1
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Wang K, Hu X, Zhang J. Fast clonal family inference from large-scale B cell repertoire sequencing data. CELL REPORTS METHODS 2023; 3:100601. [PMID: 37788671 PMCID: PMC10626204 DOI: 10.1016/j.crmeth.2023.100601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/31/2023] [Accepted: 09/08/2023] [Indexed: 10/05/2023]
Abstract
Advances in high-throughput sequencing technologies have facilitated the large-scale characterization of B cell receptor (BCR) repertoires. However, the vast amount and high diversity of the BCR sequences pose challenges for efficient and biologically meaningful analysis. Here, we introduce fastBCR, an efficient computational approach for inferring B cell clonal families from massive BCR heavy chain sequences. We demonstrate that fastBCR substantially reduces the running time while ensuring high accuracy on simulated datasets with diverse numbers of B cell lineages and varying mutation rates. We apply fastBCR to real BCR sequencing data from peripheral blood samples of COVID-19 patients, showing that the inferred clonal families display disease-associated features, as well as corresponding antigen-binding specificity and affinity. Overall, our results demonstrate the advantages of fastBCR for analyzing BCR repertoire data, which will facilitate the identification of disease-associated antibodies and improve our understanding of the B cell immune response.
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Affiliation(s)
- Kaixuan Wang
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, China
| | - Xihao Hu
- GV20 Therapeutics, Cambridge, MA, USA
| | - Jian Zhang
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, China.
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2
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Hao Q, Zhan C, Lian C, Luo S, Cao W, Wang B, Xie X, Ye X, Gui T, Voena C, Pighi C, Wang Y, Tian Y, Wang X, Dai P, Cai Y, Liu X, Ouyang S, Sun S, Hu Q, Liu J, Ye Y, Zhao J, Lu A, Wang JY, Huang C, Su B, Meng FL, Chiarle R, Pan-Hammarström Q, Yeap LS. DNA repair mechanisms that promote insertion-deletion events during immunoglobulin gene diversification. Sci Immunol 2023; 8:eade1167. [PMID: 36961908 PMCID: PMC10351598 DOI: 10.1126/sciimmunol.ade1167] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 03/01/2023] [Indexed: 03/26/2023]
Abstract
Insertions and deletions (indels) are low-frequency deleterious genomic DNA alterations. Despite their rarity, indels are common, and insertions leading to long complementarity-determining region 3 (CDR3) are vital for antigen-binding functions in broadly neutralizing and polyreactive antibodies targeting viruses. Because of challenges in detecting indels, the mechanism that generates indels during immunoglobulin diversification processes remains poorly understood. We carried out ultra-deep profiling of indels and systematically dissected the underlying mechanisms using passenger-immunoglobulin mouse models. We found that activation-induced cytidine deaminase-dependent ±1-base pair (bp) indels are the most prevalent indel events, biasing deleterious outcomes, whereas longer in-frame indels, especially insertions that can extend the CDR3 length, are rare outcomes. The ±1-bp indels are channeled by base excision repair, but longer indels require additional DNA-processing factors. Ectopic expression of a DNA exonuclease or perturbation of the balance of DNA polymerases can increase the frequency of longer indels, thus paving the way for models that can generate antibodies with long CDR3. Our study reveals the mechanisms that generate beneficial and deleterious indels during the process of antibody somatic hypermutation and has implications in understanding the detrimental genomic alterations in various conditions, including tumorigenesis.
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Affiliation(s)
- Qian Hao
- 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
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Chuanzong Zhan
- 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
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Chaoyang Lian
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Simin Luo
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Wenyi Cao
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Binbin Wang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Xia Xie
- 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; 320 Yueyang Road, Shanghai 200031, China
| | - Xiaofei Ye
- Department of Biosciences and Nutrition, Karolinska Institutet; SE141-83, Huddinge, Stockholm, Sweden
- Present address: Kindstar Global Precision Medicine Institute, Wuhan, China and Kindstar Biotech, Wuhan, China
| | - Tuantuan Gui
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Claudia Voena
- Department of Molecular Biotechnology and Health Sciences, University of Torino; 10126 Torino, Italy
| | - Chiara Pighi
- Department of Molecular Biotechnology and Health Sciences, University of Torino; 10126 Torino, Italy
- Department of Pathology, Boston Children’s Hospital, and Harvard Medical School; Boston, MA 02115, USA
| | - Yanyan Wang
- 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; 320 Yueyang Road, Shanghai 200031, China
| | - Ying Tian
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Xin Wang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Pengfei Dai
- 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; 320 Yueyang Road, Shanghai 200031, China
| | - Yanni Cai
- 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; 320 Yueyang Road, Shanghai 200031, China
| | - Xiaojing Liu
- 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; 320 Yueyang Road, Shanghai 200031, China
| | - Shengqun Ouyang
- 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
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Shiqi Sun
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Qianwen Hu
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Jun Liu
- Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Youqiong Ye
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Jingkun Zhao
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Aiguo Lu
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Ji-Yang Wang
- Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
- Department of Microbiology and Immunology, College of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Chuanxin Huang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Bing Su
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Departments of Endocrinology and Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Jiao Tong University School of Medicine-Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai 200025
| | - 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; 320 Yueyang Road, Shanghai 200031, China
| | - Roberto Chiarle
- Department of Molecular Biotechnology and Health Sciences, University of Torino; 10126 Torino, Italy
- Department of Pathology, Boston Children’s Hospital, and Harvard Medical School; Boston, MA 02115, USA
| | - Qiang Pan-Hammarström
- Department of Biosciences and Nutrition, Karolinska Institutet; SE141-83, Huddinge, Stockholm, Sweden
| | - Leng-Siew Yeap
- 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
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
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3
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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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4
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In vitro evolution of antibody affinity via insertional scanning mutagenesis of an entire antibody variable region. Proc Natl Acad Sci U S A 2020; 117:27307-27318. [PMID: 33067389 DOI: 10.1073/pnas.2002954117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
We report a systematic combinatorial exploration of affinity enhancement of antibodies by insertions and deletions (InDels). Transposon-based introduction of InDels via the method TRIAD (transposition-based random insertion and deletion mutagenesis) was used to generate large libraries with random in-frame InDels across the entire single-chain variable fragment gene that were further recombined and screened by ribosome display. Knowledge of potential insertion points from TRIAD libraries formed the basis of exploration of length and sequence diversity of novel insertions by insertional-scanning mutagenesis (InScaM). An overall 256-fold affinity improvement of an anti-IL-13 antibody BAK1 as a result of InDel mutagenesis and combination with known point mutations validates this approach, and suggests that the results of this InDel mutagenesis and conventional exploration of point mutations can synergize to generate antibodies with higher affinity.
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5
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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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6
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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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7
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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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8
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Kaur H, Sain N, Mohanty D, Salunke DM. Deciphering evolution of immune recognition in antibodies. BMC STRUCTURAL BIOLOGY 2018; 18:19. [PMID: 30563492 PMCID: PMC6299584 DOI: 10.1186/s12900-018-0096-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 11/14/2018] [Indexed: 11/29/2022]
Abstract
Background Antibody, the primary effector molecule of the immune system, evolves after initial encounter with the antigen from a precursor form to a mature one to effectively deal with the antigen. Antibodies of a lineage diverge through antigen-directed isolated pathways of maturation to exhibit distinct recognition potential. In the context of evolution in immune recognition, diversity of antigen cannot be ignored. While there are reports on antibody lineage, structural perspective with respect to diverse recognition potential in a lineage has never been studied. Hence, it is crucial to evaluate how maturation leads to topological tailoring within a lineage enabling them to interact with significantly distinct antigens. Results A data-driven approach was undertaken for the study. Global experimental mouse and human antibody-antigen complex structures from PDB were compiled into a coherent database of germline-linked antibodies bound with distinct antigens. Structural analysis of all lineages showed variations in CDRs of both H and L chains. Observations of conformational adaptation made from analysis of static structures were further evaluated by characterizing dynamics of interaction in two lineages, mouse VH1–84 and human VH5–51. Sequence and structure analysis of the lineages explained that somatic mutations altered the geometries of individual antibodies with common structural constraints in some CDRs. Additionally, conformational landscape obtained from molecular dynamics simulations revealed that incoming pathogen led to further conformational divergence in the paratope (as observed across datasets) even while maintaining similar overall backbone topology. MM-GB/SA analysis showed binding energies to be in physiological range. Results of the study are coherent with experimental observations. Conclusions The findings of this study highlight basic structural principles shaping the molecular evolution of a lineage for significantly diverse antigens. Antibodies of a lineage follow different developmental pathways while preserving the imprint of the germline. From the study, it can be generalized that structural diversification of the paratope is an outcome of natural selection of a conformation from an available ensemble, which is further optimized for antigen interaction. The study establishes that starting from a common lineage, antibodies can mature to recognize a wide range of antigens. This hypothesis can be further tested and validated experimentally. Electronic supplementary material The online version of this article (10.1186/s12900-018-0096-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Harmeet Kaur
- Regional Centre for Biotechnology, Biotech Science Cluster, Faridabad, Haryana, 121001, India.,Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Neetu Sain
- National Institute of Immunology, New Delhi, Delhi, 110067, India
| | - Debasisa Mohanty
- National Institute of Immunology, New Delhi, Delhi, 110067, India
| | - Dinakar M Salunke
- Regional Centre for Biotechnology, Biotech Science Cluster, Faridabad, Haryana, 121001, India. .,International Centre for Genetic Engineering and Biotechnology, New Delhi, Delhi, 110067, India.
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9
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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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10
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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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11
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Bowers PM, Verdino P, Wang Z, da Silva Correia J, Chhoa M, Macondray G, Do M, Neben TY, Horlick RA, Stanfield RL, Wilson IA, King DJ. Nucleotide insertions and deletions complement point mutations to massively expand the diversity created by somatic hypermutation of antibodies. J Biol Chem 2014; 289:33557-67. [PMID: 25320089 DOI: 10.1074/jbc.m114.607176] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
During somatic hypermutation (SHM), deamination of cytidine by activation-induced cytidine deaminase and subsequent DNA repair generates mutations within immunoglobulin V-regions. Nucleotide insertions and deletions (indels) have recently been shown to be critical for the evolution of antibody binding. Affinity maturation of 53 antibodies using in vitro SHM in a non-B cell context was compared with mutation patterns observed for SHM in vivo. The origin and frequency of indels seen during in vitro maturation were similar to that in vivo. Indels are localized to CDRs, and secondary mutations within insertions further optimize antigen binding. Structural determination of an antibody matured in vitro and comparison with human-derived antibodies containing insertions reveal conserved patterns of antibody maturation. These findings indicate that activation-induced cytidine deaminase acting on V-region sequences is sufficient to initiate authentic formation of indels in vitro and in vivo and that point mutations, indel formation, and clonal selection form a robust tripartite system for antibody evolution.
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Affiliation(s)
| | - Petra Verdino
- From Anaptysbio Inc., San Diego, California 92121 and
| | | | | | - Mark Chhoa
- From Anaptysbio Inc., San Diego, California 92121 and
| | | | - Minjee Do
- From Anaptysbio Inc., San Diego, California 92121 and
| | | | | | - Robyn L Stanfield
- the Department of Integrative Structural and Computational Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037
| | - Ian A Wilson
- the Department of Integrative Structural and Computational Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037
| | - David J King
- From Anaptysbio Inc., San Diego, California 92121 and
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12
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Yu L, Guan Y. Immunologic Basis for Long HCDR3s in Broadly Neutralizing Antibodies Against HIV-1. Front Immunol 2014; 5:250. [PMID: 24917864 PMCID: PMC4040451 DOI: 10.3389/fimmu.2014.00250] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 05/12/2014] [Indexed: 01/18/2023] Open
Abstract
A large number of potent broadly neutralizing antibodies (bnAbs) against HIV-1 have been reported in recent years, raising hope for the possibility of an effective vaccine based on epitopes recognized by these protective antibodies. However, many of these bnAbs contain the long heavy chain complementarity-determining region 3 (HCDR3), which is viewed as an obstacle to the development of an HIV-1 vaccine targeting the bnAb responses. This mini-review summarizes the current literature and discusses the different potential immunologic mechanisms for generating long HCDR3, including D–D fusion, VH replacement, long N region addition, and skewed D–J gene usage, among which potential VH replacement products appear to be significant contributors. VH replacement occurs through recombinase activated gene-mediated secondary recombination and contributes to the diversified naïve B cell repertoire. During VH replacement, a short stretch of nucleotides from previously rearranged VH genes remains within the newly formed HCDR3, thus elongating its length. Accumulating evidence suggests that long HCDR3s are present in significant numbers in the human mature naïve B cell repertoire and are primarily generated by recombination during B cell development. These new observations indicate that long HCDR3s, though low in frequency, are a normal feature of the human antibody naïve repertoire and they appear to be selected to target conserved epitopes located in deep, partially obscured regions of the HIV-1 envelope trimer. Therefore, the presence of long HCDR3 sequences should not necessarily be viewed as an obstacle to the development of an HIV-1 vaccine based upon bnAb responses.
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Affiliation(s)
- Lei Yu
- Division of Basic Science and Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine , Baltimore, MD , USA
| | - Yongjun Guan
- Division of Basic Science and Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine , Baltimore, MD , USA ; Department of Microbiology and Immunology, University of Maryland School of Medicine , Baltimore, MD , USA
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13
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Briney BS, Jr. JEC. Secondary mechanisms of diversification in the human antibody repertoire. Front Immunol 2013; 4:42. [PMID: 23483107 PMCID: PMC3593266 DOI: 10.3389/fimmu.2013.00042] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 02/05/2013] [Indexed: 12/25/2022] Open
Abstract
V(D)J recombination and somatic hypermutation (SHM) are the primary mechanisms for diversification of the human antibody repertoire. These mechanisms allow for rapid humoral immune responses to a wide range of pathogenic challenges. V(D)J recombination efficiently generate a virtually limitless diversity through random recombination of variable (V), diversity (D), and joining (J) genes with diverse non-templated junctions between the selected gene segments. Following antigen stimulation, affinity maturation by SHM produces antibodies with refined specificity mediated by mutations typically focused in complementarity determining regions (CDRs), which form the bulk of the antigen recognition site. While V(D)J recombination and SHM are responsible for much of the diversity of the antibody repertoire, there are several secondary mechanisms that, while less frequent, make substantial contributions to antibody diversity including V(DD)J recombination (or D-D fusion), SHM-associated insertions and deletions, and affinity maturation and antigen contact by non-CDR regions of the antibody. In addition to enhanced diversity, these mechanisms allow the production of antibodies that are critical to response to a variety of viral and bacterial pathogens but that would be difficult to generate using only the primary mechanisms of diversification.
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Affiliation(s)
- Bryan S. Briney
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical CenterNashville, TN, USA
| | - James E. Crowe Jr.
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical CenterNashville, TN, USA
- Department of Pediatrics, Vanderbilt University Medical CenterNashville, TN, USA
- The Vanderbilt Vaccine Center, Vanderbilt University Medical CenterNashville, TN, USA
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14
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Alharbi KK, Khan IA, Abed ASA, Syed R. Insertion/Deletion polymorphisms do play any role in G6PD deficiency individuals in the Kingdom of the Saudi Arabia. Bioinformation 2013; 9:49-53. [PMID: 23390344 PMCID: PMC3563416 DOI: 10.6026/97320630009049] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 12/04/2012] [Indexed: 11/23/2022] Open
Abstract
Glucose-6-phosphate dehydrogenase (G6PD) is an enzyme in the pentose phosphate pathway (PPP) that plays an important role in protecting cells from oxidative damage by producing NADPH and reduced glutathione. G6PD deficiency is considered one of the most common genetic disorders present in the X chromosome and is the most common of enzymopathic red blood cell disorder. Angiotensin converting enzyme (ACE) plays an essential role in two physiological systems, one leading to the production of angiotensin II and the other to the degradation of bradykinin. Most studies focused on an insertion/deletion (I/D) polymorphism in intron 16 of the ACE gene as a marker for a functional polymorphism. The α(2B)-adrenergic receptor gene (α(2B)AR) is a three-amino acid deletion (12Glu9) polymorphism is located on chromosome 2. (Glu(9)/Glu(9)) of this polymorphism has been first time studies in G6PD individuals. We have selected 39 G6PD deficiency male individuals and PCR was carried out with the I/D polymorphisms. ACE I/D polymorphism study was carried out in G6PD individuals and showed strong association with DD genotypes and D alleles OR=39.38, p<0.0001 (95% CI=8.80-176.1) and OR=38.58, p<0.0001 (95% CI=13.21-112.6). Another gene of α(2B)AR I/D polymorphism study cannot show any association in DD genotype OR-0.6882,p=0.9388 (95% CI=0.2035-2.327) and with D allele OR-0.9614,p=0.9388 (95% CI=0.3482-2.653). Our study shows that G6PD deficiency is showing strong association in DD genotype and D allele of ACE gene and α(2B)AR gene have not shown any important role and one of the reason could be the low sample size.
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Affiliation(s)
- Khalid K Alharbi
- Clinical Laboratory Sciences Department, College of Applied Medical Sciences, King Saud University, P.O. Box 10219, Riyadh 11433, Kingdom of Saudi Arabia
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15
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Location and length distribution of somatic hypermutation-associated DNA insertions and deletions reveals regions of antibody structural plasticity. Genes Immun 2012; 13:523-9. [PMID: 22717702 PMCID: PMC3449029 DOI: 10.1038/gene.2012.28] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Following the initial diversity generated by V(D)J recombination, somatic hypermutation is the principal mechanism for producing further antibody repertoire diversity in antigen-experienced B cells. While somatic hypermutation typically results in single nucleotide substitutions, the infrequent incorporation of genetic insertions and deletions has also been associated with the somatic hypermutation process. We used high throughput antibody sequencing to determine the sequence of thousands of antibody genes containing somatic hypermutation-associated insertions and deletions (SHA indels), which revealed significant differences between the location of SHA indels and somatic mutations. Further, we identified a cluster of insertions and deletions in the antibody framework 3 region which corresponds to the hypervariable region 4 (HV4) in T cell receptors. We propose that this HV4-like region, identified by SHA indel analysis, represents a region of under-appreciated affinity maturation potential. Finally, through analysis of both location and length distribution of SHA indels, we have determined regions of structural plasticity within the antibody protein.
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16
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Human peripheral blood antibodies with long HCDR3s are established primarily at original recombination using a limited subset of germline genes. PLoS One 2012; 7:e36750. [PMID: 22590602 PMCID: PMC3348910 DOI: 10.1371/journal.pone.0036750] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Accepted: 04/07/2012] [Indexed: 12/27/2022] Open
Abstract
A number of antibodies that efficiently neutralize microbial targets contain long heavy chain complementarity determining region 3 (HCDR3) loops. For HIV, several of the most broad and potently neutralizing antibodies have exceptionally long HCDR3s. Two broad potently neutralizing HIV-specific antibodies, PG9 and PG16, exhibit secondary structure. Two other long HCDR3 antibodies, 2F5 and 4E10, protect against mucosal challenge with SHIV. Induction of such long HCDR3 antibodies may be critical to the design of an effective vaccine strategy for HIV and other pathogens, however it is unclear at present how to induce such antibodies. Here, we present genetic evidence that human peripheral blood antibodies containing long HCDR3s are not primarily generated by insertions introduced during the somatic hypermutation process. Instead, they are typically formed by processes occurring as part of the original recombination event. Thus, the response of B cells encoding antibodies with long HCDR3s results from selection of unusual clones from the naïve repertoire rather than through accumulation of insertions. These antibodies typically use a small subset of D and J gene segments that are particularly suited to encoding long HCDR3s, resulting in the incorporation of highly conserved genetic elements in the majority of antibody sequences encoding long HCDR3s.
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17
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Coupling mammalian cell surface display with somatic hypermutation for the discovery and maturation of human antibodies. Proc Natl Acad Sci U S A 2011; 108:20455-60. [PMID: 22158898 DOI: 10.1073/pnas.1114010108] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel approach has been developed for the isolation and maturation of human antibodies that replicates key features of the adaptive immune system by coupling in vitro somatic hypermutation (SHM) with mammalian cell display. SHM is dependent on the action of the B cell specific enzyme, activation-induced cytidine deaminase (AID), and can be replicated in non-B cells through expression of recombinant AID. A library of human antibodies, based on germline V-gene segments with recombined human regions was used to isolate low-affinity antibodies to human β nerve growth factor (hβNGF). These antibodies, initially naïve to SHM, were subjected to AID-directed SHM in vitro and selected using the same mammalian cell display system, as illustrated by the maturation of one of the antibodies to low pM K(D). This approach overcomes many of the previous limitations of mammalian cell display, enabling direct selection and maturation of antibodies as full-length, glycosylated IgGs.
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18
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Mechanism of lethal toxin neutralization by a human monoclonal antibody specific for the PA(20) region of Bacillus anthracis protective antigen. Toxins (Basel) 2011; 3:979-90. [PMID: 22069752 PMCID: PMC3202870 DOI: 10.3390/toxins3080979] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Revised: 07/07/2011] [Accepted: 08/04/2011] [Indexed: 11/17/2022] Open
Abstract
The primary immunogenic component of the currently approved anthrax vaccine is the protective antigen (PA) unit of the binary toxin system. PA-specific antibodies neutralize anthrax toxins and protect against infection. Recent research has determined that in humans, only antibodies specific for particular determinants are capable of effecting toxin neutralization, and that the neutralizing epitopes recognized by these antibodies are distributed throughout the PA monomer. The mechanisms by which the majority of these epitopes effect neutralization remain unknown. In this report we investigate the process by which a human monoclonal antibody specific for the amino-terminal domain of PA neutralizes lethal toxin in an in vitro assay of cytotoxicity, and find that it neutralizes LT by blocking the requisite cleavage of the amino-terminal 20 kD portion of the molecule (PA20) from the remainder of the PA monomer. We also demonstrate that the epitope recognized by this human monoclonal does not encompass the 166RKKR169 furin recognition sequence in domain 1 of PA.
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19
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Domain specificity of the human antibody response to Bacillus anthracis protective antigen. Vaccine 2008; 26:4041-7. [PMID: 18565627 DOI: 10.1016/j.vaccine.2008.05.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2008] [Revised: 05/01/2008] [Accepted: 05/09/2008] [Indexed: 11/22/2022]
Abstract
Protective antigen (PA) is the cell surface recognition moiety of the Bacillus anthracis A-B toxin system, and the active immunogenic component in the currently licensed human anthrax vaccine (BioThrax, or AVA). The serum antibody response to the PA protein is polyclonal and complex both in terms of the antibody combining sites utilized to bind PA and the PA-associated epitopes recognized. We have cloned, sequenced, and expressed a large panel of PA-specific human monoclonal antibodies from seven AVA-immunized donors. Dot blots, Western blots, and radiolabeled antigen capture assays employing both proteolytic fragments of PA and engineered PA sub-domain fusion proteins were used to determine the region (domain) of the PA monomer to which each of the cloned human antibodies bound. The domain specificity of the isolated monoclonals was highly biased towards the amino-terminal 20kDa fragment of PA (PA(20)), with the majority (62%) of independently arising antibody clones reacting with determinants located on this PA fragment. A similar bias in domain specificity was also demonstrated in the serum response of AVA-vaccinated donors. Since PA(20) is cleaved from the remainder of the monomer rapidly following cell surface binding and has no known role in the intoxication process, the immunodominance of PA(20)-associated epitopes may directly affect the efficacy of PA-based anthrax vaccines.
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20
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Zhou J, Ullal A, Liberato J, Sun J, Keitel W, Reason DC. Paratope diversity in the human antibody response to Bacillus anthracis protective antigen. Mol Immunol 2007; 45:338-47. [PMID: 17707509 PMCID: PMC2063455 DOI: 10.1016/j.molimm.2007.06.159] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2007] [Revised: 06/11/2007] [Accepted: 06/17/2007] [Indexed: 11/15/2022]
Abstract
The active component of the licensed human anthrax vaccine (BioThrax, or AVA) is a Bacillus anthracis toxin known as protective antigen (PA). Second generation anthrax vaccines currently under development are also based on a recombinant form of PA. Since the current and future anthrax vaccines are based on this toxin, it is important that the immunobiology of this protein in vaccinated humans be understood in detail. We have isolated and analyzed the PA-specific antibody repertoire from an AVA-vaccinated individual. When examined at the clonal level, we find an antibody response that is complex in terms of the combinatorial elements and immunoglobulin variable genes employed. All PA-specific antibodies had undergone somatic hypermutation and class switch recombination, both signs of affinity maturation. Although the antigenic epitopes recognized by the response were distributed throughout the PA monomer, the majority of antibodies arising in this individual following vaccination recognize determinants located on the amino-terminal (PA20) sub-domain of the molecule. This latter finding may have implications for the rational design of future PA-based anthrax vaccines.
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Affiliation(s)
- Jianhui Zhou
- Children's Hospital Oakland Research Institute, 5700 Martin Luther King Jr. Way, Oakland, CA 94609, USA
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