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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Mavridis G, Arya R, Domnick A, Zoidakis J, Makridakis M, Vlahou A, Mpakali A, Lelis A, Georgiadis D, Tampé R, Papakyriakou A, Stern LJ, Stratikos E. A systematic re-examination of processing of MHCI-bound antigenic peptide precursors by endoplasmic reticulum aminopeptidase 1. J Biol Chem 2020; 295:7193-7210. [PMID: 32184355 PMCID: PMC7247305 DOI: 10.1074/jbc.ra120.012976] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 03/09/2020] [Indexed: 11/06/2022] Open
Abstract
Endoplasmic reticulum aminopeptidase 1 (ERAP1) trims antigenic peptide precursors to generate mature antigenic peptides for presentation by major histocompatibility complex class I (MHCI) molecules and regulates adaptive immune responses. ERAP1 has been proposed to trim peptide precursors both in solution and in preformed MHCI-peptide complexes, but which mode is more relevant to its biological function remains controversial. Here, we compared ERAP1-mediated trimming of antigenic peptide precursors in solution or when bound to three MHCI alleles, HLA-B*58, HLA-B*08, and HLA-A*02. For all MHCI-peptide combinations, peptide binding onto MHCI protected against ERAP1-mediated trimming. In only a single MHCI-peptide combination, trimming of an HLA-B*08-bound 12-mer progressed at a considerable rate, albeit still slower than in solution. Results from thermodynamic, kinetic, and computational analyses suggested that this 12-mer is highly labile and that apparent on-MHC trimming rates are always slower than that of MHCI-peptide dissociation. Both ERAP2 and leucine aminopeptidase, an enzyme unrelated to antigen processing, could trim this labile peptide from preformed MHCI complexes as efficiently as ERAP1. A pseudopeptide analogue with high affinity for both HLA-B*08 and the ERAP1 active site could not promote the formation of a ternary ERAP1/MHCI/peptide complex. Similarly, no interactions between ERAP1 and purified peptide-loading complex were detected in the absence or presence of a pseudopeptide trap. We conclude that MHCI binding protects peptides from ERAP1 degradation and that trimming in solution along with the dynamic nature of peptide binding to MHCI are sufficient to explain ERAP1 processing of antigenic peptide precursors.
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Affiliation(s)
- George Mavridis
- National Centre for Scientific Research Demokritos, Agia Paraskevi 15341, Greece
| | - Richa Arya
- University of Massachusetts Medical School, Worcester, Massachusetts 01655
| | - Alexander Domnick
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Strasse 9, D-60438 Frankfurt/Main, Germany
| | - Jerome Zoidakis
- Centre of Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens 11527, Greece
| | - Manousos Makridakis
- Centre of Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens 11527, Greece
| | - Antonia Vlahou
- Centre of Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens 11527, Greece
| | - Anastasia Mpakali
- National Centre for Scientific Research Demokritos, Agia Paraskevi 15341, Greece
| | - Angelos Lelis
- Laboratory of Organic Chemistry, Chemistry Department, University of Athens, Athens 15772, Greece
| | - Dimitris Georgiadis
- Laboratory of Organic Chemistry, Chemistry Department, University of Athens, Athens 15772, Greece
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Strasse 9, D-60438 Frankfurt/Main, Germany
| | | | - Lawrence J Stern
- University of Massachusetts Medical School, Worcester, Massachusetts 01655
| | - Efstratios Stratikos
- National Centre for Scientific Research Demokritos, Agia Paraskevi 15341, Greece.
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Zimmermann C, Kowalewski D, Bauersfeld L, Hildenbrand A, Gerke C, Schwarzmüller M, Le-Trilling VTK, Stevanovic S, Hengel H, Momburg F, Halenius A. HLA-B locus products resist degradation by the human cytomegalovirus immunoevasin US11. PLoS Pathog 2019; 15:e1008040. [PMID: 31527904 PMCID: PMC6764698 DOI: 10.1371/journal.ppat.1008040] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 09/27/2019] [Accepted: 08/22/2019] [Indexed: 12/27/2022] Open
Abstract
To escape CD8+ T-cell immunity, human cytomegalovirus (HCMV) US11 redirects MHC-I for rapid ER-associated proteolytic degradation (ERAD). In humans, classical MHC-I molecules are encoded by the highly polymorphic HLA-A, -B and -C gene loci. While HLA-C resists US11 degradation, the specificity for HLA-A and HLA-B products has not been systematically studied. In this study we analyzed the MHC-I peptide ligands in HCMV-infected cells. A US11-dependent loss of HLA-A ligands was observed, but not of HLA-B. We revealed a general ability of HLA-B to assemble with β2m and exit from the ER in the presence of US11. Surprisingly, a low-complexity region between the signal peptide sequence and the Ig-like domain of US11, was necessary to form a stable interaction with assembled MHC-I and, moreover, this region was also responsible for changing the pool of HLA-B ligands. Our data suggest a two-pronged strategy by US11 to escape CD8+ T-cell immunity, firstly, by degrading HLA-A molecules, and secondly, by manipulating the HLA-B ligandome. The human immune system can cover the presentation of a wide array of pathogen derived antigens owing to the three extraordinary polymorphic MHC class I (MHC-I) gene loci, called HLA-A, -B and -C in humans. Studying the HLA peptide ligands of human cytomegalovirus (HCMV) infected cells, we realized that the HCMV encoded glycoprotein US11 targeted different HLA gene products in distinct manners. More than 20 years ago the first HCMV encoded MHC-I inhibitors were identified, including US11, targeting MHC-I for proteasomal degradation. Here, we describe that the prime target for US11-mediated degradation is HLA-A, whereas HLA-B can resist degradation. Our further mechanistic analysis revealed that US11 uses various domains for distinct functions. Remarkably, the ability of US11 to interact with assembled MHC-I and modify peptide loading of degradation-resistant HLA-B was dependent on a low-complexity region (LCR) located between the signal peptide and the immunoglobulin-like domain of US11. To redirect MHC-I for proteasomal degradation the LCR was dispensable. These findings now raise the intriguing question why US11 has evolved to target HLA-A and -B differentially. Possibly, HLA-B molecules are spared in order to dampen NK cell attack against infected cells.
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Affiliation(s)
- Cosima Zimmermann
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Daniel Kowalewski
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Liane Bauersfeld
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Andreas Hildenbrand
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Carolin Gerke
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Magdalena Schwarzmüller
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | | | - Stefan Stevanovic
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Hartmut Hengel
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Frank Momburg
- Clinical Cooperation Unit Applied Tumor Immunity, Antigen Presentation and T/NK Cell Activation Group, German Cancer Research Center, Heidelberg, Germany
| | - Anne Halenius
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- * E-mail:
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Schellens IMM, Hoof I, Meiring HD, Spijkers SNM, Poelen MCM, van Gaans-van den Brink JAM, van der Poel K, Costa AI, van Els CACM, van Baarle D, Kesmir C. Comprehensive Analysis of the Naturally Processed Peptide Repertoire: Differences between HLA-A and B in the Immunopeptidome. PLoS One 2015; 10:e0136417. [PMID: 26375851 PMCID: PMC4574158 DOI: 10.1371/journal.pone.0136417] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 08/04/2015] [Indexed: 01/23/2023] Open
Abstract
The cytotoxic T cell (CTL) response is determined by the peptide repertoire presented by the HLA class I molecules of an individual. We performed an in-depth analysis of the peptide repertoire presented by a broad panel of common HLA class I molecules on four B lymphoblastoid cell-lines (BLCL). Peptide elution and mass spectrometry analysis were utilised to investigate the number and abundance of self-peptides. Altogether, 7897 unique self-peptides, derived of 4344 proteins, were eluted. After viral infection, the number of unique self-peptides eluted significantly decreased compared to uninfected cells, paralleled by a decrease in the number of source proteins. In the overall dataset, the total number of unique self-peptides eluted from HLA-B molecules was larger than from HLA-A molecules, and they were derived from a larger number of source proteins. These results in B cells suggest that HLA-B molecules possibly present a more diverse repertoire compared to their HLA-A counterparts, which may contribute to their immunodominance. This study provides a unique data set giving new insights into the complex system of antigen presentation for a broad panel of HLA molecules, many of which were never studied this extensively before.
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Affiliation(s)
- Ingrid M. M. Schellens
- Laboratory of Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
- Department of Internal Medicine and Infectious Diseases, University Medical Center Utrecht, Utrecht, the Netherlands
- Centre for Immunology of Infectious Diseases and Vaccines, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Ilka Hoof
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
| | - Hugo D. Meiring
- Centre for Immunology of Infectious Diseases and Vaccines, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Institute for Translational Vaccinology (Intravacc), Bilthoven, The Netherlands
| | - Sanne N. M. Spijkers
- Laboratory of Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Martien C. M. Poelen
- Centre for Immunology of Infectious Diseases and Vaccines, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | | | - Kees van der Poel
- Laboratory of Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Ana I. Costa
- Laboratory of Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Cecile A. C. M. van Els
- Centre for Immunology of Infectious Diseases and Vaccines, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Debbie van Baarle
- Laboratory of Translational Immunology, Department of Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
- Department of Internal Medicine and Infectious Diseases, University Medical Center Utrecht, Utrecht, the Netherlands
- Centre for Immunology of Infectious Diseases and Vaccines, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- * E-mail:
| | - Can Kesmir
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
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Moradi S, Berry R, Pymm P, Hitchen C, Beckham SA, Wilce MCJ, Walpole NG, Clements CS, Reid HH, Perugini MA, Brooks AG, Rossjohn J, Vivian JP. The structure of the atypical killer cell immunoglobulin-like receptor, KIR2DL4. J Biol Chem 2015; 290:10460-71. [PMID: 25759384 PMCID: PMC4400354 DOI: 10.1074/jbc.m114.612291] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 02/10/2015] [Indexed: 01/31/2023] Open
Abstract
The engagement of natural killer cell immunoglobulin-like receptors (KIRs) with their target ligands, human leukocyte antigen (HLA) molecules, is a critical component of innate immunity. Structurally, KIRs typically have either two (D1-D2) or three (D0-D1-D2) extracellular immunoglobulin domains, with the D1 and D2 domain recognizing the α1 and α2 helices of HLA, respectively, whereas the D0 domain of the KIR3DLs binds a loop region flanking the α1 helix of the HLA molecule. KIR2DL4 is distinct from other KIRs (except KIR2DL5) in that it does not contain a D1 domain and instead has a D0-D2 arrangement. Functionally, KIR2DL4 is also atypical in that, unlike all other KIRs, KIR2DL4 has both activating and inhibitory signaling domains. Here, we determined the 2.8 Å crystal structure of the extracellular domains of KIR2DL4. Structurally, KIR2DL4 is reminiscent of other KIR2DL receptors, with the D0 and D2 adopting the C2-type immunoglobulin fold arranged with an acute elbow angle. However, KIR2DL4 self-associated via the D0 domain in a concentration-dependent manner and was observed as a tetramer in the crystal lattice by size exclusion chromatography, dynamic light scattering, analytical ultracentrifugation, and small angle x-ray scattering experiments. The assignment of residues in the D0 domain to forming the KIR2DL4 tetramer precludes an interaction with HLA akin to that observed for KIR3DL1. Accordingly, no interaction was observed to HLA by direct binding studies. Our data suggest that the unique functional properties of KIR2DL4 may be mediated by self-association of the receptor.
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Affiliation(s)
- Shoeib Moradi
- From the Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, and
| | - Richard Berry
- From the Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, and the Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Phillip Pymm
- From the Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, and
| | - Corinne Hitchen
- From the Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, and
| | - Simone A Beckham
- From the Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, and
| | - Matthew C J Wilce
- From the Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, and
| | - Nicholas G Walpole
- From the Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, and
| | - Craig S Clements
- From the Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, and
| | - Hugh H Reid
- From the Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, and
| | - Matthew A Perugini
- the Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne Victoria 3086 Australia
| | - Andrew G Brooks
- the Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3010, Australia, and
| | - Jamie Rossjohn
- From the Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, and the Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia, the Institute of Infection and Immunity, Cardiff University, School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Julian P Vivian
- From the Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, and the Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia,
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Lauterbach N, Wieten L, Popeijus HE, Vanderlocht J, van Zon PMH, Voorter CEM, Tilanus MGJ. Peptide-induced HLA-E expression in human PBMCs is dependent on peptide sequence and the HLA-E genotype. Tissue Antigens 2015; 85:242-51. [PMID: 25735891 DOI: 10.1111/tan.12525] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 11/13/2014] [Accepted: 01/18/2015] [Indexed: 12/31/2022]
Abstract
Human Leukocyte Antigen (HLA)-E is a low-polymorphic non-classical HLA class I molecule which plays a crucial role in immune surveillance by presentation of peptides to T and natural killer (NK) cells. HLA-E polymorphism is related to HLA-E surface expression and is associated with patient outcome after stem cell transplantation. We aim to investigate the regulation of HLA-E expression level in peripheral blood mononuclear cells (PBMCs) of healthy individuals homozygous for HLA-E*01:01 or HLA-E*01:03, by using a panel of HLA-E binding peptides derived from CMV, Hsp60 and HLA class I. Basal and peptide-induced HLA-E surface expression levels were higher in PBMC from HLA-E*01:03 homozygous subjects as compared to PBMC from HLA-E*01:01 homozygous subjects. HLA-E mRNA levels were comparable between the two genotypes and remained constant after peptide stimulation. HLA-E surface expression seemed to be not only dependent on the HLA-E genotype, but also on the sequence of the peptide as evidenced by the profound difference in HLA-E upregulation with the Hsp60 and the B7 peptide. Our results showed that peptide-induced HLA-E expression is regulated at the posttranscriptional level as extracellular peptide stimulation did not influence RNA expression. This study provides new insights in the mechanism by which HLA-E expression is regulated and underlines a new role for extracellular peptides in inducing HLA-E translation, which may represent a defense mechanism against lytic viral infections and necrosis.
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Affiliation(s)
- N Lauterbach
- Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center, Maastricht, the Netherlands
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Baharav E, Weinberger A. The HLA-B*5101 molecule-binding capacity to antigens used in animal models of Behçet's disease: a bioinformatics study. Isr Med Assoc J 2012; 14:424-428. [PMID: 22953618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
BACKGROUND The human lymphocyte antigen (HLA) molecule B*5101 is a functioning receptor of the immune system and is generally accepted as a genetic marker for Behçet disease (BD), a multi-organ, chronic inflammatory disorder. The role of the HLA-B*5101 in the pathogenesis of BD is elusive. The assumption that HLA-B*5101 has an active role in BD is suggestive, but no antigen has yet been identified. OBJECTIVES To evaluate the potential binding capacity of various antigens to the HLA-B*5101 molecule. METHODS Using bioinformatics programs, we studied the binding capacity of HLA-B*5101 and its corresponding rat molecule RT.A1 to the following antigens: heatshock protein-60 (HSP60), major histocompatibility complex class I chain-related gene A (MICA), retinal S-antigen (S-Ag), HLA-B27 molecule and its peptide (PD) and tropomyosin (TPM), all of which serve as antigens in animal models corresponding to BD. RESULTS In each protein including the B*5101 molecule itself, the computerized programs revealed several short sequences with potential high binding capacity to HLA-B*5101 with the exception of B-27PD. The rat MHC RT1. Al. had no binding capacity to S-Ag. CONCLUSIONS The evaluated proteins have the potential to bind to and to serve as potential antigens to the HLA-B*5101 and the rat MHC RT1.Al. molecules. The pathogenicity of these suggested short peptides should be evaluated in animal models of BD.
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Affiliation(s)
- Ehud Baharav
- Department of Medicine C, Rabin Medical Center (Beilinson Campus), Petah Tikva, Israel.
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Gadewal NS, Joshi NN. In silico analysis of peptide binding features of HLA-B*4006. Indian J Exp Biol 2012; 50:93-100. [PMID: 22670471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
HLA-B*4006 is the most common allele amongst Indians. It belongs to the 'HLA-B44 supertype' family of alleles that constitute an important component of the peptide binding repertoire in populations world over. Its peptide binding characteristics remain poorly examined. The amino acid sequence and structural considerations suggest a small, poorly hydrophobic 'F' pocket for this allele that may adversely affect the interaction with the C terminal residue of the antigenic peptide. Contribution of auxiliary anchor residues (P3) of the peptide has also been indicated. To examine these aspects by in silico analysis, HLA-B*4001, 4002, and 4006 alleles were modeled using HLA-B*4402 as a template. Eleven peptides, known to bind alleles of this family, were used for docking and molecular dynamics studies. Interaction between the amino group (main-chain) of P3 residue and Tyr99 of the alleles was seen in majority of peptide-complexes. Hydrophobic interactions between Tyr7 and Tyr159 with N terminal residues of the peptide were also seen in all the complexes. Replacement of Trp95 by leucine in HLA-B*4006 resulted in reduction of binding free energy in 8 out of 9 complexes. In summary, the analysis of the modeled structures and HLA-peptide complexes strongly supports the adverse effect of Trp95 at pocket F and the possible role of the third residue of the antigenic peptide as an auxiliary anchor in HLA-B*4006 peptide complexes. In the light of suggested promiscuous peptide binding pattern and association with risk for tuberculosis/HIV for this allele, the ascertainment of the predicted effects of Trp95 and role of P3 residue as an auxiliary anchor by this preliminary in silico analysis thus helps define direction of the further studies.
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Affiliation(s)
- Nikhil S Gadewal
- Bioinformatics Centre (BTIS), Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210, India.
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Lu CX, Zhu N, Zhang Q, Huang H, Ke BS, Hou HS, Shen BJ. [Sequence analysis of a novel human leukocyte antigen allele B*5827]. Zhonghua Yi Xue Yi Chuan Xue Za Zhi 2011; 28:88-91. [PMID: 21287518 DOI: 10.3760/cma.j.issn.1003-9406.2011.01.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
OBJECTIVE To investigate the molecular basis for a novel human leukocyte antigen (HLA) allele B*5827. METHODS DNA from the proband was analyzed by polymerase chain reaction-sequence specific oligonucleotide (PCR-SSO) typing. The amplified product was sequenced bidirectionally. RESULTS Abnormal HLA-B locus was observed and its nucleotide sequence was different from the known HLA-B allele sequences, with highest homology to HLA-B*5820 allele. It differs from HLA-B*5820 by 8 nucleotide substitutions in exon 3, i.e., nt 290 (G > C), nt 346 (T > A), nt 390 (A > C), nt 404 (G > C), nt 413 (C > G), nt 471 (A > G), nt 486 (A > G) and nt 487 (C > A), resulting in an amino acid change from ser > arg at nt 97, phe >tyr at nt 115, ser > arg at nt 130, thr > ala at nt 157 and thr > glu at nt 162. Nucleotide differences of nt 404 (G > C) and nt 413( C > G) did not change amino acid. CONCLUSION The sequences of the novel allele have been submitted to GenBank (access No.GU071234). A novel HLA class I allele B*5827 has been officially assigned by the WHO HLA Nomenclature Committee in Jan. 2010.
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Affiliation(s)
- Chao-xia Lu
- Shandong Umbilical Cord Blood Bank, Jinan, Shandong, 250102 PR China
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Pereyra F, Jia X, McLaren PJ, Telenti A, de Bakker PI, Walker BD, Jia X, McLaren PJ, Ripke S, Brumme CJ, Pulit SL, Telenti A, Carrington M, Kadie CM, Carlson JM, Heckerman D, de Bakker PI, Pereyra F, de Bakker PI, Graham RR, Plenge RM, Deeks SG, Walker BD, Gianniny L, Crawford G, Sullivan J, Gonzalez E, Davies L, Camargo A, Moore JM, Beattie N, Gupta S, Crenshaw A, Burtt NP, Guiducci C, Gupta N, Carrington M, Gao X, Qi Y, Yuki Y, Pereyra F, Piechocka-Trocha A, Cutrell E, Rosenberg R, Moss KL, Lemay P, O’Leary J, Schaefer T, Verma P, Toth I, Block B, Baker B, Rothchild A, Lian J, Proudfoot J, Alvino DML, Vine S, Addo MM, Allen TM, Altfeld M, Henn MR, Le Gall S, Streeck H, Walker BD, Haas DW, Kuritzkes DR, Robbins GK, Shafer RW, Gulick RM, Shikuma CM, Haubrich R, Riddler S, Sax PE, Daar ES, Ribaudo HJ, Agan B, Agarwal S, Ahern RL, Allen BL, Altidor S, Altschuler EL, Ambardar S, Anastos K, Anderson B, Anderson V, Andrady U, Antoniskis D, Bangsberg D, Barbaro D, Barrie W, Bartczak J, Barton S, Basden P, Basgoz N, Bazner S, Bellos NC, Benson AM, Berger J, Bernard NF, Bernard AM, Birch C, Bodner SJ, Bolan RK, Boudreaux ET, Bradley M, Braun JF, Brndjar JE, Brown SJ, Brown K, Brown ST, Burack J, Bush LM, Cafaro V, Campbell O, Campbell J, Carlson RH, Carmichael JK, Casey KK, Cavacuiti C, Celestin G, Chambers ST, Chez N, Chirch LM, Cimoch PJ, Cohen D, Cohn LE, Conway B, Cooper DA, Cornelson B, Cox DT, Cristofano MV, Cuchural G, Czartoski JL, Dahman JM, Daly JS, Davis BT, Davis K, Davod SM, Deeks SG, DeJesus E, Dietz CA, Dunham E, Dunn ME, Ellerin TB, Eron JJ, Fangman JJ, Farel CE, Ferlazzo H, Fidler S, Fleenor-Ford A, Frankel R, Freedberg KA, French NK, Fuchs JD, Fuller JD, Gaberman J, Gallant JE, Gandhi RT, Garcia E, Garmon D, Gathe JC, Gaultier CR, Gebre W, Gilman FD, Gilson I, Goepfert PA, Gottlieb MS, Goulston C, Groger RK, Gurley TD, Haber S, Hardwicke R, Hardy WD, Harrigan PR, Hawkins TN, Heath S, Hecht FM, Henry WK, Hladek M, Hoffman RP, Horton JM, Hsu RK, Huhn GD, Hunt P, Hupert MJ, Illeman ML, Jaeger H, Jellinger RM, John M, Johnson JA, Johnson KL, Johnson H, Johnson K, Joly J, Jordan WC, Kauffman CA, Khanlou H, Killian RK, Kim AY, Kim DD, Kinder CA, Kirchner JT, Kogelman L, Kojic EM, Korthuis PT, Kurisu W, Kwon DS, LaMar M, Lampiris H, Lanzafame M, Lederman MM, Lee DM, Lee JM, Lee MJ, Lee ET, Lemoine J, Levy JA, Llibre JM, Liguori MA, Little SJ, Liu AY, Lopez AJ, Loutfy MR, Loy D, Mohammed DY, Man A, Mansour MK, Marconi VC, Markowitz M, Marques R, Martin JN, Martin HL, Mayer KH, McElrath MJ, McGhee TA, McGovern BH, McGowan K, McIntyre D, Mcleod GX, Menezes P, Mesa G, Metroka CE, Meyer-Olson D, Miller AO, Montgomery K, Mounzer KC, Nagami EH, Nagin I, Nahass RG, Nelson MO, Nielsen C, Norene DL, O’Connor DH, Ojikutu BO, Okulicz J, Oladehin OO, Oldfield EC, Olender SA, Ostrowski M, Owen WF, Pae E, Parsonnet J, Pavlatos AM, Perlmutter AM, Pierce MN, Pincus JM, Pisani L, Price LJ, Proia L, Prokesch RC, Pujet HC, Ramgopal M, Rathod A, Rausch M, Ravishankar J, Rhame FS, Richards CS, Richman DD, Robbins GK, Rodes B, Rodriguez M, Rose RC, Rosenberg ES, Rosenthal D, Ross PE, Rubin DS, Rumbaugh E, Saenz L, Salvaggio MR, Sanchez WC, Sanjana VM, Santiago S, Schmidt W, Schuitemaker H, Sestak PM, Shalit P, Shay W, Shirvani VN, Silebi VI, Sizemore JM, Skolnik PR, Sokol-Anderson M, Sosman JM, Stabile P, Stapleton JT, Starrett S, Stein F, Stellbrink HJ, Sterman FL, Stone VE, Stone DR, Tambussi G, Taplitz RA, Tedaldi EM, Telenti A, Theisen W, Torres R, Tosiello L, Tremblay C, Tribble MA, Trinh PD, Tsao A, Ueda P, Vaccaro A, Valadas E, Vanig TJ, Vecino I, Vega VM, Veikley W, Wade BH, Walworth C, Wanidworanun C, Ward DJ, Warner DA, Weber RD, Webster D, Weis S, Wheeler DA, White DJ, Wilkins E, Winston A, Wlodaver CG, Wout AV, Wright DP, Yang OO, Yurdin DL, Zabukovic BW, Zachary KC, Zeeman B, Zhao M. The major genetic determinants of HIV-1 control affect HLA class I peptide presentation. Science 2010; 330:1551-7. [PMID: 21051598 PMCID: PMC3235490 DOI: 10.1126/science.1195271] [Citation(s) in RCA: 911] [Impact Index Per Article: 65.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Infectious and inflammatory diseases have repeatedly shown strong genetic associations within the major histocompatibility complex (MHC); however, the basis for these associations remains elusive. To define host genetic effects on the outcome of a chronic viral infection, we performed genome-wide association analysis in a multiethnic cohort of HIV-1 controllers and progressors, and we analyzed the effects of individual amino acids within the classical human leukocyte antigen (HLA) proteins. We identified >300 genome-wide significant single-nucleotide polymorphisms (SNPs) within the MHC and none elsewhere. Specific amino acids in the HLA-B peptide binding groove, as well as an independent HLA-C effect, explain the SNP associations and reconcile both protective and risk HLA alleles. These results implicate the nature of the HLA-viral peptide interaction as the major factor modulating durable control of HIV infection.
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Affiliation(s)
| | | | - Florencia Pereyra
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
- Department of Medicine, Division of Infectious Disease, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Xiaoming Jia
- Harvard-MIT Division of Health Sciences and Technology, Boston, MA, USA
| | - Paul J. McLaren
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Amalio Telenti
- Institute of Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Paul I.W. de Bakker
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Medical Genetics, Division of Biomedical Genetics, University Medical Center Utrecht, Netherlands
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Netherlands
| | - Bruce D. Walker
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | | | - Xiaoming Jia
- Harvard-MIT Division of Health Sciences and Technology, Boston, MA, USA
| | - Paul J. McLaren
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Stephan Ripke
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Center for Human Genetic Research, MGH, Harvard Medical School, Boston, MA, USA
| | - Chanson J. Brumme
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Sara L. Pulit
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Amalio Telenti
- Institute of Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Mary Carrington
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, NCI-Frederick, Frederick, MD, USA
| | | | | | | | - Paul I.W. de Bakker
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Medical Genetics, Division of Biomedical Genetics, University Medical Center Utrecht, Netherlands
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Netherlands
| | | | - Florencia Pereyra
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
- Department of Medicine, Division of Infectious Disease, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Paul I.W. de Bakker
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Medical Genetics, Division of Biomedical Genetics, University Medical Center Utrecht, Netherlands
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Netherlands
| | | | - Robert M. Plenge
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Steven G. Deeks
- University of California San Francisco, San Francisco, CA, USA
| | - Bruce D. Walker
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | | | | | | | | | | | - Leela Davies
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Amy Camargo
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | | | - Supriya Gupta
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Noël P. Burtt
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Namrata Gupta
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Mary Carrington
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, NCI-Frederick, Frederick, MD, USA
| | - Xiaojiang Gao
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, NCI-Frederick, Frederick, MD, USA
| | - Ying Qi
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, NCI-Frederick, Frederick, MD, USA
| | - Yuko Yuki
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, NCI-Frederick, Frederick, MD, USA
| | | | - Florencia Pereyra
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
- Department of Medicine, Division of Infectious Disease, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Alicja Piechocka-Trocha
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Emily Cutrell
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Rachel Rosenberg
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Kristin L. Moss
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Paul Lemay
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Jessica O’Leary
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Todd Schaefer
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Pranshu Verma
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Ildiko Toth
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Brian Block
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Brett Baker
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Alissa Rothchild
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Jeffrey Lian
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Jacqueline Proudfoot
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Donna Marie L. Alvino
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Seanna Vine
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Marylyn M. Addo
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Todd M. Allen
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Marcus Altfeld
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | | | - Sylvie Le Gall
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Hendrik Streeck
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Bruce D. Walker
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | | | - David W. Haas
- Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Daniel R. Kuritzkes
- Department of Medicine, Division of Infectious Disease, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | - Roy M. Gulick
- Weill Medical College of Cornell University, New York, NY, USA
| | - Cecilia M. Shikuma
- Hawaii Center for AIDS, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, USA
| | | | | | - Paul E. Sax
- Department of Medicine, Division of Infectious Disease, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Eric S. Daar
- University of California Los Angeles, Los Angeles, CA, USA
| | - Heather J. Ribaudo
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA
| | | | - Brian Agan
- Infectious Disease Clinical Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | | | | | | | | | | | | | - Kathryn Anastos
- Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Ben Anderson
- St. Leonards Medical Centre, St. Leonards, Australia
| | | | | | | | - David Bangsberg
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
- MGH, Harvard Medical School, Boston, MA, USA
| | - Daniel Barbaro
- Tarrant County Infectious Disease Associates, Fort Worth, TX, USA
| | | | | | - Simon Barton
- Chelsea and Westminster Hospital, St. Stephen’s Centre, London, UK
| | | | | | - Suzane Bazner
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | | | | | | | - Nicole F. Bernard
- Research Institute, McGill University Health Centre, Montreal General Hospital, Montreal, Canada
| | | | - Christopher Birch
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | | | | | - Emilie T. Boudreaux
- Louisiana State University Health Sciences Center, University Medical Center East Clinic, Lafayatte, LA, USA
| | - Meg Bradley
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - James F. Braun
- Physicians’ Research Network, Callen-Lorde Community Health Center, New York, NY, USA
| | | | | | | | | | | | - Larry M. Bush
- University of Miami-Miller School of Medicine, Lake Worth, FL, USA
| | | | | | | | | | | | | | | | | | | | - Nancy Chez
- H.E.L.P./Project Samaritan, Bronx, NY, USA
| | - Lisa M. Chirch
- David E. Rogers Center for HIV/AIDS Care, Southampton, NY, USA
| | | | | | - Lillian E. Cohn
- 9th Street Internal Medicine Associates, Philadelphia, PA, USA
| | - Brian Conway
- University of British Columbia, Vancouver, Canada
| | - David A. Cooper
- National Centre in HIV Epidemiology and Clinical Research, Sydney, Australia
| | | | - David T. Cox
- Metro Infectious Disease Consultants, Indianapolis, IN, USA
| | | | | | | | | | - Jennifer S. Daly
- University of Massachusetts Memorial Medical Center, Worcester, MA, USA
| | | | - Kristine Davis
- University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | | | - Steven G. Deeks
- University of California San Francisco, San Francisco, CA, USA
| | | | - Craig A. Dietz
- The Kansas City Free Health Clinic, Kansas City, MO, USA
| | - Eleanor Dunham
- David E. Rogers Center for HIV/AIDS Care, Southampton, NY, USA
| | | | | | - Joseph J. Eron
- University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Claire E. Farel
- Department of Medicine, Division of Infectious Disease, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Helen Ferlazzo
- Visiting Nurse Association of Central New Jersey, Community Health Center, Asbury Park, NJ, USA
| | | | | | | | | | - Neel K. French
- Private Practice of Neel K. French, M.D., Chicago, IL, USA
| | | | | | | | - Joel E. Gallant
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Efrain Garcia
- Private Practice of Efrain Garcia, M.D., Miami, FL, USA
| | | | - Joseph C. Gathe
- Private Practice of Joseph C. Gathe Jr., M.D., Houston, TX, USA
| | | | | | | | - Ian Gilson
- Medical College of Wisconsin, Milwaukee, WI, USA
| | | | | | | | | | | | | | | | - W. David Hardy
- University of California Los Angeles, Los Angeles, CA, USA
| | | | | | - Sonya Heath
- University of Alabama, Birmingham, Birmingham, AL, USA
| | | | | | - Melissa Hladek
- The Catholic University of America, School of Nursing, Washington, DC, USA
| | | | | | - Ricky K. Hsu
- New York University Medical Center, New York, NY, USA
| | | | - Peter Hunt
- University of California San Francisco, San Francisco, CA, USA
| | - Mark J. Hupert
- Tarrant County Infectious Disease Associates, Fort Worth, TX, USA
| | | | - Hans Jaeger
- HIV Research and Clinical Care Centre, Munich, Germany
| | | | - Mina John
- Murdoch University, Murdoch, Australia
| | - Jennifer A. Johnson
- Department of Medicine, Division of Infectious Disease, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Heather Johnson
- Tarrant County Infectious Disease Associates, Fort Worth, TX, USA
| | - Kay Johnson
- University of Cincinnati, Cincinnati, OH, USA
| | - Jennifer Joly
- David E. Rogers Center for HIV/AIDS Care, Southampton, NY, USA
| | | | | | | | | | | | | | | | | | | | | | | | - Wayne Kurisu
- Sharp Rees Stealy Medical Center, San Diego, CA, USA
| | - Douglas S. Kwon
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | | | - Harry Lampiris
- University of California San Francisco, San Francisco, CA, USA
| | | | | | | | - Jean M.L. Lee
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | | | - Janice Lemoine
- Greater Lawrence Family Health Center, Lawrence, MA, USA
| | - Jay A. Levy
- University of California San Francisco, San Francisco, CA, USA
| | - Josep M. Llibre
- Hospital Universitari Germans Trias i Pujol, Barcelona, Spain
| | | | | | - Anne Y. Liu
- Department of Medicine, Division of Infectious Disease, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | - Dawn Loy
- Infectious Disease Associates, Sarasota, FL, USA
| | | | - Alan Man
- Kaiser Permanente, Portland, OR, USA
| | | | | | - Martin Markowitz
- Aaron Diamond AIDS Research Center, Rockefeller University, New York, NY, USA
| | - Rui Marques
- Deruico Doencas Infecciosas, Porto, Portugal
| | | | | | | | | | | | | | - Katherine McGowan
- Department of Medicine, Division of Infectious Disease, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Dawn McIntyre
- Jersey Shore University Medical Center, Neptune, NJ, USA
| | - Gavin X. Mcleod
- College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Prema Menezes
- University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Greg Mesa
- Highland Medical Associates, Hendersonville, NC, USA
| | | | - Dirk Meyer-Olson
- Medizinische Hochschule, Abteilung Klinische Immunologie, Hannover, Germany
| | | | | | | | - Ellen H. Nagami
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Iris Nagin
- Lower East Side Service Center, New York, NY, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | - Eunice Pae
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | | | | | | | | | | | | | | | | | | | | | - Moti Ramgopal
- Midway Immunology and Research Center, Fort Pierce, FL, USA
| | - Almas Rathod
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | | | - J. Ravishankar
- State University of New York Downstate Medical Center, Brooklyn, NY, USA
| | | | | | | | | | - Berta Rodes
- Fundacion para la Investigacion Biomedica del Hospital Carlos III, Madrid, Spain
| | | | | | | | | | - Polly E. Ross
- Western North Carolina Community Health Services, Asheville, NC, USA
| | - David S. Rubin
- New York Hospital Medical Center of Queens, Flushing, NY, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Paul Stabile
- William F. Ryan Community Health Center, New York, NY, USA
| | | | | | - Francine Stein
- Visiting Nurse Association of Central New Jersey, Community Health Center, Asbury Park, NJ, USA
| | | | | | | | | | | | | | | | - Amalio Telenti
- Institute of Microbiology, University of Lausanne, Lausanne, Switzerland
| | - William Theisen
- Department of Medicine, Division of Infectious Disease, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | | | | | - Phuong D. Trinh
- Montgomery Infectious Disease Associates, Silver Spring, MD, USA
| | - Alice Tsao
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Peggy Ueda
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | | | - Emilia Valadas
- Hospital de Santa Maria, Faculdade de Medicina de Lisboa, Lisbon, Portugal
| | | | - Isabel Vecino
- University of North Texas Health Science Center, Fort Worth, TX, USA
| | | | | | - Barbara H. Wade
- Infectious Diseases Associates of Northwest Florida, Pensacola, FL, USA
| | | | | | | | | | | | | | - Steve Weis
- University of North Texas Health Science Center, Fort Worth, TX, USA
| | - David A. Wheeler
- Clinical Alliance for Research and Education-Infectious Diseases, Annandale, VA, USA
| | - David J. White
- Hawthorn House, Birmingham Heartlands Hospital, Birmingham, UK
| | - Ed Wilkins
- North Manchester General Hospital, Manchester, UK
| | | | | | | | | | - Otto O. Yang
- University of California Los Angeles, Los Angeles, CA, USA
| | | | | | | | - Beth Zeeman
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard, Boston, MA, USA
| | - Meng Zhao
- United Health Services Hospitals, Binghamton, NY, USA
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Hurley CK, Oudshoorn M, Setterholm M, Spellman SR, Petersdorf E, Lee SJ, Gooley T, Malkki M, Horowitz MM. Re: An approach to predicting HSCT outcome using HLA-mismatch information mapped on protein structure data. Biol Blood Marrow Transplant 2010; 16:865-6. [PMID: 20172039 DOI: 10.1016/j.bbmt.2010.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2010] [Accepted: 02/05/2010] [Indexed: 11/15/2022]
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12
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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El-Awar N, Terasaki PI, Cai J, Deng CT, Ozawa M, Nguyen A, Lias M, Conger N. Epitopes of HLA-A, B, C, DR, DQ, DP and MICA antigens. Clin Transpl 2009:295-321. [PMID: 20524293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
This chapter presents lists of HLA epitopes that have been defined to date. It also presents examples of reactions of mAb and eluted allosera with the class I, class II and MICAsingle antigen beads. To date, we have identified 110 class I epitopes, of which 47 were defined by mAbs and 63 by alloantibodies that were eluted from rHLA class I single antigen cell lines. We listed 34 epitopes shared by the HLA-A locus antigens, 44 epitopes shared by HLA-B locus antigens, 4 epitopes shared by HLA-C locus antigens, 20 inter-locus epitopes shared by HLA-A-B locus antigens, 5 inter-locus epitopes shared by HLA-B-C locus antigens and 3 inter-locus epitopes shared by HLA-A-B-C locus antigens. Sixty HLA-DR epitopes have been defined mostly by one amino acid (aa) residue on the HLA-DR beta chain. Eighteen HLA-DQ epitopes have been defined on the HLA-DQB chain and on the HLA-DQA chain of the HLA-DQ antigens. A few DQ epitopes were defined by one aa residue. However, most can be defined by several alternative combinations of aa residues. DQA and DP epitopes--few in number at this time--were identified. Only seven MICA epitopes have been defined to date. All epitopes can be defined by an exclusive amino acid.
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14
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Wölfel C, Lennerz V, Lindemann E, Hess G, Derigs HG, Huber C, Herr W, Wölfel T. Dissection and molecular analysis of alloreactive CD8+ T cell responses in allogeneic haematopoietic stem cell transplantation. Cancer Immunol Immunother 2008; 57:849-57. [PMID: 18004563 PMCID: PMC11030130 DOI: 10.1007/s00262-007-0421-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2007] [Accepted: 10/27/2007] [Indexed: 10/22/2022]
Abstract
We applied a cDNA expression screening procedure with cryopreserved non-clonal CD8+ T cell populations (Lennerz et al., Proc. Natl. Acad. Sci. USA 102:16013-8, 2005) to the identification of candidate antigens for graft-versus-host disease (GvHD) and graft-versus-leukaemia (GvL) effects in allogeneic haematopoietic stem cell transplantation (allo-HSCT). In a patient-donor model system with HLA class I disparities, we identified an HLA-B*44 mismatch allele, HLA-B*4405, as the dominant target of alloreactive T cells expanded in vitro from donor peripheral blood mononuclear cells (PBMC). HLA-B*4405-reactive T cells were detectable after multiple in vitro stimulations in the patient's post-HSCT PBMC. In a patient-donor model with full HLA compatibility, the major target antigen of donor lymphocytes stimulated in vitro with the respective patient's pre-HSCT PBMC was restricted by HLA-A*0201 and was encoded by TRIM22-442 C, a newly detected polymorphic allele of the tripartite motif family member TRIM22 (synonym: STAF50), preferentially expressed in cells of the haematopoietic system. An arginine(R)-to-cysteine(C) exchange at position 442 generated an immunogenic T cell epitope equivalent to a minor histocompatibility antigen (mHag). TRIM22-442C-specific T cells persisted long-term in the patient's post-HSCT PBMC. Approximately, 1.3% of Caucasians carry TRIM22.442 C in association with HLA-A*0201. In particular, the knowledge of a large and diverse panel of such mHags may be crucial for further improvement of donor selection and adoptive T cell transfer strategies. The procedure applied herein will help to accelerate and facilitate their identification.
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Affiliation(s)
- Catherine Wölfel
- III. Department of Internal Medicine, Haematology/Oncology, Johannes Gutenberg University, 55101 Mainz, Germany
| | - Volker Lennerz
- III. Department of Internal Medicine, Haematology/Oncology, Johannes Gutenberg University, 55101 Mainz, Germany
| | - Eva Lindemann
- III. Department of Internal Medicine, Haematology/Oncology, Johannes Gutenberg University, 55101 Mainz, Germany
| | - Georg Hess
- III. Department of Internal Medicine, Haematology/Oncology, Johannes Gutenberg University, 55101 Mainz, Germany
| | - Hans G. Derigs
- III. Department of Internal Medicine, Haematology/Oncology, Johannes Gutenberg University, 55101 Mainz, Germany
| | - Christoph Huber
- III. Department of Internal Medicine, Haematology/Oncology, Johannes Gutenberg University, 55101 Mainz, Germany
| | - Wolfgang Herr
- III. Department of Internal Medicine, Haematology/Oncology, Johannes Gutenberg University, 55101 Mainz, Germany
| | - Thomas Wölfel
- III. Department of Internal Medicine, Haematology/Oncology, Johannes Gutenberg University, 55101 Mainz, Germany
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15
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Li H, Dai Y, Huang H, Li L, Leng S, Cheng J, Niu Y, Duan H, Liu Q, Zhang X, Huang X, Xie J, Feng Z, Wang J, He J, Zheng Y. HLA-B*1301 as a biomarker for genetic susceptibility to hypersensitivity dermatitis induced by trichloroethylene among workers in China. Environ Health Perspect 2007; 115:1553-1556. [PMID: 18007983 PMCID: PMC2072824 DOI: 10.1289/ehp.10325] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2007] [Accepted: 08/24/2007] [Indexed: 05/25/2023]
Abstract
BACKGROUND Trichloroethylene (TCE) is used extensively as an industrial solvent and has been recognized as one of the major environmental pollutants. To date, > 200 cases of TCE-induced hypersensitivity dermatitis among exposed workers have been reported worldwide, and TCE exposure has become one of the critical occupational health issues in Asia. OBJECTIVES The study aimed to identify genetic susceptible biomarkers associated with the TCE-induced hypersensitivity dermatitis in genes located in the human leukocyte antigen (HLA) region. METHODS From 1998 to 2006, 121 cases with TCE-induced hypersensitivity dermatitis and 142 tolerant controls were recruited into the population-based case-control study. We determined HLA alleles B, DRB1, DQA1, and DQB1, by sequence-based typing. p-Values were corrected for comparisons of multiple HLA alleles. In addition, we compared and analyzed the structure character of amino acid residues of HLA molecules found in participants. RESULTS We obtained complete genotyping data of 113 cases and 142 controls. The allele HLA-B*1301 was present in 83 (73.5%) of 113 patients compared with 13 (9.2%) of 142 tolerant workers (odds ratio = 27.5; 95% confidence interval, 13.5-55.7; corrected p = 1.48 x 10(-21)). In addition, the HLA-B*44 alleles were present in 6.2% (7/113) of patients, but were absent in TCE-tolerant workers. Residue 95 shared by HLA-B*1301 and HLA-B*44 molecules formed a different pocket F than other residues. CONCLUSIONS The allele HLA-B*1301 is strongly associated with TCE-induced hypersensitivity dermatitis among exposed workers and might be used as a biomarker to predict high risk individuals to TCE.
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Affiliation(s)
- Haishan Li
- Key Laboratory, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yufei Dai
- Key Laboratory, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hanlin Huang
- Department of Toxicology, Hospital for Occupational Diseases Control of Guangdong Province, Guangzhou, Guangdong, China
| | - Laiyu Li
- Department of Toxicology, Hospital for Occupational Diseases Control of Guangdong Province, Guangzhou, Guangdong, China
| | - Shuguang Leng
- Key Laboratory, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Juan Cheng
- Key Laboratory, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yong Niu
- Key Laboratory, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Huawei Duan
- Key Laboratory, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Qingjun Liu
- Key Laboratory, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xing Zhang
- Key Laboratory, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xianqing Huang
- Hospital for Occupational Diseases Control of Shenzhen, Shenzhen, Guangdong, China
| | - Jinxin Xie
- Institute of Health Inspection of Longgang District, Shenzhen, Guangdong, China
| | - Zhiming Feng
- Institute of Health Inspection of Longgang District, Shenzhen, Guangdong, China
| | - Juncai Wang
- Institute of Health Inspection of Longgang District, Shenzhen, Guangdong, China
| | - Jiaxi He
- Hospital for Occupational Diseases Control of Shenzhen, Shenzhen, Guangdong, China
| | - Yuxin Zheng
- Key Laboratory, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
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16
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Schlaf G, Erhuma ME, Seliger B, Foell J, Altermann WW. A novel HLA-B*35 (B*3570) allele of a Caucasian family differing with one amino acid mismatch from HLA-B*3503 allele in exon 4. ACTA ACUST UNITED AC 2007; 70:72-3. [PMID: 17559587 DOI: 10.1111/j.1399-0039.2007.00845.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A novel human leucocyte antigen (HLA)-B35 (HLA-B*3570) allele has been identified in a Caucasian family from Middle Europe using single allele-specific sequencing strategy. This allele is identical to the HLA-B*3503 allele except for one point mutation in exon 4 at codon 188 (CAC-->CGC), resulting in an amino acid change from histidine to arginine.
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Affiliation(s)
- G Schlaf
- Institute of Medical Immunology, Interbranch HLA-Laboratory, Martin Luther University Halle-Wittenberg, Magdeburger Strasse 16, D-06097 Halle, Germany
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17
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Nielsen M, Lundegaard C, Blicher T, Lamberth K, Harndahl M, Justesen S, Røder G, Peters B, Sette A, Lund O, Buus S. NetMHCpan, a method for quantitative predictions of peptide binding to any HLA-A and -B locus protein of known sequence. PLoS One 2007; 2:e796. [PMID: 17726526 PMCID: PMC1949492 DOI: 10.1371/journal.pone.0000796] [Citation(s) in RCA: 443] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2007] [Accepted: 07/29/2007] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Binding of peptides to Major Histocompatibility Complex (MHC) molecules is the single most selective step in the recognition of pathogens by the cellular immune system. The human MHC class I system (HLA-I) is extremely polymorphic. The number of registered HLA-I molecules has now surpassed 1500. Characterizing the specificity of each separately would be a major undertaking. PRINCIPAL FINDINGS Here, we have drawn on a large database of known peptide-HLA-I interactions to develop a bioinformatics method, which takes both peptide and HLA sequence information into account, and generates quantitative predictions of the affinity of any peptide-HLA-I interaction. Prospective experimental validation of peptides predicted to bind to previously untested HLA-I molecules, cross-validation, and retrospective prediction of known HIV immune epitopes and endogenous presented peptides, all successfully validate this method. We further demonstrate that the method can be applied to perform a clustering analysis of MHC specificities and suggest using this clustering to select particularly informative novel MHC molecules for future biochemical and functional analysis. CONCLUSIONS Encompassing all HLA molecules, this high-throughput computational method lends itself to epitope searches that are not only genome- and pathogen-wide, but also HLA-wide. Thus, it offers a truly global analysis of immune responses supporting rational development of vaccines and immunotherapy. It also promises to provide new basic insights into HLA structure-function relationships. The method is available at http://www.cbs.dtu.dk/services/NetMHCpan.
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Affiliation(s)
- Morten Nielsen
- Center for Biological Sequence Analysis, BioCentrum-DTU, Technical University of Denmark, Lyngby, Denmark.
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Brockman MA, Schneidewind A, Lahaie M, Schmidt A, Miura T, Desouza I, Ryvkin F, Derdeyn CA, Allen S, Hunter E, Mulenga J, Goepfert PA, Walker BD, Allen TM. Escape and compensation from early HLA-B57-mediated cytotoxic T-lymphocyte pressure on human immunodeficiency virus type 1 Gag alter capsid interactions with cyclophilin A. J Virol 2007; 81:12608-18. [PMID: 17728232 PMCID: PMC2169025 DOI: 10.1128/jvi.01369-07] [Citation(s) in RCA: 230] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Certain histocompatibility leukocyte antigen (HLA) alleles are associated with improved clinical outcomes for individuals infected with human immunodeficiency virus type 1 (HIV-1), but the mechanisms for their effects remain undefined. An early CD8(+) T-cell escape mutation in the dominant HLA-B57-restricted Gag epitope TW10 (TSTLQEQIGW) has been shown to impair HIV-1 replication capacity in vitro. We demonstrate here that this T(242)N substitution in the capsid protein is associated with upstream mutations at residues H(219), I(223), and M(228) in the cyclophilin A (CypA)-binding loop in B57(+) individuals with progressive disease. In an independent cohort of epidemiologically linked transmission pairs, the presence of these substitutions in viruses encoding T(242)N was associated with significantly higher plasma viremia in donors, further suggesting that these secondary mutations compensated for the replication defect of T(242)N. Using NL4-3 constructs, we illustrate the ability of these CypA loop changes to partially restore replication of the T(242)N variant in vitro. Notably, these mutations also enhanced viral resistance to the drug cyclosporine A, indicating a reduced dependence of the compensated virus on CypA that is normally essential for optimal infectivity. Therefore, mutations in TW10 allow HIV-1 to evade a dominant early CD8(+) T-cell response, but the benefits of escape are offset by a defect in capsid function. These data suggest that TW10 escape variants undergo a postentry block that is partially overcome by changes in the CypA-binding loop and identify a mechanism for an HIV-1 fitness defect that may contribute to the slower disease progression associated with HLA-B57.
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Affiliation(s)
- Mark A Brockman
- Partners AIDS Research Center, Massachusetts General Hospital-East, CNY 6625, Charlestown, MA 02129, USA
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Norman PJ, Abi-Rached L, Gendzekhadze K, Korbel D, Gleimer M, Rowley D, Bruno D, Carrington CVF, Chandanayingyong D, Chang YH, Crespí C, Saruhan-Direskeneli G, Fraser PA, Hameed K, Kamkamidze G, Koram KA, Layrisse Z, Matamoros N, Milà J, Park MH, Pitchappan RM, Ramdath DD, Shiau MY, Stephens HAF, Struik S, Verity DH, Vaughan RW, Tyan D, Davis RW, Riley EM, Ronaghi M, Parham P. Unusual selection on the KIR3DL1/S1 natural killer cell receptor in Africans. Nat Genet 2007; 39:1092-9. [PMID: 17694054 DOI: 10.1038/ng2111] [Citation(s) in RCA: 181] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2007] [Accepted: 07/06/2007] [Indexed: 12/12/2022]
Abstract
Interactions of killer cell immunoglobulin-like receptors (KIRs) with major histocompatibility complex (MHC) class I ligands diversify natural killer cell responses to infection. By analyzing sequence variation in diverse human populations, we show that the KIR3DL1/S1 locus encodes two lineages of polymorphic inhibitory KIR3DL1 allotypes that recognize Bw4 epitopes of protein">HLA-A and HLA-B and one lineage of conserved activating KIR3DS1 allotypes, also implicated in Bw4 recognition. Balancing selection has maintained these three lineages for over 3 million years. Variation was selected at D1 and D2 domain residues that contact HLA class I and at two sites on D0, the domain that enhances the binding of KIR3D to HLA class I. HLA-B variants that gained Bw4 through interallelic microconversion are also products of selection. A worldwide comparison uncovers unusual KIR3DL1/S1 evolution in modern sub-Saharan Africans. Balancing selection is weak and confined to D0, KIR3DS1 is rare and KIR3DL1 allotypes with similar binding sites predominate. Natural killer cells express the dominant KIR3DL1 at a high frequency and with high surface density, providing strong responses to cells perturbed in Bw4 expression.
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Affiliation(s)
- Paul J Norman
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, USA.
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20
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Kumar P, Vahedi-Faridi A, Merino E, López de Castro JA, Volz A, Ziegler A, Saenger W, Uchanska-Ziegler B. Expression, purification and preliminary X-ray crystallographic analysis of the human major histocompatibility antigen HLA-B*1402 in complex with a viral peptide and with a self-peptide. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:631-4. [PMID: 17620730 PMCID: PMC2335130 DOI: 10.1107/s1744309107029077] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2007] [Accepted: 06/13/2007] [Indexed: 05/16/2023]
Abstract
The product of the human major histocompatibility (HLA) class I allele HLA-B*1402 only differs from that of allele HLA-B*1403 at amino-acid position 156 of the heavy chain (Leu in HLA-B*1402 and Arg in HLA-B*1403). However, both subtypes are known to be differentially associated with the inflammatory rheumatic disease ankylosing spondylitis (AS) in black populations in Cameroon and Togo. HLA-B*1402 is not associated with AS, in contrast to HLA-B*1403, which is associated with this disease in the Togolese population. The products of these alleles can present peptides with Arg at position 2, a feature shared by a small group of other HLA-B antigens, including HLA-B*2705, the prototypical AS-associated subtype. Complexes of HLA-B*1402 with a viral peptide (RRRWRRLTV, termed pLMP2) and a self-peptide (IRAAPPPLF, termed pCatA) were prepared and were crystallized using polyethylene glycol as precipitant. The complexes crystallized in space groups P2(1) (pLMP2) and P2(1)2(1)2(1) (pCatA) and diffracted synchrotron radiation to 2.55 and 1.86 A resolution, respectively. Unambiguous solutions for both data sets were obtained by molecular replacement using a peptide-complexed HLA-B*2705 molecule (PDB code 1jge) as a search model.
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Affiliation(s)
- Pravin Kumar
- Institut für Immungenetik, Charité – Universitätsmedizin Berlin, Humboldt-Universität zu Berlin, Thielallee 73, 14195 Berlin, Germany
| | - Ardeschir Vahedi-Faridi
- Institut für Chemie und Biochemie/Kristallographie, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany
| | - Elena Merino
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Cientificas, Universidad Autónoma de Madrid, Facultad de Ciencias, Universidad Autónoma, 28049 Madrid, Spain
| | - José A. López de Castro
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Cientificas, Universidad Autónoma de Madrid, Facultad de Ciencias, Universidad Autónoma, 28049 Madrid, Spain
| | - Armin Volz
- Institut für Immungenetik, Charité – Universitätsmedizin Berlin, Humboldt-Universität zu Berlin, Thielallee 73, 14195 Berlin, Germany
| | - Andreas Ziegler
- Institut für Immungenetik, Charité – Universitätsmedizin Berlin, Humboldt-Universität zu Berlin, Thielallee 73, 14195 Berlin, Germany
| | - Wolfram Saenger
- Institut für Chemie und Biochemie/Kristallographie, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany
- Correspondence e-mail: ,
| | - Barbara Uchanska-Ziegler
- Institut für Immungenetik, Charité – Universitätsmedizin Berlin, Humboldt-Universität zu Berlin, Thielallee 73, 14195 Berlin, Germany
- Correspondence e-mail: ,
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Burrows JM, Wynn KK, Tynan FE, Archbold J, Miles JJ, Bell MJ, Brennan RM, Walker S, McCluskey J, Rossjohn J, Khanna R, Burrows SR. The impact of HLA-B micropolymorphism outside primary peptide anchor pockets on the CTL response to CMV. Eur J Immunol 2007; 37:946-53. [PMID: 17357107 DOI: 10.1002/eji.200636588] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The factors controlling epitope selection in the T cell response to persistent viruses are not fully understood, and we have examined this issue in the context of four HLA-B*35-binding peptides from the pp65 antigen of human cytomegalovirus, two of which are previously undescribed. Striking differences in the hierarchy of immunodominance between these four epitopes were observed in healthy virus carriers expressing HLA-B*3501 versus B*3508, two HLA-B allotypes that differ by a single amino acid at position 156 (HLA-B*3501, (156)Leucine; HLA-B*3508, (156)Arginine) that projects from the alpha2 helix into the centre of the peptide-binding groove. While HLA-B*3501(+) individuals responded most strongly to the (123)IPSINVHHY(131) and (366)HPTFTSQY(373) epitopes, HLA-B*3508(+) individuals responded preferentially to (103)CPSQEPMSIYVY(114) and (188)FPTKDVAL(195). By comparing peptide-MHC association and disassociation rates with peptide immunogenicity, it was clear that dissociation rates correlate more closely with the hierarchy of immunodominance among the four pp65 peptides. These findings demonstrate that MHC micropolymorphism at positions outside the primary anchor residue binding pockets can have a major impact on determinant selection in antiviral T cell responses. Such influences may provide the evolutionary pressure that maintains closely related MHC molecules in diverse human populations.
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Affiliation(s)
- Jacqueline M Burrows
- Division of Infectious Diseases and Immunology, Queensland Institute of Medical Research, Brisbane, Australia.
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22
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Hourigan CS, Harkiolaki M, Peterson NA, Bell JI, Jones EY, O'Callaghan CA. The structure of the human allo-ligand HLA-B*3501 in complex with a cytochrome p450 peptide: steric hindrance influences TCR allo-recognition. Eur J Immunol 2007; 36:3288-93. [PMID: 17109469 DOI: 10.1002/eji.200636234] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Virus-specific T cell populations have been implicated in allo-recognition. The subdominant T cell receptor JL12 recognizes both HLA-B*0801 presenting the Epstein-Barr virus-derived peptide FLRGRAYGL and also HLA-B*3501 presenting the cytochrome p450 self peptide KPIVVLHGY. This cross-reactivity could promote the rejection of HLA-B*3501-positive cells in Epstein-Barr virus-exposed HLA-B*0801 recipients. LC13, the dominant TCR against the HLA-B*0801:FLRGRAYGL complex, fails to recognize HLA-B*3501:KPIVVLHGY. We report the 1.75-Angstrom resolution crystal structure of the human allo-ligand HLA-B*3501:KPIVVLHGY. Similarities between this structure and that of HLA-B*0801:FLRGRAYGL may facilitate cross-recognition by JL12. Moreover, the elevated peptide position in HLA-B*3501:KPIVVLHGY would provide steric hindrance to LC13, preventing it from interacting in the manner in which it interacts with HLA-B*0801:FLRGRAYGL. These findings are relevant to understanding the basis of T cell cross-reactivity in allo-recognition, optimal transplant donor-recipient matching and developing specific molecular inhibitors of allo-recognition.
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Bade-Doeding C, DeLuca DS, Seltsam A, Blasczyk R, Eiz-Vesper B. Amino acid 95 causes strong alteration of peptide position Pomega in HLA-B*41 variants. Immunogenetics 2007; 59:253-9. [PMID: 17294180 DOI: 10.1007/s00251-007-0197-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2006] [Accepted: 01/08/2007] [Indexed: 11/24/2022]
Abstract
There have been several attempts over the years to identify positions in the peptide-binding region (PBR) of human leukocyte antigens (HLA) that influence the specificity of bound amino acids (AAs) at each position in the peptide. Originally, six pockets (A-F) were defined by calculating the surface area of the PBR on the crystal structure of HLA-A2 molecules. More recent crystallographic analyses of a variety of HLA alleles have led to broader pocket definitions. In this study, we examined the peptide-binding specificity of HLA-B*41 alleles and compared our results with the available pocket definitions. By generating recombinant HLA-B molecules and studying the eluted peptides by mass spectrometry and pool sequencing, we detected two different POmega peptide motifs within the B*41 group: Leu vs Val/Pro. Specificity was dependent on the presence of Leu (B*4102, B*4103, and B*4104) vs Trp (B*4101, B*4105, and B*4106) at AA position 95 in the HLA molecule, whose impact on POmega has been a subject of controversy in current pocket definitions. In contrast, the Arg97Ser mutation did not affect pocket F binding specificity in B*41 subtypes although residue 97 was previously identified as a modulator of peptide binding for several HLA class I alleles. According to most pocket definitions, this study shows that the Asn80Lys substitution in B*4105 impels the peptide's POmega anchor toward more promiscuity. Our sequencing results of peptides eluted from HLA-B*41 variants demonstrate the limitations of current pocket definitions and underline the need for an extended peptide motif database for improved understanding of peptide-major histocompatibility complex interactions.
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Honeyborne I, Prendergast A, Pereyra F, Leslie A, Crawford H, Payne R, Reddy S, Bishop K, Moodley E, Nair K, van der Stok M, McCarthy N, Rousseau CM, Addo M, Mullins JI, Brander C, Kiepiela P, Walker BD, Goulder PJR. Control of human immunodeficiency virus type 1 is associated with HLA-B*13 and targeting of multiple gag-specific CD8+ T-cell epitopes. J Virol 2007; 81:3667-72. [PMID: 17251285 PMCID: PMC1866034 DOI: 10.1128/jvi.02689-06] [Citation(s) in RCA: 125] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To better understand relationships between CD8+ T-cell specificity and the immune control of human immunodeficiency virus type 1 (HIV-1), we analyzed the role of HLA-B*13, an allele associated with low viremia, in a cohort of 578 C clade-infected individuals in Durban, South Africa. Six novel B*13-restricted cytotoxic T lymphocyte epitopes were defined from analyses of 37 B*13-positive subjects, including three Gag epitopes. These B*13-restricted epitopes contribute to a broad Gag-specific CD8+ response that is associated with the control of viremia. These data are consistent with data from studies of other HLA-class I alleles associated with HIV control that have shown that the targeting of multiple Gag epitopes is associated with relative suppression of viremia.
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Affiliation(s)
- Isobella Honeyborne
- Department of Paediatrics, Peter Medawar Building for Pathogen Research, South Parks Road, Oxford OX1 3SY, United Kingdom
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25
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Røder G, Blicher T, Justesen S, Johannesen B, Kristensen O, Kastrup J, Buus S, Gajhede M. Crystal structures of two peptide-HLA-B*1501 complexes; structural characterization of the HLA-B62 supertype. Acta Crystallogr D Biol Crystallogr 2006; 62:1300-10. [PMID: 17057332 DOI: 10.1107/s0907444906027636] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2006] [Accepted: 07/17/2006] [Indexed: 11/10/2022]
Abstract
MHC class I molecules govern human cytotoxic T cell responses. Their specificity determines which peptides they sample from the intracellular protein environment and then present to human cytotoxic T cells. More than 1100 different MHC class I proteins have been found in human populations and it would be a major undertaking to address each of these specificities individually. Based upon their peptide binding specificity, they are currently subdivided into 12 supertypes. Several of these HLA supertypes have not yet been described at the structural level. To support a comprehensive understanding of human immune responses, the structure of at least one member of each supertype should be determined. Here, the structures of two immunogenic peptide-HLA-B*1501 complexes are described. The structure of HLA-B*1501 in complex with a peptide (LEKARGSTY, corresponding to positions 274-282 in the Epstein-Barr virus nuclear antigen-3A) was determined to 2.3 A resolution. The structure of HLA-B*1501 in complex with a peptide (ILGPPGSVY) derived from human ubiquitin-conjugating enzyme-E2 corresponding to positions 91-99 was solved to 1.8 A resolution. Mutual comparisons of these two structures with structures from other HLA supertypes define and explain the specificity of the P2 and P9 peptide anchor preferences in the B62 HLA supertype. The P2 peptide residue binds to the B-pocket in HLA-B*1501. This pocket is relatively large because of the small Ser67 residue located at the bottom. The peptide proximal part of the B-pocket is hydrophobic, which is consistent with P2 anchor residue preference for Leu. The specificity of the B-pocket is determined by the Met45, Ile66 and Ser67 residues. The apex of the B-pocket is hydrophilic because of the Ser67 residue. The P9 peptide residue binds to the F-pocket in HLA-B*1501. The residues most important for the specificity of this pocket are Tyr74, Leu81, Leu95, Tyr123 and Trp147. These residues create a hydrophobic interior in the F-pocket and their spatial arrangement makes the pocket capable of containing large, bulky peptide side chains. Ser116 is located at the bottom of the F-pocket and makes the bottom of this pocket hydrophilic. Ser116, may act as a hydrogen-bonding partner and as such is a perfect place for binding of a Tyr9 peptide residue. Thus, based on structure information it is now possible to explain the peptide sequence specificity of HLA-B*1501 as previously determined by peptide binding and pool sequencing experiments.
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Affiliation(s)
- Gustav Røder
- Institute of Medical Microbiology and Immunology, Panum Institute 18.3.20, Blegdamsvej 3B, 2200N Copenhagen, Denmark.
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26
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Elsner HA, Horn PA, Schoenemann C, Altermann WW, Blasczyk R. Aberrant expression of HLA-B*3565Q is associated with a disrupted disulfide bond. Immunogenetics 2006; 58:929-31. [PMID: 17021858 DOI: 10.1007/s00251-006-0158-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2006] [Accepted: 08/31/2006] [Indexed: 11/28/2022]
Abstract
The identification of expression variants is a challenge in HLA diagnostics. We here describe the identification of the novel allele HLA-B*3565Q. The serological HLA class I type, as determined by a lymphocytotoxicity test, was A11,24; B38; Bw4; Cw-; whereas PCR-sequence-specific primers resulted in A*11,*24, B*35,*38; Cw*12, thus suggesting the presence of a nonexpressed B*35 allele. To clarify the lack of serological HLA-B35 reactivity, exons 2 and 3 were sequenced following haplotype-specific amplification. At position 564 from the beginning of the coding region (exon 3), a transversion (C-->G) was observed, which, at the amino acid level, results in a substitution from cysteine to tryptophane at position 164 of the mature polypeptide. Because this position is essential for the formation of a disulfide bond linking the cysteine residues at positions 101 and 164, which is strongly conserved in functional class I molecules of vertebrates, the disruption of this bond is very likely to be the reason for the lack of serological detectability. We later found the same novel allele in a second unrelated individual, of whom we were able to establish a lymphoblastoid cell line (B-LCL). Serological testing of this B-LCL indicated a very low aberrant expression of HLA-B*3565Q, which cannot be expected to be detected by standard serology techniques.
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27
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Affiliation(s)
- S M Jeong
- Department of Physiology, College of Veterinary Medicine, Konkuk University, Seoul, Republic of Korea
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28
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Affiliation(s)
- C-C Chu
- Transfusion Medicine Laboratory, Medical Research Department, Mackay Memorial Hospital, Taipei, Taiwan
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29
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Hoelsch K, Lenggeler I, Knabe H, Hartel K, Klein HG, Woelpl A. Identification of a novel HLA-B*44 variant (B*4441) in three unrelated Caucasian individuals. ACTA ACUST UNITED AC 2006; 67:247-9. [PMID: 16573564 DOI: 10.1111/j.1399-0039.2006.00563.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Here, we report the identification of a new human leukocyte antigen (HLA)-B*44 allele found almost simultaneous in three DNA samples which were part of routine bone marrow donor typing by order of the German registry 'Aktion Knochenmarkspende Bayern'. The samples appeared noticeable in different polymerase chain reactions using sequence-specific primers (PCR-SSP) or sequence-specific oligonucleotides (PCR-SSO). Sequence-based typing revealed a novel allele officially designated as B*4441*. This sequence differs from HLA-B*44020101/4427 by two nucleotide positions at the beginning of exon 3: by position 353 (T to C) and by position 355 (A to C). These differences in sequence result in deviant amino acids at codon 94 (Ile94Thr) and codon 95 (Ile95Leu).
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Affiliation(s)
- K Hoelsch
- Laboratory for Medical Genetics, Dr Klein, Martinsried, Munich, Germany
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30
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Affiliation(s)
- L-X Yan
- HLA typing laboratory, Blood Center of Zhejiang Province, Hangzhou, China.
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31
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Affiliation(s)
- P A Horn
- Institute for Transfusion Medicine, Hannover Medical School, Germany
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32
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Knights AJ, Weinzierl AO, Flad T, Guinn BA, Mueller L, Mufti GJ, Stevanovic S, Pawelec G. A novel MHC-associated Proteinase 3 peptide isolated from primary chronic myeloid leukaemia cells further supports the significance of this antigen for the immunotherapy of myeloid leukaemias. Leukemia 2006; 20:1067-72. [PMID: 16628186 DOI: 10.1038/sj.leu.2404234] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Three of the most promising antigens for immunotherapy of chronic myelogenous leukaemia (CML) include the specific fusion-protein, Bcr/Abl, and the overexpressed proteins WT1 and Proteinase 3. The clinical significance of Proteinase 3 as a target in myelogenous leukaemias has been bolstered by detection of high frequencies of cytotoxic CD8+ lymphocytes specific for this antigen in patients undergoing immune therapies. Our investigation aimed to directly identify MHC-ligands derived from these antigens and presented on CML blasts by means of affinity-purification and mass spectrometric peptide-sequencing. Although no known or potential new epitopes were discovered for Bcr/Abl or WT1, a novel peptide from Proteinase 3 was detected among the more abundant MHC-ligands. Additionally, MHC-ligands derived from known immunogenic proteins overexpressed as a result of Bcr/Abl transformation were also identified. Our investigation is the second of only a small number of studies to identify a peptide from Proteinase 3 among the more abundant MHC-associated peptides and thus implies that peptides from this antigen are among the more abundantly presented of the known leukaemic antigens. Taken in conjunction with clinical observations of functional Proteinase 3 specific CTL in patients', these data further support the application of this antigen as an immunotherapeutical target for myelogenous leukaemias.
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Affiliation(s)
- A J Knights
- Section for Transplantation Immunology and Immunohaematology, University Hospital Tübingen, ZMF, Waldhörnlestrasse 22, Tübingen, Germany.
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Ely LK, Beddoe T, Clements CS, Matthews JM, Purcell AW, Kjer-Nielsen L, McCluskey J, Rossjohn J. Disparate thermodynamics governing T cell receptor-MHC-I interactions implicate extrinsic factors in guiding MHC restriction. Proc Natl Acad Sci U S A 2006; 103:6641-6. [PMID: 16617112 PMCID: PMC1564203 DOI: 10.1073/pnas.0600743103] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The underlying basis of major histocompatibility complex (MHC) restriction is unclear. Nevertheless, current data suggest that a common thermodynamic signature dictates alphabeta T cell receptor (TcR) ligation. To evaluate whether this thermodynamic signature defines MHC restriction, we have examined the thermodynamic basis of a highly characterized immunodominant TcR interacting with its cognate peptide-MHC-I ligand. Surprisingly, we observed this interaction to be governed by favorable enthalpic and entropic forces, which is in contrast to the prevailing generality, namely, enthalpically driven interactions combined with markedly unfavorable entropic forces. We conclude that extrinsic molecular factors, such as coreceptor ligation, conformational adjustments involved in TcR signaling, or constraints dictated by higher-order arrangement of ligated TcRs, might play a greater role in guiding MHC restriction than appreciated previously.
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Affiliation(s)
- Lauren K. Ely
- Protein Crystallography Unit, Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Travis Beddoe
- Protein Crystallography Unit, Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Craig S. Clements
- Protein Crystallography Unit, Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Jacqueline M. Matthews
- School of Molecular and Microbial Biosciences, University of Sydney, Sydney, New South Wales 2006, Australia; and
| | | | - Lars Kjer-Nielsen
- Microbiology and Immunology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - James McCluskey
- Microbiology and Immunology, University of Melbourne, Parkville, Victoria 3010, Australia
- To whom correspondence may be addressed. E-mail:
or
| | - Jamie Rossjohn
- Protein Crystallography Unit, Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, Australia
- To whom correspondence may be addressed. E-mail:
or
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34
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Kögler G, Enczmann J, Rocha V, Gluckman E, Wernet P. High-resolution HLA typing by sequencing for HLA-A, -B, -C, -DR, -DQ in 122 unrelated cord blood/patient pair transplants hardly improves long-term clinical outcome. Bone Marrow Transplant 2006; 36:1033-41. [PMID: 16247425 DOI: 10.1038/sj.bmt.1705189] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
To determine the impact of high-resolution (HR) HLA typing with outcomes after UCBT, DNAs of 122 pairs were analysed for HLA class I and class II mismatches (MM) based on HR typing. For HLA-A, -B on low-resolution typing and -DRB1 on HR typing, the following MM situation resulted: no MM (13%), one MM (40%), two MM (36%), three MM (8%), four MM (3%). For A, B, C, DR and DQ based on HR typing the following MM occurred: No MM (4%), one MM (10%), two MM (15%), three MM (22%), four MM (25%), five MM (12%), six MM (6%), seven MM (3%), eight MM (2%). There was no significant association between number of MM (HR) for both HLA-A, -B and -DRB1 and HLA-A, -B, -C, -DRB1 and DQB1 and aGvHD grade II-IV. There was a trend that MM in class I HR were associated with neutrophil recovery; HLA-A locus typing analysed in HvG direction was associated with reduced cumulative incidence of engraftment (P=0.04), the same for C-KIR in HvG direction (P=0.01). No significant correlation was found between numbers of HLA-MM on the HR level with 2-year survival. The analysis shows that the degree of mismatching in UCBT is even higher than expected.
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Affiliation(s)
- G Kögler
- José Carreras EUROCORD/NETCORD Bank Germany at the Institute for Transplantation Diagnostics and Cell Therapeutics, University of Duesseldorf Medical School, Düsseldorf, Germany.
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35
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Bihl F, Frahm N, Di Giammarino L, Sidney J, John M, Yusim K, Woodberry T, Sango K, Hewitt HS, Henry L, Linde CH, Chisholm JV, Zaman TM, Pae E, Mallal S, Walker BD, Sette A, Korber BT, Heckerman D, Brander C. Impact of HLA-B Alleles, Epitope Binding Affinity, Functional Avidity, and Viral Coinfection on the Immunodominance of Virus-Specific CTL Responses. J Immunol 2006; 176:4094-101. [PMID: 16547245 DOI: 10.4049/jimmunol.176.7.4094] [Citation(s) in RCA: 131] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Immunodominance is variably used to describe either the most frequently detectable response among tested individuals or the strongest response within a single individual, yet factors determining either inter- or intraindividual immunodominance are still poorly understood. More than 90 individuals were tested against 184 HIV- and 92 EBV-derived, previously defined CTL epitopes. The data show that HLA-B-restricted epitopes were significantly more frequently recognized than HLA-A- or HLA-C-restricted epitopes. HLA-B-restricted epitopes also induced responses of higher magnitude than did either HLA-A- or HLA-C-restricted epitopes, although this comparison only reached statistical significance for EBV epitopes. For both viruses, the magnitude and frequency of recognition were correlated with each other, but not with the epitope binding affinity to the restricting HLA allele. The presence or absence of HIV coinfection did not impact EBV epitope immunodominance patterns significantly. Peptide titration studies showed that the magnitude of responses was associated with high functional avidity, requiring low concentration of cognate peptide to respond in in vitro assays. The data support the important role of HLA-B alleles in antiviral immunity and afford a better understanding of the factors contributing to inter- and intraindividual immunodominance.
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Affiliation(s)
- Florian Bihl
- Partners AIDS Research Center, Massachusetts General Hospital, Charlestown, 02129, USA
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36
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Affiliation(s)
- J-Y Baek
- College of Medicine, Pochon CHA University, Seoul, Korea
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37
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de Rijke B, van Horssen-Zoetbrood A, Beekman JM, Otterud B, Maas F, Woestenenk R, Kester M, Leppert M, Schattenberg AV, de Witte T, van de Wiel-van Kemenade E, Dolstra H. A frameshift polymorphism in P2X5 elicits an allogeneic cytotoxic T lymphocyte response associated with remission of chronic myeloid leukemia. J Clin Invest 2006; 115:3506-16. [PMID: 16322791 PMCID: PMC1297240 DOI: 10.1172/jci24832] [Citation(s) in RCA: 112] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2005] [Accepted: 09/13/2005] [Indexed: 11/17/2022] Open
Abstract
Minor histocompatibility antigens (mHAgs) constitute the targets of the graft-versus-leukemia response after HLA-identical allogeneic stem cell transplantation. Here, we have used genetic linkage analysis to identify a novel mHAg, designated lymphoid-restricted histocompatibility antigen-1 (LRH-1), which is encoded by the P2X5 gene and elicited an allogeneic CTL response in a patient with chronic myeloid leukemia after donor lymphocyte infusion. We demonstrate that immunogenicity for LRH-1 is due to differential protein expression in recipient and donor cells as a consequence of a homozygous frameshift polymorphism in the donor. Tetramer analysis showed that emergence of LRH-1-specific CD8+ cytotoxic T cells in peripheral blood and bone marrow correlated with complete remission of chronic myeloid leukemia. Furthermore, the restricted expression of LRH-1 in hematopoietic cells including leukemic CD34+ progenitor cells provides evidence of a role for LRH-1-specific CD8+ cytotoxic T cells in selective graft-versus-leukemia reactivity in the absence of severe graft-versus-host disease. These findings illustrate that the P2X5-encoded mHAg LRH-1 could be an attractive target for specific immunotherapy to treat hematological malignancies recurring after allogeneic stem cell transplantation.
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MESH Headings
- Adult
- Amino Acid Sequence
- Antigens, CD34/biosynthesis
- Base Sequence
- Bone Marrow Cells/cytology
- CD8-Positive T-Lymphocytes/metabolism
- Cell Line
- Cells, Cultured
- Chromium/metabolism
- Chromosome Mapping
- Chromosomes, Human, Pair 17
- DNA-Binding Proteins/genetics
- Epitopes/chemistry
- Female
- Frameshift Mutation
- Fusion Proteins, bcr-abl/chemistry
- Genetic Linkage
- Genetic Markers
- Genotype
- Graft vs Leukemia Effect
- HLA-B Antigens/chemistry
- HLA-B7 Antigen
- Haplotypes
- Homozygote
- Humans
- Interferon-gamma/metabolism
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/immunology
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/therapy
- Leukocyte Common Antigens/chemistry
- Lod Score
- Male
- Models, Genetic
- Molecular Sequence Data
- Neurons/metabolism
- Pedigree
- Peptides/chemistry
- Plasmids/metabolism
- Polymorphism, Genetic
- Receptors, Purinergic P2/genetics
- Receptors, Purinergic P2/metabolism
- Receptors, Purinergic P2X5
- Recurrence
- Retroviridae/genetics
- Reverse Transcriptase Polymerase Chain Reaction
- Stem Cell Transplantation
- Stem Cells
- T-Lymphocytes/cytology
- T-Lymphocytes/immunology
- T-Lymphocytes, Cytotoxic/cytology
- Time Factors
- Transcription Factors/genetics
- Transplantation, Homologous
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Affiliation(s)
- Björn de Rijke
- Central Hematology Laboratory, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
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38
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Affiliation(s)
- O-J Kwon
- BioSewoom Institute of Bioscience & Biotechnology, Seoul, Korea
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39
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Jones MA, Hislop AD, Snaith JS. Synthesis and biological evaluation of two chemically modified peptide epitopes for the class I MHC protein HLA-B*2705. Org Biomol Chem 2006; 4:3769-77. [PMID: 17024283 DOI: 10.1039/b611170j] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The T-cell receptor of a CD8(+) T-cell recognises peptide epitopes bound by class I major histocompatibility complex (MHC) glycoproteins presented in a groove on their upper surface. Within the groove of the MHC molecule are 6 pockets, two of which mostly display a high degree of specificity for binding amino acids capable of making conserved and energetically favourable contacts with the MHC. One type of MHC molecule, HLA-B*2705, preferentially binds peptides containing an arginine at position 2. In an effort to increase the affinity of peptides for HLA-B*2705, potentially leading to better immune responses to such a peptide, we synthesised two modified epitopes where the amino acid at position 2 involved in anchoring the peptide to the class I molecule was replaced with the alpha-methylated beta,gamma-unsaturated arginine analogue 2-(S)-amino-5-guanidino-2-methyl-pent-3-enoic acid. The latter was prepared via a multi-step synthetic sequence, starting from alpha-methyl serine, and incorporated into dipeptides which were fragment-coupled to resin-bound heptameric peptides yielding the target nonameric sequences. Biological characterisation indicated that the modified peptides were poorer than the native peptides at stabilising empty class I MHC complexes, and cells sensitised with these peptides were not recognised as well by cognate CD8(+) T-cells, where available, compared to those sensitised with the native peptide. We suggest that the modifications made to the peptide have decreased its ability to bind to the peptide binding groove of HLA-B*2705 molecules which may explain the decrease in recognition by cytotoxic T-cells when compared to the native peptide.
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Affiliation(s)
- Matthew A Jones
- School of Chemistry, University of Birmingham, Birmingham, UK B15 2TT.
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40
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Zawacka A, Loll B, Biesiadka J, Saenger W, Uchanska-Ziegler B, Ziegler A. X-ray diffraction analysis of crystals from the human major histocompatibility antigen HLA-B*2706 in complex with a viral peptide and with a self-peptide. Acta Crystallogr Sect F Struct Biol Cryst Commun 2005; 61:1097-9. [PMID: 16511245 PMCID: PMC1978159 DOI: 10.1107/s1744309105037966] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2005] [Accepted: 11/17/2005] [Indexed: 01/05/2023]
Abstract
The human leukocyte antigen (HLA) alleles HLA-B*2704 and HLA-B*2706 show an ethnically restricted distribution and are differentially associated with ankylosing spondylitis, with HLA-B*2706 lacking association with this autoimmune disease. However, the products of the two alleles differ by only two amino acids, at heavy-chain residues 114 (His in HLA-B*2704; Asp in HLA-B*2706) and 116 (Asp in HLA-B*2704; Tyr in HLA-B*2706). Both residues could be involved in contacting amino acids of a bound peptide, suggesting that peptides presented by these subtypes play a role in disease pathogenesis. Two HLA-B*2706-peptide complexes were crystallized using the hanging-drop vapour-diffusion method with PEG as precipitant. Data sets were collected to resolutions of 2.70 A (viral peptide pLMP2, RRRWRRLTV; space group P2(1)2(1)2(1)) and 1.83 A (self-peptide pVIPR, RRKWRRWHL; space group P2(1)). Using HLA-B*2705 complexed with the pGR peptide (RRRWHRWRL) as a search model, unambiguous molecular-replacement solutions were found for both HLA-B*2706 complexes.
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Affiliation(s)
- Anna Zawacka
- Institut für Immungenetik, Charité – Universitätsmedizin Berlin, Campus Virchow-Klinikum, Humboldt-Universität zu Berlin, Spandauer Damm 130, 14050 Berlin, Germany
| | - Bernhard Loll
- Institut für Chemie und Biochemie/Kristallographie, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany
| | - Jacek Biesiadka
- Institut für Chemie und Biochemie/Kristallographie, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany
| | - Wolfram Saenger
- Institut für Chemie und Biochemie/Kristallographie, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany
| | - Barbara Uchanska-Ziegler
- Institut für Immungenetik, Charité – Universitätsmedizin Berlin, Campus Virchow-Klinikum, Humboldt-Universität zu Berlin, Spandauer Damm 130, 14050 Berlin, Germany
| | - Andreas Ziegler
- Institut für Immungenetik, Charité – Universitätsmedizin Berlin, Campus Virchow-Klinikum, Humboldt-Universität zu Berlin, Spandauer Damm 130, 14050 Berlin, Germany
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41
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Stewart-Jones GBE, Gillespie G, Overton IM, Kaul R, Roche P, McMichael AJ, Rowland-Jones S, Jones EY. Structures of three HIV-1 HLA-B*5703-peptide complexes and identification of related HLAs potentially associated with long-term nonprogression. J Immunol 2005; 175:2459-68. [PMID: 16081817 DOI: 10.4049/jimmunol.175.4.2459] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Long-term nonprogression during acute HIV infection has been strongly associated with HLA-B*5701 or HLA-B*5703. In this study, we present the high resolution crystal structures of HLA-B*5703 complexes with three HIV-1 epitopes: ISPRTLNAW (ISP), KAFSPEVIPMF (KAF-11), and KAFSPEVI (KAF-8). These reveal peptide anchoring at position 2 and their C termini. The different peptide lengths and primary sequences are accommodated by variation in the specific contacts made to the HLA-B*5703, flexibility in water structure, and conformational adjustment of side chains within the peptide-binding groove. The peptides adopt markedly different conformations, and trap variable numbers of water molecules, near a cluster of tyrosine side chains located in the central region of the peptide-binding groove. The KAF-11 epitope completely encompasses the shorter KAF-8 epitope but the peptides are presented in different conformations; the KAF-11 peptide arches out of the peptide-binding groove, exposing a significant main chain surface area. Bioinformatic analysis of the MHC side chains observed to contribute to the peptide anchor specificity, and other specific peptide contacts, reveals HLA alleles associated with long-term nonprogression and a number of related HLA alleles that may share overlapping peptide repertoires with HLA-B*5703 and thus may display a similar capacity for efficient immune control of HIV-1 infection.
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Affiliation(s)
- Guillaume B E Stewart-Jones
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
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42
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Abstract
CD4(+)CD25(+) regulatory T cells are selected in the thymus to control autoreactive thymic escapees preventing autoimmunity that cannot be achieved by negative selection or deletion alone, thus playing an important role in the maintenance of immunological homeostasis. Not only significant in preventing autoimmunity, CD4(+)CD25(+) regulatory T cells have also been shown to be involved in allograft tolerance in organ transplantation. We have formerly introduced two lines of HLA class I transgenic mice to elucidate the role of HLA class I molecules in transplantation biology. Using a heterotopic cardiac transplantation model, we show herein that intrathymic inoculation of donor HLA class I-derived synthetic peptide results in the generation of CD4(+)CD25(+) regulatory T cells, which induce graft specific tolerance without any preconditioning of the recipient or use of immunosuppressive drugs. This study provides evidence of the novel therapeutic potential of CD4(+)CD25(+) regulatory T cells for clinical transplantation.
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Affiliation(s)
- S Tamura
- Department of Surgery and Bioengineering, Advanced Clinical Research Center, Institution of Medical Science, University of Tokyo, Tokyo, Japan.
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43
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Rückert C, Fiorillo MT, Loll B, Moretti R, Biesiadka J, Saenger W, Ziegler A, Sorrentino R, Uchanska-Ziegler B. Conformational dimorphism of self-peptides and molecular mimicry in a disease-associated HLA-B27 subtype. J Biol Chem 2005; 281:2306-16. [PMID: 16221670 DOI: 10.1074/jbc.m508528200] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
An interesting property of certain peptides presented by major histocompatibility complex (MHC) molecules is their acquisition of a dual binding mode within the peptide binding groove. Using x-ray crystallography at 1.4 A resolution, we show here that the glucagon receptor-derived self-peptide pGR ((412)RRRWHRWRL(420)) is presented by the disease-associated human MHC class I subtype HLA-B*2705 in a dual conformation as well, with the middle of the peptide bent toward the floor of the peptide binding groove of the molecule in both binding modes. The conformations of pGR are compared here with those of another self-peptide (pVIPR, RRKWRRWHL) that is also displayed in two binding modes by HLA-B*2705 antigens and with that of the viral peptide pLMP2 (RRRWRRLTV). Conserved structural features suggest that the N-terminal halves of the peptides are crucial in allowing cytotoxic T lymphocyte (CTL) cross-reactivity. In addition, an analysis of T cell receptors (TCRs) from pGR- or pVIPR-directed, HLA-B27-restricted CTL clones demonstrates that TCR from distinct clones but with comparable reactivity may share CDR3alpha but not CDR3beta regions. Therefore, the cross-reactivity of these CTLs depends on TCR-CDR3alpha, is modulated by TCR-CDR3beta sequences, and is ultimately a consequence of the conformational dimorphism that characterizes binding of the self-peptides to HLA-B*2705. These results lend support to the concept that conformational dimorphisms of MHC class I-bound peptides might be connected with the occurrence of self-reactive CTL.
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MESH Headings
- Antigens/chemistry
- Cell Line, Tumor
- Chromium/chemistry
- Crystallography, X-Ray
- Electrons
- Female
- HLA-B Antigens/chemistry
- HLA-B27 Antigen/chemistry
- HLA-B27 Antigen/metabolism
- Histocompatibility Antigens Class I/chemistry
- Humans
- Hydrogen Bonding
- Leukocytes, Mononuclear/cytology
- Major Histocompatibility Complex
- Male
- Models, Molecular
- Molecular Mimicry
- Peptides/chemistry
- Protein Binding
- Protein Conformation
- Protein Structure, Tertiary
- Receptors, Antigen, T-Cell/metabolism
- Receptors, Glucagon/chemistry
- Spondylitis, Ankylosing/immunology
- Spondylitis, Ankylosing/metabolism
- T-Lymphocytes/metabolism
- T-Lymphocytes, Cytotoxic/metabolism
- Viral Matrix Proteins/chemistry
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Affiliation(s)
- Christine Rückert
- Institut für Immungenetik, Charité-Universitätsmedizin Berlin, Campus Virchow-Klinikum, Humboldt-Universität zu Berlin, Spandauer Damm 130, 14050 Berlin, Germany
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44
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Loll B, Zawacka A, Biesiadka J, Petter C, Rückert C, Saenger W, Uchanska-Ziegler B, Ziegler A. Preliminary X-ray diffraction analysis of crystals from the recombinantly expressed human major histocompatibility antigen HLA-B*2704 in complex with a viral peptide and with a self-peptide. Acta Crystallogr Sect F Struct Biol Cryst Commun 2005; 61:939-41. [PMID: 16511201 PMCID: PMC1991317 DOI: 10.1107/s1744309105029234] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2005] [Accepted: 09/14/2005] [Indexed: 11/10/2022]
Abstract
The product of the human leukocyte antigen (HLA) gene HLA-B*2704 differs from that of the prototypical subtype HLA-B*2705 by three amino acids at heavy-chain residues 77 (Ser instead of Asp), 152 (Glu instead of Val) and 211 (Gly instead of Ala). In contrast to the ubiquitous HLA-B*2705 subtype, HLA-B*2704 occurs only in orientals. Both subtypes are strongly associated with spondyloarthropathies and the peptides presented by these subtypes are suspected to play a role in disease pathogenesis. HLA-B*2704 was crystallized in complex with a viral peptide and with a self-peptide using the hanging-drop vapour-diffusion method with PEG as a precipitant. Both crystals belong to space group P2(1)2(1)2(1). Data sets were collected to 1.60 A (complex with the self-peptide pVIPR) or to 1.90 A (complex with the viral peptide pLMP2) resolution using synchrotron radiation. With HLA-B*2705 complexed with pVIPR as a search model, unambiguous molecular-replacement solutions were found for the complexes of HLA-B*2704 with both peptides.
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Affiliation(s)
- Bernhard Loll
- Institut für Chemie/Kristallographie, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany
| | - Anna Zawacka
- Institut für Immungenetik, Charité–Universitätsmedizin Berlin, Campus Virchow-Klinikum, Humboldt-Universität zu Berlin, Spandauer Damm 130, 14050 Berlin, Germany
| | - Jacek Biesiadka
- Institut für Chemie/Kristallographie, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany
| | - Cordula Petter
- Institut für Immungenetik, Charité–Universitätsmedizin Berlin, Campus Virchow-Klinikum, Humboldt-Universität zu Berlin, Spandauer Damm 130, 14050 Berlin, Germany
| | - Christine Rückert
- Institut für Immungenetik, Charité–Universitätsmedizin Berlin, Campus Virchow-Klinikum, Humboldt-Universität zu Berlin, Spandauer Damm 130, 14050 Berlin, Germany
| | - Wolfram Saenger
- Institut für Chemie/Kristallographie, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany
| | - Barbara Uchanska-Ziegler
- Institut für Immungenetik, Charité–Universitätsmedizin Berlin, Campus Virchow-Klinikum, Humboldt-Universität zu Berlin, Spandauer Damm 130, 14050 Berlin, Germany
| | - Andreas Ziegler
- Institut für Immungenetik, Charité–Universitätsmedizin Berlin, Campus Virchow-Klinikum, Humboldt-Universität zu Berlin, Spandauer Damm 130, 14050 Berlin, Germany
- Correspondence e-mail:
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45
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Tynan FE, Burrows SR, Buckle AM, Clements CS, Borg NA, Miles JJ, Beddoe T, Whisstock JC, Wilce MC, Silins SL, Burrows JM, Kjer-Nielsen L, Kostenko L, Purcell AW, McCluskey J, Rossjohn J. T cell receptor recognition of a 'super-bulged' major histocompatibility complex class I-bound peptide. Nat Immunol 2005; 6:1114-22. [PMID: 16186824 DOI: 10.1038/ni1257] [Citation(s) in RCA: 227] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2005] [Accepted: 08/23/2005] [Indexed: 11/08/2022]
Abstract
Unusually long major histocompatibility complex (MHC) class I-restricted epitopes are important in immunity, but their 'bulged' conformation represents a potential obstacle to alphabeta T cell receptor (TCR)-MHC class I docking. To elucidate how such recognition is achieved while still preserving MHC restriction, we have determined here the structure of a TCR in complex with HLA-B(*)3508 presenting a peptide 13 amino acids in length. This complex was atypical of TCR-peptide-MHC class I interactions, being dominated at the interface by peptide-mediated interactions. The TCR assumed two distinct orientations, swiveling on top of the centrally bulged, rigid peptide such that only limited contacts were made with MHC class I. Although the TCR-peptide recognition resembled an antibody-antigen interaction, the TCR-MHC class I contacts defined a minimal 'generic footprint' of MHC-restriction. Thus our findings simultaneously demonstrate the considerable adaptability of the TCR and the 'shape' of MHC restriction.
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MESH Headings
- Amino Acid Sequence
- Antigen Presentation
- Cell Line
- Crystallography, X-Ray
- Epitopes, T-Lymphocyte/chemistry
- Epitopes, T-Lymphocyte/immunology
- HLA-B Antigens/chemistry
- HLA-B Antigens/immunology
- Humans
- Molecular Sequence Data
- Peptides/chemistry
- Peptides/immunology
- Protein Conformation
- Receptors, Antigen, T-Cell, alpha-beta/chemistry
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- T-Lymphocytes, Cytotoxic/immunology
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Affiliation(s)
- Fleur E Tynan
- The Protein Crystallography Unit, Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, Australia
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46
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Abstract
Three novel human leucocyte antigen (HLA) class I alleles have been characterized by means of direct DNA sequencing analysis. HLA-A* 0261 showed sequence variation at conserved codon. It differs from HLA-A* 020601 by a single-nucleotide substitution at codon 57 (CCG-->GCG) resulting in an amino acid change from Pro to Ala. The sequences of HLA-B*1585 are similar to those of HLA-B*15010101, but differed five nucleotides on exon 3 resulting in three amino acid changes at residues 94 (Thr-->Ile), 95 (Leu-->Ile) and 103 (Val-->Leu). Likewise, HLA-B*1587 is identical to HLA-B*15010101 except at codons 80-83 (Asn-Leu-Arg-Gly-->Ile-Ala-Leu-Arg) which has been replaced by HLA-Bw4 motif. These alleles seemed to be generated by either a point mutation or a gene conversion-like event from alleles existing in the population with high frequencies.
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Affiliation(s)
- K W Lee
- Hallym Institution for Genome Application, Hallym University, Sacred Heart Hospital, #896 Pyungchon-Dong, Dongan-Ku, Anyang, Kyungki-Do 431-070, Korea.
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47
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Hickman-Miller HD, Bardet W, Gilb A, Luis AD, Jackson KW, Watkins DI, Hildebrand WH. Rhesus macaque MHC class I molecules present HLA-B-like peptides. J Immunol 2005; 175:367-75. [PMID: 15972670 DOI: 10.4049/jimmunol.175.1.367] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
SIV-infected Indian rhesus macaques (Macaca mulatta) are an important animal model for humans infected with HIV. Understanding macaque (M. mulatta class I (Mamu)) MHC class I-peptide binding facilitates the comparison of SIV- and HIV-specific cellular immune responses. In this study, we characterized the endogenous peptide-binding properties of three Mamu-A (A*02, A*08, A*11) and three Mamu-B (B*01, B*03, B*12) class I molecules. Motif comparisons revealed that five of the six macaque class I molecules (A*02, A*08, A*11, B*01, and B*03) have peptide-binding motifs similar to those of human class I molecules. Of the 65 macaque endogenous peptide ligands that we sequenced by tandem mass spectroscopy, 5 were previously eluted from HLA class I molecules. Nonamers predominated among the individual ligands, and both the motifs and the individual ligands indicated P2, P9, and various ancillary anchors. Interestingly, peptide binding of the Mamu-A and Mamu-B molecules exhibited cross-species peptide-presentation overlap primarily with HLA-B molecules. Indeed, all of the macaque class I molecules appeared HLA-B-like in peptide presentation. Remarkably, the overlap in macaque- and HLA-peptide presentation occurred despite divergent class I peptide-binding grooves. Macaque and human class I differing by up to 42 aa (13-23%) within the alpha-1 and alpha-2 domains, including substantial divergence within specificity pockets A-F, bound the same endogenous peptide. Therefore, endogenous peptide characterization indicates that macaque class I molecules may be the functional equivalents of HLA-B molecules.
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Affiliation(s)
- Heather D Hickman-Miller
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
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48
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Merino E, Montserrat V, Paradela A, López de Castro JA. Two HLA-B14 subtypes (B*1402 and B*1403) differentially associated with ankylosing spondylitis differ substantially in peptide specificity but have limited peptide and T-cell epitope sharing with HLA-B27. J Biol Chem 2005; 280:35868-80. [PMID: 16115862 DOI: 10.1074/jbc.m505641200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The peptide specificity of HLA-B*1403, an allotype associated with ankylosing spondylitis (Lopez-Larrea, C., Mijiyawa, M., Gonzalez, S., Fernandez-Morera, J. L., Blanco-Gelaz, M. A., Martinez-Borra, J., and Lopez-Vazquez, A. (2002) Arthritis Rheum. 46, 2968-2971) was compared with those of the non-associated B*1402 and the prototypic disease-associated B*2705 allotypes. Although differing by a single residue (L156R), B*1402 and B*1403 shared only 32-35% of their peptide repertoires. Subtype-related differences observed in multiple peptide positions, including P3 and P7, were largely explained by a direct effect of the L156R change on peptide specificity. The HLA-B14 subtypes shared only approximately 3% of their peptide repertoires with B*2705. This was due to distinct residue usage at most positions, as revealed by statistical comparison of B*1402, B*1403, and B*2705-bound nonamers. Nevertheless, shared ligands between B*2705 and B*1403 were formally identified, although ligands common to B*2705 and B*1403, but absent from B*1402, were not found. Alloreactive T-cells were used as a tool to analyze epitope sharing among B*1402, B*1403, and B*2705. The percentage of cross-reactive T-cell clones closely paralleled peptide overlap, suggesting that shared ligands tend to maintain their antigenic features when bound to the different allotypes. Our results indicate that B*1403 and B*2705 can present common peptides. However, both the disparity of their peptide repertoires and the lack of binding features shared by these two allotypes, but not B*1402, argue against, although do not exclude, a mechanism of spondyloarthritis mediated by specific ligands of B*2705 and B*1403.
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Affiliation(s)
- Elena Merino
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Facultad de Ciencias, Universidad Autónoma, 28049 Madrid, Spain
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49
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Sesma L, Galocha B, Vázquez M, Purcell AW, Marcilla M, McCluskey J, López de Castro JA. Qualitative and Quantitative Differences in Peptides Bound to HLA-B27 in the Presence of Mouse versus Human Tapasin Define a Role for Tapasin as a Size-Dependent Peptide Editor. J Immunol 2005; 174:7833-44. [PMID: 15944288 DOI: 10.4049/jimmunol.174.12.7833] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Tapasin (Tpn) is a chaperone of the endoplasmic reticulum involved in peptide loading to MHC class I proteins. The influence of mouse Tpn (mTpn) on the HLA-B*2705-bound peptide repertoire was analyzed to characterize the species specificity of this chaperone. B*2705 was expressed on Tpn-deficient human 721.220 cells cotransfected with human (hTpn) or mTpn. The heterodimer to beta(2)-microglobulin-free H chain ratio on the cell surface was reduced with mTpn, suggesting lower B*2705 stability. The B*2705-bound peptide repertoires loaded with hTpn or mTpn shared 94-97% identity, although significant differences in peptide amount were observed in 16-17% of the shared ligands. About 3-6% of peptides were bound only with either hTpn or mTpn. Nonamers differentially bound with mTpn had less suitable anchor residues and bound B*2705 less efficiently in vitro than those loaded only with hTpn or shared nonamers. Decamers showed a different pattern: those found only with mTpn had similarly suitable residues as shared decamers and bound B*2705 with high efficiency. Peptides differentially presented by B*2705 on human or mouse cells showed an analogous pattern of residue suitability, suggesting that the effect of mTpn on B*2705 loading is comparable in both cell types. Thus, mTpn has quantitative and qualitative effects on the B*2705-bound peptide repertoire, impairing presentation of some suitable ligands and allowing others with suboptimal anchor residues and lower affinity to be presented. Our results favor a size-dependent peptide editing role of Tpn for HLA-B*2705 that is species-dependent and suboptimally performed, at least for nonamers, by mTpn.
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Affiliation(s)
- Laura Sesma
- Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid), Facultad de Ciencias, Universidad Autónoma, Madrid, Spain
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50
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Witter K, Volgger A, Zahn R, Scholz S, Albert ED. Bone marrow donor routine HLA typing identified a novel B*07 allele, B*0734, confirmed by allele-specific DNA cycle sequencing. ACTA ACUST UNITED AC 2005; 65:497-9. [PMID: 15853907 DOI: 10.1111/j.1399-0039.2005.00390.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this article, we report the identification of a new human leukocyte antigen-B allele in a sample that was tested in our routine typing for bone marrow donors. This novel allele officially designed B*0734 was found in a female donor of Bavarian Caucasoid origin (Laboratory code 121036). The search for unrelated bone marrow donors was initiated by the Aktion Knochenmarkspende Bayern. In comparison to the common B*070201, B*0734 differs at four nucleotide positions, 412 (G-->A), 539 (G-->T), 559 (G-->A) and 560 (A-->C) causing three amino acid substitutions, at postion 138 Asp-->Asn, at position 180 Arg-->Leu and at position 187 Glu-->Thr.
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Affiliation(s)
- K Witter
- Laboratory of Immunogenetics, University Munich, Paul-Heyse-Strasse 33, 80336 Munich, Germany.
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