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Flender D, Vilenne F, Adams C, Boonen K, Valkenborg D, Baggerman G. Exploring the dynamic landscape of immunopeptidomics: Unravelling posttranslational modifications and navigating bioinformatics terrain. MASS SPECTROMETRY REVIEWS 2024. [PMID: 39152539 DOI: 10.1002/mas.21905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 07/30/2024] [Accepted: 08/01/2024] [Indexed: 08/19/2024]
Abstract
Immunopeptidomics is becoming an increasingly important field of study. The capability to identify immunopeptides with pivotal roles in the human immune system is essential to shift the current curative medicine towards personalized medicine. Throughout the years, the field has matured, giving insight into the current pitfalls. Nowadays, it is commonly accepted that generalizing shotgun proteomics workflows is malpractice because immunopeptidomics faces numerous challenges. While many of these difficulties have been addressed, the road towards the ideal workflow remains complicated. Although the presence of Posttranslational modifications (PTMs) in the immunopeptidome has been demonstrated, their identification remains highly challenging despite their significance for immunotherapies. The large number of unpredictable modifications in the immunopeptidome plays a pivotal role in the functionality and these challenges. This review provides a comprehensive overview of the current advancements in immunopeptidomics. We delve into the challenges associated with identifying PTMs within the immunopeptidome, aiming to address the current state of the field.
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Affiliation(s)
- Daniel Flender
- Centre for Proteomics, University of Antwerp, Antwerpen, Belgium
- Health Unit, VITO, Mol, Belgium
| | - Frédérique Vilenne
- Health Unit, VITO, Mol, Belgium
- Data Science Institute, University of Hasselt, Hasselt, Belgium
| | - Charlotte Adams
- Department of Computer Science, University of Antwerp, Antwerp, Belgium
| | - Kurt Boonen
- Centre for Proteomics, University of Antwerp, Antwerpen, Belgium
- ImmuneSpec, Niel, Belgium
| | - Dirk Valkenborg
- Data Science Institute, University of Hasselt, Hasselt, Belgium
| | - Geert Baggerman
- Department of Computer Science, University of Antwerp, Antwerp, Belgium
- ImmuneSpec, Niel, Belgium
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2
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Santambrogio L, Franco A. The yin/yang balance of the MHC-self -immunopeptidome. Front Immunol 2022; 13:1035363. [PMID: 36405763 PMCID: PMC9666884 DOI: 10.3389/fimmu.2022.1035363] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/07/2022] [Indexed: 07/22/2023] Open
Abstract
The MHC-self immunopeptidome of professional antigen presenting cells is a cognate ligand for the TCRs expressed on both conventional and thymic-derived natural regulatory T cells. In regulatory T cells, the TCR signaling associated with MHC-peptide recognition induces antigen specific as well as bystander immunosuppression. On the other hand, TCR activation of conventional T cells is associated with protective immunity. As such the peripheral T cell repertoire is populated by a number of T cells with different phenotypes and different TCRs, which can recognize the same MHC-self-peptide complex, resulting in opposite immunological outcomes. This article summarizes what is known about regulatory and conventional T cell recognition of the MHC-self-immunopeptidome at steady state and in inflammatory conditions associated with increased T and B cell self-reactivity, discussing how changes in the MHC-ligandome including epitope copy number and post-translational modifications can tilt the balance toward the expansion of pro-inflammatory or regulatory T cells.
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Affiliation(s)
- Laura Santambrogio
- Department of Radiation Oncology, Physiology and Biophysics, Englander Institute of Precision Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Alessandra Franco
- University of California San Diego School of Medicine, Department of Pediatrics, La Jolla, CA, United States
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3
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Sandalova T, Sala BM, Achour A. Structural aspects of chemical modifications in the MHC-restricted immunopeptidome; Implications for immune recognition. Front Chem 2022; 10:861609. [PMID: 36017166 PMCID: PMC9395651 DOI: 10.3389/fchem.2022.861609] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 07/12/2022] [Indexed: 11/26/2022] Open
Abstract
Significant advances in mass-spectroscopy (MS) have made it possible to investigate the cellular immunopeptidome, a large collection of MHC-associated epitopes presented on the surface of healthy, stressed and infected cells. These approaches have hitherto allowed the unambiguous identification of large cohorts of epitope sequences that are restricted to specific MHC class I and II molecules, enhancing our understanding of the quantities, qualities and origins of these peptide populations. Most importantly these analyses provide essential information about the immunopeptidome in responses to pathogens, autoimmunity and cancer, and will hopefully allow for future tailored individual therapies. Protein post-translational modifications (PTM) play a key role in cellular functions, and are essential for both maintaining cellular homeostasis and increasing the diversity of the proteome. A significant proportion of proteins is post-translationally modified, and thus a deeper understanding of the importance of PTM epitopes in immunopeptidomes is essential for a thorough and stringent understanding of these peptide populations. The aim of the present review is to provide a structural insight into the impact of PTM peptides on stability of MHC/peptide complexes, and how these may alter/modulate immune responses.
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Affiliation(s)
- Tatyana Sandalova
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Section for Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Benedetta Maria Sala
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Section for Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Adnane Achour
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Section for Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- *Correspondence: Adnane Achour,
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4
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Zhao Y, Sun M, Zhang N, Liu X, Yue C, Feng L, Ji S, Liu X, Qi J, Wong CC, Gao GF, Liu WJ. Phosphosite-dependent presentation of dual phosphorylated peptides by MHC class I molecules. iScience 2022; 25:104013. [PMID: 35310951 PMCID: PMC8931367 DOI: 10.1016/j.isci.2022.104013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 02/14/2022] [Accepted: 02/25/2022] [Indexed: 11/30/2022] Open
Abstract
Phosphopeptides presented by major histocompatibility complex (MHC) class I have been regarded as a pivotal type of cancer neoantigens that are recognized by T cells. The structural basis of single-phosphorylated peptide presentation has been well studied. Diphosphorylation with one interval between two sites is one of the prevalent forms of multisite-phosphorylated peptides. Herein, we determined the molecular basis of presentation of two P4/P6 double pS-containing peptides by HLA-B27 and compared them with unmodified and single-phosphorylated peptide complexes. These data clarified not only the HLA allele-specific presentation of phosphopeptides by MHC class I molecules but also the cooperativity of peptide conformation within P4 and P6 phosphorylation sites. The phosphorylation of P6 site can influence the binding mode of P4 phosphorylated site to HLA-B27. And we found the diphospho-dependent attenuated effect of peptide binding affinity. This study provides insights into the MHC presentation features of diphosphopeptides, which is different from monophosphopeptides. Diphosphorylation with an interval is prevalent among multiphosphorylated peptides Diphosphopeptide presentation is HLA specific and different from monophosphopeptide The cooperativity of peptide conformation within P4 and P6 phosphorylation sites The diphosphorylation attenuates peptide binding affinity to HLA-B27
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Affiliation(s)
- Yingze Zhao
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing 100052, China
- Research Unit of Adaptive Evolution and Control of Emerging Viruses (2018RU009), Chinese Academy of Medical Sciences, Beijing 102206, China
| | - Mingwei Sun
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Nan Zhang
- Center for Precision Medicine Multi-Omics Research, Peking University Health Science Center, Peking University, Beijing 100191, China
| | - Xueyuan Liu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing 100052, China
- School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Can Yue
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing 100052, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Feng
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing 100052, China
| | - Shushen Ji
- Center for Precision Medicine Multi-Omics Research, Peking University Health Science Center, Peking University, Beijing 100191, China
| | - Xiao Liu
- Center for Precision Medicine Multi-Omics Research, Peking University Health Science Center, Peking University, Beijing 100191, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Catherine C.L. Wong
- Center for Precision Medicine Multi-Omics Research, Peking University Health Science Center, Peking University, Beijing 100191, China
- Corresponding author
| | - George F. Gao
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing 100052, China
- Research Unit of Adaptive Evolution and Control of Emerging Viruses (2018RU009), Chinese Academy of Medical Sciences, Beijing 102206, China
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
- Corresponding author
| | - William J. Liu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing 100052, China
- Research Unit of Adaptive Evolution and Control of Emerging Viruses (2018RU009), Chinese Academy of Medical Sciences, Beijing 102206, China
- Corresponding author
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5
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Loll B, Rückert C, Uchanska-Ziegler B, Ziegler A. Conformational Plasticity of HLA-B27 Molecules Correlates Inversely With Efficiency of Negative T Cell Selection. Front Immunol 2020; 11:179. [PMID: 32117305 PMCID: PMC7027375 DOI: 10.3389/fimmu.2020.00179] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 01/23/2020] [Indexed: 01/07/2023] Open
Abstract
The development of autoimmune disorders is incompletely understood. Inefficient thymic T cell selection against self-peptides presented by major histocompatibility antigens (HLA in humans) may contribute to the emergence of auto-reactive effector cells, and molecular mimicry between foreign and self-peptides could promote T cell cross-reactivity. A pair of class I subtypes, HLA-B2705 and HLA-B2709, have previously been intensely studied, because they are distinguished from each other only by a single amino acid exchange at the floor of the peptide-binding groove, yet are differentially associated with the autoinflammatory disorder ankylosing spondylitis. Using X-ray crystallography in combination with ensemble refinement, we find that the non-disease-associated subtype HLA-B2709, when presenting the self-peptide pGR (RRRWHRWRL), exhibits elevated conformational dynamics, and the complex can also be recognized by T cells. Both features are not observed in case of the sequence-related self-peptide pVIPR (RRKWRRWHL) in complex with this subtype, and T cell cross-reactivity between pGR, pVIPR, and the viral peptide pLMP2 (RRRWRRLTV) is only rarely observed. The disease-associated subtype HLA-B2705, however, exhibits extensive conformational flexibility in case of the three complexes, all of which are also recognized by frequently occurring cross-reactive T cells. A comparison of the structural and dynamic properties of the six HLA-B27 complexes, together with their individual ability to interact with T cells, permits us to correlate the flexibility of HLA-B27 complexes with effector cell reactivity. The results suggest the existence of an inverse relationship between conformational plasticity of peptide-HLA-B27 complexes and the efficiency of negative selection of self-reactive cells within the thymus.
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Affiliation(s)
- Bernhard Loll
- Institut für Chemie und Biochemie, Abteilung Strukturbiochemie, Freie Universität Berlin, Berlin, Germany,*Correspondence: Bernhard Loll
| | - Christine Rückert
- Institut für Immungenetik, Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Berlin, Germany
| | - Barbara Uchanska-Ziegler
- Institut für Immungenetik, Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Berlin, Germany,Ziegler Biosolutions, Waldshut-Tiengen, Germany
| | - Andreas Ziegler
- Ziegler Biosolutions, Waldshut-Tiengen, Germany,Andreas Ziegler
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Driller R, Ballaschk M, Schmieder P, Uchanska-Ziegler B, Ziegler A, Loll B. Metal-triggered conformational reorientation of a self-peptide bound to a disease-associated HLA-B*27 subtype. J Biol Chem 2019; 294:13269-13279. [PMID: 31296658 DOI: 10.1074/jbc.ra119.008937] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 07/08/2019] [Indexed: 01/03/2023] Open
Abstract
Conformational changes of major histocompatibility complex (MHC) antigens have the potential to be recognized by T cells and may arise from polymorphic variation of the MHC molecule, the binding of modifying ligands, or both. Here, we investigated whether metal ions could affect allele-dependent structural variation of the two minimally distinct human leukocyte antigen (HLA)-B*27:05 and HLA-B*27:09 subtypes, which exhibit differential association with the rheumatic disease ankylosing spondylitis (AS). We employed NMR spectroscopy and X-ray crystallography coupled with ensemble refinement to study the AS-associated HLA-B*27:05 subtype and the AS-nonassociated HLA-B* 27:09 in complex with the self-peptide pVIPR (RRKWRRWHL). Both techniques revealed that pVIPR exhibits a higher degree of flexibility when complexed with HLA-B*27:05 than with HLA-B*27:09. Furthermore, we found that the binding of the metal ion Cu2+ or Ni2+, but not Mn2+, Zn2+, or Hg2+, affects the structure of a pVIPR-bound HLA-B*27 molecule in a subtype-dependent manner. In HLA-B*27:05, the metals triggered conformational reorientations of pVIPR, but no such structural changes were observed in the HLA-B*27:09 subtype, with or without bound metal ion. These observations provide the first demonstration that not only major histocompatibility complex class II, but also class I, molecules can undergo metal ion-induced conformational alterations. Our findings suggest that metals may have a role in triggering rheumatic diseases such as AS and also have implications for the molecular basis of metal-induced hypersensitivities and allergies.
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Affiliation(s)
- Ronja Driller
- Institut für Chemie/Biochemie, AG Strukturbiochemie, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany
| | - Martin Ballaschk
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Peter Schmieder
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Barbara Uchanska-Ziegler
- Institut für Immungenetik, Charité-Universitätsmedizin Berlin, Freie Universität Berlin, Thielallee 73, 14195 Berlin, Germany; Ziegler Biosolutions, Fahrgasse 5, 79761 Waldshut-Tiengen, Germany
| | - Andreas Ziegler
- Ziegler Biosolutions, Fahrgasse 5, 79761 Waldshut-Tiengen, Germany.
| | - Bernhard Loll
- Institut für Chemie/Biochemie, AG Strukturbiochemie, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany; MoloX GmbH, Takustrasse 6, 14195 Berlin, Germany.
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7
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Carbamazepine-Mediated Adverse Drug Reactions: CBZ-10,11-epoxide but Not Carbamazepine Induces the Alteration of Peptides Presented by HLA-B∗15:02. J Immunol Res 2018; 2018:5086503. [PMID: 30302345 PMCID: PMC6158965 DOI: 10.1155/2018/5086503] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 07/19/2018] [Accepted: 07/31/2018] [Indexed: 01/11/2023] Open
Abstract
Among patients treated with the anticonvulsive and psychotropic drug carbamazepine (CBZ), approximately 10% develop severe and life-threatening adverse drug reactions. These immunological conditions are resolved upon withdrawal of the medicament, suggesting that the drug does not manifest in the body in long term. The HLA allele B∗15:02 has been described to be a genomic biomarker for CBZ-mediated immune reactions. It is not well understood if the immune reactions are triggered by the original drug or by its metabolite carbamazepine-10,11-epoxide (EPX) and how the interaction between the drug and the distinct HLA molecule occurs. Genetically engineered human B-lymphoblastoid cells expressing soluble HLA-B∗15:02 molecules were treated with the drug or its metabolite. Functional pHLA complexes were purified; peptides were eluted and sequenced. Applying mass spectrometric analysis, CBZ and EPX were monitored by analyzing the heavy chain and peptide fractions separately for the presence of the drug. This method enabled the detection of the drug in a biological situation post-pHLA assembly. Both drugs were bound to the HLA-B∗15:02 heavy chain; however, solely EPX altered the peptide-binding motif of B∗15:02-restricted peptides. This observation could be explained through structural insight; EPX binds to the peptide-binding region and alters the biochemical features of the F pocket and thus the peptide motif. Understanding the nature of immunogenic interactions between CBZ and EPX with the HLA immune complex will guide towards effective and safe medications.
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8
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Morita D, Sugita M. Lipopeptides: a novel antigen repertoire presented by major histocompatibility complex class I molecules. Immunology 2016; 149:139-45. [PMID: 27402593 DOI: 10.1111/imm.12646] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 07/04/2016] [Accepted: 07/06/2016] [Indexed: 01/13/2023] Open
Abstract
Post-translationally modified peptides, such as those containing either phosphorylated or O-glycosylated serine/threonine residues, may be presented to cytotoxic T lymphocytes (CTLs) by MHC class I molecules. Most of these modified peptides are captured in the MHC class I groove in a similar manner to that for unmodified peptides. N-Myristoylated 5-mer lipopeptides have recently been identified as a novel chemical class of MHC class I-presented antigens. The rhesus classical MHC class I allele, Mamu-B*098, was found to be capable of binding N-myristoylated lipopeptides and presenting them to CTLs. A high-resolution X-ray crystallographic analysis of the Mamu-B*098:lipopeptide complex revealed that the myristic group as well as conserved C-terminal serine residue of the lipopeptide ligand functioned as anchors, whereas the short stretch of three amino acid residues located in the middle of the lipopeptides was only exposed externally with the potential to interact directly with specific T-cell receptors. Therefore, the modes of lipopeptide-ligand interactions with MHC class I and with T-cell receptors are novel and fundamentally distinct from that for MHC class I-presented peptides. Another lipopeptide-presenting MHC class I allele has now been identified, leading us to the prediction that MHC class I molecules may be separated on a functional basis into two groups: one presenting long peptides and the other presenting short lipopeptides. Since the N-myristoylation of viral proteins is often linked to pathogenesis, CTLs capable of sensing N-myristoylation may serve to control pathogenic viruses, raising the possibility for the development of a new type of lipopeptide vaccine.
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Affiliation(s)
- Daisuke Morita
- Laboratory of Cell Regulation, Institute for Virus Research, Kyoto University, Kyoto, Japan
| | - Masahiko Sugita
- Laboratory of Cell Regulation, Institute for Virus Research, Kyoto University, Kyoto, Japan
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Tedeschi V, Vitulano C, Cauli A, Paladini F, Piga M, Mathieu A, Sorrentino R, Fiorillo MT. The Ankylosing Spondylitis-associated HLA-B*2705 presents a B*0702-restricted EBV epitope and sustains the clonal amplification of cytotoxic T cells in patients. Mol Med 2016; 22:215-223. [PMID: 27254288 DOI: 10.2119/molmed.2016.00031] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 05/11/2016] [Indexed: 12/16/2022] Open
Abstract
HLA-B*27 is strongly associated with an inflammatory autoimmune disorder, the Ankylosing Spondylitis (AS) and plays a protective role in viral infections. The two aspects might be linked. In this work, we compared in B*2705/B*07 positive patients with AS, the CD8+ T cell responses to two immunodominant EBV-derived epitopes restricted for either the HLA-B*27 (pEBNA3C) or the HLA-B*07 (pEBNA3A). We have unexpectedly found that the HLA-B*07-restricted EBNA3A peptide is presented by both the B*0702 and the B*2705 but not by the non AS-associated B*2709, that differs from the AS-associated B*2705 for a single amino acid in the peptide-binding groove (His116Asp). We then analysed 38 B*2705-positive/B*07-negative (31 AS-patients and 7 healthy donors) and 8 B*2709-positive/B*07-negative subjects. EBNA3A-specific CD8+ T lymphocytes were present in 55.3% of the HLA-B*2705 but in none of the B*2709 donors (p=0.0049). TCR β-chain analysis identified common TCRBV and TCRBJ gene segments and shared CDR3β sequences in pEBNA3A-responsive CTLs of B*2705 carriers, suggesting the existence of a shared TCR repertoire for recognition of the uncanonical B*2705/pEBNA3A complex. These data highlight the plasticity of the AS-associated HLA-B*2705, which presents peptides with suboptimal binding motifs, possibly contributing both to its enhanced capacity to protect against pathogens and to predispose to autoimmunity.
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Affiliation(s)
- Valentina Tedeschi
- Department of Biology and Biotechnology "C. Darwin", Sapienza University, Rome, Italy
| | - Carolina Vitulano
- Department of Biology and Biotechnology "C. Darwin", Sapienza University, Rome, Italy
| | - Alberto Cauli
- 2nd Chair of Rheumatology, Department of Medical Sciences, University of Cagliari, Cagliari, Italy
| | - Fabiana Paladini
- Department of Biology and Biotechnology "C. Darwin", Sapienza University, Rome, Italy
| | - Matteo Piga
- 2nd Chair of Rheumatology, Department of Medical Sciences, University of Cagliari, Cagliari, Italy
| | - Alessandro Mathieu
- 2nd Chair of Rheumatology, Department of Medical Sciences, University of Cagliari, Cagliari, Italy
| | - Rosa Sorrentino
- Department of Biology and Biotechnology "C. Darwin", Sapienza University, Rome, Italy
| | - Maria Teresa Fiorillo
- Department of Biology and Biotechnology "C. Darwin", Sapienza University, Rome, Italy
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10
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Sun M, Liu J, Qi J, Tefsen B, Shi Y, Yan J, Gao GF. Nα-terminal acetylation for T cell recognition: molecular basis of MHC class I-restricted nα-acetylpeptide presentation. THE JOURNAL OF IMMUNOLOGY 2014; 192:5509-19. [PMID: 24829406 DOI: 10.4049/jimmunol.1400199] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
As one of the most common posttranslational modifications (PTMs) of eukaryotic proteins, N(α)-terminal acetylation (Nt-acetylation) generates a class of N(α)-acetylpeptides that are known to be presented by MHC class I at the cell surface. Although such PTM plays a pivotal role in adjusting proteolysis, the molecular basis for the presentation and T cell recognition of N(α)-acetylpeptides remains largely unknown. In this study, we determined a high-resolution crystallographic structure of HLA (HLA)-B*3901 complexed with an N(α)-acetylpeptide derived from natural cellular processing, also in comparison with the unmodified-peptide complex. Unlike the α-amino-free P1 residues of unmodified peptide, of which the α-amino group inserts into pocket A of the Ag-binding groove, the N(α)-linked acetyl of the acetylated P1-Ser protrudes out of the groove for T cell recognition. Moreover, the Nt-acetylation not only alters the conformation of the peptide but also switches the residues in the α1-helix of HLA-B*3901, which may impact the T cell engagement. The thermostability measurements of complexes between N(α)-acetylpeptides and a series of MHC class I molecules derived from different species reveal reduced stability. Our findings provide the insight into the mode of N(α)-acetylpeptide-specific presentation by classical MHC class I molecules and shed light on the potential of acetylepitope-based immune intervene and vaccine development.
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Affiliation(s)
- Mingwei Sun
- School of Life Sciences, University of Science and Technology of China, Hefei 230027, China; CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jun Liu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; and
| | - Jianxun Qi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Boris Tefsen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yi Shi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Research Network of Immunity and Health, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Jinghua Yan
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - George F Gao
- School of Life Sciences, University of Science and Technology of China, Hefei 230027, China; CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; and Research Network of Immunity and Health, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
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11
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The role of dendritic cells in tissue-specific autoimmunity. J Immunol Res 2014; 2014:857143. [PMID: 24877157 PMCID: PMC4022068 DOI: 10.1155/2014/857143] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Revised: 03/20/2014] [Accepted: 04/08/2014] [Indexed: 01/24/2023] Open
Abstract
In this review, we explore the role of dendritic cell subsets in the development of tissue-specific autoimmune diseases. From the increasing list of dendritic cell subclasses, it is becoming clear that we are only at the beginning of understanding the role of these antigen presenting cells in mediating autoimmunity. Emerging research areas for the study of dendritic cell involvement in the onset and inhibition of tissue-specific autoimmunity are presented. Further, we compare tissue specific to systemic autoimmunity to demonstrate how development of dendritic cell-based therapies may be broadly applicable to both classes of autoimmunity. Continued development of these research areas will lead us closer to clinical assessment of novel immunosuppressive therapy for the reversal and prevention of tissue-specific autoimmunity. Through description of dendritic cell functions in the modulation of tissue-specific autoimmunity, we hope to stimulate a greater appreciation and understanding of the role dendritic cells play in the development and treatment of autoimmunity.
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12
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Wendling D, Prati C. Spondyloarthritis and smoking: towards a new insight into the disease. Expert Rev Clin Immunol 2014; 9:511-6. [DOI: 10.1586/eci.13.35] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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13
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Ireland JM, Unanue ER. Autophagy in antigen-presenting cells results in presentation of citrullinated peptides to CD4 T cells. ACTA ACUST UNITED AC 2011; 208:2625-32. [PMID: 22162830 PMCID: PMC3244027 DOI: 10.1084/jem.20110640] [Citation(s) in RCA: 187] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Citrullinated peptide presentation by DCs and macrophages is constitutive, whereas B cells present modified peptides only with autophagy induced by serum starvation or BCR ligation. Antibody responses to citrullinated self-proteins are found in autoimmunities, particularly in rheumatoid arthritis, where they serve as a diagnostic indicator. We show here that processing of the protein hen egg-white lysozyme (HEL) resulted in citrullination of peptides presented on class II MHC molecules by antigen-presenting cells. The presentation of the citrullinated peptides but not of the unmodified peptides was associated with autophagy. Dendritic cells (DCs), macrophages, and thymic DCs presented citrullinated peptides constitutively. Their treatment with 3-methyladenine (3MA) blocked presentation of citrullinated HEL peptides, but presentation of unmodified peptides was not affected. Presentation of citrullinated peptides was not detected on B cells or B lymphoma cells under normal culture conditions. In B cells, engagement of the B cell antigen receptor was required for presentation of the citrullinated peptides, also inhibited by 3MA. B lymphoma–expressing HEL cells presented citrullinated peptides only after brief serum starvation. This presentation was reduced by 3MA or by reduction in Atg5 expression. Presentation of the unmodified peptides was not changed. The findings indicate a linkage between autophagy and autoreactivity through the generation of this neo-epitope.
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Affiliation(s)
- Jamie M Ireland
- Department of Pathology and Immunology, School of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA
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Anti-mutated citrullinated vimentin (anti-MCV) and anti-65 kDa heat shock protein (anti-hsp65): new biomarkers in ankylosing spondylitis. Joint Bone Spine 2011; 79:63-6. [PMID: 21683641 DOI: 10.1016/j.jbspin.2011.03.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Accepted: 03/15/2011] [Indexed: 10/18/2022]
Abstract
INTRODUCTION Citrullination as well as anti-citrullinated protein/peptide antibodies (ACPA) have been implicated in the pathogenesis of rheumatoid arthritis (RA). While ACPAs are specific and sensitive markers for RA, there have been hardly any reports regarding ACPAs in ankylosing spondylitis (AS). The possible role of antibodies to Mycobacterial 65 kDa heat shock protein (hsp65) has not been characterized in AS. As new laboratory biomarkers of AS are needed, we investigated the prevalence of anti-mutated citrullinated vimentin (MCV) and anti-hsp65 antibodies in AS. METHODS Altogether 43 AS and 44 healthy controls were included in the study. Anti-MCV and anti-hsp65 were determined in sera by commercial and in-house ELISA, respectively. Serum autoantibody levels were correlated with ESR, CRP, HLA-B27 status, smoking habits, pain intensity, BASDAI, BASFI and BASMI indices. RESULTS Patients with AS had significantly higher serum anti-MCV levels (17.3 U/mL, range: 8.3-31.5 U/mL) in comparison to healthy subjects (8.9 U/mL, range: 5.4-13.3 U/mL) (p<0.01). Sixteen of the 43 AS patients (37%) and none of the 44 healthy controls (0%) were anti-MCV positive using the cut-off value recommended by the manufacturer (>20 U/mL). The mean anti-hsp65 concentration in AS sera was 124.8 AU/mL (range: 27.2-1000 AU/mL), while controls exerted significantly lower anti-hsp65 levels (mean: 51.8 AU/mL; range: 22.5-88.5 AU/mL) (p<0.001). Correlation analysis revealed that both anti-MCV positivity (r=0.613; p=0.012) and absolute serum anti-MCV levels (r=0.553; p=0.021) correlated with anti-hsp65 levels. Anti-MCV positivity also correlated with ESR (r=0.437; p=0.03). CONCLUSIONS Anti-MCV and anti-hsp65 may be novel biomarkers in AS.
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Uchanska-Ziegler B, Loll B, Fabian H, Hee CS, Saenger W, Ziegler A. HLA class I-associated diseases with a suspected autoimmune etiology: HLA-B27 subtypes as a model system. Eur J Cell Biol 2011; 91:274-86. [PMID: 21665321 DOI: 10.1016/j.ejcb.2011.03.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2010] [Revised: 03/15/2011] [Accepted: 03/15/2011] [Indexed: 01/05/2023] Open
Abstract
Although most autoimmune diseases are connected to major histocompatibility complex (MHC) class II alleles, a small number of these disorders exhibit a variable degree of association with selected MHC class I genes, like certain human HLA-A and HLA-B alleles. The basis for these associations, however, has so far remained elusive. An understanding might be obtained by comparing functional, biochemical, and biophysical properties of alleles that are minimally distinct from each other, but are nevertheless differentially associated to a given disease, like the HLA-B*27:05 and HLA-B*27:09 antigens, which differ only by a single amino acid residue (Asp116His) that is deeply buried within the binding groove. We have employed a number of approaches, including X-ray crystallography and isotope-edited infrared spectroscopy, to investigate biophysical characteristics of the two HLA-B27 subtypes complexed with up to ten different peptides. Our findings demonstrate that the binding of these peptides as well as the conformational flexibility of the subtypes is greatly influenced by interactions of the C-terminal peptide residue. In particular, a basic C-terminal peptide residue is favoured by the disease-associated subtype HLA-B*27:05, but not by HLA-B*27:09. This property appears also as the only common denominator of distinct HLA class I alleles, among them HLA-B*27:05, HLA-A*03:01 or HLA-A*11:01, that are associated with diseases suspected to have an autoimmune etiology. We postulate here that the products of these alleles, due to their unusual ability to bind with high affinity to a particular peptide set during positive T cell selection in the thymus, are involved in shaping an abnormal T cell repertoire which predisposes to the acquisition of autoimmune diseases.
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Affiliation(s)
- Barbara Uchanska-Ziegler
- Institut für Immungenetik, Charité - Universitätmedizin Berlin, Campus Benjamin Franklin, Freie Universität Berlin, Thielallee 73, 14195 Berlin, Germany.
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Fabian H, Loll B, Huser H, Naumann D, Uchanska-Ziegler B, Ziegler A. Influence of inflammation-related changes on conformational characteristics of HLA-B27 subtypes as detected by IR spectroscopy. FEBS J 2011; 278:1713-27. [DOI: 10.1111/j.1742-4658.2011.08097.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Loll B, Rückert C, Hee CS, Saenger W, Uchanska-Ziegler B, Ziegler A. Loss of recognition by cross-reactive T cells and its relation to a C-terminus-induced conformational reorientation of an HLA-B*2705-bound peptide. Protein Sci 2011; 20:278-90. [PMID: 21280120 PMCID: PMC3048413 DOI: 10.1002/pro.559] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2010] [Revised: 11/10/2010] [Accepted: 11/10/2010] [Indexed: 01/07/2023]
Abstract
The human major histocompatibility complex class I antigen HLA-B*2705 binds several sequence-related peptides (pVIPR, RRKWRRWHL; pLPM2, RRRWRRLTV; pGR, RRRWHRWRL). Cross-reactivity of cytotoxic T cells (CTL) against these HLA-B*2705:peptide complexes seemed to depend on a particular peptide conformation that is facilitated by the engagement of a crucial residue within the binding groove (Asp116), associated with a noncanonical bulging-in of the middle portion of the bound peptide. We were interested whether a conformational reorientation of the ligand might contribute to the lack of cross-reactivity of these CTL with a peptide derived from voltage-dependent calcium channel α1 subunit (pCAC, SRRWRRWNR), in which the C-terminal peptide residue pArg9 could engage Asp116. Analyses of the HLA-B*2705:pCAC complex by X-ray crystallography at 1.94 Å resolution demonstrated that the peptide had indeed undergone a drastic reorientation, leading it to adopt a canonical binding mode accompanied by the loss of molecular mimicry between pCAC and sequence-related peptides such as pVIPR, pLMP2, and pGR. This was clearly a consequence of interactions of pArg9 with Asp116 and other F-pocket residues. Furthermore, we observed an unprecedented reorientation of several additional residues of the HLA-B*2705 heavy chain near the N-terminal region of the peptide, including also the presence of double conformations of two glutamate residues, Glu63 and Glu163, on opposing sides of the peptide binding groove. Together with the Arg-Ser exchange at peptide position 1, there are thus multiple structural reasons that may explain the observed failure of pVIPR-directed, HLA-B*2705-restricted CTL to cross-react with HLA-B*2705:pCAC complexes.
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Affiliation(s)
- Bernhard Loll
- Institut für Chemie und Biochemie, Abteilung Strukturbiochemie, Freie Universität BerlinTakustrasse 6, Berlin 14195, Germany,*Correspondence to: Bernhard Loll, Institut für Chemie und Biochemie, Abteilung Strukturbiochemie, Freie Universität Berlin, Takustrasse 6, Berlin 14195, Germany. E-mail:
| | - Christine Rückert
- Institut für Immungenetik, Charité - Universitätsmedizin Berlin, Campus Benjamin Franklin, Freie Universität BerlinThielallee 73, Berlin 14195, Germany
| | - Chee Seng Hee
- Institut für Immungenetik, Charité - Universitätsmedizin Berlin, Campus Benjamin Franklin, Freie Universität BerlinThielallee 73, Berlin 14195, Germany
| | - Wolfram Saenger
- Institut für Chemie und Biochemie, Abteilung Kristallographie, Freie Universität BerlinTakustrasse 6, Berlin 14195, Germany
| | - Barbara Uchanska-Ziegler
- Institut für Immungenetik, Charité - Universitätsmedizin Berlin, Campus Benjamin Franklin, Freie Universität BerlinThielallee 73, Berlin 14195, Germany
| | - Andreas Ziegler
- Institut für Immungenetik, Charité - Universitätsmedizin Berlin, Campus Benjamin Franklin, Freie Universität BerlinThielallee 73, Berlin 14195, Germany
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Structure of a classical MHC class I molecule that binds "non-classical" ligands. PLoS Biol 2010; 8:e1000557. [PMID: 21151886 PMCID: PMC2998441 DOI: 10.1371/journal.pbio.1000557] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2010] [Accepted: 10/27/2010] [Indexed: 11/19/2022] Open
Abstract
The chicken MHC YF1*7.1 X-ray structures reveal that this protein binds lipids and thus represents a "hybrid" class I complex with features of classical as well as non-classical MHC molecules. Chicken YF1 genes share a close sequence relationship with classical MHC class I loci but map outside of the core MHC region. To obtain insights into their function, we determined the structure of the YF1*7.1/β2-microgloblin complex by X-ray crystallography at 1.3 Å resolution. It exhibits the architecture typical of classical MHC class I molecules but possesses a hydrophobic binding groove that contains a non-peptidic ligand. This finding prompted us to reconstitute YF1*7.1 also with various self-lipids. Seven additional YF1*7.1 structures were solved, but only polyethyleneglycol molecules could be modeled into the electron density within the binding groove. However, an assessment of YF1*7.1 by native isoelectric focusing indicated that the molecules were also able to bind nonself-lipids. The ability of YF1*7.1 to interact with hydrophobic ligands is unprecedented among classical MHC class I proteins and might aid the chicken immune system to recognize a diverse ligand repertoire with a minimal number of MHC class I molecules. Proteins encoded by the major histocompatibility complex (MHC) play crucial roles in vertebrate immune systems, presenting pathogen-derived protein fragments to receptors on effector cells. In contrast, some non-classical MHC class I proteins such as CD1 molecules possess a hydrophobic groove that allows them to display lipids. Chicken MHC-Y is a genetic region outside the core MHC that harbors several immune-related genes, among them YF1*7.1, which encodes a protein whose structure we solved in this study. YF1*7.1 is an MHC class I molecule that exhibits the architecture typical of classical MHC class I antigens but possesses a hydrophobic binding groove that binds non-peptidic ligands. By using lipid-binding assays, we show that this molecule can indeed bind lipids. Therefore, YF1*7.1 bridges, at least in structural terms, the traditional gap between classical and non-classical MHC class I molecules. Lipid-binding YF1 proteins might serve the chicken to enlarge its otherwise very small repertoire of antigen-presenting MHC class I molecules. Furthermore, comparative analyses of the two protein subunits of classical MHC molecules revealed a structural feature in chickens that appears to be shared by non-mammalian but not by mammalian vertebrates. This unique feature is indicative of a structure-dependent co-evolution of two genetically unlinked genes in non-mammalian species.
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A reductionist cell-free major histocompatibility complex class II antigen processing system identifies immunodominant epitopes. Nat Med 2010; 16:1333-40. [PMID: 21037588 PMCID: PMC3058316 DOI: 10.1038/nm.2248] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2009] [Accepted: 07/23/2010] [Indexed: 12/18/2022]
Abstract
Immunodominance is defined as restricted responsiveness of T cells to a few selected epitopes from complex antigens. Strategies currently used for elucidating CD4+ T cell epitopes are inadequate. To understand the mechanism of epitope selection for helper T cells, we established a cell-free antigen processing system composed of defined proteins: MHC class II, cathepsins, and HLA-DM. Our minimalist system successfully identified the physiologically selected immunodominant epitopes of model antigens, HA1 from influenza virus (A/Texas/1/77) and type II collagen. When applied for de novo epitope identification to a malaria antigen, or HA1 from H5N1 virus (Avian Flu), the system selected a single epitope from each protein that were confirmed to be immunodominant by their capacity to activate CD4+ T cells in HLA-DR1 positive human volunteers or transgenic mice immunized with the corresponding proteins. Thus, we provide a powerful new tool for the identification of physiologically relevant helper T cell epitopes from antigens.
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Haliloglu T, Gul A, Erman B. Predicting important residues and interaction pathways in proteins using Gaussian Network Model: binding and stability of HLA proteins. PLoS Comput Biol 2010; 6:e1000845. [PMID: 20628622 PMCID: PMC2900293 DOI: 10.1371/journal.pcbi.1000845] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2010] [Accepted: 06/02/2010] [Indexed: 01/07/2023] Open
Abstract
A statistical thermodynamics approach is proposed to determine structurally and functionally important residues in native proteins that are involved in energy exchange with a ligand and other residues along an interaction pathway. The structure-function relationships, ligand binding and allosteric activities of ten structures of HLA Class I proteins of the immune system are studied by the Gaussian Network Model. Five of these models are associated with inflammatory rheumatic disease and the remaining five are properly functioning. In the Gaussian Network Model, the protein structures are modeled as an elastic network where the inter-residue interactions are harmonic. Important residues and the interaction pathways in the proteins are identified by focusing on the largest eigenvalue of the residue interaction matrix. Predicted important residues match those known from previous experimental and clinical work. Graph perturbation is used to determine the response of the important residues along the interaction pathway. Differences in response patterns of the two sets of proteins are identified and their relations to disease are discussed. We propose a statistical thermodynamics model for determining structurally and functionally important residues in ligand-protein interactions. Our method identifies the path that the protein uses in transferring information from one point to the other. We show that a few energetically active residues are most efficient in energy exchange with the surroundings acting as ‘energy gates’. The remaining important residues that we identify are situated along the interaction path. These are the hub residues. Strong correlations exist between energy gates and hub residues along the interaction path, thus relating to allostery and cooperative binding. We studied the structure-function, ligand binding and allosteric activities of ten models of HLA Class I proteins of the immune system. Five of these models belong to the HLA-B*2705 allele and are strongly associated with a chronic inflammatory rheumatic disease. The remaining five from the HLA-B*2709 allele of the same protein are the corresponding properly functioning ones. We show that differences in the contact maps of the two types lead to significant and consistent changes in the fluctuation profile, making the HLA-B*2705 alleles respond too strongly to perturbation.
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Affiliation(s)
- Turkan Haliloglu
- Polymer Research Center, Bogazici University, Bebek, Istanbul, Turkey
- * E-mail: (TH); (BE)
| | - Ahmet Gul
- Division of Rheumatology, Department of Internal Medicine, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Burak Erman
- Center for Computational Biology and Bioinformatics, Koc University, Istanbul, Turkey
- * E-mail: (TH); (BE)
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Fabian H, Huser H, Loll B, Ziegler A, Naumann D, Uchanska-Ziegler B. HLA-B27 heavy chains distinguished by a micropolymorphism exhibit differential flexibility. ACTA ACUST UNITED AC 2010; 62:978-87. [DOI: 10.1002/art.27316] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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22
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Nurzia E, Panimolle F, Cauli A, Mathieu A, Magnacca A, Paladini F, Sorrentino R, Fiorillo MT. CD8+ T-cell mediated self-reactivity in HLA-B27 context as a consequence of dual peptide conformation. Clin Immunol 2010; 135:476-82. [PMID: 20167541 DOI: 10.1016/j.clim.2010.01.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2009] [Revised: 01/18/2010] [Accepted: 01/21/2010] [Indexed: 12/11/2022]
Abstract
HLA-B2709 does not predispose for Ankylosing Spondylitis although it differs from B2705, the most common and AS-associated subtype in different ethnic groups, only for the substitution His116Asp. Therefore, a productive approach to elucidate the molecular mechanisms of the disease could be the comparison of these alleles. B2705 has been shown to display certain self-peptides enriched in basic residues i.e., pVIPR and pGR, in a dual conformation and this is accompanied by the presence of specific cytotoxic T cells in patients with AS. In this study, we convalidate our previous observation that B2709 healthy subjects do not possess primary reactivity towards pVIPR while showing a prompt CD8+ T cell response driven by pGR. Notably, in the B2709 context of presentation, pVIPR assumes only a single conformation in contrast with pGR which is dimorphic. These results suggest a possible general connection between the occurrence of double peptide conformation and the property of inducing specific autoimmune responses.
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Affiliation(s)
- Elisa Nurzia
- Department of Cell Biology and Development, Sapienza University of Rome, 00185 Roma, Italy
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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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