1
|
Cullum E, Perez-Betancourt Y, Shi M, Gkika E, Schneewind O, Missiakas D, Golovkina T. Deficiency in non-classical major histocompatibility class II-like molecule, H2-O confers protection against Staphylococcus aureus in mice. PLoS Pathog 2024; 20:e1012306. [PMID: 38843309 PMCID: PMC11185455 DOI: 10.1371/journal.ppat.1012306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 06/18/2024] [Accepted: 05/29/2024] [Indexed: 06/19/2024] Open
Abstract
Staphylococcus aureus is a human-adapted pathogen that replicates by asymptomatically colonizing its host. S. aureus is also the causative agent of purulent skin and soft tissue infections as well as bloodstream infections that result in the metastatic seeding of abscess lesions in all organ tissues. Prolonged colonization, infection, disease relapse, and recurrence point to the versatile capacity of S. aureus to bypass innate and adaptive immune defenses as well as the notion that some hosts fail to generate protective immune responses. Here, we find a genetic trait that provides protection against this pathogen. Mice lacking functional H2-O, the equivalent of human HLA-DO, inoculated with a mouse-adapted strain of S. aureus, efficiently decolonize the pathogen. Further, these decolonized animals resist subsequent bloodstream challenge with methicillin-resistant S. aureus. A genetic approach demonstrates that T-cell dependent B cell responses are required to control S. aureus colonization and infection in H2-O-deficient mice. Reduced bacterial burdens in these animals correlate with increased titers and enhanced phagocytic activity of S. aureus-specific antibodies. H2-O negatively regulates the loading of high affinity peptides on major histocompatibility class II (MHC-II) molecules. Thus, we hypothesize that immune responses against S. aureus are derepressed in mice lacking H2-O because more high affinity peptides are presented by MHC-II. We speculate that loss-of-function HLA-DO alleles may similarly control S. aureus replication in humans.
Collapse
Affiliation(s)
- Emily Cullum
- Department of Microbiology, University of Chicago, Chicago, Illinois, United States of America
- Committee on Immunology, University of Chicago, Chicago, Illinois, United States of America
| | - Yunys Perez-Betancourt
- Department of Microbiology, University of Chicago, Chicago, Illinois, United States of America
- Howard T. Ricketts Laboratory, University of Chicago, Chicago, Illinois, United States of America
| | - Miaomiao Shi
- Department of Microbiology, University of Chicago, Chicago, Illinois, United States of America
- Howard T. Ricketts Laboratory, University of Chicago, Chicago, Illinois, United States of America
| | - Eirinaios Gkika
- Department of Microbiology, University of Chicago, Chicago, Illinois, United States of America
| | - Olaf Schneewind
- Department of Microbiology, University of Chicago, Chicago, Illinois, United States of America
| | - Dominique Missiakas
- Department of Microbiology, University of Chicago, Chicago, Illinois, United States of America
- Howard T. Ricketts Laboratory, University of Chicago, Chicago, Illinois, United States of America
| | - Tatyana Golovkina
- Department of Microbiology, University of Chicago, Chicago, Illinois, United States of America
- Committee on Immunology, University of Chicago, Chicago, Illinois, United States of America
- Committee on Microbiology, University of Chicago, Chicago, Illinois, United States of America
- Committee on Genetics, Genomics and System Biology, University of Chicago, Chicago, Illinois, United States of America
| |
Collapse
|
2
|
Wang N, Waghray D, Caveney NA, Jude KM, Garcia KC. Structural insights into human MHC-II association with invariant chain. Proc Natl Acad Sci U S A 2024; 121:e2403031121. [PMID: 38687785 PMCID: PMC11087810 DOI: 10.1073/pnas.2403031121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 03/29/2024] [Indexed: 05/02/2024] Open
Abstract
The loading of processed peptides on to major histocompatibility complex II (MHC-II) molecules for recognition by T cells is vital to cell-mediated adaptive immunity. As part of this process, MHC-II associates with the invariant chain (Ii) during biosynthesis in the endoplasmic reticulum to prevent premature peptide loading and to serve as a scaffold for subsequent proteolytic processing into MHC-II-CLIP. Cryo-electron microscopy structures of full-length Human Leukocyte Antigen-DR (HLA-DR) and HLA-DQ complexes associated with Ii, resolved at 3.0 to 3.1 Å, elucidate the trimeric assembly of the HLA/Ii complex and define atomic-level interactions between HLA, Ii transmembrane domains, loop domains, and class II-associated invariant chain peptides (CLIP). Together with previous structures of MHC-II peptide loading intermediates DO and DM, our findings complete the structural path governing class II antigen presentation.
Collapse
Affiliation(s)
- Nan Wang
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA94305
- HHMI, Stanford University School of Medicine, Stanford, CA94305
| | - Deepa Waghray
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA94305
| | - Nathanael A. Caveney
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA94305
| | - Kevin M. Jude
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA94305
- HHMI, Stanford University School of Medicine, Stanford, CA94305
| | - K. Christopher Garcia
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA94305
- HHMI, Stanford University School of Medicine, Stanford, CA94305
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA94305
| |
Collapse
|
3
|
Mariuzza RA, Shahid S, Karade SS. The immune checkpoint receptor LAG3: Structure, function, and target for cancer immunotherapy. J Biol Chem 2024; 300:107241. [PMID: 38556085 PMCID: PMC11061240 DOI: 10.1016/j.jbc.2024.107241] [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: 01/29/2024] [Revised: 03/21/2024] [Accepted: 03/25/2024] [Indexed: 04/02/2024] Open
Abstract
Lymphocyte activation gene 3 protein (LAG3) is an immune checkpoint receptor that is highly upregulated on exhausted T cells in the tumor microenvironment. LAG3 transmits inhibitory signals to T cells upon binding to MHC class II and other ligands, rendering T cells dysfunctional. Consequently, LAG3 is a major target for cancer immunotherapy with many anti-LAG3 monoclonal antibodies (mAbs) that block LAG3 inhibitory activity in clinical trials. In this review, we examine the molecular basis for LAG3 function in light of recently determined crystal and cryoEM structures of this inhibitory receptor. We review what is known about LAG3 interactions with MHC class II, its canonical ligand, and the newly discovered ligands FGL1 and the T cell receptor (TCR)-CD3 complex, including current controversies over the relative importance of these ligands. We then address the development and mechanisms of action of anti-LAG3 mAbs in clinical trials for cancer immunotherapy. We discuss new strategies to therapeutically target LAG3 using mAbs that not only block the LAG3-MHC class II interaction, but also LAG3 interactions with FGL1 or TCR-CD3, or that disrupt LAG3 dimerization. Finally, we assess the possibility of developing mAbs that enhance, rather than block, LAG3 inhibitory activity as treatments for autoimmune diseases.
Collapse
Affiliation(s)
- Roy A Mariuzza
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA.
| | - Salman Shahid
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
| | - Sharanbasappa S Karade
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland, USA; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
| |
Collapse
|
4
|
Jiang J, Natarajan K, Margulies DH. Chaperone-mediated MHC-I peptide exchange in antigen presentation. IUCRJ 2024; 11:287-298. [PMID: 38656309 PMCID: PMC11067752 DOI: 10.1107/s2052252524002768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 03/26/2024] [Indexed: 04/26/2024]
Abstract
This work focuses on molecules that are encoded by the major histocompatibility complex (MHC) and that bind self-, foreign- or tumor-derived peptides and display these at the cell surface for recognition by receptors on T lymphocytes (T cell receptors, TCR) and natural killer (NK) cells. The past few decades have accumulated a vast knowledge base of the structures of MHC molecules and the complexes of MHC/TCR with specificity for many different peptides. In recent years, the structures of MHC-I molecules complexed with chaperones that assist in peptide loading have been revealed by X-ray crystallography and cryogenic electron microscopy. These structures have been further studied using mutagenesis, molecular dynamics and NMR approaches. This review summarizes the current structures and dynamic principles that govern peptide exchange as these relate to the process of antigen presentation.
Collapse
Affiliation(s)
- Jiansheng Jiang
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA
| | - Kannan Natarajan
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA
| | - David H. Margulies
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA
| |
Collapse
|
5
|
Fu M. Evolutionary analysis of major histocompatibility complex variants in chytrid-resistant and susceptible amphibians. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 118:105544. [PMID: 38216106 DOI: 10.1016/j.meegid.2023.105544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 10/09/2023] [Accepted: 12/17/2023] [Indexed: 01/14/2024]
Abstract
An amphibian emerging infectious disease (EID), chytridiomycosis, caused by Batrachochytrium dendrobatidis (Bd), originated in Asia but primarily led to declines and extinctions in amphibian populations outside of Asia. Host major histocompatibility complex (MHC) molecules exhibit high polymorphism, and the evolution of MHC can be influenced by recombination and pathogens. Previous studies have indicated that host MHC class II is associated with Bd resistance. In this study, I conducted recombination and selection tests on functional MHC IIß1 alleles from an Asian Bd-resistant anuran species (Bufo gargarizans) and an Australasian Bd-susceptible species (Litoria caerulea). Recombination at the same site was identified in both species, supporting the hypothesis that recombination contributes to MHC IIß1 diversity in amphibians. Positive selection was observed in MHC IIß1 alleles in both species. In L. caerulea, at least four amino acid sites were identified under significant positive selection in the MHC IIß1, whereas these sites were either negatively selected or conserved in B. gargarizans. This suggests these sites might be selected for Bd resistance. Hydrophobicity was detected in certain amino acid sites relating to Bd resistance, suggesting this physicochemical property may be a factor selected to counteract Bd infection. These findings of this study provide an evolutionary basis for understanding how amphibian MHC IIß1 may undergo selection in response to chytrid infection.
Collapse
Affiliation(s)
- Minjie Fu
- School of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul 08826, Republic of Korea; Research Institute of Basic Sciences, Seoul National University, Seoul 08826, Republic of Korea.
| |
Collapse
|
6
|
Hu J, Song L, Ning M, Niu X, Han M, Gao C, Feng X, Cai H, Li T, Li F, Li H, Gong D, Song W, Liu L, Pu J, Liu J, Smith J, Sun H, Huang Y. A new chromosome-scale duck genome shows a major histocompatibility complex with several expanded multigene families. BMC Biol 2024; 22:31. [PMID: 38317190 PMCID: PMC10845735 DOI: 10.1186/s12915-024-01817-0] [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: 09/01/2022] [Accepted: 01/04/2024] [Indexed: 02/07/2024] Open
Abstract
BACKGROUND The duck (Anas platyrhynchos) is one of the principal natural hosts of influenza A virus (IAV), harbors almost all subtypes of IAVs and resists to many IAVs which cause extreme virulence in chicken and human. However, the response of duck's adaptive immune system to IAV infection is poorly characterized due to lack of a detailed gene map of the major histocompatibility complex (MHC). RESULTS We herein reported a chromosome-scale Beijing duck assembly by integrating Nanopore, Bionano, and Hi-C data. This new reference genome SKLA1.0 covers 40 chromosomes, improves the contig N50 of the previous duck assembly with highest contiguity (ZJU1.0) of more than a 5.79-fold, surpasses the chicken and zebra finch references in sequence contiguity and contains a complete genomic map of the MHC. Our 3D MHC genomic map demonstrated that gene family arrangement in this region was primordial; however, families such as AnplMHCI, AnplMHCIIβ, AnplDMB, NKRL (NK cell receptor-like genes) and BTN underwent gene expansion events making this area complex. These gene families are distributed in two TADs and genes sharing the same TAD may work in a co-regulated model. CONCLUSIONS These observations supported the hypothesis that duck's adaptive immunity had been optimized with expanded and diversified key immune genes which might help duck to combat influenza virus. This work provided a high-quality Beijing duck genome for biological research and shed light on new strategies for AIV control.
Collapse
Affiliation(s)
- Jiaxiang Hu
- State Key Laboratory of Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China
| | - Linfei Song
- State Key Laboratory of Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China
| | - Mengfei Ning
- State Key Laboratory of Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China
| | - Xinyu Niu
- State Key Laboratory of Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China
| | - Mengying Han
- State Key Laboratory of Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China
| | - Chuze Gao
- State Key Laboratory of Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China
| | - Xingwei Feng
- State Key Laboratory of Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China
| | - Han Cai
- State Key Laboratory of Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China
| | - Te Li
- State Key Laboratory of Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China
| | - Fangtao Li
- Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China
| | - Huifang Li
- Jiangsu Institute of Poultry Science, Yangzhou, China
| | - Daoqing Gong
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Weitao Song
- Jiangsu Institute of Poultry Science, Yangzhou, China
| | - Long Liu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Juan Pu
- Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China
| | - Jinhua Liu
- Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China
| | - Jacqueline Smith
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK
| | - Honglei Sun
- Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China.
| | - Yinhua Huang
- State Key Laboratory of Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, No.2 Yuan Ming Yuan West Road, Hai Dian District, Beijing, 100193, China.
| |
Collapse
|
7
|
Song N, Welsh RA, Sadegh-Nasseri S. Proper development of long-lived memory CD4 T cells requires HLA-DO function. Front Immunol 2023; 14:1277609. [PMID: 37908352 PMCID: PMC10613709 DOI: 10.3389/fimmu.2023.1277609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 10/03/2023] [Indexed: 11/02/2023] Open
Abstract
Introduction HLA-DO (DO) is an accessory protein that binds DM for trafficking to MIIC and has peptide editing functions. DO is mainly expressed in thymic medulla and B cells. Using biochemical experiments, our lab has discovered that DO has differential effects on editing peptides of different sequences: DO increases binding of DM-resistant peptides and reduces the binding of DM-sensitive peptides to the HLA-DR1 molecules. In a separate line of work, we have established that appropriate densities of antigen presentation by B cells during the contraction phase of an infection, induces quiescence in antigen experienced CD4 T cells, as they differentiate into memory T cells. This quiescence phenotype helps memory CD4 T cell survival and promotes effective memory responses to secondary Ag challenge. Methods Based on our mechanistic understanding of DO function, it would be expected that if the immunodominant epitope of antigen is DM-resistant, presentation of decreased densities of pMHCII by B cells would lead to faulty development of memory CD4 T cells in the absence of DO. We explored the effects of DO on development of memory CD4 T cells and B cells utilizing two model antigens, H5N1-Flu Ag bearing DM-resistant, and OVA protein, which has a DM-sensitive immunodominant epitope and four mouse strains including two DO-deficient Tg mice. Using Tetramers and multiple antibodies against markers of memory CD4 T cells and B cells, we tracked memory development. Results We found that immunized DR1+DO-KO mice had fewer CD4 memory T cells and memory B cells as compared to the DR1+DO-WT counterpart and had compromised recall responses. Conversely, OVA specific memory responses elicited in HA immunized DR1+DO-KO mice were normal. Conclusion These results demonstrate that in the absence of DO, the presentation of cognate foreign antigens in the DO-KO mice is altered and can impact the proper development of memory cells. These findings provide new insights on vaccination design leading to better immune memory responses.
Collapse
|
8
|
Abualrous ET, Stolzenberg S, Sticht J, Wieczorek M, Roske Y, Günther M, Dähn S, Boesen BB, Calvo MM, Biese C, Kuppler F, Medina-García Á, Álvaro-Benito M, Höfer T, Noé F, Freund C. MHC-II dynamics are maintained in HLA-DR allotypes to ensure catalyzed peptide exchange. Nat Chem Biol 2023; 19:1196-1204. [PMID: 37142807 PMCID: PMC10522485 DOI: 10.1038/s41589-023-01316-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 03/17/2023] [Indexed: 05/06/2023]
Abstract
Presentation of antigenic peptides by major histocompatibility complex class II (MHC-II) proteins determines T helper cell reactivity. The MHC-II genetic locus displays a large degree of allelic polymorphism influencing the peptide repertoire presented by the resulting MHC-II protein allotypes. During antigen processing, the human leukocyte antigen (HLA) molecule HLA-DM (DM) encounters these distinct allotypes and catalyzes exchange of the placeholder peptide CLIP by exploiting dynamic features of MHC-II. Here, we investigate 12 highly abundant CLIP-bound HLA-DRB1 allotypes and correlate dynamics to catalysis by DM. Despite large differences in thermodynamic stability, peptide exchange rates fall into a target range that maintains DM responsiveness. A DM-susceptible conformation is conserved in MHC-II molecules, and allosteric coupling between polymorphic sites affects dynamic states that influence DM catalysis. As exemplified for rheumatoid arthritis, we postulate that intrinsic dynamic features of peptide-MHC-II complexes contribute to the association of individual MHC-II allotypes with autoimmune disease.
Collapse
Affiliation(s)
- Esam T Abualrous
- Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
- Department of Physics, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Sebastian Stolzenberg
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | - Jana Sticht
- Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
- Core Facility BioSupraMol, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Marek Wieczorek
- Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Yvette Roske
- Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Matthias Günther
- Theoretische Systembiologie (B086), Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - Steffen Dähn
- Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Benedikt B Boesen
- Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Marcos Martínez Calvo
- Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Charlotte Biese
- Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Frank Kuppler
- Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Álvaro Medina-García
- Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Miguel Álvaro-Benito
- Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Thomas Höfer
- Theoretische Systembiologie (B086), Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - Frank Noé
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany.
- Microsoft Research AI4Science, Berlin, Germany.
- Department of Physics, Freie Universität Berlin, Berlin, Germany.
- Department of Chemistry, Rice University, Houston, TX, USA.
| | - Christian Freund
- Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany.
| |
Collapse
|
9
|
Landry SJ, Mettu RR, Kolls JK, Aberle JH, Norton E, Zwezdaryk K, Robinson J. Structural Framework for Analysis of CD4+ T-Cell Epitope Dominance in Viral Fusion Proteins. Biochemistry 2023; 62:2517-2529. [PMID: 37554055 PMCID: PMC10483696 DOI: 10.1021/acs.biochem.3c00335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/31/2023] [Indexed: 08/10/2023]
Abstract
Antigen conformation shapes CD4+ T-cell specificity through mechanisms of antigen processing, and the consequences for immunity may rival those from conformational effects on antibody specificity. CD4+ T cells initiate and control immunity to pathogens and cancer and are at least partly responsible for immunopathology associated with infection, autoimmunity, and allergy. The primary trigger for CD4+ T-cell maturation is the presentation of an epitope peptide in the MHC class II antigen-presenting protein (MHCII), most commonly on an activated dendritic cell, and then the T-cell responses are recalled by subsequent presentations of the epitope peptide by the same or other antigen-presenting cells. Peptide presentation depends on the proteolytic fragmentation of the antigen in an endosomal/lysosomal compartment and concomitant loading of the fragments into the MHCII, a multistep mechanism called antigen processing and presentation. Although the role of peptide affinity for MHCII has been well studied, the role of proteolytic fragmentation has received less attention. In this Perspective, we will briefly summarize evidence that antigen resistance to unfolding and proteolytic fragmentation shapes the specificity of the CD4+ T-cell response to selected viral envelope proteins, identify several remarkable examples in which the immunodominant CD4+ epitopes most likely depend on the interaction of processing machinery with antigen conformation, and outline how knowledge of antigen conformation can inform future efforts to design vaccines.
Collapse
Affiliation(s)
- Samuel J. Landry
- Department
of Biochemistry and Molecular Biology, Tulane
University School of Medicine, New Orleans, Louisiana 70112, United States
| | - Ramgopal R. Mettu
- Department
of Computer Science, Tulane University, New Orleans, Louisiana 70118, United States
| | - Jay K. Kolls
- John
W. Deming Department of Internal Medicine, Center for Translational
Research in Infection and Inflammation, Tulane University School of Medicine, New Orleans, Louisiana 70112, United States
| | - Judith H. Aberle
- Center
for Virology, Medical University of Vienna, 1090 Vienna, Austria
| | - Elizabeth Norton
- Department
of Microbiology & Immunology, Tulane
University School of Medicine, New Orleans, Louisiana 70112, United States
| | - Kevin Zwezdaryk
- Department
of Microbiology & Immunology, Tulane
University School of Medicine, New Orleans, Louisiana 70112, United States
| | - James Robinson
- Department
of Pediatrics, Tulane University School
of Medicine, New Orleans, Louisiana 70112, United States
| |
Collapse
|
10
|
Fu M, Eimes JA, Kong S, Lamichhaney S, Waldman B. Identification of major histocompatibility complex genotypes associated with resistance to an amphibian emerging infectious disease. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 113:105470. [PMID: 37336279 DOI: 10.1016/j.meegid.2023.105470] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 06/12/2023] [Accepted: 06/16/2023] [Indexed: 06/21/2023]
Abstract
Amphibian chytridiomycosis, caused by Batrachochytrium dendrobatidis (Bd), emerged from Asia and spread globally. By comparing functional MHC IIß1 alleles from an Asian Bd-resistant anuran species (Bufo gargarizans) with those of an Australasian Bd-susceptible species (Litoria caerulea), we identified MHC genotypes associated with Bd resistance. These alleles encode a glycine deletion (G90β1) and adjacent motifs in the deepest pathogen-derived peptide-binding groove. Every Bd-resistant individual, but no susceptible individuals, possessed at least one allele encoding the variant. We detected trans-species polymorphism at the end of the MHC IIβ1 sequences. The G90β1 deletion was encoded by different alleles in the two species, suggesting it may have evolved independently in each species rather than having been derived from a common ancestor. These results are consistent with a scenario by which MHC adaptations that confer resistance to the pathogen have evolved by convergent evolution. Immunogenetic studies such as this are critical to ongoing conservation efforts.
Collapse
Affiliation(s)
- Minjie Fu
- School of Biological Sciences, Seoul National University, Seoul 08826, South Korea.
| | - John A Eimes
- University College, Sungkyunkwan University, Suwon 16419, South Korea.
| | - Sungsik Kong
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Sangeet Lamichhaney
- Department of Biological Sciences, Kent State University, Kent, OH 44243, USA
| | - Bruce Waldman
- School of Biological Sciences, Seoul National University, Seoul 08826, South Korea; Department of Integrative Biology, Oklahoma State University, Stillwater, OK 74078, USA
| |
Collapse
|
11
|
Li L, Peng X, Batliwala M, Bouvier M. Crystal structures of MHC class I complexes reveal the elusive intermediate conformations explored during peptide editing. Nat Commun 2023; 14:5020. [PMID: 37596268 PMCID: PMC10439229 DOI: 10.1038/s41467-023-40736-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 08/08/2023] [Indexed: 08/20/2023] Open
Abstract
Studies have suggested that MHC class I (MHC I) molecules fluctuate rapidly between numerous conformational states and these motions support peptide sampling. To date, MHC I intermediates are largely uncharacterized experimentally and remain elusive. Here, we present x-ray crystal structures of HLA-B8 loaded with 20mer peptides that show pronounced distortions at the N-terminus of the groove. Long stretches of N-terminal amino acid residues are missing in the electron density maps creating an open-ended groove. Our structures also reveal highly unusual features in MHC I-peptide interaction at the N-terminus of the groove. Molecular dynamics simulations indicate that the complexes have varying degrees of conformational flexibility in a manner consistent with the structures. We suggest that our structures have captured the remarkable molecular dynamics of MHC I-peptide interaction. The visualization of peptide-dependent conformational motions in MHC I is a major step forward in our conceptual understanding of dynamics in high-affinity peptide selection.
Collapse
Affiliation(s)
- Lenong Li
- Department of Microbiology and Immunology, University of Illinois, Chicago, IL, 60612, USA
| | - Xubiao Peng
- Center for Quantum Technology Research and Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurements, School of Physics, Beijing Institute of Technology, Beijing, 100081, China
| | - Mansoor Batliwala
- Department of Microbiology and Immunology, University of Illinois, Chicago, IL, 60612, USA
| | - Marlene Bouvier
- Department of Microbiology and Immunology, University of Illinois, Chicago, IL, 60612, USA.
| |
Collapse
|
12
|
Stražar M, Park J, Abelin JG, Taylor HB, Pedersen TK, Plichta DR, Brown EM, Eraslan B, Hung YM, Ortiz K, Clauser KR, Carr SA, Xavier RJ, Graham DB. HLA-II immunopeptidome profiling and deep learning reveal features of antigenicity to inform antigen discovery. Immunity 2023; 56:1681-1698.e13. [PMID: 37301199 PMCID: PMC10519123 DOI: 10.1016/j.immuni.2023.05.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 02/08/2023] [Accepted: 05/11/2023] [Indexed: 06/12/2023]
Abstract
CD4+ T cell responses are exquisitely antigen specific and directed toward peptide epitopes displayed by human leukocyte antigen class II (HLA-II) on antigen-presenting cells. Underrepresentation of diverse alleles in ligand databases and an incomplete understanding of factors affecting antigen presentation in vivo have limited progress in defining principles of peptide immunogenicity. Here, we employed monoallelic immunopeptidomics to identify 358,024 HLA-II binders, with a particular focus on HLA-DQ and HLA-DP. We uncovered peptide-binding patterns across a spectrum of binding affinities and enrichment of structural antigen features. These aspects underpinned the development of context-aware predictor of T cell antigens (CAPTAn), a deep learning model that predicts peptide antigens based on their affinity to HLA-II and full sequence of their source proteins. CAPTAn was instrumental in discovering prevalent T cell epitopes from bacteria in the human microbiome and a pan-variant epitope from SARS-CoV-2. Together CAPTAn and associated datasets present a resource for antigen discovery and the unraveling genetic associations of HLA alleles with immunopathologies.
Collapse
Affiliation(s)
- Martin Stražar
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jihye Park
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Hannah B Taylor
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Thomas K Pedersen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Eric M Brown
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Basak Eraslan
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yuan-Mao Hung
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Kayla Ortiz
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Karl R Clauser
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Daniel B Graham
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| |
Collapse
|
13
|
Olajide OM, Osman MK, Robert J, Kessler S, Toews LK, Thamamongood T, Neefjes J, Wrobel AG, Schwemmle M, Ciminski K, Reuther P. Evolutionarily conserved amino acids in MHC-II mediate bat influenza A virus entry into human cells. PLoS Biol 2023; 21:e3002182. [PMID: 37410798 DOI: 10.1371/journal.pbio.3002182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 06/02/2023] [Indexed: 07/08/2023] Open
Abstract
The viral hemagglutinins of conventional influenza A viruses (IAVs) bind to sialylated glycans on host cell surfaces for attachment and subsequent infection. In contrast, hemagglutinins of bat-derived IAVs target major histocompatibility complex class II (MHC-II) for cell entry. MHC-II proteins from various vertebrate species can facilitate infection with the bat IAV H18N11. Yet, it has been difficult to biochemically determine the H18:MHC-II binding. Here, we followed a different approach and generated MHC-II chimeras from the human leukocyte antigen DR (HLA-DR), which supports H18-mediated entry, and the nonclassical MHC-II molecule HLA-DM, which does not. In this context, viral entry was supported only by a chimera containing the HLA-DR α1, α2, and β1 domains. Subsequent modeling of the H18:HLA-DR interaction identified the α2 domain as central for this interaction. Further mutational analyses revealed highly conserved amino acids within loop 4 (N149) and β-sheet 6 (V190) of the α2 domain as critical for virus entry. This suggests that conserved residues in the α1, α2, and β1 domains of MHC-II mediate H18-binding and virus propagation. The conservation of MHC-II amino acids, which are critical for H18N11 binding, may explain the broad species specificity of this virus.
Collapse
Affiliation(s)
- Okikiola M Olajide
- Institute of Virology, Medical Center - University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Maria Kaukab Osman
- Institute of Virology, Medical Center - University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Jonathan Robert
- Institute of Virology, Medical Center - University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Susanne Kessler
- Institute of Virology, Medical Center - University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Lina Kathrin Toews
- Institute of Virology, Medical Center - University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Thiprampai Thamamongood
- Virology and Cell Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Khlong Nueng, Khlong Luang District, Pathum Thani, Thailand
| | - Jacques Neefjes
- Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, Leiden, the Netherlands
| | - Antoni G Wrobel
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Martin Schwemmle
- Institute of Virology, Medical Center - University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Kevin Ciminski
- Institute of Virology, Medical Center - University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Peter Reuther
- Institute of Virology, Medical Center - University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| |
Collapse
|
14
|
Margulies DH, Jiang J, Ahmad J, Boyd LF, Natarajan K. Chaperone function in antigen presentation by MHC class I molecules-tapasin in the PLC and TAPBPR beyond. Front Immunol 2023; 14:1179846. [PMID: 37398669 PMCID: PMC10308438 DOI: 10.3389/fimmu.2023.1179846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 05/30/2023] [Indexed: 07/04/2023] Open
Abstract
Peptide loading of MHC-I molecules plays a critical role in the T cell response to infections and tumors as well as to interactions with inhibitory receptors on natural killer (NK) cells. To facilitate and optimize peptide acquisition, vertebrates have evolved specialized chaperones to stabilize MHC-I molecules during their biosynthesis and to catalyze peptide exchange favoring high affinity or optimal peptides to permit transport to the cell surface where stable peptide/MHC-I (pMHC-I) complexes are displayed and are available for interaction with T cell receptors and any of a host of inhibitory and activating receptors. Although components of the endoplasmic reticulum (ER) resident peptide loading complex (PLC) were identified some 30 years ago, the detailed biophysical parameters that govern peptide selection, binding, and surface display have recently been understood better with advances in structural methods including X-ray crystallography, cryogenic electron microscopy (cryo-EM), and computational modeling. These approaches have provided refined mechanistic illustration of the molecular events involved in the folding of the MHC-I heavy chain, its coordinate glycosylation, assembly with its light chain, β2-microglobulin (β2m), its association with the PLC, and its binding of peptides. Our current view of this important cellular process as it relates to antigen presentation to CD8+ T cells is based on many different approaches: biochemical, genetic, structural, computational, cell biological, and immunological. In this review, taking advantage of recent X-ray and cryo-EM structural evidence and molecular dynamics simulations, examined in the context of past experiments, we attempt a dispassionate evaluation of the details of peptide loading in the MHC-I pathway. By critical evaluation of several decades of investigation, we outline aspects of the peptide loading process that are well-understood and indicate those that demand further detailed investigation. Further studies should contribute not only to basic understanding, but also to applications for immunization and therapy of tumors and infections.
Collapse
|
15
|
Li L, Peng X, Batliwala M, Bouvier M. Unusual crystal structures of MHC class I complexes reveal the elusive intermediate conformations explored during peptide editing in antigen presentation. RESEARCH SQUARE 2023:rs.3.rs-2500847. [PMID: 36747752 PMCID: PMC9901037 DOI: 10.21203/rs.3.rs-2500847/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Studies have suggested that MHC class I (MHC I) molecules fluctuate rapidly between conformational states as they sample peptides for potential ligands. To date, MHC I intermediates are largely uncharacterized experimentally and remain elusive. We present x-ray crystal structures of HLA-B8 loaded with 20mer peptides that show significant conformational heterogeneity at the N-terminus of the groove. Long stretches of N-terminal residues were missing in the electron density maps creating an unstructured and widely open-ended groove. Our structures also revealed highly unusual features in MHC I and peptide conformations, and in MHC I-peptide interaction at the N-terminus of the groove. Molecular dynamics simulations showed that the complexes have varying degrees of flexibility in a manner consistent with the structures. We suggest that our structures represent transient substates explored by MHC I molecules during peptide editing. The visualization of peptide-dependent conformational flexibility in MHC I groove is a major step forward in our conceptual understanding of peptide repertoire development in antigen presentation. Our study also raises questions about the role of the N-terminus of the groove in peptide editing.
Collapse
Affiliation(s)
- Lenong Li
- Department of Microbiology and Immunology, University of Illinois, Chicago, IL, 60612, USA
| | - Xubiao Peng
- Center for Quantum Technology Research and Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurements (MOE), School of Physics, Beijing Institute of Technology, Beijing 100081, China
| | - Mansoor Batliwala
- Department of Microbiology and Immunology, University of Illinois, Chicago, IL, 60612, USA
| | - Marlene Bouvier
- Department of Microbiology and Immunology, University of Illinois, Chicago, IL, 60612, USA
| |
Collapse
|
16
|
Quantitative affinity measurement of small molecule ligand binding to major histocompatibility complex class-I-related protein 1 MR1. J Biol Chem 2022; 298:102714. [PMID: 36403855 PMCID: PMC9764189 DOI: 10.1016/j.jbc.2022.102714] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/10/2022] [Accepted: 11/14/2022] [Indexed: 11/18/2022] Open
Abstract
The Major Histocompatibility Complex class I-related protein 1 (MR1) presents small molecule metabolites, drugs, and drug-like molecules that are recognized by MR1-reactive T cells. While we have an understanding of how antigens bind to MR1 and upregulate MR1 cell surface expression, a quantitative, cell-free, assessment of MR1 ligand-binding affinity was lacking. Here, we developed a fluorescence polarization-based assay in which fluorescent MR1 ligand was loaded into MR1 protein in vitro and competitively displaced by candidate ligands over a range of concentrations. Using this assay, ligand affinity for MR1 could be differentiated as strong (IC50 < 1 μM), moderate (1 μM < IC50 < 100 μM), and weak (IC50 > 100 μM). We demonstrated a clear correlation between ligand-binding affinity for MR1, the presence of a covalent bond between MR1 and ligand, and the number of salt bridge and hydrogen bonds formed between MR1 and ligand. Using this newly developed fluorescence polarization-based assay to screen for candidate ligands, we identified the dietary molecules vanillin and ethylvanillin as weak bona fide MR1 ligands. Both upregulated MR1 on the surface of C1R.MR1 cells and the crystal structure of a MAIT cell T cell receptor-MR1-ethylvanillin complex revealed that ethylvanillin formed a Schiff base with K43 of MR1 and was buried within the A'-pocket. Collectively, we developed and validated a method to quantitate the binding affinities of ligands for MR1 that will enable an efficient and rapid screening of candidate MR1 ligands.
Collapse
|
17
|
Cancer-specific T helper shared and neo-epitopes uncovered by expression of the MHC class II master regulator CIITA. Cell Rep 2022; 41:111485. [DOI: 10.1016/j.celrep.2022.111485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 05/13/2022] [Accepted: 09/19/2022] [Indexed: 11/22/2022] Open
|
18
|
Ayres CM, Baker BM. Peptide-dependent tuning of major histocompatibility complex motional properties and the consequences for cellular immunity. Curr Opin Immunol 2022; 76:102184. [PMID: 35550277 PMCID: PMC10052791 DOI: 10.1016/j.coi.2022.102184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 03/15/2022] [Accepted: 04/05/2022] [Indexed: 12/22/2022]
Abstract
T cell receptors (TCRs) and other receptors of the immune system recognize peptides presented by class I or class II major histocompatibility complex (MHC) proteins. Although we generally distinguish between the MHC protein and its peptide, at an atomic level the two form a structural composite, which allows peptides to influence MHC properties and vice versa. One consequence is the peptide-dependent tuning of MHC structural dynamics, which contributes to protein structural adaptability and influences how receptors identify and bind targets. Peptide-dependent tuning of MHC protein dynamics can impact processes such as antigenicity, TCR cross-reactivity, and T cell repertoire selection. Motional tuning extends beyond the binding groove, influencing peptide selection and exchange, as well as interactions with other immune receptors. Here, we review recent findings showing how peptides can affect the dynamic and adaptable nature of MHC proteins. We highlight consequences for immunity and demonstrate how MHC proteins have evolved to be highly sensitive dynamic reporters, with broad immunological consequences.
Collapse
Affiliation(s)
- Cory M Ayres
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Brian M Baker
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA.
| |
Collapse
|
19
|
Pishesha N, Harmand TJ, Ploegh HL. A guide to antigen processing and presentation. Nat Rev Immunol 2022; 22:751-764. [PMID: 35418563 DOI: 10.1038/s41577-022-00707-2] [Citation(s) in RCA: 212] [Impact Index Per Article: 106.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2022] [Indexed: 12/13/2022]
Abstract
Antigen processing and presentation are the cornerstones of adaptive immunity. B cells cannot generate high-affinity antibodies without T cell help. CD4+ T cells, which provide such help, use antigen-specific receptors that recognize major histocompatibility complex (MHC) molecules in complex with peptide cargo. Similarly, eradication of virus-infected cells often depends on cytotoxic CD8+ T cells, which rely on the recognition of peptide-MHC complexes for their action. The two major classes of glycoproteins entrusted with antigen presentation are the MHC class I and class II molecules, which present antigenic peptides to CD8+ T cells and CD4+ T cells, respectively. This Review describes the essentials of antigen processing and presentation. These pathways are divided into six discrete steps that allow a comparison of the various means by which antigens destined for presentation are acquired and how the source proteins for these antigens are tagged for degradation, destroyed and ultimately displayed as peptides in complex with MHC molecules for T cell recognition.
Collapse
Affiliation(s)
- Novalia Pishesha
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Society of Fellows, Harvard University, Cambridge, MA, USA.,Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Thibault J Harmand
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Hidde L Ploegh
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
20
|
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.
Collapse
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
| |
Collapse
|
21
|
Olsson N, Jiang W, Adler LN, Mellins ED, Elias JE. Tuning DO:DM ratios modulates MHC class II immunopeptidomes. Mol Cell Proteomics 2022; 21:100204. [DOI: 10.1016/j.mcpro.2022.100204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 01/07/2022] [Accepted: 01/16/2022] [Indexed: 10/19/2022] Open
|
22
|
Wang X, Zhang X, Han Y, Duan X, Wang J, Yan H, Wang S, Xu Y, Zhu Z, Wang L, Huang Y, Lin Q, Tan X, Zhuo J, Zhang H, Mao M, Gou W, Yi Z, Li X. Role of the major histocompatibility complex class II protein presentation pathway in bone immunity imbalance in postmenopausal osteoporosis. Front Endocrinol (Lausanne) 2022; 13:876067. [PMID: 36034452 PMCID: PMC9402988 DOI: 10.3389/fendo.2022.876067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 07/13/2022] [Indexed: 11/13/2022] Open
Abstract
Bone immunity regulates osteoclast differentiation and bone resorption and is a potential target for the treatment of postmenopausal osteoporosis (PMOP). The molecular network between bone metabolism and the immune system is complex. However, the molecular mechanism underlying the involvement of the major histocompatibility complex class II (MHC-II) molecule protein presentation pathway in PMOP remains to be elucidated. The MHC-II molecule is a core molecule of the protein presentation pathway. It is combined with the processed short peptide and presented to T lymphocytes, thereby activating them to become effector T cells. T-cell-derived inflammatory factors promote bone remodeling in PMOP. Moreover, the MHC-II molecule is highly expressed in osteoclast precursors. MHC-II transactivator (CIITA) is the main regulator of MHC-II gene expression and the switch for protein presentation. CIITA is also a major regulator of osteoclast differentiation and bone homeostasis. Therefore, we hypothesized that the MHC-II promotes osteoclast differentiation, providing a novel pathogenic mechanism and a potential target for the treatment of PMOP.
Collapse
Affiliation(s)
- Xiaoning Wang
- College of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Xin Zhang
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Yidan Han
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Xinwei Duan
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Jianchang Wang
- College of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Hui Yan
- College of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Shanshan Wang
- College of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Yunteng Xu
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Zaishi Zhu
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Lili Wang
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China
- Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Yanfeng Huang
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Qing Lin
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Xue Tan
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Junkuan Zhuo
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Haifeng Zhang
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Min Mao
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Weiying Gou
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Zhouping Yi
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Xihai Li
- College of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China
- Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou, China
- *Correspondence: Xihai Li,
| |
Collapse
|
23
|
Amin M, Barzegari E, Pourshohod A, Zeinali M, Jamalan M. 3D structure prediction, dynamic investigation and rational construction of an epitope-masked thermostable bovine hyaluronidase. Int J Biol Macromol 2021; 187:544-553. [PMID: 34298049 DOI: 10.1016/j.ijbiomac.2021.07.098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 07/14/2021] [Accepted: 07/14/2021] [Indexed: 01/11/2023]
Abstract
Hyaluronidase (HAase) from bovine testes (BTH) has long been used in broad pharmaceutical areas, while it is associated with drawbacks in aspects of solubility, immunogenicity and pharmacokinetics. These issues can be addressed by gaining structural insights and designing rational modifications to the enzyme structure, as proposed in this study. A 3D structural model was built for HAase and underwent 40 ns of molecular dynamic simulation to examine its thermostability under normal, melting, and extreme conditions. The enzyme activity of BTH was measured against temperature and pH by kinetic assays. The interaction of bovine HAase with HA and chondroitin was defined by molecular docking. Furthermore, immunogenic properties of the enzyme were explored by immunoinformatics. Thermal effects on bovine HAase structural model and the HAase interactions with its substrates were described. We identified some B- and T-cell epitopes and showed that the protein could be recognized by human immune receptor molecules. Epitope masking by adding polyethylene glycol (PEG) to amine groups of residues presenting on the surface of the protein structure was adopted as a surface modification to enhance pharmacological properties of BTH. Assays showed that PEGylated BTH had higher thermostability and similar activity compared to the native enzyme.
Collapse
Affiliation(s)
- Mansour Amin
- Department of Microbiology, School of Medicine, Dezful University of Medical Sciences, Dezful, Iran
| | - Ebrahim Barzegari
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Aminollah Pourshohod
- Department of Biochemistry, Cellular and Molecular Research Center, Ahvaz Jundishapur University of Medical Science, Medical School, Ahvaz, Iran
| | - Majid Zeinali
- Biotechnology Research Center, Research Institute of Petroleum Industry (RIPI), Tehran, Iran
| | - Mostafa Jamalan
- Department of Biochemistry, Abadan University of Medical Sciences, Abadan, Iran.
| |
Collapse
|
24
|
Ghosh D, Jiang W, Mukhopadhyay D, Mellins ED. New insights into B cells as antigen presenting cells. Curr Opin Immunol 2021; 70:129-137. [PMID: 34242927 DOI: 10.1016/j.coi.2021.06.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/07/2021] [Accepted: 06/09/2021] [Indexed: 01/06/2023]
Abstract
In addition to their role as antibody producing cells, B cells make a critical contribution to adaptive immune responses by functioning as professional antigen-presenting cells (APC). Distinctive features of B cells as APC include the expression of the B cell receptor (BCR) for antigen and regulated expression of HLA-DO. Here, we discuss recent progress in investigation of B cells as APC. We start with an update on the canonical MHC class II antigen presentation pathway in B cells and alternative pathways, including generation of extracellular vesicles. Turning to APC function, we highlight the roles of B cells as thymic APC, as APC for T follicular helper (TFH), as APC for CD4 memory T cells and as presenters of idiotypic BCR determinants. We also note recent examples that link B cell Ag-presentation to disease. Emerging evidence indicates that, in addition to unique features of B cells compared to other professional APC, there is appreciable heterogeneity among B cells, arising from, for example, B cell activation state or the microenvironment.
Collapse
Affiliation(s)
- Debopam Ghosh
- Department of Pediatrics, Program in Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Wei Jiang
- Department of Pediatrics, Program in Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Dhriti Mukhopadhyay
- Department of Surgery, University of Arizona, Tucson, AZ 85724, USA; Tuba City Regional Health Care, Tuba City, AZ 86045, USA
| | - Elizabeth D Mellins
- Department of Pediatrics, Program in Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
| |
Collapse
|
25
|
Aflalo A, Boyle LH. Polymorphisms in MHC class I molecules influence their interactions with components of the antigen processing and presentation pathway. Int J Immunogenet 2021; 48:317-325. [PMID: 34176210 DOI: 10.1111/iji.12546] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/12/2021] [Accepted: 05/24/2021] [Indexed: 10/21/2022]
Abstract
MHC class I (MHC-I) molecules undergo an intricate folding process in order to pick up antigenic peptide to present to the immune system. In recent years, the discovery of a new peptide editor for MHC-I has added an extra level of complexity in our understanding of how peptide presentation is regulated. On top of this, the incredible diversity in MHC-I molecules leads to significant variation in the interaction between MHC-I and components of the antigen processing and presentation pathway. Here, we review our current understanding regarding how polymorphisms in human leukocyte antigen class I molecules influence their interactions with key components of the antigen processing and presentation pathway. A deeper understanding of this may offer new insights regarding how apparently subtle variation in MHC-I can have a significant impact on susceptibility to disease.
Collapse
Affiliation(s)
- Aure Aflalo
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Louise H Boyle
- Department of Pathology, University of Cambridge, Cambridge, UK
| |
Collapse
|
26
|
Partnering for the major histocompatibility complex class II and antigenic determinant requires flexibility and chaperons. Curr Opin Immunol 2021; 70:112-121. [PMID: 34146954 DOI: 10.1016/j.coi.2021.05.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 05/12/2021] [Indexed: 11/22/2022]
Abstract
Cytotoxic, or helper T cells recognize antigen via T cell receptors (TCRs) that can see their target antigen as short sequences of peptides bound to the groove of proteins of major histocompatibility complex (MHC) class I, and class II respectively. For MHC class II epitope selection from exogenous pathogens or self-antigens, participation of several accessory proteins, molecular chaperons, processing enzymes within multiple vesicular compartments is necessary. A major contributing factor is the MHC class II structure itself that uniquely offers a dynamic and flexible groove essential for epitope selection. In this review, I have taken a historical perspective focusing on the flexibility of the MHC II molecules as the driving force in determinant selection and interactions with the accessory molecules in antigen processing, HLA-DM and HLA-DO.
Collapse
|
27
|
Wu Y, Zhang N, Hashimoto K, Xia C, Dijkstra JM. Structural Comparison Between MHC Classes I and II; in Evolution, a Class-II-Like Molecule Probably Came First. Front Immunol 2021; 12:621153. [PMID: 34194421 PMCID: PMC8236899 DOI: 10.3389/fimmu.2021.621153] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 05/04/2021] [Indexed: 01/03/2023] Open
Abstract
Structures of peptide-loaded major histocompatibility complex class I (pMHC-I) and class II (pMHC-II) complexes are similar. However, whereas pMHC-II complexes include similar-sized IIα and IIβ chains, pMHC-I complexes include a heavy chain (HC) and a single domain molecule β2-microglobulin (β2-m). Recently, we elucidated several pMHC-I and pMHC-II structures of primitive vertebrate species. In the present study, a comprehensive comparison of pMHC-I and pMHC-II structures helps to understand pMHC structural evolution and supports the earlier proposed—though debated—direction of MHC evolution from class II-type to class I. Extant pMHC-II structures share major functional characteristics with a deduced MHC-II-type homodimer ancestor. Evolutionary establishment of pMHC-I presumably involved important new functions such as (i) increased peptide selectivity by binding the peptides in a closed groove (ii), structural amplification of peptide ligand sequence differences by binding in a non-relaxed fashion, and (iii) increased peptide selectivity by syngeneic heterotrimer complex formation between peptide, HC, and β2-m. These new functions were associated with structures that since their establishment in early pMHC-I have been very well conserved, including a shifted and reorganized P1 pocket (aka A pocket), and insertion of a β2-m hydrophobic knob into the peptide binding domain β-sheet floor. A comparison between divergent species indicates better sequence conservation of peptide binding domains among MHC-I than among MHC-II, agreeing with more demanding interactions within pMHC-I complexes. In lungfishes, genes encoding fusions of all MHC-IIα and MHC-IIβ extracellular domains were identified, and although these lungfish genes presumably derived from classical MHC-II, they provide an alternative mechanistic hypothesis for how evolution from class II-type to class I may have occurred.
Collapse
Affiliation(s)
- Yanan Wu
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Nianzhi Zhang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Keiichiro Hashimoto
- Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Japan
| | - Chun Xia
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Johannes M Dijkstra
- Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Japan
| |
Collapse
|
28
|
Welsh RA, Song N, Sadegh-Nasseri S. How Does B Cell Antigen Presentation Affect Memory CD4 T Cell Differentiation and Longevity? Front Immunol 2021; 12:677036. [PMID: 34177919 PMCID: PMC8224923 DOI: 10.3389/fimmu.2021.677036] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 05/18/2021] [Indexed: 11/13/2022] Open
Abstract
Dendritic cells are the antigen presenting cells that process antigens effectively and prime the immune system, a characteristic that have gained them the spotlights in recent years. B cell antigen presentation, although less prominent, deserves equal attention. B cells select antigen experienced CD4 T cells to become memory and initiate an orchestrated genetic program that maintains memory CD4 T cells for life of the individual. Over years of research, we have demonstrated that low levels of antigens captured by B cells during the resolution of an infection render antigen experienced CD4 T cells into a quiescent/resting state. Our studies suggest that in the absence of antigen, the resting state associated with low-energy utilization and proliferation can help memory CD4 T cells to survive nearly throughout the lifetime of mice. In this review we would discuss the primary findings from our lab as well as others that highlight our understanding of B cell antigen presentation and the contributions of the MHC Class II accessory molecules to this outcome. We propose that the quiescence induced by the low levels of antigen presentation might be a mechanism necessary to regulate long-term survival of CD4 memory T cells and to prevent cross-reactivity to autoantigens, hence autoimmunity.
Collapse
Affiliation(s)
- Robin A Welsh
- Graduate Program in Immunology, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Nianbin Song
- Department of Biology, Krieger School of Arts & Sciences, Johns Hopkins University, Baltimore, MD, United States
| | - Scheherazade Sadegh-Nasseri
- Graduate Program in Immunology, Johns Hopkins School of Medicine, Baltimore, MD, United States.,Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, United States
| |
Collapse
|
29
|
Hafstrand I, Aflalo A, Boyle LH. Why TAPBPR? Implications of an additional player in MHC class I peptide presentation. Curr Opin Immunol 2021; 70:90-94. [PMID: 34052734 DOI: 10.1016/j.coi.2021.04.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/15/2021] [Accepted: 04/30/2021] [Indexed: 10/21/2022]
Abstract
The peptide editor TAPBPR is the newest member of the major histocompatibility complex class I (MHC-I) antigen processing and presentation pathway. Since 2013, studies have explored the functions and mechanisms of action of this tapasin homolog. Here, we review the key insights gained from structural studies of the TAPBPR:MHC-I complex and the involvement of the TAPBPR loop in peptide exchange. However, despite recent advances, the question still remains: why do we need TAPBPR? The recent appreciation that different MHC-I allotypes vary in their ability to interact with TAPBPR, together with a role for TAPBPR in alternative presentation pathways highlights that much remains unknown concerning the biological need for TAPBPR.
Collapse
Affiliation(s)
- Ida Hafstrand
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, United Kingdom; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Aure Aflalo
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, United Kingdom
| | - Louise H Boyle
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, United Kingdom.
| |
Collapse
|
30
|
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.
Collapse
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.
| |
Collapse
|
31
|
Halabi S, Ghosh M, Stevanović S, Rammensee HG, Bertzbach LD, Kaufer BB, Moncrieffe MC, Kaspers B, Härtle S, Kaufman J. The dominantly expressed class II molecule from a resistant MHC haplotype presents only a few Marek's disease virus peptides by using an unprecedented binding motif. PLoS Biol 2021; 19:e3001057. [PMID: 33901176 PMCID: PMC8101999 DOI: 10.1371/journal.pbio.3001057] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 05/06/2021] [Accepted: 03/31/2021] [Indexed: 12/14/2022] Open
Abstract
Viral diseases pose major threats to humans and other animals, including the billions of chickens that are an important food source as well as a public health concern due to zoonotic pathogens. Unlike humans and other typical mammals, the major histocompatibility complex (MHC) of chickens can confer decisive resistance or susceptibility to many viral diseases. An iconic example is Marek's disease, caused by an oncogenic herpesvirus with over 100 genes. Classical MHC class I and class II molecules present antigenic peptides to T lymphocytes, and it has been hard to understand how such MHC molecules could be involved in susceptibility to Marek's disease, given the potential number of peptides from over 100 genes. We used a new in vitro infection system and immunopeptidomics to determine peptide motifs for the 2 class II molecules expressed by the MHC haplotype B2, which is known to confer resistance to Marek's disease. Surprisingly, we found that the vast majority of viral peptide epitopes presented by chicken class II molecules arise from only 4 viral genes, nearly all having the peptide motif for BL2*02, the dominantly expressed class II molecule in chickens. We expressed BL2*02 linked to several Marek's disease virus (MDV) peptides and determined one X-ray crystal structure, showing how a single small amino acid in the binding site causes a crinkle in the peptide, leading to a core binding peptide of 10 amino acids, compared to the 9 amino acids in all other reported class II molecules. The limited number of potential T cell epitopes from such a complex virus can explain the differential MHC-determined resistance to MDV, but raises questions of mechanism and opportunities for vaccine targets in this important food species, as well as providing a basis for understanding class II molecules in other species including humans.
Collapse
Affiliation(s)
- Samer Halabi
- University of Cambridge, Department of Pathology, Cambridge, United Kingdom
- University of Edinburgh, Institute for Immunology and Infection Research, Edinburgh, United Kingdom
| | - Michael Ghosh
- University of Tübingen, Department of Immunology, Institute of Cell Biology, Tübingen, Germany
| | - Stefan Stevanović
- University of Tübingen, Department of Immunology, Institute of Cell Biology, Tübingen, Germany
| | - Hans-Georg Rammensee
- University of Tübingen, Department of Immunology, Institute of Cell Biology, Tübingen, Germany
| | | | | | | | - Bernd Kaspers
- Ludwig Maximillians University, Veterinary Faculty, Planegg, Germany
| | - Sonja Härtle
- Ludwig Maximillians University, Veterinary Faculty, Planegg, Germany
| | - Jim Kaufman
- University of Cambridge, Department of Pathology, Cambridge, United Kingdom
- University of Edinburgh, Institute for Immunology and Infection Research, Edinburgh, United Kingdom
- University of Cambridge, Department of Veterinary Medicine, Cambridge, United Kingdom
| |
Collapse
|
32
|
Pleiotropic consequences of metabolic stress for the major histocompatibility complex class II molecule antigen processing and presentation machinery. Immunity 2021; 54:721-736.e10. [PMID: 33725478 DOI: 10.1016/j.immuni.2021.02.019] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 12/30/2020] [Accepted: 02/24/2021] [Indexed: 01/11/2023]
Abstract
Hyperglycemia and hyperlipidemia are often observed in individuals with type II diabetes (T2D) and related mouse models. One dysmetabolic biochemical consequence is the non-enzymatic reaction between sugars, lipids, and proteins, favoring protein glycation, glycoxidation, and lipoxidation. Here, we identified oxidative alterations in key components of the major histocompatibility complex (MHC) class II molecule antigen processing and presentation machinery in vivo under conditions of hyperglycemia-induced metabolic stress. These modifications were linked to epitope-specific changes in endosomal processing efficiency, MHC class II-peptide binding, and DM editing activity. Moreover, we observed some quantitative and qualitative changes in the MHC class II immunopeptidome of Ob/Ob mice on a high-fat diet compared with controls, including changes in the presentation of an apolipoprotein B100 peptide associated previously with T2D and metabolic syndrome-related clinical complications. These findings highlight a link between glycation reactions and altered MHC class II antigen presentation that may contribute to T2D complications.
Collapse
|
33
|
张 建, 王 玉, 何 金, 李 焕, 陈 劲, 陈 达, 陈 建. [Construction and Expression of Eukaryotic and Prokaryotic Recombinant Vectors of Pepck and Gp63 Dominant Epitopes of Leishmania infantum]. SICHUAN DA XUE XUE BAO. YI XUE BAN = JOURNAL OF SICHUAN UNIVERSITY. MEDICAL SCIENCE EDITION 2021; 52:194-201. [PMID: 33829691 PMCID: PMC10408922 DOI: 10.12182/20210160104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Indexed: 11/23/2022]
Abstract
OBJECTIVE To construct eukaryotic and prokaryotic recombinant vectors containing Pepck- Gp63 and to achieve protein expression by selecting the dominant epitope genes of Pepck and Gp63 of Leishmania infantum. METHODS The secondary structure and HLA epitopes of phosphoenolpyruvate carboxylase (PEPCK) were predicted by in silico analysis, and the dominant epitopes were picked out. According to the analysis results of glycoprotein of 63×10 3(GP63) epitopes identified by the same method in our laboratory, the dominant epitope genes of Pepck and Gp63 were used to construct pET32a- Pepck- Gp63 and pVAX1- Pepck- Gp63 by overlapping PCR and enzyme reaction. Then, for protein expression, the prokaryotic vectors were transfected into E.coil while the eukaryotic vectors were transfected into NIH3T3 cells by liposome transfection. RESULTS There were multiple dominant epitopes in Pepckand there were Pepck-Gp63 sequences in the polyclonal site of expression vector. The expression of Pepck-Gp63 in E.coil appeared in inclusion form and led to 74 kDa band in SDS-PAGE. The immunofluorescence results of NIH3T3 cells transfected by pVAX1- Pepck-Gp63 were positive. CONCLUSION The recombinant prokaryotic expression plasmids pET32a- Pepck-Gp63 and eukaryotic expression plasmids pVAX1- P epck -Gp63 were successfully constructed, and it was shown that the recombinant plasmids were able to express the corresponding target proteins in E. coli and NIH3T3 cells, respectively, providing a preliminary experimental basis for the subsequent study of immunization strategies.
Collapse
Affiliation(s)
- 建辉 张
- 四川大学华西基础医学与法医学院 病原生物学系寄生虫教研室 (成都 610041)Parasitology Teaching and Research Center, Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - 玉洁 王
- 四川大学华西基础医学与法医学院 病原生物学系寄生虫教研室 (成都 610041)Parasitology Teaching and Research Center, Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - 金蕾 何
- 四川大学华西基础医学与法医学院 病原生物学系寄生虫教研室 (成都 610041)Parasitology Teaching and Research Center, Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - 焕卿 李
- 四川大学华西基础医学与法医学院 病原生物学系寄生虫教研室 (成都 610041)Parasitology Teaching and Research Center, Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - 劲宇 陈
- 四川大学华西基础医学与法医学院 病原生物学系寄生虫教研室 (成都 610041)Parasitology Teaching and Research Center, Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - 达丽 陈
- 四川大学华西基础医学与法医学院 病原生物学系寄生虫教研室 (成都 610041)Parasitology Teaching and Research Center, Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - 建平 陈
- 四川大学华西基础医学与法医学院 病原生物学系寄生虫教研室 (成都 610041)Parasitology Teaching and Research Center, Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610041, China
| |
Collapse
|
34
|
Münz C. The Macroautophagy Machinery in MHC Restricted Antigen Presentation. Front Immunol 2021; 12:628429. [PMID: 33717153 PMCID: PMC7947692 DOI: 10.3389/fimmu.2021.628429] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 01/18/2021] [Indexed: 11/18/2022] Open
Abstract
Autophagy-related (ATG) gene products regulate macroautophagy, LC3-associated phagocytosis (LAP) and LC3-dependent extracellular vesicle loading and secretion (LDELS). These processes also influence antigen processing for presentation on major histocompatibility complex (MHC) molecules to T cells. Here, I summarize how these different pathways use the macroautophagy machinery, contribute to MHC class I and II restricted antigen presentation and influence autoimmunity, tumor immunology and immune control of infectious diseases. Targeting these different pathways should allow the regulation of intracellular and extracellular antigen presentation to T cells to modulate protective and pathological immune responses.
Collapse
Affiliation(s)
- Christian Münz
- Viral Immunobiology, Institute of Experimental Immunology, University of Zürich, Zürich, Switzerland
| |
Collapse
|
35
|
Almeida T, Gaigher A, Muñoz-Mérida A, Neves F, Castro LFC, Flajnik MF, Ohta Y, Esteves PJ, Veríssimo A. Cartilaginous fish class II genes reveal unprecedented old allelic lineages and confirm the late evolutionary emergence of DM. Mol Immunol 2020; 128:125-138. [PMID: 33126081 PMCID: PMC8010645 DOI: 10.1016/j.molimm.2020.10.003] [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: 08/14/2020] [Revised: 09/22/2020] [Accepted: 10/03/2020] [Indexed: 12/16/2022]
Abstract
Cartilaginous fish (chimaeras, rays and sharks) are the most basal extant jawed vertebrates with an adaptive immune system based on the Major Histocompatibility Complex (MHC). Despite being a key taxon in the evolution of vertebrate adaptive immunity, no comprehensive characterization of MHC class II genes has been undertaken for the group. We performed extensive bioinformatic searches on a taxonomically diverse dataset of transcriptomes and genomes of cartilaginous fish targeting MHC class II sequences. Class IIα and IIβ sequences were retrieved from all taxa analyzed and showed typical features of classical class II genes. Phylogenetic trees of the immunoglobulin superfamily domain showed two divergent and remarkably ancient lineages of class II genes in Selachians (sharks), originating >350 million years ago. Close linkage of lineage-specific pairs of IIα and IIβ genes was found, confirming previous results, with genes from distinct lineages segregating as alleles. Nonclassical class II DM sequences were not retrieved from these data and classical class II sequences lacked the conserved residues shown to interact with DM molecules, supporting claims that the DM system arose only in the lobe-finned fish lineage leading to tetrapods. Based on our search methods, other divergent class II genes are unlikely in cartilaginous fish.
Collapse
Affiliation(s)
- Tereza Almeida
- CIBIO-InBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661 Vairão, Portugal; Department of Biology, Faculty of Sciences - University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal; Department of Microbiology and Immunology, University of Maryland, Baltimore, MD 21201, USA
| | - Arnaud Gaigher
- CIBIO-InBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - Antonio Muñoz-Mérida
- CIBIO-InBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - Fabiana Neves
- CIBIO-InBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - L Filipe C Castro
- Department of Biology, Faculty of Sciences - University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal; CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, 4450-208 Matosinhos, Portugal
| | - Martin F Flajnik
- Department of Microbiology and Immunology, University of Maryland, Baltimore, MD 21201, USA
| | - Yuko Ohta
- Department of Microbiology and Immunology, University of Maryland, Baltimore, MD 21201, USA
| | - Pedro J Esteves
- CIBIO-InBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661 Vairão, Portugal; Department of Biology, Faculty of Sciences - University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Ana Veríssimo
- CIBIO-InBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661 Vairão, Portugal.
| |
Collapse
|
36
|
Szeto C, Bloom JI, Sloane H, Lobos CA, Fodor J, Jayasinghe D, Chatzileontiadou DSM, Grant EJ, Buckle AM, Gras S. Impact of HLA-DR Antigen Binding Cleft Rigidity on T Cell Recognition. Int J Mol Sci 2020; 21:ijms21197081. [PMID: 32992915 PMCID: PMC7582474 DOI: 10.3390/ijms21197081] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 09/22/2020] [Accepted: 09/23/2020] [Indexed: 01/22/2023] Open
Abstract
The interaction between T cell receptor (TCR) and peptide (p)-Human Leukocyte Antigen (HLA) complexes is the critical first step in determining T cell responses. X-ray crystallographic studies of pHLA in TCR-bound and free states provide a structural perspective that can help understand T cell activation. These structures represent a static “snapshot”, yet the nature of pHLAs and their interactions with TCRs are highly dynamic. This has been demonstrated for HLA class I molecules with in silico techniques showing that some interactions, thought to stabilise pHLA-I, are only transient and prone to high flexibility. Here, we investigated the dynamics of HLA class II molecules by focusing on three allomorphs (HLA-DR1, -DR11 and -DR15) that are able to present the same epitope and activate CD4+ T cells. A single TCR (F24) has been shown to recognise all three HLA-DR molecules, albeit with different affinities. Using molecular dynamics and crystallographic ensemble refinement, we investigate the molecular basis of these different affinities and uncover hidden roles for HLA polymorphic residues. These polymorphisms were responsible for the widening of the antigen binding cleft and disruption of pHLA-TCR interactions, underpinning the hierarchy of F24 TCR binding affinity, and ultimately T cell activation. We expanded this approach to all available pHLA-DR structures and discovered that all HLA-DR molecules were inherently rigid. Together with in vitro protein stability and peptide affinity measurements, our results suggest that HLA-DR1 possesses inherently high protein stability, and low HLA-DM susceptibility.
Collapse
Affiliation(s)
- Christopher Szeto
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; (C.S.); (J.I.B.); (H.S.); (C.A.L.); (J.F.); (D.J.); (D.S.M.C.); (E.J.G.); (A.M.B.)
| | - Joseph I. Bloom
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; (C.S.); (J.I.B.); (H.S.); (C.A.L.); (J.F.); (D.J.); (D.S.M.C.); (E.J.G.); (A.M.B.)
| | - Hannah Sloane
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; (C.S.); (J.I.B.); (H.S.); (C.A.L.); (J.F.); (D.J.); (D.S.M.C.); (E.J.G.); (A.M.B.)
| | - Christian A. Lobos
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; (C.S.); (J.I.B.); (H.S.); (C.A.L.); (J.F.); (D.J.); (D.S.M.C.); (E.J.G.); (A.M.B.)
| | - James Fodor
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; (C.S.); (J.I.B.); (H.S.); (C.A.L.); (J.F.); (D.J.); (D.S.M.C.); (E.J.G.); (A.M.B.)
- Eccles Institute of Neuroscience, John Curtin School of Medical Research, The Australian National University, Canberra, ACT 0200, Australia
| | - Dhilshan Jayasinghe
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; (C.S.); (J.I.B.); (H.S.); (C.A.L.); (J.F.); (D.J.); (D.S.M.C.); (E.J.G.); (A.M.B.)
| | - Demetra S. M. Chatzileontiadou
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; (C.S.); (J.I.B.); (H.S.); (C.A.L.); (J.F.); (D.J.); (D.S.M.C.); (E.J.G.); (A.M.B.)
| | - Emma J. Grant
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; (C.S.); (J.I.B.); (H.S.); (C.A.L.); (J.F.); (D.J.); (D.S.M.C.); (E.J.G.); (A.M.B.)
| | - Ashley M. Buckle
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; (C.S.); (J.I.B.); (H.S.); (C.A.L.); (J.F.); (D.J.); (D.S.M.C.); (E.J.G.); (A.M.B.)
| | - Stephanie Gras
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; (C.S.); (J.I.B.); (H.S.); (C.A.L.); (J.F.); (D.J.); (D.S.M.C.); (E.J.G.); (A.M.B.)
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC 3800, Australia
- Correspondence:
| |
Collapse
|
37
|
Álvaro-Benito M, Freund C. Revisiting nonclassical HLA II functions in antigen presentation: Peptide editing and its modulation. HLA 2020; 96:415-429. [PMID: 32767512 DOI: 10.1111/tan.14007] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 08/04/2020] [Indexed: 01/08/2023]
Abstract
The nonclassical major histocompatibility complex of class II molecules (ncMHCII) HLA-DM (DM) and HLA-DO (DO) feature essential functions for the selection of the peptides that are displayed by classical MHCII proteins (MHCII) for CD4+ Th cell surveillance. Thus, although the binding groove of classical MHCII dictates the main features of the peptides displayed, ncMHCII function defines the preferential loading of peptides from specific cellular compartments and the extent to which they are presented. DM acts as a chaperone for classical MHCII molecules facilitating peptide exchange and thereby favoring the binding of peptide-MHCII complexes of high kinetic stability mostly in late endosomal compartments. DO on the other hand binds to DM blocking its peptide-editing function in B cells and thymic epithelial cells, limiting DM activity in these cellular subsets. DM and DO distinct expression patterns therefore define specific antigen presentation profiles that select unique peptide pools for each set of antigen presenting cell. We have come a long way understanding the mechanistic underpinnings of such distinct editing profiles and start to grasp the implications for ncMHCII biological function. DM acts as filter for the selection of immunodominant, pathogen-derived epitopes while DO blocks DM activity under certain physiological conditions to promote tolerance to self. Interestingly, recent findings have shown that the unexplored and neglected ncMHCII genetic diversity modulates retroviral infection in mouse, and affects human ncMHCII function. This review aims at highlighting the importance of ncMHCII function for CD4+ Th cell responses while integrating and evaluating what could be the impact of distinct editing profiles because of natural genetic variations.
Collapse
Affiliation(s)
- Miguel Álvaro-Benito
- Laboratory of Protein Biochemistry, Institute für Chemie und Biochemie, Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Christian Freund
- Laboratory of Protein Biochemistry, Institute für Chemie und Biochemie, Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Berlin, Germany
| |
Collapse
|
38
|
Graves AM, Virdis F, Morrison E, Álvaro-Benito M, Khan AA, Freund C, Golovkina TV, Denzin LK. Human Hepatitis B Viral Infection Outcomes Are Linked to Naturally Occurring Variants of HLA-DOA That Have Altered Function. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2020; 205:923-935. [PMID: 32690655 PMCID: PMC7415708 DOI: 10.4049/jimmunol.2000476] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 06/11/2020] [Indexed: 12/21/2022]
Abstract
HLA molecules of the MHC class II (MHCII) bind and present pathogen-derived peptides for CD4 T cell activation. Peptide loading of MHCII in the endosomes of cells is controlled by the interplay of the nonclassical MHCII molecules, HLA-DM (DM) and HLA-DO (DO). DM catalyzes peptide loading, whereas DO, an MHCII substrate mimic, prevents DM from interacting with MHCII, resulting in an altered MHCII-peptide repertoire and increased MHCII-CLIP. Although the two genes encoding DO (DOA and DOB) are considered nonpolymorphic, there are rare natural variants. Our previous work identified DOB variants that altered DO function. In this study, we show that natural variation in the DOA gene also impacts DO function. Using the 1000 Genomes Project database, we show that ∼98% of individuals express the canonical DOA*0101 allele, and the remaining individuals mostly express DOA*0102, which we found was a gain-of-function allele. Analysis of 25 natural occurring DOα variants, which included the common alleles, identified three null variants and one variant with reduced and nine with increased ability to modulate DM activity. Unexpectedly, several of the variants produced reduced DO protein levels yet efficiently inhibited DM activity. Finally, analysis of associated single-nucleotide polymorphisms genetically linked the DOA*0102 common allele, a gain-of-function variant, with human hepatitis B viral persistence. In contrast, we found that the DOα F114L null allele was linked with viral clearance. Collectively, these studies show that natural variation occurring in the human DOA gene impacts DO function and can be linked to specific outcomes of viral infections.
Collapse
Affiliation(s)
- Austin M Graves
- Child Health Institute of New Jersey, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901
- Rutgers Graduate School of Biomedical Sciences, Piscataway, NJ 08854
| | - Francesca Virdis
- Child Health Institute of New Jersey, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901
| | - Eliot Morrison
- Laboratory of Protein Biochemistry, Department of Biology, Chemistry and Pharmacy, Free University of Berlin, 14195 Berlin, Germany
| | - Miguel Álvaro-Benito
- Laboratory of Protein Biochemistry, Department of Biology, Chemistry and Pharmacy, Free University of Berlin, 14195 Berlin, Germany
| | - Aly A Khan
- Department of Pathology, The University of Chicago, Chicago, IL 60637
| | - Christian Freund
- Laboratory of Protein Biochemistry, Department of Biology, Chemistry and Pharmacy, Free University of Berlin, 14195 Berlin, Germany
| | | | - Lisa K Denzin
- Child Health Institute of New Jersey, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901;
- Department of Pediatrics, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901; and
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901
| |
Collapse
|
39
|
Welsh RA, Sadegh-Nasseri S. The love and hate relationship of HLA-DM/DO in the selection of immunodominant epitopes. Curr Opin Immunol 2020; 64:117-123. [PMID: 32599219 DOI: 10.1016/j.coi.2020.05.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 05/20/2020] [Indexed: 12/11/2022]
Abstract
Successful activation of CD4 T cells is centered around the ability of antigen presenting cells to successfully process, select Class II immunodominant epitopes from exogenous antigens and to present it to cognate T cells. To achieve this, newly synthesized MHC-II molecules are transferred to a specialized compartment which contain both exogenous antigens and the Class II processing machinery. Here in a process known as 'editing,' the Class II accessory molecule DM (HLA-DM human; murine H2-M) facilitates the loading and selection of exogenous peptides to MHC class II molecules thereby assuring proper selection of immunodominant epitopes. A second Class II accessory molecule, DO (HLA-DO human; murine H2-O), mainly present in B cells and thymic epithelium also contributes to the selection of immunodominant epitopes. Yet, despite a wealth of mechanistic insights into how DM functions, understanding the contributions of DO to epitope selection has proven to be highly challenging. In this review, we have attempted to discuss published in vitro and in vivo data during the past three years with insights into the biology of DO.
Collapse
Affiliation(s)
- Robin A Welsh
- Graduate Program in Immunology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Scheherazade Sadegh-Nasseri
- Graduate Program in Immunology, Johns Hopkins University School of Medicine, Baltimore, MD, United States; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States.
| |
Collapse
|
40
|
Carabali-Isajar ML, Ocampo M, Varela Y, Díaz-Arévalo D, Patarroyo MA, Patarroyo ME. Antibodies targeting Mycobacterium tuberculosis peptides inhibit mycobacterial entry to infection target cells. Int J Biol Macromol 2020; 161:712-720. [PMID: 32522539 DOI: 10.1016/j.ijbiomac.2020.06.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 05/13/2020] [Accepted: 06/01/2020] [Indexed: 01/26/2023]
Abstract
The humoral immunity regarding tuberculosis can contribute towards controlling the mycobacteria and the disease. Antigens mediating such type of immunity should thus be evaluated for formulating anti-tuberculosis vaccines. The antigen recognition of seven peptides derived from proteins on Mtb H37Rv envelope and a further seven peptides modified from them was evaluated in sera taken from people suffering Mtb infection and others free from it. Peptide sequences' ability to inhibit Mtb entry to human macrophages was determined in vitro and, after isolating peptide-specific IgG antibodies, it was ascertained which ones were exercising such inhibitory function. Aotus were inoculated with the modified peptides for evaluating the activity of the antibodies so produced. Human QTF+ and QTF- sera recognised some of the peptides and inhibited Mtb entry. The same effect was seen with peptide-specific IgG regarding all the native sequences and modified ones. Sera taken from inoculated Aotus was also able to reduce the pathogen's entry. The data showed that some peptides evaluated in this study could induce antibodies able to inhibit the pathogen's entry to human macrophages, i.e. they could represent candidates for part of an anti-tuberculosis vaccine. The methodology used here complements the evaluation of promising antigens for designing effective vaccines.
Collapse
Affiliation(s)
- Mary L Carabali-Isajar
- Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50 No. 26-20, 111321 Bogotá, Colombia; Universidad del Rosario, Carrera 24 No. 63C-69, 111321 Bogotá, Colombia
| | - Marisol Ocampo
- Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50 No. 26-20, 111321 Bogotá, Colombia; Universidad Distrital Francisco José de Caldas, Carrera 3 # 26A - 40, 11021 Bogotá, Colombia.
| | - Yahson Varela
- Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50 No. 26-20, 111321 Bogotá, Colombia; Universidad del Rosario, Carrera 24 No. 63C-69, 111321 Bogotá, Colombia
| | - Diana Díaz-Arévalo
- Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50 No. 26-20, 111321 Bogotá, Colombia; Universidad del Rosario, Carrera 24 No. 63C-69, 111321 Bogotá, Colombia
| | - Manuel A Patarroyo
- Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50 No. 26-20, 111321 Bogotá, Colombia; Universidad del Rosario, Carrera 24 No. 63C-69, 111321 Bogotá, Colombia
| | - Manuel E Patarroyo
- Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50 No. 26-20, 111321 Bogotá, Colombia; Universidad Nacional de Colombia, Carrera 45 No. 26-85, 11001 Bogotá, Colombia
| |
Collapse
|
41
|
Margulies DH, Jiang J, Natarajan K. Structural and dynamic studies of TAPBPR and Tapasin reveal the mechanism of peptide loading of MHC-I molecules. Curr Opin Immunol 2020; 64:71-79. [DOI: 10.1016/j.coi.2020.04.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 03/24/2020] [Accepted: 04/03/2020] [Indexed: 12/17/2022]
|
42
|
Srivastava R, Coulon PGA, Prakash S, Dhanushkodi NR, Roy S, Nguyen AM, Alomari NI, Mai UT, Amezquita C, Ye C, Maillère B, BenMohamed L. Human Epitopes Identified from Herpes Simplex Virus Tegument Protein VP11/12 (UL46) Recall Multifunctional Effector Memory CD4 + T EM Cells in Asymptomatic Individuals and Protect from Ocular Herpes Infection and Disease in "Humanized" HLA-DR Transgenic Mice. J Virol 2020; 94:e01991-19. [PMID: 31915285 PMCID: PMC7081904 DOI: 10.1128/jvi.01991-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 01/02/2020] [Indexed: 01/17/2023] Open
Abstract
While the role of CD8+ T cells in the control of herpes simplex virus 1 (HSV-1) infection and disease is gaining wider acceptance, a direct involvement of effector CD4+ T cells in this protection and the phenotype and function of HSV-specific human CD4+ T cell epitopes remain to be fully elucidated. In the present study, we report that several epitopes from the HSV-1 virion tegument protein (VP11/12) encoded by UL46 are targeted by CD4+ T cells from HSV-seropositive asymptomatic individuals (who, despite being infected, never develop any recurrent herpetic disease). Among these, we identified two immunodominant effector memory CD4+ TEM cell epitopes, amino acids (aa) 129 to 143 of VP11/12 (VP11/12129-143) and VP11/12483-497, using in silico, in vitro, and in vivo approaches based on the following: (i) a combination of the TEPITOPE algorithm and PepScan library scanning of the entire 718 aa of HSV-1 VP11/12 sequence; (ii) an in silico peptide-protein docking analysis and in vitro binding assay that identify epitopes with high affinity to soluble HLA-DRB1 molecules; and (iii) an ELISpot assay and intracellular detection of gamma interferon (IFN-γ), CD107a/b degranulation, and CD4+ T cell carboxyfluorescein succinimidyl ester (CFSE) proliferation assays. We demonstrated that native VP11/12129-143 and VP11/12483-497 epitopes presented by HSV-1-infected HLA-DR-positive target cells were recognized mainly by effector memory CD4+ TEM cells while being less targeted by FOXP3+ CD4+ CD25+ regulatory T cells. Furthermore, immunization of HLA-DR transgenic mice with a mixture of the two immunodominant human VP11/12 CD4+ TEM cell epitopes, but not with cryptic epitopes, induced HSV-specific polyfunctional IFN-γ-producing CD107ab+ CD4+ T cells associated with protective immunity against ocular herpes infection and disease.IMPORTANCE We report that naturally protected HSV-1-seropositive asymptomatic individuals develop a higher frequency of antiviral effector memory CD4+ TEM cells specific to two immunodominant epitopes derived from the HSV-1 tegument protein VP11/12. Immunization of HLA-DR transgenic mice with a mixture of these two immunodominant CD4+ T cell epitopes induced a robust antiviral CD4+ T cell response in the cornea that was associated with protective immunity against ocular herpes. The emerging concept of developing an asymptomatic herpes vaccine that would boost effector memory CD4+ and CD8+ TEM cell responses is discussed.
Collapse
Affiliation(s)
- Ruchi Srivastava
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, California, USA
| | - Pierre-Gregoire A Coulon
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, California, USA
| | - Swayam Prakash
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, California, USA
| | - Nisha R Dhanushkodi
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, California, USA
| | - Soumyabrata Roy
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, California, USA
| | - Angela M Nguyen
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, California, USA
| | - Nuha I Alomari
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, California, USA
| | - Uyen T Mai
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, California, USA
| | - Cassendra Amezquita
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, California, USA
| | - Caitlin Ye
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, California, USA
| | - Bernard Maillère
- Commissariat à l'Energie Atomique et aux Energies Alternatives-Saclay, Université Paris-Saclay, Service d'Ingénierie Moléculaire des Protéines, Gif-sur-Yvette, France
| | - Lbachir BenMohamed
- Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, California, USA
- Department of Molecular Biology and Biochemistry, University of California Irvine, School of Medicine, Irvine, California, USA
- Institute for Immunology, University of California Irvine, School of Medicine, Irvine, California, USA
| |
Collapse
|
43
|
Zhang J, He J, Li J, Zhou Q, Chen H, Zheng Z, Chen Q, Chen D, Chen J. The immunogenicity and protective immunity of multi-epitopes DNA prime-protein boost vaccines encoding Amastin-Kmp-11, Kmp11-Gp63 and Amastin-Gp63 against visceral leishmaniasis. PLoS One 2020; 15:e0230381. [PMID: 32176727 PMCID: PMC7075555 DOI: 10.1371/journal.pone.0230381] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 02/28/2020] [Indexed: 11/27/2022] Open
Abstract
Visceral leishmaniasis (VL) is the most fatal form of leishmaniasis if left untreated and 50,000 to 90,000 new cases of VL occur worldwide each year. Although various vaccines had been studied in animal models, none of them was eligible to prevent human from infections. In this study, according to the silico analysis of Leishmania Amastin, Kmp-11 and Gp63 protein, dominant epitope sequences of these proteins were selected and linked to construct dominant multi-epitopes DNA and protein vaccines (Amastin-Kmp-11, Amastin-Gp63 and Kmp-11-Gp63) against VL. BALB/c mice were immunized with a DNA prime-protein boost immunization strategy and challenged with a new Leishmania parasite strain isolated from a VL patient. After immunization, the results including specific antibody titers, IL-4 and TNF-α levels, and CD4 and CD8 T cell proportion suggested the potent immunogenicity of the three vaccines. After infection, the results of spleen parasite burdens in the three vaccine groups were significantly lower than those of control groups, and the parasite reduction rates of Amastin-Kmp-11, Amastin-Gp63 and Kmp-11-Gp63 groups were 89.38%, 91.01% and 88.42%, respectively. Spleen smear observation and liver histopathological changes showed that all vaccine groups could produce significant immunoprotection against VL and Amastin-Gp63 vaccine was the best. In conclusion, our work demonstrated that the three dominant multi-epitopes Amastin-Kmp-11, Amastin-Gp63 and Kmp-11-Gp63 DNA prime-protein boost vaccines might be new vaccine candidates for VL, and the Amastin-Gp63 vaccine have best efficacy.
Collapse
Affiliation(s)
- Jianhui Zhang
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Jinlei He
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Jiao Li
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Qi Zhou
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Han Chen
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Zhiwan Zheng
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Qiwei Chen
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Dali Chen
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Jianping Chen
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China.,Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Sichuan University, Chengdu, Sichuan, China
| |
Collapse
|
44
|
Welsh RA, Song N, Foss CA, Boronina T, Cole RN, Sadegh-Nasseri S. Lack of the MHC class II chaperone H2-O causes susceptibility to autoimmune diseases. PLoS Biol 2020; 18:e3000590. [PMID: 32069316 PMCID: PMC7028248 DOI: 10.1371/journal.pbio.3000590] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 01/13/2020] [Indexed: 01/14/2023] Open
Abstract
DO (HLA-DO, in human; murine H2-O) is a highly conserved nonclassical major histocompatibility complex class II (MHC II) accessory molecule mainly expressed in the thymic medulla and B cells. Previous reports have suggested possible links between DO and autoimmunity, Hepatitis C (HCV) infection, and cancer, but the mechanism of how DO contributes to these diseases remains unclear. Here, using a combination of various in vivo approaches, including peptide elution, mixed lymphocyte reaction, T-cell receptor (TCR) deep sequencing, tetramer-guided naïve CD4 T-cell precursor enumeration, and whole-body imaging, we report that DO affects the repertoire of presented self-peptides by B cells and thymic epithelium. DO induces differential effects on epitope presentation and thymic selection, thereby altering CD4 T-cell precursor frequencies. Our findings were validated in two autoimmune disease models by demonstrating that lack of DO increases autoreactivity and susceptibility to autoimmune disease development. A combination of cellular, molecular and in vivo approaches reveals that the non-classical MHC class II chaperone DO controls CD4 T cell thymic selection; its absence leads to susceptibility to two murine autoimmune diseases, collagen-induced arthritis and experimental autoimmune encephalomyelitis.
Collapse
Affiliation(s)
- Robin A. Welsh
- Graduate Program in Immunology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Nianbin Song
- Graduate Program in Immunology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Catherine A. Foss
- Russel H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Tatiana Boronina
- Mass Spectrometry and Proteomics Core, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Robert N. Cole
- Mass Spectrometry and Proteomics Core, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Scheherazade Sadegh-Nasseri
- Graduate Program in Immunology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- * E-mail:
| |
Collapse
|
45
|
Zhang L, Li X, Ma L, Zhang B, Meng G, Xia C. A Newly Recognized Pairing Mechanism of the α- and β-Chains of the Chicken Peptide-MHC Class II Complex. THE JOURNAL OF IMMUNOLOGY 2020; 204:1630-1640. [PMID: 32034060 DOI: 10.4049/jimmunol.1901305] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 01/09/2020] [Indexed: 01/24/2023]
Abstract
MHC class II (MHC-II) molecules play a crucial role in cellular and humoral immunity by forming peptide-MHC-II (pMHC-II) complexes. The three-dimensional structures of pMHC-II complexes have been well resolved in humans and mice. However, there is no structural information for pMHC-II complexes in nonmammals. In chickens, there are two closely related and highly polymorphic β-chains and one monomorphic α-chain, and the mechanism by which one monomorphic α-chain combines with two polymorphic β-chains to form a functional heterodimer remains unknown. In this study, we report the crystal structure of a chicken pMHC-II complex (pBL2*019:01) at 1.9-Å resolution as the first nonmammalian structure of a pMHC-II complex. The structure reveals an increase in hydrogen bonding between the α and β main chains at the central interface that is introduced by the insertion of four residues in the α-chain. The residues in the β-chain that form hydrogen bonds with the α-chain are conserved among all β alleles. These structural characteristics explain the phenomenon of only one BLA allele without sequence variation pairing with highly diverse BLB alleles from two loci in the genome. Additionally, the characteristics of the peptide in the peptide-binding groove were confirmed. These results provide a new understanding of the pairing mechanism of the α- and β-chains in a pMHC-II complex and establish a structural principle to design epitope-related vaccines for the prevention of chicken diseases.
Collapse
Affiliation(s)
- Lijie Zhang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Haidian District, Beijing 100193, China; and
| | - Xiaoying Li
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Haidian District, Beijing 100193, China; and
| | - Lizhen Ma
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Haidian District, Beijing 100193, China; and
| | - Bing Zhang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Haidian District, Beijing 100193, China; and
| | - Geng Meng
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Haidian District, Beijing 100193, China
| | - Chun Xia
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Haidian District, Beijing 100193, China; and
| |
Collapse
|
46
|
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.
Collapse
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.
| |
Collapse
|
47
|
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.
Collapse
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.
| |
Collapse
|
48
|
Mamedov A, Vorobyeva N, Filimonova I, Zakharova M, Kiselev I, Bashinskaya V, Baulina N, Boyko A, Favorov A, Kulakova O, Ziganshin R, Smirnov I, Poroshina A, Shilovskiy I, Khaitov M, Sykulev Y, Favorova O, Vlassov V, Gabibov A, Belogurov A. Protective Allele for Multiple Sclerosis HLA-DRB1*01:01 Provides Kinetic Discrimination of Myelin and Exogenous Antigenic Peptides. Front Immunol 2020; 10:3088. [PMID: 32010139 PMCID: PMC6978714 DOI: 10.3389/fimmu.2019.03088] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 12/17/2019] [Indexed: 12/15/2022] Open
Abstract
Risk of the development of multiple sclerosis (MS) is known to be increased in individuals bearing distinct class II human leukocyte antigen (HLA) variants, whereas some of them may have a protective effect. Here we analyzed distribution of a highly polymorphous HLA-DRB1 locus in more than one thousand relapsing-remitting MS patients and healthy individuals of Russian ethnicity. Carriage of HLA-DRB1*15 and HLA-DRB1*03 alleles was associated with MS risk, whereas carriage of HLA-DRB1*01 and HLA-DRB1*11 was found to be protective. Analysis of genotypes revealed the compensatory effect of risk and resistance alleles in trans. We have identified previously unknown MBP153-161 peptide located at the C-terminus of MBP protein and MBP90-98 peptide that bound to recombinant HLA-DRB1*01:01 protein with affinity comparable to that of classical antigenic peptide 306-318 from the hemagglutinin (HA) of the influenza virus demonstrating the ability of HLA-DRB1*01:01 to present newly identified MBP153-161 and MBP90-98 peptides. Measurements of kinetic parameters of MBP and HA peptides binding to HLA-DRB1*01:01 catalyzed by HLA-DM revealed a significantly lower rate of CLIP exchange for MBP153-161 and MBP90-98 peptides as opposed to HA peptide. Analysis of the binding of chimeric MBP-HA peptides demonstrated that the observed difference between MBP153-161, MBP90-98, and HA peptide epitopes is caused by the lack of anchor residues in the C-terminal part of the MBP peptides resulting in a moderate occupation of P6/7 and P9 pockets of HLA-DRB1*01:01 by MBP153-161 and MBP90-98 peptides in contrast to HA308-316 peptide. This leads to the P1 and P4 docking failure and rapid peptide dissociation and release of empty HLA-DM-HLA-DR complex. We would like to propose that protective properties of the HLA-DRB1*01 allele could be directly linked to the ability of HLA-DRB1*01:01 to kinetically discriminate between antigenic exogenous peptides and endogenous MBP derived peptides.
Collapse
Affiliation(s)
- Azad Mamedov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | | | - Ioanna Filimonova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Maria Zakharova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia
| | - Ivan Kiselev
- Pirogov Russian National Research Medical University, Moscow, Russia
| | | | - Natalia Baulina
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Alexey Boyko
- Pirogov Russian National Research Medical University, Moscow, Russia.,Neuroimmunological Department of the Federal Center of Cerebrovascular Diseases and Stroke, Moscow, Russia
| | - Alexander Favorov
- Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University, Baltimore, MD, United States.,Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Olga Kulakova
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Rustam Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Ivan Smirnov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Institute of Fundamental Medicine and Biology, Kazan (Volga) Federal University, Kazan, Russia
| | - Alina Poroshina
- National Research Center Institute of Immunology FMBA of Russia, Moscow, Russia
| | - Igor Shilovskiy
- National Research Center Institute of Immunology FMBA of Russia, Moscow, Russia
| | - Musa Khaitov
- National Research Center Institute of Immunology FMBA of Russia, Moscow, Russia
| | - Yuri Sykulev
- Department of Microbiology, Thomas Jefferson University, Philadelphia, PA, United States
| | - Olga Favorova
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Valentin Vlassov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Alexander Gabibov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Department of Fundamental Medicine, Lomonosov Moscow State University, Moscow, Russia
| | - Alexey Belogurov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Department of Fundamental Medicine, Lomonosov Moscow State University, Moscow, Russia
| |
Collapse
|
49
|
Sadegh-Nasseri S. How a Proposed Hypothesis during My PhD Training Shaped My Career. Crit Rev Immunol 2020; 40:449-464. [PMID: 33463956 PMCID: PMC11014643 DOI: 10.1615/critrevimmunol.2020035324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In this memoir-style essay, I have narrated the evolution of my scientific career, as deeply influenced by my PhD training and the mentorship of Professor Eli Sercarz. Starting in his lab, and continuing to my own laboratory, many of the questions we have pursued link in some way to Eli's ideas. In this essay, I have summarized the path that I followed after graduating from his lab and highlight findings along the way. I apologize to my colleagues whose work was not discussed here due to the nature of this review and space limitations.
Collapse
|
50
|
Shamin M, Benedyk TH, Graham SC, Deane JE. The lipid transfer protein Saposin B does not directly bind CD1d for lipid antigen loading. Wellcome Open Res 2019; 4:117. [PMID: 31667358 PMCID: PMC6807164 DOI: 10.12688/wellcomeopenres.15368.2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/14/2019] [Indexed: 12/13/2022] Open
Abstract
Background: Lipid antigens are presented on the surface of cells by the CD1 family of glycoproteins, which have structural and functional similarity to MHC class I molecules. The hydrophobic lipid antigens are embedded in membranes and inaccessible to the lumenal lipid-binding domain of CD1 molecules. Therefore, CD1 molecules require lipid transfer proteins for lipid loading and editing. CD1d is loaded with lipids in late endocytic compartments, and lipid transfer proteins of the saposin family have been shown to play a crucial role in this process. However, the mechanism by which saposins facilitate lipid binding to CD1 molecules is not known and is thought to involve transient interactions between protein components to ensure CD1-lipid complexes can be efficiently trafficked to the plasma membrane for antigen presentation. Of the four saposin proteins, the importance of Saposin B (SapB) for loading of CD1d is the most well-characterised. However, a direct interaction between CD1d and SapB has yet to be described. Methods: In order to determine how SapB might load lipids onto CD1d, we used purified, recombinant CD1d and SapB and carried out a series of highly sensitive binding assays to monitor direct interactions. We performed equilibrium binding analysis, chemical cross-linking and co-crystallisation experiments, under a range of different conditions. Results: We could not demonstrate a direct interaction between SapB and CD1d using any of these binding assays. Conclusions: This work strongly indicates that the role of SapB in lipid loading does not involve direct binding to CD1d. We discuss the implication of this for our understanding of lipid loading of CD1d and propose several factors that may influence this process.
Collapse
Affiliation(s)
- Maria Shamin
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
| | - Tomasz H. Benedyk
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
| | - Stephen C. Graham
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
| | - Janet E. Deane
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0QQ, UK
| |
Collapse
|