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Lobos CA, Chatzileontiadou DSM, Sok B, Almedia C, Halim H, D'Orsogna L, Gras S. Molecular insights into the HLA-B35 molecules' classification associated with HIV control. Immunol Cell Biol 2024; 102:34-45. [PMID: 37811811 PMCID: PMC10952751 DOI: 10.1111/imcb.12698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 07/04/2023] [Accepted: 09/19/2023] [Indexed: 10/10/2023]
Abstract
Human leukocyte antigen (HLA) class I molecules have been shown to influence the immune response to HIV infection and acquired immunodeficiency syndrome progression. Polymorphisms within the HLA-B35 molecules divide the family into two groups, namely, Px and PY. The Px group is associated with deleterious effects and accelerated disease progression in HIV+ patients, whereas the PY group is not. The classification is based on the preferential binding of a tyrosine at the C-terminal part of the peptide in the PY group, and a nontyrosine residue in the Px group. However, there is a lack of knowledge on the molecular differences between the two groups. Here, we have investigated three HLA-B35 molecules, namely, HLA-B*35:01 (PY), HLA-B*35:03 (Px) and HLA-B*35:05 (unclassified). We selected an HIV-derived peptide, NY9, and demonstrated that it can trigger a polyfunctional CD8+ T-cell response in HLA-B*35:01+ /HIV+ patients. We determined that in the complex with the NY9 peptide, the PY molecule was more stable than the Px molecule. We solved the crystal structures of the three HLA molecules in complex with the NY9 peptide, and structural similarities with HLA-B*35:01 would classify the HLA-B*35:05 within the PY group. Interestingly, we found that HLA-B*35:05 can also bind a small molecule in its cleft, suggesting that small drugs could bind as well.
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Affiliation(s)
- Christian A Lobos
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular ScienceLa Trobe UniversityBundooraVICAustralia
- Department of Biochemistry and Molecular BiologyMonash UniversityClaytonVICAustralia
| | - Demetra SM Chatzileontiadou
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular ScienceLa Trobe UniversityBundooraVICAustralia
- Department of Biochemistry and Molecular BiologyMonash UniversityClaytonVICAustralia
| | - Bonin Sok
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular ScienceLa Trobe UniversityBundooraVICAustralia
| | - Coral‐Ann Almedia
- Department of Clinical Immunology and PathWestFiona Stanley HospitalPerthWAAustralia
- School of MedicineUniversity of Western AustraliaPerthWAAustralia
| | - Hanim Halim
- Department of Biochemistry and Molecular BiologyMonash UniversityClaytonVICAustralia
| | - Lloyd D'Orsogna
- Department of Clinical Immunology and PathWestFiona Stanley HospitalPerthWAAustralia
- School of MedicineUniversity of Western AustraliaPerthWAAustralia
| | - Stephanie Gras
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular ScienceLa Trobe UniversityBundooraVICAustralia
- Department of Biochemistry and Molecular BiologyMonash UniversityClaytonVICAustralia
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2
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Tirado-Herranz A, Guasp P, Pastor-Moreno A, Area-Navarro M, Alvarez I. Analysis of the different subpeptidomes presented by the HLA class I molecules of the B7 supertype. Cell Immunol 2023; 387:104707. [PMID: 36933326 DOI: 10.1016/j.cellimm.2023.104707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/03/2023] [Accepted: 03/07/2023] [Indexed: 03/14/2023]
Abstract
MHC-I molecules of the HLA-B7 supertype preferentially bind peptides with proline at position 2. HLA-B*51:01 and B*51:08 present two predominant subpeptidomes, one with Pro2 and hydrophobic residues at P1, and another with Ala2 and Asp enriched at position 1. Here, we present a meta-analysis of the peptidomes presented by molecules of the B7 supertype to investigate the presence of subpeptidomes across different allotypes. Several allotypes presented subpeptidomes differing in the presence of Pro or another residue at P2. The Ala2 subpeptidomes preferred Asp1 except in HLA-B*54:01, where ligands with Ala2 contained Glu1. Sequence alignment and the analysis of crystal structures allowed us to propose positions 45 and 67 of the MHC heavy chain as relevant for the presence of subpeptidomes. Deciphering the principles behind the presence of subpeptidomes could improve our understanding of antigen presentation in other MHC-I molecules. Running title: HLA-B7 supertype subpeptidomes.
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Affiliation(s)
- Adrián Tirado-Herranz
- Immunology Unit, Department of Cell Biology, Physiology and Immunology, Autonomous University of Barcelona, 08193 Bellaterra, Spain; Institute of Biotechnology and Biomedicine, Autonomous University of Barcelona, 08193 Bellaterra, Spain
| | - Pablo Guasp
- Immuno-Oncology Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alba Pastor-Moreno
- Immunology Unit, Department of Cell Biology, Physiology and Immunology, Autonomous University of Barcelona, 08193 Bellaterra, Spain; Institute of Biotechnology and Biomedicine, Autonomous University of Barcelona, 08193 Bellaterra, Spain
| | - María Area-Navarro
- Immunology Unit, Department of Cell Biology, Physiology and Immunology, Autonomous University of Barcelona, 08193 Bellaterra, Spain; Institute of Biotechnology and Biomedicine, Autonomous University of Barcelona, 08193 Bellaterra, Spain
| | - Iñaki Alvarez
- Immunology Unit, Department of Cell Biology, Physiology and Immunology, Autonomous University of Barcelona, 08193 Bellaterra, Spain; Institute of Biotechnology and Biomedicine, Autonomous University of Barcelona, 08193 Bellaterra, Spain.
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3
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Li X, Lin X, Mei X, Chen P, Liu A, Liang W, Chang S, Li J. HLA3D: an integrated structure-based computational toolkit for immunotherapy. Brief Bioinform 2022; 23:6548371. [PMID: 35289353 PMCID: PMC9116210 DOI: 10.1093/bib/bbac076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/12/2022] [Accepted: 02/14/2022] [Indexed: 01/02/2023] Open
Abstract
Motivation The human major histocompatibility complex (MHC), also known as human leukocyte antigen (HLA), plays an important role in the adaptive immune system by presenting non-self-peptides to T cell receptors. The MHC region has been shown to be associated with a variety of diseases, including autoimmune diseases, organ transplantation and tumours. However, structural analytic tools of HLA are still sparse compared to the number of identified HLA alleles, which hinders the disclosure of its pathogenic mechanism. Result To provide an integrative analysis of HLA, we first collected 1296 amino acid sequences, 256 protein data bank structures, 120 000 frequency data of HLA alleles in different populations, 73 000 publications and 39 000 disease-associated single nucleotide polymorphism sites, as well as 212 modelled HLA heterodimer structures. Then, we put forward two new strategies for building up a toolkit for transplantation and tumour immunotherapy, designing risk alignment pipeline and antigenic peptide prediction pipeline by integrating different resources and bioinformatic tools. By integrating 100 000 calculated HLA conformation difference and online tools, risk alignment pipeline provides users with the functions of structural alignment, sequence alignment, residue visualization and risk report generation of mismatched HLA molecules. For tumour antigen prediction, we first predicted 370 000 immunogenic peptides based on the affinity between peptides and MHC to generate the neoantigen catalogue for 11 common tumours. We then designed an antigenic peptide prediction pipeline to provide the functions of mutation prediction, peptide prediction, immunogenicity assessment and docking simulation. We also present a case study of hepatitis B virus mutations associated with liver cancer that demonstrates the high legitimacy of our antigenic peptide prediction process. HLA3D, including different HLA analytic tools and the prediction pipelines, is available at http://www.hla3d.cn/.
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Affiliation(s)
- Xingyu Li
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Xue Lin
- Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, China
| | - Xueyin Mei
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Pin Chen
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Anna Liu
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Weicheng Liang
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Shan Chang
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
| | - Jian Li
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China
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Sim MJW, Stotz Z, Lu J, Brennan P, Long EO, Sun PD. T cells discriminate between groups C1 and C2 HLA-C. eLife 2022; 11:75670. [PMID: 35587797 PMCID: PMC9177145 DOI: 10.7554/elife.75670] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 05/15/2022] [Indexed: 01/09/2023] Open
Abstract
Dimorphic amino acids at positions 77 and 80 delineate HLA-C allotypes into two groups, C1 and C2, which associate with disease through interactions with C1 and C2-specific natural killer cell receptors. How the C1/C2 dimorphism affects T cell recognition is unknown. Using HLA-C allotypes that differ only by the C1/C2-defining residues, we found that KRAS-G12D neoantigen-specific T cell receptors (TCRs) discriminated between C1 and C2 presenting the same KRAS-G12D peptides. Structural and functional experiments, and immunopeptidomics analysis revealed that Ser77 in C1 and Asn77 in C2 influence amino acid preference near the peptide C-terminus (pΩ), including the pΩ-1 position, in which C1 favors small and C2 prefers large residues. This resulted in weaker TCR affinity for KRAS-G12D-bound C2-HLA-C despite conserved TCR contacts. Thus, the C1/C2 dimorphism on its own impacts peptide presentation and HLA-C-restricted T cell responses, with implications in disease, including adoptive T cell therapy targeting KRAS-G12D-induced cancers.
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Affiliation(s)
- Malcolm J W Sim
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of HealthRockvilleUnited States
| | - Zachary Stotz
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of HealthRockvilleUnited States
| | - Jinghua Lu
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of HealthRockvilleUnited States
| | - Paul Brennan
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of HealthRockvilleUnited States
| | - Eric O Long
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of HealthRockvilleUnited States
| | - Peter D Sun
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of HealthRockvilleUnited States
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Jantz-Naeem N, Springer S. Venus flytrap or pas de trois? The dynamics of MHC class I molecules. Curr Opin Immunol 2021; 70:82-89. [PMID: 33993034 DOI: 10.1016/j.coi.2021.04.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/05/2021] [Accepted: 04/08/2021] [Indexed: 11/25/2022]
Abstract
The peptide binding site of major histocompatibility complex (MHC) class I molecules is natively unfolded when devoid of peptides. Peptide binding stabilizes the structure and slows the dynamics, but peptide-specific and subtype-specific motions influence, and are influenced by, interaction with assembly chaperones, the T cell receptor, and other class I-binding proteins. The molecular mechanisms of cooperation between peptide, class I heavy chain, and beta-2 microglobulin are insufficiently known but are being elucidated by nuclear magnetic resonance and other modern methods. It appears that micropolymorphic clusters of charged amino acids, often hidden in the molecule interior, determine the dynamics and thus chaperone dependence, cellular fate, and disease association of class I.
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Affiliation(s)
- Nouria Jantz-Naeem
- Department of Life Sciences and Chemistry, Jacobs University, Bremen, Germany
| | - Sebastian Springer
- Department of Life Sciences and Chemistry, Jacobs University, Bremen, Germany.
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6
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Kedzierska K, Koutsakos M. The ABC of Major Histocompatibility Complexes and T Cell Receptors in Health and Disease. Viral Immunol 2021; 33:160-178. [PMID: 32286182 PMCID: PMC7185345 DOI: 10.1089/vim.2019.0184] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
A seminal discovery of major histocompatibility complex (MHC) restriction in T cell recognition by Peter Doherty and Rolf Zinkernagel has led to 45 years of exciting research on the mechanisms governing peptide MHC (pMHC) recognition by T cell receptors (TCRs) and their importance in health and disease. T cells provide a significant level of protection against viral, bacterial, and parasitic infections, as well as tumors, hence, the generation of protective T cell responses is a primary goal for cell-mediated vaccines and immunotherapies. Understanding the mechanisms underlying generation of optimal high-avidity effector T cell responses, memory development, maintenance, and recall is of major importance for the rational design of preventative and therapeutic vaccines/immunotherapies. In this review, we summarize the lessons learned over the last four decades and outline our current understanding of the basis and consequences of pMHC/TCR interactions on T cell development and function, and TCR diversity and composition, driving better clinical outcomes and prevention of viral escape. We also discuss the current models of T cell memory formation and determinants of immunodominant T cell responses in animal models and humans. As TCR composition and diversity can affect both the protective capacity of T cells and protection against viral escape, defining the spectrum of TCR selection has implications for improving the functional efficacy of effector T cell responsiveness and memory formation.
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Affiliation(s)
- Katherine Kedzierska
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Marios Koutsakos
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
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7
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Oncogenic Properties of the EBV ZEBRA Protein. Cancers (Basel) 2020; 12:cancers12061479. [PMID: 32517128 PMCID: PMC7352903 DOI: 10.3390/cancers12061479] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/03/2020] [Accepted: 06/04/2020] [Indexed: 12/14/2022] Open
Abstract
Epstein Barr Virus (EBV) is one of the most common human herpesviruses. After primary infection, it can persist in the host throughout their lifetime in a latent form, from which it can reactivate following specific stimuli. EBV reactivation is triggered by transcriptional transactivator proteins ZEBRA (also known as Z, EB-1, Zta or BZLF1) and RTA (also known as BRLF1). Here we discuss the structural and functional features of ZEBRA, its role in oncogenesis and its possible implication as a prognostic or diagnostic marker. Modulation of host gene expression by ZEBRA can deregulate the immune surveillance, allow the immune escape, and favor tumor progression. It also interacts with host proteins, thereby modifying their functions. ZEBRA is released into the bloodstream by infected cells and can potentially penetrate any cell through its cell-penetrating domain; therefore, it can also change the fate of non-infected cells. The features of ZEBRA described in this review outline its importance in EBV-related malignancies.
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8
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The molecular basis of how buried human leukocyte antigen polymorphism modulates natural killer cell function. Proc Natl Acad Sci U S A 2020; 117:11636-11647. [PMID: 32404419 DOI: 10.1073/pnas.1920570117] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Micropolymorphisms within human leukocyte antigen (HLA) class I molecules can change the architecture of the peptide-binding cleft, leading to differences in peptide presentation and T cell recognition. The impact of such HLA variation on natural killer (NK) cell recognition remains unclear. Given the differential association of HLA-B*57:01 and HLA-B*57:03 with the control of HIV, recognition of these HLA-B57 allomorphs by the killer cell immunoglobulin-like receptor (KIR) 3DL1 was compared. Despite differing by only two polymorphic residues, both buried within the peptide-binding cleft, HLA-B*57:01 more potently inhibited NK cell activation. Direct-binding studies showed KIR3DL1 to preferentially recognize HLA-B*57:01, particularly when presenting peptides with positively charged position (P)Ω-2 residues. In HLA-B*57:01, charged PΩ-2 residues were oriented toward the peptide-binding cleft and away from KIR3DL1. In HLA-B*57:03, the charged PΩ-2 residues protruded out from the cleft and directly impacted KIR3DL1 engagement. Accordingly, KIR3DL1 recognition of HLA class I ligands is modulated by both the peptide sequence and conformation, as determined by the HLA polymorphic framework, providing a rationale for understanding differences in clinical associations.
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9
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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: 13] [Impact Index Per Article: 3.3] [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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10
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Lérias JR, Paraschoudi G, de Sousa E, Martins J, Condeço C, Figueiredo N, Carvalho C, Dodoo E, Castillo-Martin M, Beltrán A, Ligeiro D, Rao M, Zumla A, Maeurer M. Microbes as Master Immunomodulators: Immunopathology, Cancer and Personalized Immunotherapies. Front Cell Dev Biol 2020; 7:362. [PMID: 32039196 PMCID: PMC6989410 DOI: 10.3389/fcell.2019.00362] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 12/12/2019] [Indexed: 12/12/2022] Open
Abstract
The intricate interplay between the immune system and microbes is an essential part of the physiological homeostasis in health and disease. Immunological recognition of commensal microbes, such as bacterial species resident in the gut or lung as well as dormant viral species, i.e., cytomegalovirus (CMV) or Epstein-Barr virus (EBV), in combination with a balanced immune regulation, is central to achieve immune-protection. Emerging evidence suggests that immune responses primed to guard against commensal microbes may cause unexpected pathological outcomes, e.g., chronic inflammation and/or malignant transformation. Furthermore, translocation of immune cells from one anatomical compartment to another, i.e., the gut-lung axis via the lymphatics or blood has been identified as an important factor in perpetrating systemic inflammation, tissue destruction, as well as modulating host-protective immune responses. We present in this review immune response patterns to pathogenic as well as non-pathogenic microbes and how these immune-recognition profiles affect local immune responses or malignant transformation. We discuss personalized immunological therapies which, directly or indirectly, target host biological pathways modulated by antimicrobial immune responses.
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Affiliation(s)
- Joana R. Lérias
- ImmunoSurgery Unit, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | | | - Eric de Sousa
- ImmunoSurgery Unit, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - João Martins
- ImmunoSurgery Unit, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Carolina Condeço
- ImmunoSurgery Unit, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Nuno Figueiredo
- Digestive Unit, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Carlos Carvalho
- Digestive Unit, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | | | | | - Antonio Beltrán
- Department of Pathology, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Dário Ligeiro
- Lisbon Centre for Blood and Transplantation, Instituto Português do Sangue e Transplantação, Lisbon, Portugal
| | - Martin Rao
- ImmunoSurgery Unit, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Alimuddin Zumla
- Division of Infection and Immunity, NIHR Biomedical Research Centre, University College London Hospitals NHS Foundation Trust, University College London, London, United Kingdom
| | - Markus Maeurer
- ImmunoSurgery Unit, Champalimaud Centre for the Unknown, Lisbon, Portugal
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11
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Singh G, Pritam M, Banerjee M, Singh AK, Singh SP. Genome based screening of epitope ensemble vaccine candidates against dreadful visceral leishmaniasis using immunoinformatics approach. Microb Pathog 2019; 136:103704. [PMID: 31479726 DOI: 10.1016/j.micpath.2019.103704] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 08/12/2019] [Accepted: 08/31/2019] [Indexed: 01/09/2023]
Abstract
Visceral leishmaniasis (VL) is a dreadful protozoan disease caused by Leishmania donovani that severely affects huge populations in tropical and sub-tropical regions. The present study reports an unbiased genome based screening of 4 potent vaccine antigens against 8023 L. donovani proteins by following the criteria of presence of signal peptides, GPI-anchors and ≤1 transmembrane helix using advanced bioinformatics tools viz. SignalP4.0, PredGPI and TMHMM2.0, respectively. They are designated as genome based predicted signal peptide antigens (GBPSPA). The antigenicity/immunogenicity of chosen vaccine antigens (GBPSPA) with 4 randomly selected known leishmanial antigens (RSKLA) was compared by simulation study employing C-ImmSim software for human immune responses. This revealed better immunological responses. These antigens were further evaluated for the presence of B- and T-cell epitopes using immune epitope database (IEDB) based recommended consensus method of MHC class I and II tools. It was found to forecast CD4+ and CD8+ T-cell responses in genetically diverse human population worldwide as well as different endemic regions through IEDB based predicted population coverage (PPC) analysis tool. The worldwide percent PPC value of combined (HLA class I and II) epitope ensemble forecast was found to be 99.98, 99.96 and 50.04, respectively for GBPSPA, RSKLA and experimentally known epitopes (EKE) of L. donovani. Therefore, these potential antigens/epitope ensembles could favor the design of prospective and novel vaccine constructs like self-assembled epitopes as nano vaccine formulations against VL. Overall, the present study will serve as a model framework that might improve the effectiveness of designed vaccine against L. donovani and other related pathogens.
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Affiliation(s)
- Garima Singh
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow-226028, India.
| | - Manisha Pritam
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow-226028, India.
| | - Monisha Banerjee
- Molecular and Human Genetics Laboratory, Department of Zoology, University of Lucknow, Lucknow- 226007, India.
| | - Akhilesh Kumar Singh
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow-226028, India.
| | - Satarudra Prakash Singh
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow-226028, India; Department of Biotech and Genome, School of Life Sciences, Mahatma Gandhi Central University, Motihari-845401, India.
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12
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Gfeller D, Guillaume P, Michaux J, Pak HS, Daniel RT, Racle J, Coukos G, Bassani-Sternberg M. The Length Distribution and Multiple Specificity of Naturally Presented HLA-I Ligands. THE JOURNAL OF IMMUNOLOGY 2018; 201:3705-3716. [DOI: 10.4049/jimmunol.1800914] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 10/12/2018] [Indexed: 11/19/2022]
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13
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Illing PT, Pymm P, Croft NP, Hilton HG, Jojic V, Han AS, Mendoza JL, Mifsud NA, Dudek NL, McCluskey J, Parham P, Rossjohn J, Vivian JP, Purcell AW. HLA-B57 micropolymorphism defines the sequence and conformational breadth of the immunopeptidome. Nat Commun 2018; 9:4693. [PMID: 30410026 PMCID: PMC6224591 DOI: 10.1038/s41467-018-07109-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 10/12/2018] [Indexed: 12/17/2022] Open
Abstract
Immunophenotypic differences between closely related human leukocyte antigen (HLA) alleles have been associated with divergent clinical outcomes in infection, autoimmunity, transplantation and drug hypersensitivity. Here we explore the impact of micropolymorphism on peptide antigen presentation by three closely related HLA molecules, HLA-B*57:01, HLA-B*57:03 and HLA-B*58:01, that are differentially associated with the HIV elite controller phenotype and adverse drug reactions. For each allotype, we mine HLA ligand data sets derived from the same parental cell proteome to define qualitative differences in peptide presentation using classical peptide binding motifs and an unbiased statistical approach. The peptide repertoires show marked qualitative overlap, with 982 peptides presented by all allomorphs. However, differences in peptide abundance, HLA-peptide stability, and HLA-bound conformation demonstrate that HLA micropolymorphism impacts more than simply the range of peptide ligands. These differences provide grounds for distinct immune reactivity and insights into the capacity of micropolymorphism to diversify immune outcomes. Human leukocyte antigens (HLA) are multi-allelic and polymorphic genes that present antigens to immune cells for inducing protective immunity. Here, using systems biology and structural approaches, the authors show that micropolymorphism of three HLA has effects beyond the modulation of antigen diversity.
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Affiliation(s)
- Patricia T Illing
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Phillip Pymm
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia.,Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC, 3800, Australia
| | - Nathan P Croft
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Hugo G Hilton
- Departments of Structural Biology and Microbiology & Immunology, School of Medicine, Stanford University, Stanford, 94305, CA, USA.,Calico Life Sciences LLC, South San Francisco, 94080, CA, USA
| | - Vladimir Jojic
- Calico Life Sciences LLC, South San Francisco, 94080, CA, USA
| | - Alex S Han
- Department of Genetics, School of Medicine, Stanford University, Stanford, 94305, CA, USA
| | - Juan L Mendoza
- Department of Molecular and Cellular Physiology, School of Medicine, Stanford University, Stanford, 94305, CA, USA.,Institute for Molecular Engineering and Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, 60637, IL, USA
| | - Nicole A Mifsud
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Nadine L Dudek
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - James McCluskey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Peter Parham
- Departments of Structural Biology and Microbiology & Immunology, School of Medicine, Stanford University, Stanford, 94305, CA, USA
| | - Jamie Rossjohn
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia.,Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC, 3800, Australia.,Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, CF14 4XN, UK
| | - Julian P Vivian
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia. .,Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC, 3800, Australia.
| | - Anthony W Purcell
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia.
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14
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Abels WC, Manandhar T, Kunze-Schumacher H, Blasczyk R, Bade-Döding C. The polymorphism at residue 156 determines the HLA-B*35 restricted peptide repertoire during HCMV infection. Immunogenetics 2018; 70:639-646. [PMID: 30128813 PMCID: PMC6182399 DOI: 10.1007/s00251-018-1077-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 08/16/2018] [Indexed: 12/27/2022]
Abstract
Peptide selection in infected cells is not fully understood yet, but several indications point to the fact that there are differences to uninfected cells, especially in productive HCMV infection, since HCMV evolved various strategies to disable the hosts immune system, including presentation of peptide-HLA complexes to immune effector cells. Therefore, peptide predictions for specific HLA alleles are limited in these cases and the naturally presented peptide repertoire of HCMV-infected cells is of major interest to optimize adoptive T cell therapies. The allotypes HLA-B*35:01 and B*35:08 differ at a single amino acid at position 156 and have been described to differ in their peptide features and in their association with the peptide loading complex. Virus specific T cells recognizing the allelic pHLA-B*35 complexes could be detected, indicating a significant role of this HLA subtypes in viral immunity. However, naturally selected and presented viral peptides have not been described so far. In this study, we analyzed the peptide binding repertoire for HLA-B*35:01 and HLA-B*35:08 in HCMV-infected cells. The isolated peptides from both allelic subtypes were of extraordinary length, however differed in their features, origin, and sequence. For these HCMV-originated peptides, no overlap in the peptide repertoire could be observed between the two allelic subtypes. These findings reveal the discrepancies between predicted and naturally presented immunogenic epitopes and support the need of comprehensive peptide recruitment data for personalized and effective cellular therapies.
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Affiliation(s)
- Wiebke C Abels
- Institute for Transfusion Medicine, Hannover Medical School, Hannover, Germany
| | - Trishna Manandhar
- Institute for Transfusion Medicine, Hannover Medical School, Hannover, Germany
| | | | - Rainer Blasczyk
- Institute for Transfusion Medicine, Hannover Medical School, Hannover, Germany
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15
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Lytic EBV infection investigated by detection of Soluble Epstein-Barr virus ZEBRA in the serum of patients with PTLD. Sci Rep 2017; 7:10479. [PMID: 28874674 PMCID: PMC5585268 DOI: 10.1038/s41598-017-09798-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 07/28/2017] [Indexed: 12/14/2022] Open
Abstract
The ZEBRA protein (encoded by the BZLF1 gene), is the major transcription factor of EBV, expressed upon EBV lytic cycle activation. Several studies highlighted the critical role of EBV lytic infection as a risk factor for lymphoproliferative disorders like post-transplant lymphoproliferative disease (PTLD). Here, we use an antigen-capture ELISA assay specifically designed to detecting the circulating soluble ZEBRA (sZEBRA) in serum samples (threshold value determined at 40ng/mL). We retrospectively investigated a population of 66 transplanted patients comprising 35 PTLD. All the samples from a control population (30 EBV-seronegative subjects and 25 immunocompetent individuals with EBV serological reactivation), classified as sZEBRA < 40ng/mL were assigned as negative. At PTLD diagnosis, EBV genome (quantified by qPCR with EBV DNA>200 copies/mL) and sZEBRA were detectable in 51% and 60% of cases, respectively. In the patients who developed a pathologically-confirmed PTLD, the mean sZEBRA value in cases, was 399 ng/mL +/− 141 versus 53ng/mL +/− 7 in patients who did not (p < 0,001). This is the first report relating to the detection of the circulating ZEBRA in serum specimens, as well as the first analysis dealing with the lytic cycle of EBV in PTLD patients with this new biomarker.
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16
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Pender MP, Csurhes PA, Burrows JM, Burrows SR. Defective T-cell control of Epstein-Barr virus infection in multiple sclerosis. Clin Transl Immunology 2017; 6:e126. [PMID: 28197337 PMCID: PMC5292561 DOI: 10.1038/cti.2016.87] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 12/02/2016] [Accepted: 12/02/2016] [Indexed: 02/07/2023] Open
Abstract
Mounting evidence indicates that infection with Epstein–Barr virus (EBV) has a
major role in the pathogenesis of multiple sclerosis (MS). Defective elimination of
EBV-infected B cells by CD8+ T cells might cause MS by allowing
EBV-infected autoreactive B cells to accumulate in the brain. Here we undertake a
comprehensive analysis of the T-cell response to EBV in MS, using flow cytometry and
intracellular IFN-γ staining to measure T-cell responses to EBV-infected
autologous lymphoblastoid cell lines and pools of human leukocyte antigen
(HLA)-class-I-restricted peptides from EBV lytic or latent proteins and
cytomegalovirus (CMV), in 95 patients and 56 EBV-seropositive healthy subjects. In 20
HLA-A2+ healthy subjects and 20 HLA-A2+ patients
we also analysed CD8+ T cells specific for individual peptides,
measured by binding to HLA-peptide complexes and production of IFN-γ,
TNF-α and IL-2. We found a decreased CD8+ T-cell response to
EBV lytic, but not CMV lytic, antigens at the onset of MS and at all subsequent
disease stages. CD8+ T cells directed against EBV latent antigens
were increased but had reduced cytokine polyfunctionality indicating T-cell
exhaustion. During attacks the EBV-specific CD4+ and
CD8+ T-cell populations expanded, with increased functionality of
latent-specific CD8+ T cells. With increasing disease duration,
EBV-specific CD4+ and CD8+ T cells progressively
declined, consistent with T-cell exhaustion. The anti-EBNA1 IgG titre correlated
inversely with the EBV-specific CD8+ T-cell frequency. We postulate
that defective CD8+ T-cell control of EBV reactivation leads to an
expanded population of latently infected cells, including autoreactive B cells.
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Affiliation(s)
- Michael P Pender
- School of Medicine, The University of Queensland, Brisbane, Queensland, Australia; Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia; Cellular ImmunoIogy Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Peter A Csurhes
- School of Medicine, The University of Queensland, Brisbane, Queensland, Australia; Cellular ImmunoIogy Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia; The University of Queensland Centre for Clinical Research, Brisbane, Queensland, Australia
| | - Jacqueline M Burrows
- Cellular ImmunoIogy Laboratory, QIMR Berghofer Medical Research Institute , Brisbane, Queensland, Australia
| | - Scott R Burrows
- School of Medicine, The University of Queensland, Brisbane, Queensland, Australia; Cellular ImmunoIogy Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
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17
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Structural and Biochemical Analyses of Swine Major Histocompatibility Complex Class I Complexes and Prediction of the Epitope Map of Important Influenza A Virus Strains. J Virol 2016; 90:6625-6641. [PMID: 27170754 DOI: 10.1128/jvi.00119-16] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Accepted: 05/03/2016] [Indexed: 12/29/2022] Open
Abstract
UNLABELLED The lack of a peptide-swine leukocyte antigen class I (pSLA I) complex structure presents difficulties for the study of swine cytotoxic T lymphocyte (CTL) immunity and molecule vaccine development to eliminate important swine viral diseases, such as influenza A virus (IAV). Here, after cloning and comparing 28 SLA I allelic genes from Chinese Heishan pigs, pSLA-3*hs0202 was crystalized and solved. SLA-3*hs0202 binding with sβ2m and a KMNTQFTAV (hemagglutinin [HA]-KMN9) peptide from the 2009 pandemic swine H1N1 strain clearly displayed two distinct conformations with HA-KMN9 peptides in the structures, which are believed to be beneficial to stimulate a broad spectrum of CTL immune responses. Notably, we found that different HA-KMN9 conformations are caused, not only by the flexibility of the side chains of residues in the peptide-binding groove (PBG), but also by the skewing of α1 and α2 helixes forming the PBG. In addition, alanine scanning and circular-dichroism (CD) spectra confirmed that the B, D, and F pockets play critical biochemical roles in determining the peptide-binding motif of SLA-3*hs0202. Based on biochemical parameters and comparisons to similar pockets in other known major histocompatibility complex class I (MHC-I) structures, the fundamental motif for SLA-3*hs0202 was determined to be X-(M/A/R)-(N/Q/R/F)-X-X-X-X-X-(V/I) by refolding in vitro and multiple mutant peptides. Finally, 28 SLA-3*hs0202-restricted epitope candidates were identified from important IAV strains, and two of them have been found in humans as HLA-A*0201-specific IAV epitopes. Structural and biochemical illumination of pSLA-3*hs0202 can benefit vaccine development to control IAV in swine. IMPORTANCE We crystalized and solved the first SLA-3 structure, SLA-3*hs0202, and found that it could present the same IAV peptide with two distinct conformations. Unlike previous findings showing that variable peptide conformations are caused only by the flexibility of the side chains in the groove, the skewing of the α1 and α2 helixes is important in the different peptide conformations in SLA-3*hs0202. We also determined the fundamental motif for SLA-3*hs0202 to be X-(M/A/R)-(N/Q/R/F)-X-X-X-X-X-(V/I) based on a series of structural and biochemical analyses, and 28 SLA-3*hs0202-restricted epitope candidates were identified from important IAV strains. We believe our structure and analyses of pSLA-3*hs0202 can benefit vaccine development to control IAV in swine.
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18
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Manandhar T, Kunze-Schumacher H, Huyton T, Celik AA, Blasczyk R, Bade-Doeding C. Understanding the obstacle of incompatibility at residue 156 within HLA-B*35 subtypes. Immunogenetics 2016; 68:247-60. [PMID: 26758079 PMCID: PMC4799800 DOI: 10.1007/s00251-015-0896-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 12/23/2015] [Indexed: 01/22/2023]
Abstract
Defining permissive and non-permissive mismatches for transplantation is a demanding challenge. Single mismatches at amino acid (AA) position 156 of human leucocyte antigen (HLA) class I have been described to alter the peptide motif, repertoire, or mode of peptide loading through differential interaction with the peptide-loading complex. Hence, a single mismatch can tip the balance and trigger an immunological reaction. HLA-B*35 subtypes have been described to evade the loading complex, 156 mismatch distinguishing B*35:01 and B*35:08 changes the binding groove sufficiently to alter the sequence features of the selected peptide repertoire. To understand the functional influences of residue 156 in B*35 variants, we analyzed the peptide binding profiles of HLA-B*35:01156Leu, B*35:08156Arg and B*35:62156Trp. The glycoprotein tapasin represents a target for immune evasions and functions within the multimeric peptide-loading complex to stabilize empty class I molecules and promote acquisition of high-affinity peptides. All three B*35 subtypes showed a tapasin-independent mode of peptide acquisition. HLA-B*35-restricted peptides of low- and high-binding affinities were recovered in the presence and absence of tapasin and subsequently sequenced utilizing mass spectrometry. The peptides derived from B*35 variants differ substantially in their features dependent on their mode of recruitment; all peptides were preferentially anchored by Pro at p2 and Tyr, Phe, Leu, or Lys at pΩ. However, the Trp at residue 156 altered the p2 motif to an Ala and restricted the pΩ to a Trp. Our results highlight the importance of understanding the impact of key micropolymorphism and how a single AA mismatch orchestrates the neighboring AAs.
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Affiliation(s)
- Trishna Manandhar
- Hannover Medical School, Institute for Transfusion Medicine, Feodor-Lynen-Str. 5, 30625, Hannover, Germany
| | - Heike Kunze-Schumacher
- Hannover Medical School, Institute for Transfusion Medicine, Feodor-Lynen-Str. 5, 30625, Hannover, Germany
| | - Trevor Huyton
- Hannover Medical School, Institute for Transfusion Medicine, Feodor-Lynen-Str. 5, 30625, Hannover, Germany
| | - Alexander A Celik
- Hannover Medical School, Institute for Transfusion Medicine, Feodor-Lynen-Str. 5, 30625, Hannover, Germany
| | - Rainer Blasczyk
- Hannover Medical School, Institute for Transfusion Medicine, Feodor-Lynen-Str. 5, 30625, Hannover, Germany
| | - Christina Bade-Doeding
- Hannover Medical School, Institute for Transfusion Medicine, Feodor-Lynen-Str. 5, 30625, Hannover, Germany.
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Miles JJ, McCluskey J, Rossjohn J, Gras S. Understanding the complexity and malleability of T-cell recognition. Immunol Cell Biol 2015; 93:433-41. [PMID: 25582337 DOI: 10.1038/icb.2014.112] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 11/21/2014] [Accepted: 11/23/2014] [Indexed: 12/15/2022]
Abstract
T cells are the master regulators of immune system function, continually walking the biological tightrope between adequate host defence and accidental host pathology. Tolerance is maintained or broken through an intricate structural interplay between the T-cell receptor (TCR) and major histocompatibility complex (MHC) molecule cradling peptide antigens (p). Recent advances in structural biology have shown that the TCR/pMHC interface is surprising precise and extraordinarily malleable. We have seen that seemingly minor changes in the TCR/pMHC interface can abrogate function, as well as substantial conformational changes before and after TCR docking. Our understanding of T-cell biology has also been altered with the knowledge that MHC molecules can bind not only peptides, but also an array of natural and synthetic compounds. Here, we review some examples of the precision and flexibility intrinsic to the TCR/p/MHCI axis.
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Affiliation(s)
- John J Miles
- 1] QIMR Berghofer Medical Research Institute and QIMR Berghofer Centre for Immunotherapy and Vaccine Development, Brisbane, Queensland, Australia [2] School of Medicine, The University of Queensland, Brisbane, Queensland, Australia [3] Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, Wales, UK
| | - James McCluskey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia
| | - Jamie Rossjohn
- 1] Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, Wales, UK [2] Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria, Australia [3] ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | - Stephanie Gras
- 1] Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria, Australia [2] ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
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20
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A Micropolymorphism Altering the Residue Triad 97/114/156 Determines the Relative Levels of Tapasin Independence and Distinct Peptide Profiles for HLA-A(*)24 Allotypes. J Immunol Res 2014; 2014:298145. [PMID: 25802875 PMCID: PMC4353853 DOI: 10.1155/2014/298145] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 11/12/2014] [Accepted: 11/12/2014] [Indexed: 11/17/2022] Open
Abstract
While many HLA class I molecules interact directly with the peptide loading complex (PLC) for conventional loading of peptides certain class I molecules are able to present peptides in a way that circumvents the PLC components. We investigated micropolymorphisms at position 156 of HLA-A(*)24 allotypes and their effects on PLC dependence for assembly and peptide binding specificities. HLA-A(*)24:06(156Trp) and HLA-A(*)24:13(156Leu) showed high levels of cell surface expression while HLA-A(*)24:02(156Gln) was expressed at low levels in tapasin deficient cells. Peptides presented by these allelic variants showed distinct differences in features and repertoire. Immunoprecipitation experiments demonstrated all the HLA-A(*)24/156 variants to associate at similar levels with tapasin when present. Structurally, HLA-A(*)24:02 contains the residue triad Met97/His114/Gln156 and a Trp156 or Leu156 polymorphism provides tapasin independence by stabilizing these triad residues, thus generating an energetically stable and a more peptide receptive environment. Micropolymorphisms at position 156 can influence the generic peptide loading pathway for HLA-A(*)24 by altering their tapasin dependence for peptide selection. The trade-off for this tapasin independence could be the presentation of unusual ligands by these alleles, imposing significant risk following hematopoietic stem cell transplantation (HSCT).
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21
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Pender MP, Burrows SR. Epstein-Barr virus and multiple sclerosis: potential opportunities for immunotherapy. Clin Transl Immunology 2014; 3:e27. [PMID: 25505955 PMCID: PMC4237030 DOI: 10.1038/cti.2014.25] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2014] [Revised: 09/30/2014] [Accepted: 09/30/2014] [Indexed: 01/04/2023] Open
Abstract
Multiple sclerosis (MS) is a common chronic inflammatory demyelinating disease of the central nervous system (CNS) causing progressive disability. Many observations implicate Epstein–Barr virus (EBV) in the pathogenesis of MS, namely universal EBV seropositivity, high anti-EBV antibody levels, alterations in EBV-specific CD8+ T-cell immunity, increased spontaneous EBV-induced transformation of peripheral blood B cells, increased shedding of EBV from saliva and accumulation of EBV-infected B cells and plasma cells in the brain. Several mechanisms have been postulated to explain the role of EBV in the development of MS including cross-reactivity between EBV and CNS antigens, bystander damage to the CNS by EBV-specific CD8+ T cells, activation of innate immunity by EBV-encoded small RNA molecules in the CNS, expression of αB-crystallin in EBV-infected B cells leading to a CD4+ T-cell response against oligodendrocyte-derived αB-crystallin and EBV infection of autoreactive B cells, which produce pathogenic autoantibodies and provide costimulatory survival signals to autoreactive T cells in the CNS. The rapidly accumulating evidence for a pathogenic role of EBV in MS provides ground for optimism that it might be possible to prevent and cure MS by effectively controlling EBV infection through vaccination, antiviral drugs or treatment with EBV-specific cytotoxic CD8+ T cells. Adoptive immunotherapy with in vitro-expanded autologous EBV-specific CD8+ T cells directed against viral latent proteins was recently used to treat a patient with secondary progressive MS. Following the therapy, there was clinical improvement, decreased disease activity on magnetic resonance imaging and reduced intrathecal immunoglobulin production.
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Affiliation(s)
- Michael P Pender
- School of Medicine, The University of Queensland , Brisbane, QLD, Australia ; Department of Neurology, Royal Brisbane and Women's Hospital , Brisbane, QLD, Australia ; QIMR Berghofer Medical Research Institute , Brisbane, QLD, Australia
| | - Scott R Burrows
- School of Medicine, The University of Queensland , Brisbane, QLD, Australia ; QIMR Berghofer Medical Research Institute , Brisbane, QLD, Australia
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22
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T cell epitope clustering in the highly immunogenic BZLF1 antigen of Epstein-Barr virus. J Virol 2014; 89:703-12. [PMID: 25355876 DOI: 10.1128/jvi.02642-14] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
UNLABELLED Polymorphism in the human leukocyte antigen (HLA) loci ensures that the CD8(+) T cell response to viruses is directed against a diverse range of antigenic epitopes, thereby minimizing the impact of virus escape mutation across the population. The BZLF1 antigen of Epstein-Barr virus is an immunodominant target for CD8(+) T cells, but the response has been characterized only in the context of a limited number of HLA molecules due to incomplete epitope mapping. We have now greatly expanded the number of defined CD8(+) T cell epitopes from BZLF1, allowing the response to be evaluated in a much larger proportion of the population. Some regions of the antigen fail to be recognized by CD8(+) T cells, while others include clusters of overlapping epitopes presented by different HLA molecules. These highly immunogenic regions of BZLF1 include polymorphic sequences, such that up to four overlapping epitopes are impacted by a single amino acid variation common in different regions of the world. This focusing of the immune response to limited regions of the viral protein could be due to sequence similarity to human proteins creating "immune blind spots" through self-tolerance. This study significantly enhances the understanding of the immune response to BZLF1, and the precisely mapped T cell epitopes may be directly exploited in vaccine development and adoptive immunotherapy. IMPORTANCE Epstein-Barr virus (EBV) is an important human pathogen, associated with several malignancies, including nasopharyngeal carcinoma and Hodgkin lymphoma. T lymphocytes are critical for virus control, and clinical trials aimed at manipulating this arm of the immune system have demonstrated efficacy in treating these EBV-associated diseases. These trials have utilized information on the precise location of viral epitopes for T cell recognition, for either measuring or enhancing responses. In this study, we have characterized the T cell response to the highly immunogenic BZLF1 antigen of EBV by greatly expanding the number of defined T cell epitopes. An unusual clustering of epitopes was identified, highlighting a small region of BZLF1 that is targeted by the immune response of a high proportion of the world's population. This focusing of the immune response could be utilized in developing vaccines/therapies with wide coverage, or it could potentially be exploited by the virus to escape the immune response.
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23
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Soluble HLA technology as a strategy to evaluate the impact of HLA mismatches. J Immunol Res 2014; 2014:246171. [PMID: 25254222 PMCID: PMC4165401 DOI: 10.1155/2014/246171] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 07/15/2014] [Accepted: 08/05/2014] [Indexed: 11/17/2022] Open
Abstract
HLA class I incompatibilities still remain one of the main barriers for unrelated bone marrow transplantation (BMT); hence the molecular understanding of how to mismatch patients and donors and still have successful clinical outcomes will guide towards the future of unrelated BMT. One way to estimate the magnitude of polymorphisms within the PBR is to determine which peptides can be selected by individual HLA alleles and subsequently presented for recognition by T cells. The features (structure, length, and sequence) of different peptides each confer an individual pHLA landscape and thus directly shape the individual immune response. The elution and sequencing of peptides by mass spectrometric analysis enable determining the bona fide repertoire of presented peptides for a given allele. This is an effective and simple way to compare the functions of allelic variants and make a first assessment of their degree of permissivity. We describe the methodology used for peptide sequencing and the limitations of peptide prediction tools compared to experimental methods. We highlight the altered peptide features that are observed between allelic variants and the need to discover the altered peptide repertoire in situations of "artificial" graft versus host disease (GvHD) that occur in HLA-specific hypersensitive immune responses to drugs.
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24
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Yanaka S, Ueno T, Shi Y, Qi J, Gao GF, Tsumoto K, Sugase K. Peptide-dependent conformational fluctuation determines the stability of the human leukocyte antigen class I complex. J Biol Chem 2014; 289:24680-90. [PMID: 25028510 DOI: 10.1074/jbc.m114.566174] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In immune-mediated control of pathogens, human leukocyte antigen (HLA) class I presents various antigenic peptides to CD8(+) T-cells. Long-lived peptide presentation is important for efficient antigen-specific T-cell activation. Presentation time depends on the peptide sequence and the stability of the peptide-HLA complex (pHLA). However, the determinant of peptide-dependent pHLA stability remains elusive. Here, to reveal the pHLA stabilization mechanism, we examined the crystal structures of an HLA class I allomorph in complex with HIV-derived peptides and evaluated site-specific conformational fluctuations using NMR. Although the crystal structures of various pHLAs were almost identical independent of the peptides, fluctuation analyses identified a peptide-dependent minor state that would be more tightly packed toward the peptide. The minor population correlated well with the thermostability and cell surface presentation of pHLA, indicating that this newly identified minor state is important for stabilizing the pHLA and facilitating T-cell recognition.
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Affiliation(s)
- Saeko Yanaka
- From the Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo 277-8562, Japan
| | - Takamasa Ueno
- Center for AIDS Research, Kumamoto University, Kumamoto 860-0811, Japan, International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto 860-0811, Japan
| | - Yi Shi
- Research Network of Immunity and Health, Beijing Institute of Life Science, Chinese Academy of Sciences, Beijing 100101, China, CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianxun Qi
- Research Network of Immunity and Health, Beijing Institute of Life Science, Chinese Academy of Sciences, Beijing 100101, China, CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - George F Gao
- Research Network of Immunity and Health, Beijing Institute of Life Science, Chinese Academy of Sciences, Beijing 100101, China, CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Kouhei Tsumoto
- From the Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo 277-8562, Japan, Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Tokyo 108-8693, Japan, Medical Proteomics Laboratory, Institute of Medical Science, The University of Tokyo, Tokyo 108-8693, Japan, and
| | - Kenji Sugase
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Osaka 618-8503, Japan
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25
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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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26
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Liu YC, Chen Z, Neller MA, Miles JJ, Purcell AW, McCluskey J, Burrows SR, Rossjohn J, Gras S. A molecular basis for the interplay between T cells, viral mutants, and human leukocyte antigen micropolymorphism. J Biol Chem 2014; 289:16688-98. [PMID: 24759101 DOI: 10.1074/jbc.m114.563502] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mutations within T cell epitopes represent a common mechanism of viral escape from the host protective immune response. The diverse T cell repertoire and the extensive human leukocyte antigen (HLA) polymorphism across populations is the evolutionary response to viral mutation. However, the molecular basis underpinning the interplay between HLA polymorphism, the T cell repertoire, and viral escape is unclear. Here we investigate the T cell response to a HLA-B*35:01- and HLA-B*35:08-restricted (407)HPVGEADYFEY(417) epitope from Epstein-Barr virus and naturally occurring variants at positions 4 and 5 thereof. Each viral variant differently impacted on the epitope's flexibility and conformation when bound to HLA-B*35:08 or HLA-B*35:01. We provide a molecular basis for understanding how the single residue polymorphism that discriminates between HLA-B*35:01/08 profoundly impacts on T cell receptor recognition. Surprisingly, one viral variant (P5-Glu to P5-Asp) effectively changed restriction preference from HLA-B*35:01 to HLA-B*35:08. Collectively, our study portrays the interplay between the T cell response, viral escape, and HLA polymorphism, whereby HLA polymorphism enables altered presentation of epitopes from different strains of Epstein-Barr virus.
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Affiliation(s)
- Yu Chih Liu
- From the Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Melbourne 3800, Australia
| | - Zhenjun Chen
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Michelle A Neller
- QIMR Berghofer Medical Research Institute and QIMR Berghofer Centre for Immunotherapy and Vaccine Development, Brisbane, Queensland 4006, Australia
| | - John J Miles
- QIMR Berghofer Medical Research Institute and QIMR Berghofer Centre for Immunotherapy and Vaccine Development, Brisbane, Queensland 4006, Australia
| | - Anthony W Purcell
- From the Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Melbourne 3800, Australia
| | - James McCluskey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Scott R Burrows
- QIMR Berghofer Medical Research Institute and QIMR Berghofer Centre for Immunotherapy and Vaccine Development, Brisbane, Queensland 4006, Australia
| | - Jamie Rossjohn
- From the Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Melbourne 3800, Australia, Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, CF14 4XN Wales, United Kingdom, and Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Stephanie Gras
- From the Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Melbourne 3800, Australia, Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
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Molecular imprint of exposure to naturally occurring genetic variants of human cytomegalovirus on the T cell repertoire. Sci Rep 2014; 4:3993. [PMID: 24509977 PMCID: PMC3918921 DOI: 10.1038/srep03993] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 01/20/2014] [Indexed: 11/14/2022] Open
Abstract
Exposure to naturally occurring variants of herpesviruses in clinical settings can have a dramatic impact on anti-viral immunity. Here we have evaluated the molecular imprint of variant peptide-MHC complexes on the T-cell repertoire during human cytomegalovirus (CMV) infection and demonstrate that primary co-infection with genetic variants of CMV was coincident with development of strain-specific T-cell immunity followed by emergence of cross-reactive virus-specific T-cells. Cross-reactive CMV-specific T cells exhibited a highly conserved public T cell repertoire, while T cells directed towards specific genetic variants displayed oligoclonal repertoires, unique to each individual. T cell recognition foot–print and pMHC-I structural analyses revealed that the cross-reactive T cells accommodate alterations in the pMHC complex with a broader foot-print focussing on the core of the peptide epitope. These findings provide novel molecular insight into how infection with naturally occurring genetic variants of persistent human herpesviruses imprints on the evolution of the anti-viral T-cell repertoire.
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Bhati M, Cole DK, McCluskey J, Sewell AK, Rossjohn J. The versatility of the αβ T-cell antigen receptor. Protein Sci 2014; 23:260-72. [PMID: 24375592 DOI: 10.1002/pro.2412] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Revised: 12/20/2013] [Accepted: 12/20/2013] [Indexed: 02/06/2023]
Abstract
The T-cell antigen receptor is a heterodimeric αβ protein (TCR) expressed on the surface of T-lymphocytes, with each chain of the TCR comprising three complementarity-determining regions (CDRs) that collectively form the antigen-binding site. Unlike antibodies, which are closely related proteins that recognize intact protein antigens, TCRs classically bind, via their CDR loops, to peptides (p) that are presented by molecules of the major histocompatibility complex (MHC). This TCR-pMHC interaction is crucially important in cell-mediated immunity, with the specificity in the cellular immune response being attributable to MHC polymorphism, an extensive TCR repertoire and a variable peptide cargo. The ensuing structural and biophysical studies within the TCR-pMHC axis have been highly informative in understanding the fundamental events that underpin protective immunity and dysfunctional T-cell responses that occur during autoimmunity. In addition, TCRs can recognize the CD1 family, a family of MHC-related molecules that instead of presenting peptides are ideally suited to bind lipid-based antigens. Structural studies within the CD1-lipid antigen system are beginning to inform us how lipid antigens are specifically presented by CD1, and how such CD1-lipid antigen complexes are recognized by the TCR. Moreover, it has recently been shown that certain TCRs can bind to vitamin B based metabolites that are bound to an MHC-like molecule termed MR1. Thus, TCRs can recognize peptides, lipids, and small molecule metabolites, and here we review the basic principles underpinning this versatile and fascinating receptor recognition system that is vital to a host's survival.
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Affiliation(s)
- Mugdha Bhati
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria, 3800, Australia
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29
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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: 524] [Impact Index Per Article: 47.6] [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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Norman PJ, Hollenbach JA, Nemat-Gorgani N, Guethlein LA, Hilton HG, Pando MJ, Koram KA, Riley EM, Abi-Rached L, Parham P. Co-evolution of human leukocyte antigen (HLA) class I ligands with killer-cell immunoglobulin-like receptors (KIR) in a genetically diverse population of sub-Saharan Africans. PLoS Genet 2013; 9:e1003938. [PMID: 24204327 PMCID: PMC3814319 DOI: 10.1371/journal.pgen.1003938] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 09/16/2013] [Indexed: 02/06/2023] Open
Abstract
Interactions between HLA class I molecules and killer-cell immunoglobulin-like receptors (KIR) control natural killer cell (NK) functions in immunity and reproduction. Encoded by genes on different chromosomes, these polymorphic ligands and receptors correlate highly with disease resistance and susceptibility. Although studied at low-resolution in many populations, high-resolution analysis of combinatorial diversity of HLA class I and KIR is limited to Asian and Amerindian populations with low genetic diversity. At the other end of the spectrum is the West African population investigated here: we studied 235 individuals, including 104 mother-child pairs, from the Ga-Adangbe of Ghana. This population has a rich diversity of 175 KIR variants forming 208 KIR haplotypes, and 81 HLA-A, -B and -C variants forming 190 HLA class I haplotypes. Each individual we studied has a unique compound genotype of HLA class I and KIR, forming 1-14 functional ligand-receptor interactions. Maintaining this exceptionally high polymorphism is balancing selection. The centromeric region of the KIR locus, encoding HLA-C receptors, is highly diverse whereas the telomeric region encoding Bw4-specific KIR3DL1, lacks diversity in Africans. Present in the Ga-Adangbe are high frequencies of Bw4-bearing HLA-B*53:01 and Bw4-lacking HLA-B*35:01, which otherwise are identical. Balancing selection at key residues maintains numerous HLA-B allotypes having and lacking Bw4, and also those of stronger and weaker interaction with LILRB1, a KIR-related receptor. Correspondingly, there is a balance at key residues of KIR3DL1 that modulate its level of cell-surface expression. Thus, capacity to interact with NK cells synergizes with peptide binding diversity to drive HLA-B allele frequency distribution. These features of KIR and HLA are consistent with ongoing co-evolution and selection imposed by a pathogen endemic to West Africa. Because of the prevalence of malaria in the Ga-Adangbe and previous associations of cerebral malaria with HLA-B*53:01 and KIR, Plasmodium falciparum is a candidate pathogen.
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Affiliation(s)
- Paul J. Norman
- Departments of Structural Biology and Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail:
| | - Jill A. Hollenbach
- Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, California, United States of America
| | - Neda Nemat-Gorgani
- Departments of Structural Biology and Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Lisbeth A. Guethlein
- Departments of Structural Biology and Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Hugo G. Hilton
- Departments of Structural Biology and Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Marcelo J. Pando
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Kwadwo A. Koram
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Eleanor M. Riley
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Laurent Abi-Rached
- Departments of Structural Biology and Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- Centre National de la Recherche Scientifique, Laboratoire d'Analyse, Topologie, Probabilités - Unité Mixte de Recherche 7353, Equipe ATIP, Aix-Marseille Université, Marseille, France
| | - Peter Parham
- Departments of Structural Biology and Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, United States of America
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Liu YC, Miles JJ, Neller MA, Gostick E, Price DA, Purcell AW, McCluskey J, Burrows SR, Rossjohn J, Gras S. Highly divergent T-cell receptor binding modes underlie specific recognition of a bulged viral peptide bound to a human leukocyte antigen class I molecule. J Biol Chem 2013; 288:15442-54. [PMID: 23569211 PMCID: PMC3668706 DOI: 10.1074/jbc.m112.447185] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Human leukocyte antigen (HLA)-I molecules can present long peptides, yet the mechanisms by which T-cell receptors (TCRs) recognize featured pHLA-I landscapes are unclear. We compared the binding modes of three distinct human TCRs, CA5, SB27, and SB47, complexed with a “super-bulged” viral peptide (LPEPLPQGQLTAY) restricted by HLA-B*35:08. The CA5 and SB27 TCRs engaged HLA-B*35:08LPEP similarly, straddling the central region of the peptide but making limited contacts with HLA-B*35:08. Remarkably, the CA5 TCR did not contact the α1-helix of HLA-B*35:08. Differences in the CDR3β loop between the CA5 and SB27 TCRs caused altered fine specificities. Surprisingly, the SB47 TCR engaged HLA-B*35:08LPEP using a completely distinct binding mechanism, namely “bypassing” the bulged peptide and making extensive contacts with the extreme N-terminal end of HLA-B*35:08. This docking footprint included HLA-I residues not observed previously as TCR contact sites. The three TCRs exhibited differing patterns of alloreactivity toward closely related or distinct HLA-I allotypes. Thus, the human T-cell repertoire comprises a range of TCRs that can interact with “bulged” pHLA-I epitopes using unpredictable strategies, including the adoption of atypical footprints on the MHC-I.
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Affiliation(s)
- Yu Chih Liu
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton 3800, Australia
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Axelsson-Robertson R, Loxton AG, Walzl G, Ehlers MM, Kock MM, Zumla A, Maeurer M. A broad profile of co-dominant epitopes shapes the peripheral Mycobacterium tuberculosis specific CD8+ T-cell immune response in South African patients with active tuberculosis. PLoS One 2013; 8:e58309. [PMID: 23555576 PMCID: PMC3608651 DOI: 10.1371/journal.pone.0058309] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Accepted: 02/01/2013] [Indexed: 11/18/2022] Open
Abstract
We studied major histocompatibility complex (MHC) class I peptide-presentation and nature of the antigen-specific CD8+ T-cell response from South African tuberculosis (TB) patients with active TB. 361 MHC class I binding epitopes were identified from three immunogenic TB proteins (ESAT-6 [Rv3875], Ag85B [Rv1886c], and TB10.4 [Rv0288], including amino acid variations for Rv0288, i.e., A10T, G13D, S27N, and A71S for MHC allotypes common in a South African population (e.g., human leukocyte antigen [HLA]-A*30, B*58, and C*07). Inter-allelic differences were identified regarding the broadness of the peptide-binding capacity. Mapping of frequencies of Mycobacterium tuberculosis (M. tb) antigen-specific CD8+ T-cells using 48 different multimers, including the newly constructed recombinant MHC class I alleles HLA-B*58:01 and C*0701, revealed a low frequency of CD8+ T-cell responses directed against a broad panel of co-dominant M. tb epitopes in the peripheral circulation of most patients. The antigen-specific responses were dominated by CD8+ T-cells with a precursor-like phenotype (CD45RA+CCR7+). The data show that the CD8+ T-cell response from patients with pulmonary TB (prior to treatment) is directed against subdominant epitopes derived from secreted and non-secreted M. tb antigens and that variant, natural occurring M. tb Rv0288 ligands, have a profound impact on T-cell recognition.
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Affiliation(s)
| | - André G. Loxton
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research and MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Health Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Gerhard Walzl
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research and MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Health Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Marthie M. Ehlers
- Department of Medical Microbiology, University of Pretoria/NHLS, Pretoria, South Africa
| | - Marleen M. Kock
- Department of Medical Microbiology, University of Pretoria/NHLS, Pretoria, South Africa
| | - Alimuddin Zumla
- Division of Infection and Immunity, University College London Medical School, London, United Kingdom
| | - Markus Maeurer
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
- Therapeutic Immunology (TIM), Department of Laboratory Medicine, Karolinska Institutet and CAST, Karolinska University Hospital, Stockholm, Sweden
- * E-mail:
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Structural features underlying T-cell receptor sensitivity to concealed MHC class I micropolymorphisms. Proc Natl Acad Sci U S A 2012; 109:E3483-92. [PMID: 23161907 DOI: 10.1073/pnas.1207896109] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Polymorphic differences distinguishing MHC class I subtypes often permit the presentation of shared epitopes in conformationally identical formats but can affect T-cell repertoire selection, differentially impacting autoimmune susceptibilities and viral clearance in vivo. The molecular mechanisms underlying this effect are not well understood. We performed structural, thermodynamic, and functional analyses of a conserved T-cell receptor (TCR) which is frequently expanded in response to a HIV-1 epitope when presented by HLA-B*5701 but is not selected by HLA-B*5703, which differs from HLA-B*5701 by two concealed polymorphisms. Our findings illustrate that although both HLA-B*57 subtypes display the epitope in structurally conserved formats, the impact of their polymorphic differences occurs directly as a consequence of TCR ligation, primarily because of peptide adjustments required for TCR binding, which involves the interplay of polymorphic residues and water molecules. These minor differences culminate in subtype-specific differential TCR-binding kinetics and cellular function. Our data demonstrate a potential mechanism whereby the most subtle MHC class I micropolymorphisms can influence TCR use and highlight their implications for disease outcomes.
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Gras S, Burrows SR, Turner SJ, Sewell AK, McCluskey J, Rossjohn J. A structural voyage toward an understanding of the MHC-I-restricted immune response: lessons learned and much to be learned. Immunol Rev 2012; 250:61-81. [DOI: 10.1111/j.1600-065x.2012.01159.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Stephanie Gras
- Department of Biochemistry and Molecular Biology; School of Biomedical Sciences; Monash University; Clayton; Australia
| | - Scott R. Burrows
- Queensland Institute of Medical Research and Australian Centre for Vaccine Development; Brisbane; Australia
| | - Stephen J. Turner
- Department of Microbiology and Immunology; University of Melbourne; Parkville; Australia
| | - Andrew K. Sewell
- Institute of Infection and Immunity; Cardiff University School of Medicine; Cardiff; UK
| | - James McCluskey
- Department of Microbiology and Immunology; University of Melbourne; Parkville; Australia
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Calis JJA, de Boer RJ, Keşmir C. Degenerate T-cell recognition of peptides on MHC molecules creates large holes in the T-cell repertoire. PLoS Comput Biol 2012; 8:e1002412. [PMID: 22396638 PMCID: PMC3291541 DOI: 10.1371/journal.pcbi.1002412] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Accepted: 01/18/2012] [Indexed: 11/18/2022] Open
Abstract
The cellular immune system screens peptides presented by host cells on MHC molecules to assess if the cells are infected. In this study we examined whether the presented peptides contain enough information for a proper self/nonself assessment by comparing the presented human (self) and bacterial or viral (nonself) peptides on a large number of MHC molecules. For all MHC molecules tested, only a small fraction of the presented nonself peptides from 174 species of bacteria and 1000 viral proteomes ([Formula: see text]0.2%) is shown to be identical to a presented self peptide. Next, we use available data on T-cell receptor-peptide-MHC interactions to estimate how well T-cells distinguish between similar peptides. The recognition of a peptide-MHC by the T-cell receptor is flexible, and as a result, about one-third of the presented nonself peptides is expected to be indistinguishable (by T-cells) from presented self peptides. This suggests that T-cells are expected to remain tolerant for a large fraction of the presented nonself peptides, which provides an explanation for the "holes in the T-cell repertoire" that are found for a large fraction of foreign epitopes. Additionally, this overlap with self increases the need for efficient self tolerance, as many self-similar nonself peptides could initiate an autoimmune response. Degenerate recognition of peptide-MHC-I complexes by T-cells thus creates large and potentially dangerous overlaps between self and nonself.
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Affiliation(s)
- Jorg J A Calis
- Theoretical Biology & Bioinformatics, Utrecht University, Utrecht, The Netherlands.
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Badrinath S, Saunders P, Huyton T, Aufderbeck S, Hiller O, Blasczyk R, Bade-Doeding C. Position 156 influences the peptide repertoire and tapasin dependency of human leukocyte antigen B*44 allotypes. Haematologica 2011; 97:98-106. [PMID: 21993680 DOI: 10.3324/haematol.2011.046037] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Polymorphic differences between donor and recipient human leukocyte antigen class I molecules can result in graft-versus-host disease due to distinct peptide presentation. As part of the peptide-loading complex, tapasin plays an important role in selecting peptides from the pool of potential ligands. Class I polymorphisms can significantly alter the tapasin-mediated interaction with the peptide-loading complex and although most class I allotypes are highly dependent upon tapasin, some are able to load peptides independently of tapasin. Several human leukocyte antigen B*44 allotypes differ exclusively at position 156 (B*44:02(156Asp), 44:03(156Leu), 44:28(156Arg), 44:35(156Glu)). From these alleles, only the high tapasin-dependency of human leukocyte antigen B*44:02 has been reported. DESIGN AND METHODS We investigated the influence of position 156 polymorphisms on both the requirement of tapasin for efficient surface expression of each allotype and their peptide features. Genes encoding human leukocyte antigen B*44 variants bearing all possible substitutions at position 156 were lentivirally transduced into human leukocyte antigen class I-negative LCL 721.221 cells and the tapasin-deficient cell line LCL 721.220. RESULTS Exclusively human leukocyte antigen B*44:28(156Arg) was expressed on the surface of tapasin-deficient cells, suggesting that the remaining B*44/156 variants are highly tapasin-dependent. Our computational analysis suggests that the tapasin-independence of human leukocyte antigen B*44:28(156Arg) is a result of stabilization of the peptide binding region and generation of a more peptide receptive state. Sequencing of peptides eluted from human leukocyte antigen B*44 molecules by liquid chromatography-electrospray ionization-mass spectrometry (LTQ-Orbitrap) demonstrated that both B*44:02 and B*44:28 share the same overall peptide motif and a certain percentage of their individual peptide repertoires in the presence and/or absence of tapasin. CONCLUSIONS Here we report for the first time the influence of position 156 on the human leukocyte antigen/tapasin association. Additionally, the results of peptide sequencing suggest that tapasin chaperoning is needed to acquire peptides of unusual length.
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Affiliation(s)
- Soumya Badrinath
- Institute for Transfusion Medicine, Hannover Medical School, Hannover, Germany
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37
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Miconnet I, Marrau A, Farina A, Taffé P, Vigano S, Harari A, Pantaleo G. Large TCR Diversity of Virus-Specific CD8 T Cells Provides the Mechanistic Basis for Massive TCR Renewal after Antigen Exposure. THE JOURNAL OF IMMUNOLOGY 2011; 186:7039-49. [DOI: 10.4049/jimmunol.1003309] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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38
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Luo G, Quan G, Guo J, Zhang H, Li S, Wu W, Nie L, Dong Y, Wu S, Zheng G, Yang J, Xu J, Wang W. A basic phenylalanine-rich oligo-peptide causes antibody cross-reactivity. Electrophoresis 2011; 32:752-63. [PMID: 21365653 DOI: 10.1002/elps.201000446] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2010] [Revised: 12/23/2010] [Accepted: 01/05/2011] [Indexed: 11/08/2022]
Abstract
Glycolate oxidase (GO) and ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) are the two enzymes that serve key functions in the photorespiration and photosynthesis of plants. A 2 kDa highly basic phenylalanine-rich oligo-peptide (BOP) binds to the surface of acidic GO via ionic and hydrophobic interactions, forming the GO-BOP complex (GC). Previously, RubisCO was thought to exist as a single species composed of a large (rbc L, 54 kDa) and a small subunit (rbc S, 14 kDa). Here we show for the first time, using 2-DE, SDS-PAGE, immunoassays and amino acid determination, that BOP also interacts with RubisCO and that many RubisCO-BOP complexes (RCs), differing in pI, hydrophobicity and activity, coexist in green leaves. GCs, RCs and crude extract from green leaves analyzed by SDS-PAGE Western blotting showed that BOP exists either in subunit-BOP complexes (GO subunit-BOP, rbc L-BOP and rbc S-BOP etc.), with a wide variation in the number and the position of BOPs bound to each subunit molecular, or alone without a binding partner. When rbc L-BOP and rbc S-BOP were assayed by SDS-PAGE, BOP was dissociated from the subunit and it self-assembled to form 37 different BOP polymers (basic phenylalanine-rich protein) whose molecular weights (M(r)s) ranged from 34.0 to 91.6 kDa, indicating that the M(r) of BOP is about 2 kDa. Thus, the addition of BOP changes the M(r) of the subunit-BOP complexes so minimally that the rbc L and rbc S run at their predicted M(r)s on SDS-PAGE. In summary, the results described here demonstrate that the presence of BOP in complexes (both subunit-BOP complex and protein-BOP complex) can cause cross-reactivity of antibodies against different proteins.
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Affiliation(s)
- Gangyue Luo
- Guangdong Provincial Key Lab of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou, P. R. China
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The structural bases of direct T‐cell allorecognition: implications for T‐cell‐mediated transplant rejection. Immunol Cell Biol 2011; 89:388-95. [DOI: 10.1038/icb.2010.150] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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40
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Burrows SR, Moss DJ, Khanna R. Understanding human T-cell-mediated immunoregulation through herpesviruses. Immunol Cell Biol 2011; 89:352-8. [PMID: 21301481 DOI: 10.1038/icb.2010.136] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Human herpesviruses have coevolved with humans over millions of years, and adaptation of latent infection within the cells of the immune system is a unique characteristic of many of these viruses. Following primary infection, these herpesviruses establish an asymptomatic-persistent infection in healthy individuals that is strictly controlled by virus-specific CD8(+) and CD4(+) T cells. Here, we provide a brief overview of how the human immune system interacts with these latent viruses and regulates the lifelong host-virus relationship in healthy virus carriers. Extensive studies on T-cell-mediated immune regulation over the last decade has allowed researchers to successfully translate these findings into the clinical setting to treat various herpesvirus-associated diseases in transplant patients and individuals with virus-associated malignancies. It is highly likely that these newly emerging T-cell-based therapeutic and diagnostic technologies will revolutionize the clinical management of patients with herpesvirus-associated diseases.
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Affiliation(s)
- Scott R Burrows
- Australian Centre for Vaccine Development, Queensland Institute of Medical Research, Brisbane, Queensland, Australia.
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Abstract
There is increasing evidence that infection with the Epstein-Barr virus (EBV) plays a role in the development of multiple sclerosis (MS), a chronic inflammatory demyelinating disease of the CNS. This article provides a four-tier hypothesis proposing (1) EBV infection is essential for the development of MS; (2) EBV causes MS in genetically susceptible individuals by infecting autoreactive B cells, which seed the CNS where they produce pathogenic autoantibodies and provide costimulatory survival signals to autoreactive T cells that would otherwise die in the CNS by apoptosis; (3) the susceptibility to develop MS after EBV infection is dependent on a genetically determined quantitative deficiency of the cytotoxic CD8+ T cells that normally keep EBV infection under tight control; and (4) sunlight and vitamin D protect against MS by increasing the number of CD8+ T cells available to control EBV infection. The hypothesis makes predictions that can be tested, including the prevention and successful treatment of MS by controlling EBV infection.
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Affiliation(s)
- Michael P Pender
- School of Medicine, The University of Queensland, Queensland, Australia.
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Hwang SH, Oh HB, Choi SE, Seo JJ, Lee JH, Cho SW, Chae JM, Heo YS, Chang CL, Lee EY. Impact of amino acid substitution at residue 9 of HLA-A2 on the development of acute GVHD in Korean pediatric patients receiving unrelated hematopoietic stem cell transplantation. Transpl Int 2010; 23:1216-22. [DOI: 10.1111/j.1432-2277.2010.01117.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Gras S, Chen Z, Miles JJ, Liu YC, Bell MJ, Sullivan LC, Kjer-Nielsen L, Brennan RM, Burrows JM, Neller MA, Khanna R, Purcell AW, Brooks AG, McCluskey J, Rossjohn J, Burrows SR. Allelic polymorphism in the T cell receptor and its impact on immune responses. ACTA ACUST UNITED AC 2010; 207:1555-67. [PMID: 20566715 PMCID: PMC2901058 DOI: 10.1084/jem.20100603] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
In comparison to human leukocyte antigen (HLA) polymorphism, the impact of allelic sequence variation within T cell receptor (TCR) loci is much less understood. Particular TCR loci have been associated with autoimmunity, but the molecular basis for this phenomenon is undefined. We examined the T cell response to an HLA-B*3501-restricted epitope (HPVGEADYFEY) from Epstein-Barr virus (EBV), which is frequently dominated by a TRBV9*01(+) public TCR (TK3). However, the common allelic variant TRBV9*02, which differs by a single amino acid near the CDR2beta loop (Gln55-->His55), was never used in this response. The structure of the TK3 TCR, its allelic variant, and a nonnaturally occurring mutant (Gln55-->Ala55) in complex with HLA-B*3501(HPVGEADYFEY) revealed that the Gln55-->His55 polymorphism affected the charge complementarity at the TCR-peptide-MHC interface, resulting in reduced functional recognition of the cognate and naturally occurring variants of this EBV peptide. Thus, polymorphism in the TCR loci may contribute toward variability in immune responses and the outcome of infection.
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Affiliation(s)
- Stephanie Gras
- The Protein Crystallography Unit, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
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Burrows SR, Chen Z, Archbold JK, Tynan FE, Beddoe T, Kjer-Nielsen L, Miles JJ, Khanna R, Moss DJ, Liu YC, Gras S, Kostenko L, Brennan RM, Clements CS, Brooks AG, Purcell AW, McCluskey J, Rossjohn J. Hard wiring of T cell receptor specificity for the major histocompatibility complex is underpinned by TCR adaptability. Proc Natl Acad Sci U S A 2010; 107:10608-13. [PMID: 20483993 PMCID: PMC2890827 DOI: 10.1073/pnas.1004926107] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
alphabeta T cell receptors (TCRs) are genetically restricted to corecognize peptide antigens bound to self-major histocompatibility complex (pMHC) molecules; however, the basis for this MHC specificity remains unclear. Despite the current dogma, evaluation of the TCR-pMHC-I structural database shows that the nongermline-encoded complementarity-determining region (CDR)-3 loops often contact the MHC-I, and the germline-encoded CDR1 and -2 loops frequently participate in peptide-mediated interactions. Nevertheless, different TCRs adopt a roughly conserved docking mode over the pMHC-I, in which three MHC-I residues (65, 69, and 155) are invariably contacted by the TCR in one way or another. Nonetheless, the impact of mutations at these three positions, either individually or together, was not uniformly detrimental to TCR recognition of pHLA-B*0801 or pHLA-B*3508. Moreover, when TCR-pMHC-I recognition was impaired, this could be partially restored by expression of the CD8 coreceptor. The structure of a TCR-pMHC-I complex in which these three (65, 69, and 155) MHC-I positions were all mutated resulted in shifting of the TCR footprint relative to the cognate complex and formation of compensatory interactions. Collectively, our findings reveal the inherent adaptability of the TCR in maintaining peptide recognition while accommodating changes to the central docking site on the pMHC-I.
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MESH Headings
- Adaptive Immunity
- Cell Line, Tumor
- Cytotoxicity, Immunologic
- Databases, Genetic
- Humans
- Lymphocyte Activation
- Major Histocompatibility Complex
- Models, Molecular
- Mutation
- Protein Structure, Quaternary
- Protein Structure, Tertiary
- Receptors, Antigen, T-Cell/chemistry
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
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Affiliation(s)
- Scott R. Burrows
- Cellular Immunology Laboratory, Queensland Institute of Medical Research and Australian Centre for Vaccine Development, Brisbane 4029, Australia
| | - Zhenjun Chen
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Julia K. Archbold
- The Protein Crystallography Unit, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; and
| | - Fleur E. Tynan
- The Protein Crystallography Unit, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; and
| | - Travis Beddoe
- The Protein Crystallography Unit, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; and
| | - Lars Kjer-Nielsen
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - John J. Miles
- Cellular Immunology Laboratory, Queensland Institute of Medical Research and Australian Centre for Vaccine Development, Brisbane 4029, Australia
| | - Rajiv Khanna
- Cellular Immunology Laboratory, Queensland Institute of Medical Research and Australian Centre for Vaccine Development, Brisbane 4029, Australia
| | - Denis J. Moss
- Cellular Immunology Laboratory, Queensland Institute of Medical Research and Australian Centre for Vaccine Development, Brisbane 4029, Australia
| | - Yu Chih Liu
- The Protein Crystallography Unit, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; and
| | - Stephanie Gras
- The Protein Crystallography Unit, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; and
| | - Lyudmila Kostenko
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Rebekah M. Brennan
- Cellular Immunology Laboratory, Queensland Institute of Medical Research and Australian Centre for Vaccine Development, Brisbane 4029, Australia
| | - Craig S. Clements
- The Protein Crystallography Unit, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; and
| | - Andrew G. Brooks
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Anthony W. Purcell
- Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - James McCluskey
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Jamie Rossjohn
- The Protein Crystallography Unit, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; and
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Constraints within major histocompatibility complex class I restricted peptides: presentation and consequences for T-cell recognition. Proc Natl Acad Sci U S A 2010; 107:5534-9. [PMID: 20212169 DOI: 10.1073/pnas.1000032107] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Residues within processed protein fragments bound to major histocompatibility complex class I (MHC-I) glycoproteins have been considered to function as a series of "independent pegs" that either anchor the peptide (p) to the MHC-I and/or interact with the spectrum of alphabeta-T-cell receptors (TCRs) specific for the pMHC-I epitope in question. Mining of the extensive pMHC-I structural database established that many self- and viral peptides show extensive and direct interresidue interactions, an unexpected finding that has led us to the idea of "constrained" peptides. Mutational analysis of two constrained peptides (the HLA B44 restricted self-peptide (B44DPalpha-EEFGRAFSF) and an H2-D(b) restricted influenza peptide (D(b)PA, SSLENFRAYV) demonstrated that the conformation of the prominently exposed arginine in both peptides was governed by interactions with MHC-I-orientated flanking residues from the peptide itself. Using reverse genetics in a murine influenza model, we revealed that mutation of an MHC-I-orientated residue (SSLENFRAYV --> SSLENARAYV) within the constrained PA peptide resulted in a diminished cytotoxic T lymphocyte (CTL) response and the recruitment of a limited pMHC-I specific TCR repertoire. Interactions between individual peptide positions can thus impose fine control on the conformation of pMHC-I epitopes, whereas the perturbation of such constraints can lead to a previously unappreciated mechanism of viral escape.
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Karp DR, Marthandan N, Marsh SGE, Ahn C, Arnett FC, Deluca DS, Diehl AD, Dunivin R, Eilbeck K, Feolo M, Guidry PA, Helmberg W, Lewis S, Mayes MD, Mungall C, Natale DA, Peters B, Petersdorf E, Reveille JD, Smith B, Thomson G, Waller MJ, Scheuermann RH. Novel sequence feature variant type analysis of the HLA genetic association in systemic sclerosis. Hum Mol Genet 2009; 19:707-19. [PMID: 19933168 DOI: 10.1093/hmg/ddp521] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
We describe a novel approach to genetic association analyses with proteins sub-divided into biologically relevant smaller sequence features (SFs), and their variant types (VTs). SFVT analyses are particularly informative for study of highly polymorphic proteins such as the human leukocyte antigen (HLA), given the nature of its genetic variation: the high level of polymorphism, the pattern of amino acid variability, and that most HLA variation occurs at functionally important sites, as well as its known role in organ transplant rejection, autoimmune disease development and response to infection. Further, combinations of variable amino acid sites shared by several HLA alleles (shared epitopes) are most likely better descriptors of the actual causative genetic variants. In a cohort of systemic sclerosis patients/controls, SFVT analysis shows that a combination of SFs implicating specific amino acid residues in peptide binding pockets 4 and 7 of HLA-DRB1 explains much of the molecular determinant of risk.
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Affiliation(s)
- David R Karp
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX 75390-8884, USA.
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Sung FY, Jung CM, Wu CF, Lin CL, Liu CJ, Liaw YF, Tsai KS, Yu MW. Hepatitis B virus core variants modify natural course of viral infection and hepatocellular carcinoma progression. Gastroenterology 2009; 137:1687-97. [PMID: 19664630 DOI: 10.1053/j.gastro.2009.07.063] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2009] [Revised: 06/11/2009] [Accepted: 07/23/2009] [Indexed: 12/26/2022]
Abstract
BACKGROUND & AIMS We assessed the influence of genetic variants in the hepatitis B virus (HBV) core, which is a principal immunologic target, on the progression to hepatocellular carcinoma (HCC) in a cohort of 4841 male HBV carriers followed up for 16 years. METHODS First, baseline sera from 116 HCC cases and 154 controls nested within the cohort were used for sequencing of the HBV core gene to screen for variants with effects on HCC progression. By applying a high-throughput assay for detecting viral single nucleotide substitutions, we then used a longitudinal study (n = 1143) to examine whether 2 identified variants that lie in the region within or flanking epitopes affected the natural course of hepatitis B through investigating their relationships with time trends for viral load and clinical features. RESULTS In the nested case-control study, there were 6 core variants associated with decreased risk of HCC after accounting for viral genotype; 5 lie in the region within or flanking epitopes (P < .04). Each variant correlated with a 0.7- to 1-log decrease in viral load and hepatitis B virus e antigen negativity at baseline. The longitudinal study further showed that the appearance of 2 such variants (T1938C and T2045A) was preceded by long-term diminished viral load and decreased rate of liver abnormalities and was significantly less frequent in individuals with a prolonged immune clearance phase that associated with spectrum of liver disease than those in inactive carrier or reactivation phase. CONCLUSIONS HBV core variants affecting the kinetics of host-virus interplay may influence longitudinal viral load and HCC progression.
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Affiliation(s)
- Feng-Yu Sung
- Graduate Institute of Epidemiology, College of Public Health, National Taiwan University, Taipei, Taiwan
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Kumar P, Vahedi-Faridi A, Saenger W, Merino E, López de Castro JA, Uchanska-Ziegler B, Ziegler A. Structural basis for T cell alloreactivity among three HLA-B14 and HLA-B27 antigens. J Biol Chem 2009; 284:29784-97. [PMID: 19617632 PMCID: PMC2785609 DOI: 10.1074/jbc.m109.038497] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2009] [Revised: 07/09/2009] [Indexed: 01/07/2023] Open
Abstract
The existence of cytotoxic T cells (CTL) cross-reacting with the human major histocompatibility antigens HLA-B14 and HLA-B27 suggests that their alloreactivity could be due to presentation of shared peptides in similar binding modes by these molecules. We therefore determined the crystal structures of the subtypes HLA-B*1402, HLA-B*2705, and HLA-B*2709 in complex with a proven self-ligand, pCatA (peptide with the sequence IRAAPPPLF derived from cathepsin A (residues 2-10)), and of HLA-B*1402 in complex with a viral peptide, pLMP2 (RRRWRRLTV, derived from latent membrane protein 2 (residues 236-244) of Epstein-Barr virus). Despite the exchange of 18 residues within the binding grooves of HLA-B*1402 and HLA-B*2705 or HLA-B*2709, the pCatA peptide is presented in nearly identical conformations. However, pLMP2 is displayed by HLA-B*1402 in a conformation distinct from those previously found in the two HLA-B27 subtypes. In addition, the complexes of HLA-B*1402 with the two peptides reveal a nonstandard, tetragonal mode of the peptide N terminus anchoring in the binding groove because of the exchange of the common Tyr-171 by His-171 of the HLA-B*1402 heavy chain. This exchange appears also responsible for reduced stability of HLA-B14-peptide complexes in vivo and slow assembly in vitro. The studies with the pCatA peptide uncover that CTL cross-reactive between HLA-B14 and HLA-B27 might primarily recognize the common structural features of the bound peptide, thus neglecting amino acid replacements within the rim of the binding grooves. In contrast, structural alterations between the three complexes with the pLMP2 peptide indicate how heavy chain polymorphisms can influence peptide display and prevent CTL cross-reactivity between HLA-B14 and HLA-B27 antigens.
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Affiliation(s)
- Pravin Kumar
- From the Institut für Immungenetik, Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, Freie Universität Berlin, Thielallee 73, 14195 Berlin, Germany
| | - Ardeschir Vahedi-Faridi
- the Institut für Chemie und Biochemie/Kristallographie, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany, and
| | - Wolfram Saenger
- the Institut für Chemie und Biochemie/Kristallographie, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany, and
| | - Elena Merino
- the Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Cientificas and Universidad Autónoma de Madrid, Nicolás Cabrera, N.1, Universidad Autónoma, 28049 Madrid, Spain
| | - José A. López de Castro
- the Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Cientificas and Universidad Autónoma de Madrid, Nicolás Cabrera, N.1, Universidad Autónoma, 28049 Madrid, Spain
| | - Barbara Uchanska-Ziegler
- From the Institut für Immungenetik, Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, Freie Universität Berlin, Thielallee 73, 14195 Berlin, Germany
| | - Andreas Ziegler
- From the Institut für Immungenetik, Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, Freie Universität Berlin, Thielallee 73, 14195 Berlin, Germany
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49
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Hassen E, Nahla G, Bouaouina N, Chouchane L. The human leukocyte antigen class I genes in nasopharyngeal carcinoma risk. Mol Biol Rep 2009; 37:119-26. [PMID: 19449168 DOI: 10.1007/s11033-009-9548-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2008] [Accepted: 04/30/2009] [Indexed: 10/20/2022]
Abstract
Nasopharyngeal carcinoma (NPC) is a virally associated cancer which is highly prevalent in Southeast Asia and North Africa. Several linkage analysis studies suggested the association of susceptibility HLA (Human Leukocyte Antigen) alleles and haplotypes with NPC development. The HLA system is very polymorphic and according to the ethnic group studied, it has been found to have the capacity to confer susceptibility or resistance to NPC. Our aim was to review the most important described genetic associations of HLA class I in NPC and to comment on the inconsistent associations found in the different NPC incidence areas. We believe that the mechanisms of these associations may involve HLA genes through the differential capacity of each allele to present antigens. However, because HLA genes contain various linked candidate genes, HLA-NPC associations should be carefully interpreted.
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Affiliation(s)
- Elham Hassen
- Faculty of Medicine of Monastir, Molecular Immuno-oncology Laboratory, Monastir University, Monastir, Tunisia.
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50
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Pender MP, Csurhes PA, Lenarczyk A, Pfluger CMM, Burrows SR. Decreased T cell reactivity to Epstein-Barr virus infected lymphoblastoid cell lines in multiple sclerosis. J Neurol Neurosurg Psychiatry 2009; 80:498-505. [PMID: 19015225 PMCID: PMC2663364 DOI: 10.1136/jnnp.2008.161018] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
OBJECTIVE To investigate T cell and antibody immunity to Epstein-Barr virus (EBV) in multiple sclerosis (MS). METHODS Immunoglobulin G (IgG) immunity to EBV nuclear antigen 1 (EBNA1) and viral capsid antigen was measured by enzyme linked immunosorbent assays, and T cell immunity was assessed using enzyme linked immunospot assays to measure the frequency of peripheral blood mononuclear cells (PBMC) producing interferon gamma in response to autologous EBV infected B cell lymphoblastoid cell lines (LCL) in 34 EBV seropositive healthy subjects and 34 EBV seropositive patients with MS who had not received immunomodulatory therapy in the previous 3 months. RESULTS Patients with MS had increased levels of anti-EBNA1 IgG but a decreased frequency of LCL specific T cells compared with healthy subjects. Using purified populations of CD4(+) T cells and CD8(+) T cells, we showed that the LCL specific response resides predominantly in the CD8(+) population, with a frequency 5-7-fold higher than in the CD4(+) population. The decreased CD8(+) T cell response to LCL in MS was not caused by decreased HLA class I expression by LCL, and LCL from MS patients could be killed normally by HLA matched EBV specific cytotoxic CD8(+) T cell clones from healthy subjects. Furthermore, the decreased CD8(+) T cell immunity to EBV was not due to a primary defect in the function of CD8(+) T cells because EBV specific cytotoxic CD8(+) T cell lines could be generated normally from the PBMC of patients with MS. CONCLUSION This quantitative deficiency in CD8(+) T cell immunity to EBV might be responsible for the accumulation of EBV infected B cells in the brains of patients with MS.
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Affiliation(s)
- M P Pender
- University of Queensland, School of Medicine, Royal Brisbane and Women's Hospital, Queensland, Australia.
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