1
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Zhang T, Yang D, Tang L, Hu Y. Current development of severe acute respiratory syndrome coronavirus 2 neutralizing antibodies (Review). Mol Med Rep 2024; 30:148. [PMID: 38940338 PMCID: PMC11228696 DOI: 10.3892/mmr.2024.13272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 05/21/2024] [Indexed: 06/29/2024] Open
Abstract
The coronavirus disease 2019 pandemic due to severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) seriously affected global public health security. Studies on vaccines, neutralizing antibodies (NAbs) and small molecule antiviral drugs are currently ongoing. In particular, NAbs have emerged as promising therapeutic agents due to their well‑defined mechanism, high specificity, superior safety profile, ease of large‑scale production and simultaneous application for both prevention and treatment of viral infection. Numerous NAb therapeutics have entered the clinical research stages, demonstrating promising therapeutic and preventive effects. These agents have been used for outbreak prevention and control under urgent authorization processes. The present review summarizes the molecular targets of SARS‑CoV‑2‑associated NAbs and screening and identification techniques for NAb development. Moreover, the current shortcomings and challenges that persist with the use of NAbs are discussed. The aim of the present review is to offer a reference for the development of NAbs for any future emergent infectious diseases, including SARS‑CoV‑2.
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Affiliation(s)
- Tong Zhang
- Department of Hematology, Wuhan Union Hospital, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Di Yang
- Department of Hematology, Wuhan Union Hospital, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Liang Tang
- Department of Hematology, Wuhan Union Hospital, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
| | - Yu Hu
- Department of Hematology, Wuhan Union Hospital, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
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2
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Beaulaurier J, Ly L, Duty JA, Tyer C, Stevens C, Hung CT, Sookdeo A, Drong AW, Kowdle S, Turner DJ, Juul S, Hickey S, Lee B. De novo antibody discovery in human blood from full-length single B cell transcriptomics and matching haplotyped-resolved germline assemblies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.26.586834. [PMID: 38585716 PMCID: PMC10996687 DOI: 10.1101/2024.03.26.586834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Immunoglobulin (IGH, IGK, IGL) loci in the human genome are highly polymorphic regions that encode the building blocks of the light and heavy chain IG proteins that dimerize to form antibodies. The processes of V(D)J recombination and somatic hypermutation in B cells are responsible for creating an enormous reservoir of highly specific antibodies capable of binding a vast array of possible antigens. However, the antibody repertoire is fundamentally limited by the set of variable (V), diversity (D), and joining (J) alleles present in the germline IG loci. To better understand how the germline IG haplotypes contribute to the expressed antibody repertoire, we combined genome sequencing of the germline IG loci with single-cell transcriptome sequencing of B cells from the same donor. Sequencing and assembly of the germline IG loci captured the IGH locus in a single fully-phased contig where the maternal and paternal contributions to the germline V, D, and J repertoire can be fully resolved. The B cells were collected following a measles, mumps, and rubella (MMR) vaccination, resulting in a population of cells that were activated in response to this specific immune challenge. Single-cell, full-length transcriptome sequencing of these B cells resulted in whole transcriptome characterization of each cell, as well as highly-accurate consensus sequences for the somatically rearranged and hypermutated light and heavy chain IG transcripts. A subset of antibodies synthesized based on their consensus heavy and light chain transcript sequences demonstrated binding to measles antigens and neutralization of measles live virus.
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3
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Zhu Y, Tang H, Xie W, Chen S, Zeng H, Lan C, Guan J, Ma C, Yang X, Wang Q, Wei L, Zhang Z, Yu X. The multilevel extensive diversity across the cynomolgus macaque captured by ultra-deep adaptive immune receptor repertoire sequencing. SCIENCE ADVANCES 2024; 10:eadj5640. [PMID: 38266093 PMCID: PMC10807814 DOI: 10.1126/sciadv.adj5640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 12/22/2023] [Indexed: 01/26/2024]
Abstract
The extent to which AIRRs differ among and within individuals remains elusive. Via ultra-deep repertoire sequencing of 22 and 25 tissues in three cynomolgus macaques, respectively, we identified 84 and 114 novel IGHV and TRBV alleles, confirming 72 (85.71%) and 100 (87.72%) of them. The heterogeneous V gene usage patterns were influenced, in turn, by genetics, isotype (for BCRs only), tissue group, and tissue. A higher proportion of intragroup shared clones in the intestinal tissues than those in other tissues suggests a close intra-intestinal adaptive immunity network. Significantly higher mutation burdens in the public clones and the inter-tissue shared IgM and IgD clones indicate that they might target the shared antigens. This study reveals the extensive heterogeneity of the AIRRs at various levels and has broad fundamental and clinical implications. The data generated here will serve as an invaluable resource for future studies on adaptive immunity in health and diseases.
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Affiliation(s)
- Yan Zhu
- Center for Precision Medicine, Medical Research Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
- Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Haipei Tang
- Center for Precision Medicine, Medical Research Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
| | - Wenxi Xie
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Sen Chen
- Center for Precision Medicine, Medical Research Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Huikun Zeng
- Center for Precision Medicine, Medical Research Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
- Division of Nephrology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China
| | - Chunhong Lan
- Center for Precision Medicine, Medical Research Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Junjie Guan
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Cuiyu Ma
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Xiujia Yang
- Center for Precision Medicine, Medical Research Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
- Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
| | - Qilong Wang
- Center for Precision Medicine, Medical Research Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
| | - Lai Wei
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Zhenhai Zhang
- Center for Precision Medicine, Medical Research Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Southern Medical University, Guangzhou 510515, China
| | - Xueqing Yu
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou 510080, China
- Division of Nephrology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China
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4
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Feng F, Yuen R, Wang Y, Hua A, Kepler TB, Wetzler LM. Characterizing adjuvants' effects at murine immunoglobulin repertoire level. iScience 2024; 27:108749. [PMID: 38269092 PMCID: PMC10805652 DOI: 10.1016/j.isci.2023.108749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 09/29/2023] [Accepted: 12/12/2023] [Indexed: 01/26/2024] Open
Abstract
Generating large-scale, high-fidelity sequencing data is challenging and, furthermore, not much has been done to characterize adjuvants' effects at the repertoire level. Thus, we introduced an IgSeq pipeline that standardized library prep protocols and data analysis functions for accurate repertoire profiling. We then studied systemically effects of CpG and Alum on the Ig heavy chain repertoire using the ovalbumin (OVA) murine model. Ig repertoires of different tissues (spleen and bone marrow) and isotypes (IgG and IgM) were examined and compared in IGHV mutation, gene usage, CDR3 length, clonal diversity, and clonal selection. We found Ig repertoires of different compartments exhibited distinguishable profiles at the non-immunized steady state, and distinctions became more pronounced upon adjuvanted immunizations. Notably, Alum and CpG effects exhibited different tissue- and isotype-preferences. The former led to increased diversity of abundant clones in bone marrow, and the latter promoted the selection of IgG clones in both tissues.
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Affiliation(s)
- Feng Feng
- Department of Microbiology, Boston University, Boston, MA 02118, USA
| | - Rachel Yuen
- Department of Microbiology, Boston University, Boston, MA 02118, USA
| | - Yumei Wang
- Department of Microbiology, Boston University, Boston, MA 02118, USA
| | - Axin Hua
- Department of Microbiology, Boston University, Boston, MA 02118, USA
| | - Thomas B. Kepler
- Department of Microbiology, Boston University, Boston, MA 02118, USA
- Department of Mathematics and Statistics, Boston University, Boston, MA 02118, USA
| | - Lee M. Wetzler
- Department of Microbiology, Boston University, Boston, MA 02118, USA
- Department of Medicine, Boston University School of Medicine, Boston University, Boston, MA 02118, USA
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5
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Teo QW, Wang Y, Lv H, Tan TJC, Lei R, Mao KJ, Wu NC. Stringent and complex sequence constraints of an IGHV1-69 broadly neutralizing antibody to influenza HA stem. Cell Rep 2023; 42:113410. [PMID: 37976161 PMCID: PMC10872586 DOI: 10.1016/j.celrep.2023.113410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/29/2023] [Accepted: 10/24/2023] [Indexed: 11/19/2023] Open
Abstract
IGHV1-69 is frequently utilized by broadly neutralizing influenza antibodies to the hemagglutinin (HA) stem. These IGHV1-69 HA stem antibodies have diverse complementarity-determining region (CDR) H3 sequences. Besides, their light chains have minimal to no contact with the epitope. Consequently, sequence determinants that confer IGHV1-69 antibodies with HA stem specificity remain largely elusive. Using high-throughput experiments, this study reveals the importance of light-chain sequence for the IGHV1-69 HA stem antibody CR9114, which is the broadest influenza antibody known to date. Moreover, we demonstrate that the CDR H3 sequences from many other IGHV1-69 antibodies, including those to the HA stem, are incompatible with CR9114. Along with mutagenesis and structural analysis, our results indicate that light-chain and CDR H3 sequences coordinately determine the HA stem specificity of IGHV1-69 antibodies. Overall, this work provides molecular insights into broadly neutralizing antibody responses to influenza virus, which have important implications for universal influenza vaccine development.
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Affiliation(s)
- Qi Wen Teo
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Yiquan Wang
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Huibin Lv
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Timothy J C Tan
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Ruipeng Lei
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Kevin J Mao
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Nicholas C Wu
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; Carle Illinois College of Medicine, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA.
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6
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Kreer C, Lupo C, Ercanoglu MS, Gieselmann L, Spisak N, Grossbach J, Schlotz M, Schommers P, Gruell H, Dold L, Beyer A, Nourmohammad A, Mora T, Walczak AM, Klein F. Probabilities of developing HIV-1 bNAb sequence features in uninfected and chronically infected individuals. Nat Commun 2023; 14:7137. [PMID: 37932288 PMCID: PMC10628170 DOI: 10.1038/s41467-023-42906-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 10/24/2023] [Indexed: 11/08/2023] Open
Abstract
HIV-1 broadly neutralizing antibodies (bNAbs) are able to suppress viremia and prevent infection. Their induction by vaccination is therefore a major goal. However, in contrast to antibodies that neutralize other pathogens, HIV-1-specific bNAbs frequently carry uncommon molecular characteristics that might prevent their induction. Here, we perform unbiased sequence analyses of B cell receptor repertoires from 57 uninfected and 46 chronically HIV-1- or HCV-infected individuals and learn probabilistic models to predict the likelihood of bNAb development. We formally show that lower probabilities for bNAbs are predictive of higher HIV-1 neutralization activity. Moreover, ranking bNAbs by their probabilities allows to identify highly potent antibodies with superior generation probabilities as preferential targets for vaccination approaches. Importantly, we find equal bNAb probabilities across infected and uninfected individuals. This implies that chronic infection is not a prerequisite for the generation of bNAbs, fostering the hope that HIV-1 vaccines can induce bNAb development in uninfected people.
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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
| | - Cosimo Lupo
- Laboratoire de physique de l'Ecole normale supérieure, CNRS, PSL University, Sorbonne Université, and Université Paris Cité, 75005, Paris, France
- Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Roma I, 00185, Rome, Italy
| | - Meryem S Ercanoglu
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Lutz Gieselmann
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- German Center for Infection Research, Partner Site Bonn-Cologne, 50931, Cologne, Germany
| | - Natanael Spisak
- Laboratoire de physique de l'Ecole normale supérieure, CNRS, PSL University, Sorbonne Université, and Université Paris Cité, 75005, Paris, France
| | - Jan Grossbach
- Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases & Institute for Genetics, Faculty of Mathematics and Natural Sciences, University of Cologne, 50931, Cologne, Germany
| | - Maike Schlotz
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Philipp Schommers
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- German Center for Infection Research, Partner Site Bonn-Cologne, 50931, Cologne, Germany
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50931, Cologne, Germany
| | - Henning Gruell
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937, Cologne, Germany
| | - Leona Dold
- Department of Internal Medicine I, University Hospital of Bonn, Bonn, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Bonn, Germany
| | - Andreas Beyer
- Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases & Institute for Genetics, Faculty of Mathematics and Natural Sciences, University of Cologne, 50931, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50931, Cologne, Germany
| | - Armita Nourmohammad
- Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, 37077, Göttingen, Germany
- Department of Physics, University of Washington, 3910 15th Ave Northeast, Seattle, WA, 98195, USA
- Department of Applied Mathematics, University of Washington, 4182 W Stevens Way NE, Seattle, WA, 98105, USA
- Paul G. Allen School of Computer Science and Engineering, University of Washington, 85 E Stevens Way NE, Seattle, WA, 98195, USA
- Fred Hutchinson Cancer Center, 1241 Eastlake Ave E, Seattle, WA, 98102, USA
| | - Thierry Mora
- Laboratoire de physique de l'Ecole normale supérieure, CNRS, PSL University, Sorbonne Université, and Université Paris Cité, 75005, Paris, France
| | - Aleksandra M Walczak
- Laboratoire de physique de l'Ecole normale supérieure, CNRS, PSL University, Sorbonne Université, and Université Paris Cité, 75005, Paris, France
| | - Florian Klein
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany.
- German Center for Infection Research, Partner Site Bonn-Cologne, 50931, Cologne, Germany.
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50931, Cologne, Germany.
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7
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Gazzola A, Navari M, Mannu C, Donelli R, Etebari M, Piccaluga PP. Single-Step IGHV Next-Generation Sequencing Detects Clonality and Somatic Hypermutation in Lymphoid Malignancies: A Phase III Diagnostic Accuracy Study. Cancers (Basel) 2023; 15:4624. [PMID: 37760593 PMCID: PMC10526376 DOI: 10.3390/cancers15184624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/05/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND Multiplex PCR based on consensus primers followed by capillary electrophoresis and Sanger sequencing are considered as the gold standard method for the evaluation of clonality and somatic hypermutation in lymphoid malignancies. As an alternative, the next-generation sequencing (NGS) of immune receptor genes has recently been proposed as a solution, due to being highly effective and sensitive. Here, we designed a phase III diagnostic accuracy study intended to compare the current gold standard methods versus the first commercially available NGS approaches for testing immunoglobulin heavy chain gene rearrangements. METHODS We assessed IGH rearrangements in 68 samples by means of both the NGS approach (LymphoTrack® IGH assay, and LymphoTrack® IGH somatic hypermutation assay, run on Illumina MiSeq) and capillary electrophoresis/Sanger sequencing to assess clonality and somatic hypermutations (SHM). RESULTS In comparison to the routine capillary-based analysis, the NGS clonality assay had an overall diagnostic accuracy of 96% (63/66 cases). Other studied criteria included sensitivity (95%), specificity (100%), positive predictive value (100%) and negative predictive value (75%). In discrepant cases, the NGS results were confirmed by a different set of primers that provided coverage of the IGH leader sequence. Furthermore, there was excellent agreement of the SHM determination with both the LymphoTrack® FR1 and leader assays when compared to the Sanger sequencing analysis (84%), with NGS able to assess the SHM rate even in cases where the conventional approach failed. CONCLUSION Overall, conventional Sanger sequencing and next-generation-sequencing-based clonality and somatic hypermutation analyses gave comparable results. For future use in a routine diagnostic workflow, NGS-based approaches should be evaluated prospectively and an analysis of cost-effectiveness should be performed.
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Affiliation(s)
- Anna Gazzola
- Hematopathology Unit, IRCCS Azienda Opedaliera-Universitaria di Bologna S. Orsola-Malpighi, 40138 Bologna, Italy; (A.G.); (C.M.)
| | - Mohsen Navari
- Department of Medical Biotechnology, School of Paramedical Sciences, Torbat Heydariyeh University of Medical Sciences, Torbat Heydariyeh 95196-33787, Iran;
- Research Center of Advanced Technologies in Medicine, Torbat Heydariyeh University of Medical Sciences, Torbat Heydariyeh 95196-33787, Iran
- Bioinformatics Research Center, Mashhad University of Medical Sciences, Mashhad 91779-48564, Iran
| | - Claudia Mannu
- Hematopathology Unit, IRCCS Azienda Opedaliera-Universitaria di Bologna S. Orsola-Malpighi, 40138 Bologna, Italy; (A.G.); (C.M.)
| | - Riccardo Donelli
- Biobank of Research, IRCCS Azienda Opedaliera-Universitaria di Bologna, 40138 Bologna, Italy;
- Department of Medical and Surgical Sciences, Institute of Hematology and Medical Oncology “L&A Seràgnoli”, Bologna University School of Medicine, 40126 Bologna, Italy
| | - Maryam Etebari
- Health Sciences Research Center, Torbat Heydariyeh University of Medical Sciences, Torbat Heydariyeh 33787-95196, Iran;
| | - Pier Paolo Piccaluga
- Biobank of Research, IRCCS Azienda Opedaliera-Universitaria di Bologna, 40138 Bologna, Italy;
- Department of Medical and Surgical Sciences, Institute of Hematology and Medical Oncology “L&A Seràgnoli”, Bologna University School of Medicine, 40126 Bologna, Italy
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8
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Peres A, Lees WD, Rodriguez OL, Lee NY, Polak P, Hope R, Kedmi M, Collins AM, Ohlin M, Kleinstein S, Watson C, Yaari G. IGHV allele similarity clustering improves genotype inference from adaptive immune receptor repertoire sequencing data. Nucleic Acids Res 2023; 51:e86. [PMID: 37548401 PMCID: PMC10484671 DOI: 10.1093/nar/gkad603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 06/26/2023] [Accepted: 08/03/2023] [Indexed: 08/08/2023] Open
Abstract
In adaptive immune receptor repertoire analysis, determining the germline variable (V) allele associated with each T- and B-cell receptor sequence is a crucial step. This process is highly impacted by allele annotations. Aligning sequences, assigning them to specific germline alleles, and inferring individual genotypes are challenging when the repertoire is highly mutated, or sequence reads do not cover the whole V region. Here, we propose an alternative naming scheme for the V alleles, as well as a novel method to infer individual genotypes. We demonstrate the strengths of the two by comparing their outcomes to other genotype inference methods. We validate the genotype approach with independent genomic long-read data. The naming scheme is compatible with current annotation tools and pipelines. Analysis results can be converted from the proposed naming scheme to the nomenclature determined by the International Union of Immunological Societies (IUIS). Both the naming scheme and the genotype procedure are implemented in a freely available R package (PIgLET https://bitbucket.org/yaarilab/piglet). To allow researchers to further explore the approach on real data and to adapt it for their uses, we also created an interactive website (https://yaarilab.github.io/IGHV_reference_book).
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Affiliation(s)
- Ayelet Peres
- Faculty of Engineering, Bar Ilan University, 5290002 Ramat Gan, Israel
- Bar Ilan Institute of Nanotechnology and Advanced Materials, Bar Ilan University, 5290002 Ramat Gan, Israel
| | - William D Lees
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, WC1E 7JE, UK
| | - Oscar L Rodriguez
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - Noah Y Lee
- Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06511, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Pazit Polak
- Faculty of Engineering, Bar Ilan University, 5290002 Ramat Gan, Israel
- Bar Ilan Institute of Nanotechnology and Advanced Materials, Bar Ilan University, 5290002 Ramat Gan, Israel
| | - Ronen Hope
- Faculty of Engineering, Bar Ilan University, 5290002 Ramat Gan, Israel
| | - Meirav Kedmi
- Department of Pathology, Yale School of Medicine, New Haven, CT, 06520, USA
- Division of Hematology and Bone Marrow Transplantation, Chaim Sheba Medical Center, Tel-Hashomer, 5262000, Israel
- Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, 69978, Israel
| | - Andrew M Collins
- School of Biotechnology and Biomedical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Mats Ohlin
- Department of Immunotechnology Lund University, Lund, 221 00, Sweden
| | - Steven H Kleinstein
- Program in Computational Biology & Bioinformatics, Yale University, New Haven, CT, 06511, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - Gur Yaari
- Faculty of Engineering, Bar Ilan University, 5290002 Ramat Gan, Israel
- Bar Ilan Institute of Nanotechnology and Advanced Materials, Bar Ilan University, 5290002 Ramat Gan, Israel
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9
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Rodriguez OL, Safonova Y, Silver CA, Shields K, Gibson WS, Kos JT, Tieri D, Ke H, Jackson KJL, Boyd SD, Smith ML, Marasco WA, Watson CT. Genetic variation in the immunoglobulin heavy chain locus shapes the human antibody repertoire. Nat Commun 2023; 14:4419. [PMID: 37479682 PMCID: PMC10362067 DOI: 10.1038/s41467-023-40070-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 07/11/2023] [Indexed: 07/23/2023] Open
Abstract
Variation in the antibody response has been linked to differential outcomes in disease, and suboptimal vaccine and therapeutic responsiveness, the determinants of which have not been fully elucidated. Countering models that presume antibodies are generated largely by stochastic processes, we demonstrate that polymorphisms within the immunoglobulin heavy chain locus (IGH) impact the naive and antigen-experienced antibody repertoire, indicating that genetics predisposes individuals to mount qualitatively and quantitatively different antibody responses. We pair recently developed long-read genomic sequencing methods with antibody repertoire profiling to comprehensively resolve IGH genetic variation, including novel structural variants, single nucleotide variants, and genes and alleles. We show that IGH germline variants determine the presence and frequency of antibody genes in the expressed repertoire, including those enriched in functional elements linked to V(D)J recombination, and overlapping disease-associated variants. These results illuminate the power of leveraging IGH genetics to better understand the regulation, function, and dynamics of the antibody response in disease.
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Affiliation(s)
- Oscar L Rodriguez
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Yana Safonova
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Catherine A Silver
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Kaitlyn Shields
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - William S Gibson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Justin T Kos
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - David Tieri
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Hanzhong Ke
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | | | - Scott D Boyd
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Melissa L Smith
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA.
| | - Wayne A Marasco
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA.
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10
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Teo QW, Wang Y, Lv H, Tan TJ, Lei R, Mao KJ, Wu NC. Stringent and complex sequence constraints of an IGHV1-69 broadly neutralizing antibody to influenza HA stem. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.06.547908. [PMID: 37461670 PMCID: PMC10350038 DOI: 10.1101/2023.07.06.547908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
IGHV1-69 is frequently utilized by broadly neutralizing influenza antibodies to the hemagglutinin (HA) stem. These IGHV1-69 HA stem antibodies have diverse complementarity-determining region (CDR) H3 sequences. Besides, their light chains have minimal to no contact with the epitope. Consequently, sequence determinants that confer IGHV1-69 antibodies with HA stem specificity remain largely elusive. Using high-throughput experiments, this study revealed the importance of light chain sequence for the IGHV1-69 HA stem antibody CR9114, which is the broadest influenza antibody known to date. Moreover, we demonstrated that the CDR H3 sequences from many other IGHV1-69 antibodies, including those to HA stem, were incompatible with CR9114. Along with mutagenesis and structural analysis, our results indicate that light chain and CDR H3 sequences coordinately determine the HA stem specificity of IGHV1-69 antibodies. Overall, this work provides molecular insights into broadly neutralizing antibody responses to influenza virus, which have important implications for universal influenza vaccine development.
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Affiliation(s)
- Qi Wen Teo
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Yiquan Wang
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Huibin Lv
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Timothy J.C. Tan
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Ruipeng Lei
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Kevin J. Mao
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Nicholas C. Wu
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Carle Illinois College of Medicine, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
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11
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Hardt U, Corcoran MM, Narang S, Malmström V, Padyukov L, Karlsson Hedestam GB. Analysis of IGH allele content in a sample group of rheumatoid arthritis patients demonstrates unrevealed population heterogeneity. Front Immunol 2023; 14:1073414. [PMID: 36798124 PMCID: PMC9927645 DOI: 10.3389/fimmu.2023.1073414] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 01/09/2023] [Indexed: 02/04/2023] Open
Abstract
Immunoglobulin heavy chain (IGH) germline gene variations influence the B cell receptor repertoire, with resulting biological consequences such as shaping our response to infections and altering disease susceptibilities. However, the lack of information on polymorphism frequencies in the IGH loci at the population level makes association studies challenging. Here, we genotyped a pilot group of 30 individuals with rheumatoid arthritis (RA) to examine IGH allele content and frequencies in this group. Eight novel IGHV alleles and one novel IGHJ allele were identified in the study. 15 cases were haplotypable using heterozygous IGHJ6 or IGHD anchors. One variant, IGHV4-34*01_S0742, was found in three out of 30 cases and included a single nucleotide change resulting in a non-canonical recombination signal sequence (RSS) heptamer. This variant allele, shown by haplotype analysis to be non-expressed, was also found in three out of 30 healthy controls and matched a single nucleotide polymorphism (SNP) described in the 1000 Genomes Project (1KGP) collection with frequencies that varied between population groups. Our finding of previously unreported alleles in a relatively small group of individuals with RA illustrates the need for baseline information about IG allelic frequencies in targeted study groups in preparation for future analysis of these genes in disease association studies.
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Affiliation(s)
- Uta Hardt
- Division of Rheumatology, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden and Karolinska University Hospital, Stockholm, Sweden
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Martin M. Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Sanjana Narang
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Vivianne Malmström
- Division of Rheumatology, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden and Karolinska University Hospital, Stockholm, Sweden
| | - Leonid Padyukov
- Division of Rheumatology, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden and Karolinska University Hospital, Stockholm, Sweden
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12
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Pennell M, Rodriguez OL, Watson CT, Greiff V. The evolutionary and functional significance of germline immunoglobulin gene variation. Trends Immunol 2023; 44:7-21. [PMID: 36470826 DOI: 10.1016/j.it.2022.11.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 11/07/2022] [Indexed: 12/04/2022]
Abstract
The recombination between immunoglobulin (IG) gene segments determines an individual's naïve antibody repertoire and, consequently, (auto)antigen recognition. Emerging evidence suggests that mammalian IG germline variation impacts humoral immune responses associated with vaccination, infection, and autoimmunity - from the molecular level of epitope specificity, up to profound changes in the architecture of antibody repertoires. These links between IG germline variants and immunophenotype raise the question on the evolutionary causes and consequences of diversity within IG loci. We discuss why the extreme diversity in IG loci remains a mystery, why resolving this is important for the design of more effective vaccines and therapeutics, and how recent evidence from multiple lines of inquiry may help us do so.
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Affiliation(s)
- Matt Pennell
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA; Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.
| | - Oscar L Rodriguez
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Victor Greiff
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway.
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13
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Olson BJ, Schattgen SA, Thomas PG, Bradley P, Matsen IV FA. Comparing T cell receptor repertoires using optimal transport. PLoS Comput Biol 2022; 18:e1010681. [PMID: 36476997 PMCID: PMC9728925 DOI: 10.1371/journal.pcbi.1010681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 10/24/2022] [Indexed: 12/12/2022] Open
Abstract
The complexity of entire T cell receptor (TCR) repertoires makes their comparison a difficult but important task. Current methods of TCR repertoire comparison can incur a high loss of distributional information by considering overly simplistic sequence- or repertoire-level characteristics. Optimal transport methods form a suitable approach for such comparison given some distance or metric between values in the sample space, with appealing theoretical and computational properties. In this paper we introduce a nonparametric approach to comparing empirical TCR repertoires that applies the Sinkhorn distance, a fast, contemporary optimal transport method, and a recently-created distance between TCRs called TCRdist. We show that our methods identify meaningful differences between samples from distinct TCR distributions for several case studies, and compete with more complicated methods despite minimal modeling assumptions and a simpler pipeline.
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Affiliation(s)
- Branden J. Olson
- Department of Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Statistics, University of Washington, Seattle, Washington, United States of America
| | - Stefan A. Schattgen
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Paul G. Thomas
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Philip Bradley
- Department of Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Institute for Protein Design, Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- * E-mail: (PB); (FAM)
| | - Frederick A. Matsen IV
- Department of Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Statistics, University of Washington, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Seattle, Washington, United States of America
- * E-mail: (PB); (FAM)
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14
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Michaeli M, Carlotti E, Hazanov H, Gribben JG, Mehr R. Mutational patterns along different evolution paths of follicular lymphoma. Front Oncol 2022; 12:1029995. [DOI: 10.3389/fonc.2022.1029995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 10/24/2022] [Indexed: 11/11/2022] Open
Abstract
Follicular lymphoma (FL) is an indolent disease, characterized by a median life expectancy of 18-20 years and by intermittent periods of relapse and remission. FL frequently transforms into the more aggressive diffuse large B cell lymphoma (t-FL). In previous studies, the analysis of immunoglobulin heavy chain variable region (IgHV) genes in sequential biopsies from the same patient revealed two different patterns of tumor clonal evolution: direct evolution, through acquisition of additional IgHV mutations over time, or divergent evolution, in which lymphoma clones from serial biopsies independently develop from a less-mutated common progenitor cell (CPC). Our goal in this study was to characterize the somatic hypermutation (SHM) patterns of IgHV genes in sequential FL samples from the same patients, and address the question of whether the mutation mechanisms (SHM targeting, DNA repair or both), or selection forces acting on the tumor clones, were different in FL samples compared to healthy control samples, or in late relapsed/transformed FL samples compared to earlier ones. Our analysis revealed differences in the distribution of mutations from each of the nucleotides when tumor and non-tumor clones were compared, while FL and transformed FL (t-FL) tumor clones displayed similar mutation distributions. Lineage tree measurements suggested that either initial clone affinity or selection thresholds were lower in FL samples compared to controls, but similar between FL and t-FL samples. Finally, we observed that both FL and t-FL tumor clones tend to accumulate larger numbers of potential N-glycosylation sites due to the introduction of new SHM. Taken together, these results suggest that transformation into t-FL, in contrast to initial FL development, is not associated with any major changes in DNA targeting or repair, or the selection threshold of the tumor clone.
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15
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Chen Z, Zhang P, Matsuoka Y, Tsybovsky Y, West K, Santos C, Boyd LF, Nguyen H, Pomerenke A, Stephens T, Olia AS, Zhang B, De Giorgi V, Holbrook MR, Gross R, Postnikova E, Garza NL, Johnson RF, Margulies DH, Kwong PD, Alter HJ, Buchholz UJ, Lusso P, Farci P. Potent monoclonal antibodies neutralize Omicron sublineages and other SARS-CoV-2 variants. Cell Rep 2022; 41:111528. [PMID: 36302375 PMCID: PMC9554601 DOI: 10.1016/j.celrep.2022.111528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 07/29/2022] [Accepted: 09/28/2022] [Indexed: 11/17/2022] Open
Abstract
The emergence and global spread of the SARS-CoV-2 Omicron variants, which carry an unprecedented number of mutations, raise serious concerns due to the reduced efficacy of current vaccines and resistance to therapeutic antibodies. Here, we report the generation and characterization of two potent human monoclonal antibodies, NA8 and NE12, against the receptor-binding domain of the SARS-CoV-2 spike protein. NA8 interacts with a highly conserved region and has a breadth of neutralization with picomolar potency against the Beta variant and the Omicron BA.1 and BA.2 sublineages and nanomolar potency against BA.2.12.1 and BA.4. Combination of NA8 and NE12 retains potent neutralizing activity against the major SARS-CoV-2 variants of concern. Cryo-EM analysis provides the structural basis for the broad and complementary neutralizing activity of these two antibodies. We confirm the in vivo protective and therapeutic efficacies of NA8 and NE12 in the hamster model. These results show that broad and potent human antibodies can overcome the continuous immune escape of evolving SARS-CoV-2 variants.
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Affiliation(s)
- Zhaochun Chen
- Hepatic Pathogenesis Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Peng Zhang
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Yumiko Matsuoka
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Yaroslav Tsybovsky
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kamille West
- Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Celia Santos
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Lisa F Boyd
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Hanh Nguyen
- Hepatic Pathogenesis Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Anna Pomerenke
- Hepatic Pathogenesis Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Tyler Stephens
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Adam S Olia
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Valeria De Giorgi
- Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Michael R Holbrook
- National Institute of Allergy and Infectious Diseases (NIAID) Integrated Research Facility, National Institutes of Health, Frederick, MD, USA
| | - Robin Gross
- National Institute of Allergy and Infectious Diseases (NIAID) Integrated Research Facility, National Institutes of Health, Frederick, MD, USA
| | - Elena Postnikova
- National Institute of Allergy and Infectious Diseases (NIAID) Integrated Research Facility, National Institutes of Health, Frederick, MD, USA
| | - Nicole L Garza
- SARS-CoV-2 Virology Core, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Reed F Johnson
- SARS-CoV-2 Virology Core, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - David H Margulies
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Harvey J Alter
- Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Ursula J Buchholz
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Paolo Lusso
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Patrizia Farci
- Hepatic Pathogenesis Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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16
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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: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [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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17
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Collins AM, Watson CT, Breden F. Immunoglobulin genes, reproductive isolation and vertebrate speciation. Immunol Cell Biol 2022; 100:497-506. [PMID: 35781330 PMCID: PMC9545137 DOI: 10.1111/imcb.12567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 06/19/2022] [Accepted: 06/21/2022] [Indexed: 12/15/2022]
Abstract
Reproductive isolation drives the formation of new species, and many genes contribute to this through Dobzhansky–Muller incompatibilities (DMIs). These incompatibilities occur when gene divergence affects loci encoding interacting products such as receptors and their ligands. We suggest here that the nature of vertebrate immunoglobulin (IG) genes must make them prone to DMIs. The genes of these complex loci form functional genes through the process of recombination, giving rise to a repertoire of heterodimeric receptors of incredible diversity. This repertoire, within individuals and within species, must defend against pathogens but must also avoid pathogenic self‐reactivity. We suggest that this avoidance of autoimmunity is only achieved through a coordination of evolution between heavy‐ and light‐chain genes, and between these genes and the rest of the genome. Without coordinated evolution, the hybrid offspring of two diverging populations will carry a heavy burden of DMIs, resulting in a loss of fitness. Critical incompatibilities could manifest as incompatibilities between a mother and her divergent offspring. During fetal development, biochemical differences between the parents of hybrid offspring could make their offspring a target of the maternal immune system. This hypothesis was conceived in the light of recent insights into the population genetics of IG genes. This has suggested that antibody genes are probably as susceptible to evolutionary forces as other parts of the genome. Further repertoire studies in human and nonhuman species should now help determine whether antibody genes have been part of the evolutionary forces that drive the development of species.
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Affiliation(s)
- Andrew M Collins
- School of Biotechnology and Biomolecular Sciences University of New South Wales Sydney NSW Australia
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics University of Louisville School of Medicine Louisville KY USA
| | - Felix Breden
- Department of Biological Sciences Simon Fraser University Burnaby BC Canada
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18
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Young C, Lau AWY, Burnett DL. B cells in the balance: Offsetting self-reactivity avoidance with protection against foreign. Front Immunol 2022; 13:951385. [PMID: 35967439 PMCID: PMC9364820 DOI: 10.3389/fimmu.2022.951385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 06/29/2022] [Indexed: 11/21/2022] Open
Abstract
Antibodies are theoretically limitless in their diversity and specificity to foreign antigens; however they are constrained by the need to avoid binding to self. Germinal centers (GC) allow diversification and maturation of the antibody response towards the foreign antigen. While self-tolerance mechanisms controlling self-reactivity during B cell maturation are well recognized, the mechanisms by which GCs balance self-tolerance and foreign binding especially in the face of cross-reactivity between self and foreign, remain much less well defined. In this review we explore the extent to which GC self-tolerance restricts affinity maturation. We present studies suggesting that the outcome is situationally dependent, affected by affinity and avidity to self-antigen, and the extent to which self-binding and foreign-binding are interdependent. While auto-reactive GC B cells can mutate away from self while maturing towards the foreign antigen, if no mutational trajectories allow for self-reactive redemption, self-tolerance prevails and GC responses to the foreign pathogen are restricted, except when self-tolerance checkpoints are relaxed. Finally, we consider whether polyreactivity is subject to the same level of restriction in GC responses, especially if polyreactivity is linked to an increase in foreign protection, as occurs in certain broadly neutralizing antibodies. Overall, the outcomes for GC B cells that bind self-antigen can range from redemption, transient relaxation in self-tolerance or restriction of the antibody response to the foreign pathogen.
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Affiliation(s)
- Clara Young
- Immunology Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst, NSW, Australia
- *Correspondence: Clara Young, ; Deborah L. Burnett,
| | - Angelica W. Y. Lau
- Immunology Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst, NSW, Australia
| | - Deborah L. Burnett
- Immunology Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst, NSW, Australia
- *Correspondence: Clara Young, ; Deborah L. Burnett,
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19
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Jackson KJL, Kos JT, Lees W, Gibson WS, Smith ML, Peres A, Yaari G, Corcoran M, Busse CE, Ohlin M, Watson CT, Collins AM. A BALB/c IGHV Reference Set, Defined by Haplotype Analysis of Long-Read VDJ-C Sequences From F1 (BALB/c x C57BL/6) Mice. Front Immunol 2022; 13:888555. [PMID: 35720344 PMCID: PMC9205180 DOI: 10.3389/fimmu.2022.888555] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 04/28/2022] [Indexed: 11/13/2022] Open
Abstract
The immunoglobulin genes of inbred mouse strains that are commonly used in models of antibody-mediated human diseases are poorly characterized. This compromises data analysis. To infer the immunoglobulin genes of BALB/c mice, we used long-read SMRT sequencing to amplify VDJ-C sequences from F1 (BALB/c x C57BL/6) hybrid animals. Strain variations were identified in the Ighm and Ighg2b genes, and analysis of VDJ rearrangements led to the inference of 278 germline IGHV alleles. 169 alleles are not present in the C57BL/6 genome reference sequence. To establish a set of expressed BALB/c IGHV germline gene sequences, we computationally retrieved IGHV haplotypes from the IgM dataset. Haplotyping led to the confirmation of 162 BALB/c IGHV gene sequences. A musIGHV398 pseudogene variant also appears to be present in the BALB/cByJ substrain, while a functional musIGHV398 gene is highly expressed in the BALB/cJ substrain. Only four of the BALB/c alleles were also observed in the C57BL/6 haplotype. The full set of inferred BALB/c sequences has been used to establish a BALB/c IGHV reference set, hosted at https://ogrdb.airr-community.org. We assessed whether assemblies from the Mouse Genome Project (MGP) are suitable for the determination of the genes of the IGH loci. Only 37 (43.5%) of the 85 confirmed IMGT-named BALB/c IGHV and 33 (42.9%) of the 77 confirmed non-IMGT IGHV were found in a search of the MGP BALB/cJ genome assembly. This suggests that current MGP assemblies are unsuitable for the comprehensive documentation of germline IGHVs and more efforts will be needed to establish strain-specific reference sets.
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Affiliation(s)
| | - Justin T. Kos
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, United States
| | - William Lees
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom
| | - William S. Gibson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, United States
| | - Melissa Laird Smith
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, United States
| | - Ayelet Peres
- Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel
| | - Gur Yaari
- Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel
| | - Martin Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Christian E. Busse
- Division of B Cell Immunology, German Cancer Research Center, Heidelberg, Germany
| | - Mats Ohlin
- Department of Immunotechnology, Lund University, Lund, Sweden
| | - Corey T. Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, United States
| | - Andrew M. Collins
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
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20
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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] [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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21
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Reincke SM, Yuan M, Kornau HC, Corman VM, van Hoof S, Sánchez-Sendin E, Ramberger M, Yu W, Hua Y, Tien H, Schmidt ML, Schwarz T, Jeworowski LM, Brandl SE, Rasmussen HF, Homeyer MA, Stöffler L, Barner M, Kunkel D, Huo S, Horler J, von Wardenburg N, Kroidl I, Eser TM, Wieser A, Geldmacher C, Hoelscher M, Gänzer H, Weiss G, Schmitz D, Drosten C, Prüss H, Wilson IA, Kreye J. SARS-CoV-2 Beta variant infection elicits potent lineage-specific and cross-reactive antibodies. Science 2022; 375:782-787. [PMID: 35076281 PMCID: PMC8939768 DOI: 10.1126/science.abm5835] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 01/18/2022] [Indexed: 12/16/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Beta variant of concern (VOC) resists neutralization by major classes of antibodies from COVID-19 patients and vaccinated individuals. In this study, serum of Beta-infected patients revealed reduced cross-neutralization of wild-type virus. From these patients, we isolated Beta-specific and cross-reactive receptor-binding domain (RBD) antibodies. The Beta-specificity results from recruitment of VOC-specific clonotypes and accommodation of mutations present in Beta and Omicron into a major antibody class that is normally sensitive to these mutations. The Beta-elicited cross-reactive antibodies share genetic and structural features with wild type-elicited antibodies, including a public VH1-58 clonotype that targets the RBD ridge. These findings advance our understanding of the antibody response to SARS-CoV-2 shaped by antigenic drift, with implications for design of next-generation vaccines and therapeutics.
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MESH Headings
- Adolescent
- Adult
- Aged
- Aged, 80 and over
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/genetics
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/genetics
- Antibodies, Viral/immunology
- Antibodies, Viral/metabolism
- Antigenic Drift and Shift
- COVID-19/immunology
- COVID-19/virology
- Cross Reactions
- Female
- Humans
- Male
- Middle Aged
- Neutralization Tests
- Protein Binding
- Protein Domains
- Protein Interaction Domains and Motifs
- SARS-CoV-2/chemistry
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/metabolism
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Affiliation(s)
- S. Momsen Reincke
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neurology and Experimental Neurology, Berlin, Germany
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Helmholtz Innovation Lab BaoBab (Brain antibody-omics and B-cell Lab), Berlin, Germany
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hans-Christian Kornau
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Neuroscience Research Center (NWFZ), Cluster NeuroCure, Berlin, Germany
| | - Victor M. Corman
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany and German Centre for Infection Research (DZIF), Berlin, Germany
- Labor Berlin–Charité Vivantes GmbH, Berlin
| | - Scott van Hoof
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neurology and Experimental Neurology, Berlin, Germany
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Helmholtz Innovation Lab BaoBab (Brain antibody-omics and B-cell Lab), Berlin, Germany
| | - Elisa Sánchez-Sendin
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neurology and Experimental Neurology, Berlin, Germany
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Helmholtz Innovation Lab BaoBab (Brain antibody-omics and B-cell Lab), Berlin, Germany
| | - Melanie Ramberger
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Helmholtz Innovation Lab BaoBab (Brain antibody-omics and B-cell Lab), Berlin, Germany
| | - Wenli Yu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yuanzi Hua
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Henry Tien
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Marie Luisa Schmidt
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany and German Centre for Infection Research (DZIF), Berlin, Germany
| | - Tatjana Schwarz
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany and German Centre for Infection Research (DZIF), Berlin, Germany
| | - Lara Maria Jeworowski
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany and German Centre for Infection Research (DZIF), Berlin, Germany
| | - Sarah E. Brandl
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neurology and Experimental Neurology, Berlin, Germany
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Helmholtz Innovation Lab BaoBab (Brain antibody-omics and B-cell Lab), Berlin, Germany
| | - Helle Foverskov Rasmussen
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neurology and Experimental Neurology, Berlin, Germany
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Helmholtz Innovation Lab BaoBab (Brain antibody-omics and B-cell Lab), Berlin, Germany
| | - Marie A. Homeyer
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neurology and Experimental Neurology, Berlin, Germany
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Helmholtz Innovation Lab BaoBab (Brain antibody-omics and B-cell Lab), Berlin, Germany
| | - Laura Stöffler
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neurology and Experimental Neurology, Berlin, Germany
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Helmholtz Innovation Lab BaoBab (Brain antibody-omics and B-cell Lab), Berlin, Germany
| | - Martin Barner
- Helmholtz Innovation Lab BaoBab (Brain antibody-omics and B-cell Lab), Berlin, Germany
| | - Désirée Kunkel
- Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Flow and Mass Cytometry Core Facility, Berlin, Germany
| | - Shufan Huo
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neurology and Experimental Neurology, Berlin, Germany
| | - Johannes Horler
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neurology and Experimental Neurology, Berlin, Germany
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Helmholtz Innovation Lab BaoBab (Brain antibody-omics and B-cell Lab), Berlin, Germany
| | - Niels von Wardenburg
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neurology and Experimental Neurology, Berlin, Germany
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Helmholtz Innovation Lab BaoBab (Brain antibody-omics and B-cell Lab), Berlin, Germany
| | - Inge Kroidl
- Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich (LMU), Germany
- German Center for Infection Research (DZIF), partner site Munich, Germany
| | - Tabea M. Eser
- Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich (LMU), Germany
- German Center for Infection Research (DZIF), partner site Munich, Germany
| | - Andreas Wieser
- Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich (LMU), Germany
- German Center for Infection Research (DZIF), partner site Munich, Germany
| | - Christof Geldmacher
- Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich (LMU), Germany
- German Center for Infection Research (DZIF), partner site Munich, Germany
| | - Michael Hoelscher
- Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich (LMU), Germany
- German Center for Infection Research (DZIF), partner site Munich, Germany
| | - Hannes Gänzer
- Department of Internal Medicine, BKH Schwaz, Schwaz, Austria
| | - Günter Weiss
- Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria
| | - Dietmar Schmitz
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Neuroscience Research Center (NWFZ), Cluster NeuroCure, Berlin, Germany
| | - Christian Drosten
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Virology, Berlin, Germany and German Centre for Infection Research (DZIF), Berlin, Germany
| | - Harald Prüss
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neurology and Experimental Neurology, Berlin, Germany
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Helmholtz Innovation Lab BaoBab (Brain antibody-omics and B-cell Lab), Berlin, Germany
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jakob Kreye
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neurology and Experimental Neurology, Berlin, Germany
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Helmholtz Innovation Lab BaoBab (Brain antibody-omics and B-cell Lab), Berlin, Germany
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Pediatric Neurology, Berlin, Germany
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22
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Chen Z, Zhang P, Matsuoka Y, Tsybovsky Y, West K, Santos C, Boyd LF, Nguyen H, Pomerenke A, Stephens T, Olia AS, De Giorgi V, Holbrook MR, Gross R, Postnikova E, Garza NL, Johnson RF, Margulies DH, Kwong PD, Alter HJ, Buchholz UJ, Lusso P, Farci P. Extremely potent monoclonal antibodies neutralize Omicron and other SARS-CoV-2 variants. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022. [PMID: 35043120 DOI: 10.1101/2022.01.12.22269023] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The ongoing coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has triggered a devastating global health, social and economic crisis. The RNA nature and broad circulation of this virus facilitate the accumulation of mutations, leading to the continuous emergence of variants of concern with increased transmissibility or pathogenicity 1 . This poses a major challenge to the effectiveness of current vaccines and therapeutic antibodies 1, 2 . Thus, there is an urgent need for effective therapeutic and preventive measures with a broad spectrum of action, especially against variants with an unparalleled number of mutations such as the recently emerged Omicron variant, which is rapidly spreading across the globe 3 . Here, we used combinatorial antibody phage-display libraries from convalescent COVID-19 patients to generate monoclonal antibodies against the receptor-binding domain of the SARS-CoV-2 spike protein with ultrapotent neutralizing activity. One such antibody, NE12, neutralizes an early isolate, the WA-1 strain, as well as the Alpha and Delta variants with half-maximal inhibitory concentrations at picomolar level. A second antibody, NA8, has an unusual breadth of neutralization, with picomolar activity against both the Beta and Omicron variants. The prophylactic and therapeutic efficacy of NE12 and NA8 was confirmed in preclinical studies in the golden Syrian hamster model. Analysis by cryo-EM illustrated the structural basis for the neutralization properties of NE12 and NA8. Potent and broadly neutralizing antibodies against conserved regions of the SARS-CoV-2 spike protein may play a key role against future variants of concern that evade immune control.
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23
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Omer A, Peres A, Rodriguez OL, Watson CT, Lees W, Polak P, Collins AM, Yaari G. T cell receptor beta germline variability is revealed by inference from repertoire data. Genome Med 2022; 14:2. [PMID: 34991709 PMCID: PMC8740489 DOI: 10.1186/s13073-021-01008-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 12/08/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND T and B cell receptor (TCR, BCR) repertoires constitute the foundation of adaptive immunity. Adaptive immune receptor repertoire sequencing (AIRR-seq) is a common approach to study immune system dynamics. Understanding the genetic factors influencing the composition and dynamics of these repertoires is of major scientific and clinical importance. The chromosomal loci encoding for the variable regions of TCRs and BCRs are challenging to decipher due to repetitive elements and undocumented structural variants. METHODS To confront this challenge, AIRR-seq-based methods have recently been developed for B cells, enabling genotype and haplotype inference and discovery of undocumented alleles. However, this approach relies on complete coverage of the receptors' variable regions, whereas most T cell studies sequence a small fraction of that region. Here, we adapted a B cell pipeline for undocumented alleles, genotype, and haplotype inference for full and partial AIRR-seq TCR data sets. The pipeline also deals with gene assignment ambiguities, which is especially important in the analysis of data sets of partial sequences. RESULTS From the full and partial AIRR-seq TCR data sets, we identified 39 undocumented polymorphisms in T cell receptor Beta V (TRBV) and 31 undocumented 5 ' UTR sequences. A subset of these inferences was also observed using independent genomic approaches. We found that a single nucleotide polymorphism differentiating between the two documented T cell receptor Beta D2 (TRBD2) alleles is strongly associated with dramatic changes in the expressed repertoire. CONCLUSIONS We reveal a rich picture of germline variability and demonstrate how a single nucleotide polymorphism dramatically affects the composition of the whole repertoire. Our findings provide a basis for annotation of TCR repertoires for future basic and clinical studies.
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Affiliation(s)
- Aviv Omer
- Faculty of Engineering, Bar Ilan University, Ramat Gan, 5290002, Israel
- Bar Ilan institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, 5290002, Israel
| | - Ayelet Peres
- Faculty of Engineering, Bar Ilan University, Ramat Gan, 5290002, Israel
- Bar Ilan institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, 5290002, Israel
| | - Oscar L Rodriguez
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - William Lees
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, UK
| | - Pazit Polak
- Faculty of Engineering, Bar Ilan University, Ramat Gan, 5290002, Israel
- Bar Ilan institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, 5290002, Israel
| | - Andrew M Collins
- School of Biotechnology and Biomedical Sciences, University of New South Wales, Sydney, Australia
| | - Gur Yaari
- Faculty of Engineering, Bar Ilan University, Ramat Gan, 5290002, Israel.
- Bar Ilan institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, 5290002, Israel.
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24
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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] [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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25
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Huang Y, Thörnqvist L, Ohlin M. Computational Inference, Validation, and Analysis of 5'UTR-Leader Sequences of Alleles of Immunoglobulin Heavy Chain Variable Genes. Front Immunol 2021; 12:730105. [PMID: 34671351 PMCID: PMC8521166 DOI: 10.3389/fimmu.2021.730105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 09/06/2021] [Indexed: 12/05/2022] Open
Abstract
Upstream and downstream sequences of immunoglobulin genes may affect the expression of such genes. However, these sequences are rarely studied or characterized in most studies of immunoglobulin repertoires. Inference from large, rearranged immunoglobulin transcriptome data sets offers an opportunity to define the upstream regions (5'-untranslated regions and leader sequences). We have now established a new data pre-processing procedure to eliminate artifacts caused by a 5'-RACE library generation process, reanalyzed a previously studied data set defining human immunoglobulin heavy chain genes, and identified novel upstream regions, as well as previously identified upstream regions that may have been identified in error. Upstream sequences were also identified for a set of previously uncharacterized germline gene alleles. Several novel upstream region variants were validated, for instance by their segregation to a single haplotype in heterozygotic subjects. SNPs representing several sequence variants were identified from population data. Finally, based on the outcomes of the analysis, we define a set of testable hypotheses with respect to the placement of particular alleles in complex IGHV locus haplotypes, and discuss the evolutionary relatedness of particular heavy chain variable genes based on sequences of their upstream regions.
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Affiliation(s)
| | | | - Mats Ohlin
- Department of Immunotechnology, Lund University, Lund, Sweden
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26
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Schraven AL, Hansen VL, Morrissey KA, Stannard HJ, Ong OT, Douek DC, Miller RD, Old JM. Developmental and comparative immunology single-cell transcriptome analysis of the B-cell repertoire reveals the usage of immunoglobulins in the gray short-tailed opossum (Monodelphis domestica). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 123:104141. [PMID: 34038789 DOI: 10.1016/j.dci.2021.104141] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 05/18/2021] [Accepted: 05/19/2021] [Indexed: 06/12/2023]
Abstract
B-cells are key to humoral immunity, are found in multiple lymphoid organs, and have the unique ability to mediate the production of antigen-specific antibodies in the presence of pathogens. The marsupial immunoglobulin (Ig) heavy (H) chain locus encodes four constant region isotypes, IgA, IgG, IgM and IgE, but no IgD, and there are two light (L) chain isotypes, lambda (Igλ) and kappa (Igκ). To gain an understanding of the marsupial humoral immune system, B-cell transcriptomes generated by single-cell RNA sequencing from gray short-tailed opossum (Monodelphis domestica) splenocytes, and peripheral blood mononuclear cells were analysed. The cells used were from a single unimmunized animal and the majority of B-cells were transcribing IgM heavy chains. The ratio of Ig light chain use was roughly 2:1, Igλ:Igκ in this individual. This was not predicted due to Igκ being the more complex of the two L chain loci. The variable (V) gene segment pairs used in individual B-cells confirm greater diversity provided by the L chain V. This study is the first to report on using single cell analysis to investigate Ig repertoires in a marsupial and confirms a number of prior hypothesis, as well as revealing some surprises.
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Affiliation(s)
- Andrea L Schraven
- School of Science and Health, Hawkesbury Campus, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
| | - Victoria L Hansen
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico Albuquerque, New Mexico, USA
| | - Kimberly A Morrissey
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico Albuquerque, New Mexico, USA
| | - Hayley J Stannard
- Charles Sturt University, School of Animal and Veterinary Sciences, Wagga Wagga, NSW, 2678, Australia
| | - Oselyne Tw Ong
- Children's Medical Research Institute, Westmead, NSW, 2145, Australia
| | - Daniel C Douek
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Robert D Miller
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico Albuquerque, New Mexico, USA
| | - Julie M Old
- School of Science and Health, Hawkesbury Campus, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia.
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27
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Lee JH, Toy L, Kos JT, Safonova Y, Schief WR, Havenar-Daughton C, Watson CT, Crotty S. Vaccine genetics of IGHV1-2 VRC01-class broadly neutralizing antibody precursor naïve human B cells. NPJ Vaccines 2021; 6:113. [PMID: 34489473 PMCID: PMC8421370 DOI: 10.1038/s41541-021-00376-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 07/29/2021] [Indexed: 02/07/2023] Open
Abstract
A successful HIV vaccine eliciting broadly neutralizing antibodies (bnAbs) must overcome the hurdle of being able to activate naive precursor B cells encoding features within their germline B cell receptors (BCR) that allow recognition of broadly neutralizing epitopes. Knowledge of whether bnAb precursor B cells are circulating at sufficient frequencies within individuals in communities heavily impacted by HIV may be important. Using a germline-targeting eOD-GT8 immunogen and high-throughput droplet-based single-cell BCR sequencing, we demonstrate that large numbers of paired BCR sequences from multiple donors can be efficiently screened to elucidate precursor frequencies of rare, naive VRC01-class B cells. Further, we analyzed IGHV1-2 allelic usage among three different cohorts; we find that IGHV1-2 alleles traditionally thought to be incompatible with VRC01-class responses are relatively common in various human populations and that germline variation within IGHV1-2 associates with gene usage frequencies in the naive BCR repertoire.
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Affiliation(s)
- Jeong Hyun Lee
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Laura Toy
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Justin T Kos
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Yana Safonova
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
- Computer Science and Engineering Department, University of California San Diego, San Diego, CA, USA
| | - William R Schief
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Colin Havenar-Daughton
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA.
| | - Shane Crotty
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, USA.
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, USA.
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA, USA.
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28
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Qiu Q, Zhang P, Zhang N, Shen Y, Lou S, Deng J. Development of a Prognostic Nomogram for Acute Myeloid Leukemia on IGHD Gene Family. Int J Gen Med 2021; 14:4303-4316. [PMID: 34408473 PMCID: PMC8364394 DOI: 10.2147/ijgm.s317528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/15/2021] [Indexed: 11/29/2022] Open
Abstract
Purpose Acute myeloid leukaemia (AML) is a common haematological disease in adults. The overall survival (OS) remains unsatisfactory. It is critical to identify potential prognostic biomarkers and develop a nomogram that predicts overall survival in patients with AML. Patients and Methods We used gene expression dataset and clinical data from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) to identify differential expression analysis, survival analysis, and prognostic value of IGHD gene family (IGHDs) in AML patients. A risk score model was built through Lasso analysis and multivariate Cox regression. We also developed a nomogram and evaluated its accuracy with Harrell’s Harmony Index (C-index) and calibration curve. Last, the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) database was used for external validation. Results IGHD1-20 mRNA expression level was an independent prognostic factor for patients with AML by multivariate analysis. After Lasso analysis and multivariate Cox regression, we constructed a 3-gene model (IGHD1-1, IGHD1-20, IGHD3-16) associated with OS in AML. Risk score and age were validated as independent risk factors for prognosis and were used to build a nomogram. The C index and calibration curve results show that its ability to predict 1-year, 3-year and 5-year overall survival is accurate. Conclusion The mRNA level of IGHDs was increased in AML patients. IGHD1-20 was an independent risk factor for OS in AML patients. The IGHDs risk model (IGHD1-1, IGHD1-20, IGHD3-16) relates to the OS of AML patients. The nomogram, including risk score and age, can conveniently and effectively predict the overall survival rate of patients.
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Affiliation(s)
- Qunxiang Qiu
- Department of Hematology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, People's Republic of China
| | - Ping Zhang
- Hematology Laboratory, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, People's Republic of China
| | - Nan Zhang
- Department of Hematology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, People's Republic of China
| | - Yan Shen
- Department of Hematology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, People's Republic of China
| | - Shifeng Lou
- Department of Hematology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, People's Republic of China
| | - Jianchuan Deng
- Department of Hematology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, People's Republic of China
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29
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Yuan M, Huang D, Lee CCD, Wu NC, Jackson AM, Zhu X, Liu H, Peng L, van Gils MJ, Sanders RW, Burton DR, Reincke SM, Prüss H, Kreye J, Nemazee D, Ward AB, Wilson IA. Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. Science 2021; 373:818-823. [PMID: 34016740 PMCID: PMC8284396 DOI: 10.1126/science.abh1139] [Citation(s) in RCA: 255] [Impact Index Per Article: 85.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 05/12/2021] [Indexed: 12/12/2022]
Abstract
Neutralizing antibodies (nAbs) elicited against the receptor binding site (RBS) of the spike protein of wild-type severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are generally less effective against recent variants of concern. RBS residues Glu484, Lys417, and Asn501 are mutated in variants first described in South Africa (B.1.351) and Brazil (P.1). We analyzed their effects on angiotensin-converting enzyme 2 binding, as well as the effects of two of these mutations (K417N and E484K) on nAbs isolated from COVID-19 patients. Binding and neutralization of the two most frequently elicited antibody families (IGHV3-53/3-66 and IGHV1-2), which can both bind the RBS in alternative binding modes, are abrogated by K417N, E484K, or both. These effects can be structurally explained by their extensive interactions with RBS nAbs. However, nAbs to the more conserved, cross-neutralizing CR3022 and S309 sites were largely unaffected. The results have implications for next-generation vaccines and antibody therapies.
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MESH Headings
- Angiotensin-Converting Enzyme 2/metabolism
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/metabolism
- Antibodies, Viral/immunology
- Antibodies, Viral/metabolism
- Antigenic Variation
- Antigens, Viral/chemistry
- Antigens, Viral/genetics
- Antigens, Viral/immunology
- Antigens, Viral/metabolism
- Binding Sites
- Binding Sites, Antibody
- COVID-19/immunology
- COVID-19/virology
- Epitopes
- Humans
- Immune Evasion
- Mutation
- Protein Binding
- Protein Domains
- Receptors, Coronavirus/metabolism
- SARS-CoV-2/chemistry
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/metabolism
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Affiliation(s)
- Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Deli Huang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Chang-Chun D Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nicholas C Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Abigail M Jackson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xueyong Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hejun Liu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Linghang Peng
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Marit J van Gils
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Rogier W Sanders
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam, Netherlands
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Ragon Institute of MGH, Harvard, and MIT, Cambridge, MA 02139, USA
| | - S Momsen Reincke
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Harald Prüss
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Jakob Kreye
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
| | - David Nemazee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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30
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Mikocziova I, Greiff V, Sollid LM. Immunoglobulin germline gene variation and its impact on human disease. Genes Immun 2021; 22:205-217. [PMID: 34175903 PMCID: PMC8234759 DOI: 10.1038/s41435-021-00145-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 06/01/2021] [Accepted: 06/10/2021] [Indexed: 02/06/2023]
Abstract
Immunoglobulins (Ig) play an important role in the immune system both when expressed as antigen receptors on the cell surface of B cells and as antibodies secreted into extracellular fluids. The advent of high-throughput sequencing methods has enabled the investigation of human Ig repertoires at unprecedented depth. This has led to the discovery of many previously unreported germline Ig alleles. Moreover, it is becoming clear that convergent and stereotypic antibody responses are common where different individuals recognise defined antigenic epitopes with the use of the same Ig V genes. Thus, germline V gene variation is increasingly being linked to the differential capacity of generating an effective immune response, which might lead to varying disease susceptibility. Here, we review recent evidence of how germline variation in Ig genes impacts the Ig repertoire and its subsequent effects on the adaptive immune response in vaccination, infection, and autoimmunity.
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Affiliation(s)
- Ivana Mikocziova
- Department of Immunology, University of Oslo, Oslo, Norway
- K. G. Jebsen Centre for Coeliac Disease Research, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Victor Greiff
- Department of Immunology, University of Oslo, Oslo, Norway
| | - Ludvig M Sollid
- Department of Immunology, University of Oslo, Oslo, Norway.
- K. G. Jebsen Centre for Coeliac Disease Research, University of Oslo and Oslo University Hospital, Oslo, Norway.
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31
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Khatri I, Berkowska MA, van den Akker EB, Teodosio C, Reinders MJT, van Dongen JJM. Population matched (pm) germline allelic variants of immunoglobulin (IG) loci: Relevance in infectious diseases and vaccination studies in human populations. Genes Immun 2021; 22:172-186. [PMID: 34120151 PMCID: PMC8196923 DOI: 10.1038/s41435-021-00143-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/12/2021] [Accepted: 06/01/2021] [Indexed: 02/05/2023]
Abstract
Immunoglobulin (IG) loci harbor inter-individual allelic variants in many different germline IG variable, diversity and joining genes of the IG heavy (IGH), kappa (IGK) and lambda (IGL) loci, which together form the genetic basis of the highly diverse antigen-specific B-cell receptors. These allelic variants can be shared between or be specific to human populations. The current immunogenetics resources gather the germline alleles, however, lack the population specificity of the alleles which poses limitations for disease-association studies related to immune responses in different human populations. Therefore, we systematically identified germline alleles from 26 different human populations around the world, profiled by "1000 Genomes" data. We identified 409 IGHV, 179 IGKV, and 199 IGLV germline alleles supported by at least seven haplotypes. The diversity of germline alleles is the highest in Africans. Remarkably, the variants in the identified novel alleles show strikingly conserved patterns, the same as found in other IG databases, suggesting over-time evolutionary selection processes. We could relate the genetic variants to population-specific immune responses, e.g. IGHV1-69 for flu in Africans. The population matched IG (pmIG) resource will enhance our understanding of the SHM-related B-cell receptor selection processes in (infectious) diseases and vaccination within and between different human populations.
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Affiliation(s)
- Indu Khatri
- Department Immunology, Leiden University Medical Center, Leiden, The Netherlands
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Erik B van den Akker
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands
- Department Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
- Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
| | - Cristina Teodosio
- Department Immunology, Leiden University Medical Center, Leiden, The Netherlands
| | - Marcel J T Reinders
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands
- Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
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32
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Zhang Z, Jara CJ, Singh M, Xu H, Goodnow CC, Jackson KJ, Reed JH. Human transitional and IgM low mature naïve B cells preserve permissive B-cell receptors. Immunol Cell Biol 2021; 99:865-878. [PMID: 33988890 PMCID: PMC8453828 DOI: 10.1111/imcb.12478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/11/2021] [Accepted: 05/11/2021] [Indexed: 12/02/2022]
Abstract
The level of immunoglobulin M (IgM) displayed on the surface of peripheral blood B cells exhibits a broad dynamic range and has been associated with both development and selection. To determine whether IgM surface expression associates with distinct immunoglobulin heavy‐chain (IGH) repertoire properties, we performed deep IgM sequencing of peripheral blood transitional and mature naïve B cells in the upper and lower quartiles of surface IgM expression for 12 healthy donors. Mature naïve B cells within the lowest quartile for surface IgM expression displayed more diverse IGH features including increased complementarity‐determining region 3 length, IGHJ6 segment usage and aromatic amino acids compared with mature naïve B cells with high surface IgM. There were no differences between IGH repertoires for transitional B cells with high or low surface IgM. These findings suggest that a selection checkpoint during progression of transitional to mature naïve B cells reduces the breadth of the IGH repertoire among high surface IgM B cells but that diversity is preserved in B cells expressing low levels of surface IgM.
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Affiliation(s)
- Zhiguo Zhang
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,Department of Rheumatology and Immunology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Christopher J Jara
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,Faculty of Medicine, St. Vincent's Clinical School, UNSW, Sydney, NSW, Australia
| | - Mandeep Singh
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,Faculty of Medicine, St. Vincent's Clinical School, UNSW, Sydney, NSW, Australia
| | - Huji Xu
- Department of Rheumatology and Immunology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Christopher C Goodnow
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,School of Medical Sciences and Cellular Genomics Futures Institute, UNSW, Sydney, NSW, Australia
| | | | - Joanne H Reed
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,Faculty of Medicine, St. Vincent's Clinical School, UNSW, Sydney, NSW, Australia
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33
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Voss WN, Hou YJ, Johnson NV, Delidakis G, Kim JE, Javanmardi K, Horton AP, Bartzoka F, Paresi CJ, Tanno Y, Chou CW, Abbasi SA, Pickens W, George K, Boutz DR, Towers DM, McDaniel JR, Billick D, Goike J, Rowe L, Batra D, Pohl J, Lee J, Gangappa S, Sambhara S, Gadush M, Wang N, Person MD, Iverson BL, Gollihar JD, Dye JM, Herbert AS, Finkelstein IJ, Baric RS, McLellan JS, Georgiou G, Lavinder JJ, Ippolito GC. Prevalent, protective, and convergent IgG recognition of SARS-CoV-2 non-RBD spike epitopes. Science 2021; 372:1108-1112. [PMID: 33947773 PMCID: PMC8224265 DOI: 10.1126/science.abg5268] [Citation(s) in RCA: 177] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 04/29/2021] [Indexed: 12/12/2022]
Abstract
The molecular composition and binding epitopes of the immunoglobulin G (IgG) antibodies that circulate in blood plasma after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are unknown. Proteomic deconvolution of the IgG repertoire to the spike glycoprotein in convalescent subjects revealed that the response is directed predominantly (>80%) against epitopes residing outside the receptor binding domain (RBD). In one subject, just four IgG lineages accounted for 93.5% of the response, including an amino (N)-terminal domain (NTD)-directed antibody that was protective against lethal viral challenge. Genetic, structural, and functional characterization of a multidonor class of "public" antibodies revealed an NTD epitope that is recurrently mutated among emerging SARS-CoV-2 variants of concern. These data show that "public" NTD-directed and other non-RBD plasma antibodies are prevalent and have implications for SARS-CoV-2 protection and antibody escape.
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MESH Headings
- Animals
- Antibodies, Monoclonal/blood
- Antibodies, Monoclonal/chemistry
- Antibodies, Monoclonal/immunology
- Antibodies, Neutralizing/blood
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/blood
- Antibodies, Viral/chemistry
- Antibodies, Viral/immunology
- Antibody Affinity
- COVID-19/immunology
- COVID-19/prevention & control
- Epitopes/immunology
- Humans
- Immune Evasion
- Immunoglobulin G/blood
- Immunoglobulin G/chemistry
- Immunoglobulin G/immunology
- Immunoglobulin Heavy Chains/immunology
- Immunoglobulin Variable Region/immunology
- Mice
- Mice, Inbred BALB C
- Mutation
- Protein Domains
- Proteomics
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
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Affiliation(s)
- William N Voss
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Yixuan J Hou
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Nicole V Johnson
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - George Delidakis
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Jin Eyun Kim
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Kamyab Javanmardi
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Andrew P Horton
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Foteini Bartzoka
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Chelsea J Paresi
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Yuri Tanno
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Chia-Wei Chou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Shawn A Abbasi
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Whitney Pickens
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Katia George
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Daniel R Boutz
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- CCDC Army Research Laboratory-South, The University of Texas at Austin, Austin, TX, USA
| | - Dalton M Towers
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | | | - Daniel Billick
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Jule Goike
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Lori Rowe
- Biotechnology Core Facility Branch, Division of Scientific Resources, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Tulane National Primate Research Center Department of Microbiology 18703 Three Rivers Road Covington, LA, USA
| | - Dhwani Batra
- Biotechnology Core Facility Branch, Division of Scientific Resources, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jan Pohl
- Biotechnology Core Facility Branch, Division of Scientific Resources, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Justin Lee
- Biotechnology Core Facility Branch, Division of Scientific Resources, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Shivaprakash Gangappa
- Immunology and Pathogenesis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Suryaprakash Sambhara
- Immunology and Pathogenesis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Michelle Gadush
- Center for Biomedical Research Support, The University of Texas at Austin, Austin, TX, USA
| | - Nianshuang Wang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Maria D Person
- Center for Biomedical Research Support, The University of Texas at Austin, Austin, TX, USA
| | - Brent L Iverson
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Jimmy D Gollihar
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- CCDC Army Research Laboratory-South, The University of Texas at Austin, Austin, TX, USA
- Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA
| | - John M Dye
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Andrew S Herbert
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - George Georgiou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
| | - Jason J Lavinder
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Gregory C Ippolito
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
- Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
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34
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Bhardwaj V, Pevzner PA, Rashtchian C, Safonova Y. Trace Reconstruction Problems in Computational Biology. IEEE TRANSACTIONS ON INFORMATION THEORY 2021; 67:3295-3314. [PMID: 34176957 PMCID: PMC8224466 DOI: 10.1109/tit.2020.3030569] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The problem of reconstructing a string from its error-prone copies, the trace reconstruction problem, was introduced by Vladimir Levenshtein two decades ago. While there has been considerable theoretical work on trace reconstruction, practical solutions have only recently started to emerge in the context of two rapidly developing research areas: immunogenomics and DNA data storage. In immunogenomics, traces correspond to mutated copies of genes, with mutations generated naturally by the adaptive immune system. In DNA data storage, traces correspond to noisy copies of DNA molecules that encode digital data, with errors being artifacts of the data retrieval process. In this paper, we introduce several new trace generation models and open questions relevant to trace reconstruction for immunogenomics and DNA data storage, survey theoretical results on trace reconstruction, and highlight their connections to computational biology. Throughout, we discuss the applicability and shortcomings of known solutions and suggest future research directions.
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Affiliation(s)
- Vinnu Bhardwaj
- Electrical and Computer Engineering Department, University of California San Diego, La Jolla, USA
| | - Pavel A. Pevzner
- Computer Science and Engineering Department, University of California San Diego, La Jolla, USA
| | - Cyrus Rashtchian
- Computer Science and Engineering Department, University of California San Diego, La Jolla, USA
- Qualcomm Institute, University of California San Diego, La Jolla, USA
| | - Yana Safonova
- Computer Science and Engineering Department, University of California San Diego, La Jolla, USA
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35
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Abstract
Immunogenomics studies have been largely limited to individuals of European ancestry, restricting the ability to identify variation in human adaptive immune responses across populations. Inclusion of a greater diversity of individuals in immunogenomics studies will substantially enhance our understanding of human immunology.
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36
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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] [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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37
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A single donor is sufficient to produce a highly functional in vitro antibody library. Commun Biol 2021; 4:350. [PMID: 33742103 PMCID: PMC7979914 DOI: 10.1038/s42003-021-01881-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 02/19/2021] [Indexed: 01/31/2023] Open
Abstract
Antibody complementarity determining region diversity has been considered to be the most important metric for the production of a functional antibody library. Generally, the greater the antibody library diversity, the greater the probability of selecting a diverse array of high affinity leads. According to this paradigm, the primary means of elevating library diversity has been by increasing the number of donors. In the present study we explored the possibility of creating an in vitro antibody library from a single healthy individual, showing that the number of lymphocytes, rather than the number of donors, is the key criterion in the production of a diverse and functional antibody library. We describe the construction of a high-quality phage display library comprising 5 × 109 human antibodies by applying an efficient B cell extraction protocol from a single donor and a targeted V-gene amplification strategy favoring specific antibody families for their improved developability profiles. Each step of the library generation process was followed and validated by next generation sequencing to monitor the library quality and diversity. The functionality of the library was tested using several therapeutically relevant targets for which a vast number of different antibodies with desired biophysical properties were obtained.
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38
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Ohlin M. Poorly Expressed Alleles of Several Human Immunoglobulin Heavy Chain Variable Genes are Common in the Human Population. Front Immunol 2021; 11:603980. [PMID: 33717051 PMCID: PMC7943739 DOI: 10.3389/fimmu.2020.603980] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 12/08/2020] [Indexed: 12/23/2022] Open
Abstract
Extensive diversity has been identified in the human heavy chain immunoglobulin locus, including allelic variation, gene duplication, and insertion/deletion events. Several genes have been suggested to be deleted in many haplotypes. Such findings have commonly been based on inference of the germline repertoire from data sets covering antibody heavy chain encoding transcripts. The inference process operates under conditions that may limit identification of genes transcribed at low levels. The presence of rare transcripts that would indicate the existence of poorly expressed alleles in haplotypes that otherwise appear to have deleted these genes has been assessed in the present study. Alleles IGHV1-2*05, IGHV1-3*02, IGHV4-4*01, and IGHV7-4-1*01 were all identified as being expressed from multiple haplotypes, but only at low levels, haplotypes that by inference often appeared not to express these genes at all. These genes are thus not as commonly deleted as previously thought. An assessment of the 5' untranslated region (up to and including the TATA-box), the signal peptide-encoding part of the gene, and the 3'-heptamer suggests that the alleles have no or minimal sequence difference in these regions in comparison to highly expressed alleles. This suggest that they may be able to participate in immunoglobulin gene rearrangement, transcription and translation. However, all four poorly expressed alleles harbor unusual sequence variants within their coding region that may compromise the functionality of the encoded products, thereby limiting their incorporation into the immunoglobulin repertoire. Transcripts based on IGHV7-4-1*01 that had undergone somatic hypermutation and class switch had mutated the codon that encoded the unusual residue in framework region 3 (cysteine 92; located far from the antigen binding site). This finding further supports the poor compatibility of this unusual residue in a fully functional protein product. Indications of a linkage disequilibrium were identified as IGHV1-2*05 and IGHV4-4*01 co-localized to the same haplotypes. Furthermore, transcripts of two of the poorly expressed alleles (IGHV1-3*02 and IGHV4-4*01) mostly do not encode in-frame, functional products, suggesting that these alleles might be essentially non-functional. It is proposed that the functionality status of immunoglobulin genes should also include assessment of their ability to encode functional protein products.
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Affiliation(s)
- Mats Ohlin
- Department of Immunotechnology, Lund University, Lund, Sweden
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39
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Yuan M, Huang D, Lee CCD, Wu NC, Jackson AM, Zhu X, Liu H, Peng L, van Gils MJ, Sanders RW, Burton DR, Reincke SM, Prüss H, Kreye J, Nemazee D, Ward AB, Wilson IA. Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.02.16.430500. [PMID: 33619487 PMCID: PMC7899451 DOI: 10.1101/2021.02.16.430500] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The protective efficacy of neutralizing antibodies (nAbs) elicited during natural infection with SARS-CoV-2 and by vaccination based on its spike protein has been compromised with emergence of the recent SARS-CoV-2 variants. Residues E484 and K417 in the receptor-binding site (RBS) are both mutated in lineages first described in South Africa (B.1.351) and Brazil (B.1.1.28.1). The nAbs isolated from SARS-CoV-2 patients are preferentially encoded by certain heavy-chain germline genes and the two most frequently elicited antibody families (IGHV3-53/3-66 and IGHV1-2) can each bind the RBS in two different binding modes. However, their binding and neutralization are abrogated by either the E484K or K417N mutation, whereas nAbs to the cross-reactive CR3022 and S309 sites are largely unaffected. This structural and functional analysis illustrates why mutations at E484 and K417 adversely affect major classes of nAbs to SARS-CoV-2 with consequences for next-generation COVID-19 vaccines.
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Affiliation(s)
- Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Deli Huang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Chang-Chun D. Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nicholas C. Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Abigail M. Jackson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xueyong Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hejun Liu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Linghang Peng
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Marit J. van Gils
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Rogier W. Sanders
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, Location AMC, University of Amsterdam, Amsterdam, The Netherlands
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Dennis R. Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Ragon Institute of MGH, Harvard and MIT, Cambridge, MA 02139, USA
| | - S. Momsen Reincke
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Harald Prüss
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Jakob Kreye
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
| | - David Nemazee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
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40
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Yuan M, Liu H, Wu NC, Wilson IA. Recognition of the SARS-CoV-2 receptor binding domain by neutralizing antibodies. Biochem Biophys Res Commun 2021; 538:192-203. [PMID: 33069360 PMCID: PMC7547570 DOI: 10.1016/j.bbrc.2020.10.012] [Citation(s) in RCA: 143] [Impact Index Per Article: 47.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 10/07/2020] [Indexed: 12/21/2022]
Abstract
Immediately from the outset of the COVID-19 pandemic, researchers from diverse biomedical and biological disciplines have united to study the novel pandemic virus, SARS-CoV-2. The antibody response to SARS-CoV-2 has been a major focus of COVID-19 research due to its clinical relevance and importance in vaccine and therapeutic development. Isolation and characterization of antibodies to SARS-CoV-2 have been accumulating at an unprecedented pace. Most of the SARS-CoV-2 neutralizing antibodies to date target the spike (S) protein receptor binding domain (RBD), which engages the host receptor ACE2 for viral entry. Here we review the binding sites and molecular features of monoclonal antibodies that target the SARS-CoV-2 RBD, including a few that also cross-neutralize SARS-CoV.
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Affiliation(s)
- Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Hejun Liu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Nicholas C Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA; IAVI Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery (CAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
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41
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Rhesus and cynomolgus macaque immunoglobulin heavy-chain genotyping yields comprehensive databases of germline VDJ alleles. Immunity 2021; 54:355-366.e4. [PMID: 33484642 DOI: 10.1016/j.immuni.2020.12.018] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 10/19/2020] [Accepted: 12/30/2020] [Indexed: 12/20/2022]
Abstract
Definition of the specific germline immunoglobulin (Ig) alleles present in an individual is a critical first step to delineate the ontogeny and evolution of antigen-specific antibody responses. Rhesus and cynomolgus macaques are important animal models for pre-clinical studies, with four main sub-groups being used: Indian- and Chinese-origin rhesus macaques and Mauritian and Indonesian cynomolgus macaques. We applied the (Ig) gene inference tool IgDiscover and performed extensive Sanger sequencing-based genomic validation to define germline VDJ alleles in these 4 sub-groups, comprising 45 macaques in total. There was allelic overlap between Chinese- and Indian-origin rhesus macaques and also between the two macaque species, which is consistent with substantial admixture. The island-restricted Mauritian cynomolgus population displayed the lowest number of alleles of the sub-groups, yet maintained high individual allelic diversity. These comprehensive databases of germline IGH alleles for rhesus and cynomolgus macaques provide a resource toward the study of B cell responses in these important pre-clinical models.
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42
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Raybould MIJ, Rees AR, Deane CM. Current strategies for detecting functional convergence across B-cell receptor repertoires. MAbs 2021; 13:1996732. [PMID: 34781829 PMCID: PMC8604390 DOI: 10.1080/19420862.2021.1996732] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 10/10/2021] [Accepted: 10/12/2021] [Indexed: 12/11/2022] Open
Abstract
Convergence across B-cell receptor (BCR) and antibody repertoires has become instrumental in prioritizing candidates in recent rapid therapeutic antibody discovery campaigns. It has also increased our understanding of the immune system, providing evidence for the preferential selection of BCRs to particular (immunodominant) epitopes post vaccination/infection. These important implications for both drug discovery and immunology mean that it is essential to consider the optimal way to combine experimental and computational technology when probing BCR repertoires for convergence signatures. Here, we discuss the theoretical basis for observing BCR repertoire functional convergence and explore factors of study design that can impact functional signal. We also review the computational arsenal available to detect antibodies with similar functional properties, highlighting opportunities enabled by recent clustering algorithms that exploit structural similarities between BCRs. Finally, we suggest future areas of development that should increase the power of BCR repertoire functional clustering.
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Affiliation(s)
- Matthew I. J. Raybould
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, UK
| | | | - Charlotte M. Deane
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, UK
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43
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Voss WN, Hou YJ, Johnson NV, Kim JE, Delidakis G, Horton AP, Bartzoka F, Paresi CJ, Tanno Y, Abbasi SA, Pickens W, George K, Boutz DR, Towers DM, McDaniel JR, Billick D, Goike J, Rowe L, Batra D, Pohl J, Lee J, Gangappa S, Sambhara S, Gadush M, Wang N, Person MD, Iverson BL, Gollihar JD, Dye J, Herbert A, Baric RS, McLellan JS, Georgiou G, Lavinder JJ, Ippolito GC. Prevalent, protective, and convergent IgG recognition of SARS-CoV-2 non-RBD spike epitopes in COVID-19 convalescent plasma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 33398269 DOI: 10.1101/2020.12.20.423708] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Although humoral immunity is essential for control of SARS-CoV-2, the molecular composition, binding epitopes and effector functions of the immunoglobulin G (IgG) antibodies that circulate in blood plasma following infection are unknown. Proteomic deconvolution of the circulating IgG repertoire (Ig-Seq 1 ) to the spike ectodomain (S-ECD 2 ) in four convalescent study subjects revealed that the plasma response is oligoclonal and directed predominantly (>80%) to S-ECD epitopes that lie outside the receptor binding domain (RBD). When comparing antibodies directed to either the RBD, the N-terminal domain (NTD) or the S2 subunit (S2) in one subject, just four IgG lineages (1 anti-S2, 2 anti-NTD and 1 anti-RBD) accounted for 93.5% of the repertoire. Although the anti-RBD and one of the anti-NTD antibodies were equally potently neutralizing in vitro , we nonetheless found that the anti-NTD antibody was sufficient for protection to lethal viral challenge, either alone or in combination as a cocktail where it dominated the effect of the other plasma antibodies. We identified in vivo protective plasma anti-NTD antibodies in 3/4 subjects analyzed and discovered a shared class of antibodies targeting the NTD that utilize unmutated or near-germline IGHV1-24, the most electronegative IGHV gene in the human genome. Structural analysis revealed that binding to NTD is dominated by interactions with the heavy chain, accounting for 89% of the entire interfacial area, with germline residues uniquely encoded by IGHV1-24 contributing 20% (149 Å 2 ). Together with recent reports of germline IGHV1-24 antibodies isolated by B-cell cloning 3,4 our data reveal a class of shared IgG antibodies that are readily observed in convalescent plasma and underscore the role of NTD-directed antibodies in protection against SARS-CoV-2 infection.
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44
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van Zelm MC, Ziegler-Heitbrock L, Collins AM, Chan SK, Engel P. Editorial: Nomenclature - Avoiding Babylonian Speech Confusion in Present Day Immunology. Front Immunol 2020; 11:621100. [PMID: 33381126 PMCID: PMC7767845 DOI: 10.3389/fimmu.2020.621100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 11/20/2020] [Indexed: 11/13/2022] Open
Affiliation(s)
- Menno C. van Zelm
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, VIC, Australia
- Department of Allergy, Immunology & Respiratory Medicine, Central Clinical School, Monash University, Melbourne, VIC, Australia
- Allergy, Asthma and Clinical Immunology, Alfred Health, Melbourne, IC, Australia
| | | | - Andrew M. Collins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Sanny K. Chan
- Department of Pediatrics, Division of Allergy and Immunology, National Jewish Health, Denver, CO, United States
- Department of Biomedical Research, National Jewish Health, Denver, CO, United States
| | - Pablo Engel
- Immunology Unit, Department of Biomedical Sciences, Medical School of the University of Barcelona, Barcelona, Spain
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45
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Rodriguez OL, Gibson WS, Parks T, Emery M, Powell J, Strahl M, Deikus G, Auckland K, Eichler EE, Marasco WA, Sebra R, Sharp AJ, Smith ML, Bashir A, Watson CT. A Novel Framework for Characterizing Genomic Haplotype Diversity in the Human Immunoglobulin Heavy Chain Locus. Front Immunol 2020; 11:2136. [PMID: 33072076 PMCID: PMC7539625 DOI: 10.3389/fimmu.2020.02136] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 08/06/2020] [Indexed: 02/06/2023] Open
Abstract
An incomplete ascertainment of genetic variation within the highly polymorphic immunoglobulin heavy chain locus (IGH) has hindered our ability to define genetic factors that influence antibody-mediated processes. Due to locus complexity, standard high-throughput approaches have failed to accurately and comprehensively capture IGH polymorphism. As a result, the locus has only been fully characterized two times, severely limiting our knowledge of human IGH diversity. Here, we combine targeted long-read sequencing with a novel bioinformatics tool, IGenotyper, to fully characterize IGH variation in a haplotype-specific manner. We apply this approach to eight human samples, including a haploid cell line and two mother-father-child trios, and demonstrate the ability to generate high-quality assemblies (>98% complete and >99% accurate), genotypes, and gene annotations, identifying 2 novel structural variants and 15 novel IGH alleles. We show multiplexing allows for scaling of the approach without impacting data quality, and that our genotype call sets are more accurate than short-read (>35% increase in true positives and >97% decrease in false-positives) and array/imputation-based datasets. This framework establishes a desperately needed foundation for leveraging IG genomic data to study population-level variation in antibody-mediated immunity, critical for bettering our understanding of disease risk, and responses to vaccines and therapeutics.
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Affiliation(s)
- Oscar L Rodriguez
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - William S Gibson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, United States
| | - Tom Parks
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Matthew Emery
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - James Powell
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Maya Strahl
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Gintaras Deikus
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Kathryn Auckland
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, United States.,Howard Hughes Medical Institute, University of Washington, Seattle, WA, United States
| | - Wayne A Marasco
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Department of Medicine, Harvard Medical School, Boston, MA, United States
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Icahn Institute of Data Science and Genomic Technology, New York, NY, United States
| | - Andrew J Sharp
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Melissa L Smith
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, United States.,Icahn Institute of Data Science and Genomic Technology, New York, NY, United States
| | - Ali Bashir
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, United States
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46
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Yuan M, Liu H, Wu NC, Lee CCD, Zhu X, Zhao F, Huang D, Yu W, Hua Y, Tien H, Rogers TF, Landais E, Sok D, Jardine JG, Burton DR, Wilson IA. Structural basis of a shared antibody response to SARS-CoV-2. Science 2020; 369:1119-1123. [PMID: 32661058 PMCID: PMC7402627 DOI: 10.1126/science.abd2321] [Citation(s) in RCA: 451] [Impact Index Per Article: 112.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 07/07/2020] [Indexed: 12/12/2022]
Abstract
Molecular understanding of neutralizing antibody responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) could accelerate vaccine design and drug discovery. We analyzed 294 anti-SARS-CoV-2 antibodies and found that immunoglobulin G heavy-chain variable region 3-53 (IGHV3-53) is the most frequently used IGHV gene for targeting the receptor-binding domain (RBD) of the spike protein. Co-crystal structures of two IGHV3-53-neutralizing antibodies with RBD, with or without Fab CR3022, at 2.33- to 3.20-angstrom resolution revealed that the germline-encoded residues dominate recognition of the angiotensin I converting enzyme 2 (ACE2)-binding site. This binding mode limits the IGHV3-53 antibodies to short complementarity-determining region H3 loops but accommodates light-chain diversity. These IGHV3-53 antibodies show minimal affinity maturation and high potency, which is promising for vaccine design. Knowledge of these structural motifs and binding mode should facilitate the design of antigens that elicit this type of neutralizing response.
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Affiliation(s)
- Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hejun Liu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nicholas C Wu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Chang-Chun D Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xueyong Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Fangzhu Zhao
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Deli Huang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Wenli Yu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yuanzi Hua
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Henry Tien
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Thomas F Rogers
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Elise Landais
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI, New York, NY 10004, USA
| | - Devin Sok
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI, New York, NY 10004, USA
| | - Joseph G Jardine
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI, New York, NY 10004, USA
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
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47
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Yuan M, Liu H, Wu NC, Lee CCD, Zhu X, Zhao F, Huang D, Yu W, Hua Y, Tien H, Rogers TF, Landais E, Sok D, Jardine JG, Burton DR, Wilson IA. Structural basis of a public antibody response to SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.06.08.141267. [PMID: 32577642 PMCID: PMC7302194 DOI: 10.1101/2020.06.08.141267] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Molecular-level understanding of human neutralizing antibody responses to SARS-CoV-2 could accelerate vaccine design and facilitate drug discovery. We analyzed 294 SARS-CoV-2 antibodies and found that IGHV3-53 is the most frequently used IGHV gene for targeting the receptor binding domain (RBD) of the spike (S) protein. We determined crystal structures of two IGHV3-53 neutralizing antibodies +/- Fab CR3022 ranging from 2.33 to 3.11 Å resolution. The germline-encoded residues of IGHV3-53 dominate binding to the ACE2 binding site epitope with no overlap with the CR3022 epitope. Moreover, IGHV3-53 is used in combination with a very short CDR H3 and different light chains. Overall, IGHV3-53 represents a versatile public VH in neutralizing SARS-CoV-2 antibodies, where their specific germline features and minimal affinity maturation provide important insights for vaccine design and assessing outcomes.
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Affiliation(s)
- Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hejun Liu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nicholas C. Wu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Chang-Chun D. Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xueyong Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Fangzhu Zhao
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Deli Huang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Wenli Yu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yuanzi Hua
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Henry Tien
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Thomas F. Rogers
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Elise Landais
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI, New York, NY10004, USA
| | - Devin Sok
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI, New York, NY10004, USA
| | - Joseph G. Jardine
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI, New York, NY10004, USA
| | - Dennis R. Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
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48
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Inter- and intraspecies comparison of phylogenetic fingerprints and sequence diversity of immunoglobulin variable genes. Immunogenetics 2020; 72:279-294. [PMID: 32367185 DOI: 10.1007/s00251-020-01164-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 04/13/2020] [Indexed: 10/24/2022]
Abstract
Protection and neutralization of a vast array of pathogens is accomplished by the tremendous diversity of the B cell receptor (BCR) repertoire. For jawed vertebrates, this diversity is initiated via the somatic recombination of immunoglobulin (Ig) germline elements. While it is clear that the number of these germline segments differs from species to species, the extent of cross-species sequence diversity remains largely uncharacterized. Here we use extensive computational and statistical methods to investigate the sequence diversity and evolutionary relationship between Ig variable (V), diversity (D), and joining (J) germline segments across nine commonly studied species ranging from zebrafish to human. Metrics such as guanine-cytosine (GC) content showed low redundancy across Ig germline genes within a given species. Other comparisons, including amino acid motifs, evolutionary selection, and sequence diversity, revealed species-specific properties. Additionally, we showed that the germline-encoded diversity differs across antibody (recombined V-D-J) repertoires of various B cell subsets. To facilitate future comparative immunogenomics analysis, we created VDJgermlines, an R package that contains the germline sequences from multiple species. Our study informs strategies for the humanization and engineering of therapeutic antibodies.
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49
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Dynamics of heavy chain junctional length biases in antibody repertoires. Commun Biol 2020; 3:207. [PMID: 32358517 PMCID: PMC7195405 DOI: 10.1038/s42003-020-0931-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 04/01/2020] [Indexed: 11/21/2022] Open
Abstract
Antibody variable domain sequence diversity is generated by recombination of germline segments. The third complementarity-determining region of the heavy chain (CDR H3) is the region of highest sequence diversity and is formed by the joining of heavy chain VH, DH and JH germline segments combined with random nucleotide trimming and additions between these segments. We show that CDR H3 and junctional segment length distributions are biased in human antibody repertoires as a function of VH, VL and JH germline segment utilization. Most length biases are apparent in the naive and antigen experienced B cell compartments but not in nonproductive recombination products, indicating B cell selection as a major driver of these biases. Our findings reveal biases in the antibody CDR H3 diversity landscape shaped by VH, VL, and JH germline segment use during naive and antigen-experienced repertoire selection. Sankar et al. investigate the junctional length biases (determining antibody binding potential) as a function of germline gene usage in antibody repertoires. They show that CDR H3 and junction length are biased by VH, VL, and JH germline segment usage and these biases are apparent in both naive and antigen-experienced repertoires but not in non-productive repertoires.
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50
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Bhardwaj V, Franceschetti M, Rao R, Pevzner PA, Safonova Y. Automated analysis of immunosequencing datasets reveals novel immunoglobulin D genes across diverse species. PLoS Comput Biol 2020; 16:e1007837. [PMID: 32339161 PMCID: PMC7295240 DOI: 10.1371/journal.pcbi.1007837] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 06/15/2020] [Accepted: 04/01/2020] [Indexed: 12/30/2022] Open
Abstract
Immunoglobulin genes are formed through V(D)J recombination, which joins the variable (V), diversity (D), and joining (J) germline genes. Since variations in germline genes have been linked to various diseases, personalized immunogenomics focuses on finding alleles of germline genes across various patients. Although reconstruction of V and J genes is a well-studied problem, the more challenging task of reconstructing D genes remained open until the IgScout algorithm was developed in 2019. In this work, we address limitations of IgScout by developing a probabilistic MINING-D algorithm for D gene reconstruction, apply it to hundreds of immunosequencing datasets from multiple species, and validate the newly inferred D genes by analyzing diverse whole genome sequencing datasets and haplotyping heterozygous V genes. Antibodies provide specific binding to an enormous range of antigens and represent a key component of the adaptive immune system. Immunosequencing has emerged as a method of choice for generating millions of reads that sample antibody repertoires and provides insights into monitoring immune response to disease and vaccination. Most of the previous immunogenomics studies rely on the reference germline genes in the immunoglobulin locus rather than the germline genes in a specific patient. This approach is deficient since the set of known germline genes is incomplete (particularly for non-European humans and non-human species) and contains alleles that resulted from sequencing and annotation errors. The problem of de novo inference of diversity (D) genes from immunosequencing data remained open until the IgScout algorithm was developed in 2019. We address limitations of IgScout by developing a probabilistic MINING-D algorithm for D gene reconstruction and infer multiple D genes across multiple species that are not present in standard databases.
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Affiliation(s)
- Vinnu Bhardwaj
- Electrical and Computer Engineering Department, University of California San Diego, San Diego, California, United States of America
| | - Massimo Franceschetti
- Electrical and Computer Engineering Department, University of California San Diego, San Diego, California, United States of America
| | - Ramesh Rao
- Electrical and Computer Engineering Department, University of California San Diego, San Diego, California, United States of America
- Qualcomm Institute, University of California San Diego, San Diego, California, United States of America
| | - Pavel A. Pevzner
- Computer Science and Engineering Department, University of California San Diego, San Diego, California, United States of America
- * E-mail:
| | - Yana Safonova
- Computer Science and Engineering Department, University of California San Diego, San Diego, California, United States of America
- Center for Information Theory and Applications, University of California San Diego, San Diego, California, United States of America
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