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Yan Q, Zhang Y, Hou R, Pan W, Liang H, Gao X, Deng W, Huang X, Qu L, Tang C, He P, Liu B, Wang Q, Zhao X, Lin Z, Chen Z, Li P, Han J, Xiong X, Zhao J, Li S, Niu X, Chen L. Deep immunoglobulin repertoire sequencing depicts a comprehensive atlas of spike-specific antibody lineages shared among COVID-19 convalescents. Emerg Microbes Infect 2024; 13:2290841. [PMID: 38044868 PMCID: PMC10810631 DOI: 10.1080/22221751.2023.2290841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 11/29/2023] [Indexed: 12/05/2023]
Abstract
Neutralizing antibodies are a key component in protective humoral immunity against SARS-CoV-2. Currently, available technologies cannot track epitope-specific antibodies in global antibody repertoires. Thus, the comprehensive repertoire of spike-specific neutralizing antibodies elicited by SARS-CoV-2 infection is not fully understood. We therefore combined high-throughput immunoglobulin heavy chain (IgH) repertoire sequencing, and structural and bioinformatics analysis to establish an antibodyomics pipeline, which enables tracking spike-specific antibody lineages that target certain neutralizing epitopes. We mapped the neutralizing epitopes on the spike and determined the epitope-preferential antibody lineages. This analysis also revealed numerous overlaps between immunodominant neutralizing antibody-binding sites and mutation hotspots on spikes as observed so far in SARS-CoV-2 variants. By clustering 2677 spike-specific antibodies with 360 million IgH sequences that we sequenced, a total of 329 shared spike-specific antibody clonotypes were identified from 33 COVID-19 convalescents and 24 SARS-CoV-2-naïve individuals. Epitope mapping showed that the shared antibody responses target not only neutralizing epitopes on RBD and NTD but also non-neutralizing epitopes on S2. The immunodominance of neutralizing antibody response is determined by the occurrence of specific precursors in human naïve B-cell repertoires. We identified that only 28 out of the 329 shared spike-specific antibody clonotypes persisted for at least 12 months. Among them, long-lived IGHV3-53 antibodies are likely to evolve cross-reactivity to Omicron variants through accumulating somatic hypermutations. Altogether, we created a comprehensive atlas of spike-targeting antibody lineages in COVID-19 convalescents and antibody precursors in human naïve B cell repertoires, providing a valuable reference for future vaccine design and evaluation.
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Affiliation(s)
- Qihong Yan
- State Key Laboratory of Respiratory Disease, 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, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Yudi Zhang
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- University of Chinese Academy of Science, Beijing, People’s Republic of China
| | - Ruitian Hou
- Guangzhou Institute of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Wenjing Pan
- Hengyang Medical School, University of South China, Hengyang, People’s Republic of China
- Nanjing ARP Biotechnology Co., Ltd, Nanjing, People’s Republic of China
| | - Huan Liang
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of 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, People’s Republic of China
| | - Weiqi Deng
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- University of Chinese Academy of Science, Beijing, People’s Republic of China
| | - Xiaohan Huang
- State Key Laboratory of Respiratory Disease, 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, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Linbing Qu
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
| | - Congli Tang
- Nanjing ARP Biotechnology Co., Ltd, Nanjing, People’s Republic of China
| | - Ping He
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- Guangzhou National Laboratory, Guangzhou, People’s Republic of China
| | - Banghui Liu
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
| | - Qian Wang
- Guangzhou National Laboratory, Guangzhou, People’s Republic of China
| | - Xinwei Zhao
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- Guangzhou National Laboratory, Guangzhou, People’s Republic of China
| | - Zihan Lin
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- University of Chinese Academy of Science, Beijing, People’s Republic of China
| | - Zhaoming Chen
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
| | - Pingchao Li
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
| | - Jian Han
- iRepertoire Inc., Huntsville, AL, USA
| | - Xiaoli Xiong
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
- Guangzhou National Laboratory, Guangzhou, People’s Republic of China
| | - Song Li
- Hengyang Medical School, University of South China, Hengyang, People’s Republic of China
| | - Xuefeng Niu
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Ling Chen
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 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
- Guangzhou National Laboratory, Guangzhou, People’s Republic of China
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2
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Lee H, Shin K, Lee Y, Lee S, Lee S, Lee E, Kim SW, Shin HY, Kim JH, Chung J, Kwon S. Identification of B cell subsets based on antigen receptor sequences using deep learning. Front Immunol 2024; 15:1342285. [PMID: 38576618 PMCID: PMC10991714 DOI: 10.3389/fimmu.2024.1342285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 03/07/2024] [Indexed: 04/06/2024] Open
Abstract
B cell receptors (BCRs) denote antigen specificity, while corresponding cell subsets indicate B cell functionality. Since each B cell uniquely encodes this combination, physical isolation and subsequent processing of individual B cells become indispensable to identify both attributes. However, this approach accompanies high costs and inevitable information loss, hindering high-throughput investigation of B cell populations. Here, we present BCR-SORT, a deep learning model that predicts cell subsets from their corresponding BCR sequences by leveraging B cell activation and maturation signatures encoded within BCR sequences. Subsequently, BCR-SORT is demonstrated to improve reconstruction of BCR phylogenetic trees, and reproduce results consistent with those verified using physical isolation-based methods or prior knowledge. Notably, when applied to BCR sequences from COVID-19 vaccine recipients, it revealed inter-individual heterogeneity of evolutionary trajectories towards Omicron-binding memory B cells. Overall, BCR-SORT offers great potential to improve our understanding of B cell responses.
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Affiliation(s)
- Hyunho Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
| | - Kyoungseob Shin
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
| | - Yongju Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
| | - Soobin Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
| | - Seungyoun Lee
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Science, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Eunjae Lee
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Science, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Seung Woo Kim
- Department of Neurology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Ha Young Shin
- Department of Neurology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jong Hoon Kim
- Department of Dermatology and Cutaneous Biology Research Institute, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Junho Chung
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Science, Seoul National University College of Medicine, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sunghoon Kwon
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, Republic of Korea
- Bio-MAX Institute, Seoul National University, Seoul, Republic of Korea
- Inter-University Semiconductor Research Center, Seoul National University, Seoul, Republic of Korea
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3
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Shingai M, Iida S, Kawai N, Kawahara M, Sekiya T, Ohno M, Nomura N, Handabile C, Kawakita T, Omori R, Yamagishi J, Sano K, Ainai A, Suzuki T, Ohnishi K, Ito K, Kida H. Extraction of the CDRH3 sequence of the mouse antibody repertoire selected upon influenza virus infection by subtraction of the background antibody repertoire. J Virol 2024; 98:e0199523. [PMID: 38323813 PMCID: PMC10949447 DOI: 10.1128/jvi.01995-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 01/14/2024] [Indexed: 02/08/2024] Open
Abstract
Historically, antibody reactivity to pathogens and vaccine antigens has been evaluated using serological measurements of antigen-specific antibodies. However, it is difficult to evaluate all antibodies that contribute to various functions in a single assay, such as the measurement of the neutralizing antibody titer. Bulk antibody repertoire analysis using next-generation sequencing is a comprehensive method for analyzing the overall antibody response; however, it is unreliable for estimating antigen-specific antibodies due to individual variation. To address this issue, we propose a method to subtract the background signal from the repertoire of data of interest. In this study, we analyzed changes in antibody diversity and inferred the heavy-chain complementarity-determining region 3 (CDRH3) sequences of antibody clones that were selected upon influenza virus infection in a mouse model using bulk repertoire analysis. A decrease in the diversity of the antibody repertoire was observed upon viral infection, along with an increase in neutralizing antibody titers. Using kernel density estimation of sequences in a high-dimensional sequence space with background signal subtraction, we identified several clusters of CDRH3 sequences induced upon influenza virus infection. Most of these repertoires were detected more frequently in infected mice than in uninfected control mice, suggesting that infection-specific antibody sequences can be extracted using this method. Such an accurate extraction of antigen- or infection-specific repertoire information will be a useful tool for vaccine evaluation in the future. IMPORTANCE As specific interactions between antigens and cell-surface antibodies trigger the proliferation of B-cell clones, the frequency of each antibody sequence in the samples reflects the size of each clonal population. Nevertheless, it is extremely difficult to extract antigen-specific antibody sequences from the comprehensive bulk antibody sequences obtained from blood samples due to repertoire bias influenced by exposure to dietary antigens and other infectious agents. This issue can be addressed by subtracting the background noise from the post-immunization or post-infection repertoire data. In the present study, we propose a method to quantify repertoire data from comprehensive repertoire data. This method allowed subtraction of the background repertoire, resulting in more accurate extraction of expanded antibody repertoires upon influenza virus infection. This accurate extraction of antigen- or infection-specific repertoire information is a useful tool for vaccine evaluation.
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Affiliation(s)
- Masashi Shingai
- Division of Biologics Development, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
- Division of Vaccine Immunology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Sayaka Iida
- Division of Bioinformatics, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Naoko Kawai
- Division of Collaboration and Education, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Mamiko Kawahara
- Division of Biologics Development, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Toshiki Sekiya
- Division of Biologics Development, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Marumi Ohno
- Division of Biologics Development, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
| | - Naoki Nomura
- Division of Biologics Development, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
| | - Chimuka Handabile
- Division of Biologics Development, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
| | - Tomomi Kawakita
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
- Division of Vaccine Immunology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Ryosuke Omori
- Division of Bioinformatics, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Junya Yamagishi
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Division of Collaboration and Education, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Kaori Sano
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Akira Ainai
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tadaki Suzuki
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kazuo Ohnishi
- Department of Immunology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kimihito Ito
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Division of Bioinformatics, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Hiroshi Kida
- Division of Biologics Development, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
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4
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Carzaniga T, Casiraghi L, Nava G, Zanchetta G, Inzani T, Chiari M, Bollati V, Epis S, Bandi C, Lai A, Zehender G, Bellini T, Buscaglia M. Serum antibody fingerprinting of SARS-CoV-2 variants in infected and vaccinated subjects by label-free microarray biosensor. Front Immunol 2024; 15:1323406. [PMID: 38476234 PMCID: PMC10927789 DOI: 10.3389/fimmu.2024.1323406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 02/06/2024] [Indexed: 03/14/2024] Open
Abstract
Both viral infection and vaccination affect the antibody repertoire of a person. Here, we demonstrate that the analysis of serum antibodies generates information not only on the virus type that caused the infection but also on the specific virus variant. We developed a rapid multiplex assay providing a fingerprint of serum antibodies against five different SARS-CoV-2 variants based on a microarray of virus antigens immobilized on the surface of a label-free reflectometric biosensor. We analyzed serum from the plasma of convalescent subjects and vaccinated volunteers and extracted individual antibody profiles of both total immunoglobulin Ig and IgA fractions. We found that Ig level profiles were strongly correlated with the specific variant of infection or vaccination and that vaccinated subjects displayed a larger quantity of total Ig and a lower fraction of IgA relative to the population of convalescent unvaccinated subjects.
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Affiliation(s)
- Thomas Carzaniga
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milan, Italy
| | - Luca Casiraghi
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milan, Italy
| | - Giovanni Nava
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milan, Italy
| | - Giuliano Zanchetta
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milan, Italy
| | - Tommaso Inzani
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milan, Italy
| | - Marcella Chiari
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta”, National Research Council of Italy (SCITEC-CNR), Milano, Italy
| | - Valentina Bollati
- Dipartimento di Scienze Cliniche e di Comunità, Università degli Studi di Milano, Milano, Italy
| | - Sara Epis
- Dipartimento di Bioscienze and Pediatric Clinical Research Center (CRC) ‘Fondazione Romeo ed Enrica Invernizzi’, Università degli Studi di Milano, Milano, Italy
| | - Claudio Bandi
- Dipartimento di Bioscienze and Pediatric Clinical Research Center (CRC) ‘Fondazione Romeo ed Enrica Invernizzi’, Università degli Studi di Milano, Milano, Italy
| | - Alessia Lai
- Dipartimento di Scienze Biomediche e Cliniche, Università degli Studi di Milano, Milano, Italy
| | - Gianguglielmo Zehender
- Dipartimento di Scienze Biomediche e Cliniche, Università degli Studi di Milano, Milano, Italy
| | - Tommaso Bellini
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milan, Italy
| | - Marco Buscaglia
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milan, Italy
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Troelnikov A, Armour B, Putty T, Aggarwal A, Akerman A, Milogiannakis V, Chataway T, King J, Turville SG, Gordon TP, Wang JJ. Immunoglobulin repertoire restriction characterizes the serological responses of patients with predominantly antibody deficiency. J Allergy Clin Immunol 2023; 152:290-301.e7. [PMID: 36965845 DOI: 10.1016/j.jaci.2023.02.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 02/06/2023] [Accepted: 02/09/2023] [Indexed: 03/27/2023]
Abstract
BACKGROUND Predominantly antibody deficiency (PAD) is the most common category of inborn errors of immunity and is underpinned by impaired generation of appropriate antibody diversity and quantity. In the clinic, responses are interrogated by assessment of vaccination responses, which is central to many PAD diagnoses. However, the composition of the generated antibody repertoire is concealed from traditional quantitative measures of serological responses. Leveraging modern mass spectrometry-based proteomics (MS-proteomics), it is possible to elaborate the molecular features of specific antibody repertoires, which may address current limitations of diagnostic vaccinology. OBJECTIVES We sought to evaluate serum antibody responses in patients with PAD following vaccination with a neo-antigen (severe acute respiratory syndrome coronavirus-2 vaccination) using MS-proteomics. METHODS Following severe acute respiratory syndrome coronavirus-2 vaccination, serological responses in individuals with PAD and healthy controls (HCs) were assessed by anti-S1 subunit ELISA and neutralization assays. Purified anti-S1 subunit IgG and IgM was profiled by MS-proteomics for IGHV subfamily usage and somatic hypermutation analysis. RESULTS Twelve patients with PAD who were vaccine-responsive were recruited with 11 matched vaccinated HCs. Neutralization and end point anti-S1 titers were lower in PAD. All subjects with PAD demonstrated restricted anti-S1 IgG antibody repertoires, with usage of <5 IGHV subfamilies (median: 3; range 2-4), compared to ≥5 for the 11 HC subjects (P < .001). IGHV3-7 utilization was far less common in patients with PAD than in HCs (2 of 12 vs 10 of 11; P = .001). Amino acid substitutions due to somatic hypermutation per subfamily did not differ between groups. Anti-S1 IgM was present in 64% and 50% of HC and PAD cohorts, respectively, and did not differ significantly between HCs and patients with PAD. CONCLUSIONS This study demonstrates the breadth of anti-S1 antibodies elicited by vaccination at the proteome level and identifies stereotypical restriction of IGHV utilization in the IgG repertoire in patients with PAD compared with HC subjects. Despite uniformly pauci-clonal antibody repertoires some patients with PAD generated potent serological responses, highlighting a possible limitation of traditional serological techniques. These findings suggest that IgG repertoire restriction is a key feature of antibody repertoires in PAD.
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Affiliation(s)
- Alexander Troelnikov
- College of Medicine and Public Health, Flinders University, Bedford Park, Australia; SA Pathology, Adelaide, Australia.
| | - Bridie Armour
- College of Medicine and Public Health, Flinders University, Bedford Park, Australia; SA Pathology, Adelaide, Australia
| | - Trishni Putty
- College of Medicine and Public Health, Flinders University, Bedford Park, Australia; SA Pathology, Adelaide, Australia
| | | | | | | | - Tim Chataway
- College of Medicine and Public Health, Flinders University, Bedford Park, Australia
| | - Jovanka King
- SA Pathology, Adelaide, Australia; Women's and Children's Hospital Network, Adelaide, Australia; Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
| | | | - Tom P Gordon
- College of Medicine and Public Health, Flinders University, Bedford Park, Australia; SA Pathology, Adelaide, Australia; Flinders Medical Centre, Bedford Park, Australia
| | - Jing Jing Wang
- College of Medicine and Public Health, Flinders University, Bedford Park, Australia; SA Pathology, Adelaide, Australia
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6
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Abd Alhadi M, Friedman LM, Karlsson EA, Cohen-Lavi L, Burkovitz A, Schultz-Cherry S, Noah TL, Weir SS, Shulman LM, Beck MA, Hertz T. Obesity Is Associated with an Impaired Baseline Repertoire of Anti-Influenza Virus Antibodies. Microbiol Spectr 2023; 11:e0001023. [PMID: 37098954 PMCID: PMC10269616 DOI: 10.1128/spectrum.00010-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 03/27/2023] [Indexed: 04/27/2023] Open
Abstract
Obesity is a risk factor for severe disease and mortality for both influenza and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. While previous studies show that individuals with obesity generate antibody responses following influenza vaccination, infection rates within the obese group were twice as high as those in the healthy-weight group. The repertoire of antibodies raised against influenza viruses following previous vaccinations and/or natural exposures is referred to here as baseline immune history (BIH). To investigate the hypothesis that obesity impacts immune memory to infections and vaccines, we profiled the BIH of obese and healthy-weight adults vaccinated with the 2010-2011 seasonal influenza vaccine in response to conformational and linear antigens. Despite the extensive heterogeneity of the BIH profiles in both groups, there were striking differences between obese and healthy subjects, especially with regard to A/H1N1 strains and the 2009 pandemic virus (Cal09). Individuals with obesity had lower IgG and IgA magnitude and breadth for a panel of A/H1N1 whole viruses and hemagglutinin proteins from 1933 to 2009 but increased IgG magnitude and breadth for linear peptides from the Cal09 H1 and N1 proteins. Age was also associated with A/H1N1 BIH, with young individuals with obesity being more likely to have reduced A/H1N1 BIH. We found that individuals with low IgG BIH had significantly lower neutralizing antibody titers than individuals with high IgG BIH. Taken together, our findings suggest that increased susceptibility of obese participants to influenza infection may be mediated in part by obesity-associated differences in the memory B-cell repertoire, which cannot be ameliorated by current seasonal vaccination regimens. Overall, these data have vital implications for the next generation of influenza virus and SARS-CoV-2 vaccines. IMPORTANCE Obesity is associated with increased morbidity and mortality from influenza and SARS-CoV-2 infection. While vaccination is the most effective strategy for preventing influenza virus infection, our previous studies showed that influenza vaccines fail to provide optimal protection in obese individuals despite reaching canonical correlates of protection. Here, we show that obesity may impair immune history in humans and cannot be overcome by seasonal vaccination, especially in younger individuals with decreased lifetime exposure to infections and seasonal vaccines. Low baseline immune history is associated with decreased protective antibody responses. Obesity potentially handicaps overall responses to vaccination, biasing it toward responses to linear epitopes, which may reduce protective capacity. Taken together, our data suggest that young obese individuals are at an increased risk of reduced protection by vaccination, likely due to altered immune history biased toward nonprotective antibody responses. Given the worldwide obesity epidemic coupled with seasonal respiratory virus infections and the inevitable next pandemic, it is imperative that we understand and improve vaccine efficacy in this high-risk population. The design, development, and usage of vaccines for and in obese individuals may need critical evaluation, and immune history should be considered an alternate correlate of protection in future vaccine clinical trials.
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Affiliation(s)
- Marwa Abd Alhadi
- Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Lilach M. Friedman
- Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Erik A. Karlsson
- Virology Unit, Institute Pasteur du Cambodge, Phnom Penh, Cambodia
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Liel Cohen-Lavi
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- Department of Industrial Engineering and Management, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Anat Burkovitz
- Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Stacey Schultz-Cherry
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Terry L. Noah
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Samuel S. Weir
- Department of Family Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Lester M. Shulman
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Melinda A. Beck
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Tomer Hertz
- Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
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7
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Ramirez Valdez K, Nzau B, Dorey-Robinson D, Jarman M, Nyagwange J, Schwartz JC, Freimanis G, Steyn AW, Warimwe GM, Morrison LJ, Mwangi W, Charleston B, Bonnet-Di Placido M, Hammond JA. A Customizable Suite of Methods to Sequence and Annotate Cattle Antibodies. Vaccines (Basel) 2023; 11:1099. [PMID: 37376488 PMCID: PMC10302312 DOI: 10.3390/vaccines11061099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/07/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
Studying the antibody response to infection or vaccination is essential for developing more effective vaccines and therapeutics. Advances in high-throughput antibody sequencing technologies and immunoinformatic tools now allow the fast and comprehensive analysis of antibody repertoires at high resolution in any species. Here, we detail a flexible and customizable suite of methods from flow cytometry, single cell sorting, heavy and light chain amplification to antibody sequencing in cattle. These methods were used successfully, including adaptation to the 10x Genomics platform, to isolate native heavy-light chain pairs. When combined with the Ig-Sequence Multi-Species Annotation Tool, this suite represents a powerful toolkit for studying the cattle antibody response with high resolution and precision. Using three workflows, we processed 84, 96, and 8313 cattle B cells from which we sequenced 24, 31, and 4756 antibody heavy-light chain pairs, respectively. Each method has strengths and limitations in terms of the throughput, timeline, specialist equipment, and cost that are each discussed. Moreover, the principles outlined here can be applied to study antibody responses in other mammalian species.
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Affiliation(s)
| | - Benjamin Nzau
- The Pirbright Institute, Pirbright GU24 0NF, UK
- Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK
| | | | | | - James Nyagwange
- The Pirbright Institute, Pirbright GU24 0NF, UK
- KEMRI-Wellcome Trust Research Programme CGMRC, Kilifi P.O. Box 230-80108, Kenya
| | | | | | | | - George M Warimwe
- KEMRI-Wellcome Trust Research Programme CGMRC, Kilifi P.O. Box 230-80108, Kenya
| | - Liam J Morrison
- Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK
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8
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Andreu-Sánchez S, Bourgonje AR, Vogl T, Kurilshikov A, Leviatan S, Ruiz-Moreno AJ, Hu S, Sinha T, Vich Vila A, Klompus S, Kalka IN, de Leeuw K, Arends S, Jonkers I, Withoff S, Brouwer E, Weinberger A, Wijmenga C, Segal E, Weersma RK, Fu J, Zhernakova A. Phage display sequencing reveals that genetic, environmental, and intrinsic factors influence variation of human antibody epitope repertoire. Immunity 2023; 56:1376-1392.e8. [PMID: 37164013 DOI: 10.1016/j.immuni.2023.04.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 12/13/2022] [Accepted: 04/06/2023] [Indexed: 05/12/2023]
Abstract
Phage-displayed immunoprecipitation sequencing (PhIP-seq) has enabled high-throughput profiling of human antibody repertoires. However, a comprehensive overview of environmental and genetic determinants shaping human adaptive immunity is lacking. In this study, we investigated the effects of genetic, environmental, and intrinsic factors on the variation in human antibody repertoires. We characterized serological antibody repertoires against 344,000 peptides using PhIP-seq libraries from a wide range of microbial and environmental antigens in 1,443 participants from a population cohort. We detected individual-specificity, temporal consistency, and co-housing similarities in antibody repertoires. Genetic analyses showed the involvement of the HLA, IGHV, and FUT2 gene regions in antibody-bound peptide reactivity. Furthermore, we uncovered associations between phenotypic factors (including age, cell counts, sex, smoking behavior, and allergies, among others) and particular antibody-bound peptides. Our results indicate that human antibody epitope repertoires are shaped by both genetics and environmental exposures and highlight specific signatures of distinct phenotypes and genotypes.
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Affiliation(s)
- Sergio Andreu-Sánchez
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Arno R Bourgonje
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Thomas Vogl
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel; Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Graz, Austria; Center for Cancer Research, Medical University of Vienna, Wien, Austria.
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Sigal Leviatan
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Angel J Ruiz-Moreno
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Shixian Hu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Trishla Sinha
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Arnau Vich Vila
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Shelley Klompus
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Iris N Kalka
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Karina de Leeuw
- Department of Rheumatology and Clinical Immunology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Suzanne Arends
- Department of Rheumatology and Clinical Immunology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Iris Jonkers
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Sebo Withoff
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Elisabeth Brouwer
- Department of Rheumatology and Clinical Immunology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Adina Weinberger
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
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9
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Bourgonje AR, Andreu-Sánchez S, Vogl T, Hu S, Vich Vila A, Gacesa R, Leviatan S, Kurilshikov A, Klompus S, Kalka IN, van Dullemen HM, Weinberger A, Visschedijk MC, Festen EAM, Faber KN, Wijmenga C, Dijkstra G, Segal E, Fu J, Zhernakova A, Weersma RK. Phage-display immunoprecipitation sequencing of the antibody epitope repertoire in inflammatory bowel disease reveals distinct antibody signatures. Immunity 2023; 56:1393-1409.e6. [PMID: 37164015 DOI: 10.1016/j.immuni.2023.04.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 12/13/2022] [Accepted: 04/14/2023] [Indexed: 05/12/2023]
Abstract
Inflammatory bowel diseases (IBDs), e.g., Crohn's disease (CD) and ulcerative colitis (UC), are chronic immune-mediated inflammatory diseases. A comprehensive overview of an IBD-specific antibody epitope repertoire is, however, lacking. Using high-throughput phage-display immunoprecipitation sequencing (PhIP-Seq), we identified antibodies against 344,000 antimicrobial, immune, and food antigens in 497 individuals with IBD compared with 1,326 controls. IBD was characterized by 373 differentially abundant antibody responses (202 overrepresented and 171 underrepresented), with 17% shared by both IBDs, 55% unique to CD, and 28% unique to UC. Antibody reactivities against bacterial flagellins dominated in CD and were associated with ileal involvement, fibrostenotic disease, and anti-Saccharomyces cerevisiae antibody positivity, but not with fecal microbiome composition. Antibody epitope repertoires accurately discriminated CD from controls (area under the curve [AUC] = 0.89), and similar discrimination was achieved when using only ten antibodies (AUC = 0.87). Individuals with IBD thus show a distinct antibody repertoire against selected peptides, allowing clinical stratification and discovery of immunological targets.
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Affiliation(s)
- Arno R Bourgonje
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Sergio Andreu-Sánchez
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Thomas Vogl
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel; Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Graz, Austria; Center for Cancer Research, Medical University of Vienna, Wien, Austria
| | - Shixian Hu
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Arnau Vich Vila
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Ranko Gacesa
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Sigal Leviatan
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Shelley Klompus
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Iris N Kalka
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Hendrik M van Dullemen
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Adina Weinberger
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Marijn C Visschedijk
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Eleonora A M Festen
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Klaas Nico Faber
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Gerard Dijkstra
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
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10
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Basu M, Fucile C, Piepenbrink MS, Bunce CA, Man LX, Liesveld J, Rosenberg AF, Keefer MC, Kobie JJ. Mixed Origins: HIV gp120-Specific Memory Develops from Pre-Existing Memory and Naive B Cells Following Vaccination in Humans. AIDS Res Hum Retroviruses 2023. [PMID: 36762930 PMCID: PMC10398743 DOI: 10.1089/aid.2022.0104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023] Open
Abstract
The most potent and broad HIV envelope (Env)-specific antibodies often when reverted to their inferred germline versions representing the naive B cell receptor, fail to bind Env, suggesting that the initial responding B cell population not only exclusively comprises a naive population, but also a pre-existing cross-reactive antigen-experienced B cell pool that expands following Env exposure. Previously we isolated gp120-reactive monoclonal antibodies (mAbs) from participants in HVTN 105, an HIV vaccine trial. Using deep sequencing, focused on immunoglobulin G (IgG), IgA, and IgM, VH-lineage tracking, we identified four of these mAb lineages in pre-immune peripheral blood. We also looked through the ∼7 month postvaccination bone marrow, and interestingly, several of these lineages that were found in prevaccination blood were still persistent in the postvaccination bone marrow, including the CD138+ long-lived plasma cell compartment. The majority of the pre-immune lineage members included IgM, however, IgG and IgA members were also prevalent and exhibited somatic hypermutation. These results suggest that vaccine-induced gp120-specific antibody lineages originate from both naive and cross-reactive memory B cells. ClinicalTrials.gov NCT02207920.
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Affiliation(s)
- Madhubanti Basu
- Infectious Diseases Division, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Christopher Fucile
- Informatics Institute, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Michael S Piepenbrink
- Infectious Diseases Division, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Catherine A Bunce
- Infectious Diseases Division, University of Rochester, Rochester, New York, USA
| | - Li-Xing Man
- Department of Otolaryngology Head and Neck Surgery, University of Rochester, Rochester, New York, USA
| | - Jane Liesveld
- Division of Hematology/Oncology, University of Rochester, Rochester, New York, USA
| | - Alexander F Rosenberg
- Informatics Institute, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Michael C Keefer
- Infectious Diseases Division, University of Rochester, Rochester, New York, USA
| | - James J Kobie
- Infectious Diseases Division, University of Alabama at Birmingham, Birmingham, Alabama, USA
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11
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Deshpande S, Ansari MY, Sutar J, Das P, Hingankar N, Mukherjee S, Jayal P, Singh S, Anantharaj A, Singh J, Chattopadhyay S, Raghavan S, Gosain M, Chauhan S, Shrivas S, Prasad C, Chauhan S, Sharma N, Jana P, Thiruvengadam R, Kshetrapal P, Wadhwa N, Das B, Batra G, Medigeshi G, Sok D, Bhatnagar S, Garg PK, Bhattacharya J. Ancestral SARS-CoV-2-Driven Antibody Repertoire Diversity in an Unvaccinated Individual Correlates with Expanded Neutralization Breadth. Microbiol Spectr 2023; 11:e0433222. [PMID: 36946746 PMCID: PMC10100905 DOI: 10.1128/spectrum.04332-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 03/06/2023] [Indexed: 03/23/2023] Open
Abstract
Understanding the quality of immune repertoire triggered during natural infection can provide vital clues that form the basis for development of a humoral immune response in some individuals capable of broadly neutralizing pan-SARS-CoV-2 variants. In the present study, we report variations in neutralization potential against Omicron variants of two novel neutralizing monoclonal antibodies (MAbs), THSC20.HVTR11 and THSC20.HVTR55, isolated from an unvaccinated convalescent individual that represent distinct B cell lineage origins and epitope specificity compared to five MAbs we previously reported that were isolated from the same individual. In addition, we observed neutralization of Omicron variants by plasma antibodies obtained from this particular individual postvaccination with increased magnitude. Interestingly, this observation was found to be comparable with six additional individuals who initially were also infected with ancestral SARS-CoV-2 and then received vaccines, indicating that hybrid immunity can provide robust humoral immunity likely by antibody affinity maturation. Development of a distinct antigen-specific B cell repertoire capable of producing polyclonal antibodies with distinct affinity and specificities offers the highest probability of protecting against evolving SARS-CoV-2 variants. IMPORTANCE Development of robust neutralizing antibodies in SARS-CoV-2 convalescent individuals is known; however, it varies at the population level. We isolated monoclonal antibodies from an individual infected with ancestral SARS-CoV-2 in early 2020 that not only varied in their B cell lineage origin but also varied in their capability and potency to neutralize all the known variants of concern (VOCs) and currently circulating Omicron variants. This indicated establishment of unique lineages that contributed in forming a B cell repertoire in this particular individual immediately following infection, giving rise to diverse antibody responses that could complement each other in providing a broadly neutralizing polyclonal antibody response. Individuals who were able to produce polyclonal antibody responses with higher magnitude have a higher chance of being protected from evolving SARS-CoV-2 variants.
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Affiliation(s)
- Suprit Deshpande
- IAVI-Antibody Translational Research Program, Translational Health Science & Technology Institute, Faridabad, Haryana, India
| | - Mohammed Yousuf Ansari
- IAVI-Antibody Translational Research Program, Translational Health Science & Technology Institute, Faridabad, Haryana, India
| | - Jyoti Sutar
- IAVI-Antibody Translational Research Program, Translational Health Science & Technology Institute, Faridabad, Haryana, India
- IAVI, New York, New York, USA
| | - Payel Das
- IAVI-Antibody Translational Research Program, Translational Health Science & Technology Institute, Faridabad, Haryana, India
| | - Nitin Hingankar
- IAVI-Antibody Translational Research Program, Translational Health Science & Technology Institute, Faridabad, Haryana, India
| | - Sohini Mukherjee
- IAVI-Antibody Translational Research Program, Translational Health Science & Technology Institute, Faridabad, Haryana, India
- IAVI, New York, New York, USA
| | - Priyanka Jayal
- IAVI-Antibody Translational Research Program, Translational Health Science & Technology Institute, Faridabad, Haryana, India
| | - Savita Singh
- Translational Health Science & Technology Institute, Faridabad, Haryana, India
| | - Anbalagan Anantharaj
- Translational Health Science & Technology Institute, Faridabad, Haryana, India
- Bioassay Laboratory, Translational Health Science & Technology Institute, Faridabad, Haryana, India
| | - Janmejay Singh
- Translational Health Science & Technology Institute, Faridabad, Haryana, India
- Bioassay Laboratory, Translational Health Science & Technology Institute, Faridabad, Haryana, India
| | | | - Sreevatsan Raghavan
- Translational Health Science & Technology Institute, Faridabad, Haryana, India
| | - Mudita Gosain
- Translational Health Science & Technology Institute, Faridabad, Haryana, India
| | - Supriya Chauhan
- IAVI-Antibody Translational Research Program, Translational Health Science & Technology Institute, Faridabad, Haryana, India
| | - Shweta Shrivas
- IAVI-Antibody Translational Research Program, Translational Health Science & Technology Institute, Faridabad, Haryana, India
| | - Chaman Prasad
- IAVI-Antibody Translational Research Program, Translational Health Science & Technology Institute, Faridabad, Haryana, India
| | - Sangeeta Chauhan
- IAVI-Antibody Translational Research Program, Translational Health Science & Technology Institute, Faridabad, Haryana, India
| | - Neha Sharma
- IAVI-Antibody Translational Research Program, Translational Health Science & Technology Institute, Faridabad, Haryana, India
| | - Pradipta Jana
- Translational Health Science & Technology Institute, Faridabad, Haryana, India
| | | | - Pallavi Kshetrapal
- Translational Health Science & Technology Institute, Faridabad, Haryana, India
| | - Nitya Wadhwa
- Translational Health Science & Technology Institute, Faridabad, Haryana, India
| | - Bhabatosh Das
- Translational Health Science & Technology Institute, Faridabad, Haryana, India
| | - Gaurav Batra
- Translational Health Science & Technology Institute, Faridabad, Haryana, India
| | - Guruprasad Medigeshi
- Translational Health Science & Technology Institute, Faridabad, Haryana, India
- Bioassay Laboratory, Translational Health Science & Technology Institute, Faridabad, Haryana, India
| | - Devin Sok
- IAVI-Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery (CAVD), The Scripps Research Institute, La Jolla, California, USA
- Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, USA
- IAVI, New York, New York, USA
| | - Shinjini Bhatnagar
- Translational Health Science & Technology Institute, Faridabad, Haryana, India
| | - Pramod Kumar Garg
- Translational Health Science & Technology Institute, Faridabad, Haryana, India
| | - Jayanta Bhattacharya
- IAVI-Antibody Translational Research Program, Translational Health Science & Technology Institute, Faridabad, Haryana, India
- IAVI, New York, New York, USA
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12
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Kazieva LS, Farafonova TE, Zgoda VG. [Antibody proteomics]. Biomed Khim 2023; 69:5-18. [PMID: 36857423 DOI: 10.18097/pbmc20236901005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Antibodies represent an essential component of humoral immunity; therefore their study is important for molecular biology and medicine. The unique property of antibodies to specifically recognize and bind a certain molecular target (an antigen) determines their widespread application in treatment and diagnostics of diseases, as well as in laboratory and biotechnological practices. High specificity and affinity of antibodies is determined by the presence of primary structure variable regions, which are not encoded in the human genome and are unique for each antibody-producing B cell clone. Hence, there is little or no information about amino acid sequences of the variable regions in the databases. This differs identification of antibody primary structure from most of the proteomic studies because it requires either B cell genome sequencing or de novo amino acid sequencing of the antibody. The present review demonstrates some examples of proteomic and proteogenomic approaches and the methodological arsenal that proteomics can offer for studying antibodies, in particular, for identification of primary structure, evaluation of posttranslational modifications and application of bioinformatics tools for their decoding.
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Affiliation(s)
- L Sh Kazieva
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | - V G Zgoda
- Institute of Biomedical Chemistry, Moscow, Russia
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13
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Rush SA, Brar G, Hsieh CL, Chautard E, Rainho-Tomko JN, Slade CD, Bricault CA, Kume A, Kearns J, Groppo R, Mundle ST, Zhang L, Casimiro D, Fu TM, DiNapoli JM, McLellan JS. Characterization of prefusion-F-specific antibodies elicited by natural infection with human metapneumovirus. Cell Rep 2022; 40:111399. [PMID: 36130517 DOI: 10.1016/j.celrep.2022.111399] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 06/23/2022] [Accepted: 09/01/2022] [Indexed: 12/20/2022] Open
Abstract
Human metapneumovirus (hMPV) is a major cause of acute respiratory infections in infants and older adults, for which no vaccines or therapeutics are available. The viral fusion (F) glycoprotein is required for entry and is the primary target of neutralizing antibodies; however, little is known about the humoral immune response generated from natural infection. Here, using prefusion-stabilized F proteins to interrogate memory B cells from two older adults, we obtain over 700 paired non-IgM antibody sequences representing 563 clonotypes, indicative of a highly polyclonal response. Characterization of 136 monoclonal antibodies reveals broad recognition of the protein surface, with potently neutralizing antibodies targeting each antigenic site. Cryo-EM studies further reveal two non-canonical sites and the molecular basis for recognition of the apex of hMPV F by two prefusion-specific neutralizing antibodies. Collectively, these results provide insight into the humoral response to hMPV infection in older adults and will help guide vaccine development.
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14
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Lebedin M, Foglierini M, Khorkova S, Vázquez García C, Ratswohl C, Davydov AN, Turchaninova MA, Daubenberger C, Chudakov DM, Lanzavecchia A, de la Rosa K. Different classes of genomic inserts contribute to human antibody diversity. Proc Natl Acad Sci U S A 2022; 119:e2205470119. [PMID: 36037353 DOI: 10.1073/pnas.2205470119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The enormous diversity of antibodies is a key element to combat infections. Antibodies containing pathogen receptors were a surprising discovery that contrasted antibody diversification through classic recombination events. However, such insert-containing antibodies were thus far exclusively detected in African individuals exposed to malaria parasites and were identified as screening byproducts or through hypothesis-driven search. The prevalence and complexity of insertion events remained elusive. In this study, we devise an unbiased, systematic approach to identify inserts in the human antibody repertoire. We show that inserts from distant genomic regions occur in the majority of donors and are independent of Plasmodium falciparum preexposure. Our findings suggest that four distinct classes of insertion events contribute diversity to the human antibody repertoire. Recombination of antibody genes in B cells can involve distant genomic loci and contribute a foreign antigen-binding element to form hybrid antibodies with broad reactivity for Plasmodium falciparum. So far, antibodies containing the extracellular domain of the LAIR1 and LILRB1 receptors represent unique examples of cross-chromosomal antibody diversification. Here, we devise a technique to profile non-VDJ elements from distant genes in antibody transcripts. Independent of the preexposure of donors to malaria parasites, non-VDJ inserts were detected in 80% of individuals at frequencies of 1 in 104 to 105 B cells. We detected insertions in heavy, but not in light chain or T cell receptor transcripts. We classify the insertions into four types depending on the insert origin and destination: 1) mitochondrial and 2) nuclear DNA inserts integrated at VDJ junctions; 3) inserts originating from telomere proximal genes; and 4) fragile sites incorporated between J-to-constant junctions. The latter class of inserts was exclusively found in memory and in in vitro activated B cells, while all other classes were already detected in naïve B cells. More than 10% of inserts preserved the reading frame, including transcripts with signs of antigen-driven affinity maturation. Collectively, our study unravels a mechanism of antibody diversification that is layered on the classical V(D)J and switch recombination.
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15
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Vaidehi Narayanan H, Hoffmann A. From Antibody Repertoires to Cell-Cell Interactions to Molecular Networks: Bridging Scales in the Germinal Center. Front Immunol 2022; 13:898078. [PMID: 35603162 PMCID: PMC9114758 DOI: 10.3389/fimmu.2022.898078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 04/08/2022] [Indexed: 01/02/2023] Open
Abstract
Antibody-mediated adaptive immunity must provide effective long-term protection with minimal adverse effects, against rapidly mutating pathogens, in a human population with diverse ages, genetics, and immune histories. In order to grasp and leverage the complexities of the antibody response, we advocate for a mechanistic understanding of the multiscale germinal center (GC) reaction - the process by which precursor B-cells evolve high-affinity antigen-specific antibodies, forming an effector repertoire of plasma and memory cells for decades-long protection. The regulatory dynamics of B-cells within the GC are complex, and unfold across multiple interacting spatial and temporal scales. At the organism scale, over weeks to years, the antibody sequence repertoire formed by various B-cell clonal lineages modulates antibody quantity and quality over time. At the tissue and cellular scale, over hours to weeks, B-cells undergo selection via spatially distributed interactions with local stroma, antigen, and helper T-cells. At the molecular scale, over seconds to days, intracellular signaling, transcriptional, and epigenetic networks modulate B-cell fates and shape their clonal lineages. We summarize our current understanding within each of these scales, and identify missing links in connecting them. We suggest that quantitative multi-scale mathematical models of B-cell and GC reaction dynamics provide predictive frameworks that can apply basic immunological knowledge to practical challenges such as rational vaccine design.
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Affiliation(s)
- Haripriya Vaidehi Narayanan
- Signaling Systems Laboratory, Department of Microbiology, Immunology, and Molecular Genetics, and Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, CA, United States
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16
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Pashova S, Balabanski L, Elmadjian G, Savov A, Stoyanova E, Shivarov V, Petrov P, Pashov A. Restriction of the Global IgM Repertoire in Antiphospholipid Syndrome. Front Immunol 2022; 13:865232. [PMID: 35493489 PMCID: PMC9043687 DOI: 10.3389/fimmu.2022.865232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 03/21/2022] [Indexed: 11/22/2022] Open
Abstract
The typical anti-phospholipid antibodies (APLA) in the anti-phospholipid syndrome (APS) are reactive with the phospholipid-binding protein β2GPI as well as a growing list of other protein targets. The relation of APLA to natural antibodies and the fuzzy set of autoantigens involved provoked us to study the changes in the IgM repertoire in APS. To this end, peptides selected by serum IgM from a 7-residue linear peptide phage display library (PDL) were deep sequenced. The analysis was aided by a novel formal representation of the Igome (the mimotope set reflecting the IgM specificities) in the form of a sequence graph. The study involved women with APLA and habitual abortions (n=24) compared to age-matched clinically healthy pregnant women (n=20). Their pooled Igomes (297 028 mimotope sequences) were compared also to the global public repertoire Igome of pooled donor plasma IgM (n=2 796 484) and a set of 7-mer sequences found in the J regions of human immunoglobulins (n=4 433 252). The pooled Igome was represented as a graph connecting the sequences as similar as the mimotopes of the same monoclonal antibody. The criterion was based on previously published data. In the resulting graph, identifiable clusters of vertices were considered related to the footprints of overlapping antibody cross-reactivities. A subgraph based on the clusters with a significant differential expression of APS patients’ mimotopes contained predominantly specificities underrepresented in APS. The differentially expressed IgM footprints showed also an increased cross-reactivity with immunoglobulin J regions. The specificities underexpressed in APS had a higher correlation with public specificities than those overexpressed. The APS associated specificities were strongly related also to the human peptidome with 1 072 mimotope sequences found in 7 519 human proteins. These regions were characterized by low complexity. Thus, the IgM repertoire of the APS patients was found to be characterized by a significant reduction of certain public specificities found in the healthy controls with targets representing low complexity linear self-epitopes homologous to human antibody J regions.
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Affiliation(s)
- Shina Pashova
- Institute of Biology and Immunology of Reproduction, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Lubomir Balabanski
- Department of Medical Genetics, Medical University-Sofia, Sofia, Bulgaria.,Genomics Laboratory, Hospital "Malinov", Sofia, Bulgaria
| | - Gabriel Elmadjian
- Institute of Biology and Immunology of Reproduction, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Alexey Savov
- Department of Medical Genetics, Medical University-Sofia, Sofia, Bulgaria
| | - Elena Stoyanova
- Institute of Biology and Immunology of Reproduction, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | | | - Peter Petrov
- Institute Mathematics and Informatics, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Anastas Pashov
- Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
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17
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Kaduk M, Corcoran M, Karlsson Hedestam GB. Addressing IGHV Gene Structural Diversity Enhances Immunoglobulin Repertoire Analysis: Lessons From Rhesus Macaque. Front Immunol 2022; 13:818440. [PMID: 35419009 PMCID: PMC8995469 DOI: 10.3389/fimmu.2022.818440] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 03/01/2022] [Indexed: 11/13/2022] Open
Abstract
The accurate germline gene assignment and assessment of somatic hypermutation in antibodies induced by immunization or infection are important in immunological studies. Here, we illustrate issues specific to the construction of comprehensive immunoglobulin (IG) germline gene reference databases for outbred animal species using rhesus macaques, a frequently used non-human primate model, as a model test case. We demonstrate that the genotypic variation found in macaque germline inference studies is reflected in similar levels of gene diversity in genomic assemblies. We show that the high frequency of IG heavy chain V (IGHV) region structural and gene copy number variation between subjects means that individual animals lack genes that are present in other animals. Therefore, gene databases compiled from a single or too few animals will inevitably result in inaccurate gene assignment and erroneous SHM level assessment for those genes it lacks. We demonstrate this by assigning a test macaque IgG library to the KIMDB, a database compiled of germline IGHV sequences from 27 rhesus macaques, and, alternatively, to the IMGT rhesus macaque database, based on IGHV genes inferred primarily from the genomic sequence of the rheMac10 reference assembly, supplemented with 10 genes from the Mmul_051212 assembly. We found that the use of a gene-restricted database led to overestimations of SHM by up to 5% due to misassignments. The principles described in the current study provide a model for the creation of comprehensive immunoglobulin reference databases from outbred species to ensure accurate gene assignment, lineage tracing and SHM calculations.
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Affiliation(s)
- Mateusz Kaduk
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Martin Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
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18
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Ehling RA, Weber CR, Mason DM, Friedensohn S, Wagner B, Bieberich F, Kapetanovic E, Vazquez-Lombardi R, Di Roberto RB, Hong KL, Wagner C, Pataia M, Overath MD, Sheward DJ, Murrell B, Yermanos A, Cuny AP, Savic M, Rudolf F, Reddy ST. SARS-CoV-2 reactive and neutralizing antibodies discovered by single-cell sequencing of plasma cells and mammalian display. Cell Rep 2022; 38:110242. [PMID: 34998467 PMCID: PMC8692065 DOI: 10.1016/j.celrep.2021.110242] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 09/22/2021] [Accepted: 12/20/2021] [Indexed: 01/05/2023] Open
Abstract
Characterization of COVID-19 antibodies has largely focused on memory B cells; however, it is the antibody-secreting plasma cells that are directly responsible for the production of serum antibodies, which play a critical role in resolving SARS-CoV-2 infection. Little is known about the specificity of plasma cells, largely because plasma cells lack surface antibody expression, thereby complicating their screening. Here, we describe a technology pipeline that integrates single-cell antibody repertoire sequencing and mammalian display to interrogate the specificity of plasma cells from 16 convalescent patients. Single-cell sequencing allows us to profile antibody repertoire features and identify expanded clonal lineages. Mammalian display screening is used to reveal that 43 antibodies (of 132 candidates) derived from expanded plasma cell lineages are specific to SARS-CoV-2 antigens, including antibodies with high affinity to the SARS-CoV-2 receptor-binding domain (RBD) that exhibit potent neutralization and broad binding to the RBD of SARS-CoV-2 variants (of concern/interest).
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Affiliation(s)
- Roy A Ehling
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Cédric R Weber
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; deepCDR Biologics AG, Basel, Switzerland
| | - Derek M Mason
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; deepCDR Biologics AG, Basel, Switzerland
| | - Simon Friedensohn
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; deepCDR Biologics AG, Basel, Switzerland
| | - Bastian Wagner
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Florian Bieberich
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Edo Kapetanovic
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | | | - Raphaël B Di Roberto
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Kai-Lin Hong
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; Botnar Research Centre for Child Health, Basel, Switzerland
| | | | - Michele Pataia
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; deepCDR Biologics AG, Basel, Switzerland
| | - Max D Overath
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Daniel J Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Alexander Yermanos
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; Botnar Research Centre for Child Health, Basel, Switzerland; Institute of Microbiology and Immunology, Department of Biology, ETH Zurich, Zurich, Switzerland; Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
| | - Andreas P Cuny
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; Swiss Institute of Bioinformatics, Mattenstr. 26, 4058 Basel, Switzerland
| | - Miodrag Savic
- Department of Biomedical Engineering, University of Basel, Allschwil, Switzerland; Department of Surgery, Oral and Cranio-Maxillofacial Surgery, University Hospital Basel, Basel, Switzerland; Department of Health, Economics and Health Directorate, Canton Basel-Landschaft, Switzerland
| | - Fabian Rudolf
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; Swiss Institute of Bioinformatics, Mattenstr. 26, 4058 Basel, Switzerland
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; Botnar Research Centre for Child Health, Basel, Switzerland.
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19
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Yang X, Zhu Y, Chen S, Zeng H, Guan J, Wang Q, Lan C, Sun D, Yu X, Zhang Z. Novel Allele Detection Tool Benchmark and Application With Antibody Repertoire Sequencing Dataset. Front Immunol 2021; 12:739179. [PMID: 34764956 PMCID: PMC8576399 DOI: 10.3389/fimmu.2021.739179] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 10/11/2021] [Indexed: 11/29/2022] Open
Abstract
Detailed knowledge of the diverse immunoglobulin germline genes is critical for the study of humoral immunity. Hundreds of alleles have been discovered by analyzing antibody repertoire sequencing (Rep-seq or Ig-seq) data via multiple novel allele detection tools (NADTs). However, the performance of these NADTs through antibody sequences with intrinsic somatic hypermutations (SHMs) is unclear. Here, we developed a tool to simulate repertoires by integrating the full spectrum features of an antibody repertoire such as germline gene usage, junctional modification, position-specific SHM and clonal expansion based on 2152 high-quality datasets. We then systematically evaluated these NADTs using both simulated and genuine Ig-seq datasets. Finally, we applied these NADTs to 687 Ig-seq datasets and identified 43 novel allele candidates (NACs) using defined criteria. Twenty-five alleles were validated through findings of other sources. In addition to the NACs detected, our simulation tool, the results of our comparison, and the streamline of this process may benefit further humoral immunity studies via Ig-seq.
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Affiliation(s)
- Xiujia Yang
- 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
| | - Yan Zhu
- Center for Precision Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Sen Chen
- 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
| | - 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
| | - Junjie Guan
- 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
| | - 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
| | - Chunhong Lan
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Deqiang Sun
- Department of Center Laboratory, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - 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
| | - 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
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20
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Chen G, Shrock EL, Li MZ, Spergel JM, Nadeau KC, Pongracic JA, Umetsu DT, Rachid R, MacGinnitie AJ, Phipatanakul W, Schneider L, Oettgen HC, Elledge SJ. High-resolution epitope mapping by AllerScan reveals relationships between IgE and IgG repertoires during peanut oral immunotherapy. Cell Rep Med 2021; 2:100410. [PMID: 34755130 PMCID: PMC8563412 DOI: 10.1016/j.xcrm.2021.100410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 07/18/2021] [Accepted: 09/21/2021] [Indexed: 10/24/2022]
Abstract
Peanut allergy can result in life-threatening reactions and is a major public health concern. Oral immunotherapy (OIT) induces desensitization to food allergens through administration of increasing amounts of allergen. To dissect peanut-specific immunoglobulin E (IgE) and IgG responses in subjects undergoing OIT, we have developed AllerScan, a method that leverages phage-display and next-generation sequencing to identify the epitope targets of peanut-specific antibodies. We observe a striking diversification and boosting of the peanut-specific IgG repertoire after OIT and a reduction in pre-existing IgE levels against individual epitopes. High-resolution epitope mapping reveals shared recognition of public epitopes in Ara h 1, 2, 3, and 7. In individual subjects, OIT-induced IgG specificities overlap extensively with IgE and exhibit strikingly similar antibody footprints, suggesting related clonal lineages or convergent evolution of peanut-specific IgE and IgG B cells. Individual differences in epitope recognition identified via AllerScan could inform safer and more effective personalized immunotherapy.
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Affiliation(s)
- Genghao Chen
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA 02115, USA.,Program in Biological and Biomedical Sciences, Harvard University, Cambridge, MA 02115, USA
| | - Ellen L Shrock
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA 02115, USA.,Program in Biological and Biomedical Sciences, Harvard University, Cambridge, MA 02115, USA
| | - Mamie Z Li
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Jonathan M Spergel
- Division of Allergy and Immunology, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pediatrics, Perelman School of Medicine of University of Pennsylvania, Philadelphia, PA, USA
| | - Kari C Nadeau
- Department of Medicine, Sean N Parker Center for Allergy and Asthma Research, Stanford University, Palo Alto, CA, USA
| | - Jacqueline A Pongracic
- Division of Pediatric Allergy and Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.,Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA
| | - Dale T Umetsu
- Division of Immunology, Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Rima Rachid
- Division of Immunology, Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Andrew J MacGinnitie
- Division of Immunology, Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Wanda Phipatanakul
- Division of Immunology, Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Lynda Schneider
- Division of Immunology, Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Hans C Oettgen
- Division of Immunology, Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Stephen J Elledge
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA 02115, USA
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21
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Olsen TH, Boyles F, Deane CM. Observed Antibody Space: A diverse database of cleaned, annotated, and translated unpaired and paired antibody sequences. Protein Sci 2021; 31:141-146. [PMID: 34655133 PMCID: PMC8740823 DOI: 10.1002/pro.4205] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/09/2021] [Accepted: 10/12/2021] [Indexed: 11/17/2022]
Abstract
The antibody repertoires of individuals and groups have been used to explore disease states, understand vaccine responses, and drive therapeutic development. The arrival of B‐cell receptor repertoire sequencing has enabled researchers to get a snapshot of these antibody repertoires, and as more data are generated, increasingly in‐depth studies are possible. However, most publicly available data only exist as raw FASTQ files, making the data hard to access, process, and compare. The Observed Antibody Space (OAS) database was created in 2018 to offer clean, annotated, and translated repertoire data. In this paper, we describe an update to OAS that has been driven by the increasing volume of data and the appearance of paired (VH/VL) sequence data. OAS is now accessible via a new web server, with standardized search parameters and a new sequence‐based search option. The new database provides both nucleotides and amino acids for every sequence, with additional sequence annotations to make the data Minimal Information about Adaptive Immune Receptor Repertoire compliant, and comments on potential problems with the sequence. OAS now contains 25 new studies, including severe acute respiratory syndrome coronavirus 2 data and paired sequencing data. The new database is accessible at http://opig.stats.ox.ac.uk/webapps/oas/, and all data are freely available for download.
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Affiliation(s)
- Tobias H Olsen
- Department of Statistics, University of Oxford, Oxford, UK
| | - Fergus Boyles
- Department of Statistics, University of Oxford, Oxford, UK
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22
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Snapkov I, Chernigovskaya M, Sinitcyn P, Lê Quý K, Nyman TA, Greiff V. Progress and challenges in mass spectrometry-based analysis of antibody repertoires. Trends Biotechnol 2021:S0167-7799(21)00193-1. [PMID: 34535228 DOI: 10.1016/j.tibtech.2021.08.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/16/2021] [Accepted: 08/17/2021] [Indexed: 12/22/2022]
Abstract
Humoral immunity is divided into the cellular B cell and protein-level antibody responses. High-throughput sequencing has advanced our understanding of both these fundamental aspects of B cell immunology as well as aspects pertaining to vaccine and therapeutics biotechnology. Although the protein-level serum and mucosal antibody repertoire make major contributions to humoral protection, the sequence composition and dynamics of antibody repertoires remain underexplored. This limits insight into important immunological and biotechnological parameters such as the number of antigen-specific antibodies, which are for example, relevant for pathogen neutralization, microbiota regulation, severity of autoimmunity, and therapeutic efficacy. High-resolution mass spectrometry (MS) has allowed initial insights into the antibody repertoire. We outline current challenges in MS-based sequence analysis of antibody repertoires and propose strategies for their resolution.
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23
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Aizik L, Dror Y, Taussig D, Barzel A, Carmi Y, Wine Y. Antibody Repertoire Analysis of Tumor-Infiltrating B Cells Reveals Distinct Signatures and Distributions Across Tissues. Front Immunol 2021; 12:705381. [PMID: 34349765 PMCID: PMC8327180 DOI: 10.3389/fimmu.2021.705381] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 06/29/2021] [Indexed: 12/12/2022] Open
Abstract
The role of B cells in the tumor microenvironment (TME) has largely been under investigated, and data regarding the antibody repertoire encoded by B cells in the TME and the adjacent lymphoid organs are scarce. Here, we utilized B cell receptor high-throughput sequencing (BCR-Seq) to profile the antibody repertoire signature of tumor-infiltrating lymphocyte B cells (TIL−Bs) in comparison to B cells from three anatomic compartments in a mouse model of triple-negative breast cancer. We found that TIL-Bs exhibit distinct antibody repertoire measures, including high clonal polarization and elevated somatic hypermutation rates, suggesting a local antigen-driven B-cell response. Importantly, TIL-Bs were highly mutated but non-class switched, suggesting that class-switch recombination may be inhibited in the TME. Tracing the distribution of TIL-B clones across various compartments indicated that they migrate to and from the TME. The data thus suggests that antibody repertoire signatures can serve as indicators for identifying tumor-reactive B cells.
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Affiliation(s)
- Ligal Aizik
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Yael Dror
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - David Taussig
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Adi Barzel
- The School of Neurobiology, Biochemistry and Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Yaron Carmi
- Department of Pathology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yariv Wine
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
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24
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Guthmiller JJ, Utset HA, Henry C, Li L, Zheng NY, Sun W, Costa Vieira M, Zost S, Huang M, Hensley SE, Cobey S, Palese P, Wilson PC. An Egg-Derived Sulfated N-Acetyllactosamine Glycan Is an Antigenic Decoy of Influenza Virus Vaccines. mBio 2021; 12:e0083821. [PMID: 34126773 DOI: 10.1128/mBio.00838-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Influenza viruses grown in eggs for the purposes of vaccine generation often acquire mutations during egg adaptation or possess different glycosylation patterns than viruses circulating among humans. Here, we report that seasonal influenza virus vaccines possess an egg-derived glycan that is an antigenic decoy, with egg-binding MAbs reacting with a sulfated N-acetyllactosamine (LacNAc). Half of subjects that received an egg-grown vaccine mounted an antibody response against this egg-derived antigen. Egg-binding monoclonal antibodies specifically bind viruses grown in eggs, but not viruses grown in other chicken-derived cells, suggesting that only egg-grown vaccines can induce antiegg antibodies. Notably, antibodies against the egg antigen utilized a restricted antibody repertoire and possessed features of natural antibodies, as most antibodies were IgM and had a simple heavy-chain complementarity-determining region 3. By analyzing a public data set of influenza virus vaccine-induced plasmablasts, we discovered egg-binding public clonotypes that were shared across studies. Together, this study shows that egg-grown vaccines can induce antibodies against an egg-associated glycan, which may divert the host immune response away from protective epitopes.
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25
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Yang X, Wang M, Wu J, Shi D, Zhang Y, Zeng H, Zhu Y, Lan C, Deng Y, Guo S, Xu L, Ma C, Zhang Y, Ou J, Liu CJ, Chen Y, Wang Q, Xie W, Guan J, Ding J, Wang Z, Chang C, Yang W, Zhang H, Chen J, Qin L, Zhou H, Bei JX, Wei L, Cao G, Yu X, Zhang Z. Large-scale analysis of 2,152 Ig-seq datasets reveals key features of B cell biology and the antibody repertoire. Cell Rep 2021; 35:109110. [PMID: 33979623 DOI: 10.1016/j.celrep.2021.109110] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 03/09/2021] [Accepted: 04/20/2021] [Indexed: 12/20/2022] Open
Abstract
Antibody repertoire sequencing enables researchers to acquire millions of B cell receptors and investigate these molecules at the single-nucleotide level. This power and resolution in studying humoral responses have led to its wide applications. However, most of these studies were conducted with a limited number of samples. Given the extraordinary diversity, assessment of these key features with a large sample set is demanded. Thus, we collect and systematically analyze 2,152 high-quality heavy-chain antibody repertoires. Our study reveals that 52 core variable genes universally contribute to more than 99% of each individual's repertoire; a distal interspersed preferences characterize V gene recombination; the number of public clones between two repertoires follows a linear model, and the positive selection dominates at RGYW motif in somatic hypermutations. Thus, this population-level analysis resolves some critical features of the antibody repertoire and may have significant value to the large cadre of scientists.
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Prabakaran P, Chowdhury PS. Landscape of Non-canonical Cysteines in Human V H Repertoire Revealed by Immunogenetic Analysis. Cell Rep 2021; 31:107831. [PMID: 32610132 PMCID: PMC7326410 DOI: 10.1016/j.celrep.2020.107831] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 04/02/2020] [Accepted: 06/08/2020] [Indexed: 12/21/2022] Open
Abstract
Human antibody repertoire data captured through next-generation sequencing (NGS) has enabled deeper insights into B cell immunogenetics and paratope diversity. By analyzing large public NGS datasets, we map the landscape of non-canonical cysteines in human variable heavy-chain domains (VHs) at the repertoire level. We identify remarkable usage of non-canonical cysteines within the heavy-chain complementarity-determining region 3 (CDR-H3) and other CDRs and framework regions. Furthermore, our study reveals the diversity and location of non-canonical cysteines and their associated motifs in human VHs, which are reminiscent of and more complex than those found in other non-human species such as chicken, camel, llama, shark, and cow. These results explain how non-canonical cysteines strategically occur in the human antibodyome to expand its paratope space. This study will guide the design of human antibodies harboring disulfide-stabilized long CDR-H3s to access difficult-to-target epitopes and influence a paradigm shift in developability involving non-canonical cysteines. NGS-based non-canonical cysteine landscape in human VHs 1 to 8 non-canonical cysteines and up to 30% in long CDR-H3s An array of potential disulfide motifs adds paratope diversity Non-canonical cysteines in human VHs are reminiscent of lower animals
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Mukhamedova M, Wrapp D, Shen CH, Gilman MSA, Ruckwardt TJ, Schramm CA, Ault L, Chang L, Derrien-Colemyn A, Lucas SAM, Ransier A, Darko S, Phung E, Wang L, Zhang Y, Rush SA, Madan B, Stewart-Jones GBE, Costner PJ, Holman LA, Hickman SP, Berkowitz NM, Doria-Rose NA, Morabito KM, DeKosky BJ, Gaudinski MR, Chen GL, Crank MC, Misasi J, Sullivan NJ, Douek DC, Kwong PD, Graham BS, McLellan JS, Mascola JR. Vaccination with prefusion-stabilized respiratory syncytial virus fusion protein induces genetically and antigenically diverse antibody responses. Immunity 2021; 54:769-780.e6. [PMID: 33823129 DOI: 10.1016/j.immuni.2021.03.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 01/21/2021] [Accepted: 03/05/2021] [Indexed: 12/14/2022]
Abstract
An effective vaccine for respiratory syncytial virus (RSV) is an unrealized public health goal. A single dose of the prefusion-stabilized fusion (F) glycoprotein subunit vaccine (DS-Cav1) substantially increases serum-neutralizing activity in healthy adults. We sought to determine whether DS-Cav1 vaccination induces a repertoire mirroring the pre-existing diversity from natural infection or whether antibody lineages targeting specific epitopes predominate. We evaluated RSV F-specific B cell responses before and after vaccination in six participants using complementary B cell sequencing methodologies and identified 555 clonal lineages. DS-Cav1-induced lineages recognized the prefusion conformation of F (pre-F) and were genetically diverse. Expressed antibodies recognized all six antigenic sites on the pre-F trimer. We identified 34 public clonotypes, and structural analysis of two antibodies from a predominant clonotype revealed a common mode of recognition. Thus, vaccination with DS-Cav1 generates a diverse polyclonal response targeting the antigenic sites on pre-F, supporting the development and advanced testing of pre-F-based vaccines against RSV.
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Affiliation(s)
- Maryam Mukhamedova
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Daniel Wrapp
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Chen-Hsiang Shen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Morgan S A Gilman
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Tracy J Ruckwardt
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chaim A Schramm
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Larissa Ault
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lauren Chang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alexandrine Derrien-Colemyn
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sarah A M Lucas
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amy Ransier
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Samuel Darko
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Emily Phung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Institute for Biomedical Sciences, George Washington University, Washington, DC 20052, USA
| | - Lingshu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yi Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Scott A Rush
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Bharat Madan
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66045, USA
| | - Guillaume B E Stewart-Jones
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Pamela J Costner
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - LaSonji A Holman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Somia P Hickman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nina M Berkowitz
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicole A Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kaitlyn M Morabito
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Brandon J DeKosky
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66045, USA; Department of Chemical Engineering, The University of Kansas, Lawrence, KS 66045, USA
| | - Martin R Gaudinski
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Grace L Chen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michelle C Crank
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - John Misasi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nancy J Sullivan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Barney S Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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Wang Y, Howell KA, Brannan J, Agans KN, Turner HL, Wirchnianski AS, Kailasan S, Fusco M, Galkin A, Chiang CI, Zhao X, Saphire EO, Chandran K, Ward AB, Dye JM, Aman MJ, Geisbert TW, Li Y. Prominent Neutralizing Antibody Response Targeting the Ebolavirus Glycoprotein Subunit Interface Elicited by Immunization. J Virol 2021; 95:JVI.01907-20. [PMID: 33536172 PMCID: PMC8103683 DOI: 10.1128/jvi.01907-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 01/13/2021] [Indexed: 12/21/2022] Open
Abstract
The severe death toll caused by the recent outbreak of Ebola virus disease reinforces the importance of developing ebolavirus prevention and treatment strategies. Here, we have explored the immunogenicity of a novel immunization regimen priming with vesicular stomatitis virus particles bearing Sudan Ebola virus (SUDV) glycoprotein (GP) that consists of GP1 & GP2 subunits and boosting with soluble SUDV GP in macaques, which developed robust neutralizing antibody (nAb) responses following immunizations. Moreover, EB46, a protective nAb isolated from one of the immune macaques, is found to target the GP1/GP2 interface, with GP-binding mode and neutralization mechanism similar to a number of ebolavirus nAbs from human and mouse, indicating that the ebolavirus GP1/GP2 interface is a common immunological target in different species. Importantly, selected immune macaque polyclonal sera showed nAb specificity similar to EB46 at substantial titers, suggesting that the GP1/GP2 interface region is a viable target for ebolavirus vaccine.Importance: The elicitation of sustained neutralizing antibody (nAb) responses against diverse ebolavirus strains remains as a high priority for the vaccine field. The most clinically advanced rVSV-ZEBOV vaccine could elicit moderate nAb responses against only one ebolavirus strain, EBOV, among the five ebolavirus strains, which last less than 6 months. Boost immunization strategies are desirable to effectively recall the rVSV vector-primed nAb responses to prevent infections in prospective epidemics, while an in-depth understanding of the specificity of immunization-elicited nAb responses is essential for improving vaccine performance. Here, using non-human primate animal model, we demonstrated that booster immunization with a stabilized trimeric soluble form of recombinant glycoprotein derived from the ebolavirus Sudan strain following the priming rVSV vector immunization led to robust nAb responses that substantially map to the subunit interface of ebolavirus glycoprotein, a common B cell repertoire target of multiple species including primates and rodents.
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Affiliation(s)
- Yimeng Wang
- Institute for Bioscience and Biotechnology Research, Rockville, MD
| | | | - Jennifer Brannan
- US Army Medical Research Institute of Infectious Diseases, Frederick, MD
| | - Krystle N Agans
- Galveston National Laboratory and Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX
- Galveston National Laboratory and Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX
| | - Hannah L Turner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA
| | - Ariel S Wirchnianski
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY
| | | | - Marnie Fusco
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA
| | - Andrey Galkin
- Institute for Bioscience and Biotechnology Research, Rockville, MD
- La Jolla Institute for Immunology, La Jolla, CA
| | - Chi-I Chiang
- Institute for Bioscience and Biotechnology Research, Rockville, MD
| | - Xuelian Zhao
- Institute for Bioscience and Biotechnology Research, Rockville, MD
| | | | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA
| | - John M Dye
- US Army Medical Research Institute of Infectious Diseases, Frederick, MD
| | | | - Thomas W Geisbert
- Galveston National Laboratory and Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX
- Galveston National Laboratory and Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX
| | - Yuxing Li
- Institute for Bioscience and Biotechnology Research, Rockville, MD
- Department of Microbiology and Immunology and Center of Biomolecular Therapeutics, University of Maryland School of Medicine, Baltimore, MD
- Department of Microbiology and Immunology and Center of Biomolecular Therapeutics, University of Maryland School of Medicine, Baltimore, MD
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Abstract
It is increasingly clear that an extraordinarily diverse range of clinically important conditions—including infections, vaccinations, autoimmune diseases, transplants, transfusion reactions, aging, and cancers—leave telltale signatures in the millions of V(D)J-rearranged antibody and T cell receptor [TR per the Human Genome Organization (HUGO) nomenclature but more commonly known as TCR] genes collectively expressed by a person’s B cells (antibodies) and T cells. We refer to these as the immunome. Because of its diversity and complexity, the immunome provides singular opportunities for advancing personalized medicine by serving as the substrate for a highly multiplexed, near-universal blood test. Here we discuss some of these opportunities, the current state of immunome-based diagnostics, and highlight some of the challenges involved. We conclude with a call to clinicians, researchers, and others to join efforts with the Adaptive Immune Receptor Repertoire Community (AIRR-C) to realize the diagnostic potential of the immunome.
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Affiliation(s)
- Ramy A Arnaout
- Department of Pathology and Division of Clinical Informatics, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, United States.,Department of Pathology, Harvard Medical School, Boston, MA, United States
| | - Eline T Luning Prak
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Nicholas Schwab
- Department of Neurology and Institute of Translational Neurology, University of Muenster, Muenster, Germany
| | - Florian Rubelt
- Roche Sequencing Solutions, Pleasanton, CA, United States
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30
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Meyer TC, Michalik S, Holtfreter S, Weiss S, Friedrich N, Völzke H, Kocher T, Kohler C, Schmidt F, Bröker BM, Völker U. A Comprehensive View on the Human Antibody Repertoire Against Staphylococcus aureus Antigens in the General Population. Front Immunol 2021; 12:651619. [PMID: 33777051 PMCID: PMC7987813 DOI: 10.3389/fimmu.2021.651619] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 02/16/2021] [Indexed: 12/20/2022] Open
Abstract
Our goal was to provide a comprehensive overview of the antibody response to Staphylococcus aureus antigens in the general population as a basis for defining disease-specific profiles and diagnostic signatures. We tested the specific IgG and IgA responses to 79 staphylococcal antigens in 996 individuals from the population-based Study of Health in Pomerania. Using a dilution-based multiplex suspension array, we extended the dynamic range of specific antibody detection to seven orders of magnitude, allowing the precise quantification of high and low abundant antibody specificities in the same sample. The observed IgG and IgA antibody responses were highly heterogeneous with differences between individuals as well as between bacterial antigens that spanned several orders of magnitude. Some antigens elicited significantly more IgG than IgA and vice versa. We confirmed a strong influence of colonization on the antibody response and quantified the influence of sex, smoking, age, body mass index, and serum glucose on anti-staphylococcal IgG and IgA. However, all host parameters tested explain only a small part of the extensive variability in individual response to the different antigens of S. aureus.
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Affiliation(s)
- Tanja C Meyer
- Department Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Stephan Michalik
- Department Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Silva Holtfreter
- Department of Immunology, Institute of Immunology and Transfusion Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Stefan Weiss
- Department Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Nele Friedrich
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Henry Völzke
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Thomas Kocher
- Unit of Periodontology, University Medicine Greifswald, Greifswald, Germany
| | - Christian Kohler
- Friedrich Loeffler Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
| | - Frank Schmidt
- Department Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany.,Proteomics Core, Weill Cornell Medicine-Qatar, Qatar Foundation-Education City, Doha, Qatar
| | - Barbara M Bröker
- Department of Immunology, Institute of Immunology and Transfusion Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Uwe Völker
- Department Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
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31
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Reifert J, Kamath K, Bozekowski J, Lis E, Horn EJ, Granger D, Theel ES, Shon J, Sawyer JR, Daugherty PS. Serum Epitope Repertoire Analysis Enables Early Detection of Lyme Disease with Improved Sensitivity in an Expandable Multiplex Format. J Clin Microbiol 2021; 59:e01836-20. [PMID: 33148704 PMCID: PMC8111119 DOI: 10.1128/jcm.01836-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 10/27/2020] [Indexed: 12/25/2022] Open
Abstract
Widely employed diagnostic antibody serology for Lyme disease, known as standard two-tier testing (STTT), exhibits insufficient sensitivity in early Lyme disease, yielding many thousands of false-negative test results each year. Given this problem, we applied serum antibody repertoire analysis (SERA), or next-generation sequencing (NGS)-based serology, to discover IgG and IgM antibody epitope motifs capable of detecting Lyme disease-specific antibodies with high sensitivity and specificity. Iterative motif discovery and bioinformatic analysis of epitope repertoires from subjects with Lyme disease (n = 264) and controls (n = 391) yielded a set of 28 epitope motifs representing 20 distinct IgG antibody epitopes and a set of 38 epitope motifs representing 21 distinct IgM epitopes, which performed equivalently in a large validation cohort of STTT-positive samples. In a second validation set from subjects with clinically defined early Lyme disease (n = 119) and controls (n = 257), the SERA Lyme IgG and IgM assay exhibited significantly improved sensitivity relative to STTT (77% versus 62%; Z-test; P = 0.013) and improved specificity (99% versus 97%). Early Lyme disease subjects exhibited significantly fewer reactive epitopes (Mann-Whitney U test; P < 0.0001) relative to subjects with Lyme arthritis. Thus, SERA Lyme IgG and M panels provided increased accuracy in early Lyme disease in a readily expandable multiplex assay format.
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Affiliation(s)
| | | | | | - Ewa Lis
- Serimmune Inc., Goleta, California, USA
| | | | - Dane Granger
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester Minnesota, USA
| | - Elitza S Theel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester Minnesota, USA
| | - John Shon
- Serimmune Inc., Goleta, California, USA
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Hong B, Wang L, Huang C, Hong X, Liu A, Li Q, Liu Q, Su L, Wang L, Wang C, Ying T. Decrease of Clone Diversity in IgM Repertoires of HBV Chronically Infected Individuals With High Level of Viral Replication. Front Microbiol 2021; 11:615669. [PMID: 33519772 PMCID: PMC7843509 DOI: 10.3389/fmicb.2020.615669] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 12/22/2020] [Indexed: 01/05/2023] Open
Abstract
High-throughput antibody sequencing allows in-depth insights into human antibody repertoires. To investigate the characteristics of antibody repertoires in patients with chronic HBV infection, we performed Illumina sequencing and IMGT/HighV-QUEST analysis of B lymphocytes from healthy adults and the HBV carriers with high or low level of viral replication. The comparative study revealed high levels of similarity between the IgM and IgG repertoires of the HBV carriers and the healthy adults, including the somatic mutations in V regions, the average CDR3 length, and the occurrence of junctional modifications. Nevertheless, the diversity of the unique clones decreased and some clusters of unique clones expanded in the IgM repertoire of chronic HBV carriers (CHB) compared with healthy adults (HH) and inactive HBV carriers (IHB). Such difference in clone diversity and expansion was not observed in the IgG repertoires of the three populations. More shared antibody clones were found between the IgM repertoires of IHB and HH than that found between CHB and HH (7079 clones vs. 2304 clones). Besides, the biased used IGHD genes were IGHD2-2 and IGHD3-3 in CHB library but were IGHD3-10 and IGHD3-22 in IHB and HH library. In contrast, for IgG repertories, the preferred used VDJ genes were similar in all the three populations. These results indicated that low level of serum HBV might not induce significant changes in BCR repertoires, and high level of HBV replication could have more impacts on IgM repertories than IgG repertoires. Taken together, our findings provide a better understanding of the antibody repertoires of HBV chronically infected individuals.
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Affiliation(s)
- Binbin Hong
- Central Laboratory, Second Affiliated Hospital, Fujian Medical University, Quanzhou, China
| | - Lizhi Wang
- Traditional Chinese Medicine Department, Rehabilitation Hospital, Quanzhou, China
| | - Chunlan Huang
- Traditional Chinese Medicine Department, Rehabilitation Hospital, Quanzhou, China
| | - Xiaoju Hong
- Traditional Chinese Medicine Department, Rehabilitation Hospital, Quanzhou, China
| | - Alan Liu
- Traditional Chinese Medicine Department, Rehabilitation Hospital, Quanzhou, China
| | - Qiulan Li
- Central Laboratory, Second Affiliated Hospital, Fujian Medical University, Quanzhou, China
| | - Qiaoling Liu
- Central Laboratory, Second Affiliated Hospital, Fujian Medical University, Quanzhou, China
| | - Lili Su
- Central Laboratory, Second Affiliated Hospital, Fujian Medical University, Quanzhou, China
| | - Lixing Wang
- Central Laboratory, Second Affiliated Hospital, Fujian Medical University, Quanzhou, China
| | - Chunyu Wang
- Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Tianlei Ying
- Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan University, Shanghai, China
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33
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Keating R, Johnson JL, Brice DC, Labombarde JG, Dent AL, McGargill MA. Broadly Reactive Influenza Antibodies Are Not Limited by Germinal Center Competition with High-Affinity Antibodies. mBio 2020; 11:e01859-20. [PMID: 33144374 DOI: 10.1128/mBio.01859-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
It is estimated that 250,000 to 650,000 individuals worldwide die each year from seasonal influenza A virus (IAV) infections. Current vaccines provide little protection against newly emerging strains. Thus, considerable effort is focused on enhancing the generation of broadly reactive IAV antibodies in order to develop a universal IAV vaccine. However, broadly reactive IAV antibodies are rare and the factors that limit their generation are not completely understood. Our data disprove the prevailing hypothesis that broadly reactive IAV antibodies are uncommon due to competition in the germinal centers with antibodies specific for the variable, hemagglutinin (HA) head. Understanding the factors that constrain development of antibodies specific for conserved regions of IAV is imperative for developing an effective universal IAV vaccine, which could potentially circumvent a catastrophic pandemic. These findings are significant as they highlight the importance of investigating other mechanisms that contribute to the paucity of broadly reactive IAV antibodies. Enhancing the generation of broadly reactive antibodies against influenza A virus (IAV) is a pertinent goal toward developing a universal IAV vaccine. While antibodies that bind conserved IAV epitopes have been identified in humans, antibodies specific for the variable epitopes are much more prevalent than antibodies recognizing conserved epitopes. It is important to define the factors that limit the generation of broadly reactive IAV antibodies in order to develop an effective universal IAV vaccine. The predominant theory is that competition within germinal centers favors the synthesis of high-affinity antibodies specific for the variable region of the virus, and limits antibodies specific for conserved IAV epitopes. Here, we show that reducing germinal center formation and removing competition with high-affinity antibodies was not sufficient to increase broadly reactive IAV antibodies or enhance protection against distinct IAV subtypes. These data disprove the prevailing hypothesis that broadly reactive IAV antibodies are rare due to competition within germinal centers, and reveal the critical need to further investigate factors that limit broadly reactive IAV antibodies. Additionally, our data show that IAV-specific IgM antibodies persist in mice in the absence of germinal centers, highlighting the protective capacity of germinal center-independent IgM antibodies, which are not typically considered when testing correlates of protection, and offer an alternate target for delivering a universal IAV vaccine.
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34
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Kräutler NJ, Yermanos A, Pedrioli A, Welten SPM, Lorgé D, Greczmiel U, Bartsch I, Scheuermann J, Kiefer JD, Eyer K, Menzel U, Greiff V, Neri D, Stadler T, Reddy ST, Oxenius A. Quantitative and Qualitative Analysis of Humoral Immunity Reveals Continued and Personalized Evolution in Chronic Viral Infection. Cell Rep 2020; 30:997-1012.e6. [PMID: 31995768 DOI: 10.1016/j.celrep.2019.12.088] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 11/20/2019] [Accepted: 12/23/2019] [Indexed: 12/31/2022] Open
Abstract
Control of established chronic lymphocytic choriomeningitis virus (LCMV) infection requires the production of neutralizing antibodies, but it remains unknown how the ensemble of antibodies evolves during ongoing infection. Here, we analyze the evolution of antibody responses during acute or chronic LCMV infection, combining quantitative functional assays and time-resolved antibody repertoire sequencing. We establish that antibody responses initially converge in both infection types on a functional and repertoire level, but diverge later during chronic infection, showing increased clonal diversity, the appearance of mouse-specific persistent clones, and distinct phylogenetic signatures. Chronic infection is characterized by a longer-lasting germinal center reaction and a continuous differentiation of plasma cells, resulting in the emergence of higher-affinity plasma cells exhibiting increased antibody secretion rates. Taken together, our findings reveal the emergence of a personalized antibody response in chronic infection and support the concept that maintaining B cell diversity throughout chronic LCMV infection correlates with the development of infection-resolving antibodies.
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Affiliation(s)
- Nike Julia Kräutler
- Institute of Microbiology, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Alexander Yermanos
- Institute of Microbiology, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland; Department of Biosystems and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Alessandro Pedrioli
- Institute of Microbiology, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Suzanne P M Welten
- Institute of Microbiology, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Dominique Lorgé
- Institute of Microbiology, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Ute Greczmiel
- Institute of Microbiology, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Ilka Bartsch
- Institute of Microbiology, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Jörg Scheuermann
- Institute for Pharmaceutical Sciences, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Jonathan D Kiefer
- Institute for Pharmaceutical Sciences, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Klaus Eyer
- Laboratory for Functional Immune Repertoire Analysis, Institute of Pharmaceutical Sciences, D-CHAB, ETH Zürich, Zürich, Switzerland
| | - Ulrike Menzel
- Department of Biosystems and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Victor Greiff
- Department of Biosystems and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland; Department of Immunology, University of Oslo, Sognsvannsveien 20 Rikshospitalet, 0372 Oslo, Norway
| | - Dario Neri
- Institute for Pharmaceutical Sciences, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
| | - Tanja Stadler
- Department of Biosystems and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Sai T Reddy
- Department of Biosystems and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Annette Oxenius
- Institute of Microbiology, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland.
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Nielsen SCA, Yang F, Jackson KJL, Hoh RA, Röltgen K, Jean GH, Stevens BA, Lee JY, Rustagi A, Rogers AJ, Powell AE, Hunter M, Najeeb J, Otrelo-Cardoso AR, Yost KE, Daniel B, Nadeau KC, Chang HY, Satpathy AT, Jardetzky TS, Kim PS, Wang TT, Pinsky BA, Blish CA, Boyd SD. Human B Cell Clonal Expansion and Convergent Antibody Responses to SARS-CoV-2. Cell Host Microbe 2020; 28:516-525.e5. [PMID: 32941787 PMCID: PMC7470783 DOI: 10.1016/j.chom.2020.09.002] [Citation(s) in RCA: 167] [Impact Index Per Article: 41.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/13/2020] [Accepted: 08/27/2020] [Indexed: 02/07/2023]
Abstract
B cells are critical for the production of antibodies and protective immunity to viruses. Here we show that patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) who develop coronavirus disease 2019 (COVID-19) display early recruitment of B cells expressing a limited subset of IGHV genes, progressing to a highly polyclonal response of B cells with broader IGHV gene usage and extensive class switching to IgG and IgA subclasses with limited somatic hypermutation in the initial weeks of infection. We identify convergence of antibody sequences across SARS-CoV-2-infected patients, highlighting stereotyped naive responses to this virus. Notably, sequence-based detection in COVID-19 patients of convergent B cell clonotypes previously reported in SARS-CoV infection predicts the presence of SARS-CoV/SARS-CoV-2 cross-reactive antibody titers specific for the receptor-binding domain. These findings offer molecular insights into shared features of human B cell responses to SARS-CoV-2 and SARS-CoV.
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Affiliation(s)
| | - Fan Yang
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | | | - Ramona A Hoh
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Katharina Röltgen
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Grace H Jean
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Bryan A Stevens
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Ji-Yeun Lee
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Arjun Rustagi
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA 94305, USA
| | - Angela J Rogers
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Stanford University, Stanford, CA 94305, USA
| | - Abigail E Powell
- Stanford ChEM-H and Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | | | - Javaria Najeeb
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
| | | | - Kathryn E Yost
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Bence Daniel
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Kari C Nadeau
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Stanford University, Stanford, CA 94305, USA; Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | | | - Theodore S Jardetzky
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA; Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Peter S Kim
- Stanford ChEM-H and Department of Biochemistry, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Taia T Wang
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Benjamin A Pinsky
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Catherine A Blish
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
| | - Scott D Boyd
- Department of Pathology, Stanford University, Stanford, CA 94305, USA; Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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36
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Suprun M, Getts R, Grishina G, Tsuang A, Suárez‐Fariñas M, Sampson HA. Ovomucoid epitope-specific repertoire of IgE, IgG 4 , IgG 1 , IgA 1 , and IgD antibodies in egg-allergic children. Allergy 2020; 75:2633-2643. [PMID: 32391917 DOI: 10.1111/all.14357] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 03/24/2020] [Accepted: 04/08/2020] [Indexed: 12/29/2022]
Abstract
BACKGROUND Egg-white ovomucoid, that is, Gal d 1, is associated with IgE-mediated allergic reactions in most egg-allergic children. Epitope-specific IgE levels have been correlated with the severity of egg allergy, while emerging evidence suggests that other antibody isotypes (IgG1 , IgG4 , IgA, and IgD) may have a protective function; yet, their epitope-specific repertoires and associations with atopic comorbidities have not been studied. METHODS Bead-based epitope assay (BBEA) was used to quantitate the levels of epitope-specific (es)IgA, esIgE, esIgD, esIgG1 , and esIgG4 antibodies directed at 58 (15-mer) overlapping peptides, covering the entire sequence of ovomucoid, in plasma of 38 egg-allergic and 6 atopic children. Intraclass correlation (ICC) and coefficient of variation (CV) were used for the reliability assessment. The relationships across esIgs were evaluated using network analysis; linear and logistic regressions were used to compare groups based on egg allergy status and comorbidities. RESULTS BBEA had high reliability (ICC >0.75) and low variability (CV <20%) and could detect known IgE-binding epitopes. Egg-allergic children had lower esIgA1 (P = .010) and esIgG1 (P = .016) and higher esIgE (P < .001) and esIgD (P = .015) levels compared to the atopic controls. Interestingly, within the allergic group, children with higher esIgD had decreased odds of anaphylactic reactions (OR =0.48, P = .038). Network analysis identified most associations between esIgE with either esIgG4 or esIgD; indicating that IgE-secreting plasma cells could originate from either sequential isotype switch from antigen-experienced intermediate isotypes or directly from the IgD+ B cells. CONCLUSIONS Collectively, these data point toward a contribution of epitope-specific antibody repertoires to the pathogenesis of egg allergy.
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Affiliation(s)
- Maria Suprun
- Icahn School of Medicine at Mount Sinai New Yok NY USA
| | | | | | - Angela Tsuang
- Icahn School of Medicine at Mount Sinai New Yok NY USA
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37
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Nielsen SCA, Yang F, Jackson KJL, Hoh RA, Röltgen K, Stevens B, Lee JY, Rustagi A, Rogers AJ, Powell AE, Najeeb J, Otrelo-Cardoso AR, Yost KE, Daniel B, Chang HY, Satpathy AT, Jardetzky TS, Kim PS, Wang TT, Pinsky BA, Blish CA, Boyd SD. Human B cell clonal expansion and convergent antibody responses to SARS-CoV-2. bioRxiv 2020:2020.07.08.194456. [PMID: 32676593 PMCID: PMC7359515 DOI: 10.1101/2020.07.08.194456] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
During virus infection B cells are critical for the production of antibodies and protective immunity. Here we show that the human B cell compartment in patients with diagnostically confirmed SARS-CoV-2 and clinical COVID-19 is rapidly altered with the early recruitment of B cells expressing a limited subset of IGHV genes, progressing to a highly polyclonal response of B cells with broader IGHV gene usage and extensive class switching to IgG and IgA subclasses with limited somatic hypermutation in the initial weeks of infection. We identify extensive convergence of antibody sequences across SARS-CoV-2 patients, highlighting stereotyped naïve responses to this virus. Notably, sequence-based detection in COVID-19 patients of convergent B cell clonotypes previously reported in SARS-CoV infection predicts the presence of SARS-CoV/SARS-CoV-2 cross-reactive antibody titers specific for the receptor-binding domain. These findings offer molecular insights into shared features of human B cell responses to SARS-CoV-2 and other zoonotic spillover coronaviruses.
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Affiliation(s)
- Sandra C. A. Nielsen
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
- These authors contributed equally
| | - Fan Yang
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
- These authors contributed equally
| | - Katherine J. L. Jackson
- Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
- These authors contributed equally
| | - Ramona A. Hoh
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
- These authors contributed equally
| | - Katharina Röltgen
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Bryan Stevens
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Ji-Yeun Lee
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Arjun Rustagi
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA 94305, USA
| | - Angela J. Rogers
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, Stanford University, Stanford, CA 94305, USA
| | - Abigail E. Powell
- Stanford ChEM-H and Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Javaria Najeeb
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
| | | | - Kathryn E. Yost
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Bence Daniel
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Howard Y. Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | | | - Theodore S. Jardetzky
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA 94305, USA
| | - Peter S. Kim
- Stanford ChEM-H and Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Taia T. Wang
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | | | - Catherine A. Blish
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Scott D. Boyd
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA 94305, USA
- Lead Contact
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38
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Yermanos A, Kräutler NJ, Pedrioli A, Menzel U, Greiff V, Stadler T, Oxenius A, Reddy ST. IgM Antibody Repertoire Fingerprints in Mice Are Personalized but Robust to Viral Infection Status. Front Cell Infect Microbiol 2020; 10:254. [PMID: 32547966 PMCID: PMC7270205 DOI: 10.3389/fcimb.2020.00254] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 04/30/2020] [Indexed: 01/11/2023] Open
Abstract
Antibody repertoire sequencing provides a molecular fingerprint of current and past pathogens encountered by the immune system. Most repertoire studies in humans require measuring the B cell response in the blood, resulting in a large bias to the IgM isotype. The extent to which the circulating IgM antibody repertoire correlates to lymphoid tissue-resident B cells in the setting of viral infection remains largely uncharacterized. Therefore, we compared the IgM repertoires from both blood and bone marrow (BM) plasma cells (PCs) following acute or chronic lymphocytic choriomeningitis virus (LCMV) infection in mice. Despite previously reported serum alterations between acute and chronic infection, IgM repertoire signatures based on clonal diversity metrics, public clones, network, and phylogenetic analysis were largely unable to distinguish infection cohorts. Our findings, however, revealed mouse-specific repertoire fingerprints between the blood and PC repertoires irrespective of infection status.
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Affiliation(s)
- Alexander Yermanos
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland.,Department of Biosystems and Engineering, ETH Zurich, Basel, Switzerland
| | | | | | - Ulrike Menzel
- Department of Biosystems and Engineering, ETH Zurich, Basel, Switzerland
| | - Victor Greiff
- Department of Immunology, University of Oslo, Oslo, Norway
| | - Tanja Stadler
- Department of Biosystems and Engineering, ETH Zurich, Basel, Switzerland
| | | | - Sai T Reddy
- Department of Biosystems and Engineering, ETH Zurich, Basel, Switzerland
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39
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Hernandez DN, Tam K, Shopsin B, Radke EE, Kolahi P, Copin R, Stubbe FX, Cardozo T, Torres VJ, Silverman GJ. Unbiased Identification of Immunogenic Staphylococcus aureus Leukotoxin B-Cell Epitopes. Infect Immun 2020; 88:e00785-19. [PMID: 32014894 DOI: 10.1128/IAI.00785-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 01/26/2020] [Indexed: 12/26/2022] Open
Abstract
Unbiased identification of individual immunogenic B-cell epitopes in major antigens of a pathogen remains a technology challenge for vaccine discovery. We therefore developed a platform for rapid phage display screening of deep recombinant libraries consisting of as few as one major pathogen antigen. Using the bicomponent pore-forming leukocidin (Luk) exotoxins of the major pathogen Staphylococcus aureus as a prototype, we randomly fragmented and separately ligated the hemolysin gamma A (HlgA) and LukS genes into a custom-built phage display system, termed pComb-Opti8. Deep sequence analysis of barcoded amplimers of the HlgA and LukS gene fragment libraries demonstrated that biopannng against a cross-reactive anti-Luk monoclonal antibody (MAb) recovered convergent molecular clones with short overlapping homologous sequences. We thereby identified an 11-amino-acid sequence that is highly conserved in four Luk toxin subunits and is ubiquitous in representation within S. aureus clinical isolates. The isolated 11-amino-acid peptide probe was predicted to retain the native three-dimensional (3D) conformation seen within the Luk holotoxin. Indeed, this peptide was recognized by the selecting anti-Luk MAb, and, using mutated peptides, we showed that a particular amino acid side chain was essential for these interactions. Furthermore, murine immunization with this peptide elicited IgG responses that were highly reactive with both the autologous synthetic peptide and the full-length Luk toxin homologues. Thus, using a gene fragment- and phage display-based pipeline, we have identified and validated immunogenic B-cell epitopes that are cross-reactive between members of the pore-forming leukocidin family. This approach could be harnessed to identify novel epitopes for a much-needed S. aureus-protective subunit vaccine.
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40
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Honjo K, Won WJ, King RG, Ianov L, Crossman DK, Easlick JL, Shakhmatov MA, Khass M, Vale AM, Stephan RP, Li R, Davis RS. Fc Receptor-Like 6 (FCRL6) Discloses Progenitor B Cell Heterogeneity That Correlates With Pre-BCR Dependent and Independent Pathways of Natural Antibody Selection. Front Immunol 2020; 11:82. [PMID: 32117244 PMCID: PMC7033751 DOI: 10.3389/fimmu.2020.00082] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 01/13/2020] [Indexed: 11/24/2022] Open
Abstract
B-1a cells produce "natural" antibodies (Abs) to neutralize pathogens and clear neo self-antigens, but the fundamental selection mechanisms that shape their polyreactive repertoires are poorly understood. Here, we identified a B cell progenitor subset defined by Fc receptor-like 6 (FCRL6) expression, harboring innate-like defense, migration, and differentiation properties conducive for natural Ab generation. Compared to FCRL6- pro B cells, the repressed mitotic, DNA damage repair, and signaling activity of FCRL6+ progenitors, yielded VH repertoires with biased distal Ighv segment accessibility, constrained diversity, and hydrophobic and charged CDR-H3 sequences. Beyond nascent autoreactivity, VH11 productivity, which predominates phosphatidylcholine-specific B-1a B cell receptors (BCRs), was higher for FCRL6+ cells as was pre-BCR formation, which was required for Myc induction and VH11, but not VH12, B-1a development. Thus, FCRL6 revealed unexpected heterogeneity in the developmental origins, regulation, and selection of natural Abs at the pre-BCR checkpoint with implications for autoimmunity and lymphoproliferative disorders.
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MESH Headings
- Animals
- Antibodies/immunology
- Antibodies/metabolism
- B-Lymphocytes/immunology
- B-Lymphocytes/metabolism
- Cell Differentiation/genetics
- Cell Differentiation/immunology
- Female
- Humans
- Immunoglobulin Heavy Chains/genetics
- Immunoglobulin Heavy Chains/immunology
- Immunoglobulin Variable Region/genetics
- Immunoglobulin Variable Region/immunology
- Mice, Inbred BALB C
- Mice, Inbred C57BL
- Mice, Knockout
- Phosphatidylcholines/immunology
- Phosphatidylcholines/metabolism
- Precursor Cells, B-Lymphoid/immunology
- Precursor Cells, B-Lymphoid/metabolism
- Receptors, Antigen, B-Cell/genetics
- Receptors, Antigen, B-Cell/immunology
- Receptors, Antigen, B-Cell/metabolism
- Receptors, Fc/genetics
- Receptors, Fc/immunology
- Receptors, Fc/metabolism
- Signal Transduction/genetics
- Signal Transduction/immunology
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Affiliation(s)
- Kazuhito Honjo
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Woong-Jai Won
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Rodney G. King
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Lara Ianov
- Civitan International Research Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | - David K. Crossman
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Juliet L. Easlick
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Mikhail A. Shakhmatov
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Mohamed Khass
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- Genetic Engineering and Biotechnology Division, National Research Center, Cairo, Egypt
| | - Andre M. Vale
- Program in Immunobiology, Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Robert P. Stephan
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Ran Li
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Randall S. Davis
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, United States
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, United States
- Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, United States
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41
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Kreer C, Gruell H, Mora T, Walczak AM, Klein F. Exploiting B Cell Receptor Analyses to Inform on HIV-1 Vaccination Strategies. Vaccines (Basel) 2020; 8:vaccines8010013. [PMID: 31906351 PMCID: PMC7157687 DOI: 10.3390/vaccines8010013] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 12/23/2019] [Accepted: 12/24/2019] [Indexed: 12/22/2022] Open
Abstract
The human antibody repertoire is generated by the recombination of different gene segments as well as by processes of somatic mutation. Together these mechanisms result in a tremendous diversity of antibodies that are able to combat various pathogens including viruses and bacteria, or malignant cells. In this review, we summarize the opportunities and challenges that are associated with the analyses of the B cell receptor repertoire and the antigen-specific B cell response. We will discuss how recent advances have increased our understanding of the antibody response and how repertoire analyses can be exploited to inform on vaccine strategies, particularly against HIV-1.
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Affiliation(s)
- Christoph Kreer
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; (C.K.); (H.G.)
| | - Henning Gruell
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; (C.K.); (H.G.)
- German Center for Infection Research, Partner Site Bonn-Cologne, 50931 Cologne, Germany
| | - Thierry Mora
- Laboratoire de Physique de l’École Normale Supérieure (PSL University), CNRS, Sorbonne Université, Université de Paris, 75005 Paris, France; (T.M.); (A.M.W.)
| | - Aleksandra M. Walczak
- Laboratoire de Physique de l’École Normale Supérieure (PSL University), CNRS, Sorbonne Université, Université de Paris, 75005 Paris, France; (T.M.); (A.M.W.)
| | - Florian Klein
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; (C.K.); (H.G.)
- German Center for Infection Research, Partner Site Bonn-Cologne, 50931 Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
- Correspondence:
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42
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Vaisman-Mentesh A, Rosenstein S, Yavzori M, Dror Y, Fudim E, Ungar B, Kopylov U, Picard O, Kigel A, Ben-Horin S, Benhar I, Wine Y. Molecular Landscape of Anti-Drug Antibodies Reveals the Mechanism of the Immune Response Following Treatment With TNFα Antagonists. Front Immunol 2019; 10:2921. [PMID: 31921180 PMCID: PMC6930160 DOI: 10.3389/fimmu.2019.02921] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 11/28/2019] [Indexed: 12/25/2022] Open
Abstract
Drugs formulated from monoclonal antibodies (mAbs) are clinically effective in various diseases. Repeated administration of mAbs, however, elicits an immune response in the form of anti-drug-antibodies (ADA), thereby reducing the drug's efficacy. Notwithstanding their importance, the molecular landscape of ADA and the mechanisms involved in their formation are not fully understood. Using a newly developed quantitative bio-immunoassay, we found that ADA concentrations specific to TNFα antagonists can exceed extreme concentrations of 1 mg/ml with a wide range of neutralization capacity. Our data further suggest a preferential use of the λ light chain in a subset of neutralizing ADA. Moreover, we show that administration of TNFα antagonists result in a vaccine-like response whereby ADA formation is governed by the extrafollicular T cell-independent immune response. Our bio-immunoassay coupled with insights on the nature of the immune response can be leveraged to improve mAb immunogenicity assessment and facilitate improvement in therapeutic intervention strategies.
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Affiliation(s)
- Anna Vaisman-Mentesh
- George S. Wise Faculty of Life Sciences, School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Shai Rosenstein
- George S. Wise Faculty of Life Sciences, School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Miri Yavzori
- Gastroenterology Department, Sheba Medical Center and Sackler School of Medicine, Tel-Aviv University, Tel Aviv-Yafo, Israel
| | - Yael Dror
- George S. Wise Faculty of Life Sciences, School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Ella Fudim
- Gastroenterology Department, Sheba Medical Center and Sackler School of Medicine, Tel-Aviv University, Tel Aviv-Yafo, Israel
| | - Bella Ungar
- Gastroenterology Department, Sheba Medical Center and Sackler School of Medicine, Tel-Aviv University, Tel Aviv-Yafo, Israel
| | - Uri Kopylov
- Gastroenterology Department, Sheba Medical Center and Sackler School of Medicine, Tel-Aviv University, Tel Aviv-Yafo, Israel
| | - Orit Picard
- Gastroenterology Department, Sheba Medical Center and Sackler School of Medicine, Tel-Aviv University, Tel Aviv-Yafo, Israel
| | - Aya Kigel
- George S. Wise Faculty of Life Sciences, School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Shomron Ben-Horin
- Gastroenterology Department, Sheba Medical Center and Sackler School of Medicine, Tel-Aviv University, Tel Aviv-Yafo, Israel
| | - Itai Benhar
- George S. Wise Faculty of Life Sciences, School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Yariv Wine
- George S. Wise Faculty of Life Sciences, School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Tel Aviv-Yafo, Israel
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Abstract
Enhancers are defined as regulatory elements that control transcription in a cell-type and developmental stage-specific manner. They achieve this by physically interacting with their cognate gene promoters. Significantly, these interactions can occur through long genomic distances since enhancers may not be near their cognate promoters. The optimal coordination of enhancer-regulated transcription is essential for the function and identity of the cell. Although great efforts to fully understand the principles of this type of regulation are ongoing, other potential functions of the long-range chromatin interactions (LRCIs) involving enhancers are largely unexplored. We recently uncovered a new role for enhancer elements in determining the three-dimensional (3D) structure of the immunoglobulin kappa (Igκ) light chain receptor locus suggesting a structural function for these DNA elements. This enhancer-mediated locus configuration shapes the resulting Igκ repertoire. We also propose a role for enhancers as critical components of sub-topologically associating domain (subTAD) formation and nuclear spatial localization.
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Affiliation(s)
- E Mauricio Barajas-Mora
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.,Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Ann J Feeney
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
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44
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Pashov A, Shivarov V, Hadzhieva M, Kostov V, Ferdinandov D, Heintz KM, Pashova S, Todorova M, Vassilev T, Kieber-Emmons T, Meza-Zepeda LA, Hovig E. Diagnostic Profiling of the Human Public IgM Repertoire With Scalable Mimotope Libraries. Front Immunol 2019; 10:2796. [PMID: 31849974 PMCID: PMC6901697 DOI: 10.3389/fimmu.2019.02796] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 11/14/2019] [Indexed: 12/12/2022] Open
Abstract
Specific antibody reactivities are routinely used as biomarkers, but the antibody repertoire reactivity (igome) profiles are still neglected. Here, we propose rationally designed peptide arrays as efficient probes for these system level biomarkers. Most IgM antibodies are characterized by few somatic mutations, polyspecificity, and physiological autoreactivity with housekeeping function. Previously, probing this repertoire with a set of immunodominant self-proteins provided a coarse analysis of the respective repertoire profiles. In contrast, here, we describe the generation of a peptide mimotope library that reflects the common IgM repertoire of 10,000 healthy donors. In addition, an appropriately sized subset of this quasi-complete mimotope library was further designed as a potential diagnostic tool. A 7-mer random peptide phage display library was panned on pooled human IgM. Next-generation sequencing of the selected phage yielded 224,087 sequences, which clustered in 790 sequence clusters. A set of 594 mimotopes, representative of the most significant sequence clusters, was shown to probe symmetrically the space of IgM reactivities in patients' sera. This set of mimotopes can be easily scaled including a greater proportion of the mimotope library. The trade-off between the array size and the resolution can be explored while preserving the symmetric sampling of the mimotope sequence and reactivity spaces. BLAST search of the non-redundant protein database with the mimotopes sequences yielded significantly more immunoglobulin J region hits than random peptides, indicating a considerable idiotypic connectivity of the targeted igome. The proof of principle predictors for random diagnoses was represented by profiles of mimotopes. The number of potential reactivity profiles that can be extracted from this library is estimated at more than 1070. Thus, a quasi-complete IgM mimotope library and a scalable representative subset thereof are found to address very efficiently the dynamic diversity of the human public IgM repertoire, providing informationally dense and structurally interpretable IgM reactivity profiles.
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Affiliation(s)
- Anastas Pashov
- Laboratory of Experimental Immunotherapy, Department of Immunology, Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Velizar Shivarov
- Laboratory of Clinical Immunology, Department of Clinical Hematology, Sofiamed University Hospital, Sofia, Bulgaria.,Faculty of Biology, Sofia University "St. Kliment Ohridski," Sofia, Bulgaria
| | - Maya Hadzhieva
- Laboratory of Experimental Immunotherapy, Department of Immunology, Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Victor Kostov
- Laboratory of Experimental Immunotherapy, Department of Immunology, Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria.,Neurosurgery Clinic, St. Ivan Rilsky Hospital, Sofia MU, Sofia, Bulgaria
| | - Dilyan Ferdinandov
- Neurosurgery Clinic, St. Ivan Rilsky Hospital, Sofia MU, Sofia, Bulgaria
| | - Karen-Marie Heintz
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Shina Pashova
- Laboratory of Experimental Immunotherapy, Department of Immunology, Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria.,Department of Molecular Immunology, Institute of Biology and Immunology of Reproduction, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Milena Todorova
- Laboratory of Experimental Immunotherapy, Department of Immunology, Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Tchavdar Vassilev
- Institute of Biology and Biomedicine, N.I. Lobachevsky University, Nizhny Novgorod, Russia
| | - Thomas Kieber-Emmons
- Winthrop P. Rockefeller Cancer Research Center, UAMS, Little Rock, AR, United States
| | - Leonardo A Meza-Zepeda
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Eivind Hovig
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,Centre for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
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45
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Setliff I, Shiakolas AR, Pilewski KA, Murji AA, Mapengo RE, Janowska K, Richardson S, Oosthuysen C, Raju N, Ronsard L, Kanekiyo M, Qin JS, Kramer KJ, Greenplate AR, McDonnell WJ, Graham BS, Connors M, Lingwood D, Acharya P, Morris L, Georgiev IS. High-Throughput Mapping of B Cell Receptor Sequences to Antigen Specificity. Cell 2019; 179:1636-1646.e15. [PMID: 31787378 DOI: 10.1016/j.cell.2019.11.003] [Citation(s) in RCA: 172] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 08/28/2019] [Accepted: 10/31/2019] [Indexed: 12/15/2022]
Abstract
B cell receptor (BCR) sequencing is a powerful tool for interrogating immune responses to infection and vaccination, but it provides limited information about the antigen specificity of the sequenced BCRs. Here, we present LIBRA-seq (linking B cell receptor to antigen specificity through sequencing), a technology for high-throughput mapping of paired heavy- and light-chain BCR sequences to their cognate antigen specificities. B cells are mixed with a panel of DNA-barcoded antigens so that both the antigen barcode(s) and BCR sequence are recovered via single-cell next-generation sequencing. Using LIBRA-seq, we mapped the antigen specificity of thousands of B cells from two HIV-infected subjects. The predicted specificities were confirmed for a number of HIV- and influenza-specific antibodies, including known and novel broadly neutralizing antibodies. LIBRA-seq will be an integral tool for antibody discovery and vaccine development efforts against a wide range of antigen targets.
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Affiliation(s)
- Ian Setliff
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Program in Chemical and Physical Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Andrea R Shiakolas
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Kelsey A Pilewski
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Amyn A Murji
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Rutendo E Mapengo
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa
| | - Katarzyna Janowska
- Division of Structural Biology, Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Simone Richardson
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa; Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2000, South Africa
| | - Charissa Oosthuysen
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa; Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2000, South Africa
| | - Nagarajan Raju
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Larance Ronsard
- Ragon Institute of Massachusetts General Hospital, Harvard and Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Juliana S Qin
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Kevin J Kramer
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Allison R Greenplate
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Wyatt J McDonnell
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Center for Translational and Clinical Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Barney S Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Mark Connors
- National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Daniel Lingwood
- Ragon Institute of Massachusetts General Hospital, Harvard and Massachusetts Institute of Technology, Cambridge, MA 02139, 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; 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
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, 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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46
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Magadan S, Krasnov A, Hadi-Saljoqi S, Afanasyev S, Mondot S, Lallias D, Castro R, Salinas I, Sunyer O, Hansen J, Koop BF, Lefranc MP, Boudinot P. Standardized IMGT® Nomenclature of Salmonidae IGH Genes, the Paradigm of Atlantic Salmon and Rainbow Trout: From Genomics to Repertoires. Front Immunol 2019; 10:2541. [PMID: 31798572 PMCID: PMC6866254 DOI: 10.3389/fimmu.2019.02541] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 10/14/2019] [Indexed: 12/11/2022] Open
Abstract
In teleost fish as in mammals, humoral adaptive immunity is based on B lymphocytes expressing highly diverse immunoglobulins (IG). During B cell differentiation, IG loci are subjected to genomic rearrangements of V, D, and J genes, producing a unique antigen receptor expressed on the surface of each lymphocyte. During the course of an immune response to infections or immunizations, B cell clones specific of epitopes from the immunogen are expanded and activated, leading to production of specific antibodies. Among teleost fish, salmonids comprise key species for aquaculture. Rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar) are especially important from a commercial point of view and have emerged as critical models for fish immunology. The growing interest to capture accurate and comprehensive antibody responses against common pathogens and vaccines has resulted in recent efforts to sequence the IG repertoire in these species. In this context, a unified and standardized nomenclature of salmonid IG heavy chain (IGH) genes is urgently required, to improve accuracy of annotation of adaptive immune receptor repertoire dataset generated by high-throughput sequencing (AIRRseq) and facilitate comparisons between studies and species. Interestingly, the assembly of salmonids IGH genomic sequences is challenging due to the presence of two large size duplicated IGH loci and high numbers of IG genes and pseudogenes. We used data available for Atlantic salmon to establish an IMGT standardized nomenclature of IGH genes in this species and then applied the IMGT rules to the rainbow trout IGH loci to set up a nomenclature, which takes into account the specificities of Salmonid loci. This unique, consistent nomenclature for Salmonid IGH genes was then used to construct IMGT sequence reference directories allowing accurate annotation of AIRRseq data. The complex issues raised by the genetic diversity of salmon and trout strains are discussed in the context of IG repertoire annotation.
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Affiliation(s)
- Susana Magadan
- Immunology Laboratory, Biomedical Research Center, University of Vigo, Vigo, Spain
- Department of Biology, Center of Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, NM, United States
| | - Aleksei Krasnov
- Nofima AS, Norwegian Institute of Food, Fisheries and Aquaculture Research, Tromsø, Norway
| | - Saida Hadi-Saljoqi
- IMGT®, The International ImMunoGeneTics Information System® (IMGT), Laboratoire d'ImmunoGénétique Moléculaire (LIGM), Institut de Génétique Humaine (IGH), CNRS, University of Montpellier, Montpellier, France
| | - Sergey Afanasyev
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Saint Petersburg, Russia
| | - Stanislas Mondot
- MICALIS, Institut National de la Recherche Agronomique, Université Paris-Saclay, Jouy-en-Josas, France
| | - Delphine Lallias
- Génétique Animale et Biologie Intégrative (GABI), INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Rosario Castro
- Virologie et Immunologie Moléculaires (VIM), Institut National de la Recherche Agronomique (INRA), Université Paris-Saclay, Jouy-en-Josas, France
| | - Irene Salinas
- Department of Biology, Center of Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, NM, United States
| | - Oriol Sunyer
- Pathobiology Department, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - John Hansen
- Western Fisheries Research Center, U.S. Geological Survey, Seattle, WA, United States
| | - Ben F. Koop
- Department of Biology, University of Victoria, Victoria, BC, Canada
| | - Marie-Paule Lefranc
- IMGT®, The International ImMunoGeneTics Information System® (IMGT), Laboratoire d'ImmunoGénétique Moléculaire (LIGM), Institut de Génétique Humaine (IGH), CNRS, University of Montpellier, Montpellier, France
| | - Pierre Boudinot
- Virologie et Immunologie Moléculaires (VIM), Institut National de la Recherche Agronomique (INRA), Université Paris-Saclay, Jouy-en-Josas, France
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47
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Gao F, Lin X, He L, Wang R, Wang H, Shi X, Zhang F, Yin C, Zhang L, Zhu J, Yu L. Development of a Potent and Protective Germline-Like Antibody Lineage Against Zika Virus in a Convalescent Human. Front Immunol 2019; 10:2424. [PMID: 31708914 PMCID: PMC6821881 DOI: 10.3389/fimmu.2019.02424] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 09/27/2019] [Indexed: 12/31/2022] Open
Abstract
Zika virus (ZIKV) specific neutralizing antibodies hold great promise for antibody-based interventions and vaccine design against ZIKV infection. However, their development in infected patients remains unclear. Here, we applied next-generation sequencing (NGS) to probe the dynamic development of a potent and protective ZIKV E DIII-specific antibody ZK2B10 isolated from a ZIKV convalescent individual. The unbiased repertoire analysis showed dramatic changes in the usage of antibody variable region germline genes. However, lineage tracing of ZK2B10 revealed limited somatic hypermutation and transient expansion during the 12 months following the onset of symptoms. The NGS-derived, germline-like ZK2B10 somatic variants neutralized ZIKV potently and protected mice from lethal challenge of ZIKV without detectable cross-reactivity with Dengue virus (DENV). Site-directed mutagenesis identified two residues within the λ chain, N31 and S91, that are essential to the functional maturation of ZK2B10. The repertoire and lineage features unveiled here will help elucidate the developmental process and protective potential of E DIII-directed antibodies against ZIKV infection.
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Affiliation(s)
- Fei Gao
- Department of Basic Medical Sciences, Comprehensive AIDS Research Center, Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Tsinghua University, Beijing, China
| | - Xiaohe Lin
- Department of Integrative Structural and Computational Biology, Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
| | - Linling He
- Department of Integrative Structural and Computational Biology, Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
| | - Ruoke Wang
- Department of Basic Medical Sciences, Comprehensive AIDS Research Center, Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Tsinghua University, Beijing, China
| | - Han Wang
- Department of Basic Medical Sciences, Comprehensive AIDS Research Center, Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Tsinghua University, Beijing, China
| | - Xuanling Shi
- Department of Basic Medical Sciences, Comprehensive AIDS Research Center, Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Tsinghua University, Beijing, China
| | - Fuchun Zhang
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Chibiao Yin
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Linqi Zhang
- Department of Basic Medical Sciences, Comprehensive AIDS Research Center, Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Tsinghua University, Beijing, China
| | - Jiang Zhu
- Department of Integrative Structural and Computational Biology, Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
| | - Lei Yu
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
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48
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Bennett MR, Dong J, Bombardi RG, Soto C, Parrington HM, Nargi RS, Schoeder CT, Nagel MB, Schey KL, Meiler J, Skaar EP, Crowe JE. Human VH1-69 Gene-Encoded Human Monoclonal Antibodies against Staphylococcus aureus IsdB Use at Least Three Distinct Modes of Binding To Inhibit Bacterial Growth and Pathogenesis. mBio 2019; 10:e02473-19. [PMID: 31641091 PMCID: PMC6805997 DOI: 10.1128/mbio.02473-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 09/18/2019] [Indexed: 12/30/2022] Open
Abstract
Staphylococcus aureus is an important human pathogen that infects nearly every human tissue. Like most organisms, the acquisition of nutrient iron is necessary for its survival. One route by which it obtains this metal is through the iron-regulated surface determinant (Isd) system that scavenges iron from the hemoglobin of the host. We show that the heavy chain variable region IGHV1-69 gene commonly encodes human monoclonal antibodies (mAbs) targeting IsdB-NEAT2. Remarkably, these antibodies bind to multiple antigenic sites. One class of IGHV1-69-encoded mAbs blocks S. aureus heme acquisition by binding to the heme-binding site of NEAT2, while two additional classes reduce the bacterial burden in vivo by an alternative Fc receptor-mediated mechanism. We further identified clonal lineages of IGHV1-69-encoded mAbs using donor samples, showing that each lineage diversifies during infection by somatic hypermutation. These studies reveal that IGHV1-69-encoded antibodies contribute to a protective immune response, furthering our understanding of the correlates of protection against S. aureus infection.IMPORTANCE The human pathogen Staphylococcus aureus causes a wide range of infections, including skin abscesses and sepsis. There is currently no licensed vaccine to prevent S. aureus infection, and its treatment has become increasingly difficult due to antibiotic resistance. One potential way to inhibit S. aureus pathogenesis is to prevent iron acquisition. The iron-regulated surface determinant (Isd) system has evolved in S. aureus to acquire hemoglobin from the human host as a source of heme-iron. In this study, we investigated the molecular and structural basis for antibody-mediated correlates against a member of the Isd system, IsdB. The association of immunoglobulin heavy chain variable region IGHV1-69 gene-encoded human monoclonal antibodies with the response against S. aureus IsdB is described using structural and functional studies to define the importance of this antibody class. We also determine that somatic hypermutation in the development of these antibodies hinders rather than fine-tunes the immune response to IsdB.
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Affiliation(s)
- Monique R Bennett
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jinhui Dong
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Robin G Bombardi
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Cinque Soto
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Helen M Parrington
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Rachel S Nargi
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Clara T Schoeder
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Marcus B Nagel
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Kevin L Schey
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Jens Meiler
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Eric P Skaar
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - James E Crowe
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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49
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Guo Y, Chen K, Kwong PD, Shapiro L, Sheng Z. cAb-Rep: A Database of Curated Antibody Repertoires for Exploring Antibody Diversity and Predicting Antibody Prevalence. Front Immunol 2019; 10:2365. [PMID: 31649674 PMCID: PMC6794461 DOI: 10.3389/fimmu.2019.02365] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 09/20/2019] [Indexed: 12/18/2022] Open
Abstract
The diversity of B cell receptors provides a basis for recognizing numerous pathogens. Antibody repertoire sequencing has revealed relationships between B cell receptor sequences, their diversity, and their function in infection, vaccination, and disease. However, many repertoire datasets have been deposited without annotation or quality control, limiting their utility. To accelerate investigations of B cell immunoglobulin sequence repertoires and to facilitate development of algorithms for their analysis, we constructed a comprehensive public database of curated human B cell immunoglobulin sequence repertoires, cAb-Rep (https://cab-rep.c2b2.columbia.edu), which currently includes 306 immunoglobulin repertoires from 121 human donors, who were healthy, vaccinated, or had autoimmune disease. The database contains a total of 267.9 million V(D)J heavy chain and 72.9 million VJ light chain transcripts. These transcripts are full-length or near full-length, have been annotated with gene origin, antibody isotype, somatic hypermutations, and other biological characteristics, and are stored in FASTA format to facilitate their direct use by most current repertoire-analysis programs. We describe a website to search cAb-Rep for similar antibodies along with methods for analysis of the prevalence of antibodies with specific genetic signatures, for estimation of reproducibility of somatic hypermutation patterns of interest, and for delineating frequencies of somatically introduced N-glycosylation. cAb-Rep should be useful for investigating attributes of B cell sequence repertoires, for understanding characteristics of affinity maturation, and for identifying potential barriers to the elicitation of effective neutralizing antibodies in infection or by vaccination.
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Affiliation(s)
- Yicheng Guo
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States
| | - Kevin Chen
- College of Arts and Science, Stony Brook University, Stony Brook, NY, United States
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, United States
| | - Lawrence Shapiro
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States.,Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, United States
| | - Zizhang Sheng
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States
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50
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Li R, Fu F, Feng L, Liu P. Next-generation sequencing and single-cell RT-PCR reveal a distinct variable gene usage of porcine antibody repertoire following PEDV vaccination. Sci China Life Sci 2019; 63:1240-1250. [PMID: 31321668 PMCID: PMC7088813 DOI: 10.1007/s11427-019-9576-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 05/12/2019] [Indexed: 11/24/2022]
Abstract
Porcine epidemic diarrhea virus (PEDV) is the most common diarrhea-causing pathogen in newborn piglets. The clarifications of the overall antibody repertoire and antigen-specific antibody repertoire are essential to provide important insights into the B-cell response and reshape new vaccines. Here, we applied next-generation sequencing (NGS) technology to investigate immunoglobulin (Ig) variable (V) gene segment usage of swine B-cells from peripheral blood lymphocytes (PBL) and mesenteric lymph node (MLN) cells following PEDV vaccination. We identified the transcripts of all functional Ig V-genes in antibody repertoire. IgHV1S2, IgKV1-11, and IgLV3-4 were the most prevalent gene segments for heavy, kappa, and lambda chains, respectively, in PBL and MLN. Unlike previous studies, IgKV1, instead of IgKV2, and IgLV3, instead of IgLV8, were the prevalent Ig V-gene families for kappa and lambda light chains, respectively. We further examined the antibody repertoire of PEDV spike-specific B cells by single-cell RT-PCR. In contrast to the overall antibody repertoire, Ig V-gene segments of PEDV spike-specific B cells preferentially adopted IgHV1-4 and IgHV1-14 for heavy chain, IgKV1-11 for kappa chain, and IgLV3-3 for lambda chain. These results represent a comprehensive analysis to characterize the Ig V-gene segment usage in the overall and PEDV spike-specific antibody repertoire in PBL and MLN.
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Affiliation(s)
- Ren Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150001, China
| | - Fang Fu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150001, China
| | - Li Feng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150001, China.
| | - PingHuang Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150001, China.
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