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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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Falco M, Sivori S, Meazza R, Pende D. Report from the Eleventh Killer Immunoglobulin-like Receptor (KIR) Workshop: Novel insights on KIR polymorphism, ligand recognition, expression and function. HLA 2020; 94:100-110. [PMID: 31177639 DOI: 10.1111/tan.13608] [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: 04/26/2019] [Revised: 05/24/2019] [Accepted: 06/04/2019] [Indexed: 11/27/2022]
Abstract
The Eleventh Killer Immunoglobulin-like Receptor (KIR) Workshop was held in Camogli (Genoa, Italy) in October 2018. This congress brought together 113 participants working on KIR field. Fifty-eight studies have been presented, the majority of which included unpublished data. Thus, KIR workshop, allowing the meeting of people sharing their knowledge and experience in a friendly atmosphere, still represents a special event of fruitful discussion and exchange of novel breakthrough, results, and ideas. In this report, we summarize all the scientific contributions highlighting the most recent advances in KIR field. Forty abstracts presented at the KIR Workshop are published in this issue.
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Affiliation(s)
- Michela Falco
- Laboratorio di Immunologia Clinica e Sperimentale, IRCCS Istituto G. Gaslini, Genoa, Italy
| | - Simona Sivori
- Dipartimento di Medicina Sperimentale (DIMES) e Centro di Eccellenza per la Ricerca Biomedica (CEBR), Università degli Studi di Genova, Genoa, Italy
| | - Raffaella Meazza
- Laboratorio di Immunologia, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Daniela Pende
- Laboratorio di Immunologia, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
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Shimizu C, Kim J, Eleftherohorinou H, Wright VJ, Hoang LT, Tremoulet AH, Franco A, Hibberd ML, Takahashi A, Kubo M, Ito K, Tanaka T, Onouchi Y, Coin LJM, Levin M, Burns JC, Shike H. HLA-C variants associated with amino acid substitutions in the peptide binding groove influence susceptibility to Kawasaki disease. Hum Immunol 2019; 80:731-738. [PMID: 31122742 PMCID: PMC10793643 DOI: 10.1016/j.humimm.2019.04.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 04/26/2019] [Accepted: 04/27/2019] [Indexed: 10/26/2022]
Abstract
Kawasaki disease (KD) is a pediatric vasculitis caused by an unknown trigger in genetically susceptible children. The incidence varies widely across genetically diverse populations. Several associations with HLA Class I alleles have been reported in single cohort studies. Using a genetic approach, from the nine single nucleotide variants (SNVs) associated with KD susceptibility in children of European descent, we identified SNVs near the HLA-C (rs6906846) and HLA-B genes (rs2254556) whose association was replicated in a Japanese descent cohort (rs6906846 p = 0.01, rs2254556 p = 0.005). The risk allele (A at rs6906846) was also associated with HLA-C*07:02 and HLA-C*04:01 in both US multi-ethnic and Japanese cohorts and HLA-C*12:02 only in the Japanese cohort. The risk A-allele was associated with eight non-conservative amino acid substitutions (amino acid positions); Asp or Ser (9), Arg (14), Ala (49), Ala (73), Ala (90), Arg (97), Phe or Ser (99), and Phe or Ser (116) in the HLA-C peptide binding groove that binds peptides for presentation to cytotoxic T cells (CTL). This raises the possibility of increased affinity to a "KD peptide" that contributes to the vasculitis of KD in genetically susceptible children.
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Affiliation(s)
- Chisato Shimizu
- Department of Pediatrics, University California San Diego, La Jolla, CA, USA.
| | - Jihoon Kim
- Division of Biomedical Informatics, Department of Medicine, University California San Diego, La Jolla, CA, USA
| | - Hariklia Eleftherohorinou
- Section of Paediatrics, Division of Infectious Diseases, Department of Medicine, Imperial College London, London, UK
| | - Victoria J Wright
- Section of Paediatrics, Division of Infectious Diseases, Department of Medicine, Imperial College London, London, UK
| | | | - Adriana H Tremoulet
- Department of Pediatrics, University California San Diego, La Jolla, CA, USA; Department of Cardiology, Rady Childrens' Hospital San Diego, San Diego, CA, USA
| | - Alessandra Franco
- Department of Pediatrics, University California San Diego, La Jolla, CA, USA
| | | | - Atsushi Takahashi
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan; Department of Genomic Medicine, Research Institute, National Cerebral and Cardiovascular Center, Suita, Osaka, Japan
| | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Kaoru Ito
- Laboratory for Cardiovascular Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Toshihiro Tanaka
- Department of Human Genetics and Disease Diversity, Tokyo Medical and Dental University Graduate School of Medical and Dental Sciences, Bunkyo-ku, Tokyo, Japan
| | - Yoshihiro Onouchi
- Laboratory for Cardiovascular Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan; Department of Public Health, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Lachlan J M Coin
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Australia
| | - Michael Levin
- Section of Paediatrics, Division of Infectious Diseases, Department of Medicine, Imperial College London, London, UK
| | - Jane C Burns
- Department of Pediatrics, University California San Diego, La Jolla, CA, USA; Department of Cardiology, Rady Childrens' Hospital San Diego, San Diego, CA, USA
| | - Hiroko Shike
- Department of Pathology, HLA Laboratory, Penn State Hershey Medical Center, Hershey, PA, USA
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Mele D, Pasi A, Cacciatore R, Mantovani S, Oliviero B, Mondelli MU, Varchetta S. Decreased interferon-γ production by NK cells from KIR haplotype B carriers in hepatitis C virus infection. Liver Int 2019; 39:1237-1245. [PMID: 31177636 DOI: 10.1111/liv.14172] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 06/03/2019] [Accepted: 06/04/2019] [Indexed: 01/13/2023]
Abstract
BACKGROUND AND AIMS Different population genetics studies showed that interactions between killer-cell immunoglobulin-like receptors (KIR) and HLA play a role in viral disease outcome, but functional correlates are missing. Building upon our previous work pointing to a regulatory role for KIR3DL1/DS1 in hepatitis C virus (HCV) infection, we analysed whether its expression may affect natural killer (NK) cell function in the presence or absence of its principal ligand HLA-Bw4 in KIR haplotype A and B carriers, which are characterized by a different representation of activating and inhibitory KIRs. METHODS We performed KIR and HLA class I genotypic analysis in 54 healthy donors (HD) and 50 HCV+ subjects and examined NK cell cytokine secretion and degranulation in the context of KIR3DL1-HLA-Bw4 match stratified by KIR haplotype. RESULTS KIR3DL1-HLA-Bw4 match induced functional NK cell modulation, reflected by reduced interferon (IFN)γ production in haplotype B HCV+ patients compared to HD. This functional impairment could be ascribed to the KIR3DS1 negative HCV-infected patient population, whose NK cells also showed a significantly decreased proportion of KIR3DL1. Haplotype A HCV-infected patients showed increased NK cell degranulation compared with HD in the absence of KIR-HLA-Bw4 match and this activity was associated with increased phosphorylation of signal transducer and activator of transcription (STAT) 1. CONCLUSIONS Our data show that NK cells from HCV+ patients have an unbalanced ability to produce IFNγ and to kill target cells in haplotype A and B carriers, suggesting the existence of complex functional differences governed by KIR-HLA interaction, particularly on KIR3DL1 expressing NK cells.
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Affiliation(s)
- Dalila Mele
- Division of Infectious Diseases and Immunology, Department of Medical Sciences and Infectious Diseases, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Annamaria Pasi
- Laboratory of Immunogenetics, Department of Transfusion Medicine and Immuno-Hematology, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Rosalia Cacciatore
- Laboratory of Immunogenetics, Department of Transfusion Medicine and Immuno-Hematology, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Stefania Mantovani
- Division of Infectious Diseases and Immunology, Department of Medical Sciences and Infectious Diseases, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Barbara Oliviero
- Division of Infectious Diseases and Immunology, Department of Medical Sciences and Infectious Diseases, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Mario U Mondelli
- Division of Infectious Diseases and Immunology, Department of Medical Sciences and Infectious Diseases, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.,Department of Internal Medicine and Therapeutics, University of Pavia, Pavia, Italy
| | - Stefania Varchetta
- Division of Infectious Diseases and Immunology, Department of Medical Sciences and Infectious Diseases, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
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Boudreau JE, Hsu KC. Natural killer cell education in human health and disease. Curr Opin Immunol 2018; 50:102-111. [PMID: 29413815 DOI: 10.1016/j.coi.2017.11.003] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 11/18/2017] [Indexed: 02/06/2023]
Abstract
Natural killer (NK) cells maintain immune homeostasis by detecting and eliminating damaged cells. Simultaneous activating and inhibitory input are integrated by NK cells, with the net signal prompting cytotoxicity and cytokine production, or inhibition. Chief among the inhibitory ligands for NK cells are 'self' human leukocyte antigen (HLA) molecules, which are sensed by killer immunoglobulin-like receptors (KIR). Through a process called 'education', the functional capabilities of each NK cell are counterbalanced by their sensitivity for inhibition by co-inherited 'self' HLA. HLA and their ligands, the killer immunoglobulin-like receptors (KIR), are encoded by polymorphic, polygenic gene loci that segregate independently, therefore, NK education and function differ even between related individuals. In this review, we describe how variation in NK education, reactivity and sensitivity for inhibition impacts reproductive success, infection, cancer, inflammatory and autoimmune diseases.
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Affiliation(s)
- Jeanette E Boudreau
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Canada; Department of Pathology, Dalhousie University, Halifax, Canada
| | - Katharine C Hsu
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA.
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Capittini C, Emmi G, Mannarino S, Bossi G, Dellepiane RM, Salice P, Pietrogrande MC, Pasi A, De Silvestri A, Tinelli C, Martinetti M. An immune-molecular hypothesis supporting infectious aetiopathogenesis of Kawasaki disease in children. Eur J Immunol 2018; 48:543-545. [PMID: 29193035 DOI: 10.1002/eji.201747226] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 10/18/2017] [Accepted: 11/23/2017] [Indexed: 01/10/2023]
Abstract
The competitive binding between CpG-ODN (single-stranded DNA from pathogens) and HLA-B and HLA-A ligands for the inhibitory Killer Immunoglobulin-like Receptors (KIR)3DL1/2 may lead to possible hypo-sensing of pathogens and ineffective clearance. We observed an overabundance of HLA ligands for inhibitory KIR with three domains in KD subjects.
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Affiliation(s)
- Cristina Capittini
- Biometry and Clinical Epidemiology, IRCCS Policlinico San Matteo Foundation, Pavia, Italy
| | - Giacomo Emmi
- Department of Experimental and Clinical Medicine, University of Firenze, Italy
| | - Savina Mannarino
- Department of Pediatrics, Pediatric Cardiology, IRCCS Policlinico San Matteo Foundation, Pavia, Italy
| | - Grazia Bossi
- Department of Pediatrics, IRCCS Policlinico San Matteo Foundation, Pavia, Italy
| | - Rosa Maria Dellepiane
- Pediatric Clinic II, University of Milan, IRCCS Ca' Granda Foundation, Ospedale Maggiore Policlinico, Milan, Italy
| | - Patrizia Salice
- Pediatric Cardiology, Cardiology Unit, IRCCS Ca' Granda Foundation, Ospedale Maggiore Policlinico, Milan, Italy
| | - Maria Cristina Pietrogrande
- Pediatric Clinic II, University of Milan, IRCCS Ca' Granda Foundation, Ospedale Maggiore Policlinico, Milan, Italy
| | - Annamaria Pasi
- Immunohematology and Transfusion Center, IRCCS Policlinico San Matteo Foundation, Pavia, Italy
| | - Annalisa De Silvestri
- Biometry and Clinical Epidemiology, IRCCS Policlinico San Matteo Foundation, Pavia, Italy
| | - Carmine Tinelli
- Biometry and Clinical Epidemiology, IRCCS Policlinico San Matteo Foundation, Pavia, Italy
| | - Miryam Martinetti
- Immunohematology and Transfusion Center, IRCCS Policlinico San Matteo Foundation, Pavia, Italy
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Del Principe D, Pietraforte D, Gambardella L, Marchesi A, Tarissi de Jacobis I, Villani A, Malorni W, Straface E. Pathogenetic determinants in Kawasaki disease: the haematological point of view. J Cell Mol Med 2017; 21:632-639. [PMID: 28063205 PMCID: PMC5345614 DOI: 10.1111/jcmm.12992] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 08/18/2016] [Indexed: 12/12/2022] Open
Abstract
Kawasaki disease is a multisystemic vasculitis that can result in coronary artery lesions. It predominantly affects young children and is characterized by prolonged fever, diffuse mucosal inflammation, indurative oedema of the hands and feet, a polymorphous skin rash and non‐suppurative lymphadenopathy. Coronary artery involvement is the most important complication of Kawasaki disease and may cause significant coronary stenosis resulting in ischemic heart disease. The introduction of intravenous immunoglobulin decreases the incidence of coronary artery lesions to less than 5%. The etiopathogenesis of this disease remains unclear. Several lines of evidence suggest that an interplay between a microbial infection and a genetic predisposition could take place in the development of the disease. In this review, we summarize the state of the art of pathogenetic mechanisms of Kawasaki disease underscoring the relevance of haematological features as a novel field of investigation.
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Affiliation(s)
- Domenico Del Principe
- Department of Therapeutic Research and Medicine Evaluation, Section of Cell Aging and Gender Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Donatella Pietraforte
- Department of Neurosciences, Section of Cell Aging and Gender Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Lucrezia Gambardella
- Department of Therapeutic Research and Medicine Evaluation, Section of Cell Aging and Gender Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Alessandra Marchesi
- General Pediatric and Infectious Disease Unit, Internal Care Department, Bambino Gesù Children's Hospital, Rome, Italy
| | - Isabella Tarissi de Jacobis
- General Pediatric and Infectious Disease Unit, Internal Care Department, Bambino Gesù Children's Hospital, Rome, Italy
| | - Alberto Villani
- General Pediatric and Infectious Disease Unit, Internal Care Department, Bambino Gesù Children's Hospital, Rome, Italy
| | - Walter Malorni
- Department of Therapeutic Research and Medicine Evaluation, Section of Cell Aging and Gender Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Elisabetta Straface
- Department of Therapeutic Research and Medicine Evaluation, Section of Cell Aging and Gender Medicine, Istituto Superiore di Sanità, Rome, Italy
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