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Zhang Q, Zhang L, Zhou C, Yang Y, Yin Z, Wu D, Tang K, Cao Z. DSab-origin: a novel IGHD sensitive VDJ mapping method and its application on antibody response after influenza vaccination. BMC Bioinformatics 2019; 20:137. [PMID: 30871465 PMCID: PMC6417009 DOI: 10.1186/s12859-019-2715-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 03/06/2019] [Indexed: 12/04/2022] Open
Abstract
Background Functional antibody genes are often assembled by VDJ recombination and then diversified by somatic hypermutation. Identifying the combination of sourcing germline genes is critical to understand the process of antibody maturation, which may facilitate the diagnostics and rapid generation of human monoclonal antibodies in therapeutics. Despite of successful efforts in V and J fragment assignment, method in D segment tracing remains weak for immunoglobulin heavy diversity (IGHD). Results In this paper, we presented a D-sensitive mapping method called DSab-origin with accuracies around 90% in human monoclonal antibody data and average 95.8% in mouse data. Besides, DSab-origin achieved the best performance in holistic prediction of VDJ segments assignment comparing with other methods commonly used in simulation data. After that, an application example was explored on the antibody response based on a time-series antibody sequencing data after influenza vaccination. The result indicated that, despite the personal response among different donors, IGHV3–7 and IGHD4–17 were likely to be dominated gene segments in these three donors. Conclusions This work filled in a computational gap in D segment assignment for VDJ germline gene identification in antibody research. And it offered an application example of DSab-origin for studying the antibody maturation process after influenza vaccination. Electronic supplementary material The online version of this article (10.1186/s12859-019-2715-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Qingchen Zhang
- Shanghai 10th people's hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, People's Republic of China
| | - Lu Zhang
- Shanghai 10th people's hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, People's Republic of China
| | - Chen Zhou
- Shanghai 10th people's hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, People's Republic of China
| | - Yiyan Yang
- Shanghai 10th people's hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, People's Republic of China
| | - Zuojing Yin
- Shanghai 10th people's hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, People's Republic of China
| | - Dingfeng Wu
- Shanghai 10th people's hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, People's Republic of China
| | - Kailin Tang
- Shanghai 10th people's hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, People's Republic of China
| | - Zhiwei Cao
- Shanghai 10th people's hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, People's Republic of China.
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2
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Giesecke C, Meyer T, Durek P, Maul J, Preiß J, Jacobs JFM, Thiel A, Radbruch A, Ullrich R, Dörner T. Simultaneous Presence of Non- and Highly Mutated Keyhole Limpet Hemocyanin (KLH)-Specific Plasmablasts Early after Primary KLH Immunization Suggests Cross-Reactive Memory B Cell Activation. THE JOURNAL OF IMMUNOLOGY 2018; 200:3981-3992. [DOI: 10.4049/jimmunol.1701728] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 04/13/2018] [Indexed: 12/25/2022]
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Abstract
Somatic assembly of T cell receptor and B cell receptor (BCR) genes produces a vast diversity of lymphocyte antigen recognition capacity. The advent of efficient high-throughput sequencing of lymphocyte antigen receptor genes has recently generated unprecedented opportunities for exploration of adaptive immune responses. With these opportunities have come significant challenges in understanding the analysis techniques that most accurately reflect underlying biological phenomena. In this regard, sample preparation and sequence analysis techniques, which have largely been borrowed and adapted from other fields, continue to evolve. Here, we review current methods and challenges of library preparation, sequencing and statistical analysis of lymphocyte receptor repertoire studies. We discuss the general steps in the process of immune repertoire generation including sample preparation, platforms available for sequencing, processing of sequencing data, measurable features of the immune repertoire, and the statistical tools that can be used for analysis and interpretation of the data. Because BCR analysis harbors additional complexities, such as immunoglobulin (Ig) (i.e., antibody) gene somatic hypermutation and class switch recombination, the emphasis of this review is on Ig/BCR sequence analysis.
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Affiliation(s)
- Neha Chaudhary
- Division of Rheumatology, Department of Medicine, Immunology and Allergy, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Duane R. Wesemann
- Division of Rheumatology, Department of Medicine, Immunology and Allergy, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
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4
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Fu X, Sun J, Tan E, Shimizu K, Reza MS, Watabe S, Asakawa S. High-Throughput Sequencing of the Expressed Torafugu ( Takifugu rubripes) Antibody Sequences Distinguishes IgM and IgT Repertoires and Reveals Evidence of Convergent Evolution. Front Immunol 2018. [PMID: 29515575 PMCID: PMC5826340 DOI: 10.3389/fimmu.2018.00251] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
B-cell antigen receptor (BCR) or antibody diversity arises from somatic recombination of immunoglobulin (Ig) gene segments and is concentrated within the Ig heavy (H) chain complementarity-determining region 3 (CDR-H3). We performed high-throughput sequencing of the expressed antibody heavy-chain repertoire from adult torafugu. We found that torafugu use between 70 and 82% of all possible V (variable), D (diversity), and J (joining) gene segment combinations and that they share a similar frequency distribution of these VDJ combinations. The CDR-H3 sequence repertoire observed in individuals is biased with the preferential use of a small number of VDJ, dominated by sequences containing inserted nucleotides. We uncovered the common CDR-H3 amino-acid (aa) sequences shared by individuals. Common CDR-H3 sequences feature highly convergent nucleic-acid recombination compared with private ones. Finally, we observed differences in repertoires between IgM and IgT, including the unequal usage frequencies of V gene segment and the biased number of nucleotide insertion/deletion at VDJ junction regions that leads to distinct distributions of CDR-H3 lengths.
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Affiliation(s)
- Xi Fu
- State Key Laboratory of Biotherapy, West China Hospital, Collaborative Innovation Center and Sichuan University, Chengdu, China.,Laboratory of Aquatic Molecular Biology and Biotechnology, Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Jianqiang Sun
- Bioinformational Engineering Laboratory, Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Engkong Tan
- Laboratory of Aquatic Molecular Biology and Biotechnology, Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Kentaro Shimizu
- Bioinformational Engineering Laboratory, Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Md Shaheed Reza
- School of Marine Biosciences, Kitasato University, Kanagawa, Japan.,Department of Fisheries Technology, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Shugo Watabe
- School of Marine Biosciences, Kitasato University, Kanagawa, Japan
| | - Shuichi Asakawa
- Laboratory of Aquatic Molecular Biology and Biotechnology, Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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5
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Abstract
Next-generation sequencing is making it possible to study the antibody repertoire of an organism in unprecedented detail, and, by so doing, to characterize its behavior in the response to infection and in pathological conditions such as autoimmunity and cancer. The polymorphic nature of the repertoire poses unique challenges that rule out the use of many commonly used NGS methods and require tradeoffs to be made when considering experimental design.We outline the main contexts in which antibody repertoire analysis has been used, and summarize the key tools that are available. The humoral immune response to vaccination has been a particular focus of repertoire analyses, and we review the key conclusions and methods used in these studies.
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Affiliation(s)
- William D Lees
- Department of Biological Sciences and Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet Street, London, WC1E 7HX, UK
| | - Adrian J Shepherd
- Department of Biological Sciences and Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet Street, London, WC1E 7HX, UK.
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6
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HashClone: a new tool to quantify the minimal residual disease in B-cell lymphoma from deep sequencing data. BMC Bioinformatics 2017; 18:516. [PMID: 29169317 PMCID: PMC5701356 DOI: 10.1186/s12859-017-1923-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 11/06/2017] [Indexed: 01/27/2023] Open
Abstract
Background Mantle Cell Lymphoma (MCL) is a B cell aggressive neoplasia accounting for about the 6% of all lymphomas. The most common molecular marker of clonality in MCL, as in other B lymphoproliferative disorders, is the ImmunoGlobulin Heavy chain (IGH) rearrangement, occurring in B-lymphocytes. The patient-specific IGH rearrangement is extensively used to monitor the Minimal Residual Disease (MRD) after treatment through the standardized Allele-Specific Oligonucleotides Quantitative Polymerase Chain Reaction based technique. Recently, several studies have suggested that the IGH monitoring through deep sequencing techniques can produce not only comparable results to Polymerase Chain Reaction-based methods, but also might overcome the classical technique in terms of feasibility and sensitivity. However, no standard bioinformatics tool is available at the moment for data analysis in this context. Results In this paper we present HashClone, an easy-to-use and reliable bioinformatics tool that provides B-cells clonality assessment and MRD monitoring over time analyzing data from Next-Generation Sequencing (NGS) technique. The HashClone strategy-based is composed of three steps: the first and second steps implement an alignment-free prediction method that identifies a set of putative clones belonging to the repertoire of the patient under study. In the third step the IGH variable region, diversity region, and joining region identification is obtained by the alignment of rearrangements with respect to the international ImMunoGenetics information system database. Moreover, a provided graphical user interface for HashClone execution and clonality visualization over time facilitate the tool use and the results interpretation. The HashClone performance was tested on the NGS data derived from MCL patients to assess the major B-cell clone in the diagnostic samples and to monitor the MRD in the real and artificial follow up samples. Conclusions Our experiments show that in all the experimental settings, HashClone was able to correctly detect the major B-cell clones and to precisely follow them in several samples showing better accuracy than the state-of-art tool. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1923-2) contains supplementary material, which is available to authorized users.
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7
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Shi J, Darrah E, Sims GP, Mustelin T, Sampson K, Konig MF, Bingham CO, Rosen A, Andrade F. Affinity maturation shapes the function of agonistic antibodies to peptidylarginine deiminase type 4 in rheumatoid arthritis. Ann Rheum Dis 2017; 77:141-148. [PMID: 29070531 DOI: 10.1136/annrheumdis-2017-211489] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 09/08/2017] [Accepted: 09/09/2017] [Indexed: 12/28/2022]
Abstract
OBJECTIVES The citrullinating enzyme peptidylarginine deiminase type 4 (PAD4) is the target of a polyclonal group of autoantibodies in patients with rheumatoid arthritis (RA). A subgroup of such antibodies, initially identified by cross-reactivity with peptidylarginine deiminase type 3 (PAD3), is strongly associated with progression of radiographic joint damage and interstitial lung disease and has the unique ability to activate PAD4. The features of these antibodies in terms of their T cell-dependent origin, genetic characteristics and effect of individual antibody specificities on PAD4 function remain to be defined. METHODS We used PAD4 tagged with the monomeric fluorescent protein mWasabi to isolate PAD4-specific memory B cells from anti-PAD4 positive patients with RA and applied single cell cloning technologies to obtain monoclonal antibodies. RESULTS Among 44 single B cells, we cloned five antibodies with PAD4-activating properties. Sequence analysis, germline reversion experiments and antigen specificity assays suggested that autoantibodies to PAD4 are not polyreactive and arise from PAD4-reactive precursors. Somatic mutations increase the agonistic activity of these antibodies at low calcium concentrations by facilitating their interaction with structural epitopes that modulate calcium-binding site 5 in PAD4. CONCLUSIONS PAD4-activating antibodies directly amplify a key process in disease pathogenesis, making them unique among other autoantibodies in RA. Understanding the molecular basis for their functionality may inform the design of future PAD4 inhibitors.
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Affiliation(s)
- Jing Shi
- Division of Rheumatology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Erika Darrah
- Division of Rheumatology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Gary P Sims
- Respiratory, Inflammation, and Autoimmunity, MedImmune LLC, Gaithersburg, Maryland, USA
| | - Tomas Mustelin
- Respiratory, Inflammation, and Autoimmunity, MedImmune LLC, Gaithersburg, Maryland, USA
| | - Kevon Sampson
- Division of Rheumatology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Maximilian F Konig
- Division of Rheumatology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Clifton O Bingham
- Division of Rheumatology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Antony Rosen
- Division of Rheumatology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Felipe Andrade
- Division of Rheumatology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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8
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Moore PL, Gorman J, Doria-Rose NA, Morris L. Ontogeny-based immunogens for the induction of V2-directed HIV broadly neutralizing antibodies. Immunol Rev 2017; 275:217-229. [PMID: 28133797 PMCID: PMC5300058 DOI: 10.1111/imr.12501] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The development of a preventative HIV vaccine able to elicit broadly neutralizing antibodies (bNAbs) remains a major challenge. Antibodies that recognize the V2 region at the apex of the HIV envelope trimer are among the most common bNAb specificities during chronic infection and many exhibit remarkable breadth and potency. Understanding the developmental pathway of these antibodies has provided insights into their precursors, and the viral strains that engage them, as well as defined how such antibodies mature to acquire breadth. V2‐apex bNAbs are derived from rare precursors with long anionic CDR H3s that are often deleted in the B cell repertoire. However, longitudinal studies suggest that once engaged, these precursors contain many of the structural elements required for neutralization, and can rapidly acquire breadth through moderate levels of somatic hypermutation in response to emerging viral variants. These commonalities in the precursors and mechanism of neutralization have enabled the identification of viral strains that show enhanced reactivity for V2 precursors from multiple donors, and may form the basis of germline targeting approaches. In parallel, new structural insights into the HIV trimer, the target of these quaternary antibodies, has created invaluable new opportunities for ontogeny‐based immunogens designed to select for rare V2‐bNAb precursors, and drive them toward breadth.
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Affiliation(s)
- Penny L Moore
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.,Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Jason Gorman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Nicole A Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Lynn Morris
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.,Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
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9
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Henderson LA, Volpi S, Frugoni F, Janssen E, Kim S, Sundel RP, Dedeoglu F, Lo MS, Hazen MM, Beth Son M, Mathieu R, Zurakowski D, Yu N, Lebedeva T, Fuhlbrigge RC, Walter JE, Nee Lee Y, Nigrovic PA, Notarangelo LD. Next-Generation Sequencing Reveals Restriction and Clonotypic Expansion of Treg Cells in Juvenile Idiopathic Arthritis. Arthritis Rheumatol 2017; 68:1758-68. [PMID: 26815131 DOI: 10.1002/art.39606] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 01/19/2016] [Indexed: 01/12/2023]
Abstract
OBJECTIVE Treg cell-mediated suppression of Teff cells is impaired in juvenile idiopathic arthritis (JIA); however, the basis for this dysfunction is incompletely understood. Animal models of autoimmunity and immunodeficiency demonstrate that a diverse Treg cell repertoire is essential to maintain Treg cell function. The present study was undertaken to investigate the Treg and Teff cell repertoires in JIA. METHODS Treg cells (CD4+CD25+CD127(low) ) and Teff cells (CD4+CD25-) were isolated from peripheral blood and synovial fluid obtained from JIA patients, healthy controls, and children with Lyme arthritis. Treg cell function was measured in suppressive assays. The T cell receptor β chain (TRB) was amplified by multiplex polymerase chain reaction and next-generation sequencing was performed, with amplicons sequenced using an Illumina HiSeq platform. Data were analyzed using ImmunoSEQ, International ImMunoGeneTics system, and the Immunoglobulin Analysis Tools. RESULTS Compared to findings in controls, the JIA peripheral blood Treg cell repertoire was restricted, and clonotypic expansions were found in both blood and synovial fluid Treg cells. Skewed usage and pairing of TRB variable and joining genes, including overuse of gene segments that have been associated with other autoimmune conditions, was observed. JIA patients shared a substantial portion of synovial fluid Treg cell clonotypes that were private to JIA and not identified in Lyme arthritis. CONCLUSION We identified restriction and clonotypic expansions in the JIA Treg cell repertoire with sharing of Treg cell clonotypes across patients. These findings suggest that abnormalities in the Treg cell repertoire, possibly engendered by shared antigenic triggers, may contribute to disease pathogenesis in JIA.
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Affiliation(s)
| | | | | | - Erin Janssen
- Boston Children's Hospital, Boston, Massachusetts
| | - Susan Kim
- Boston Children's Hospital, Boston, Massachusetts
| | | | | | - Mindy S Lo
- Boston Children's Hospital, Boston, Massachusetts
| | | | | | | | | | - Neng Yu
- American Red Cross Blood Services-East Division, New England HLA Services, Dedham, Massachusetts
| | - Tatiana Lebedeva
- American Red Cross Blood Services-East Division, New England HLA Services, Dedham, Massachusetts
| | - Robert C Fuhlbrigge
- Boston Children's Hospital and Brigham and Women's Hospital, Boston, Massachusetts
| | - Jolan E Walter
- Boston Children's Hospital and Massachusetts General Hospital for Children, Boston, Massachusetts
| | - Yu Nee Lee
- Boston Children's Hospital, Boston, Massachusetts
| | - Peter A Nigrovic
- Boston Children's Hospital and Brigham and Women's Hospital, Boston, Massachusetts
| | - Luigi D Notarangelo
- Boston Children's Hospital, Harvard Medical School, and Harvard Stem Cell Institute, Boston, Massachusetts
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10
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Longo NS, Rogosch T, Zemlin M, Zouali M, Lipsky PE. Mechanisms That Shape Human Antibody Repertoire Development in Mice Transgenic for Human Ig H and L Chain Loci. THE JOURNAL OF IMMUNOLOGY 2017; 198:3963-3977. [PMID: 28438896 DOI: 10.4049/jimmunol.1700133] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 03/17/2017] [Indexed: 02/03/2023]
Abstract
To determine the impact of the milieu on the development of the human B cell repertoire, we carried out a comprehensive analysis of productive and nonproductive Ig gene rearrangements from transgenic mice engineered to express single copies of the unrearranged human H chain and L chain Ig gene loci. By examining the nonproductive repertoire as an indication of the immediate product of the rearrangement machinery without an impact of selection, we discovered that the distribution of human rearrangements arising in the mouse was generally comparable to that seen in humans. However, differences between the distribution of nonproductive and productive rearrangements that reflect the impact of selection suggested species-specific selection played a role in shaping the respective repertoires. Although expression of some VH genes was similar in mouse and human (IGHV3-23, IGHV3-30, and IGHV4-59), other genes behaved differently (IGHV3-33, IGHV3-48, IGHV4-31, IGHV4-34, and IGHV1-18). Gene selection differences were also noted in L chains. Notably, nonproductive human VH rearrangements in the transgenic mice expressed shorter CDRH3 with less N addition. Even the CDRH3s in the productive rearrangements were shorter in length than those of the normal human productive repertoire. Amino acids in the CDRH3s in both species showed positive selection of tyrosines and glycines, and negative selection of leucines. The data indicate that the environment in which B cells develop can affect the expressed Ig repertoire by exerting influences on the distribution of expressed VH and VL genes and by influencing the amino acid composition of the Ag binding site.
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Affiliation(s)
- Nancy S Longo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Tobias Rogosch
- Pediatric Immunology and Allergology, Department of Pediatrics, Philipps-University Marburg, D-35033 Marburg, Germany
| | - Michael Zemlin
- Klinik für Kinder-und Jugendmedizin, Universitätsklinikum Gießen und Marburg GmbH, Standort Marburg, D-35033 Marburg, Germany.,Department of General Pediatrics and Neonatology, Saarland University Medical School, D-66421 Homburg, Germany
| | - Moncef Zouali
- INSERM & Université Paris Diderot, Sorbonne Paris Cité Centre Viggo Petersen, Hôpital Lariboisière, 75475 Paris, France; and
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11
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Lee DW, Khavrutskii IV, Wallqvist A, Bavari S, Cooper CL, Chaudhury S. BRILIA: Integrated Tool for High-Throughput Annotation and Lineage Tree Assembly of B-Cell Repertoires. Front Immunol 2017; 7:681. [PMID: 28144239 PMCID: PMC5239784 DOI: 10.3389/fimmu.2016.00681] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 12/21/2016] [Indexed: 11/13/2022] Open
Abstract
The somatic diversity of antigen-recognizing B-cell receptors (BCRs) arises from Variable (V), Diversity (D), and Joining (J) (VDJ) recombination and somatic hypermutation (SHM) during B-cell development and affinity maturation. The VDJ junction of the BCR heavy chain forms the highly variable complementarity determining region 3 (CDR3), which plays a critical role in antigen specificity and binding affinity. Tracking the selection and mutation of the CDR3 can be useful in characterizing humoral responses to infection and vaccination. Although tens to hundreds of thousands of unique BCR genes within an expressed B-cell repertoire can now be resolved with high-throughput sequencing, tracking SHMs is still challenging because existing annotation methods are often limited by poor annotation coverage, inconsistent SHM identification across the VDJ junction, or lack of B-cell lineage data. Here, we present B-cell repertoire inductive lineage and immunosequence annotator (BRILIA), an algorithm that leverages repertoire-wide sequencing data to globally improve the VDJ annotation coverage, lineage tree assembly, and SHM identification. On benchmark tests against simulated human and mouse BCR repertoires, BRILIA correctly annotated germline and clonally expanded sequences with 94 and 70% accuracy, respectively, and it has a 90% SHM-positive prediction rate in the CDR3 of heavily mutated sequences; these are substantial improvements over existing methods. We used BRILIA to process BCR sequences obtained from splenic germinal center B cells extracted from C57BL/6 mice. BRILIA returned robust B-cell lineage trees and yielded SHM patterns that are consistent across the VDJ junction and agree with known biological mechanisms of SHM. By contrast, existing BCR annotation tools, which do not account for repertoire-wide clonal relationships, systematically underestimated both the size of clonally related B-cell clusters and yielded inconsistent SHM frequencies. We demonstrate BRILIA’s utility in B-cell repertoire studies related to VDJ gene usage, mechanisms for adenosine mutations, and SHM hot spot motifs. Furthermore, we show that the complete gene usage annotation and SHM identification across the entire CDR3 are essential for studying the B-cell affinity maturation process through immunosequencing methods.
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Affiliation(s)
- Donald W Lee
- Biotechnology HPC Software Applications Institute (BHSAI), Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command , Fort Detrick, MD , USA
| | - Ilja V Khavrutskii
- Biotechnology HPC Software Applications Institute (BHSAI), Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command , Fort Detrick, MD , USA
| | - Anders Wallqvist
- Biotechnology HPC Software Applications Institute (BHSAI), Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command , Fort Detrick, MD , USA
| | - Sina Bavari
- Molecular and Translational Sciences, U.S. Army Medical Research Institute of Infectious Diseases , Frederick, MD , USA
| | - Christopher L Cooper
- Molecular and Translational Sciences, U.S. Army Medical Research Institute of Infectious Diseases , Frederick, MD , USA
| | - Sidhartha Chaudhury
- Biotechnology HPC Software Applications Institute (BHSAI), Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command , Fort Detrick, MD , USA
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12
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Multiple Antibody Lineages in One Donor Target the Glycan-V3 Supersite of the HIV-1 Envelope Glycoprotein and Display a Preference for Quaternary Binding. J Virol 2016; 90:10574-10586. [PMID: 27654288 DOI: 10.1128/jvi.01012-16] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 08/31/2016] [Indexed: 11/20/2022] Open
Abstract
One of the goals of HIV-1 vaccine development is the elicitation of neutralizing antibodies against vulnerable regions on the envelope glycoprotein (Env) viral spike. Broadly neutralizing antibodies targeting the Env glycan-V3 region (also called the N332 glycan supersite) have been described previously, with several single lineages each derived from different individual donors. We used a high-throughput B-cell culture method to isolate neutralizing antibodies from an HIV-1-infected donor with high serum neutralization breadth. Clonal relatives from three distinct antibody lineages were isolated. Each of these antibody lineages displayed modest breadth and potency but shared several characteristics with the well-characterized glycan-V3 antibodies, including dependence on glycans N332 and N301, VH4 family gene utilization, a heavy chain complementarity-determining region 2 (CDRH2) insertion, and a longer-than-average CDRH3. In contrast to previously described glycan-V3 antibodies, these antibodies preferentially recognized the native Env trimer compared to monomeric gp120. These data indicate the diversity of antibody specificities that target the glycan-V3 site. The quaternary binding preference of these antibodies suggests that that their elicitation likely requires the presentation of a native-like trimeric Env immunogen. IMPORTANCE Broadly neutralizing antibodies targeting the HIV-1 glycan-V3 region with single lineages from individual donors have been described previously. Here we describe three lineages from a single donor, each of which targets glycan-V3. Unlike previously described glycan-V3 antibodies, these mature antibodies bind preferentially to the native Env trimer and weakly to the gp120 monomer. These data extend our knowledge of the immune response recognition of the N332 supersite region and suggest that the mode of epitope recognition is more complex than previously anticipated.
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13
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Walther S, Tietze M, Czerny CP, König S, Diesterbeck US. Development of a Bioinformatics Framework for the Detection of Gene Conversion and the Analysis of Combinatorial Diversity in Immunoglobulin Heavy Chains in Four Cattle Breeds. PLoS One 2016; 11:e0164567. [PMID: 27828971 PMCID: PMC5102495 DOI: 10.1371/journal.pone.0164567] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 09/06/2016] [Indexed: 02/06/2023] Open
Abstract
We have developed a new bioinformatics framework for the analysis of rearranged bovine heavy chain immunoglobulin (Ig) variable regions by combining and refining widely used alignment algorithms. This bioinformatics framework allowed us to investigate alignments of heavy chain framework regions (FRHs) and the separate alignments of FRHs and heavy chain complementarity determining regions (CDRHs) to determine their germline origin in the four cattle breeds Aubrac, German Black Pied, German Simmental, and Holstein Friesian. Now it is also possible to specifically analyze Ig heavy chains possessing exceptionally long CDR3Hs. In order to gain more insight into breed specific differences in Ig combinatorial diversity, somatic hypermutations and putative gene conversions of IgG, we compared the dominantly transcribed variable (IGHV), diversity (IGHD), and joining (IGHJ) segments and their recombination in the four cattle breeds. The analysis revealed the use of 15 different IGHV segments, 21 IGHD segments, and two IGHJ segments with significant different transcription levels within the breeds. Furthermore, there are preferred rearrangements within the three groups of CDR3H lengths. In the sequences of group 2 (CDR3H lengths (L) of 11–47 amino acid residues (aa)) a higher number of recombination was observed than in sequences of group 1 (L≤10 aa) and 3 (L≥48 aa). The combinatorial diversity of germline IGHV, IGHD, and IGHJ-segments revealed 162 rearrangements that were significantly different. The few preferably rearranged gene segments within group 3 CDR3H regions may indicate specialized antibodies because this length is unique in cattle. The most important finding of this study, which was enabled by using the bioinformatics framework, is the discovery of strong evidence for gene conversion as a rare event using pseudogenes fulfilling all definitions for this particular diversification mechanism.
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Affiliation(s)
- Stefanie Walther
- Department of Animal Sciences, Institute of Veterinary Medicine, Division of Microbiology and Animal Hygiene, Faculty of Agricultural Sciences, Georg-August University Goettingen, Goettingen, Germany
| | - Manfred Tietze
- Department of Animal Breeding, University of Kassel, Witzenhausen, Germany
| | - Claus-Peter Czerny
- Department of Animal Sciences, Institute of Veterinary Medicine, Division of Microbiology and Animal Hygiene, Faculty of Agricultural Sciences, Georg-August University Goettingen, Goettingen, Germany
| | - Sven König
- Department of Animal Breeding, University of Kassel, Witzenhausen, Germany
| | - Ulrike S. Diesterbeck
- Department of Animal Sciences, Institute of Veterinary Medicine, Division of Microbiology and Animal Hygiene, Faculty of Agricultural Sciences, Georg-August University Goettingen, Goettingen, Germany
- * E-mail:
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14
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Toby IT, Levin MK, Salinas EA, Christley S, Bhattacharya S, Breden F, Buntzman A, Corrie B, Fonner J, Gupta NT, Hershberg U, Marthandan N, Rosenfeld A, Rounds W, Rubelt F, Scarborough W, Scott JK, Uduman M, Vander Heiden JA, Scheuermann RH, Monson N, Kleinstein SH, Cowell LG. VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements. BMC Bioinformatics 2016; 17:333. [PMID: 27766961 PMCID: PMC5073965 DOI: 10.1186/s12859-016-1214-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Background The genes that produce antibodies and the immune receptors expressed on lymphocytes are not germline encoded; rather, they are somatically generated in each developing lymphocyte by a process called V(D)J recombination, which assembles specific, independent gene segments into mature composite genes. The full set of composite genes in an individual at a single point in time is referred to as the immune repertoire. V(D)J recombination is the distinguishing feature of adaptive immunity and enables effective immune responses against an essentially infinite array of antigens. Characterization of immune repertoires is critical in both basic research and clinical contexts. Recent technological advances in repertoire profiling via high-throughput sequencing have resulted in an explosion of research activity in the field. This has been accompanied by a proliferation of software tools for analysis of repertoire sequencing data. Despite the widespread use of immune repertoire profiling and analysis software, there is currently no standardized format for output files from V(D)J analysis. Researchers utilize software such as IgBLAST and IMGT/High V-QUEST to perform V(D)J analysis and infer the structure of germline rearrangements. However, each of these software tools produces results in a different file format, and can annotate the same result using different labels. These differences make it challenging for users to perform additional downstream analyses. Results To help address this problem, we propose a standardized file format for representing V(D)J analysis results. The proposed format, VDJML, provides a common standardized format for different V(D)J analysis applications to facilitate downstream processing of the results in an application-agnostic manner. The VDJML file format specification is accompanied by a support library, written in C++ and Python, for reading and writing the VDJML file format. Conclusions The VDJML suite will allow users to streamline their V(D)J analysis and facilitate the sharing of scientific knowledge within the community. The VDJML suite and documentation are available from https://vdjserver.org/vdjml/. We welcome participation from the community in developing the file format standard, as well as code contributions.
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Affiliation(s)
- Inimary T Toby
- Department of Clinical Sciences, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-9066, USA
| | - Mikhail K Levin
- Bank of America Corporate Center, 100 North Tryon Street, Charlotte, NC, 28202, USA
| | | | - Scott Christley
- Department of Clinical Sciences, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-9066, USA
| | - Sanchita Bhattacharya
- Institute for Computational Health Sciences, University of California San Francisco, Mission Hall, 550 16th Street, 4th Floor, Box 0110, San Francisco, CA, 94158, USA
| | - Felix Breden
- Department of Biological Sciences and The IRMACS Centre, Simon Fraser University, 8888 University Drive, Burnaby, V5A 1S6, British Columbia, Canada
| | - Adam Buntzman
- Department of Immunobiology, University of Arizona School of Medicine, 1656 E. Mabel Street, P.O. Box 245221, Tucson, AZ, 85724-5221, USA
| | - Brian Corrie
- New Zealand eScience Infrastructure, University of Auckland, Level 10, 49 Symonds Street, Auckland, New Zealand
| | - John Fonner
- Texas Advanced Computing Center, Research Office Complex 1.101, J.J. Pickle Research Campus, Building 196, 10100 Burnet Road (R8700), Austin, TX, 78758-4497, USA
| | - Namita T Gupta
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, 300 George Street, Suite 505, New Haven, CT, 06511, USA
| | - Uri Hershberg
- School of Biomedical Engineering, Science and Health Systems and Department of Microbiology and Immunology, College of Medicine, Drexel University, 3141 Chestnut Street, Philadelphia, PA, 19104, USA
| | - Nishanth Marthandan
- The IRMACS Centre (ASB 10905), Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Aaron Rosenfeld
- School of Biomedical Engineering, Science and Health Systems, Drexel University, 3141 Chestnut Street, Philadelphia, PA, 19104, USA
| | - William Rounds
- Department of Neurology and Neurotherapeutics, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-9036, USA
| | - Florian Rubelt
- Stanford University School of Medicine, 279 Campus Drive, Stanford, CA, 94305-5101, USA
| | - Walter Scarborough
- Texas Advanced Computing Center, Research Office Complex 1.101, J.J. Pickle Research Campus, Building 196, 10100 Burnet Road (R8700), Austin, TX, 78758-4497, USA
| | - Jamie K Scott
- Department of Molecular Biology and Biochemistry and Faculty of Health Sciences, Simon Fraser University, Blusson Hall, Room 11300, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Mohamed Uduman
- Department of Pathology, Yale School of Medicine, 300 George Street, Suite 505, New Haven, CT, 06511, USA
| | - Jason A Vander Heiden
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, 300 George Street, Suite 505, New Haven, CT, 06511, USA
| | - Richard H Scheuermann
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA.,Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.,Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - Nancy Monson
- Department of Neurology and Neurotherapeutics, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-9036, USA
| | - Steven H Kleinstein
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, 300 George Street, Suite 505, New Haven, CT, 06511, USA.,Department of Pathology, Yale School of Medicine, 300 George Street, Suite 505, New Haven, CT, 06511, USA.,Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Lindsay G Cowell
- Department of Clinical Sciences, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-9066, USA.
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Schramm CA, Sheng Z, Zhang Z, Mascola JR, Kwong PD, Shapiro L. SONAR: A High-Throughput Pipeline for Inferring Antibody Ontogenies from Longitudinal Sequencing of B Cell Transcripts. Front Immunol 2016; 7:372. [PMID: 27708645 PMCID: PMC5030719 DOI: 10.3389/fimmu.2016.00372] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 09/07/2016] [Indexed: 02/01/2023] Open
Abstract
The rapid advance of massively parallel or next-generation sequencing technologies has made possible the characterization of B cell receptor repertoires in ever greater detail, and these developments have triggered a proliferation of software tools for processing and annotating these data. Of especial interest, however, is the capability to track the development of specific antibody lineages across time, which remains beyond the scope of most current programs. We have previously reported on the use of techniques such as inter- and intradonor analysis and CDR3 tracing to identify transcripts related to an antibody of interest. Here, we present Software for the Ontogenic aNalysis of Antibody Repertoires (SONAR), capable of automating both general repertoire analysis and specialized techniques for investigating specific lineages. SONAR annotates next-generation sequencing data, identifies transcripts in a lineage of interest, and tracks lineage development across multiple time points. SONAR also generates figures, such as identity-divergence plots and longitudinal phylogenetic "birthday" trees, and provides interfaces to other programs such as DNAML and BEAST. SONAR can be downloaded as a ready-to-run Docker image or manually installed on a local machine. In the latter case, it can also be configured to take advantage of a high-performance computing cluster for the most computationally intensive steps, if available. In summary, this software provides a useful new tool for the processing of large next-generation sequencing datasets and the ontogenic analysis of neutralizing antibody lineages. SONAR can be found at https://github.com/scharch/SONAR, and the Docker image can be obtained from https://hub.docker.com/r/scharch/sonar/.
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Affiliation(s)
- Chaim A Schramm
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA; Department of Systems Biology, Columbia University, New York, NY, USA; Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Zizhang Sheng
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA; Department of Systems Biology, Columbia University, New York, NY, USA
| | - Zhenhai Zhang
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA; Department of Systems Biology, Columbia University, New York, NY, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health , Bethesda, MD , USA
| | - Peter D Kwong
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA; Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Lawrence Shapiro
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA; Department of Systems Biology, Columbia University, New York, NY, USA; Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
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16
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Andrews SF, Huang Y, Kaur K, Popova LI, Ho IY, Pauli NT, Henry Dunand CJ, Taylor WM, Lim S, Huang M, Qu X, Lee JH, Salgado-Ferrer M, Krammer F, Palese P, Wrammert J, Ahmed R, Wilson PC. Immune history profoundly affects broadly protective B cell responses to influenza. Sci Transl Med 2016; 7:316ra192. [PMID: 26631631 DOI: 10.1126/scitranslmed.aad0522] [Citation(s) in RCA: 297] [Impact Index Per Article: 37.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Generating a broadly protective influenza vaccine is critical to global health. Understanding how immune memory influences influenza immunity is central to this goal. We undertook an in-depth study of the B cell response to the pandemic 2009 H1N1 vaccine over consecutive years. Analysis of monoclonal antibodies generated from vaccine-induced plasmablasts demonstrated that individuals with low preexisting serological titers to the vaccinating strain generated a broadly reactive, hemagglutinin (HA) stalk-biased response. Higher preexisting serum antibody levels correlated with a strain-specific HA head-dominated response. We demonstrate that this HA head immunodominance encompasses poor accessibility of the HA stalk epitopes. Further, we show polyreactivity of HA stalk-reactive antibodies that could cause counterselection of these cells. Thus, preexisting memory B cells against HA head epitopes predominate, inhibiting a broadly protective response against the HA stalk upon revaccination with similar strains. Consideration of influenza exposure history is critical for new vaccine strategies designed to elicit broadly neutralizing antibodies.
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Affiliation(s)
- Sarah F Andrews
- Department of Medicine, Section of Rheumatology, Gwen Knapp Center for Lupus and Immunology Research, The University of Chicago, Chicago, IL 60637, USA
| | - Yunping Huang
- Department of Medicine, Section of Rheumatology, Gwen Knapp Center for Lupus and Immunology Research, The University of Chicago, Chicago, IL 60637, USA
| | - Kaval Kaur
- Department of Medicine, Section of Rheumatology, Gwen Knapp Center for Lupus and Immunology Research, The University of Chicago, Chicago, IL 60637, USA. Committee on Immunology, The University of Chicago, Chicago, IL 60637, USA
| | - Lyubov I Popova
- Department of Medicine, Section of Rheumatology, Gwen Knapp Center for Lupus and Immunology Research, The University of Chicago, Chicago, IL 60637, USA
| | - Irvin Y Ho
- Department of Medicine, Section of Rheumatology, Gwen Knapp Center for Lupus and Immunology Research, The University of Chicago, Chicago, IL 60637, USA
| | - Noel T Pauli
- Department of Medicine, Section of Rheumatology, Gwen Knapp Center for Lupus and Immunology Research, The University of Chicago, Chicago, IL 60637, USA. Committee on Immunology, The University of Chicago, Chicago, IL 60637, USA
| | - Carole J Henry Dunand
- Department of Medicine, Section of Rheumatology, Gwen Knapp Center for Lupus and Immunology Research, The University of Chicago, Chicago, IL 60637, USA
| | - William M Taylor
- Department of Medicine, Section of Rheumatology, Gwen Knapp Center for Lupus and Immunology Research, The University of Chicago, Chicago, IL 60637, USA
| | - Samuel Lim
- Department of Medicine, Section of Rheumatology, Gwen Knapp Center for Lupus and Immunology Research, The University of Chicago, Chicago, IL 60637, USA
| | - Min Huang
- Department of Medicine, Section of Rheumatology, Gwen Knapp Center for Lupus and Immunology Research, The University of Chicago, Chicago, IL 60637, USA
| | - Xinyan Qu
- Department of Medicine, Section of Rheumatology, Gwen Knapp Center for Lupus and Immunology Research, The University of Chicago, Chicago, IL 60637, USA
| | - Jane-Hwei Lee
- Department of Medicine, Section of Rheumatology, Gwen Knapp Center for Lupus and Immunology Research, The University of Chicago, Chicago, IL 60637, USA
| | - Marlene Salgado-Ferrer
- Department of Medicine, Section of Rheumatology, Gwen Knapp Center for Lupus and Immunology Research, The University of Chicago, Chicago, IL 60637, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Peter Palese
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jens Wrammert
- Emory Vaccine Center, Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Rafi Ahmed
- Emory Vaccine Center, Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Patrick C Wilson
- Department of Medicine, Section of Rheumatology, Gwen Knapp Center for Lupus and Immunology Research, The University of Chicago, Chicago, IL 60637, USA. Committee on Immunology, The University of Chicago, Chicago, IL 60637, USA.
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17
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Glanville J, D'Angelo S, Khan TA, Reddy ST, Naranjo L, Ferrara F, Bradbury ARM. Deep sequencing in library selection projects: what insight does it bring? Curr Opin Struct Biol 2016; 33:146-60. [PMID: 26451649 DOI: 10.1016/j.sbi.2015.09.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 08/19/2015] [Accepted: 09/17/2015] [Indexed: 11/17/2022]
Abstract
High throughput sequencing is poised to change all aspects of the way antibodies and other binders are discovered and engineered. Millions of available sequence reads provide an unprecedented sampling depth able to guide the design and construction of effective, high quality naïve libraries containing tens of billions of unique molecules. Furthermore, during selections, high throughput sequencing enables quantitative tracing of enriched clones and position-specific guidance to amino acid variation under positive selection during antibody engineering. Successful application of the technologies relies on specific PCR reagent design, correct sequencing platform selection, and effective use of computational tools and statistical measures to remove error, identify antibodies, estimate diversity, and extract signatures of selection from the clone down to individual structural positions. Here we review these considerations and discuss some of the remaining challenges to the widespread adoption of the technology.
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Affiliation(s)
- J Glanville
- Program in Computational and Systems Immunology, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - S D'Angelo
- University of New Mexico Comprehensive Cancer Center, and Division of Molecular Medicine, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - T A Khan
- ETH Zurich, Department of Biosystems Science and Engineering, Basel, Switzerland
| | - S T Reddy
- ETH Zurich, Department of Biosystems Science and Engineering, Basel, Switzerland
| | - L Naranjo
- Bioscience division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - F Ferrara
- University of New Mexico Comprehensive Cancer Center, and Division of Molecular Medicine, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - A R M Bradbury
- Bioscience division, Los Alamos National Laboratory, Los Alamos, NM, USA.
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18
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Foster MH, Buckley ES, Chen BJ, Hwang KK, Clark AG. Uncommon structural motifs dominate the antigen binding site in human autoantibodies reactive with basement membrane collagen. Mol Immunol 2016; 76:123-33. [PMID: 27450516 PMCID: PMC4979994 DOI: 10.1016/j.molimm.2016.07.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Revised: 07/01/2016] [Accepted: 07/05/2016] [Indexed: 11/26/2022]
Abstract
Autoantibodies mediate organ destruction in multiple autoimmune diseases, yet their origins in patients remain poorly understood. To probe the genetic origins and structure of disease-associated autoantibodies, we engrafted immunodeficient mice with human CD34+ hematopoietic stem cells and immunized with the non-collagenous-1 (NC1) domain of the alpha3 chain of type IV collagen. This antigen is expressed in lungs and kidneys and is targeted by autoantibodies in anti-glomerular basement membrane (GBM) nephritis and Goodpasture syndrome (GPS), prototypic human organ-specific autoimmune diseases. Using Epstein Barr virus transformation and cell fusion, six human anti-alpha3(IV)NC1 collagen monoclonal autoantibodies (mAb) were recovered, including subsets reactive with human kidney and with epitopes recognized by patients' IgG. Sequence analysis reveals a long to exceptionally long heavy chain complementarity determining region3 (HCDR3), the major site of antigen binding, in all six mAb. Mean HCDR3 length is 25.5 amino acids (range 20-36), generated from inherently long DH and JH genes and extended regions of non-templated N-nucleotides. Long HCDR3 are suited to forming noncontiguous antigen contacts and to binding recessed, immunologically silent epitopes hidden from conventional antibodies, as seen with self-antigen crossreactive broadly neutralizing anti-HIV Ig (bnAb). The anti-alpha3(IV)NC1 collagen mAb also show preferential use of unmutated variable region genes that are enriched among human chronic lymphocytic leukemia antibodies that share features with natural polyreactive Ig. Our findings suggest unexpected relationships between pathogenic anti-collagen Ig, bnAb, and autoreactive Ig associated with malignancy, all of which arise from B cells expressing unconventional structural elements that may require transient escape from tolerance for successful expansion.
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Affiliation(s)
- Mary H Foster
- Department of Medicine, Duke University Medical Center, Durham, N.C., USA; Durham VA Medical Center, Durham, N.C., USA; Duke Cancer Institute, Duke University Medical Center, Durham, N.C., USA.
| | | | - Benny J Chen
- Department of Medicine, Duke University Medical Center, Durham, N.C., USA; Duke Cancer Institute, Duke University Medical Center, Durham, N.C., USA.
| | - Kwan-Ki Hwang
- Department of Medicine, Duke University Medical Center, Durham, N.C., USA; Duke Human Vaccine Institute, Duke University Medical Center, Durham, N.C., USA.
| | - Amy G Clark
- Department of Medicine, Duke University Medical Center, Durham, N.C., USA; Durham VA Medical Center, Durham, N.C., USA.
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19
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Bonissone SR, Pevzner PA. Immunoglobulin Classification Using the Colored Antibody Graph. J Comput Biol 2016; 23:483-94. [PMID: 27149636 DOI: 10.1089/cmb.2016.0010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The somatic recombination of V, D, and J gene segments in B-cells introduces a great deal of diversity, and divergence from reference segments. Many recent studies of antibodies focus on the population of antibody transcripts that show which V, D, and J gene segments have been favored for a particular antigen, a repertoire. To properly describe the antibody repertoire, each antibody must be labeled by its constituting V, D, and J gene segment, a task made difficult by somatic recombination and hypermutation events. While previous approaches to repertoire analysis were based on sequential alignments, we describe a new de Bruijn graph-based algorithm to perform VDJ labeling and benchmark its performance.
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Affiliation(s)
- Stefano R Bonissone
- 1 Bioinformatics and Systems Biology Program, University of California San diego , La Jolla, California
| | - Pavel A Pevzner
- 2 Department of Computer Science and Engineering, University of California San diego , La Jolla, California
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20
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Frost SDW, Murrell B, Hossain ASMM, Silverman GJ, Pond SLK. Assigning and visualizing germline genes in antibody repertoires. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2014.0240. [PMID: 26194754 PMCID: PMC4528417 DOI: 10.1098/rstb.2014.0240] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Identifying the germline genes involved in immunoglobulin rearrangements is an essential first step in the analysis of antibody repertoires. Based on our prior work in analysing diverse recombinant viruses, we present IgSCUEAL (Immunoglobulin Subtype Classification Using Evolutionary ALgorithms), a phylogenetic approach to assign V and J regions of immunoglobulin sequences to their corresponding germline alleles, with D regions assigned using a simple pairwise alignment algorithm. We also develop an interactive web application for viewing the results, allowing the user to explore the frequency distribution of sequence assignments and CDR3 region length statistics, which is useful for summarizing repertoires, as well as a detailed viewer of rearrangements and region alignments for individual query sequences. We demonstrate the accuracy and utility of our method compared with sequence similarity-based approaches and other non-phylogenetic model-based approaches, using both simulated data and a set of evaluation datasets of human immunoglobulin heavy chain sequences. IgSCUEAL demonstrates the highest accuracy of V and J assignment amongst existing approaches, even when the reassorted sequence is highly mutated, and can successfully cluster sequences on the basis of shared V/J germline alleles.
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Affiliation(s)
- Simon D W Frost
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, Cambridgeshire CB3 0ES, UK
| | - Ben Murrell
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - A S Md Mukarram Hossain
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, Cambridgeshire CB3 0ES, UK
| | - Gregg J Silverman
- Department of Medicine, New York University School of Medicine, New York, NY 10016, USA Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
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21
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Cortina-Ceballos B, Godoy-Lozano EE, Sámano-Sánchez H, Aguilar-Salgado A, Velasco-Herrera MDC, Vargas-Chávez C, Velázquez-Ramírez D, Romero G, Moreno J, Téllez-Sosa J, Martínez-Barnetche J. Reconstructing and mining the B cell repertoire with ImmunediveRsity. MAbs 2016; 7:516-24. [PMID: 25875140 PMCID: PMC4622655 DOI: 10.1080/19420862.2015.1026502] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The B cell antigen receptor repertoire is highly diverse and constantly modified by clonal selection. High-throughput DNA sequencing (HTS) of the lymphocyte repertoire (Rep-Seq) represents a promising technology to explore such diversity ex-vivo and assist in the identification of antigen-specific antibodies based on molecular signatures of clonal selection. Therefore, integrative tools for repertoire reconstruction and analysis from antibody sequences are needed. We developed ImmunediveRity, a stand-alone pipeline primarily based in R programming for the integral analysis of B cell repertoire data generated by HTS. The pipeline integrates GNU software and in house scripts to perform quality filtering, sequencing noise correction and repertoire reconstruction based on V, D and J segment assignment, clonal origin and unique heavy chain identification. Post-analysis scripts generate a wealth of repertoire metrics that in conjunction with a rich graphical output facilitates sample comparison and repertoire mining. Its performance was tested with raw and curated human and mouse 454-Roche sequencing benchmarks providing good approximations of repertoire structure. Furthermore, ImmunediveRsity was used to mine the B cell repertoire of immunized mice with a model antigen, allowing the identification of previously validated antigen-specific antibodies, and revealing different and unexpected clonal diversity patterns in the post-immunization IgM and IgG compartments. Although ImmunediveRsity is similar to other recently developed tools, it offers significant advantages that facilitate repertoire analysis and repertoire mining. ImmunediveRsity is open source and free for academic purposes and it runs on 64 bit GNU/Linux and MacOS. Available at: https://bitbucket.org/ImmunediveRsity/immunediversity/
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Affiliation(s)
- Bernardo Cortina-Ceballos
- a Centro de Investigación Sobre Enfermedades Infecciosas; Instituto Nacional de Salud Pública (CISEI-INSP); Cuernavaca , Morelos , México
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22
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Elhanati Y, Marcou Q, Mora T, Walczak AM. repgenHMM: a dynamic programming tool to infer the rules of immune receptor generation from sequence data. Bioinformatics 2016; 32:1943-51. [PMID: 27153709 PMCID: PMC4920122 DOI: 10.1093/bioinformatics/btw112] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 02/20/2016] [Indexed: 01/01/2023] Open
Abstract
MOTIVATION The diversity of the immune repertoire is initially generated by random rearrangements of the receptor gene during early T and B cell development. Rearrangement scenarios are composed of random events-choices of gene templates, base pair deletions and insertions-described by probability distributions. Not all scenarios are equally likely, and the same receptor sequence may be obtained in several different ways. Quantifying the distribution of these rearrangements is an essential baseline for studying the immune system diversity. Inferring the properties of the distributions from receptor sequences is a computationally hard problem, requiring enumerating every possible scenario for every sampled receptor sequence. RESULTS We present a Hidden Markov model, which accounts for all plausible scenarios that can generate the receptor sequences. We developed and implemented a method based on the Baum-Welch algorithm that can efficiently infer the parameters for the different events of the rearrangement process. We tested our software tool on sequence data for both the alpha and beta chains of the T cell receptor. To test the validity of our algorithm, we also generated synthetic sequences produced by a known model, and confirmed that its parameters could be accurately inferred back from the sequences. The inferred model can be used to generate synthetic sequences, to calculate the probability of generation of any receptor sequence, as well as the theoretical diversity of the repertoire. We estimate this diversity to be [Formula: see text] for human T cells. The model gives a baseline to investigate the selection and dynamics of immune repertoires. AVAILABILITY AND IMPLEMENTATION Source code and sample sequence files are available at https://bitbucket.org/yuvalel/repgenhmm/downloads CONTACT elhanati@lpt.ens.fr or tmora@lps.ens.fr or awalczak@lpt.ens.fr.
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Affiliation(s)
- Yuval Elhanati
- Laboratoire de physique théorique, CNRS, UPMC and Ecole normale supérieure, Paris, France
| | - Quentin Marcou
- Laboratoire de physique théorique, CNRS, UPMC and Ecole normale supérieure, Paris, France
| | - Thierry Mora
- Laboratoire de physique statistique, CNRS, UPMC and Ecole normale supérieure, Paris, France
| | - Aleksandra M Walczak
- Laboratoire de physique théorique, CNRS, UPMC and Ecole normale supérieure, Paris, France
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23
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Ralph DK, Matsen FA. Consistency of VDJ Rearrangement and Substitution Parameters Enables Accurate B Cell Receptor Sequence Annotation. PLoS Comput Biol 2016; 12:e1004409. [PMID: 26751373 PMCID: PMC4709141 DOI: 10.1371/journal.pcbi.1004409] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 06/20/2015] [Indexed: 11/18/2022] Open
Abstract
VDJ rearrangement and somatic hypermutation work together to produce antibody-coding B cell receptor (BCR) sequences for a remarkable diversity of antigens. It is now possible to sequence these BCRs in high throughput; analysis of these sequences is bringing new insight into how antibodies develop, in particular for broadly-neutralizing antibodies against HIV and influenza. A fundamental step in such sequence analysis is to annotate each base as coming from a specific one of the V, D, or J genes, or from an N-addition (a.k.a. non-templated insertion). Previous work has used simple parametric distributions to model transitions from state to state in a hidden Markov model (HMM) of VDJ recombination, and assumed that mutations occur via the same process across sites. However, codon frame and other effects have been observed to violate these parametric assumptions for such coding sequences, suggesting that a non-parametric approach to modeling the recombination process could be useful. In our paper, we find that indeed large modern data sets suggest a model using parameter-rich per-allele categorical distributions for HMM transition probabilities and per-allele-per-position mutation probabilities, and that using such a model for inference leads to significantly improved results. We present an accurate and efficient BCR sequence annotation software package using a novel HMM "factorization" strategy. This package, called partis (https://github.com/psathyrella/partis/), is built on a new general-purpose HMM compiler that can perform efficient inference given a simple text description of an HMM.
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Affiliation(s)
- Duncan K. Ralph
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Frederick A. Matsen
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail:
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24
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Kidd MJ, Jackson KJL, Boyd SD, Collins AM. DJ Pairing during VDJ Recombination Shows Positional Biases That Vary among Individuals with Differing IGHD Locus Immunogenotypes. THE JOURNAL OF IMMUNOLOGY 2015; 196:1158-64. [PMID: 26700767 DOI: 10.4049/jimmunol.1501401] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 10/20/2015] [Indexed: 11/19/2022]
Abstract
Human IgH diversity is influenced by biases in the pairing of IGHD and IGHJ genes, but these biases have not been described in detail. We used high-throughput sequencing of VDJ rearrangements to explore DJ pairing biases in 29 individuals. It was possible to infer three contrasting IGHD-IGHJ haplotypes in nine of these individuals, and two of these haplotypes include deletion polymorphisms involving multiple contiguous IGHD genes. Therefore, we were able to explore how the underlying genetic makeup of the H chain locus influences the formation of particular DJ pairs. Analysis of nonproductive rearrangements demonstrates that 3' IGHD genes tend to pair preferentially with 5' IGHJ genes, whereas 5' IGHD genes pair preferentially with 3' IGHJ genes; the relationship between IGHD gene pairing frequencies and IGHD gene position is a near linear one for each IGHJ gene. However, striking differences are seen in individuals who carry deletion polymorphisms in the D locus. The absence of different blocks of IGHD genes leads to increases in the utilization frequencies of just a handful of genes, and these genes have no clear positional relationships to the deleted genes. This suggests that pairing frequencies may be influenced by additional complex positional relationships that perhaps arise from chromatin structure. In contrast to IGHD gene usage, IGHJ gene usage is unaffected by the IGHD gene-deletion polymorphisms. Such an outcome would be expected if the recombinase complex associates with an IGHJ gene before associating with an IGHD gene partner.
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Affiliation(s)
- Marie J Kidd
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, Sydney, New South Wales 2052, Australia; and
| | - Katherine J L Jackson
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, Sydney, New South Wales 2052, Australia; and Department of Pathology, Stanford University, Stanford, CA 94305
| | - Scott D Boyd
- Department of Pathology, Stanford University, Stanford, CA 94305
| | - Andrew M Collins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, Sydney, New South Wales 2052, Australia; and
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25
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Murira A, Lapierre P, Lamarre A. Evolution of the Humoral Response during HCV Infection: Theories on the Origin of Broadly Neutralizing Antibodies and Implications for Vaccine Design. Adv Immunol 2015; 129:55-107. [PMID: 26791858 DOI: 10.1016/bs.ai.2015.09.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Similar to human immunodeficiency virus (HIV)-1, vaccine-induced elicitation of broadly neutralizing (bNt) antibodies (Abs) is gaining traction as a key goal toward the eradication of the hepatitis C virus (HCV) pandemic. Previously, the significance of the Ab response against HCV was underappreciated given the prevailing evidence advancing the role of the cellular immune response in clearance and overall control of the infection. However, recent findings have driven growing interest in the humoral arm of the immune response and in particular the role of bNt responses due to their ability to confer protective immunity upon passive transfer in animal models. Nevertheless, the origin and development of bNt Abs is poorly understood and their occurrence is rare as well as delayed with emergence only observed in the chronic phase of infection. In this review, we characterize the interplay between the host immune response and HCV as it progresses from the acute to chronic phase of infection. In addition, we place these events in the context of current hypotheses on the origin of bNt Abs against the HIV-1, whose humoral immune response is better characterized. Based on the increasing significance of the humoral immune response against HCV, characterization of these events may be critical in understanding the development of the bNt responses and, thus, provide strategies toward effective vaccine design.
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Affiliation(s)
- Armstrong Murira
- Immunovirology Laboratory, Institut national de la recherche scientifique (INRS), INRS-Institut Armand-Frappier, Laval, Quebec, Canada.
| | - Pascal Lapierre
- Immunovirology Laboratory, Institut national de la recherche scientifique (INRS), INRS-Institut Armand-Frappier, Laval, Quebec, Canada
| | - Alain Lamarre
- Immunovirology Laboratory, Institut national de la recherche scientifique (INRS), INRS-Institut Armand-Frappier, Laval, Quebec, Canada.
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26
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Sim JH, Kim HR, Chang SH, Kim IJ, Lipsky PE, Lee J. Autoregulatory function of interleukin-10-producing pre-naïve B cells is defective in systemic lupus erythematosus. Arthritis Res Ther 2015. [PMID: 26209442 PMCID: PMC4515025 DOI: 10.1186/s13075-015-0687-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
INTRODUCTION Pre-naïve B cells represent an intermediate stage in human B-cell development with some functions of mature cells, but their involvement in immune responses is unknown. The aim of this study was to determine the functional role of normal pre-naïve B cells during immune responses and possible abnormalities in systemic lupus erythematosus (SLE) that might contribute to disease pathogenesis. METHODS Pre-naïve, naïve, and memory B cells from healthy individuals and SLE patients were stimulated through CD40 and were analyzed for interleukin-10 (IL-10) production and co-stimulatory molecule expression and their regulation of T-cell activation. Autoreactivity of antibodies produced by pre-naïve B cells was tested by measuring immunoglobulin M (IgM) autoantibodies in culture supernatants after differentiation. RESULTS CD40-stimulated pre-naïve B cells produce larger amounts of IL-10 but did not suppress CD4(+) T-cell cytokine production. Activated pre-naïve B cells demonstrated IL-10-mediated ineffective promotion of CD4(+) T-cell proliferation and induction of CD4(+)FoxP3(+) T cells and IL-10 independent impairment of co-stimulatory molecule expression and tumor necrosis factor-alpha (TNF-α) and IL-6 production. IgM antibodies produced by differentiated pre-naïve B cells were reactive to single-stranded deoxyribonucleic acid. SLE pre-naïve B cells were defective in producing IL-10, and co-stimulatory molecule expression was enhanced, resulting in promotion of robust CD4(+) T-cell proliferation. CONCLUSIONS There is an inherent and IL-10-mediated mechanism that limits the capacity of normal pre-naïve B cells from participating in cellular immune response, but these cells can differentiate into autoantibody-secreting plasma cells. In SLE, defects in IL-10 secretion permit pre-naïve B cells to promote CD4(+) T-cell activation and may thereby enhance the development of autoimmunity.
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Affiliation(s)
- Ji Hyun Sim
- Department of Anatomy, Seoul National University College of Medicine, Daehak-ro 103, Seoul, 110-799, Republic of Korea.
| | - Hang-Rae Kim
- Department of Anatomy, Seoul National University College of Medicine, Daehak-ro 103, Seoul, 110-799, Republic of Korea. .,Department of Biomedical Sciences, Seoul National University College of Medicine, Daehak-ro 103, Seoul, 110-799, Republic of Korea.
| | - Soog-Hee Chang
- Department of Anatomy, Seoul National University College of Medicine, Daehak-ro 103, Seoul, 110-799, Republic of Korea.
| | - In Je Kim
- Division of Rheumatology, Ewha Womans University School of Medicine, Anyangcheon-gil 1071, Seoul, 158-710, Korea.
| | | | - Jisoo Lee
- Division of Rheumatology, Ewha Womans University School of Medicine, Anyangcheon-gil 1071, Seoul, 158-710, Korea.
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27
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Jardine JG, Ota T, Sok D, Pauthner M, Kulp DW, Kalyuzhniy O, Skog PD, Thinnes TC, Bhullar D, Briney B, Menis S, Jones M, Kubitz M, Spencer S, Adachi Y, Burton DR, Schief WR, Nemazee D. HIV-1 VACCINES. Priming a broadly neutralizing antibody response to HIV-1 using a germline-targeting immunogen. Science 2015; 349:156-61. [PMID: 26089355 DOI: 10.1126/science.aac5894] [Citation(s) in RCA: 299] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Accepted: 06/11/2015] [Indexed: 12/19/2022]
Abstract
A major goal of HIV-1 vaccine research is the design of immunogens capable of inducing broadly neutralizing antibodies (bnAbs) that bind to the viral envelope glycoprotein (Env). Poor binding of Env to unmutated precursors of bnAbs, including those of the VRC01 class, appears to be a major problem for bnAb induction. We engineered an immunogen that binds to VRC01-class bnAb precursors and immunized knock-in mice expressing germline-reverted VRC01 heavy chains. Induced antibodies showed characteristics of VRC01-class bnAbs, including a short CDRL3 (light-chain complementarity-determining region 3) and mutations that favored binding to near-native HIV-1 gp120 constructs. In contrast, native-like immunogens failed to activate VRC01-class precursors. The results suggest that rational epitope design can prime rare B cell precursors for affinity maturation to desired targets.
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Affiliation(s)
- Joseph G Jardine
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center (NAC), The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Takayuki Ota
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Devin Sok
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center (NAC), The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Matthias Pauthner
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center (NAC), The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Daniel W Kulp
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center (NAC), The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Oleksandr Kalyuzhniy
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center (NAC), The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Patrick D Skog
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Theresa C Thinnes
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Deepika Bhullar
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bryan Briney
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center (NAC), The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sergey Menis
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center (NAC), The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Meaghan Jones
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center (NAC), The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Mike Kubitz
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center (NAC), The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Skye Spencer
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center (NAC), The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yumiko Adachi
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center (NAC), The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Dennis R Burton
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center (NAC), The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA. Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02129, USA.
| | - William R Schief
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center (NAC), The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA. Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02129, USA.
| | - David Nemazee
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA.
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Yoon H, Macke J, West AP, Foley B, Bjorkman PJ, Korber B, Yusim K. CATNAP: a tool to compile, analyze and tally neutralizing antibody panels. Nucleic Acids Res 2015; 43:W213-9. [PMID: 26044712 PMCID: PMC4489231 DOI: 10.1093/nar/gkv404] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 04/15/2015] [Indexed: 02/01/2023] Open
Abstract
CATNAP (Compile, Analyze and Tally NAb Panels) is a new web server at Los Alamos HIV Database, created to respond to the newest advances in HIV neutralizing antibody research. It is a comprehensive platform focusing on neutralizing antibody potencies in conjunction with viral sequences. CATNAP integrates neutralization and sequence data from published studies, and allows users to analyze that data for each HIV Envelope protein sequence position and each antibody. The tool has multiple data retrieval and analysis options. As input, the user can pick specific antibodies and viruses, choose a panel from a published study, or supply their own data. The output superimposes neutralization panel data, virus epidemiological data, and viral protein sequence alignments on one page, and provides further information and analyses. The user can highlight alignment positions, or select antibody contact residues and view position-specific information from the HIV databases. The tool calculates tallies of amino acids and N-linked glycosylation motifs, counts of antibody-sensitive and -resistant viruses in conjunction with each amino acid or N-glycosylation motif, and performs Fisher's exact test to detect potential positive or negative amino acid associations for the selected antibody. Website name: CATNAP (Compile, Analyze and Tally NAb Panels). Website address: http://hiv.lanl.gov/catnap.
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Affiliation(s)
- Hyejin Yoon
- Los Alamos National Laboratory, Los Alamos, NM, USA
| | | | | | - Brian Foley
- Los Alamos National Laboratory, Los Alamos, NM, USA
| | | | - Bette Korber
- Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Karina Yusim
- Los Alamos National Laboratory, Los Alamos, NM, USA
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29
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Russ DE, Ho KY, Longo NS. HTJoinSolver: Human immunoglobulin VDJ partitioning using approximate dynamic programming constrained by conserved motifs. BMC Bioinformatics 2015; 16:170. [PMID: 26001675 PMCID: PMC4492005 DOI: 10.1186/s12859-015-0589-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 04/22/2015] [Indexed: 11/13/2022] Open
Abstract
Background Partitioning the human immunoglobulin variable region into variable (V), diversity (D), and joining (J) segments is a common sequence analysis step. We introduce a novel approximate dynamic programming method that uses conserved immunoglobulin gene motifs to improve performance of aligning V-segments of rearranged immunoglobulin (Ig) genes. Our new algorithm enhances the former JOINSOLVER algorithm by processing sequences with insertions and/or deletions (indels) and improves the efficiency for large datasets provided by high throughput sequencing. Results In our simulations, which include rearrangements with indels, the V-matching success rate improved from 61% for partial alignments of sequences with indels in the original algorithm to over 99% in the approximate algorithm. An improvement in the alignment of human VDJ rearrangements over the initial JOINSOLVER algorithm was also seen when compared to the Stanford.S22 human Ig dataset with an online VDJ partitioning software evaluation tool. Conclusions HTJoinSolver can rapidly identify V- and J-segments with indels to high accuracy for mutated sequences when the mutation probability is around 30% and 20% respectively. The D-segment is much harder to fit even at 20% mutation probability. For all segments, the probability of correctly matching V, D, and J increases with our alignment score.
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Affiliation(s)
- Daniel E Russ
- Division of Computational Bioscience, Center for Information Technology, NIH, 12 South Drive, Bethesda, MD, 20892, USA.
| | - Kwan-Yuet Ho
- Division of Computational Bioscience, Center for Information Technology, NIH, 12 South Drive, Bethesda, MD, 20892, USA.
| | - Nancy S Longo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, 40 Convent Drive, Bethesda, MD, 20892, USA.
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30
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Wu X, Zhang Z, Schramm CA, Joyce MG, Kwon YD, Zhou T, Sheng Z, Zhang B, O'Dell S, McKee K, Georgiev IS, Chuang GY, Longo NS, Lynch RM, Saunders KO, Soto C, Srivatsan S, Yang Y, Bailer RT, Louder MK, Mullikin JC, Connors M, Kwong PD, Mascola JR, Shapiro L. Maturation and Diversity of the VRC01-Antibody Lineage over 15 Years of Chronic HIV-1 Infection. Cell 2015; 161:470-485. [PMID: 25865483 DOI: 10.1016/j.cell.2015.03.004] [Citation(s) in RCA: 179] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 12/01/2014] [Accepted: 02/09/2015] [Indexed: 11/29/2022]
Abstract
HIV-1-neutralizing antibodies develop in most HIV-1-infected individuals, although highly effective antibodies are generally observed only after years of chronic infection. Here, we characterize the rate of maturation and extent of diversity for the lineage that produced the broadly neutralizing antibody VRC01 through longitudinal sampling of peripheral B cell transcripts over 15 years and co-crystal structures of lineage members. Next-generation sequencing identified VRC01-lineage transcripts, which encompassed diverse antibodies organized into distinct phylogenetic clades. Prevalent clades maintained characteristic features of antigen recognition, though each evolved binding loops and disulfides that formed distinct recognition surfaces. Over the course of the study period, VRC01-lineage clades showed continuous evolution, with rates of ∼2 substitutions per 100 nucleotides per year, comparable to that of HIV-1 evolution. This high rate of antibody evolution provides a mechanism by which antibody lineages can achieve extraordinary diversity and, over years of chronic infection, develop effective HIV-1 neutralization.
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Affiliation(s)
- Xueling Wu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Aaron Diamond AIDS Research Center, Rockefeller University, New York, NY 10016, USA
| | - Zhenhai Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Department of Biochemistry and Molecular Biophysics and Department of Systems Biology, Columbia University, New York, NY 10032, USA; State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China; National Clinical Research Center for Kidney Disease, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Chaim A Schramm
- Department of Biochemistry and Molecular Biophysics and Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - M Gordon Joyce
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Young Do Kwon
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zizhang Sheng
- Department of Biochemistry and Molecular Biophysics and Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sijy O'Dell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Krisha McKee
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ivelin S Georgiev
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gwo-Yu Chuang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nancy S Longo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rebecca M Lynch
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kevin O Saunders
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Cinque Soto
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sanjay Srivatsan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yongping Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Robert T Bailer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mark K Louder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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- NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - James C Mullikin
- NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mark Connors
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Lawrence Shapiro
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Department of Biochemistry and Molecular Biophysics and Department of Systems Biology, Columbia University, New York, NY 10032, USA.
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Paciello G, Acquaviva A, Pighi C, Ferrarini A, Macii E, Zamo’ A, Ficarra E. VDJSeq-Solver: in silico V(D)J recombination detection tool. PLoS One 2015; 10:e0118192. [PMID: 25799103 PMCID: PMC4370828 DOI: 10.1371/journal.pone.0118192] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 01/05/2015] [Indexed: 11/29/2022] Open
Abstract
In this paper we present VDJSeq-Solver, a methodology and tool to identify clonal lymphocyte populations from paired-end RNA Sequencing reads derived from the sequencing of mRNA neoplastic cells. The tool detects the main clone that characterises the tissue of interest by recognizing the most abundant V(D)J rearrangement among the existing ones in the sample under study. The exact sequence of the clone identified is capable of accounting for the modifications introduced by the enzymatic processes. The proposed tool overcomes limitations of currently available lymphocyte rearrangements recognition methods, working on a single sequence at a time, that are not applicable to high-throughput sequencing data. In this work, VDJSeq-Solver has been applied to correctly detect the main clone and identify its sequence on five Mantle Cell Lymphoma samples; then the tool has been tested on twelve Diffuse Large B-Cell Lymphoma samples. In order to comply with the privacy, ethics and intellectual property policies of the University Hospital and the University of Verona, data is available upon request to supporto.utenti@ateneo.univr.it after signing a mandatory Materials Transfer Agreement. VDJSeq-Solver JAVA/Perl/Bash software implementation is free and available at http://eda.polito.it/VDJSeq-Solver/.
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Affiliation(s)
- Giulia Paciello
- Department of Control and Computer Engineering, Politecnico di Torino, Torino, Italy
- * E-mail:
| | - Andrea Acquaviva
- Department of Control and Computer Engineering, Politecnico di Torino, Torino, Italy
| | - Chiara Pighi
- Department of Pathology and Diagnostics, University of Verona, Verona, Italy
- Department of Pathology, Children Hospital Boston, Harvard Medical School, Boston, USA
| | | | - Enrico Macii
- Department of Control and Computer Engineering, Politecnico di Torino, Torino, Italy
| | - Alberto Zamo’
- Department of Pathology and Diagnostics, University of Verona, Verona, Italy
| | - Elisa Ficarra
- Department of Control and Computer Engineering, Politecnico di Torino, Torino, Italy
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CD27-IgD- memory B cells are modulated by in vivo interleukin-6 receptor (IL-6R) blockade in rheumatoid arthritis. Arthritis Res Ther 2015; 17:61. [PMID: 25888920 PMCID: PMC4415279 DOI: 10.1186/s13075-015-0580-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 02/23/2015] [Indexed: 01/07/2023] Open
Abstract
Introduction Enhanced B cell activity, particularly memory B cells have gained interest in evaluating response during therapies with biologics. CD27-IgD- double-negative (DN) B cells lacking the conventional memory marker CD27 are reported to be part of the memory compartment, however, only scarce data is available for rheumatoid arthritis (RA). We therefore focused on DN B cells in RA, studied their isotypes and modulation during interleukin-6 receptor (IL-6R) inhibition by tocilizumab (TCZ). Methods DN B cells were phenotypically analyzed from 40 RA patients during TCZ at baseline week 12, week 24 and 1 year. A single B cell polymerase chain reaction (PCR) approach was used to study Ig receptors, VH gene rearrangements and specific isotypes. Results Phenotypic analysis showed a significantly expanded population of DN B cells in RA which contain a heterogeneous mixture of IgG-, IgA- and IgM-expressing cells with a clear dominance of IgG+ cells. DN B cells carry rearranged heavy chain gene sequences with a diversified mutational pattern consistent with memory B cells. In contrast to tumor necrosis factor alpha (TNF-α) inhibition, a significant reduction in mutational frequency of BCR gene rearrangements at week 12, 24 and 1 year (P <0.0001) was observed by in vivo IL-6R inhibition. These changes were observed for all BCR isotypes IgG, IgA and IgM at week 12, 24 and 1 year (P <0.0001). IgA-RF, IgA serum level and IgA+ DN B cells decreased significantly (P <0.05) at week 12 and week 24 during TCZ. Patients with a good European League Against Rheumatism (EULAR) response to TCZ had less DN B cells at baseline as compared to moderate responders (P = 0.006). Univariate logistic regression analysis revealed that the frequency of DN B cells at baseline is inversely correlated to a subsequent good EULAR response (P = 0.024) with an odds ratio of 1.48 (95% confidence interval as 1.05 to 2.06). Conclusions In RA, the heterogeneous DN B cell compartment is expanded and dominated by IgG isotype. TCZ can modulate the mutational status of DN Ig isotype receptors over 1 year. Interestingly, the frequency of DN B cells in RA may serve as a baseline predictor of subsequent EULAR response to TCZ. Electronic supplementary material The online version of this article (doi:10.1186/s13075-015-0580-y) contains supplementary material, which is available to authorized users.
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Roll P, Muhammad K, Stuhler G, Grigoleit U, Einsele H, Tony HP. Effect of ATG-F on B-cell reconstitution after hematopoietic stem cell transplantation. Eur J Haematol 2015; 95:514-23. [PMID: 25677646 DOI: 10.1111/ejh.12524] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/16/2015] [Indexed: 01/03/2023]
Abstract
Antithymocyte globulin Fresenius (ATG-F) is used before hematopoietic stem cell transplantation to prevent graft rejection and graft-versus-host disease in patients with HLA-matched unrelated donors or mismatched volunteers. However, little is known about the effect of ATG-F on the reconstitution of B-cell subsets. Sixty-seven patients were longitudinally studied at day 15, day 30, and then monthly after hematopoietic stem cell transplantation. Conditioning regimes included ATG-F, which was infused at days 3, 2 and 1 at a dosage of 10 mg/kg/d. Twenty-seven patients received conditioning regimes without ATG. ATG-treated patients showed a significant delay of CD19+ B cells in the early recovery period. The absolute numbers of circulating CD19+ B cells were significantly lower (P < 0.05) up to 5 months post-transplantation compared to non-ATG patients. The recovery of the memory compartment was delayed in both groups and did not reach normal values 1-year post-transplantation. ATG-treated patient showed significantly lower absolute numbers of circulating CD27+ memory B cells in the first-month after transplantation compared to non-ATG patients. In conclusion, treatment with ATG in the conditioning regime of patients undergoing allogeneic hematopoietic stem cell transplantation leads to a significant delay of CD19+ B cells. Thus, ATG seems also to negatively influence B-cell immune reconstitution.
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Affiliation(s)
- Petra Roll
- Department of Medicine II, University of Würzburg, Würzburg, Germany
| | - Khalid Muhammad
- Department of Medicine II, University of Würzburg, Würzburg, Germany
| | - Gernot Stuhler
- Department of Medicine II, University of Würzburg, Würzburg, Germany
| | - Ulrich Grigoleit
- Department of Medicine II, University of Würzburg, Würzburg, Germany
| | - Hermann Einsele
- Department of Medicine II, University of Würzburg, Würzburg, Germany
| | - Hans-Peter Tony
- Department of Medicine II, University of Würzburg, Würzburg, Germany
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34
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The Immunogenicity of Antibody Aggregates in a Novel Transgenic Mouse Model. Pharm Res 2015; 32:2344-59. [DOI: 10.1007/s11095-015-1627-0] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 01/12/2015] [Indexed: 11/25/2022]
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35
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Bonissone SR, Pevzner PA. Immunoglobulin Classification Using the Colored Antibody Graph. LECTURE NOTES IN COMPUTER SCIENCE 2015. [DOI: 10.1007/978-3-319-16706-0_7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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36
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Old questions, new tools: does next-generation sequencing hold the key to unraveling intestinal B-cell responses? Mucosal Immunol 2015; 8:29-37. [PMID: 25389035 DOI: 10.1038/mi.2014.103] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 09/18/2014] [Indexed: 02/04/2023]
Abstract
Analysis of the intestinal B-cell system and properties of immunoglobulin A, the main antibody isotype produced in the gut, has dominated the rise of mucosal immunology as a discipline. Seminal work established concepts describing the induction, transport, and function of mucosal antibodies. Still, open questions remain and we lack a comprehensive view of how the various sites and pathways of immunoglobulin A induction are integrated to respond to gut antigens. Next-generation sequencing (NGS) offers a novel approach to study B-cell responses, which might substantially enhance our tool box to answer key questions in the field and to take the next steps toward therapeutic exploitation of the mucosal B-cell system. In this review we discuss the potential, challenges, and emerging solutions for gut B-cell repertoire analysis by NGS.
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37
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Calis JJA, Rosenberg BR. Characterizing immune repertoires by high throughput sequencing: strategies and applications. Trends Immunol 2014; 35:581-590. [PMID: 25306219 PMCID: PMC4390416 DOI: 10.1016/j.it.2014.09.004] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 09/05/2014] [Accepted: 09/09/2014] [Indexed: 01/09/2023]
Abstract
As the key cellular effectors of adaptive immunity, T and B lymphocytes utilize specialized receptors to recognize, respond to, and neutralize a diverse array of extrinsic threats. These receptors (immunoglobulins in B lymphocytes, T cell receptors in T lymphocytes) are incredibly variable, the products of specialized genetic diversification mechanisms that generate complex lymphocyte repertoires with extensive collections of antigen specificities. Recent advances in high throughput sequencing (HTS) technologies have transformed our ability to examine antigen receptor repertoires at single nucleotide, and more recently, single cell, resolution. Here we review current approaches to examining antigen receptor repertoires by HTS, and discuss inherent biological and technical challenges. We further describe emerging applications of this powerful methodology for exploring the adaptive immune system.
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Affiliation(s)
| | - Brad R Rosenberg
- The Rockefeller University, New York, NY, USA; John C. Whitehead Presidential Fellows Program, The Rockefeller University, New York, NY, USA.
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38
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Vaccine-induced plasmablast responses in rhesus macaques: phenotypic characterization and a source for generating antigen-specific monoclonal antibodies. J Immunol Methods 2014; 416:69-83. [PMID: 25445326 DOI: 10.1016/j.jim.2014.11.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 10/09/2014] [Accepted: 11/03/2014] [Indexed: 12/25/2022]
Abstract
Over 100 broadly neutralizing antibodies have been isolated from a minority of HIV infected patients, but the steps leading to the selection of plasma cells producing such antibodies remain incompletely understood, hampering the development of vaccines able to elicit them. Rhesus macaques have become a preferred animal model system used to study SIV/HIV, for the characterization and development of novel therapeutics and vaccines as well as to understand pathogenesis. However, most of our knowledge about the dynamics of antibody responses is limited to the analysis of serum antibodies or monoclonal antibodies generated from memory B cells. In a vaccine setting, relatively little is known about the early cellular responses that elicit long-lived plasma cells and memory B cells and the tools to dissect plasmablast responses are not available in macaques. In the current study, we show that the majority (>80%) of the vaccine-induced plasmablast response are antigen-specific by functional ELISPOT assays. While plasmablasts are easily defined and isolated in humans, those same phenotypic markers have not been useful for identifying macaque plasmablasts. Here we describe an approach that allows for the isolation and single cell sorting of vaccine-induced plasmablasts. Finally, we show that isolated plasmablasts can be used to efficiently recover antigen-specific monoclonal antibodies through single cell expression cloning. This will allow detailed studies of the early plasmablast responses in rhesus macaques, enabling the characterization of both their repertoire breadth as well as the epitope specificity and functional qualities of the antibodies they produce, not only in the context of SIV/HIV vaccines but for many other pathogens/vaccines as well.
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van Schouwenburg PA, Kruithof S, Votsmeier C, van Schie K, Hart MH, de Jong RN, van Buren EEL, van Ham M, Aarden L, Wolbink G, Wouters D, Rispens T. Functional analysis of the anti-adalimumab response using patient-derived monoclonal antibodies. J Biol Chem 2014; 289:34482-8. [PMID: 25326381 DOI: 10.1074/jbc.m114.615500] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The production of antibodies to adalimumab in autoimmune patients treated with adalimumab is shown to diminish treatment efficacy. We previously showed that these antibodies are almost exclusively neutralizing, indicating a restricted response. Here, we investigated the characteristics of a panel of patient-derived monoclonal antibodies for binding to adalimumab. Single B-cells were isolated from two patients, cultured, and screened for adalimumab specificity. Analysis of variable region sequences of 16 clones suggests that the immune response against adalimumab is broad, involving multiple B-cell clones each using different combinations of V(D)J segments. A strong bias for replacement mutations in the complementarity determining regions was found, indicating an antigen-driven response. We recombinantly expressed 11 different monoclonal antibodies and investigated their affinity and specificity. All clones except one are of high affinity (Kd between 0.6 and 233 pm) and compete with TNF as well as each other for binding to adalimumab. However, binding to a panel of single-point mutants of adalimumab indicates markedly different fine specificities that also result in a differential tendency of each clone to form dimeric and multimeric immune complexes. We conclude that although all anti-adalimumab antibodies compete for binding to TNF, the response is clonally diverse and involves multiple epitopes on adalimumab. These results are important for understanding the relationship between self and non-self or idiotypic determinants on therapeutic antibodies and their potential immunogenicity.
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Affiliation(s)
- Pauline A van Schouwenburg
- From the Department of Immunopathology, Sanquin Research and Landsteiner Laboratory Academic Medical Centre, 1105 AZ Amsterdam, The Netherlands
| | - Simone Kruithof
- From the Department of Immunopathology, Sanquin Research and Landsteiner Laboratory Academic Medical Centre, 1105 AZ Amsterdam, The Netherlands
| | - Christian Votsmeier
- Global Drug Discovery, Global Biologics, Bayer HealthCare AG, 51061 Cologne, Germany, and
| | - Karin van Schie
- From the Department of Immunopathology, Sanquin Research and Landsteiner Laboratory Academic Medical Centre, 1105 AZ Amsterdam, The Netherlands
| | - Margreet H Hart
- From the Department of Immunopathology, Sanquin Research and Landsteiner Laboratory Academic Medical Centre, 1105 AZ Amsterdam, The Netherlands
| | | | | | - Marieke van Ham
- From the Department of Immunopathology, Sanquin Research and Landsteiner Laboratory Academic Medical Centre, 1105 AZ Amsterdam, The Netherlands
| | - Lucien Aarden
- From the Department of Immunopathology, Sanquin Research and Landsteiner Laboratory Academic Medical Centre, 1105 AZ Amsterdam, The Netherlands
| | - Gertjan Wolbink
- From the Department of Immunopathology, Sanquin Research and Landsteiner Laboratory Academic Medical Centre, 1105 AZ Amsterdam, The Netherlands, the Jan van Breemen Research Institute/Reade, 1056 AB Amsterdam, The Netherlands
| | - Diana Wouters
- From the Department of Immunopathology, Sanquin Research and Landsteiner Laboratory Academic Medical Centre, 1105 AZ Amsterdam, The Netherlands
| | - Theo Rispens
- From the Department of Immunopathology, Sanquin Research and Landsteiner Laboratory Academic Medical Centre, 1105 AZ Amsterdam, The Netherlands,
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Finton KAK, Friend D, Jaffe J, Gewe M, Holmes MA, Larman HB, Stuart A, Larimore K, Greenberg PD, Elledge SJ, Stamatatos L, Strong RK. Ontogeny of recognition specificity and functionality for the broadly neutralizing anti-HIV antibody 4E10. PLoS Pathog 2014; 10:e1004403. [PMID: 25254371 PMCID: PMC4177983 DOI: 10.1371/journal.ppat.1004403] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 08/16/2014] [Indexed: 01/07/2023] Open
Abstract
The process of antibody ontogeny typically improves affinity, on-rate, and thermostability, narrows polyspecificity, and rigidifies the combining site to the conformer optimal for binding from the broader ensemble accessible to the precursor. However, many broadly-neutralizing anti-HIV antibodies incorporate unusual structural elements and recognition specificities or properties that often lead to autoreactivity. The ontogeny of 4E10, an autoreactive antibody with unexpected combining site flexibility, was delineated through structural and biophysical comparisons of the mature antibody with multiple potential precursors. 4E10 gained affinity primarily by off-rate enhancement through a small number of mutations to a highly conserved recognition surface. Controverting the conventional paradigm, the combining site gained flexibility and autoreactivity during ontogeny, while losing thermostability, though polyspecificity was unaffected. Details of the recognition mechanism, including inferred global effects due to 4E10 binding, suggest that neutralization by 4E10 may involve mechanisms beyond simply binding, also requiring the ability of the antibody to induce conformational changes distant from its binding site. 4E10 is, therefore, unlikely to be re-elicited by conventional vaccination strategies.
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Affiliation(s)
- Kathryn A. K. Finton
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Della Friend
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - James Jaffe
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Mesfin Gewe
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Margaret A. Holmes
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - H. Benjamin Larman
- Department of Genetics, Harvard University Medical School, and Division of Genetics, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Andrew Stuart
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Kevin Larimore
- Department of Immunology, University of Washington, Seattle, Washington, United States of America
| | - Philip D. Greenberg
- Department of Immunology, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
- Program in Immunology, Cancer Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Stephen J. Elledge
- Department of Genetics, Harvard University Medical School, and Division of Genetics, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Leonidas Stamatatos
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - Roland K. Strong
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail:
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Giraud M, Salson M, Duez M, Villenet C, Quief S, Caillault A, Grardel N, Roumier C, Preudhomme C, Figeac M. Fast multiclonal clusterization of V(D)J recombinations from high-throughput sequencing. BMC Genomics 2014; 15:409. [PMID: 24885090 PMCID: PMC4070559 DOI: 10.1186/1471-2164-15-409] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 05/08/2014] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND V(D)J recombinations in lymphocytes are essential for immunological diversity. They are also useful markers of pathologies. In leukemia, they are used to quantify the minimal residual disease during patient follow-up. However, the full breadth of lymphocyte diversity is not fully understood. RESULTS We propose new algorithms that process high-throughput sequencing (HTS) data to extract unnamed V(D)J junctions and gather them into clones for quantification. This analysis is based on a seed heuristic and is fast and scalable because in the first phase, no alignment is performed with germline database sequences. The algorithms were applied to TR γ HTS data from a patient with acute lymphoblastic leukemia, and also on data simulating hypermutations. Our methods identified the main clone, as well as additional clones that were not identified with standard protocols. CONCLUSIONS The proposed algorithms provide new insight into the analysis of high-throughput sequencing data for leukemia, and also to the quantitative assessment of any immunological profile. The methods described here are implemented in a C++ open-source program called Vidjil.
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Affiliation(s)
- Mathieu Giraud
- />Laboratoire d’Informatique Fondamentale de Lille (LIFL, UMR CNRS 8022, Université Lille 1) and Inria Lille – Cité scientifique – Bâtiment M3, 59655 Villeneuve d’Ascq, France
| | - Mikaël Salson
- />Laboratoire d’Informatique Fondamentale de Lille (LIFL, UMR CNRS 8022, Université Lille 1) and Inria Lille – Cité scientifique – Bâtiment M3, 59655 Villeneuve d’Ascq, France
| | - Marc Duez
- />Laboratoire d’Informatique Fondamentale de Lille (LIFL, UMR CNRS 8022, Université Lille 1) and Inria Lille – Cité scientifique – Bâtiment M3, 59655 Villeneuve d’Ascq, France
- />SIRIC OncoLille, Lille, France
| | - Céline Villenet
- />Functional and Structural Genomic Platform, Université Lille 2, IFR 114 Lille, France
| | - Sabine Quief
- />Functional and Structural Genomic Platform, Université Lille 2, IFR 114 Lille, France
- />Lille Institute for Cancer Research (IRCL), Lille, France
| | - Aurélie Caillault
- />Department of Hematology, Biology and Pathology Center, Lille, France
| | - Nathalie Grardel
- />Department of Hematology, Biology and Pathology Center, Lille, France
| | - Christophe Roumier
- />Department of Hematology, Biology and Pathology Center, Lille, France
- />Inserm U-837, Cancer Research Institute, Lille, France
| | - Claude Preudhomme
- />Department of Hematology, Biology and Pathology Center, Lille, France
- />Inserm U-837, Cancer Research Institute, Lille, France
| | - Martin Figeac
- />Functional and Structural Genomic Platform, Université Lille 2, IFR 114 Lille, France
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Developmental pathway for potent V1V2-directed HIV-neutralizing antibodies. Nature 2014; 509:55-62. [PMID: 24590074 DOI: 10.1038/nature13036] [Citation(s) in RCA: 576] [Impact Index Per Article: 57.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 01/16/2014] [Indexed: 02/08/2023]
Abstract
Antibodies capable of neutralizing HIV-1 often target variable regions 1 and 2 (V1V2) of the HIV-1 envelope, but the mechanism of their elicitation has been unclear. Here we define the developmental pathway by which such antibodies are generated and acquire the requisite molecular characteristics for neutralization. Twelve somatically related neutralizing antibodies (CAP256-VRC26.01-12) were isolated from donor CAP256 (from the Centre for the AIDS Programme of Research in South Africa (CAPRISA)); each antibody contained the protruding tyrosine-sulphated, anionic antigen-binding loop (complementarity-determining region (CDR) H3) characteristic of this category of antibodies. Their unmutated ancestor emerged between weeks 30-38 post-infection with a 35-residue CDR H3, and neutralized the virus that superinfected this individual 15 weeks after initial infection. Improved neutralization breadth and potency occurred by week 59 with modest affinity maturation, and was preceded by extensive diversification of the virus population. HIV-1 V1V2-directed neutralizing antibodies can thus develop relatively rapidly through initial selection of B cells with a long CDR H3, and limited subsequent somatic hypermutation. These data provide important insights relevant to HIV-1 vaccine development.
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Giesecke C, Frölich D, Reiter K, Mei HE, Wirries I, Kuhly R, Killig M, Glatzer T, Stölzel K, Perka C, Lipsky PE, Dörner T. Tissue Distribution and Dependence of Responsiveness of Human Antigen-Specific Memory B Cells. THE JOURNAL OF IMMUNOLOGY 2014; 192:3091-100. [DOI: 10.4049/jimmunol.1302783] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Illegitimate V(D)J recombination-mediated deletions in Notch1 and Bcl11b are not sufficient for extensive clonal expansion and show minimal age or sex bias in frequency or junctional processing. Mutat Res 2014; 761:34-48. [PMID: 24530429 DOI: 10.1016/j.mrfmmm.2014.01.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 12/23/2013] [Accepted: 01/28/2014] [Indexed: 01/22/2023]
Abstract
Illegitimate V(D)J recombination at oncogenes and tumor suppressor genes is implicated in formation of several T cell malignancies. Notch1 and Bcl11b, genes involved in developing T cell specification, selection, proliferation, and survival, were previously shown to contain hotspots for deletional illegitimate V(D)J recombination associated with radiation-induced thymic lymphoma. Interestingly, these deletions were also observed in wild-type animals. In this study, we conducted frequency, clonality, and junctional processing analyses of Notch1 and Bcl11b deletions during mouse development and compared results to published analyses of authentic V(D)J rearrangements at the T cell receptor beta (TCRβ) locus and illegitimate V(D)J deletions observed at the human, nonimmune HPRT1 locus not involved in T cell malignancies. We detect deletions in Notch1 and Bcl11b in thymic and splenic T cell populations, consistent with cells bearing deletions in the circulating lymphocyte pool. Deletions in thymus can occur in utero, increase in frequency between fetal and postnatal stages, are detected at all ages examined between fetal and 7 months, exhibit only limited clonality (contrasting with previous results in radiation-sensitive mouse strains), and consistent with previous reports are more frequent in Bcl11b, partially explained by relatively high Recombination Signal Information Content (RIC) scores. Deletion junctions in Bcl11b exhibit greater germline nucleotide loss, while in Notch1 palindromic (P) nucleotides are more abundant, although average P nucleotide length is similar for both genes and consistent with results at the TCRβ locus. Non-templated (N) nucleotide insertions appear to increase between fetal and postnatal stages for Notch1, consistent with normal terminal deoxynucleotidyl transferase (TdT) activity; however, neonatal Bcl11b junctions contain elevated levels of N insertions. Finally, contrasting with results at the HPRT1 locus, we find no obvious age or gender bias in junctional processing, and inverted repeats at recessed coding ends (Pr nucleotides) correspond mostly to single-base additions consistent with normal TdT activity.
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45
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McIntyre D, Zuckerman NS, Field M, Mehr R, Stott DI. The V(H) repertoire and clonal diversification of B cells in inflammatory myopathies. Eur J Immunol 2014; 44:585-96. [PMID: 24343314 DOI: 10.1002/eji.201343315] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 07/24/2013] [Accepted: 12/11/2013] [Indexed: 01/12/2023]
Abstract
The contribution of antigen-driven B-cell adaptive immune responses within the inflamed muscle of inflammatory myopathies (IMs) is largely unknown. In this study, we investigated the immunoglobulin V(H) gene repertoire, somatic hypermutation, clonal diversification, and selection of infiltrating B cells in muscle biopsies from IM patients (dermatomyositis and polymyositis), to determine whether B cells and/or plasma cells contribute to the associated pathologies of these diseases. The data reveal that Ig V(H) gene repertoires of muscle-infiltrating B cells deviate from the normal V(H) gene repertoire in individual patients, and differ between different types of IMs. Analysis of somatic mutations revealed clonal diversification of muscle-infiltrating B cells and evidence for a chronic B-cell response within the inflamed muscle. We conclude that muscle-infiltrating B cells undergo selection, somatic hypermutation and clonal diversification in situ during antigen-driven immune responses in patients with IMs, providing insight into the contribution of B cells to the pathological mechanisms of these disorders.
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Affiliation(s)
- Donna McIntyre
- Institute of Infection, Immunity and Inflammation, Glasgow Biomedical Research Centre, University of Glasgow, Glasgow, Scotland, UK
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Vrolix K, Fraussen J, Losen M, Stevens J, Lazaridis K, Molenaar PC, Somers V, Bracho MA, Le Panse R, Stinissen P, Berrih-Aknin S, Maessen JG, Van Garsse L, Buurman WA, Tzartos SJ, De Baets MH, Martinez-Martinez P. Clonal heterogeneity of thymic B cells from early-onset myasthenia gravis patients with antibodies against the acetylcholine receptor. J Autoimmun 2014; 52:101-12. [PMID: 24439114 DOI: 10.1016/j.jaut.2013.12.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 12/12/2013] [Indexed: 10/25/2022]
Abstract
Myasthenia gravis (MG) with antibodies against the acetylcholine receptor (AChR-MG) is considered as a prototypic autoimmune disease. The thymus is important in the pathophysiology of the disease since thymus hyperplasia is a characteristic of early-onset AChR-MG and patients often improve after thymectomy. We hypothesized that thymic B cell and antibody repertoires of AChR-MG patients differ intrinsically from those of control individuals. Using immortalization with Epstein-Barr Virus and Toll-like receptor 9 activation, we isolated and characterized monoclonal B cell lines from 5 MG patients and 8 controls. Only 2 of 570 immortalized B cell clones from MG patients produced antibodies against the AChR (both clones were from the same patient), suggesting that AChR-specific B cells are not enriched in the thymus. Surprisingly, many B cell lines from both AChR-MG and control thymus samples displayed reactivity against striated muscle proteins. Striational antibodies were produced by 15% of B cell clones from AChR-MG versus 6% in control thymus. The IgVH gene sequence analysis showed remarkable similarities, concerning VH family gene distribution, mutation frequency and CDR3 composition, between B cells of AChR-MG patients and controls. MG patients showed clear evidence of clonal B cell expansion in contrast to controls. In this latter aspect, MG resembles multiple sclerosis and clinically isolated syndrome, but differs from systemic lupus erythematosus. Our results support an antigen driven immune response in the MG thymus, but the paucity of AChR-specific B cells, in combination with the observed polyclonal expansions suggest a more diverse immune response than expected.
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Affiliation(s)
- Kathleen Vrolix
- Department of Neuroscience, School of Mental Health and Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, Universiteitssingel 50, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - Judith Fraussen
- Neuroimmunology group, Biomedical Research Institute and Transnationale Universiteit Limburg, School of Life Sciences, Hasselt University, Diepenbeek, Belgium
| | - Mario Losen
- Department of Neuroscience, School of Mental Health and Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, Universiteitssingel 50, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - Jo Stevens
- Department of Neuroscience, School of Mental Health and Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, Universiteitssingel 50, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | | | - Peter C Molenaar
- Department of Neuroscience, School of Mental Health and Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, Universiteitssingel 50, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - Veerle Somers
- Neuroimmunology group, Biomedical Research Institute and Transnationale Universiteit Limburg, School of Life Sciences, Hasselt University, Diepenbeek, Belgium
| | - Maria Alma Bracho
- Centre Superior d'Investigació en Salut Pública (CSISP), Àrea de Genòmica i Salut, Conselleria de Sanitat, Generalitat Valenciana, València, Spain; Institut "Cavanilles" de Biodiversitat i Biologia Evolutiva (ICBiBE), Universitat de València, València, Spain; Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Ministerio de Ciencia e Innovación, Spain
| | - Rozen Le Panse
- UPMC UM 76/INSERM U974/CNRS UMR7215/Institute of Myology, 105 Bd de l'hôpital, Paris, France
| | - Piet Stinissen
- Neuroimmunology group, Biomedical Research Institute and Transnationale Universiteit Limburg, School of Life Sciences, Hasselt University, Diepenbeek, Belgium
| | - Sonia Berrih-Aknin
- UPMC UM 76/INSERM U974/CNRS UMR7215/Institute of Myology, 105 Bd de l'hôpital, Paris, France
| | - Jos G Maessen
- Department of Cardiothoracic Surgery, University Hospital, Maastricht, The Netherlands
| | - Leen Van Garsse
- Department of Cardiothoracic Surgery, University Hospital, Maastricht, The Netherlands
| | - Wim A Buurman
- Department of Neuroscience, School of Mental Health and Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, Universiteitssingel 50, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - Socrates J Tzartos
- Department of Biochemistry, Hellenic Pasteur Institute, GR 11521 Athens, Greece
| | - Marc H De Baets
- Department of Neuroscience, School of Mental Health and Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, Universiteitssingel 50, P.O. Box 616, 6200 MD Maastricht, The Netherlands; Neuroimmunology group, Biomedical Research Institute and Transnationale Universiteit Limburg, School of Life Sciences, Hasselt University, Diepenbeek, Belgium
| | - Pilar Martinez-Martinez
- Department of Neuroscience, School of Mental Health and Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, Universiteitssingel 50, P.O. Box 616, 6200 MD Maastricht, The Netherlands.
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Bowers E, Scamurra RW, Asrani A, Beniguel L, MaWhinney S, Keays KM, Thurn JR, Janoff EN. Decreased mutation frequencies among immunoglobulin G variable region genes during viremic HIV-1 infection. PLoS One 2014; 9:e81913. [PMID: 24409278 PMCID: PMC3883639 DOI: 10.1371/journal.pone.0081913] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Accepted: 10/28/2013] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND/OBJECTIVE HIV-1 infection is complicated by high rates of opportunistic infections against which specific antibodies contribute to immune defense. Antibody function depends on somatic hypermutation (SHM) of variable regions of immunoglobulin heavy chain genes (VH-D-J). We characterized the frequency of SHM in expressed IgG mRNA immunoglobulin transcripts from control and HIV-1-infected patients. DESIGN We compared utilization of genes in the most prominent VH family (VH3) and mutation frequencies and patterns of cDNA from VH3-IgG genes from 10 seronegative control subjects and 21 patients with HIV-1 infection (6 without and 15 patients with detectable plasma viremia). METHODS Unique IgG VH3 family cDNA sequences (n = 1,565) were PCR amplified, cloned, and sequenced from blood. Sequences were analyzed using online (Vbase) and in-house immunoglobulin alignment resources. RESULTS Mutation frequencies in the antigen-binding hypervariable complementarity determining regions (CDR1/2) of IgG class-switched B cells were lower among viremic HIV-1-infected patients vs. controls for nucleotides (CDR1/2: 10±5% vs. 13.5±6%, p = 0.03) and amino acids (CDR: 20%±10 vs. 25%±12, p = 0.02) and in structural framework regions. Mutation patterns were similar among groups. The most common VH3 gene, VH3-23, was utilized less frequently among viremic HIV-1-infected patients (p = 0.03), and overall, mutation frequencies were decreased in nearly all VH3 genes compared with controls. CONCLUSIONS B cells from HIV-1-infected patients show decreased mutation frequencies, especially in antigen-binding VH3 CDR genes, and selective defects in gene utilization. Similar mutation patterns suggest defects in the quantity, but not quality, of mutator activity. Lower levels of SHM in IgG class-switched B cells from HIV-1-infected patients may contribute to the increased risk of opportunistic infections and impaired humoral responses to preventative vaccines.
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Affiliation(s)
- Elisabeth Bowers
- Mucosal and Vaccine Research Program Colorado (MAVRC), University of Colorado Denver, Aurora, Colorado, United States of America ; Infectious Disease Division, University of Colorado Denver, Aurora, Colorado, United States of America ; Department of Microbiology, University of Colorado Denver, Aurora, Colorado, United States of America ; Denver Veterans Affairs Medical Center, Denver, Colorado, United States of America
| | - Ronald W Scamurra
- Minneapolis VA Health Care System, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Anil Asrani
- Minneapolis VA Health Care System, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Lydie Beniguel
- GIMAP EA 3064, Faculté de Médecine, Université Jean Monnet, Saint Etienne, France
| | - Samantha MaWhinney
- Mucosal and Vaccine Research Program Colorado (MAVRC), University of Colorado Denver, Aurora, Colorado, United States of America ; Colorado School of Public Health, University of Colorado Denver, Aurora, Colorado, United States of America
| | - Kathryne M Keays
- Mucosal and Vaccine Research Program Colorado (MAVRC), University of Colorado Denver, Aurora, Colorado, United States of America ; Infectious Disease Division, University of Colorado Denver, Aurora, Colorado, United States of America
| | - Joseph R Thurn
- Minneapolis VA Health Care System, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Edward N Janoff
- Mucosal and Vaccine Research Program Colorado (MAVRC), University of Colorado Denver, Aurora, Colorado, United States of America ; Infectious Disease Division, University of Colorado Denver, Aurora, Colorado, United States of America ; Department of Microbiology, University of Colorado Denver, Aurora, Colorado, United States of America ; Denver Veterans Affairs Medical Center, Denver, Colorado, United States of America
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48
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Finn JA, Crowe JE. Impact of new sequencing technologies on studies of the human B cell repertoire. Curr Opin Immunol 2013; 25:613-8. [PMID: 24161653 DOI: 10.1016/j.coi.2013.09.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Revised: 09/24/2013] [Accepted: 09/30/2013] [Indexed: 12/01/2022]
Affiliation(s)
- Jessica A Finn
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
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De novo identification of VRC01 class HIV-1-neutralizing antibodies by next-generation sequencing of B-cell transcripts. Proc Natl Acad Sci U S A 2013; 110:E4088-97. [PMID: 24106303 DOI: 10.1073/pnas.1306262110] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Next-generation sequencing of antibody transcripts provides a wealth of data, but the ability to identify function-specific antibodies solely on the basis of sequence has remained elusive. We previously characterized the VRC01 class of antibodies, which target the CD4-binding site on gp120, appear in multiple donors, and broadly neutralize HIV-1. Antibodies of this class have developmental commonalities, but typically share only ∼50% amino acid sequence identity among different donors. Here we apply next-generation sequencing to identify VRC01 class antibodies in a new donor, C38, directly from B cell transcript sequences. We first tested a lineage rank approach, but this was unsuccessful, likely because VRC01 class antibody sequences were not highly prevalent in this donor. We next identified VRC01 class heavy chains through a phylogenetic analysis that included thousands of sequences from C38 and a few known VRC01 class sequences from other donors. This "cross-donor analysis" yielded heavy chains with little sequence homology to previously identified VRC01 class heavy chains. Nonetheless, when reconstituted with the light chain from VRC01, half of the heavy chain chimeric antibodies showed substantial neutralization potency and breadth. We then identified VRC01 class light chains through a five-amino-acid sequence motif necessary for VRC01 light chain recognition. From over a million light chain sequences, we identified 13 candidate VRC01 class members. Pairing of these light chains with the phylogenetically identified C38 heavy chains yielded functional antibodies that effectively neutralized HIV-1. Bioinformatics analysis can thus directly identify functional HIV-1-neutralizing antibodies of the VRC01 class from a sequenced antibody repertoire.
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Jackson KJL, Kidd MJ, Wang Y, Collins AM. The shape of the lymphocyte receptor repertoire: lessons from the B cell receptor. Front Immunol 2013; 4:263. [PMID: 24032032 PMCID: PMC3759170 DOI: 10.3389/fimmu.2013.00263] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 08/19/2013] [Indexed: 11/13/2022] Open
Abstract
Both the B cell receptor (BCR) and the T cell receptor (TCR) repertoires are generated through essentially identical processes of V(D)J recombination, exonuclease trimming of germline genes, and the random addition of non-template encoded nucleotides. The naïve TCR repertoire is constrained by thymic selection, and TCR repertoire studies have therefore focused strongly on the diversity of MHC-binding complementarity determining region (CDR) CDR3. The process of somatic point mutations has given B cell studies a major focus on variable (IGHV, IGLV, and IGKV) genes. This in turn has influenced how both the naïve and memory BCR repertoires have been studied. Diversity (D) genes are also more easily identified in BCR VDJ rearrangements than in TCR VDJ rearrangements, and this has allowed the processes and elements that contribute to the incredible diversity of the immunoglobulin heavy chain CDR3 to be analyzed in detail. This diversity can be contrasted with that of the light chain where a small number of polypeptide sequences dominate the repertoire. Biases in the use of different germline genes, in gene processing, and in the addition of non-template encoded nucleotides appear to be intrinsic to the recombination process, imparting "shape" to the repertoire of rearranged genes as a result of differences spanning many orders of magnitude in the probabilities that different BCRs will be generated. This may function to increase the precursor frequency of naïve B cells with important specificities, and the likely emergence of such B cell lineages upon antigen exposure is discussed with reference to public and private T cell clonotypes.
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Affiliation(s)
- Katherine J. L. Jackson
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Marie J. Kidd
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Yan Wang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Andrew M. Collins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
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