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Zacharias M, Springer S. Peptide vaccines get an OS update. Nat Chem Biol 2024; 20:549-550. [PMID: 38580838 DOI: 10.1038/s41589-024-01608-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2024]
Affiliation(s)
- Martin Zacharias
- Center for Protein Assemblies, Technical University Munich, Munich, Germany.
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2
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Jiang J, Natarajan K, Margulies DH. Chaperone-mediated MHC-I peptide exchange in antigen presentation. IUCRJ 2024; 11:287-298. [PMID: 38656309 PMCID: PMC11067752 DOI: 10.1107/s2052252524002768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 03/26/2024] [Indexed: 04/26/2024]
Abstract
This work focuses on molecules that are encoded by the major histocompatibility complex (MHC) and that bind self-, foreign- or tumor-derived peptides and display these at the cell surface for recognition by receptors on T lymphocytes (T cell receptors, TCR) and natural killer (NK) cells. The past few decades have accumulated a vast knowledge base of the structures of MHC molecules and the complexes of MHC/TCR with specificity for many different peptides. In recent years, the structures of MHC-I molecules complexed with chaperones that assist in peptide loading have been revealed by X-ray crystallography and cryogenic electron microscopy. These structures have been further studied using mutagenesis, molecular dynamics and NMR approaches. This review summarizes the current structures and dynamic principles that govern peptide exchange as these relate to the process of antigen presentation.
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Affiliation(s)
- Jiansheng Jiang
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA
| | - Kannan Natarajan
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA
| | - David H. Margulies
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA
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3
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Cong Z, Xiong Y, Lyu L, Fu B, Guo D, Sha Z, Yang B, Wu H. The relationship between Listeria infections and host immune responses: Listeriolysin O as a potential target. Biomed Pharmacother 2024; 171:116129. [PMID: 38194738 DOI: 10.1016/j.biopha.2024.116129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 12/31/2023] [Accepted: 01/02/2024] [Indexed: 01/11/2024] Open
Abstract
Listeria monocytogenes (Lm), a foodborne bacterium, can infect people and has a high fatality rate in immunocompromised individuals. Listeriolysin O (LLO), the primary virulence factor of Lm, is critical in regulating the pathogenicity of Lm. This review concludes that LLO may either directly or indirectly activate a number of host cell viral pathophysiology processes, such as apoptosis, pyroptosis, autophagy, necrosis and necroptosis. We describe the invasion of host cells by Lm and the subsequent removal of Lm by CD8 T cells and CD4 T cells upon receipt of the LLO epitopes from major histocompatibility complex class I (MHC-I) and major histocompatibility complex class II (MHC-II). The development of several LLO-based vaccines that make use of the pore-forming capabilities of LLO and the immune response of the host cells is then described. Finally, we conclude by outlining the several natural substances that have been shown to alter the three-dimensional conformation of LLO by binding to particular amino acid residues of LLO, which reduces LLO pathogenicity and may be a possible pharmacological treatment for Lm.
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Affiliation(s)
- Zixuan Cong
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Yan Xiong
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Lyu Lyu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, China
| | - Beibei Fu
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Dong Guo
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Zhou Sha
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Bo Yang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu 730046, China.
| | - Haibo Wu
- School of Life Sciences, Chongqing University, Chongqing 401331, China.
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4
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Liu J, Li M, Fu J, Dong M, Fan X, Zhong L, Xu G, Li Y, Xi Q. sTRBC1 and cyTRBC1 Expression Distinguishes Indolent T-Lymphoblastic Proliferations From T-Lymphoblastic Leukemia/Lymphoma. Am J Surg Pathol 2023; 47:1325-1331. [PMID: 37515427 DOI: 10.1097/pas.0000000000002103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
Indolent T-lymphoblastic proliferation (iT-LBP) consists of a proliferation of non-neoplastic TdT + T cells in extrathymic tissues, requiring no treatment. However, due to overlapping clinical and histologic features, distinguishing iT-LBP from T-cell acute lymphoblastic leukemia/lymphoblastic lymphoma (T-ALL/LBL) can be challenging. Recently, flow cytometry-based evaluation of TRBC1 has been used to detect of T-cell clonality in TCRαβ + mature T-cell lymphomas and aid in the differential diagnosis between T-ALL and normal thymocytes. We present a case of iT-LBP with high-grade serous ovarian carcinoma (HGSOC). To investigate the potential utility of TRBC1 expression in distinguishing iT-LBP from T-ALL/LBL, we assessed both surface (s) and cytoplasmic (cy) TRBC1 expression patterns on blast cells from the patient with iT-LBP and HGSOC as well as 11 patients diagnosed with T-ALL/LBL. The results revealed that sTRBC1 and cyTRBC1 exhibited polytypic expression patterns in patient with iT-LBP and HGSOC, while cyTRBC1 showed monotypic expression in those with T-ALL/LBL. This suggests that evaluation of sTRBC1 and cyTRBC1 expression can serve as a simple, rapid, and effective approach to differentiate between iT-LBP and T-ALL/LBL.
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Affiliation(s)
| | | | | | | | | | - Ling Zhong
- Sichuan Provincial Key Laboratory for Human Disease Gene Study and Department of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan Province, China
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Trier NH, Houen G. Antibody Cross-Reactivity in Auto-Immune Diseases. Int J Mol Sci 2023; 24:13609. [PMID: 37686415 PMCID: PMC10487534 DOI: 10.3390/ijms241713609] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/25/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023] Open
Abstract
Autoimmunity is defined by the presence of antibodies and/or T cells directed against self-components. Although of unknown etiology, autoimmunity commonly is associated with environmental factors such as infections, which have been reported to increase the risk of developing autoimmune diseases. Occasionally, similarities between infectious non-self and self-tissue antigens may contribute to immunological cross-reactivity in autoimmune diseases. These reactions may be interpreted as molecular mimicry, which describes cross-reactivity between foreign pathogens and self-antigens that have been reported to cause tissue damage and to contribute to the development of autoimmunity. By focusing on the nature of antibodies, cross-reactivity in general, and antibody-antigen interactions, this review aims to characterize the nature of potential cross-reactive immune reactions between infectious non-self and self-tissue antigens which may be associated with autoimmunity but may not actually be the cause of disease onset.
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Affiliation(s)
- Nicole Hartwig Trier
- Department of Neurology, Rigshospitalet Glostrup, Valdemar Hansens Vej 1-23, 2600 Glostrup, Denmark
| | - Gunnar Houen
- Department of Neurology, Rigshospitalet Glostrup, Valdemar Hansens Vej 1-23, 2600 Glostrup, Denmark
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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6
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Janarthanam R, Kuang FL, Zalewski A, Amsden K, Wang MY, Ostilla L, Keeley K, Hirano I, Kagalwalla A, Wershil BK, Gonsalves N, Wechsler JB. Bulk T-cell receptor sequencing confirms clonality in pediatric eosinophilic esophagitis and identifies a food-specific repertoire. Allergy 2023; 78:2487-2496. [PMID: 37203302 PMCID: PMC10768854 DOI: 10.1111/all.15773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 03/15/2023] [Accepted: 04/04/2023] [Indexed: 05/20/2023]
Abstract
BACKGROUND Eosinophilic esophagitis (EoE) involves a chronic immune-mediated response to dietary antigens. Recent work identifies T-cell clonality in children with EoE, however, it is unknown whether this is true in adults or whether there is a restricted food-specific T-cell repertoire. We sought to confirm T-cell receptor (TCR) clonality in EoE and assess for differences with specific food triggers. METHODS Bulk TCR sequencing was performed on mRNA isolated from esophageal biopsies obtained from adults and children with EoE (n = 15) who had food triggers confirmed by endoscopic evaluation. Non-EoE adult and pediatric controls (n = 10) were included. Differences in TCR clonality by disease and treatment status were assessed. Shared and similar V-J-CDR3s were assessed based on specific food triggers. RESULTS Active EoE biopsies from children but not adults displayed decreased unique TCRα/β clonotypes and increased relative abundance of TCRs comprising >1% of the total compared to non-EoE controls and paired inactive EoE samples. Among patients in which baseline, post diet elimination, and food trigger reintroduction samples (n = 6) were obtained, we observed ~1% of TCRs were shared only between pre-diet elimination and trigger reintroduction. Patients with a shared EoE trigger (milk) had a greater degree of shared and similar TCRs compared to patients with differing triggers (seafood, wheat, egg, soy). CONCLUSION We confirmed relative clonality in children but not adults with active EoE and identified potential food-specific TCRs, particularly for milk-triggered EoE. Further studies are needed to better identify the broad TCR repertoire relevant to food triggers.
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Affiliation(s)
- Rethavathi Janarthanam
- Division of Gastroenterology, Hepatology & Nutrition, Ann & Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg school of Medicine, Chicago, Illinois, USA
| | - Fei Li Kuang
- Division of Allergy-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Angelika Zalewski
- Division of Gastroenterology and Hepatology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Katie Amsden
- Division of Gastroenterology, Hepatology & Nutrition, Ann & Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg school of Medicine, Chicago, Illinois, USA
| | - Ming-Yu Wang
- Division of Gastroenterology, Hepatology & Nutrition, Ann & Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg school of Medicine, Chicago, Illinois, USA
| | - Lorena Ostilla
- Division of Gastroenterology, Hepatology & Nutrition, Ann & Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg school of Medicine, Chicago, Illinois, USA
| | - Kaitlyn Keeley
- Division of Gastroenterology, Hepatology & Nutrition, Ann & Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg school of Medicine, Chicago, Illinois, USA
| | - Ikuo Hirano
- Division of Gastroenterology and Hepatology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Amir Kagalwalla
- Department of Pediatrics, John H. Stroger Cook County Hospital of Chicago, Chicago, Illinois, USA
| | - Barry K Wershil
- Division of Gastroenterology, Hepatology & Nutrition, Ann & Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg school of Medicine, Chicago, Illinois, USA
| | - Nirmala Gonsalves
- Division of Gastroenterology and Hepatology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Joshua B Wechsler
- Division of Gastroenterology, Hepatology & Nutrition, Ann & Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg school of Medicine, Chicago, Illinois, USA
- Division of Allergy-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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Sun Y, Young MC, Woodward CH, Danon JN, Truong HV, Gupta S, Winters TJ, Font-Burgada J, Burslem GM, Sgourakis NG. Universal open MHC-I molecules for rapid peptide loading and enhanced complex stability across HLA allotypes. Proc Natl Acad Sci U S A 2023; 120:e2304055120. [PMID: 37310998 PMCID: PMC10288639 DOI: 10.1073/pnas.2304055120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/18/2023] [Indexed: 06/15/2023] Open
Abstract
The polymorphic nature and intrinsic instability of class I major histocompatibility complex (MHC-I) and MHC-like molecules loaded with suboptimal peptides, metabolites, or glycolipids presents a fundamental challenge for identifying disease-relevant antigens and antigen-specific T cell receptors (TCRs), hindering the development of autologous therapeutics. Here, we leverage the positive allosteric coupling between the peptide and light chain (β2 microglobulin, β2m) subunits for binding to the MHC-I heavy chain (HC) through an engineered disulfide bond bridging conserved epitopes across the HC/β2m interface, to generate conformationally stable, peptide-receptive molecules named "open MHC-I." Biophysical characterization shows that open MHC-I molecules are properly folded protein complexes of enhanced thermal stability compared to the wild type when loaded with low- to moderate-affinity peptides. Using solution NMR, we characterize the effects of the disulfide bond on the conformation and dynamics of the MHC-I structure, ranging from local changes in β2m-interacting sites of the peptide-binding groove to long-range effects on the α2-1 helix and α3 domain. The interchain disulfide bond stabilizes MHC-I molecules in an open conformation to promote peptide exchange across multiple human leukocyte antigen (HLA) allotypes, covering representatives from five HLA-A supertypes, six HLA-B supertypes, and oligomorphic HLA-Ib molecules. Our structure-guided design, combined with conditional β-peptide ligands, provides a universal platform to generate ready-to-load MHC-I systems of enhanced stability, enabling a range of approaches to screen antigenic epitope libraries and probe polyclonal TCR repertoires covering highly polymorphic HLA-I allotypes, as well as oligomorphic nonclassical molecules.
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Affiliation(s)
- Yi Sun
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Michael C. Young
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Claire H. Woodward
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Julia N. Danon
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Hau V. Truong
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Sagar Gupta
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Trenton J. Winters
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Joan Font-Burgada
- Cancer Signaling and Microenvironment Program, Fox Chase Cancer Center, Philadelphia, PA19111
| | - George M. Burslem
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- Department of Cancer Biology and Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Nikolaos G. Sgourakis
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
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8
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Sun Y, Young MC, Woodward CH, Danon JN, Truong H, Gupta S, Winters TJ, Burslem G, Sgourakis NG. Universal open MHC-I molecules for rapid peptide loading and enhanced complex stability across HLA allotypes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.18.533266. [PMID: 36993702 PMCID: PMC10055308 DOI: 10.1101/2023.03.18.533266] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The polymorphic nature and intrinsic instability of class I major histocompatibility complex (MHC-I) and MHC-like molecules loaded with suboptimal peptides, metabolites, or glycolipids presents a fundamental challenge for identifying disease-relevant antigens and antigen-specific T cell receptors (TCRs), hindering the development of autologous therapeutics. Here, we leverage the positive allosteric coupling between the peptide and light chain (β 2 microglobulin, β 2 m) subunits for binding to the MHC-I heavy chain (HC) through an engineered disulfide bond bridging conserved epitopes across the HC/β 2 m interface, to generate conformationally stable, open MHC-I molecules. Biophysical characterization shows that open MHC-I molecules are properly folded protein complexes of enhanced thermal stability compared to the wild type, when loaded with low- to intermediate-affinity peptides. Using solution NMR, we characterize the effects of the disulfide bond on the conformation and dynamics of the MHC-I structure, ranging from local changes in β 2 m interacting sites of the peptide binding groove to long-range effects on the α 2-1 helix and α 3 domain. The interchain disulfide bond stabilizes empty MHC-I molecules in a peptide-receptive, open conformation to promote peptide exchange across multiple human leucocyte antigen (HLA) allotypes, covering representatives from five HLA-A, six HLA-B supertypes, and oligomorphic HLA-Ib molecules. Our structural design, combined with conditional β-peptide ligands, provides a universal platform for generating ready-to-load MHC-I systems of enhanced stability, enabling a range of approaches to screen antigenic epitope libraries and probe polyclonal TCR repertoires in the context of highly polymorphic HLA-I allotypes, as well as oligomorphic nonclassical molecules. Significance Statement We outline a structure-guided approach for generating conformationally stable, open MHC-I molecules with enhanced ligand exchange kinetics spanning five HLA-A, all HLA-B supertypes, and oligomorphic HLA-Ib allotypes. We present direct evidence of positive allosteric cooperativity between peptide binding and β 2 m association with the heavy chain by solution NMR and HDX-MS spectroscopy. We demonstrate that covalently linked β 2 m serves as a conformational chaperone to stabilize empty MHC-I molecules in a peptide-receptive state, by inducing an open conformation and preventing intrinsically unstable heterodimers from irreversible aggregation. Our study provides structural and biophysical insights into the conformational properties of MHC-I ternary complexes, which can be further applied to improve the design of ultra-stable, universal ligand exchange systems in a pan-HLA allelic setting.
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Wang F, Yang M, Luo W, Zhou Q. Characteristics of tumor microenvironment and novel immunotherapeutic strategies for non-small cell lung cancer. JOURNAL OF THE NATIONAL CANCER CENTER 2022; 2:243-262. [PMID: 39036549 PMCID: PMC11256730 DOI: 10.1016/j.jncc.2022.10.002] [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: 07/29/2022] [Revised: 10/12/2022] [Accepted: 10/14/2022] [Indexed: 11/08/2022] Open
Abstract
Immune checkpoint inhibitor-based immunotherapy has revolutionized the treatment approach of non-small cell lung cancer (NSCLC). Monoclonal antibodies against programmed cell death-1 (PD-1) and PD-ligand 1 (PD-L1) are widely used in clinical practice, but other antibodies that can circumvent innate and acquired resistance are bound to undergo preclinical and clinical studies. However, tumor cells can develop and facilitate the tolerogenic nature of the tumor microenvironment (TME), resulting in tumor progression. Therefore, the immune escape mechanisms exploited by growing lung cancer involve a fine interplay between all actors in the TME. A better understanding of the molecular biology of lung cancer and the cellular/molecular mechanisms involved in the crosstalk between lung cancer cells and immune cells in the TME could identify novel therapeutic weapons in the old war against lung cancer. This article discusses the role of TME in the progression of lung cancer and pinpoints possible advances and challenges of immunotherapy for NSCLC.
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Affiliation(s)
- Fen Wang
- Department of Oncology, Shenzhen Key Laboratory of Gastrointestinal Cancer Translational Research, Cancer Institute, Peking University Shenzhen Hospital, Shenzhen-Peking University-Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Mingyi Yang
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- School of Medicine, South China University of Technology, Guangzhou, China
| | - Weichi Luo
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Qing Zhou
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
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Ruibal P, Franken KLMC, van Meijgaarden KE, van Wolfswinkel M, Derksen I, Scheeren FA, Janssen GMC, van Veelen PA, Sarfas C, White AD, Sharpe SA, Palmieri F, Petrone L, Goletti D, Abeel T, Ottenhoff THM, Joosten SA. Identification of HLA-E Binding Mycobacterium tuberculosis-Derived Epitopes through Improved Prediction Models. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 209:1555-1565. [PMID: 36096642 PMCID: PMC9536328 DOI: 10.4049/jimmunol.2200122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 08/03/2022] [Indexed: 01/04/2023]
Abstract
Tuberculosis (TB) remains one of the deadliest infectious diseases worldwide, posing great social and economic burden to affected countries. Novel vaccine approaches are needed to increase protective immunity against the causative agent Mycobacterium tuberculosis (Mtb) and to reduce the development of active TB disease in latently infected individuals. Donor-unrestricted T cell responses represent such novel potential vaccine targets. HLA-E-restricted T cell responses have been shown to play an important role in protection against TB and other infections, and recent studies have demonstrated that these cells can be primed in vitro. However, the identification of novel pathogen-derived HLA-E binding peptides presented by infected target cells has been limited by the lack of accurate prediction algorithms for HLA-E binding. In this study, we developed an improved HLA-E binding peptide prediction algorithm and implemented it to identify (to our knowledge) novel Mtb-derived peptides with capacity to induce CD8+ T cell activation and that were recognized by specific HLA-E-restricted T cells in Mycobacterium-exposed humans. Altogether, we present a novel algorithm for the identification of pathogen- or self-derived HLA-E-presented peptides.
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Affiliation(s)
- Paula Ruibal
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands
| | - Kees L M C Franken
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands
| | | | | | - Ian Derksen
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Ferenc A Scheeren
- Department of Dermatology, Leiden University Medical Center, Leiden, the Netherlands
| | - George M C Janssen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Peter A van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Charlotte Sarfas
- Research and Development Department, UK Health Security Agency, Salisbury, United Kingdom
| | - Andrew D White
- Research and Development Department, UK Health Security Agency, Salisbury, United Kingdom
| | - Sally A Sharpe
- Research and Development Department, UK Health Security Agency, Salisbury, United Kingdom
| | - Fabrizio Palmieri
- National Institute for Infectious Diseases Lazzaro Spallanzani Scientific Institute for Research, Hospitalization and Healthcare, Rome, Italy
| | - Linda Petrone
- National Institute for Infectious Diseases Lazzaro Spallanzani Scientific Institute for Research, Hospitalization and Healthcare, Rome, Italy
| | - Delia Goletti
- National Institute for Infectious Diseases Lazzaro Spallanzani Scientific Institute for Research, Hospitalization and Healthcare, Rome, Italy
| | - Thomas Abeel
- Delft Bioinformatics Lab, Delft University of Technology, Delft, the Netherlands; and
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Tom H M Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands
| | - Simone A Joosten
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands;
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11
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Niemann M, Matern BM, Spierings E. Snowflake: A deep learning-based human leukocyte antigen matching algorithm considering allele-specific surface accessibility. Front Immunol 2022; 13:937587. [PMID: 35967374 PMCID: PMC9372366 DOI: 10.3389/fimmu.2022.937587] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/11/2022] [Indexed: 12/12/2022] Open
Abstract
Histocompatibility in solid-organ transplantation has a strong impact on long-term graft survival. Although recent advances in matching of both B-cell epitopes and T-cell epitopes have improved understanding of allorecognition, the immunogenic determinants are still not fully understood. We hypothesized that HLA solvent accessibility is allele-specific, thus supporting refinement of HLA B-cell epitope prediction. We developed a computational pipeline named Snowflake to calculate solvent accessibility of HLA Class I proteins for deposited HLA crystal structures, supplemented by constructed HLA structures through the AlphaFold protein folding predictor and peptide binding predictions of the APE-Gen docking framework. This dataset trained a four-layer long short-term memory bidirectional recurrent neural network, which in turn inferred solvent accessibility of all known HLA Class I proteins. We extracted 676 HLA Class-I experimental structures from the Protein Data Bank and supplemented it by 37 Class-I alleles for which structures were predicted. For each of the predicted structures, 10 known binding peptides as reported by the Immune Epitope DataBase were rendered into the binding groove. Although HLA Class I proteins predominantly are folded similarly, we found higher variation in root mean square difference of solvent accessibility between experimental structures of different HLAs compared to structures with identical amino acid sequence, suggesting HLA’s solvent accessible surface is protein specific. Hence, residues may be surface-accessible on e.g. HLA-A*02:01, but not on HLA-A*01:01. Mapping these data to antibody-verified epitopes as defined by the HLA Epitope Registry reveals patterns of (1) consistently accessible residues, (2) only subsets of an epitope’s residues being consistently accessible and (3) varying surface accessibility of residues of epitopes. Our data suggest B-cell epitope definitions can be refined by considering allele-specific solvent-accessibility, rather than aggregating HLA protein surface maps by HLA class or locus. To support studies on epitope analyses in organ transplantation, the calculation of donor-allele-specific solvent-accessible amino acid mismatches was implemented as a cloud-based web service.
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Affiliation(s)
- Matthias Niemann
- Research and Development, PIRCHE AG, Berlin, Germany
- *Correspondence: Matthias Niemann,
| | - Benedict M. Matern
- Center for Translational Immunology, University Medical Center, Utrecht, Netherlands
| | - Eric Spierings
- Center for Translational Immunology, University Medical Center, Utrecht, Netherlands
- Central Diagnostic Laboratory, University Medical Center, Utrecht, Netherlands
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12
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Tomasiak L, Karch R, Schreiner W. Conformational flexibility of a free and TCR-bound pMHC-I protein investigated by long-term molecular dynamics simulations. BMC Immunol 2022; 23:36. [PMID: 35902791 PMCID: PMC9335952 DOI: 10.1186/s12865-022-00510-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 07/13/2022] [Indexed: 11/10/2022] Open
Abstract
Background Major histocompatibility complexes (MHCs) play a crucial role in the cell-mediated adaptive immune response as they present antigenic peptides (p) which are recognized by host T cells through a complex formation of the T cell receptor (TCR) with pMHC. In the present study, we report on changes in conformational flexibility within a pMHC molecule upon TCR binding by looking at molecular dynamics (MD) simulations of the free and the TCR-bound pMHC-I protein of the LC13-HLA-B*44:05-pEEYLQAFTY complex. Results We performed long-term MD simulations with a total simulation time of 8 µs, employing 10 independent 400 ns replicas for the free and the TCR-bound pMHC system. Upon TCR ligation, we observed a reduced dynamic flexibility in the central residues of the peptide and the MHC α1-helix, altered occurrences of hydrogen bonds between the peptide and the MHC, a reduced conformational entropy of the peptide-binding groove, as well as a decreased solvent accessible surface area. Conclusions In summary, our results from 8 µs MD simulations indicate a restricted conformational space of the MHC peptide-binding groove upon TCR ligation and suggest a minimum simulation time of approximately 100 ns for biomolecules of comparable complexity to draw meaningful conclusions. Given the relatively long total simulation time, our results contribute to a more detailed view on conformational flexibility properties of the investigated free and TCR-bound pMHC-I system. Supplementary Information The online version contains supplementary material available at 10.1186/s12865-022-00510-7.
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Affiliation(s)
- Lisa Tomasiak
- Institute of Biosimulation and Bioinformatics, Center for Medical Statistics, Informatics and Intelligent Systems, Medical University of Vienna, Spitalgasse 23, 1090, Vienna, Austria
| | - Rudolf Karch
- Institute of Biosimulation and Bioinformatics, Center for Medical Statistics, Informatics and Intelligent Systems, Medical University of Vienna, Spitalgasse 23, 1090, Vienna, Austria.
| | - Wolfgang Schreiner
- Institute of Biosimulation and Bioinformatics, Center for Medical Statistics, Informatics and Intelligent Systems, Medical University of Vienna, Spitalgasse 23, 1090, Vienna, Austria
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13
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Liu M, Goo J, Liu Y, Sun W, Wu MC, Hsu L, He Q. TCR-L: an analysis tool for evaluating the association between the T-cell receptor repertoire and clinical phenotypes. BMC Bioinformatics 2022; 23:152. [PMID: 35484495 PMCID: PMC9052542 DOI: 10.1186/s12859-022-04690-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 04/13/2022] [Indexed: 11/10/2022] Open
Abstract
Background T cell receptors (TCRs) play critical roles in adaptive immune responses, and recent advances in genome technology have made it possible to examine the T cell receptor (TCR) repertoire at the individual sequence level. The analysis of the TCR repertoire with respect to clinical phenotypes can yield novel insights into the etiology and progression of immune-mediated diseases. However, methods for association analysis of the TCR repertoire have not been well developed. Methods We introduce an analysis tool, TCR-L, for evaluating the association between the TCR repertoire and disease outcomes. Our approach is developed under a mixed effect modeling, where the fixed effect represents features that can be explicitly extracted from TCR sequences while the random effect represents features that are hidden in TCR sequences and are difficult to be extracted. Statistical tests are developed to examine the two types of effects independently, and then the p values are combined. Results Simulation studies demonstrate that (1) the proposed approach can control the type I error well; and (2) the power of the proposed approach is greater than approaches that consider fixed effect only or random effect only. The analysis of real data from a skin cutaneous melanoma study identifies an association between the TCR repertoire and the short/long-term survival of patients. Conclusion The TCR-L can accommodate features that can be extracted as well as features that are hidden in TCR sequences. TCR-L provides a powerful approach for identifying association between TCR repertoire and disease outcomes.
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Affiliation(s)
- Meiling Liu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, USA
| | - Juna Goo
- Department of Mathematics, Boise State University, Boise, USA
| | - Yang Liu
- Department of Mathematics and Statistics, Wright State University, Dayton, USA
| | - Wei Sun
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, USA
| | - Michael C Wu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, USA
| | - Li Hsu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, USA
| | - Qianchuan He
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, USA.
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14
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Gupta S, Azadvari N, Hosseinzadeh P. Design of Protein Segments and Peptides for Binding to Protein Targets. BIODESIGN RESEARCH 2022; 2022:9783197. [PMID: 37850124 PMCID: PMC10521657 DOI: 10.34133/2022/9783197] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 03/16/2022] [Indexed: 10/19/2023] Open
Abstract
Recent years have witnessed a rise in methods for accurate prediction of structure and design of novel functional proteins. Design of functional protein fragments and peptides occupy a small, albeit unique, space within the general field of protein design. While the smaller size of these peptides allows for more exhaustive computational methods, flexibility in their structure and sparsity of data compared to proteins, as well as presence of noncanonical building blocks, add additional challenges to their design. This review summarizes the current advances in the design of protein fragments and peptides for binding to targets and discusses the challenges in the field, with an eye toward future directions.
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Affiliation(s)
- Suchetana Gupta
- Knight Campus Center for Accelerating Scientific Impact, University of Oregon, Eugene OR 97403, USA
| | - Noora Azadvari
- Knight Campus Center for Accelerating Scientific Impact, University of Oregon, Eugene OR 97403, USA
| | - Parisa Hosseinzadeh
- Knight Campus Center for Accelerating Scientific Impact, University of Oregon, Eugene OR 97403, USA
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15
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Ballabio F, Broggini L, Paissoni C, Han X, Peqini K, Sala BM, Sun R, Sandalova T, Barbiroli A, Achour A, Pellegrino S, Ricagno S, Camilloni C. l- to d-Amino Acid Substitution in the Immunodominant LCMV-Derived Epitope gp33 Highlights the Sensitivity of the TCR Recognition Mechanism for the MHC/Peptide Structure and Dynamics. ACS OMEGA 2022; 7:9622-9635. [PMID: 35350306 PMCID: PMC8945122 DOI: 10.1021/acsomega.1c06964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/04/2022] [Indexed: 06/14/2023]
Abstract
Presentation of pathogen-derived epitopes by major histocompatibility complex I (MHC-I) can lead to the activation and expansion of specific CD8+ T cell clones, eventually resulting in the destruction of infected target cells. Altered peptide ligands (APLs), designed to elicit immunogenicity toward a wild-type peptide, may affect the overall stability of MHC-I/peptide (pMHC) complexes and modulate the recognition by T cell receptors (TCR). Previous works have demonstrated that proline substitution at position 3 (p3P) of different MHC-restricted epitopes, including the immunodominant LCMV-derived epitope gp33 and escape variants, may be an effective design strategy to increase epitope immunogenicity. These studies hypothesized that the p3P substitution increases peptide rigidity, facilitating TCR binding. Here, molecular dynamics simulations indicate that the p3P modification rigidifies the APLs in solution predisposing them for the MHC-I loading as well as once bound to H-2Db, predisposing them for TCR binding. Our results also indicate that peptide position 6, key for interaction of H-2Db/gp33 with the TCR P14, takes a suboptimal conformation before as well as after binding to the TCR. Analyses of H-2Db in complex with APLs, in which position 6 was subjected to an l- to d-amino acid modification, revealed small conformational changes and comparable pMHC thermal stability. However, the l- to d-modification reduced significantly the binding to P14 even in the presence of the p3P modification. Our combined data highlight the sensitivity of the TCR for the conformational dynamics of pMHC and provide further tools to dissect and modulate TCR binding and immunogenicity via APLs.
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Affiliation(s)
- Federico Ballabio
- Dipartimento
di Bioscienze, Università degli Studi
di Milano, Milano 20133, Italy
| | - Luca Broggini
- Dipartimento
di Bioscienze, Università degli Studi
di Milano, Milano 20133, Italy
- Institute
of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, San Donato Milanese 20097, Italy
| | - Cristina Paissoni
- Dipartimento
di Bioscienze, Università degli Studi
di Milano, Milano 20133, Italy
| | - Xiao Han
- Science
for Life Laboratory, Department of Medicine, Karolinska Institute,
& Division of Infectious Diseases, Karolinska
University Hospital, Stockholm 14186, Sweden
| | - Kaliroi Peqini
- DISFARM,
Dipartimento di Scienze Farmaceutiche, Sezione Chimica Generale e
Organica, Università degli Studi
di Milano, Milano 20122, Italy
| | - Benedetta Maria Sala
- Science
for Life Laboratory, Department of Medicine, Karolinska Institute,
& Division of Infectious Diseases, Karolinska
University Hospital, Stockholm 14186, Sweden
| | - Renhua Sun
- Science
for Life Laboratory, Department of Medicine, Karolinska Institute,
& Division of Infectious Diseases, Karolinska
University Hospital, Stockholm 14186, Sweden
| | - Tatyana Sandalova
- Science
for Life Laboratory, Department of Medicine, Karolinska Institute,
& Division of Infectious Diseases, Karolinska
University Hospital, Stockholm 14186, Sweden
| | - Alberto Barbiroli
- Dipartimento
di Scienze per gli Alimenti, la Nutrizione e l’Ambiente, Università degli Studi di Milano, Milano 20122, Italy
| | - Adnane Achour
- Science
for Life Laboratory, Department of Medicine, Karolinska Institute,
& Division of Infectious Diseases, Karolinska
University Hospital, Stockholm 14186, Sweden
| | - Sara Pellegrino
- DISFARM,
Dipartimento di Scienze Farmaceutiche, Sezione Chimica Generale e
Organica, Università degli Studi
di Milano, Milano 20122, Italy
| | - Stefano Ricagno
- Dipartimento
di Bioscienze, Università degli Studi
di Milano, Milano 20133, Italy
- Institute
of Molecular and Translational Cardiology, IRCCS Policlinico San Donato, San Donato Milanese 20097, Italy
| | - Carlo Camilloni
- Dipartimento
di Bioscienze, Università degli Studi
di Milano, Milano 20133, Italy
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16
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Strand A, Shen ST, Tomchick D, Wang J, Wang CR, Deisenhofer J. Structure and dynamics of major histocompatibility class Ib molecule H2-M3 complexed with mitochondrial-derived peptides. J Biomol Struct Dyn 2022; 40:10300-10312. [PMID: 34176438 PMCID: PMC8722451 DOI: 10.1080/07391102.2021.1942214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Presentation of antigenic peptides to T-cell receptors is an essential step in the adaptive immune response. In the mouse the class Ib major histocompatibility complex molecule, H2-M3, presents bacterial- and mitochondrial-derived peptides to T-cell receptors on cytotoxic T cells. Four mitochondrial heptapeptides, differing only at residue 6, form complexes with H2-M3 which can be distinguished by T cells. No structures of relevant receptors are available. To investigate the structural basis for this distinction, crystal structures were determined and molecular dynamics simulations over one microsecond were done for each complex. In the crystal structures of the heptapeptide complexes with H2-M3, presented here, the side chains of the peptide residues at position 6 all point into the H2-M3 binding groove, and are thus inaccessible, so that the very similar structures do not suggest how recognition and initiation of responses by the T cells may occur. However, conformational differences, which could be crucial to T-cell discrimination, appear within one microsecond during molecular dynamics simulations of the four complexes. Specifically, the three C-terminal residues of peptide ligands with alanine or threonine at position 6 partially exit the binding groove; this does not occur in peptide ligands with isoleucine or valine at position 6. Structural changes associated with partial peptide exit from the binding groove, along with relevant peptide binding energetics and immunological results are discussed. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Arne Strand
- Green Center for Systems Biology, UT Southwestern Medical Center, Dallas, Texas, United States of America
| | - San-Tai Shen
- AnTaimmu Biomed Co., Ltd., Zhubei City, Hsinchu County, Taiwan
| | - Diana Tomchick
- Department of Biophysics, UT Southwestern Medical Center, Dallas, Texas, United States of America,Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas, United States of America
| | - Junmei Wang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Chyung-Ru Wang
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Johann Deisenhofer
- Green Center for Systems Biology, UT Southwestern Medical Center, Dallas, Texas, United States of America,Department of Biophysics, UT Southwestern Medical Center, Dallas, Texas, United States of America,Corresponding author
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17
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Luzuriaga MA, Herbert FC, Brohlin OR, Gadhvi J, Howlett T, Shahrivarkevishahi A, Wijesundara YH, Venkitapathi S, Veera K, Ehrman R, Benjamin CE, Popal S, Burton MD, Ingersoll MA, De Nisco NJ, Gassensmith JJ. Metal-Organic Framework Encapsulated Whole-Cell Vaccines Enhance Humoral Immunity against Bacterial Infection. ACS NANO 2021; 15:17426-17438. [PMID: 34546723 DOI: 10.1021/acsnano.1c03092] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The increasing rate of resistance of bacterial infection against antibiotics requires next generation approaches to fight potential pandemic spread. The development of vaccines against pathogenic bacteria has been difficult owing, in part, to the genetic diversity of bacteria. Hence, there are many potential target antigens and little a priori knowledge of which antigen/s will elicit protective immunity. The painstaking process of selecting appropriate antigens could be avoided with whole-cell bacteria; however, whole-cell formulations typically fail to produce long-term and durable immune responses. These complications are one reason why no vaccine against any type of pathogenic E. coli has been successfully clinically translated. As a proof of principle, we demonstrate a method to enhance the immunogenicity of a model pathogenic E. coli strain by forming a slow releasing depot. The E. coli strain CFT073 was biomimetically mineralized within a metal-organic framework (MOF). This process encapsulates the bacteria within 30 min in water and at ambient temperatures. Vaccination with this formulation substantially enhances antibody production and results in significantly enhanced survival in a mouse model of bacteremia compared to standard inactivated formulations.
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18
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Muñoz-García N, Lima M, Villamor N, Morán-Plata FJ, Barrena S, Mateos S, Caldas C, Balanzategui A, Alcoceba M, Domínguez A, Gómez F, Langerak AW, van Dongen JJM, Orfao A, Almeida J. Anti-TRBC1 Antibody-Based Flow Cytometric Detection of T-Cell Clonality: Standardization of Sample Preparation and Diagnostic Implementation. Cancers (Basel) 2021; 13:cancers13174379. [PMID: 34503189 PMCID: PMC8430560 DOI: 10.3390/cancers13174379] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/17/2021] [Accepted: 08/23/2021] [Indexed: 11/16/2022] Open
Abstract
A single antibody (anti-TRBC1; JOVI-1 antibody clone) against one of the two mutually exclusive T-cell receptor β-chain constant domains was identified as a potentially useful flow-cytometry (FCM) marker to assess Tαβ-cell clonality. We optimized the TRBC1-FCM approach for detecting clonal Tαβ-cells and validated the method in 211 normal, reactive and pathological samples. TRBC1 labeling significantly improved in the presence of CD3. Purified TRBC1+ and TRBC1- monoclonal and polyclonal Tαβ-cells rearranged TRBJ1 in 44/47 (94%) and TRBJ1+TRBJ2 in 48 of 48 (100%) populations, respectively, which confirmed the high specificity of this assay. Additionally, TRBC1+/TRBC1- ratios within different Tαβ-cell subsets are provided as reference for polyclonal cells, among which a bimodal pattern of TRBC1-expression profile was found for all TCRVβ families, whereas highly-variable TRBC1+/TRBC1- ratios were observed in more mature vs. naïve Tαβ-cell subsets (vs. total T-cells). In 112/117 (96%) samples containing clonal Tαβ-cells in which the approach was validated, monotypic expression of TRBC1 was confirmed. Dilutional experiments showed a level of detection for detecting clonal Tαβ-cells of ≤10-4 in seven out of eight pathological samples. These results support implementation of the optimized TRBC1-FCM approach as a fast, specific and accurate method for assessing T-cell clonality in diagnostic-FCM panels, and for minimal (residual) disease detection in mature Tαβ+ leukemia/lymphoma patients.
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Affiliation(s)
- Noemí Muñoz-García
- Translational and Clinical Research Program, Centro de Investigación del Cáncer and IBMCC (CSIC-University of Salamanca), Cytometry Service, NUCLEUS, Department of Medicine, University of Salamanca (USAL) and Institute of Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain; (N.M.-G.); (F.J.M.-P.); (S.B.); (S.M.); (C.C.); (A.O.)
- Biomedical Research Networking Centre Consortium of Oncology (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain; (N.V.); (A.B.); (M.A.)
| | - Margarida Lima
- Department of Hematology, Laboratory of Cytometry, Hospital de Santo António, Centro Hospitalar do Porto, 4099-001 Porto, Portugal;
- Unit for Multidisciplinary Research in Biomedicine (UMIB), Abel Salazar Institute of Biomedical Sciences (ICBAS), University of Porto, 4050-313 Porto, Portugal
| | - Neus Villamor
- Biomedical Research Networking Centre Consortium of Oncology (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain; (N.V.); (A.B.); (M.A.)
- Department of Pathology, Hematopathology Unit, Hospital Clínic, IDIBAPS, 08036 Barcelona, Spain
| | - F. Javier Morán-Plata
- Translational and Clinical Research Program, Centro de Investigación del Cáncer and IBMCC (CSIC-University of Salamanca), Cytometry Service, NUCLEUS, Department of Medicine, University of Salamanca (USAL) and Institute of Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain; (N.M.-G.); (F.J.M.-P.); (S.B.); (S.M.); (C.C.); (A.O.)
- Biomedical Research Networking Centre Consortium of Oncology (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain; (N.V.); (A.B.); (M.A.)
| | - Susana Barrena
- Translational and Clinical Research Program, Centro de Investigación del Cáncer and IBMCC (CSIC-University of Salamanca), Cytometry Service, NUCLEUS, Department of Medicine, University of Salamanca (USAL) and Institute of Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain; (N.M.-G.); (F.J.M.-P.); (S.B.); (S.M.); (C.C.); (A.O.)
- Biomedical Research Networking Centre Consortium of Oncology (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain; (N.V.); (A.B.); (M.A.)
| | - Sheila Mateos
- Translational and Clinical Research Program, Centro de Investigación del Cáncer and IBMCC (CSIC-University of Salamanca), Cytometry Service, NUCLEUS, Department of Medicine, University of Salamanca (USAL) and Institute of Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain; (N.M.-G.); (F.J.M.-P.); (S.B.); (S.M.); (C.C.); (A.O.)
- Biomedical Research Networking Centre Consortium of Oncology (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain; (N.V.); (A.B.); (M.A.)
| | - Carolina Caldas
- Translational and Clinical Research Program, Centro de Investigación del Cáncer and IBMCC (CSIC-University of Salamanca), Cytometry Service, NUCLEUS, Department of Medicine, University of Salamanca (USAL) and Institute of Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain; (N.M.-G.); (F.J.M.-P.); (S.B.); (S.M.); (C.C.); (A.O.)
- Biomedical Research Networking Centre Consortium of Oncology (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain; (N.V.); (A.B.); (M.A.)
| | - Ana Balanzategui
- Biomedical Research Networking Centre Consortium of Oncology (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain; (N.V.); (A.B.); (M.A.)
- Hematology Service, University Hospital of Salamanca, Translational and Clinical Research Program, Centro de Investigación del Cáncer/IBMCC and IBSAL, 37007 Salamanca, Spain
| | - Miguel Alcoceba
- Biomedical Research Networking Centre Consortium of Oncology (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain; (N.V.); (A.B.); (M.A.)
- Hematology Service, University Hospital of Salamanca, Translational and Clinical Research Program, Centro de Investigación del Cáncer/IBMCC and IBSAL, 37007 Salamanca, Spain
| | - Alejandro Domínguez
- Centro de Salud Miguel Armijo, Sanidad de Castilla y León (SACYL), 37007 Salamanca, Spain; (A.D.); (F.G.)
| | - Fabio Gómez
- Centro de Salud Miguel Armijo, Sanidad de Castilla y León (SACYL), 37007 Salamanca, Spain; (A.D.); (F.G.)
| | - Anton W. Langerak
- Department of Immunology, Laboratory Medical immunology, Erasmus MC, University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands;
| | - Jacques J. M. van Dongen
- Department of Immunology, Leiden University Medical Center (LUMC), 2333 ZA Leiden, The Netherlands;
| | - Alberto Orfao
- Translational and Clinical Research Program, Centro de Investigación del Cáncer and IBMCC (CSIC-University of Salamanca), Cytometry Service, NUCLEUS, Department of Medicine, University of Salamanca (USAL) and Institute of Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain; (N.M.-G.); (F.J.M.-P.); (S.B.); (S.M.); (C.C.); (A.O.)
- Biomedical Research Networking Centre Consortium of Oncology (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain; (N.V.); (A.B.); (M.A.)
| | - Julia Almeida
- Translational and Clinical Research Program, Centro de Investigación del Cáncer and IBMCC (CSIC-University of Salamanca), Cytometry Service, NUCLEUS, Department of Medicine, University of Salamanca (USAL) and Institute of Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain; (N.M.-G.); (F.J.M.-P.); (S.B.); (S.M.); (C.C.); (A.O.)
- Biomedical Research Networking Centre Consortium of Oncology (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain; (N.V.); (A.B.); (M.A.)
- Correspondence:
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19
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Niebuhr M, Belde J, Fähnrich A, Serge A, Irla M, Ellebrecht CT, Hammers CM, Bieber K, Westermann J, Kalies K. Receptor repertoires of murine follicular T helper cells reveal a high clonal overlap in separate lymph nodes in autoimmunity. eLife 2021; 10:70053. [PMID: 34402793 PMCID: PMC8370764 DOI: 10.7554/elife.70053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 08/02/2021] [Indexed: 12/21/2022] Open
Abstract
Follicular T helper cells (Tfh) are a specialized subset of CD4 effector T cells that are crucial for germinal center (GC) reactions and for selecting B cells to undergo affinity maturation. Despite this central role for humoral immunity, only few data exist about their clonal distribution when multiple lymphoid organs are exposed to the same antigen (Ag) as it is the case in autoimmunity. Here, we used an autoantibody-mediated disease model of the skin and injected one auto-Ag into the two footpads of the same mouse and analyzed the T cell receptor (TCR)β sequences of Tfh located in GCs of both contralateral draining lymph nodes. We found that over 90% of the dominant GC-Tfh clonotypes were shared in both lymph nodes but only transiently. The initially dominant Tfh clonotypes especially declined after establishment of chronic disease while GC reaction and autoimmune disease continued. Our data demonstrates a dynamic behavior of Tfh clonotypes under autoimmune conditions and emphasizes the importance of the time point for distinguishing auto-Ag-specific Tfh clonotypes from potential bystander activated ones.
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Affiliation(s)
- Markus Niebuhr
- Institute for Anatomy, University of Lübeck, Lübeck, Germany
| | - Julia Belde
- Institute for Anatomy, University of Lübeck, Lübeck, Germany
| | - Anke Fähnrich
- Institute for Anatomy, University of Lübeck, Lübeck, Germany.,Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Arnauld Serge
- Laboratoire Adhésion et Inflammation, Inserm U1067 CNRS, Aix-Marseille Université, Marseille, France
| | - Magali Irla
- Centre d'Immunologie de Marseille Luminy (CIML), INSERM U1104, Aix-Marseille Université UM2, Marseille, France
| | - Christoph T Ellebrecht
- Institute for Anatomy, University of Lübeck, Lübeck, Germany.,Department of Dermatology, University of Pennsylvania, Philadelphia, United States
| | - Christoph M Hammers
- Institute for Anatomy, University of Lübeck, Lübeck, Germany.,Department of Dermatology, University of Lübeck, Lübeck, Germany
| | - Katja Bieber
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | | | - Kathrin Kalies
- Institute for Anatomy, University of Lübeck, Lübeck, Germany
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20
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Jantz-Naeem N, Springer S. Venus flytrap or pas de trois? The dynamics of MHC class I molecules. Curr Opin Immunol 2021; 70:82-89. [PMID: 33993034 DOI: 10.1016/j.coi.2021.04.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/05/2021] [Accepted: 04/08/2021] [Indexed: 11/25/2022]
Abstract
The peptide binding site of major histocompatibility complex (MHC) class I molecules is natively unfolded when devoid of peptides. Peptide binding stabilizes the structure and slows the dynamics, but peptide-specific and subtype-specific motions influence, and are influenced by, interaction with assembly chaperones, the T cell receptor, and other class I-binding proteins. The molecular mechanisms of cooperation between peptide, class I heavy chain, and beta-2 microglobulin are insufficiently known but are being elucidated by nuclear magnetic resonance and other modern methods. It appears that micropolymorphic clusters of charged amino acids, often hidden in the molecule interior, determine the dynamics and thus chaperone dependence, cellular fate, and disease association of class I.
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Affiliation(s)
- Nouria Jantz-Naeem
- Department of Life Sciences and Chemistry, Jacobs University, Bremen, Germany
| | - Sebastian Springer
- Department of Life Sciences and Chemistry, Jacobs University, Bremen, Germany.
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21
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Bingöl EN, Serçinoğlu O, Ozbek P. Unraveling the Allosteric Communication Mechanisms in T-Cell Receptor-Peptide-Loaded Major Histocompatibility Complex Dynamics Using Molecular Dynamics Simulations: An Approach Based on Dynamic Cross Correlation Maps and Residue Interaction Energy Calculations. J Chem Inf Model 2021; 61:2444-2453. [PMID: 33930270 DOI: 10.1021/acs.jcim.1c00338] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Antigen presentation by major histocompatibility complex (MHC) proteins to T-cell receptors (TCRs) plays a crucial role in triggering the adaptive immune response. Most of our knowledge on TCR-peptide-loaded major histocompatibility complex (pMHC) interaction stemmed from experiments yielding static structures, yet the dynamic aspects of this molecular interaction are equally important to understand the underlying molecular mechanisms and to develop treatment strategies against diseases such as cancer and autoimmune diseases. To this end, computational biophysics studies including all-atom molecular dynamics simulations have provided useful insights; however, we still lack a basic understanding of an overall allosteric mechanism that results in conformational changes in the TCR and subsequent T-cell activation. Previous hydrogen-deuterium exchange and nuclear magnetic resonance studies provided clues regarding these molecular mechanisms, including global rigidification and allosteric effects on the constant domain of TCRs away from the pMHC interaction site. Here, we show that molecular dynamics simulations can be used to identify how this overall rigidification may be related to the allosteric communication within TCRs upon pMHC interaction via essential dynamics and nonbonded residue-residue interaction energy analyses. The residues taking part in the rigidification effect are highlighted with an intricate analysis on residue interaction changes, which lead to a detailed outline of the complex formation event. Our results indicate that residues of the Cβ domain of TCRs show significant differences in their nonbonded interactions upon complex formation. Moreover, the dynamic cross correlations between these residues are also increased, in line with their nonbonded interaction energy changes. Altogether, our approach may be valuable for elucidating intramolecular allosteric changes in the TCR structure upon pMHC interaction in molecular dynamics simulations.
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Affiliation(s)
- Elif Naz Bingöl
- Department of Bioengineering, Institute of Pure and Applied Sciences, Marmara University, 34722 Istanbul, Turkey
| | - Onur Serçinoğlu
- Department of Bioengineering, Faculty of Engineering, Gebze Technical University, Kocaeli 41400, Turkey
| | - Pemra Ozbek
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul 34722, Turkey
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22
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Thomas C, Tampé R. MHC I assembly and peptide editing - chaperones, clients, and molecular plasticity in immunity. Curr Opin Immunol 2021; 70:48-56. [PMID: 33689959 DOI: 10.1016/j.coi.2021.02.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 02/07/2021] [Indexed: 11/24/2022]
Abstract
Peptides presented on MHC I molecules allow the immune system to detect diseased cells. The displayed peptides typically stem from proteasomal degradation of cytoplasmic proteins and are translocated into the ER lumen where they are trimmed and loaded onto MHC I. Peptide translocation is carried out by the transporter associated with antigen processing, which forms the central building block of a dynamic assembly called the peptide-loading complex (PLC). By coordinating peptide transfer with MHC I loading and peptide optimization, the PLC is a linchpin in the adaptive immune system. Peptide loading and optimization is catalyzed by the PLC component tapasin and the PLC-independent TAPBPR, two MHC I-dedicated enzymes chaperoning empty or suboptimally loaded MHC I and selecting stable peptide-MHC I complexes in a process called peptide editing or proofreading. Recent structural and functional studies of peptide editing have dramatically improved our understanding of this pivotal event in antigen processing/presentation. This review is dedicated to Vincenzo Cerundolo (1959-2020) for his pioneering work in the field of antigen processing/presentation.
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Affiliation(s)
- Christoph Thomas
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue Str. 9, Frankfurt, 60438 Main, Germany.
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue Str. 9, Frankfurt, 60438 Main, Germany.
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23
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Gunasinghe SD, Peres NG, Goyette J, Gaus K. Biomechanics of T Cell Dysfunctions in Chronic Diseases. Front Immunol 2021; 12:600829. [PMID: 33717081 PMCID: PMC7948521 DOI: 10.3389/fimmu.2021.600829] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 01/12/2021] [Indexed: 12/12/2022] Open
Abstract
Understanding the mechanisms behind T cell dysfunctions during chronic diseases is critical in developing effective immunotherapies. As demonstrated by several animal models and human studies, T cell dysfunctions are induced during chronic diseases, spanning from infections to cancer. Although factors governing the onset and the extent of the functional impairment of T cells can differ during infections and cancer, most dysfunctional phenotypes share common phenotypic traits in their immune receptor and biophysical landscape. Through the latest developments in biophysical techniques applied to explore cell membrane and receptor-ligand dynamics, we are able to dissect and gain further insights into the driving mechanisms behind T cell dysfunctions. These insights may prove useful in developing immunotherapies aimed at reinvigorating our immune system to fight off infections and malignancies more effectively. The recent success with checkpoint inhibitors in treating cancer opens new avenues to develop more effective, targeted immunotherapies. Here, we highlight the studies focused on the transformation of the biophysical landscape during infections and cancer, and how T cell biomechanics shaped the immunopathology associated with chronic diseases.
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Affiliation(s)
- Sachith D Gunasinghe
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Sydney, NSW, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, NSW, Australia
| | - Newton G Peres
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Sydney, NSW, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, NSW, Australia
| | - Jesse Goyette
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Sydney, NSW, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, NSW, Australia
| | - Katharina Gaus
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Sydney, NSW, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, NSW, Australia
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24
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Mizsei R, Li X, Chen WN, Szabo M, Wang JH, Wagner G, Reinherz EL, Mallis RJ. A general chemical crosslinking strategy for structural analyses of weakly interacting proteins applied to preTCR-pMHC complexes. J Biol Chem 2021; 296:100255. [PMID: 33837736 PMCID: PMC7948749 DOI: 10.1016/j.jbc.2021.100255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 12/29/2020] [Accepted: 01/04/2021] [Indexed: 11/04/2022] Open
Abstract
T lymphocytes discriminate between healthy and infected or cancerous cells via T-cell receptor-mediated recognition of peptides bound and presented by cell-surface-expressed major histocompatibility complex molecules (MHCs). Pre-T-cell receptors (preTCRs) on thymocytes foster development of αβT lymphocytes through their β chain interaction with MHC displaying self-peptides on thymic epithelia. The specific binding of a preTCR with a peptide-MHC complex (pMHC) has been identified previously as forming a weak affinity complex with a distinct interface from that of mature αβTCR. However, a lack of appropriate tools has limited prior efforts to investigate this unique interface. Here we designed a small-scale linkage screening protocol using bismaleimide linkers for determining residue-specific distance constraints between transiently interacting protein pairs in solution. Employing linkage distance restraint-guided molecular modeling, we report the oriented solution docking geometry of a preTCRβ-pMHC interaction. The linkage model of preTCRβ-pMHC complex was independently verified with paramagnetic pseudocontact chemical shift (PCS) NMR of the unlinked protein mixtures. Using linkage screens, we show that the preTCR binds with differing affinities to peptides presented by MHC in solution. Moreover, the C-terminal peptide segment is a key determinant in preTCR-pMHC recognition. We also describe the process for future large-scale production and purification of the linked constructs for NMR, X-ray crystallography, and single-molecule electron microscopy studies.
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MESH Headings
- Antigens, Surface/chemistry
- Antigens, Surface/genetics
- Antigens, Surface/ultrastructure
- Humans
- Major Histocompatibility Complex/genetics
- Membrane Glycoproteins/chemistry
- Membrane Glycoproteins/ultrastructure
- Nuclear Magnetic Resonance, Biomolecular
- Peptides/chemistry
- Peptides/genetics
- Protein Binding/genetics
- Protein Interaction Domains and Motifs/genetics
- Receptors, Antigen, T-Cell/chemistry
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/ultrastructure
- Receptors, Antigen, T-Cell, alpha-beta/chemistry
- Receptors, Antigen, T-Cell, alpha-beta/ultrastructure
- T-Lymphocytes/chemistry
- T-Lymphocytes/immunology
- T-Lymphocytes/ultrastructure
- Thymocytes/chemistry
- Thymocytes/ultrastructure
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Affiliation(s)
- Réka Mizsei
- Laboratory of Immunobiology, Dana Farber Cancer Institute, Boston, Massachusetts, USA; Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Xiaolong Li
- Laboratory of Immunobiology, Dana Farber Cancer Institute, Boston, Massachusetts, USA; Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA; Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Wan-Na Chen
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Monika Szabo
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Jia-Huai Wang
- Laboratory of Immunobiology, Dana Farber Cancer Institute, Boston, Massachusetts, USA; Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA; Department of Cancer Biology, Dana Farber Cancer Institute, Boston, Massachusetts, USA; Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Ellis L Reinherz
- Laboratory of Immunobiology, Dana Farber Cancer Institute, Boston, Massachusetts, USA; Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA; Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA.
| | - Robert J Mallis
- Laboratory of Immunobiology, Dana Farber Cancer Institute, Boston, Massachusetts, USA; Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA; Department of Dermatology, Harvard Medical School, Boston, Massachusetts, USA.
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25
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Wei X, Gu L, Heng W. T lymphocytes related biomarkers for predicting immunotherapy efficacy in non-small cell lung cancer. Oncol Lett 2020; 21:89. [PMID: 33376522 PMCID: PMC7751340 DOI: 10.3892/ol.2020.12350] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 11/20/2020] [Indexed: 02/07/2023] Open
Abstract
The immune environment is a determinant of whether patients with cancer can benefit from immunotherapy. Immune checkpoint inhibitors (ICIs) have improved the prognosis of patients with different types of malignancies and have initiated a transformation in tumor therapy. However, some patients cannot achieve a long-term response and several patients even have no response to ICIs therapy. Thus, potential biomarkers that can effectively predict the efficacy of ICIs are essential for their clinical application and for the selection of patients. The accuracy of well-known biomarkers, such as expression of programmed cell death ligand 1 and tumor mutational burden, remains controversial. One of the critical factors for immune responses in the tumor microenvironment is tumor antigen-specific T cell. The density and distribution of tumor-infiltrating lymphocytes, T cells activation and T lymphocytes phenotypes in peripheral blood and serum cytokines have been observed in different types of solid cancer. Although the association with immunotherapy prognosis is in dispute, the prospect of T cell-related biomarkers is encouraged. The present review discusses whether these factors are associated with clinical outcomes of patients with non-small cell lung cancer. The association between several serum cytokines and ICIs therapy efficacy is also discussed.
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Affiliation(s)
- Xiaoying Wei
- Department of Medicine, Respiratory, Emergency and Intensive Care Medicine, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215000, P.R. China
| | - Ling Gu
- Department of Medicine, Respiratory, Emergency and Intensive Care Medicine, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215000, P.R. China
| | - Wei Heng
- Department of Medicine, Respiratory, Emergency and Intensive Care Medicine, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215000, P.R. China
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26
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He Y, Agnihotri P, Rangarajan S, Chen Y, Kerzic MC, Ma B, Nussinov R, Mariuzza RA, Orban J. Peptide-MHC Binding Reveals Conserved Allosteric Sites in MHC Class I- and Class II-Restricted T Cell Receptors (TCRs). J Mol Biol 2020; 432:166697. [PMID: 33157083 PMCID: PMC8356565 DOI: 10.1016/j.jmb.2020.10.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/29/2020] [Accepted: 10/27/2020] [Indexed: 12/31/2022]
Abstract
T cells are vital for adaptive immune responses that protect against pathogens and cancers. The T cell receptor (TCR)-CD3 complex comprises a diverse αβ TCR heterodimer in noncovalent association with three invariant CD3 dimers. The TCR is responsible for recognizing antigenic peptides bound to MHC molecules (pMHC), while the CD3 dimers relay activation signals to the T cell. However, the mechanisms by which TCR engagement by pMHC is transmitted to CD3 remain mysterious, although there is growing evidence that mechanosensing and allostery both play a role. Here, we carried out NMR analysis of a human autoimmune TCR (MS2-3C8) that recognizes a self-peptide from myelin basic protein presented by the MHC class II molecule HLA-DR4. We observed pMHC-induced NMR signal perturbations in MS2-3C8 that indicate long-range effects on TCR β chain conformation and dynamics. Our results demonstrate that, in addition to expected changes in the NMR resonances of pMHC-contacting residues, perturbations extend to the Vβ/Vα, Vβ/Cβ, and Cβ/Cα interfacial regions. Moreover, the pattern of long-range perturbations is similar to that detected previously in the β chains of two MHC class I-restricted TCRs, thereby revealing a common allosteric pathway among three unrelated TCRs. Molecular dynamics (MD) simulations predict similar pMHC-induced effects. Taken together, our results demonstrate that pMHC binding induces long-range allosteric changes in the TCR β chain at conserved sites in both representative MHC class I- and class II-restricted TCRs, and that these sites may play a role in the transmission of signaling information.
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Affiliation(s)
- Yanan He
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA; Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | - Pragati Agnihotri
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Sneha Rangarajan
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Yihong Chen
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA; Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | - Melissa C Kerzic
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Buyong Ma
- Engineering Research Center of Cell & Therapeutic Antibody, MOE, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China; Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Roy A Mariuzza
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA.
| | - John Orban
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA; Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA.
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27
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Attia JVD, Dessens CE, van de Water R, Houvast RD, Kuppen PJK, Krijgsman D. The Molecular and Functional Characteristics of HLA-G and the Interaction with Its Receptors: Where to Intervene for Cancer Immunotherapy? Int J Mol Sci 2020; 21:ijms21228678. [PMID: 33213057 PMCID: PMC7698525 DOI: 10.3390/ijms21228678] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/06/2020] [Accepted: 11/13/2020] [Indexed: 12/12/2022] Open
Abstract
Human leukocyte antigen G (HLA-G) mediates maternal-fetal immune tolerance. It is also considered an immune checkpoint in cancer since it may mediate immune evasion and thus promote tumor growth. HLA-G is, therefore, a potential target for immunotherapy. However, existing monoclonal antibodies directed against HLA-G lack sufficient specificity and are not suitable for immune checkpoint inhibition in a clinical setting. For this reason, it is essential that alternative approaches are explored to block the interaction between HLA-G and its receptors. In this review, we discuss the structure and peptide presentation of HLA-G, and its interaction with the receptors Ig-like transcript (ILT) 2, ILT4, and Killer cell immunoglobulin-like receptor 2DL4 (KIR2DL4). Based on our findings, we propose three alternative strategies to block the interaction between HLA-G and its receptors in cancer immunotherapy: (1) prevention of HLA-G dimerization, (2) targeting the peptide-binding groove of HLA-G, and (3) targeting the HLA-G receptors. These strategies should be an important focus of future studies that aim to develop immune checkpoint inhibitors to block the interaction between HLA-G and its receptors for the treatment of cancer.
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28
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Qi X, Qi C, Wu T, Hu Y. CSF1R and HCST: Novel Candidate Biomarkers Predicting the Response to Immunotherapy in Non-Small Cell Lung Cancer. Technol Cancer Res Treat 2020; 19:1533033820970663. [PMID: 33153411 PMCID: PMC7658512 DOI: 10.1177/1533033820970663] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Objective: Precision immunotherapy in non-small cell lung cancer (NSCLC) have been the focus of tumor immunity research. The aim of this study is to identify novel candidate biomarkers predicting the response to immunotherapy in NSCLC. Methods: GSE126044 was obtained from Gene Expression Omnibus (GEO). According to the response to anti-PD-1 antibody, 2 groups were divided: response group and non-response group. Differentially expressed genes (DEGs) were screened using R. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed. ROC curves and possible pathways of the seed genes were further analyzed. Results: In total, 588 DEGs (487 upregulated DEGs and 101 downregulated) were identified. GO and KEGG analyses showed that upregulated DEGs were mainly enriched in immune response and cell adhesion pathways, while VEGF signaling pathway and metabolic pathways were mainly enriched in downregulated DEGs. In addition, CSF1 R and HCST showed more powerful predictive ability than PDL1. More importantly, these candidate genes were not only positively correlated with the expression of PDL1 and the infiltration of CD8+ T cells in the immune microenvironment, but also might improve the prognosis in lung squamous cell carcinoma. Conclusions: CSF1 R and HCST might be novel predictive markers for immunotherapy in NSCLC.
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Affiliation(s)
- Xiaoguang Qi
- Department of Oncology, the First Medical Center, 104607Chinese PLA General Hospital, Beijing China
| | - Chunyan Qi
- Department of Special Ward, the Second Medical Center, 104607Chinese PLA General Hospital, Beijing, China
| | - Tao Wu
- Department of Outpatient Pharmacy, the First Medical Center, 74495Chinese PLA General Hospital, Beijing, China
| | - Yi Hu
- Department of Oncology, the First Medical Center, 104607Chinese PLA General Hospital, Beijing China
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29
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Bertolini M, McElwee K, Gilhar A, Bulfone‐Paus S, Paus R. Hair follicle immune privilege and its collapse in alopecia areata. Exp Dermatol 2020; 29:703-725. [DOI: 10.1111/exd.14155] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/18/2020] [Accepted: 07/10/2020] [Indexed: 12/11/2022]
Affiliation(s)
| | - Kevin McElwee
- Monasterium Laboratory Münster Germany
- Centre for Skin Sciences University of Bradford Bradford UK
- Department of Dermatology and Skin Science University of British Columbia Vancouver British Columbia Canada
| | - Amos Gilhar
- Laboratory for Skin Research Rappaport Faculty of Medicine Technion‐Israel Institute of Technology Haifa Israel
| | - Silvia Bulfone‐Paus
- Monasterium Laboratory Münster Germany
- Centre for Dermatology Research University of Manchester and NIHR Manchester Biomedical Research Centre Manchester UK
| | - Ralf Paus
- Monasterium Laboratory Münster Germany
- Centre for Dermatology Research University of Manchester and NIHR Manchester Biomedical Research Centre Manchester UK
- Dr. Philip Frost Department of Dermatology & Cutaneous Surgery University of Miami Miller School of Medicine Miami FL USA
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30
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Wang X, Li S, Liu J, Kong D, Han X, Lei P, Xu M, Guan H, Hou D. Ameliorative effects of sea buckthorn oil on DNCB induced atopic dermatitis model mice via regulation the balance of Th1/Th2. BMC Complement Med Ther 2020; 20:263. [PMID: 32843010 PMCID: PMC7449066 DOI: 10.1186/s12906-020-02997-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 06/22/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Atopic dermatitis (AD) is a worldwide chronic skin disease which burden public health. Sea buckthorn (SBT) (Hippophae rhamnoides L., Elaeagnaceae) oil, as a traditional herbal medicine, has been used for disease treatment for many years. The effects of SBT oil on AD mouse model induced by repeated administration of 2,4-dinitrochlorobenzene (DNCB) in BALB/c mice was evaluated in this study. METHODS Mice were divided into four groups including the normal control group, AD model group, AD model group treated with SBT oil (5 ml/kg) and AD model group treated with SBT oil (10 ml/kg). Same volume at different concentrations of SBT oil was applied daily on the latter two groups by gavage for 15 days following AD model induction. The function of skin barrier and the production of IL-4, IFN-γ, TNF-α and TSLP were examined after animal sacrifice. The migration and mature of langerhans cell (LCs) in lymph node was further assessed by flow cytometry. RESULTS SBT oil alleviated dermatitis scores, decreased ear thickness, prevented infiltration of mast cell, reduced lymph node weight and depressed activity of Th2 cells. SBT oil also reduced the expression of IL-4, IFN-γ, TNF-α and TSLP in ear tissue, IgE level in serum and mRNA relative expression of IL-4, IFN-γ, TNF-α in lymph node. Moreover, SBT oil inhibited the migration of LCs cells from local lesions to lymph node and it's mature in lymph node. CONCLUSIONS These results suggest SBT oil had a beneficial effect either systemic or regional on DNCB-induced AD mice via maintain the balance of Th1/Th2 and may be a potential complementary candidate for AD treatment.
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Affiliation(s)
- Xinxin Wang
- Liaoning University of Traditional Chinese Medicine, Shenyang, Liaoning, PR China.,Basic Medical and Forensic Medicine, Baotou Medical college, Baotou, Inner Mongolia, PR China
| | - Sijia Li
- Liaoning University of Traditional Chinese Medicine, Shenyang, Liaoning, PR China
| | - Jiping Liu
- Neurosurgery Department, Northern Hospital of Inner Mongolia, Baotou, Inner Mongolia, PR China
| | - Dongning Kong
- Liaoning Dongning Pharmceutical Co., Ltd., Fuxin, Liaoning, PR China
| | - Xiaowei Han
- College of Integrated Traditional Chinese and Western Medicine, Liaoning University of Traditional Chinese Medicine, Chongshan Road NO.79, Shenyang, Liaoning, 110847, P.R. China
| | - Ping Lei
- College of Integrated Traditional Chinese and Western Medicine, Liaoning University of Traditional Chinese Medicine, Chongshan Road NO.79, Shenyang, Liaoning, 110847, P.R. China
| | - Ming Xu
- College of Integrated Traditional Chinese and Western Medicine, Liaoning University of Traditional Chinese Medicine, Chongshan Road NO.79, Shenyang, Liaoning, 110847, P.R. China
| | - Hongquan Guan
- College of Integrated Traditional Chinese and Western Medicine, Liaoning University of Traditional Chinese Medicine, Chongshan Road NO.79, Shenyang, Liaoning, 110847, P.R. China.
| | - Diandong Hou
- College of Integrated Traditional Chinese and Western Medicine, Liaoning University of Traditional Chinese Medicine, Chongshan Road NO.79, Shenyang, Liaoning, 110847, P.R. China.
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31
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Margulies DH, Jiang J, Natarajan K. Structural and dynamic studies of TAPBPR and Tapasin reveal the mechanism of peptide loading of MHC-I molecules. Curr Opin Immunol 2020; 64:71-79. [DOI: 10.1016/j.coi.2020.04.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 03/24/2020] [Accepted: 04/03/2020] [Indexed: 12/17/2022]
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32
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Ferreira JM, Santos LDS, Oliveira SP, Dos Santos BRC, Dos Santos ACM, de Moura EL, de Souza EVM, de Lima Filho JL. Chikungunya Virus Infection Outcome: A Systematic Review of Host Genetics. Immunol Invest 2020; 50:58-79. [PMID: 32204641 DOI: 10.1080/08820139.2020.1733011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Background: Chikungunya virus (CHIKV) is a global concern, inducing chikungunya fever and trigging an arthritogenic chronic phase beyond some severe forms. Outcomes of CHIKV infections in humans are dependent on genetic variations. Here, a systematic review was performed to show evidence of genetic variations on infection outcomes of patients. Methods: Searches were performed in Scopus, SciELO, MEDLINE/PubMed, Web of Science, OneFile (GALE), Periódicos CAPES and ScienceDirect Journals databases. The PICOS approach was used to assess the eligibility of records. A meta-analysis was also conducted to show an association between described alleles/genes and CHIKV infection outcome. Results: Reviews of genetic variants were conducted on genes: CD 209, OAS1, OAS2, OAS3, MIF, TLR-3, TLR-7, TLR-8, MYD-88, KIR, HLA-B; HLA-C; DRB1 and DQB1. Studies were performed on Gabon, Singapore, and India, including Indians, Malay, Gabonese and Chinese ethnicities and published between 2009-2017. The meta-analysis was performed with DRB1 *01; *03; *04; *07; *10; *11; *13; *14 and *15 and DQB1 *02; *03; *05 and *06 alleles with Indian population sample. Sampling power was >80% and a significant positive association between DRB1*14 and CHIKV infection was found (OR = 1.67, 95% CI = 1.04-2.67; p = .03). Conclusion: Majority of the studies were conducted in India. Meta-analysis suggests that DRB1*14 is related to the susceptibility of symptomatic CHIKV infection in Indian population. The literature about CHIKV infection and genetic variations is scarce. The precise role of genetic variation in CHIKV is not clear yet. Further studies are necessary to provide more concrete evidences.
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Affiliation(s)
- Jean Moisés Ferreira
- Laboratório de Imunopatologia Keizo Asami - LIKA, Centro de Biociências, Universidade Federal de Pernambuco (UFPE) , Recife, Pernambuco, Brazil
| | - Leandro Douglas Silva Santos
- Laboratório de Biologia Molecular E Expressão Gênica - LABMEG, Universidade Federal de Alagoas (UFAL) - Campus Arapiraca , Arapiraca, Alagoas, Brazil
| | - Susana Paiva Oliveira
- Laboratório de Biologia Molecular E Expressão Gênica - LABMEG, Universidade Federal de Alagoas (UFAL) - Campus Arapiraca , Arapiraca, Alagoas, Brazil
| | - Bárbara Rayssa Correia Dos Santos
- Laboratório de Biologia Molecular E Expressão Gênica - LABMEG, Universidade Federal de Alagoas (UFAL) - Campus Arapiraca , Arapiraca, Alagoas, Brazil
| | - Ana Caroline Melo Dos Santos
- Laboratório de Biologia Molecular E Expressão Gênica - LABMEG, Universidade Federal de Alagoas (UFAL) - Campus Arapiraca , Arapiraca, Alagoas, Brazil
| | - Edilson Leite de Moura
- Laboratório de Biologia Molecular E Expressão Gênica - LABMEG, Universidade Federal de Alagoas (UFAL) - Campus Arapiraca , Arapiraca, Alagoas, Brazil
| | - Elaine Virginia Martins de Souza
- Laboratório de Biologia Molecular E Expressão Gênica - LABMEG, Universidade Federal de Alagoas (UFAL) - Campus Arapiraca , Arapiraca, Alagoas, Brazil
| | - José Luiz de Lima Filho
- Laboratório de Imunopatologia Keizo Asami - LIKA, Centro de Biociências, Universidade Federal de Pernambuco (UFPE) , Recife, Pernambuco, Brazil
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Sagert L, Hennig F, Thomas C, Tampé R. A loop structure allows TAPBPR to exert its dual function as MHC I chaperone and peptide editor. eLife 2020; 9:55326. [PMID: 32167472 PMCID: PMC7117912 DOI: 10.7554/elife.55326] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 03/12/2020] [Indexed: 01/18/2023] Open
Abstract
Adaptive immunity vitally depends on major histocompatibility complex class I (MHC I) molecules loaded with peptides. Selective loading of peptides onto MHC I, referred to as peptide editing, is catalyzed by tapasin and the tapasin-related TAPBPR. An important catalytic role has been ascribed to a structural feature in TAPBPR called the scoop loop, but the exact function of the scoop loop remains elusive. Here, using a reconstituted system of defined peptide-exchange components including human TAPBPR variants, we uncover a substantial contribution of the scoop loop to the stability of the MHC I-chaperone complex and to peptide editing. We reveal that the scoop loop of TAPBPR functions as an internal peptide surrogate in peptide-depleted environments stabilizing empty MHC I and impeding peptide rebinding. The scoop loop thereby acts as an additional selectivity filter in shaping the repertoire of presented peptide epitopes and the formation of a hierarchical immune response.
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Affiliation(s)
- Lina Sagert
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt, Germany
| | - Felix Hennig
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt, Germany
| | - Christoph Thomas
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt, Germany
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt, Germany
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Loll B, Rückert C, Uchanska-Ziegler B, Ziegler A. Conformational Plasticity of HLA-B27 Molecules Correlates Inversely With Efficiency of Negative T Cell Selection. Front Immunol 2020; 11:179. [PMID: 32117305 PMCID: PMC7027375 DOI: 10.3389/fimmu.2020.00179] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 01/23/2020] [Indexed: 01/07/2023] Open
Abstract
The development of autoimmune disorders is incompletely understood. Inefficient thymic T cell selection against self-peptides presented by major histocompatibility antigens (HLA in humans) may contribute to the emergence of auto-reactive effector cells, and molecular mimicry between foreign and self-peptides could promote T cell cross-reactivity. A pair of class I subtypes, HLA-B2705 and HLA-B2709, have previously been intensely studied, because they are distinguished from each other only by a single amino acid exchange at the floor of the peptide-binding groove, yet are differentially associated with the autoinflammatory disorder ankylosing spondylitis. Using X-ray crystallography in combination with ensemble refinement, we find that the non-disease-associated subtype HLA-B2709, when presenting the self-peptide pGR (RRRWHRWRL), exhibits elevated conformational dynamics, and the complex can also be recognized by T cells. Both features are not observed in case of the sequence-related self-peptide pVIPR (RRKWRRWHL) in complex with this subtype, and T cell cross-reactivity between pGR, pVIPR, and the viral peptide pLMP2 (RRRWRRLTV) is only rarely observed. The disease-associated subtype HLA-B2705, however, exhibits extensive conformational flexibility in case of the three complexes, all of which are also recognized by frequently occurring cross-reactive T cells. A comparison of the structural and dynamic properties of the six HLA-B27 complexes, together with their individual ability to interact with T cells, permits us to correlate the flexibility of HLA-B27 complexes with effector cell reactivity. The results suggest the existence of an inverse relationship between conformational plasticity of peptide-HLA-B27 complexes and the efficiency of negative selection of self-reactive cells within the thymus.
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Affiliation(s)
- Bernhard Loll
- Institut für Chemie und Biochemie, Abteilung Strukturbiochemie, Freie Universität Berlin, Berlin, Germany,*Correspondence: Bernhard Loll
| | - Christine Rückert
- Institut für Immungenetik, Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Berlin, Germany
| | - Barbara Uchanska-Ziegler
- Institut für Immungenetik, Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Berlin, Germany,Ziegler Biosolutions, Waldshut-Tiengen, Germany
| | - Andreas Ziegler
- Ziegler Biosolutions, Waldshut-Tiengen, Germany,Andreas Ziegler
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35
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Trowitzsch S, Tampé R. Multifunctional Chaperone and Quality Control Complexes in Adaptive Immunity. Annu Rev Biophys 2020; 49:135-161. [PMID: 32004089 DOI: 10.1146/annurev-biophys-121219-081643] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The fundamental process of adaptive immunity relies on the differentiation of self from nonself. Nucleated cells are continuously monitored by effector cells of the immune system, which police the peptide status presented via cell surface molecules. Recent integrative structural approaches have provided insights toward our understanding of how sophisticated cellular machineries shape such hierarchical immune surveillance. Biophysical and structural achievements were invaluable for defining the interconnection of many key factors during antigen processing and presentation, and helped to solve several conundrums that persisted for many years. In this review, we illuminate the numerous quality control machineries involved in different steps during the maturation of major histocompatibility complex class I (MHC I) proteins, from their synthesis in the endoplasmic reticulum to folding and trafficking via the secretory pathway, optimization of antigenic cargo, final release to the cell surface, and engagement with their cognate receptors on cytotoxic T lymphocytes.
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Affiliation(s)
- Simon Trowitzsch
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany; ,
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany; ,
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36
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Mariuzza RA, Agnihotri P, Orban J. The structural basis of T-cell receptor (TCR) activation: An enduring enigma. J Biol Chem 2020. [DOI: 10.1016/s0021-9258(17)49904-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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37
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Mariuzza RA, Agnihotri P, Orban J. The structural basis of T-cell receptor (TCR) activation: An enduring enigma. J Biol Chem 2019; 295:914-925. [PMID: 31848223 DOI: 10.1074/jbc.rev119.009411] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
T cells are critical for protective immune responses to pathogens and tumors. The T-cell receptor (TCR)-CD3 complex is composed of a diverse αβ TCR heterodimer noncovalently associated with the invariant CD3 dimers CD3ϵγ, CD3ϵδ, and CD3ζζ. The TCR mediates recognition of antigenic peptides bound to MHC molecules (pMHC), whereas the CD3 molecules transduce activation signals to the T cell. Whereas much is known about downstream T-cell signaling pathways, the mechanism whereby TCR engagement by pMHC is first communicated to the CD3 signaling apparatus, a process termed early T-cell activation, remains largely a mystery. In this review, we examine the molecular basis for TCR activation in light of the recently determined cryoEM structure of a complete TCR-CD3 complex. This structure provides an unprecedented opportunity to assess various signaling models that have been proposed for the TCR. We review evidence from single-molecule and structural studies for force-induced conformational changes in the TCR-CD3 complex, for dynamically-driven TCR allostery, and for pMHC-induced structural changes in the transmembrane and cytoplasmic regions of CD3 subunits. We identify major knowledge gaps that must be filled in order to arrive at a comprehensive model of TCR activation that explains, at the molecular level, how pMHC-specific information is transmitted across the T-cell membrane to initiate intracellular signaling. An in-depth understanding of this process will accelerate the rational design of immunotherapeutic agents targeting the TCR-CD3 complex.
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Affiliation(s)
- Roy A Mariuzza
- W. M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland 20850 .,Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742
| | - Pragati Agnihotri
- W. M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland 20850.,Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742
| | - John Orban
- W. M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, Maryland 20850 .,Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742
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38
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Molecular determinants of chaperone interactions on MHC-I for folding and antigen repertoire selection. Proc Natl Acad Sci U S A 2019; 116:25602-25613. [PMID: 31796585 PMCID: PMC6926029 DOI: 10.1073/pnas.1915562116] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The interplay between a highly polymorphic set of MHC-I alleles and molecular chaperones shapes the repertoire of peptide antigens displayed on the cell surface for T cell surveillance. Here, we demonstrate that the molecular chaperone TAP-binding protein related (TAPBPR) associates with a broad range of partially folded MHC-I species inside the cell. Bimolecular fluorescence complementation and deep mutational scanning reveal that TAPBPR recognition is polarized toward the α2 domain of the peptide-binding groove, and depends on the formation of a conserved MHC-I disulfide epitope in the α2 domain. Conversely, thermodynamic measurements of TAPBPR binding for a representative set of properly conformed, peptide-loaded molecules suggest a narrower MHC-I specificity range. Using solution NMR, we find that the extent of dynamics at "hotspot" surfaces confers TAPBPR recognition of a sparsely populated MHC-I state attained through a global conformational change. Consistently, restriction of MHC-I groove plasticity through the introduction of a disulfide bond between the α1/α2 helices abrogates TAPBPR binding, both in solution and on a cellular membrane, while intracellular binding is tolerant of many destabilizing MHC-I substitutions. Our data support parallel TAPBPR functions of 1) chaperoning unstable MHC-I molecules with broad allele-specificity at early stages of their folding process, and 2) editing the peptide cargo of properly conformed MHC-I molecules en route to the surface, which demonstrates a narrower specificity. Our results suggest that TAPBPR exploits localized structural adaptations, both near and distant to the peptide-binding groove, to selectively recognize discrete conformational states sampled by MHC-I alleles, toward editing the repertoire of displayed antigens.
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Ler GJM, Xu W, Mak JYW, Liu L, Bernhardt PV, Fairlie DP. Computer Modelling and Synthesis of Deoxy and Monohydroxy Analogues of a Ribitylaminouracil Bacterial Metabolite that Potently Activates Human T Cells. Chemistry 2019; 25:15594-15608. [DOI: 10.1002/chem.201903732] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 09/13/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Geraldine J. M. Ler
- Division of Chemistry and Structural Biology ARC Centre of Excellence in Advanced Molecular Imaging and Centre for Inflammation and Disease Research Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Weijun Xu
- Division of Chemistry and Structural Biology ARC Centre of Excellence in Advanced Molecular Imaging and Centre for Inflammation and Disease Research Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Jeffrey Y. W. Mak
- Division of Chemistry and Structural Biology ARC Centre of Excellence in Advanced Molecular Imaging and Centre for Inflammation and Disease Research Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Ligong Liu
- Division of Chemistry and Structural Biology ARC Centre of Excellence in Advanced Molecular Imaging and Centre for Inflammation and Disease Research Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Paul V. Bernhardt
- School of Chemistry and Molecular Biosciences The University of Queensland Brisbane QLD 4072 Australia
| | - David P. Fairlie
- Division of Chemistry and Structural Biology ARC Centre of Excellence in Advanced Molecular Imaging and Centre for Inflammation and Disease Research Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
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Karch R, Stocsits C, Ilieva N, Schreiner W. Intramolecular Domain Movements of Free and Bound pMHC and TCR Proteins: A Molecular Dynamics Simulation Study. Cells 2019; 8:cells8070720. [PMID: 31337065 PMCID: PMC6678086 DOI: 10.3390/cells8070720] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/02/2019] [Accepted: 07/12/2019] [Indexed: 12/11/2022] Open
Abstract
The interaction of antigenic peptides (p) and major histocompatibility complexes (pMHC) with T-cell receptors (TCR) is one of the most important steps during the immune response. Here we present a molecular dynamics simulation study of bound and unbound TCR and pMHC proteins of the LC13-HLA-B*44:05-pEEYLQAFTY complex to monitor differences in relative orientations and movements of domains between bound and unbound states of TCR-pMHC. We generated local coordinate systems for MHC α1- and MHC α2-helices and the variable T-cell receptor regions TCR Vα and TCR Vβ and monitored changes in the distances and mutual orientations of these domains. In comparison to unbound states, we found decreased inter-domain movements in the simulations of bound states. Moreover, increased conformational flexibility was observed for the MHC α2-helix, the peptide, and for the complementary determining regions of the TCR in TCR-unbound states as compared to TCR-bound states.
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Affiliation(s)
- Rudolf Karch
- Section of Biosimulation and Bioinformatics, Center for Medical Statistics, Informatics and Intelligent Systems (CeMSIIS), Medical University of Vienna, Spitalgasse 23, A-1090 Vienna, Austria
| | - Claudia Stocsits
- Section of Biosimulation and Bioinformatics, Center for Medical Statistics, Informatics and Intelligent Systems (CeMSIIS), Medical University of Vienna, Spitalgasse 23, A-1090 Vienna, Austria
| | - Nevena Ilieva
- Institute of Information and Communication Technologies (IICT), Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Block 25A, 1113 Sofia, Bulgaria
- CERN-TH, Esplanade des Particules 1, 1211 Geneva, Switzerland
| | - Wolfgang Schreiner
- Section of Biosimulation and Bioinformatics, Center for Medical Statistics, Informatics and Intelligent Systems (CeMSIIS), Medical University of Vienna, Spitalgasse 23, A-1090 Vienna, Austria.
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41
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Salutari I, Martin R, Caflisch A. The 3A6-TCR/superagonist/HLA-DR2a complex shows similar interface and reduced flexibility compared to the complex with self-peptide. Proteins 2019; 88:31-46. [PMID: 31237711 DOI: 10.1002/prot.25764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 06/10/2019] [Accepted: 06/15/2019] [Indexed: 11/11/2022]
Abstract
T-cell receptor (TCR) recognition of the myelin basic protein (MBP) peptide presented by major histocompatibility complex (MHC) protein HLA-DR2a, one of the MHC class II alleles associated with multiple sclerosis, is highly variable. Interactions in the trimolecular complex between the TCR of the MBP83-99-specific T cell clone 3A6 with the MBP-peptide/HLA-DR2a (abbreviated TCR/pMHC) lead to substantially different proliferative responses when comparing the wild-type decapeptide MBP90-99 and a superagonist peptide, which differs mainly in the residues that point toward the TCR. Here, we investigate the influence of the peptide sequence on the interface and intrinsic plasticity of the TCR/pMHC trimolecular and pMHC bimolecular complexes by molecular dynamics simulations. The intermolecular contacts at the TCR/pMHC interface are similar for the complexes with the superagonist and the MBP self-peptide. The orientation angle between TCR and pMHC fluctuates less in the complex with the superagonist peptide. Thus, the higher structural stability of the TCR/pMHC tripartite complex with the superagonist peptide, rather than a major difference in binding mode with respect to the self-peptide, seems to be responsible for the stronger proliferative response.
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Affiliation(s)
- Ilaria Salutari
- Department of Biochemistry, University of Zürich, Zürich, Switzerland
| | - Roland Martin
- Department of Neurology, University Hospital Zürich, Zürich, Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zürich, Zürich, Switzerland
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42
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Thomas C, Tampé R. MHC I chaperone complexes shaping immunity. Curr Opin Immunol 2019; 58:9-15. [DOI: 10.1016/j.coi.2019.01.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 12/16/2018] [Accepted: 01/04/2019] [Indexed: 01/21/2023]
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43
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Natarajan K, Jiang J, Margulies DH. Structural aspects of chaperone-mediated peptide loading in the MHC-I antigen presentation pathway. Crit Rev Biochem Mol Biol 2019; 54:164-173. [PMID: 31084439 DOI: 10.1080/10409238.2019.1610352] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Recognition of foreign and dysregulated antigens by the cellular innate and adaptive immune systems is in large part dependent on the cell surface display of peptide/MHC (pMHC) complexes. The formation of such complexes requires the generation of antigenic peptides, proper folding of MHC molecules, loading of peptides onto MHC molecules, glycosylation, and transport to the plasma membrane. This complex series of biosynthetic, biochemical, and cell biological reactions is known as "antigen processing and presentation". Here, we summarize recent work, focused on the structural and functional characterization of the key MHC-I-dedicated chaperones, tapasin, and TAPBPR. The mechanisms reflect the ability of conformationally flexible molecules to adapt to their ligands, and are comparable to similar processes that are exploited in peptide antigen loading in the MHC-II pathway.
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Affiliation(s)
- Kannan Natarajan
- a Molecular Biology Section, Laboratory of Immune System Biology , National Institute of Allergy and Infectious Diseases, National Institutes of Health , Bethesda , MD , USA
| | - Jiansheng Jiang
- a Molecular Biology Section, Laboratory of Immune System Biology , National Institute of Allergy and Infectious Diseases, National Institutes of Health , Bethesda , MD , USA
| | - David H Margulies
- a Molecular Biology Section, Laboratory of Immune System Biology , National Institute of Allergy and Infectious Diseases, National Institutes of Health , Bethesda , MD , USA
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44
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Jiang J, Natarajan K, Margulies DH. MHC Molecules, T cell Receptors, Natural Killer Cell Receptors, and Viral Immunoevasins-Key Elements of Adaptive and Innate Immunity. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1172:21-62. [PMID: 31628650 DOI: 10.1007/978-981-13-9367-9_2] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Molecules encoded by the Major Histocompatibility Complex (MHC) bind self or foreign peptides and display these at the cell surface for recognition by receptors on T lymphocytes (designated T cell receptors-TCR) or on natural killer (NK) cells. These ligand/receptor interactions govern T cell and NK cell development as well as activation of T memory and effector cells. Such cells participate in immunological processes that regulate immunity to various pathogens, resistance and susceptibility to cancer, and autoimmunity. The past few decades have witnessed the accumulation of a huge knowledge base of the molecular structures of MHC molecules bound to numerous peptides, of TCRs with specificity for many different peptide/MHC (pMHC) complexes, of NK cell receptors (NKR), of MHC-like viral immunoevasins, and of pMHC/TCR and pMHC/NKR complexes. This chapter reviews the structural principles that govern peptide/MHC (pMHC), pMHC/TCR, and pMHC/NKR interactions, for both MHC class I (MHC-I) and MHC class II (MHC-II) molecules. In addition, we discuss the structures of several representative MHC-like molecules. These include host molecules that have distinct biological functions, as well as virus-encoded molecules that contribute to the evasion of the immune response.
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Affiliation(s)
- Jiansheng Jiang
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bldg. 10, Room 11D07, 10 Center Drive, Bethesda, MD, 20892-1892, USA.
| | - Kannan Natarajan
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bldg. 10, Room 11D07, 10 Center Drive, Bethesda, MD, 20892-1892, USA
| | - David H Margulies
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bldg. 10, Room 11D12, 10 Center Drive, Bethesda, MD, 20892-1892, USA
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45
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Buckle AM, Borg NA. Integrating Experiment and Theory to Understand TCR-pMHC Dynamics. Front Immunol 2018; 9:2898. [PMID: 30581442 PMCID: PMC6293202 DOI: 10.3389/fimmu.2018.02898] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 11/26/2018] [Indexed: 11/13/2022] Open
Abstract
The conformational dynamism of proteins is well established. Rather than having a single structure, proteins are more accurately described as a conformational ensemble that exists across a rugged energy landscape, where different conformational sub-states interconvert. The interaction between αβ T cell receptors (TCR) and cognate peptide-MHC (pMHC) is no exception, and is a dynamic process that involves substantial conformational change. This review focuses on technological advances that have begun to establish the role of conformational dynamics and dynamic allostery in TCR recognition of the pMHC and the early stages of signaling. We discuss how the marriage of molecular dynamics (MD) simulations with experimental techniques provides us with new ways to dissect and interpret the process of TCR ligation. Notably, application of simulation techniques lags behind other fields, but is predicted to make substantial contributions. Finally, we highlight integrated approaches that are being used to shed light on some of the key outstanding questions in the early events leading to TCR signaling.
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Affiliation(s)
- Ashley M Buckle
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Natalie A Borg
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
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