1
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Chuang L, Qifeng J, Shaolei Y. The tumor immune microenvironment and T-cell-related immunotherapies in colorectal cancer. Discov Oncol 2024; 15:244. [PMID: 38918278 PMCID: PMC11199466 DOI: 10.1007/s12672-024-01117-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 06/21/2024] [Indexed: 06/27/2024] Open
Abstract
The tumor microenvironment includes a complex network of immune T-cell subsets that play important roles in colorectal cancer (CRC) progression and are key elements of CRC immunotherapy. T cells develop and migrate within tumors, recognizing tumor-specific antigens to regulate immune surveillance. Current immunotherapies are divided into the following main categories based on the regulatory role of T-cell subsets in the tumor immune microenvironment (TIME): cytokines, monoclonal antibodies, peptide vaccines, CAR-T cells and more. This review describes the composition of the tumor immune microenvironment in colorectal cancer and the involvement of T cells in the pathogenesis and progression of CRC as well as current T-cell-related immunotherapies. Further studies on CRC-specific tumor antigens, the gene regulation of T cells, and the regulation of immune activity are needed.
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Affiliation(s)
- Liu Chuang
- Hanan Branch of the Second Affiliated Hospital of Heilongjiang University of Chinese Medicine, Guogoli Street, Nangang District, Harbin, China
| | - Ju Qifeng
- The First Affiliated Hospital Heilongjiang University of Chinese Medicine, Harbin, China
| | - Yu Shaolei
- Hanan Branch of the Second Affiliated Hospital of Heilongjiang University of Chinese Medicine, Guogoli Street, Nangang District, Harbin, China.
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2
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Chan YW, Tan CH, Heh CH, Tan KY. An immunoinformatic approach to assessing the immunogenic capacity of alpha-neurotoxins in elapid snake venoms. Front Pharmacol 2023; 14:1143437. [PMID: 37153801 PMCID: PMC10155835 DOI: 10.3389/fphar.2023.1143437] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/27/2023] [Indexed: 05/10/2023] Open
Abstract
Introduction: Most elapid snakes produce venoms that contain alpha-neurotoxins (α-NTXs), which are proteins that cause post-synaptic blockade and paralysis in snakebite envenoming. However, existing elapid antivenoms are known for their low potency in neutralizing the neurotoxic activity of α-NTXs, while the immunological basis has not been elucidated. Methods: In this study, a structure-based major histocompatibility complex II (MHCII) epitope predictor of horse (Equus caballus), complemented with DM-editing determinant screening algorithm was adopted to assess the immunogenicity of α-NTXs in the venoms of major Asiatic elapids (Naja kaouthia, Ophiophagus hannah, Laticauda colubrina, Hydrophis schistosus, Hydrophis curtus). Results: The scoring metric M2R, representing the relative immunogenic performance of respective α-NTXs, showed all α-NTXs have an overall low M2R of <0.3, and most of the predicted binders feature non-optimal P1 anchor residues. The M2R scores correlate strongly (R2 = 0.82) with the potency scores (p-score) generated based on the relative abundances of α-NTXs and the neutralization potency of commercial antivenoms. Discussion: The immunoinformatic analysis indicates that the inferior antigenicity of α-NTXs is not only due to their small molecular size but also the subpar immunogenicity affected by their amino acid composition. Structural modification with conjugation and synthetic epitope as immunogen may potentially enhance the immunogenicity for improved antivenom potency against α-NTXs of elapid snakes.
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Affiliation(s)
- Yi Wei Chan
- Protein and Interactomics Laboratory, Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Choo Hock Tan
- Venom Research and Toxicology Laboratory, Department of Pharmacology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Choon Han Heh
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Malaya, Kuala Lumpur, Malaysia
| | - Kae Yi Tan
- Protein and Interactomics Laboratory, Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
- *Correspondence: Kae Yi Tan,
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3
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Halabi S, Kaufman J. New vistas unfold: Chicken MHC molecules reveal unexpected ways to present peptides to the immune system. Front Immunol 2022; 13:886672. [PMID: 35967451 PMCID: PMC9372762 DOI: 10.3389/fimmu.2022.886672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 07/07/2022] [Indexed: 11/27/2022] Open
Abstract
The functions of a wide variety of molecules with structures similar to the classical class I and class II molecules encoded by the major histocompatibility complex (MHC) have been studied by biochemical and structural studies over decades, with many aspects for humans and mice now enshrined in textbooks as dogma. However, there is much variation of the MHC and MHC molecules among the other jawed vertebrates, understood in the most detail for the domestic chicken. Among the many unexpected features in chickens is the co-evolution between polymorphic TAP and tapasin genes with a dominantly-expressed class I gene based on a different genomic arrangement compared to typical mammals. Another important discovery was the hierarchy of class I alleles for a suite of properties including size of peptide repertoire, stability and cell surface expression level, which is also found in humans although not as extreme, and which led to the concept of generalists and specialists in response to infectious pathogens. Structural studies of chicken class I molecules have provided molecular explanations for the differences in peptide binding compared to typical mammals. These unexpected phenomena include the stringent binding with three anchor residues and acidic residues at the peptide C-terminus for fastidious alleles, and the remodelling binding sites, relaxed binding of anchor residues in broad hydrophobic pockets and extension at the peptide C-terminus for promiscuous alleles. The first few studies for chicken class II molecules have already uncovered unanticipated structural features, including an allele that binds peptides by a decamer core. It seems likely that the understanding of how MHC molecules bind and present peptides to lymphocytes will broaden considerably with further unexpected discoveries through biochemical and structural studies for chickens and other non-mammalian vertebrates.
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Affiliation(s)
- Samer Halabi
- Institute for Immunology and Infection Research, University of Edinburgh, Edinburgh, United Kingdom
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Jim Kaufman
- Institute for Immunology and Infection Research, University of Edinburgh, Edinburgh, United Kingdom
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
- *Correspondence: Jim Kaufman,
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4
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Breed ER, Vobořil M, Ashby KM, Martinez RJ, Qian L, Wang H, Salgado OC, O'Connor CH, Hogquist KA. Type 2 cytokines in the thymus activate Sirpα + dendritic cells to promote clonal deletion. Nat Immunol 2022; 23:1042-1051. [PMID: 35637352 PMCID: PMC10037932 DOI: 10.1038/s41590-022-01218-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 04/18/2022] [Indexed: 12/30/2022]
Abstract
The thymus contains a diversity of dendritic cells (DCs) that exist in defined locations and have different antigen-processing and -presenting features. This suggests that they play nonredundant roles in mediating thymocyte selection. In an effort to eliminate SIRPα+ classic DC2 subsets, we discovered that a substantial proportion expresses the surface lectin, CD301b, in the thymus. These cells resemble the CD301b+ type 2 immune response promoting DCs that are present in the skin-draining lymph nodes. Transcriptional and phenotypic comparison to other DC subsets in the thymus revealed that thymic CD301b+ cDCs represent an activated state that exhibits enhanced antigen processing and presentation. Furthermore, a CD301b+ cDC2 subset demonstrated a type 2 cytokine signature and required steady-state interleukin-4 receptor signaling. Selective ablation of CD301b+ cDC2 subsets impaired clonal deletion without affecting regulatory T cells (Treg cells). The T cell receptor α repertoire sequencing confirmed that a cDC2 subset promotes deletion of conventional T cells with minimal effect on Treg cell selection. Together, these findings suggest that cytokine-induced activation of DCs in the thymus substantially enforces central tolerance.
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Affiliation(s)
- Elise R Breed
- Department of Laboratory Medicine and Pathology, Center for Immunology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Matouš Vobořil
- Department of Laboratory Medicine and Pathology, Center for Immunology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Katherine M Ashby
- Department of Laboratory Medicine and Pathology, Center for Immunology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Ryan J Martinez
- Department of Laboratory Medicine and Pathology, Center for Immunology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Lily Qian
- Department of Laboratory Medicine and Pathology, Center for Immunology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Haiguang Wang
- Department of Laboratory Medicine and Pathology, Center for Immunology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Oscar C Salgado
- Department of Laboratory Medicine and Pathology, Center for Immunology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Christine H O'Connor
- Research Informatics Solutions, Laboratory Medicine and Pathology Group, Minnesota Supercomputing Institute, Minneapolis, MN, USA
| | - Kristin A Hogquist
- Department of Laboratory Medicine and Pathology, Center for Immunology, University of Minnesota Medical School, Minneapolis, MN, USA.
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5
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Sim MJW, Sun PD. T Cell Recognition of Tumor Neoantigens and Insights Into T Cell Immunotherapy. Front Immunol 2022; 13:833017. [PMID: 35222422 PMCID: PMC8867076 DOI: 10.3389/fimmu.2022.833017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 01/21/2022] [Indexed: 12/13/2022] Open
Abstract
In cancer, non-synonymous DNA base changes alter protein sequence and produce neoantigens that are detected by the immune system. For immune detection, neoantigens must first be presented on class I or II human leukocyte antigens (HLA) followed by recognition by peptide-specific receptors, exemplified by the T-cell receptor (TCR). Detection of neoantigens represents a unique challenge to the immune system due to their high similarity with endogenous ‘self’ proteins. Here, we review insights into how TCRs detect neoantigens from structural studies and delineate two broad mechanistic categories: 1) recognition of mutated ‘self’ peptides and 2) recognition of novel ‘non-self’ peptides generated through anchor residue modifications. While mutated ‘self’ peptides differ only by a single amino acid from an existing ‘self’ epitope, mutations that form anchor residues generate an entirely new epitope, hitherto unknown to the immune system. We review recent structural studies that highlight these structurally distinct mechanisms and discuss how they may lead to differential anti-tumor immune responses. We discuss how T cells specific for neoantigens derived from anchor mutations can be of high affinity and provide insights to their use in adoptive T cell transfer-based immunotherapy.
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Affiliation(s)
- Malcolm J W Sim
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Rockville, MD, United States
| | - Peter D Sun
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Rockville, MD, United States
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6
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He J, Chen J, Han X, Gu Q, Liang J, Sun M, Liu S, Yao Y, Shi L. Association of HLA-DM and HLA class II Genes with Antibody Response Induced by Inactivated Japanese Encephalitis Vaccine. HLA 2022; 99:357-367. [PMID: 35118816 DOI: 10.1111/tan.14575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 01/29/2022] [Accepted: 01/31/2022] [Indexed: 11/04/2022]
Abstract
HLA (HLA) class II molecules, HLA-DR, DP, and DQ, together with HLA II-like protein DM, play a dominant role in the processing and presentation of antigens, which may influence vaccine effectiveness. We previously demonstrated that variations in the HLA-DRB1, DPB1, and DQB1 genes may affect the neutralising antibody (NAb) response induced by the inactivated Japanese encephalitis vaccine (IJEV). In the present study, we genotyped HLA-DPA1, DQA1, DMA, and DMB genes and used previous HLA-DRB1, DPB1, and DQB1 data to evaluate the association of these genes with IJEV-induced NAbs, at both the seroconversion and geometric mean titres (GMTs). We confirmed the seropositive association of DQB1*02:01 and NAbs (0.156 vs. 0.075, Padj = 0.018; OR = 2.270; 95% CI = 1.285-3.999) and seronegative association of DQB1*02:02 (0.014 vs. 0.09, Padj = 0.0002; OR = 0.130; 95% CI = 0.047-0.400). Furthermore, the DMB*01:03-DMA*01:01-DPA1*01:03-DPB1*04:01 haplotype was associated with a negative response (0.020 vs. 0.074; Padj = 0.03; OR = 0.250; 95% CI = 0.097-0.649), whereas DRB1*15:02-DMB*01:01-DMA*01:01 was associated with a positive response (0.034 vs. 0; Padj = 0.044). In addition, DRB1*12:02, DRB1*13:02, DPB1*04:01, DPB1*05:01, DPB1*09:01, DQA1*06:01, and DQA1*01:02 were associated with a higher GMT of NAbs, whereas DRB1*11:01, DPB1*13:01, and DQA1*05:05 were associated with a lower GMT of NAbs. In conclusion, the present study suggests that variations in the HLA-DM and HLA class II genes, as well as their combined allotypes, may influence the IJEV NAbs at seroconversion and GMT levels. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Jihong He
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China
| | - Jun Chen
- Department of Immunogenetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China
| | - Xue Han
- Department of Immunogenetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China
| | - Qin Gu
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China.,Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Disease, Kunming, China
| | - Jiangli Liang
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China.,Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Disease, Kunming, China
| | - Mingbo Sun
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China.,Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Disease, Kunming, China
| | - Shuyuan Liu
- Department of Immunogenetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China
| | - Yufeng Yao
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China
| | - Li Shi
- Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Disease, Kunming, China
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7
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Regulation of the BCR signalosome by the class II peptide editor, H2-M, affects the development and repertoire of innate-like B cells. Cell Rep 2022; 38:110200. [DOI: 10.1016/j.celrep.2021.110200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 09/23/2021] [Accepted: 12/13/2021] [Indexed: 11/21/2022] Open
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8
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Heidari M, Pakdel A, Bakhtiarizadeh MR, Dehghanian F. Integrated Analysis of lncRNAs, mRNAs, and TFs to Identify Regulatory Networks Underlying MAP Infection in Cattle. Front Genet 2021; 12:668448. [PMID: 34290737 PMCID: PMC8287970 DOI: 10.3389/fgene.2021.668448] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 06/04/2021] [Indexed: 11/29/2022] Open
Abstract
Johne’s disease is a chronic infection of ruminants that burdens dairy herds with a significant economic loss. The pathogenesis of the disease has not been revealed clearly due to its complex nature. In order to achieve deeper biological insights into molecular mechanisms involved in MAP infection resulting in Johne’s disease, a system biology approach was used. As far as is known, this is the first study that considers lncRNAs, TFs, and mRNAs, simultaneously, to construct an integrated gene regulatory network involved in MAP infection. Weighted gene coexpression network analysis (WGCNA) and functional enrichment analysis were conducted to explore coexpression modules from which nonpreserved modules had altered connectivity patterns. After identification of hub and hub-hub genes as well as TFs and lncRNAs in the nonpreserved modules, integrated networks of lncRNA-mRNA-TF were constructed, and cis and trans targets of lncRNAs were identified. Both cis and trans targets of lncRNAs were found in eight nonpreserved modules. Twenty-one of 47 nonpreserved modules showed significant biological processes related to the immune system and MAP infection. Some of the MAP infection’s related pathways in the most important nonpreserved modules comprise “positive regulation of cytokine-mediated signaling pathway,” “negative regulation of leukocyte migration,” “T-cell differentiation,” “neutrophil activation,” and “defense response.” Furthermore, several genes were identified in these modules, including SLC11A1, MAPK8IP1, HMGCR, IFNGR1, CMPK2, CORO1A, IRF1, LDLR, BOLA-DMB, and BOLA-DMA, which are potentially associated with MAP pathogenesis. This study not only enhanced our knowledge of molecular mechanisms behind MAP infection but also highlighted several promising hub and hub-hub genes involved in macrophage-pathogen interaction.
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Affiliation(s)
- Maryam Heidari
- Department of Animal Sciences, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Abbas Pakdel
- Department of Animal Sciences, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
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9
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Taylor HB, Klaeger S, Clauser KR, Sarkizova S, Weingarten-Gabbay S, Graham DB, Carr SA, Abelin JG. MS-Based HLA-II Peptidomics Combined With Multiomics Will Aid the Development of Future Immunotherapies. Mol Cell Proteomics 2021; 20:100116. [PMID: 34146720 PMCID: PMC8327157 DOI: 10.1016/j.mcpro.2021.100116] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 06/02/2021] [Accepted: 06/03/2021] [Indexed: 12/25/2022] Open
Abstract
Immunotherapies have emerged to treat diseases by selectively modulating a patient's immune response. Although the roles of T and B cells in adaptive immunity have been well studied, it remains difficult to select targets for immunotherapeutic strategies. Because human leukocyte antigen class II (HLA-II) peptides activate CD4+ T cells and regulate B cell activation, proliferation, and differentiation, these peptide antigens represent a class of potential immunotherapy targets and biomarkers. To better understand the molecular basis of how HLA-II antigen presentation is involved in disease progression and treatment, systematic HLA-II peptidomics combined with multiomic analyses of diverse cell types in healthy and diseased states is required. For this reason, MS-based innovations that facilitate investigations into the interplay between disease pathologies and the presentation of HLA-II peptides to CD4+ T cells will aid in the development of patient-focused immunotherapies.
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Affiliation(s)
- Hannah B Taylor
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Susan Klaeger
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Karl R Clauser
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | - Shira Weingarten-Gabbay
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Daniel B Graham
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA; Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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10
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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.
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11
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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.
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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
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12
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Frommer L, Kahaly GJ. Type 1 Diabetes and Autoimmune Thyroid Disease-The Genetic Link. Front Endocrinol (Lausanne) 2021; 12:618213. [PMID: 33776915 PMCID: PMC7988207 DOI: 10.3389/fendo.2021.618213] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 01/06/2021] [Indexed: 12/12/2022] Open
Abstract
Type 1 diabetes (T1D) and autoimmune thyroid disease (AITD) are the most frequent chronic autoimmune diseases worldwide. Several autoimmune endocrine and non-endocrine disorders tend to occur together. T1D and AITD often cluster in individuals and families, seen in the formation of autoimmune polyendocrinopathy (AP). The close relationship between these two diseases is largely explained by sharing a common genetic background. The HLA antigens DQ2 (DQA1*0501-DQB1*0201) and DQ8 (DQA1*0301-DQB1*0302), tightly linked with DR3 and DR4, are the major common genetic predisposition. Moreover, functional single nucleotide polymorphisms (or rare variants) of various genes, such as the cytotoxic T-lymphocyte- associated antigen (CTLA4), the protein tyrosine phosphatase non-receptor type 22 (PTPN22), the interleukin-2 Receptor (IL2Ra), the Vitamin D receptor (VDR), and the tumor-necrosis-factor-α (TNF) that are involved in immune regulation have been identified to confer susceptibility to both T1D and AITD. Other genes including cluster of differentiation 40 (CD40), the forkhead box P3 (FOXP3), the MHC Class I Polypeptide-Related Sequence A (MICA), insulin variable number of tandem repeats (INS-VNTR), the C-Type Lectin Domain Containing 16A (CLEC16A), the Erb-B2 Receptor Tyrosine Kinase 3 (ERBB3) gene, the interferon-induced helicase C domain-containing protein 1 (IFIH1), and various cytokine genes are also under suspicion to increase susceptibility to T1D and AITD. Further, BTB domain and CNC homolog 2 (BACH2), C-C motif chemokine receptor 5 (CCR5), SH2B adaptor protein 3 (SH2B3), and Rac family small GTPase 2 (RAC2) are found to be associated with T1D and AITD by various independent genome wide association studies and overlap in our list, indicating a strong common genetic link for T1D and AITD. As several susceptibility genes and environmental factors contribute to the disease aetiology of both T1D and AITD and/or AP subtype III variant (T1D+AITD) simultaneously, all patients with T1D should be screened for AITD, and vice versa.
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13
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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.
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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:
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14
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Zhou C, Liu Y, Qiao L, Lan Y, Price M, Meng Y, Yang N, Yue B. Genome-Wide Analyses Provide Insights into the Scavenging Lifestyle of the Striped Hyena ( Hyaena hyaena). DNA Cell Biol 2020; 39:1872-1885. [PMID: 32936023 DOI: 10.1089/dna.2020.5537] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Hyenas (family Hyaenidae) occupy a variety of different niches, of which the striped hyena (Hyaena hyaena) scavenges mainly on the carcasses of animals. We compared its genome with the genomes of nine other mammals, focusing on similarities and differences in chemoreception, detoxification, digestive, and immune systems. The results showed that the striped hyena's immune and digestive system-related gene families have significantly expanded, which was likely to be an adaptive response to its scavenging lifestyle. In addition, 88 and 26 positive selected genes (PSGs) were identified in the immune system and digestive system, respectively, which may be the molecular basis for immune defense system to effectively resist pathogen invasion. Functional enrichment analysis of PSGs revealed that most of them were involved in the immune regulation process. Among them, eight specific missense mutations were found in two PSGs (MHC class II antigen DOA and MHC class II antigen DOB), suggesting important reorganization of the immune system in the striped hyena. Moreover, we identified one cathelicidin gene and four defensin genes in the striped hyenas by genome mining, which have high-efficiency and broad-spectrum antimicrobial activity. Of particular interest, a striped hyena-specific missense mutation was found in the cathelicidin gene. PolyPhen-2 classified the missense mutation as a harmful mutation, which may have aided in immune adaptation to carrion feeding. Our genomic analyses on the striped hyena provided insights into its success in the adaptation to the scavenging lifestyle.
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Affiliation(s)
- Chuang Zhou
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, P.R. China
| | - Yi Liu
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, P.R. China
| | - Lu Qiao
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, P.R. China
| | - Yue Lan
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, P.R. China
| | - Megan Price
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, P.R. China
| | - Yang Meng
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, P.R. China
| | - Nan Yang
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, P.R. China
| | - Bisong Yue
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, P.R. China
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15
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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.
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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
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16
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Knowlden ZAG, Richards KA, Moritzky SA, Sant AJ. Peptide Epitope Hot Spots of CD4 T Cell Recognition Within Influenza Hemagglutinin During the Primary Response to Infection. Pathogens 2019; 8:pathogens8040220. [PMID: 31694141 PMCID: PMC6963931 DOI: 10.3390/pathogens8040220] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 10/22/2019] [Accepted: 10/29/2019] [Indexed: 01/15/2023] Open
Abstract
Antibodies specific for the hemagglutinin (HA) protein of influenza virus are critical for protective immunity to infection. Our studies show that CD4 T cells specific for epitopes derived from HA are the most effective in providing help for the HA-specific B cell responses to infection and vaccination. In this study, we asked whether HA epitopes recognized by CD4 T cells in the primary response to infection are equally distributed across the HA protein or if certain segments are enriched in CD4 T cell epitopes. Mice that collectively expressed eight alternative MHC (Major Histocompatibility Complex) class II molecules, that would each have different peptide binding specificities, were infected with an H1N1 influenza virus. CD4 T cell peptide epitope specificities were identified by cytokine EliSpots. These studies revealed that the HA-specific CD4 T cell epitopes cluster in two distinct regions of HA and that some segments of HA are completely devoid of CD4 T cell epitopes. When located on the HA structure, it appears that the regions that most poorly recruit CD4 T cells are sequestered within the interior of the HA trimer, perhaps inaccessible to the proteolytic machinery inside the endosomal compartments of antigen presenting cells.
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17
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Zakharova MY, Belyanina TA, Sokolov AV, Kiselev IS, Mamedov AE. The Contribution of Major Histocompatibility Complex Class II Genes to an Association with Autoimmune Diseases. Acta Naturae 2019; 11:4-12. [PMID: 31993230 PMCID: PMC6977962 DOI: 10.32607/20758251-2019-11-4-4-12] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Genetic studies of patients with autoimmune diseases have shown that one of the most important roles in the developing of these diseases is played by a cluster of genes of the major histocompatibility complex (MHC), as compared with other genome areas. Information on the specific contribution of MHC alleles, mostly MHC class II ones, to the genetic predisposition to autoimmune diseases is crucial for understanding their pathogenesis. This review dwells on the most relevant aspects of this problem: namely, the correlation between carriage of certain MHC II alleles and an increased (positively associated allele) or reduced (negatively associated allele) probability of developing the most common autoimmune diseases, such as type 1 diabetes, rheumatoid arthritis, multiple sclerosis, systemic lupus erythematosus, autoimmune thyroiditis, etc. The most universal haplotypes, DR3-DQ2 and DR4-DQ8, are positively associated with many of these diseases, while the universal allele HLA-DRB1*0701 is protective.
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Affiliation(s)
- M. Yu. Zakharova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997 Russia
- Pirogov Russian National Research Medical University, Moscow, 117997 Russia
| | - T. A. Belyanina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997 Russia
| | - A. V. Sokolov
- I.M. Sechenov First Moscow State Medical University, Moscow, 119991 Russia
| | - I. S. Kiselev
- Pirogov Russian National Research Medical University, Moscow, 117997 Russia
| | - A. E. Mamedov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997 Russia
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18
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Pourjafar-Dehkordi D, Vieweg S, Itzen A, Zacharias M. Phosphorylation of Ser111 in Rab8a Modulates Rabin8-Dependent Activation by Perturbation of Side Chain Interaction Networks. Biochemistry 2019; 58:3546-3554. [PMID: 31361120 DOI: 10.1021/acs.biochem.9b00516] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
GTPases are key players during cellular signaling. Phosphorylation of Rab proteins, which belong to the Ras superfamily of small GTPases regulating intracellular transport, has been implicated in the pathogenesis of Parkinson's disease. For Rab8a, it was shown that serine 111 phosphorylation (pS111) is dependent on the protein kinase PINK1 and that mimicking the phosphorylation at S111 by a serine/glutamate substitution (S111E) impaired Rab8a activation by its cognate nucleotide exchange factor (GEF) Rabin8. However, Ser111 is not part of the interface of the Rab8a:Rabin8 complex. Here, we performed comparative molecular dynamics and free energy simulations on Rab8a and Rab8a:Rabin8 complexes to elucidate the molecular details of how pS111 and S111E may influence the interaction with Rabin8. The simulations indicate that S111E and pS111 establish an intramolecular interaction with arginine 79 (R79). The interaction persists in the complex and perturbs a favorable intermolecular salt-bridge contact between R79 in Rab8a and aspartate 187 in Rabin8. Binding free energy analysis reveals that S111E and pS111, as well as the R79A mutation, drastically decrease the binding affinity for Rabin8. Combining the R79A mutation with S111E or pS111 nearly diminishes Rab8a-Rabin8 binding. In vitro experiments confirm our computational results showing a >80% decrease in the nucleotide exchange rate of the respective Rab8a mutants in the presence of Rabin8 compared to that of the wild type. In addition to insights into how S111 phosphorylation of Rab8a influences GEF-mediated activation, the simulations demonstrate how side chain modifications in general can allosterically influence the surface side chain interaction network between binding partners.
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Affiliation(s)
- Danial Pourjafar-Dehkordi
- Physics Department T38 , Technical University of Munich , James-Franck-Strasse 1 , 85748 Garching , Germany
| | - Sophie Vieweg
- Department of Chemistry , Technical University of Munich , Lichtenbergstraße 1 , 85748 Garching , Germany
| | - Aymelt Itzen
- Universitätsklinikum Hamburg-Eppendorf , Institut für Biochemie und Signaltransduktion , Martinistraße 52 , 20246 Hamburg , Germany
| | - Martin Zacharias
- Physics Department T38 , Technical University of Munich , James-Franck-Strasse 1 , 85748 Garching , Germany
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19
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Wang HY, Cui Z, Pei ZY, Fang SB, Chen SF, Zhu L, Chen M, Chen N, Zhao MH. Risk HLA class II alleles and amino acid residues in myeloperoxidase-ANCA-associated vasculitis. Kidney Int 2019; 96:1010-1019. [PMID: 31471160 DOI: 10.1016/j.kint.2019.06.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 06/05/2019] [Accepted: 06/19/2019] [Indexed: 01/09/2023]
Abstract
A genome-wide association study (GWAS) indicated that myeloperoxidase-ANCA associated vasculitis (AAV) is associated with HLA-DQ. However, susceptibility alleles in these loci have been under-investigated. Here we genotyped 258 Chinese patients with myeloperoxidase-AAV and 597 healthy control individuals at HLA DRB1, DQA1, DQB1 and DPB1, and extracted the encoded amino acid sequences from the IMGT/HLA database. The replication cohort included 97 cases and 107 controls. T cell epitopes of myeloperoxidase were predicted and docked to the HLA molecules. We found DQA1∗0302 (odds ratio 2.34 (95% confidence interval 1.75-3.14)) and DQB1∗0303 (odds ratio 1.89 (1.45-2.48)) were risk alleles for myeloperoxidase-AAV. They are in overt linkage disequilibrium (r2 0.69) and the haplotype DQA1∗0302-DQB1∗0303 presents a significant risk (haplotype score 6.39) as well. Aspartate160 on the DQ α chain (odds ratio 2.06 (1.60-2.67)), encoded by DQA1∗0302, and isoleucine185 on the DQ β chain (odds ratio 1.73 (1.38-2.18)), encoded by DQB1∗0303, both located in the α2β2 domains, conferred significant risk for myeloperoxidase-AAV. Homologous modeling showed that DQα∗160D may confer susceptibility to myeloperoxidase-AAV by altering dimerization of the HLA molecules. Thus, more attention should be paid to the roles of amino acids in the α2β2 domains in addition to the α1β1 binding groove of HLA class II molecules.
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Affiliation(s)
- Huai-Yu Wang
- Renal Division, Department of Medicine, Peking University First Hospital, Beijing, China; Institute of Nephrology, Peking University, Beijing, China; Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China
| | - Zhao Cui
- Renal Division, Department of Medicine, Peking University First Hospital, Beijing, China; Institute of Nephrology, Peking University, Beijing, China; Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China.
| | | | | | - Su-Fang Chen
- Renal Division, Department of Medicine, Peking University First Hospital, Beijing, China; Institute of Nephrology, Peking University, Beijing, China; Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China
| | - Li Zhu
- Renal Division, Department of Medicine, Peking University First Hospital, Beijing, China; Institute of Nephrology, Peking University, Beijing, China; Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China
| | - Min Chen
- Renal Division, Department of Medicine, Peking University First Hospital, Beijing, China; Institute of Nephrology, Peking University, Beijing, China; Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China
| | - Nan Chen
- Department of Nephrology, Institute of Nephrology, Shanghai Ruijin Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Ming-Hui Zhao
- Renal Division, Department of Medicine, Peking University First Hospital, Beijing, China; Institute of Nephrology, Peking University, Beijing, China; Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China; Peking-Tsinghua Center for Life Sciences, Beijing, China
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20
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Nanaware PP, Jurewicz MM, Leszyk JD, Shaffer SA, Stern LJ. HLA-DO Modulates the Diversity of the MHC-II Self-peptidome. Mol Cell Proteomics 2019; 18:490-503. [PMID: 30573663 PMCID: PMC6398211 DOI: 10.1074/mcp.ra118.000956] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 11/26/2018] [Indexed: 12/30/2022] Open
Abstract
Presentation of antigenic peptides on MHC-II molecules is essential for tolerance to self and for initiation of immune responses against foreign antigens. DO (HLA-DO in humans, H2-O in mice) is a nonclassical MHC-II protein that has been implicated in control of autoimmunity and regulation of neutralizing antibody responses to viruses. These effects likely are related to a role of DO in selecting MHC-II epitopes, but previous studies examining the effect of DO on presentation of selected CD4 T cell epitopes have been contradictory. To understand how DO modulates MHC-II antigen presentation, we characterized the full spectrum of peptides presented by MHC-II molecules expressed by DO-sufficient and DO-deficient antigen-presenting cells in vivo and in vitro using quantitative mass spectrometry approaches. We found that DO controlled the diversity of the presented peptide repertoire, with a subset of peptides presented only when DO was expressed. Antigen-presenting cells express another nonclassical MHC-II protein, DM, which acts as a peptide editor by preferentially catalyzing the exchange of less stable MHC-II peptide complexes, and which is inhibited when bound to DO. Peptides presented uniquely in the presence of DO were sensitive to DM-mediated exchange, suggesting that decreased DM editing was responsible for the increased diversity. DO-deficient mice mounted CD4 T cell responses against wild-type antigen-presenting cells, but not vice versa, indicating that DO-dependent alterations in the MHC-II peptidome could be recognized by circulating T cells. These data suggest that cell-specific and regulated expression of HLA-DO serves to fine-tune MHC-II peptidomes, in order to enhance self-tolerance to a wide spectrum of epitopes while allowing focused presentation of immunodominant epitopes during an immune response.
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Affiliation(s)
- Padma P Nanaware
- From the ‡Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Mollie M Jurewicz
- From the ‡Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - John D Leszyk
- §Mass Spectrometry Facility, University of Massachusetts Medical School, Shrewsbury, Massachusetts 01545
| | - Scott A Shaffer
- §Mass Spectrometry Facility, University of Massachusetts Medical School, Shrewsbury, Massachusetts 01545
- ¶Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Lawrence J Stern
- From the ‡Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts 01605;
- ¶Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
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21
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Sant AJ. Overview of T-Cell Recognition. Clin Immunol 2019. [DOI: 10.1016/b978-0-7020-6896-6.00006-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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22
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Class II MHC antigen processing in immune tolerance and inflammation. Immunogenetics 2018; 71:171-187. [PMID: 30421030 DOI: 10.1007/s00251-018-1095-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 10/31/2018] [Indexed: 01/22/2023]
Abstract
Presentation of peptide antigens by MHC-II proteins is prerequisite to effective CD4 T cell tolerance to self and to recognition of foreign antigens. Antigen uptake and processing pathways as well as expression of the peptide exchange factors HLA-DM and HLA-DO differ among the various professional and non-professional antigen-presenting cells and are modulated by cell developmental state and activation. Recent studies have highlighted the importance of these cell-specific factors in controlling the source and breadth of peptides presented by MHC-II under different conditions. During inflammation, increased presentation of selected self-peptides has implications for maintenance of peripheral tolerance and autoimmunity.
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23
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Ancient features of the MHC class II presentation pathway, and a model for the possible origin of MHC molecules. Immunogenetics 2018; 71:233-249. [DOI: 10.1007/s00251-018-1090-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 10/06/2018] [Indexed: 10/28/2022]
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24
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Alvaro-Benito M, Morrison E, Wieczorek M, Sticht J, Freund C. Human leukocyte Antigen-DM polymorphisms in autoimmune diseases. Open Biol 2017; 6:rsob.160165. [PMID: 27534821 PMCID: PMC5008016 DOI: 10.1098/rsob.160165] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Accepted: 07/19/2016] [Indexed: 12/20/2022] Open
Abstract
Classical MHC class II (MHCII) proteins present peptides for CD4+ T-cell surveillance and are by far the most prominent risk factor for a number of autoimmune disorders. To date, many studies have shown that this link between particular MHCII alleles and disease depends on the MHCII's particular ability to bind and present certain peptides in specific physiological contexts. However, less attention has been paid to the non-classical MHCII molecule human leucocyte antigen-DM, which catalyses peptide exchange on classical MHCII proteins acting as a peptide editor. DM function impacts the presentation of both antigenic peptides in the periphery and key self-peptides during T-cell development in the thymus. In this way, DM activity directly influences the response to pathogens, as well as mechanisms of self-tolerance acquisition. While decreased DM editing of particular MHCII proteins has been proposed to be related to autoimmune disorders, no experimental evidence for different DM catalytic properties had been reported until recently. Biochemical and structural investigations, together with new animal models of loss of DM activity, have provided an attractive foundation for identifying different catalytic efficiencies for DM allotypes. Here, we revisit the current knowledge of DM function and discuss how DM function may impart autoimmunity at the organism level.
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Affiliation(s)
- Miguel Alvaro-Benito
- Protein Biochemistry Group, Institute for Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Eliot Morrison
- Protein Biochemistry Group, Institute for Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Marek Wieczorek
- Protein Biochemistry Group, Institute for Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Jana Sticht
- Protein Biochemistry Group, Institute for Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Christian Freund
- Protein Biochemistry Group, Institute for Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
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25
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Marino R, Capoferri R, Panelli S, Minozzi G, Strozzi F, Trevisi E, Snel GGM, Ajmone-Marsan P, Williams JL. Johne's disease in cattle: an in vitro model to study early response to infection of Mycobacterium avium subsp. paratuberculosis using RNA-seq. Mol Immunol 2017; 91:259-271. [PMID: 28988040 DOI: 10.1016/j.molimm.2017.08.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/07/2017] [Accepted: 08/21/2017] [Indexed: 02/07/2023]
Abstract
Johne's disease is a chronic granulomatous enteritis caused by Mycobacterium avium subsp. paratubercolosis (MAP) which affects ruminants worldwide and has a significant economic impact. MAP has also been associated with human Crohn's disease, although this connection is not well established. MAP is highly adapted for survival within host macrophages and prevents macrophage activation, blocks phagosome acidification and maturation, and attenuates presentation of antigens to the immune system. The consequence is a very long silent infection before clinical signs are observed. The present work examined the transcriptome of bovine monocyte-derived macrophages (MDM) infected with the L1 strain of MAP at 2h, 6h and 24h post infection using RNA-seq. Pathway over-representation analysis of genes differentially expressed between infected vs. control MDM identified that immune related pathways were affected. Genes belonging to the cytokine-cytokine receptor interaction pathway and members of the JAK-STAT pathway, which is involved in the regulation of immune response, were up-regulated. However, in parallel inhibitors of immune functions were activated, including suppressor of cytokine signaling (SOCS) and cytokine-inducible SH2-containing protein (CISH), which most likely suppresses IFNγ and the JAK/STAT signaling cascade in infected MDM, which may favour MAP survival. After exposure, macrophages phagocytise pathogens, activate the complement cascade and the adaptive immune system through the antigen presentation process. However, data presented here suggest that genes related to phagocytosis and lysosome function are down regulated in MAP infected MDM. Genes of MHC class II and complement pathway were also down-regulated. This study therefore shows that MAP infection is associated with changes in expression of genes related to the host immune response that may affect its ability to survive and multiply inside the host cell.
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Affiliation(s)
- Rosanna Marino
- CREA Research Centre for Animal Production and Aquaculture, Via Antonio Lombardo 11, 26900 Lodi, Italy; Istituto Sperimentale Italiano "Lazzaro Spallanzani", 26027, Rivolta d'Adda, Cremona, Italy; Institute of Zootechnics, Università Cattolica del S. Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy.
| | - Rossana Capoferri
- Istituto Sperimentale Italiano "Lazzaro Spallanzani", 26027, Rivolta d'Adda, Cremona, Italy.
| | - Simona Panelli
- Parco Tecnologico Padano, via Einstein, 26900 Lodi, Italy.
| | | | | | - Erminio Trevisi
- Institute of Zootechnics, Università Cattolica del S. Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy; Nutrigenomics and Proteomic Research Center - PRONUTRIGEN, Università Cattolica del S. Cuore, via Emilia Parmense 84, 29122 Piacenza, Italy.
| | | | - Paolo Ajmone-Marsan
- Institute of Zootechnics, Università Cattolica del S. Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy; Nutrigenomics and Proteomic Research Center - PRONUTRIGEN, Università Cattolica del S. Cuore, via Emilia Parmense 84, 29122 Piacenza, Italy.
| | - John L Williams
- Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA 5371, Australia.
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26
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Evolving Insights for MHC Class II Antigen Processing and Presentation in Health and Disease. ACTA ACUST UNITED AC 2017. [DOI: 10.1007/s40495-017-0097-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Cruz FM, Colbert JD, Merino E, Kriegsman BA, Rock KL. The Biology and Underlying Mechanisms of Cross-Presentation of Exogenous Antigens on MHC-I Molecules. Annu Rev Immunol 2017; 35:149-176. [PMID: 28125356 PMCID: PMC5508990 DOI: 10.1146/annurev-immunol-041015-055254] [Citation(s) in RCA: 191] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
To monitor the health of cells, the immune system tasks antigen-presenting cells with gathering antigens from other cells and bringing them to CD8 T cells in the form of peptides bound to MHC-I molecules. Most cells would be unable to perform this function because they use their MHC-I molecules to exclusively present peptides derived from the cell's own proteins. However, the immune system evolved mechanisms for dendritic cells and some other phagocytes to sample and present antigens from the extracellular milieu on MHC-I through a process called cross-presentation. How this important task is accomplished, its role in health and disease, and its potential for exploitation are the subject of this review.
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Affiliation(s)
- Freidrich M Cruz
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts 01655; , , , ,
| | - Jeff D Colbert
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts 01655; , , , ,
| | - Elena Merino
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts 01655; , , , ,
| | - Barry A Kriegsman
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts 01655; , , , ,
| | - Kenneth L Rock
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts 01655; , , , ,
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28
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Wieczorek M, Sticht J, Stolzenberg S, Günther S, Wehmeyer C, El Habre Z, Álvaro-Benito M, Noé F, Freund C. MHC class II complexes sample intermediate states along the peptide exchange pathway. Nat Commun 2016; 7:13224. [PMID: 27827392 PMCID: PMC5105163 DOI: 10.1038/ncomms13224] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 09/13/2016] [Indexed: 01/07/2023] Open
Abstract
The presentation of peptide-MHCII complexes (pMHCIIs) for surveillance by T cells is a well-known immunological concept in vertebrates, yet the conformational dynamics of antigen exchange remain elusive. By combining NMR-detected H/D exchange with Markov modelling analysis of an aggregate of 275 microseconds molecular dynamics simulations, we reveal that a stable pMHCII spontaneously samples intermediate conformations relevant for peptide exchange. More specifically, we observe two major peptide exchange pathways: the kinetic stability of a pMHCII's ground state defines its propensity for intrinsic peptide exchange, while the population of a rare, intermediate conformation correlates with the propensity of the HLA-DM-catalysed pathway. Helix-destabilizing mutants designed based on our model shift the exchange behaviour towards the HLA-DM-catalysed pathway and further allow us to conceptualize how allelic variation can shape an individual's MHC restricted immune response. MHCII proteins bind and present both foreign and self-antigens to potentially activate CD4+ T cells via cognate T cell receptors (TCRs) during the adaptive immune response. Here, the authors combine NMR-detected H/D exchange with Markov modelling analysis to shed light on the dynamics of MHCII peptide exchange.
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Affiliation(s)
- Marek Wieczorek
- Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Jana Sticht
- Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Sebastian Stolzenberg
- Computational Molecular Biology group, Institute for Mathematics, Arnimallee 6, 14195 Berlin, Germany
| | - Sebastian Günther
- Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany.,Institute of Human Virology, University of Maryland School of Medicine, 725 West Lombard Street, Baltimore, Maryland 21201, USA
| | - Christoph Wehmeyer
- Computational Molecular Biology group, Institute for Mathematics, Arnimallee 6, 14195 Berlin, Germany
| | - Zeina El Habre
- Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Miguel Álvaro-Benito
- Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Frank Noé
- Computational Molecular Biology group, Institute for Mathematics, Arnimallee 6, 14195 Berlin, Germany
| | - Christian Freund
- Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
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29
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Rosskopf S, Jutz S, Neunkirchner A, Candia MR, Jahn-Schmid B, Bohle B, Pickl WF, Steinberger P. Creation of an engineered APC system to explore and optimize the presentation of immunodominant peptides of major allergens. Sci Rep 2016; 6:31580. [PMID: 27539532 PMCID: PMC4990899 DOI: 10.1038/srep31580] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 07/26/2016] [Indexed: 01/08/2023] Open
Abstract
We have generated engineered APC to present immunodominant peptides derived from the major aero-allergens of birch and mugwort pollen, Bet v 1142-153 and Art v 125-36, respectively. Jurkat-based T cell reporter lines expressing the cognate allergen-specific T cell receptors were used to read out the presentation of allergenic peptides on the engineered APC. Different modalities of peptide loading and presentation on MHC class II molecules were compared. Upon exogenous loading with allergenic peptides, the engineered APC elicited a dose-dependent response in the reporter T cells and the presence of chemical loading enhancers strongly increased reporter activation. Invariant chain-based MHC class II targeting strategies of endogenously expressed peptides resulted in stronger activation of the reporters than exogenous loading. Moreover, we used Bet v 1 as model allergen to study the ability of K562 cells to present antigenic peptides derived from whole proteins either taken up or endogenously expressed as LAMP-1 fusion protein. In both cases the ability of these cells to process and present peptides derived from whole proteins critically depended on the expression of HLA-DM. We have identified strategies to achieve efficient presentation of allergenic peptides on engineered APC and demonstrate their use to stimulate T cells from allergic individuals.
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Affiliation(s)
- Sandra Rosskopf
- Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Sabrina Jutz
- Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Alina Neunkirchner
- Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Martín R Candia
- Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Beatrice Jahn-Schmid
- Department of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Barbara Bohle
- Department of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Winfried F Pickl
- Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Peter Steinberger
- Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
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30
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Bailey A, Dalchau N, Carter R, Emmott S, Phillips A, Werner JM, Elliott T. Selector function of MHC I molecules is determined by protein plasticity. Sci Rep 2015; 5:14928. [PMID: 26482009 PMCID: PMC5224517 DOI: 10.1038/srep14928] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 09/09/2015] [Indexed: 12/27/2022] Open
Abstract
The selection of peptides for presentation at the surface of most nucleated cells by major histocompatibility complex class I molecules (MHC I) is crucial to the immune response in vertebrates. However, the mechanisms of the rapid selection of high affinity peptides by MHC I from amongst thousands of mostly low affinity peptides are not well understood. We developed computational systems models encoding distinct mechanistic hypotheses for two molecules, HLA-B*44:02 (B*4402) and HLA-B*44:05 (B*4405), which differ by a single residue yet lie at opposite ends of the spectrum in their intrinsic ability to select high affinity peptides. We used in vivo biochemical data to infer that a conformational intermediate of MHC I is significant for peptide selection. We used molecular dynamics simulations to show that peptide selector function correlates with protein plasticity, and confirmed this experimentally by altering the plasticity of MHC I with a single point mutation, which altered in vivo selector function in a predictable way. Finally, we investigated the mechanisms by which the co-factor tapasin influences MHC I plasticity. We propose that tapasin modulates MHC I plasticity by dynamically coupling the peptide binding region and α3 domain of MHC I allosterically, resulting in enhanced peptide selector function.
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Affiliation(s)
- Alistair Bailey
- Institute for Life Sciences, Building 85, University of Southampton, SO17 1BJ, UK
- Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK
- Centre for Biological Sciences, Faculty of Natural & Environmental Sciences, Building 85, University of Southampton, SO17 1BJ, UK
| | - Neil Dalchau
- Computational Science Laboratory, Microsoft Research, 21 Station Road, Cambridge, CB1 2FB, UK
| | - Rachel Carter
- Institute for Life Sciences, Building 85, University of Southampton, SO17 1BJ, UK
- Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK
| | - Stephen Emmott
- Computational Science Laboratory, Microsoft Research, 21 Station Road, Cambridge, CB1 2FB, UK
| | - Andrew Phillips
- Computational Science Laboratory, Microsoft Research, 21 Station Road, Cambridge, CB1 2FB, UK
| | - Jörn M. Werner
- Institute for Life Sciences, Building 85, University of Southampton, SO17 1BJ, UK
- Centre for Biological Sciences, Faculty of Natural & Environmental Sciences, Building 85, University of Southampton, SO17 1BJ, UK
| | - Tim Elliott
- Institute for Life Sciences, Building 85, University of Southampton, SO17 1BJ, UK
- Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK
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31
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Yin L, Maben ZJ, Becerra A, Stern LJ. Evaluating the Role of HLA-DM in MHC Class II-Peptide Association Reactions. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2015; 195:706-16. [PMID: 26062997 PMCID: PMC4490944 DOI: 10.4049/jimmunol.1403190] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 05/15/2015] [Indexed: 01/07/2023]
Abstract
Ag presentation by MHC class II (MHC II) molecules to CD4(+) T cells plays a key role in the regulation of the adaptive immune response. Loading of antigenic peptides onto MHC II is catalyzed by HLA-DM (DM), a nonclassical MHC II molecule. The mechanism of DM-facilitated peptide loading is an outstanding problem in the field of Ag presentation. In this study, we systemically explored possible kinetic mechanisms for DM-catalyzed peptide association by measuring real-time peptide association kinetics using fluorescence polarization assays and comparing the experimental data with numerically modeled peptide association reactions. We found that DM does not facilitate peptide association by stabilizing peptide-free MHC II against aggregation. Moreover, DM does not promote transition of an inactive peptide-averse conformation of MHC II to an active peptide-receptive conformation. Instead, DM forms an intermediate with MHC II that binds peptide with faster kinetics than MHC II in the absence of DM. In the absence of peptides, interaction of MHC II with DM leads to inactivation and formation of a peptide-averse form. This study provides novel insights into how DM efficiently catalyzes peptide loading during Ag presentation.
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Affiliation(s)
- Liusong Yin
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01605; and
| | - Zachary J Maben
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01605; and
| | - Aniuska Becerra
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01605; and
| | - Lawrence J Stern
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01605; and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
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32
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Sharma S, Patnaik SK, Taggart RT, Kannisto ED, Enriquez SM, Gollnick P, Baysal BE. APOBEC3A cytidine deaminase induces RNA editing in monocytes and macrophages. Nat Commun 2015; 6:6881. [PMID: 25898173 PMCID: PMC4411297 DOI: 10.1038/ncomms7881] [Citation(s) in RCA: 163] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 03/10/2015] [Indexed: 01/01/2023] Open
Abstract
The extent, regulation and enzymatic basis of RNA editing by cytidine deamination are incompletely understood. Here we show that transcripts of hundreds of genes undergo site-specific C>U RNA editing in macrophages during M1 polarization and in monocytes in response to hypoxia and interferons. This editing alters the amino acid sequences for scores of proteins, including many that are involved in pathogenesis of viral diseases. APOBEC3A, which is known to deaminate cytidines of single-stranded DNA and to inhibit viruses and retrotransposons, mediates this RNA editing. Amino acid residues of APOBEC3A that are known to be required for its DNA deamination and anti-retrotransposition activities were also found to affect its RNA deamination activity. Our study demonstrates the cellular RNA editing activity of a member of the APOBEC3 family of innate restriction factors and expands the understanding of C>U RNA editing in mammals. Aberrant RNA editing is linked to a range of neuropsychiatric and chronic diseases. Here Sharma et al. show that APOBEC3A can function as an RNA editing protein in response to physiological stimuli, significantly expanding our understanding of RNA editing and the role this may play in diseases.
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Affiliation(s)
- Shraddha Sharma
- Department of Pathology, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, New York 14203, USA
| | - Santosh K Patnaik
- Department of Thoracic Surgery, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, New York 14203, USA
| | - R Thomas Taggart
- Department of Pathology, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, New York 14203, USA
| | - Eric D Kannisto
- Department of Thoracic Surgery, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, New York 14203, USA
| | - Sally M Enriquez
- Department of Biological Sciences, University at Buffalo, State University of New York, Buffalo, New York 14260, USA
| | - Paul Gollnick
- Department of Biological Sciences, University at Buffalo, State University of New York, Buffalo, New York 14260, USA
| | - Bora E Baysal
- Department of Pathology, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, New York 14203, USA
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33
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Haag S, Tuncel J, Thordardottir S, Mason DE, Yau ACY, Dobritzsch D, Bäcklund J, Peters EC, Holmdahl R. Positional identification of RT1-B (HLA-DQ) as susceptibility locus for autoimmune arthritis. THE JOURNAL OF IMMUNOLOGY 2015; 194:2539-50. [PMID: 25672758 DOI: 10.4049/jimmunol.1402238] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Rheumatoid arthritis (RA) is associated with amino acid variants in multiple MHC molecules. The association to MHC class II (MHC-II) has been studied in several animal models of RA. In most cases these models depend on T cells restricted to a single immunodominant peptide of the immunizing Ag, which does not resemble the autoreactive T cells in RA. An exception is pristane-induced arthritis (PIA) in the rat where polyclonal T cells induce chronic arthritis after being primed against endogenous Ags. In this study, we used a mixed genetic and functional approach to show that RT1-Ba and RT1-Bb (RT1-B locus), the rat orthologs of HLA-DQA and HLA-DQB, determine the onset and severity of PIA. We isolated a 0.2-Mb interval within the MHC-II locus of three MHC-congenic strains, of which two were protected from severe PIA. Comparison of sequence and expression variation, as well as in vivo blocking of RT1-B and RT1-D (HLA-DR), showed that arthritis in these strains is regulated by coding polymorphisms in the RT1-B genes. Motif prediction based on MHC-II eluted peptides and structural homology modeling suggested that variants in the RT1-B P1 pocket, which likely affect the editing capacity by RT1-DM, are important for the development of PIA.
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Affiliation(s)
- Sabrina Haag
- Division of Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77, Stockholm, Sweden
| | - Jonatan Tuncel
- Division of Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77, Stockholm, Sweden;
| | - Soley Thordardottir
- Division of Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77, Stockholm, Sweden
| | - Daniel E Mason
- Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121
| | - Anthony C Y Yau
- Division of Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77, Stockholm, Sweden
| | - Doreen Dobritzsch
- Division of Molecular Structural Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden; and Department of Chemistry, Biomedical Center, Uppsala University, S-751 24 Uppsala, Sweden
| | - Johan Bäcklund
- Division of Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77, Stockholm, Sweden
| | - Eric C Peters
- Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121
| | - Rikard Holmdahl
- Division of Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77, Stockholm, Sweden;
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Álvaro-Benito M, Wieczorek M, Sticht J, Kipar C, Freund C. HLA-DMA polymorphisms differentially affect MHC class II peptide loading. THE JOURNAL OF IMMUNOLOGY 2014; 194:803-16. [PMID: 25505276 DOI: 10.4049/jimmunol.1401389] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
During the adaptive immune response, MHCII proteins display antigenic peptides on the cell surface of APCs for CD4(+) T cell surveillance. HLA-DM, a nonclassical MHCII protein, acts as a peptide exchange catalyst for MHCII, editing the peptide repertoire. Although they map to the same gene locus, MHCII proteins exhibit a high degree of polymorphism, whereas only low variability has been observed for HLA-DM. As HLA-DM activity directly favors immunodominant peptide presentation, polymorphisms in HLA-DM (DMA or DMB chain) might well be a contributing risk factor for autoimmunity and immune disorders. Our systematic comparison of DMA*0103/DMB*0101 (DMA-G155A and DMA-R184H) with DMA*0101/DMB*0101 in terms of catalyzed peptide exchange and dissociation, as well as direct interaction with several HLA-DR/peptide complexes, reveals an attenuated catalytic activity of DMA*0103/DMB*0101. The G155A substitution dominates the catalytic behavior of DMA*0103/DMB*0101 by decreasing peptide release velocity. Preloaded peptide-MHCII complexes exhibit ∼2-fold increase in half-life in the presence of DMA*0103/DMB*0101 when compared with DMA*0101/DMB*0101. We show that this effect leads to a greater persistence of autoimmunity-related Ags in the presence of high-affinity competitor peptide. Our study therefore reveals that HLA-DM polymorphic residues have a considerable impact on HLA-DM catalytic activity.
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Affiliation(s)
- Miguel Álvaro-Benito
- Institut für Chemie und Biochemie, Freie Universität Berlin, 14195 Berlin, Germany; and
| | - Marek Wieczorek
- Institut für Chemie und Biochemie, Freie Universität Berlin, 14195 Berlin, Germany; and Leibniz Institute for Molecular Pharmacology, 13125 Berlin, Germany
| | - Jana Sticht
- Institut für Chemie und Biochemie, Freie Universität Berlin, 14195 Berlin, Germany; and
| | - Claudia Kipar
- Institut für Chemie und Biochemie, Freie Universität Berlin, 14195 Berlin, Germany; and
| | - Christian Freund
- Institut für Chemie und Biochemie, Freie Universität Berlin, 14195 Berlin, Germany; and Leibniz Institute for Molecular Pharmacology, 13125 Berlin, Germany
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35
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Kremer AN, van der Meijden ED, Honders MW, Pont MJ, Goeman JJ, Falkenburg JHF, Griffioen M. Human leukocyte antigen-DO regulates surface presentation of human leukocyte antigen class II-restricted antigens on B cell malignancies. Biol Blood Marrow Transplant 2014; 20:742-7. [PMID: 24530695 DOI: 10.1016/j.bbmt.2014.02.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 02/06/2014] [Indexed: 11/29/2022]
Abstract
Hematological malignancies often express surface HLA class II, making them attractive targets for CD4+ T cell therapy. We previously demonstrated that HLA class II ligands can be divided into DM-resistant and DM-sensitive antigens. In contrast to presentation of DM-resistant antigens, presentation of DM-sensitive antigens is suppressed by HLA-DM but can be rescued by HLA-DO. We also showed that HLA-DO expression remains low in nonhematopoietic cells under inflammatory conditions, suggesting that DM-sensitive antigens may be ideal T cell targets with a low risk for graft-versus-host disease. Here, we demonstrated that B cell malignancies often express HLA-DO and that levels are in particular high in chronic lymphocytic leukemia. Moreover, we showed that surface presentation of DM-sensitive antigens is regulated by HLA-DO, and that DM-sensitive antigens are relevant T cell targets for B cell malignancies and, especially, chronic lymphocytic leukemia. These data open the perspective to target HLA class II ligands with specific processing and presentation behavior for CD4+ T cell therapy of hematological malignancies.
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Affiliation(s)
- Anita N Kremer
- Department of Hematology, Leiden University Medical Center, RC Leiden, The Netherlands; Department of Internal Medicine 5, Hematology and Oncology, University Hospital Erlangen, Erlangen, Germany
| | | | - M Willy Honders
- Department of Hematology, Leiden University Medical Center, RC Leiden, The Netherlands
| | - Margot J Pont
- Department of Hematology, Leiden University Medical Center, RC Leiden, The Netherlands
| | - Jelle J Goeman
- Department of Medical Statistics, Leiden University Medical Center, RC Leiden, The Netherlands
| | | | - Marieke Griffioen
- Department of Hematology, Leiden University Medical Center, RC Leiden, The Netherlands.
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36
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Denzin LK. Inhibition of HLA-DM Mediated MHC Class II Peptide Loading by HLA-DO Promotes Self Tolerance. Front Immunol 2013; 4:465. [PMID: 24381574 PMCID: PMC3865790 DOI: 10.3389/fimmu.2013.00465] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 12/03/2013] [Indexed: 12/05/2022] Open
Abstract
Major histocompatibility class II (MHCII) molecules are loaded with peptides derived from foreign and self-proteins within the endosomes and lysosomes of antigen presenting cells (APCs). This process is mediated by interaction of MHCII with the conserved, non-polymorphic MHCII like molecule HLA-DM (DM). DM activity is directly opposed by HLA-DO (DO), another conserved, non-polymorphic MHCII like molecule. DO is an MHCII substrate mimic. Binding of DO to DM prevents MHCII from binding to DM, thereby inhibiting peptide loading. Inhibition of DM function enables low stability MHC complexes to survive and populate the surface of APCs. As a consequence, DO promotes the display of a broader pool of low abundance self-peptides. Broadening the peptide repertoire theoretically reduces the likelihood of inadvertently acquiring a density of self-ligands that is sufficient to activate self-reactive T cells. One function of DO, therefore, is to promote T cell tolerance by shaping the visible image of self. Recent data also shows that DO influences the adaptive immune response by controlling B cell entry into the germinal center reaction. This review explores the data supporting these concepts.
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Affiliation(s)
- Lisa K Denzin
- Department of Pediatrics, Robert Wood Johnson Medical School, Child Health Institute of New Jersey, Rutgers, The State University of New Jersey , New Brunswick, NJ , USA
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Mellins ED, Stern LJ. HLA-DM and HLA-DO, key regulators of MHC-II processing and presentation. Curr Opin Immunol 2013; 26:115-22. [PMID: 24463216 DOI: 10.1016/j.coi.2013.11.005] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 11/14/2013] [Accepted: 11/15/2013] [Indexed: 11/28/2022]
Abstract
Peptide loading of class II MHC molecules in endosomal compartments is regulated by HLA-DM. HLA-DO modulates HLA-DM function, with consequences for the spectrum of MHC-bound epitopes presented at the cell surface for interaction with T cells. Here, we summarize and discuss recent progress in investigating the molecular mechanisms of action of HLA-DM and HLA-DO and in understanding their roles in immune responses. Key findings are the long-awaited structures of HLA-DM in complex with its class II substrate and with HLA-DO, and observation of a novel phenotype--autoimmunity combined with immunodeficiency--in mice lacking HLA-DO. We also highlight several areas where gaps persist in our knowledge about this pair of proteins and their molecular biology and immunobiology.
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Affiliation(s)
- Elizabeth D Mellins
- Department of Pediatrics, Program in Immunology, Stanford University, Stanford, CA 94305, United States
| | - Lawrence J Stern
- Department of Pathology, Immunology and Microbiology Program, University of Massachusetts Medical School, Worcester, MA 01655, United States.
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Newell EW. Higher throughput methods of identifying T cell epitopes for studying outcomes of altered antigen processing and presentation. Front Immunol 2013; 4:430. [PMID: 24367368 PMCID: PMC3851853 DOI: 10.3389/fimmu.2013.00430] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Accepted: 11/21/2013] [Indexed: 01/09/2023] Open
Abstract
Variation in the mechanisms that mediate antigen processing, MHC-loading, and presentation of peptides allows cells to significantly modulate the repertoire of peptides presented by both MHC class I or class II. To more quickly determine how these different modes or modulations of presentation translate into altered immune responses, higher throughput methods for identifying T cell epitopes are needed. Proteomics-based comprehensive cataloging of peptides eluted from MHC is a challenging but ideal way of identifying peptide sequences influenced by variable modes of processing and presentation. Several groups have already been successful with this approach and ongoing technical improvements will broaden its applicability. Subsequently, high content combinatorial peptide-MHC tetramer staining using mass cytometry, as we have recently described, should enable the broad assessment of how these changes are perceived by T cells and translated into an altered immune response. The importance of this analysis is highlighted by evidence that physiologically relevant variation in antigen processing and presentation as well as other factors can give rise to unpredictably different T cell responses.
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Affiliation(s)
- Evan W Newell
- Singapore Immunology Network, Agency for Science Technology and Research , Singapore
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Sant AJ, Chaves FA, Leddon SA, Tung J. The control of the specificity of CD4 T cell responses: thresholds, breakpoints, and ceilings. Front Immunol 2013; 4:340. [PMID: 24167504 PMCID: PMC3805957 DOI: 10.3389/fimmu.2013.00340] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 10/04/2013] [Indexed: 12/31/2022] Open
Abstract
It has been known for over 25 years that CD4 T cell responses are restricted to a finite number of peptide epitopes within pathogens or protein vaccines. These selected peptide epitopes are termed "immunodominant." Other peptides within the antigen that can bind to host MHC molecules and recruit CD4 T cells as single peptides are termed "cryptic" because they fail to induce responses when expressed in complex proteins or when in competition with other peptides during the immune response. In the last decade, our laboratory has evaluated the mechanisms that underlie the preferential specificity of CD4 T cells and have discovered that both intracellular events within antigen presenting cells, particular selective DM editing, and intercellular regulatory pathways, involving IFN-γ, indoleamine 2,3-dioxygenase, and regulatory T cells, play a role in selecting the final peptide specificity of CD4 T cells. In this review, we summarize our findings, discuss the implications of this work on responses to pathogens and vaccines and speculate on the logic of these regulatory events.
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Affiliation(s)
- Andrea J. Sant
- Department of Microbiology and Immunology, David H. Smith Center for Vaccine Biology and Immunology, University of Rochester Medical Center, Rochester, NY, USA
| | - Francisco A. Chaves
- Department of Microbiology and Immunology, David H. Smith Center for Vaccine Biology and Immunology, University of Rochester Medical Center, Rochester, NY, USA
| | - Scott A. Leddon
- Department of Microbiology and Immunology, David H. Smith Center for Vaccine Biology and Immunology, University of Rochester Medical Center, Rochester, NY, USA
| | - Jacqueline Tung
- Department of Microbiology and Immunology, David H. Smith Center for Vaccine Biology and Immunology, University of Rochester Medical Center, Rochester, NY, USA
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Poluektov YO, Kim A, Sadegh-Nasseri S. HLA-DO and Its Role in MHC Class II Antigen Presentation. Front Immunol 2013; 4:260. [PMID: 24009612 PMCID: PMC3756479 DOI: 10.3389/fimmu.2013.00260] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 08/15/2013] [Indexed: 11/25/2022] Open
Abstract
Helper T cells are stimulated to fight infections or diseases upon recognition of peptides from antigens that are processed and presented by the proteins of Major Histocompatibility Complex (MHC) Class II molecules. Degradation of a full protein into small peptide fragments is a lengthy process consisting of many steps and chaperones. Malfunctions during any step of antigen processing could lead to the development of self-reactive T cells or defective immune response to pathogens. Although much has been accomplished regarding how antigens are processed and presented to T cells, many questions still remain unanswered, preventing the design of therapeutics for direct intervention with antigen processing. Here, we review published work on the discovery and function of a MHC class II molecular chaperone, HLA-DO, in human, and its mouse analog H2-O, herein called DO. While DO was originally discovered decades ago, elucidating its function has proven challenging. DO was discovered in association with another chaperone HLA-DM (DM) but unlike DM, its distribution is more tissue specific, and its function more subtle.
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Affiliation(s)
- Yuri O Poluektov
- Graduate Program in Immunology, Johns Hopkins University , Baltimore, MD , USA
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