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Abbate MF, Dupic T, Vigne E, Shahsavarian MA, Walczak AM, Mora T. Computational detection of antigen-specific B cell receptors following immunization. Proc Natl Acad Sci U S A 2024; 121:e2401058121. [PMID: 39163333 PMCID: PMC11363332 DOI: 10.1073/pnas.2401058121] [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: 01/16/2024] [Accepted: 07/10/2024] [Indexed: 08/22/2024] Open
Abstract
B cell receptors (BCRs) play a crucial role in recognizing and fighting foreign antigens. High-throughput sequencing enables in-depth sampling of the BCRs repertoire after immunization. However, only a minor fraction of BCRs actively participate in any given infection. To what extent can we accurately identify antigen-specific sequences directly from BCRs repertoires? We present a computational method grounded on sequence similarity, aimed at identifying statistically significant responsive BCRs. This method leverages well-known characteristics of affinity maturation and expected diversity. We validate its effectiveness using longitudinally sampled human immune repertoire data following influenza vaccination and SARS-CoV-2 infections. We show that different lineages converge to the same responding Complementarity Determining Region 3, demonstrating convergent selection within an individual. The outcomes of this method hold promise for application in vaccine development, personalized medicine, and antibody-derived therapeutics.
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Affiliation(s)
- Maria Francesca Abbate
- Laboratoire de physique de l’École normale supérieure, CNRS, Paris Sciences et Lettres University, Sorbonne Université, and Université Paris-Cité, Paris75005, France
- Large Molecule Research, Sanofi, Vitry-sur-Seine94 400, France
| | - Thomas Dupic
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA02138
| | | | | | - Aleksandra M. Walczak
- Laboratoire de physique de l’École normale supérieure, CNRS, Paris Sciences et Lettres University, Sorbonne Université, and Université Paris-Cité, Paris75005, France
| | - Thierry Mora
- Laboratoire de physique de l’École normale supérieure, CNRS, Paris Sciences et Lettres University, Sorbonne Université, and Université Paris-Cité, Paris75005, France
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Umeda M, Kojima K, Michitsuji T, Tsuji Y, Shimizu T, Fukui S, Sumiyoshi R, Koga T, Kawashiri SY, Naoki I, Iagawa T, Tamai M, Origuchi T, Furuyama M, Tsuboi M, Matsuoka N, Okada A, Aramaki T, Kawakami A. Successful treatment of systemic lupus erythematosus with residual disease activity by switching from belimumab to anifrolumab. Mod Rheumatol 2024:roae038. [PMID: 38756072 DOI: 10.1093/mr/roae038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 04/23/2024] [Indexed: 05/18/2024]
Affiliation(s)
- Masataka Umeda
- Department of Immunology and Rheumatology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
- Research Unit for Preventive and Clinical Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Kanako Kojima
- Department of Immunology and Rheumatology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Toru Michitsuji
- Department of Immunology and Rheumatology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Yoshika Tsuji
- Department of Immunology and Rheumatology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Toshimasa Shimizu
- Department of Immunology and Rheumatology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Shoichi Fukui
- Department of Immunology and Rheumatology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Remi Sumiyoshi
- Department of Immunology and Rheumatology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Tomohiro Koga
- Department of Immunology and Rheumatology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Shin-Ya Kawashiri
- Department of Immunology and Rheumatology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Iwamoto Naoki
- Department of Immunology and Rheumatology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Takashi Iagawa
- Department of Immunology and Rheumatology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Mami Tamai
- Department of Immunology and Rheumatology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Tomoki Origuchi
- Department of Immunology and Rheumatology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Masako Furuyama
- Department of Rheumatology, Nagasaki Kita Hospital, Nagasaki, Japan
| | | | - Naoki Matsuoka
- Nagasaki Medical Hospital of Rheumatology, Nagasaki, Japan
| | - Akitomo Okada
- Department of Rheumatology, National Hospital Organization Nagasaki Medical Center, Omura, Japan
| | | | - Atsushi Kawakami
- Department of Immunology and Rheumatology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
- Research Unit for Preventive and Clinical Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
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3
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Mahla RS. Bone marrow B cell developmental aberrations and systemic lupus erythematosus: comment on the article by Dong et al. Arthritis Rheumatol 2024; 76:813-814. [PMID: 38115794 DOI: 10.1002/art.42786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 12/13/2023] [Indexed: 12/21/2023]
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Dong C, Chen Z, Zhang X, Gu Z. Reply. Arthritis Rheumatol 2024; 76:814-815. [PMID: 38146093 DOI: 10.1002/art.42787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 12/27/2023]
Affiliation(s)
- Chen Dong
- Department of Rheumatology, Research Center of Clinical Immunology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong university, Nantong, China
| | - Zechuan Chen
- The Center for Microbes, Development and Health, Key Laboratory of Molecular Virology & Immunology, Shanghai Institute of Immunity and Immunology, Chinese Academy of Sciences/University of Chinese Academy of Sciences, Shanghai, China
| | - Xiaoming Zhang
- The Center for Microbes, Development and Health, Key Laboratory of Molecular Virology & Immunology, Shanghai Institute of Immunity and Immunology, Chinese Academy of Sciences/University of Chinese Academy of Sciences, Shanghai, China
| | - Zhifeng Gu
- Department of Rheumatology, Research Center of Clinical Immunology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong university, Nantong, China
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He Y, Vinuesa CG. Germinal center versus extrafollicular responses in systemic autoimmunity: Who turns the blade on self? Adv Immunol 2024; 162:109-133. [PMID: 38866437 PMCID: PMC7616122 DOI: 10.1016/bs.ai.2024.02.002] [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] [Indexed: 06/14/2024]
Abstract
Spontaneously formed germinal centers (GCs) have been reported in most mouse models of human autoimmune disease and autoimmune patients, and have long been considered a source of somatically-mutated and thus high affinity autoantibodies, but their role in autoimmunity is becoming increasingly controversial, particularly in the context of systemic autoimmune diseases like lupus. On the one hand, there is good evidence that some pathogenic lupus antibodies have acquired somatic mutations that increase affinity for self-antigens. On the other hand, recent studies that have genetically prevented GC formation, suggest that GCs are dispensable for systemic autoimmunity, pointing instead to pathogenic extrafollicular (EF) B-cell responses. Furthermore, several lines of evidence suggest germinal centers may in fact be somewhat protective in the context of autoimmunity. Here we review how some of the conflicting evidence arose, and current views on the role of GCs in autoimmunity, outlining mechanisms by which GC may eliminate self-reactivity. We also discuss recent advances in understanding extrafollicular B cell subsets that participate in autoimmunity.
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Affiliation(s)
- Yuke He
- China-Australia Centre for Personalised Immunology, Department of Rheumatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Carola G Vinuesa
- China-Australia Centre for Personalised Immunology, Department of Rheumatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China; Francis Crick Institute, London, United Kingdom.
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Wang Q, Feng D, Jia S, Lu Q, Zhao M. B-Cell Receptor Repertoire: Recent Advances in Autoimmune Diseases. Clin Rev Allergy Immunol 2024; 66:76-98. [PMID: 38459209 DOI: 10.1007/s12016-024-08984-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2024] [Indexed: 03/10/2024]
Abstract
In the field of contemporary medicine, autoimmune diseases (AIDs) are a prevalent and debilitating group of illnesses. However, they present extensive and profound challenges in terms of etiology, pathogenesis, and treatment. A major reason for this is the elusive pathophysiological mechanisms driving disease onset. Increasing evidence suggests the indispensable role of B cells in the pathogenesis of autoimmune diseases. Interestingly, B-cell receptor (BCR) repertoires in autoimmune diseases display a distinct skewing that can provide insights into disease pathogenesis. Over the past few years, advances in high-throughput sequencing have provided powerful tools for analyzing B-cell repertoire to understand the mechanisms during the period of B-cell immune response. In this paper, we have provided an overview of the mechanisms and analytical methods for generating BCR repertoire diversity and summarize the latest research progress on BCR repertoire in autoimmune diseases, including systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), primary Sjögren's syndrome (pSS), multiple sclerosis (MS), and type 1 diabetes (T1D). Overall, B-cell repertoire analysis is a potent tool to understand the involvement of B cells in autoimmune diseases, facilitating the creation of innovative therapeutic strategies targeting specific B-cell clones or subsets.
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Affiliation(s)
- Qian Wang
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, the Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Clinical Medical Research Center of Major Skin Diseases and Skin Health of Hunan Province, Changsha, China
| | - Delong Feng
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, the Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Clinical Medical Research Center of Major Skin Diseases and Skin Health of Hunan Province, Changsha, China
| | - Sujie Jia
- Department of Pharmacy, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, 210042, China
| | - Qianjin Lu
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, 210042, China.
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences, Nanjing, China.
| | - Ming Zhao
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, the Second Xiangya Hospital of Central South University, Changsha, Hunan, China.
- Clinical Medical Research Center of Major Skin Diseases and Skin Health of Hunan Province, Changsha, China.
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, 210042, China.
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences, Nanjing, China.
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Yuuki H, Itamiya T, Nagafuchi Y, Ota M, Fujio K. B cell receptor repertoire abnormalities in autoimmune disease. Front Immunol 2024; 15:1326823. [PMID: 38361948 PMCID: PMC10867955 DOI: 10.3389/fimmu.2024.1326823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 01/15/2024] [Indexed: 02/17/2024] Open
Abstract
B cells play a crucial role in the immune response and contribute to various autoimmune diseases. Recent studies have revealed abnormalities in the B cell receptor (BCR) repertoire of patients with autoimmune diseases, with distinct features observed among different diseases and B cell subsets. Classically, BCR repertoire was used as an identifier of distinct antigen-specific clonotypes, but the recent advancement of analyzing large-scale repertoire has enabled us to use it as a tool for characterizing cellular biology. In this review, we provide an overview of the BCR repertoire in autoimmune diseases incorporating insights from our latest research findings. In systemic lupus erythematosus (SLE), we observed a significant skew in the usage of VDJ genes, particularly in CD27+IgD+ unswitched memory B cells and plasmablasts. Notably, autoreactive clones within unswitched memory B cells were found to be increased and strongly associated with disease activity, underscoring the clinical significance of this subset. Similarly, various abnormalities in the BCR repertoire have been reported in other autoimmune diseases such as rheumatoid arthritis. Thus, BCR repertoire analysis holds potential for enhancing our understanding of the underlying mechanisms involved in autoimmune diseases. Moreover, it has the potential to predict treatment effects and identify therapeutic targets in autoimmune diseases.
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Affiliation(s)
- Hayato Yuuki
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takahiro Itamiya
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yasuo Nagafuchi
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Mineto Ota
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Keishi Fujio
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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Budeus B, Kibler A, Küppers R. Human IgM-expressing memory B cells. Front Immunol 2023; 14:1308378. [PMID: 38143767 PMCID: PMC10748387 DOI: 10.3389/fimmu.2023.1308378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 11/27/2023] [Indexed: 12/26/2023] Open
Abstract
A hallmark of T cell dependent (TD) humoral immune responses is the generation of long-lived memory B cells. The generation of these cells occurs primarily in the germinal center (GC) reaction, where antigen-activated B cells undergo affinity maturation as a major consequence of the combined processes of proliferation, somatic hypermutation of their immunoglobulin V (IgV) region genes, and selection for improved affinity of their B-cell antigen receptors. As many B cells also undergo class-switching to IgG or IgA in these TD responses, there was traditionally a focus on class-switched memory B cells in both murine and human studies on memory B cells. However, it has become clear that there is also a large subset of IgM-expressing memory B cells, which have important phenotypic and functional similarities but also differences to class-switched memory B cells. There is an ongoing discussion about the origin of distinct subsets of human IgM+ B cells with somatically mutated IgV genes. We argue here that the vast majority of human IgM-expressing B cells with somatically mutated IgV genes in adults is indeed derived from GC reactions, even though a generation of some mostly lowly mutated IgM+ B cells from other differentiation pathways, mainly in early life, may exist.
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Affiliation(s)
| | | | - Ralf Küppers
- Institute of Cell Biology (Cancer Research), Medical Faculty, University of Duisburg–Essen, Essen, Germany
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Atisha-Fregoso Y, Diamond B. Decoding B cell receptors in autoimmune diseases. Ann Rheum Dis 2023; 82:1369-1370. [PMID: 37591659 DOI: 10.1136/ard-2023-224779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 08/03/2023] [Indexed: 08/19/2023]
Affiliation(s)
- Yemil Atisha-Fregoso
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research, Manhasset, New York, USA
| | - Betty Diamond
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research, Manhasset, New York, USA
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