1
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Chen L, Hu Y, Zheng B, Luo L, Su Z. Human TCR repertoire in cancer. Cancer Med 2024; 13:e70164. [PMID: 39240157 DOI: 10.1002/cam4.70164] [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: 05/06/2024] [Revised: 08/02/2024] [Accepted: 08/19/2024] [Indexed: 09/07/2024] Open
Abstract
BACKGROUND T cells, the "superstar" of the immune system, play a crucial role in antitumor immunity. T-cell receptors (TCR) are crucial molecules that enable T cells to identify antigens and start immunological responses. The body has evolved a unique method for rearrangement, resulting in a vast diversity of TCR repertoires. A healthy TCR repertoire is essential for the particular identification of antigens by T cells. METHODS In this article, we systematically summarized the TCR creation mechanisms and analysis methodologies, particularly focusing on the application of next-generation sequencing (NGS) technology. We explore the TCR repertoire in health and cancer, and discuss the implications of TCR repertoire analysis in understanding carcinogenesis, cancer progression, and treatment. RESULTS The TCR repertoire analysis has enormous potential for monitoring the emergence and progression of malignancies, as well as assessing therapy response and prognosis. The application of NGS has dramatically accelerated our comprehension of TCR diversity and its role in cancer immunity. CONCLUSIONS To substantiate the significance of TCR repertoires as biomarkers, more thorough and exhaustive research should be conducted. The TCR repertoire analysis, enabled by advanced sequencing technologies, is poised to become a crucial tool in the future of cancer diagnosis, monitoring, and therapy evaluation.
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Affiliation(s)
- Lin Chen
- Department of Medical Genetics/Prenatal Diagnostic Center, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Yuan Hu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
- Department of Anesthesia Nursing, West China Second University Hospital, Sichuan University/West China School of Nursing, Sichuan University, Chengdu, China
| | - Bohao Zheng
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Limei Luo
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Zhenzhen Su
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu, China
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2
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Yan Q, Gao X, Liu B, Hou R, He P, Ma Y, Zhang Y, Zhang Y, Li Z, Chen Q, Wang J, Huang X, Liang H, Zheng H, Yao Y, Chen X, Niu X, He J, Chen L, Zhao J, Xiong X. Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein and potentially drive the genesis of Omicron variants. Nat Commun 2024; 15:7585. [PMID: 39217172 PMCID: PMC11366018 DOI: 10.1038/s41467-024-51770-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 08/17/2024] [Indexed: 09/04/2024] Open
Abstract
Continued evolution of SARS-CoV-2 generates variants to challenge antibody immunity established by infection and vaccination. A connection between population immunity and genesis of virus variants has long been suggested but its molecular basis remains poorly understood. Here, we identify a class of SARS-CoV-2 neutralizing public antibodies defined by their shared usage of VL6-57 light chains. Although heavy chains of diverse genotypes are utilized, convergent HCDR3 rearrangements have been observed among these public antibodies to cooperate with germline VL6-57 LCDRs to target a convergent epitope defined by RBD residues S371-S373-S375. Antibody repertoire analysis identifies that this class of VL6-57 antibodies is present in SARS-CoV-2-naive individuals and is clonally expanded in most COVID-19 patients. We confirm that Omicron-specific substitutions at S371, S373 and S375 mediate escape of antibodies of the VL6-57 class. These findings support that this class of public antibodies constitutes a potential immune pressure promoting the introduction of S371L/F-S373P-S375F in Omicron variants. The results provide further molecular evidence to support that antigenic evolution of SARS-CoV-2 is driven by antibody mediated population immunity.
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Affiliation(s)
- Qihong Yan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xijie Gao
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Banghui Liu
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Ruitian Hou
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Ping He
- Guangzhou National Laboratory, Guangzhou, China
| | - Yong Ma
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yudi Zhang
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yanjun Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zimu Li
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Qiuluan Chen
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health - Guangdong Laboratory), Guangzhou, China
| | - Jingjing Wang
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Xiaohan Huang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Huan Liang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Huiran Zheng
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yichen Yao
- Shanghai Institute for Advanced Immunochemical Studies, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Xianying Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xuefeng Niu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jun He
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
| | - Ling Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
- Guangzhou National Laboratory, Guangzhou, China.
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
- Guangzhou National Laboratory, Guangzhou, China.
- Shanghai Institute for Advanced Immunochemical Studies, School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
| | - Xiaoli Xiong
- State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
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3
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Zia A, Orozco A, Fang ISY, Tang AM, Mendoza Viruega AS, Dong S, Leung LYT, Devraj VM, Oludada OE, Ehrhardt GRA. High throughput long-read sequencing of circulating lymphocytes of the evolutionarily distant sea lamprey reveals diversity and common elements of the variable lymphocyte receptor B (VLRB) repertoire. Front Immunol 2024; 15:1427075. [PMID: 39170622 PMCID: PMC11335541 DOI: 10.3389/fimmu.2024.1427075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 07/22/2024] [Indexed: 08/23/2024] Open
Abstract
The leucine-rich repeat-based variable lymphocyte receptor B (VLRB) antibody system of jawless vertebrates is capable of generating an antibody repertoire equal to or exceeding the diversity of antibody repertoires of jawed vertebrates. Unlike immunoglobulin-based immune repertoires, the VLRB repertoire diversity is characterized by variable lengths of VLRB encoding transcripts, rendering conventional immunoreceptor repertoire sequencing approaches unsuitable for VLRB repertoire sequencing. Here we demonstrate that long-read single-molecule real-time (SMRT) sequencing (PacBio) approaches permit the efficient large-scale assessment of the VLRB repertoire. We present a computational pipeline for sequence data processing and provide the first repertoire-based analysis of VLRB protein characteristics including properties of its subunits and regions of diversity within each structural leucine-rich repeat subunit. Our study provides a template to explore changes in the VLRB repertoire during immune responses and to establish large scale VLRB repertoire databases for computational approaches aimed at isolating monoclonal VLRB reagents for biomedical research and clinical applications.
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Affiliation(s)
| | - Ariel Orozco
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Irene S. Y. Fang
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Aspen M. Tang
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | | | - Shilan Dong
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | | | - Vijaya M. Devraj
- Department of Immunology, University of Toronto, Toronto, ON, Canada
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4
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Kushwaha S, Shome P, Sehgal D. Antigen-driven Convergent Evolution of Polysaccharide-specific "DH-less" B Cells in Glycoconjugate Immunized Mice. Immunohorizons 2024; 8:511-526. [PMID: 39093310 PMCID: PMC11374756 DOI: 10.4049/immunohorizons.2400055] [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: 07/08/2024] [Accepted: 07/10/2024] [Indexed: 08/04/2024] Open
Abstract
Glycoconjugate vaccines elicit robust anti-polysaccharide Ab response by recruiting T-cell help. Multiple doses of glycoconjugate vaccine are required to induce long-lasting immunity. The characteristics of anti-polysaccharide Ab response have been reported previously. However, the effect of glycoconjugate booster immunization on anti-polysaccharide and anti-carrier protein Ab repertoire remains poorly understood. In this study, we used clinically relevant pneumococcal capsular polysaccharide type 14 (PCP14) conjugated with cross-reactive material 197 (CRM197) as a model glycoconjugate Ag (PCP14-CRM197). We performed a comprehensive sequence analysis of mouse mAbs generated against PCP14 and CRM197 following immunization with one or three doses of PCP14-CRM197. Analysis of the paired Ig H and L chain transcripts revealed that anti-PCP14 Ab repertoire is extremely restricted. The reoccurrence of five replacement mutations at identical positions in anti-polysaccharide mAbs generated from different mice provided evidence for Ag-driven selection in PCP14-specific B cells. Convergent evolution was observed wherein distinct V(D)J rearrangements resulted in identical or nearly identical CDR3 in anti-PCP14 mAbs. Abs that lacked DH encoded amino acids dominated the anti-PCP14 Ab response. In contrast, anti-CRM197 Ab response was quite diverse, with fewer mutations compared with the anti-PCP14 mAbs, suggesting that conjugation of the polysaccharide to a carrier protein interferes with the development of carrier protein-specific Ab responses. Our findings provide molecular insights into the maturation of Ab responses driven by booster doses of glycoconjugate. This has fundamental implications for the design of glycoconjugate vaccines, especially where the development of Ab response against the carrier protein is also crucial.
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Affiliation(s)
- Sachin Kushwaha
- Molecular Immunology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India
| | - Pratiksha Shome
- Molecular Immunology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India
| | - Devinder Sehgal
- Molecular Immunology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India
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5
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Natsrita P, Charoenkwan P, Shoombuatong W, Mahalapbutr P, Faksri K, Chareonsudjai S, Rungrotmongkol T, Pipattanaboon C. Machine-learning-assisted high-throughput identification of potent and stable neutralizing antibodies against all four dengue virus serotypes. Sci Rep 2024; 14:17165. [PMID: 39060292 PMCID: PMC11282219 DOI: 10.1038/s41598-024-67487-8] [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: 12/15/2023] [Accepted: 07/11/2024] [Indexed: 07/28/2024] Open
Abstract
Several computational methods have been developed to identify neutralizing antibodies (NAbs) covering four dengue virus serotypes (DENV-1 to DENV-4); however, limitations of the dataset and the resulting performance remain. Here, we developed a new computational framework to predict potent and stable NAbs against DENV-1 to DENV-4 using only antibody (CDR-H3) and epitope sequences as input. Specifically, our proposed computational framework employed sequence-based ML and molecular dynamic simulation (MD) methods to achieve more accurate identification. First, we built a novel dataset (n = 1108) by compiling the interactions of CDR-H3 and epitope sequences with the half maximum inhibitory concentration (IC50) values, which represent neutralizing activities. Second, we achieved an accurately predictive ML model that showed high AUC values of 0.879 and 0.885 by tenfold cross-validation and independent tests, respectively. Finally, our computational framework could be applied to filter approximately 2.5 million unseen antibodies into two final candidates that showed strong and stable binding to all four serotypes. In addition, the most potent and stable candidate (1B3B9_V21) was evaluated for its development potential as a therapeutic agent by molecular docking and MD simulations. This study provides an antibody computational approach to facilitate the high-throughput identification of NAbs and accelerate the development of therapeutic antibodies.
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Affiliation(s)
- Piyatida Natsrita
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Phasit Charoenkwan
- Modern Management and Information Technology, College of Arts, Media and Technology, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Watshara Shoombuatong
- Center for Research Innovation and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, 10700, Thailand
| | - Panupong Mahalapbutr
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Kiatichai Faksri
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
- Research and Diagnostic Center for Emerging Infectious Diseases, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Sorujsiri Chareonsudjai
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Thanyada Rungrotmongkol
- Center of Excellent in Biocatalyst and Sustainable Biotechnology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Chonlatip Pipattanaboon
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand.
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6
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Richardson E, Bibi S, McLean F, Schimanski L, Rijal P, Ghraichy M, von Niederhäusern V, Trück J, Clutterbuck EA, O’Connor D, Luhn K, Townsend A, Peters B, Pollard AJ, Deane CM, Kelly DF. Computational mining of B cell receptor repertoires reveals antigen-specific and convergent responses to Ebola vaccination. Front Immunol 2024; 15:1383753. [PMID: 39040106 PMCID: PMC11260629 DOI: 10.3389/fimmu.2024.1383753] [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: 02/08/2024] [Accepted: 06/11/2024] [Indexed: 07/24/2024] Open
Abstract
Outbreaks of Ebolaviruses, such as Sudanvirus (SUDV) in Uganda in 2022, demonstrate that species other than the Zaire ebolavirus (EBOV), which is currently the sole virus represented in current licensed vaccines, remain a major threat to global health. There is a pressing need to develop effective pan-species vaccines and novel monoclonal antibody-based therapeutics for Ebolavirus disease. In response to recent outbreaks, the two dose, heterologous Ad26.ZEBOV/MVA-BN-Filo vaccine regimen was developed and was tested in a large phase II clinical trial (EBL2001) as part of the EBOVAC2 consortium. Here, we perform bulk sequencing of the variable heavy chain (VH) of B cell receptors (BCR) in forty participants from the EBL2001 trial in order to characterize the BCR repertoire in response to vaccination with Ad26.ZEBOV/MVA-BN-Filo. We develop a comprehensive database, EBOV-AbDab, of publicly available Ebolavirus-specific antibody sequences. We then use our database to predict the antigen-specific component of the vaccinee repertoires. Our results show striking convergence in VH germline gene usage across participants following the MVA-BN-Filo dose, and provide further evidence of the role of IGHV3-15 and IGHV3-13 antibodies in the B cell response to Ebolavirus glycoprotein. Furthermore, we found that previously described Ebola-specific mAb sequences present in EBOV-AbDab were sufficient to describe at least one of the ten most expanded BCR clonotypes in more than two thirds of our cohort of vaccinees following the boost, providing proof of principle for the utility of computational mining of immune repertoires.
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Affiliation(s)
- Eve Richardson
- Department of Statistics, University of Oxford, Oxford, United Kingdom
- Oxford Vaccine Group, Department of Pediatrics, University of Oxford, Oxford, United Kingdom
- La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Sagida Bibi
- Oxford Vaccine Group, Department of Pediatrics, University of Oxford, Oxford, United Kingdom
| | - Florence McLean
- Oxford Vaccine Group, Department of Pediatrics, University of Oxford, Oxford, United Kingdom
| | - Lisa Schimanski
- Weatherall Institute for Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Pramila Rijal
- Weatherall Institute for Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Marie Ghraichy
- Divisions of Allergy and Immunology, University Children’s Hospital and Children’s Research Center, University of Zurich (UZH), Zurich, Switzerland
| | - Valentin von Niederhäusern
- Divisions of Allergy and Immunology, University Children’s Hospital and Children’s Research Center, University of Zurich (UZH), Zurich, Switzerland
| | - Johannes Trück
- Divisions of Allergy and Immunology, University Children’s Hospital and Children’s Research Center, University of Zurich (UZH), Zurich, Switzerland
| | | | - Daniel O’Connor
- Oxford Vaccine Group, Department of Pediatrics, University of Oxford, Oxford, United Kingdom
| | - Kerstin Luhn
- Janssen Vaccines and Prevention, Leiden, Netherlands
| | - Alain Townsend
- Weatherall Institute for Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Bjoern Peters
- La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Andrew J. Pollard
- Oxford Vaccine Group, Department of Pediatrics, University of Oxford, Oxford, United Kingdom
| | | | - Dominic F. Kelly
- Oxford Vaccine Group, Department of Pediatrics, University of Oxford, Oxford, United Kingdom
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
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7
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Gabernet G, Marquez S, Bjornson R, Peltzer A, Meng H, Aron E, Lee NY, Jensen CG, Ladd D, Polster M, 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. PLoS Comput Biol 2024; 20:e1012265. [PMID: 39058741 PMCID: PMC11305553 DOI: 10.1371/journal.pcbi.1012265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 08/07/2024] [Accepted: 06/20/2024] [Indexed: 07/28/2024] Open
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.
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Affiliation(s)
- Gisela Gabernet
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, United States of America
- Quantitative Biology Center, Eberhard-Karls University of Tübingen, Tübingen, Germany
| | - Susanna Marquez
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Robert Bjornson
- Yale Center for Research Computing, New Haven, Connecticut, United States of America
| | | | - Hailong Meng
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Edel Aron
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
| | - Noah Y. Lee
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
| | - Cole G. Jensen
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
| | - David Ladd
- oNKo-Innate Pty Ltd, Melbourne, Victoria, Australia
| | - Mark Polster
- Quantitative Biology Center, Eberhard-Karls University of Tübingen, Tübingen, Germany
- Department of Computer Science, Eberhard-Karls University of Tübingen, Tübingen, Germany
- M3 Research Center, University Hospital, Tübingen, Germany
| | - Friederike Hanssen
- Quantitative Biology Center, Eberhard-Karls University of Tübingen, Tübingen, Germany
- Department of Computer Science, Eberhard-Karls University of Tübingen, Tübingen, Germany
- M3 Research Center, University Hospital, Tübingen, Germany
| | - Simon Heumos
- Quantitative Biology Center, Eberhard-Karls University of Tübingen, Tübingen, Germany
- Department of Computer Science, Eberhard-Karls University of Tübingen, Tübingen, Germany
- M3 Research Center, University Hospital, Tübingen, Germany
| | | | - Gur Yaari
- Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel
| | - Markus C. Kowarik
- Department of Neurology and Stroke, Center for Neurology, Eberhard-Karls University of Tübingen, Tübingen, Germany
- Hertie Institute for Clinical Brain Research, Eberhard-Karls University of Tübingen, Tübingen, Germany
| | - Sven Nahnsen
- Quantitative Biology Center, Eberhard-Karls University of Tübingen, Tübingen, Germany
- Department of Computer Science, Eberhard-Karls University of Tübingen, Tübingen, Germany
- M3 Research Center, University Hospital, Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics (IBMI), Eberhard-Karls University of Tübingen, Tübingen, Germany
| | - Steven H. Kleinstein
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, United States of America
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, United States of America
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8
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Singh T, Miller IG, Venkatayogi S, Webster H, Heimsath HJ, Eudailey JA, Dudley DM, Kumar A, Mangan RJ, Thein A, Aliota MT, Newman CM, Mohns MS, Breitbach ME, Berry M, Friedrich TC, Wiehe K, O'Connor DH, Permar SR. Prior dengue virus serotype 3 infection modulates subsequent plasmablast responses to Zika virus infection in rhesus macaques. mBio 2024; 15:e0316023. [PMID: 38349142 PMCID: PMC10936420 DOI: 10.1128/mbio.03160-23] [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: 12/17/2023] [Accepted: 01/17/2024] [Indexed: 03/14/2024] Open
Abstract
Immunodominant and highly conserved flavivirus envelope proteins can trigger cross-reactive IgG antibodies against related flaviviruses, which shapes subsequent protection or disease severity. This study examined how prior dengue serotype 3 (DENV-3) infection affects subsequent Zika virus (ZIKV) plasmablast responses in rhesus macaques (n = 4). We found that prior DENV-3 infection was not associated with diminished ZIKV-neutralizing antibodies or magnitude of plasmablast activation. Rather, characterization of 363 plasmablasts and their derivative 177 monoclonal antibody supernatants from acute ZIKV infection revealed that prior DENV-3 infection was associated with a differential isotype distribution toward IgG, lower somatic hypermutation, and lesser B cell receptor variable gene diversity as compared with repeat ZIKV challenge. We did not find long-lasting DENV-3 cross-reactive IgG after a ZIKV infection but did find persistent ZIKV-binding cross-reactive IgG after a DENV-3 infection, suggesting non-reciprocal cross-reactive immunity. Infection with ZIKV after DENV-3 boosted pre-existing DENV-3-neutralizing antibodies by two- to threefold, demonstrating immune imprinting. These findings suggest that the order of DENV and ZIKV infections has impact on the quality of early B cell immunity which has implications for optimal immunization strategies. IMPORTANCE The Zika virus epidemic of 2015-2016 in the Americas revealed that this mosquito-transmitted virus could be congenitally transmitted during pregnancy and cause birth defects in newborns. Currently, there are no interventions to mitigate this disease and Zika virus is likely to re-emerge. Understanding how protective antibody responses are generated against Zika virus can help in the development of a safe and effective vaccine. One main challenge is that Zika virus co-circulates with related viruses like dengue, such that prior exposure to one can generate cross-reactive antibodies against the other which may enhance infection and disease from the second virus. In this study, we sought to understand how prior dengue virus infection impacts subsequent immunity to Zika virus by single-cell sequencing of antibody producing cells in a second Zika virus infection. Identifying specific qualities of Zika virus immunity that are modulated by prior dengue virus immunity will enable optimal immunization strategies.
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Affiliation(s)
- Tulika Singh
- Human Vaccine Institute, School of Medicine, Duke University, Durham, North Carolina, USA
- Division of Infectious Disease and Vaccinology, School of Public Health, University of California, Berkeley, California, USA
| | | | - Sravani Venkatayogi
- Human Vaccine Institute, School of Medicine, Duke University, Durham, North Carolina, USA
| | - Helen Webster
- Human Vaccine Institute, School of Medicine, Duke University, Durham, North Carolina, USA
| | - Holly J. Heimsath
- Human Vaccine Institute, School of Medicine, Duke University, Durham, North Carolina, USA
| | - Josh A. Eudailey
- Human Vaccine Institute, School of Medicine, Duke University, Durham, North Carolina, USA
- Department of Pediatrics, Weill Cornell Medicine, New York, USA
| | - Dawn M. Dudley
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Amit Kumar
- Human Vaccine Institute, School of Medicine, Duke University, Durham, North Carolina, USA
| | - Riley J. Mangan
- Human Vaccine Institute, School of Medicine, Duke University, Durham, North Carolina, USA
| | - Amelia Thein
- Department of Pediatrics, Weill Cornell Medicine, New York, USA
| | - Matthew T. Aliota
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Twin Cities, St. Paul, Minnesota, USA
| | - Christina M. Newman
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Mariel S. Mohns
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Meghan E. Breitbach
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Madison Berry
- Human Vaccine Institute, School of Medicine, Duke University, Durham, North Carolina, USA
| | - Thomas C. Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Kevin Wiehe
- Human Vaccine Institute, School of Medicine, Duke University, Durham, North Carolina, USA
| | - David H. O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Sallie R. Permar
- Human Vaccine Institute, School of Medicine, Duke University, Durham, North Carolina, USA
- Department of Pediatrics, Weill Cornell Medicine, New York, USA
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9
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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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10
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Zhu Y, Tang H, Xie W, Chen S, Zeng H, Lan C, Guan J, Ma C, Yang X, Wang Q, Wei L, Zhang Z, Yu X. The multilevel extensive diversity across the cynomolgus macaque captured by ultra-deep adaptive immune receptor repertoire sequencing. SCIENCE ADVANCES 2024; 10:eadj5640. [PMID: 38266093 PMCID: PMC10807814 DOI: 10.1126/sciadv.adj5640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 12/22/2023] [Indexed: 01/26/2024]
Abstract
The extent to which AIRRs differ among and within individuals remains elusive. Via ultra-deep repertoire sequencing of 22 and 25 tissues in three cynomolgus macaques, respectively, we identified 84 and 114 novel IGHV and TRBV alleles, confirming 72 (85.71%) and 100 (87.72%) of them. The heterogeneous V gene usage patterns were influenced, in turn, by genetics, isotype (for BCRs only), tissue group, and tissue. A higher proportion of intragroup shared clones in the intestinal tissues than those in other tissues suggests a close intra-intestinal adaptive immunity network. Significantly higher mutation burdens in the public clones and the inter-tissue shared IgM and IgD clones indicate that they might target the shared antigens. This study reveals the extensive heterogeneity of the AIRRs at various levels and has broad fundamental and clinical implications. The data generated here will serve as an invaluable resource for future studies on adaptive immunity in health and diseases.
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Affiliation(s)
- Yan Zhu
- Center for Precision Medicine, Medical Research Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
- Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Haipei Tang
- Center for Precision Medicine, Medical Research Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
| | - Wenxi Xie
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Sen Chen
- Center for Precision Medicine, Medical Research Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Huikun Zeng
- Center for Precision Medicine, Medical Research Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
- Division of Nephrology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China
| | - Chunhong Lan
- Center for Precision Medicine, Medical Research Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Junjie Guan
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Cuiyu Ma
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Xiujia Yang
- Center for Precision Medicine, Medical Research Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
- Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
| | - Qilong Wang
- Center for Precision Medicine, Medical Research Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
| | - Lai Wei
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Zhenhai Zhang
- Center for Precision Medicine, Medical Research Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Southern Medical University, Guangzhou 510515, China
| | - Xueqing Yu
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
- Division of Nephrology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China
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11
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Natali EN, Horst A, Meier P, Greiff V, Nuvolone M, Babrak LM, Fink K, Miho E. The dengue-specific immune response and antibody identification with machine learning. NPJ Vaccines 2024; 9:16. [PMID: 38245547 PMCID: PMC10799860 DOI: 10.1038/s41541-023-00788-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 12/07/2023] [Indexed: 01/22/2024] Open
Abstract
Dengue virus poses a serious threat to global health and there is no specific therapeutic for it. Broadly neutralizing antibodies recognizing all serotypes may be an effective treatment. High-throughput adaptive immune receptor repertoire sequencing (AIRR-seq) and bioinformatic analysis enable in-depth understanding of the B-cell immune response. Here, we investigate the dengue antibody response with these technologies and apply machine learning to identify rare and underrepresented broadly neutralizing antibody sequences. Dengue immunization elicited the following signatures on the antibody repertoire: (i) an increase of CDR3 and germline gene diversity; (ii) a change in the antibody repertoire architecture by eliciting power-law network distributions and CDR3 enrichment in polar amino acids; (iii) an increase in the expression of JNK/Fos transcription factors and ribosomal proteins. Furthermore, we demonstrate the applicability of computational methods and machine learning to AIRR-seq datasets for neutralizing antibody candidate sequence identification. Antibody expression and functional assays have validated the obtained results.
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Affiliation(s)
- Eriberto Noel Natali
- FHNW University of Applied Sciences and Arts Northwestern Switzerland, School of Life Sciences, Muttenz, Switzerland
| | - Alexander Horst
- FHNW University of Applied Sciences and Arts Northwestern Switzerland, School of Life Sciences, Muttenz, Switzerland
| | - Patrick Meier
- FHNW University of Applied Sciences and Arts Northwestern Switzerland, School of Life Sciences, Muttenz, Switzerland
| | - Victor Greiff
- Department of Immunology, Oslo University Hospital Rikshospitalet and University of Oslo, Oslo, Norway
| | - Mario Nuvolone
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Lmar Marie Babrak
- FHNW University of Applied Sciences and Arts Northwestern Switzerland, School of Life Sciences, Muttenz, Switzerland
| | | | - Enkelejda Miho
- FHNW University of Applied Sciences and Arts Northwestern Switzerland, School of Life Sciences, Muttenz, Switzerland.
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- aiNET GmbH, Basel, Switzerland.
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12
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Ivanova EN, Shwetar J, Devlin JC, Buus TB, Gray-Gaillard S, Koide A, Cornelius A, Samanovic MI, Herrera A, Mimitou EP, Zhang C, Karmacharya T, Desvignes L, Ødum N, Smibert P, Ulrich RJ, Mulligan MJ, Koide S, Ruggles KV, Herati RS, Koralov SB. mRNA COVID-19 vaccine elicits potent adaptive immune response without the persistent inflammation seen in SARS-CoV-2 infection. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2021.04.20.21255677. [PMID: 33907755 PMCID: PMC8077568 DOI: 10.1101/2021.04.20.21255677] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
SARS-CoV-2 infection and vaccination elicit potent immune responses. Our study presents a comprehensive multimodal single-cell dataset of peripheral blood of patients with acute COVID-19 and of healthy volunteers before and after receiving the SARS-CoV-2 mRNA vaccine and booster. We compared host immune responses to the virus and vaccine using transcriptional profiling, coupled with B/T cell receptor repertoire reconstruction. COVID-19 patients displayed an enhanced interferon signature and cytotoxic gene upregulation, absent in vaccine recipients. These findings were validated in an independent dataset. Analysis of B and T cell repertoires revealed that, while the majority of clonal lymphocytes in COVID-19 patients were effector cells, clonal expansion was more evident among circulating memory cells in vaccine recipients. Furthermore, while clonal αβ T cell responses were observed in both COVID-19 patients and vaccine recipients, dramatic expansion of clonal γδT cells was found only in infected individuals. Our dataset enables comparative analyses of immune responses to infection versus vaccination, including clonal B and T cell responses. Integrating our data with publicly available datasets allowed us to validate our findings in larger cohorts. To our knowledge, this is the first dataset to include comprehensive profiling of longitudinal samples from healthy volunteers pre/post SARS-CoV-2 vaccine and booster.
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13
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Vieira MC, Palm AKE, Stamper CT, Tepora ME, Nguyen KD, Pham TD, Boyd SD, Wilson PC, Cobey S. Germline-encoded specificities and the predictability of the B cell response. PLoS Pathog 2023; 19:e1011603. [PMID: 37624867 PMCID: PMC10484431 DOI: 10.1371/journal.ppat.1011603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 09/07/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
Antibodies result from the competition of B cell lineages evolving under selection for improved antigen recognition, a process known as affinity maturation. High-affinity antibodies to pathogens such as HIV, influenza, and SARS-CoV-2 are frequently reported to arise from B cells whose receptors, the precursors to antibodies, are encoded by particular immunoglobulin alleles. This raises the possibility that the presence of particular germline alleles in the B cell repertoire is a major determinant of the quality of the antibody response. Alternatively, initial differences in germline alleles' propensities to form high-affinity receptors might be overcome by chance events during affinity maturation. We first investigate these scenarios in simulations: when germline-encoded fitness differences are large relative to the rate and effect size variation of somatic mutations, the same germline alleles persistently dominate the response of different individuals. In contrast, if germline-encoded advantages can be easily overcome by subsequent mutations, allele usage becomes increasingly divergent over time, a pattern we then observe in mice experimentally infected with influenza virus. We investigated whether affinity maturation might nonetheless strongly select for particular amino acid motifs across diverse genetic backgrounds, but we found no evidence of convergence to similar CDR3 sequences or amino acid substitutions. These results suggest that although germline-encoded specificities can lead to similar immune responses between individuals, diverse evolutionary routes to high affinity limit the genetic predictability of responses to infection and vaccination.
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Affiliation(s)
- Marcos C. Vieira
- Department of Ecology and Evolution, University of Chicago, Chicago, United States of America
| | - Anna-Karin E. Palm
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, United States of America
| | - Christopher T. Stamper
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
- Committee on Immunology, University of Chicago, Chicago, United States of America
| | - Micah E. Tepora
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, United States of America
| | - Khoa D. Nguyen
- Department of Pathology, Stanford University School of Medicine, Stanford, United States of America
| | - Tho D. Pham
- Department of Pathology, Stanford University School of Medicine, Stanford, United States of America
| | - Scott D. Boyd
- Department of Pathology, Stanford University School of Medicine, Stanford, United States of America
| | - Patrick C. Wilson
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, United States of America
- Gale and Ira Drukier Institute for Children’s Health, Weill Cornell Medicine, New York City, United States of America
| | - Sarah Cobey
- Department of Ecology and Evolution, University of Chicago, Chicago, United States of America
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14
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Patel A, Kumar S, Lai L, Chakravarthy C, Valanparambil R, Reddy ES, Gottimukkala K, Bajpai P, Raju DR, Edara VV, Davis-Gardner ME, Linderman S, Dixit K, Sharma P, Mantus G, Cheedarla N, Verkerke HP, Frank F, Neish AS, Roback JD, Davis CW, Wrammert J, Ahmed R, Suthar MS, Sharma A, Murali-Krishna K, Chandele A, Ortlund EA. Molecular basis of SARS-CoV-2 Omicron variant evasion from shared neutralizing antibody response. Structure 2023; 31:801-811.e5. [PMID: 37167972 PMCID: PMC10171968 DOI: 10.1016/j.str.2023.04.010] [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: 11/09/2022] [Revised: 03/09/2023] [Accepted: 04/21/2023] [Indexed: 05/13/2023]
Abstract
Understanding the molecular features of neutralizing epitopes is important for developing vaccines/therapeutics against emerging SARS-CoV-2 variants. We describe three monoclonal antibodies (mAbs) generated from COVID-19 recovered individuals during the first wave of the pandemic in India. These mAbs had publicly shared near germline gene usage and potently neutralized Alpha and Delta, poorly neutralized Beta, and failed to neutralize Omicron BA.1 SARS-CoV-2 variants. Structural analysis of these mAbs in complex with trimeric spike protein showed that all three mAbs bivalently bind spike with two mAbs targeting class 1 and one targeting a class 4 receptor binding domain epitope. The immunogenetic makeup, structure, and function of these mAbs revealed specific molecular interactions associated with the potent multi-variant binding/neutralization efficacy. This knowledge shows how mutational combinations can affect the binding or neutralization of an antibody, which in turn relates to the efficacy of immune responses to emerging SARS-CoV-2 escape variants.
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Affiliation(s)
- Anamika Patel
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Sanjeev Kumar
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Lilin Lai
- Department of Pediatrics, Division of Infectious Diseases, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Chennareddy Chakravarthy
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Rajesh Valanparambil
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Elluri Seetharami Reddy
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi 110067, India; Kusuma School of Biological Sciences, Indian Institute of Technology, New Delhi 110016, India
| | - Kamalvishnu Gottimukkala
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Prashant Bajpai
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Dinesh Ravindra Raju
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA; Georgia Tech, Atlanta, GA 30332, USA
| | - Venkata Viswanadh Edara
- Department of Pediatrics, Division of Infectious Diseases, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Meredith E Davis-Gardner
- Department of Pediatrics, Division of Infectious Diseases, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Susanne Linderman
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Kritika Dixit
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Pragati Sharma
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Grace Mantus
- Department of Pediatrics, Division of Infectious Diseases, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Narayanaiah Cheedarla
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Hans P Verkerke
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02215, USA
| | - Filipp Frank
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Andrew S Neish
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - John D Roback
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Carl W Davis
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Jens Wrammert
- Department of Pediatrics, Division of Infectious Diseases, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Rafi Ahmed
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Mehul S Suthar
- Department of Pediatrics, Division of Infectious Diseases, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA; Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Amit Sharma
- Structural Parasitology Group, International Center for Genetic Engineering and Biotechnology, New Delhi 110067, India.
| | - Kaja Murali-Krishna
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi 110067, India; Department of Pediatrics, Division of Infectious Diseases, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA.
| | - Anmol Chandele
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi 110067, India.
| | - Eric A Ortlund
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA.
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15
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Hoh RA, Thörnqvist L, Yang F, Godzwon M, King JJ, Lee JY, Greiff L, Boyd SD, Ohlin M. Clonal evolution and stereotyped sequences of human IgE lineages in aeroallergen-specific immunotherapy. J Allergy Clin Immunol 2023; 152:214-229. [PMID: 36828082 DOI: 10.1016/j.jaci.2023.02.009] [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: 08/02/2022] [Revised: 01/22/2023] [Accepted: 02/09/2023] [Indexed: 02/24/2023]
Abstract
BACKGROUND Allergic disease reflects specific inflammatory processes initiated by interaction between allergen and allergen-specific IgE. Specific immunotherapy (SIT) is an effective long-term treatment option, but the mechanisms by which SIT provides desensitization are not well understood. OBJECTIVE Our aim was to characterize IgE sequences expressed by allergen-specific B cells over a 3-year longitudinal study of patients with aeroallergies who were undergoing SIT. METHODS Allergen-specific IgE-expressing clones were identified by using combinatorial single-chain variable fragment libraries and tracked in PBMCs and nasal biopsy samples over a 3-year period with antibody gene repertoire sequencing. The characteristics of private IgE-expressing clones were compared with those of stereotyped or "public" IgE responses to the grass pollen allergen Phleum pratense (Phl p) 2. RESULT Members of the same allergen-specific IgE lineages were observed in nasal biopsy samples and blood, and lineages detected at baseline persisted in blood and nasal biopsy samples after 3 years of SIT, including B cells that express IgE. Evidence of progressive class switch recombination to IgG subclasses was observed after 3 years of SIT. A common stereotyped Phl p 2-specific antibody heavy chain sequence was detected in multiple donors. The amino acid residues enriched in IgE-stereotyped sequences from seropositive donors were analyzed with machine learning and k-mer motif discovery. Stereotyped IgE sequences had lower overall rates of somatic hypermutation and antigen selection than did single-chain variable fragment-derived allergen-specific sequences or IgE sequences of unknown specificity. CONCLUSION Longitudinal tracking of rare circulating and tissue-resident allergen-specific IgE+ clones demonstrates persistence of allergen-specific IgE+ clones, progressive class switch recombination to IgG subtypes, and distinct maturation of a stereotyped Phl p 2 clonotype.
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Affiliation(s)
- Ramona A Hoh
- Department of Pathology, Stanford University, Stanford, Calif
| | | | - Fan Yang
- Department of Pathology, Stanford University, Stanford, Calif
| | | | - Jasmine J King
- Department of Pathology, Stanford University, Stanford, Calif
| | - Ji-Yeun Lee
- Department of Pathology, Stanford University, Stanford, Calif
| | - Lennart Greiff
- Department of Clinical Sciences, Lund University, Lund, Sweden; Department of Otorhinolaryngology, Head and Neck Surgery, Skåne University Hospital, Lund, Sweden
| | - Scott D Boyd
- Department of Pathology, Stanford University, Stanford, Calif; Sean N. Parker Center for Allergy and Asthma Research, Stanford University, Stanford, Calif
| | - Mats Ohlin
- Department of Immunotechnology, Lund University, Lund, Sweden
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16
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Gaspar-Castillo C, Rodríguez MH, Ortiz-Navarrete V, Alpuche-Aranda CM, Martinez-Barnetche J. Structural and immunological basis of cross-reactivity between dengue and Zika infections: Implications in serosurveillance in endemic regions. Front Microbiol 2023; 14:1107496. [PMID: 37007463 PMCID: PMC10063793 DOI: 10.3389/fmicb.2023.1107496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 02/24/2023] [Indexed: 03/19/2023] Open
Abstract
Dengue and Zika are arthropod-borne viral diseases present in more than 100 countries around the world. In the past decade, Zika emerged causing widespread outbreaks in new regions, where dengue has been endemic-epidemic for a long period. The wide and extensive dissemination of the mosquito vectors, Aedes aegypti, and Ae. albopictus, favor the co-existence of both infections in the same regions. Together with an important proportion of asymptomatic infections, similar clinical manifestations, and a short time window for acute infection confirmatory tests, it is difficult to differentially estimate both dengue and Zika incidence and prevalence. DENV and ZIKV flavivirus share high structural similarity, inducing a cross-reactive immune response that leads to false positives in serological tests particularly in secondary infections. This results in overestimation of recent Zika outbreaks seroprevalence in dengue endemic regions. In this review, we address the biological basis underlying DENV and ZIKV structural homology; the structural and cellular basis of immunological cross reactivity; and the resulting difficulties in measuring dengue and Zika seroprevalence. Finally, we offer a perspective about the need for more research to improve serological tests performance.
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Affiliation(s)
- Carlos Gaspar-Castillo
- Center for Infectious Diseases Research, National Institute of Public Health, Cuernavaca, Mexico
| | - Mario H. Rodríguez
- Center for Infectious Diseases Research, National Institute of Public Health, Cuernavaca, Mexico
| | - Vianney Ortiz-Navarrete
- Department of Molecular Biomedicine, Center for Research and Advanced Studies of the National Polytechnic Institute, Mexico City, Mexico
| | - Celia M. Alpuche-Aranda
- Center for Infectious Diseases Research, National Institute of Public Health, Cuernavaca, Mexico
- Celia M. Alpuche-Aranda,
| | - Jesus Martinez-Barnetche
- Center for Infectious Diseases Research, National Institute of Public Health, Cuernavaca, Mexico
- *Correspondence: Jesus Martinez-Barnetche,
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17
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Ruiz Ortega M, Spisak N, Mora T, Walczak AM. Modeling and predicting the overlap of B- and T-cell receptor repertoires in healthy and SARS-CoV-2 infected individuals. PLoS Genet 2023; 19:e1010652. [PMID: 36827454 PMCID: PMC10075420 DOI: 10.1371/journal.pgen.1010652] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 04/05/2023] [Accepted: 02/02/2023] [Indexed: 02/26/2023] Open
Abstract
Adaptive immunity's success relies on the extraordinary diversity of protein receptors on B and T cell membranes. Despite this diversity, the existence of public receptors shared by many individuals gives hope for developing population-wide vaccines and therapeutics. Using probabilistic modeling, we show many of these public receptors are shared by chance in healthy individuals. This predictable overlap is driven not only by biases in the random generation process of receptors, as previously reported, but also by their common functional selection. However, the model underestimates sharing between repertoires of individuals infected with SARS-CoV-2, suggesting strong specific antigen-driven convergent selection. We exploit this discrepancy to identify COVID-associated receptors, which we validate against datasets of receptors with known viral specificity. We study their properties in terms of sequence features and network organization, and use them to design an accurate diagnostic tool for predicting SARS-CoV-2 status from repertoire data.
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Affiliation(s)
- María Ruiz Ortega
- Laboratoire de physique de l’École Normale Supérieure, CNRS, PSL University, Sorbonne Université, and Université de Paris, Paris, France
| | - Natanael Spisak
- Laboratoire de physique de l’École Normale Supérieure, CNRS, PSL University, Sorbonne Université, and Université de Paris, Paris, France
| | - Thierry Mora
- Laboratoire de physique de l’École Normale Supérieure, CNRS, PSL University, Sorbonne Université, and Université de Paris, Paris, France
| | - Aleksandra M. Walczak
- Laboratoire de physique de l’École Normale Supérieure, CNRS, PSL University, Sorbonne Université, and Université de Paris, Paris, France
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18
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Chen Y, Prévost J, Ullah I, Romero H, Lisi V, Tolbert WD, Grover JR, Ding S, Gong SY, Beaudoin-Bussières G, Gasser R, Benlarbi M, Vézina D, Anand SP, Chatterjee D, Goyette G, Grunst MW, Yang Z, Bo Y, Zhou F, Béland K, Bai X, Zeher AR, Huang RK, Nguyen DN, Sherburn R, Wu D, Piszczek G, Paré B, Matthies D, Xia D, Richard J, Kumar P, Mothes W, Côté M, Uchil PD, Lavallée VP, Smith MA, Pazgier M, Haddad E, Finzi A. Molecular basis for antiviral activity of two pediatric neutralizing antibodies targeting SARS-CoV-2 Spike RBD. iScience 2023; 26:105783. [PMID: 36514310 PMCID: PMC9733284 DOI: 10.1016/j.isci.2022.105783] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 11/07/2022] [Accepted: 12/07/2022] [Indexed: 12/13/2022] Open
Abstract
Neutralizing antibodies (NAbs) hold great promise for clinical interventions against SARS-CoV-2 variants of concern (VOCs). Understanding NAb epitope-dependent antiviral mechanisms is crucial for developing vaccines and therapeutics against VOCs. Here we characterized two potent NAbs, EH3 and EH8, isolated from an unvaccinated pediatric patient with exceptional plasma neutralization activity. EH3 and EH8 cross-neutralize the early VOCs and mediate strong Fc-dependent effector activity in vitro. Structural analyses of EH3 and EH8 in complex with the receptor-binding domain (RBD) revealed the molecular determinants of the epitope-driven protection and VOC evasion. While EH3 represents the prevalent IGHV3-53 NAb whose epitope substantially overlaps with the ACE2 binding site, EH8 recognizes a narrow epitope exposed in both RBD-up and RBD-down conformations. When tested in vivo, a single-dose prophylactic administration of EH3 fully protected stringent K18-hACE2 mice from lethal challenge with Delta VOC. Our study demonstrates that protective NAbs responses converge in pediatric and adult SARS-CoV-2 patients.
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Affiliation(s)
- Yaozong Chen
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4712, USA
| | - Jérémie Prévost
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Irfan Ullah
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Hugo Romero
- Centre de Recherche du CHU Ste-Justine, Montreal, QC H3T 1C5, Canada
| | - Veronique Lisi
- Centre de Recherche du CHU Ste-Justine, Montreal, QC H3T 1C5, Canada
| | - William D. Tolbert
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4712, USA
| | - Jonathan R. Grover
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Shilei Ding
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada
| | - Shang Yu Gong
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
| | - Guillaume Beaudoin-Bussières
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Romain Gasser
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Mehdi Benlarbi
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada
| | - Dani Vézina
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada
| | - Sai Priya Anand
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
| | | | | | - Michael W. Grunst
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Ziwei Yang
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Yuxia Bo
- Department of Biochemistry, Microbiology and Immunology, Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Fei Zhou
- Unit on Structural Biology, Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kathie Béland
- Centre de Recherche du CHU Ste-Justine, Montreal, QC H3T 1C5, Canada
| | - Xiaoyun Bai
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Allison R. Zeher
- Unit on Structural Biology, Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rick K. Huang
- Unit on Structural Biology, Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dung N. Nguyen
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4712, USA
| | - Rebekah Sherburn
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4712, USA
| | - Di Wu
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Grzegorz Piszczek
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bastien Paré
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montreal, QC H3T 1J4, Canada
| | - Doreen Matthies
- Unit on Structural Biology, Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Di Xia
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jonathan Richard
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Priti Kumar
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Walther Mothes
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Marceline Côté
- Department of Biochemistry, Microbiology and Immunology, Center for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Pradeep D. Uchil
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Vincent-Philippe Lavallée
- Centre de Recherche du CHU Ste-Justine, Montreal, QC H3T 1C5, Canada
- Division of Pediatric Hematology-Oncology, Centre Hospitalier Universitaire (CHU) Sainte-Justine, Montréal, QC, Canada
- Département de Pédiatrie, Université de Montréal, Montreal, QC H3T 1C5, Canada
| | - Martin A. Smith
- Centre de Recherche du CHU Ste-Justine, Montreal, QC H3T 1C5, Canada
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montreal, QC H3T 1J4, Canada
| | - Marzena Pazgier
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4712, USA
| | - Elie Haddad
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
- Département de Pédiatrie, Université de Montréal, Montreal, QC H3T 1C5, Canada
| | - Andrés Finzi
- Centre de Recherche du CHUM (CRCHUM), Montreal, QC H2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
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19
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Pennell M, Rodriguez OL, Watson CT, Greiff V. The evolutionary and functional significance of germline immunoglobulin gene variation. Trends Immunol 2023; 44:7-21. [PMID: 36470826 DOI: 10.1016/j.it.2022.11.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 11/07/2022] [Indexed: 12/04/2022]
Abstract
The recombination between immunoglobulin (IG) gene segments determines an individual's naïve antibody repertoire and, consequently, (auto)antigen recognition. Emerging evidence suggests that mammalian IG germline variation impacts humoral immune responses associated with vaccination, infection, and autoimmunity - from the molecular level of epitope specificity, up to profound changes in the architecture of antibody repertoires. These links between IG germline variants and immunophenotype raise the question on the evolutionary causes and consequences of diversity within IG loci. We discuss why the extreme diversity in IG loci remains a mystery, why resolving this is important for the design of more effective vaccines and therapeutics, and how recent evidence from multiple lines of inquiry may help us do so.
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Affiliation(s)
- Matt Pennell
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA; Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.
| | - Oscar L Rodriguez
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Victor Greiff
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway.
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20
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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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21
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Jaffe DB, Shahi P, Adams BA, Chrisman AM, Finnegan PM, Raman N, Royall AE, Tsai F, Vollbrecht T, Reyes DS, Hepler NL, McDonnell WJ. Functional antibodies exhibit light chain coherence. Nature 2022; 611:352-357. [PMID: 36289331 PMCID: PMC9607724 DOI: 10.1038/s41586-022-05371-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 09/21/2022] [Indexed: 11/08/2022]
Abstract
The vertebrate adaptive immune system modifies the genome of individual B cells to encode antibodies that bind particular antigens1. In most mammals, antibodies are composed of heavy and light chains that are generated sequentially by recombination of V, D (for heavy chains), J and C gene segments. Each chain contains three complementarity-determining regions (CDR1-CDR3), which contribute to antigen specificity. Certain heavy and light chains are preferred for particular antigens2-22. Here we consider pairs of B cells that share the same heavy chain V gene and CDRH3 amino acid sequence and were isolated from different donors, also known as public clonotypes23,24. We show that for naive antibodies (those not yet adapted to antigens), the probability that they use the same light chain V gene is around 10%, whereas for memory (functional) antibodies, it is around 80%, even if only one cell per clonotype is used. This property of functional antibodies is a phenomenon that we call light chain coherence. We also observe this phenomenon when similar heavy chains recur within a donor. Thus, although naive antibodies seem to recur by chance, the recurrence of functional antibodies reveals surprising constraint and determinism in the processes of V(D)J recombination and immune selection. For most functional antibodies, the heavy chain determines the light chain.
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22
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Patel A, Kumar S, Lai L, Chakravarthy C, Valanparambil R, Reddy ES, Gottimukkala K, Bajpai P, Raju DR, Edara VV, Davis-Gardner ME, Linderman S, Dixit K, Sharma P, Mantus G, Cheedarla N, Verkerke HP, Frank F, Neish AS, Roback JD, Davis CW, Wrammert J, Ahmed R, Suthar MS, Sharma A, Murali-Krishna K, Chandele A, Ortlund EA. Molecular basis of SARS-CoV-2 Omicron variant evasion from shared neutralizing antibody response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.10.24.513517. [PMID: 36324804 DOI: 10.1101/2022.10.13.512091] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
A detailed understanding of the molecular features of the neutralizing epitopes developed by viral escape mutants is important for predicting and developing vaccines or therapeutic antibodies against continuously emerging SARS-CoV-2 variants. Here, we report three human monoclonal antibodies (mAbs) generated from COVID-19 recovered individuals during first wave of pandemic in India. These mAbs had publicly shared near germline gene usage and potently neutralized Alpha and Delta, but poorly neutralized Beta and completely failed to neutralize Omicron BA.1 SARS-CoV-2 variants. Structural analysis of these three mAbs in complex with trimeric spike protein showed that all three mAbs are involved in bivalent spike binding with two mAbs targeting class-1 and one targeting class-4 Receptor Binding Domain (RBD) epitope. Comparison of immunogenetic makeup, structure, and function of these three mAbs with our recently reported class-3 RBD binding mAb that potently neutralized all SARS-CoV-2 variants revealed precise antibody footprint, specific molecular interactions associated with the most potent multi-variant binding / neutralization efficacy. This knowledge has timely significance for understanding how a combination of certain mutations affect the binding or neutralization of an antibody and thus have implications for predicting structural features of emerging SARS-CoV-2 escape variants and to develop vaccines or therapeutic antibodies against these.
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Affiliation(s)
- Anamika Patel
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Sanjeev Kumar
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Lilin Lai
- Department of Pediatrics, Emory National Primate Center, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Chennareddy Chakravarthy
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Rajesh Valanparambil
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Elluri Seetharami Reddy
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi, 110067, India
- Kusuma School of Biological Sciences, Indian Institute of Technology, New Delhi, 110016, India
| | - Kamalvishnu Gottimukkala
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Prashant Bajpai
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Dinesh Ravindra Raju
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
- Georgia Tech, Atlanta, GA 30332, USA
| | - Venkata Viswanadh Edara
- Department of Pediatrics, Emory National Primate Center, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Meredith E Davis-Gardner
- Department of Pediatrics, Emory National Primate Center, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Susanne Linderman
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Kritika Dixit
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Pragati Sharma
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Grace Mantus
- Department of Pediatrics, Emory National Primate Center, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Narayanaiah Cheedarla
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Hans P Verkerke
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02215, USA
| | - Filipp Frank
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Andrew S Neish
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - John D Roback
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Carl W Davis
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Jens Wrammert
- Department of Pediatrics, Emory National Primate Center, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Rafi Ahmed
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Mehul S Suthar
- Department of Pediatrics, Emory National Primate Center, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Amit Sharma
- Structural Parasitology Group, International Center for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Kaja Murali-Krishna
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi, 110067, India
- Department of Pediatrics, Emory National Primate Center, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Anmol Chandele
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Eric A Ortlund
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
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23
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Patel A, Kumar S, Lai L, Chakravarthy C, Valanparambil R, Reddy ES, Gottimukkala K, Bajpai P, Raju DR, Edara VV, Davis-Gardner ME, Linderman S, Dixit K, Sharma P, Mantus G, Cheedarla N, Verkerke HP, Frank F, Neish AS, Roback JD, Davis CW, Wrammert J, Ahmed R, Suthar MS, Sharma A, Murali-Krishna K, Chandele A, Ortlund EA. Molecular basis of SARS-CoV-2 Omicron variant evasion from shared neutralizing antibody response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.10.24.513517. [PMID: 36324804 PMCID: PMC9628201 DOI: 10.1101/2022.10.24.513517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A detailed understanding of the molecular features of the neutralizing epitopes developed by viral escape mutants is important for predicting and developing vaccines or therapeutic antibodies against continuously emerging SARS-CoV-2 variants. Here, we report three human monoclonal antibodies (mAbs) generated from COVID-19 recovered individuals during first wave of pandemic in India. These mAbs had publicly shared near germline gene usage and potently neutralized Alpha and Delta, but poorly neutralized Beta and completely failed to neutralize Omicron BA.1 SARS-CoV-2 variants. Structural analysis of these three mAbs in complex with trimeric spike protein showed that all three mAbs are involved in bivalent spike binding with two mAbs targeting class-1 and one targeting class-4 Receptor Binding Domain (RBD) epitope. Comparison of immunogenetic makeup, structure, and function of these three mAbs with our recently reported class-3 RBD binding mAb that potently neutralized all SARS-CoV-2 variants revealed precise antibody footprint, specific molecular interactions associated with the most potent multi-variant binding / neutralization efficacy. This knowledge has timely significance for understanding how a combination of certain mutations affect the binding or neutralization of an antibody and thus have implications for predicting structural features of emerging SARS-CoV-2 escape variants and to develop vaccines or therapeutic antibodies against these.
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Affiliation(s)
- Anamika Patel
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Sanjeev Kumar
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Lilin Lai
- Department of Pediatrics, Emory National Primate Center, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA,Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Chennareddy Chakravarthy
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA,Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Rajesh Valanparambil
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA,Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Elluri Seetharami Reddy
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi, 110067, India,Kusuma School of Biological Sciences, Indian Institute of Technology, New Delhi, 110016, India
| | - Kamalvishnu Gottimukkala
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Prashant Bajpai
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Dinesh Ravindra Raju
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA.,Georgia Tech, Atlanta, GA 30332, USA
| | - Venkata Viswanadh Edara
- Department of Pediatrics, Emory National Primate Center, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Meredith E. Davis-Gardner
- Department of Pediatrics, Emory National Primate Center, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Susanne Linderman
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA,Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Kritika Dixit
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Pragati Sharma
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Grace Mantus
- Department of Pediatrics, Emory National Primate Center, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA,Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Narayanaiah Cheedarla
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Hans P. Verkerke
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA,Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02215, USA
| | - Filipp Frank
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Andrew S. Neish
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - John D. Roback
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Carl W. Davis
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA,Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Jens Wrammert
- Department of Pediatrics, Emory National Primate Center, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA,Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Rafi Ahmed
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA,Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Mehul S. Suthar
- Department of Pediatrics, Emory National Primate Center, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA,Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA,Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
| | - Amit Sharma
- Structural Parasitology Group, International Center for Genetic Engineering and Biotechnology, New Delhi, 110067, India,Correspondence: (E.A.O.), (A.C.), (K.M.K.), (A.S.)
| | - Kaja Murali-Krishna
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi, 110067, India,Department of Pediatrics, Emory National Primate Center, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA,Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA,Correspondence: (E.A.O.), (A.C.), (K.M.K.), (A.S.)
| | - Anmol Chandele
- ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi, 110067, India,Correspondence: (E.A.O.), (A.C.), (K.M.K.), (A.S.)
| | - Eric A. Ortlund
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA.,Correspondence: (E.A.O.), (A.C.), (K.M.K.), (A.S.)
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24
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Waltari E, Nafees S, McCutcheon KM, Wong J, Pak JE. AIRRscape: An interactive tool for exploring B-cell receptor repertoires and antibody responses. PLoS Comput Biol 2022; 18:e1010052. [PMID: 36126074 PMCID: PMC9524643 DOI: 10.1371/journal.pcbi.1010052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 09/30/2022] [Accepted: 09/04/2022] [Indexed: 11/18/2022] Open
Abstract
The sequencing of antibody repertoires of B-cells at increasing coverage and depth has led to the identification of vast numbers of immunoglobulin heavy and light chains. However, the size and complexity of these Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) datasets makes it difficult to perform exploratory analyses. To aid in data exploration, we have developed AIRRscape, an R Shiny-based interactive web browser application that enables B-cell receptor (BCR) and antibody feature discovery through comparisons among multiple repertoires. Using AIRR-seq data as input, AIRRscape starts by aggregating and sorting repertoires into interactive and explorable bins of germline V-gene, germline J-gene, and CDR3 length, providing a high-level view of the entire repertoire. Interesting subsets of repertoires can be quickly identified and selected, and then network topologies of CDR3 motifs can be generated for further exploration. Here we demonstrate AIRRscape using patient BCR repertoires and sequences of published monoclonal antibodies to investigate patterns of humoral immunity to three viral pathogens: SARS-CoV-2, HIV-1, and DENV (dengue virus). AIRRscape reveals convergent antibody sequences among datasets for all three pathogens, although HIV-1 antibody datasets display limited convergence and idiosyncratic responses. We have made AIRRscape available as a web-based Shiny application, along with code on GitHub to encourage its open development and use by immuno-informaticians, virologists, immunologists, vaccine developers, and other scientists that are interested in exploring and comparing multiple immune receptor repertoires.
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Affiliation(s)
- Eric Waltari
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
- * E-mail: (EW); (JEP)
| | - Saba Nafees
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | | | - Joan Wong
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - John E. Pak
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
- * E-mail: (EW); (JEP)
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25
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Park JC, Noh J, Jang S, Kim KH, Choi H, Lee D, Kim J, Chung J, Lee DY, Lee Y, Lee H, Yoo DK, Lee AC, Byun MS, Yi D, Han SH, Kwon S, Mook-Jung I. Association of B cell profile and receptor repertoire with the progression of Alzheimer's disease. Cell Rep 2022; 40:111391. [PMID: 36130492 DOI: 10.1016/j.celrep.2022.111391] [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: 02/28/2022] [Revised: 07/04/2022] [Accepted: 08/29/2022] [Indexed: 11/16/2022] Open
Abstract
Alzheimer's disease (AD) is the most prevalent type of dementia. Reports have revealed that the peripheral immune system is linked to neuropathology; however, little is known about the contribution of B lymphocytes in AD. For this longitudinal study, 133 participants are included at baseline and second-year follow-up. Also, we analyze B cell receptor (BCR) repertoire data generated from a public dataset of three normal and 10 AD samples and perform BCR repertoire profiling and pairwise sharing analysis. As a result, longitudinal increase in B lymphocytes is associated with increased cerebral amyloid deposition and hyperactivates induced pluripotent stem cell-derived microglia with loss-of-function for beta-amyloid clearance. Patients with AD share similar class-switched BCR sequences with identical isotypes, despite the high somatic hypermutation rate. Thus, BCR repertoire profiling can lead to the development of individualized immune-based therapeutics and treatment. We provide evidence of both quantitative and qualitative changes in B lymphocytes during AD pathogenesis.
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Affiliation(s)
- Jong-Chan Park
- Department of Biochemistry and Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea; Neuroscience Research Institute, Medical Research Center, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea; SNU Dementia Research Center, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea; Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Jinsung Noh
- Department of Electrical and Computer Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea; Bio-MAX Institute, Seoul National University, Seoul 08826, Republic of Korea
| | - Sukjin Jang
- Department of Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Ki Hyun Kim
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea; Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Hayoung Choi
- Department of Biochemistry and Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea; SNU Dementia Research Center, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea
| | - Dongjoon Lee
- Department of Biochemistry and Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea; SNU Dementia Research Center, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea
| | - Jieun Kim
- Department of Biochemistry and Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea
| | - Junho Chung
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea; Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Department of Biomedical Science, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Dong Young Lee
- Institute of Human Behavioral Medicine, Medical Research Center, Seoul National University, Seoul 03080, Republic of Korea; Department of Psychiatry, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea; Department of Neuropsychiatry, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - Yonghee Lee
- Department of Electrical and Computer Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Hyunho Lee
- Department of Electrical and Computer Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Duck Kyun Yoo
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea; Department of Biomedical Science, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Amos Chungwon Lee
- Bio-MAX Institute, Seoul National University, Seoul 08826, Republic of Korea
| | - Min Soo Byun
- Department of Psychiatry, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea; Department of Neuropsychiatry, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - Dahyun Yi
- Department of Neuropsychiatry, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - Sun-Ho Han
- Department of Biochemistry and Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea; Neuroscience Research Institute, Medical Research Center, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea; SNU Dementia Research Center, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea.
| | - Sunghoon Kwon
- Department of Electrical and Computer Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea; Bio-MAX Institute, Seoul National University, Seoul 08826, Republic of Korea; BK21+ Creative Research Engineer Development for IT, Seoul National University, Seoul 08826, Republic of Korea; Biomedical Research Institute, Seoul National University Hospital, Seoul 03080, Republic of Korea; Interdisciplinary Program in Bioengineering, Seoul National University, Seoul 08826, Republic of Korea.
| | - Inhee Mook-Jung
- Department of Biochemistry and Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea; Neuroscience Research Institute, Medical Research Center, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea; SNU Dementia Research Center, College of Medicine, Seoul National University, Seoul 03080, Republic of Korea.
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26
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Abstract
Antibodies and T cell receptors (TCRs) are the fundamental building blocks of adaptive immunity. Repertoire-scale functionality derives from their epitope-binding properties, just as macroscopic properties like temperature derive from microscopic molecular properties. However, most approaches to repertoire-scale measurement, including sequence diversity and entropy, are not based on antibody or TCR function in this way. Thus, they potentially overlook key features of immunological function. Here we present a framework that describes repertoires in terms of the epitope-binding properties of their constituent antibodies and TCRs, based on analysis of thousands of antibody-antigen and TCR-peptide-major-histocompatibility-complex binding interactions and over 400 high-throughput repertoires. We show that repertoires consist of loose overlapping classes of antibodies and TCRs with similar binding properties. We demonstrate the potential of this framework to distinguish specific responses vs. bystander activation in influenza vaccinees, stratify cytomegalovirus (CMV)-infected cohorts, and identify potential immunological "super-agers." Classes add a valuable dimension to the assessment of immune function.
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27
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Clonal structure, stability and dynamics of human memory B cells and circulating plasmablasts. Nat Immunol 2022; 23:1076-1085. [PMID: 35761085 PMCID: PMC9276532 DOI: 10.1038/s41590-022-01230-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 04/26/2022] [Indexed: 12/22/2022]
Abstract
Memory B cells persist for a lifetime and rapidly differentiate into antibody-producing plasmablasts and plasma cells upon antigen re-encounter. The clonal relationship and evolution of memory B cells and circulating plasmablasts is not well understood. Using single-cell sequencing combined with isolation of specific antibodies, we found that in two healthy donors, the memory B cell repertoire was dominated by large IgM, IgA and IgG2 clonal families, whereas IgG1 families, including those specific for recall antigens, were of small size. Analysis of multiyear samples demonstrated stability of memory B cell clonal families and revealed that a large fraction of recently generated plasmablasts was derived from long-term memory B cell families and was found recurrently. Collectively, this study provides a systematic description of the structure, stability and dynamics of the human memory B cell pool and suggests that memory B cells may be active at any time point in the generation of plasmablasts.
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28
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Falconi-Agapito F, Kerkhof K, Merino X, Bakokimi D, Torres F, Van Esbroeck M, Talledo M, Ariën KK. Peptide Biomarkers for the Diagnosis of Dengue Infection. Front Immunol 2022; 13:793882. [PMID: 35154111 PMCID: PMC8826428 DOI: 10.3389/fimmu.2022.793882] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/05/2022] [Indexed: 11/13/2022] Open
Abstract
In a world with an increasing population at risk of exposure to arthropod-borne flaviviruses, access to timely and accurate diagnostic tests would impact profoundly on the management of cases. Twenty peptides previously identified using a flavivirus proteome-wide microarray were evaluated to determine their discriminatory potential to detect dengue virus (DENV) infection. This included nine peptides recognized by IgM antibodies (PM peptides) and 11 peptides recognized by IgG antibodies (PG peptides). A bead-based multiplex peptide immunoassay (MPIA) using the Luminex technology was set-up to determine Ab binding levels to each of these peptides in a panel of 323 carefully selected human serum samples. Sera are derived from individuals either infected with different viruses, namely, the four DENV serotypes, Zika virus (ZIKV), yellow fever virus (YFV), chikungunya virus (CHIKV), West Nile virus (WNV) and Human immunodeficiency virus (HIV), or receiving vaccination against YFV, tick-borne encephalitis (TBEV), and Japanese encephalitis virus (JEV). Additionally, a set of healthy controls were included. We targeted a minimum specificity of 80% for all the analysis. The PG-9 peptide had the best sensitivity (73%) when testing DENV sera from acute patients (A-DENV; <8 days since symptom onset). With sera from convalescent DENV patients (C-DENV; >10 days since symptom onset) the FPG-1 peptide was the best seromarker with a sensitivity of 86%. When combining all A-DENV and C-DENV samples, peptides PM-22 and FPG-1 had the best-diagnostic performance with a sensitivity of 60 and 61.1%, and areas under the curve (AUC) of 0.7865 and 0.8131, respectively. A Random forest (RF) algorithm was used to select the best combination of peptides to classify DENV infection at a targeted specificity >80%. The best RF model for PM peptides that included A-DENV and C-DENV samples, reached a sensitivity of 72.3%, while for PG peptides, the best RF models for A-DENV only, C-DENV only and A-DENV + C-DENV reached a sensitivity of 88.9%, 89.1%, and 88.3%, respectively. In conclusion, the combination of multiple peptides constitutes a founding set of seromarkers for the discrimination of DENV infected individuals from other flavivirus infections.
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Affiliation(s)
- Francesca Falconi-Agapito
- Department of Biomedical Sciences, Unit of Virology, Institute of Tropical Medicine, Antwerp, Belgium
- Virology Unit, Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Karen Kerkhof
- Department of Biomedical Sciences, Unit of Virology, Institute of Tropical Medicine, Antwerp, Belgium
| | - Xiomara Merino
- Virology Unit, Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Diana Bakokimi
- Department of Biomedical Sciences, Unit of Virology, Institute of Tropical Medicine, Antwerp, Belgium
| | | | - Marjan Van Esbroeck
- Department of Clinical Sciences, National Reference Center for Arboviruses, Institute of Tropical Medicine, Antwerp, Belgium
| | - Michael Talledo
- Virology Unit, Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Kevin K. Ariën
- Department of Biomedical Sciences, Unit of Virology, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
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29
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Murji AA, Raju N, Qin JS, Kaldine H, Janowska K, Fechter EF, Mapengo R, Scheepers C, Setliff I, Acharya P, Morris L, Georgiev IS. Sequence and functional characterization of a public HIV-specific antibody clonotype. iScience 2022; 25:103564. [PMID: 34984325 PMCID: PMC8692997 DOI: 10.1016/j.isci.2021.103564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 08/30/2021] [Accepted: 12/01/2021] [Indexed: 01/15/2023] Open
Abstract
Public antibody clonotypes shared among multiple individuals have been identified for several pathogens. However, little is known about the determinants of antibody "publicness". Here, we characterize the sequence and functional properties of antibodies from a public clonotype targeting the CD4 binding site on HIV-1 Env. Our results showed that HIV-1 specificity for the public antibodies studied here, comprising sequences from three individuals, was modulated by the VH, but not VL, germline gene. Non-native pairing of public heavy and light chains from different individuals suggested functional complementation of sequences within this public antibody clonotype. The strength of antigen recognition appeared to be dependent on the specific antibody light chain used, but not on other sequence features such as native-antibody or germline sequence identity. Understanding the determinants of antibody clonotype "publicness" can provide insights into the fundamental rules of host-pathogen interactions at the population level, with implications for clonotype-specific vaccine development.
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Affiliation(s)
- Amyn A. Murji
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Nagarajan Raju
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Juliana S. Qin
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Haajira Kaldine
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa
- Antibody Immunity Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2000, South Africa
| | - Katarzyna Janowska
- Division of Structural Biology, Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | | | - Rutendo Mapengo
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa
- Antibody Immunity Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2000, South Africa
| | - Cathrine Scheepers
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa
- Antibody Immunity Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2000, South Africa
| | - Ian Setliff
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Priyamvada Acharya
- Division of Structural Biology, Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Lynn Morris
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa
- Antibody Immunity Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2000, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban 4041, South Africa
| | - Ivelin S. Georgiev
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Program in Computational Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, TN 37232, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
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30
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Wang Q, Zeng H, Zhu Y, Wang M, Zhang Y, Yang X, Tang H, Li H, Chen Y, Ma C, Lan C, Liu B, Yang W, Yu X, Zhang Z. Dual UMIs and Dual Barcodes With Minimal PCR Amplification Removes Artifacts and Acquires Accurate Antibody Repertoire. Front Immunol 2021; 12:778298. [PMID: 35003093 PMCID: PMC8727365 DOI: 10.3389/fimmu.2021.778298] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/25/2021] [Indexed: 12/03/2022] Open
Abstract
Antibody repertoire sequencing (Rep-seq) has been widely used to reveal repertoire dynamics and to interrogate antibodies of interest at single nucleotide-level resolution. However, polymerase chain reaction (PCR) amplification introduces extensive artifacts including chimeras and nucleotide errors, leading to false discovery of antibodies and incorrect assessment of somatic hypermutations (SHMs) which subsequently mislead downstream investigations. Here, a novel approach named DUMPArts, which improves the accuracy of antibody repertoires by labeling each sample with dual barcodes and each molecule with dual unique molecular identifiers (UMIs) via minimal PCR amplification to remove artifacts, is developed. Tested by ultra-deep Rep-seq data, DUMPArts removed inter-sample chimeras, which cause artifactual shared clones and constitute approximately 15% of reads in the library, as well as intra-sample chimeras with erroneous SHMs and constituting approximately 20% of the reads, and corrected base errors and amplification biases by consensus building. The removal of these artifacts will provide an accurate assessment of antibody repertoires and benefit related studies, especially mAb discovery and antibody-guided vaccine design.
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Affiliation(s)
- Qilong Wang
- Center for Precision Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Huikun Zeng
- Center for Precision Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yan Zhu
- Center for Precision Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Minhui Wang
- State Key Laboratory of Organ Failure Research, National Clinical Research Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yanfang Zhang
- State Key Laboratory of Organ Failure Research, National Clinical Research Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Xiujia Yang
- State Key Laboratory of Organ Failure Research, National Clinical Research Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Haipei Tang
- Center for Precision Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Hongliang Li
- School of Computer Science and Technology, Beijing Institute of Technology, Beijing, China
| | - Yuan Chen
- Center for Precision Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Cuiyu Ma
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Chunhong Lan
- Center for Precision Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- State Key Laboratory of Organ Failure Research, National Clinical Research Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Bin Liu
- School of Computer Science and Technology, Beijing Institute of Technology, Beijing, China
| | - Wei Yang
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- *Correspondence: Wei Yang, ; Xueqing Yu, ; Zhenhai Zhang, ;
| | - Xueqing Yu
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Division of Nephrology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- *Correspondence: Wei Yang, ; Xueqing Yu, ; Zhenhai Zhang, ;
| | - Zhenhai Zhang
- Center for Precision Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- State Key Laboratory of Organ Failure Research, National Clinical Research Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Southern Medical University, Guangzhou, China
- *Correspondence: Wei Yang, ; Xueqing Yu, ; Zhenhai Zhang, ;
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Analysis of B cell receptor repertoires reveals key signatures of systemic B cell response after SARS-CoV-2 infection. J Virol 2021; 96:e0160021. [PMID: 34878902 PMCID: PMC8865482 DOI: 10.1128/jvi.01600-21] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
A comprehensive study of the B cell response against SARS-CoV-2 could be significant for understanding the immune response and developing therapeutical antibodies and vaccines. To define the dynamics and characteristics of the antibody repertoire following SARS-CoV-2 infection, we analyzed the mRNA transcripts of immunoglobulin heavy chain (IgH) repertoires of 24 peripheral blood samples collected between 3 and 111 days after symptom onset from 10 COVID-19 patients. Massive clonal expansion of naive B cells with limited somatic hypermutation (SHM) was observed in the second week after symptom onset. The proportion of low-SHM IgG clones strongly correlated with spike-specific IgG antibody titers, highlighting the significant activation of naive B cells in response to a novel virus infection. The antibody isotype switching landscape showed a transient IgA surge in the first week after symptom onset, followed by a sustained IgG elevation that lasted for at least 3 months. SARS-CoV-2 infection elicited poly-germ line reactive antibody responses. Interestingly, 17 different IGHV germ line genes recombined with IGHJ6 showed significant clonal expansion. By comparing the IgH repertoires that we sequenced with the 774 reported SARS-CoV-2–reactive monoclonal antibodies (MAbs), 13 shared spike-specific IgH clusters were found. These shared spike-specific IgH clusters are derived from the same lineage of several recently published neutralizing MAbs, including CC12.1, CC12.3, C102, REGN10977, and 4A8. Furthermore, identical spike-specific IgH sequences were found in different COVID-19 patients, suggesting a highly convergent antibody response to SARS-CoV-2. Our analysis based on sequencing antibody repertoires from different individuals revealed key signatures of the systemic B cell response induced by SARS-CoV-2 infection. IMPORTANCE Although the canonical delineation of serum antibody responses following SARS-CoV-2 infection has been well established, the dynamics of antibody repertoire at the mRNA transcriptional level has not been well understood, especially the correlation between serum antibody titers and the antibody mRNA transcripts. In this study, we analyzed the IgH transcripts and characterized the B cell clonal expansion and differentiation, isotype switching, and somatic hypermutation in COVID-19 patients. This study provided insights at the repertoire level for the B cell response after SARS-CoV-2 infection.
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32
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The immuneML ecosystem for machine learning analysis of adaptive immune receptor repertoires. NAT MACH INTELL 2021. [DOI: 10.1038/s42256-021-00413-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Landscapes and dynamic diversifications of B-cell receptor repertoires in COVID-19 patients. Hum Immunol 2021; 83:119-129. [PMID: 34785098 PMCID: PMC8566346 DOI: 10.1016/j.humimm.2021.10.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 10/29/2021] [Accepted: 10/29/2021] [Indexed: 01/08/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the pandemic of coronavirus disease 2019 (COVID-19). Great international efforts have been put into the development of prophylactic vaccines and neutralizing antibodies. However, the knowledge about the B cell immune response induced by the SARS-CoV-2 virus is still limited. Here, we report a comprehensive characterization of the dynamics of immunoglobin heavy chain (IGH) repertoire in COVID-19 patients. By using next-generation sequencing technology, we examined the temporal changes in the landscape of the patient's immunological status and found dramatic changes in the IGH within the patient's immune system after the onset of COVID-19 symptoms. Although different patients have distinct immune responses to SARS-CoV-2 infection, by employing clonotype overlap, lineage expansion, and clonotype network analyses, we observed a higher clonotype overlap and substantial lineage expansion of B cell clones 2-3 weeks after the onset of illness, which is of great importance to B-cell immune responses. Meanwhile, for preferences of V gene usage during SARS-CoV-2 infection, IGHV3-74 and IGHV4-34, and IGHV4-39 in COVID-19 patients were more abundant than those of healthy controls. Overall, we present an immunological resource for SARS-CoV-2 that could promote both therapeutic development as well as mechanistic research.
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Horst A, Smakaj E, Natali EN, Tosoni D, Babrak LM, Meier P, Miho E. Machine Learning Detects Anti-DENV Signatures in Antibody Repertoire Sequences. Front Artif Intell 2021; 4:715462. [PMID: 34708197 PMCID: PMC8542978 DOI: 10.3389/frai.2021.715462] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 07/30/2021] [Indexed: 11/13/2022] Open
Abstract
Dengue infection is a global threat. As of today, there is no universal dengue fever treatment or vaccines unreservedly recommended by the World Health Organization. The investigation of the specific immune response to dengue virus would support antibody discovery as therapeutics for passive immunization and vaccine design. High-throughput sequencing enables the identification of the multitude of antibodies elicited in response to dengue infection at the sequence level. Artificial intelligence can mine the complex data generated and has the potential to uncover patterns in entire antibody repertoires and detect signatures distinctive of single virus-binding antibodies. However, these machine learning have not been harnessed to determine the immune response to dengue virus. In order to enable the application of machine learning, we have benchmarked existing methods for encoding biological and chemical knowledge as inputs and have investigated novel encoding techniques. We have applied different machine learning methods such as neural networks, random forests, and support vector machines and have investigated the parameter space to determine best performing algorithms for the detection and prediction of antibody patterns at the repertoire and antibody sequence levels in dengue-infected individuals. Our results show that immune response signatures to dengue are detectable both at the antibody repertoire and at the antibody sequence levels. By combining machine learning with phylogenies and network analysis, we generated novel sequences that present dengue-binding specific signatures. These results might aid further antibody discovery and support vaccine design.
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Affiliation(s)
- Alexander Horst
- School of Life Sciences, Institute of Medical Engineering and Medical Informatics, University of Applied Sciences and Arts Northwestern Switzerland FHNW, Muttenz, Switzerland
| | - Erand Smakaj
- School of Life Sciences, Institute of Medical Engineering and Medical Informatics, University of Applied Sciences and Arts Northwestern Switzerland FHNW, Muttenz, Switzerland
| | - Eriberto Noel Natali
- School of Life Sciences, Institute of Medical Engineering and Medical Informatics, University of Applied Sciences and Arts Northwestern Switzerland FHNW, Muttenz, Switzerland
| | - Deniz Tosoni
- School of Life Sciences, Institute of Medical Engineering and Medical Informatics, University of Applied Sciences and Arts Northwestern Switzerland FHNW, Muttenz, Switzerland
| | - Lmar Marie Babrak
- School of Life Sciences, Institute of Medical Engineering and Medical Informatics, University of Applied Sciences and Arts Northwestern Switzerland FHNW, Muttenz, Switzerland
| | - Patrick Meier
- School of Life Sciences, Institute of Medical Engineering and Medical Informatics, University of Applied Sciences and Arts Northwestern Switzerland FHNW, Muttenz, Switzerland
| | - Enkelejda Miho
- School of Life Sciences, Institute of Medical Engineering and Medical Informatics, University of Applied Sciences and Arts Northwestern Switzerland FHNW, Muttenz, Switzerland.,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.,aiNET GmbH, Basel, Switzerland
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35
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Current Trends and Limitations in Dengue Antiviral Research. Trop Med Infect Dis 2021; 6:tropicalmed6040180. [PMID: 34698303 PMCID: PMC8544673 DOI: 10.3390/tropicalmed6040180] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 12/13/2022] Open
Abstract
Dengue is the most prevalent arthropod-borne viral disease worldwide and affects approximately 2.5 billion people living in over 100 countries. Increasing geographic expansion of Aedes aegypti mosquitoes (which transmit the virus) has made dengue a global health concern. There are currently no approved antivirals available to treat dengue, and the only approved vaccine used in some countries is limited to seropositive patients. Treatment of dengue, therefore, remains largely supportive to date; hence, research efforts are being intensified for the development of antivirals. The nonstructural proteins, 3 and 5 (NS3 and NS5), have been the major targets for dengue antiviral development due to their indispensable enzymatic and biological functions in the viral replication process. NS5 is the largest and most conserved nonstructural protein encoded by flaviviruses. Its multifunctionality makes it an attractive target for antiviral development, but research efforts have, this far, not resulted in the successful development of an antiviral targeting NS5. Increase in structural insights into the dengue NS5 protein will accelerate drug discovery efforts focused on NS5 as an antiviral target. In this review, we will give an overview of the current state of therapeutic development, with a focus on NS5 as a therapeutic target against dengue.
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Castro R, Navelsaker S, Collet B, Jouneau L, Bochet P, Quillet E, Evensen Ø, Sunyer JO, Fillatreau S, Bruhns P, Rose T, Huetz F, Boudinot P. Cutting Edge: Neutralizing Public Antibody Responses Are an Ancient Form of Defense Conserved in Fish and Mammals. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2021; 207:371-375. [PMID: 34233911 PMCID: PMC11152318 DOI: 10.4049/jimmunol.2100149] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 05/16/2021] [Indexed: 11/19/2022]
Abstract
The repertoire of Abs is generated by genomic rearrangements during B cell differentiation. Although V(D)J rearrangements lead to repertoires mostly different between individuals, recent studies have shown that they contain a substantial fraction of overrepresented and shared "public" clones. We previously reported a strong public IgHμ clonotypic response against the rhabdovirus viral hemorrhagic septicemia virus in a teleost fish. In this study, we identified an IgL chain associated with this public response that allowed us to characterize its functionality. We show that this public Ab response has a potent neutralizing capacity that is typically associated with host protection during rhabdovirus infections. We also demonstrate that the public response is not restricted to a particular trout isogenic line but expressed in multiple genetic backgrounds and may be used as a marker of successful vaccination. Our work reveals that public B cell responses producing generic Abs constitute a mechanism of protection against infection conserved across vertebrates.
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Affiliation(s)
- Rosario Castro
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France
| | - Sofie Navelsaker
- Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine, Oslo, Norway
| | - Bertrand Collet
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France
| | - Luc Jouneau
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France
| | - Pascal Bochet
- Bioimage Analysis Unit, Department of Cell Biology and Infection, Institut Pasteur, CNRS-UMR3691, Paris, France
| | - Edwige Quillet
- Université Paris-Saclay, INRAE, GABI, Jouy-en-Josas, France
| | - Øystein Evensen
- Department of Basic Sciences and Aquatic Medicine, Faculty of Veterinary Medicine, Oslo, Norway
| | - J Oriol Sunyer
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA
| | - Simon Fillatreau
- Department of Immunology, Infectiology and Haematology (I2H), Institut Necker-Enfants Malades, INSERM U1151-CNRS UMR 8253, Paris, France
- Faculté de Médecine, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
- AP-HP, Hôpital Necker-Enfants Malades, Paris, France
| | - Pierre Bruhns
- Unit of Antibodies in Therapy and Pathology, Institut Pasteur, UMR 1222 INSERM, Paris, France; and
| | - Thierry Rose
- Lymphocyte Cell Biology Unit, INSERM 1221, Institut Pasteur, Paris, France
| | - François Huetz
- Unit of Antibodies in Therapy and Pathology, Institut Pasteur, UMR 1222 INSERM, Paris, France; and
| | - Pierre Boudinot
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France;
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37
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Zhang Q, Ju B, Ge J, Chan JFW, Cheng L, Wang R, Huang W, Fang M, Chen P, Zhou B, Song S, Shan S, Yan B, Zhang S, Ge X, Yu J, Zhao J, Wang H, Liu L, Lv Q, Fu L, Shi X, Yuen KY, Liu L, Wang Y, Chen Z, Zhang L, Wang X, Zhang Z. Potent and protective IGHV3-53/3-66 public antibodies and their shared escape mutant on the spike of SARS-CoV-2. Nat Commun 2021; 12:4210. [PMID: 34244522 PMCID: PMC8270942 DOI: 10.1038/s41467-021-24514-w] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 06/07/2021] [Indexed: 12/23/2022] Open
Abstract
Neutralizing antibodies (nAbs) to SARS-CoV-2 hold powerful potentials for clinical interventions against COVID-19 disease. However, their common genetic and biologic features remain elusive. Here we interrogate a total of 165 antibodies from eight COVID-19 patients, and find that potent nAbs from different patients have disproportionally high representation of IGHV3-53/3-66 usage, and therefore termed as public antibodies. Crystal structural comparison of these antibodies reveals they share similar angle of approach to RBD, overlap in buried surface and binding residues on RBD, and have substantial spatial clash with receptor angiotensin-converting enzyme-2 (ACE2) in binding to RBD. Site-directed mutagenesis confirms these common binding features although some minor differences are found. One representative antibody, P5A-3C8, demonstrates extraordinarily protective efficacy in a golden Syrian hamster model against SARS-CoV-2 infection. However, virus escape analysis identifies a single natural mutation in RBD, namely K417N found in B.1.351 variant from South Africa, abolished the neutralizing activity of these public antibodies. The discovery of public antibodies and shared escape mutation highlight the intricate relationship between antibody response and SARS-CoV-2, and provide critical reference for the development of antibody and vaccine strategies to overcome the antigenic variation of SARS-CoV-2.
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Affiliation(s)
- Qi Zhang
- NexVac Research Center, Comprehensive AIDS Research Center, Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Tsinghua University, Beijing, China
| | - Bin Ju
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital; The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Jiwan Ge
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jasper Fuk-Woo Chan
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong SAR, People's Republic of China
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, People's Republic of China
| | - Lin Cheng
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital; The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Ruoke Wang
- NexVac Research Center, Comprehensive AIDS Research Center, Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Tsinghua University, Beijing, China
| | - Weijin Huang
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, National Institutes for Food and Drug Control, Beijing, China
| | - Mengqi Fang
- NexVac Research Center, Comprehensive AIDS Research Center, Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Tsinghua University, Beijing, China
| | - Peng Chen
- NexVac Research Center, Comprehensive AIDS Research Center, Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Tsinghua University, Beijing, China
| | - Bing Zhou
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital; The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Shuo Song
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital; The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Sisi Shan
- NexVac Research Center, Comprehensive AIDS Research Center, Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Tsinghua University, Beijing, China
| | - Baohua Yan
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing, China
| | - Senyan Zhang
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xiangyang Ge
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital; The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Jiazhen Yu
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital; The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Juanjuan Zhao
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital; The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
- Shenzhen Bay Laboratory, Shenzhen, Guangdong Province, China
| | - Haiyan Wang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital; The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Li Liu
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, People's Republic of China
- AIDS Institute, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, People's Republic of China
| | - Qining Lv
- NexVac Research Center, Comprehensive AIDS Research Center, Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Tsinghua University, Beijing, China
| | - Lili Fu
- NexVac Research Center, Comprehensive AIDS Research Center, Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Tsinghua University, Beijing, China
| | - Xuanling Shi
- NexVac Research Center, Comprehensive AIDS Research Center, Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Tsinghua University, Beijing, China
| | - Kwok Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong SAR, People's Republic of China
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, People's Republic of China
| | - Lei Liu
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital; The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Youchun Wang
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, National Institutes for Food and Drug Control, Beijing, China.
| | - Zhiwei Chen
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong SAR, People's Republic of China.
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, People's Republic of China.
- AIDS Institute, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, People's Republic of China.
| | - Linqi Zhang
- NexVac Research Center, Comprehensive AIDS Research Center, Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Tsinghua University, Beijing, China.
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China.
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen, China.
| | - Xinquan Wang
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing, China.
| | - Zheng Zhang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital; The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China.
- Shenzhen Bay Laboratory, Shenzhen, Guangdong Province, China.
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38
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Tan TJC, Yuan M, Kuzelka K, Padron GC, Beal JR, Chen X, Wang Y, Rivera-Cardona J, Zhu X, Stadtmueller BM, Brooke CB, Wilson IA, Wu NC. Sequence signatures of two public antibody clonotypes that bind SARS-CoV-2 receptor binding domain. Nat Commun 2021; 12:3815. [PMID: 34155209 PMCID: PMC8217500 DOI: 10.1038/s41467-021-24123-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 05/28/2021] [Indexed: 02/05/2023] Open
Abstract
Since the COVID-19 pandemic onset, the antibody response to SARS-CoV-2 has been extensively characterized. Antibodies to the receptor binding domain (RBD) on the spike protein are frequently encoded by IGHV3-53/3-66 with a short complementarity-determining region (CDR) H3. Germline-encoded sequence motifs in heavy chain CDRs H1 and H2 have a major function, but whether any common motifs are present in CDR H3, which is often critical for binding specificity, is not clear. Here, we identify two public clonotypes of IGHV3-53/3-66 RBD antibodies with a 9-residue CDR H3 that pair with different light chains. Distinct sequence motifs on CDR H3 are present in the two public clonotypes that seem to be related to differential light chain pairing. Additionally, we show that Y58F is a common somatic hypermutation that results in increased binding affinity of IGHV3-53/3-66 RBD antibodies with a short CDR H3. These results advance understanding of the antibody response to SARS-CoV-2.
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Affiliation(s)
- Timothy J C Tan
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Kaylee Kuzelka
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Gilberto C Padron
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jacob R Beal
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Xin Chen
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yiquan Wang
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Joel Rivera-Cardona
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Xueyong Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Beth M Stadtmueller
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Christopher B Brooke
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA.
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA.
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA.
| | - Nicholas C Wu
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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39
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Natali EN, Babrak LM, Miho E. Prospective Artificial Intelligence to Dissect the Dengue Immune Response and Discover Therapeutics. Front Immunol 2021; 12:574411. [PMID: 34211454 PMCID: PMC8239437 DOI: 10.3389/fimmu.2021.574411] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 05/17/2021] [Indexed: 01/02/2023] Open
Abstract
Dengue virus (DENV) poses a serious threat to global health as the causative agent of dengue fever. The virus is endemic in more than 128 countries resulting in approximately 390 million infection cases each year. Currently, there is no approved therapeutic for treatment nor a fully efficacious vaccine. The development of therapeutics is confounded and hampered by the complexity of the immune response to DENV, in particular to sequential infection with different DENV serotypes (DENV1-5). Researchers have shown that the DENV envelope (E) antigen is primarily responsible for the interaction and subsequent invasion of host cells for all serotypes and can elicit neutralizing antibodies in humans. The advent of high-throughput sequencing and the rapid advancements in computational analysis of complex data, has provided tools for the deconvolution of the DENV immune response. Several types of complex statistical analyses, machine learning models and complex visualizations can be applied to begin answering questions about the B- and T-cell immune responses to multiple infections, antibody-dependent enhancement, identification of novel therapeutics and advance vaccine research.
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Affiliation(s)
- Eriberto N. Natali
- Institute of Medical Engineering and Medical Informatics, School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland FHNW, Muttenz, Switzerland
| | - Lmar M. Babrak
- Institute of Medical Engineering and Medical Informatics, School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland FHNW, Muttenz, Switzerland
| | - Enkelejda Miho
- Institute of Medical Engineering and Medical Informatics, School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland FHNW, Muttenz, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- aiNET GmbH, Basel, Switzerland
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40
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Bullen G, Galson JD, Hall G, Villar P, Moreels L, Ledsgaard L, Mattiuzzo G, Bentley EM, Masters EW, Tang D, Millett S, Tongue D, Brown R, Diamantopoulos I, Parthiban K, Tebbutt C, Leah R, Chaitanya K, Ergueta-Carballo S, Pazeraitis D, Surade SB, Ashiru O, Crippa L, Cowan R, Bowler MW, Campbell JI, Lee WYJ, Carr MD, Matthews D, Pfeffer P, Hufton SE, Sawmynaden K, Osbourn J, McCafferty J, Karatt-Vellatt A. Cross-Reactive SARS-CoV-2 Neutralizing Antibodies From Deep Mining of Early Patient Responses. Front Immunol 2021; 12:678570. [PMID: 34211469 PMCID: PMC8239432 DOI: 10.3389/fimmu.2021.678570] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 05/13/2021] [Indexed: 12/22/2022] Open
Abstract
Passive immunization using monoclonal antibodies will play a vital role in the fight against COVID-19. The recent emergence of viral variants with reduced sensitivity to some current antibodies and vaccines highlights the importance of broad cross-reactivity. This study describes deep-mining of the antibody repertoires of hospitalized COVID-19 patients using phage display technology and B cell receptor (BCR) repertoire sequencing to isolate neutralizing antibodies and gain insights into the early antibody response. This comprehensive discovery approach has yielded a panel of potent neutralizing antibodies which bind distinct viral epitopes including epitopes conserved in SARS-CoV-1. Structural determination of a non-ACE2 receptor blocking antibody reveals a previously undescribed binding epitope, which is unlikely to be affected by the mutations in any of the recently reported major viral variants including B.1.1.7 (from the UK), B.1.351 (from South Africa) and B.1.1.28 (from Brazil). Finally, by combining sequences of the RBD binding and neutralizing antibodies with the B cell receptor repertoire sequencing, we also describe a highly convergent early antibody response. Similar IgM-derived sequences occur within this study group and also within patient responses described by multiple independent studies published previously.
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Affiliation(s)
| | | | - Gareth Hall
- Leicester Institute of Structural and Chemical Biology and Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
| | | | | | | | - Giada Mattiuzzo
- National Institute for Biological Standards and Control, Potters Bar, United Kingdom
| | - Emma M Bentley
- National Institute for Biological Standards and Control, Potters Bar, United Kingdom
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Richard Cowan
- Leicester Institute of Structural and Chemical Biology and Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
| | | | | | - Wing-Yiu Jason Lee
- Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Mark D Carr
- Leicester Institute of Structural and Chemical Biology and Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
| | | | - Paul Pfeffer
- Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Simon E Hufton
- National Institute for Biological Standards and Control, Potters Bar, United Kingdom
| | | | - Jane Osbourn
- Alchemab Therapeutics Ltd., London, United Kingdom
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41
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Wang H, Yan K, Wang R, Yang Y, Shen Y, Yu C, Chen L. Antibody heavy chain CDR3 length-dependent usage of human IGHJ4 and IGHJ6 germline genes. Antib Ther 2021; 4:101-108. [PMID: 34195544 PMCID: PMC8237691 DOI: 10.1093/abt/tbab010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/07/2021] [Accepted: 06/10/2021] [Indexed: 12/26/2022] Open
Abstract
Therapeutic antibody discovery using synthetic diversity has been proved productive, especially for target proteins not suitable for traditional animal immunization-based antibody discovery approaches. Recently, many lines of evidences suggest that the quality of synthetic diversity design limits the development success of synthetic antibody hits. The aim of our study is to understand the quality limitation and to properly address the challenges with a better design. Using VH3–23 as a model framework, we observed and quantitatively mapped CDR-H3 loop length-dependent usage of human IGHJ4 and IGHJ6 germline genes in the natural human immune repertoire. Skewed usage of DH2-JH6 and DH3-JH6 rearrangements was quantitatively determined in a CDR-H3 length-dependent manner in natural human antibodies with long CDR-H3 loops. Structural modeling suggests choices of JH help to stabilize antibody CDR-H3 loop and JH only partially contributes to the paratope. Our observations shed light on the design of next-generation synthetic diversity with improved probability of success.
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Affiliation(s)
- Huimin Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, #15 Beisanhuandong Rd, Chaoyang District, Beijing 100029, China
| | - Kai Yan
- Biotherapeutics, Biocytogen Pharmaceuticals (Beijing) Co. Ltd., #12 Baoshennan St, Daxing District, Beijing 102629, China
| | - Ruixue Wang
- Biotherapeutics, Biocytogen Pharmaceuticals (Beijing) Co. Ltd., #12 Baoshennan St, Daxing District, Beijing 102629, China
| | - Yi Yang
- Biotherapeutics, Biocytogen Pharmaceuticals (Beijing) Co. Ltd., #12 Baoshennan St, Daxing District, Beijing 102629, China
| | - Yuelei Shen
- Biotherapeutics, Biocytogen Pharmaceuticals (Beijing) Co. Ltd., #12 Baoshennan St, Daxing District, Beijing 102629, China
| | - Changyuan Yu
- College of Life Science and Technology, Beijing University of Chemical Technology, #15 Beisanhuandong Rd, Chaoyang District, Beijing 100029, China
| | - Lei Chen
- Biotherapeutics, Biocytogen Pharmaceuticals (Beijing) Co. Ltd., #12 Baoshennan St, Daxing District, Beijing 102629, China
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42
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Yan Q, He P, Huang X, Luo K, Zhang Y, Yi H, Wang Q, Li F, Hou R, Fan X, Li P, Liu X, Liang H, Deng Y, Chen Z, Chen Y, Mo X, Feng L, Xiong X, Li S, Han J, Qu L, Niu X, Chen L. Germline IGHV3-53-encoded RBD-targeting neutralizing antibodies are commonly present in the antibody repertoires of COVID-19 patients. Emerg Microbes Infect 2021; 10:1097-1111. [PMID: 33944697 PMCID: PMC8183521 DOI: 10.1080/22221751.2021.1925594] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Monoclonal antibodies (mAbs) encoded by IGHV3-53 (VH3-53) targeting the spike receptor-binding domain (RBD) have been isolated from different COVID-19 patients. However, the existence and prevalence of shared VH3-53-encoded antibodies in the antibody repertoires is not clear. Using antibody repertoire sequencing, we found that the usage of VH3-53 increased after SARS-CoV-2 infection. A highly shared VH3-53-J6 clonotype was identified in 9 out of 13 COVID-19 patients. This clonotype was derived from convergent gene rearrangements with few somatic hypermutations and was evolutionary conserved. We synthesized 34 repertoire-deduced novel VH3-53-J6 heavy chains and paired with a common IGKV1-9 light chain to produce recombinant mAbs. Most of these recombinant mAbs (23/34) possess RBD binding and virus-neutralizing activities, and recognize ACE2 binding site via the same molecular interface. Our computational analysis, validated by laboratory experiments, revealed that VH3-53 antibodies targeting RBD are commonly present in COVID-19 patients’ antibody repertoires, indicating many people have germline-like precursor sequences to rapidly generate SARS-CoV-2 neutralizing antibodies. Moreover, antigen-specific mAbs can be digitally obtained through antibody repertoire sequencing and computational analysis.
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Affiliation(s)
- Qihong Yan
- Bioland Laboratory, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People's Republic of China.,Savaid Medical School, University of Chinese Academy of Science, Beijing, People's Republic of China
| | - Ping He
- Bioland Laboratory, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People's Republic of China.,Savaid Medical School, University of Chinese Academy of Science, Beijing, People's Republic of China
| | - Xiaohan Huang
- Bioland Laboratory, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People's Republic of China.,Savaid Medical School, University of Chinese Academy of Science, Beijing, People's Republic of China
| | - Kun Luo
- Bioland Laboratory, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People's Republic of China.,Savaid Medical School, University of Chinese Academy of Science, Beijing, People's Republic of China
| | - Yudi Zhang
- Bioland Laboratory, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People's Republic of China.,Savaid Medical School, University of Chinese Academy of Science, Beijing, People's Republic of China
| | - Haisu Yi
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Qian Wang
- Bioland Laboratory, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People's Republic of China
| | - Feng Li
- Guangzhou Institute of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Ruitian Hou
- Bioland Laboratory, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People's Republic of China.,Savaid Medical School, University of Chinese Academy of Science, Beijing, People's Republic of China
| | - Xiaodi Fan
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Pingchao Li
- Bioland Laboratory, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People's Republic of China
| | - Xinglong Liu
- Bioland Laboratory, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People's Republic of China
| | - Huan Liang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Yijun Deng
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Zhaoming Chen
- Bioland Laboratory, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People's Republic of China
| | - Yunfei Chen
- Bioland Laboratory, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People's Republic of China
| | - Xiaoneng Mo
- Guangzhou Institute of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Liqiang Feng
- Bioland Laboratory, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People's Republic of China
| | - Xiaoli Xiong
- Bioland Laboratory, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People's Republic of China
| | - Song Li
- iRepertoire Inc. , Huntsville, AL, USA.,College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou, People's Republic of China
| | - Jian Han
- iRepertoire Inc. , Huntsville, AL, USA
| | - Linbing Qu
- Bioland Laboratory, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People's Republic of China
| | - Xuefeng Niu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China
| | - Ling Chen
- Bioland Laboratory, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People's Republic of China.,State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People's Republic of China.,Guangzhou Institute of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, People's Republic of China
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43
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Cai F, Chen WH, Wu W, Jones JA, Choe M, Gohain N, Shen X, LaBranche C, Eaton A, Sutherland L, Lee EM, Hernandez GE, Wu NR, Scearce R, Seaman MS, Moody MA, Santra S, Wiehe K, Tomaras GD, Wagh K, Korber B, Bonsignori M, Montefiori DC, Haynes BF, de Val N, Joyce MG, Saunders KO. Structural and genetic convergence of HIV-1 neutralizing antibodies in vaccinated non-human primates. PLoS Pathog 2021; 17:e1009624. [PMID: 34086838 PMCID: PMC8216552 DOI: 10.1371/journal.ppat.1009624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 06/21/2021] [Accepted: 05/07/2021] [Indexed: 11/19/2022] Open
Abstract
A primary goal of HIV-1 vaccine development is the consistent elicitation of protective, neutralizing antibodies. While highly similar neutralizing antibodies (nAbs) have been isolated from multiple HIV-infected individuals, it is unclear whether vaccination can consistently elicit highly similar nAbs in genetically diverse primates. Here, we show in three outbred rhesus macaques that immunization with Env elicits a genotypically and phenotypically conserved nAb response. From these vaccinated macaques, we isolated four antibody lineages that had commonalities in immunoglobulin variable, diversity, and joining gene segment usage. Atomic-level structures of the antigen binding fragments of the two most similar antibodies showed nearly identical paratopes. The Env binding modes of each of the four vaccine-induced nAbs were distinct from previously known monoclonal HIV-1 neutralizing antibodies, but were nearly identical to each other. The similarities of these antibodies show that the immune system in outbred primates can respond to HIV-1 Env vaccination with a similar structural and genotypic solution for recognizing a particular neutralizing epitope. These results support rational vaccine design for HIV-1 that aims to reproducibly elicit, in genetically diverse primates, nAbs with specific paratope structures capable of binding conserved epitopes.
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Affiliation(s)
- Fangping Cai
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Wei-Hung Chen
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Weimin Wu
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, United States of America
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, Maryland, United States of America
| | - Julia A. Jones
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Misook Choe
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Neelakshi Gohain
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Xiaoying Shen
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Celia LaBranche
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Amanda Eaton
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Laura Sutherland
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Esther M. Lee
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Giovanna E. Hernandez
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Nelson R. Wu
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Richard Scearce
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Michael S. Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - M. Anthony Moody
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Sampa Santra
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Georgia D. Tomaras
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Immunology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Kshitij Wagh
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Bette Korber
- Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Mattia Bonsignori
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - David C. Montefiori
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Barton F. Haynes
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Immunology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Natalia de Val
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, United States of America
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, Maryland, United States of America
| | - M. Gordon Joyce
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, United States of America
| | - Kevin O. Saunders
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Immunology, Duke University Medical Center, Durham, North Carolina, United States of America
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44
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Bhardwaj V, Pevzner PA, Rashtchian C, Safonova Y. Trace Reconstruction Problems in Computational Biology. IEEE TRANSACTIONS ON INFORMATION THEORY 2021; 67:3295-3314. [PMID: 34176957 PMCID: PMC8224466 DOI: 10.1109/tit.2020.3030569] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The problem of reconstructing a string from its error-prone copies, the trace reconstruction problem, was introduced by Vladimir Levenshtein two decades ago. While there has been considerable theoretical work on trace reconstruction, practical solutions have only recently started to emerge in the context of two rapidly developing research areas: immunogenomics and DNA data storage. In immunogenomics, traces correspond to mutated copies of genes, with mutations generated naturally by the adaptive immune system. In DNA data storage, traces correspond to noisy copies of DNA molecules that encode digital data, with errors being artifacts of the data retrieval process. In this paper, we introduce several new trace generation models and open questions relevant to trace reconstruction for immunogenomics and DNA data storage, survey theoretical results on trace reconstruction, and highlight their connections to computational biology. Throughout, we discuss the applicability and shortcomings of known solutions and suggest future research directions.
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Affiliation(s)
- Vinnu Bhardwaj
- Electrical and Computer Engineering Department, University of California San Diego, La Jolla, USA
| | - Pavel A. Pevzner
- Computer Science and Engineering Department, University of California San Diego, La Jolla, USA
| | - Cyrus Rashtchian
- Computer Science and Engineering Department, University of California San Diego, La Jolla, USA
- Qualcomm Institute, University of California San Diego, La Jolla, USA
| | - Yana Safonova
- Computer Science and Engineering Department, University of California San Diego, La Jolla, USA
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45
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Chuang GY, Shen CH, Cheung CSF, Gorman J, Creanga A, Joyce MG, Leung K, Rawi R, Wang L, Yang ES, Yang Y, Zhang B, Zhang Y, Kanekiyo M, Zhou T, DeKosky BJ, Graham BS, Mascola JR, Kwong PD. Sequence-Signature Optimization Enables Improved Identification of Human HV6-1-Derived Class Antibodies That Neutralize Diverse Influenza A Viruses. Front Immunol 2021; 12:662909. [PMID: 34135892 PMCID: PMC8201785 DOI: 10.3389/fimmu.2021.662909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/26/2021] [Indexed: 11/13/2022] Open
Abstract
Sequence signatures of multidonor broadly neutralizing influenza antibodies can be used to quantify the prevalence of B cells with virus-neutralizing potential to accelerate development of broadly protective vaccine strategies. Antibodies of the same class share similar recognition modes and developmental pathways, and several antibody classes have been identified that neutralize diverse group 1- and group 2-influenza A viruses and have been observed in multiple human donors. One such multidonor antibody class, the HV6-1-derived class, targets the stem region of hemagglutinin with extraordinary neutralization breadth. Here, we use an iterative process to combine informatics, biochemical, and structural analyses to delineate an improved sequence signature for HV6-1-class antibodies. Based on sequence and structure analyses of known HV6-1 class antibodies, we derived a more inclusive signature (version 1), which we used to search for matching B-cell transcripts from published next-generation sequencing datasets of influenza vaccination studies. We expressed selected antibodies, evaluated their function, and identified amino acid-level requirements from which to refine the sequence signature (version 2). The cryo-electron microscopy structure for one of the signature-identified antibodies in complex with hemagglutinin confirmed motif recognition to be similar to known HV6-1-class members, MEDI8852 and 56.a.09, despite differences in recognition-loop length. Threading indicated the refined signature to have increased accuracy, and signature-identified heavy chains, when paired with the light chain of MEDI8852, showed neutralization comparable to the most potent members of the class. Incorporating sequences of additional class members thus enables an improved sequence signature for HV6-1-class antibodies, which can identify class members with increased accuracy.
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Affiliation(s)
- Gwo-Yu Chuang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Chen-Hsiang Shen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Crystal Sao-Fong Cheung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Jason Gorman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Adrian Creanga
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - M Gordon Joyce
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Kwanyee Leung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Reda Rawi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Lingshu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Eun Sung Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Yongping Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Yi Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Brandon J DeKosky
- Department of Pharmaceutical Chemistry and Department of Chemical Engineering, University of Kansas, Lawrence, KS, United States
| | - Barney S Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
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46
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Sun H, Yang HQ, Zhai K, Tong ZH. Signatures of B Cell Receptor Repertoire Following Pneumocystis Infection. Front Microbiol 2021; 12:636250. [PMID: 34135870 PMCID: PMC8202503 DOI: 10.3389/fmicb.2021.636250] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 04/01/2021] [Indexed: 11/13/2022] Open
Abstract
B cells play vital roles in host defense against Pneumocystis infection. However, the features of the B cell receptor (BCR) repertoire in disease progression remain unclear. Here, we integrated single-cell RNA sequencing and single-cell BCR sequencing of immune cells from mouse lungs in an uninfected state and 1–4 weeks post-infection in order to illustrate the dynamic nature of B cell responses during Pneumocystis infection. We identified continuously increased plasma cells and an elevated ratio of (IgA + IgG) to (IgD + IgM) after infection. Moreover, Pneumocystis infection was associated with an increasing naïve B subset characterized by elevated expression of the transcription factor ATF3. The proportion of clonal expanded cells progressively increased, while BCR diversity decreased. Plasma cells exhibited higher levels of somatic hypermutation than naïve B cells. Biased usage of V(D)J genes was observed, and the usage frequency of IGHV9-3 rose. Overall, these results present a detailed atlas of B cell transcriptional changes and BCR repertoire features in the context of Pneumocystis infection, which provides valuable information for finding diagnostic biomarkers and developing potential immunotherapeutic targets.
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Affiliation(s)
- Han Sun
- Department of Respiratory and Critical Care Medicine, Beijing Institute of Respiratory Medicine, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Hu-Qin Yang
- Department of Respiratory and Critical Care Medicine, Beijing Institute of Respiratory Medicine, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Kan Zhai
- Department of Respiratory and Critical Care Medicine, Beijing Institute of Respiratory Medicine, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Zhao-Hui Tong
- Department of Respiratory and Critical Care Medicine, Beijing Institute of Respiratory Medicine, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
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47
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He B, Liu S, Wang Y, Xu M, Cai W, Liu J, Bai W, Ye S, Ma Y, Hu H, Meng H, Sun T, Li Y, Luo H, Shi M, Du X, Zhao W, Chen S, Yang J, Zhu H, Jie Y, Yang Y, Guo D, Wang Q, Liu Y, Yan H, Wang M, Chen YQ. Rapid isolation and immune profiling of SARS-CoV-2 specific memory B cell in convalescent COVID-19 patients via LIBRA-seq. Signal Transduct Target Ther 2021; 6:195. [PMID: 34001847 PMCID: PMC8127497 DOI: 10.1038/s41392-021-00610-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 03/24/2021] [Accepted: 03/31/2021] [Indexed: 02/06/2023] Open
Abstract
B cell response plays a critical role against SARS-CoV-2 infection. However, little is known about the diversity and frequency of the paired SARS-CoV-2 antigen-specific BCR repertoire after SARS-CoV-2 infection. Here, we performed single-cell RNA sequencing and VDJ sequencing using the memory and plasma B cells isolated from five convalescent COVID-19 patients, and analyzed the spectrum and transcriptional heterogeneity of antibody immune responses. Via linking BCR to antigen specificity through sequencing (LIBRA-seq), we identified a distinct activated memory B cell subgroup (CD11chigh CD95high) had a higher proportion of SARS-CoV-2 antigen-labeled cells compared with memory B cells. Our results revealed the diversity of paired BCR repertoire and the non-stochastic pairing of SARS-CoV-2 antigen-specific immunoglobulin heavy and light chains after SARS-CoV-2 infection. The public antibody clonotypes were shared by distinct convalescent individuals. Moreover, several antibodies isolated by LIBRA-seq showed high binding affinity against SARS-CoV-2 receptor-binding domain (RBD) or nucleoprotein (NP) via ELISA assay. Two RBD-reactive antibodies C14646P3S and C2767P3S isolated by LIBRA-seq exhibited high neutralizing activities against both pseudotyped and authentic SARS-CoV-2 viruses in vitro. Our study provides fundamental insights into B cell response following SARS-CoV-2 infection at the single-cell level.
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Affiliation(s)
- Bing He
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Shuning Liu
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Yuanyuan Wang
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Mengxin Xu
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Wei Cai
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Jia Liu
- Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Wendi Bai
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Shupei Ye
- Pulmonary and critical care medicine, The Third People's Hospital of Dongguan City, Dongguan, Guangdong Province, China
| | - Yong Ma
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Hengrui Hu
- Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Huicui Meng
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Tao Sun
- Hangzhou ImmuQuad Biotechnologies, Hangzhou, China.,Zhejiang-California International NanoSystems Institute, Zhejiang University, Hangzhou, China
| | - Yanling Li
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Huanle Luo
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Mang Shi
- Infection and Immunity Center, School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Xiangjun Du
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Wenjing Zhao
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Shoudeng Chen
- Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
| | - Jingyi Yang
- Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Haipeng Zhu
- Department of Infectious Diseases, The Ninth People's Hospital of Dongguan City, Dongguan, Guangdong Province, China
| | - Yusheng Jie
- Department of Infectious Diseases, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong Province, China
| | - Yuedong Yang
- School of Data and Computer Science, Sun Yat-sen University, Guangzhou, China
| | - Deyin Guo
- Infection and Immunity Center, School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Qiao Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yuwen Liu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen, China.,Genome Analysis Laboratory of the Ministry of Agriculture, Shenzhen, China.,Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Huimin Yan
- Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Manli Wang
- Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Yao-Qing Chen
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, China. .,Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China.
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48
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Zhou X, Ma F, Xie J, Yuan M, Li Y, Shaabani N, Zhao F, Huang D, Wu NC, Lee CCD, Liu H, Li J, Chen Z, Hong Y, Liu WH, Xiao N, Burton DR, Tu H, Li H, Chen X, Teijaro JR, Wilson IA, Xiao C, Huang Z. Diverse immunoglobulin gene usage and convergent epitope targeting in neutralizing antibody responses to SARS-CoV-2. Cell Rep 2021; 35:109109. [PMID: 33932326 PMCID: PMC8064889 DOI: 10.1016/j.celrep.2021.109109] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 03/07/2021] [Accepted: 04/20/2021] [Indexed: 12/23/2022] Open
Abstract
It is unclear whether individuals with enormous diversity in B cell receptor repertoires are consistently able to mount effective antibody responses against SARS-CoV-2. We analyzed antibody responses in a cohort of 55 convalescent patients and isolated 54 potent neutralizing monoclonal antibodies (mAbs). While most of the mAbs target the angiotensin-converting enzyme 2 (ACE2) binding surface on the receptor binding domain (RBD) of SARS-CoV-2 spike protein, mAb 47D1 binds only to one side of the receptor binding surface on the RBD. Neutralization by 47D1 is achieved independent of interfering RBD-ACE2 binding. A crystal structure of the mAb-RBD complex shows that the IF motif at the tip of 47D1 CDR H2 interacts with a hydrophobic pocket in the RBD. Diverse immunoglobulin gene usage and convergent epitope targeting characterize neutralizing antibody responses to SARS-CoV-2, suggesting that vaccines that effectively present the receptor binding site on the RBD will likely elicit neutralizing antibody responses in a large fraction of the population.
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Affiliation(s)
- Xiaojuan Zhou
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Fengge Ma
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Jun Xie
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yunqiao Li
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Namir Shaabani
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Fangzhu Zhao
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Deli Huang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nicholas C Wu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Chang-Chun D Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hejun Liu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jiali Li
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Zhonghui Chen
- Affiliated Hospital of Putian University, Putian, Fujian 351100, China
| | - Yazhen Hong
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Wen-Hsien Liu
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Nengming Xiao
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA
| | - Haijian Tu
- Affiliated Hospital of Putian University, Putian, Fujian 351100, China
| | - Hang Li
- Affiliated Hospital of Putian University, Putian, Fujian 351100, China
| | - Xin Chen
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - John R Teijaro
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Changchun Xiao
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Zhe Huang
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China.
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49
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From Structural Studies to HCV Vaccine Design. Viruses 2021; 13:v13050833. [PMID: 34064532 PMCID: PMC8147963 DOI: 10.3390/v13050833] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 04/21/2021] [Accepted: 04/28/2021] [Indexed: 02/06/2023] Open
Abstract
Hepatitis C virus (HCV) is a serious and growing public health problem despite recent developments of antiviral therapeutics. To achieve global elimination of HCV, an effective cross-genotype vaccine is needed. The failure of previous vaccination trials to elicit an effective cross-reactive immune response demands better vaccine antigens to induce a potent cross-neutralizing response to improve vaccine efficacy. HCV E1 and E2 envelope (Env) glycoproteins are the main targets for neutralizing antibodies (nAbs), which aid in HCV clearance and protection. Therefore, a molecular-level understanding of the nAb responses against HCV is imperative for the rational design of cross-genotype vaccine antigens. Here we summarize the recent advances in structural studies of HCV Env and Env-nAb complexes and how they improve our understanding of immune recognition of HCV. We review the structural data defining HCV neutralization epitopes and conformational plasticity of the Env proteins, and the knowledge applicable to rational vaccine design.
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50
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Wec AZ, Lin KS, Kwasnieski JC, Sinai S, Gerold J, Kelsic ED. Overcoming Immunological Challenges Limiting Capsid-Mediated Gene Therapy With Machine Learning. Front Immunol 2021; 12:674021. [PMID: 33986759 PMCID: PMC8112259 DOI: 10.3389/fimmu.2021.674021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 04/09/2021] [Indexed: 12/11/2022] Open
Abstract
A key hurdle to making adeno-associated virus (AAV) capsid mediated gene therapy broadly beneficial to all patients is overcoming pre-existing and therapy-induced immune responses to these vectors. Recent advances in high-throughput DNA synthesis, multiplexing and sequencing technologies have accelerated engineering of improved capsid properties such as production yield, packaging efficiency, biodistribution and transduction efficiency. Here we outline how machine learning, advances in viral immunology, and high-throughput measurements can enable engineering of a new generation of de-immunized capsids beyond the antigenic landscape of natural AAVs, towards expanding the therapeutic reach of gene therapy.
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Affiliation(s)
- Anna Z. Wec
- Applied Biology, Dyno Therapeutics Inc, Cambridge, MA, United States
| | - Kathy S. Lin
- Data Science, Dyno Therapeutics Inc, Cambridge, MA, United States
| | | | - Sam Sinai
- Data Science, Dyno Therapeutics Inc, Cambridge, MA, United States
| | - Jeff Gerold
- Data Science, Dyno Therapeutics Inc, Cambridge, MA, United States
| | - Eric D. Kelsic
- Applied Biology, Dyno Therapeutics Inc, Cambridge, MA, United States
- Data Science, Dyno Therapeutics Inc, Cambridge, MA, United States
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