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Gilles A, Hu L, Virdis F, Sant’Angelo DB, Dimitrova N, Hedrick JA, Denzin LK. The MHC Class II Antigen-Processing and Presentation Pathway Is Dysregulated in Type 1 Diabetes. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 211:1630-1642. [PMID: 37811896 PMCID: PMC10872857 DOI: 10.4049/jimmunol.2300213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 09/20/2023] [Indexed: 10/10/2023]
Abstract
Peptide loading of MHC class II (MHCII) molecules is facilitated by HLA-DM (DM), which catalyzes CLIP release, stabilizes empty MHCII, and edits the MHCII-bound peptide repertoire. HLA-DO (DO) binds to DM and modulates its activity, resulting in an altered set of peptides presented at the cell surface. MHCII-peptide presentation in individuals with type 1 diabetes (T1D) is abnormal, leading to a breakdown in tolerance; however, no direct measurement of the MHCII pathway activity in T1D patients has been performed. In this study, we measured MHCII Ag-processing pathway activity in humans by determining MHCII, MHCII-CLIP, DM, and DO levels by flow cytometry for peripheral blood B cells, dendritic cells, and monocytes from 99 T1D patients and 97 controls. Results showed that MHCII levels were similar for all three APC subsets. In contrast, MHCII-CLIP levels, independent of sex, age at blood draw, disease duration, and diagnosis age, were significantly increased for all three APCs, with B cells showing the largest increase (3.4-fold). DM and DO levels, which usually directly correlate with MHCII-CLIP levels, were unexpectedly identical in T1D patients and controls. Gene expression profiling on PBMC RNA showed that DMB mRNA was significantly elevated in T1D patients with residual C-peptide. This resulted in higher levels of DM protein in B cells and dendritic cells. DO levels were also increased, suggesting that the MHCII pathway maybe differentially regulated in individuals with residual C-peptide. Collectively, these studies show a dysregulation of the MHCII Ag-processing pathway in patients with T1D.
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Affiliation(s)
- Ambroise Gilles
- Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ 08901, Current address: Division of Plastic Surgery, Department of Surgery, Penn State Health Milton S. Hershey Medical Center, Hershey, PA
| | - Lan Hu
- Oncology Informatics & Genomics, Philips North America, Cambridge, MA, 02141
| | - Francesca Virdis
- Child Health Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ 08901, Current address: Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Monserrato, Cagliari, Italy
| | - Derek B. Sant’Angelo
- Child Health Institute of New Jersey, Department of Pediatrics and Department of Pharmacology, Rutgers Robert Wood Johnson Medical School, and Graduate School of Biomedical Sciences, The State University of NJ, New Brunswick, NJ, 08901
| | - Nevenka Dimitrova
- Oncology Informatics and Genomics, Philips North America, Valhalla, NY 10598, Current address: Memorial Sloan-Kettering Cancer Center, New York, NY, 10065
| | | | - Lisa K. Denzin
- Child Health Institute of New Jersey, Department of Pediatrics and Department of Pharmacology, Rutgers Robert Wood Johnson Medical School, and Graduate School of Biomedical Sciences, The State University of NJ, New Brunswick, NJ, 08901
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2
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Tomer R, Patiyal S, Dhall A, Raghava GPS. Prediction of celiac disease associated epitopes and motifs in a protein. Front Immunol 2023; 14:1056101. [PMID: 36742312 PMCID: PMC9893285 DOI: 10.3389/fimmu.2023.1056101] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 01/02/2023] [Indexed: 01/20/2023] Open
Abstract
Introduction Celiac disease (CD) is an autoimmune gastrointestinal disorder causes immune-mediated enteropathy against gluten. Gluten immunogenic peptides have the potential to trigger immune responses which leads to damage the small intestine. HLA-DQ2/DQ8 are major alleles that bind to epitope/antigenic region of gluten and induce celiac disease. There is a need to identify CD associated epitopes in protein-based foods and therapeutics. Methods In this study, computational tools have been developed to predict CD associated epitopes and motifs. Dataset used for training, testing and evaluation contain experimentally validated CD associated and non-CD associate peptides. We perform positional analysis to identify the most significant position of an amino acid residue in the peptide and checked the frequency of HLA alleles. We also compute amino acid composition to develop machine learning based models. We also developed ensemble method that combines motif-based approach and machine learning based models. Results and Discussion Our analysis support existing hypothesis that proline (P) and glutamine (Q) are highly abundant in CD associated peptides. A model based on density of P&Q in peptides has been developed for predicting CD associated peptides which achieve maximum AUROC 0.98 on independent data. We discovered motifs (e.g., QPF, QPQ, PYP) which occurs specifically in CD associated peptides. We also developed machine learning based models using peptide composition and achieved maximum AUROC 0.99. Finally, we developed ensemble method that combines motif-based approach and machine learning based models. The ensemble model-predict CD associated motifs with 100% accuracy on an independent dataset, not used for training. Finally, the best models and motifs has been integrated in a web server and standalone software package "CDpred". We hope this server anticipate the scientific community for the prediction, designing and scanning of CD associated peptides as well as CD associated motifs in a protein/peptide sequence (https://webs.iiitd.edu.in/raghava/cdpred/).
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3
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Hernández-Doño S, Sánchez-González RA, Trujillo-Vizuet MG, Zamudio-Castellanos FY, García-Silva R, Bulos-Rodríguez P, Vazquez-Guzmán CA, Cárdenas-Ramos X, de León Rodríguez D, Elías F, Domínguez-Arevillaga S, Pérez-Tirado JM, Vera-Lastra OL, Granados J, Sepúlveda-Delgado J. Protective HLA alleles against severe COVID-19: HLA-A*68 as an ancestral protection allele in Tapachula-Chiapas, Mexico. Clin Immunol 2022; 238:108990. [PMID: 35395388 PMCID: PMC8982524 DOI: 10.1016/j.clim.2022.108990] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 02/13/2022] [Accepted: 03/25/2022] [Indexed: 11/03/2022]
Abstract
HLA is a polymorphic antigen presenter which has provided valuable information on the susceptibility of populations to viruses. Therefore, the study of HLA can reveal specific susceptibility or resistance alleles to severe COVID-19 in an ethnically dependent manner. This pilot study investigated HLA alleles associated with COVID-19 severity in Tapachula, Chiapas, Mexico. A total of 146 Mexican Mestizos were typed for HLA class I and II using PCR-SSP. The patients were classified according to the outcome (death or improvement) and the infection's severity (mild or severe). In addition, a group of exposed uninfected individuals was included. HLA-A*68 was found to be a protective allele against the severe infection and fatal outcome; pC = 0.03, OR = 0.4, 95% CI =0.20-0.86, and pC =0.009, OR = 0.3, 95% CI =0.13-0.71 respectively. HLA-DRB1*03 also appears to be a protective factor against fatal outcome pC = 0.009, OR = 0.1, 95%IC = 0.01-0.66; however, the low frequency of this allele in the studied population limits the statistical power. The severity and fatal outcome of COVID-19 patients in Tapachula, Chiapas depend more on the lack of resistance than susceptibility HLA alleles.
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Affiliation(s)
- Susana Hernández-Doño
- Department of Transplantation, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | | | | | | | - Rafael García-Silva
- Department of Transplantation, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Pedro Bulos-Rodríguez
- Department of Internal Medicine, Hospital Regional de Alta Especialidad Ciudad Salud, Tapachula, Chiapas, Mexico
| | - Carlos A Vazquez-Guzmán
- Department of Internal Medicine, Hospital Regional de Alta Especialidad Ciudad Salud, Tapachula, Chiapas, Mexico
| | | | - Diana de León Rodríguez
- Facultad de Medicina Humana Campus IV, Universidad Autónoma de Chiapas, Mexico; Becario de la Dirección General de Calidad y Educación en Salud, Secretaría de Salud, Mexico
| | - Fabiola Elías
- Facultad de Medicina Humana Campus IV, Universidad Autónoma de Chiapas, Mexico
| | | | | | - Olga Lidia Vera-Lastra
- Department of Internal Medicine, Hospital de Especialidades, Centro Médico la Raza, Chile
| | - Julio Granados
- Department of Transplantation, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Jesús Sepúlveda-Delgado
- Research Division, Hospital Regional de Alta Especialidad Ciudad Salud, Tapachula, Chiapas, Mexico.
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4
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He J, Chen J, Han X, Gu Q, Liang J, Sun M, Liu S, Yao Y, Shi L. Association of HLA-DM and HLA class II Genes with Antibody Response Induced by Inactivated Japanese Encephalitis Vaccine. HLA 2022; 99:357-367. [PMID: 35118816 DOI: 10.1111/tan.14575] [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: 08/20/2021] [Revised: 01/29/2022] [Accepted: 01/31/2022] [Indexed: 11/04/2022]
Abstract
HLA (HLA) class II molecules, HLA-DR, DP, and DQ, together with HLA II-like protein DM, play a dominant role in the processing and presentation of antigens, which may influence vaccine effectiveness. We previously demonstrated that variations in the HLA-DRB1, DPB1, and DQB1 genes may affect the neutralising antibody (NAb) response induced by the inactivated Japanese encephalitis vaccine (IJEV). In the present study, we genotyped HLA-DPA1, DQA1, DMA, and DMB genes and used previous HLA-DRB1, DPB1, and DQB1 data to evaluate the association of these genes with IJEV-induced NAbs, at both the seroconversion and geometric mean titres (GMTs). We confirmed the seropositive association of DQB1*02:01 and NAbs (0.156 vs. 0.075, Padj = 0.018; OR = 2.270; 95% CI = 1.285-3.999) and seronegative association of DQB1*02:02 (0.014 vs. 0.09, Padj = 0.0002; OR = 0.130; 95% CI = 0.047-0.400). Furthermore, the DMB*01:03-DMA*01:01-DPA1*01:03-DPB1*04:01 haplotype was associated with a negative response (0.020 vs. 0.074; Padj = 0.03; OR = 0.250; 95% CI = 0.097-0.649), whereas DRB1*15:02-DMB*01:01-DMA*01:01 was associated with a positive response (0.034 vs. 0; Padj = 0.044). In addition, DRB1*12:02, DRB1*13:02, DPB1*04:01, DPB1*05:01, DPB1*09:01, DQA1*06:01, and DQA1*01:02 were associated with a higher GMT of NAbs, whereas DRB1*11:01, DPB1*13:01, and DQA1*05:05 were associated with a lower GMT of NAbs. In conclusion, the present study suggests that variations in the HLA-DM and HLA class II genes, as well as their combined allotypes, may influence the IJEV NAbs at seroconversion and GMT levels. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Jihong He
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China
| | - Jun Chen
- Department of Immunogenetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China
| | - Xue Han
- Department of Immunogenetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China
| | - Qin Gu
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China.,Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Disease, Kunming, China
| | - Jiangli Liang
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China.,Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Disease, Kunming, China
| | - Mingbo Sun
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China.,Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Disease, Kunming, China
| | - Shuyuan Liu
- Department of Immunogenetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China
| | - Yufeng Yao
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China
| | - Li Shi
- Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Disease, Kunming, China
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5
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Regulation of the BCR signalosome by the class II peptide editor, H2-M, affects the development and repertoire of innate-like B cells. Cell Rep 2022; 38:110200. [DOI: 10.1016/j.celrep.2021.110200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 09/23/2021] [Accepted: 12/13/2021] [Indexed: 11/21/2022] Open
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6
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Abualrous ET, Sticht J, Freund C. Major histocompatibility complex (MHC) class I and class II proteins: impact of polymorphism on antigen presentation. Curr Opin Immunol 2021; 70:95-104. [PMID: 34052735 DOI: 10.1016/j.coi.2021.04.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/23/2021] [Accepted: 04/25/2021] [Indexed: 01/01/2023]
Abstract
The major histocompatibility complex (MHC) loci are amongst the most polymorphic regions in the genomes of vertebrates. In the human population, thousands of MHC gene variants (alleles) exist that translate into distinct allotypes equipped with overlapping but unique peptide binding profiles. Understanding the differential structural and dynamic properties of MHC alleles and their interaction with critical regulators of peptide exchange bears the potential for more personalized strategies of immune modulation in the context of HLA-associated diseases.
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Affiliation(s)
- Esam T Abualrous
- Protein Biochemistry, Institute for Biochemistry, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Jana Sticht
- Protein Biochemistry, Institute for Biochemistry, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Christian Freund
- Protein Biochemistry, Institute for Biochemistry, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany.
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7
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Willis RA, Ramachandiran V, Shires JC, Bai G, Jeter K, Bell DL, Han L, Kazarian T, Ugwu KC, Laur O, Contreras-Alcantara S, Long DL, Altman JD. Production of Class II MHC Proteins in Lentiviral Vector-Transduced HEK-293T Cells for Tetramer Staining Reagents. Curr Protoc 2021; 1:e36. [PMID: 33539685 PMCID: PMC7880703 DOI: 10.1002/cpz1.36] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Class II major histocompatibility complex peptide (MHC-IIp) multimers are precisely engineered reagents used to detect T cells specific for antigens from pathogens, tumors, and self-proteins. While the related Class I MHC/peptide (MHC-Ip) multimers are usually produced from subunits expressed in E. coli, most Class II MHC alleles cannot be produced in bacteria, and this has contributed to the perception that MHC-IIp reagents are harder to produce. Herein, we present a robust constitutive expression system for soluble biotinylated MHC-IIp proteins that uses stable lentiviral vector-transduced derivatives of HEK-293T cells. The expression design includes allele-specific peptide ligands tethered to the amino-terminus of the MHC-II β chain via a protease-cleavable linker. Following cleavage of the linker, HLA-DM is used to catalyze efficient peptide exchange, enabling high-throughput production of many distinct MHC-IIp complexes from a single production cell line. Peptide exchange is monitored using either of two label-free methods, native isoelectric focusing gel electrophoresis or matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry of eluted peptides. Together, these methods produce MHC-IIp complexes that are highly homogeneous and that form the basis for excellent MHC-IIp multimer reagents. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Lentivirus production and expression line creation Support Protocol 1: Six-well assay for estimation of production cell line yield Support Protocol 2: Universal ELISA for quantifying proteins with fused leucine zippers and His-tags Basic Protocol 2: Cultures for production of Class II MHC proteins Basic Protocol 3: Purification of Class II MHC proteins by anti-leucine zipper affinity chromatography Alternate Protocol 1: IMAC purification of His-tagged Class II MHC Support Protocol 3: Protein concentration measurements and adjustments Support Protocol 4: Polishing purification by anion-exchange chromatography Support Protocol 5: Estimating biotinylation percentage by streptavidin precipitation Basic Protocol 4: Peptide exchange Basic Protocol 5: Analysis of peptide exchange by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry Alternate Protocol 2: Native isoelectric focusing to validate MHC-II peptide loading Basic Protocol 6: Multimerization Basic Protocol 7: Staining cells with Class II MHC tetramers.
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Affiliation(s)
- Richard A Willis
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia
- Yerkes National Primate Research Center, Atlanta, Georgia
| | - Vasanthi Ramachandiran
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia
- Yerkes National Primate Research Center, Atlanta, Georgia
| | - John C Shires
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia
- Yerkes National Primate Research Center, Atlanta, Georgia
| | - Ge Bai
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia
- Yerkes National Primate Research Center, Atlanta, Georgia
| | - Kelly Jeter
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia
- Yerkes National Primate Research Center, Atlanta, Georgia
| | - Donielle L Bell
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia
- Yerkes National Primate Research Center, Atlanta, Georgia
| | - Lixia Han
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia
- Yerkes National Primate Research Center, Atlanta, Georgia
| | - Tamara Kazarian
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia
- Yerkes National Primate Research Center, Atlanta, Georgia
| | - Kyla C Ugwu
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia
- Yerkes National Primate Research Center, Atlanta, Georgia
| | - Oskar Laur
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia
- Emory Custom Cloning Core Facility, Emory University School of Medicine, Atlanta, Georgia
| | - Susana Contreras-Alcantara
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia
- Yerkes National Primate Research Center, Atlanta, Georgia
| | - Dale L Long
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia
- Yerkes National Primate Research Center, Atlanta, Georgia
| | - John D Altman
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia
- Yerkes National Primate Research Center, Atlanta, Georgia
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia
- Center for AIDS Research, Emory University, Atlanta, Georgia
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8
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James EA, Mallone R, Kent SC, DiLorenzo TP. T-Cell Epitopes and Neo-epitopes in Type 1 Diabetes: A Comprehensive Update and Reappraisal. Diabetes 2020; 69:1311-1335. [PMID: 32561620 PMCID: PMC7306130 DOI: 10.2337/dbi19-0022] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 04/23/2020] [Indexed: 02/06/2023]
Abstract
The autoimmune disease type 1 diabetes is characterized by effector T-cell responses to pancreatic β-cell-derived peptides presented by HLA class I and class II molecules, leading ultimately to β-cell demise and insulin insufficiency. Although a given HLA molecule presents a vast array of peptides, only those recognized by T cells are designated as epitopes. Given their intimate link to etiology, the discovery and characterization of T-cell epitopes is a critical aspect of type 1 diabetes research. Understanding epitope recognition is also crucial for the pursuit of antigen-specific immunotherapies and implementation of strategies for T-cell monitoring. For these reasons, a cataloging and appraisal of the T-cell epitopes targeted in type 1 diabetes was completed over a decade ago, providing an important resource for both the research and the clinical communities. Here we present a much needed update and reappraisal of this earlier work and include online supplementary material where we cross-index each epitope with its primary references and Immune Epitope Database (IEDB) identifier. Our analysis includes a grading scale to score the degree of evidence available for each epitope, which conveys our perspective on several useful criteria for epitope evaluation. While providing an efficient summary of the arguably impressive current state of knowledge, this work also brings to light several deficiencies. These include the need for improved epitope validation, as few epitopes score highly by the criteria employed, and the dearth of investigations of the epitopes recognized in the context of several understudied type 1 diabetes-associated HLA molecules.
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Affiliation(s)
- Eddie A James
- Department of Translational Research, Benaroya Research Institute at Virginia Mason, Seattle, WA
| | - Roberto Mallone
- Université de Paris, Institut Cochin, CNRS, INSERM, Paris, France
- Service de Diabétologie et Immunologie Clinique, Cochin Hospital, Hôpitaux Universitaires de Paris Centre-Université de Paris, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Sally C Kent
- Diabetes Center of Excellence, Division of Diabetes, Department of Medicine, University of Massachusetts Medical School, Worcester, MA
| | - Teresa P DiLorenzo
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY
- Division of Endocrinology, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY
- Einstein-Mount Sinai Diabetes Research Center, Albert Einstein College of Medicine, Bronx, NY
- The Fleischer Institute for Diabetes and Metabolism, Albert Einstein College of Medicine, Bronx, NY
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9
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Álvaro-Benito M, Morrison E, Ebner F, Abualrous ET, Urbicht M, Wieczorek M, Freund C. Distinct editing functions of natural HLA-DM allotypes impact antigen presentation and CD4 + T cell activation. Cell Mol Immunol 2020; 17:133-142. [PMID: 30467419 PMCID: PMC7000412 DOI: 10.1038/s41423-018-0181-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 10/16/2018] [Indexed: 12/31/2022] Open
Abstract
Classical human leukocyte antigen (HLA) molecules of the major histocompatibility class II (MHCII) complex present peptides for the development, surveillance and activation of CD4+ T cells. The nonclassical MHCII-like protein HLA-DM (DM) catalyzes the exchange and loading of peptides onto MHCII molecules, thereby shaping MHCII immunopeptidomes. Natural variations of DM in both chains of the protein (DMA and DMB) have been hypothesized to impact peptide presentation, but no evidence for altered function has been reported. Here we define the presence of DM allotypes in human populations covered by the 1000 Genomes Project and probe their activity. The functional properties of several allotypes are investigated and show strong enhancement of peptide-induced T cell activation for a particular combination of DMA and DMB. Biochemical evidence suggests a broader pH activity profile for the new variant relative to that of the most commonly expressed DM allotype. Immunopeptidome analysis indicates that the compartmental activity of the new DM heterodimer extends beyond the late endosome and suggests that the natural variation of DM has profound effects on adaptive immunity when antigens bypass the canonical processing pathway.
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Affiliation(s)
- Miguel Álvaro-Benito
- Laboratory of Protein Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany.
| | - Eliot Morrison
- Laboratory of Protein Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany
| | - Friederike Ebner
- Institut für Immunologie, Department of Veterinary Medicine, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, 14163, Berlin, Germany
| | - Esam T Abualrous
- Computational Molecular Biology Group, Institute for Mathematics, Freie Universität Berlin, Berlin, Germany
| | - Marie Urbicht
- Laboratory of Protein Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany
| | - Marek Wieczorek
- Laboratory of Protein Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany
| | - Christian Freund
- Laboratory of Protein Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany.
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10
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Reyes-Vargas E, Barker AP, Zhou Z, He X, Jensen PE. HLA-DM catalytically enhances peptide dissociation by sensing peptide-MHC class II interactions throughout the peptide-binding cleft. J Biol Chem 2020; 295:2959-2973. [PMID: 31969393 PMCID: PMC7062162 DOI: 10.1074/jbc.ra119.010645] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 01/13/2020] [Indexed: 11/06/2022] Open
Abstract
Human leukocyte antigen-DM (HLA-DM) is an integral component of the major histocompatibility complex class II (MHCII) antigen-processing and -presentation pathway. HLA-DM shapes the immune system by differentially catalyzing peptide exchange on MHCII molecules, thereby editing the peptide-MHCII (pMHCII) repertoire by imposing a bias on the foreign and self-derived peptide cargos that are presented on the cell surface for immune surveillance and tolerance induction by CD4+ T cells. To better understand DM selectivity, here we developed a real-time fluorescence anisotropy assay to delineate the pMHCII intrinsic stability, DM-binding affinity, and catalytic turnover, independent kinetic parameters of HLA-DM enzymatic activity. We analyzed prominent pMHCII contacts by differentiating the kinetic parameters in pMHCII homologs, observing that peptide interactions throughout the MHCII-binding cleft influence both the rate of peptide dissociation from the DM-pMHCII catalytic complex and the binding affinity of HLA-DM for a pMHCII. We show that the intrinsic stability of a pMHCII linearly correlates with DM catalytic turnover, but is nonlinearly correlated with its binding affinity. Surprisingly, interactions at the peptides N terminus up to and including MHCII position one (P1) anchor affected the catalytic turnover, suggesting that the active DM-pMHCII catalytic complex operates on pMHCII complexes with full peptide occupancy. Furthermore, interactions at the peptide C terminus modulated DM-binding affinity, suggesting distal communication between peptide interactions with the MHCII and the DM-pMHCII binding interface. Our results imply an intimate linkage between the DM-pMHCII interface and peptide-MHCII interactions throughout the peptide-binding cleft.
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Affiliation(s)
- Eduardo Reyes-Vargas
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112
| | - Adam P Barker
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112; Department of Pathology, ARUP Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah 84108
| | - Zemin Zhou
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112
| | - Xiao He
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112.
| | - Peter E Jensen
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112; Department of Pathology, ARUP Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah 84108.
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11
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Hung SC, Hou T, Jiang W, Wang N, Qiao SW, Chow IT, Liu X, van der Burg SH, Koelle DM, Kwok WW, Sollid LM, Mellins ED. Epitope Selection for HLA-DQ2 Presentation: Implications for Celiac Disease and Viral Defense. THE JOURNAL OF IMMUNOLOGY 2019; 202:2558-2569. [PMID: 30926644 DOI: 10.4049/jimmunol.1801454] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 03/01/2019] [Indexed: 01/28/2023]
Abstract
We have reported that the major histocompatibility molecule HLA-DQ2 (DQA1*05:01/DQB1*02:01) (DQ2) is relatively resistant to HLA-DM (DM), a peptide exchange catalyst for MHC class II. In this study, we analyzed the role of DQ2/DM interaction in the generation of DQ2-restricted gliadin epitopes, relevant to celiac disease, or DQ2-restricted viral epitopes, relevant to host defense. We used paired human APC, differing in DM expression (DMnull versus DMhigh) or differing by expression of wild-type DQ2, versus a DM-susceptible, DQ2 point mutant DQ2α+53G. The APC pairs were compared for their ability to stimulate human CD4+ T cell clones. Despite higher DQ2 levels, DMhigh APC attenuated T cell responses compared with DMnull APC after intracellular generation of four tested gliadin epitopes. DMhigh APC expressing the DQ2α+53G mutant further suppressed these gliadin-mediated responses. The gliadin epitopes were found to have moderate affinity for DQ2, and even lower affinity for the DQ2 mutant, consistent with DM suppression of their presentation. In contrast, DMhigh APC significantly promoted the presentation of DQ2-restricted epitopes derived intracellularly from inactivated HSV type 2, influenza hemagglutinin, and human papillomavirus E7 protein. When extracellular peptide epitopes were used as Ag, the DQ2 surface levels and peptide affinity were the major regulators of T cell responses. The differential effect of DM on stimulation of the two groups of T cell clones implies differences in DQ2 presentation pathways associated with nonpathogen- and pathogen-derived Ags in vivo.
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Affiliation(s)
- Shu-Chen Hung
- Division of Human Gene Therapy, Department of Pediatrics, Stanford University, Stanford, CA 94305.,Program in Immunology, Stanford University, Stanford, CA 94305
| | - Tieying Hou
- Division of Human Gene Therapy, Department of Pediatrics, Stanford University, Stanford, CA 94305.,Program in Immunology, Stanford University, Stanford, CA 94305
| | - Wei Jiang
- Division of Human Gene Therapy, Department of Pediatrics, Stanford University, Stanford, CA 94305.,Program in Immunology, Stanford University, Stanford, CA 94305
| | - Nan Wang
- Division of Human Gene Therapy, Department of Pediatrics, Stanford University, Stanford, CA 94305.,Program in Immunology, Stanford University, Stanford, CA 94305
| | - Shuo-Wang Qiao
- Centre for Immune Regulation, Department of Immunology, University of Oslo and Oslo University Hospital, Rikshospitalet, 0372 Oslo, Norway.,K.G. Jebsen Coeliac Disease Research Centre, University of Oslo, 0424 Oslo, Norway
| | - I-Ting Chow
- Benaroya Research Institute at Virginia Mason, Seattle, WA 98101
| | - Xiaodan Liu
- Division of Human Gene Therapy, Department of Pediatrics, Stanford University, Stanford, CA 94305.,Program in Immunology, Stanford University, Stanford, CA 94305
| | - Sjoerd H van der Burg
- Department of Medical Oncology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - David M Koelle
- Department of Medicine, University of Washington, Seattle, WA 98195.,Department of Laboratory Medicine, University of Washington, Seattle, WA 98195; and.,Department of Global Health, University of Washington, Seattle, WA 98195
| | - William W Kwok
- Benaroya Research Institute at Virginia Mason, Seattle, WA 98101
| | - Ludvig M Sollid
- Centre for Immune Regulation, Department of Immunology, University of Oslo and Oslo University Hospital, Rikshospitalet, 0372 Oslo, Norway.,K.G. Jebsen Coeliac Disease Research Centre, University of Oslo, 0424 Oslo, Norway
| | - Elizabeth D Mellins
- Division of Human Gene Therapy, Department of Pediatrics, Stanford University, Stanford, CA 94305; .,Program in Immunology, Stanford University, Stanford, CA 94305
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12
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Class II MHC antigen processing in immune tolerance and inflammation. Immunogenetics 2018; 71:171-187. [PMID: 30421030 DOI: 10.1007/s00251-018-1095-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 10/31/2018] [Indexed: 01/22/2023]
Abstract
Presentation of peptide antigens by MHC-II proteins is prerequisite to effective CD4 T cell tolerance to self and to recognition of foreign antigens. Antigen uptake and processing pathways as well as expression of the peptide exchange factors HLA-DM and HLA-DO differ among the various professional and non-professional antigen-presenting cells and are modulated by cell developmental state and activation. Recent studies have highlighted the importance of these cell-specific factors in controlling the source and breadth of peptides presented by MHC-II under different conditions. During inflammation, increased presentation of selected self-peptides has implications for maintenance of peripheral tolerance and autoimmunity.
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13
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Ito Y, Ashenberg O, Pyrdol J, Luoma AM, Rozenblatt-Rosen O, Hofree M, Christian E, Ferrari de Andrade L, Tay RE, Teyton L, Regev A, Dougan SK, Wucherpfennig KW. Rapid CLIP dissociation from MHC II promotes an unusual antigen presentation pathway in autoimmunity. J Exp Med 2018; 215:2617-2635. [PMID: 30185635 PMCID: PMC6170167 DOI: 10.1084/jem.20180300] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 07/03/2018] [Accepted: 08/15/2018] [Indexed: 11/19/2022] Open
Abstract
Spontaneous CLIP dissociation from an autoimmunity-associated MHC II protein enhances presentation of peptides released by insulin-producing β cells. Presentation of such extracellular peptides does not require endosomal antigen processing and augments islet infiltration by CD4 T cells. A number of autoimmunity-associated MHC class II proteins interact only weakly with the invariant chain–derived class II–associated invariant chain peptide (CLIP). CLIP dissociates rapidly from I-Ag7 even in the absence of DM, and this property is related to the type 1 diabetes–associated β57 polymorphism. We generated knock-in non-obese diabetic (NOD) mice with a single amino acid change in the CLIP segment of the invariant chain in order to moderately slow CLIP dissociation from I-Ag7. These knock-in mice had a significantly reduced incidence of spontaneous type 1 diabetes and diminished islet infiltration by CD4 T cells, in particular T cells specific for fusion peptides generated by covalent linkage of proteolytic fragments within β cell secretory granules. Rapid CLIP dissociation enhanced the presentation of such extracellular peptides, thus bypassing the conventional MHC class II antigen-processing pathway. Autoimmunity-associated MHC class II polymorphisms therefore not only modify binding of self-peptides, but also alter the biochemistry of peptide acquisition.
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Affiliation(s)
- Yoshinaga Ito
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA.,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA
| | - Orr Ashenberg
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
| | - Jason Pyrdol
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA
| | - Adrienne M Luoma
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA.,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA
| | | | - Matan Hofree
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
| | - Elena Christian
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
| | - Lucas Ferrari de Andrade
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA.,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA
| | - Rong En Tay
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA.,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA
| | - Luc Teyton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA
| | - Aviv Regev
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
| | - Stephanie K Dougan
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA .,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA
| | - Kai W Wucherpfennig
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA .,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA
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14
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Alvaro-Benito M, Morrison E, Wieczorek M, Sticht J, Freund C. Human leukocyte Antigen-DM polymorphisms in autoimmune diseases. Open Biol 2017; 6:rsob.160165. [PMID: 27534821 PMCID: PMC5008016 DOI: 10.1098/rsob.160165] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Accepted: 07/19/2016] [Indexed: 12/20/2022] Open
Abstract
Classical MHC class II (MHCII) proteins present peptides for CD4+ T-cell surveillance and are by far the most prominent risk factor for a number of autoimmune disorders. To date, many studies have shown that this link between particular MHCII alleles and disease depends on the MHCII's particular ability to bind and present certain peptides in specific physiological contexts. However, less attention has been paid to the non-classical MHCII molecule human leucocyte antigen-DM, which catalyses peptide exchange on classical MHCII proteins acting as a peptide editor. DM function impacts the presentation of both antigenic peptides in the periphery and key self-peptides during T-cell development in the thymus. In this way, DM activity directly influences the response to pathogens, as well as mechanisms of self-tolerance acquisition. While decreased DM editing of particular MHCII proteins has been proposed to be related to autoimmune disorders, no experimental evidence for different DM catalytic properties had been reported until recently. Biochemical and structural investigations, together with new animal models of loss of DM activity, have provided an attractive foundation for identifying different catalytic efficiencies for DM allotypes. Here, we revisit the current knowledge of DM function and discuss how DM function may impart autoimmunity at the organism level.
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Affiliation(s)
- Miguel Alvaro-Benito
- Protein Biochemistry Group, Institute for Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Eliot Morrison
- Protein Biochemistry Group, Institute for Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Marek Wieczorek
- Protein Biochemistry Group, Institute for Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Jana Sticht
- Protein Biochemistry Group, Institute for Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Christian Freund
- Protein Biochemistry Group, Institute for Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
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15
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Evolving Insights for MHC Class II Antigen Processing and Presentation in Health and Disease. ACTA ACUST UNITED AC 2017. [DOI: 10.1007/s40495-017-0097-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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16
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Wieczorek M, Abualrous ET, Sticht J, Álvaro-Benito M, Stolzenberg S, Noé F, Freund C. Major Histocompatibility Complex (MHC) Class I and MHC Class II Proteins: Conformational Plasticity in Antigen Presentation. Front Immunol 2017. [PMID: 28367149 DOI: 10.3389/fimmu.2017.00292.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Antigen presentation by major histocompatibility complex (MHC) proteins is essential for adaptive immunity. Prior to presentation, peptides need to be generated from proteins that are either produced by the cell's own translational machinery or that are funneled into the endo-lysosomal vesicular system. The prolonged interaction between a T cell receptor and specific pMHC complexes, after an extensive search process in secondary lymphatic organs, eventually triggers T cells to proliferate and to mount a specific cellular immune response. Once processed, the peptide repertoire presented by MHC proteins largely depends on structural features of the binding groove of each particular MHC allelic variant. Additionally, two peptide editors-tapasin for class I and HLA-DM for class II-contribute to the shaping of the presented peptidome by favoring the binding of high-affinity antigens. Although there is a vast amount of biochemical and structural information, the mechanism of the catalyzed peptide exchange for MHC class I and class II proteins still remains controversial, and it is not well understood why certain MHC allelic variants are more susceptible to peptide editing than others. Recent studies predict a high impact of protein intermediate states on MHC allele-specific peptide presentation, which implies a profound influence of MHC dynamics on the phenomenon of immunodominance and the development of autoimmune diseases. Here, we review the recent literature that describe MHC class I and II dynamics from a theoretical and experimental point of view and we highlight the similarities between MHC class I and class II dynamics despite the distinct functions they fulfill in adaptive immunity.
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Affiliation(s)
- Marek Wieczorek
- Protein Biochemistry, Institute for Biochemistry, Freie Universität Berlin , Berlin , Germany
| | - Esam T Abualrous
- Computational Molecular Biology Group, Institute for Mathematics , Berlin , Germany
| | - Jana Sticht
- Protein Biochemistry, Institute for Biochemistry, Freie Universität Berlin , Berlin , Germany
| | - Miguel Álvaro-Benito
- Protein Biochemistry, Institute for Biochemistry, Freie Universität Berlin , Berlin , Germany
| | | | - Frank Noé
- Computational Molecular Biology Group, Institute for Mathematics , Berlin , Germany
| | - Christian Freund
- Protein Biochemistry, Institute for Biochemistry, Freie Universität Berlin , Berlin , Germany
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17
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Nguyen TB, Jayaraman P, Bergseng E, Madhusudhan MS, Kim CY, Sollid LM. Unraveling the structural basis for the unusually rich association of human leukocyte antigen DQ2.5 with class-II-associated invariant chain peptides. J Biol Chem 2017; 292:9218-9228. [PMID: 28364043 DOI: 10.1074/jbc.m117.785139] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 03/28/2017] [Indexed: 11/06/2022] Open
Abstract
Human leukocyte antigen (HLA)-DQ2.5 (DQA1*05/DQB1*02) is a class-II major histocompatibility complex protein associated with both type 1 diabetes and celiac disease. One unusual feature of DQ2.5 is its high class-II-associated invariant chain peptide (CLIP) content. Moreover, HLA-DQ2.5 preferentially binds the non-canonical CLIP2 over the canonical CLIP1. To better understand the structural basis of HLA-DQ2.5's unusual CLIP association characteristics, better insight into the HLA-DQ2.5·CLIP complex structures is required. To this end, we determined the X-ray crystal structure of the HLA-DQ2.5· CLIP1 and HLA-DQ2.5·CLIP2 complexes at 2.73 and 2.20 Å, respectively. We found that HLA-DQ2.5 has an unusually large P4 pocket and a positively charged peptide-binding groove that together promote preferential binding of CLIP2 over CLIP1. An α9-α22-α24-α31-β86-β90 hydrogen bond network located at the bottom of the peptide-binding groove, spanning from the P1 to P4 pockets, renders the residues in this region relatively immobile. This hydrogen bond network, along with a deletion mutation at α53, may lead to HLA-DM insensitivity in HLA-DQ2.5. A molecular dynamics simulation experiment reported here and recent biochemical studies by others support this hypothesis. The diminished HLA-DM sensitivity is the likely reason for the CLIP-rich phenotype of HLA-DQ2.5.
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Affiliation(s)
- Thanh-Binh Nguyen
- the Bioinformatics Institute, Singapore 138671, Singapore.,the Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Priya Jayaraman
- the Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Elin Bergseng
- the Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital, N-0372 Oslo, Norway
| | - M S Madhusudhan
- the Bioinformatics Institute, Singapore 138671, Singapore.,the Indian Institute of Science Education and Research, Pune 411008, India, and
| | - Chu-Young Kim
- From the Department of Chemistry and .,School of Pharmacy, University of Texas at El Paso, El Paso, Texas 79968.,Synthetic Biology for Clinical and Technological Innovation, Life Sciences Institute, National University of Singapore, 117456 Singapore, Singapore
| | - Ludvig M Sollid
- the Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital, N-0372 Oslo, Norway
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18
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Wieczorek M, Abualrous ET, Sticht J, Álvaro-Benito M, Stolzenberg S, Noé F, Freund C. Major Histocompatibility Complex (MHC) Class I and MHC Class II Proteins: Conformational Plasticity in Antigen Presentation. Front Immunol 2017; 8:292. [PMID: 28367149 PMCID: PMC5355494 DOI: 10.3389/fimmu.2017.00292] [Citation(s) in RCA: 564] [Impact Index Per Article: 80.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 02/28/2017] [Indexed: 11/21/2022] Open
Abstract
Antigen presentation by major histocompatibility complex (MHC) proteins is essential for adaptive immunity. Prior to presentation, peptides need to be generated from proteins that are either produced by the cell’s own translational machinery or that are funneled into the endo-lysosomal vesicular system. The prolonged interaction between a T cell receptor and specific pMHC complexes, after an extensive search process in secondary lymphatic organs, eventually triggers T cells to proliferate and to mount a specific cellular immune response. Once processed, the peptide repertoire presented by MHC proteins largely depends on structural features of the binding groove of each particular MHC allelic variant. Additionally, two peptide editors—tapasin for class I and HLA-DM for class II—contribute to the shaping of the presented peptidome by favoring the binding of high-affinity antigens. Although there is a vast amount of biochemical and structural information, the mechanism of the catalyzed peptide exchange for MHC class I and class II proteins still remains controversial, and it is not well understood why certain MHC allelic variants are more susceptible to peptide editing than others. Recent studies predict a high impact of protein intermediate states on MHC allele-specific peptide presentation, which implies a profound influence of MHC dynamics on the phenomenon of immunodominance and the development of autoimmune diseases. Here, we review the recent literature that describe MHC class I and II dynamics from a theoretical and experimental point of view and we highlight the similarities between MHC class I and class II dynamics despite the distinct functions they fulfill in adaptive immunity.
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Affiliation(s)
- Marek Wieczorek
- Protein Biochemistry, Institute for Biochemistry, Freie Universität Berlin , Berlin , Germany
| | - Esam T Abualrous
- Computational Molecular Biology Group, Institute for Mathematics , Berlin , Germany
| | - Jana Sticht
- Protein Biochemistry, Institute for Biochemistry, Freie Universität Berlin , Berlin , Germany
| | - Miguel Álvaro-Benito
- Protein Biochemistry, Institute for Biochemistry, Freie Universität Berlin , Berlin , Germany
| | | | - Frank Noé
- Computational Molecular Biology Group, Institute for Mathematics , Berlin , Germany
| | - Christian Freund
- Protein Biochemistry, Institute for Biochemistry, Freie Universität Berlin , Berlin , Germany
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19
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Zhou Z, Reyes-Vargas E, Escobar H, Chang KY, Barker AP, Rockwood AL, Delgado JC, He X, Jensen PE. Peptidomic analysis of type 1 diabetes associated HLA-DQ molecules and the impact of HLA-DM on peptide repertoire editing. Eur J Immunol 2016; 47:314-326. [PMID: 27861808 DOI: 10.1002/eji.201646656] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 10/21/2016] [Accepted: 11/10/2016] [Indexed: 11/08/2022]
Abstract
HLA-DM and class II associated invariant chain (Ii) are key cofactors in the MHC class II (MHCII) antigen processing pathway. We used tandem mass spectrometry sequencing to directly interrogate the global impact of DM and Ii on the repertoire of MHCII-bound peptides in human embryonic kidney 293T cells expressing HLA-DQ molecules in the absence or presence of these cofactors. We found that Ii and DM have a major impact on the repertoire of peptides presented by DQ1 and DQ6, with the caveat that this technology is not quantitative. The peptide repertoires of type 1 diabetes (T1D) associated DQ8, DQ2, and DQ8/2 are altered to a lesser degree by DM expression, and these molecules share overlapping features in their peptide binding motifs that are distinct from control DQ1 and DQ6 molecules. Peptides were categorized into DM-resistant, DM-dependent, or DM-sensitive groups based on the mass spectrometry data, and representative peptides were tested in competitive binding assays and peptide dissociation rate experiments with soluble DQ6. Our data support the conclusion that high intrinsic stability of DQ-peptide complexes is necessary but not sufficient to confer resistance to DM editing, and provide candidate parameters that may be useful in predicting the sensitivity of T-cell epitopes to DM editing.
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Affiliation(s)
- Zemin Zhou
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | | | | | - Kuan Y Chang
- Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung, Taiwan
| | - Adam P Barker
- Department of Pathology, University of Utah, Salt Lake City, UT, USA.,ARUP Laboratories, University of Utah, Salt Lake City, UT, USA
| | - Alan L Rockwood
- Department of Pathology, University of Utah, Salt Lake City, UT, USA.,ARUP Laboratories, University of Utah, Salt Lake City, UT, USA
| | - Julio C Delgado
- Department of Pathology, University of Utah, Salt Lake City, UT, USA.,ARUP Laboratories, University of Utah, Salt Lake City, UT, USA
| | - Xiao He
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Peter E Jensen
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
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20
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Stern LJ, Santambrogio L. The melting pot of the MHC II peptidome. Curr Opin Immunol 2016; 40:70-7. [PMID: 27018930 DOI: 10.1016/j.coi.2016.03.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 03/14/2016] [Accepted: 03/15/2016] [Indexed: 02/07/2023]
Abstract
Recent advances in mass spectrometry technology have facilitated detailed examination of MHC-II immunopeptidomes, for example the repertoires of peptides bound to MHC-II molecules expressed in antigen presenting cells. These studies have deepened our view of MHC-II presentation. Other studies have broadened our view of pathways leading up to peptide loading. Here we review these recent studies in the context of earlier work on conventional and non-conventional MHC-II processing. The message that emerges is that sources of antigen beyond conventional endosomal processing of endocytosed proteins are important for generation of cellular immune responses to pathogens and maintenance of central and peripheral tolerance. The multiplicity of pathways results in a broad MHC II immunopeptidome that conveys the sampled environment to patrolling T cells.
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Affiliation(s)
- Lawrence J Stern
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01655, United States; Department of Biochemistry & Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, United States; Graduate Program in Immunology and Microbiology, University of Massachusetts Medical School, Worcester, MA 01655, United States.
| | - Laura Santambrogio
- Department of Pathology, Albert Einstein College of Medicine, NY 10461, United States; Department of Microbiology & Immunology, Albert Einstein College of Medicine, NY 10461, United States
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