1
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Rosenberg AM, Ayres CM, Medina-Cucurella AV, Whitehead TA, Baker BM. Enhanced T cell receptor specificity through framework engineering. Front Immunol 2024; 15:1345368. [PMID: 38545094 PMCID: PMC10967027 DOI: 10.3389/fimmu.2024.1345368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 02/15/2024] [Indexed: 04/12/2024] Open
Abstract
Development of T cell receptors (TCRs) as immunotherapeutics is hindered by inherent TCR cross-reactivity. Engineering more specific TCRs has proven challenging, as unlike antibodies, improving TCR affinity does not usually improve specificity. Although various protein design approaches have been explored to surmount this, mutations in TCR binding interfaces risk broadening specificity or introducing new reactivities. Here we explored if TCR specificity could alternatively be tuned through framework mutations distant from the interface. Studying the 868 TCR specific for the HIV SL9 epitope presented by HLA-A2, we used deep mutational scanning to identify a framework mutation above the mobile CDR3β loop. This glycine to proline mutation had no discernable impact on binding affinity or functional avidity towards the SL9 epitope but weakened recognition of SL9 escape variants and led to fewer responses in a SL9-derived positional scanning library. In contrast, an interfacial mutation near the tip of CDR3α that also did not impact affinity or functional avidity towards SL9 weakened specificity. Simulations indicated that the specificity-enhancing mutation functions by reducing the range of loop motions, limiting the ability of the TCR to adjust to different ligands. Although our results are likely to be TCR dependent, using framework engineering to control TCR loop motions may be a viable strategy for improving the specificity of TCR-based immunotherapies.
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Affiliation(s)
- Aaron M. Rosenberg
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, United States
| | - Cory M. Ayres
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, United States
| | | | - Timothy A. Whitehead
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, United States
| | - Brian M. Baker
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, United States
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2
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Gao Y, Barton JP. A binary trait model reveals the fitness effects of HIV-1 escape from T cell responses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.03.583183. [PMID: 38464239 PMCID: PMC10925374 DOI: 10.1101/2024.03.03.583183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Natural selection often acts on multiple traits simultaneously. For example, the virus HIV-1 faces pressure to evade host immunity while also preserving replicative fitness. While past work has studied selection during HIV-1 evolution, it is challenging to quantitatively separate different contributions to fitness. This task is made more difficult because a single mutation can affect both immune escape and replication. Here, we develop an evolutionary model that disentangles the effects of escaping CD8+ T cell-mediated immunity, which we model as a binary trait, from other contributions to fitness. After validation in simulations, we applied this model to study within-host HIV-1 evolution in a clinical data set. We observed strong selection for immune escape, sometimes greatly exceeding past estimates, especially early in infection. Conservative estimates suggest that roughly half of HIV-1 fitness gains during the first months to years of infection can be attributed to T cell escape. Our approach is not limited to HIV-1 or viruses, and could be adapted to study the evolution of quantitative traits in other contexts.
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Affiliation(s)
- Yirui Gao
- Department of Physics and Astronomy, University of California, Riverside, USA
| | - John P. Barton
- Department of Physics and Astronomy, University of California, Riverside, USA
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, USA
- Department of Physics and Astronomy, University of Pittsburgh, USA
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3
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Chang-Gonzalez AC, Mallis RJ, Lang MJ, Reinherz EL, Hwang W. Asymmetric framework motion of TCRαβ controls load-dependent peptide discrimination. eLife 2024; 13:e91881. [PMID: 38167271 PMCID: PMC10869138 DOI: 10.7554/elife.91881] [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: 08/14/2023] [Accepted: 12/21/2023] [Indexed: 01/05/2024] Open
Abstract
Mechanical force is critical for the interaction between an αβ T cell receptor (TCR) and a peptide-bound major histocompatibility complex (pMHC) molecule to initiate productive T-cell activation. However, the underlying mechanism remains unclear. We use all-atom molecular dynamics simulations to examine the A6 TCR bound to HLA-A*02:01 presenting agonist or antagonist peptides under different extensions to simulate the effects of applied load on the complex, elucidating their divergent biological responses. We found that TCR α and β chains move asymmetrically, which impacts the interface with pMHC, in particular the peptide-sensing CDR3 loops. For the wild-type agonist, the complex stabilizes in a load-dependent manner while antagonists destabilize it. Simulations of the Cβ FG-loop deletion, which reduces the catch bond response, and simulations with in silico mutant peptides further support the observed behaviors. The present results highlight the combined role of interdomain motion, fluctuating forces, and interfacial contacts in determining the mechanical response and fine peptide discrimination by a TCR, thereby resolving the conundrum of nearly identical crystal structures of TCRαβ-pMHC agonist and antagonist complexes.
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Affiliation(s)
- Ana C Chang-Gonzalez
- Department of Biomedical Engineering, Texas A&M UniversityCollege StationUnited States
| | - Robert J Mallis
- Department of Dermatology, Harvard Medical SchoolBostonUnited States
- Laboratory of Immunobiology, Dana-Farber Cancer InstituteBostonUnited States
- Department of Medicine, Oncology, Dana-Farber Cancer InstituteBostonUnited States
| | - Matthew J Lang
- Department of Chemistry and Biomolecular Engineering, Vanderbilt UniversityNashvilleUnited States
- Department of Molecular Physiology and Biophysics, Vanderbilt UniversityNashvilleUnited States
| | - Ellis L Reinherz
- Laboratory of Immunobiology, Dana-Farber Cancer InstituteBostonUnited States
- Department of Medicine, Oncology, Dana-Farber Cancer InstituteBostonUnited States
- Department of Medicine, Harvard Medical SchoolBostonUnited States
| | - Wonmuk Hwang
- Department of Biomedical Engineering, Texas A&M UniversityCollege StationUnited States
- Department of Materials Science & Engineering, Texas A&M UniversityCollege StationUnited States
- Department of Physics & Astronomy, Texas A&M UniversityCollege StationUnited States
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4
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Chang-Gonzalez AC, Mallis RJ, Lang MJ, Reinherz EL, Hwang W. Asymmetric framework motion of TCR αβ controls load-dependent peptide discrimination. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.10.557064. [PMID: 37745603 PMCID: PMC10515854 DOI: 10.1101/2023.09.10.557064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Mechanical force is critical for the interaction between an αβT cell receptor (TCR) and a peptide-bound major histocompatibility complex (pMHC) molecule to initiate productive T-cell activation. However, the underlying mechanism remains unclear. We use all-atom molecular dynamics simulations to examine the A6 TCR bound to HLA-A*02:01 presenting agonist or antagonist peptides under different extensions to simulate the effects of applied load on the complex, elucidating their divergent biological responses. We found that TCR α and β chains move asymmetrically, which impacts the interface with pMHC, in particular the peptide-sensing CDR3 loops. For the wild-type agonist, the complex stabilizes in a load-dependent manner while antagonists destabilize it. Simulations of the Cβ FG-loop deletion, which reduces the catch bond response, and simulations with in silico mutant peptides further support the observed behaviors. The present results highlight the combined role of interdomain motion, fluctuating forces, and interfacial contacts in determining the mechanical response and fine peptide discrimination by a TCR, thereby resolving the conundrum of nearly identical crystal structures of TCRαβ-pMHC agonist and antagonist complexes.
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Affiliation(s)
- Ana C. Chang-Gonzalez
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, USA
| | - Robert J. Mallis
- Dept. Dermatology, Harvard Medical School, Boston, MA, USA
- Lab. of Immunobio., Dana-Farber Cancer Inst., Boston, MA, USA
- Dept. Med. Oncology, Dana-Farber Cancer Inst., Boston, MA, USA
| | - Matthew J. Lang
- Dept. Chem. and Biomolec. Eng., Vanderbilt Univ., Nashville, TN, USA
- Dept. Molec. Physiology and Biophys., Vanderbilt Univ., Nashville, TN, USA
| | - Ellis L. Reinherz
- Dept. Medicine, Harvard Medical School, Boston, MA, USA
- Lab. of Immunobio., Dana-Farber Cancer Inst., Boston, MA, USA
- Dept. Med. Oncology, Dana-Farber Cancer Inst., Boston, MA, USA
| | - Wonmuk Hwang
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, USA
- Department of Materials Science & Engineering, Texas A&M University, College Station, TX, USA
- Dept. Phys. & Astronomy, Texas A&M Univ., College Station, TX, USA
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5
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Isaeva OI, Ketelaars SLC, Kvistborg P. In Silico Analysis Predicts a Limited Impact of SARS-CoV-2 Variants on CD8 T Cell Recognition. Front Immunol 2022; 13:891524. [PMID: 35572563 PMCID: PMC9094405 DOI: 10.3389/fimmu.2022.891524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
Since the start of the COVID-19 pandemic, mutations have led to the emergence of new SARS-CoV-2 variants, and some of these have become prominent or dominant variants of concern. This natural course of development can have an impact on how protective the previously naturally or vaccine induced immunity is. Therefore, it is crucial to understand whether and how variant specific mutations influence host immunity. To address this, we have investigated how mutations in the recent SARS-CoV-2 variants of interest and concern influence epitope sequence similarity, predicted binding affinity to HLA, and immunogenicity of previously reported SARS-CoV-2 CD8 T cell epitopes. Our data suggests that the vast majority of SARS-CoV-2 CD8 T cell recognized epitopes are not altered by variant specific mutations. Interestingly, for the CD8 T cell epitopes that are altered due to variant specific mutations, our analyses show there is a high degree of sequence similarity between mutated and reference SARS-CoV-2 CD8 T cell epitopes. However, mutated epitopes, primarily derived from the spike protein, in SARS-CoV-2 variants Delta, AY.4.2 and Mu display reduced predicted binding affinity to their restriction element. These findings indicate that the recent SARS-CoV-2 variants of interest and concern have limited ability to escape memory CD8 T cell responses raised by vaccination or prior infection with SARS-CoV-2 early in the pandemic. The overall low impact of the mutations on CD8 T cell cross-recognition is in accordance with the notion that mutations in SARS-CoV-2 are primarily the result of receptor binding affinity and antibody selection pressures exerted on the spike protein, unrelated to T cell immunity.
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Affiliation(s)
- Olga I Isaeva
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands.,Department of Tumor Biology and Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands.,Oncode Institute, Utrecht, Netherlands
| | - Steven L C Ketelaars
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Pia Kvistborg
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands
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6
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Perez MAS, Cuendet MA, Röhrig UF, Michielin O, Zoete V. Structural Prediction of Peptide-MHC Binding Modes. Methods Mol Biol 2022; 2405:245-282. [PMID: 35298818 DOI: 10.1007/978-1-0716-1855-4_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The immune system is constantly protecting its host from the invasion of pathogens and the development of cancer cells. The specific CD8+ T-cell immune response against virus-infected cells and tumor cells is based on the T-cell receptor recognition of antigenic peptides bound to class I major histocompatibility complexes (MHC) at the surface of antigen presenting cells. Consequently, the peptide binding specificities of the highly polymorphic MHC have important implications for the design of vaccines, for the treatment of autoimmune diseases, and for personalized cancer immunotherapy. Evidence-based machine-learning approaches have been successfully used for the prediction of peptide binders and are currently being developed for the prediction of peptide immunogenicity. However, understanding and modeling the structural details of peptide/MHC binding is crucial for a better understanding of the molecular mechanisms triggering the immunological processes, estimating peptide/MHC affinity using universal physics-based approaches, and driving the design of novel peptide ligands. Unfortunately, due to the large diversity of MHC allotypes and possible peptides, the growing number of 3D structures of peptide/MHC (pMHC) complexes in the Protein Data Bank only covers a small fraction of the possibilities. Consequently, there is a growing need for rapid and efficient approaches to predict 3D structures of pMHC complexes. Here, we review the key characteristics of the 3D structure of pMHC complexes before listing databases and other sources of information on pMHC structures and MHC specificities. Finally, we discuss some of the most prominent pMHC docking software.
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Affiliation(s)
- Marta A S Perez
- Computer-aided Molecular Engineering Group, Department of Oncology UNIL-CHUV, Lausanne University, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, Lausanne, Switzerland
- Molecular Modelling Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Michel A Cuendet
- Molecular Modelling Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Oncology Department, Centre Hospitalier Universitaire Vaudois (CHUV), Precision Oncology Center, Lausanne, Switzerland
| | - Ute F Röhrig
- Molecular Modelling Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Olivier Michielin
- Molecular Modelling Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- Oncology Department, Centre Hospitalier Universitaire Vaudois (CHUV), Precision Oncology Center, Lausanne, Switzerland.
| | - Vincent Zoete
- Computer-aided Molecular Engineering Group, Department of Oncology UNIL-CHUV, Lausanne University, Lausanne, Switzerland.
- Ludwig Institute for Cancer Research, Lausanne, Switzerland.
- Molecular Modelling Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
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7
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Vakilian M. A review on the effect of prolyl isomerization on immune response aberration and hypersensitivity reactions: A unifying hypothesis. Clin Immunol 2021; 234:108896. [PMID: 34848356 DOI: 10.1016/j.clim.2021.108896] [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: 08/27/2021] [Revised: 11/19/2021] [Accepted: 11/21/2021] [Indexed: 12/01/2022]
Abstract
Little is known about the causes and mechanisms of ectopic immune responses, including different types of hypersensitivity, superantigens, and cytokine storms. Two of the most questionable phenomena observed in immunology are why the intensity and extent of immune responses to different antigens are different, and why some self-antigens are attacked as foreign. The secondary structure of the peptides involved in the immune system, such as the epitope-paratope interfaces plays a pivotal role in the resulting immune responses. Prolyl cis/trans isomerization plays a fundamental role in the form of the secondary structure and the folding of proteins. This review covers some of the emerging evidence indicating the impact of prolyl isomerization on protein conformation, aberration of immune responses, and the development of hypersensitivity reactions.
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Affiliation(s)
- Mehrdad Vakilian
- Department of Cell Biology, Genetics and Physiology, University of Malaga (UMA), The Institute of Biomedical Research in Malaga (IBIMA), Málaga, Spain.
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8
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Abstract
T cell activation is a critical event in the adaptive immune response, indispensable for cell-mediated and humoral immunity as well as for immune regulation. Recent years have witnessed an emerging trend emphasizing the essential role that physical force and mechanical properties play at the T cell interface. In this review, we integrate current knowledge of T cell antigen recognition and the different models of T cell activation from the perspective of mechanobiology, focusing on the interaction between the T cell receptor (TCR) and the peptide-major histocompatibility complex (pMHC) antigen. We address the shortcomings of TCR affinity alone in explaining T cell functional outcomes and the rising status of force-regulated TCR bond lifetimes, most notably the TCR catch bond. Ultimately, T cell activation and the ensuing physiological responses result from mechanical interaction between TCRs and the pMHC. Expected final online publication date for the Annual Review of Cell and Developmental Biology, Volume 37 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Baoyu Liu
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA; , ,
| | - Elizabeth M Kolawole
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA; , ,
| | - Brian D Evavold
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA; , ,
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9
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Lehmann AA, Kirchenbaum GA, Zhang T, Reche PA, Lehmann PV. Deconvoluting the T Cell Response to SARS-CoV-2: Specificity Versus Chance and Cognate Cross-Reactivity. Front Immunol 2021; 12:635942. [PMID: 34127926 PMCID: PMC8196231 DOI: 10.3389/fimmu.2021.635942] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 03/11/2021] [Indexed: 01/08/2023] Open
Abstract
SARS-CoV-2 infection takes a mild or clinically inapparent course in the majority of humans who contract this virus. After such individuals have cleared the virus, only the detection of SARS-CoV-2-specific immunological memory can reveal the exposure, and hopefully the establishment of immune protection. With most viral infections, the presence of specific serum antibodies has provided a reliable biomarker for the exposure to the virus of interest. SARS-CoV-2 infection, however, does not reliably induce a durable antibody response, especially in sub-clinically infected individuals. Consequently, it is plausible for a recently infected individual to yield a false negative result within only a few months after exposure. Immunodiagnostic attention has therefore shifted to studies of specific T cell memory to SARS-CoV-2. Most reports published so far agree that a T cell response is engaged during SARS-CoV-2 infection, but they also state that in 20-81% of SARS-CoV-2-unexposed individuals, T cells respond to SARS-CoV-2 antigens (mega peptide pools), allegedly due to T cell cross-reactivity with Common Cold coronaviruses (CCC), or other antigens. Here we show that, by introducing irrelevant mega peptide pools as negative controls to account for chance cross-reactivity, and by establishing the antigen dose-response characteristic of the T cells, one can clearly discern between cognate T cell memory induced by SARS-CoV-2 infection vs. cross-reactive T cell responses in individuals who have not been infected with SARS-CoV-2.
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Affiliation(s)
- Alexander A Lehmann
- Research and Development, Cellular Technology Ltd., Shaker Heights, OH, United States
| | - Greg A Kirchenbaum
- Research and Development, Cellular Technology Ltd., Shaker Heights, OH, United States
| | - Ting Zhang
- Research and Development, Cellular Technology Ltd., Shaker Heights, OH, United States
| | - Pedro A Reche
- Laboratorio de Inmunomedicina & Inmunoinformatica, Departamento de Immunologia & O2, Facultad de Medicina, Universidad Complutense de Madrid, Madrid, Spain
| | - Paul V Lehmann
- Research and Development, Cellular Technology Ltd., Shaker Heights, OH, United States
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10
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Meng Q, Wu Y, Sui X, Meng J, Wang T, Lin Y, Wang Z, Zhou X, Qi Y, Du J, Gao Y. POTN: A Human Leukocyte Antigen-A2 Immunogenic Peptides Screening Model and Its Applications in Tumor Antigens Prediction. Front Immunol 2020; 11:02193. [PMID: 33133063 PMCID: PMC7579403 DOI: 10.3389/fimmu.2020.02193] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 08/11/2020] [Indexed: 12/23/2022] Open
Abstract
Whole genome/exome sequencing data for tumors are now abundant, and many tumor antigens, especially mutant antigens (neoantigens), have been identified for cancer immunotherapy. However, only a small fraction of the peptides from these antigens induce cytotoxic T cell responses. Therefore, efficient methods to identify these antigenic peptides are crucial. The current models of major histocompatibility complex (MHC) binding and antigenic prediction are still inaccurate. In this study, 360 9-mer peptides with verified immunological activity were selected to construct a prediction of tumor neoantigen (POTN) model, an immunogenic prediction model specifically for the human leukocyte antigen-A2 allele. Based on the physicochemical properties of amino acids, such as the residue propensity, hydrophobicity, and organic solvent/water, we found that the predictive capability of POTN is superior to that of the prediction programs SYPEITHI, IEDB, and NetMHCpan 4.0. We used POTN to screen peptides for the cancer-testis antigen located on the X chromosome, and we identified several peptides that may trigger immunogenicity. We synthesized and measured the binding affinity and immunogenicity of these peptides and found that the accuracy of POTN is higher than that of NetMHCpan 4.0. Identifying the properties related to the T cell response or immunogenicity paves the way to understanding the MHC/peptide/T cell receptor complex. In conclusion, POTN is an efficient prediction model for screening high-affinity immunogenic peptides from tumor antigens, and thus provides useful information for developing cancer immunotherapy.
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Affiliation(s)
- Qingqing Meng
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Yahong Wu
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Xinghua Sui
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Jingjie Meng
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Tingting Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Yan Lin
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Zhiwei Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Xiuman Zhou
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Yuanming Qi
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Jiangfeng Du
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Yanfeng Gao
- School of Life Sciences, Zhengzhou University, Zhengzhou, China.,School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, China
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11
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Yamazaki R, Furukawa A, Hirayasu K, Yumoto K, Fukuhara H, Arase H, Maenaka K. Molecular mechanism of the recognition of bacterially cleaved immunoglobulin by the immune regulatory receptor LILRA2. J Biol Chem 2020; 295:9531-9541. [PMID: 32424043 DOI: 10.1074/jbc.ra120.013354] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/14/2020] [Indexed: 12/14/2022] Open
Abstract
Human leukocyte immunoglobulin-like receptors (LILRs) typically regulate immune activation by binding to the human leukocyte antigen class I molecules. LILRA2, a member of the LILR family, was recently reported to bind to other unique ligands, the bacterially degraded Igs (N-truncated Igs), for the activation of immune cells. Therefore, LILRA2 is currently attracting significant attention as a novel innate immune receptor. However, the detailed recognition mechanisms required for this interaction remain unclear. In this study, using several biophysical techniques, we uncovered the molecular mechanism of N-truncated Ig recognition by LILRA2. Surface plasmon resonance analysis disclosed that LILRA2 specifically binds to N-truncated Ig with weak affinity (Kd = 4.8 μm) and fast kinetics. However, immobilized LILRA2 exhibited a significantly enhanced interaction with N-truncated Ig due to avidity effects. This suggests that cell surface-bound LILRA2 rapidly monitors and identifies bi- or multivalent abnormal N-truncated Igs through specific cross-linking to induce immune activation. Van't Hoff analysis revealed that this interaction is enthalpy-driven, with a small entropy loss, and results from differential scanning calorimetry indicated the instability of the putative LILRA2-binding site, the Fab region of the N-truncated Ig. Atomic force microscopy revealed that N truncation does not cause significant structural changes in Ig. Furthermore, mutagenesis analysis identified the hydrophobic region of LILRA2 domain 2 as the N-truncated Ig-binding site, representing a novel ligand-binding site for the LILR family. These results provide detailed insights into the molecular regulation of LILR-mediated immune responses targeting ligands that have been modified by bacteria.
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Affiliation(s)
- Rika Yamazaki
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Atsushi Furukawa
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Kouyuki Hirayasu
- WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan.,Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan.,Advanced Preventive Medical Sciences Research Center, Kanazawa University, Kanazawa, Japan
| | - Kohei Yumoto
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Hideo Fukuhara
- Center for Research and Education on Drug Discovery, Hokkaido University, Sapporo, Japan
| | - Hisashi Arase
- WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan.,Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Katsumi Maenaka
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan .,Center for Research and Education on Drug Discovery, Hokkaido University, Sapporo, Japan.,Global Station for Biosurfaces and Drug Discovery, Hokkaido University, Sapporo, Japan.,Center for Life Innovation, Hokkaido University, Sapporo, Japan
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12
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Toptygina AP. Heterologous immune responses in health and disease. RUSSIAN JOURNAL OF INFECTION AND IMMUNITY 2020. [DOI: 10.15789/2220-7619-hir-1292] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Immunological memory and tolerance represent major achievements and advantages of adaptive immunity. Organisms bearing adaptive immunity display prominent competitive advantages in the fight against infections. Memory immune cells are preserved for decades and are able to repel a second attack of an infectious agent. However, studies performed in the XXI century have shown that even unrelated pathogens may be quickly and effectively destroyed by memory cells. This type of response is called heterologous so that heterologous immune response is mainly typical to viral infections and other intracellular infections, where T-cells play a lead role in protection. This review will discuss various mechanisms involved in implementing T-cell cross-reactivity, describe molecular prerequisites for heterologous T-cell responses. Experimental evidence of memory T-cell potential to heterologous immune response in mouse models and in human infections are also discussed. Heterologous immune response is an important immune arm in adults and the elderly when the yield of naive cells to the periphery declines due to thymus involution. Along with obvious advantages, heterologous immune response leads to imbalanced memory T-cell repertoire, replacement of immunodominant epitopes with minor ones allowing viruses to evade immune response that results in virus persistence, or, conversely, fulminant infection course. Another threat of heterologous immune response due to switch in dominant repertoire of recognizable epitopes is presented by random self-epitope recognition, which can lead to development of autoimmune pathology. Heterologous immunity can also disrupt drug-induced tolerance in organ and tissue transplants and lead to graft rejection. Heterologous immune response should be taken into consideration while developing and using new vaccines, especially in adults and the elderly.
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13
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Debebe BJ, Boelen L, Lee JC, Thio CL, Astemborski J, Kirk G, Khakoo SI, Donfield SM, Goedert JJ, Asquith B. Identifying the immune interactions underlying HLA class I disease associations. eLife 2020; 9:54558. [PMID: 32238263 PMCID: PMC7253178 DOI: 10.7554/elife.54558] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 03/06/2020] [Indexed: 12/11/2022] Open
Abstract
Variation in the risk and severity of many autoimmune diseases, malignancies and infections is strongly associated with polymorphisms at the HLA class I loci. These genetic associations provide a powerful opportunity for understanding the etiology of human disease. HLA class I associations are often interpreted in the light of 'protective' or 'detrimental' CD8+ T cell responses which are restricted by the host HLA class I allotype. However, given the diverse receptors which are bound by HLA class I molecules, alternative interpretations are possible. As well as binding T cell receptors on CD8+ T cells, HLA class I molecules are important ligands for inhibitory and activating killer immunoglobulin-like receptors (KIRs) which are found on natural killer cells and some T cells; for the CD94:NKG2 family of receptors also expressed mainly by NK cells and for leukocyte immunoglobulin-like receptors (LILRs) on myeloid cells. The aim of this study is to develop an immunogenetic approach for identifying and quantifying the relative contribution of different receptor-ligand interactions to a given HLA class I disease association and then to use this approach to investigate the immune interactions underlying HLA class I disease associations in three viral infections: Human T cell Leukemia Virus type 1, Human Immunodeficiency Virus type 1 and Hepatitis C Virus as well as in the inflammatory condition Crohn's disease.
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Affiliation(s)
- Bisrat J Debebe
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Lies Boelen
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - James C Lee
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
| | -
- Johns Hopkins University, Baltimore, United States.,Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Chloe L Thio
- Johns Hopkins University, Baltimore, United States
| | | | - Gregory Kirk
- Johns Hopkins University, Baltimore, United States
| | - Salim I Khakoo
- Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | | | - James J Goedert
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, United States
| | - Becca Asquith
- Department of Infectious Disease, Imperial College London, London, United Kingdom
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14
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Abstract
The immune response is orchestrated by a variety of immune cells. The function of each cell is determined by the collective signals from various immunoreceptors, whose expression and activity depend on the developmental stages of the cell and its environmental context. Recent studies have highlighted the presence of mechanical force on several immunoreceptor-ligand pairs and the important role of force in regulating their interaction and function. In this Perspective, we use the T cell antigen receptor as an example with which to review the current understanding of the mechanosensing properties of immunoreceptors. We discuss the types of forces that immunoreceptors may encounter and the effects of force on ligand bonding, conformational change and the triggering of immunoreceptors, as well as the effects of force on the downstream signal transduction, cell-fate decisions and effector function of immune cells.
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15
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Karch R, Stocsits C, Ilieva N, Schreiner W. Intramolecular Domain Movements of Free and Bound pMHC and TCR Proteins: A Molecular Dynamics Simulation Study. Cells 2019; 8:cells8070720. [PMID: 31337065 PMCID: PMC6678086 DOI: 10.3390/cells8070720] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/02/2019] [Accepted: 07/12/2019] [Indexed: 12/11/2022] Open
Abstract
The interaction of antigenic peptides (p) and major histocompatibility complexes (pMHC) with T-cell receptors (TCR) is one of the most important steps during the immune response. Here we present a molecular dynamics simulation study of bound and unbound TCR and pMHC proteins of the LC13-HLA-B*44:05-pEEYLQAFTY complex to monitor differences in relative orientations and movements of domains between bound and unbound states of TCR-pMHC. We generated local coordinate systems for MHC α1- and MHC α2-helices and the variable T-cell receptor regions TCR Vα and TCR Vβ and monitored changes in the distances and mutual orientations of these domains. In comparison to unbound states, we found decreased inter-domain movements in the simulations of bound states. Moreover, increased conformational flexibility was observed for the MHC α2-helix, the peptide, and for the complementary determining regions of the TCR in TCR-unbound states as compared to TCR-bound states.
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Affiliation(s)
- Rudolf Karch
- Section of Biosimulation and Bioinformatics, Center for Medical Statistics, Informatics and Intelligent Systems (CeMSIIS), Medical University of Vienna, Spitalgasse 23, A-1090 Vienna, Austria
| | - Claudia Stocsits
- Section of Biosimulation and Bioinformatics, Center for Medical Statistics, Informatics and Intelligent Systems (CeMSIIS), Medical University of Vienna, Spitalgasse 23, A-1090 Vienna, Austria
| | - Nevena Ilieva
- Institute of Information and Communication Technologies (IICT), Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Block 25A, 1113 Sofia, Bulgaria
- CERN-TH, Esplanade des Particules 1, 1211 Geneva, Switzerland
| | - Wolfgang Schreiner
- Section of Biosimulation and Bioinformatics, Center for Medical Statistics, Informatics and Intelligent Systems (CeMSIIS), Medical University of Vienna, Spitalgasse 23, A-1090 Vienna, Austria.
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16
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Ogishi M, Yotsuyanagi H. Quantitative Prediction of the Landscape of T Cell Epitope Immunogenicity in Sequence Space. Front Immunol 2019; 10:827. [PMID: 31057550 PMCID: PMC6477061 DOI: 10.3389/fimmu.2019.00827] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 03/28/2019] [Indexed: 01/02/2023] Open
Abstract
Immunodominant T cell epitopes preferentially targeted in multiple individuals are the critical element of successful vaccines and targeted immunotherapies. However, the underlying principles of this “convergence” of adaptive immunity among different individuals remain poorly understood. To quantitatively describe epitope immunogenicity, here we propose a supervised machine learning framework generating probabilistic estimates of immunogenicity, termed “immunogenicity scores,” based on the numerical features computed through sequence-based simulation approximating the molecular scanning process of peptides presented onto major histocompatibility complex (MHC) by the human T cell receptor (TCR) repertoire. Notably, overlapping sets of intermolecular interaction parameters were commonly utilized in MHC-I and MHC-II prediction. Moreover, a similar simulation of individual TCR-peptide interaction using the same set of interaction parameters yielded correlates of TCR affinity. Pathogen-derived epitopes and tumor-associated epitopes with positive T cell reactivity generally had higher immunogenicity scores than non-immunogenic counterparts, whereas thymically expressed self-epitopes were assigned relatively low scores regardless of their immunogenicity annotation. Immunogenicity score dynamics among single amino acid mutants delineated the landscape of position- and residue-specific mutational impacts. Simulation of position-specific immunogenicity score dynamics detected residues with high escape potential in multiple epitopes, consistent with known escape mutations in the literature. This study indicates that targeting of epitopes by human adaptive immunity is to some extent directed by defined thermodynamic principles. The proposed framework also has a practical implication in that it may enable to more efficiently prioritize epitope candidates highly prone to T cell recognition in multiple individuals, warranting prospective validation across different cohorts.
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Affiliation(s)
- Masato Ogishi
- Division of Infectious Diseases and Applied Immunology, The Institute of Medical Sciences Research Hospital, The University of Tokyo, Tokyo, Japan
| | - Hiroshi Yotsuyanagi
- Division of Infectious Diseases and Applied Immunology, The Institute of Medical Sciences Research Hospital, The University of Tokyo, Tokyo, Japan
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17
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Warren JA, Clutton G, Goonetilleke N. Harnessing CD8 + T Cells Under HIV Antiretroviral Therapy. Front Immunol 2019; 10:291. [PMID: 30863403 PMCID: PMC6400228 DOI: 10.3389/fimmu.2019.00291] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 02/04/2019] [Indexed: 12/16/2022] Open
Abstract
Antiretroviral therapy (ART) has transformed HIV from a fatal disease to a chronic condition. In recent years there has been considerable interest in strategies to enable HIV-infected individuals to cease ART without viral rebound, either by purging all cells infected harboring replication-competent virus (HIV eradication), or by boosting immune responses to allow durable suppression of virus without rebound (HIV remission). Both of these approaches may need to harness HIV-specific CD8+ T cells to eliminate infected cells and/or prevent viral spread. In untreated infection, both HIV-specific and total CD8+ T cells are dysfunctional. Here, we review our current understanding of both global and HIV-specific CD8+ T cell immunity in HIV-infected individuals with durably suppressed viral load under ART, and its implications for HIV cure, eradication or remission. Overall, the literature indicates significant normalization of global T cell parameters, including CD4/8 ratio, activation status, and telomere length. Global characteristics of CD8+ T cells from HIV+ART+ individuals align more closely with those of HIV-seronegative individuals than of viremic HIV-infected individuals. However, markers of senescence remain elevated, leading to the hypothesis that immune aging is accelerated in HIV-infected individuals on ART. This phenomenon could have implications for attempts to prime de novo, or boost existing HIV-specific CD8+ T cell responses. A major challenge for both HIV cure and remission strategies is to elicit HIV-specific CD8+ T cell responses superior to that elicited by natural infection in terms of response kinetics, magnitude, breadth, viral suppressive capacity, and tissue localization. Addressing these issues will be critical to the success of HIV cure and remission attempts.
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Affiliation(s)
- Joanna A Warren
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, United States
| | - Genevieve Clutton
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, United States
| | - Nilu Goonetilleke
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, United States.,UNC HIV Cure Center, University of North Carolina, Chapel Hill, NC, United States
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18
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Jurtz VI, Olsen LR. Computational Methods for Identification of T Cell Neoepitopes in Tumors. Methods Mol Biol 2019; 1878:157-172. [PMID: 30378075 DOI: 10.1007/978-1-4939-8868-6_9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Cancer immunotherapy has experienced several major breakthroughs in the past decade. Most recently, technical advances in next-generation sequencing methods have enabled discovery of tumor-specific mutations leading to protective T cell neoepitopes. Many of the successes are enabled by computational methods, which facilitate processing of raw data, mapping of mutations, and prediction of neoepitopes. In this book chapter, we provide an overview of the computational tasks related to the identification of neoepitopes, propose specific tools and best practices, and discuss strengths, weaknesses, and future challenges.
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Affiliation(s)
- Vanessa Isabell Jurtz
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | - Lars Rønn Olsen
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark.
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19
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Moyo N, Vogel AB, Buus S, Erbar S, Wee EG, Sahin U, Hanke T. Efficient Induction of T Cells against Conserved HIV-1 Regions by Mosaic Vaccines Delivered as Self-Amplifying mRNA. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2018; 12:32-46. [PMID: 30547051 PMCID: PMC6258890 DOI: 10.1016/j.omtm.2018.10.010] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 10/21/2018] [Indexed: 12/20/2022]
Abstract
Focusing T cell responses on the most vulnerable parts of HIV-1, the functionally conserved regions of HIV-1 proteins, is likely a key prerequisite for vaccine success. For a T cell vaccine to efficiently control HIV-1 replication, the vaccine-elicited individual CD8+ T cells and as a population have to display a number of critical traits. If any one of these traits is suboptimal, the vaccine is likely to fail. Fine-tuning of individual protective characteristics of T cells will require iterative stepwise improvements in clinical trials. Although the second-generation tHIVconsvX immunogens direct CD8+ T cells to predominantly protective and conserved epitopes, in the present work, we have used formulated self-amplifying mRNA (saRNA) to deliver tHIVconsvX to the immune system. We demonstrated in BALB/c and outbred mice that regimens employing saRNA vaccines induced broadly specific, plurifunctional CD8+ and CD4+ T cells, which displayed structured memory subpopulations and were maintained at relatively high frequencies over at least 22 weeks post-administration. This is one of the first thorough analyses of mRNA vaccine-elicited T cell responses. The combination of tHIVconsvX immunogens and the highly versatile and easily manufacturable saRNA platform may provide a long-awaited opportunity to define and optimize induction of truly protective CD8+ T cell parameters in human volunteers.
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Affiliation(s)
- Nathifa Moyo
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Annette B Vogel
- Biopharmaceutical New Technologies (BioNTech) Corporation, Mainz 55131, Germany
| | - Søren Buus
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen 2200, Denmark
| | - Stephanie Erbar
- Biopharmaceutical New Technologies (BioNTech) Corporation, Mainz 55131, Germany
| | - Edmund G Wee
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Ugur Sahin
- Biopharmaceutical New Technologies (BioNTech) Corporation, Mainz 55131, Germany
| | - Tomáš Hanke
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK.,International Research Center for Medical Sciences, Kumamoto University, Kumamoto 860-0811, Japan
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20
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Fodor J, Riley BT, Borg NA, Buckle AM. Previously Hidden Dynamics at the TCR-Peptide-MHC Interface Revealed. THE JOURNAL OF IMMUNOLOGY 2018; 200:4134-4145. [PMID: 29728507 DOI: 10.4049/jimmunol.1800315] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 04/10/2018] [Indexed: 12/28/2022]
Abstract
A structural characterization of the interaction between αβ TCRs and cognate peptide-MHC (pMHC) is central to understanding adaptive T cell-mediated immunity. X-ray crystallography, although the source of much structural data, traditionally provides only a static snapshot of the protein. Given the emerging evidence for the important role of conformational dynamics in protein function, we interrogated 309 crystallographic structures of pMHC complexes using ensemble refinement, a technique that can extract dynamic information from the x-ray data. Focusing on a subset of human pMHC class I systems, we found that in many cases, ensemble methods were able to uncover previously hidden evidence of significant conformational plasticity, thereby revealing additional information that can build upon and significantly enhance functional interpretations that are based on a single static structure. Notable examples include the interpretation of differences in the disease association of HLA subtypes, the relationship between peptide prominence and TCR recognition, the role of conformational flexibility in vaccine design, and the discrimination between induced fit and conformational selection models of TCR binding. We show that the currently widespread practice of analyzing pMHC interactions via the study of a single crystallographic structure does not make use of pertinent and easily accessible information from x-ray data concerning alternative protein conformations. This new analysis therefore not only highlights the capacity for ensemble methods to significantly enrich the interpretation of decades of structural data but also provides previously missing information concerning the dynamics of existing characterized TCR-pMHC interactions.
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Affiliation(s)
- James Fodor
- Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia; and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Blake T Riley
- Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia; and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Natalie A Borg
- Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia; and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Ashley M Buckle
- Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia; and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
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21
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Cole DK, Fuller A, Dolton G, Zervoudi E, Legut M, Miles K, Blanchfield L, Madura F, Holland CJ, Bulek AM, Bridgeman JS, Miles JJ, Schauenburg AJA, Beck K, Evavold BD, Rizkallah PJ, Sewell AK. Dual Molecular Mechanisms Govern Escape at Immunodominant HLA A2-Restricted HIV Epitope. Front Immunol 2017; 8:1503. [PMID: 29209312 PMCID: PMC5701626 DOI: 10.3389/fimmu.2017.01503] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 10/25/2017] [Indexed: 12/05/2022] Open
Abstract
Serial accumulation of mutations to fixation in the SLYNTVATL (SL9) immunodominant, HIV p17 Gag-derived, HLA A2-restricted cytotoxic T lymphocyte epitope produce the SLFNTIAVL triple mutant “ultimate” escape variant. These mutations in solvent-exposed residues are believed to interfere with TCR recognition, although confirmation has awaited structural verification. Here, we solved a TCR co-complex structure with SL9 and the triple escape mutant to determine the mechanism of immune escape in this eminent system. We show that, in contrast to prevailing hypotheses, the main TCR contact residue is 4N and the dominant mechanism of escape is not via lack of TCR engagement. Instead, mutation of solvent-exposed residues in the peptide destabilise the peptide–HLA and reduce peptide density at the cell surface. These results highlight the extraordinary lengths that HIV employs to evade detection by high-affinity TCRs with a broad peptide-binding footprint and necessitate re-evaluation of this exemplar model of HIV TCR escape.
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Affiliation(s)
- David K Cole
- Cardiff University School of Medicine, University Hospital, Heath Park, Cardiff, United Kingdom
| | - Anna Fuller
- Cardiff University School of Medicine, University Hospital, Heath Park, Cardiff, United Kingdom
| | - Garry Dolton
- Cardiff University School of Medicine, University Hospital, Heath Park, Cardiff, United Kingdom
| | - Efthalia Zervoudi
- Cardiff University School of Medicine, University Hospital, Heath Park, Cardiff, United Kingdom
| | - Mateusz Legut
- Cardiff University School of Medicine, University Hospital, Heath Park, Cardiff, United Kingdom
| | - Kim Miles
- Cardiff University School of Medicine, University Hospital, Heath Park, Cardiff, United Kingdom
| | - Lori Blanchfield
- Department of Microbiology and Immunology, Emory University, Atlanta, GA, United States
| | - Florian Madura
- Cardiff University School of Medicine, University Hospital, Heath Park, Cardiff, United Kingdom
| | - Christopher J Holland
- Cardiff University School of Medicine, University Hospital, Heath Park, Cardiff, United Kingdom
| | - Anna M Bulek
- Cardiff University School of Medicine, University Hospital, Heath Park, Cardiff, United Kingdom
| | - John S Bridgeman
- Cardiff University School of Medicine, University Hospital, Heath Park, Cardiff, United Kingdom
| | - John J Miles
- Cardiff University School of Medicine, University Hospital, Heath Park, Cardiff, United Kingdom.,James Cook University, Cairns, QLD, Australia
| | - Andrea J A Schauenburg
- Cardiff University School of Medicine, University Hospital, Heath Park, Cardiff, United Kingdom
| | - Konrad Beck
- Cardiff University School of Dentistry, University Hospital, Heath Park, Cardiff, United Kingdom
| | - Brian D Evavold
- Department of Microbiology and Immunology, Emory University, Atlanta, GA, United States
| | - Pierre J Rizkallah
- Cardiff University School of Medicine, University Hospital, Heath Park, Cardiff, United Kingdom
| | - Andrew K Sewell
- Cardiff University School of Medicine, University Hospital, Heath Park, Cardiff, United Kingdom
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22
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Ayres CM, Corcelli SA, Baker BM. Peptide and Peptide-Dependent Motions in MHC Proteins: Immunological Implications and Biophysical Underpinnings. Front Immunol 2017; 8:935. [PMID: 28824655 PMCID: PMC5545744 DOI: 10.3389/fimmu.2017.00935] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 07/21/2017] [Indexed: 01/28/2023] Open
Abstract
Structural biology of peptides presented by class I and class II MHC proteins has transformed immunology, impacting our understanding of fundamental immune mechanisms and allowing researchers to rationalize immunogenicity and design novel vaccines. However, proteins are not static structures as often inferred from crystallographic structures. Their components move and breathe individually and collectively over a range of timescales. Peptides bound within MHC peptide-binding grooves are no exception and their motions have been shown to impact recognition by T cell and other receptors in ways that influence function. Furthermore, peptides tune the motions of MHC proteins themselves, which impacts recognition of peptide/MHC complexes by other proteins. Here, we review the motional properties of peptides in MHC binding grooves and discuss how peptide properties can influence MHC motions. We briefly review theoretical concepts about protein motion and highlight key data that illustrate immunological consequences. We focus primarily on class I systems due to greater availability of data, but segue into class II systems as the concepts and consequences overlap. We suggest that characterization of the dynamic “energy landscapes” of peptide/MHC complexes and the resulting functional consequences is one of the next frontiers in structural immunology.
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Affiliation(s)
- Cory M Ayres
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States.,Harper Cancer Research Institute, University of Notre Dame, South Bend, IN, United States
| | - Steven A Corcelli
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States
| | - Brian M Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States.,Harper Cancer Research Institute, University of Notre Dame, South Bend, IN, United States
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23
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Moyo N, Borthwick NJ, Wee EG, Capucci S, Crook A, Dorrell L, Hanke T. Long-term follow up of human T-cell responses to conserved HIV-1 regions elicited by DNA/simian adenovirus/MVA vaccine regimens. PLoS One 2017; 12:e0181382. [PMID: 28719652 PMCID: PMC5515449 DOI: 10.1371/journal.pone.0181382] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 06/29/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Durability of vaccine-elicited immune responses is one of the key determinants for vaccine success. Our aim is to develop a vaccination strategy against the human immunodeficiency virus type 1 (HIV-1), which induces protective and durable CD8+ T-cell responses. The central theorem of our approach is to focus T cells on highly conserved regions of the HIV-1 proteome and this is achieved through the use of the first-generation conserved vaccine immunogen HIVconsv. This immunogen vectored by plasmid DNA, simian adenovirus and poxvirus MVA was tested in healthy, HIV-1-negative adults in UK and induced high magnitudes of HIVconsv-specific plurifunctional CD8+ T cells capable of in vitro HIV-1 inhibition. Here, we assessed the durability of these responses. METHODS Vaccine recipients in trial HIV-CORE 002 were invited to provide a blood sample at 1 and 2 years after vaccination. Their PBMCs were tested in IFN-γ ELISPOT, 25-analyte Luminex, CFSE proliferation and intracellular cytokine staining assays, the last enhanced by HLA-peptide dextramer analysis. RESULTS 12/12 (1 year) and 8/8 (2 years) returning subjects had median (range) of 990 (150-2495) and 763 (70-1745) IFN-γ SFU/106 PBMC specific for HIVconsv, respectively, and recognized 5 (1-6) out of 6 peptide pools at 2 years. Over one-half of the HIVconsv-specific cells expressed at least 3 functions IFN-γ, TNF-α and CD107a, and were capable of proliferation. Among dextramer-reactive cells, naïve, transitional, effector and terminally differentiated memory subsets were similarly represented. CONCLUSIONS First generation HIVconsv vaccine induced human T cells, which were plurifunctional and persisted for at least 2 years. TRIAL REGISTRATION ClinicalTrials.gov NCT01151319.
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Affiliation(s)
- Nathifa Moyo
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Nicola J Borthwick
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Edmund G Wee
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Silvia Capucci
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Alison Crook
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Lucy Dorrell
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- NDM Research Building, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Tomáš Hanke
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
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24
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Chakraborty AK, Barton JP. Rational design of vaccine targets and strategies for HIV: a crossroad of statistical physics, biology, and medicine. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2017; 80:032601. [PMID: 28059778 DOI: 10.1088/1361-6633/aa574a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Vaccination has saved more lives than any other medical procedure. Pathogens have now evolved that have not succumbed to vaccination using the empirical paradigms pioneered by Pasteur and Jenner. Vaccine design strategies that are based on a mechanistic understanding of the pertinent immunology and virology are required to confront and eliminate these scourges. In this perspective, we describe just a few examples of work aimed to achieve this goal by bringing together approaches from statistical physics with biology and clinical research.
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Affiliation(s)
- Arup K Chakraborty
- Departments of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America. Departments of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America. Departments of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America. Departments of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America. Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America. Ragon Institute of MIT, MGH, & Harvard, Cambridge, MA 02139, United States of America
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25
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Zhang H, Lim HS, Knapp B, Deane CM, Aleksic M, Dushek O, van der Merwe PA. The contribution of major histocompatibility complex contacts to the affinity and kinetics of T cell receptor binding. Sci Rep 2016; 6:35326. [PMID: 27734930 PMCID: PMC5062128 DOI: 10.1038/srep35326] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 09/28/2016] [Indexed: 11/09/2022] Open
Abstract
The interaction between the T cell antigen receptor (TCR) and antigenic peptide in complex with major histocompatibility complex (MHC) molecules is a crucial step in T cell activation. The relative contributions of TCR:peptide and TCR:MHC contacts to the overall binding energy remain unclear. This has important implications for our understanding of T cell development and function. In this study we used site directed mutagenesis to estimate the contribution of HLA-A2 side-chains to the binding of four TCRs. Our results show that these TCRs have very different energetic ‘footprints’ on HLA-A2, with no residues contributing to all TCR interactions. The estimated overall contribution of MHC side-chains to the total interaction energy was variable, with lower limits ranging from 11% to 50%. Kinetic analysis suggested a minor and variable contribution of MHC side-chains to the transition state complex, arguing against a two-step mechanism for TCR binding.
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Affiliation(s)
- Hao Zhang
- Sir William Dunn School of Pathology, University of Oxford, United Kingdom
| | - Hong-Sheng Lim
- Sir William Dunn School of Pathology, University of Oxford, United Kingdom
| | - Berhard Knapp
- Department of Statistics, University of Oxford, United Kingdom
| | | | - Milos Aleksic
- Sir William Dunn School of Pathology, University of Oxford, United Kingdom
| | - Omer Dushek
- Sir William Dunn School of Pathology, University of Oxford, United Kingdom
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Connelley TK, Li X, MacHugh N, Colau D, Graham SP, van der Bruggen P, Taracha EL, Gill A, Morrison WI. CD8 T-cell responses against the immunodominant Theileria parva peptide Tp249-59 are composed of two distinct populations specific for overlapping 11-mer and 10-mer epitopes. Immunology 2016; 149:172-85. [PMID: 27317384 PMCID: PMC5011678 DOI: 10.1111/imm.12637] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 06/07/2016] [Accepted: 06/07/2016] [Indexed: 01/30/2023] Open
Abstract
Immunity against Theileria parva is associated with CD8 T-cell responses that exhibit immunodominance, focusing the response against limited numbers of epitopes. As candidates for inclusion in vaccines, characterization of responses against immunodominant epitopes is a key component in novel vaccine development. We have previously demonstrated that the Tp249-59 and Tp1214-224 epitopes dominate CD8 T-cell responses in BoLA-A10 and BoLA-18 MHC I homozygous animals, respectively. In this study, peptide-MHC I tetramers for these epitopes, and a subdominant BoLA-A10-restricted epitope (Tp298-106 ), were generated to facilitate accurate and rapid enumeration of epitope-specific CD8 T cells. During validation of these tetramers a substantial proportion of Tp249-59 -reactive T cells failed to bind the tetramer, suggesting that this population was heterogeneous with respect to the recognized epitope. We demonstrate that Tp250-59 represents a distinct epitope and that tetramers produced with Tp50-59 and Tp49-59 show no cross-reactivity. The Tp249-59 and Tp250-59 epitopes use different serine residues as the N-terminal anchor for binding to the presenting MHC I molecule. Molecular dynamic modelling predicts that the two peptide-MHC I complexes adopt structurally different conformations and Tcell receptor β sequence analysis showed that Tp249-59 and Tp250-59 are recognized by non-overlapping T-cell receptor repertoires. Together these data demonstrate that although differing by only a single residue, Tp249-59 and Tp250-59 epitopes form distinct ligands for T-cell receptor recognition. Tetramer analysis of T. parva-specific CD8 T-cell lines confirmed the immunodominance of Tp1214-224 in BoLA-A18 animals and showed in BoLA-A10 animals that the Tp249-59 epitope response was generally more dominant than the Tp250-59 response and confirmed that the Tp298-106 response was subdominant.
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Affiliation(s)
- Timothy K. Connelley
- Division of Immunity and InfectionThe Roslin InstituteThe University of EdinburghMidlothianUK
| | - Xiaoying Li
- Division of Immunity and InfectionThe Roslin InstituteThe University of EdinburghMidlothianUK
- Present address: School of Life Sciences and TechnologyXinxiang Medical UniversityLaboratory Building Room 232XinxiangHenanCN 453003China
| | - Niall MacHugh
- Division of Immunity and InfectionThe Roslin InstituteThe University of EdinburghMidlothianUK
| | - Didier Colau
- Ludwig Institute for Cancer Research and de Duve InstituteUniversite catholique de LouvainBrusselsBelgium
| | - Simon P. Graham
- The International Livestock Research InstituteNairobiKenya
- Present address: The Pirbright InstituteAsh RoadPirbrightGU24 0NFUK
| | - Pierre van der Bruggen
- Ludwig Institute for Cancer Research and de Duve InstituteUniversite catholique de LouvainBrusselsBelgium
| | - Evans L. Taracha
- The International Livestock Research InstituteNairobiKenya
- Present address: Institute of Primate ResearchPO Box 24481‐00502KarenKenya
| | - Andy Gill
- Division of NeurobiologyThe Roslin InstituteThe University of EdinburghMidlothianUK
| | - William Ivan Morrison
- Division of Immunity and InfectionThe Roslin InstituteThe University of EdinburghMidlothianUK
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Li X, Li W, Zhong P, Fang K, Zhu K, Musa TH, Song Y, Du G, Gao R, Guo Y, Yan W, Xuan Y, Wei P. Nationwide Trends in Molecular Epidemiology of HIV-1 in China. AIDS Res Hum Retroviruses 2016; 32:851-9. [PMID: 27080587 DOI: 10.1089/aid.2016.0029] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
To estimate the nationwide and regional distribution of HIV-1 genotypes in China in the past three decades, province-specific HIV-1 molecular epidemiology data were derived from 260 independent studies of HIV molecular prevalence through searching PubMed, VIP Chinese Journal Database (VIP), China National Knowledge Infrastructure, and Wanfang Data from January 1981 to December 2015. The nationwide and regional distribution of HIV-1 genotypes was estimated by weighting the genotype distribution from each province- and risk-specific subpopulation with the number of reported cases in the corresponding subgroups in the relevant periods. A sharp transition of HIV-1 subtypes and recombinant distribution was observed in various risk groups and regions over time. CRF01_AE has rapidly surged among almost all risk groups and in all areas, and it has become dominant among men who have sex with men and heterosexuals. A wide variety of new circulating recombinant forms (CRFs) and unique recombinant forms (URFs) were rapidly appearing in several risk groups and regions. After 2007, CRF01_AE was the most prevalent strain, accounting for 42.5% of all national infections, followed by CRF07_BC (28.9%), subtype B'/B (10.9%), CRF08_BC (10.0%), and subtype C (2.8%). URFs and other CRFs were responsible for 2.6% and fewer than 1% of infections nationwide, respectively. The nationwide and regional distributions of HIV-1 subtypes and recombinants were sharply shifting in China. CRF01_AE and new CRFs played an increasing role in the nationwide or regional HIV pandemic. The nationwide diversity of HIV-1 poses a formidable challenge to HIV vaccine development and disease prevention.
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Affiliation(s)
- Xiaoshan Li
- Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Wei Li
- Department of Infectious Disease Prevention and School Health, Nanjing Municipal Center for Disease Control and Prevention, Nanjing, China
| | - Ping Zhong
- Department of AIDS and STD, Shanghai Municipal Center for Disease Control and Prevention, Shanghai Municipal Institutes for Preventive Medicine, Shanghai, China
| | - Kun Fang
- Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Kexin Zhu
- School of Public Health, Nantong University, Nantong, China
| | - Taha Hussein Musa
- Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Yue Song
- Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Guoping Du
- Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Rong Gao
- Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Yan Guo
- Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Wenjuan Yan
- Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Yang Xuan
- Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Pingmin Wei
- Teaching and Research Office of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
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Mutua G, Farah B, Langat R, Indangasi J, Ogola S, Onsembe B, Kopycinski JT, Hayes P, Borthwick NJ, Ashraf A, Dally L, Barin B, Tillander A, Gilmour J, De Bont J, Crook A, Hannaman D, Cox JH, Anzala O, Fast PE, Reilly M, Chinyenze K, Jaoko W, Hanke T, HIV-CORE 004 study group T. Broad HIV-1 inhibition in vitro by vaccine-elicited CD8(+) T cells in African adults. Mol Ther Methods Clin Dev 2016; 3:16061. [PMID: 27617268 PMCID: PMC5006719 DOI: 10.1038/mtm.2016.61] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 07/22/2016] [Indexed: 02/07/2023]
Abstract
We are developing a pan-clade HIV-1 T-cell vaccine HIVconsv, which could complement Env vaccines for prophylaxis and be a key to HIV cure. Our strategy focuses vaccine-elicited effector T-cells on functionally and structurally conserved regions (not full-length proteins and not only epitopes) of the HIV-1 proteome, which are common to most global variants and which, if mutated, cause a replicative fitness loss. Our first clinical trial in low risk HIV-1-negative adults in Oxford demonstrated the principle that naturally mostly subdominant epitopes, when taken out of the context of full-length proteins/virus and delivered by potent regimens involving combinations of simian adenovirus and poxvirus modified vaccinia virus Ankara, can induce robust CD8(+) T cells of broad specificities and functions capable of inhibiting in vitro HIV-1 replication. Here and for the first time, we tested this strategy in low risk HIV-1-negative adults in Africa. We showed that the vaccines were well tolerated and induced high frequencies of broadly HIVconsv-specific plurifunctional T cells, which inhibited in vitro viruses from four major clades A, B, C, and D. Because sub-Saharan Africa is globally the region most affected by HIV-1/AIDS, trial HIV-CORE 004 represents an important stage in the path toward efficacy evaluation of this highly rational and promising vaccine strategy.
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Affiliation(s)
- Gaudensia Mutua
- KAVI-Institute of Clinical Research, University of Nairobi, Kenya
| | - Bashir Farah
- KAVI-Institute of Clinical Research, University of Nairobi, Kenya
| | - Robert Langat
- KAVI-Institute of Clinical Research, University of Nairobi, Kenya
| | | | - Simon Ogola
- KAVI-Institute of Clinical Research, University of Nairobi, Kenya
| | - Brian Onsembe
- KAVI-Institute of Clinical Research, University of Nairobi, Kenya
| | - Jakub T Kopycinski
- Human Immunology Laboratory, International AIDS Vaccine Initiative, Imperial College, London, UK
| | - Peter Hayes
- Human Immunology Laboratory, International AIDS Vaccine Initiative, Imperial College, London, UK
| | | | - Ambreen Ashraf
- Human Immunology Laboratory, International AIDS Vaccine Initiative, Imperial College, London, UK
| | - Len Dally
- Emmes Corporation, Rockville, Maryland, USA
| | - Burc Barin
- Emmes Corporation, Rockville, Maryland, USA
| | | | - Jill Gilmour
- Human Immunology Laboratory, International AIDS Vaccine Initiative, Imperial College, London, UK
| | - Jan De Bont
- International AIDS Vaccine Initiative-New York, New York, New York, USA
| | - Alison Crook
- Jenner Institute, University of Oxford, Oxford, UK
| | - Drew Hannaman
- ICHOR Medical Systems, Inc., San Diego, California, USA
| | - Josephine H Cox
- Human Immunology Laboratory, International AIDS Vaccine Initiative, Imperial College, London, UK
| | - Omu Anzala
- KAVI-Institute of Clinical Research, University of Nairobi, Kenya
| | - Patricia E Fast
- International AIDS Vaccine Initiative-New York, New York, New York, USA
| | | | - Kundai Chinyenze
- International AIDS Vaccine Initiative-New York, New York, New York, USA
| | - Walter Jaoko
- KAVI-Institute of Clinical Research, University of Nairobi, Kenya
| | - Tomáš Hanke
- Jenner Institute, University of Oxford, Oxford, UK
- International Research Center for Medical Sciences, Kumamoto University, Japan
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Barton JP, Goonetilleke N, Butler TC, Walker BD, McMichael AJ, Chakraborty AK. Relative rate and location of intra-host HIV evolution to evade cellular immunity are predictable. Nat Commun 2016; 7:11660. [PMID: 27212475 PMCID: PMC4879252 DOI: 10.1038/ncomms11660] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 04/18/2016] [Indexed: 12/05/2022] Open
Abstract
Human immunodeficiency virus (HIV) evolves within infected persons to escape being destroyed by the host immune system, thereby preventing effective immune control of infection. Here, we combine methods from evolutionary dynamics and statistical physics to simulate in vivo HIV sequence evolution, predicting the relative rate of escape and the location of escape mutations in response to T-cell-mediated immune pressure in a cohort of 17 persons with acute HIV infection. Predicted and clinically observed times to escape immune responses agree well, and we show that the mutational pathways to escape depend on the viral sequence background due to epistatic interactions. The ability to predict escape pathways and the duration over which control is maintained by specific immune responses open the door to rational design of immunotherapeutic strategies that might enable long-term control of HIV infection. Our approach enables intra-host evolution of a human pathogen to be predicted in a probabilistic framework.
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Affiliation(s)
- John P. Barton
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts 02139, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Nilu Goonetilleke
- Department of Microbiology, Immunology and Medicine, University of North Carolina, Chapel Hill, North Carolina 27599, USA
- Nuffield Department of Medicine, University of Oxford, Old Road Campus, Headington, Oxford OX3 7FZ, UK
| | - Thomas C. Butler
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Bruce D. Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts 02139, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Andrew J. McMichael
- Nuffield Department of Medicine, University of Oxford, Old Road Campus, Headington, Oxford OX3 7FZ, UK
| | - Arup K. Chakraborty
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts 02139, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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30
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Comrie WA, Burkhardt JK. Action and Traction: Cytoskeletal Control of Receptor Triggering at the Immunological Synapse. Front Immunol 2016; 7:68. [PMID: 27014258 PMCID: PMC4779853 DOI: 10.3389/fimmu.2016.00068] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Accepted: 02/12/2016] [Indexed: 01/03/2023] Open
Abstract
It is well known that F-actin dynamics drive the micron-scale cell shape changes required for migration and immunological synapse (IS) formation. In addition, recent evidence points to a more intimate role for the actin cytoskeleton in promoting T cell activation. Mechanotransduction, the conversion of mechanical input into intracellular biochemical changes, is thought to play a critical role in several aspects of immunoreceptor triggering and downstream signal transduction. Multiple molecules associated with signaling events at the IS have been shown to respond to physical force, including the TCR, costimulatory molecules, adhesion molecules, and several downstream adapters. In at least some cases, it is clear that the relevant forces are exerted by dynamics of the T cell actomyosin cytoskeleton. Interestingly, there is evidence that the cytoskeleton of the antigen-presenting cell also plays an active role in T cell activation, by countering the molecular forces exerted by the T cell at the IS. Since actin polymerization is itself driven by TCR and costimulatory signaling pathways, a complex relationship exists between actin dynamics and receptor activation. This review will focus on recent advances in our understanding of the mechanosensitive aspects of T cell activation, paying specific attention to how F-actin-directed forces applied from both sides of the IS fit into current models of receptor triggering and activation.
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Affiliation(s)
- William A Comrie
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA , USA
| | - Janis K Burkhardt
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA , USA
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31
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Bello M, Correa-Basurto J. Energetic and flexibility properties captured by long molecular dynamics simulations of a membrane-embedded pMHCII-TCR complex. MOLECULAR BIOSYSTEMS 2016; 12:1350-66. [PMID: 26926952 DOI: 10.1039/c6mb00058d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Although crystallographic data have provided important molecular insight into the interactions in the pMHC-TCR complex, the inherent features of this structural approach cause it to only provide a static picture of the interactions. While unbiased molecular dynamics simulations (UMDSs) have provided important information about the dynamic structural behavior of the pMHC-TCR complex, most of them have modeled the pMHC-TCR complex as soluble, when in physiological conditions, this complex is membrane bound; therefore, following this latter UMDS protocol might hamper important dynamic results. In this contribution, we performed three independent 300 ns-long UMDSs of the pMHCII-TCR complex anchored in two opposing membranes to explore the structural and energetic properties of the recognition of pMHCII by the TCR. The conformational ensemble generated through UMDSs was subjected to clustering and Cartesian principal component analyses (cPCA) to explore the dynamical behavior of the pMHCII-TCR association. Furthermore, based on the conformational population sampled through UMDSs, the effective binding free energy, per-residue free energy decomposition, and alanine scanning mutations were explored for the native pMHCII-TCR complex, as well as for 12 mutations (p1-p12MHCII-TCR) introduced in the native peptide. Clustering analyses and cPCA provide insight into the rocking motion of the TCR onto pMHCII, together with the presence of new electrostatic interactions not observed through crystallographic methods. Energetic results provide evidence of the main contributors to the pMHC-TCR complex formation as well as the key residues involved in this molecular recognition process.
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Affiliation(s)
- Martiniano Bello
- Laboratorio de Modelado Molecular, Bioinformática y Diseño de Fármacos de la Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis Y Diaz Mirón S/N, Col. Casco de Santo Tomas, Mexico City, CP: 11340, Mexico.
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Abdul-Jawad S, Ondondo B, van Hateren A, Gardner A, Elliott T, Korber B, Hanke T. Increased Valency of Conserved-mosaic Vaccines Enhances the Breadth and Depth of Epitope Recognition. Mol Ther 2016; 24:375-384. [PMID: 26581160 PMCID: PMC4817818 DOI: 10.1038/mt.2015.210] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 11/09/2015] [Indexed: 12/19/2022] Open
Abstract
The biggest roadblock in development of effective vaccines against human immunodeficiency virus type 1 (HIV-1) is the virus genetic diversity. For T-cell vaccine, this can be tackled by focusing the vaccine-elicited T-cells on the highly functionally conserved regions of HIV-1 proteins, mutations in which typically cause a replicative fitness loss, and by computing multivalent mosaic proteins, which maximize the coverage of potential 9-mer T-cell epitopes of the input viral sequences. Our first conserved region vaccines HIVconsv employed clade alternating consensus sequences and showed promise in the initial clinical trials in terms of magnitude and breadth of elicited CD8(+) T-cells. Here, monitoring T-cells restricted by HLA-A*02:01 in transgenic mice, we assessed whether or not the tHIVconsv design (HIVconsv with a tissue plasminogen activator leader sequence) benefits from combining with a complementing conserved mosaic immunogen tHIVcmo, and compared the bivalent immunization to that with trivalent conserved mosaic vaccines. A hierarchy of tHIVconsv ≤ tHIVconsv+tHIVcmo < tCmo1+tCmo2+tCmo3 vaccinations for induction of CD8(+) T-cell responses was observed in terms of recognition of tested peptide variants. Thus, our HLA-A*02:01-restricted epitope data concur with previously published mouse and macaque observations and suggest that even conserved region vaccines benefit from oligovalent mosaic design.
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Affiliation(s)
| | | | - Andy van Hateren
- Faculty of Medicine and Institute for Life Science, University of Southampton, Southampton, UK
| | | | - Tim Elliott
- Faculty of Medicine and Institute for Life Science, University of Southampton, Southampton, UK
| | - Bette Korber
- Los Alamos National Laboratory, Theoretical Biology and Biophysics, Los Alamos, New Mexico, USA; The New Mexico Consortium, Los Alamos, New Mexico, USA
| | - Tomáš Hanke
- The Jenner Institute, University of Oxford, Oxford, UK; International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan.
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Ahmed T, Borthwick NJ, Gilmour J, Hayes P, Dorrell L, Hanke T. Control of HIV-1 replication in vitro by vaccine-induced human CD8(+) T cells through conserved subdominant Pol epitopes. Vaccine 2016; 34:1215-24. [PMID: 26784683 PMCID: PMC4769096 DOI: 10.1016/j.vaccine.2015.12.021] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Revised: 09/21/2015] [Accepted: 12/09/2015] [Indexed: 02/07/2023]
Abstract
Objective The specificity of CD8+ T cells is critical for early control of founder/transmitted and reactivated HIV-1. To tackle HIV-1 variability and escape, we designed vaccine immunogen HIVconsv assembled from 14 highly conserved regions of mainly Gag and Pol proteins. When administered to HIV-1-negative human volunteers in trial HIV-CORE 002, HIVconsv vaccines elicited CD8+ effector T cells which inhibited replication of up to 8 HIV-1 isolates in autologous CD4+ cells. This inhibition correlated with interferon-γ production in response to Gag and Pol peptide pools, but direct evidence of the inhibitory specificity was missing. Here, we aimed to define through recognition of which epitopes these effectors inhibit HIV-1 replication. Design CD8+ T-cells from the 3 broadest HIV-1 inhibitors out of 23 vaccine recipients were expanded in culture by Gag or Pol peptide restimulation and tested in viral inhibition assay (VIA) using HIV-1 clade B and A isolates. Methods Frozen PBMCs were expanded first using peptide pools from Gag or Pol conserved regions and tested on HIV-1-infected cells in VIA or by individual peptides for their effector functions. Single peptide specificities responsible for inhibition of HIV-1 replication were then confirmed by single-peptide expanded effectors tested on HIV-1-infected cells. Results We formally demonstrated that the vaccine-elicited inhibitory human CD8+ T cells recognized conserved epitopes of both Pol and Gag proteins. We defined 7 minimum epitopes, of which 3 were novel, presumably naturally subdominant. The effectors were oligofunctional producing several cytokines and chemokines and killing peptide-pulsed target cells. Conclusions These results implicate the use of functionally conserved regions of Pol in addition to the widely used Gag for T-cell vaccine design. Proportion of volunteers developing these effectors and their frequency in circulating PBMC are separate issues, which can be addressed, if needed, by more efficient vector and regimen delivery of conserved immunogens.
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Affiliation(s)
- Tina Ahmed
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Nicola J Borthwick
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Jill Gilmour
- Human Immunology Laboratory, International AIDS Vaccine Initiative, London SW10 9NH, United Kingdom; Faculty of Medicine, Imperial College, London SW7 2AZ, United Kingdom
| | - Peter Hayes
- Human Immunology Laboratory, International AIDS Vaccine Initiative, London SW10 9NH, United Kingdom
| | - Lucy Dorrell
- Human Immunology Laboratory, International AIDS Vaccine Initiative, London SW10 9NH, United Kingdom; Nuffield Department of Medicine, NDM Research Building, University of Oxford, Oxford OX3 7FZ, United Kingdom; Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Tomáš Hanke
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom; International Research Center for Medical Sciences, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Japan.
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DockTope: a Web-based tool for automated pMHC-I modelling. Sci Rep 2015; 5:18413. [PMID: 26674250 PMCID: PMC4682062 DOI: 10.1038/srep18413] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 11/18/2015] [Indexed: 11/08/2022] Open
Abstract
The immune system is constantly challenged, being required to protect the organism against a wide variety of infectious pathogens and, at the same time, to avoid autoimmune disorders. One of the most important molecules involved in these events is the Major Histocompatibility Complex class I (MHC-I), responsible for binding and presenting small peptides from the intracellular environment to CD8+ T cells. The study of peptide:MHC-I (pMHC-I) molecules at a structural level is crucial to understand the molecular mechanisms underlying immunologic responses. Unfortunately, there are few pMHC-I structures in the Protein Data Bank (PDB) (especially considering the total number of complexes that could be formed combining different peptides), and pMHC-I modelling tools are scarce. Here, we present DockTope, a free and reliable web-based tool for pMHC-I modelling, based on crystal structures from the PDB. DockTope is fully automated and allows any researcher to construct a pMHC-I complex in an efficient way. We have reproduced a dataset of 135 non-redundant pMHC-I structures from the PDB (Cα RMSD below 1 Å). Modelling of pMHC-I complexes is remarkably important, contributing to the knowledge of important events such as cross-reactivity, autoimmunity, cancer therapy, transplantation and rational vaccine design.
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Abstract
An effective human immunodeficiency virus type 1 (HIV-1) vaccine is expected to have the greatest impact on HIV-1 spread and remains a global scientific priority. Only one candidate vaccine has significantly reduced HIV-1 acquisition, yet at a limited efficacy of 31%, and none have delayed disease progression in vaccinated individuals. Thus, the challenge remains to develop HIV-1 immunogens that will elicit protective immunity. A combination of two independent approaches - namely the elicitation of broadly neutralising antibodies (bNAb) to prevent or reduce acquisition of infection and stimulation of effective cytotoxic T lymphocyte (CTL) responses to slow disease progression in breakthrough infections (recent evidence suggests that CTLs could also block HIV-1 from establishing persistent infection) - is the current ideal. The purpose of this review is to summarise strategies and progress in the design and testing of HIV-1 immunogens to elicit bNAb and protective CTL immune responses. Recent advances in mimicking the functional native envelope trimer structure and in designing structurally-stabilised bNAb epitope forms to drive development of germline precursors to mature bNAb are highlighted. Systematic or computational approaches to T cell immunogen design aimed at covering viral diversity, increasing the breadth of immune responses and/or reducing viable viral escape are discussed. We also discuss a recent novel vaccine vector approach shown to induce extremely broad and persistent T cell responses that could clear highly pathogenic simian immunodeficiency virus (SIV) early after infection in the monkey model. While in vitro and animal model data are promising, Phase II and III human clinical trials are ultimately needed to determine the efficacy of immunogen design approaches.
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Affiliation(s)
- Jaclyn K Mann
- />HIV Pathogenesis Programme, University of KwaZulu-Natal, 719 Umbilo Road, Durban, 4001 South Africa
- />KwaZulu-Natal Research Institute for Tuberculosis and HIV, University of KwaZulu-Natal, Durban, 4001 South Africa
| | - Thumbi Ndung’u
- />HIV Pathogenesis Programme, University of KwaZulu-Natal, 719 Umbilo Road, Durban, 4001 South Africa
- />KwaZulu-Natal Research Institute for Tuberculosis and HIV, University of KwaZulu-Natal, Durban, 4001 South Africa
- />Ragon Institute of MGH, MIT and Harvard University, Cambridge, MA 02139 USA
- />Max Planck Institute for Infection Biology, Chariteplatz, D-10117 Berlin, Germany
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Understanding the structural dynamics of TCR-pMHC interactions. Trends Immunol 2014; 35:604-612. [DOI: 10.1016/j.it.2014.10.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 10/20/2014] [Accepted: 10/20/2014] [Indexed: 12/23/2022]
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Reiser JB, Legoux F, Gras S, Trudel E, Chouquet A, Léger A, Le Gorrec M, Machillot P, Bonneville M, Saulquin X, Housset D. Analysis of relationships between peptide/MHC structural features and naive T cell frequency in humans. THE JOURNAL OF IMMUNOLOGY 2014; 193:5816-26. [PMID: 25392532 DOI: 10.4049/jimmunol.1303084] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The structural rules governing peptide/MHC (pMHC) recognition by T cells remain unclear. To address this question, we performed a structural characterization of several HLA-A2/peptide complexes and assessed in parallel their antigenicity, by analyzing the frequency of the corresponding Ag-specific naive T cells in A2(+) and A2(-) individuals, as well as within CD4(+) and CD8(+) subsets. We were able to find a correlation between specific naive T cell frequency and peptide solvent accessibility and/or mobility for a subset of moderately prominent peptides. However, one single structural parameter of the pMHC complexes could not be identified to explain each peptide antigenicity. Enhanced pMHC antigenicity was associated with both highly biased TRAV usage, possibly reflecting favored interaction between particular pMHC complexes and germline TRAV loops, and peptide structural features allowing interactions with a broad range of permissive CDR3 loops. In this context of constrained TCR docking mode, an optimal peptide solvent exposed surface leading to an optimal complementarity with TCR interface may constitute one of the key features leading to high frequency of specific T cells. Altogether our results suggest that frequency of specific T cells depends on the fine-tuning of several parameters, the structural determinants governing TCR-pMHC interaction being just one of them.
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Affiliation(s)
- Jean-Baptiste Reiser
- Université de Grenoble Alpes, Institut de Biologie Structurale, F-38044 Grenoble, France; Commissariat à l'énergie atomique et aux énergies alternatives, Direction des sciences du vivant, Institut de Biologie Structurale, F-38044 Grenoble, France; Centre national de la recherche scientifique, Institut de Biologie Structurale, F-38044 Grenoble, France
| | - François Legoux
- Institut national de la santé et de la recherche médicale, Unité mixte de recherche 892, Centre de Recherche en Cancérologie Nantes Angers, F-44000 Nantes, France; and
| | - Stéphanie Gras
- Université de Grenoble Alpes, Institut de Biologie Structurale, F-38044 Grenoble, France; Commissariat à l'énergie atomique et aux énergies alternatives, Direction des sciences du vivant, Institut de Biologie Structurale, F-38044 Grenoble, France; Centre national de la recherche scientifique, Institut de Biologie Structurale, F-38044 Grenoble, France
| | - Eric Trudel
- Université de Grenoble Alpes, Institut de Biologie Structurale, F-38044 Grenoble, France; Commissariat à l'énergie atomique et aux énergies alternatives, Direction des sciences du vivant, Institut de Biologie Structurale, F-38044 Grenoble, France; Centre national de la recherche scientifique, Institut de Biologie Structurale, F-38044 Grenoble, France
| | - Anne Chouquet
- Université de Grenoble Alpes, Institut de Biologie Structurale, F-38044 Grenoble, France; Commissariat à l'énergie atomique et aux énergies alternatives, Direction des sciences du vivant, Institut de Biologie Structurale, F-38044 Grenoble, France; Centre national de la recherche scientifique, Institut de Biologie Structurale, F-38044 Grenoble, France
| | - Alexandra Léger
- Institut national de la santé et de la recherche médicale, Unité mixte de recherche 892, Centre de Recherche en Cancérologie Nantes Angers, F-44000 Nantes, France; and
| | - Madalen Le Gorrec
- Université de Grenoble Alpes, Institut de Biologie Structurale, F-38044 Grenoble, France; Commissariat à l'énergie atomique et aux énergies alternatives, Direction des sciences du vivant, Institut de Biologie Structurale, F-38044 Grenoble, France; Centre national de la recherche scientifique, Institut de Biologie Structurale, F-38044 Grenoble, France
| | - Paul Machillot
- Université de Grenoble Alpes, Institut de Biologie Structurale, F-38044 Grenoble, France; Commissariat à l'énergie atomique et aux énergies alternatives, Direction des sciences du vivant, Institut de Biologie Structurale, F-38044 Grenoble, France; Centre national de la recherche scientifique, Institut de Biologie Structurale, F-38044 Grenoble, France
| | - Marc Bonneville
- Institut national de la santé et de la recherche médicale, Unité mixte de recherche 892, Centre de Recherche en Cancérologie Nantes Angers, F-44000 Nantes, France; and
| | - Xavier Saulquin
- Institut national de la santé et de la recherche médicale, Unité mixte de recherche 892, Centre de Recherche en Cancérologie Nantes Angers, F-44000 Nantes, France; and Université de Nantes, F-44000 Nantes, France
| | - Dominique Housset
- Université de Grenoble Alpes, Institut de Biologie Structurale, F-38044 Grenoble, France; Commissariat à l'énergie atomique et aux énergies alternatives, Direction des sciences du vivant, Institut de Biologie Structurale, F-38044 Grenoble, France; Centre national de la recherche scientifique, Institut de Biologie Structurale, F-38044 Grenoble, France;
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Hoppes R, Oostvogels R, Luimstra JJ, Wals K, Toebes M, Bies L, Ekkebus R, Rijal P, Celie PHN, Huang JH, Emmelot ME, Spaapen RM, Lokhorst H, Schumacher TNM, Mutis T, Rodenko B, Ovaa H. Altered peptide ligands revisited: vaccine design through chemically modified HLA-A2-restricted T cell epitopes. THE JOURNAL OF IMMUNOLOGY 2014; 193:4803-13. [PMID: 25311806 DOI: 10.4049/jimmunol.1400800] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Virus or tumor Ag-derived peptides that are displayed by MHC class I molecules are attractive starting points for vaccine development because they induce strong protective and therapeutic cytotoxic T cell responses. In thus study, we show that the MHC binding and consequent T cell reactivity against several HLA-A*02 restricted epitopes can be further improved through the incorporation of nonproteogenic amino acids at primary and secondary anchor positions. We screened more than 90 nonproteogenic, synthetic amino acids through a range of epitopes and tested more than 3000 chemically enhanced altered peptide ligands (CPLs) for binding affinity to HLA-A*0201. With this approach, we designed CPLs of viral epitopes, of melanoma-associated Ags, and of the minor histocompatibility Ag UTA2-1, which is currently being evaluated for its antileukemic activity in clinical dendritic cell vaccination trials. The crystal structure of one of the CPLs in complex with HLA-A*0201 revealed the molecular interactions likely responsible for improved binding. The best CPLs displayed enhanced affinity for MHC, increasing MHC stability and prolonging recognition by Ag-specific T cells and, most importantly, they induced accelerated expansion of antitumor T cell frequencies in vitro and in vivo as compared with the native epitope. Eventually, we were able to construct a toolbox of preferred nonproteogenic residues with which practically any given HLA-A*02 restricted epitope can be readily optimized. These CPLs could improve the therapeutic outcome of vaccination strategies or can be used for ex vivo enrichment and faster expansion of Ag-specific T cells for transfer into patients.
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Affiliation(s)
- Rieuwert Hoppes
- Division of Cell Biology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Rimke Oostvogels
- Department of Clinical Chemistry and Haematology, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands Department of Haematology, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Jolien J Luimstra
- Division of Cell Biology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Kim Wals
- Division of Cell Biology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Mireille Toebes
- Division of Immunology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Laura Bies
- Division of Immunology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Reggy Ekkebus
- Division of Cell Biology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Pramila Rijal
- Division of Cell Biology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Patrick H N Celie
- Division of Biochemistry, The Netherlands Cancer Institute Protein Facility, 1066 CX Amsterdam, the Netherlands; and
| | - Julie H Huang
- Department of Clinical Chemistry and Haematology, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Maarten E Emmelot
- Department of Clinical Chemistry and Haematology, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Robbert M Spaapen
- Division of Cell Biology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Henk Lokhorst
- Department of Haematology, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Ton N M Schumacher
- Division of Immunology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Tuna Mutis
- Department of Clinical Chemistry and Haematology, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Boris Rodenko
- Division of Cell Biology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8TA, United Kingdom
| | - Huib Ovaa
- Division of Cell Biology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
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NetTepi: an integrated method for the prediction of T cell epitopes. Immunogenetics 2014; 66:449-56. [DOI: 10.1007/s00251-014-0779-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 05/06/2014] [Indexed: 02/07/2023]
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McMichael AJ, Koff WC. Vaccines that stimulate T cell immunity to HIV-1: the next step. Nat Immunol 2014; 15:319-22. [PMID: 24646598 PMCID: PMC4324504 DOI: 10.1038/ni.2844] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 02/05/2014] [Indexed: 12/20/2022]
Abstract
The search for a vaccine against human immunodeficiency virus type 1 (HIV-1) has many hurdles to overcome. Ideally, the stimulation of both broadly neutralizing antibodies and cell-mediated immune responses remains the best option, but no candidate in clinical trials at present has elicited such antibodies, and efficacy trials have not demonstrated any benefit for vaccines designed to stimulate immune responses of CD8(+) T cells. Findings obtained with the simian immunodeficiency virus (SIV) monkey model have provided new evidence that stimulating effective CD8(+) T cell immunity could provide protection, and in this Perspective we explore the path forward for optimizing such responses in humans.
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Affiliation(s)
| | - Wayne C Koff
- International AIDS Vaccine Initiative, New York, New York, USA
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Hanke T. Conserved immunogens in prime-boost strategies for the next-generation HIV-1 vaccines. Expert Opin Biol Ther 2014; 14:601-16. [PMID: 24490585 DOI: 10.1517/14712598.2014.885946] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
INTRODUCTION Effective vaccines are the best solution for stopping the spread of HIV/AIDS and other infectious diseases. Their development and in-depth understanding of pathogen-host interactions rely on technological advances. AREAS COVERED Rational vaccine development can be effectively approached by conceptual separation of, on one hand, design of immunogens from improving their presentation to the immune system and, on the other, induction of antibodies from induction of killer CD8(+) T cells. The biggest roadblock for many vaccines is the pathogens' variability. This is best tackled by focusing both antibodies and T cells on the functionally most conserved regions of proteins common to many variants, including escape mutants. For vectored vaccines, these 'universal' subunit immunogens are most efficiently delivered using heterologous prime-boost regimens, which can be further optimised by adjuvantation and route of delivery. EXPERT OPINION Development of vaccines against human diseases has many features in common. Acceleration of vaccine discovery depends on basic research and new technologies. Novel strategies should be safely, but rapidly tested in humans. While out-of-the-box thinking is important, vaccine success largely depends on incremental advances best achieved through small, systematic, iterative clinical studies. Failures are inevitable, but the end rewards are huge. The future will be exciting.
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Affiliation(s)
- Tomáš Hanke
- The Jenner Institute, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ , UK
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42
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Zarnitsyna VI, Evavold BD, Schoettle LN, Blattman JN, Antia R. Estimating the diversity, completeness, and cross-reactivity of the T cell repertoire. Front Immunol 2013; 4:485. [PMID: 24421780 PMCID: PMC3872652 DOI: 10.3389/fimmu.2013.00485] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2013] [Accepted: 12/10/2013] [Indexed: 11/13/2022] Open
Abstract
In order to recognize and combat a diverse array of pathogens the immune system has a large repertoire of T cells having unique T cell receptors (TCRs) with only a few clones specific for any given antigen. We discuss how the number of different possible TCRs encoded in the genome (the potential repertoire) and the number of different TCRs present in an individual (the realized repertoire) can be measured. One puzzle is that the potential repertoire greatly exceeds the realized diversity of naïve T cells within any individual. We show that the existing hypotheses fail to explain why the immune system has the potential to generate far more diversity than is used in an individual, and propose an alternative hypothesis of “evolutionary sloppiness.” Another immunological puzzle is why mice and humans have similar repertoires even though humans have over 1000-fold more T cells. We discuss how the idea of the “protecton,” the smallest unit of protection, might explain this discrepancy and estimate the size of “protecton” based on available precursor frequencies data. We then consider T cell cross-reactivity – the ability of a T cell clone to respond to more than one epitope. We extend existing calculations to estimate the extent of expected cross-reactivity between the responses to different pathogens. Our results are consistent with two observations: a low probability of observing cross-reactivity between the immune responses to two randomly chosen pathogens; and the ensemble of memory cells being sufficiently diverse to generate cross-reactive responses to new pathogens.
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Affiliation(s)
| | - Brian D Evavold
- Department of Microbiology and Immunology, Emory University , Atlanta, GA , USA
| | - Louis N Schoettle
- Center for Infectious Diseases and Vaccinology, School of Life Sciences, Arizona State University , Tempe, AZ , USA
| | - Joseph N Blattman
- Center for Infectious Diseases and Vaccinology, School of Life Sciences, Arizona State University , Tempe, AZ , USA
| | - Rustom Antia
- Department of Biology, Emory University , Atlanta, GA , USA
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Calis JJA, Maybeno M, Greenbaum JA, Weiskopf D, De Silva AD, Sette A, Keşmir C, Peters B. Properties of MHC class I presented peptides that enhance immunogenicity. PLoS Comput Biol 2013; 9:e1003266. [PMID: 24204222 PMCID: PMC3808449 DOI: 10.1371/journal.pcbi.1003266] [Citation(s) in RCA: 530] [Impact Index Per Article: 48.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 08/23/2013] [Indexed: 12/14/2022] Open
Abstract
T-cells have to recognize peptides presented on MHC molecules to be activated and elicit their effector functions. Several studies demonstrate that some peptides are more immunogenic than others and therefore more likely to be T-cell epitopes. We set out to determine which properties cause such differences in immunogenicity. To this end, we collected and analyzed a large set of data describing the immunogenicity of peptides presented on various MHC-I molecules. Two main conclusions could be drawn from this analysis: First, in line with previous observations, we showed that positions P4–6 of a presented peptide are more important for immunogenicity. Second, some amino acids, especially those with large and aromatic side chains, are associated with immunogenicity. This information was combined into a simple model that was used to demonstrate that immunogenicity is, to a certain extent, predictable. This model (made available at http://tools.iedb.org/immunogenicity/) was validated with data from two independent epitope discovery studies. Interestingly, with this model we could show that T-cells are equipped to better recognize viral than human (self) peptides. After the past successful elucidation of different steps in the MHC-I presentation pathway, the identification of variables that influence immunogenicity will be an important next step in the investigation of T-cell epitopes and our understanding of cellular immune responses. T-cells have to recognize peptides presented on MHC molecules to be activated and elicit their effector functions. Some peptide-MHC-I complexes (pMHCs) are better recognized by T-cells; we call such pMHCs more immunogenic. For other pMHCs, no recognizing T-cells seem to exist; we call such pMHCs non-immunogenic. We set out to determine which properties of pMHCs cause such differences in immunogenicity, by carefully collecting a large set of immunogenic and non-immunogenic pMHCs, and analysing the difference between these sets. Two important observations were made: First, in line with previous observations, we showed that positions P4–6 of a presented peptide are more important for immunogenicity. Second, some amino acids, especially those with large and aromatic side chains, seem to be better recognized by T-cells as they associate with immunogenicity. Next, this information was combined into a simple model to predict the immunogenicity of new pMHCs (this model is made available at http://tools.iedb.org/immunogenicity/). Interestingly, with this model we could show that T-cells are equipped to strongly recognize viral peptides. After the past successful elucidation of different steps in the MHC-I presentation pathway, the identification of variables that influence immunogenicity will be an important next step in the investigation of T-cell epitopes and our understanding of cellular immune responses.
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Affiliation(s)
- Jorg J. A. Calis
- Theoretical Biology & Bioinformatics, Utrecht University, Utrecht, The Netherlands
- * E-mail:
| | - Matt Maybeno
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America
| | - Jason A. Greenbaum
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America
| | - Daniela Weiskopf
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America
| | - Aruna D. De Silva
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America
- Genetech Research Institute, Colombo, Sri Lanka
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America
| | - Can Keşmir
- Theoretical Biology & Bioinformatics, Utrecht University, Utrecht, The Netherlands
| | - Bjoern Peters
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America
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Sulfamethoxazole induces a switch mechanism in T cell receptors containing TCRVβ20-1, altering pHLA recognition. PLoS One 2013; 8:e76211. [PMID: 24116097 PMCID: PMC3792127 DOI: 10.1371/journal.pone.0076211] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Accepted: 08/21/2013] [Indexed: 11/19/2022] Open
Abstract
T cell receptors (TCR) containing Vβ20-1 have been implicated in a wide range of T cell mediated disease and allergic reactions, making it a target for understanding these. Mechanics of T cell receptors are largely unexplained by static structures available from x-ray crystallographic studies. A small number of molecular dynamic simulations have been conducted on TCR, however are currently lacking either portions of the receptor or explanations for differences between binding and non-binding TCR recognition of respective peptide-HLA. We performed molecular dynamic simulations of a TCR containing variable domain Vβ20-1, sequenced from drug responsive T cells. These were initially from a patient showing maculopapular eruptions in response to the sulfanilamide-antibiotic sulfamethoxazole (SMX). The CDR2β domain of this TCR was found to dock SMX with high affinity. Using this compound as a perturbation, overall mechanisms involved in responses mediated by this receptor were explored, showing a chemical action on the TCR free from HLA or peptide interaction. Our simulations show two completely separate modes of binding cognate peptide-HLA complexes, with an increased affinity induced by SMX bound to the Vβ20-1. Overall binding of the TCR is mediated through a primary recognition by either the variable β or α domain, and a switch in recognition within these across TCR loops contacting the peptide and HLA occurs when SMX is present in the CDR2β loop. Large binding affinity differences are induced by summed small amino acid changes primarily by SMX modifying only three critical CDR2β loop amino acid positions. These residues, TYRβ57, ASPβ64, and LYSβ65 initially hold hydrogen bonds from the CDR2β to adjacent CDR loops. Effects from SMX binding are amplified and traverse longer distances through internal TCR hydrogen bonding networks, controlling the overall TCR conformation. Thus, the CDR2β of Vβ20-1 acts as a ligand controlled switch affecting overall TCR binding affinity.
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Abstract
Since the discovery of hepatitis C virus (HCV) by molecular cloning almost a quarter of a century ago, unprecedented at the time because the virus had never been grown in cell culture or detected serologically, there have been impressive strides in many facets of our understanding of the natural history of the disease, the viral life cycle, the pathogenesis, and antiviral therapy. It is apparent that the virus has developed multiple strategies to evade immune surveillance and eradication. This Review covers what we currently understand of the temporal and spatial immunological changes within the human innate and adaptive host immune responses that ultimately determine the outcomes of HCV infection.
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46
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Wooldridge L. Individual MHCI-Restricted T-Cell Receptors are Characterized by a Unique Peptide Recognition Signature. Front Immunol 2013; 4:199. [PMID: 23888160 PMCID: PMC3719040 DOI: 10.3389/fimmu.2013.00199] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 07/03/2013] [Indexed: 11/13/2022] Open
Abstract
Effective immunity requires that a limited TCR repertoire is able to recognize a vast number of foreign peptide-MHCI (peptide-major histocompatibility complex class I) molecules. This challenge is overcome by the ability of individual TCRs to recognize large numbers of peptides. Recently, it was demonstrated that MHCI-restricted TCRs can recognize up to 106 peptides of a defined length. Astonishingly, this remarkable level of promiscuity does not extend to peptides of different lengths, a fundamental observation that has broad implications for CD8+ T-cell immunity. In particular, the findings suggest that effective immunity can only be achieved by mobilization of “length-matched” CD8+ T-cell clonotypes. Overall, recent findings suggest that every TCR is specific for a unique set of peptides, which can be described as a unique “peptide recognition signature” (PRS) and consists of three components: (1) peptide length preference, (2) number of peptides recognized; and, (3) sequence identity (e.g., self versus pathogen derived). In future, the ability to de-convolute peptide recognition signatures across the normal and pathogenic repertoire will be essential for understanding the system requirements for effective CD8+ T-cell immunity and elucidating mechanisms which underlie CD8+ T-cell mediated disease.
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Affiliation(s)
- Linda Wooldridge
- Institute of Infection and Immunity, Cardiff University School of Medicine , Heath Park, Cardiff , UK
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47
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Motozono C, Miles JJ, Hasan Z, Gatanaga H, Meribe SC, Price DA, Oka S, Sewell AK, Ueno T. CD8(+) T cell cross-reactivity profiles and HIV-1 immune escape towards an HLA-B35-restricted immunodominant Nef epitope. PLoS One 2013; 8:e66152. [PMID: 23799076 PMCID: PMC3684606 DOI: 10.1371/journal.pone.0066152] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Accepted: 05/01/2013] [Indexed: 11/23/2022] Open
Abstract
Antigen cross-reactivity is an inbuilt feature of the T cell compartment. However, little is known about the flexibility of T cell recognition in the context of genetically variable pathogens such as HIV-1. In this study, we used a combinatorial library containing 24 billion octamer peptides to characterize the cross-reactivity profiles of CD8+ T cells specific for the immunodominant HIV-1 subtype B Nef epitope VY8 (VPLRPMTY) presented by HLA-B*35∶01. In conjunction, we examined naturally occurring antigenic variations within the VY8 epitope. Sequence analysis of plasma viral RNA isolated from 336 HIV-1-infected individuals revealed variability at position (P) 3 and P8 of VY8; Phe at P8, but not Val at P3, was identified as an HLA-B*35∶01-associated polymorphism. VY8-specific T cells generated from several different HIV-1-infected patients showed unique and clonotype-dependent cross-reactivity footprints. Nonetheless, all T cells recognized both the index Leu and mutant Val at P3 equally well. In contrast, competitive titration assays revealed that the Tyr to Phe substitution at P8 reduced T cell recognition by 50–130 fold despite intact peptide binding to HLA-B*35∶01. These findings explain the preferential selection of Phe at the C-terminus of VY8 in HLA-B*35∶01+ individuals and demonstrate that HIV-1 can exploit the limitations of T cell recognition in vivo.
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Affiliation(s)
- Chihiro Motozono
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
| | - John J. Miles
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
- Australian Centre for Vaccine Development, Human Immunity Laboratory, Queensland Institute of Medical Research, Brisbane, Australia
- School of Medicine, The University of Queensland, Brisbane, Australia
| | - Zafrul Hasan
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
| | - Hiroyuki Gatanaga
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
- AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan
| | | | - David A. Price
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
| | - Shinichi Oka
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
- AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Andrew K. Sewell
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
- * E-mail: (TU); (AKS)
| | - Takamasa Ueno
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
- * E-mail: (TU); (AKS)
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48
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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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49
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Yin Y, Li Y, Mariuzza RA. Structural basis for self-recognition by autoimmune T-cell receptors. Immunol Rev 2013; 250:32-48. [PMID: 23046121 DOI: 10.1111/imr.12002] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
T-cell receptors (TCRs) recognize peptides presented by major histocompatibility complex molecules (pMHC) to discriminate between foreign and self-antigens. Whereas T-cell recognition of foreign peptides is essential for protection against microbial pathogens, recognition of self-peptides by T cells that have escaped negative selection in the thymus can lead to autoimmune disease. Structural studies of autoimmune TCR-pMHC complexes have provided insights into the mechanisms underlying self-recognition and escape from thymic deletion. Two broad categories of self-reactive TCRs can be clearly distinguished: (i) TCRs with altered binding topologies to self-pMHC and (ii) TCRs that bind self-pMHC in the canonical diagonal orientation, but where there are structural defects or suboptimal anchors in the self-ligand. For both categories, however, the overall stability of the autoimmune TCR-pMHC complex is markedly reduced compared to anti-microbial complexes, allowing the autoreactive T cells to evade negative selection, yet retain the ability to be activated by self-antigens in target organs. Additionally, the structures provide insights into TCR cross-reactivity, which can contribute to autoimmunity by increasing the likelihood of self-pMHC recognition. Efforts are now underway to understand the impact of structural alterations in autoimmune TCR-pMHC complexes on higher order assemblies involved in TCR signaling, as well as on immunological synapse formation.
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Affiliation(s)
- Yiyuan Yin
- Department of Antibody Engineering, Genentech, South San Francisco, CA, USA
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Baker BM, Scott DR, Blevins SJ, Hawse WF. Structural and dynamic control of T-cell receptor specificity, cross-reactivity, and binding mechanism. Immunol Rev 2013; 250:10-31. [PMID: 23046120 DOI: 10.1111/j.1600-065x.2012.01165.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Over the past two decades, structural biology has shown how T-cell receptors engage peptide/major histocompatibility complex (MHC) complexes and provided insight into the mechanisms underlying antigen specificity and cross-reactivity. Here we review and contextualize our contributions, which have emphasized the influence of structural changes and molecular flexibility. A repeated observation is the presence of conformational melding, in which the T-cell receptor (TCR), peptide, and in some cases, MHC protein cooperatively adjust in order for recognition to proceed. The structural changes reflect the intrinsic dynamics of the unligated proteins. Characterization of the dynamics of unligated TCR shows how binding loop motion can influence TCR cross-reactivity as well as specificity towards peptide and MHC. Examination of peptide dynamics indicates not only peptide-specific variation but also a peptide dependence to MHC flexibility. This latter point emphasizes that the TCR engages a composite peptide/MHC surface and that physically the receptor makes little distinction between the peptide and MHC. Much additional evidence for this can be found within the database of available structures, including our observations of a peptide dependence to the TCR binding mode and structural compensations for altered interatomic interactions, in which lost TCR-peptide interactions are replaced with TCR-MHC interactions. The lack of a hard-coded physical distinction between peptide and MHC has implications not only for specificity and cross-reactivity but also the mechanisms underlying MHC restriction as well as attempts to modulate and control TCR recognition.
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Affiliation(s)
- Brian M Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, IN, USA.
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