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Blunt MD, Fisher H, Schittenhelm RB, Mbiribindi B, Fulton R, Khan S, Espana-Serrano L, Graham LV, Bastidas-Legarda L, Burns D, Khakoo SM, Mansour S, Essex JW, Ayala R, Das J, Purcell AW, Khakoo SI. The nuclear export protein XPO1 provides a peptide ligand for natural killer cells. SCIENCE ADVANCES 2024; 10:eado6566. [PMID: 39178254 PMCID: PMC11343027 DOI: 10.1126/sciadv.ado6566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 07/22/2024] [Indexed: 08/25/2024]
Abstract
XPO1 (Exportin-1/CRM1) is a nuclear export protein that is frequently overexpressed in cancer and functions as a driver of oncogenesis. Currently small molecules that target XPO1 are being used in the clinic as anticancer agents. We identify XPO1 as a target for natural killer (NK) cells. Using immunopeptidomics, we have identified a peptide derived from XPO1 that can be recognized by the activating NK cell receptor KIR2DS2 in the context of human leukocyte antigen-C. The peptide can be endogenously processed and presented to activate NK cells specifically through this receptor. Although high XPO1 expression in cancer is commonly associated with a poor prognosis, we show that the outcome of specific cancers, such as hepatocellular carcinoma, can be substantially improved if there is concomitant evidence of NK cell infiltration. We thus identify XPO1 as a bona fide tumor antigen recognized by NK cells that offers an opportunity for a personalized approach to NK cell therapy for solid tumors.
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Affiliation(s)
- Matthew D. Blunt
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Hayden Fisher
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- School of Chemistry, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, UK
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, UK
| | - Ralf B. Schittenhelm
- Monash Proteomics & Metabolomics Platform, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Berenice Mbiribindi
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Rebecca Fulton
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Sajida Khan
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Laura Espana-Serrano
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Lara V. Graham
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Leidy Bastidas-Legarda
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- School of Chemistry, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, UK
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, UK
- Monash Proteomics & Metabolomics Platform, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute, and The Department of Pediatrics, Pelotonia Institute for Immuno-Oncology, Ohio State University, Columbus, OH, USA
| | - Daniel Burns
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Sophie M.S. Khakoo
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Salah Mansour
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Jonathan W. Essex
- School of Chemistry, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, UK
| | - Rochelle Ayala
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Jayajit Das
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute, and The Department of Pediatrics, Pelotonia Institute for Immuno-Oncology, Ohio State University, Columbus, OH, USA
| | - Anthony W. Purcell
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Salim I. Khakoo
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
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2
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Weisbrod L, Capriotti L, Hofmann M, Spieler V, Dersch H, Voedisch B, Schmidt P, Knake S. FASTMAP-a flexible and scalable immunopeptidomics pipeline for HLA- and antigen-specific T-cell epitope mapping based on artificial antigen-presenting cells. Front Immunol 2024; 15:1386160. [PMID: 38779658 PMCID: PMC11109385 DOI: 10.3389/fimmu.2024.1386160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 04/17/2024] [Indexed: 05/25/2024] Open
Abstract
The study of peptide repertoires presented by major histocompatibility complex (MHC) molecules and the identification of potential T-cell epitopes contribute to a multitude of immunopeptidome-based treatment approaches. Epitope mapping is essential for the development of promising epitope-based approaches in vaccination as well as for innovative therapeutics for autoimmune diseases, infectious diseases, and cancer. It also plays a critical role in the immunogenicity assessment of protein therapeutics with regard to safety and efficacy concerns. The main challenge emerges from the highly polymorphic nature of the human leukocyte antigen (HLA) molecules leading to the requirement of a peptide mapping strategy for a single HLA allele. As many autoimmune diseases are linked to at least one specific antigen, we established FASTMAP, an innovative strategy to transiently co-transfect a single HLA allele combined with a disease-specific antigen into a human cell line. This approach allows the specific identification of HLA-bound peptides using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Using FASTMAP, we found a comparable spectrum of endogenous peptides presented by the most frequently expressed HLA alleles in the world's population compared to what has been described in literature. To ensure a reliable peptide mapping workflow, we combined the HLA alleles with well-known human model antigens like coagulation factor VIII, acetylcholine receptor subunit alpha, protein structures of the SARS-CoV-2 virus, and myelin basic protein. Using these model antigens, we have been able to identify a broad range of peptides that are in line with already published and in silico predicted T-cell epitopes of the specific HLA/model antigen combination. The transient co-expression of a single affinity-tagged MHC molecule combined with a disease-specific antigen in a human cell line in our FASTMAP pipeline provides the opportunity to identify potential T-cell epitopes/endogenously processed MHC-bound peptides in a very cost-effective, fast, and customizable system with high-throughput potential.
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Affiliation(s)
- Luisa Weisbrod
- Recombinant Protein Discovery, CSL Innovation GmbH, Marburg, Germany
| | - Luigi Capriotti
- Analytical Biochemistry, Research and Development, CSL Behring AG, Bern, Switzerland
| | - Marco Hofmann
- Recombinant Protein Discovery, CSL Innovation GmbH, Marburg, Germany
| | - Valerie Spieler
- Recombinant Protein Discovery, CSL Innovation GmbH, Marburg, Germany
| | - Herbert Dersch
- Recombinant Protein Discovery, CSL Innovation GmbH, Marburg, Germany
| | - Bernd Voedisch
- Recombinant Protein Discovery, CSL Innovation GmbH, Marburg, Germany
| | - Peter Schmidt
- Protein Biochemistry, Bio21 Institute, CSL Limited, Parkville, VIC, Australia
| | - Susanne Knake
- Department of Neurology, Epilepsy Center Hessen, Philipps University Marburg, Marburg, Germany
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3
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Tang Z, Wang S, Du L, Hu D, Chen X, Zheng H, Ding H, Chen S, Zhang L, Zhang N. The impact of micropolymorphism in Anpl-UAA on structural stability and peptide presentation. Int J Biol Macromol 2024; 267:131665. [PMID: 38636758 DOI: 10.1016/j.ijbiomac.2024.131665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 04/13/2024] [Accepted: 04/15/2024] [Indexed: 04/20/2024]
Abstract
Micropolymorphism significantly shapes the peptide-binding characteristics of major histocompatibility complex class I (MHC-I) molecules, affecting the host's resistance to pathogens, which is particularly pronounced in avian species displaying the "minimal essential MHC" expression pattern. In this study, we compared two duck MHC-I alleles, Anpl-UAA*77 and Anpl-UAA*78, that exhibit markedly different peptide binding properties despite their high sequence homology. Through mutagenesis experiments and crystallographic analysis of complexes with the influenza virus-derived peptide AEAIIVAMV (AEV9), we identified a critical role for the residue at position 62 in regulating hydrogen-bonding interactions between the peptide backbone and the peptide-binding groove. This modulation affects the characteristics of the B pocket and the stability of the loop region between the 310 helix and the α1 helix, leading to significant changes in the structure and stability of the peptide-MHC-I complex (pMHC-I). Moreover, the proportion of different residues at position 62 among Anpl-UAAs may reflect the correlation between pAnpl-UAA stability and duck body temperature. This research not only advances our understanding of the Anpl-UAA structure but also deepens our insight into the impact of MHC-I micropolymorphism on peptide binding.
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Affiliation(s)
- Ziche Tang
- National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Suqiu Wang
- National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Liubao Du
- National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Dongmei Hu
- National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Xiaoming Chen
- National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Hanyin Zheng
- National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Han Ding
- National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Shiwen Chen
- National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Lin Zhang
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, Shandong, China; Key Laboratory of Livestock and Poultry Multi-omics of MARA, Jinan 250100, Shandong, China.
| | - Nianzhi Zhang
- National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China..
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4
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Jacquot R, Kodjikian L, Chapurlat R, Sève P. Targeted therapies for uveitis in spondyloarthritis: A narrative review. Joint Bone Spine 2024; 91:105697. [PMID: 38309516 DOI: 10.1016/j.jbspin.2024.105697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 01/01/2024] [Accepted: 01/23/2024] [Indexed: 02/05/2024]
Abstract
Spondyloarthritis (SpA) encompasses a group of chronic inflammatory disorders of the joints frequently associated with uveitis in almost a quarter of cases. SpA-related uveitis typically affects the eye anterior chamber with sudden onset, causing pain, redness, photophobia, and blurred vision. Ophthalmologists will describe an acute anterior unilateral uveitis. Most patients present with episodic acute anterior non-granulomatous uveitis and retain excellent visual acuity. However, systemic treatments are recommended in the event of frequent relapses (2-3/year) or in rare cases of sight-threatening with ocular complications. The improved understanding of the pathogenesis of SpA has led to the management of this disease by biologics. Here, we review the main data regarding the opportunity to target specific components in inflammatory pathways for the treatment of SpA-related uveitis. These therapies are recommended for long-term control when uveitis relapses occur too frequently despite conventional systemic treatments. Significant benefits have been obtained with the tumor necrosis factor-α inhibitors (TNFis), particularly infliximab and adalimumab. Paradoxically, a high number of uveitis occurrences have been shown on etanercept. Mixed results have been demonstrated with interleukin-17 antagonists (secukinumab) and interleukin-12/interleukin-23 antagonists (ustekinumab) in cases of failure of TNFis. JAK inhibitors seem to be a valuable class of medications for these patients in the future. Although SpA-related uveitis is typically managed with conventional local and/or systemic treatments, these biological/targeted therapies may provide avenues to control both the underlying SpA and uveitis manifestations. Thus, a close collaboration between patients, rheumatologists, internists, and ophthalmologists is needed to optimally manage ocular inflammation in SpA.
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Affiliation(s)
- Robin Jacquot
- Department of Internal Medicine, Hospices Civils de Lyon, Hôpital Universitaire de la Croix-Rousse, University Claude-Bernard Lyon 1, Lyon, France; Inserm U1290, Research on Healthcare Performance (RESHAPE), University Claude-Bernard Lyon 1, Lyon, France.
| | - Laurent Kodjikian
- Department of Ophthalmology, Hospices Civils de Lyon, Hôpital Universitaire de la Croix-Rousse, University Claude-Bernard Lyon 1, Lyon, France; UMR5510 MATEIS, CNRS, INSA Lyon, University Claude-Bernard Lyon 1, Villeurbanne, France
| | - Roland Chapurlat
- Department of Rheumatology, Hospices Civils de Lyon, Hôpital Universitaire Édouard-Herriot, University Claude-Bernard Lyon 1, Lyon, France
| | - Pascal Sève
- Department of Internal Medicine, Hospices Civils de Lyon, Hôpital Universitaire de la Croix-Rousse, University Claude-Bernard Lyon 1, Lyon, France; Inserm U1290, Research on Healthcare Performance (RESHAPE), University Claude-Bernard Lyon 1, Lyon, France
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5
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van de Sande MGH, Elewaut D. Pathophysiology and immunolgical basis of axial spondyloarthritis. Best Pract Res Clin Rheumatol 2023; 37:101897. [PMID: 38030467 DOI: 10.1016/j.berh.2023.101897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 11/13/2023] [Indexed: 12/01/2023]
Abstract
Over the recent years the wider availability and application of state-of-the-art immunological technologies greatly advanced the insight into the mechanisms that play an important role in axial spondyloarthritis (axSpA) pathophysiology. This increased understanding has facilitated the development of novel treatments that target disease relevant pathways, hereby improving outcome for axSpA patients. In axSpA pathophysiology genetic and environmental factors as well as immune activation by mechanical or bacterial stress resulting in a chronic inflammatory response have a central role. The TNF and IL-23/IL-17 immune pathways play a pivotal role in these disease mechanisms. This review provides an outline of the immunological basis of axSpA with a focus on key genetic risk factors and their link to activation of the pathological immune response, as well as on the role of the gut and entheses in the initiation of inflammation with subsequent new bone formation in axSpA.
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Affiliation(s)
- Marleen G H van de Sande
- Department of Rheumatology & Clinical Immunology and Department of Experimental Immunology, Amsterdam UMC Location University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Infection and Immunity Institute, Amsterdam, the Netherlands; Amsterdam Rheumatology & Immunology Center (ARC), Academic Medical Center, Amsterdam, the Netherlands.
| | - Dirk Elewaut
- Unit Molecular Immunology and Inflammation, VIB Centre for Inflammation Research, Ghent University and Department of Rheumatology, Ghent University Hospital, C. Heymanslaan 10, Ghent, 9000, Belgium.
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6
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Shahbazy M, Ramarathinam SH, Illing PT, Jappe EC, Faridi P, Croft NP, Purcell AW. Benchmarking bioinformatics pipelines in data-independent acquisition mass spectrometry for immunopeptidomics. Mol Cell Proteomics 2023; 22:100515. [PMID: 36796644 PMCID: PMC10060114 DOI: 10.1016/j.mcpro.2023.100515] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 01/26/2023] [Accepted: 02/06/2023] [Indexed: 02/16/2023] Open
Abstract
Immunopeptidomes are the peptide repertoires bound by the molecules encoded by the major histocompatibility complex (MHC) (human leukocyte antigen (HLA) in humans). These HLA-peptide complexes are presented on the cell surface for immune T-cell recognition. Immunopeptidomics denotes the utilization of tandem mass spectrometry (MS/MS) to identify and quantify peptides bound to HLA molecules. Data-independent acquisition (DIA) has emerged as a powerful strategy for quantitative proteomics and deep proteome-wide identification; however, DIA application to immunopeptidomics analyses has so far seen limited use. Further, of the many DIA data processing tools currently available, there is no consensus in the immunopeptidomics community on the most appropriate pipeline(s) for in-depth and accurate HLA peptide identification. Herein, we benchmarked four commonly used spectral library-based DIA pipelines developed for proteomics applications (Skyline, Spectronaut, DIA-NN, and PEAKS) for their ability to perform immunopeptidome quantification. We validated and assessed the capability of each tool to identify and quantify HLA-bound peptides. Generally, DIA-NN and PEAKS provided higher immunopeptidome coverage with more reproducible results. Skyline and Spectronaut conferred more accurate peptide identification with lower experimental false-positive rates. All tools demonstrated reasonable correlations in quantifying precursors of HLA-bound peptides. Our benchmarking study suggests a combined strategy of applying at least two complementary DIA software tools to achieve the greatest degree of confidence and in-depth coverage of immunopeptidome data.
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Affiliation(s)
- Mohammad Shahbazy
- Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Sri H Ramarathinam
- Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Patricia T Illing
- Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Emma C Jappe
- Evaxion Biotech, Bredgade 34E, DK-1260 Copenhagen, Denmark
| | - Pouya Faridi
- Department of Medicine, School of Clinical Sciences, Monash University, Clayton, VIC 3800, Australia.
| | - Nathan P Croft
- Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia.
| | - Anthony W Purcell
- Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia.
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7
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Yang X, Garner LI, Zvyagin IV, Paley MA, Komech EA, Jude KM, Zhao X, Fernandes RA, Hassman LM, Paley GL, Savvides CS, Brackenridge S, Quastel MN, Chudakov DM, Bowness P, Yokoyama WM, McMichael AJ, Gillespie GM, Garcia KC. Autoimmunity-associated T cell receptors recognize HLA-B*27-bound peptides. Nature 2022; 612:771-777. [PMID: 36477533 PMCID: PMC10511244 DOI: 10.1038/s41586-022-05501-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 11/01/2022] [Indexed: 12/12/2022]
Abstract
Human leucocyte antigen B*27 (HLA-B*27) is strongly associated with inflammatory diseases of the spine and pelvis (for example, ankylosing spondylitis (AS)) and the eye (that is, acute anterior uveitis (AAU))1. How HLA-B*27 facilitates disease remains unknown, but one possible mechanism could involve presentation of pathogenic peptides to CD8+ T cells. Here we isolated orphan T cell receptors (TCRs) expressing a disease-associated public β-chain variable region-complementary-determining region 3β (BV9-CDR3β) motif2-4 from blood and synovial fluid T cells from individuals with AS and from the eye in individuals with AAU. These TCRs showed consistent α-chain variable region (AV21) chain pairing and were clonally expanded in the joint and eye. We used HLA-B*27:05 yeast display peptide libraries to identify shared self-peptides and microbial peptides that activated the AS- and AAU-derived TCRs. Structural analysis revealed that TCR cross-reactivity for peptide-MHC was rooted in a shared binding motif present in both self-antigens and microbial antigens that engages the BV9-CDR3β TCRs. These findings support the hypothesis that microbial antigens and self-antigens could play a pathogenic role in HLA-B*27-associated disease.
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Affiliation(s)
- Xinbo Yang
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lee I Garner
- NDM Research Building, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Centre for Immuno-oncology, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Ivan V Zvyagin
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russian Federation
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
| | - Michael A Paley
- Rheumatology Division, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Ekaterina A Komech
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russian Federation
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
| | - Kevin M Jude
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Xiang Zhao
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ricardo A Fernandes
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lynn M Hassman
- Department of Ophthalmology, Washington University School of Medicine, St Louis, MO, USA
| | - Grace L Paley
- Department of Ophthalmology, Washington University School of Medicine, St Louis, MO, USA
| | - Christina S Savvides
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Simon Brackenridge
- NDM Research Building, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Centre for Immuno-oncology, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Max N Quastel
- NDM Research Building, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Centre for Immuno-oncology, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Dmitriy M Chudakov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russian Federation
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
| | - Paul Bowness
- Nuffield Department of Orthopaedics Rheumatology and Muscuoskeletal Science (NDORMS), Botnar Research Center, University of Oxford, Oxford, UK
| | - Wayne M Yokoyama
- Rheumatology Division, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA.
- Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St Louis, MO, USA.
| | - Andrew J McMichael
- NDM Research Building, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Centre for Immuno-oncology, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - Geraldine M Gillespie
- NDM Research Building, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Centre for Immuno-oncology, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
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Xiong Y, Cai M, Xu Y, Dong P, Chen H, He W, Zhang J. Joint together: The etiology and pathogenesis of ankylosing spondylitis. Front Immunol 2022; 13:996103. [PMID: 36325352 PMCID: PMC9619093 DOI: 10.3389/fimmu.2022.996103] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 09/28/2022] [Indexed: 08/16/2023] Open
Abstract
Spondyloarthritis (SpA) refers to a group of diseases with inflammation in joints and spines. In this family, ankylosing spondylitis (AS) is a rare but classic form that mainly involves the spine and sacroiliac joint, leading to the loss of flexibility and fusion of the spine. Compared to other diseases in SpA, AS has a very distinct hereditary disposition and pattern of involvement, and several hypotheses about its etiopathogenesis have been proposed. In spite of significant advances made in Th17 dynamics and AS treatment, the underlying mechanism remains concealed. To this end, we covered several topics, including the nature of the immune response, the microenvironment in the articulation that is behind the disease's progression, and the split between the hypotheses and the evidence on how the intestine affects arthritis. In this review, we describe the current findings of AS and SpA, with the aim of providing an integrated view of the initiation of inflammation and the development of the disease.
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Affiliation(s)
- Yuehan Xiong
- Department of Immunology, Chinese Academy of Medical Sciences (CAMS) Key Laboratory of T Cell and Cancer Immunotherapy, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) and School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Menghua Cai
- Department of Immunology, Chinese Academy of Medical Sciences (CAMS) Key Laboratory of T Cell and Cancer Immunotherapy, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) and School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Yi Xu
- Department of Immunology, Chinese Academy of Medical Sciences (CAMS) Key Laboratory of T Cell and Cancer Immunotherapy, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) and School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Peng Dong
- Changzhou Xitaihu Institute for Frontier Technology of Cell Therapy, Changzhou, China
| | - Hui Chen
- Department of Immunology, Chinese Academy of Medical Sciences (CAMS) Key Laboratory of T Cell and Cancer Immunotherapy, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) and School of Basic Medicine, Peking Union Medical College, Beijing, China
- Changzhou Xitaihu Institute for Frontier Technology of Cell Therapy, Changzhou, China
| | - Wei He
- Department of Immunology, Chinese Academy of Medical Sciences (CAMS) Key Laboratory of T Cell and Cancer Immunotherapy, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) and School of Basic Medicine, Peking Union Medical College, Beijing, China
- Changzhou Xitaihu Institute for Frontier Technology of Cell Therapy, Changzhou, China
| | - Jianmin Zhang
- Department of Immunology, Chinese Academy of Medical Sciences (CAMS) Key Laboratory of T Cell and Cancer Immunotherapy, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) and School of Basic Medicine, Peking Union Medical College, Beijing, China
- Changzhou Xitaihu Institute for Frontier Technology of Cell Therapy, Changzhou, China
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9
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Garrido-Mesa J, Brown MA. T cell Repertoire Profiling and the Mechanism by which HLA-B27 Causes Ankylosing Spondylitis. Curr Rheumatol Rep 2022; 24:398-410. [PMID: 36197645 PMCID: PMC9666335 DOI: 10.1007/s11926-022-01090-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/25/2022] [Indexed: 11/25/2022]
Abstract
Purpose of Review Ankylosing spondylitis (AS) is strongly associated with the HLA-B27 gene. The canonical function of HLA-B27 is to present antigenic peptides to CD8 lymphocytes, leading to adaptive immune responses. The ‘arthritogenic peptide’ theory as to the mechanism by which HLA-B27 induces ankylosing spondylitis proposes that HLA-B27 presents peptides derived from exogenous sources such as bacteria to CD8 lymphocytes, which subsequently cross-react with antigens at the site of inflammation of the disease, causing inflammation. This review describes findings of studies in AS involving profiling of T cell expansions and discusses future research opportunities based on these findings. Recent Findings Consistent with this theory, there is an expanding body of data showing that expansion of a restricted pool of CD8 lymphocytes is found in most AS patients yet only in a small proportion of healthy HLA-B27 carriers. Summary These exciting findings strongly support the theory that AS is driven by presentation of antigenic peptides to the adaptive immune system by HLA-B27. They point to new potential approaches to identify the exogenous and endogenous antigens involved and to potential therapies for the disease.
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Affiliation(s)
- Jose Garrido-Mesa
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, England
| | - Matthew A Brown
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, England.
- Genomics England, Charterhouse Square, London, EC1M 6BQ, England.
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10
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Hensen L, Illing PT, Rowntree LC, Davies J, Miller A, Tong SYC, Habel JR, van de Sandt CE, Flanagan K, Purcell AW, Kedzierska K, Clemens EB. T Cell Epitope Discovery in the Context of Distinct and Unique Indigenous HLA Profiles. Front Immunol 2022; 13:812393. [PMID: 35603215 PMCID: PMC9121770 DOI: 10.3389/fimmu.2022.812393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
CD8+ T cells are a pivotal part of the immune response to viruses, playing a key role in disease outcome and providing long-lasting immunity to conserved pathogen epitopes. Understanding CD8+ T cell immunity in humans is complex due to CD8+ T cell restriction by highly polymorphic Human Leukocyte Antigen (HLA) proteins, requiring T cell epitopes to be defined for different HLA allotypes across different ethnicities. Here we evaluate strategies that have been developed to facilitate epitope identification and study immunogenic T cell responses. We describe an immunopeptidomics approach to sequence HLA-bound peptides presented on virus-infected cells by liquid chromatography with tandem mass spectrometry (LC-MS/MS). Using antigen presenting cell lines that stably express the HLA alleles characteristic of Indigenous Australians, this approach has been successfully used to comprehensively identify influenza-specific CD8+ T cell epitopes restricted by HLA allotypes predominant in Indigenous Australians, including HLA-A*24:02 and HLA-A*11:01. This is an essential step in ensuring high vaccine coverage and efficacy in Indigenous populations globally, known to be at high risk from influenza disease and other respiratory infections.
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Affiliation(s)
- Luca Hensen
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Patricia T. Illing
- Department of Biochemistry and Molecular Biology & Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Louise C. Rowntree
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Jane Davies
- Menzies School of Health Research, Darwin, NT, Australia
| | - Adrian Miller
- Indigenous Engagement, CQUniversity, Townsville, QLD, Australia
| | - Steven Y. C. Tong
- Menzies School of Health Research, Darwin, NT, Australia
- Victorian Infectious Diseases Service, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Jennifer R. Habel
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Carolien E. van de Sandt
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Katie L. Flanagan
- Department of Infectious Diseases and Tasmanian Vaccine Trial Centre, Launceston General Hospital, Launceston, TAS, Australia
- School of Health Sciences and School of Medicine, University of Tasmania, Launceston, TAS, Australia
- Department of Immunology and Pathology, Monash University, Melbourne, VIC, Australia
- School of Health and Biomedical Science, RMIT University, Melbourne, VIC, Australia
| | - Anthony W. Purcell
- Department of Biochemistry and Molecular Biology & Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - E. Bridie Clemens
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
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11
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Tay SH, Yeo JG, Leong JY, Albani S, Arkachaisri T. Juvenile Spondyloarthritis: What More Do We Know About HLA-B27, Enthesitis, and New Bone Formation? Front Med (Lausanne) 2021; 8:666772. [PMID: 34095174 PMCID: PMC8174582 DOI: 10.3389/fmed.2021.666772] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 04/20/2021] [Indexed: 12/13/2022] Open
Abstract
Juvenile spondyloarthritis (JSpA) refers to a diverse spectrum of immune-mediated inflammatory arthritides whose onset occurs in late childhood and adolescence. Like its adult counterpart, JSpA is typified by a strong association with human leukocyte antigen-B27 (HLA-B27) and potential axial involvement, while lacking rheumatoid factor (RF) and distinguishing autoantibodies. A characteristic manifestation of JSpA is enthesitis (inflammation of insertion sites of tendons, ligaments, joint capsules or fascia to bone), which is commonly accompanied by bone resorption and new bone formation at affected sites. In this Review, advances in the role of HLA-B27, enthesitis and its associated osteoproliferation in JSpA pathophysiology and treatment options will be discussed. A deeper appreciation of how these elements contribute to the JSpA disease mechanism will better inform diagnosis, prognosis and therapy, which in turn translates to an improved quality of life for patients.
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Affiliation(s)
- Shi Huan Tay
- SingHealth Duke-National University of Singapore Academic Medical Centre, Translational Immunology Institute, Singapore, Singapore.,Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Joo Guan Yeo
- SingHealth Duke-National University of Singapore Academic Medical Centre, Translational Immunology Institute, Singapore, Singapore.,Duke-National University of Singapore Medical School, Singapore, Singapore.,Rheumatology and Immunology Service, Department of Pediatric Subspecialties, KK Women's and Children's Hospital, Singapore, Singapore
| | - Jing Yao Leong
- SingHealth Duke-National University of Singapore Academic Medical Centre, Translational Immunology Institute, Singapore, Singapore.,Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Salvatore Albani
- SingHealth Duke-National University of Singapore Academic Medical Centre, Translational Immunology Institute, Singapore, Singapore.,Duke-National University of Singapore Medical School, Singapore, Singapore.,Rheumatology and Immunology Service, Department of Pediatric Subspecialties, KK Women's and Children's Hospital, Singapore, Singapore
| | - Thaschawee Arkachaisri
- Duke-National University of Singapore Medical School, Singapore, Singapore.,Rheumatology and Immunology Service, Department of Pediatric Subspecialties, KK Women's and Children's Hospital, Singapore, Singapore
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12
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Pak H, Michaux J, Huber F, Chong C, Stevenson BJ, Müller M, Coukos G, Bassani-Sternberg M. Sensitive Immunopeptidomics by Leveraging Available Large-Scale Multi-HLA Spectral Libraries, Data-Independent Acquisition, and MS/MS Prediction. Mol Cell Proteomics 2021; 20:100080. [PMID: 33845167 PMCID: PMC8724634 DOI: 10.1016/j.mcpro.2021.100080] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 03/18/2021] [Accepted: 04/05/2021] [Indexed: 12/15/2022] Open
Abstract
Mass spectrometry (MS) is the state-of-the-art methodology for capturing the breadth and depth of the immunopeptidome across human leukocyte antigen (HLA) allotypes and cell types. The majority of studies in the immunopeptidomics field are discovery driven. Hence, data-dependent tandem MS (MS/MS) acquisition (DDA) is widely used, as it generates high-quality references of peptide fingerprints. However, DDA suffers from the stochastic selection of abundant ions that impairs sensitivity and reproducibility. In contrast, in data-independent acquisition (DIA), the systematic fragmentation and acquisition of all fragment ions within given isolation m/z windows yield a comprehensive map for a given sample. However, many DIA approaches commonly require generating comprehensive DDA-based spectrum libraries, which can become impractical for studying noncanonical and personalized neoantigens. Because the amount of HLA peptides eluted from biological samples such as small tissue biopsies is typically not sufficient for acquiring both meaningful DDA data necessary for generating comprehensive spectral libraries and DIA MS measurements, the implementation of DIA in the immunopeptidomics translational research domain has remained limited. We implemented a DIA immunopeptidomics workflow and assessed its sensitivity and accuracy by matching DIA data against libraries with growing complexity-from sample-specific libraries to libraries combining 2 to 40 different immunopeptidomics samples. Analyzing DIA immunopeptidomics data against a complex multi-HLA spectral library resulted in a two-fold increase in peptide identification compared with sample-specific library and in a three-fold increase compared with DDA measurements, yet with no detrimental effect on the specificity. Furthermore, we demonstrated the implementation of DIA for sensitive personalized neoantigen discovery through the analysis of DIA data with predicted MS/MS spectra of clinically relevant HLA ligands. We conclude that a comprehensive multi-HLA library for DIA approach in combination with MS/MS prediction is highly advantageous for clinical immunopeptidomics, especially when low amounts of biological samples are available.
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Affiliation(s)
- HuiSong Pak
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital and the University of Lausanne, Lausanne, Switzerland
| | - Justine Michaux
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital and the University of Lausanne, Lausanne, Switzerland
| | - Florian Huber
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital and the University of Lausanne, Lausanne, Switzerland
| | - Chloe Chong
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital and the University of Lausanne, Lausanne, Switzerland
| | | | - Markus Müller
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital and the University of Lausanne, Lausanne, Switzerland; SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - George Coukos
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital and the University of Lausanne, Lausanne, Switzerland
| | - Michal Bassani-Sternberg
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital and the University of Lausanne, Lausanne, Switzerland.
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13
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Wei X, Wang S, Li Z, Li Z, Qu Z, Wang S, Zou B, Liang R, Xia C, Zhang N. Peptidomes and Structures Illustrate Two Distinguishing Mechanisms of Alternating the Peptide Plasticity Caused by Swine MHC Class I Micropolymorphism. Front Immunol 2021; 12:592447. [PMID: 33717070 PMCID: PMC7952875 DOI: 10.3389/fimmu.2021.592447] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 01/13/2021] [Indexed: 01/24/2023] Open
Abstract
The micropolymorphism of major histocompatibility complex class I (MHC-I) can greatly alter the plasticity of peptide presentation, but elucidating the underlying mechanism remains a challenge. Here we investigated the impact of the micropolymorphism on peptide presentation of swine MHC-I (termed swine leukocyte antigen class I, SLA-I) molecules via immunopeptidomes that were determined by our newly developed random peptide library combined with the mass spectrometry (MS) de novo sequencing method (termed RPLD–MS) and the corresponding crystal structures. The immunopeptidomes of SLA-1*04:01, SLA-1*13:01, and their mutants showed that mutations of residues 156 and 99 could expand and narrow the ranges of peptides presented by SLA-I molecules, respectively. R156A mutation of SLA-1*04:01 altered the charge properties and enlarged the volume size of pocket D, which eliminated the harsh restriction to accommodate the third (P3) anchor residue of the peptide and expanded the peptide binding scope. Compared with 99Tyr of SLA-1*0401, 99Phe of SLA-1*13:01 could not form a conservative hydrogen bond with the backbone of the P3 residues, leading to fewer changes in the pocket properties but a significant decrease in quantitative of immunopeptidomes. This absent force could be compensated by the salt bridge formed by P1-E and 170Arg. These data illustrate two distinguishing manners that show how micropolymorphism alters the peptide-binding plasticity of SLA-I alleles, verifying the sensitivity and accuracy of the RPLD-MS method for determining the peptide binding characteristics of MHC-I in vitro and helping to more accurately predict and identify MHC-I restricted epitopes.
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Affiliation(s)
- Xiaohui Wei
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Song Wang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Zhuolin Li
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Zibin Li
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Zehui Qu
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Suqiu Wang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Baohua Zou
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Ruiying Liang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Chun Xia
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China.,Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, China Agricultural University, Beijing, China
| | - Nianzhi Zhang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
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14
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Nakamura A, Boroojeni SF, Haroon N. Aberrant antigen processing and presentation: Key pathogenic factors leading to immune activation in Ankylosing spondylitis. Semin Immunopathol 2021; 43:245-253. [PMID: 33532928 DOI: 10.1007/s00281-020-00833-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 12/18/2020] [Indexed: 12/12/2022]
Abstract
The strong association of HLA-B*27 with ankylosing spondylitis (AS) was first reported nearly 50 years ago. However, the mechanistic link between HLA-B*27 and AS has remained an enigma. While 85-90% of AS patients possess HLA-B*27, majority of HLA-B*27 healthy individuals do not develop AS. This suggests that additional genes and genetic regions interplay with HLA-B*27 to cause AS. Previous genome-wide association studies (GWAS) identified key genes that are distinctively expressed in AS, including the Endoplasmic Reticulum Aminopeptidase (ERAP) 1 and ERAP2. As these gene-encoding molecules are primarily implicated in the process of peptide processing and presentation, potential pathological interaction of these molecules with HLA-B*27 may operate to cause AS by activating downstream immune responses. The aberrant peptide processing also gives rise to the accumulation of unstable protein complex in endoplasmic reticulum (ER), which drives endoplasmic reticulum-associated protein degradation (ERAD) and unfolded protein response (UPR) and activates autophagy. In this review, we describe the current hypotheses of AS pathogenesis, focusing on antigen processing and presentation operated by HLA-B*27 and associated molecules that may contribute to the disease initiation and progression of AS.
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Affiliation(s)
- Akihiro Nakamura
- Schroeder Arthritis Institute, University Health Network, Toronto, Ontario, Canada.,Spondylitis Program, University Health Network, Toronto, Ontario, Canada.,Division of Genetics and Development, Krembil Research Institute, University Health Network, 60 Leonard Avenue, Toronto, Ontario, M5T 2S8, Canada.,Division of Rheumatology, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada.,Institute of Medical Science, Department of Medicine, University of Toronto, 399 Bathurst Street, Toronto, Ontario, M5T 2S8, Canada
| | - Shaghayegh Foroozan Boroojeni
- Schroeder Arthritis Institute, University Health Network, Toronto, Ontario, Canada.,Spondylitis Program, University Health Network, Toronto, Ontario, Canada.,Division of Genetics and Development, Krembil Research Institute, University Health Network, 60 Leonard Avenue, Toronto, Ontario, M5T 2S8, Canada.,Institute of Medical Science, Department of Medicine, University of Toronto, 399 Bathurst Street, Toronto, Ontario, M5T 2S8, Canada
| | - Nigil Haroon
- Schroeder Arthritis Institute, University Health Network, Toronto, Ontario, Canada. .,Spondylitis Program, University Health Network, Toronto, Ontario, Canada. .,Division of Genetics and Development, Krembil Research Institute, University Health Network, 60 Leonard Avenue, Toronto, Ontario, M5T 2S8, Canada. .,Division of Rheumatology, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada. .,Institute of Medical Science, Department of Medicine, University of Toronto, 399 Bathurst Street, Toronto, Ontario, M5T 2S8, Canada.
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15
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Wakefield D, Clarke D, McCluskey P. Recent Developments in HLA B27 Anterior Uveitis. Front Immunol 2021; 11:608134. [PMID: 33469457 PMCID: PMC7813675 DOI: 10.3389/fimmu.2020.608134] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 11/23/2020] [Indexed: 02/03/2023] Open
Abstract
There has been steady progress in understanding the pathogenesis, clinical features, and effective treatment of acute anterior uveitis (AU) over the past 5 years. Large gene wide association studies have confirmed that AU is a polygenic disease, with overlaps with the seronegative arthropathies and inflammatory bowel diseases, associations that have been repeatedly confirmed in clinical studies. The role of the microbiome in AU has received increased research attention, with recent evidence indicating that human leukocyte antigen B27 (HLA B27) may influence the composition of the gut microbiome in experimental animals. Extensive clinical investigations have confirmed the typical features of acute AU (AAU) and its response to topical, regional and systemic immunosuppressive treatment. Increased understanding of the role of cytokines has resulted in studies confirming the value of anti-cytokine therapy [anti-tumor necrosis factor (anti-TNF) and interleukin 6 (IL-6) therapy] in severe and recurrent cases of AAU, particularly in subjects with an associated spondyloarthopathy (SpA) and in juvenile idiopathic arthritis (JIA)-associated AAU.
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Affiliation(s)
- Denis Wakefield
- Faculty of Medicine, University of NSW Sydney, Kensington, NSW, Australia
- NSW Health Pathology and South Eastern Sydney, LHD, Sydney, NSW, Australia
| | - Daniel Clarke
- Department of Medicine, South Eastern Sydney, LHD, Sydney, NSW, Australia
| | - Peter McCluskey
- Save Sight Institute, The University of Sydney, Sydney, NSW, Australia
- Discipline of Clinical Ophthalmology and Eye Health, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
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16
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Rademacher J, Poddubnyy D, Pleyer U. Uveitis in spondyloarthritis. Ther Adv Musculoskelet Dis 2020; 12:1759720X20951733. [PMID: 32963592 PMCID: PMC7488890 DOI: 10.1177/1759720x20951733] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 07/30/2020] [Indexed: 12/17/2022] Open
Abstract
Uveitis is the most frequent extra-articular manifestation of axial spondyloarthritis (SpA), occurring in up to one-third of the patients. In the majority of patients, uveitis is acute, anterior and unilateral and presents with photosensitivity, sudden onset of pain and blurred vision. Topical steroids are an effective treatment; however, recurrent or refractory cases may need conventional disease-modifying antirheumatic drugs or biological treatment with monoclonal tumor necrosis factor (TNF) inhibitors, thus also influencing treatment strategy of the underlying SpA. Though the exact pathogenesis of SpA and uveitis remains unknown, both seem to result from the interaction of a specific, mostly shared genetical background (among other HLA-B27 positivity), external influences such as microbiome, bacterial infection or mechanical stress and activation of the immune system resulting in inflammation. Up to 40% of patients presenting with acute anterior uveitis (AAU) have an undiagnosed SpA. Therefore, an effective referral strategy for AAU patients is needed to shorten the diagnostic delay of SpA and enable an early effective treatment. Further, the risk for ophthalmological manifestations increases with the disease duration in SpA; and patients presenting with ocular symptoms should be referred to an ophthalmologist. Thus, a close collaboration between patient, rheumatologist and ophthalmologist is needed to optimally manage ocular inflammation in SpA.
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Affiliation(s)
- Judith Rademacher
- Department of Gastroenterology, Infectiology and Rheumatology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Hindenburgdamm 30, Berlin, 10117, Germany
| | - Denis Poddubnyy
- Department of Gastroenterology, Infectiology and Rheumatology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Uwe Pleyer
- Department of Ophthalmology, Campus Virchow, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
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17
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HLA risk alleles and gut microbiome in ankylosing spondylitis and rheumatoid arthritis. Best Pract Res Clin Rheumatol 2019; 33:101499. [DOI: 10.1016/j.berh.2020.101499] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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18
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Ternette N, Purcell AW. Immunopeptidomics Special Issue. Proteomics 2019; 18:e1800145. [PMID: 29949244 DOI: 10.1002/pmic.201800145] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 06/04/2018] [Indexed: 12/29/2022]
Affiliation(s)
- Nicola Ternette
- The Jenner Institute, Target Discovery Institute Mass Spectrometry Laboratory, University of Oxford, OX3, 7FZ, UK
| | - Anthony W Purcell
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia
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19
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Driller R, Ballaschk M, Schmieder P, Uchanska-Ziegler B, Ziegler A, Loll B. Metal-triggered conformational reorientation of a self-peptide bound to a disease-associated HLA-B*27 subtype. J Biol Chem 2019; 294:13269-13279. [PMID: 31296658 DOI: 10.1074/jbc.ra119.008937] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 07/08/2019] [Indexed: 01/03/2023] Open
Abstract
Conformational changes of major histocompatibility complex (MHC) antigens have the potential to be recognized by T cells and may arise from polymorphic variation of the MHC molecule, the binding of modifying ligands, or both. Here, we investigated whether metal ions could affect allele-dependent structural variation of the two minimally distinct human leukocyte antigen (HLA)-B*27:05 and HLA-B*27:09 subtypes, which exhibit differential association with the rheumatic disease ankylosing spondylitis (AS). We employed NMR spectroscopy and X-ray crystallography coupled with ensemble refinement to study the AS-associated HLA-B*27:05 subtype and the AS-nonassociated HLA-B* 27:09 in complex with the self-peptide pVIPR (RRKWRRWHL). Both techniques revealed that pVIPR exhibits a higher degree of flexibility when complexed with HLA-B*27:05 than with HLA-B*27:09. Furthermore, we found that the binding of the metal ion Cu2+ or Ni2+, but not Mn2+, Zn2+, or Hg2+, affects the structure of a pVIPR-bound HLA-B*27 molecule in a subtype-dependent manner. In HLA-B*27:05, the metals triggered conformational reorientations of pVIPR, but no such structural changes were observed in the HLA-B*27:09 subtype, with or without bound metal ion. These observations provide the first demonstration that not only major histocompatibility complex class II, but also class I, molecules can undergo metal ion-induced conformational alterations. Our findings suggest that metals may have a role in triggering rheumatic diseases such as AS and also have implications for the molecular basis of metal-induced hypersensitivities and allergies.
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Affiliation(s)
- Ronja Driller
- Institut für Chemie/Biochemie, AG Strukturbiochemie, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany
| | - Martin Ballaschk
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Peter Schmieder
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Barbara Uchanska-Ziegler
- Institut für Immungenetik, Charité-Universitätsmedizin Berlin, Freie Universität Berlin, Thielallee 73, 14195 Berlin, Germany; Ziegler Biosolutions, Fahrgasse 5, 79761 Waldshut-Tiengen, Germany
| | - Andreas Ziegler
- Ziegler Biosolutions, Fahrgasse 5, 79761 Waldshut-Tiengen, Germany.
| | - Bernhard Loll
- Institut für Chemie/Biochemie, AG Strukturbiochemie, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany; MoloX GmbH, Takustrasse 6, 14195 Berlin, Germany.
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20
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Shraibman B, Barnea E, Kadosh DM, Haimovich Y, Slobodin G, Rosner I, López-Larrea C, Hilf N, Kuttruff S, Song C, Britten C, Castle J, Kreiter S, Frenzel K, Tatagiba M, Tabatabai G, Dietrich PY, Dutoit V, Wick W, Platten M, Winkler F, von Deimling A, Kroep J, Sahuquillo J, Martinez-Ricarte F, Rodon J, Lassen U, Ottensmeier C, van der Burg SH, Thor Straten P, Poulsen HS, Ponsati B, Okada H, Rammensee HG, Sahin U, Singh H, Admon A. Identification of Tumor Antigens Among the HLA Peptidomes of Glioblastoma Tumors and Plasma. Mol Cell Proteomics 2019; 18:1255-1268. [PMID: 31154438 PMCID: PMC6553928 DOI: 10.1074/mcp.ra119.001524] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Indexed: 12/24/2022] Open
Abstract
Glioblastoma multiforme (GBM) is the most aggressive brain tumor with poor prognosis to most patients. Immunotherapy of GBM is a potentially beneficial treatment option, whose optimal implementation may depend on familiarity with tumor specific antigens, presented as HLA peptides by the GBM cells. Further, early detection of GBM, such as by a routine blood test, may improve survival, even with the current treatment modalities. This study includes large-scale analyses of the HLA peptidome (immunopeptidome) of the plasma-soluble HLA molecules (sHLA) of 142 plasma samples, and the membranal HLA of GBM tumors of 10 of these patients' tumor samples. Tumor samples were fresh-frozen immediately after surgery and the plasma samples were collected before, and at multiple visits after surgery. In total, this HLA peptidome analysis involved 52 different HLA allotypes and resulted in the identification of more than 35,000 different HLA peptides. Strong correlations were observed in the signal intensities and in the repertoires of identified peptides between the tumors and plasma-soluble HLA peptidomes of the individual patients, whereas low correlations were observed between these HLA peptidomes and the tumors' proteomes. HLA peptides derived from Cancer/Testis Antigens (CTAs) were selected based on their presence among the HLA peptidomes of the patients and absence of expression of their source genes from any healthy and essential human tissues, except from immune-privileged sites. Additionally, peptides were selected as potential biomarkers if their levels in the plasma-sHLA peptidome were significantly reduced after the removal of tumor mass. The CTAs identified among the analyzed HLA peptidomes provide new opportunities for personalized immunotherapy and for early diagnosis of GBM.
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Affiliation(s)
- Bracha Shraibman
- From the ‡Department of Biology, Technion, Israel Institute of Technology, Haifa 32000, Israel
| | - Eilon Barnea
- From the ‡Department of Biology, Technion, Israel Institute of Technology, Haifa 32000, Israel
| | - Dganit Melamed Kadosh
- From the ‡Department of Biology, Technion, Israel Institute of Technology, Haifa 32000, Israel
| | - Yael Haimovich
- From the ‡Department of Biology, Technion, Israel Institute of Technology, Haifa 32000, Israel
| | - Gleb Slobodin
- §Rheumatology Unit, Bnai Zion Medical Center, Haifa 31048, Israel
| | - Itzhak Rosner
- §Rheumatology Unit, Bnai Zion Medical Center, Haifa 31048, Israel
| | | | - Norbert Hilf
- ‖Immatics Biotechnologies GmbH, Paul-Ehrlich-Str. 15,72076 Tuebingen, Germany
| | - Sabrina Kuttruff
- ‖Immatics Biotechnologies GmbH, Paul-Ehrlich-Str. 15,72076 Tuebingen, Germany
| | - Colette Song
- ‖Immatics Biotechnologies GmbH, Paul-Ehrlich-Str. 15,72076 Tuebingen, Germany
| | - Cedrik Britten
- **BioNTech AG, Holderlinstr. 8,55131 Mainz, Germany
- ¶¶¶Association for Cancer Immunotherapy (CIMT), Langenbeckstr. 1,55131 Mainz, Germany
| | - John Castle
- **BioNTech AG, Holderlinstr. 8,55131 Mainz, Germany
| | | | | | - Marcos Tatagiba
- ‡‡Eberhard Karls Universität Tübingen, Department of Immunology, Auf der Morgenstelle 15,72076 Tubingen, Germany
| | - Ghazaleh Tabatabai
- ‡‡Eberhard Karls Universität Tübingen, Department of Immunology, Auf der Morgenstelle 15,72076 Tubingen, Germany
| | - Pierre-Yves Dietrich
- §§Université de Genève, Rue Gabrielle Perret Gentil 4; 1211 Geneve 14, Switzerland
| | - Valérie Dutoit
- §§Université de Genève, Rue Gabrielle Perret Gentil 4; 1211 Geneve 14, Switzerland
| | - Wolfgang Wick
- ¶¶Heidelberg University Medical Center, Im Neuenheimer Feld 672, D-69120 Heidelberg, Germany
| | - Michael Platten
- ¶¶Heidelberg University Medical Center, Im Neuenheimer Feld 672, D-69120 Heidelberg, Germany
| | - Frank Winkler
- ¶¶Heidelberg University Medical Center, Im Neuenheimer Feld 672, D-69120 Heidelberg, Germany
| | - Andreas von Deimling
- ¶¶Heidelberg University Medical Center, Im Neuenheimer Feld 672, D-69120 Heidelberg, Germany
| | - Judith Kroep
- ‖‖Leiden University Medical Center, Department of Medical Oncology, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Juan Sahuquillo
- ‡‡‡Vall d'Hebron University Hospital, Institut Catala de la Salut, Pg. Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Francisco Martinez-Ricarte
- ‡‡‡Vall d'Hebron University Hospital, Institut Catala de la Salut, Pg. Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Jordi Rodon
- ‡‡‡Vall d'Hebron University Hospital, Institut Catala de la Salut, Pg. Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Ulrik Lassen
- ‖‖‖Region Hovedstaden (Center for Cancer Immune Therapy (CCIT), Herlev Hospital, Herlev Ringvej 75, DK-2730, Copenhagen, Denmark
| | - Christian Ottensmeier
- §§§Cancer Sciences Division, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Sjoerd H van der Burg
- ‖‖Leiden University Medical Center, Department of Medical Oncology, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
- ¶¶¶Association for Cancer Immunotherapy (CIMT), Langenbeckstr. 1,55131 Mainz, Germany
| | - Per Thor Straten
- ‖‖‖Region Hovedstaden (Center for Cancer Immune Therapy (CCIT), Herlev Hospital, Herlev Ringvej 75, DK-2730, Copenhagen, Denmark
| | - Hans Skovgaard Poulsen
- ‡‡‡‡Rigshospitalet, Departments of Radiation Biology and Oncology, Rigshospitalet 9, Blegdamsvej, DK-2100, Copenhagen, Denmark
| | - Berta Ponsati
- §§§§BCN Peptides, Pol. Ind. Els Vinyets-Els Fogars II. 08777 Sant Quinti de Mediona (Barcelona), Spain
| | - Hideho Okada
- ¶¶¶¶University of California and the Parker Institute for Cancer Immunotherapy, San Francisco, CA 94131
| | - Hans-Georg Rammensee
- ‡‡Eberhard Karls Universität Tübingen, Department of Immunology, Auf der Morgenstelle 15,72076 Tubingen, Germany
| | - Ugur Sahin
- **BioNTech AG, Holderlinstr. 8,55131 Mainz, Germany
| | - Harpreet Singh
- ‖Immatics Biotechnologies GmbH, Paul-Ehrlich-Str. 15,72076 Tuebingen, Germany
| | - Arie Admon
- From the ‡Department of Biology, Technion, Israel Institute of Technology, Haifa 32000, Israel;
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21
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Purcell AW, Ramarathinam SH, Ternette N. Mass spectrometry-based identification of MHC-bound peptides for immunopeptidomics. Nat Protoc 2019; 14:1687-1707. [PMID: 31092913 DOI: 10.1038/s41596-019-0133-y] [Citation(s) in RCA: 190] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 01/08/2019] [Indexed: 01/13/2023]
Abstract
Peptide antigens bound to molecules encoded by the major histocompatibility complex (MHC) and presented on the cell surface form the targets of T lymphocytes. This critical arm of the adaptive immune system facilitates the eradication of pathogen-infected and cancerous cells, as well as the production of antibodies. Methods to identify these peptide antigens are critical to the development of new vaccines, for which the goal is the generation of effective adaptive immune responses and long-lasting immune memory. Here, we describe a robust protocol for the identification of MHC-bound peptides from cell lines and tissues, using nano-ultra-performance liquid chromatography coupled to high-resolution mass spectrometry (nUPLC-MS/MS) and recent improvements in methods for isolation and characterization of these peptides. The protocol starts with the immunoaffinity capture of naturally processed MHC-peptide complexes. The peptides dissociate from the class I human leukocyte antigens (HLAs) upon acid denaturation. This peptide cargo is then extracted and separated into fractions by HPLC, and the peptides in these fractions are identified using nUPLC-MS/MS. With this protocol, several thousand peptides can be identified from a wide variety of cell types, including cancerous and infected cells and those from tissues, with a turnaround time of 2-3 d.
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Affiliation(s)
- Anthony W Purcell
- Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.
| | - Sri H Ramarathinam
- Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Nicola Ternette
- The Jenner Institute, Mass Spectrometry Laboratory, Target Discovery Institute, University of Oxford, Oxford, UK.
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22
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Paladini F, Fiorillo MT, Tedeschi V, Cauli A, Mathieu A, Sorrentino R. Ankylosing Spondylitis: A Trade Off of HLA-B27, ERAP, and Pathogen Interconnections? Focus on Sardinia. Front Immunol 2019; 10:35. [PMID: 30740100 PMCID: PMC6355666 DOI: 10.3389/fimmu.2019.00035] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 01/08/2019] [Indexed: 01/04/2023] Open
Abstract
The frequency of HLA-B27 in patients with Ankylosing Spondylitis (AS) is over 85%. There are more than 170 recognized HLA-B27 alleles but the majority of them is not sufficiently represented for genetic association studies. So far only two alleles, the HLA-B*2706 in Asia and the HLA-B*2709 in Sardinia, have not been found to be associated with AS. The highly homogenous genetic structure of the Sardinian population has favored the search of relevant variants for disease-association studies. Moreover, malaria, once endemic in the island, has been shown to have contributed to shape the native population genome affecting the relative allele frequency of relevant genes. In Sardinia, the prevalence of HLA-B*2709, which differs from the strongly AS-associated B*2705 prototype for one amino acid (His/Asp116) in the F pocket of the peptide binding groove, is around 20% of all HLA-B27 alleles. We have previously hypothesized that malaria could have contributed to the establishment of this allele in Sardinia. Based on our recent findings, in this perspective article we speculate that the Endoplasmic Reticulum Amino Peptidases, ERAP1 and 2, associated with AS and involved in antigen presentation, underwent co-selection by malaria. These genes, besides shaping the immunopeptidome of HLA-class I molecules, have other biological functions that could also be involved in the immunosurveillance against malaria.
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Affiliation(s)
- Fabiana Paladini
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University, Rome, Italy
| | - Maria Teresa Fiorillo
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University, Rome, Italy
| | - Valentina Tedeschi
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University, Rome, Italy
| | - Alberto Cauli
- Department of Medical Sciences and Public Health, Chair of Rheumatology and Rheumatology Unit, University and AOU of Cagliari, Cagliari, Italy
| | - Alessandro Mathieu
- Department of Medical Sciences and Public Health, Chair of Rheumatology and Rheumatology Unit, University and AOU of Cagliari, Cagliari, Italy
| | - Rosa Sorrentino
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University, Rome, Italy
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23
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Illing PT, Pymm P, Croft NP, Hilton HG, Jojic V, Han AS, Mendoza JL, Mifsud NA, Dudek NL, McCluskey J, Parham P, Rossjohn J, Vivian JP, Purcell AW. HLA-B57 micropolymorphism defines the sequence and conformational breadth of the immunopeptidome. Nat Commun 2018; 9:4693. [PMID: 30410026 PMCID: PMC6224591 DOI: 10.1038/s41467-018-07109-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 10/12/2018] [Indexed: 12/17/2022] Open
Abstract
Immunophenotypic differences between closely related human leukocyte antigen (HLA) alleles have been associated with divergent clinical outcomes in infection, autoimmunity, transplantation and drug hypersensitivity. Here we explore the impact of micropolymorphism on peptide antigen presentation by three closely related HLA molecules, HLA-B*57:01, HLA-B*57:03 and HLA-B*58:01, that are differentially associated with the HIV elite controller phenotype and adverse drug reactions. For each allotype, we mine HLA ligand data sets derived from the same parental cell proteome to define qualitative differences in peptide presentation using classical peptide binding motifs and an unbiased statistical approach. The peptide repertoires show marked qualitative overlap, with 982 peptides presented by all allomorphs. However, differences in peptide abundance, HLA-peptide stability, and HLA-bound conformation demonstrate that HLA micropolymorphism impacts more than simply the range of peptide ligands. These differences provide grounds for distinct immune reactivity and insights into the capacity of micropolymorphism to diversify immune outcomes. Human leukocyte antigens (HLA) are multi-allelic and polymorphic genes that present antigens to immune cells for inducing protective immunity. Here, using systems biology and structural approaches, the authors show that micropolymorphism of three HLA has effects beyond the modulation of antigen diversity.
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Affiliation(s)
- Patricia T Illing
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Phillip Pymm
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia.,Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC, 3800, Australia
| | - Nathan P Croft
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Hugo G Hilton
- Departments of Structural Biology and Microbiology & Immunology, School of Medicine, Stanford University, Stanford, 94305, CA, USA.,Calico Life Sciences LLC, South San Francisco, 94080, CA, USA
| | - Vladimir Jojic
- Calico Life Sciences LLC, South San Francisco, 94080, CA, USA
| | - Alex S Han
- Department of Genetics, School of Medicine, Stanford University, Stanford, 94305, CA, USA
| | - Juan L Mendoza
- Department of Molecular and Cellular Physiology, School of Medicine, Stanford University, Stanford, 94305, CA, USA.,Institute for Molecular Engineering and Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, 60637, IL, USA
| | - Nicole A Mifsud
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Nadine L Dudek
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - James McCluskey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Peter Parham
- Departments of Structural Biology and Microbiology & Immunology, School of Medicine, Stanford University, Stanford, 94305, CA, USA
| | - Jamie Rossjohn
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia.,Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC, 3800, Australia.,Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, CF14 4XN, UK
| | - Julian P Vivian
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia. .,Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC, 3800, Australia.
| | - Anthony W Purcell
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia.
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24
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Shraibman B, Barnea E, Kadosh DM, Haimovich Y, Slobodin G, Rosner I, López-Larrea C, Hilf N, Kuttruff S, Song C, Britten C, Castle J, Kreiter S, Frenzel K, Tatagiba M, Tabatabai G, Dietrich PY, Dutoit V, Wick W, Platten M, Winkler F, von Deimling A, Kroep J, Sahuquillo J, Martinez-Ricarte F, Rodon J, Lassen U, Ottensmeier C, van der Burg SH, Thor Straten P, Poulsen HS, Ponsati B, Okada H, Rammensee HG, Sahin U, Singh H, Admon A. Identification of Tumor Antigens Among the HLA Peptidomes of Glioblastoma Tumors and Plasma. Mol Cell Proteomics 2018; 17:2132-2145. [PMID: 30072578 PMCID: PMC6210219 DOI: 10.1074/mcp.ra118.000792] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 07/22/2018] [Indexed: 12/22/2022] Open
Abstract
Glioblastoma multiforme (GBM) is the most aggressive brain tumor with poor prognosis to most patients. Immunotherapy of GBM is a potentially beneficial treatment option, whose optimal implementation may depend on familiarity with tumor specific antigens, presented as HLA peptides by the GBM cells. Furthermore, early detection of GBM, such as by a routine blood test, may improve survival, even with the current treatment modalities. This study includes large-scale analyses of the HLA peptidome (immunopeptidome) of the plasma-soluble HLA molecules (sHLA) of 142 plasma samples, and the membranal HLA of GBM tumors of 10 of these patients' tumor samples. Tumor samples were fresh-frozen immediately after surgery and the plasma samples were collected before, and at multiple visits after surgery. In total, this HLA peptidome analysis involved 52 different HLA allotypes and resulted in the identification of more than 35,000 different HLA peptides. Strong correlations were observed in the signal intensities and in the repertoires of identified peptides between the tumors and plasma-soluble HLA peptidomes of the individual patients, whereas low correlations were observed between these HLA peptidomes and the tumors' proteomes. HLA peptides derived from Cancer/Testis Antigens (CTAs) were selected based on their presence among the HLA peptidomes of the patients and absence of expression of their source genes from any healthy and essential human tissues, except from immune-privileged sites. Additionally, peptides were selected as potential biomarkers if their levels in the plasma-sHLA peptidome were significantly reduced after the removal of tumor mass. The CTAs identified among the analyzed HLA peptidomes provide new opportunities for personalized immunotherapy and for early diagnosis of GBM.
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Affiliation(s)
- Bracha Shraibman
- From the ‡Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel
| | - Eilon Barnea
- From the ‡Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel
| | | | - Yael Haimovich
- From the ‡Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel
| | - Gleb Slobodin
- §Rheumatology Unit Bnai Zion Medical Center, Haifa 31048, Israel
| | - Itzhak Rosner
- §Rheumatology Unit Bnai Zion Medical Center, Haifa 31048, Israel
| | | | - Norbert Hilf
- ‖Immatics Biotechnologies GmbH, Paul-Ehrlich-Str. 15,72076 Tuebingen, Germany
| | - Sabrina Kuttruff
- ‖Immatics Biotechnologies GmbH, Paul-Ehrlich-Str. 15,72076 Tuebingen, Germany
| | - Colette Song
- ‖Immatics Biotechnologies GmbH, Paul-Ehrlich-Str. 15,72076 Tuebingen, Germany
| | - Cedrik Britten
- **BioNTech AG, Holderlinstr. 8,55131 Mainz, Germany
- ¶¶¶Association for Cancer Immunotherapy (CIMT), Langenbeckstr. 1,55131 Mainz, Germany
| | - John Castle
- **BioNTech AG, Holderlinstr. 8,55131 Mainz, Germany
| | | | | | - Marcos Tatagiba
- ‡‡Eberhard Karls Universität Tübingen, Department of Immunology, Auf der Morgenstelle 15,72076 Tubingen, Germany
| | - Ghazaleh Tabatabai
- ‡‡Eberhard Karls Universität Tübingen, Department of Immunology, Auf der Morgenstelle 15,72076 Tubingen, Germany
| | - Pierre-Yves Dietrich
- §§Université de Genève, Rue Gabrielle Perret Gentil 4; 1211 Geneve 14, Switzerland
| | - Valérie Dutoit
- §§Université de Genève, Rue Gabrielle Perret Gentil 4; 1211 Geneve 14, Switzerland
| | - Wolfgang Wick
- ¶¶Heidelberg University Medical Center, Im Neuenheimer Feld 672, D-69120 Heidelberg, Germany
| | - Michael Platten
- ¶¶Heidelberg University Medical Center, Im Neuenheimer Feld 672, D-69120 Heidelberg, Germany
| | - Frank Winkler
- ¶¶Heidelberg University Medical Center, Im Neuenheimer Feld 672, D-69120 Heidelberg, Germany
| | - Andreas von Deimling
- ¶¶Heidelberg University Medical Center, Im Neuenheimer Feld 672, D-69120 Heidelberg, Germany
| | - Judith Kroep
- ‖‖Leiden University Medical Center, Department of Medical Oncology, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Juan Sahuquillo
- ***Vall d'Hebron University Hospital, Institut Catala de la Salut, Pg. Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Francisco Martinez-Ricarte
- ***Vall d'Hebron University Hospital, Institut Catala de la Salut, Pg. Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Jordi Rodon
- ***Vall d'Hebron University Hospital, Institut Catala de la Salut, Pg. Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Ulrik Lassen
- ‡‡‡Region Hovedstaden (Center for Cancer Immune Therapy (CCIT), Herlev Hospital, Herlev Ringvej 75, DK-2730, Copenhagen, Denmark
| | - Christian Ottensmeier
- §§§Cancer Sciences Division, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Sjoerd H van der Burg
- ‖‖Leiden University Medical Center, Department of Medical Oncology, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
- ¶¶¶Association for Cancer Immunotherapy (CIMT), Langenbeckstr. 1,55131 Mainz, Germany
| | - Per Thor Straten
- ‡‡‡Region Hovedstaden (Center for Cancer Immune Therapy (CCIT), Herlev Hospital, Herlev Ringvej 75, DK-2730, Copenhagen, Denmark
| | - Hans Skovgaard Poulsen
- ‖‖‖Rigshospitalet, Departments of Radiation Biology and Oncology, Rigshospitalet 9, Blegdamsvej, DK-2100, Copenhagen, Denmark
| | - Berta Ponsati
- ****BCN Peptides, Pol. Ind. Els Vinyets-Els Fogars II. 08777 Sant Quinti de Mediona (Barcelona), Spain
| | - Hideho Okada
- ‡‡‡‡University of California, San Francisco, CA 94131 USA
| | - Hans-Georg Rammensee
- ‡‡Eberhard Karls Universität Tübingen, Department of Immunology, Auf der Morgenstelle 15,72076 Tubingen, Germany
| | - Ugur Sahin
- **BioNTech AG, Holderlinstr. 8,55131 Mainz, Germany
| | - Harpreet Singh
- ‖Immatics Biotechnologies GmbH, Paul-Ehrlich-Str. 15,72076 Tuebingen, Germany
| | - Arie Admon
- From the ‡Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel;
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25
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Colbert RA, Navid F, Gill T. The role of HLA-B*27 in spondyloarthritis. Best Pract Res Clin Rheumatol 2018; 31:797-815. [PMID: 30509441 DOI: 10.1016/j.berh.2018.07.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 07/20/2018] [Indexed: 02/08/2023]
Abstract
The mechanism by which HLA-B*27 predisposes to spondyloarthritis remains unresolved. Arthritogenic peptides have not been defined in humans and are not involved in experimental models of spondyloarthritis. Aberrant properties of HLA-B*27 can activate the IL-23/IL-17 axis in HLA-B*27 transgenic rats and humans. In HLA-B*27-independent rodent models, spondyloarthritis can be driven by IL-23 triggering entheseal-resident CD4-/CD8- T cells or CD4+ Th17 T cells. These findings point toward noncanonical mechanisms linking HLA-B*27 to the disease and provide a potential explanation for HLA-B*27-negative spondyloarthritis. Gut microbial dysbiosis may be important in the development of spondyloarthritis. HLA-B*27-induced changes in gut microbiota are complex and suggest an ecological model of dysbiosis in rodents. The importance of the IL-23/IL-17 axis in ankylosing spondylitis has been demonstrated by studies showing efficacy of IL-17. Although deciphering the precise role(s) of HLA-B*27 in disease requires further investigation, considerable progress has been made in understanding this complex relationship.
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Affiliation(s)
- Robert A Colbert
- Pediatric Translational Research Branch, NIAMS Intramural Research Program, NIH, USA.
| | - Fatemeh Navid
- Pediatric Translational Research Branch, NIAMS Intramural Research Program, NIH, USA.
| | - Tejpal Gill
- Pediatric Translational Research Branch, NIAMS Intramural Research Program, NIH, USA.
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26
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Ramarathinam SH, Croft NP, Illing PT, Faridi P, Purcell AW. Employing proteomics in the study of antigen presentation: an update. Expert Rev Proteomics 2018; 15:637-645. [PMID: 30080115 DOI: 10.1080/14789450.2018.1509000] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Our immune system discriminates self from non-self by examining the peptide cargo of human leukocyte antigen (HLA) molecules displayed on the cell surface. Successful recognition of HLA-bound non-self peptides can induce T cell responses leading to, for example, the destruction of infected cells. Today, largely due to advances in technology, we have an unprecedented capability to identify the nature of these presented peptides and unravel the true complexity of antigen presentation. Areas covered: In addition to conventional linear peptides, HLA molecules also present post-translationally modified sequences comprising a wealth of chemical and structural modifications, including a novel class of noncontiguous spliced peptides. This review focuses on these emerging themes in antigen presentation and how mass spectrometry in particular has contributed to a new view of the antigenic landscape that is presented to the immune system. Expert Commentary: Advances in the sensitivity of mass spectrometers and use of hybrid fragmentation technologies will provide more information-rich spectra of HLA bound peptides leading to more definitive identification of T cell epitopes. Coupled with improvements in sample preparation and new informatics workflows, studies will access novel classes of peptide antigen and allow interrogation of rare and clinically relevant samples.
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Affiliation(s)
- Sri H Ramarathinam
- a Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute , Monash University , Clayton , VIC , Australia
| | - Nathan P Croft
- a Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute , Monash University , Clayton , VIC , Australia
| | - Patricia T Illing
- a Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute , Monash University , Clayton , VIC , Australia
| | - Pouya Faridi
- a Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute , Monash University , Clayton , VIC , Australia
| | - Anthony W Purcell
- a Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute , Monash University , Clayton , VIC , Australia
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27
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Blatnik R, Mohan N, Bonsack M, Falkenby LG, Hoppe S, Josef K, Steinbach A, Becker S, Nadler WM, Rucevic M, Larsen MR, Salek M, Riemer AB. A Targeted LC-MS Strategy for Low-Abundant HLA Class-I-Presented Peptide Detection Identifies Novel Human Papillomavirus T-Cell Epitopes. Proteomics 2018; 18:e1700390. [PMID: 29603667 PMCID: PMC6033010 DOI: 10.1002/pmic.201700390] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Revised: 03/16/2018] [Indexed: 12/12/2022]
Abstract
For rational design of therapeutic vaccines, detailed knowledge about target epitopes that are endogenously processed and truly presented on infected or transformed cells is essential. Many potential target epitopes (viral or mutation-derived), are presented at low abundance. Therefore, direct detection of these peptides remains a challenge. This study presents a method for the isolation and LC-MS3 -based targeted detection of low-abundant human leukocyte antigen (HLA) class-I-presented peptides from transformed cells. Human papillomavirus (HPV) was used as a model system, as the HPV oncoproteins E6 and E7 are attractive therapeutic vaccination targets and expressed in all transformed cells, but present at low abundance due to viral immune evasion mechanisms. The presented approach included preselection of target antigen-derived peptides by in silico predictions and in vitro binding assays. The peptide purification process was tailored to minimize contaminants after immunoprecipitation of HLA-peptide complexes, while keeping high isolation yields of low-abundant target peptides. The subsequent targeted LC-MS3 detection allowed for increased sensitivity, which resulted in successful detection of the known HLA-A2-restricted epitope E711-19 and ten additional E7-derived peptides on the surface of HPV16-transformed cells. T-cell reactivity was shown for all the 11 detected peptides in ELISpot assays, which shows that detection by our approach has high predictive value for immunogenicity. The presented strategy is suitable for validating even low-abundant candidate epitopes to be true immunotherapy targets.
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Affiliation(s)
- Renata Blatnik
- Immunotherapy and ImmunopreventionGerman Cancer Research Center (DKFZ)Im Neuenheimer Feld 28069120 HeidelbergGermany
- Molecular Vaccine DesignGerman Center for Infection Research (DZIF)Partner Site HeidelbergHeidelbergGermany
| | - Nitya Mohan
- Immunotherapy and ImmunopreventionGerman Cancer Research Center (DKFZ)Im Neuenheimer Feld 28069120 HeidelbergGermany
| | - Maria Bonsack
- Immunotherapy and ImmunopreventionGerman Cancer Research Center (DKFZ)Im Neuenheimer Feld 28069120 HeidelbergGermany
- Molecular Vaccine DesignGerman Center for Infection Research (DZIF)Partner Site HeidelbergHeidelbergGermany
| | - Lasse G. Falkenby
- Department of Biochemistry and Molecular BiologyUniversity of Southern DenmarkOdense MDenmark
| | - Stephanie Hoppe
- Immunotherapy and ImmunopreventionGerman Cancer Research Center (DKFZ)Im Neuenheimer Feld 28069120 HeidelbergGermany
- Molecular Vaccine DesignGerman Center for Infection Research (DZIF)Partner Site HeidelbergHeidelbergGermany
| | - Kathrin Josef
- Immunotherapy and ImmunopreventionGerman Cancer Research Center (DKFZ)Im Neuenheimer Feld 28069120 HeidelbergGermany
- Molecular Vaccine DesignGerman Center for Infection Research (DZIF)Partner Site HeidelbergHeidelbergGermany
| | - Alina Steinbach
- Immunotherapy and ImmunopreventionGerman Cancer Research Center (DKFZ)Im Neuenheimer Feld 28069120 HeidelbergGermany
- Molecular Vaccine DesignGerman Center for Infection Research (DZIF)Partner Site HeidelbergHeidelbergGermany
| | - Sara Becker
- Immunotherapy and ImmunopreventionGerman Cancer Research Center (DKFZ)Im Neuenheimer Feld 28069120 HeidelbergGermany
| | - Wiebke M. Nadler
- Division of Stem Cells and CancerGerman Cancer Research Center (DKFZ) and Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI‐STEM)HeidelbergGermany
| | - Marijana Rucevic
- Massachusetts General HospitalCenter for Cancer ResearchCharlestownMAUSA
| | - Martin R. Larsen
- Department of Biochemistry and Molecular BiologyUniversity of Southern DenmarkOdense MDenmark
| | - Mogjiborahman Salek
- Immunotherapy and ImmunopreventionGerman Cancer Research Center (DKFZ)Im Neuenheimer Feld 28069120 HeidelbergGermany
- Molecular Vaccine DesignGerman Center for Infection Research (DZIF)Partner Site HeidelbergHeidelbergGermany
| | - Angelika B. Riemer
- Immunotherapy and ImmunopreventionGerman Cancer Research Center (DKFZ)Im Neuenheimer Feld 28069120 HeidelbergGermany
- Molecular Vaccine DesignGerman Center for Infection Research (DZIF)Partner Site HeidelbergHeidelbergGermany
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28
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Dashti N, Mahmoudi M, Aslani S, Jamshidi A. HLA-B*27 subtypes and their implications in the pathogenesis of ankylosing spondylitis. Gene 2018; 670:15-21. [PMID: 29803000 DOI: 10.1016/j.gene.2018.05.092] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 05/14/2018] [Accepted: 05/23/2018] [Indexed: 12/25/2022]
Abstract
Ankylosing spondylitis (AS) is a highly heritable kind of arthritis that affects the vertebral column. AS risk has been associated strongly with Human leukocyte antigen (HLA)-B*27. In fact, some HLA-B*27 subtypes have been associated with the increased disease risk, although some specific subtypes have not shown such associations. It is supposed that HLA-B*27 plays a major role in the etiopathogenesis of the disease. However, the difference in pathogenic outcomes of HLA-B*27 certain subtypes needs to be clarified. The purpose of this review article is to overview on the detailed implications of the HLA-B*27 subtypes in the etiopathogenesis of AS. Moreover, the role of ERAP1 in AS and its epistasis with HLA-B*27 have been reviewed.
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Affiliation(s)
- Navid Dashti
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran; Department of Immunology, School of Medicine, TehranUniversity of Medical Sciences, Tehran, Iran
| | - Mahdi Mahmoudi
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran.
| | - Saeed Aslani
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Ahmadreza Jamshidi
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran.
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29
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Yair-Sabag S, Tedeschi V, Vitulano C, Barnea E, Glaser F, Melamed Kadosh D, Taurog JD, Fiorillo MT, Sorrentino R, Admon A. The Peptide Repertoire of HLA-B27 may include Ligands with Lysine at P2 Anchor Position. Proteomics 2018; 18:e1700249. [DOI: 10.1002/pmic.201700249] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 12/21/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Shira Yair-Sabag
- Department of Biology; Technion-Israel Institute of Technology; Haifa Israel
| | - Valentina Tedeschi
- Department of Biology and Biotechnology “C. Darwin”; Sapienza University of Rome; Rome Italy
| | - Carolina Vitulano
- Department of Biology and Biotechnology “C. Darwin”; Sapienza University of Rome; Rome Italy
| | - Eilon Barnea
- Department of Biology; Technion-Israel Institute of Technology; Haifa Israel
| | - Fabian Glaser
- Bioinformatics Knowledge Unit; The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering; Technion-Israel Institute of Technology; Haifa Israel
| | | | - Joel D. Taurog
- Department of Internal Medicine; University of Texas Southwestern Medical Center; Dallas USA
| | - Maria Teresa Fiorillo
- Department of Biology and Biotechnology “C. Darwin”; Sapienza University of Rome; Rome Italy
| | - Rosa Sorrentino
- Department of Biology and Biotechnology “C. Darwin”; Sapienza University of Rome; Rome Italy
| | - Arie Admon
- Department of Biology; Technion-Israel Institute of Technology; Haifa Israel
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30
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Ritz D, Kinzi J, Neri D, Fugmann T. Data-Independent Acquisition of HLA Class I Peptidomes on the Q Exactive Mass Spectrometer Platform. Proteomics 2018; 17. [PMID: 28834231 DOI: 10.1002/pmic.201700177] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 07/07/2017] [Indexed: 12/18/2022]
Abstract
The characterization of peptides presented by human leukocyte antigen (HLA) class I molecules is crucial for understanding immune processes, biomarker discovery, and the development of novel immunotherapies or vaccines. Mass spectrometry allows the direct identification of thousands of HLA-bound peptides from cell lines, blood, or tissue. In recent years, data-independent acquisition (DIA) mass spectrometry methods have evolved, promising to increase reproducibility and sensitivity over classical data-dependent acquisition (DDA) workflows. Here, we describe a DIA setup on the Q Exactive mass spectrometer, optimized regarding the unique properties of HLA class I peptides. The methodology enables sensitive and highly reproducible characterization of HLA peptidomes from individual cell lines. From up to 16 DDA analyses of 100 million human cells, more than 10 000 peptides could be confidently identified, serving as basis for the generation of spectral libraries. This knowledge enabled the subsequent interrogation of DIA data, leading to the identification of peptide sets with >90% overlap between replicate samples, a prerequisite for the comparative study of closely related specimens. Furthermore, >3000 peptides could be identified from just one million cells after DIA analysis using a library generated from 300 million cells. The reduction in sample quantity and the high reproducibility of DIA-based HLA peptidome analysis should facilitate personalized medicine applications.
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Affiliation(s)
| | - Jonny Kinzi
- Institute of Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland
| | - Dario Neri
- Institute of Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland
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31
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Vitulano C, Tedeschi V, Paladini F, Sorrentino R, Fiorillo MT. The interplay between HLA-B27 and ERAP1/ERAP2 aminopeptidases: from anti-viral protection to spondyloarthritis. Clin Exp Immunol 2017; 190:281-290. [PMID: 28759104 DOI: 10.1111/cei.13020] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/26/2017] [Indexed: 01/06/2023] Open
Abstract
The human leukocyte antigen class I gene HLA-B27 is the strongest risk factor for ankylosing spondylitis (AS), a chronic inflammatory arthritic disorder. More recently, the Endoplasmic Reticulum Aminopeptidase (ERAP) 1 and 2 genes have been identified by genome wide association studies (GWAS) as additional susceptibility factors. In the ER, these aminopeptidases trim the peptides to a length suitable to fit into the groove of the major histocompatibility complex (MHC) class I molecules. It is noteworthy that an epistatic interaction between HLA-B27 and ERAP1, but not between HLA-B27 and ERAP2, has been highlighted. However, these observations suggest a paramount centrality for the HLA-B27 peptide repertoire that determines the natural B27 immunological function, i.e. the T cell antigen presentation and, as a by-product, elicits HLA-B27 aberrant behaviours: (i) the misfolding leading to ER stress responses and autophagy and (ii) the surface expression of homodimers acting as ligands for innate immune receptors. In this context, it has been observed that the HLA-B27 carriers, besides being prone to autoimmunity, display a far better surveillance to some viral infections. This review focuses on the ambivalent role of HLA-B27 in autoimmunity and viral protection correlating its functions to the quantitative and qualitative effects of ERAP1 and ERAP2 polymorphisms on their enzymatic activity.
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Affiliation(s)
- C Vitulano
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, Rome, Italy
| | - V Tedeschi
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, Rome, Italy
| | - F Paladini
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, Rome, Italy
| | - R Sorrentino
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, Rome, Italy
| | - M T Fiorillo
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, Rome, Italy
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32
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Solving the pathogenesis of ankylosing spondylitis. Clin Immunol 2017; 186:46-50. [PMID: 28736277 DOI: 10.1016/j.clim.2017.07.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 07/19/2017] [Indexed: 12/12/2022]
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Abstract
Over the past 5 years, advances in high-throughput techniques and studies involving large cohorts of patients have led to considerable advances in the identification of novel genetic associations and immune pathways involved in ankylosing spondylitis (AS). These discoveries include genes encoding cytokine receptors, transcription factors, signalling molecules and transport proteins. Although progress has been made in understanding the functions and potential pathogenic roles of some of these molecules, much work remains to be done to comprehend their complex interactions and therapeutic potential in AS. In this Review, we outline the current knowledge of AS pathogenesis, including genetic risk associations, HLA-B27-mediated pathology, perturbations in antigen-presentation pathways and the contribution of the type 3 immune response.
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34
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Khan MA. An Update on the Genetic Polymorphism of HLA-B*27 With 213 Alleles Encompassing 160 Subtypes (and Still Counting). Curr Rheumatol Rep 2017; 19:9. [DOI: 10.1007/s11926-017-0640-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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35
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Barnea E, Melamed Kadosh D, Haimovich Y, Satumtira N, Dorris ML, Nguyen MT, Hammer RE, Tran TM, Colbert RA, Taurog JD, Admon A. The Human Leukocyte Antigen (HLA)-B27 Peptidome in Vivo, in Spondyloarthritis-susceptible HLA-B27 Transgenic Rats and the Effect of Erap1 Deletion. Mol Cell Proteomics 2017; 16:642-662. [PMID: 28188227 DOI: 10.1074/mcp.m116.066241] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 02/05/2017] [Indexed: 01/20/2023] Open
Abstract
HLA-B27 is a class I major histocompatibility (MHC-I) allele that confers susceptibility to the rheumatic disease ankylosing spondylitis (AS) by an unknown mechanism. ERAP1 is an aminopeptidase that trims peptides in the endoplasmic reticulum for binding to MHC-I molecules. ERAP1 shows genetic epistasis with HLA-B27 in conferring susceptibility to AS. Male HLA-B27 transgenic rats develop arthritis and serve as an animal model of AS, whereas female B27 transgenic rats remain healthy. We used large scale quantitative mass spectrometry to identify over 15,000 unique HLA-B27 peptide ligands, isolated after immunoaffinity purification of the B27 molecules from the spleens of HLA-B27 transgenic rats. Heterozygous deletion of Erap1, which reduced the Erap1 level to less than half, had no qualitative or quantitative effects on the B27 peptidome. Homozygous deletion of Erap1 affected approximately one-third of the B27 peptidome but left most of the B27 peptidome unchanged, suggesting the possibility that some of the HLA-B27 immunopeptidome is not processed in the presence of Erap1. Deletion of Erap1 was permissive for the AS-like phenotype, increased mean peptide length and increased the frequency of C-terminal hydrophobic residues and of N-terminal Ala, Ser, or Lys. The presence of Erap1 increased the frequency of C-terminal Lys and Arg, of Glu and Asp at intermediate residues, and of N-terminal Gly. Several peptides of potential interest in AS pathogenesis, previously identified in human cell lines, were isolated. However, rats susceptible to arthritis had B27 peptidomes similar to those of non-susceptible rats, and no peptides were found to be uniquely associated with arthritis. Whether specific B27-bound peptides are required for AS pathogenesis remains to be determined. Data are available via ProteomeXchange with identifier PXD005502.
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Affiliation(s)
- Eilon Barnea
- From the ‡Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Dganit Melamed Kadosh
- From the ‡Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Yael Haimovich
- From the ‡Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Nimman Satumtira
- §Department of Internal Medicine, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390-8884
| | - Martha L Dorris
- §Department of Internal Medicine, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390-8884
| | - Mylinh T Nguyen
- ¶Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390-8816
| | - Robert E Hammer
- ¶Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390-8816
| | - Tri M Tran
- ‖NIAMS, National Institutes of Health, Bethesda, Maryland 20892-1560
| | - Robert A Colbert
- ‖NIAMS, National Institutes of Health, Bethesda, Maryland 20892-1560
| | - Joel D Taurog
- §Department of Internal Medicine, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390-8884;
| | - Arie Admon
- From the ‡Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel;
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