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Yoon B, Kim H, Jung SW, Park J. Single-cell lineage tracing approaches to track kidney cell development and maintenance. Kidney Int 2024; 105:1186-1199. [PMID: 38554991 DOI: 10.1016/j.kint.2024.01.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 12/06/2023] [Accepted: 01/09/2024] [Indexed: 04/02/2024]
Abstract
The kidney is a complex organ consisting of various cell types. Previous studies have aimed to elucidate the cellular relationships among these cell types in developing and mature kidneys using Cre-loxP-based lineage tracing. However, this methodology falls short of fully capturing the heterogeneous nature of the kidney, making it less than ideal for comprehensively tracing cellular progression during kidney development and maintenance. Recent technological advancements in single-cell genomics have revolutionized lineage tracing methods. Single-cell lineage tracing enables the simultaneous tracing of multiple cell types within complex tissues and their transcriptomic profiles, thereby allowing the reconstruction of their lineage tree with cell state information. Although single-cell lineage tracing has been successfully applied to investigate cellular hierarchies in various organs and tissues, its application in kidney research is currently lacking. This review comprehensively consolidates the single-cell lineage tracing methods, divided into 4 categories (clustered regularly interspaced short palindromic repeat [CRISPR]/CRISPR-associated protein 9 [Cas9]-based, transposon-based, Polylox-based, and native barcoding methods), and outlines their technical advantages and disadvantages. Furthermore, we propose potential future research topics in kidney research that could benefit from single-cell lineage tracing and suggest suitable technical strategies to apply to these topics.
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Affiliation(s)
- Baul Yoon
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Hayoung Kim
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Su Woong Jung
- Division of Nephrology, Department of Internal Medicine, College of Medicine, Kyung Hee University, Seoul, Republic of Korea; Division of Nephrology, Department of Internal Medicine, Kyung Hee University Hospital at Gangdong, Seoul, Republic of Korea.
| | - Jihwan Park
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea.
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2
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Irac SE, Soon MSF, Borcherding N, Tuong ZK. Single-cell immune repertoire analysis. Nat Methods 2024; 21:777-792. [PMID: 38637691 DOI: 10.1038/s41592-024-02243-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 03/12/2024] [Indexed: 04/20/2024]
Abstract
Single-cell T cell and B cell antigen receptor-sequencing data analysis can potentially perform in-depth assessments of adaptive immune cells that inform on understanding immune cell development to tracking clonal expansion in disease and therapy. However, it has been extremely challenging to analyze and interpret T cells and B cells and their adaptive immune receptor repertoires at the single-cell level due to not only the complexity of the data but also the underlying biology. In this Review, we delve into the computational breakthroughs that have transformed the analysis of single-cell T cell and B cell antigen receptor-sequencing data.
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Affiliation(s)
- Sergio E Irac
- Cancer Immunoregulation and Immunotherapy, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Megan Sioe Fei Soon
- Ian Frazer Centre for Children's Immunotherapy Research, Child Health Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Nicholas Borcherding
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
- Omniscope, Palo Alto, CA, USA
| | - Zewen Kelvin Tuong
- Ian Frazer Centre for Children's Immunotherapy Research, Child Health Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia.
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia.
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3
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He S, Liu SQ, Teng XY, He JY, Liu Y, Gao JH, Wu Y, Hu W, Dong ZJ, Bei JX, Xu JH. Comparative single-cell RNA sequencing analysis of immune response to inactivated vaccine and natural SARS-CoV-2 infection. J Med Virol 2024; 96:e29577. [PMID: 38572977 DOI: 10.1002/jmv.29577] [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: 10/27/2023] [Revised: 03/02/2024] [Accepted: 03/22/2024] [Indexed: 04/05/2024]
Abstract
Uncovering the immune response to an inactivated SARS-CoV-2 vaccine (In-Vac) and natural infection is crucial for comprehending COVID-19 immunology. Here we conducted an integrated analysis of single-cell RNA sequencing (scRNA-seq) data from serial peripheral blood mononuclear cell (PBMC) samples derived from 12 individuals receiving In-Vac compared with those from COVID-19 patients. Our study reveals that In-Vac induces subtle immunological changes in PBMC, including cell proportions and transcriptomes, compared with profound changes for natural infection. In-Vac modestly upregulates IFN-α but downregulates NF-κB pathways, while natural infection triggers hyperactive IFN-α and NF-κB pathways. Both In-Vac and natural infection alter T/B cell receptor repertoires, but COVID-19 has more significant change in preferential VJ gene, indicating a vigorous immune response. Our study reveals distinct patterns of cellular communications, including a selective activation of IL-15RA/IL-15 receptor pathway after In-Vac boost, suggesting its potential role in enhancing In-Vac-induced immunity. Collectively, our study illuminates multifaceted immune responses to In-Vac and natural infection, providing insights for optimizing SARS-CoV-2 vaccine efficacy.
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Affiliation(s)
- Shuai He
- Medical Laboratory Center, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Shu-Qiang Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xiang-Yun Teng
- Medical Laboratory Center, Maoming Hospital of Guangzhou University of Chinese Medicine, Maoming, China
| | - Jin-Yong He
- Medical Laboratory Center, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, China
| | - Yang Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jia-Hui Gao
- Medical Laboratory Center, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, China
| | - Yue Wu
- Medical Laboratory Center, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, China
| | - Wei Hu
- Medical Laboratory Center, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, China
| | - Zhong-Jun Dong
- School of Medicine and Institute for Immunology, Tsinghua University, Beijing, China
| | - Jin-Xin Bei
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jian-Hua Xu
- Medical Laboratory Center, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, China
- Medical Laboratory Center, Maoming Hospital of Guangzhou University of Chinese Medicine, Maoming, China
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4
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Xiao J, Luo Y, Li Y, Yao X. The characteristics of BCR-CDR3 repertoire in COVID-19 patients and SARS-CoV-2 vaccinated volunteers. J Med Virol 2024; 96:e29488. [PMID: 38415507 DOI: 10.1002/jmv.29488] [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: 11/04/2023] [Revised: 02/02/2024] [Accepted: 02/13/2024] [Indexed: 02/29/2024]
Abstract
The global COVID-19 pandemic has caused more than 1 billion infections, and numerous SARS-CoV-2 vaccines developed rapidly have been administered over 10 billion doses. The world is continuously concerned about the cytokine storms induced by the interaction between SARS-CoV-2 and host, long COVID, breakthrough infections postvaccination, and the impact of SARS-CoV-2 variants. BCR-CDR3 repertoire serves as a molecular target for monitoring the antiviral response "trace" of B cells, evaluating the effects, mechanisms, and memory abilities of individual responses to B cells, and has been successfully applied in analyzing the infection mechanisms, vaccine improvement, and neutralizing antibodies preparation of influenza virus, HIV, MERS, and Ebola virus. Based on research on BCR-CDR3 repertoire of COVID-19 patients and volunteers who received different SARS-CoV-2 vaccines in multiple laboratories worldwide, we focus on analyzing the characteristics and changes of BCR-CDR3 repertoire, such as diversity, clonality, V&J genes usage and pairing, SHM, CSR, shared CDR3 clones, as well as the summary on BCR sequences targeting virus-specific epitopes in the preparation and application research of SARS-CoV-2 potential therapeutic monoclonal antibodies. This review provides comparative data and new research schemes for studying the possible mechanisms of differences in B cell response between SARS-CoV-2 infection or vaccination, and supplies a foundation for improving vaccines after SARS-CoV-2 mutations and potential antibody therapy for infected individuals.
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Affiliation(s)
- Jiaping Xiao
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, Guizhou, China
- Fushun People's Hospital, Zigong, Sichuan, China
| | - Yan Luo
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, Guizhou, China
| | - Yangyang Li
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, Guizhou, China
| | - Xinsheng Yao
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, Guizhou, China
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5
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Tranter E, Frentsch M, Hütter-Krönke ML, Vuong GL, Busch D, Loyal L, Henze L, Rosnev S, Blau IW, Thiel A, Beule D, Bullinger L, Obermayer B, Na IK. Comparable CD8 + T-cell responses to SARS-CoV-2 vaccination in single-cell transcriptomics of recently allogeneic transplanted patients and healthy individuals. J Med Virol 2024; 96:e29539. [PMID: 38516755 DOI: 10.1002/jmv.29539] [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: 11/29/2023] [Revised: 03/05/2024] [Accepted: 03/06/2024] [Indexed: 03/23/2024]
Abstract
Despite extensive research on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccination responses in healthy individuals, there is comparatively little known beyond antibody titers and T-cell responses in the vulnerable cohort of patients after allogeneic hematopoietic stem cell transplantation (ASCT). In this study, we assessed the serological response and performed longitudinal multimodal analyses including T-cell functionality and single-cell RNA sequencing combined with T cell receptor (TCR)/B cell receptor (BCR) profiling in the context of BNT162b2 vaccination in ASCT patients. In addition, these data were compared to publicly available data sets of healthy vaccinees. Protective antibody titers were achieved in 40% of patients. We identified a distorted B- and T-cell distribution, a reduced TCR diversity, and increased levels of exhaustion marker expression as possible causes for the poorer vaccine response rates in ASCT patients. Immunoglobulin heavy chain gene rearrangement after vaccination proved to be highly variable in ASCT patients. Changes in TCRα and TCRβ gene rearrangement after vaccination differed from patterns observed in healthy vaccinees. Crucially, ASCT patients elicited comparable proportions of SARS-CoV-2 vaccine-induced (VI) CD8+ T-cells, characterized by a distinct gene expression pattern that is associated with SARS-CoV-2 specificity in healthy individuals. Our study underlines the impaired immune system and thus the lower vaccine response rates in ASCT patients. However, since protective vaccine responses and VI CD8+ T-cells can be induced in part of ASCT patients, our data advocate early posttransplant vaccination due to the high risk of infection in this vulnerable group.
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Affiliation(s)
- Eva Tranter
- Medizinische Klinik m. S. Hämatologie, Onkologie und Tumorimmunologie, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Marco Frentsch
- Medizinische Klinik m. S. Hämatologie, Onkologie und Tumorimmunologie, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Charité-Universitätsmedizin Berlin, Berlin, Germany
- BIH Center for Regenerative Therapies, Berlin Institute of Health at Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Marie Luise Hütter-Krönke
- Medizinische Klinik m. S. Hämatologie, Onkologie und Tumorimmunologie, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Giang Lam Vuong
- Medizinische Klinik m. S. Hämatologie, Onkologie und Tumorimmunologie, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - David Busch
- Medizinische Klinik m. S. Hämatologie, Onkologie und Tumorimmunologie, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Lucie Loyal
- Si-M/"Der Simulierte Mensch", A Science Framework of Technische Universität Berlin and Charité-Universitätsmedizin Berlin, Berlin, Germany
- BIH Center of Immunomics-Regenerative Immunology and Aging, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Larissa Henze
- Si-M/"Der Simulierte Mensch", A Science Framework of Technische Universität Berlin and Charité-Universitätsmedizin Berlin, Berlin, Germany
- BIH Center of Immunomics-Regenerative Immunology and Aging, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Stanislav Rosnev
- Medizinische Klinik m. S. Hämatologie, Onkologie und Tumorimmunologie, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Igor-Wolfgang Blau
- Medizinische Klinik m. S. Hämatologie, Onkologie und Tumorimmunologie, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Andreas Thiel
- Si-M/"Der Simulierte Mensch", A Science Framework of Technische Universität Berlin and Charité-Universitätsmedizin Berlin, Berlin, Germany
- BIH Center of Immunomics-Regenerative Immunology and Aging, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Dieter Beule
- Core Unit Bioinformatics, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Lars Bullinger
- Medizinische Klinik m. S. Hämatologie, Onkologie und Tumorimmunologie, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Charité-Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charité Universitätsmedizin Berlin, Berlin, Germany
- ECRC Experimental and Clinical Research Center, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Benedikt Obermayer
- Core Unit Bioinformatics, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Il-Kang Na
- Medizinische Klinik m. S. Hämatologie, Onkologie und Tumorimmunologie, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Charité-Universitätsmedizin Berlin, Berlin, Germany
- BIH Center for Regenerative Therapies, Berlin Institute of Health at Charité Universitätsmedizin Berlin, Berlin, Germany
- Si-M/"Der Simulierte Mensch", A Science Framework of Technische Universität Berlin and Charité-Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charité Universitätsmedizin Berlin, Berlin, Germany
- ECRC Experimental and Clinical Research Center, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Charité Universitätsmedizin Berlin, Berlin, Germany
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6
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Li F, Gragert L, Giovanni Biagini D, Patel JK, Kobashigawa JA, Trück J, Rodriguez O, Watson CT, Gibb DR, Zhang X, Kransdorf EP. IgM marks persistent IgG anti-human leukocyte antigen antibodies in highly sensitized heart transplant patients. J Heart Lung Transplant 2024; 43:314-323. [PMID: 37793509 DOI: 10.1016/j.healun.2023.09.022] [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: 02/05/2023] [Revised: 09/25/2023] [Accepted: 09/27/2023] [Indexed: 10/06/2023] Open
Abstract
BACKGROUND Sensitization to human leukocyte antigens (HLA) is a persistent problem in heart transplant (HT) candidates. We sought to characterize the anti-HLA antibody and circulating B cell repertoire in a cohort of highly sensitized HT candidates. METHODS We assessed immunoglobulin G (IgG) and immunoglobulin M (IgM) anti-HLA antibodies using Luminex single antigen bead assays in a cohort of 11 highly sensitized (HS; calculated panel reactive antibody ≥ 90%) and 3 mildly sensitized (MS) candidates. We also performed B cell receptor repertoire sequencing (BCRseq) in HS candidates and 33 non-candidate controls. HLA antibody strength was measured by mean fluorescence intensity (MFI). RESULTS We found that IgM anti-HLA antibodies were present in all HS candidates, but with a lower breadth and strength as compared to IgG. When anti-HLA IgG specificities intersected with IgM, binding strength was higher. In contrast, there were IgM but no intersecting IgG specificities for the MS group. In four candidates in the HS group, IgG anti-HLA antibodies decreased in both breadth and strength after HT, but the decrease in strength was smaller if the IgG possessed a specificity that intersected with pre-transplant IgM. BCRseq revealed larger B cell clonotypes in HS candidates but similar diversity as compared to controls. CONCLUSIONS IgM marks IgG anti-HLA antibodies with higher strength before HT and persistence after HT. The presence of IgM intersecting IgG for an anti-HLA specificity may be a useful approach to determine which donor HLA should be avoided for a sensitized candidate.
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Affiliation(s)
- Fang Li
- Comprehensive Transplant Center, Cedars-Sinai Medical Center, Los Angeles, California
| | - Loren Gragert
- Department of Pathology, Tulane University School of Medicine, New Orleans, Louisiana
| | - D Giovanni Biagini
- Department of Pathology, Tulane University School of Medicine, New Orleans, Louisiana
| | - Jignesh K Patel
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Jon A Kobashigawa
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Johannes Trück
- Division of Immunology, University Children's Hospital and Children's Research Center, University of Zurich (UZH), Zurich, Switzerland
| | - Oscar Rodriguez
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, Kentucky
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, Kentucky
| | - David R Gibb
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Xiaohai Zhang
- Comprehensive Transplant Center, Cedars-Sinai Medical Center, Los Angeles, California
| | - Evan P Kransdorf
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California.
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7
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Gabernet G, Marquez S, Bjornson R, Peltzer A, Meng H, Aron E, Lee NY, Jensen C, Ladd D, Hanssen F, Heumos S, Yaari G, Kowarik MC, Nahnsen S, Kleinstein SH. nf-core/airrflow: an adaptive immune receptor repertoire analysis workflow employing the Immcantation framework. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.18.576147. [PMID: 38293151 PMCID: PMC10827190 DOI: 10.1101/2024.01.18.576147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) is a valuable experimental tool to study the immune state in health and following immune challenges such as infectious diseases, (auto)immune diseases, and cancer. Several tools have been developed to reconstruct B cell and T cell receptor sequences from AIRR-seq data and infer B and T cell clonal relationships. However, currently available tools offer limited parallelization across samples, scalability or portability to high-performance computing infrastructures. To address this need, we developed nf-core/airrflow, an end-to-end bulk and single-cell AIRR-seq processing workflow which integrates the Immcantation Framework following BCR and TCR sequencing data analysis best practices. The Immcantation Framework is a comprehensive toolset, which allows the processing of bulk and single-cell AIRR-seq data from raw read processing to clonal inference. nf-core/airrflow is written in Nextflow and is part of the nf-core project, which collects community contributed and curated Nextflow workflows for a wide variety of analysis tasks. We assessed the performance of nf-core/airrflow on simulated sequencing data with sequencing errors and show example results with real datasets. To demonstrate the applicability of nf-core/airrflow to the high-throughput processing of large AIRR-seq datasets, we validated and extended previously reported findings of convergent antibody responses to SARS-CoV-2 by analyzing 97 COVID-19 infected individuals and 99 healthy controls, including a mixture of bulk and single-cell sequencing datasets. Using this dataset, we extended the convergence findings to 20 additional subjects, highlighting the applicability of nf-core/airrflow to validate findings in small in-house cohorts with reanalysis of large publicly available AIRR datasets. nf-core/airrflow is available free of charge, under the MIT license on GitHub (https://github.com/nf-core/airrflow). Detailed documentation and example results are available on the nf-core website at (https://nf-co.re/airrflow).
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8
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Gu Y, Shunmuganathan B, Qian X, Gupta R, Tan RSW, Kozma M, Purushotorman K, Murali TM, Tan NYJ, Preiser PR, Lescar J, Nasir H, Somani J, Tambyah PA, Smith KGC, Renia L, Ng LFP, Lye DC, Young BE, MacAry PA. Employment of a high throughput functional assay to define the critical factors that influence vaccine induced cross-variant neutralizing antibodies for SARS-CoV-2. Sci Rep 2023; 13:21810. [PMID: 38071323 PMCID: PMC10710454 DOI: 10.1038/s41598-023-49231-w] [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: 05/21/2023] [Accepted: 12/06/2023] [Indexed: 12/18/2023] Open
Abstract
The scale and duration of neutralizing antibody responses targeting SARS-CoV-2 viral variants represents a critically important serological parameter that predicts protective immunity for COVID-19. In this study, we describe the development and employment of a new functional assay that measures neutralizing antibodies for SARS-CoV-2 and present longitudinal data illustrating the impact of age, sex and comorbidities on the kinetics and strength of vaccine-induced antibody responses for key variants in an Asian volunteer cohort. We also present an accurate quantitation of serological responses for SARS-CoV-2 that exploits a unique set of in-house, recombinant human monoclonal antibodies targeting the viral Spike and nucleocapsid proteins and demonstrate a reduction in neutralizing antibody titres across all groups 6 months post-vaccination. We also observe a marked reduction in the serological binding activity and neutralizing responses targeting recently newly emerged Omicron variants including XBB 1.5 and highlight a significant increase in cross-protective neutralizing antibody responses following a third dose (boost) of vaccine. These data illustrate how key virological factors such as immune escape mutations combined with host demographic factors such as age and sex of the vaccinated individual influence the strength and duration of cross-protective serological immunity for COVID-19.
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Affiliation(s)
- Yue Gu
- Antibody Engineering Programme, Life Sciences Institute, National University of Singapore, Singapore, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUH-Cambridge Immune Phenotyping Centre, National University of Singapore, Singapore, Singapore
| | - Bhuvaneshwari Shunmuganathan
- Antibody Engineering Programme, Life Sciences Institute, National University of Singapore, Singapore, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Xinlei Qian
- Antibody Engineering Programme, Life Sciences Institute, National University of Singapore, Singapore, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Rashi Gupta
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Rebecca S W Tan
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Mary Kozma
- Antibody Engineering Programme, Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Kiren Purushotorman
- Antibody Engineering Programme, Life Sciences Institute, National University of Singapore, Singapore, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Tanusya M Murali
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Nikki Y J Tan
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Peter R Preiser
- Antimicrobial Resistance Interdisciplinary Research Group (AMR-IRG), Singapore-MIT Alliance in Research and Technology (SMART), Singapore, 138602, Singapore
- School of Biological Science (SBS), Nanyang Technological University (NTU), 60 Nanyang Dr, Singapore, 637551, Singapore
| | - Julien Lescar
- School of Biological Science (SBS), Nanyang Technological University (NTU), 60 Nanyang Dr, Singapore, 637551, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore, 636921, Singapore
| | - Haziq Nasir
- Division of Infectious Disease, University Medicine Cluster, National University Hospital, Singapore, Singapore
| | - Jyoti Somani
- Division of Infectious Disease, University Medicine Cluster, National University Hospital, Singapore, Singapore
| | - Paul A Tambyah
- Division of Infectious Disease, University Medicine Cluster, National University Hospital, Singapore, Singapore
| | - Kenneth G C Smith
- NUH-Cambridge Immune Phenotyping Centre, National University of Singapore, Singapore, Singapore
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, CB2 0AW, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, UK
| | - Laurent Renia
- A*STAR Infectious Diseases Labs, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Lisa F P Ng
- A*STAR Infectious Diseases Labs, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - David C Lye
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- National Centre for Infectious Diseases (NCID), Singapore, Singapore
- Tan Tock Seng Hospital, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Barnaby E Young
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- National Centre for Infectious Diseases (NCID), Singapore, Singapore
- Tan Tock Seng Hospital, Singapore, Singapore
| | - Paul A MacAry
- Antibody Engineering Programme, Life Sciences Institute, National University of Singapore, Singapore, Singapore.
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- NUH-Cambridge Immune Phenotyping Centre, National University of Singapore, Singapore, Singapore.
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9
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Arons E, Henry K, Haas C, Gould M, Tsintolas J, Mauter J, Zhou H, Burbelo PD, Cohen JI, Kreitman RJ. Characterization of B-cell receptor clonality and immunoglobulin gene usage at multiple time points during active SARS-CoV-2 infection. J Med Virol 2023; 95:e29179. [PMID: 37877800 DOI: 10.1002/jmv.29179] [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: 08/08/2023] [Revised: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 10/26/2023]
Abstract
Although monoclonal antibodies to the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) are known, B-cell receptor repertoire and its change in patients during coronavirus disease-2019 (COVID-19) progression is underreported. We aimed to study this molecularly. We used immunoglobulin heavy chain (IGH) variable region (IGHV) spectratyping and next-generation sequencing of peripheral blood B-cell genomic DNA collected at multiple time points during disease evolution to study B-cell response to SARS-CoV-2 infection in 14 individuals with acute COVID-19. We found a broad distribution of responding B-cell clones. The IGH gene usage was not significantly skewed but frequencies of individual IGH genes changed repeatedly. We found predominant usage of unmutated and low mutation-loaded IGHV rearrangements characterizing naïve and extrafollicular B cells among the majority of expanded peripheral B-cell clonal lineages at most tested time points in most patients. IGH rearrangement usage showed no apparent relation to anti-SARS-CoV-2 antibody titers. Some patients demonstrated mono/oligoclonal populations carrying highly mutated IGHV rearrangements indicating antigen experience at some of the time points tested, including even before anti-SARS-CoV-2 antibodies were detected. We present evidence demonstrating that the B-cell response to SARS-CoV-2 is individual and includes different lineages of B cells at various time points during COVID-19 progression.
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Affiliation(s)
- Evgeny Arons
- Laboratory of Molecular Biology, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | | | - Christopher Haas
- Medstar Franklin Square Medical Center, Baltimore, Maryland, USA
| | - Mory Gould
- Laboratory of Molecular Biology, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Jack Tsintolas
- Laboratory of Molecular Biology, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Jack Mauter
- Laboratory of Molecular Biology, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Hong Zhou
- Laboratory of Molecular Biology, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Peter D Burbelo
- National Institute of Dental and Craniofacial Research, NIH, Bethesda, Maryland, USA
| | - Jeffrey I Cohen
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Robert J Kreitman
- Laboratory of Molecular Biology, National Cancer Institute, NIH, Bethesda, Maryland, USA
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10
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Curtis NC, Shin S, Hederman AP, Connor RI, Wieland-Alter WF, Ionov S, Boylston J, Rose J, Sakharkar M, Dorman DB, Dessaint JA, Gwilt LL, Crowley AR, Feldman J, Hauser BM, Schmidt AG, Ashare A, Walker LM, Wright PF, Ackerman ME, Lee J. Characterization of SARS-CoV-2 Convalescent Patients' Serological Repertoire Reveals High Prevalence of Iso-RBD Antibodies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.08.556349. [PMID: 37745524 PMCID: PMC10515772 DOI: 10.1101/2023.09.08.556349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
While our understanding of SARS-CoV-2 pathogenesis and antibody responses following infection and vaccination has improved tremendously since the outbreak in 2019, the sequence identities and relative abundances of the individual constituent antibody molecules in circulation remain understudied. Using Ig-Seq, we proteomically profiled the serological repertoire specific to the whole ectodomain of SARS-CoV-2 prefusion-stabilized spike (S) as well as to the receptor binding domain (RBD) over a 6-month period in four subjects following SARS-CoV-2 infection before SARS-CoV-2 vaccines were available. In each individual, we identified between 59 and 167 unique IgG clonotypes in serum. To our surprise, we discovered that ∼50% of serum IgG specific for RBD did not recognize prefusion-stabilized S (referred to as iso-RBD antibodies), suggesting that a significant fraction of serum IgG targets epitopes on RBD inaccessible on the prefusion-stabilized conformation of S. On the other hand, the abundance of iso-RBD antibodies in nine individuals who received mRNA-based COVID-19 vaccines encoding prefusion-stabilized S was significantly lower (∼8%). We expressed a panel of 12 monoclonal antibodies (mAbs) that were abundantly present in serum from two SARS-CoV-2 infected individuals, and their binding specificities to prefusion-stabilized S and RBD were all in agreement with the binding specificities assigned based on the proteomics data, including 1 iso-RBD mAb which bound to RBD but not to prefusion-stabilized S. 2 of 12 mAbs demonstrated neutralizing activity, while other mAbs were non-neutralizing. 11 of 12 mAbs also bound to S (B.1.351), but only 1 maintained binding to S (B.1.1.529). This particular mAb binding to S (B.1.1.529) 1) represented an antibody lineage that comprised 43% of the individual's total S-reactive serum IgG binding titer 6 months post-infection, 2) bound to the S from a related human coronavirus, HKU1, and 3) had a high somatic hypermutation level (10.9%), suggesting that this antibody lineage likely had been elicited previously by pre-pandemic coronavirus and was re-activated following the SARS-CoV-2 infection. All 12 mAbs demonstrated their ability to engage in Fc-mediated effector function activities. Collectively, our study provides a quantitative overview of the serological repertoire following SARS-CoV-2 infection and the significant contribution of iso-RBD antibodies, demonstrating how vaccination strategies involving prefusion-stabilized S may have reduced the elicitation of iso-RBD serum antibodies which are unlikely to contribute to protection.
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11
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Uzun S, Zinner CP, Beenen AC, Alborelli I, Bartoszek EM, Yeung J, Calgua B, Reinscheid M, Bronsert P, Stalder AK, Haslbauer JD, Vosbeck J, Mazzucchelli L, Hoffmann T, Terracciano LM, Hutter G, Manz M, Panne I, Boettler T, Hofmann M, Bengsch B, Heim MH, Bernsmeier C, Jiang S, Tzankov A, Terziroli Beretta-Piccoli B, Matter MS. Morphologic and molecular analysis of liver injury after SARS-CoV-2 vaccination reveals distinct characteristics. J Hepatol 2023; 79:666-676. [PMID: 37290592 PMCID: PMC10245467 DOI: 10.1016/j.jhep.2023.05.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 05/10/2023] [Accepted: 05/19/2023] [Indexed: 06/10/2023]
Abstract
BACKGROUND & AIMS Liver injury after COVID-19 vaccination is very rare and shows clinical and histomorphological similarities with autoimmune hepatitis (AIH). Little is known about the pathophysiology of COVID-19 vaccine-induced liver injury (VILI) and its relationship to AIH. Therefore, we compared VILI with AIH. METHODS Formalin-fixed and paraffin-embedded liver biopsy samples from patients with VILI (n = 6) and from patients with an initial diagnosis of AIH (n = 9) were included. Both cohorts were compared by histomorphological evaluation, whole-transcriptome and spatial transcriptome sequencing, multiplex immunofluorescence, and immune repertoire sequencing. RESULTS Histomorphology was similar in both cohorts but showed more pronounced centrilobular necrosis in VILI. Gene expression profiling showed that mitochondrial metabolism and oxidative stress-related pathways were more and interferon response pathways were less enriched in VILI. Multiplex analysis revealed that inflammation in VILI was dominated by CD8+ effector T cells, similar to drug-induced autoimmune-like hepatitis. In contrast, AIH showed a dominance of CD4+ effector T cells and CD79a+ B and plasma cells. T-cell receptor (TCR) and B-cell receptor sequencing showed that T and B cell clones were more dominant in VILI than in AIH. In addition, many T cell clones detected in the liver were also found in the blood. Interestingly, analysis of TCR beta chain and Ig heavy chain variable-joining gene usage further showed that TRBV6-1, TRBV5-1, TRBV7-6, and IgHV1-24 genes are used differently in VILI than in AIH. CONCLUSIONS Our analyses support that SARS-CoV-2 VILI is related to AIH but also shows distinct differences from AIH in histomorphology, pathway activation, cellular immune infiltrates, and TCR usage. Therefore, VILI may be a separate entity, which is distinct from AIH and more closely related to drug-induced autoimmune-like hepatitis. IMPACT AND IMPLICATIONS Little is known about the pathophysiology of COVID-19 vaccine-induced liver injury (VILI). Our analysis shows that COVID-19 VILI shares some similarities with autoimmune hepatitis, but also has distinct differences such as increased activation of metabolic pathways, a more prominent CD8+ T cell infiltrate, and an oligoclonal T and B cell response. Our findings suggest that VILI is a distinct disease entity. Therefore, there is a good chance that many patients with COVID-19 VILI will recover completely and will not develop long-term autoimmune hepatitis.
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Affiliation(s)
- Sarp Uzun
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Carl P Zinner
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Amke C Beenen
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Ilaria Alborelli
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Ewelina M Bartoszek
- Microscopy Core Facility, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Jason Yeung
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Byron Calgua
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Matthias Reinscheid
- Department of Medicine II (Gastroenterology, Hepatology, Endocrinology and Infectious Diseases), Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Peter Bronsert
- Institute for Surgical Pathology, Freiburg University Medical Center, University of Freiburg, Freiburg, Germany; Core Facility for Histopathology and Digital Pathology, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Anna K Stalder
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | | | - Juerg Vosbeck
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | | | | | - Luigi M Terracciano
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy; IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Gregor Hutter
- Brain Tumor Immunotherapy Lab, Department of Biomedicine, University of Basel, Basel, Switzerland; Department of Neurosurgery, University Hospital Basel, Basel, Switzerland
| | - Michael Manz
- Gastroenterology and Hepatology, University Centre for Gastrointestinal and Liver Diseases Basel, Switzerland
| | - Isabelle Panne
- Gastroenterology and Hepatology, University Centre for Gastrointestinal and Liver Diseases Basel, Switzerland
| | - Tobias Boettler
- Department of Medicine II (Gastroenterology, Hepatology, Endocrinology and Infectious Diseases), Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Maike Hofmann
- Department of Medicine II (Gastroenterology, Hepatology, Endocrinology and Infectious Diseases), Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Bertram Bengsch
- Department of Medicine II (Gastroenterology, Hepatology, Endocrinology and Infectious Diseases), Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany; Partner Site Freiburg, German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Markus H Heim
- Gastroenterology and Hepatology, University Centre for Gastrointestinal and Liver Diseases Basel, Switzerland; Department of Biomedicine, University of Basel, Switzerland
| | - Christine Bernsmeier
- Gastroenterology and Hepatology, University Centre for Gastrointestinal and Liver Diseases Basel, Switzerland; Department of Biomedicine, University of Basel, Switzerland
| | - Sizun Jiang
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA; Department of Pathology, Dana Farber Cancer Institute, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Alexandar Tzankov
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Benedetta Terziroli Beretta-Piccoli
- Faculty of Biomedical Sciences, Università Della Svizzera Italiana, Lugano, Switzerland; Epatocentro Ticino, Lugano, Switzerland; MowatLabs, Faculty of Life Sciences and Medicine, King's College London, King's College Hospital, London, UK
| | - Matthias S Matter
- Institute of Pathology, University Hospital Basel, Basel, Switzerland.
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12
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Funakoshi Y, Yakushijin K, Ohji G, Matsutani T, Hojo W, Sakai H, Matsumoto S, Watanabe M, Kitao A, Saito Y, Kawamoto S, Yamamoto K, Koyama T, Nagatani Y, Kimbara S, Imamura Y, Kiyota N, Ito M, Minami H. Response to mRNA SARS-CoV-2 vaccination evaluated by B-cell receptor repertoire after tixagevimab/cilgavimab administration. Br J Haematol 2023; 202:504-516. [PMID: 37349876 DOI: 10.1111/bjh.18932] [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: 03/22/2023] [Revised: 05/31/2023] [Accepted: 06/02/2023] [Indexed: 06/24/2023]
Abstract
The use of anti-SARS-CoV-2 antibody products like tixagevimab/cilgavimab represents an important strategy to protect immunocompromised patients with haematological malignancies from COVID-19. Although patients who receive these agents should still be vaccinated, the use of tixagevimab/cilgavimab can mask the production of anti-spike antibody after vaccination, making it hard to assess vaccine response. We have newly established a quantification method to assess the response to SARS-CoV-2 vaccination at the mRNA level using B-cell receptor (BCR) repertoire assay and the Coronavirus Antibody Database (CoV-AbDab). Repeated blood samples before and after vaccination were analysed for the BCR repertoire, and BCR sequences were searched in the database. We analysed the number and percentage frequency of matched sequences. We found that the number of matched sequences increased 2 weeks after the first vaccination and quickly decreased. Meanwhile, the number of matched sequences more rapidly increased after the second vaccination. These results show that the postvaccine immune response can be assessed at the mRNA level by analysing the fluctuation in matching sequences. Finally, BCR repertoire analysis with CoV-AbDab clearly demonstrated the response to mRNA SARS-CoV-2 vaccination even after tixagevimab/cilgavimab administration in haematological malignancy patients who underwent allogeneic haematopoietic stem cell transplantation.
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Affiliation(s)
- Yohei Funakoshi
- Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan
| | - Kimikazu Yakushijin
- Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan
| | - Goh Ohji
- Division of Infection Disease Therapeutics, Department of Microbiology and Infectious Diseases, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan
| | - Takaji Matsutani
- Research & Development Department, Repertoire Genesis Inc., Ibaraki, Japan
| | | | | | - Sakuya Matsumoto
- Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan
| | - Marika Watanabe
- Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan
| | - Akihito Kitao
- Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan
| | - Yasuyuki Saito
- Division of Molecular and Cellular Signaling, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Shinichiro Kawamoto
- Department of Transfusion Medicine and Cell Therapy, Kobe University Hospital, Kobe, Japan
| | - Katsuya Yamamoto
- Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan
| | - Taiji Koyama
- Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan
| | - Yoshiaki Nagatani
- Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan
| | - Shiro Kimbara
- Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan
| | - Yoshinori Imamura
- Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan
| | - Naomi Kiyota
- Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan
- Cancer Center, Kobe University Hospital, Kobe, Japan
| | - Mitsuhiro Ito
- Division of Medical Biophysics, Kobe University Graduate School of Health Sciences, Kobe, Japan
| | - Hironobu Minami
- Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan
- Cancer Center, Kobe University Hospital, Kobe, Japan
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13
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Yang H, Cham J, Neal BP, Fan Z, He T, Zhang L. NAIR: Network Analysis of Immune Repertoire. Front Immunol 2023; 14:1181825. [PMID: 37614227 PMCID: PMC10443597 DOI: 10.3389/fimmu.2023.1181825] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 06/07/2023] [Indexed: 08/25/2023] Open
Abstract
T cells represent a crucial component of the adaptive immune system and mediate anti-tumoral immunity as well as protection against infections, including respiratory viruses such as SARS-CoV-2. Next-generation sequencing of the T-cell receptors (TCRs) can be used to profile the T-cell repertoire. We developed a customized pipeline for Network Analysis of Immune Repertoire (NAIR) with advanced statistical methods to characterize and investigate changes in the landscape of TCR sequences. We first performed network analysis on the TCR sequence data based on sequence similarity. We then quantified the repertoire network by network properties and correlated it with clinical outcomes of interest. In addition, we identified (1) disease-specific/associated clusters and (2) shared clusters across samples based on our customized search algorithms and assessed their relationship with clinical outcomes such as recovery from COVID-19 infection. Furthermore, to identify disease-specific TCRs, we introduced a new metric that incorporates the clonal generation probability and the clonal abundance by using the Bayes factor to filter out the false positives. TCR-seq data from COVID-19 subjects and healthy donors were used to illustrate that the proposed approach to analyzing the network architecture of the immune repertoire can reveal potential disease-specific TCRs responsible for the immune response to infection.
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Affiliation(s)
- Hai Yang
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, United States
| | - Jason Cham
- Department of Medicine, Scripps Green Hospital, La Jolla, CA, United States
| | - Brian Patrick Neal
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, United States
- Department of Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Zenghua Fan
- Department of Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Tao He
- Department of Mathematics, San Francisco State University, San Francisco, CA, United States
| | - Li Zhang
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, United States
- Department of Medicine, University of California San Francisco, San Francisco, CA, United States
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, United States
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14
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Zhou H, Xu M, Hu P, Li Y, Ren C, Li M, Pan Y, Wang S, Liu X. Identifying hub genes and common biological pathways between COVID-19 and benign prostatic hyperplasia by machine learning algorithms. Front Immunol 2023; 14:1172724. [PMID: 37426635 PMCID: PMC10328422 DOI: 10.3389/fimmu.2023.1172724] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 06/07/2023] [Indexed: 07/11/2023] Open
Abstract
Background COVID-19, a serious respiratory disease that has the potential to affect numerous organs, is a serious threat to the health of people around the world. The objective of this article is to investigate the potential biological targets and mechanisms by which SARS-CoV-2 affects benign prostatic hyperplasia (BPH) and related symptoms. Methods We downloaded the COVID-19 datasets (GSE157103 and GSE166253) and the BPH datasets (GSE7307 and GSE132714) from the Gene Expression Omnibus (GEO) database. In GSE157103 and GSE7307, differentially expressed genes (DEGs) were found using the "Limma" package, and the intersection was utilized to obtain common DEGs. Further analyses followed, including those using Protein-Protein Interaction (PPI), Gene Ontology (GO) function enrichment analysis, and the Kyoto Encyclopedia of Genes and Genomes (KEGG). Potential hub genes were screened using three machine learning methods, and they were later verified using GSE132714 and GSE166253. The CIBERSORT analysis and the identification of transcription factors, miRNAs, and drugs as candidates were among the subsequent analyses. Results We identified 97 common DEGs from GSE157103 and GSE7307. According to the GO and KEGG analyses, the primary gene enrichment pathways were immune-related pathways. Machine learning methods were used to identify five hub genes (BIRC5, DNAJC4, DTL, LILRB2, and NDC80). They had good diagnostic properties in the training sets and were validated in the validation sets. According to CIBERSORT analysis, hub genes were closely related to CD4 memory activated of T cells, T cells regulatory and NK cells activated. The top 10 drug candidates (lucanthone, phytoestrogens, etoposide, dasatinib, piroxicam, pyrvinium, rapamycin, niclosamide, genistein, and testosterone) will also be evaluated by the P value, which is expected to be helpful for the treatment of COVID-19-infected patients with BPH. Conclusion Our findings reveal common signaling pathways, possible biological targets, and promising small molecule drugs for BPH and COVID-19. This is crucial to understand the potential common pathogenic and susceptibility pathways between them.
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Affiliation(s)
- Hang Zhou
- Department of Urology, Tianjin Medical University General Hospital, Tianjin, China
| | - Mingming Xu
- Department of Urology, Tianjin Medical University General Hospital, Tianjin, China
| | - Ping Hu
- Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin, China
| | - Yuezheng Li
- Department of Urology, Tianjin Medical University General Hospital, Tianjin, China
| | - Congzhe Ren
- Department of Urology, Tianjin Medical University General Hospital, Tianjin, China
| | - Muwei Li
- Department of Urology, Tianjin Medical University General Hospital, Tianjin, China
| | - Yang Pan
- Department of Urology, Tianjin Medical University General Hospital, Tianjin, China
| | - Shangren Wang
- Department of Urology, Tianjin Medical University General Hospital, Tianjin, China
| | - Xiaoqiang Liu
- Department of Urology, Tianjin Medical University General Hospital, Tianjin, China
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15
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Wang J, Huang L, Guo N, Yao YP, Zhang C, Xu R, Jiao YM, Li YQ, Song YR, Wang FS, Fan X. Dynamics of SARS-CoV-2 Antibody Responses up to 9 Months Post-Vaccination in Individuals with Previous SARS-CoV-2 Infection Receiving Inactivated Vaccines. Viruses 2023; 15:v15040917. [PMID: 37112897 PMCID: PMC10145073 DOI: 10.3390/v15040917] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/20/2023] [Accepted: 03/24/2023] [Indexed: 04/07/2023] Open
Abstract
Humoral immunity confers protection against COVID-19. The longevity of antibody responses after receiving an inactivated vaccine in individuals with previous SARS-CoV-2 infection is unclear. Plasma samples were collected from 58 individuals with previous SARS-CoV-2 infection and 25 healthy donors (HDs) who had been vaccinated with an inactivated vaccine. The neutralizing antibodies (NAbs) and S1 domain-specific antibodies against the SARS-CoV-2 wild-type and Omicron strains and nucleoside protein (NP)-specific antibodies were measured using a chemiluminescent immunoassay. Statistical analysis was performed using clinical variables and antibodies at different timepoints after SARS-CoV-2 vaccination. NAbs targeting the wild-type or Omicron strain were detected in individuals with previous SARS-CoV-2 infection at 12 months after infection (wild-type: 81%, geometric mean (GM): 20.3 AU/mL; Omicron: 44%, GM: 9.4 AU/mL), and vaccination provided further enhancement of these antibody levels (wild-type: 98%, GM: 53.3 AU/mL; Omicron: 75%, GM: 27.8 AU/mL, at 3 months after vaccination), which were significantly higher than those in HDs receiving a third dose of inactivated vaccine (wild-type: 85%, GM: 33.6 AU/mL; Omicron: 45%, GM: 11.5 AU/mL). The level of NAbs in individuals with previous infection plateaued 6 months after vaccination, but the NAb levels in HDs declined continuously. NAb levels in individuals with previous infection at 3 months post-vaccination were strongly correlated with those at 6 months post-vaccination, and weakly correlated with those before vaccination. NAb levels declined substantially in most individuals, and the rate of antibody decay was negatively correlated with the neutrophil-to-lymphocyte ratio in the blood at discharge. These results suggest that the inactivated vaccine induced robust and durable NAb responses in individuals with previous infection up to 9 months after vaccination.
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Affiliation(s)
- Jing Wang
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing 100039, China
| | - Lei Huang
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing 100039, China
| | - Nan Guo
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing 100039, China
- Chinese PLA Medical School, Beijing 100853, China
| | - Ya-Ping Yao
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China
- Senior Department of Infectious Diseases, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100039, China
| | - Chao Zhang
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing 100039, China
| | - Ruonan Xu
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing 100039, China
| | - Yan-Mei Jiao
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing 100039, China
| | - Ya-Qun Li
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing 100039, China
| | - Yao-Ru Song
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing 100039, China
- Chinese PLA Medical School, Beijing 100853, China
| | - Fu-Sheng Wang
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing 100039, China
| | - Xing Fan
- Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing 100039, China
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16
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Scharf L, Axelsson H, Emmanouilidi A, Mathew NR, Sheward DJ, Leach S, Isakson P, Smirnov IV, Marklund E, Miron N, Andersson LM, Gisslén M, Murrell B, Lundgren A, Bemark M, Angeletti D. Longitudinal single-cell analysis of SARS-CoV-2-reactive B cells uncovers persistence of early-formed, antigen-specific clones. JCI Insight 2023; 8:165299. [PMID: 36445762 PMCID: PMC9870078 DOI: 10.1172/jci.insight.165299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 11/17/2022] [Indexed: 11/30/2022] Open
Abstract
Understanding persistence and evolution of B cell clones after COVID-19 infection and vaccination is crucial for predicting responses against emerging viral variants and optimizing vaccines. Here, we collected longitudinal samples from patients with severe COVID-19 every third to seventh day during hospitalization and every third month after recovery. We profiled their antigen-specific immune cell dynamics by combining single-cell RNA-Seq, Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-Seq), and B cell receptor-Seq (BCR-Seq) with oligo-tagged antigen baits. While the proportion of Spike receptor binding domain-specific memory B cells (MBC) increased from 3 months after infection, the other Spike- and Nucleocapsid-specific B cells remained constant. All patients showed ongoing class switching and sustained affinity maturation of antigen-specific cells, and affinity maturation was not significantly increased early after vaccine. B cell analysis revealed a polyclonal response with limited clonal expansion; nevertheless, some clones detected during hospitalization, as plasmablasts, persisted for up to 1 year, as MBC. Monoclonal antibodies derived from persistent B cell families increased their binding and neutralization breadth and started recognizing viral variants by 3 months after infection. Overall, our findings provide important insights into the clonal evolution and dynamics of antigen-specific B cell responses in longitudinally sampled patients infected with COVID-19.
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Affiliation(s)
- Lydia Scharf
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Hannes Axelsson
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Aikaterini Emmanouilidi
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Nimitha R. Mathew
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Daniel J. Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Susannah Leach
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Pharmacology
| | - Pauline Isakson
- Department of Clinical Immunology and Transfusion Medicine, and
| | - Ilya V. Smirnov
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Emelie Marklund
- Department of Infectious Diseases, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden.,Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Nicolae Miron
- Department of Clinical Immunology and Transfusion Medicine, and
| | - Lars-Magnus Andersson
- Department of Infectious Diseases, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden.,Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Magnus Gisslén
- Department of Infectious Diseases, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden.,Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Anna Lundgren
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Immunology and Transfusion Medicine, and
| | - Mats Bemark
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Immunology and Transfusion Medicine, and
| | - Davide Angeletti
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
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17
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Safra M, Tamari Z, Polak P, Shiber S, Matan M, Karameh H, Helviz Y, Levy-Barda A, Yahalom V, Peretz A, Ben-Chetrit E, Brenner B, Tuller T, Gal-Tanamy M, Yaari G. Altered somatic hypermutation patterns in COVID-19 patients classifies disease severity. Front Immunol 2023; 14:1031914. [PMID: 37153628 PMCID: PMC10154551 DOI: 10.3389/fimmu.2023.1031914] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 03/22/2023] [Indexed: 05/10/2023] Open
Abstract
Introduction The success of the human body in fighting SARS-CoV2 infection relies on lymphocytes and their antigen receptors. Identifying and characterizing clinically relevant receptors is of utmost importance. Methods We report here the application of a machine learning approach, utilizing B cell receptor repertoire sequencing data from severely and mildly infected individuals with SARS-CoV2 compared with uninfected controls. Results In contrast to previous studies, our approach successfully stratifies non-infected from infected individuals, as well as disease level of severity. The features that drive this classification are based on somatic hypermutation patterns, and point to alterations in the somatic hypermutation process in COVID-19 patients. Discussion These features may be used to build and adapt therapeutic strategies to COVID-19, in particular to quantitatively assess potential diagnostic and therapeutic antibodies. These results constitute a proof of concept for future epidemiological challenges.
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Affiliation(s)
- Modi Safra
- Bio-engineering, Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel
- Bar Ilan Institute of Nanotechnologies and Advanced Materials, Bar Ilan University, Ramat Gan, Israel
| | - Zvi Tamari
- Bio-engineering, Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel
- Bar Ilan Institute of Nanotechnologies and Advanced Materials, Bar Ilan University, Ramat Gan, Israel
| | - Pazit Polak
- Bio-engineering, Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel
- Bar Ilan Institute of Nanotechnologies and Advanced Materials, Bar Ilan University, Ramat Gan, Israel
| | - Shachaf Shiber
- Emergency Department, Rabin Medical Center-Belinson Campus, Petah Tikva, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Moshe Matan
- Clinical Microbiology Laboratory, Baruch Padeh Medical Center, Poriya, Israel
| | - Hani Karameh
- Jesselson Integrated Heart Center, Shaare Zedek Medical Center, Hebrew University School of Medicine, Jerusalem, Israel
| | - Yigal Helviz
- Intensive Care Unit, Shaare Zedek Medical Center, Hebrew University School of Medicine, Jerusalem, Israel
| | - Adva Levy-Barda
- Biobank, Department of Pathology, Rabin Medical Center-Belinson Campus, Petah Tikva, Israel
| | - Vered Yahalom
- Blood Services and Apheresis Institute, Rabin Medical Center, Petah Tikva, Israel
| | - Avi Peretz
- Clinical Microbiology Laboratory, Baruch Padeh Medical Center, Poriya, Israel
- The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Eli Ben-Chetrit
- Infectious Diseases Unit, Shaare Zedek Medical Center, Hebrew University School of Medicine, Jerusalem, Israel
| | - Baruch Brenner
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Institute of Oncology, Rabin Medical Center-Belinson Campus, Petah Tikva, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering and The Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | | | - Gur Yaari
- Bio-engineering, Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel
- Bar Ilan Institute of Nanotechnologies and Advanced Materials, Bar Ilan University, Ramat Gan, Israel
- *Correspondence: Gur Yaari,
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18
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Katoh H, Komura D, Furuya G, Ishikawa S. Immune repertoire profiling for disease pathobiology. Pathol Int 2023; 73:1-11. [PMID: 36342353 PMCID: PMC10099665 DOI: 10.1111/pin.13284] [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: 05/24/2022] [Revised: 09/20/2022] [Accepted: 10/13/2022] [Indexed: 11/09/2022]
Abstract
Lymphocytes consist of highly heterogeneous populations, each expressing a specific cell surface receptor corresponding to a particular antigen. Lymphocytes are both the cause and regulator of various diseases, including autoimmune/allergic diseases, lifestyle diseases, neurodegenerative diseases, and cancers. Recently, immune repertoire sequencing has attracted much attention because it helps obtain global profiles of the immune receptor sequences of infiltrating T and B cells in specimens. Immune repertoire sequencing not only helps deepen our understanding of the molecular mechanisms of immune-related pathology but also assists in discovering novel therapeutic modalities for diseases, thereby shedding colorful light on otherwise tiny monotonous cells when observed under a microscope. In this review article, we introduce and detail the background and methodology of immune repertoire sequencing and summarize recent scientific achievements in association with human diseases. Future perspectives on this genetic technique in the field of histopathological research will also be discussed.
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Affiliation(s)
- Hiroto Katoh
- Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Daisuke Komura
- Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Genta Furuya
- Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shumpei Ishikawa
- Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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19
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He B, Liu S, Xu M, Hu Y, Lv K, Wang Y, Ma Y, Zhai Y, Yue X, Liu L, Lu H, Zhou S, Li P, Mai G, Huang X, Li C, Chen S, Ye S, Zhao P, Yang Y, Li X, Jie Y, Shi M, Yang J, Shu Y, Chen YQ. Comparative global B cell receptor repertoire difference induced by SARS-CoV-2 infection or vaccination via single-cell V(D)J sequencing. Emerg Microbes Infect 2022; 11:2007-2020. [PMID: 35899581 PMCID: PMC9377262 DOI: 10.1080/22221751.2022.2105261] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/30/2022] [Accepted: 07/19/2022] [Indexed: 02/05/2023]
Abstract
Dynamic changes of the paired heavy and light chain B cell receptor (BCR) repertoire provide an essential insight into understanding the humoral immune response post-SARS-CoV-2 infection and vaccination. However, differences between the endogenous paired BCR repertoire kinetics in SARS-CoV-2 infection and previously recovered/naïve subjects treated with the inactivated vaccine remain largely unknown. We performed single-cell V(D)J sequencing of B cells from six healthy donors with three shots of inactivated SARS-CoV-2 vaccine (BBIBP-CorV), five people who received the BBIBP-CorV vaccine after having recovered from COVID-19, five unvaccinated COVID-19 recovered patients and then integrated with public data of B cells from four SARS-CoV-2-infected subjects. We discovered that BCR variable (V) genes were more prominently used in the SARS-CoV-2 exposed groups (both in the group with active infection and in the group that had recovered) than in the vaccinated groups. The VH gene that expanded the most after SARS-CoV-2 infection was IGHV3-33, while IGHV3-23 in the vaccinated groups. SARS-CoV-2-infected group enhanced more BCR clonal expansion and somatic hypermutation than the vaccinated healthy group. A small proportion of public clonotypes were shared between the SARS-CoV-2 infected, vaccinated healthy, and recovered groups. Moreover, several public antibodies had been identified against SARS-CoV-2 spike protein. We comprehensively characterize the paired heavy and light chain BCR repertoire from SARS-CoV-2 infection to vaccination, providing further guidance for the development of the next-generation precision vaccine.
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Affiliation(s)
- Bing He
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, People’s Republic of China
| | - Shuning Liu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, People’s Republic of China
| | - Mengxin Xu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, People’s Republic of China
| | - Yunqi Hu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, People’s Republic of China
| | - Kexin Lv
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, People’s Republic of China
| | - Yuanyuan Wang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, People’s Republic of China
| | - Yong Ma
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, People’s Republic of China
| | - Yanmei Zhai
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, People’s Republic of China
| | - Xinyu Yue
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, People’s Republic of China
| | - Lin Liu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, People’s Republic of China
| | - Hongjie Lu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, People’s Republic of China
| | - Siwei Zhou
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, People’s Republic of China
| | - Pengbin Li
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, People’s Republic of China
| | - Guoqin Mai
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, People’s Republic of China
| | - Xiaoping Huang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, People’s Republic of China
| | - Chenhang Li
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, People’s Republic of China
| | - Shifeng Chen
- Department of Respiratory and Critical Care Medicine, The 74(th) Group Army Hospital, Guangzhou, People’s Republic of China
| | - Shupei Ye
- SSL Central Hospital of Dongguan City, Dongguan, People’s Republic of China
| | - Pingsen Zhao
- Laboratory for Diagnosis of Clinical Microbiology and Infection, Medical Research Center, Yuebei People’s Hospital, Shantou University Medical College, Shaoguan, People’s Republic of China
| | - Yuedong Yang
- School of Data and Computer Science, Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Xinhua Li
- Department of Infectious Diseases and Key Laboratory of Liver Disease of Guangdong Province, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Yusheng Jie
- Department of Infectious Diseases, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, People’s Republic of China
| | - Mang Shi
- The Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, People’s Republic of China
| | - Jingyi Yang
- Vaccine and Immunology Research Center, Translational Medical Research Institute, Shanghai Public Health Clinical Center, Fudan University, Shanghai, People’s Republic of China
| | - Yuelong Shu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, People’s Republic of China
| | - Yao-Qing Chen
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, People’s Republic of China
- b School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, People’s Republic of China
- k Ministry of Education, Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Guangzhou, People’s Republic of China
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20
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Pettini E, Medaglini D, Ciabattini A. Profiling the B cell immune response elicited by vaccination against the respiratory virus SARS-CoV-2. Front Immunol 2022; 13:1058748. [PMID: 36505416 PMCID: PMC9729280 DOI: 10.3389/fimmu.2022.1058748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/04/2022] [Indexed: 11/25/2022] Open
Abstract
B cells play a fundamental role in host defenses against viral infections. Profiling the B cell response elicited by SARS-CoV-2 vaccination, including the generation and persistence of antigen-specific memory B cells, is essential for improving the knowledge of vaccine immune responsiveness, beyond the antibody response. mRNA-based vaccines have shown to induce a robust class-switched memory B cell response that persists overtime and is boosted by further vaccine administration, suggesting that memory B cells are critical in driving a recall response upon re-exposure to SARS-CoV-2 antigens. Here, we focus on the role of the B cell response in the context of SARS-CoV-2 vaccination, offering an overview of the different technologies that can be used to identify spike-specific B cells, characterize their phenotype using machine learning approaches, measure their capacity to reactivate following antigen encounter, and tracking the maturation of the B cell receptor antigenic affinity.
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21
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Cheng ZJ, Huang H, Liu Q, Zhong R, Liang Z, Xue M, Liu M, Li S, Wang H, Zheng P, Zheng C, Sun B. Immunoassay and mass cytometry revealed immunological profiles induced by inactivated BBIBP COVID-19 vaccine. J Med Virol 2022; 94:5206-5216. [PMID: 35801663 PMCID: PMC9350407 DOI: 10.1002/jmv.27983] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 06/29/2022] [Indexed: 12/15/2022]
Abstract
With the global prevalence of COVID-19 and the constant emergence of viral variants, boosters for COVID-19 vaccines to enhance antibody titers in human bodies will become an inevitable trend. However, there is a lack of data on antibody levels and the protective effects of booster injections. This study monitored and analyzed the antibody potency and the antibody responses induced by the booster injection in the subjects who received three vaccine doses. The study was conducted in a multicenter collaboration and recruited 360 healthy adults aged 20-74. Participants received the first, second, and booster doses of inactivated Sinopharm/BBIBP COVID-19 vaccine at 0, 1, and 7 months. Vaccine-induced virus-specific antibody levels (SARS-COV-2-IgA/IgM/IgG) were monitored at multiple time points, surrogate virus neutralization test (sVNT), and the spatial distribution and proportion of immune cells and markers were analyzed using the CyTOF method before vaccination and a month after the second dose. The titers of SARS-CoV-2-IgA/IgM/IgG and neutralizing antibodies increased to a high level in the first month after receiving the second dose of vaccine and declined slowly after that. The antibody levels of SARS-CoV-2-IgG and sVNT were significantly increased at 0.5 months after the induction of the booster (p < 0.05). Despite a downward trend, the antibody levels were still high in the following 6 months. The B cell concentration (in humoral sample) a month after the second injection was significantly reduced compared to that before the vaccine injection (p < 0.05). The proportion of the C01 cell cluster was significantly decreased compared with that before vaccine injection (p < 0.05). Individual cell surface markers showed distinctions in spatial distribution but were not significantly different. This study has shown that serum antibody titer levels will decrease with time by monitoring and analyzing the antibody efficacy and the antibody reaction caused by the booster injection of healthy people who received the whole vaccination (completed three injections). Still, the significant peak of the antibody titer levels after booster highlights the recall immune response. It can maintain a high concentration of antibody levels for a long time, which signifies that the protection ability has been enhanced following the injection of booster immunization. Additionally, CyTOF data shows the active production of antibodies and the change in the immunity environment.
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Affiliation(s)
- Zhangkai J. Cheng
- Department of Allergy and Clinical Immunology, Department of Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory DiseaseGuangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina,Medical CollegeInner Mongolia Minzu UniversityTongliaoChina,Guangzhou LaboratoryGuangzhouChina
| | - Huimin Huang
- Department of Allergy and Clinical Immunology, Department of Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory DiseaseGuangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
| | - Qiwen Liu
- Department of Allergy and Clinical Immunology, Department of Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory DiseaseGuangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina,Nanshan SchoolGuangzhou Medical UniversityGuangzhouChina
| | | | - Zhiman Liang
- Department of Allergy and Clinical Immunology, Department of Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory DiseaseGuangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
| | - Mingshan Xue
- Department of Allergy and Clinical Immunology, Department of Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory DiseaseGuangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina,Guangzhou LaboratoryGuangzhouChina
| | - Mingtao Liu
- Department of Allergy and Clinical Immunology, Department of Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory DiseaseGuangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
| | - Siping Li
- Dongguan Eighth People's HospitalDongguanChina
| | - Hongman Wang
- Fifth Affiliated Hospital of Zunyi Medical UniversityZhuhaiChina
| | - Peiyan Zheng
- Department of Allergy and Clinical Immunology, Department of Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory DiseaseGuangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina
| | - Chunfu Zheng
- Medical CollegeInner Mongolia Minzu UniversityTongliaoChina,Key Laboratory of Zoonose Prevention and ControlUniversities of Inner Mongolia Autonomous RegionTongliaoChina,Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryAlbertaCanada
| | - Baoqing Sun
- Department of Allergy and Clinical Immunology, Department of Laboratory, National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory DiseaseGuangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical UniversityGuangzhouChina,Guangzhou LaboratoryGuangzhouChina
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22
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Scheepers C, Richardson SI, Moyo-Gwete T, Moore PL. Antibody class-switching as a strategy to improve HIV-1 neutralization. Trends Mol Med 2022; 28:979-988. [PMID: 36117072 PMCID: PMC9617786 DOI: 10.1016/j.molmed.2022.08.010] [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: 06/21/2022] [Revised: 08/11/2022] [Accepted: 08/19/2022] [Indexed: 12/01/2022]
Abstract
Broadly neutralizing antibodies (bNAbs), when administered through passive immunization, are protective against HIV-1 infection. Current HIV-1 vaccine strategies are aimed at guiding the immune system to make bNAbs by mimicking their development during infection. Somatic hypermutation of the variable region is known to be crucial for the development of bNAbs. More recently, however, studies have shown how class-switch recombination (CSR) resulting in the generation of different antibody isotypes may serve as an additional mechanism through which antibodies can gain neutralization breadth and potency. In this review, we discuss the importance of different antibody isotypes for HIV-1 neutralization breadth and potency and how this information can be leveraged to improve passive and active immunization against HIV-1.
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Affiliation(s)
- Cathrine Scheepers
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa; SA MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Simone I Richardson
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa; SA MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Thandeka Moyo-Gwete
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa; SA MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Penny L Moore
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa; SA MRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Centre for the AIDS Programme of Research in South Africa (CAPRISA), KwaZulu-Natal, South Africa, Discipline of Virology, University of KwaZulu-Natal, South Africa.
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23
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Xu Z, Ismanto HS, Zhou H, Saputri DS, Sugihara F, Standley DM. Advances in antibody discovery from human BCR repertoires. FRONTIERS IN BIOINFORMATICS 2022; 2:1044975. [PMID: 36338807 PMCID: PMC9631452 DOI: 10.3389/fbinf.2022.1044975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022] Open
Abstract
Antibodies make up an important and growing class of compounds used for the diagnosis or treatment of disease. While traditional antibody discovery utilized immunization of animals to generate lead compounds, technological innovations have made it possible to search for antibodies targeting a given antigen within the repertoires of B cells in humans. Here we group these innovations into four broad categories: cell sorting allows the collection of cells enriched in specificity to one or more antigens; BCR sequencing can be performed on bulk mRNA, genomic DNA or on paired (heavy-light) mRNA; BCR repertoire analysis generally involves clustering BCRs into specificity groups or more in-depth modeling of antibody-antigen interactions, such as antibody-specific epitope predictions; validation of antibody-antigen interactions requires expression of antibodies, followed by antigen binding assays or epitope mapping. Together with innovations in Deep learning these technologies will contribute to the future discovery of diagnostic and therapeutic antibodies directly from humans.
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Affiliation(s)
- Zichang Xu
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Hendra S. Ismanto
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Hao Zhou
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Dianita S. Saputri
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Fuminori Sugihara
- Core Instrumentation Facility, Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Daron M. Standley
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
- Department Systems Immunology, Immunology Frontier Research Center, Osaka University, Suita, Japan
- *Correspondence: Daron M. Standley,
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24
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Effects of Prior Infection with SARS-CoV-2 on B Cell Receptor Repertoire Response during Vaccination. Vaccines (Basel) 2022; 10:vaccines10091477. [PMID: 36146555 PMCID: PMC9506540 DOI: 10.3390/vaccines10091477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/24/2022] [Accepted: 08/29/2022] [Indexed: 11/24/2022] Open
Abstract
Understanding the B cell response to SARS-CoV-2 vaccines is a high priority. High-throughput sequencing of the B cell receptor (BCR) repertoire allows for dynamic characterization of B cell response. Here, we sequenced the BCR repertoire of individuals vaccinated by the Pfizer SARS-CoV-2 mRNA vaccine. We compared BCR repertoires of individuals with previous COVID-19 infection (seropositive) to individuals without previous infection (seronegative). We discovered that vaccine-induced expanded IgG clonotypes had shorter heavy-chain complementarity determining region 3 (HCDR3), and for seropositive individuals, these expanded clonotypes had higher somatic hypermutation (SHM) than seronegative individuals. We uncovered shared clonotypes present in multiple individuals, including 28 clonotypes present across all individuals. These 28 shared clonotypes had higher SHM and shorter HCDR3 lengths compared to the rest of the BCR repertoire. Shared clonotypes were present across both serotypes, indicating convergent evolution due to SARS-CoV-2 vaccination independent of prior viral exposure.
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