1
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Hao Q, Li J, Yeap LS. Molecular mechanisms of DNA lesion and repair during antibody somatic hypermutation. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-024-2615-1. [PMID: 39048716 DOI: 10.1007/s11427-024-2615-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 05/08/2024] [Indexed: 07/27/2024]
Abstract
Antibody diversification is essential for an effective immune response, with somatic hypermutation (SHM) serving as a key molecular process in this adaptation. Activation-induced cytidine deaminase (AID) initiates SHM by inducing DNA lesions, which are ultimately resolved into point mutations, as well as small insertions and deletions (indels). These mutational outcomes contribute to antibody affinity maturation. The mechanisms responsible for generating point mutations and indels involve the base excision repair (BER) and mismatch repair (MMR) pathways, which are well coordinated to maintain genomic integrity while allowing for beneficial mutations to occur. In this regard, translesion synthesis (TLS) polymerases contribute to the diversity of mutational outcomes in antibody genes by enabling the bypass of DNA lesions. This review summarizes our current understanding of the distinct molecular mechanisms that generate point mutations and indels during SHM. Understanding these mechanisms is critical for elucidating the development of broadly neutralizing antibodies (bnAbs) and autoantibodies, and has implications for vaccine design and therapeutics.
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Affiliation(s)
- Qian Hao
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Department of Endocrinology and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jinfeng Li
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Department of Endocrinology and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Leng-Siew Yeap
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Department of Endocrinology and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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2
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Rahman RS, Wesemann DR. Whence and wherefore IgE? Immunol Rev 2024. [PMID: 39041740 DOI: 10.1111/imr.13373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
Despite the near ubiquitous presence of Ig-based antibodies in vertebrates, IgE is unique to mammals. How and why it emerged remains mysterious. IgE expression is greatly constrained compared to other IgH isotypes. While other IgH isotypes are relatively abundant, soluble IgE has a truncated half-life, and IgE plasma cells are mostly short-lived. Despite its rarity, IgE is consequential and can trigger life-threatening anaphylaxis. IgE production reflects a dynamic steady state with IgG memory B cells feeding short-lived IgE production. Emerging evidence suggests that IgE may also potentially be produced in longer-lived plasma cells as well, perhaps as an aberrancy stemming from its evolutionary roots from an antibody isotype that likely functioned more like IgG. As a late derivative of an ancient systemic antibody system, the benefits of IgE in mammals likely stems from the antibody system's adaptive recognition and response capability. However, the tendency for massive, systemic, and long-lived production, common to IgH isotypes like IgG, were likely not a good fit for IgE. The evolutionary derivation of IgE from an antibody system that for millions of years was good at antigen de-sensitization to now functioning as a highly specialized antigen-sensitization function required heavy restrictions on antibody production-insufficiency of which may contribute to allergic disease.
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Affiliation(s)
- Rifat S Rahman
- Department of Internal Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Duane R Wesemann
- Department of Medicine, Division of Allergy and Clinical Immunology, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Ragon Institute of MGH, MIT, and Harvard, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Boston, Massachusetts, USA
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3
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Lee H, Shin K, Lee Y, Lee S, Lee S, Lee E, Kim SW, Shin HY, Kim JH, Chung J, Kwon S. Identification of B cell subsets based on antigen receptor sequences using deep learning. Front Immunol 2024; 15:1342285. [PMID: 38576618 PMCID: PMC10991714 DOI: 10.3389/fimmu.2024.1342285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 03/07/2024] [Indexed: 04/06/2024] Open
Abstract
B cell receptors (BCRs) denote antigen specificity, while corresponding cell subsets indicate B cell functionality. Since each B cell uniquely encodes this combination, physical isolation and subsequent processing of individual B cells become indispensable to identify both attributes. However, this approach accompanies high costs and inevitable information loss, hindering high-throughput investigation of B cell populations. Here, we present BCR-SORT, a deep learning model that predicts cell subsets from their corresponding BCR sequences by leveraging B cell activation and maturation signatures encoded within BCR sequences. Subsequently, BCR-SORT is demonstrated to improve reconstruction of BCR phylogenetic trees, and reproduce results consistent with those verified using physical isolation-based methods or prior knowledge. Notably, when applied to BCR sequences from COVID-19 vaccine recipients, it revealed inter-individual heterogeneity of evolutionary trajectories towards Omicron-binding memory B cells. Overall, BCR-SORT offers great potential to improve our understanding of B cell responses.
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Affiliation(s)
- Hyunho Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
| | - Kyoungseob Shin
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
| | - Yongju Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
| | - Soobin Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
| | - Seungyoun Lee
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Science, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Eunjae Lee
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Science, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Seung Woo Kim
- Department of Neurology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Ha Young Shin
- Department of Neurology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jong Hoon Kim
- Department of Dermatology and Cutaneous Biology Research Institute, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Junho Chung
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Science, Seoul National University College of Medicine, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sunghoon Kwon
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, Republic of Korea
- Bio-MAX Institute, Seoul National University, Seoul, Republic of Korea
- Inter-University Semiconductor Research Center, Seoul National University, Seoul, Republic of Korea
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4
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Verhaar ER, Knoflook A, Pishesha N, Liu X, van Keizerswaard WJC, Wucherpfennig KW, Ploegh HL. MICA-specific nanobodies for diagnosis and immunotherapy of MICA + tumors. Front Immunol 2024; 15:1368586. [PMID: 38550583 PMCID: PMC10973119 DOI: 10.3389/fimmu.2024.1368586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 02/29/2024] [Indexed: 04/02/2024] Open
Abstract
MICA and MICB are Class I MHC-related glycoproteins that are upregulated on the surface of cells in response to stress, for instance due to infection or malignant transformation. MICA/B are ligands for NKG2D, an activating receptor on NK cells, CD8+ T cells, and γδ T cells. Upon engagement of MICA/B with NKG2D, these cytotoxic cells eradicate MICA/B-positive targets. MICA is frequently overexpressed on the surface of cancer cells of epithelial and hematopoietic origin. Here, we created nanobodies that recognize MICA. Nanobodies, or VHHs, are the recombinantly expressed variable regions of camelid heavy chain-only immunoglobulins. They retain the capacity of antigen recognition but are characterized by their stability and ease of production. The nanobodies described here detect surface-disposed MICA on cancer cells in vitro by flow cytometry and can be used therapeutically as nanobody-drug conjugates when fused to the Maytansine derivative DM1. The nanobody-DM1 conjugate selectively kills MICA positive tumor cells in vitro.
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Affiliation(s)
- Elisha R. Verhaar
- Boston Children’s Hospital, Harvard Medical School, Boston, MA, United States
- Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, Netherlands
| | - Anouk Knoflook
- Boston Children’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Novalia Pishesha
- Division of Immunology, Boston Children’s Hospital, Boston, MA, United States
- Department of Pediatrics, Harvard Medical School, Boston, MA, United States
| | - Xin Liu
- Boston Children’s Hospital, Harvard Medical School, Boston, MA, United States
| | | | - Kai W. Wucherpfennig
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Hidde L. Ploegh
- Boston Children’s Hospital, Harvard Medical School, Boston, MA, United States
- Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, Netherlands
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5
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Wang Q, Feng D, Jia S, Lu Q, Zhao M. B-Cell Receptor Repertoire: Recent Advances in Autoimmune Diseases. Clin Rev Allergy Immunol 2024; 66:76-98. [PMID: 38459209 DOI: 10.1007/s12016-024-08984-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2024] [Indexed: 03/10/2024]
Abstract
In the field of contemporary medicine, autoimmune diseases (AIDs) are a prevalent and debilitating group of illnesses. However, they present extensive and profound challenges in terms of etiology, pathogenesis, and treatment. A major reason for this is the elusive pathophysiological mechanisms driving disease onset. Increasing evidence suggests the indispensable role of B cells in the pathogenesis of autoimmune diseases. Interestingly, B-cell receptor (BCR) repertoires in autoimmune diseases display a distinct skewing that can provide insights into disease pathogenesis. Over the past few years, advances in high-throughput sequencing have provided powerful tools for analyzing B-cell repertoire to understand the mechanisms during the period of B-cell immune response. In this paper, we have provided an overview of the mechanisms and analytical methods for generating BCR repertoire diversity and summarize the latest research progress on BCR repertoire in autoimmune diseases, including systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), primary Sjögren's syndrome (pSS), multiple sclerosis (MS), and type 1 diabetes (T1D). Overall, B-cell repertoire analysis is a potent tool to understand the involvement of B cells in autoimmune diseases, facilitating the creation of innovative therapeutic strategies targeting specific B-cell clones or subsets.
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Affiliation(s)
- Qian Wang
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, the Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Clinical Medical Research Center of Major Skin Diseases and Skin Health of Hunan Province, Changsha, China
| | - Delong Feng
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, the Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Clinical Medical Research Center of Major Skin Diseases and Skin Health of Hunan Province, Changsha, China
| | - Sujie Jia
- Department of Pharmacy, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, 210042, China
| | - Qianjin Lu
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, 210042, China.
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences, Nanjing, China.
| | - Ming Zhao
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, the Second Xiangya Hospital of Central South University, Changsha, Hunan, China.
- Clinical Medical Research Center of Major Skin Diseases and Skin Health of Hunan Province, Changsha, China.
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, 210042, China.
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences, Nanjing, China.
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6
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Weischedel J, Higgins L, Rogers S, Gramalla-Schmitz A, Wyrzykowska P, Borgoni S, MacCarthy T, Chahwan R. Modular cytosine base editing promotes epigenomic and genomic modifications. Nucleic Acids Res 2024; 52:e8. [PMID: 37994786 PMCID: PMC10810192 DOI: 10.1093/nar/gkad1118] [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: 12/08/2022] [Revised: 10/06/2023] [Accepted: 11/06/2023] [Indexed: 11/24/2023] Open
Abstract
Prokaryotic and eukaryotic adaptive immunity differ considerably. Yet, their fundamental mechanisms of gene editing via Cas9 and activation-induced deaminase (AID), respectively, can be conveniently complimentary. Cas9 is an RNA targeted dual nuclease expressed in several bacterial species. AID is a cytosine deaminase expressed in germinal centre B cells to mediate genomic antibody diversification. AID can also mediate epigenomic reprogramming via active DNA demethylation. It is known that sequence motifs, nucleic acid structures, and associated co-factors affect AID activity. But despite repeated attempts, deciphering AID's intrinsic catalytic activities and harnessing its targeted recruitment to DNA is still intractable. Even recent cytosine base editors are unable to fully recapitulate AID's genomic and epigenomic editing properties. Here, we describe the first instance of a modular AID-based editor that recapitulates the full spectrum of genomic and epigenomic editing activity. Our 'Swiss army knife' toolbox will help better understand AID biology per se as well as improve targeted genomic and epigenomic editing.
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Affiliation(s)
- Julian Weischedel
- Institute of Experimental Immunology, University of Zurich, Zurich 8057, Switzerland
| | - Laurence Higgins
- Living Systems Institute, University of Exeter, Exeter EX4 4QD, UK
| | - Sally Rogers
- Living Systems Institute, University of Exeter, Exeter EX4 4QD, UK
| | - Anna Gramalla-Schmitz
- Institute of Experimental Immunology, University of Zurich, Zurich 8057, Switzerland
| | - Paulina Wyrzykowska
- Institute of Experimental Immunology, University of Zurich, Zurich 8057, Switzerland
| | - Simone Borgoni
- Institute of Experimental Immunology, University of Zurich, Zurich 8057, Switzerland
| | - Thomas MacCarthy
- Department of Applied Mathematics & Statistics, Stony Brook University, NY 11794-3600, USA
| | - Richard Chahwan
- Institute of Experimental Immunology, University of Zurich, Zurich 8057, Switzerland
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7
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Hoehn KB, Kleinstein SH. B cell phylogenetics in the single cell era. Trends Immunol 2024; 45:62-74. [PMID: 38151443 PMCID: PMC10872299 DOI: 10.1016/j.it.2023.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/22/2023] [Accepted: 11/24/2023] [Indexed: 12/29/2023]
Abstract
The widespread availability of single-cell RNA sequencing (scRNA-seq) has led to the development of new methods for understanding immune responses. Single-cell transcriptome data can now be paired with B cell receptor (BCR) sequences. However, RNA from BCRs cannot be analyzed like most other genes because BCRs are genetically diverse within individuals. In humans, BCRs are shaped through recombination followed by mutation and selection for antigen binding. As these processes co-occur with cell division, B cells can be studied using phylogenetic trees representing the mutations within a clone. B cell trees can link experimental timepoints, tissues, or cellular subtypes. Here, we review the current state and potential of how B cell phylogenetics can be combined with single-cell data to understand immune responses.
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Affiliation(s)
- Kenneth B Hoehn
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA.
| | - Steven H Kleinstein
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
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8
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Capella-Pujol J, de Gast M, Radić L, Zon I, Chumbe A, Koekkoek S, Olijhoek W, Schinkel J, van Gils MJ, Sanders RW, Sliepen K. Signatures of V H1-69-derived hepatitis C virus neutralizing antibody precursors defined by binding to envelope glycoproteins. Nat Commun 2023; 14:4036. [PMID: 37419906 PMCID: PMC10328973 DOI: 10.1038/s41467-023-39690-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 06/23/2023] [Indexed: 07/09/2023] Open
Abstract
An effective preventive vaccine for hepatitis C virus (HCV) remains a major unmet need. Antigenic region 3 (AR3) on the E1E2 envelope glycoprotein complex overlaps with the CD81 receptor binding site and represents an important epitope for broadly neutralizing antibodies (bNAbs) and is therefore important for HCV vaccine design. Most AR3 bNAbs utilize the VH1-69 gene and share structural features that define the AR3C-class of HCV bNAbs. In this work, we identify recombinant HCV glycoproteins based on a permuted E2E1 trimer design that bind to the inferred VH1-69 germline precursors of AR3C-class bNAbs. When presented on nanoparticles, these recombinant E2E1 glycoproteins efficiently activate B cells expressing inferred germline AR3C-class bNAb precursors as B cell receptors. Furthermore, we identify critical signatures in three AR3C-class bNAbs that represent two subclasses of AR3C-class bNAbs that will allow refined protein design. These results provide a framework for germline-targeting vaccine design strategies against HCV.
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Affiliation(s)
- Joan Capella-Pujol
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, 1105, AZ, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, 1105, AZ, Amsterdam, Netherlands
| | - Marlon de Gast
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, 1105, AZ, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, 1105, AZ, Amsterdam, Netherlands
| | - Laura Radić
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, 1105, AZ, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, 1105, AZ, Amsterdam, Netherlands
| | - Ian Zon
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, 1105, AZ, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, 1105, AZ, Amsterdam, Netherlands
| | - Ana Chumbe
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, 1105, AZ, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, 1105, AZ, Amsterdam, Netherlands
| | - Sylvie Koekkoek
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, 1105, AZ, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, 1105, AZ, Amsterdam, Netherlands
| | - Wouter Olijhoek
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, 1105, AZ, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, 1105, AZ, Amsterdam, Netherlands
| | - Janke Schinkel
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, 1105, AZ, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, 1105, AZ, Amsterdam, Netherlands
| | - Marit J van Gils
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, 1105, AZ, Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, 1105, AZ, Amsterdam, Netherlands
| | - Rogier W Sanders
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, 1105, AZ, Amsterdam, Netherlands.
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, 1105, AZ, Amsterdam, Netherlands.
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, 10065, USA.
| | - Kwinten Sliepen
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, 1105, AZ, Amsterdam, Netherlands.
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, 1105, AZ, Amsterdam, Netherlands.
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9
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Yu H, Liu B, Zhang Y, Gao X, Wang Q, Xiang H, Peng X, Xie C, Wang Y, Hu P, Shi J, Shi Q, Zheng P, Feng C, Tang G, Liu X, Guo L, Lin X, Li J, Liu C, Huang Y, Yang N, Chen Q, Li Z, Su M, Yan Q, Pei R, Chen X, Liu L, Hu F, Liang D, Ke B, Ke C, Li F, He J, Wang M, Chen L, Xiong X, Tang X. Somatically hypermutated antibodies isolated from SARS-CoV-2 Delta infected patients cross-neutralize heterologous variants. Nat Commun 2023; 14:1058. [PMID: 36828833 PMCID: PMC9951844 DOI: 10.1038/s41467-023-36761-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 02/10/2023] [Indexed: 02/26/2023] Open
Abstract
SARS-CoV-2 Omicron variants feature highly mutated spike proteins with extraordinary abilities in evading antibodies isolated earlier in the pandemic. Investigation of memory B cells from patients primarily with breakthrough infections with the Delta variant enables isolation of a number of neutralizing antibodies cross-reactive to heterologous variants of concern (VOCs) including Omicron variants (BA.1-BA.4). Structural studies identify altered complementarity determining region (CDR) amino acids and highly unusual heavy chain CDR2 insertions respectively in two representative cross-neutralizing antibodies-YB9-258 and YB13-292. These features are putatively introduced by somatic hypermutation and they are heavily involved in epitope recognition to broaden neutralization breadth. Previously, insertions/deletions were rarely reported for antiviral antibodies except for those induced by HIV-1 chronic infections. These data provide molecular mechanisms for cross-neutralization of heterologous SARS-CoV-2 variants by antibodies isolated from Delta variant infected patients with implications for future vaccination strategy.
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Affiliation(s)
- Haisheng Yu
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China.
| | - Banghui Liu
- The State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, the Chinese Academy of Sciences, Guangzhou, China
| | - Yudi Zhang
- The State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, the Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xijie Gao
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health-Guangdong Laboratory), Guangzhou, China
| | - Qian Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Haitao Xiang
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Xiaofang Peng
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Caixia Xie
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Yaping Wang
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Peiyu Hu
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health-Guangdong Laboratory), Guangzhou, China
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou, China
| | - Jingrong Shi
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Quan Shi
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Pingqian Zheng
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health-Guangdong Laboratory), Guangzhou, China
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou, China
| | - Chengqian Feng
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Guofang Tang
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Xiaopan Liu
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Liliangzi Guo
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Xiumei Lin
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Jiaojiao Li
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Chuanyu Liu
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Yaling Huang
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Naibo Yang
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Qiuluan Chen
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health-Guangdong Laboratory), Guangzhou, China
| | - Zimu Li
- The State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, the Chinese Academy of Sciences, Guangzhou, China
| | - Mengzhen Su
- The State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, the Chinese Academy of Sciences, Guangzhou, China
- University of Science and Technology of China, Hefei, Anhui, China
| | - Qihong Yan
- The State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, the Chinese Academy of Sciences, Guangzhou, China
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Rongjuan Pei
- State Key Laboratory of Virology, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Xinwen Chen
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou, China
- State Key Laboratory of Virology, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Longqi Liu
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Fengyu Hu
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Dan Liang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Bixia Ke
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Changwen Ke
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China.
| | - Feng Li
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China.
| | - Jun He
- The State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, the Chinese Academy of Sciences, Guangzhou, China.
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health-Guangdong Laboratory), Guangzhou, China.
| | - Meiniang Wang
- BGI-Shenzhen, Shenzhen, China.
- China National GeneBank, BGI-Shenzhen, Shenzhen, China.
| | - Ling Chen
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China.
- The State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, the Chinese Academy of Sciences, Guangzhou, China.
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health-Guangdong Laboratory), Guangzhou, China.
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou, China.
| | - Xiaoli Xiong
- The State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Center for Cell Lineage and Development, Guangzhou Institutes of Biomedicine and Health, the Chinese Academy of Sciences, Guangzhou, China.
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health-Guangdong Laboratory), Guangzhou, China.
| | - Xiaoping Tang
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China.
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou, China.
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10
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Blazso P, Csomos K, Tipton CM, Ujhazi B, Walter JE. Lineage Reconstruction of In Vitro Identified Antigen-Specific Autoreactive B Cells from Adaptive Immune Receptor Repertoires. Int J Mol Sci 2022; 24:ijms24010225. [PMID: 36613668 PMCID: PMC9820449 DOI: 10.3390/ijms24010225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/15/2022] [Accepted: 12/20/2022] [Indexed: 12/25/2022] Open
Abstract
The emergence, survival, growth and maintenance of autoreactive (AR) B-cell clones, the hallmark of humoral autoimmunity, leave their footprints in B-cell receptor repertoires. Collecting IgH sequences related to polyreactive (PR) ones from adaptive immune receptor repertoire (AIRR) datasets make the reconstruction and analysis of PR/AR B-cell lineages possible. We developed a computational approach, named ImmChainTracer, to extract members and to visualize clonal relationships of such B-cell lineages. Our approach was successfully applied on the IgH repertoires of patients suffering from monogenic hypomorphic RAG1 and 2 deficiency (pRD) or polygenic systemic lupus erythematosus (SLE) autoimmune diseases to identify relatives of AR IgH sequences and to track their fate in AIRRs. Signs of clonal expansion, affinity maturation and class-switching events in PR/AR and non-PR/AR B-cell lineages were revealed. An extension of our method towards B-cell expansion caused by any trigger (e.g., infection, vaccination or antibody development) may provide deeper insight into antigen specific B-lymphogenesis.
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Affiliation(s)
- Peter Blazso
- Department of Pediatrics, University of Szeged, 6720 Szeged, Hungary
- Division of Pediatric Allergy/Immunology, University of South Florida at Johns Hopkins All Children’s Hospital, St. Petersburg, FL 33701, USA
- Correspondence: (P.B.); (J.E.W.)
| | - Krisztian Csomos
- Division of Pediatric Allergy/Immunology, University of South Florida at Johns Hopkins All Children’s Hospital, St. Petersburg, FL 33701, USA
| | - Christopher M. Tipton
- Department of Medicine, Division of Rheumatology, Emory University, Atlanta, GA 30322, USA
| | - Boglarka Ujhazi
- Division of Pediatric Allergy/Immunology, University of South Florida at Johns Hopkins All Children’s Hospital, St. Petersburg, FL 33701, USA
| | - Jolan E. Walter
- Division of Pediatric Allergy/Immunology, University of South Florida at Johns Hopkins All Children’s Hospital, St. Petersburg, FL 33701, USA
- Division of Allergy and Immunology, Massachusetts General Hospital for Children, Boston, MA 02114, USA
- Correspondence: (P.B.); (J.E.W.)
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11
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Bahnan W, Happonen L, Khakzad H, Kumra Ahnlide V, de Neergaard T, Wrighton S, André O, Bratanis E, Tang D, Hellmark T, Björck L, Shannon O, Malmström L, Malmström J, Nordenfelt P. A human monoclonal antibody bivalently binding two different epitopes in streptococcal M protein mediates immune function. EMBO Mol Med 2022; 15:e16208. [PMID: 36507602 PMCID: PMC9906385 DOI: 10.15252/emmm.202216208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 11/14/2022] [Accepted: 11/16/2022] [Indexed: 12/14/2022] Open
Abstract
Group A streptococci have evolved multiple strategies to evade human antibodies, making it challenging to create effective vaccines or antibody treatments. Here, we have generated antibodies derived from the memory B cells of an individual who had successfully cleared a group A streptococcal infection. The antibodies bind with high affinity in the central region of the surface-bound M protein. Such antibodies are typically non-opsonic. However, one antibody could effectively promote vital immune functions, including phagocytosis and in vivo protection. Remarkably, this antibody primarily interacts through a bivalent dual-Fab cis mode, where the Fabs bind to two distinct epitopes in the M protein. The dual-Fab cis-binding phenomenon is conserved across different groups of M types. In contrast, other antibodies binding with normal single-Fab mode to the same region cannot bypass the M protein's virulent effects. A broadly binding, protective monoclonal antibody could be a candidate for anti-streptococcal therapy. Our findings highlight the concept of dual-Fab cis binding as a means to access conserved, and normally non-opsonic regions, regions for protective antibody targeting.
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Affiliation(s)
- Wael Bahnan
- Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of MedicineLund UniversityLundSweden
| | - Lotta Happonen
- Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of MedicineLund UniversityLundSweden
| | - Hamed Khakzad
- Equipe Signalisation Calcique et Infections MicrobiennesÉcole Normale Supérieure Paris‐SaclayGif‐sur‐YvetteFrance,Institut National de la Santé et de la Recherche Médicale (INSERM) U1282Gif‐sur‐YvetteFrance,Present address:
Université de Lorraine, Inria, LORIANancyFrance
| | - Vibha Kumra Ahnlide
- Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of MedicineLund UniversityLundSweden
| | - Therese de Neergaard
- Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of MedicineLund UniversityLundSweden
| | - Sebastian Wrighton
- Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of MedicineLund UniversityLundSweden
| | - Oscar André
- Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of MedicineLund UniversityLundSweden
| | - Eleni Bratanis
- Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of MedicineLund UniversityLundSweden
| | - Di Tang
- Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of MedicineLund UniversityLundSweden
| | - Thomas Hellmark
- Department of Clinical Sciences Lund, Division of NephrologyLund UniversityLundSweden
| | - Lars Björck
- Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of MedicineLund UniversityLundSweden
| | - Oonagh Shannon
- Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of MedicineLund UniversityLundSweden
| | - Lars Malmström
- Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of MedicineLund UniversityLundSweden
| | - Johan Malmström
- Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of MedicineLund UniversityLundSweden
| | - Pontus Nordenfelt
- Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of MedicineLund UniversityLundSweden
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12
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Contribution of rare mutational outcomes to broadly neutralizing antibodies. Acta Biochim Biophys Sin (Shanghai) 2022; 54:820-827. [PMID: 35713319 PMCID: PMC9828561 DOI: 10.3724/abbs.2022065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Antibodies are important immune molecules that are elicited by B cells to protect our bodies during viral infections or vaccinations. In humans, the antibody repertoire is diversified by programmed DNA lesion processes to ensure specific and high affinity binding to various antigens. Broadly neutralizing antibodies (bnAbs) are antibodies that have strong neutralizing activities against different variants of a virus. bnAbs such as anti-HIV bnAbs often have special characteristics including insertions and deletions, long complementarity determining region 3 (CDR3), and high frequencies of mutations, often at improbable sites of the variable regions. These unique features are rare mutational outcomes that are acquired during antibody diversification processes. In this review, we will discuss possible mechanisms that generate these rare antibody mutational outcomes. The understanding of the mechanisms that generate these rare mutational outcomes during antibody diversification will have implications in vaccine design strategies to elicit bnAbs.
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13
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Lupo C, Spisak N, Walczak AM, Mora T. Learning the statistics and landscape of somatic mutation-induced insertions and deletions in antibodies. PLoS Comput Biol 2022; 18:e1010167. [PMID: 35653375 PMCID: PMC9197026 DOI: 10.1371/journal.pcbi.1010167] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 06/14/2022] [Accepted: 05/05/2022] [Indexed: 11/25/2022] Open
Abstract
Affinity maturation is crucial for improving the binding affinity of antibodies to antigens. This process is mainly driven by point substitutions caused by somatic hypermutations of the immunoglobulin gene. It also includes deletions and insertions of genomic material known as indels. While the landscape of point substitutions has been extensively studied, a detailed statistical description of indels is still lacking. Here we present a probabilistic inference tool to learn the statistics of indels from repertoire sequencing data, which overcomes the pitfalls and biases of standard annotation methods. The model includes antibody-specific maturation ages to account for variable mutational loads in the repertoire. After validation on synthetic data, we applied our tool to a large dataset of human immunoglobulin heavy chains. The inferred model allows us to identify universal statistical features of indels in heavy chains. We report distinct insertion and deletion hotspots, and show that the distribution of lengths of indels follows a geometric distribution, which puts constraints on future mechanistic models of the hypermutation process. Affinity maturation of B cell receptors is an important mechanism by which our body designs neutralizing antibodies to defend us against pathogens, including broadly neutralizing antibodies, which target a wide range of variants of the same pathogen. Such antibodies often contain key insertions and deletions to the germline gene, or “indels”, which are caused by somatic hypermutations. However, the mechanism, frequency and role of these indels are still elusive. We designed a computational method based on a probabilistic framework to infer the characteristics of this mutational process from high-throughput antibody sequencing experiments. Applied to human data, our approach provides a comprehensive quantitative description of insertions and deletions, opening avenues for better understanding the process of affinity maturation and the design of vaccines for eliciting a broad antibody response.
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Affiliation(s)
- Cosimo Lupo
- Laboratoire de physique de l’École normale supérieure, CNRS, PSL University, Sorbonne Université, and Université de Paris, Paris, France
| | - Natanael Spisak
- Laboratoire de physique de l’École normale supérieure, CNRS, PSL University, Sorbonne Université, and Université de Paris, Paris, France
| | - Aleksandra M. Walczak
- Laboratoire de physique de l’École normale supérieure, CNRS, PSL University, Sorbonne Université, and Université de Paris, Paris, France
- * E-mail: (AMW); (TM)
| | - Thierry Mora
- Laboratoire de physique de l’École normale supérieure, CNRS, PSL University, Sorbonne Université, and Université de Paris, Paris, France
- * E-mail: (AMW); (TM)
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14
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Masuda H, Sawada A, Hashimoto SI, Tamai K, Lin KY, Harigai N, Kurosawa K, Ohta K, Seo H, Itou H. Fast-tracking antibody maturation using a B cell-based display system. MAbs 2022; 14:2122275. [PMID: 36202784 PMCID: PMC9542628 DOI: 10.1080/19420862.2022.2122275] [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] [Indexed: 12/29/2022] Open
Abstract
Affinity maturation, an essential component of antibody engineering, is crucial for developing therapeutic antibodies. Cell display system coupled with somatic hypermutation (SHM) initiated by activation-induced cytidine deaminase (AID) is a commonly used technique for affinity maturation. AID introduces targeted DNA lesions into hotspots of immunoglobulin (Ig) gene loci followed by erroneous DNA repair, leading to biased mutations in the complementary determining regions. However, systems that use an in vivo mimicking mechanism often require several rounds of selection to enrich clones possessing accumulated mutations. We previously described the human ADLib® system, which features autonomous, AID-mediated diversification in Ig gene loci of a chicken B cell line DT40 and streamlines human antibody generation and optimization in one integrated platform. In this study, we further engineered DT40 capable of receiving exogenous antibody genes and examined whether the antibody could be affinity matured. The Ig genes of three representative anti-hVEGF-A antibodies originating from the human ADLib® were introduced; the resulting human IgG1 antibodies had up to 76.4-fold improvement in binding affinities (sub-picomolar KD) within just one round of optimization, owing to efficient accumulation of functional mutations. Moreover, we successfully improved the affinity of a mouse hybridoma-derived anti-hCDCP1 antibody using the engineered DT40, and the observed mutations remained effective in the post-humanized antibody as exhibited by an 8.2-fold increase of in vitro cytotoxicity without compromised physical stability. These results demonstrated the versatility of the novel B cell-based affinity maturation system as an easy-to-use antibody optimization tool regardless of the species of origin.Abbreviations: ADLib®: Autonomously diversifying library, ADLib® KI-AMP: ADLib® knock-in affinity maturation platform, AID: activation-induced cytidine deaminase, CDRs: complementary-determining regions, DIVAC: diversification activator, ECD: extracellular domain, FACS: fluorescence-activated cell sorting, FCM: flow cytometry, HC: heavy chainIg: immunoglobulin, LC: light chain, NGS: next-generation sequencing, PBD: pyrrolobenzodiazepine, SHM: somatic hypermutation, SPR: surface plasmon resonance.
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Affiliation(s)
- Hitomi Masuda
- Research Laboratories, Chiome Bioscience Inc, Tokyo, Japan,CONTACT Hitomi Masuda Research Laboratories, Chiome Bioscience Inc, Sumitomo-Fudosan Nishi-shinjuku bldg. No. 6, 3-12-1 Honmachi, Shibuya-ku, Tokyo151-0071, Japan
| | - Atsushi Sawada
- Research Laboratories, Chiome Bioscience Inc, Tokyo, Japan
| | | | - Kanako Tamai
- Research Laboratories, Chiome Bioscience Inc, Tokyo, Japan
| | - Ke-Yi Lin
- Research Laboratories, Chiome Bioscience Inc, Tokyo, Japan
| | - Naoto Harigai
- Research Laboratories, Chiome Bioscience Inc, Tokyo, Japan
| | - Kohei Kurosawa
- Research Laboratories, Chiome Bioscience Inc, Tokyo, Japan
| | - Kunihiro Ohta
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Hidetaka Seo
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Hiroshi Itou
- Research Laboratories, Chiome Bioscience Inc, Tokyo, Japan,Hiroshi Itou Research Laboratories, Chiome Bioscience Inc, Sumitomo-Fudosan Nishi-shinjuku bldg. No. 6, 3-12-1, Honmachi, Shibuya-ku, Tokyo 151-0071 Japan
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15
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Marquez S, Babrak L, Greiff V, Hoehn KB, Lees WD, Luning Prak ET, Miho E, Rosenfeld AM, Schramm CA, Stervbo U. Adaptive Immune Receptor Repertoire (AIRR) Community Guide to Repertoire Analysis. Methods Mol Biol 2022; 2453:297-316. [PMID: 35622333 PMCID: PMC9761518 DOI: 10.1007/978-1-0716-2115-8_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Adaptive immune receptor repertoires (AIRRs) are rich with information that can be mined for insights into the workings of the immune system. Gene usage, CDR3 properties, clonal lineage structure, and sequence diversity are all capable of revealing the dynamic immune response to perturbation by disease, vaccination, or other interventions. Here we focus on a conceptual introduction to the many aspects of repertoire analysis and orient the reader toward the uses and advantages of each. Along the way, we note some of the many software tools that have been developed for these investigations and link the ideas discussed to chapters on methods provided elsewhere in this volume.
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Affiliation(s)
- Susanna Marquez
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Lmar Babrak
- Institute of Biomedical Engineering and Medical Informatics, School of Life Sciences, FHNW University of Applied Sciences and Arts Northwestern Switzerland, Muttenz, Switzerland
| | - Victor Greiff
- Department of Immunology, University of Oslo, Oslo University Hospital, Oslo, Norway
| | - Kenneth B Hoehn
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - William D Lees
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, UK
| | - Eline T Luning Prak
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Enkelejda Miho
- Institute of Biomedical Engineering and Medical Informatics, School of Life Sciences, FHNW University of Applied Sciences and Arts Northwestern Switzerland, Muttenz, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- aiNET GmbH, Basel, Switzerland
| | - Aaron M Rosenfeld
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Chaim A Schramm
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Ulrik Stervbo
- Center for Translational Medicine, Immunology, and Transplantation, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Herne, Germany.
- Immundiagnostik, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Herne, Germany.
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16
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Forgacs D, Abreu RB, Sautto GA, Kirchenbaum GA, Drabek E, Williamson KS, Kim D, Emerling DE, Ross TM. Convergent antibody evolution and clonotype expansion following influenza virus vaccination. PLoS One 2021; 16:e0247253. [PMID: 33617543 PMCID: PMC7899375 DOI: 10.1371/journal.pone.0247253] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 02/03/2021] [Indexed: 12/14/2022] Open
Abstract
Recent advances in high-throughput single cell sequencing have opened up new avenues into the investigation of B cell receptor (BCR) repertoires. In this study, PBMCs were collected from 17 human participants vaccinated with the split-inactivated influenza virus vaccine during the 2016-2017 influenza season. A combination of Immune Repertoire Capture (IRCTM) technology and IgG sequencing was performed on ~7,800 plasmablast (PB) cells and preferential IgG heavy-light chain pairings were investigated. In some participants, a single expanded clonotype accounted for ~22% of their PB BCR repertoire. Approximately 60% (10/17) of participants experienced convergent evolution, possessing public PBs that were elicited independently in multiple participants. Binding profiles of one private and three public PBs confirmed they were all subtype-specific, cross-reactive hemagglutinin (HA) head-directed antibodies. Collectively, this high-resolution antibody repertoire analysis demonstrated the impact evolution can have on BCRs in response to influenza virus vaccination, which can guide future universal influenza prophylactic approaches.
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Affiliation(s)
- David Forgacs
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States of America
| | - Rodrigo B. Abreu
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States of America
| | - Giuseppe A. Sautto
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States of America
| | - Greg A. Kirchenbaum
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States of America
| | - Elliott Drabek
- Atreca, Inc., South San Francisco, CA, United States of America
| | | | - Dongkyoon Kim
- Atreca, Inc., South San Francisco, CA, United States of America
| | | | - Ted M. Ross
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States of America
- Department of Infectious Diseases, University of Georgia, Athens, GA, United States of America
- * E-mail:
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17
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Nouri N, Kleinstein SH. Somatic hypermutation analysis for improved identification of B cell clonal families from next-generation sequencing data. PLoS Comput Biol 2020; 16:e1007977. [PMID: 32574157 PMCID: PMC7347241 DOI: 10.1371/journal.pcbi.1007977] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 07/09/2020] [Accepted: 05/21/2020] [Indexed: 01/11/2023] Open
Abstract
Adaptive immune receptor repertoire sequencing (AIRR-Seq) offers the possibility of identifying and tracking B cell clonal expansions during adaptive immune responses. Members of a B cell clone are descended from a common ancestor and share the same initial V(D)J rearrangement, but their B cell receptor (BCR) sequence may differ due to the accumulation of somatic hypermutations (SHMs). Clonal relationships are learned from AIRR-seq data by analyzing the BCR sequence, with the most common methods focused on the highly diverse junction region. However, clonally related cells often share SHMs which have been accumulated during affinity maturation. Here, we investigate whether shared SHMs in the V and J segments of the BCR can be leveraged along with the junction sequence to improve the ability to identify clonally related sequences. We develop independent distance functions that capture junction similarity and shared mutations, and combine these in a spectral clustering framework to infer the BCR clonal relationships. Using both simulated and experimental data, we show that this model improves both the sensitivity and specificity for identifying B cell clones. Source code for this method is freely available in the SCOPer (Spectral Clustering for clOne Partitioning) R package (version 0.2 or newer) in the Immcantation framework: www.immcantation.org under the AGPLv3 license.
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Affiliation(s)
- Nima Nouri
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, United States of America
- Center for Medical Informatics, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Steven H. Kleinstein
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, United States of America
- Center for Medical Informatics, Yale School of Medicine, New Haven, Connecticut, United States of America
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
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18
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Kazman P, Vielberg MT, Pulido Cendales MD, Hunziger L, Weber B, Hegenbart U, Zacharias M, Köhler R, Schönland S, Groll M, Buchner J. Fatal amyloid formation in a patient's antibody light chain is caused by a single point mutation. eLife 2020; 9:52300. [PMID: 32151314 PMCID: PMC7064341 DOI: 10.7554/elife.52300] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 02/06/2020] [Indexed: 11/29/2022] Open
Abstract
In systemic light chain amyloidosis, an overexpressed antibody light chain (LC) forms fibrils which deposit in organs and cause their failure. While it is well-established that mutations in the LC’s VL domain are important prerequisites, the mechanisms which render a patient LC amyloidogenic are ill-defined. In this study, we performed an in-depth analysis of the factors and mutations responsible for the pathogenic transformation of a patient-derived λ LC, by recombinantly expressing variants in E. coli. We show that proteolytic cleavage of the patient LC resulting in an isolated VL domain is essential for fibril formation. Out of 11 mutations in the patient VL, only one, a leucine to valine mutation, is responsible for fibril formation. It disrupts a hydrophobic network rendering the C-terminal segment of VL more dynamic and decreasing domain stability. Thus, the combination of proteolytic cleavage and the destabilizing mutation trigger conformational changes that turn the LC pathogenic. Amyloid light chain amyloidosis, shortened to AL amyloidosis, is a rare and often fatal disease. It is caused by a disorder of the bone marrow. Usually, cells in the bone marrow produce Y-shaped proteins called antibodies to fight infections. In AL amyloidosis, these cells release too much of the short arm of the antibody, known as its light chain, and the light chains also carry mutations. The antibodies are no longer able to assemble properly, and instead misfold and form structures, known as amyloid fibrils. The fibrils build up outside the cells, gradually causing damage to tissues and organs that can lead to life-threatening organ failure. Due to the rareness of the disease, diagnosis is often overlooked and delayed. People experience widely varying symptoms, depending on the organs affected. Also, given the diversity of antibodies people make, every person with AL amyloidosis has a variety of mutations implicated in their disease. It is thought that mutations in the antibody light chain make it unstable and prone to misfolding, but it remains unclear which specific mutations trigger a cascade of amyloid fibril formation. Now, Kazman et al. have pinpointed the exact mechanism in one case of the disease. First, tissue biopsies from a woman with advanced AL amyloidosis were analyzed, and the defunct antibody light chain was isolated. Eleven mutations were identified in the antibody light chain, only one of which was found to be responsible for the formation of the harmful fibrils. The next step was to determine how this one small change was so damaging. The experiments showed that after the antibody light chain was cut in two, a process that happens naturally in the body, this single mutation transforms it into a protein capable of causing disease. In this ‘bedside to lab bench’ study, Kazman et al. have succeeded in determining the molecular origin of one case of AL amyloidosis. The results have also shown that the instability of antibodies due to mutation does not alone explain the formation of amyloid fibrils in this disease and that the cutting of this protein in two is also important. It is hoped that, in the long run, this work will lead to new diagnostics and treatment options for people with AL amyloidosis.
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Affiliation(s)
- Pamina Kazman
- Center for Integrated Protein Science Munich at the Department Chemie, Technische Universität München, Garching, Germany
| | - Marie-Theres Vielberg
- Center for Integrated Protein Science Munich at the Department Chemie, Technische Universität München, Garching, Germany
| | - María Daniela Pulido Cendales
- Center for Integrated Protein Science Munich at the Department Physik, Technische Universität München, Garching, Germany
| | - Lioba Hunziger
- Center for Integrated Protein Science Munich at the Department Chemie, Technische Universität München, Garching, Germany
| | - Benedikt Weber
- Center for Integrated Protein Science Munich at the Department Chemie, Technische Universität München, Garching, Germany
| | - Ute Hegenbart
- Medical Department V, Amyloidosis Center, University of Heidelberg, Heidelberg, Germany
| | - Martin Zacharias
- Center for Integrated Protein Science Munich at the Department Physik, Technische Universität München, Garching, Germany
| | - Rolf Köhler
- Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
| | - Stefan Schönland
- Medical Department V, Amyloidosis Center, University of Heidelberg, Heidelberg, Germany
| | - Michael Groll
- Center for Integrated Protein Science Munich at the Department Chemie, Technische Universität München, Garching, Germany
| | - Johannes Buchner
- Center for Integrated Protein Science Munich at the Department Chemie, Technische Universität München, Garching, Germany
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19
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Flyak AI, Ruiz SE, Salas J, Rho S, Bailey JR, Bjorkman PJ. An ultralong CDRH2 in HCV neutralizing antibody demonstrates structural plasticity of antibodies against E2 glycoprotein. eLife 2020; 9:e53169. [PMID: 32125272 PMCID: PMC7064334 DOI: 10.7554/elife.53169] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 03/02/2020] [Indexed: 12/14/2022] Open
Abstract
A vaccine protective against diverse HCV variants is needed to control the HCV epidemic. Structures of E2 complexes with front layer-specific broadly neutralizing antibodies (bNAbs) isolated from HCV-infected individuals, revealed a disulfide bond-containing CDRH3 that adopts straight (individuals who clear infection) or bent (individuals with chronic infection) conformation. To investigate whether a straight versus bent disulfide bond-containing CDRH3 is specific to particular HCV-infected individuals, we solved a crystal structure of the HCV E2 ectodomain in complex with AR3X, a bNAb with an unusually long CDRH2 that was isolated from the chronically-infected individual from whom the bent CDRH3 bNAbs were derived. The structure revealed that AR3X utilizes both its ultralong CDRH2 and a disulfide motif-containing straight CDRH3 to recognize the E2 front layer. These results demonstrate that both the straight and bent CDRH3 classes of HCV bNAb can be elicited in a single individual, revealing a structural plasticity of VH1-69-derived bNAbs.
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Affiliation(s)
- Andrew I Flyak
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Stormy E Ruiz
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
- Department of Medicine, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Jordan Salas
- Department of Medicine, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Semi Rho
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Justin R Bailey
- Department of Medicine, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
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20
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Franklin A, Steele EJ, Lindley RA. A proposed reverse transcription mechanism for (CAG)n and similar expandable repeats that cause neurological and other diseases. Heliyon 2020; 6:e03258. [PMID: 32140575 PMCID: PMC7044655 DOI: 10.1016/j.heliyon.2020.e03258] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 09/26/2019] [Accepted: 01/15/2020] [Indexed: 12/12/2022] Open
Abstract
The mechanism of (CAG)n repeat generation, and related expandable repeat diseases in non-dividing cells, is currently understood in terms of a DNA template-based DNA repair synthesis process involving hairpin stabilized slippage, local error-prone repair via MutSβ (MSH2-MSH3) hairpin protective stabilization, then nascent strand extension by DNA polymerases-β and -δ. We advance a very similar slipped hairpin-stabilized model involving MSH2-MSH3 with two key differences: the copying template may also be the nascent pre-mRNA with the repair pathway being mediated by the Y-family error-prone enzymes DNA polymerase-η and DNA polymerase-κ acting as reverse transcriptases. We argue that both DNA-based and RNA-based mechanisms could well be activated in affected non-dividing brain cells in vivo. Here, we compare the advantages of the RNA/RT-based model proposed by us as an adjunct to previously proposed models. In brief, our model depends upon dysregulated innate and adaptive immunity cascades involving AID/APOBEC and ADAR deaminases that are known to be involved in normal locus-specific immunoglobulin somatic hypermutation, cancer progression and somatic mutations at many off-target non-immunoglobulin sites across the genome: we explain how these processes could also play an active role in repeat expansion diseases at RNA polymerase II-transcribed genes.
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Affiliation(s)
- Andrew Franklin
- Medical Department, Novartis Pharmaceuticals UK Limited, 200 Frimley Business Park, Frimley, Surrey, GU16 7SR, United Kingdom
| | - Edward J. Steele
- Melville Analytics Pty Ltd, Melbourne, Vic, 3004, Australia
- CYO’Connor ERADE Village Foundation, Perth, WA, Australia
| | - Robyn A. Lindley
- GMDxgenomics, Melbourne, Vic, Australia
- Department of Clinical Pathology, Faculty of Medicine, Dentistry & Health Sciences, University of Melbourne, Vic, Australia
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21
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Yu X, Du L, Wu M, Wu J, He S, Yuan T, Sun X. The analysis of organization and diversity mechanism in goat immunoglobulin light chain gene loci. Immunobiology 2019; 225:151889. [PMID: 31812342 DOI: 10.1016/j.imbio.2019.11.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 11/26/2019] [Indexed: 11/26/2022]
Abstract
The genomic organization of goat immunoglobulin light chains (Igλ and Igκ) loci were annotated based on the goat genome database. The goat Igλ chain located on chromosome 17 contains at least 35 Vλ gene fragments (seven potential functional genes, one ORF and 27 pseudogenes), two Jλ-Cλ clusters arranged in a Vλ(35)-Jλ2-Cλ1-Jλ1-Cλ2 pattern, with another Cλ3 on scaffold. The Igκ locus included 11 Vκ (five potential functional genes, two ORFs and four pseudogene fragments), three Jκ genes and a single Cκ gene ordered in Vκ(35)-Jκ(3)-Cκ pattern on chromosome 11. By analyzing the clonies of Igλ and Igκ, we further found Vλ2 (26.23 %) &Vλ3 (73.11 %), Vκ2 (52.07 %) &Vκ4 (46.15 %) were predominately used in the expression of λ and κ chains respectively. λ chain showed more abundance in connective diversity than κ chain. Besides, somatic hypermutation with higher frequency in both immunoglobulin light chains was the major mechanism for the goat repertoire diversity. These results demonstrated goat immunoglobulin light chain variable region genome loci and repertoire diversity.
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Affiliation(s)
- Xiaohui Yu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Lijuan Du
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Mingli Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jie Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Shuai He
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Tingting Yuan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiuzhu Sun
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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22
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Glesner J, Kapingidza AB, Godzwon M, Offermann LR, Mueller GA, DeRose EF, Wright P, Richardson CM, Woodfolk JA, Vailes LD, Wünschmann S, London RE, Chapman MD, Ohlin M, Chruszcz M, Pomés A. A Human IgE Antibody Binding Site on Der p 2 for the Design of a Recombinant Allergen for Immunotherapy. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2019; 203:2545-2556. [PMID: 31554696 PMCID: PMC6810898 DOI: 10.4049/jimmunol.1900580] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 08/15/2019] [Indexed: 01/31/2023]
Abstract
Der p 2 is one of the most important allergens from the house dust mite Dermatophagoides pteronyssinus Identification of human IgE Ab binding epitopes can be used for rational design of allergens with reduced IgE reactivity for therapy. Antigenic analysis of Der p 2 was performed by site-directed mutagenesis based on the x-ray crystal structure of the allergen in complex with a Fab from the murine IgG mAb 7A1 that binds an epitope overlapping with human IgE binding sites. Conformational changes upon Ab binding were confirmed by nuclear magnetic resonance using a 7A1-single-chain variable fragment. In addition, a human IgE Ab construct that interferes with mAb 7A1 binding was isolated from a combinatorial phage-display library constructed from a mite-allergic patient and expressed as two recombinant forms (single-chain Fab in Pichia pastoris and Fab in Escherichia coli). These two IgE Ab constructs and the mAb 7A1 failed to recognize two Der p 2 epitope double mutants designed to abolish the allergen-Ab interaction while preserving the fold necessary to bind Abs at other sites of the allergen surface. A 10-100-fold reduction in binding of IgE from allergic subjects to the mutants additionally showed that the residues mutated were involved in IgE Ab binding. In summary, mutagenesis of a Der p 2 epitope defined by x-ray crystallography revealed an IgE Ab binding site that will be considered for the design of hypoallergens for immunotherapy.
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Affiliation(s)
- Jill Glesner
- Indoor Biotechnologies, Inc., Charlottesville, VA 22903
| | | | | | | | - Geoffrey A Mueller
- National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709; and
| | - Eugene F DeRose
- National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709; and
| | - Paul Wright
- University of Virginia, Charlottesville, VA 22903
| | | | | | - Lisa D Vailes
- Indoor Biotechnologies, Inc., Charlottesville, VA 22903
| | | | - Robert E London
- National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709; and
| | | | | | | | - Anna Pomés
- Indoor Biotechnologies, Inc., Charlottesville, VA 22903;
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23
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Abstract
Neutralizing antibodies against human immunodeficiency virus subtype 1 (HIV-1) bind to its envelope glycoprotein (Env). Half of the molecular mass of Env is carbohydrate making it one of the most heavily glycosylated proteins known in nature. HIV-1 Env glycans are derived from the host and present a formidable challenge for host anti-glycan antibody induction. Anti-glycan antibody induction is challenging because anti-HIV-1 glycan antibodies should recognize Env antigen while not acquiring autoreactivity. Thus, the glycan network on HIV-1 Env is referred to as the glycan shield. Despite the challenges presented by immune recognition of host-derived glycans, neutralizing antibodies capable of binding the glycans on HIV-1 Env can be generated by the host immune system in the setting of HIV-1 infection. In particular, a cluster of high mannose glycans, including an N-linked glycan at position 332, form the high mannose patch and are targeted by a variety of broadly neutralizing antibodies. These high mannose patch-directed HIV-1 antibodies can be categorized into distinct categories based on their antibody paratope structure, neutralization activity, and glycan and peptide reactivity. Below we will compare and contrast each of these classes of HIV-1 glycan-dependent antibodies and describe vaccine design efforts to elicit each of these antibody types.
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24
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Yu K, Lieber MR. Current insights into the mechanism of mammalian immunoglobulin class switch recombination. Crit Rev Biochem Mol Biol 2019; 54:333-351. [PMID: 31509023 PMCID: PMC6856442 DOI: 10.1080/10409238.2019.1659227] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/13/2019] [Accepted: 08/20/2019] [Indexed: 12/12/2022]
Abstract
Immunoglobulin (Ig) class switch recombination (CSR) is the gene rearrangement process by which B lymphocytes change the Ig heavy chain constant region to permit a switch of Ig isotype from IgM to IgG, IgA, or IgE. At the DNA level, CSR occurs via generation and joining of DNA double strand breaks (DSBs) at intronic switch regions located just upstream of each of the heavy chain constant regions. Activation-induced deaminase (AID), a B cell specific enzyme, catalyzes cytosine deaminations (converting cytosines to uracils) as the initial DNA lesions that eventually lead to DSBs and CSR. Progress on AID structure integrates very well with knowledge about Ig class switch region nucleic acid structures that are supported by functional studies. It is an ideal time to review what is known about the mechanism of Ig CSR and its relation to somatic hypermutation. There have been many comprehensive reviews on various aspects of the CSR reaction and regulation of AID expression and activity. This review is focused on the relation between AID and switch region nucleic acid structures, with a particular emphasis on R-loops.
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Affiliation(s)
- Kefei Yu
- Michigan State University, Department of Microbiology & Molecular Genetics, 5175 Biomedical Physical Sciences, East Lansing, MI 48824
| | - Michael R. Lieber
- USC Norris Comprehensive Cancer Ctr., Departments of Pathology, of Molecular Microbiology & Immunology, of Biochemistry & Molecular Biology, and of the Section of Molecular & Computational Biology within the Department of Biological Sciences, 1441 Eastlake Ave., NTT5428, Los Angeles, CA 90089-9176
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25
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Zanotti KJ, Maul RW, Yang W, Gearhart PJ. DNA Breaks in Ig V Regions Are Predominantly Single Stranded and Are Generated by UNG and MSH6 DNA Repair Pathways. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2019; 202:1573-1581. [PMID: 30665938 PMCID: PMC6382588 DOI: 10.4049/jimmunol.1801183] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 12/16/2018] [Indexed: 11/19/2022]
Abstract
Antibody diversity is initiated by activation-induced deaminase (AID), which deaminates cytosine to uracil in DNA. Uracils in the Ig gene loci can be recognized by uracil DNA glycosylase (UNG) or mutS homologs 2 and 6 (MSH2-MSH6) proteins, and then processed into DNA breaks. Breaks in switch regions of the H chain locus cause isotype switching and have been extensively characterized as staggered and blunt double-strand breaks. However, breaks in V regions that arise during somatic hypermutation are poorly understood. In this study, we characterize AID-dependent break formation in JH introns from mouse germinal center B cells. We used a ligation-mediated PCR assay to detect single-strand breaks and double-strand breaks that were either staggered or blunt. In contrast to switch regions, V regions contained predominantly single-strand breaks, which peaked 10 d after immunization. We then examined the pathways used to generate these breaks in UNG- and MSH6-deficient mice. Surprisingly, both DNA repair pathways contributed substantially to break formation, and in the absence of both UNG and MSH6, the frequency of breaks was severely reduced. When the breaks were sequenced and mapped, they were widely distributed over a 1000-bp intron region downstream of JH3 and JH4 exons and were unexpectedly located at all 4 nt. These data suggest that during DNA repair, nicks are generated at distal sites from the original deaminated cytosine, and these repair intermediates could generate both faithful and mutagenic repair. During mutagenesis, single-strand breaks would allow entry for low-fidelity DNA polymerases to generate somatic hypermutation.
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Affiliation(s)
- Kimberly J Zanotti
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224
| | - Robert W Maul
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224
| | - William Yang
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224
| | - Patricia J Gearhart
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224
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26
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Yeap LS, Meng FL. Cis- and trans-factors affecting AID targeting and mutagenic outcomes in antibody diversification. Adv Immunol 2019; 141:51-103. [PMID: 30904133 DOI: 10.1016/bs.ai.2019.01.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Antigen receptor diversification is a hallmark of adaptive immunity which allows specificity of the receptor to particular antigen. B cell receptor (BCR) or its secreted form, antibody, is diversified through antigen-independent and antigen-dependent mechanisms. During B cell development in bone marrow, BCR is diversified via V(D)J recombination mediated by RAG endonuclease. Upon stimulation by antigen, B cell undergo somatic hypermutation (SHM) to allow affinity maturation and class switch recombination (CSR) to change the effector function of the antibody. Both SHM and CSR are initiated by activation-induced cytidine deaminase (AID). Repair of AID-initiated lesions through different DNA repair pathways results in diverse mutagenic outcomes. Here, we focus on discussing cis- and trans-factors that target AID to its substrates and factors that affect different outcomes of AID-initiated lesions. The knowledge of mechanisms that govern AID targeting and outcomes could be harnessed to elicit rare functional antibodies and develop ex vivo antibody diversification approaches with diversifying base editors.
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Affiliation(s)
- Leng-Siew Yeap
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Fei-Long Meng
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.
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27
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28
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Sormanni P, Aprile FA, Vendruscolo M. Third generation antibody discovery methods: in silico rational design. Chem Soc Rev 2018; 47:9137-9157. [PMID: 30298157 DOI: 10.1039/c8cs00523k] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Owing to their outstanding performances in molecular recognition, antibodies are extensively used in research and applications in molecular biology, biotechnology and medicine. Recent advances in experimental and computational methods are making it possible to complement well-established in vivo (first generation) and in vitro (second generation) methods of antibody discovery with novel in silico (third generation) approaches. Here we describe the principles of computational antibody design and review the state of the art in this field. We then present Modular, a method that implements the rational design of antibodies in a modular manner, and describe the opportunities offered by this approach.
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Affiliation(s)
- Pietro Sormanni
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK.
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29
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Niavarani A, Shahrabi Farahani A, Sharafkhah M, Rassoulzadegan M. Pancancer analysis identifies prognostic high-APOBEC1 expression level implicated in cancer in-frame insertions and deletions. Carcinogenesis 2018; 39:327-335. [PMID: 29346513 DOI: 10.1093/carcin/bgy005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Genome insertions and deletions (indels) show tremendous functional impacts despite they are much less common than single nucleotide variants, which are at the center of studies assessing cancer mutational signatures. We studied 8891 tumor samples of 32 types from The Cancer Genome Atlas in order to explore those genes which are potentially implicated in cancer indels. Survival analysis identified in-frame indels as the most important variants predicting adverse outcome. Transcriptome-wide association study identified 16 genes overexpressed in both tumor samples and tumor types with high number of in-frame indels, of whom four (APOBEC1, BCL2L15, FOXL1 and PDX1) were identified with gene products distributed within the nucleus. APOBEC1 emerged as the mere consistently hypomethylated gene in tumor samples with high number of in-frame indels. The correlation of APOBEC1 expression levels with cancer indels was independent of age and defects in DNA homologous recombination (HR) and/or mismatch repair. Unlike frame-shift indels, triplet repeat motifs were found to occur frequently at in-frame indel sites. The splicing variant 3, making a shorter isoform b, showed essentially all the same indel correlations as of APOBEC1. Expression levels of both APOBEC1 and variant 3 were found to be predicting adverse prognosis independent of DNA HR and mismatch repair. Not less importantly, high level of variant 3 in paired normal tissues was also proved to predict cancer outcome. Our findings propose APOBEC1 and isoform b as the potential endogenous mutators implicated in cancer in-frame indels and pave the way for their use as novel prognostic tumor markers.
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Affiliation(s)
- Ahmadreza Niavarani
- Digestive Oncology Research Center, Digestive Disease Research Institute (DDRI), Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Asieh Shahrabi Farahani
- Digestive Oncology Research Center, Digestive Disease Research Institute (DDRI), Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Sharafkhah
- Digestive Oncology Research Center, Digestive Disease Research Institute (DDRI), Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Minoo Rassoulzadegan
- Institut Valrose Biologie, INSERM U1091, Université Nice Sophia Antipolis, Nice, France
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30
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Du L, Wang S, Zhu Y, Zhao H, Basit A, Yu X, Li Q, Sun X. Immunoglobulin heavy chain variable region analysis in dairy goats. Immunobiology 2018; 223:599-607. [PMID: 30025710 DOI: 10.1016/j.imbio.2018.07.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 01/12/2018] [Accepted: 07/05/2018] [Indexed: 10/28/2022]
Abstract
Based on the goat genome database, we have annotated the genomic organization of the goat immunoglobulin heavy chain variable region. The goat IgH locus is present on seven genome scaffolds, and contains ten VH, three DH and six JH segments. After the exclusion of three shorter segments, the VH genes were divided into two gene families based on sequence similarity. By analyzing the IgH cDNA sequences, we further identified that VH2 (54.2%), DH1 (61.7%) and JH1 (60.5%) segments were most frequently utilized in the expression of the immunoglobulin variable region, and that point mutations introduced by somatic hypermutation were the major mutation present in these expressed variable region. Compared with human and horses, DH-DH fusion occurred at a higher frequency in goat V(D)J recombination. These results provided variable insights into goat immunoglobulin heavy chain variable region genome loci and repertoire diversity.
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Affiliation(s)
- Lijuan Du
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China; State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Shuhui Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yanjiao Zhu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Haidong Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Abdul Basit
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xiaohui Yu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Qingwang Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiuzhu Sun
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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31
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Abstract
Probabilistic modeling is fundamental to the statistical analysis of complex data. In addition to forming a coherent description of the data-generating process, probabilistic models enable parameter inference about given datasets. This procedure is well developed in the Bayesian perspective, in which one infers probability distributions describing to what extent various possible parameters agree with the data. In this paper, we motivate and review probabilistic modeling for adaptive immune receptor repertoire data then describe progress and prospects for future work, from germline haplotyping to adaptive immune system deployment across tissues. The relevant quantities in immune sequence analysis include not only continuous parameters such as gene use frequency but also discrete objects such as B-cell clusters and lineages. Throughout this review, we unravel the many opportunities for probabilistic modeling in adaptive immune receptor analysis, including settings for which the Bayesian approach holds substantial promise (especially if one is optimistic about new computational methods). From our perspective, the greatest prospects for progress in probabilistic modeling for repertoires concern ancestral sequence estimation for B-cell receptor lineages, including uncertainty from germline genotype, rearrangement, and lineage development.
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Affiliation(s)
- Branden Olson
- Computational Biology Program Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Mail stop: M1-B514 Seattle, WA 98109-1024 phone: +1 206 667 7318
| | - Frederick A. Matsen
- Computational Biology Program Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Mail stop: M1-B514 Seattle, WA 98109-1024 phone: +1 206 667 7318
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32
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Persson H, Kirik U, Thörnqvist L, Greiff L, Levander F, Ohlin M. In Vitro Evolution of Antibodies Inspired by In Vivo Evolution. Front Immunol 2018; 9:1391. [PMID: 29977238 PMCID: PMC6021498 DOI: 10.3389/fimmu.2018.01391] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 06/05/2018] [Indexed: 01/16/2023] Open
Abstract
In vitro generation of antibodies often requires variable domain sequence evolution to adapt the protein in terms of affinity, specificity, or developability. Such antibodies, including those that are of interest for clinical development, may have their origins in a diversity of immunoglobulin germline genes. Others and we have previously shown that antibodies of different origins tend to evolve along different, preferred trajectories. Apart from substitutions within the complementary determining regions, evolution may also, in a germline gene-origin-defined manner, be focused to residues in the framework regions, and even to residues within the protein core, in many instances at a substantial distance from the antibody’s antigen-binding site. Examples of such germline origin-defined patterns of evolution are described. We propose that germline gene-preferred substitution patterns offer attractive alternatives that should be considered in efforts to evolve antibodies intended for therapeutic use with respect to appropriate affinity, specificity, and product developability. We also hypothesize that such germline gene-origin-defined in vitro evolution hold potential to result in products with limited immunogenicity, as similarly evolved antibodies will be parts of conventional, in vivo-generated antibody responses and thus are likely to have been seen by the immune system in the past.
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Affiliation(s)
- Helena Persson
- Drug Discovery and Development Platform, Science for Life Laboratory, Stockholm, Sweden.,School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology, Stockholm, Sweden
| | - Ufuk Kirik
- Department of Immunotechnology, Lund University, Lund, Sweden
| | | | - Lennart Greiff
- Department of Clinical Sciences, Lund University, Lund, Sweden.,Department of Otorhinolaryngology, Head & Neck Surgery, Skåne University Hospital, Lund, Sweden
| | | | - Mats Ohlin
- Department of Immunotechnology, Lund University, Lund, Sweden.,Human Antibody Therapeutics, Drug Discovery and Development Platform, Science for Life Laboratory, Lund University, Lund, Sweden
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33
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Haakenson JK, Huang R, Smider VV. Diversity in the Cow Ultralong CDR H3 Antibody Repertoire. Front Immunol 2018; 9:1262. [PMID: 29915599 PMCID: PMC5994613 DOI: 10.3389/fimmu.2018.01262] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 05/18/2018] [Indexed: 01/26/2023] Open
Abstract
Typical antibodies found in humans and mice usually have short CDR H3s and generally flat binding surfaces. However, cows possess a subset of antibodies with ultralong CDR H3s that can range up to 70 amino acids and form a unique “stalk and knob” structure, with the knob protruding far out of the antibody surface, where it has the potential to bind antigens with concave epitopes. Activation-induced cytidine deaminase (AID) has a proven role in diversifying antibody repertoires in humoral immunity, and it has been found to induce somatic hypermutation in bovine immunoglobulin genes both before and after contact with antigen. Due to limited use of variable and diversity genes in the V(D)J recombination events that produce ultralong CDR H3 antibodies in cows, the diversity in the bovine ultralong antibody repertoire has been proposed to rely on AID-induced mutations targeted to the IGHD8-2 gene that encodes the entire knob region. In this review, we discuss the genetics, structures, and diversity of bovine ultralong antibodies, as well as the role of AID in creating a diverse antibody repertoire.
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Affiliation(s)
- Jeremy K Haakenson
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States
| | - Ruiqi Huang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States
| | - Vaughn V Smider
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States
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Zhou D, Xu L, Huang W, Tonn T. Epitopes of MUC1 Tandem Repeats in Cancer as Revealed by Antibody Crystallography: Toward Glycopeptide Signature-Guided Therapy. Molecules 2018; 23:molecules23061326. [PMID: 29857542 PMCID: PMC6099590 DOI: 10.3390/molecules23061326] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 05/20/2018] [Accepted: 05/22/2018] [Indexed: 02/06/2023] Open
Abstract
Abnormally O-glycosylated MUC1 tandem repeat glycopeptide epitopes expressed by multiple types of cancer have long been attractive targets for therapy in the race against genetic mutations of tumor cells. Glycopeptide signature-guided therapy might be a more promising avenue than mutation signature-guided therapy. Three O-glycosylated peptide motifs, PDTR, GSTA, and GVTS, exist in a tandem repeat HGVTSAPDTRPAPGSTAPPA, containing five O-glycosylation sites. The exact peptide and sugar residues involved in antibody binding are poorly defined. Co-crystal structures of glycopeptides and respective monoclonal antibodies are very few. Here we review 3 groups of monoclonal antibodies: antibodies which only bind to peptide portion, antibodies which only bind to sugar portion, and antibodies which bind to both peptide and sugar portions. The antigenicity of peptide and sugar portions of glyco-MUC1 tandem repeat were analyzed according to available biochemical and structural data, especially the GSTA and GVTS motifs independent from the most studied PDTR. Tn is focused as a peptide-modifying residue in vaccine design, to induce glycopeptide-binding antibodies with cross reactivity to Tn-related tumor glycans, but not glycans of healthy cells. The unique requirement for the designs of antibody in antibody-drug conjugate, bi-specific antibodies, and chimeric antigen receptors are also discussed.
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Affiliation(s)
- Dapeng Zhou
- Shanghai Pulmonary Hospital Affiliated with Tongji University School of Medicine, Shanghai 200092, China.
| | - Lan Xu
- Laboratory of Antibody Structure, Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201203, China.
| | - Wei Huang
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences and iHuman Institute, ShanghaiTech University, Shanghai 201203, China.
| | - Torsten Tonn
- Institute for Transfusion Medicine Dresden, German Red Cross Blood Donation Service North-East, D-01307 Dresden, Germany.
- Medical Faculty, Carl Gustav Carus Technical University Dresden, D-01307 Dresden, Germany.
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35
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Waltari E, Jia M, Jiang CS, Lu H, Huang J, Fernandez C, Finzi A, Kaufmann DE, Markowitz M, Tsuji M, Wu X. 5' Rapid Amplification of cDNA Ends and Illumina MiSeq Reveals B Cell Receptor Features in Healthy Adults, Adults With Chronic HIV-1 Infection, Cord Blood, and Humanized Mice. Front Immunol 2018; 9:628. [PMID: 29632541 PMCID: PMC5879793 DOI: 10.3389/fimmu.2018.00628] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 03/13/2018] [Indexed: 12/17/2022] Open
Abstract
Using 5′ rapid amplification of cDNA ends, Illumina MiSeq, and basic flow cytometry, we systematically analyzed the expressed B cell receptor (BCR) repertoire in 14 healthy adult PBMCs, 5 HIV-1+ adult PBMCs, 5 cord blood samples, and 3 HIS-CD4/B mice, examining the full-length variable region of μ, γ, α, κ, and λ chains for V-gene usage, somatic hypermutation (SHM), and CDR3 length. Adding to the known repertoire of healthy adults, Illumina MiSeq consistently detected small fractions of reads with high mutation frequencies including hypermutated μ reads, and reads with long CDR3s. Additionally, the less studied IgA repertoire displayed similar characteristics to that of IgG. Compared to healthy adults, the five HIV-1 chronically infected adults displayed elevated mutation frequencies for all μ, γ, α, κ, and λ chains examined and slightly longer CDR3 lengths for γ, α, and λ. To evaluate the reconstituted human BCR sequences in a humanized mouse model, we analyzed cord blood and HIS-CD4/B mice, which all lacked the typical SHM seen in the adult reference. Furthermore, MiSeq revealed identical unmutated IgM sequences derived from separate cell aliquots, thus for the first time demonstrating rare clonal members of unmutated IgM B cells by sequencing.
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Affiliation(s)
- Eric Waltari
- Aaron Diamond AIDS Research Center, Affiliate of The Rockefeller University, New York, NY, United States
| | - Manxue Jia
- Aaron Diamond AIDS Research Center, Affiliate of The Rockefeller University, New York, NY, United States
| | - Caroline S Jiang
- Hospital Biostatistics, The Rockefeller University, New York, NY, United States
| | - Hong Lu
- Aaron Diamond AIDS Research Center, Affiliate of The Rockefeller University, New York, NY, United States
| | - Jing Huang
- Aaron Diamond AIDS Research Center, Affiliate of The Rockefeller University, New York, NY, United States
| | - Cristina Fernandez
- Aaron Diamond AIDS Research Center, Affiliate of The Rockefeller University, New York, NY, United States
| | - Andrés Finzi
- Centre de Recherche du CHUM, Université de Montréal, Montreal, QC, Canada
| | - Daniel E Kaufmann
- Centre de Recherche du CHUM, Université de Montréal, Montreal, QC, Canada.,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), La Jolla, CA, United States
| | - Martin Markowitz
- Aaron Diamond AIDS Research Center, Affiliate of The Rockefeller University, New York, NY, United States
| | - Moriya Tsuji
- Aaron Diamond AIDS Research Center, Affiliate of The Rockefeller University, New York, NY, United States
| | - Xueling Wu
- Aaron Diamond AIDS Research Center, Affiliate of The Rockefeller University, New York, NY, United States
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Immunogenetic factors driving formation of ultralong VH CDR3 in Bos taurus antibodies. Cell Mol Immunol 2017; 16:53-64. [PMID: 29200193 DOI: 10.1038/cmi.2017.117] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 09/27/2017] [Accepted: 09/28/2017] [Indexed: 12/22/2022] Open
Abstract
The antibody repertoire of Bos taurus is characterized by a subset of variable heavy (VH) chain regions with ultralong third complementarity determining regions (CDR3) which, compared to other species, can provide a potent response to challenging antigens like HIV env. These unusual CDR3 can range to over seventy highly diverse amino acids in length and form unique β-ribbon 'stalk' and disulfide bonded 'knob' structures, far from the typical antigen binding site. The genetic components and processes for forming these unusual cattle antibody VH CDR3 are not well understood. Here we analyze sequences of Bos taurus antibody VH domains and find that the subset with ultralong CDR3 exclusively uses a single variable gene, IGHV1-7 (VHBUL) rearranged to the longest diversity gene, IGHD8-2. An eight nucleotide duplication at the 3' end of IGHV1-7 encodes a longer V-region producing an extended F β-strand that contributes to the stalk in a rearranged CDR3. A low amino acid variability was observed in CDR1 and CDR2, suggesting that antigen binding for this subset most likely only depends on the CDR3. Importantly a novel, potentially AID mediated, deletional diversification mechanism of the B. taurus VH ultralong CDR3 knob was discovered, in which interior codons of the IGHD8-2 region are removed while maintaining integral structural components of the knob and descending strand of the stalk in place. These deletions serve to further diversify cysteine positions, and thus disulfide bonded loops. Hence, both germline and somatic genetic factors and processes appear to be involved in diversification of this structurally unusual cattle VH ultralong CDR3 repertoire.
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37
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Nowak J, Baker T, Georges G, Kelm S, Klostermann S, Shi J, Sridharan S, Deane CM. Length-independent structural similarities enrich the antibody CDR canonical class model. MAbs 2017; 8:751-60. [PMID: 26963563 PMCID: PMC4966832 DOI: 10.1080/19420862.2016.1158370] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Complementarity-determining regions (CDRs) are antibody loops that make up the antigen binding site. Here, we show that all CDR types have structurally similar loops of different lengths. Based on these findings, we created length-independent canonical classes for the non-H3 CDRs. Our length variable structural clusters show strong sequence patterns suggesting either that they evolved from the same original structure or result from some form of convergence. We find that our length-independent method not only clusters a larger number of CDRs, but also predicts canonical class from sequence better than the standard length-dependent approach. To demonstrate the usefulness of our findings, we predicted cluster membership of CDR-L3 sequences from 3 next-generation sequencing datasets of the antibody repertoire (over 1,000,000 sequences). Using the length-independent clusters, we can structurally classify an additional 135,000 sequences, which represents a ∼20% improvement over the standard approach. This suggests that our length-independent canonical classes might be a highly prevalent feature of antibody space, and could substantially improve our ability to accurately predict the structure of novel CDRs identified by next-generation sequencing.
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Affiliation(s)
- Jaroslaw Nowak
- a Department of Statistics , University of Oxford , Peter Medawar Building, Oxford , UK.,b Doctoral Training Center , University of Oxford , Rex Richards Building, Oxford , UK
| | - Terry Baker
- c Informatics Department , UCB Pharma , Slough , UK
| | - Guy Georges
- d Roche Pharma Research and Early Development , Therapeutic Modalities, Roche Innovation Center , Penzberg , Germany
| | | | - Stefan Klostermann
- e Roche Pharma Research and Early Development , PRED Informatics, Roche Innovation Center , Penzberg , Germany
| | - Jiye Shi
- c Informatics Department , UCB Pharma , Slough , UK
| | - Sudharsan Sridharan
- f Department of Antibody Discovery and Protein Engineering , MedImmune Ltd , Granta Park, Cambridge , UK
| | - Charlotte M Deane
- a Department of Statistics , University of Oxford , Peter Medawar Building, Oxford , UK
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De Boer RJ, Perelson AS. How Germinal Centers Evolve Broadly Neutralizing Antibodies: the Breadth of the Follicular Helper T Cell Response. J Virol 2017; 91:e00983-17. [PMID: 28878083 PMCID: PMC5660473 DOI: 10.1128/jvi.00983-17] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 08/11/2017] [Indexed: 12/20/2022] Open
Abstract
Many HIV-1-infected patients evolve broadly neutralizing antibodies (bnAbs). This evolutionary process typically takes several years and is poorly understood as selection taking place in germinal centers occurs on the basis of antibody affinity. B cells with the highest-affinity receptors tend to acquire the most antigen from the follicular dendritic cell (FDC) network and present the highest density of cognate peptides to follicular helper T (Tfh) cells, which provide survival signals to the B cell. bnAbs are therefore expected to evolve only when the B cell lineage evolving breadth is consistently capturing and presenting more peptides to Tfh cells than other lineages of more specific B cells. Here we develop mathematical models of Tfh cells in germinal centers to explicitly define the mechanisms of selection in this complex evolutionary process. Our results suggest that broadly reactive B cells presenting a high density of peptides bound to major histocompatibility complex class II molecules (pMHC) are readily outcompeted by B cells responding to lineages of HIV-1 that transiently dominate the within host viral population. Conversely, if broadly reactive B cells acquire a large variety of several HIV-1 proteins from the FDC network and present a high diversity of several pMHC, they can be rescued by a large fraction of the Tfh cell repertoire in the germinal center. Under such circumstances the evolution of bnAbs is much more consistent. Increasing either the magnitude of the Tfh cell response or the breadth of the Tfh cell repertoire markedly facilitates the evolution of bnAbs. Because both the magnitude and breadth can be increased by vaccination with several HIV-1 proteins, this calls for experimental testing.IMPORTANCE Many HIV-infected patients slowly evolve antibodies that can neutralize a large variety of viruses. Such broadly neutralizing antibodies (bnAbs) could in the future become therapeutic agents. bnAbs appear very late, and patients are typically not protected by them. At the moment, we fail to understand why this takes so long and how the immune system selects for broadly neutralizing capacity. Typically, antibodies are selected based on affinity and not on breadth. We developed mathematical models to study two different mechanisms by which the immune system can select for broadly neutralizing capacity. One of these is based upon the repertoire of different follicular helper T (Tfh) cells in germinal centers. We suggest that broadly reactive B cells may interact with a larger fraction of this repertoire and demonstrate that this would select for bnAbs. Intriguingly, this suggests that broadening the Tfh cell repertoire by vaccination may speed up the evolution of bnAbs.
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Affiliation(s)
- Rob J De Boer
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
- Santa Fe Institute, Santa Fe, New Mexico, USA
| | - Alan S Perelson
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
- Santa Fe Institute, Santa Fe, New Mexico, USA
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39
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Kirik U, Persson H, Levander F, Greiff L, Ohlin M. Antibody Heavy Chain Variable Domains of Different Germline Gene Origins Diversify through Different Paths. Front Immunol 2017; 8:1433. [PMID: 29180996 PMCID: PMC5694033 DOI: 10.3389/fimmu.2017.01433] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 10/16/2017] [Indexed: 02/04/2023] Open
Abstract
B cells produce antibodies, key effector molecules in health and disease. They mature their properties, including their affinity for antigen, through hypermutation events; processes that involve, e.g., base substitution, codon insertion and deletion, often in association with an isotype switch. Investigations of antibody evolution define modes whereby particular antibody responses are able to form, and such studies provide insight important for instance for development of efficient vaccines. Antibody evolution is also used in vitro for the design of antibodies with improved properties. To better understand the basic concepts of antibody evolution, we analyzed the mutational paths, both in terms of amino acid substitution and insertions and deletions, taken by antibodies of the IgG isotype. The analysis focused on the evolution of the heavy chain variable domain of sets of antibodies, each with an origin in 1 of 11 different germline genes representing six human heavy chain germline gene subgroups. Investigated genes were isolated from cells of human bone marrow, a major site of antibody production, and characterized by next-generation sequencing and an in-house bioinformatics pipeline. Apart from substitutions within the complementarity determining regions, multiple framework residues including those in protein cores were targets of extensive diversification. Diversity, both in terms of substitutions, and insertions and deletions, in antibodies is focused to different positions in the sequence in a germline gene-unique manner. Altogether, our findings create a framework for understanding patterns of evolution of antibodies from defined germline genes.
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Affiliation(s)
- Ufuk Kirik
- Department of Immunotechnology, Lund University, Lund, Sweden
| | - Helena Persson
- Science for Life Laboratory, Drug Discovery and Development Platform, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Fredrik Levander
- Department of Immunotechnology, Lund University, Lund, Sweden.,National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Department of Immunotechnology, Lund University, Lund, Sweden
| | - Lennart Greiff
- Department of Clinical Sciences, Lund University, Lund, Sweden.,Department of Otorhinolaryngology, Head and Neck Surgery, Skåne University Hospital, Lund, Sweden
| | - Mats Ohlin
- Department of Immunotechnology, Lund University, Lund, Sweden.,Science for Life Laboratory, Drug Discovery and Development Platform, Human Antibody Therapeutics, Lund University, Lund, Sweden.,U-READ, Lund School of Technology, Lund University, Lund, Sweden
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40
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Kennedy PJ, Oliveira C, Granja PL, Sarmento B. Monoclonal antibodies: technologies for early discovery and engineering. Crit Rev Biotechnol 2017; 38:394-408. [PMID: 28789584 DOI: 10.1080/07388551.2017.1357002] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Antibodies are essential in modern life sciences biotechnology. Their architecture and diversity allow for high specificity and affinity to a wide array of biochemicals. Combining monoclonal antibody (mAb) technology with recombinant DNA and protein expression links antibody genotype with phenotype. Yet, the ability to select and screen for high affinity binders from recombinantly-displayed, combinatorial libraries unleashes the true power of mAbs and a flood of clinical applications. The identification of novel antibodies can be accomplished by a myriad of in vitro display technologies from the proven (e.g. phage) to the emerging (e.g. mammalian cell and cell-free) based on affinity binding as well as function. Lead candidates can be further engineered for increased affinity and half-life, reduced immunogenicity and/or enhanced manufacturing, and storage capabilities. This review begins with antibody biology and how the structure and genetic machinery relate to function, diversity, and in vivo affinity maturation and follows with the general requirements of (therapeutic) antibody discovery and engineering with an emphasis on in vitro display technologies. Throughout, we highlight where antibody biology inspires technology development and where high-throughput, "big data" and in silico strategies are playing an increasing role. Antibodies dominate the growing class of targeted therapeutics, alone or as bioconjugates. However, their versatility extends to research, diagnostics, and beyond.
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Affiliation(s)
- Patrick J Kennedy
- a i3S - Instituto de Investigação e Inovação em Saúde , Universidade do Porto , Porto , Portugal.,b INEB - Instituto de Engenharia Biomédica , Universidade do Porto , Porto , Portugal.,c IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto , Porto , Portugal.,d ICBAS - Instituto de Ciências Biomédicas Abel Salazar , Universidade do Porto , Porto , Portugal
| | - Carla Oliveira
- a i3S - Instituto de Investigação e Inovação em Saúde , Universidade do Porto , Porto , Portugal.,c IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto , Porto , Portugal
| | - Pedro L Granja
- a i3S - Instituto de Investigação e Inovação em Saúde , Universidade do Porto , Porto , Portugal.,b INEB - Instituto de Engenharia Biomédica , Universidade do Porto , Porto , Portugal.,d ICBAS - Instituto de Ciências Biomédicas Abel Salazar , Universidade do Porto , Porto , Portugal.,e Departmento de Engenharia Metalúrgica e de Materiais , FEUP - Faculdade de Engenharia da Universidade do Porto , Porto , Portugal
| | - Bruno Sarmento
- a i3S - Instituto de Investigação e Inovação em Saúde , Universidade do Porto , Porto , Portugal.,b INEB - Instituto de Engenharia Biomédica , Universidade do Porto , Porto , Portugal.,f CESPU , Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde & Instituto Universitário de Ciências da Saúde , Gandra , Portugal
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41
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A Haystack Heuristic for Autoimmune Disease Biomarker Discovery Using Next-Gen Immune Repertoire Sequencing Data. Sci Rep 2017; 7:5338. [PMID: 28706301 PMCID: PMC5509648 DOI: 10.1038/s41598-017-04439-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 05/16/2017] [Indexed: 01/03/2023] Open
Abstract
Large-scale DNA sequencing of immunological repertoires offers an opportunity for the discovery of novel biomarkers for autoimmune disease. Available bioinformatics techniques however, are not adequately suited for elucidating possible biomarker candidates from within large immunosequencing datasets due to unsatisfactory scalability and sensitivity. Here, we present the Haystack Heuristic, an algorithm customized to computationally extract disease-associated motifs from next-generation-sequenced repertoires by contrasting disease and healthy subjects. This technique employs a local-search graph-theory approach to discover novel motifs in patient data. We apply the Haystack Heuristic to nine million B-cell receptor sequences obtained from nearly 100 individuals in order to elucidate a new motif that is significantly associated with multiple sclerosis. Our results demonstrate the effectiveness of the Haystack Heuristic in computing possible biomarker candidates from high throughput sequencing data and could be generalized to other datasets.
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42
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Kirik U, Greiff L, Levander F, Ohlin M. Parallel antibody germline gene and haplotype analyses support the validity of immunoglobulin germline gene inference and discovery. Mol Immunol 2017; 87:12-22. [DOI: 10.1016/j.molimm.2017.03.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 03/07/2017] [Accepted: 03/08/2017] [Indexed: 12/18/2022]
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Somatic hypermutation in immunity and cancer: Critical analysis of strand-biased and codon-context mutation signatures. DNA Repair (Amst) 2016; 45:1-24. [DOI: 10.1016/j.dnarep.2016.07.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 07/01/2016] [Indexed: 01/01/2023]
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Abstract
While searching for new therapeutics against malaria, Lanzavecchia and colleagues discovered that antibodies can be diversified by DNA sequences encoded outside of antibody genes.
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Affiliation(s)
- Davide F Robbiani
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York 10065, USA.
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York 10065, USA; Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA.
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45
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Hershberg U, Luning Prak ET. The analysis of clonal expansions in normal and autoimmune B cell repertoires. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2014.0239. [PMID: 26194753 PMCID: PMC4528416 DOI: 10.1098/rstb.2014.0239] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Clones are the fundamental building blocks of immune repertoires. The number of different clones relates to the diversity of the repertoire, whereas their size and sequence diversity are linked to selective pressures. Selective pressures act both between clones and within different sequence variants of a clone. Understanding how clonal selection shapes the immune repertoire is one of the most basic questions in all of immunology. But how are individual clones defined? Here we discuss different approaches for defining clones, starting with how antibodies are diversified during different stages of B cell development. Next, we discuss how clones are defined using different experimental methods. We focus on high-throughput sequencing datasets, and the computational challenges and opportunities that these data have for mining the antibody repertoire landscape. We discuss methods that visualize sequence variants within the same clone and allow us to consider collections of shared mutations to determine which sequences share a common ancestry. Finally, we comment on features of frequently encountered expanded B cell clones that may be of particular interest in the setting of autoimmunity and other chronic conditions.
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Affiliation(s)
- Uri Hershberg
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Bossone 7-711, 3141 Chestnut Street, Philadelphia, PA 19104, USA Department of Immunology and Microbiology, College of Medicine, Drexel University, Bossone 7-711, 3141 Chestnut Street, Philadelphia, PA 19104, USA
| | - Eline T Luning Prak
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, 405B Stellar Chance Labs, 422 Curie Boulevard, Philadelphia, PA 19104, USA
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Related Mechanisms of Antibody Somatic Hypermutation and Class Switch Recombination. Microbiol Spectr 2016; 3:MDNA3-0037-2014. [PMID: 26104555 DOI: 10.1128/microbiolspec.mdna3-0037-2014] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The primary antibody repertoire is generated by mechanisms involving the assembly of the exons that encode the antigen-binding variable regions of immunoglobulin heavy (IgH) and light (IgL) chains during the early development of B lymphocytes. After antigen-dependent activation, mature B lymphocytes can further alter their IgH and IgL variable region exons by the process of somatic hypermutation (SHM), which allows the selection of B cells in which SHMs resulted in the production of antibodies with increased antigen affinity. In addition, during antigen-dependent activation, B cells can also change the constant region of their IgH chain through a DNA double-strand-break (DSB) dependent process referred to as IgH class switch recombination (CSR), which generates B cell progeny that produce antibodies with different IgH constant region effector functions that are best suited for a elimination of a particular pathogen or in a particular setting. Both the mutations that underlie SHM and the DSBs that underlie CSR are initiated in target genes by activation-induced cytidine deaminase (AID). This review describes in depth the processes of SHM and CSR with a focus on mechanisms that direct AID cytidine deamination in activated B cells and mechanisms that promote the differential outcomes of such cytidine deamination.
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47
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Chen Z, Eder MD, Elos MT, Viboolsittiseri SS, Chen X, Wang JH. Interplay between Target Sequences and Repair Pathways Determines Distinct Outcomes of AID-Initiated Lesions. THE JOURNAL OF IMMUNOLOGY 2016; 196:2335-47. [PMID: 26810227 DOI: 10.4049/jimmunol.1502184] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 12/22/2015] [Indexed: 11/19/2022]
Abstract
Activation-induced deaminase (AID) functions by deaminating cytosines and causing U:G mismatches, a rate-limiting step of Ab gene diversification. However, precise mechanisms regulating AID deamination frequency remain incompletely understood. Moreover, it is not known whether different sequence contexts influence the preferential access of mismatch repair or uracil glycosylase (UNG) to AID-initiated U:G mismatches. In this study, we employed two knock-in models to directly compare the mutability of core Sμ and VDJ exon sequences and their ability to regulate AID deamination and subsequent repair process. We find that the switch (S) region is a much more efficient AID deamination target than the V region. Igh locus AID-initiated lesions are processed by error-free and error-prone repair. S region U:G mismatches are preferentially accessed by UNG, leading to more UNG-dependent deletions, enhanced by mismatch repair deficiency. V region mutation hotspots are largely determined by AID deamination. Recurrent and conserved S region motifs potentially function as spacers between AID deamination hotspots. We conclude that the pattern of mutation hotspots and DNA break generation is influenced by sequence-intrinsic properties, which regulate AID deamination and affect the preferential access of downstream repair. Our studies reveal an evolutionarily conserved role for substrate sequences in regulating Ab gene diversity and AID targeting specificity.
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Affiliation(s)
- Zhangguo Chen
- Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045; and Department of Biomedical Research, National Jewish Health, Denver, CO 80206
| | - Maxwell D Eder
- Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045; and
| | - Mihret T Elos
- Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045; and
| | - Sawanee S Viboolsittiseri
- Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045; and
| | - Xiaomi Chen
- Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045; and
| | - Jing H Wang
- Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045; and Department of Biomedical Research, National Jewish Health, Denver, CO 80206
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48
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A LAIR1 insertion generates broadly reactive antibodies against malaria variant antigens. Nature 2015; 529:105-109. [PMID: 26700814 PMCID: PMC4869849 DOI: 10.1038/nature16450] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 11/16/2015] [Indexed: 01/04/2023]
Abstract
Plasmodium falciparum antigens expressed on the surface of infected erythrocytes are important targets of naturally acquired immunity against malaria, but their high number and variability provide the pathogen with a powerful means of escape from host antibodies1–4. Although broadly reactive antibodies against these antigens could be useful as therapeutics and in vaccine design, their identification has proven elusive. Here, we report the isolation of human monoclonal antibodies that recognize erythrocytes infected by different P. falciparum isolates and opsonize these cells by binding to members of the RIFIN family. These antibodies acquired broad reactivity through a novel mechanism of insertion of a large DNA fragment between the V and DJ segments. The insert, which is both necessary and sufficient for binding to RIFINs, encodes the entire 100 amino acid collagen-binding domain of LAIR-1, an Ig superfamily inhibitory receptor encoded on chromosome 19. In each of the two donors studied, the antibodies are produced by a single expanded B cell clone and carry distinct somatic mutations in the LAIR-1 domain that abolish binding to collagen and increase binding to infected erythrocytes. These findings illustrate, with a biologically relevant example, a novel mechanism of antibody diversification by interchromosomal DNA transposition and demonstrate the existence of conserved epitopes that may be suitable candidates for the development of a malaria vaccine.
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Appenzeller S, Gilissen C, Rijntjes J, Tops BBJ, Kastner-van Raaij A, Hebeda KM, Nissen L, Dutilh BE, van Krieken JHJM, Groenen PJTA. Immunoglobulin rearrangement analysis from multiple lesions in the same patient using next-generation sequencing. Histopathology 2015; 67:843-58. [DOI: 10.1111/his.12714] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 04/14/2015] [Indexed: 01/16/2023]
Affiliation(s)
- Silke Appenzeller
- Center for Molecular and Biomolecular Informatics; Radboud Institute for Molecular Life Sciences; Radboud University Medical Center; Nijmegen The Netherlands
- Core Unit Systems Medicine; University of Wuerzburg; Wuerzburg Germany
| | - Christian Gilissen
- Department of Genetics; Radboud University Medical Center; Nijmegen The Netherlands
| | - Jos Rijntjes
- Department of Pathology; Radboud University Medical Center; Nijmegen The Netherlands
| | - Bastiaan B J Tops
- Department of Pathology; Radboud University Medical Center; Nijmegen The Netherlands
| | | | - Konnie M Hebeda
- Department of Pathology; Radboud University Medical Center; Nijmegen The Netherlands
| | - Loes Nissen
- Department of Gastroenterology and Hepatology; Radboud University Medical Center; Nijmegen The Netherlands
| | - Bas E Dutilh
- Center for Molecular and Biomolecular Informatics; Radboud Institute for Molecular Life Sciences; Radboud University Medical Center; Nijmegen The Netherlands
| | - J Han J M van Krieken
- Department of Pathology; Radboud University Medical Center; Nijmegen The Netherlands
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Reiche S, Dwai Y, Bussmann BM, Horn S, Sieg M, Jassoy C. High Inter-Individual Diversity of Point Mutations, Insertions, and Deletions in Human Influenza Virus Nucleoprotein-Specific Memory B Cells. PLoS One 2015; 10:e0128684. [PMID: 26086076 PMCID: PMC4472751 DOI: 10.1371/journal.pone.0128684] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 04/29/2015] [Indexed: 11/19/2022] Open
Abstract
The diversity of virus-specific antibodies and of B cells among different individuals is unknown. Using single-cell cloning of antibody genes, we generated recombinant human monoclonal antibodies from influenza nucleoprotein-specific memory B cells in four adult humans with and without preceding influenza vaccination. We examined the diversity of the antibody repertoires and found that NP-specific B cells used numerous immunoglobulin genes. The heavy chains (HCs) originated from 26 and the kappa light chains (LCs) from 19 different germ line genes. Matching HC and LC chains gave rise to 43 genetically distinct antibodies that bound influenza NP. The median lengths of the CDR3 of the HC, kappa and lambda LC were 14, 9 and 11 amino acids, respectively. We identified changes at 13.6% of the amino acid positions in the V gene of the antibody heavy chain, at 8.4% in the kappa and at 10.6 % in the lambda V gene. We identified somatic insertions or deletions in 8.1% of the variable genes. We also found several small groups of clonal relatives that were highly diversified. Our findings demonstrate broadly diverse memory B cell repertoires for the influenza nucleoprotein. We found extensive variation within individuals with a high number of point mutations, insertions, and deletions, and extensive clonal diversification. Thus, structurally conserved proteins can elicit broadly diverse and highly mutated B-cell responses.
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Affiliation(s)
- Sven Reiche
- Institute of Virology, Faculty of Medicine, University of Leipzig, Leipzig, Germany
| | - Yamen Dwai
- Institute of Virology, Faculty of Medicine, University of Leipzig, Leipzig, Germany
- Department of Biology, Faculty of Natural Sciences, Tishreen University, Latakia, Syria
| | - Bianca M. Bussmann
- Institute of Virology, Faculty of Medicine, University of Leipzig, Leipzig, Germany
| | - Susanne Horn
- Institute of Virology, Faculty of Medicine, University of Leipzig, Leipzig, Germany
| | - Michael Sieg
- Institute of Virology, Faculty of Medicine, University of Leipzig, Leipzig, Germany
- Department of Biology, Faculty of Natural Sciences, Tishreen University, Latakia, Syria
| | - Christian Jassoy
- Institute of Virology, Faculty of Medicine, University of Leipzig, Leipzig, Germany
- * E-mail:
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