-mediated type IV hypersensitivity reactions mainly manifesting as cutaneous ADRs (cADRs). Aromatic antiepileptic drugs (AEDs), used in the treatment of epilepsy as well as bipolar disorder or neuropathic pain, have been implicated as culprit drugs in a spectrum of pathologies ranging from mild maculopapular exanthema (MPE) to severe and life-threatening conditions including drug reaction with eosinophilia and systemic symptoms (DRESS), Stevens-Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN). These AED-induced cADRs are unpredictable based on pharmacological and clinical factors alone, thereby prompting investigations into genomic contributors mediating risk of pathology. The most strongly associated risk genes identified are from the human leukocyte antigen (HLA) class I alleles, which play a critical role in adaptive immunity by flagging either infected or aberrant cells for recognition by surveying T-cells. In the setting of drug hypersensitivity, the immunogenicity of HLA molecules and their peptide cargo can be modulated by interactions with small drug molecules that drive inappropriate T-cell responses. This review discusses the current understanding of HLA class I molecules in modifying risk of AED-induced cADRs.
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Affiliation(s)
- Kerry A Mullan
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Alison Anderson
- Department of Neuroscience, Central Clinical School, Monash University, Clayton, Victoria, Australia
| | - Patricia T Illing
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Patrick Kwan
- Department of Neuroscience, Central Clinical School, Monash University, Clayton, Victoria, Australia.,Department of Neuroscience, The Alfred Hospital, Melbourne, Victoria, Australia
| | - Anthony W Purcell
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Nicole A Mifsud
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
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16
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Parvizpour S, Razmara J, Pourseif MM, Omidi Y. In silico design of a triple-negative breast cancer vaccine by targeting cancer testis antigens. ACTA ACUST UNITED AC 2018; 9:45-56. [PMID: 30788259 PMCID: PMC6378095 DOI: 10.15171/bi.2019.06] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 04/10/2018] [Accepted: 04/14/2018] [Indexed: 12/14/2022]
Abstract
Introduction: Triple-negative breast cancer (TNBC) is an important subtype of breast cancer, which occurs in the absence of estrogen, progesterone and HER-2 receptors. According to the recent studies, TNBC may be a cancer testis antigen (CTA)-positive tumor, indicating that the CTA-based cancer vaccine can be a treatment option for the patients bearing such tumors. Of these antigens (Ags), the MAGE-A family and NY-ESO-1 as the most immunogenic CTAs are the potentially relevant targets for the development of an immunotherapeutic way of the breast cancer treatment. Methods: In the present study, immunoinformatics approach was used to design a multi-epitope peptide vaccine to combat the TNBC. The vaccine peptide was constructed by the fusion of three crucial components, including the CD8+ cytotoxic T lymphocytes (CTLs) epitopes, helper epitopes and adjuvant. The epitopes were predicted from the MAGE-A and NY-ESO-1 Ags. In addition, the granulocyte-macrophage-colony-stimulating factor (GM-CSF) was used as an adjuvant to promote the CD4+ T cells towards the T-helper for more strong induction of CTL responses. The components were conjugated by proper linkers. Results: The vaccine peptide was examined for different physiochemical characteristics to confirm the safety and immunogenic behavior. Furthermore, the 3D-structure of the vaccine peptide was predicted based on the homology modeling approach using the MODELLER v9.17 program. The vaccine structure was also subjected to the molecular dynamics simulation study for structure refinement. The results verified the immunogenicity and safety profile of the constructed vaccine as well as its capability for stimulating both the cellular and humoral immune responses. Conclusion: Based on our in-silico analyses, the proposed vaccine may be considered for the immunotherapy of TNBC.
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Affiliation(s)
- Sepideh Parvizpour
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jafar Razmara
- Department of Computer Science, Faculty of Mathematical Sciences, University of Tabriz, Tabriz, Iran
| | - Mohammad M Pourseif
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Yadollah Omidi
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Pharmaceutics, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
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17
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Gavvovidis I, Leisegang M, Willimsky G, Miller N, Nghiem P, Blankenstein T. Targeting Merkel Cell Carcinoma by Engineered T Cells Specific to T-Antigens of Merkel Cell Polyomavirus. Clin Cancer Res 2018; 24:3644-3655. [PMID: 29669806 DOI: 10.1158/1078-0432.ccr-17-2661] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 02/28/2018] [Accepted: 04/13/2018] [Indexed: 12/20/2022]
Abstract
Purpose: The causative agent of most cases of Merkel cell carcinoma (MCC) has been identified as the Merkel cell polyomavirus (MCV). MCV-encoded T antigens (Tag) are essential not only for virus-mediated tumorigenesis but also for maintaining MCC cell lines in vitro MCV Tags are thus an appealing target for viral oncoprotein-directed T-cell therapy for MCC. With this study, we aimed to isolate and characterize Tag-specific T-cell receptors (TCR) for potential use in gene therapy clinical trials.Experimental Design: T-cell responses against MCV Tag epitopes were investigated by immunizing transgenic mice that express a diverse human TCR repertoire restricted to HLA-A2. Human lymphocytes genetically engineered to express Tag-specific TCRs were tested for specific reactivity against MCC cell lines. The therapeutic potential of Tag-specific TCR gene therapy was tested in a syngeneic cancer model.Results: We identified naturally processed epitopes of MCV Tags and isolated Tag-specific TCRs. T cells expressing these TCRs were activated by HLA-A2-positive cells loaded with cognate peptide or cells that stably expressed MCV Tags. We showed cytotoxic potential of T cells engineered to express these TCRs in vitro and demonstrated regression of established tumors in a mouse model upon TCR gene therapy.Conclusions: Our findings demonstrate that MCC cells can be targeted by MCV Tag-specific TCRs. Although recent findings suggest that approximately half of MCC patients benefit from PD-1 pathway blockade, additional patients may benefit if their endogenous T-cell response can be augmented by infusion of transgenic MCV-specific T cells such as those described here. Clin Cancer Res; 24(15); 3644-55. ©2018 AACR.
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Affiliation(s)
- Ioannis Gavvovidis
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.,Institute of Immunology, Charité, Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Matthias Leisegang
- Institute of Immunology, Charité, Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany
| | - Gerald Willimsky
- Institute of Immunology, Charité, Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,German Cancer Research Center, Heidelberg, Germany
| | - Natalie Miller
- University of Washington, Dermatology/Medicine/Pathology, Seattle, Washington
| | - Paul Nghiem
- University of Washington, Dermatology/Medicine/Pathology, Seattle, Washington
| | - Thomas Blankenstein
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany. .,Institute of Immunology, Charité, Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany
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18
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Hafstrand I, Doorduijn EM, Sun R, Talyzina A, Sluijter M, Pellegrino S, Sandalova T, Duru AD, van Hall T, Achour A. The Immunogenicity of a Proline-Substituted Altered Peptide Ligand toward the Cancer-Associated TEIPP Neoepitope Trh4 Is Unrelated to Complex Stability. THE JOURNAL OF IMMUNOLOGY 2018; 200:2860-2868. [PMID: 29507106 DOI: 10.4049/jimmunol.1700228] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 02/07/2018] [Indexed: 01/05/2023]
Abstract
Human cancers frequently display defects in Ag processing and presentation allowing for immune evasion, and they therefore constitute a significant challenge for T cell-based immunotherapy. We have previously demonstrated that the antigenicity of tumor-associated Ags can be significantly enhanced through unconventional residue modifications as a novel tool for MHC class I (MHC-I)-based immunotherapy approaches. We have also previously identified a novel category of cancer neo-epitopes, that is, T cell epitopes associated with impaired peptide processing (TEIPP), that are selectively presented by MHC-I on cells lacking the peptide transporter TAP. In this study, we demonstrate that substitution of the nonanchoring position 3 into a proline residue of the first identified TEIPP peptide, the murine Trh4, results in significantly enhanced recognition by antitumor CTLs toward the wild-type epitope. Although higher immunogenicity has in most cases been associated with increased MHC/peptide complex stability, our results demonstrate that the overall stability of H-2Db in complex with the highly immunogenic altered peptide ligand Trh4-p3P is significantly reduced compared with wild-type H-2Db/Trh4. Comparison of the crystal structures of the H-2Db/Trh4-p3P and H-2Db/Trh4 complexes revealed that the conformation of the nonconventional methionine anchor residue p5M is altered, deleting its capacity to form adequate sulfur-π interactions with H-2Db residues, thus reducing the overall longevity of the complex. Collectively, our results indicate that vaccination with Thr4-p3P significantly enhances T cell recognition of targets presenting the wild-type TEIPP epitope and that higher immunogenicity is not necessarily directly related to MHC/peptide complex stability, opening for the possibility to design novel peptide vaccines with reduced MHC/peptide complex stability.
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Affiliation(s)
- Ida Hafstrand
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, 17165 Stockholm, Sweden.,Department of Infectious Diseases, Karolinska University Hospital, Solna, 17176 Stockholm, Sweden
| | - Elien M Doorduijn
- Medical Oncology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Renhua Sun
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, 17165 Stockholm, Sweden.,Department of Infectious Diseases, Karolinska University Hospital, Solna, 17176 Stockholm, Sweden
| | - Anna Talyzina
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, 17165 Stockholm, Sweden.,Department of Infectious Diseases, Karolinska University Hospital, Solna, 17176 Stockholm, Sweden
| | - Marjolein Sluijter
- Medical Oncology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Sara Pellegrino
- Department of Pharmaceutical Science, General and Organic Chemistry Section, University of Milan, 20133 Milan, Italy
| | - Tatyana Sandalova
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, 17165 Stockholm, Sweden.,Department of Infectious Diseases, Karolinska University Hospital, Solna, 17176 Stockholm, Sweden
| | - Adil Doganay Duru
- Cell Therapy Institute, Nova Southeastern University, Fort Lauderdale, FL 33314; and.,College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL 33328
| | - Thorbald van Hall
- Medical Oncology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands;
| | - Adnane Achour
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, 17165 Stockholm, Sweden; .,Department of Infectious Diseases, Karolinska University Hospital, Solna, 17176 Stockholm, Sweden
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19
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Mobbs JI, Illing PT, Dudek NL, Brooks AG, Baker DG, Purcell AW, Rossjohn J, Vivian JP. The molecular basis for peptide repertoire selection in the human leucocyte antigen (HLA) C*06:02 molecule. J Biol Chem 2017; 292:17203-17215. [PMID: 28855257 DOI: 10.1074/jbc.m117.806976] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 08/18/2017] [Indexed: 12/31/2022] Open
Abstract
Human leukocyte antigen (HLA)-C*06:02 is identified as the allele associated with the highest risk for the development of the autoimmune skin disease psoriasis. However, the diversity and mode of peptide presentation by the HLA-C*06:02 molecule remains unclear. Here, we describe the endogenous peptide repertoire of ∼3,000 sequences for HLA-C*06:02 that defines the peptide-binding motif for this HLA allomorph. We found that HLA-C*06:02 predominantly presents nonamer peptides with dominant arginine anchors at the P2 and P7 positions and a preference for small hydrophobic residues at the C terminus (PΩ). To determine the structural basis of this selectivity, we determined crystal structures of HLA-C*06:02 in complex with two self-peptides (ARTELYRSL and ARFNDLRFV) and an analogue of a melanocyte autoantigen (ADAMTSL5, VRSRR-abu-LRL) implicated in psoriasis. These structures revealed that HLA-C*06:02 possesses a deep peptide-binding groove comprising two electronegative B- and E-pockets that coincide with the preference for P2 and P7 arginine anchors. The ADAMTSL5 autoantigen possessed a P7-Leu instead of the P7-Arg residue, but nevertheless was accommodated within the HLA-C*06:02 antigen-binding cleft. Collectively, our results provide the structural basis for understanding peptide repertoire selection in HLA-C*06:02.
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Affiliation(s)
- Jesse I Mobbs
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia
| | - Patricia T Illing
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia
| | - Nadine L Dudek
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia
| | - Andrew G Brooks
- the Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Daniel G Baker
- Janssen Research & Development, LLC, Horsham, Philadelphia, Pennsylvania 19044
| | - Anthony W Purcell
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia,
| | - Jamie Rossjohn
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia, .,the Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton 3800, Victoria, Australia, and.,the Institute of Infection and Immunity, Cardiff University, School of Medicine, Cardiff CF14 4XN, Wales, United Kingdom
| | - Julian P Vivian
- From the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia, .,the Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton 3800, Victoria, Australia, and
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20
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Miller NJ, Church CD, Dong L, Crispin D, Fitzgibbon MP, Lachance K, Jing L, Shinohara M, Gavvovidis I, Willimsky G, McIntosh M, Blankenstein T, Koelle DM, Nghiem P. Tumor-Infiltrating Merkel Cell Polyomavirus-Specific T Cells Are Diverse and Associated with Improved Patient Survival. Cancer Immunol Res 2017; 5:137-147. [PMID: 28093446 PMCID: PMC5421625 DOI: 10.1158/2326-6066.cir-16-0210] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Revised: 11/22/2016] [Accepted: 11/28/2016] [Indexed: 01/02/2023]
Abstract
Tumor-infiltrating CD8+ T cells are associated with improved survival of patients with Merkel cell carcinoma (MCC), an aggressive skin cancer causally linked to Merkel cell polyomavirus (MCPyV). However, CD8+ T-cell infiltration is robust in only 4% to 18% of MCC tumors. We characterized the T-cell receptor (TCR) repertoire restricted to one prominent epitope of MCPyV (KLLEIAPNC, "KLL") and assessed whether TCR diversity, tumor infiltration, or T-cell avidity correlated with clinical outcome. HLA-A*02:01/KLL tetramer+ CD8+ T cells from MCC patient peripheral blood mononuclear cells (PBMC) and tumor-infiltrating lymphocytes (TIL) were isolated via flow cytometry. TCRβ (TRB) sequencing was performed on tetramer+ cells from PBMCs or TILs (n = 14) and matched tumors (n = 12). Functional avidity of T-cell clones was determined by IFNγ production. We identified KLL tetramer+ T cells in 14% of PBMC and 21% of TIL from MCC patients. TRB repertoires were strikingly diverse (397 unique TRBs were identified from 12 patients) and mostly private (only one TCRb clonotype shared between two patients). An increased fraction of KLL-specific TIL (>1.9%) was associated with significantly increased MCC-specific survival P = 0.0009). T-cell cloning from four patients identified 42 distinct KLL-specific TCRa/b pairs. T-cell clones from patients with improved MCC-specific outcomes were more avid (P < 0.05) and recognized an HLA-appropriate MCC cell line. T cells specific for a single MCPyV epitope display marked TCR diversity within and between patients. Intratumoral infiltration by MCPyV-specific T cells was associated with significantly improved MCC-specific survival, suggesting that augmenting the number or avidity of virus-specific T cells may have therapeutic benefit. Cancer Immunol Res; 5(2); 137-47. ©2017 AACR.
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MESH Headings
- CD8-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/metabolism
- Carcinoma, Merkel Cell/etiology
- Carcinoma, Merkel Cell/mortality
- Carcinoma, Merkel Cell/pathology
- Clonal Evolution/genetics
- Clonal Evolution/immunology
- Epitopes, T-Lymphocyte/chemistry
- Epitopes, T-Lymphocyte/genetics
- Epitopes, T-Lymphocyte/immunology
- Genetic Variation
- Humans
- Lymphocytes, Tumor-Infiltrating/immunology
- Lymphocytes, Tumor-Infiltrating/metabolism
- Lymphocytes, Tumor-Infiltrating/pathology
- Merkel cell polyomavirus/immunology
- Prognosis
- Receptors, Antigen, T-Cell, alpha-beta/chemistry
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Sequence Analysis, DNA
- Skin Neoplasms/etiology
- Skin Neoplasms/mortality
- Skin Neoplasms/pathology
- T-Cell Antigen Receptor Specificity/immunology
- T-Lymphocyte Subsets/immunology
- T-Lymphocyte Subsets/metabolism
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Affiliation(s)
- Natalie J Miller
- Dermatology/Medicine/Pathology, University of Washington, Seattle, Washington
| | - Candice D Church
- Dermatology/Medicine/Pathology, University of Washington, Seattle, Washington
| | - Lichun Dong
- Department of Medicine/Laboratory Medicine/Global Health, University of Washington, Seattle, Washington
| | - David Crispin
- Fred Hutchinson, Public Health Sciences Division, Seattle, Washington
| | | | - Kristina Lachance
- Dermatology/Medicine/Pathology, University of Washington, Seattle, Washington
| | - Lichen Jing
- Department of Medicine/Laboratory Medicine/Global Health, University of Washington, Seattle, Washington
| | - Michi Shinohara
- Dermatology/Medicine/Pathology, University of Washington, Seattle, Washington
| | - Ioannis Gavvovidis
- Molecular Immunology and Gene Therapy, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
- Institute of Immunology, Charité, Berlin, Germany
| | - Gerald Willimsky
- Institute of Immunology, Charité, Berlin, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin McIntosh
- Fred Hutchinson, Public Health Sciences Division, Seattle, Washington
| | - Thomas Blankenstein
- Molecular Immunology and Gene Therapy, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
- Institute of Immunology, Charité, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - David M Koelle
- Department of Medicine/Laboratory Medicine/Global Health, University of Washington, Seattle, Washington.
- Fred Hutchinson, Vaccine and Infectious Disease Division, Seattle, Washington
- Benaroya Research Institute, Seattle, Washington
| | - Paul Nghiem
- Dermatology/Medicine/Pathology, University of Washington, Seattle, Washington.
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21
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Candia M, Kratzer B, Pickl WF. On Peptides and Altered Peptide Ligands: From Origin, Mode of Action and Design to Clinical Application (Immunotherapy). Int Arch Allergy Immunol 2016; 170:211-233. [PMID: 27642756 PMCID: PMC7058415 DOI: 10.1159/000448756] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
T lymphocytes equipped with clonotypic T cell antigen receptors (TCR) recognize immunogenic peptides only when presented in the context of their own major histocompatibility complex (MHC) molecules. Peptide loading to MHC molecules occurs in intracellular compartments (ER for class I and MIIC for class II molecules) and relies on the interaction of the respective peptides and peptide binding pockets on MHC molecules. Those peptide residues not engaged in MHC binding point towards the TCR screening for possible peptide MHC complex binding partners. Natural or intentional modification of both MHC binding registers and TCR interacting residues of peptides – leading to the formation of altered peptide ligands (APLs) – might alter the way peptides interact with TCRs and hence influence subsequent T cell activation events, and consequently T cell effector functions. This review article summarizes how APLs were detected and first described, current concepts of how APLs modify T cellular signaling, which biological mechanisms might force the generation of APLs in vivo, and how peptides and APLs might be used for the benefit of patients suffering from allergic or autoimmune diseases.
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Affiliation(s)
- Martín Candia
- Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
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22
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Pandey K, Sharma M, Saarav I, Singh S, Dutta P, Bhardwaj A, Sharma S. Analysis of the DosR regulon genes to select cytotoxic T lymphocyte epitope specific vaccine candidates using a reverse vaccinology approach. Int J Mycobacteriol 2016; 5:34-43. [DOI: 10.1016/j.ijmyco.2015.10.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 10/25/2015] [Accepted: 10/27/2015] [Indexed: 10/22/2022] Open
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23
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Yao S, Liu J, Qi J, Chen R, Zhang N, Liu Y, Wang J, Wu Y, Gao GF, Xia C. Structural Illumination of Equine MHC Class I Molecules Highlights Unconventional Epitope Presentation Manner That Is Evolved in Equine Leukocyte Antigen Alleles. THE JOURNAL OF IMMUNOLOGY 2016; 196:1943-54. [DOI: 10.4049/jimmunol.1501352] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 12/03/2015] [Indexed: 01/20/2023]
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24
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Trujillo JA, Croft NP, Dudek NL, Channappanavar R, Theodossis A, Webb AI, Dunstone MA, Illing PT, Butler NS, Fett C, Tscharke DC, Rossjohn J, Perlman S, Purcell AW. The cellular redox environment alters antigen presentation. J Biol Chem 2014; 289:27979-91. [PMID: 25135637 DOI: 10.1074/jbc.m114.573402] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Cysteine-containing peptides represent an important class of T cell epitopes, yet their prevalence remains underestimated. We have established and interrogated a database of around 70,000 naturally processed MHC-bound peptides and demonstrate that cysteine-containing peptides are presented on the surface of cells in an MHC allomorph-dependent manner and comprise on average 5-10% of the immunopeptidome. A significant proportion of these peptides are oxidatively modified, most commonly through covalent linkage with the antioxidant glutathione. Unlike some of the previously reported cysteine-based modifications, this represents a true physiological alteration of cysteine residues. Furthermore, our results suggest that alterations in the cellular redox state induced by viral infection are communicated to the immune system through the presentation of S-glutathionylated viral peptides, resulting in altered T cell recognition. Our data provide a structural basis for how the glutathione modification alters recognition by virus-specific T cells. Collectively, these results suggest that oxidative stress represents a mechanism for modulating the virus-specific T cell response.
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Affiliation(s)
- Jonathan A Trujillo
- From the Department of Microbiology and the Interdisciplinary Program in Immunology, University of Iowa, Iowa City, Iowa 52242
| | - Nathan P Croft
- the Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia, the Department of Biochemistry and Molecular Biology and
| | - Nadine L Dudek
- the Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia, the Department of Biochemistry and Molecular Biology and
| | | | | | - Andrew I Webb
- the Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | | | - Patricia T Illing
- the Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Noah S Butler
- From the Department of Microbiology and the Research School of Biology, Australian National University, Canberra, Australian Capital Territory 0200, Australia, and
| | | | - David C Tscharke
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Jamie Rossjohn
- the Department of Biochemistry and Molecular Biology and Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia, the Institute of Infection and Immunity, Cardiff University, School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Stanley Perlman
- From the Department of Microbiology and the Interdisciplinary Program in Immunology, University of Iowa, Iowa City, Iowa 52242,
| | - Anthony W Purcell
- the Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia, the Department of Biochemistry and Molecular Biology and
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25
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Sun M, Liu J, Qi J, Tefsen B, Shi Y, Yan J, Gao GF. Nα-terminal acetylation for T cell recognition: molecular basis of MHC class I-restricted nα-acetylpeptide presentation. THE JOURNAL OF IMMUNOLOGY 2014; 192:5509-19. [PMID: 24829406 DOI: 10.4049/jimmunol.1400199] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
As one of the most common posttranslational modifications (PTMs) of eukaryotic proteins, N(α)-terminal acetylation (Nt-acetylation) generates a class of N(α)-acetylpeptides that are known to be presented by MHC class I at the cell surface. Although such PTM plays a pivotal role in adjusting proteolysis, the molecular basis for the presentation and T cell recognition of N(α)-acetylpeptides remains largely unknown. In this study, we determined a high-resolution crystallographic structure of HLA (HLA)-B*3901 complexed with an N(α)-acetylpeptide derived from natural cellular processing, also in comparison with the unmodified-peptide complex. Unlike the α-amino-free P1 residues of unmodified peptide, of which the α-amino group inserts into pocket A of the Ag-binding groove, the N(α)-linked acetyl of the acetylated P1-Ser protrudes out of the groove for T cell recognition. Moreover, the Nt-acetylation not only alters the conformation of the peptide but also switches the residues in the α1-helix of HLA-B*3901, which may impact the T cell engagement. The thermostability measurements of complexes between N(α)-acetylpeptides and a series of MHC class I molecules derived from different species reveal reduced stability. Our findings provide the insight into the mode of N(α)-acetylpeptide-specific presentation by classical MHC class I molecules and shed light on the potential of acetylepitope-based immune intervene and vaccine development.
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Affiliation(s)
- Mingwei Sun
- School of Life Sciences, University of Science and Technology of China, Hefei 230027, China; CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jun Liu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; and
| | - Jianxun Qi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Boris Tefsen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yi Shi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Research Network of Immunity and Health, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Jinghua Yan
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - George F Gao
- School of Life Sciences, University of Science and Technology of China, Hefei 230027, China; CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; and Research Network of Immunity and Health, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
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26
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Cruz LJ, Rueda F, Simón L, Cordobilla B, Albericio F, Domingo JC. Liposomes containing NY-ESO-1/tetanus toxoid and adjuvant peptides targeted to human dendritic cells via the Fc receptor for cancer vaccines. Nanomedicine (Lond) 2014; 9:435-49. [DOI: 10.2217/nnm.13.66] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Aim: To improve the immunological response against tumors, a vaccine based on nanoliposomes targeted to the Fcγ-receptor was developed to enhance the immunogenicity of tumor-associated antigens (TAAs). Materials & methods: Using human dendritic cells in vitro, a fragment of the TAA NY-ESO-1 combined with a T-helper peptide from the tetanus toxoid encapsulated in nanoliposomes was evaluated. In addition, peptides Palm-IL-1 and MAP-IFN-γwere coadministered as adjuvants to enhance the immunological response. Results: Coadministration of Palm-IL-1 or MAP-IFN-γpeptide adjuvants and the hybrid NY-ESO-1-tetanus toxoid (soluble or encapsulated in nanoliposomes without targeting) increased immunogenicity. However, the most potent immunological response was obtained when the peptide adjuvants were encapsulated in liposomes targeted to human dendritic cells via the Fc receptor. Conclusion: This targeted vaccine strategy is a promising tool to activate and deliver antigens to dendritic cells, thus improving immunotherapeutic response in situations in which the immune system is frequently compromised, as in advanced cancers.
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Affiliation(s)
- Luis J Cruz
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials & Nanomedicine, Barcelona Science Park, Baldiri Reixac 10, 08028 Barcelona, Spain
- Institute for Research in Biomedicine, Barcelona Science Park, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Felix Rueda
- Department of Biochemistry & Molecular Biology, University of Barcelona, Diagonal 643, 08028 Barcelona, Spain
| | - Lorena Simón
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials & Nanomedicine, Barcelona Science Park, Baldiri Reixac 10, 08028 Barcelona, Spain
- Institute for Research in Biomedicine, Barcelona Science Park, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Begoña Cordobilla
- Department of Biochemistry & Molecular Biology, University of Barcelona, Diagonal 643, 08028 Barcelona, Spain
| | - Fernando Albericio
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials & Nanomedicine, Barcelona Science Park, Baldiri Reixac 10, 08028 Barcelona, Spain
- Institute for Research in Biomedicine, Barcelona Science Park, Baldiri Reixac 10, 08028 Barcelona, Spain
- Department of Organic Chemistry, University of Barcelona, Marti i Franques 1, 08028-Barcelona, Spain
- School of Chemistry, University of KwaZulu Natal, Durban, Kwa-Zulu Natal, 4000, South Africa
| | - Joan C Domingo
- Department of Biochemistry & Molecular Biology, University of Barcelona, Diagonal 643, 08028 Barcelona, Spain
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27
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Croft NP, Purcell AW. Peptidomimetics: modifying peptides in the pursuit of better vaccines. Expert Rev Vaccines 2014; 10:211-26. [DOI: 10.1586/erv.10.161] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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28
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Halabelian L, Ricagno S, Giorgetti S, Santambrogio C, Barbiroli A, Pellegrino S, Achour A, Grandori R, Marchese L, Raimondi S, Mangione PP, Esposito G, Al-Shawi R, Simons JP, Speck I, Stoppini M, Bolognesi M, Bellotti V. Class I major histocompatibility complex, the trojan horse for secretion of amyloidogenic β2-microglobulin. J Biol Chem 2013; 289:3318-27. [PMID: 24338476 PMCID: PMC3916536 DOI: 10.1074/jbc.m113.524157] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
To form extracellular aggregates, amyloidogenic proteins bypass the intracellular quality control, which normally targets unfolded/aggregated polypeptides. Human D76N β2-microglobulin (β2m) variant is the prototype of unstable and amyloidogenic protein that forms abundant extracellular fibrillar deposits. Here we focus on the role of the class I major histocompatibility complex (MHCI) in the intracellular stabilization of D76N β2m. Using biophysical and structural approaches, we show that the MHCI containing D76N β2m (MHCI76) displays stability, dissociation patterns, and crystal structure comparable with those of the MHCI with wild type β2m. Conversely, limited proteolysis experiments show a reduced protease susceptibility for D76N β2m within the MHCI76 as compared with the free variant, suggesting that the MHCI has a chaperone-like activity in preventing D76N β2m degradation within the cell. Accordingly, D76N β2m is normally assembled in the MHCI and circulates as free plasma species in a transgenic mouse model.
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Affiliation(s)
- Levon Halabelian
- From the Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, 20133 Milano, Italy
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29
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Stone JD, Kranz DM. Role of T cell receptor affinity in the efficacy and specificity of adoptive T cell therapies. Front Immunol 2013; 4:244. [PMID: 23970885 PMCID: PMC3748443 DOI: 10.3389/fimmu.2013.00244] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Accepted: 08/05/2013] [Indexed: 01/09/2023] Open
Abstract
Over the last several years, there has been considerable progress in the treatment of cancer using gene modified adoptive T cell therapies. Two approaches have been used, one involving the introduction of a conventional αβ T cell receptor (TCR) against a pepMHC cancer antigen, and the second involving introduction of a chimeric antigen receptor (CAR) consisting of a single-chain antibody as an Fv fragment linked to transmembrane and signaling domains. In this review, we focus on one aspect of TCR-mediated adoptive T cell therapies, the impact of the affinity of the αβ TCR for the pepMHC cancer antigen on both efficacy and specificity. We discuss the advantages of higher-affinity TCRs in mediating potent activity of CD4 T cells. This is balanced with the potential disadvantage of higher-affinity TCRs in mediating greater self-reactivity against a wider range of structurally similar antigenic peptides, especially in synergy with the CD8 co-receptor. Both TCR affinity and target selection will influence potential safety issues. We suggest pre-clinical strategies that might be used to examine each TCR for possible on-target and off-target side effects due to self-reactivities, and to adjust TCR affinities accordingly.
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Affiliation(s)
- Jennifer D Stone
- Department of Biochemistry, University of Illinois , Urbana, IL , USA
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Lu X, Shi Y, Zhang W, Zhang Y, Qi J, Gao GF. Structure and receptor-binding properties of an airborne transmissible avian influenza A virus hemagglutinin H5 (VN1203mut). Protein Cell 2013; 4:502-11. [PMID: 23794001 DOI: 10.1007/s13238-013-3906-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 06/01/2013] [Indexed: 11/29/2022] Open
Abstract
Avian influenza A virus continues to pose a global threat with occasional H5N1 human infections, which is emphasized by a recent severe human infection caused by avian-origin H7N9 in China. Luckily these viruses do not transmit efficiently in human populations. With a few amino acid substitutions of the hemagglutinin H5 protein in the laboratory, two H5 mutants have been shown to obtain an air-borne transmission in a mammalian ferret model. Here in this study one of the mutant H5 proteins developed by Kawaoka's group (VN1203mut) was expressed in a baculovirus system and its receptor-binding properties were assessed. We herein show that the VN1203mut had a dramatically reduced binding affinity for the avian α2,3-linkage receptor compared to wild type but showed no detectable increase in affinity for the human α2,6-linkage receptor, using Surface Plasmon Resonance techonology. Further, the crystal structures of the VN1203mut and its complexes with either human or avian receptors demonstrate that the VN1203mut binds the human receptor in the same binding manner (cis conformation) as seen for the HAs of previously reported 1957 and 1968 pandemic influenza viruses. Our receptor binding and crystallographic data shown here further confirm that the ability to bind the avian receptor has to decrease for a higher human receptor binding affinity. As the Q226L substitution is shown important for obtaining human receptor binding, we suspect that the newly emerged H7N9 binds human receptor as H7 has a Q226L substitution.
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Affiliation(s)
- Xishan Lu
- College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
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Park MS, Park SY, Miller KR, Collins EJ, Lee HY. Accurate structure prediction of peptide-MHC complexes for identifying highly immunogenic antigens. Mol Immunol 2013; 56:81-90. [PMID: 23688437 DOI: 10.1016/j.molimm.2013.04.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 04/09/2013] [Accepted: 04/15/2013] [Indexed: 12/26/2022]
Abstract
Designing an optimal HIV-1 vaccine faces the challenge of identifying antigens that induce a broad immune capacity. One factor to control the breadth of T cell responses is the surface morphology of a peptide-MHC complex. Here, we present an in silico protocol for predicting peptide-MHC structure. A robust signature of a conformational transition was identified during all-atom molecular dynamics, which results in a model with high accuracy. A large test set was used in constructing our protocol and we went another step further using a blind test with a wild-type peptide and two highly immunogenic mutants, which predicted substantial conformational changes in both mutants. The center residues at position five of the analogs were configured to be accessible to solvent, forming a prominent surface, while the residue of the wild-type peptide was to point laterally toward the side of the binding cleft. We then experimentally determined the structures of the blind test set, using high resolution of X-ray crystallography, which verified predicted conformational changes. Our observation strongly supports a positive association of the surface morphology of a peptide-MHC complex to its immunogenicity. Our study offers the prospect of enhancing immunogenicity of vaccines by identifying MHC binding immunogens.
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Affiliation(s)
- Min-Sun Park
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, NY 14642, USA
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Zhang W, Shi Y, Lu X, Shu Y, Qi J, Gao GF. An airborne transmissible avian influenza H5 hemagglutinin seen at the atomic level. Science 2013; 340:1463-7. [PMID: 23641058 DOI: 10.1126/science.1236787] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Recent studies have identified several mutations in the hemagglutinin (HA) protein that allow the highly pathogenic avian H5N1 influenza A virus to transmit between mammals by airborne route. Here, we determined the complex structures of wild-type and mutant HAs derived from an Indonesia H5N1 virus bound to either avian or human receptor sialic acid analogs. A cis/trans conformational change in the glycosidic linkage of the receptor analog was observed, which explains how the H5N1 virus alters its receptor-binding preference. Furthermore, the mutant HA possessed low affinities for both avian and human receptors. Our findings provide a structural and biophysical basis for the H5N1 adaptation to acquire human, but maintain avian, receptor-binding properties.
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Affiliation(s)
- Wei Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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Campos-Perez J, Rice J, Escors D, Collins M, Paterson A, Savelyeva N, Stevenson FK. DNA fusion vaccine designs to induce tumor-lytic CD8+ T-cell attack via the immunodominant cysteine-containing epitope of NY-ESO 1. Int J Cancer 2013; 133:1400-7. [PMID: 23494538 DOI: 10.1002/ijc.28156] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Accepted: 03/01/2013] [Indexed: 12/31/2022]
Abstract
The cancer/testis antigen NY-ESO-1 contains an immunodominant HLA-A2-binding peptide (SLLMWITQC), designated S9C, an attractive target for vaccination against several human cancers. As cysteine contains a reactive -SH, the oxidation status of exogenous synthetic peptide is uncertain. We have designed tolerance-breaking DNA fusion vaccines incorporating a domain of tetanus toxin fused to tumor-derived peptide sequences (p.DOM-peptide), placed at the C-terminus for optimal immunogenicity. In a "humanized" HLA-A2 preclinical model, p.DOM-S9C primed S9C-specific CD8+ T cells more effectively than adjuvanted synthetic peptide. A DNA vaccine encoding the full NY-ESO-1 sequence alone induced only weak S9C-specific responses, amplified by addition of DOM sequence. The analog peptide (SLLMWITQL) also primed peptide-specific CD8+ T cells, again increased by DNA delivery. Importantly, T cells induced by S9C-encoding DNA vaccines killed tumor cells expressing endogenous NY-ESO-1. Only a fraction of T cells induced by the S9L-encoding DNA vaccines was able to recognize S9C and kill tumor cells. These data indicate that DNA vaccines mimic posttranslational modifications of -SH-containing peptides expressed by tumor cells. Instability of synthetic peptides and the potential dangers of analog peptides contrast with the ability of DNA vaccines to induce high levels of tumor-lytic peptide-specific CD8+ T cells. These findings encourage clinical exploration of this vaccine strategy to target NY-ESO-1.
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Affiliation(s)
- Juan Campos-Perez
- Genetic Vaccine Group, Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
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Liao WWP, Arthur JW. Predicting peptide binding affinities to MHC molecules using a modified semi-empirical scoring function. PLoS One 2011; 6:e25055. [PMID: 21966412 PMCID: PMC3178607 DOI: 10.1371/journal.pone.0025055] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Accepted: 08/23/2011] [Indexed: 12/19/2022] Open
Abstract
The Major Histocompatibility Complex (MHC) plays an important role in the human immune system. The MHC is involved in the antigen presentation system assisting T cells to identify foreign or pathogenic proteins. However, an MHC molecule binding a self-peptide may incorrectly trigger an immune response and cause an autoimmune disease, such as multiple sclerosis. Understanding the molecular mechanism of this process will greatly assist in determining the aetiology of various diseases and in the design of effective drugs. In the present study, we have used the Fresno semi-empirical scoring function and modify the approach to the prediction of peptide-MHC binding by using open-source and public domain software. We apply the method to HLA class II alleles DR15, DR1, and DR4, and the HLA class I allele HLA A2. Our analysis shows that using a large set of binding data and multiple crystal structures improves the predictive capability of the method. The performance of the method is also shown to be correlated to the structural similarity of the crystal structures used. We have exposed some of the obstacles faced by structure-based prediction methods and proposed possible solutions to those obstacles. It is envisaged that these obstacles need to be addressed before the performance of structure-based methods can be on par with the sequence-based methods.
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Affiliation(s)
- Webber W. P. Liao
- Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Jonathan W. Arthur
- Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
- Children's Medical Research Institute, Sydney, New South Wales, Australia
- * E-mail:
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Jones ES, Del Borgo MP, Kirsch JF, Clayton D, Bosnyak S, Welungoda I, Hausler N, Unabia S, Perlmutter P, Thomas WG, Aguilar MI, Widdop RE. A Single β-Amino Acid Substitution to Angiotensin II Confers AT
2
Receptor Selectivity and Vascular Function. Hypertension 2011; 57:570-6. [DOI: 10.1161/hypertensionaha.110.164301] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Emma S. Jones
- From the Department of Pharmacology (E.S.J., J.F.K., S.B., I.W., R.E.W.), Department of Biochemistry and Molecular Biology (M.P.D.B., D.C., S.U., M.-I.A.), and School of Chemistry (N.H., P.P.), Monash University, Clayton, Victoria, Australia; School of Biomedical Sciences (W.G.T.), University of Queensland, Brisbane, Queensland, Australia
| | - Mark P. Del Borgo
- From the Department of Pharmacology (E.S.J., J.F.K., S.B., I.W., R.E.W.), Department of Biochemistry and Molecular Biology (M.P.D.B., D.C., S.U., M.-I.A.), and School of Chemistry (N.H., P.P.), Monash University, Clayton, Victoria, Australia; School of Biomedical Sciences (W.G.T.), University of Queensland, Brisbane, Queensland, Australia
| | - Julian F. Kirsch
- From the Department of Pharmacology (E.S.J., J.F.K., S.B., I.W., R.E.W.), Department of Biochemistry and Molecular Biology (M.P.D.B., D.C., S.U., M.-I.A.), and School of Chemistry (N.H., P.P.), Monash University, Clayton, Victoria, Australia; School of Biomedical Sciences (W.G.T.), University of Queensland, Brisbane, Queensland, Australia
| | - Daniel Clayton
- From the Department of Pharmacology (E.S.J., J.F.K., S.B., I.W., R.E.W.), Department of Biochemistry and Molecular Biology (M.P.D.B., D.C., S.U., M.-I.A.), and School of Chemistry (N.H., P.P.), Monash University, Clayton, Victoria, Australia; School of Biomedical Sciences (W.G.T.), University of Queensland, Brisbane, Queensland, Australia
| | - Sanja Bosnyak
- From the Department of Pharmacology (E.S.J., J.F.K., S.B., I.W., R.E.W.), Department of Biochemistry and Molecular Biology (M.P.D.B., D.C., S.U., M.-I.A.), and School of Chemistry (N.H., P.P.), Monash University, Clayton, Victoria, Australia; School of Biomedical Sciences (W.G.T.), University of Queensland, Brisbane, Queensland, Australia
| | - Iresha Welungoda
- From the Department of Pharmacology (E.S.J., J.F.K., S.B., I.W., R.E.W.), Department of Biochemistry and Molecular Biology (M.P.D.B., D.C., S.U., M.-I.A.), and School of Chemistry (N.H., P.P.), Monash University, Clayton, Victoria, Australia; School of Biomedical Sciences (W.G.T.), University of Queensland, Brisbane, Queensland, Australia
| | - Nicholas Hausler
- From the Department of Pharmacology (E.S.J., J.F.K., S.B., I.W., R.E.W.), Department of Biochemistry and Molecular Biology (M.P.D.B., D.C., S.U., M.-I.A.), and School of Chemistry (N.H., P.P.), Monash University, Clayton, Victoria, Australia; School of Biomedical Sciences (W.G.T.), University of Queensland, Brisbane, Queensland, Australia
| | - Sharon Unabia
- From the Department of Pharmacology (E.S.J., J.F.K., S.B., I.W., R.E.W.), Department of Biochemistry and Molecular Biology (M.P.D.B., D.C., S.U., M.-I.A.), and School of Chemistry (N.H., P.P.), Monash University, Clayton, Victoria, Australia; School of Biomedical Sciences (W.G.T.), University of Queensland, Brisbane, Queensland, Australia
| | - Patrick Perlmutter
- From the Department of Pharmacology (E.S.J., J.F.K., S.B., I.W., R.E.W.), Department of Biochemistry and Molecular Biology (M.P.D.B., D.C., S.U., M.-I.A.), and School of Chemistry (N.H., P.P.), Monash University, Clayton, Victoria, Australia; School of Biomedical Sciences (W.G.T.), University of Queensland, Brisbane, Queensland, Australia
| | - Walter G. Thomas
- From the Department of Pharmacology (E.S.J., J.F.K., S.B., I.W., R.E.W.), Department of Biochemistry and Molecular Biology (M.P.D.B., D.C., S.U., M.-I.A.), and School of Chemistry (N.H., P.P.), Monash University, Clayton, Victoria, Australia; School of Biomedical Sciences (W.G.T.), University of Queensland, Brisbane, Queensland, Australia
| | - Marie-Isabel Aguilar
- From the Department of Pharmacology (E.S.J., J.F.K., S.B., I.W., R.E.W.), Department of Biochemistry and Molecular Biology (M.P.D.B., D.C., S.U., M.-I.A.), and School of Chemistry (N.H., P.P.), Monash University, Clayton, Victoria, Australia; School of Biomedical Sciences (W.G.T.), University of Queensland, Brisbane, Queensland, Australia
| | - Robert E. Widdop
- From the Department of Pharmacology (E.S.J., J.F.K., S.B., I.W., R.E.W.), Department of Biochemistry and Molecular Biology (M.P.D.B., D.C., S.U., M.-I.A.), and School of Chemistry (N.H., P.P.), Monash University, Clayton, Victoria, Australia; School of Biomedical Sciences (W.G.T.), University of Queensland, Brisbane, Queensland, Australia
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Borbulevych OY, Do P, Baker BM. Structures of native and affinity-enhanced WT1 epitopes bound to HLA-A*0201: implications for WT1-based cancer therapeutics. Mol Immunol 2010; 47:2519-24. [PMID: 20619457 DOI: 10.1016/j.molimm.2010.06.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2010] [Revised: 06/09/2010] [Accepted: 06/12/2010] [Indexed: 01/28/2023]
Abstract
Presentation of peptides by class I or class II major histocompatibility complex (MHC) molecules is required for the initiation and propagation of a T cell-mediated immune response. Peptides from the Wilms Tumor 1 transcription factor (WT1), upregulated in many hematopoetic and solid tumors, can be recognized by T cells and numerous efforts are underway to engineer WT1-based cancer vaccines. Here we determined the structures of the class I MHC molecule HLA-A*0201 bound to the native 126-134 epitope of the WT1 peptide and a recently described variant (R1Y) with improved MHC binding. The R1Y variant, a potential vaccine candidate, alters the positions of MHC charged side chains near the peptide N-terminus and significantly reduces the peptide/MHC electrostatic surface potential. These alterations indicate that the R1Y variant is an imperfect mimic of the native WT1 peptide, and suggest caution in its use as a therapeutic vaccine. Stability measurements revealed how the R1Y substitution enhances MHC binding affinity, and together with the structures suggest a strategy for engineering WT1 variants with improved MHC binding that retain the structural features of the native peptide/MHC complex.
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Affiliation(s)
- Oleg Y Borbulevych
- Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, United States
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Chen JL, Morgan AJ, Stewart-Jones G, Shepherd D, Bossi G, Wooldridge L, Hutchinson SL, Sewell AK, Griffiths GM, van der Merwe PA, Jones EY, Galione A, Cerundolo V. Ca2+ release from the endoplasmic reticulum of NY-ESO-1-specific T cells is modulated by the affinity of TCR and by the use of the CD8 coreceptor. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2010; 184:1829-1839. [PMID: 20053942 PMCID: PMC4222200 DOI: 10.4049/jimmunol.0902103] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Although several cancer immunotherapy strategies are based on the use of analog peptides and on the modulation of the TCR affinity of adoptively transferred T cells, it remains unclear whether tumor-specific T cell activation by strong and weak TCR stimuli evoke different Ca(2+) signatures from the Ca(2+) intracellular stores and whether the amplitude of Ca(2+) release from the endoplasmic reticulum (ER) can be further modulated by coreceptor binding to peptide/MHC. In this study, we combined functional, structural, and kinetic measurements to correlate the intensity of Ca(2+) signals triggered by the stimulation of the 1G4 T cell clone specific to the tumor epitope NY-ESO-1(157-165). Two analogs of the NY-ESO-1(157-165) peptide, having similar affinity to HLA-A2 molecules, but a 6-fold difference in binding affinity for the 1G4 TCR, resulted in different Ca(2+) signals and T cell activation. 1G4 stimulation by the stronger stimulus emptied the ER of stored Ca(2+), even in the absence of CD8 binding, resulting in sustained Ca(2+) influx. In contrast, the weaker stimulus induced only partial emptying of stored Ca(2+), resulting in significantly diminished and oscillatory Ca(2+) signals, which were enhanced by CD8 binding. Our data define the range of TCR/peptide MHC affinities required to induce depletion of Ca(2+) from intracellular stores and provide insights into the ability of T cells to tailor the use of the CD8 coreceptor to enhance Ca(2+) release from the ER. This, in turn, modulates Ca(2+) influx from the extracellular environment, ultimately controlling T cell activation.
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Affiliation(s)
- Ji-Li Chen
- Weatherall Institute of Molecular Medicine, OX3 9DS, Oxford
| | - Anthony J. Morgan
- Dept of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK
| | - Guillaume Stewart-Jones
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Dawn Shepherd
- Weatherall Institute of Molecular Medicine, OX3 9DS, Oxford
| | - Giovanna Bossi
- Immunocore, Limited, 57c Milton Park, Abingdon, Oxon, OX14 4RX, UK
| | - Linda Wooldridge
- Dept of Infection, Immunity and Biochemistry, The Henry Wellcome Building, Cardiff University School of Medicine, Cardiff, CF14 4XN
| | | | - Andrew K. Sewell
- Dept of Infection, Immunity and Biochemistry, The Henry Wellcome Building, Cardiff University School of Medicine, Cardiff, CF14 4XN
| | - Gillian M. Griffiths
- Cambridge Institute for Medical Research, PO Box 139, Addenbrooke’s Hospital, Hills Road, Cambridge CB2 0XY, UK
| | | | - E. Yvonne Jones
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Antony Galione
- Dept of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK
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Aleksic M, Dushek O, Zhang H, Shenderov E, Chen JL, Cerundolo V, Coombs D, van der Merwe PA. Dependence of T cell antigen recognition on T cell receptor-peptide MHC confinement time. Immunity 2010; 32:163-74. [PMID: 20137987 PMCID: PMC2862301 DOI: 10.1016/j.immuni.2009.11.013] [Citation(s) in RCA: 177] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2009] [Revised: 10/02/2009] [Accepted: 11/20/2009] [Indexed: 12/18/2022]
Abstract
T cell receptor (TCR) binding to diverse peptide-major histocompatibility complex (pMHC) ligands results in various degrees of T cell activation. Here we analyze which binding properties of the TCR-pMHC interaction are responsible for this variation in pMHC activation potency. We have analyzed activation of the 1G4 cytotoxic T lymphocyte clone by cognate pMHC variants and performed thorough correlation analysis of T cell activation with 1G4 TCR-pMHC binding properties measured in solution. We found that both the on rate (kon) and off rate (koff) contribute to activation potency. Based on our results, we propose a model in which rapid TCR rebinding to the same pMHC after chemical dissociation increases the effective half-life or “confinement time” of a TCR-pMHC interaction. This confinement time model clarifies the role of kon in T cell activation and reconciles apparently contradictory reports on the role of TCR-pMHC binding kinetics and affinity in T cell activation.
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Affiliation(s)
- Milos Aleksic
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
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van Stipdonk MJB, Badia-Martinez D, Sluijter M, Offringa R, van Hall T, Achour A. Design of agonistic altered peptides for the robust induction of CTL directed towards H-2Db in complex with the melanoma-associated epitope gp100. Cancer Res 2009; 69:7784-92. [PMID: 19789338 DOI: 10.1158/0008-5472.can-09-1724] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Immunogenicity of tumor-associated antigens (TAA) is often weak because many TAA are autoantigens for which the T-cell repertoire is sculpted by tolerance mechanisms. Substitutions at main anchor positions to increase the complementarity between the peptide and the MHC class I (MHC-I) binding cleft constitute a common procedure to improve binding capacity and immunogenicity of TAA. However, such alterations are tailored for each MHC-I allele and may recruit different CTL specificities through conformational changes in the targeted peptides. Comparative analysis of substituted melanoma-differentiation antigen gp100 in complex with H-2D(b) revealed that combined introduction of glycine and proline residues at the nonanchor positions 2 and 3, respectively, resulted in an agonistic altered peptide with dramatically enhanced binding affinity, stability, and immunogenicity of this TAA. Peptide vaccination using the p2Gp3P-altered peptide version of gp100 induced high frequencies of melanoma-specific CTL in the endogenous CD8+ repertoire. Crystal structure analysis of MHC/peptide complexes revealed that the conformation of the modified p2Gp3P-peptide was similar to the wild-type peptide, and indicated that this mimotope was stabilized through interactions between peptide residue p3P and the tyrosine residue Y159 that is conserved among most known MHC-I molecules throughout mammalian species. Our results may provide an alternative approach to enhance MHC stabilization capacity and immunogenicity of low-affinity peptides for induction of robust tumor-specific CTL.
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Affiliation(s)
- Marianne J B van Stipdonk
- Departments of Immunohematology and Blood transfusion and Clinical Oncology, Leiden University Medical Center, Leiden, the Netherlands
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40
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Post-translationally modified T cell epitopes: immune recognition and immunotherapy. J Mol Med (Berl) 2009; 87:1045-51. [DOI: 10.1007/s00109-009-0526-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2009] [Revised: 08/20/2009] [Accepted: 08/24/2009] [Indexed: 12/27/2022]
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Gehring AJ, Ho ZZ, Tan AT, Aung MO, Lee KH, Tan KC, Lim SG, Bertoletti A. Profile of tumor antigen-specific CD8 T cells in patients with hepatitis B virus-related hepatocellular carcinoma. Gastroenterology 2009; 137:682-90. [PMID: 19394336 DOI: 10.1053/j.gastro.2009.04.045] [Citation(s) in RCA: 127] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2008] [Revised: 04/06/2009] [Accepted: 04/10/2009] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS Tumor and viral antigens are expressed by hepatocellular carcinoma (HCC) in patients with chronic hepatitis B, but little is known about the immunodominance and function of tumor- and virus-specific CD8+ T cells in these patients. METHODS HLA-A2-restricted T-cell responses to 16 tumor antigens and hepatitis B virus (HBV) proteins were tested using 49 previously described epitopes. Cells from 30 HLA-A2+, HBV-infected patients (10 with HCC, 10 with HBV cirrhosis, and 10 HBV but no cirrhosis) were analyzed, after expansion, by enzyme-linked immunosorbent spot (ELISPOT). Interferon (IFN)-gamma, tumor necrosis factor (TNF)-alpha, and interleukin (IL)-2 production, as well as expression of the degranulation marker CD107a on tumor-specific CD8+ T cells, were evaluated. RESULTS Cells from all groups had tumor-specific responses. The tumor antigens NY-ESO-1 and SSX-2 were most frequently targeted and were immunogenic in the HLA-A2 subtypes that are characteristic of Asian ethnicity. Tumor-specific T cells had low affinities; T cells from non-HCC patients were polyfunctional (IFN-gamma+, TNF-alpha+, CD107a+) and those from HCC patients displayed an exhausted phenotype (IFN-gamma+, CD107a+). Programmed Death 1 (PD-1) was expressed at higher levels on T cells from tumor and liver than peripheral blood from HCC patients and might contribute to T-cell exhaustion. Blocking PD-1/PD-L1 increased the frequency of tumor-specific T cells in HCC patients but did not restore T cell function. CONCLUSIONS Patients with or without HCC have a quantitative and functional hierarchy of tumor-specific T cells. HLA-A2-restricted T cells from HCC patients target NY-ESO-1, but exist in an exhausted state that might require additional activation to restore function.
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Affiliation(s)
- Adam J Gehring
- Singapore Institute for Clinical Sciences, Agency for Science Technology and Research, Singapore
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42
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Shang X, Wang L, Niu W, Meng G, Fu X, Ni B, Lin Z, Yang Z, Chen X, Wu Y. Rational optimization of tumor epitopes using in silico
analysis-assisted substitution of TCR contact residues. Eur J Immunol 2009; 39:2248-58. [DOI: 10.1002/eji.200939338] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Petersen J, Wurzbacher SJ, Williamson NA, Ramarathinam SH, Reid HH, Nair AKN, Zhao AY, Nastovska R, Rudge G, Rossjohn J, Purcell AW. Phosphorylated self-peptides alter human leukocyte antigen class I-restricted antigen presentation and generate tumor-specific epitopes. Proc Natl Acad Sci U S A 2009; 106:2776-81. [PMID: 19196958 PMCID: PMC2650342 DOI: 10.1073/pnas.0812901106] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2008] [Indexed: 11/18/2022] Open
Abstract
Human leukocyte antigen (HLA) class I molecules present a variety of posttranslationally modified epitopes at the cell surface, although the consequences of such presentation remain largely unclear. Phosphorylation plays a critical cellular role, and deregulation in phosphate metabolism is associated with disease, including autoimmunity and tumor immunity. We have solved the high-resolution structures of 3 HLA A2-restricted phosphopeptides associated with tumor immunity and compared them with the structures of their nonphosphorylated counterparts. Phosphorylation of the epitope was observed to affect the structure and mobility of the bound epitope. In addition, the phosphoamino acid stabilized the HLA peptide complex in an epitope-specific manner and was observed to exhibit discrete flexibility within the antigen-binding cleft. Collectively, our data suggest that phosphorylation generates neoepitopes that represent demanding targets for T-cell receptor ligation. These findings provide insights into the mode of phosphopeptide presentation by HLA as well as providing a platform for the rational design of a generation of posttranslationally modified tumor vaccines.
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Affiliation(s)
- Jan Petersen
- Protein Crystallography Unit, Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Victoria 3800, Australia; and
| | - Stephanie J. Wurzbacher
- Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia
| | - Nicholas A. Williamson
- Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia
| | - Sri H. Ramarathinam
- Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia
| | - Hugh H. Reid
- Protein Crystallography Unit, Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Victoria 3800, Australia; and
| | - Ashish K. N. Nair
- Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia
| | - Anne Y. Zhao
- Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia
| | - Roza Nastovska
- Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia
| | - Geordie Rudge
- Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia
| | - Jamie Rossjohn
- Protein Crystallography Unit, Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Victoria 3800, Australia; and
| | - Anthony W. Purcell
- Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia
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Non-natural and photo-reactive amino acids as biochemical probes of immune function. PLoS One 2008; 3:e3938. [PMID: 19079589 PMCID: PMC2592539 DOI: 10.1371/journal.pone.0003938] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2008] [Accepted: 11/16/2008] [Indexed: 12/03/2022] Open
Abstract
Wilms tumor protein (WT1) is a transcription factor selectively overexpressed in leukemias and cancers; clinical trials are underway that use altered WT1 peptide sequences as vaccines. Here we report a strategy to study peptide-MHC interactions by incorporating non-natural and photo-reactive amino acids into the sequence of WT1 peptides. Thirteen WT1 peptides sequences were synthesized with chemically modified amino acids (via fluorination and photo-reactive group additions) at MHC and T cell receptor binding positions. Certain new non-natural peptide analogs could stabilize MHC class I molecules better than the native sequences and were also able to elicit specific T-cell responses and sometimes cytotoxicity to leukemia cells. Two photo-reactive peptides, also modified with a biotin handle for pull-down studies, formed covalent interactions with MHC molecules on live cells and provided kinetic data showing the rapid clearance of the peptide-MHC complex. Despite “infinite affinity” provided by the covalent peptide bonding to the MHC, immunogenicity was not enhanced by these peptides because the peptide presentation on the surface was dominated by catabolism of the complex and only a small percentage of peptide molecules covalently bound to the MHC molecules. This study shows that non-natural amino acids can be successfully incorporated into T cell epitopes to provide novel immunological, biochemical and kinetic information.
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Butler NS, Theodossis A, Webb AI, Nastovska R, Ramarathinam SH, Dunstone MA, Rossjohn J, Purcell AW, Perlman S. Prevention of cytotoxic T cell escape using a heteroclitic subdominant viral T cell determinant. PLoS Pathog 2008; 4:e1000186. [PMID: 18949029 PMCID: PMC2563037 DOI: 10.1371/journal.ppat.1000186] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2008] [Accepted: 09/24/2008] [Indexed: 01/07/2023] Open
Abstract
High affinity antigen-specific T cells play a critical role during protective immune responses. Epitope enhancement can elicit more potent T cell responses and can subsequently lead to a stronger memory pool; however, the molecular basis of such enhancement is unclear. We used the consensus peptide-binding motif for the Major Histocompatibility Complex molecule H-2K(b) to design a heteroclitic version of the mouse hepatitis virus-specific subdominant S598 determinant. We demonstrate that a single amino acid substitution at a secondary anchor residue (Q to Y at position 3) increased the stability of the engineered determinant in complex with H-2K(b). The structural basis for this enhanced stability was associated with local alterations in the pMHC conformation as a result of the Q to Y substitution. Recombinant viruses encoding this engineered determinant primed CTL responses that also reacted to the wildtype epitope with significantly higher functional avidity, and protected against selection of virus mutated at a second CTL determinant and consequent disease progression in persistently infected mice. Collectively, our findings provide a basis for the enhanced immunogenicity of an engineered determinant that will serve as a template for guiding the development of heteroclitic T cell determinants with applications in prevention of CTL escape in chronic viral infections as well as in tumor immunity.
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Affiliation(s)
- Noah S. Butler
- Department of Microbiology, University of Iowa, Iowa City, Iowa, United States of America
- Immunology Graduate Program, University of Iowa, Iowa City, Iowa, United States of America
| | - Alex Theodossis
- The Protein Crystallography Unit, Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria, Australia
| | - Andrew I. Webb
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Roza Nastovska
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Sri Harsha Ramarathinam
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Michelle A. Dunstone
- The Protein Crystallography Unit, Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria, Australia
| | - Jamie Rossjohn
- The Protein Crystallography Unit, Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria, Australia
| | - Anthony W. Purcell
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
- * E-mail: (AWP); (SP)
| | - Stanley Perlman
- Department of Microbiology, University of Iowa, Iowa City, Iowa, United States of America
- * E-mail: (AWP); (SP)
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Armstrong K, Piepenbrink K, Baker B. Conformational changes and flexibility in T-cell receptor recognition of peptide-MHC complexes. Biochem J 2008; 415:183-96. [PMID: 18800968 PMCID: PMC2782316 DOI: 10.1042/bj20080850] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2008] [Revised: 06/23/2008] [Accepted: 07/09/2008] [Indexed: 01/07/2023]
Abstract
A necessary feature of the immune system, TCR (T-cell receptor) cross-reactivity has been implicated in numerous autoimmune pathologies and is an underlying cause of transplant rejection. Early studies of the interactions of alphabeta TCRs (T-cell receptors) with their peptide-MHC ligands suggested that conformational plasticity in the TCR CDR (complementarity determining region) loops is a dominant contributor to T-cell cross-reactivity. Since these initial studies, the database of TCRs whose structures have been solved both bound and free is now large enough to permit general conclusions to be drawn about the extent of TCR plasticity and the types and locations of motion that occur. In the present paper, we review the conformational differences between free and bound TCRs, quantifying the structural changes that occur and discussing their possible roles in specificity and cross-reactivity. We show that, rather than undergoing major structural alterations or 'folding' upon binding, the majority of TCR CDR loops shift by relatively small amounts. The structural changes that do occur are dominated by hinge-bending motions, with loop remodelling usually occurring near loop apexes. As predicted from previous studies, the largest changes are in the hypervariable CDR3alpha and CDR3beta loops, although in some cases the germline-encoded CDR1alpha and CDR2alpha loops shift in magnitudes that approximate those of the CDR3 loops. Intriguingly, the smallest shifts are in the germline-encoded loops of the beta-chain, consistent with recent suggestions that the TCR beta domain may drive ligand recognition.
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Affiliation(s)
- Kathryn M. Armstrong
- *Department of Chemistry and Biochemistry, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame, IN 46556, U.S.A
| | - Kurt H. Piepenbrink
- *Department of Chemistry and Biochemistry, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame, IN 46556, U.S.A
| | - Brian M. Baker
- *Department of Chemistry and Biochemistry, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame, IN 46556, U.S.A
- †Walther Cancer Research Center, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame, IN 46556, U.S.A
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Garcia Casado J, Janda J, Wei J, Chapatte L, Colombetti S, Alves P, Ritter G, Ayyoub M, Valmori D, Chen W, Lévy F. Lentivector immunization induces tumor antigen‐specific B and T cell responsesin vivo. Eur J Immunol 2008; 38:1867-76. [DOI: 10.1002/eji.200737923] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Abstract
There are a large number of tumor antigens, which may either be specific to the tumor or inappropriately expressed or processed (tumor-associated antigen, TAA). Over the last few years, hundreds of new TAAs have been identified. Some of these represent good targets for both passive (antibody based) and active (vaccine based) therapies. Antibody treatments targeted on tumor-specific antigens, such as Herceptin and Cetuximab, have been effective in clinical trials and are now licensed. In addition, TAAs act as good surrogate markers for use in both the diagnosis and assessment of treatment in cancer patients.
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Affiliation(s)
- Angus Dalgleish
- St. George's University of London, Cranmer, London SW17 0RE, United Kingdom
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Clements CS, Dunstone MA, Macdonald WA, McCluskey J, Rossjohn J. Specificity on a knife-edge: the alphabeta T cell receptor. Curr Opin Struct Biol 2006; 16:787-95. [PMID: 17011774 DOI: 10.1016/j.sbi.2006.09.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2006] [Revised: 08/31/2006] [Accepted: 09/15/2006] [Indexed: 11/27/2022]
Abstract
The interaction between the alphabeta T cell receptor (TCR) and the peptide bound to the major histocompatibility complex class I molecule (pMHC-I) constitutes a central interaction in adaptive immunity. How these receptors interact with such low affinity while maintaining exquisite specificity for peptide antigen and host MHC (MHC-I restriction) remains a challenge to be explained by structural immunologists. Moreover, how this extracellular interaction is transmitted as an intracellular signal via the CD3 complex remains unresolved. Nevertheless, several structures of TCRs, non-liganded and ligated to a defined pMHC-I, combined with detailed biophysical analyses, have provided insight of the structural basis of MHC-I restriction. In addition, structures of isolated CD3 components have enabled T cell signalling mechanisms to be postulated. Recent findings in this area, which include seven distinct TCR/pMHC-I complexes, have fundamental implications in adaptive immunity as well as therapeutic applications to modulate the adaptive immune response.
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Affiliation(s)
- Craig S Clements
- The Protein Crystallography Unit, Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Victoria 3800, Australia
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50
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Williamson NA, Rossjohn J, Purcell AW. Tumors reveal their secrets to cytotoxic T cells. Proc Natl Acad Sci U S A 2006; 103:14649-50. [PMID: 17005729 PMCID: PMC1595405 DOI: 10.1073/pnas.0606951103] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
- Nicholas A. Williamson
- *Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia; and
| | - Jamie Rossjohn
- Protein Crystallography Unit, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Anthony W. Purcell
- *Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia; and
- To whom correspondence should be addressed. E-mail:
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