101
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Chang DK, Kurella VB, Biswas S, Avnir Y, Sui J, Wang X, Sun J, Wang Y, Panditrao M, Peterson E, Tallarico A, Fernandes S, Goodall M, Zhu Q, Brown JR, Jefferis R, Marasco WA. Humanized mouse G6 anti-idiotypic monoclonal antibody has therapeutic potential against IGHV1-69 germline gene-based B-CLL. MAbs 2016; 8:787-98. [PMID: 26963739 DOI: 10.1080/19420862.2016.1159365] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
In 10-20% of the cases of chronic lymphocytic leukemia of B-cell phenotype (B-CLL), the IGHV1-69 germline is utilized as VH gene of the B cell receptor (BCR). Mouse G6 (MuG6) is an anti-idiotypic monoclonal antibody discovered in a screen against rheumatoid factors (RFs) that binds with high affinity to an idiotope expressed on the 51p1 alleles of IGHV1-69 germline gene encoded antibodies (G6-id(+)). The finding that unmutated IGHV1-69 encoded BCRs are frequently expressed on B-CLL cells provides an opportunity for anti-idiotype monoclonal antibody immunotherapy. In this study, we first showed that MuG6 can deplete B cells encoding IGHV1-69 BCRs using a novel humanized GTL mouse model. Next, we humanized MuG6 and demonstrated that the humanized antibodies (HuG6s), especially HuG6.3, displayed ∼2-fold higher binding affinity for G6-id(+) antibody compared to the parental MuG6. Additional studies showed that HuG6.3 was able to kill G6-id(+) BCR expressing cells and patient B-CLL cells through antibody-dependent cell-mediated cytotoxicity (ADCC) and complement-dependent cytotoxicity (CDC). Finally, both MuG6 and HuG6.3 mediate in vivo depletion of B-CLL cells in NSG mice. These data suggest that HuG6.3 may provide a new precision medicine to selectively kill IGHV1-69-encoding G6-id(+) B-CLL cells.
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Affiliation(s)
- De-Kuan Chang
- a Department of Cancer Immunology and Virology , Dana-Farber Cancer Institute , Boston , MA , USA.,b Department of Medicine , Harvard Medical School , Boston , MA , USA
| | - Vinodh B Kurella
- a Department of Cancer Immunology and Virology , Dana-Farber Cancer Institute , Boston , MA , USA.,b Department of Medicine , Harvard Medical School , Boston , MA , USA
| | - Subhabrata Biswas
- a Department of Cancer Immunology and Virology , Dana-Farber Cancer Institute , Boston , MA , USA.,b Department of Medicine , Harvard Medical School , Boston , MA , USA
| | - Yuval Avnir
- a Department of Cancer Immunology and Virology , Dana-Farber Cancer Institute , Boston , MA , USA.,b Department of Medicine , Harvard Medical School , Boston , MA , USA
| | - Jianhua Sui
- a Department of Cancer Immunology and Virology , Dana-Farber Cancer Institute , Boston , MA , USA.,b Department of Medicine , Harvard Medical School , Boston , MA , USA
| | - Xueqian Wang
- a Department of Cancer Immunology and Virology , Dana-Farber Cancer Institute , Boston , MA , USA.,b Department of Medicine , Harvard Medical School , Boston , MA , USA
| | - Jiusong Sun
- a Department of Cancer Immunology and Virology , Dana-Farber Cancer Institute , Boston , MA , USA.,b Department of Medicine , Harvard Medical School , Boston , MA , USA
| | - Yanyan Wang
- a Department of Cancer Immunology and Virology , Dana-Farber Cancer Institute , Boston , MA , USA
| | - Madhura Panditrao
- a Department of Cancer Immunology and Virology , Dana-Farber Cancer Institute , Boston , MA , USA
| | - Eric Peterson
- a Department of Cancer Immunology and Virology , Dana-Farber Cancer Institute , Boston , MA , USA
| | - Aimee Tallarico
- a Department of Cancer Immunology and Virology , Dana-Farber Cancer Institute , Boston , MA , USA.,b Department of Medicine , Harvard Medical School , Boston , MA , USA
| | - Stacey Fernandes
- c Department of Medical Oncology , Dana-Farber Cancer Institute , Boston , MA , USA
| | - Margaret Goodall
- d Division of Immunity and Infection, University of Birmingham, School of Medicine , Edgbaston, Birmingham , UK
| | - Quan Zhu
- a Department of Cancer Immunology and Virology , Dana-Farber Cancer Institute , Boston , MA , USA.,b Department of Medicine , Harvard Medical School , Boston , MA , USA
| | - Jennifer R Brown
- c Department of Medical Oncology , Dana-Farber Cancer Institute , Boston , MA , USA
| | - Roy Jefferis
- d Division of Immunity and Infection, University of Birmingham, School of Medicine , Edgbaston, Birmingham , UK
| | - Wayne A Marasco
- a Department of Cancer Immunology and Virology , Dana-Farber Cancer Institute , Boston , MA , USA.,b Department of Medicine , Harvard Medical School , Boston , MA , USA
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102
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Ferret Y, Caillault A, Sebda S, Duez M, Grardel N, Duployez N, Villenet C, Figeac M, Preudhomme C, Salson M, Giraud M. Multi-loci diagnosis of acute lymphoblastic leukaemia with high-throughput sequencing and bioinformatics analysis. Br J Haematol 2016; 173:413-20. [PMID: 26898266 DOI: 10.1111/bjh.13981] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 12/21/2015] [Indexed: 12/31/2022]
Abstract
High-throughput sequencing (HTS) is considered a technical revolution that has improved our knowledge of lymphoid and autoimmune diseases, changing our approach to leukaemia both at diagnosis and during follow-up. As part of an immunoglobulin/T cell receptor-based minimal residual disease (MRD) assessment of acute lymphoblastic leukaemia patients, we assessed the performance and feasibility of the replacement of the first steps of the approach based on DNA isolation and Sanger sequencing, using a HTS protocol combined with bioinformatics analysis and visualization using the Vidjil software. We prospectively analysed the diagnostic and relapse samples of 34 paediatric patients, thus identifying 125 leukaemic clones with recombinations on multiple loci (TRG, TRD, IGH and IGK), including Dd2/Dd3 and Intron/KDE rearrangements. Sequencing failures were halved (14% vs. 34%, P = 0.0007), enabling more patients to be monitored. Furthermore, more markers per patient could be monitored, reducing the probability of false negative MRD results. The whole analysis, from sample receipt to clinical validation, was shorter than our current diagnostic protocol, with equal resources. V(D)J recombination was successfully assigned by the software, even for unusual recombinations. This study emphasizes the progress that HTS with adapted bioinformatics tools can bring to the diagnosis of leukaemia patients.
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Affiliation(s)
- Yann Ferret
- Laboratoire d'Hématologie, Centre Hospitalier Régional Universitaire de Lille, Lille, France
| | - Aurélie Caillault
- Laboratoire d'Hématologie, Centre Hospitalier Régional Universitaire de Lille, Lille, France
| | - Shéhérazade Sebda
- Functional and Structural Genomic Platform, Université de Lille, Lille, France
| | - Marc Duez
- School of Social and Community Medicine, University of Bristol, Bristol, UK.,SIRIC ONCOLille, CRIStAL, UMR 9189, Université de Lille, Lille, France
| | - Nathalie Grardel
- Laboratoire d'Hématologie, Centre Hospitalier Régional Universitaire de Lille, Lille, France
| | - Nicolas Duployez
- Laboratoire d'Hématologie, Centre Hospitalier Régional Universitaire de Lille, Lille, France
| | - Céline Villenet
- Functional and Structural Genomic Platform, Université de Lille, Lille, France
| | - Martin Figeac
- Functional and Structural Genomic Platform, Université de Lille, Lille, France
| | - Claude Preudhomme
- Laboratoire d'Hématologie, Centre Hospitalier Régional Universitaire de Lille, Lille, France
| | - Mikaël Salson
- CRIStAL, UMR 9189, CNRS, Université de Lille, Lille, France.,Inria, Lille, France
| | - Mathieu Giraud
- CRIStAL, UMR 9189, CNRS, Université de Lille, Lille, France.,Inria, Lille, France
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103
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Bornholdt ZA, Turner HL, Murin CD, Li W, Sok D, Souders CA, Piper AE, Goff A, Shamblin JD, Wollen SE, Sprague TR, Fusco ML, Pommert KBJ, Cavacini LA, Smith HL, Klempner M, Reimann KA, Krauland E, Gerngross TU, Wittrup KD, Saphire EO, Burton DR, Glass PJ, Ward AB, Walker LM. Isolation of potent neutralizing antibodies from a survivor of the 2014 Ebola virus outbreak. Science 2016; 351:1078-83. [PMID: 26912366 DOI: 10.1126/science.aad5788] [Citation(s) in RCA: 163] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 02/08/2016] [Indexed: 12/30/2022]
Abstract
Antibodies targeting the Ebola virus surface glycoprotein (EBOV GP) are implicated in protection against lethal disease, but the characteristics of the human antibody response to EBOV GP remain poorly understood. We isolated and characterized 349 GP-specific monoclonal antibodies (mAbs) from the peripheral B cells of a convalescent donor who survived the 2014 EBOV Zaire outbreak. Remarkably, 77% of the mAbs neutralize live EBOV, and several mAbs exhibit unprecedented potency. Structures of selected mAbs in complex with GP reveal a site of vulnerability located in the GP stalk region proximal to the viral membrane. Neutralizing antibodies targeting this site show potent therapeutic efficacy against lethal EBOV challenge in mice. The results provide a framework for the design of new EBOV vaccine candidates and immunotherapies.
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Affiliation(s)
- Zachary A Bornholdt
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hannah L Turner
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Charles D Murin
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA. Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Wen Li
- Adimab, Lebanon, NH 03766, USA
| | - Devin Sok
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Colby A Souders
- MassBiologics, University of Massachusetts Medical School, Boston, MA 02126, USA
| | - Ashley E Piper
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
| | - Arthur Goff
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
| | - Joshua D Shamblin
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
| | - Suzanne E Wollen
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
| | - Thomas R Sprague
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
| | - Marnie L Fusco
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kathleen B J Pommert
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Lisa A Cavacini
- MassBiologics, University of Massachusetts Medical School, Boston, MA 02126, USA
| | - Heidi L Smith
- MassBiologics, University of Massachusetts Medical School, Boston, MA 02126, USA
| | - Mark Klempner
- MassBiologics, University of Massachusetts Medical School, Boston, MA 02126, USA
| | - Keith A Reimann
- MassBiologics, University of Massachusetts Medical School, Boston, MA 02126, USA
| | | | | | | | - Erica Ollmann Saphire
- Department of Immunology and Microbial Science, 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. Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02142, USA
| | - Pamela J Glass
- U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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104
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Abstract
New high-throughput DNA sequencing (HTS) technologies developed in the past decade have begun to be applied to the study of the complex gene rearrangements that encode human antibodies. This article first reviews the genetic features of Ig loci and the HTS technologies that have been applied to human repertoire studies, then discusses key choices for experimental design and data analysis in these experiments and the insights gained in immunological and infectious disease studies with the use of these approaches.
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105
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Cole C, Volden R, Dharmadhikari S, Scelfo-Dalbey C, Vollmers C. Highly Accurate Sequencing of Full-Length Immune Repertoire Amplicons Using Tn5-Enabled and Molecular Identifier–Guided Amplicon Assembly. THE JOURNAL OF IMMUNOLOGY 2016; 196:2902-7. [DOI: 10.4049/jimmunol.1502563] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 01/11/2016] [Indexed: 12/22/2022]
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106
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Efficient construct of a large and functional scFv yeast display library derived from the ascites B cells of ovarian cancer patients by three-fragment transformation-associated recombination. Appl Microbiol Biotechnol 2016; 100:4051-61. [PMID: 26782745 DOI: 10.1007/s00253-016-7303-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Revised: 01/04/2016] [Accepted: 01/06/2016] [Indexed: 10/22/2022]
Abstract
Over the past decade, yeast display technology has emerged as a powerful tool for the isolation of high-affinity immunoglobulin fragments with potential utility as clinical diagnostic and therapeutic reagents. Despite significant refinement of the various methodologies underpinning library construction and selections, certain aspects remain challenging and process limiting. We have sought to significantly improve the robustness of the single-chain Fv (scFv) library construction step by overcoming the technical inefficiencies frequently encountered during the PCR-mediated assembly of scFvs from the discrete heavy and light V-domain repertoires. Using a novel primer set designed to provide maximum amplification coverage of the known germ-line V-domain repertoire, we have exploited the potential of the in vivo homologous gap-repair apparatus of Saccharomyces cerevisiae to assemble intact scFvs directly from co-transformed PBMC-derived VH, VL, and linearized vector component fragments. We have successfully applied this three-fragment assembly strategy to construct a large (>10(9)) scFv yeast display library from the ascites immune repertoire of ovarian cancer patients and validated the approach by applying FACS-based sorting to readily isolate scFvs that recognize various tumor marker antigens (TMAs). It is expected that this simplified construction method may find general utility, both for de novo scFv library construction and for subsequent combinatorial affinity maturation manipulations that require more than two fragments.
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107
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Abstract
Assessment of minimal residual disease (MRD) is becoming standard diagnostic care for potentially curable neoplasms such as some acute leukemias as well as chronic myeloid and lymphocytic leukemia. Although multiple myeloma (MM) remains as an incurable disease, around half of the patients achieve complete remission (CR), and recent data suggests increasing rates of curability with "total-therapy-like" programs. This landscape is likely to be improved with the advent of new antibodies and small molecules. Therefore, conventional serological and morphological techniques have become suboptimal for sensitive evaluation of highly effective treatment strategies. Although, existing data suggests that MRD could be used as a biomarker to evaluate treatment efficacy, help on therapeutic decisions, and act as surrogate for overall survival, the role of MRD in MM is still a matter of extensive debate. Here, we review the different levels of remission used to define depth of response in MM and their clinical significance, as well as the prognostic value and unique characteristics of MRD detection using immunophenotypic, molecular, and imaging techniques. Key facts The higher efficacy of new treatment strategies for MM demand the incorporation of highly sensitive techniques to monitor treatment efficacy MRD could be used as a more potent surrogate biomarker for survival than standard CR We need to understand the pros and cons of the different MRD techniques The time has come to incorporate highly sensitive, cost-effective, readily available, and standardized MRD techniques into clinical trials to assess its role in therapeutic decisions.
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Affiliation(s)
- Bruno Paiva
- Centro de Investigacion Medica Aplicada (CIMA), Clinica Universidad de Navarra, IDISNA, Pamplona, Spain
| | - Ramón García-Sanz
- Hospital Universitario de Salamanca, Centro de Investigación Del Cancer (IBMCC-USAL, CSIC), Instituto de Investigaion Biomedica de Salamanca (IBSAL), Salamanca, Spain
| | - Jesús F San Miguel
- Centro de Investigacion Medica Aplicada (CIMA), Clinica Universidad de Navarra, IDISNA, Pamplona, Spain.
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108
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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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109
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Weinberger J, Jimenez-Heredia R, Schaller S, Suessner S, Sunzenauer J, Reindl-Schwaighofer R, Weiss R, Winkler S, Gabriel C, Danzer M, Oberbauer R. Immune Repertoire Profiling Reveals that Clonally Expanded B and T Cells Infiltrating Diseased Human Kidneys Can Also Be Tracked in Blood. PLoS One 2015; 10:e0143125. [PMID: 26600245 PMCID: PMC4658119 DOI: 10.1371/journal.pone.0143125] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Accepted: 10/30/2015] [Indexed: 12/28/2022] Open
Abstract
Recent advances in high-throughput sequencing allow for the competitive analysis of the human B and T cell immune repertoire. In this study we compared Immunoglobulin and T cell receptor repertoires of lymphocytes found in kidney and blood samples of 10 patients with various renal diseases based on next-generation sequencing data. We used Biomed-2 primer panels and ImmunExplorer software to sequence, analyze and compare complementarity determining regions and V-(D)-J elements. While generally an individual's renal receptor repertoire is different from the repertoire present in blood, 94% (30/32) of the lymphocytes with clonal expansion in kidney can also be traced in blood however, not all of these clonotypes are equally abundant. Summarizing the data of all analyzed patients, 68% of highly expanded T cell clonotypes and 30% of the highly expanded B cell clonotypes that have infiltrated the kidney can be found amongst the five most abundant clonotypes in blood. In addition, complementarity determining region 3 sequences of the immunoglobulin heavy chains are on average more diverse than T cell receptor beta chains. Immune repertoire analysis of tissue infiltrating B and T cells adds new approaches to the assessment of adaptive immune response in kidney diseases. Our data suggest that expanded clonotypes in the tissues might be traceable in blood samples in the course of treatment or the natural history of the disease.
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Affiliation(s)
- Johannes Weinberger
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, Linz, Austria
- Department of Immunogenetics, Red Cross Transfusion Service of Upper Austria, Linz, Austria
| | - Raul Jimenez-Heredia
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, Linz, Austria
- Department of Immunogenetics, Red Cross Transfusion Service of Upper Austria, Linz, Austria
| | - Susanne Schaller
- Bioinformatics Research Group, University of Applied Sciences Upper Austria, Hagenberg, Austria
| | - Susanne Suessner
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, Linz, Austria
- Department of Immunogenetics, Red Cross Transfusion Service of Upper Austria, Linz, Austria
| | - Judith Sunzenauer
- Department of Internal Medicine III, KH Elisabethinen, Linz, Austria
- Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Roman Reindl-Schwaighofer
- Department of Internal Medicine III, KH Elisabethinen, Linz, Austria
- Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Richard Weiss
- Department of Molecular Biology, University of Salzburg, Salzburg, Austria
| | - Stephan Winkler
- Bioinformatics Research Group, University of Applied Sciences Upper Austria, Hagenberg, Austria
| | - Christian Gabriel
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, Linz, Austria
- Department of Immunogenetics, Red Cross Transfusion Service of Upper Austria, Linz, Austria
| | - Martin Danzer
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, Linz, Austria
- Department of Immunogenetics, Red Cross Transfusion Service of Upper Austria, Linz, Austria
- * E-mail: (MD); (RO)
| | - Rainer Oberbauer
- Department of Internal Medicine III, KH Elisabethinen, Linz, Austria
- Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
- * E-mail: (MD); (RO)
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110
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Yaari G, Kleinstein SH. Practical guidelines for B-cell receptor repertoire sequencing analysis. Genome Med 2015; 7:121. [PMID: 26589402 PMCID: PMC4654805 DOI: 10.1186/s13073-015-0243-2] [Citation(s) in RCA: 152] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
High-throughput sequencing of B-cell immunoglobulin repertoires is increasingly being applied to gain insights into the adaptive immune response in healthy individuals and in those with a wide range of diseases. Recent applications include the study of autoimmunity, infection, allergy, cancer and aging. As sequencing technologies continue to improve, these repertoire sequencing experiments are producing ever larger datasets, with tens- to hundreds-of-millions of sequences. These data require specialized bioinformatics pipelines to be analyzed effectively. Numerous methods and tools have been developed to handle different steps of the analysis, and integrated software suites have recently been made available. However, the field has yet to converge on a standard pipeline for data processing and analysis. Common file formats for data sharing are also lacking. Here we provide a set of practical guidelines for B-cell receptor repertoire sequencing analysis, starting from raw sequencing reads and proceeding through pre-processing, determination of population structure, and analysis of repertoire properties. These include methods for unique molecular identifiers and sequencing error correction, V(D)J assignment and detection of novel alleles, clonal assignment, lineage tree construction, somatic hypermutation modeling, selection analysis, and analysis of stereotyped or convergent responses. The guidelines presented here highlight the major steps involved in the analysis of B-cell repertoire sequencing data, along with recommendations on how to avoid common pitfalls.
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Affiliation(s)
- Gur Yaari
- Bioengineering Program, Faculty of Engineering, Bar-Ilan University, 5290002, Ramat Gan, Israel.
| | - Steven H Kleinstein
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06511, USA. .,Departments of Pathology and Immunobiology, Yale University School of Medicine, New Haven, CT, 06520, USA.
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111
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Levin M, King JJ, Glanville J, Jackson KJL, Looney TJ, Hoh RA, Mari A, Andersson M, Greiff L, Fire AZ, Boyd SD, Ohlin M. Persistence and evolution of allergen-specific IgE repertoires during subcutaneous specific immunotherapy. J Allergy Clin Immunol 2015; 137:1535-44. [PMID: 26559321 DOI: 10.1016/j.jaci.2015.09.027] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 07/24/2015] [Accepted: 09/23/2015] [Indexed: 10/22/2022]
Abstract
BACKGROUND Specific immunotherapy (SIT) is the only treatment with proved long-term curative potential in patients with allergic disease. Allergen-specific IgE is the causative agent of allergic disease, and antibodies contribute to SIT, but the effects of SIT on aeroallergen-specific B-cell repertoires are not well understood. OBJECTIVE We sought to characterize the IgE sequences expressed by allergen-specific B cells and track the fate of these B-cell clones during SIT. METHODS We used high-throughput antibody gene sequencing and identification of allergen-specific IgE with combinatorial antibody fragment library technology to analyze immunoglobulin repertoires of blood and the nasal mucosa from aeroallergen-sensitized subjects before and during the first year of subcutaneous SIT. RESULTS Of 52 distinct allergen-specific IgE heavy chains from 8 allergic donors, 37 were also detected by using high-throughput antibody gene sequencing of blood samples, nasal mucosal samples, or both. The allergen-specific clones had increased persistence, higher likelihood of belonging to clones expressing other switched isotypes, and possibly larger clone size than the rest of the IgE repertoire. Clone members in nasal tissue showed close mutational relationships. CONCLUSION In the future, combining functional binding studies, deep antibody repertoire sequencing, and information on clinical outcomes in larger studies might aid assessment of SIT mechanisms and efficacy.
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Affiliation(s)
- Mattias Levin
- Department of Immunotechnology, Lund University, Lund, Sweden
| | - Jasmine J King
- Department of Biology, Stanford University, Stanford, Calif; Department of Pathology, Stanford University, Stanford, Calif
| | - Jacob Glanville
- Department of Immunology, Stanford University, Stanford, Calif
| | | | | | - Ramona A Hoh
- Department of Pathology, Stanford University, Stanford, Calif
| | - Adriano Mari
- Center for Molecular Allergology, IDI-IRCCS, Rome, Italy; Associated Centers for Molecular Allergology, Rome, Italy
| | - Morgan Andersson
- Department of Otorhinolaryngology, Head and Neck Surgery, Skåne University Hospital, Lund, Sweden
| | - Lennart Greiff
- Department of Otorhinolaryngology, Head and Neck Surgery, Skåne University Hospital, Lund, Sweden
| | - Andrew Z Fire
- Department of Pathology, Stanford University, Stanford, Calif; Department of Genetics, Stanford University, Stanford, Calif
| | - Scott D Boyd
- Department of Pathology, Stanford University, Stanford, Calif
| | - Mats Ohlin
- Department of Immunotechnology, Lund University, Lund, Sweden.
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112
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Survival of human lymphoma cells requires B-cell receptor engagement by self-antigens. Proc Natl Acad Sci U S A 2015; 112:13447-54. [PMID: 26483459 DOI: 10.1073/pnas.1514944112] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The activated B-cell-like (ABC) subtype of diffuse large B-cell lymphoma (DLBCL) relies on chronic active B-cell receptor (BCR) signaling. BCR pathway inhibitors induce remissions in a subset of ABC DLBCL patients. BCR microclusters on the surface of ABC cells resemble those generated following antigen engagement of normal B cells. We speculated that binding of lymphoma BCRs to self-antigens initiates and maintains chronic active BCR signaling in ABC DLBCL. To assess whether antigenic engagement of the BCR is required for the ongoing survival of ABC cells, we developed isogenic ABC cells that differed solely with respect to the IgH V region of their BCRs. In competitive assays with wild-type cells, substitution of a heterologous V region impaired the survival of three ABC lines. The viability of one VH4-34(+) ABC line and the ability of its BCR to bind to its own cell surface depended on V region residues that mediate the intrinsic autoreactivity of VH4-34 to self-glycoproteins. The BCR of another ABC line reacted with self-antigens in apoptotic debris, and the survival of a third ABC line was sustained by reactivity of its BCR to an idiotypic epitope in its own V region. Hence, a diverse set of self-antigens is responsible for maintaining the malignant survival of ABC DLBCL cells. IgH V regions used by the BCRs of ABC DLBCL biopsy samples varied in their ability to sustain survival of these ABC lines, suggesting a screening procedure to identify patients who might benefit from BCR pathway inhibition.
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113
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Yu Y, Ceredig R, Seoighe C. LymAnalyzer: a tool for comprehensive analysis of next generation sequencing data of T cell receptors and immunoglobulins. Nucleic Acids Res 2015; 44:e31. [PMID: 26446988 PMCID: PMC4770197 DOI: 10.1093/nar/gkv1016] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 09/25/2015] [Indexed: 02/03/2023] Open
Abstract
The adaptive immune system includes populations of B and T cells capable of binding foreign epitopes via antigen specific receptors, called immunoglobulin (IG) for B cells and the T cell receptor (TCR) for T cells. In order to provide protection from a wide range of pathogens, these cells display highly diverse repertoires of IGs and TCRs. This is achieved through combinatorial rearrangement of multiple gene segments in addition, for B cells, to somatic hypermutation. Deep sequencing technologies have revolutionized analysis of the diversity of these repertoires; however, accurate TCR/IG diversity profiling requires specialist bioinformatics tools. Here we present LymAnalzyer, a software package that significantly improves the completeness and accuracy of TCR/IG profiling from deep sequence data and includes procedures to identify novel alleles of gene segments. On real and simulated data sets LymAnalyzer produces highly accurate and complete results. Although, to date we have applied it to TCR/IG data from human and mouse, it can be applied to data from any species for which an appropriate database of reference genes is available. Implemented in Java, it includes both a command line version and a graphical user interface and is freely available at https://sourceforge.net/projects/lymanalyzer/.
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Affiliation(s)
- Yaxuan Yu
- School of Mathematics, Statistics and Applied Mathematics, National University of Ireland Galway, University Road, Galway, Ireland
| | - Rhodri Ceredig
- Biosciences, National University of Ireland Galway, University Road, Dangan, Galway, Ireland
| | - Cathal Seoighe
- School of Mathematics, Statistics and Applied Mathematics, National University of Ireland Galway, University Road, Galway, Ireland
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114
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Cobey S, Wilson P, Matsen FA. The evolution within us. Philos Trans R Soc Lond B Biol Sci 2015; 370:20140235. [PMID: 26194749 PMCID: PMC4528412 DOI: 10.1098/rstb.2014.0235] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2015] [Indexed: 01/05/2023] Open
Abstract
The B-cell immune response is a remarkable evolutionary system found in jawed vertebrates. B-cell receptors, the membrane-bound form of antibodies, are capable of evolving high affinity to almost any foreign protein. High germline diversity and rapid evolution upon encounter with antigen explain the general adaptability of B-cell populations, but the dynamics of repertoires are less well understood. These dynamics are scientifically and clinically important. After highlighting the remarkable characteristics of naive and experienced B-cell repertoires, especially biased usage of genes encoding the B-cell receptors, we contrast methods of sequence analysis and their attempts to explain patterns of B-cell evolution. These phylogenetic approaches are currently unlinked to explicit models of B-cell competition, which analyse repertoire evolution at the level of phenotype, the affinities and specificities to particular antigenic sites. The models, in turn, suggest how chance, infection history and other factors contribute to different patterns of immunodominance and protection between people. Challenges in rational vaccine design, specifically vaccines to induce broadly neutralizing antibodies to HIV, underscore critical gaps in our understanding of B cells' evolutionary and ecological dynamics.
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Affiliation(s)
- Sarah Cobey
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
| | - Patrick Wilson
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA Committee on Immunology, University of Chicago, Chicago, IL 60637, USA Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, IL 60637, USA
| | - Frederick A Matsen
- Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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115
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Williams WB, Liao HX, Moody MA, Kepler TB, Alam SM, Gao F, Wiehe K, Trama AM, Jones K, Zhang R, Song H, Marshall DJ, Whitesides JF, Sawatzki K, Hua A, Liu P, Tay MZ, Seaton KE, Shen X, Foulger A, Lloyd KE, Parks R, Pollara J, Ferrari G, Yu JS, Vandergrift N, Montefiori DC, Sobieszczyk ME, Hammer S, Karuna S, Gilbert P, Grove D, Grunenberg N, McElrath MJ, Mascola JR, Koup RA, Corey L, Nabel GJ, Morgan C, Churchyard G, Maenza J, Keefer M, Graham BS, Baden LR, Tomaras GD, Haynes BF. HIV-1 VACCINES. Diversion of HIV-1 vaccine-induced immunity by gp41-microbiota cross-reactive antibodies. Science 2015; 349:aab1253. [PMID: 26229114 DOI: 10.1126/science.aab1253] [Citation(s) in RCA: 161] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Accepted: 07/09/2015] [Indexed: 01/04/2023]
Abstract
An HIV-1 DNA prime vaccine, with a recombinant adenovirus type 5 (rAd5) boost, failed to protect from HIV-1 acquisition. We studied the nature of the vaccine-induced antibody (Ab) response to HIV-1 envelope (Env). HIV-1-reactive plasma Ab titers were higher to Env gp41 than to gp120, and repertoire analysis demonstrated that 93% of HIV-1-reactive Abs from memory B cells responded to Env gp41. Vaccine-induced gp41-reactive monoclonal antibodies were non-neutralizing and frequently polyreactive with host and environmental antigens, including intestinal microbiota (IM). Next-generation sequencing of an immunoglobulin heavy chain variable region repertoire before vaccination revealed an Env-IM cross-reactive Ab that was clonally related to a subsequent vaccine-induced gp41-reactive Ab. Thus, HIV-1 Env DNA-rAd5 vaccine induced a dominant IM-polyreactive, non-neutralizing gp41-reactive Ab repertoire response that was associated with no vaccine efficacy.
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Affiliation(s)
- Wilton B Williams
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA.
| | - Hua-Xin Liao
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - M Anthony Moody
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Thomas B Kepler
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA
| | - S Munir Alam
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Feng Gao
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Ashley M Trama
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Kathryn Jones
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Ruijun Zhang
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Hongshuo Song
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Dawn J Marshall
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - John F Whitesides
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Kaitlin Sawatzki
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA
| | - Axin Hua
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA
| | - Pinghuang Liu
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Matthew Z Tay
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Kelly E Seaton
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Xiaoying Shen
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Andrew Foulger
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Krissey E Lloyd
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Robert Parks
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Justin Pollara
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Guido Ferrari
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Jae-Sung Yu
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Nathan Vandergrift
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - David C Montefiori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | | | - Scott Hammer
- Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Shelly Karuna
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Peter Gilbert
- The Statistical Center for HIV/AIDS Research and Prevention (SCHARP), Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Doug Grove
- The Statistical Center for HIV/AIDS Research and Prevention (SCHARP), Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Nicole Grunenberg
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - M Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Richard A Koup
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Lawrence Corey
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Gary J Nabel
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Cecilia Morgan
- The Statistical Center for HIV/AIDS Research and Prevention (SCHARP), Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Janine Maenza
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Michael Keefer
- University of Rochester School of Medicine, Rochester, NY, USA
| | - Barney S Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - Georgia D Tomaras
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA.
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116
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Worni-Schudel IM, Clark AG, Chien T, Hwang KK, Chen BJ, Foster MH. Recovery of a human natural antibody against the noncollagenous-1 domain of type IV collagen using humanized models. J Transl Med 2015; 13:185. [PMID: 26048777 PMCID: PMC4467618 DOI: 10.1186/s12967-015-0539-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 05/14/2015] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND Anti-glomerular basement membrane nephritis and Goodpasture syndrome result from autoantibody (Ab)-mediated destruction of kidney and lung. Ab target the noncollagenous 1 (NC1) domain of alpha3(IV) collagen, but little is known about Ab origins or structure. This ignorance is due in part to the inability to recover monoclonal Ab by transformation of patients' blood cells. The aim of this study was to assess the suitability of two humanized models for this purpose. METHODS NOD-scid-gamma immunodeficient mice were engrafted either with human CD34+ hematopoietic stem cells (HSC) (Hu-HSC mice) and immunized with alpha3(IV)NC1 collagen containing the Goodpasture epitopes or with nephritis patients' peripheral blood leukocytes (PBL) (Hu-PBL mice). After in vivo immune cell development and/or expansion, recovered human B cells were Epstein Barr virus (EBV)-transformed, screened for antigen (Ag) binding, electrofused with a mouse-human heterohybridoma, subcloned, and human Ab RNA sequenced by PCR after reverse transcription to cDNA. Flow cytometry was used to assess human B cell markers and differentiation in Hu-PBL mice. RESULTS Sequence analysis of a human Ab derived from an immunized Hu-HSC mouse and reactive with alpha3(IV)NC1 collagen reveals that it is encoded by unmutated heavy and light chain genes. The heavy chain complementarity determining region 3, a major determinant of Ag binding, contains uncommon motifs, including an N-region somatically-introduced highly hydrophobic tetrapeptide and dual cysteines encoded by a uniquely human IGHD2-2 Ab gene segment that lacks a murine counterpart. Comparison of human and mouse autoantibodies suggests that structurally similar murine Ab may arise by convergent selection. In contrast to the Hu-HSC model, transformed human B cells are rarely recovered from Hu-PBL mice, in which human B cells terminally differentiate and lose expression of EBV receptor CD21, thus precluding their transformation and recovery. CONCLUSIONS Hu-HSC mice reveal that potentially pathogenic B cells bearing unmutated Ig receptors reactive with the NC1 domain on alpha3(IV) collagen can be generated in, and not purged from, the human preimmune repertoire. Uniquely human gene elements are recruited to generate the antigen binding site in at least a subset of these autoantibodies, indicating that humanized models may provide insights inaccessible using conventional mouse models.
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Affiliation(s)
| | - Amy G Clark
- Department of Medicine, Duke University Medical Center, Durham, NC, USA.
- Durham VA Medical Center, Durham, NC, USA.
| | - Tiffany Chien
- Department of Medicine, Duke University Medical Center, Durham, NC, USA.
| | - Kwan-Ki Hwang
- Department of Medicine, Duke University Medical Center, Durham, NC, USA.
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, USA.
| | - Benny J Chen
- Department of Medicine, Duke University Medical Center, Durham, NC, USA.
- Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA.
| | - Mary H Foster
- Department of Medicine, Duke University Medical Center, Durham, NC, USA.
- Durham VA Medical Center, Durham, NC, USA.
- Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA.
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117
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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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118
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Steele EJ, Lloyd SS. Soma-to-germline feedback is implied by the extreme polymorphism at IGHV relative to MHC: The manifest polymorphism of the MHC appears greatly exceeded at Immunoglobulin loci, suggesting antigen-selected somatic V mutants penetrate Weismann's Barrier. Bioessays 2015; 37:557-69. [PMID: 25810320 DOI: 10.1002/bies.201400213] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 02/15/2015] [Accepted: 02/24/2015] [Indexed: 01/22/2023]
Abstract
Soma-to-germline feedback is forbidden under the neo-Darwinian paradigm. Nevertheless, there is a growing realization it occurs frequently in immunoglobulin (Ig) variable (V) region genes. This is a surprising development. It arises from a most unlikely source in light of the exposure of co-author EJS to the haplotype data of RL Dawkins and others on the polymorphism of the Major Histocompatibility Complex, which is generally assumed to be the most polymorphic region in the genome (spanning ∼4 Mb). The comparison between the magnitude of MHC polymorphism with estimates for the human heavy chain immunoglobulin V locus (spanning ∼1 Mb), suggests IGHV could be many orders of magnitude more polymorphic than the MHC. This conclusion needs airing in the literature as it implies generational churn and soma-to-germline gene feedback. Pedigree-based experimental strategies to resolve the IGHV issue are outlined.
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Affiliation(s)
- Edward J Steele
- C.Y. O'Connor ERADE Village Foundation, Piara Waters, WA, Australia
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119
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Paiva B, Puig N, García-Sanz R, San Miguel JF. Is This the Time to Introduce Minimal Residual Disease in Multiple Myeloma Clinical Practice? Clin Cancer Res 2015; 21:2001-8. [DOI: 10.1158/1078-0432.ccr-14-2841] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 02/06/2015] [Indexed: 11/16/2022]
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120
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Abstract
The development of high-throughput DNA sequencing technologies has enabled large-scale characterization of functional antibody repertoires, a new method of understanding protective and pathogenic immune responses. Important parameters to consider when sequencing antibody repertoires include the methodology, the B-cell population and clinical characteristics of the individuals analysed, and the bioinformatic analysis. Although focused sequencing of immunoglobulin heavy chains or complement determining regions can be utilized to monitor particular immune responses and B-cell malignancies, high-fidelity analysis of the full-length paired heavy and light chains expressed by individual B cells is critical for characterizing functional antibody repertoires. Bioinformatic identification of clonal antibody families and recombinant expression of representative members produces recombinant antibodies that can be used to identify the antigen targets of functional immune responses and to investigate the mechanisms of their protective or pathogenic functions. Integrated analysis of coexpressed functional genes provides the potential to further pinpoint the most important antibodies and clonal families generated during an immune response. Sequencing antibody repertoires is transforming our understanding of immune responses to autoimmunity, vaccination, infection and cancer. We anticipate that antibody repertoire sequencing will provide next-generation biomarkers, diagnostic tools and therapeutic antibodies for a spectrum of diseases, including rheumatic diseases.
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Affiliation(s)
- William H. Robinson
- Division of Immunology and Rheumatology, CCSR 4135, 269 Campus Drive, Stanford, CA 94305, USA.
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121
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Silva-Sanchez A, Liu CR, Vale AM, Khass M, Kapoor P, Elgavish A, Ivanov II, Ippolito GC, Schelonka RL, Schoeb TR, Burrows PD, Schroeder HW. Violation of an evolutionarily conserved immunoglobulin diversity gene sequence preference promotes production of dsDNA-specific IgG antibodies. PLoS One 2015; 10:e0118171. [PMID: 25706374 PMCID: PMC4338297 DOI: 10.1371/journal.pone.0118171] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 01/08/2015] [Indexed: 11/24/2022] Open
Abstract
Variability in the developing antibody repertoire is focused on the third complementarity determining region of the H chain (CDR-H3), which lies at the center of the antigen binding site where it often plays a decisive role in antigen binding. The power of VDJ recombination and N nucleotide addition has led to the common conception that the sequence of CDR-H3 is unrestricted in its variability and random in its composition. Under this view, the immune response is solely controlled by somatic positive and negative clonal selection mechanisms that act on individual B cells to promote production of protective antibodies and prevent the production of self-reactive antibodies. This concept of a repertoire of random antigen binding sites is inconsistent with the observation that diversity (DH) gene segment sequence content by reading frame (RF) is evolutionarily conserved, creating biases in the prevalence and distribution of individual amino acids in CDR-H3. For example, arginine, which is often found in the CDR-H3 of dsDNA binding autoantibodies, is under-represented in the commonly used DH RFs rearranged by deletion, but is a frequent component of rarely used inverted RF1 (iRF1), which is rearranged by inversion. To determine the effect of altering this germline bias in DH gene segment sequence on autoantibody production, we generated mice that by genetic manipulation are forced to utilize an iRF1 sequence encoding two arginines. Over a one year period we collected serial serum samples from these unimmunized, specific pathogen-free mice and found that more than one-fifth of them contained elevated levels of dsDNA-binding IgG, but not IgM; whereas mice with a wild type DH sequence did not. Thus, germline bias against the use of arginine enriched DH sequence helps to reduce the likelihood of producing self-reactive antibodies.
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Affiliation(s)
- Aaron Silva-Sanchez
- Department of Medicine, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Cun Ren Liu
- Department of Medicine, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Andre M. Vale
- Department of Medicine, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Program in Immunobiology, Carlos Chagas Filho Institute of Biophysics, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Mohamed Khass
- Department of Medicine, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Genetic Engineering Division, National Research Center of Egypt, Ad Doqi, Egypt
| | - Pratibha Kapoor
- Department of Medicine, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Ada Elgavish
- Department of Medicine, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Ivaylo I. Ivanov
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Gregory C. Ippolito
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Robert L. Schelonka
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Trenton R. Schoeb
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Peter D. Burrows
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Harry W. Schroeder
- Department of Medicine, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- * E-mail:
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122
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Automated analysis of high-throughput B-cell sequencing data reveals a high frequency of novel immunoglobulin V gene segment alleles. Proc Natl Acad Sci U S A 2015; 112:E862-70. [PMID: 25675496 DOI: 10.1073/pnas.1417683112] [Citation(s) in RCA: 157] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Individual variation in germline and expressed B-cell immunoglobulin (Ig) repertoires has been associated with aging, disease susceptibility, and differential response to infection and vaccination. Repertoire properties can now be studied at large-scale through next-generation sequencing of rearranged Ig genes. Accurate analysis of these repertoire-sequencing (Rep-Seq) data requires identifying the germline variable (V), diversity (D), and joining (J) gene segments used by each Ig sequence. Current V(D)J assignment methods work by aligning sequences to a database of known germline V(D)J segment alleles. However, existing databases are likely to be incomplete and novel polymorphisms are hard to differentiate from the frequent occurrence of somatic hypermutations in Ig sequences. Here we develop a Tool for Ig Genotype Elucidation via Rep-Seq (TIgGER). TIgGER analyzes mutation patterns in Rep-Seq data to identify novel V segment alleles, and also constructs a personalized germline database containing the specific set of alleles carried by a subject. This information is then used to improve the initial V segment assignments from existing tools, like IMGT/HighV-QUEST. The application of TIgGER to Rep-Seq data from seven subjects identified 11 novel V segment alleles, including at least one in every subject examined. These novel alleles constituted 13% of the total number of unique alleles in these subjects, and impacted 3% of V(D)J segment assignments. These results reinforce the highly polymorphic nature of human Ig V genes, and suggest that many novel alleles remain to be discovered. The integration of TIgGER into Rep-Seq processing pipelines will increase the accuracy of V segment assignments, thus improving B-cell repertoire analyses.
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123
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Watson CT, Steinberg KM, Graves TA, Warren RL, Malig M, Schein J, Wilson RK, Holt RA, Eichler EE, Breden F. Sequencing of the human IG light chain loci from a hydatidiform mole BAC library reveals locus-specific signatures of genetic diversity. Genes Immun 2015; 16:24-34. [PMID: 25338678 PMCID: PMC4304971 DOI: 10.1038/gene.2014.56] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 09/03/2014] [Accepted: 09/03/2014] [Indexed: 12/24/2022]
Abstract
Germline variation at immunoglobulin (IG) loci is critical for pathogen-mediated immunity, but establishing complete haplotype sequences in these regions has been problematic because of complex sequence architecture and diploid source DNA. We sequenced BAC clones from the effectively haploid human hydatidiform mole cell line, CHM1htert, across the light chain IG loci, kappa (IGK) and lambda (IGL), creating single haplotype representations of these regions. The IGL haplotype generated here is 1.25 Mb of contiguous sequence, including four novel IGLV alleles, one novel IGLC allele, and an 11.9-kb insertion. The CH17 IGK haplotype consists of two 644 kb proximal and 466 kb distal contigs separated by a large gap of unknown size; these assemblies added 49 kb of unique sequence extending into this gap. Our analysis also resulted in the characterization of seven novel IGKV alleles and a 16.7-kb region exhibiting signatures of interlocus sequence exchange between distal and proximal IGKV gene clusters. Genetic diversity in IGK/IGL was compared with that of the IG heavy chain (IGH) locus within the same haploid genome, revealing threefold (IGK) and sixfold (IGL) higher diversity in the IGH locus, potentially associated with increased levels of segmental duplication and the telomeric location of IGH.
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Affiliation(s)
- C T Watson
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - K M Steinberg
- Department of Genome Sciences, University of Washington, Seattle, WA USA
- The Genome Institute, Washington University, St Louis, MO USA
| | - T A Graves
- The Genome Institute, Washington University, St Louis, MO USA
| | - R L Warren
- Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia Canada
| | - M Malig
- Department of Genome Sciences, University of Washington, Seattle, WA USA
| | - J Schein
- Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia Canada
| | - R K Wilson
- The Genome Institute, Washington University, St Louis, MO USA
| | - R A Holt
- Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia Canada
| | - E E Eichler
- Department of Genome Sciences, University of Washington, Seattle, WA USA
- Howard Hughes Medical Institute, Seattle, WA USA
| | - F Breden
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
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124
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McGuire AT, Dreyer AM, Carbonetti S, Lippy A, Glenn J, Scheid JF, Mouquet H, Stamatatos L. HIV antibodies. Antigen modification regulates competition of broad and narrow neutralizing HIV antibodies. Science 2014; 346:1380-1383. [PMID: 25504724 DOI: 10.1126/science.1259206] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Some HIV-infected individuals develop broadly neutralizing antibodies (bNAbs), whereas most develop antibodies that neutralize only a narrow range of viruses (nNAbs). bNAbs, but not nNAbs, protect animals from experimental infection and are likely a key component of an effective vaccine. nNAbs and bNAbs target the same regions of the viral envelope glycoprotein (Env), but for reasons that remain unclear only nNAbs are elicited by Env immunization. We show that in contrast to germline-reverted (gl) bNAbs, glnNAbs recognized diverse recombinant Envs. Moreover, owing to binding affinity differences, nNAb B cell progenitors had an advantage in becoming activated and internalizing Env compared with bNAb B cell progenitors. We then identified an Env modification strategy that minimized the activation of nNAb B cells targeting epitopes that overlap those of bNAbs.
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Affiliation(s)
| | - Anita M Dreyer
- Seattle Biomedical Research Institute, Seattle, WA 98109, USA
| | - Sara Carbonetti
- Seattle Biomedical Research Institute, Seattle, WA 98109, USA
| | - Adriana Lippy
- Seattle Biomedical Research Institute, Seattle, WA 98109, USA
| | - Jolene Glenn
- Seattle Biomedical Research Institute, Seattle, WA 98109, USA
| | - Johannes F Scheid
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Hugo Mouquet
- Laboratory of Humoral Response to Pathogens, Department of Immunology, Institut Pasteur and CNRS-URA 1961, 75015 Paris, France
| | - Leonidas Stamatatos
- Seattle Biomedical Research Institute, Seattle, WA 98109, USA.,Department of Global Health, University of Washington, Seattle, WA 98109, USA
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125
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B-cell repertoire responses to varicella-zoster vaccination in human identical twins. Proc Natl Acad Sci U S A 2014; 112:500-5. [PMID: 25535378 DOI: 10.1073/pnas.1415875112] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Adaptive immune responses in humans rely on somatic genetic rearrangements of Ig and T-cell receptor loci to generate diverse antigen receptors. It is unclear to what extent an individual's genetic background affects the characteristics of the antibody repertoire used in responding to vaccination or infection. We studied the B-cell repertoires and clonal expansions in response to attenuated varicella-zoster vaccination in four pairs of adult identical twins and found that the global antibody repertoires of twin pair members showed high similarity in antibody heavy chain V, D, and J gene segment use, and in the length and features of the complementarity-determining region 3, a major determinant of antigen binding. These twin similarities were most pronounced in the IgM-expressing B-cell pools, but were seen to a lesser extent in IgG-expressing B cells. In addition, the degree of antibody somatic mutation accumulated in the B-cell repertoire was highly correlated within twin pair members. Twin pair members had greater numbers of shared convergent antibody sequences, including mutated sequences, suggesting similarity among memory B-cell clonal lineages. Despite these similarities in the memory repertoire, the B-cell clones used in acute responses to ZOSTAVAX vaccination were largely unique to each individual. Taken together, these results suggest that the overall B-cell repertoire is significantly shaped by the underlying germ-line genome, but that stochastic or individual-specific effects dominate the selection of clones in response to an acute antigenic stimulus.
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126
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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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127
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Trück J, Ramasamy MN, Galson JD, Rance R, Parkhill J, Lunter G, Pollard AJ, Kelly DF. Identification of antigen-specific B cell receptor sequences using public repertoire analysis. THE JOURNAL OF IMMUNOLOGY 2014; 194:252-261. [PMID: 25392534 DOI: 10.4049/jimmunol.1401405] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
High-throughput sequencing allows detailed study of the BCR repertoire postimmunization, but it remains unclear to what extent the de novo identification of Ag-specific sequences from the total BCR repertoire is possible. A conjugate vaccine containing Haemophilus influenzae type b (Hib) and group C meningococcal polysaccharides, as well as tetanus toxoid (TT), was used to investigate the BCR repertoire of adult humans following immunization and to test the hypothesis that public or convergent repertoire analysis could identify Ag-specific sequences. A number of Ag-specific BCR sequences have been reported for Hib and TT, which made a vaccine containing these two Ags an ideal immunological stimulus. Analysis of identical CDR3 amino acid sequences that were shared by individuals in the postvaccine repertoire identified a number of known Hib-specific sequences but only one previously described TT sequence. The extension of this analysis to nonidentical, but highly similar, CDR3 amino acid sequences revealed a number of other TT-related sequences. The anti-Hib avidity index postvaccination strongly correlated with the relative frequency of Hib-specific sequences, indicating that the postvaccination public BCR repertoire may be related to more conventional measures of immunogenicity correlating with disease protection. Analysis of public BCR repertoire provided evidence of convergent BCR evolution in individuals exposed to the same Ags. If this finding is confirmed, the public repertoire could be used for rapid and direct identification of protective Ag-specific BCR sequences from peripheral blood.
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Affiliation(s)
- Johannes Trück
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford OX3 7LE, United Kingdom
| | - Maheshi N Ramasamy
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford OX3 7LE, United Kingdom
| | - Jacob D Galson
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford OX3 7LE, United Kingdom
| | - Richard Rance
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Gerton Lunter
- The Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, United Kingdom
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford OX3 7LE, United Kingdom
| | - Dominic F Kelly
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford OX3 7LE, United Kingdom
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128
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Bremel RD, Homan EJ. Frequency Patterns of T-Cell Exposed Amino Acid Motifs in Immunoglobulin Heavy Chain Peptides Presented by MHCs. Front Immunol 2014; 5:541. [PMID: 25389426 PMCID: PMC4211557 DOI: 10.3389/fimmu.2014.00541] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 10/12/2014] [Indexed: 01/17/2023] Open
Abstract
Immunoglobulins are highly diverse protein sequences that are processed and presented to T-cells by B-cells and other antigen presenting cells. We examined a large dataset of immunoglobulin heavy chain variable regions (IGHV) to assess the diversity of T-cell exposed motifs (TCEMs). TCEM comprise those amino acids in a MHC-bound peptide, which face outwards, surrounded by the MHC histotope, and which engage the T-cell receptor. Within IGHV there is a distinct pattern of predicted MHC class II binding and a very high frequency of re-use of the TCEMs. The re-use frequency indicates that only a limited number of different cognate T-cells are required to engage many different clonal B-cells. The amino acids in each outward-facing TCEM are intercalated with the amino acids of inward-facing MHC groove-exposed motifs (GEM). Different GEM may have differing, allele-specific, MHC binding affinities. The intercalation of TCEM and GEM in a peptide allows for a vast combinatorial repertoire of epitopes, each eliciting a different response. Outcome of T-cell receptor binding is determined by overall signal strength, which is a function of the number of responding T-cells and the duration of engagement. Hence, the frequency of TCEM re-use appears to be an important determinant of whether a T-cell response is stimulatory or suppressive. The frequency distribution of TCEMs implies that somatic hypermutation is followed by T-cell clonal expansion that develops along repeated pathways. The observations of TCEM and GEM derived from immunoglobulins suggest a relatively simple, yet powerful, mechanism to correlate T-cell polyspecificity, through re-use of TCEMs, with a very high degree of specificity achieved by combination with a diversity of GEMs. The frequency profile of TCEMs also points to an economical mechanism for maintaining T-cell memory, recall, and self-discrimination based on an endogenously generated profile of motifs.
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129
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Levin M, Davies AM, Liljekvist M, Carlsson F, Gould HJ, Sutton BJ, Ohlin M. Human IgE against the major allergen Bet v 1--defining an epitope with limited cross-reactivity between different PR-10 family proteins. Clin Exp Allergy 2014; 44:288-99. [PMID: 24447087 PMCID: PMC4215112 DOI: 10.1111/cea.12230] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 09/24/2013] [Accepted: 10/25/2013] [Indexed: 02/05/2023]
Abstract
Background The interaction between IgE and allergen is a key event at the initiation of an allergic response, and its characteristics have substantial effects on the clinical manifestation. Despite this, the molecular details of the interaction between human IgE and the major birch allergen Bet v 1, one of the most potent tree allergens, still remain poorly investigated. Objective To isolate Bet v 1-specific human monoclonal IgE and characterize their interaction with the allergen. Methods Recombinant human IgE were isolated from a combinatorial antibody fragment library and their interaction with Bet v 1 assessed using various immunological assays. The structure of one such IgE in the single-chain fragment variable format was determined using X-ray crystallography. Results We present four novel Bet v 1-specific IgE, for one of which we solve the structure, all with their genetic origin in the IGHV5 germline gene, and demonstrate that they target two non-overlapping epitopes on the surface of Bet v 1, thereby fulfilling the basic criteria for FcεRI cross-linkage. We further define these epitopes and for one epitope pinpoint single amino acid residues important for the interaction with human IgE. This provides a potential explanation, at the molecular level, for the differences in recognition of isoforms of Bet v 1 and other allergens in the PR-10 protein family displayed by IgE targeting this epitope. Finally, we present the first high-resolution structure of a human allergen-specific IgE fragment in the single-chain fragment variable (scFv) format. Conclusions and Clinical Relevance We here display the usefulness of allergen-specific human monoclonal IgE as a tool in studies of the crucial molecular interaction taking place at the initiation of an allergic response. Such studies may aid us in development of better diagnostic tools and guide us in the development of new therapeutic compounds.
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Affiliation(s)
- M Levin
- Department of Immunotechnology, Lund University, Lund, Sweden
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Rounds WH, Ligocki AJ, Levin MK, Greenberg BM, Bigwood DW, Eastman EM, Cowell LG, Monson NL. The antibody genetics of multiple sclerosis: comparing next-generation sequencing to sanger sequencing. Front Neurol 2014; 5:166. [PMID: 25278930 PMCID: PMC4165282 DOI: 10.3389/fneur.2014.00166] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 08/19/2014] [Indexed: 11/29/2022] Open
Abstract
We previously identified a distinct mutation pattern in the antibody genes of B cells isolated from cerebrospinal fluid (CSF) that can identify patients who have relapsing-remitting multiple sclerosis (RRMS) and patients with clinically isolated syndromes who will convert to RRMS. This antibody gene signature (AGS) was developed using Sanger sequencing of single B cells. While potentially helpful to patients, Sanger sequencing is not an assay that can be practically deployed in clinical settings. In order to provide AGS evaluations to patients as part of their diagnostic workup, we developed protocols to generate AGS scores using next-generation DNA sequencing (NGS) on CSF-derived cell pellets without the need to isolate single cells. This approach has the potential to increase the coverage of the B-cell population being analyzed, reduce the time needed to generate AGS scores, and may improve the overall performance of the AGS approach as a diagnostic test in the future. However, no investigations have focused on whether NGS-based repertoires will properly reflect antibody gene frequencies and somatic hypermutation patterns defined by Sanger sequencing. To address this issue, we isolated paired CSF samples from eight patients who either had MS or were at risk to develop MS. Here, we present data that antibody gene frequencies and somatic hypermutation patterns are similar in Sanger and NGS-based antibody repertoires from these paired CSF samples. In addition, AGS scores derived from the NGS database correctly identified the patients who initially had or subsequently converted to RRMS, with precision similar to that of the Sanger sequencing approach. Further investigation of the utility of the AGS in predicting conversion to MS using NGS-derived antibody repertoires in a larger cohort of patients is warranted.
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Affiliation(s)
- William H Rounds
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center , Dallas, TX , USA
| | - Ann J Ligocki
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center , Dallas, TX , USA
| | - Mikhail K Levin
- Department of Clinical Sciences, University of Texas Southwestern Medical Center , Dallas, TX , USA
| | - Benjamin M Greenberg
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center , Dallas, TX , USA
| | | | | | - Lindsay G Cowell
- Department of Clinical Sciences, University of Texas Southwestern Medical Center , Dallas, TX , USA
| | - Nancy L Monson
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center , Dallas, TX , USA ; Department of Immunology, University of Texas Southwestern Medical Center , Dallas, TX , USA
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131
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Jiang Y, Redmond D, Nie K, Eng KW, Clozel T, Martin P, Tan LH, Melnick AM, Tam W, Elemento O. Deep sequencing reveals clonal evolution patterns and mutation events associated with relapse in B-cell lymphomas. Genome Biol 2014; 15:432. [PMID: 25123191 PMCID: PMC4158101 DOI: 10.1186/s13059-014-0432-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 08/07/2014] [Indexed: 12/12/2022] Open
Abstract
Background Molecular mechanisms associated with frequent relapse of diffuse large B-cell lymphoma (DLBCL) are poorly defined. It is especially unclear how primary tumor clonal heterogeneity contributes to relapse. Here, we explore unique features of B-cell lymphomas - VDJ recombination and somatic hypermutation - to address this question. Results We performed high-throughput sequencing of rearranged VDJ junctions in 14 pairs of matched diagnosis-relapse tumors, among which 7 pairs were further characterized by exome sequencing. We identify two distinctive modes of clonal evolution of DLBCL relapse: an early-divergent mode in which clonally related diagnosis and relapse tumors diverged early and developed in parallel; and a late-divergent mode in which relapse tumors developed directly from diagnosis tumors with minor divergence. By examining mutation patterns in the context of phylogenetic information provided by VDJ junctions, we identified mutations in epigenetic modifiers such as KMT2D as potential early driving events in lymphomagenesis and immune escape alterations as relapse-associated events. Conclusions Altogether, our study for the first time provides important evidence that DLBCL relapse may result from multiple, distinct tumor evolutionary mechanisms, providing rationale for therapies for each mechanism. Moreover, this study highlights the urgent need to understand the driving roles of epigenetic modifier mutations in lymphomagenesis, and immune surveillance factor genetic lesions in relapse. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0432-0) contains supplementary material, which is available to authorized users.
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132
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Bashford-Rogers RJM, Palser AL, Idris SF, Carter L, Epstein M, Callard RE, Douek DC, Vassiliou GS, Follows GA, Hubank M, Kellam P. Capturing needles in haystacks: a comparison of B-cell receptor sequencing methods. BMC Immunol 2014; 15:29. [PMID: 25189176 PMCID: PMC4243823 DOI: 10.1186/s12865-014-0029-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 07/15/2014] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Deep-sequencing methods are rapidly developing in the field of B-cell receptor (BCR) and T-cell receptor (TCR) diversity. These promise to revolutionise our understanding of adaptive immune dynamics, identify novel antibodies, and allow monitoring of minimal residual disease. However, different methods for BCR and TCR enrichment and amplification have been proposed. Here we perform the first systematic comparison between different methods of enrichment, amplification and sequencing for generating BCR and TCR repertoires using large sample numbers. RESULTS Resampling from the same RNA or cDNA pool results in highly correlated and reproducible repertoires, but resampling low frequency clones leads to stochastic variance. Repertoires generated by different sequencing methods (454 Roche and Illumina MiSeq) and amplification methods (multiplex PCR, 5' Rapid amplification of cDNA ends (5'RACE), and RNA-capture) are highly correlated, and resulting IgHV gene frequencies between the different methods were not significantly different. Read length has an impact on captured repertoire structure, and ultimately full-length BCR sequences are most informative for repertoire analysis as diversity outside of the CDR is very useful for phylogenetic analysis. Additionally, we show RNA-based BCR repertoires are more informative than using DNA. CONCLUSIONS Repertoires generated by different sequencing and amplification methods are consistent, but we show that read lengths, depths and error profiles should be considered in experimental design, and multiple sampling approaches could be employed to minimise stochastic sampling variation. This detailed investigation of immune repertoire sequencing methods is essential for informing basic and clinical research.
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Affiliation(s)
| | - Anne L Palser
- />Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Saad F Idris
- />Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Lisa Carter
- />Molecular Haematology and Cancer Biology Unit, UCL Institute of Child Health, London, WC1N 1EH UK
| | - Michael Epstein
- />Molecular Haematology and Cancer Biology Unit, UCL Institute of Child Health, London, WC1N 1EH UK
| | - Robin E Callard
- />Molecular Haematology and Cancer Biology Unit, UCL Institute of Child Health, London, WC1N 1EH UK
| | - Daniel C Douek
- />Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892 USA
| | - George S Vassiliou
- />Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - George A Follows
- />Department of Hematology, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0QQ UK
| | - Mike Hubank
- />Molecular Haematology and Cancer Biology Unit, UCL Institute of Child Health, London, WC1N 1EH UK
| | - Paul Kellam
- />Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
- />Research Department of Infection, Division of Infection and Immunity, University College London, Gower Street, London, WC1E 6BT UK
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Lavinder JJ, Hoi KH, Reddy ST, Wine Y, Georgiou G. Systematic characterization and comparative analysis of the rabbit immunoglobulin repertoire. PLoS One 2014; 9:e101322. [PMID: 24978027 PMCID: PMC4076286 DOI: 10.1371/journal.pone.0101322] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 06/04/2014] [Indexed: 11/18/2022] Open
Abstract
Rabbits have been used extensively as a model system for the elucidation of the mechanism of immunoglobulin diversification and for the production of antibodies. We employed Next Generation Sequencing to analyze Ig germline V and J gene usage, CDR3 length and amino acid composition, and gene conversion frequencies within the functional (transcribed) IgG repertoire of the New Zealand white rabbit (Oryctolagus cuniculus). Several previously unannotated rabbit heavy chain variable (VH) and light chain variable (VL) germline elements were deduced bioinformatically using multidimensional scaling and k-means clustering methods. We estimated the gene conversion frequency in the rabbit at 23% of IgG sequences with a mean gene conversion tract length of 59±36 bp. Sequencing and gene conversion analysis of the chicken, human, and mouse repertoires revealed that gene conversion occurs much more extensively in the chicken (frequency 70%, tract length 79±57 bp), was observed to a small, yet statistically significant extent in humans, but was virtually absent in mice.
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Affiliation(s)
- Jason J. Lavinder
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, United States of America
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America
| | - Kam Hon Hoi
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas, United States of America
| | - Sai T. Reddy
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, United States of America
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas, United States of America
| | - Yariv Wine
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, United States of America
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America
| | - George Georgiou
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, United States of America
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas, United States of America
- Section of Molecular Genetics and Microbiology, University of Texas at Austin, Austin, Texas, United States of America
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Gazzola A, Mannu C, Rossi M, Laginestra MA, Sapienza MR, Fuligni F, Etebari M, Melle F, Sabattini E, Agostinelli C, Bacci F, Sagramoso Sacchetti CA, Pileri SA, Piccaluga PP. The evolution of clonality testing in the diagnosis and monitoring of hematological malignancies. Ther Adv Hematol 2014; 5:35-47. [PMID: 24688753 PMCID: PMC3949299 DOI: 10.1177/2040620713519729] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Currently, distinguishing between benign and malignant lymphoid proliferations is based on a combination of clinical characteristics, cyto/histomorphology, immunophenotype and the identification of well-defined chromosomal aberrations. However, such diagnoses remain challenging in 10-15% of cases of lymphoproliferative disorders, and clonality assessments are often required to confirm diagnostic suspicions. In recent years, the development of new techniques for clonality detection has allowed researchers to better characterize, classify and monitor hematological neoplasms. In the past, clonality was primarily studied by performing Southern blotting analyses to characterize rearrangements in segments of the IG and TCR genes. Currently, the most commonly used method in the clinical molecular diagnostic laboratory is polymerase chain reaction (PCR), which is an extremely sensitive technique for detecting nucleic acids. This technique is rapid, accurate, specific, and sensitive, and it can be used to analyze small biopsies as well as formalin-fixed paraffin-embedded samples. These advantages make PCR-based approaches the current gold standard for IG/TCR clonality testing. Since the completion of the first human genome sequence, there has been a rapid development of technologies to facilitate high-throughput sequencing of DNA. These techniques have been applied to the deep characterization and classification of various diseases, patient stratification, and the monitoring of minimal residual disease. Furthermore, these novel approaches have the potential to significantly improve the sensitivity and cost of clonality assays and post-treatment monitoring of B- and T-cell malignancies. However, more studies will be required to demonstrate the utility, sensitivity, and benefits of these methods in order to warrant their adoption into clinical practice. In this review, recent developments in clonality testing are examined with an emphasis on highly sensitive systems for improving diagnostic workups and minimal residual disease assessments.
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Affiliation(s)
- Anna Gazzola
- Department of Experimental, Diagnostic, and Specialty Medicine, Bologna University Medical School, Unit of Hematopathology, S. Orsola Malpighi Hospital, Bologna, Italy
| | - Claudia Mannu
- Department of Experimental, Diagnostic, and Specialty Medicine, Bologna University Medical School, Unit of Hematopathology, S. Orsola Malpighi Hospital, Bologna, Italy
| | - Maura Rossi
- Department of Experimental, Diagnostic, and Specialty Medicine, Bologna University Medical School, Unit of Hematopathology, S. Orsola Malpighi Hospital, Bologna, Italy
| | - Maria Antonella Laginestra
- Department of Experimental, Diagnostic, and Specialty Medicine, Bologna University Medical School, Unit of Hematopathology, S. Orsola Malpighi Hospital, Bologna, Italy
| | - Maria Rosaria Sapienza
- Department of Experimental, Diagnostic, and Specialty Medicine, Bologna University Medical School, Unit of Hematopathology, S. Orsola Malpighi Hospital, Bologna, Italy
| | - Fabio Fuligni
- Department of Experimental, Diagnostic, and Specialty Medicine, Bologna University Medical School, Unit of Hematopathology, S. Orsola Malpighi Hospital, Bologna, Italy
| | - Maryam Etebari
- Department of Experimental, Diagnostic, and Specialty Medicine, Bologna University Medical School, Unit of Hematopathology, S. Orsola Malpighi Hospital, Bologna, Italy
| | - Federica Melle
- Department of Experimental, Diagnostic, and Specialty Medicine, Bologna University Medical School, Unit of Hematopathology, S. Orsola Malpighi Hospital, Bologna, Italy
| | - Elena Sabattini
- Department of Experimental, Diagnostic, and Specialty Medicine, Bologna University Medical School, Unit of Hematopathology, S. Orsola Malpighi Hospital, Bologna, Italy
| | - Claudio Agostinelli
- Department of Experimental, Diagnostic, and Specialty Medicine, Bologna University Medical School, Unit of Hematopathology, S. Orsola Malpighi Hospital, Bologna, Italy
| | - Francesco Bacci
- Department of Experimental, Diagnostic, and Specialty Medicine, Bologna University Medical School, Unit of Hematopathology, S. Orsola Malpighi Hospital, Bologna, Italy
| | - Carlo Alberto Sagramoso Sacchetti
- Department of Experimental, Diagnostic, and Specialty Medicine, Bologna University Medical School, Unit of Hematopathology, S. Orsola Malpighi Hospital, Bologna, Italy
| | - Stefano Aldo Pileri
- Department of Experimental, Diagnostic, and Specialty Medicine, Bologna University Medical School, Unit of Hematopathology, S. Orsola Malpighi Hospital, Bologna, Italy
| | - Pier Paolo Piccaluga
- Molecular Pathology Laboratory, Department of Experimental, Diagnostic, and Specialty Medicine, Bologna University Medical School, Unit of Hematopathology, S. Orsola Malpighi Hospital, Via Massarenti 9, 40138 Bologna, Italy
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Briney BS, Willis JR, Finn JA, McKinney BA, Crowe JE. Tissue-specific expressed antibody variable gene repertoires. PLoS One 2014; 9:e100839. [PMID: 24956460 PMCID: PMC4067404 DOI: 10.1371/journal.pone.0100839] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2013] [Accepted: 05/30/2014] [Indexed: 01/05/2023] Open
Abstract
Recent developments in genetic technologies allow deep analysis of the sequence diversity of immune repertoires, but little work has been reported on the architecture of immune repertoires in mucosal tissues. Antibodies are the key to prevention of infections at the mucosal surface, but it is currently unclear whether the B cell repertoire at mucosal surfaces reflects the dominant antibodies found in the systemic compartment or whether mucosal tissues harbor unique repertoires. We examined the expressed antibody variable gene repertoires from 10 different human tissues using RNA samples derived from a large number of individuals. The results revealed that mucosal tissues such as stomach, intestine and lung possess unique antibody gene repertoires that differed substantially from those found in lymphoid tissues or peripheral blood. Mutation frequency analysis of mucosal tissue repertoires revealed that they were highly mutated, with little evidence for the presence of naïve B cells, in contrast to blood. Mucosal tissue repertoires possessed longer heavy chain complementarity determining region 3 loops than lymphoid tissue repertoires. We also noted a large increase in frequency of both insertions and deletions in the small intestine antibody repertoire. These data suggest that mucosal immune repertoires are distinct in many ways from the systemic compartment.
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Affiliation(s)
- Bryan S. Briney
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Jordan R. Willis
- The Chemical and Physical Biology Program, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Jessica A. Finn
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Brett A. McKinney
- Tandy School of Computer Science and Department of Mathematics, University of Tulsa, Tulsa, Oklahoma, United States of America
| | - James E. Crowe
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- * E-mail:
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136
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Human immunoglobulin classes and subclasses show variability in VDJ gene mutation levels. Immunol Cell Biol 2014; 92:729-33. [DOI: 10.1038/icb.2014.44] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 04/30/2014] [Accepted: 04/30/2014] [Indexed: 01/30/2023]
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137
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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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138
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Galson JD, Pollard AJ, Trück J, Kelly DF. Studying the antibody repertoire after vaccination: practical applications. Trends Immunol 2014; 35:319-31. [PMID: 24856924 DOI: 10.1016/j.it.2014.04.005] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Revised: 04/17/2014] [Accepted: 04/28/2014] [Indexed: 12/25/2022]
Abstract
Nearly all licensed vaccines have been developed to confer protection against infectious diseases by stimulating the production of antibodies by B cells, but the nature of a successful antibody response has been difficult to capture. Recent advances in next-generation sequencing (NGS) technology have allowed high-resolution characterization of the antibody repertoire, and of the changes that occur following vaccination. These approaches have yielded important insights into the B cell response, and have raised the possibility of using specific antibody sequences as measures of vaccine immunogenicity. Here, we review recent findings based on antibody repertoire sequencing, and discuss potential applications of these new technologies and of the analyses of the increasing volume of antibody sequence data in the context of vaccine development.
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Affiliation(s)
- Jacob D Galson
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, Oxford, UK.
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, Oxford, UK.
| | - Johannes Trück
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Dominic F Kelly
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, Oxford, UK
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139
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Avnir Y, Tallarico AS, Zhu Q, Bennett AS, Connelly G, Sheehan J, Sui J, Fahmy A, Huang CY, Cadwell G, Bankston LA, McGuire AT, Stamatatos L, Wagner G, Liddington RC, Marasco WA. Molecular signatures of hemagglutinin stem-directed heterosubtypic human neutralizing antibodies against influenza A viruses. PLoS Pathog 2014; 10:e1004103. [PMID: 24788925 PMCID: PMC4006906 DOI: 10.1371/journal.ppat.1004103] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Accepted: 03/15/2014] [Indexed: 12/28/2022] Open
Abstract
Recent studies have shown high usage of the IGHV1-69 germline immunoglobulin gene for influenza hemagglutinin stem-directed broadly-neutralizing antibodies (HV1-69-sBnAbs). Here we show that a major structural solution for these HV1-69-sBnAbs is achieved through a critical triad comprising two CDR-H2 loop anchor residues (a hydrophobic residue at position 53 (Ile or Met) and Phe54), and CDR-H3-Tyr at positions 98±1; together with distinctive V-segment CDR amino acid substitutions that occur in positions sparse in AID/polymerase-η recognition motifs. A semi-synthetic IGHV1-69 phage-display library screen designed to investigate AID/polη restrictions resulted in the isolation of HV1-69-sBnAbs that featured a distinctive Ile52Ser mutation in the CDR-H2 loop, a universal CDR-H3 Tyr at position 98 or 99, and required as little as two additional substitutions for heterosubtypic neutralizing activity. The functional importance of the Ile52Ser mutation was confirmed by mutagenesis and by BCR studies. Structural modeling suggests that substitution of a small amino acid at position 52 (or 52a) facilitates the insertion of CDR-H2 Phe54 and CDR-H3-Tyr into adjacent pockets on the stem. These results support the concept that activation and expansion of a defined subset of IGHV1-69-encoded B cells to produce potent HV1-69-sBnAbs does not necessarily require a heavily diversified V-segment acquired through recycling/reentry into the germinal center; rather, the incorporation of distinctive amino acid substitutions by Phase 2 long-patch error-prone repair of AID-induced mutations or by random non-AID SHM events may be sufficient. We propose that these routes of B cell maturation should be further investigated and exploited as a pathway for HV1-69-sBnAb elicitation by vaccination. The quest for universal influenza vaccine has gained wide interest with the discovery of human neutralizing antibodies that are able to variably cross neutralize and protect against different influenza strains, subtypes, groups and lineages. These antibodies, which bind to a highly conserved epitope in the hemagglutinin stem, are often encoded by rearranged IGHV1-69 germline genes that alone make contact with HA and prevent virus entry and emergence of escape mutants. Our study was undertaken to gain an understanding of what structural requirements enable a rearranged IGHV1-69 Ab to become a potent cross-neutralizing antibody. We found that in addition to a critical amino acid triad consisting of a pair of anchor residues in CDR-H2 and a properly positioned CDR-H3 Tyr, distinctive V-segment substitutions that arise in positions that are distinct from phase I AID somatic hypermutation (SHM) hotspot motifs are often required. As few as two V-segment SHM can fulfill this role which appears to facilitate the optimal binding of CDR-H2 Phe54 and CHR-H3-Tyr into adjacent hydrophobic pockets in the HA stem. These studies provide new information on the SHM requirements for IGHV1-69-encoded B cells to produce HV1-69-sBnAbs and suggest that there may exist alternative routes to their elicitation by vaccination.
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Affiliation(s)
- Yuval Avnir
- Department of Cancer Immunology & AIDS, Dana-Farber Cancer Institute, Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Aimee S Tallarico
- Department of Cancer Immunology & AIDS, Dana-Farber Cancer Institute, Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Quan Zhu
- Department of Cancer Immunology & AIDS, Dana-Farber Cancer Institute, Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Andrew S Bennett
- Department of Cancer Immunology & AIDS, Dana-Farber Cancer Institute, Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Gene Connelly
- Department of Cancer Immunology & AIDS, Dana-Farber Cancer Institute, Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jared Sheehan
- Department of Cancer Immunology & AIDS, Dana-Farber Cancer Institute, Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jianhua Sui
- Department of Cancer Immunology & AIDS, Dana-Farber Cancer Institute, Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Amr Fahmy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Chiung-yu Huang
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Greg Cadwell
- Infectious and Inflammatory Disease Center, Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America
| | - Laurie A Bankston
- Infectious and Inflammatory Disease Center, Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America
| | - Andrew T McGuire
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Leonidas Stamatatos
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Robert C Liddington
- Infectious and Inflammatory Disease Center, Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America
| | - Wayne A Marasco
- Department of Cancer Immunology & AIDS, Dana-Farber Cancer Institute, Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
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140
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Identification of human neutralizing antibodies against MERS-CoV and their role in virus adaptive evolution. Proc Natl Acad Sci U S A 2014; 111:E2018-26. [PMID: 24778221 DOI: 10.1073/pnas.1402074111] [Citation(s) in RCA: 200] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The newly emerging Middle East Respiratory Syndrome coronavirus (MERS-CoV) causes a Severe Acute Respiratory Syndrome-like disease with ∼43% mortality. Given the recent detection of virus in dromedary camels, zoonotic transfer of MERS-CoV to humans is suspected. In addition, little is known about the role of human neutralizing Ab (nAb) pressure as a driving force in MERS-CoV adaptive evolution. Here, we used a well-characterized nonimmune human Ab-phage library and a panning strategy with proteoliposomes and cells to identify seven human nAbs against the receptor-binding domain (RBD) of the MERS-CoV Spike protein. These nAbs bind to three different epitopes in the RBD and human dipeptidyl peptidase 4 (hDPP4) interface with subnanomolar/nanomolar binding affinities and block the binding of MERS-CoV Spike protein with its hDPP4 receptor. Escape mutant assays identified five amino acid residues that are critical for neutralization escape. Despite the close proximity of the three epitopes on the RBD interface, escape from one epitope did not have a major impact on neutralization with Abs directed to a different epitope. Importantly, the majority of escape mutations had negative impacts on hDPP4 receptor binding and viral fitness. To our knowledge, these results provide the first report on human nAbs against MERS-CoV that may contribute to MERS-CoV clearance and evolution. Moreover, in the absence of a licensed vaccine or antiviral for MERS, this panel of nAbs offers the possibility of developing human mAb-based immunotherapy, especially for health-care workers.
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141
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Mroczek ES, Ippolito GC, Rogosch T, Hoi KH, Hwangpo TA, Brand MG, Zhuang Y, Liu CR, Schneider DA, Zemlin M, Brown EE, Georgiou G, Schroeder HW. Differences in the composition of the human antibody repertoire by B cell subsets in the blood. Front Immunol 2014; 5:96. [PMID: 24678310 PMCID: PMC3958703 DOI: 10.3389/fimmu.2014.00096] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 02/23/2014] [Indexed: 12/23/2022] Open
Abstract
The vast initial diversity of the antibody repertoire is generated centrally by means of a complex series of V(D)J gene rearrangement events, variation in the site of gene segment joining, and TdT catalyzed N-region addition. Although the diversity is great, close inspection has revealed distinct and unique characteristics in the antibody repertoires expressed by different B cell developmental subsets. In order to illustrate our approach to repertoire analysis, we present an in-depth comparison of V(D)J gene usage, hydrophobicity, length, DH reading frame, and amino acid usage between heavy chain repertoires expressed by immature, transitional, mature, memory IgD+, memory IgD−, and plasmacytes isolated from the blood of a single individual. Our results support the view that in both human and mouse, the H chain repertoires expressed by individual, developmental B cell subsets appear to differ in sequence content. Sequencing of unsorted B cells from the blood is thus likely to yield an incomplete or compressed view of what is actually happening in the immune response of the individual. Our findings support the view that studies designed to correlate repertoire expression with diseases of immune function will likely require deep sequencing of B cells sorted by subset.
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Affiliation(s)
- Eva Szymanska Mroczek
- Department of Microbiology, University of Alabama at Birmingham , Birmingham, AL , USA
| | - Gregory C Ippolito
- Department of Molecular Biosciences, University of Texas at Austin , Austin, TX , USA
| | - Tobias Rogosch
- Laboratory for Neonatology and Pediatric Immunology, Department of Pediatrics, Philipps-University , Marburg , Germany
| | - Kam Hon Hoi
- Department of Chemical Engineering, University of Texas at Austin , Austin, TX , USA ; Department of Biomedical Engineering, University of Texas at Austin , Austin, TX , USA
| | - Tracy A Hwangpo
- Department of Medicine, University of Alabama at Birmingham , Birmingham, AL , USA
| | - Marsha G Brand
- Department of Medicine, University of Alabama at Birmingham , Birmingham, AL , USA
| | - Yingxin Zhuang
- Department of Medicine, University of Alabama at Birmingham , Birmingham, AL , USA
| | - Cun Ren Liu
- Department of Medicine, University of Alabama at Birmingham , Birmingham, AL , USA
| | - David A Schneider
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham , Birmingham, AL , USA
| | - Michael Zemlin
- Laboratory for Neonatology and Pediatric Immunology, Department of Pediatrics, Philipps-University , Marburg , Germany
| | - Elizabeth E Brown
- Department of Epidemiology, University of Alabama at Birmingham , Birmingham, AL , USA
| | - George Georgiou
- Department of Molecular Biosciences, University of Texas at Austin , Austin, TX , USA ; Department of Chemical Engineering, University of Texas at Austin , Austin, TX , USA ; Department of Biomedical Engineering, University of Texas at Austin , Austin, TX , USA
| | - Harry W Schroeder
- Department of Microbiology, University of Alabama at Birmingham , Birmingham, AL , USA ; Department of Medicine, University of Alabama at Birmingham , Birmingham, AL , USA
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142
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Wang Y, Jackson KJL, Davies J, Chen Z, Gaeta BA, Rimmer J, Sewell WA, Collins AM. IgE-associated IGHV genes from venom and peanut allergic individuals lack mutational evidence of antigen selection. PLoS One 2014; 9:e89730. [PMID: 24586993 PMCID: PMC3934916 DOI: 10.1371/journal.pone.0089730] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2013] [Accepted: 01/22/2014] [Indexed: 11/18/2022] Open
Abstract
Antigen selection of B cells within the germinal center reaction generally leads to the accumulation of replacement mutations in the complementarity-determining regions (CDRs) of immunoglobulin genes. Studies of mutations in IgE-associated VDJ gene sequences have cast doubt on the role of antigen selection in the evolution of the human IgE response, and it may be that selection for high affinity antibodies is a feature of some but not all allergic diseases. The severity of IgE-mediated anaphylaxis is such that it could result from higher affinity IgE antibodies. We therefore investigated IGHV mutations in IgE-associated sequences derived from ten individuals with a history of anaphylactic reactions to bee or wasp venom or peanut allergens. IgG sequences, which more certainly experience antigen selection, served as a control dataset. A total of 6025 unique IgE and 5396 unique IgG sequences were generated using high throughput 454 pyrosequencing. The proportion of replacement mutations seen in the CDRs of the IgG dataset was significantly higher than that of the IgE dataset, and the IgE sequences showed little evidence of antigen selection. To exclude the possibility that 454 errors had compromised analysis, rigorous filtering of the datasets led to datasets of 90 core IgE sequences and 411 IgG sequences. These sequences were present as both forward and reverse reads, and so were most unlikely to include sequencing errors. The filtered datasets confirmed that antigen selection plays a greater role in the evolution of IgG sequences than of IgE sequences derived from the study participants.
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Affiliation(s)
- Yan Wang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Katherine J. L. Jackson
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Janet Davies
- The Lung and Allergy Research Centre, School of Medicine, The University of Queensland, Woolloongabba, Australia
| | - Zhiliang Chen
- School of Computer Science and Engineering, University of New South Wales, Sydney, Australia
| | - Bruno A. Gaeta
- School of Computer Science and Engineering, University of New South Wales, Sydney, Australia
| | | | - William A. Sewell
- Institute of Laboratory Medicine, St Vincent's Hospital, Darlinghurst, Australia and St Vincent's Clinical School, University of New South Wales, Darlinghurst, Australia
| | - Andrew M. Collins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
- * E-mail:
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143
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Niklas N, Pröll J, Weinberger J, Zopf A, Wiesinger K, Krismer K, Bettelheim P, Gabriel C. Qualifying high-throughput immune repertoire sequencing. Cell Immunol 2014; 288:31-8. [PMID: 24607567 DOI: 10.1016/j.cellimm.2014.02.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 11/06/2013] [Accepted: 02/12/2014] [Indexed: 10/25/2022]
Abstract
Diversity of B and T cell receptors, achieved by gene recombination and somatic hypermutation, allows the immune system for recognition and targeted reaction against various threats. Next-generation sequencing for assessment of a cell's gene composition and variation makes deep analysis of one individual's immune spectrum feasible. An easy to apply but detailed analysis and visualization strategy is necessary to process all sequences generated. We performed sequencing utilizing the 454 system for CLL and control samples, utilized the IMGT database and applied the presented analysis tools. With the applied protocol, malignant clones are found and characterized, mutational status compared to germline identity is elaborated in detail showing that the CLL mutation status is not as monoclonal as generally thought. On the other hand, this strategy is not solely applicable to the 454 sequencing system but can easily be transferred to any other next-generation sequencing platform.
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Affiliation(s)
- Norbert Niklas
- Red Cross Transfusion Service for Upper Austria, Krankenhausstraße 7, 4020 Linz, Austria.
| | - Johannes Pröll
- Red Cross Transfusion Service for Upper Austria, Krankenhausstraße 7, 4020 Linz, Austria.
| | - Johannes Weinberger
- Red Cross Transfusion Service for Upper Austria, Krankenhausstraße 7, 4020 Linz, Austria.
| | - Agnes Zopf
- Red Cross Transfusion Service for Upper Austria, Krankenhausstraße 7, 4020 Linz, Austria.
| | - Karin Wiesinger
- Red Cross Transfusion Service for Upper Austria, Krankenhausstraße 7, 4020 Linz, Austria.
| | - Konstantin Krismer
- University of Applied Sciences Upper Austria, Softwarepark 11, 4232 Hagenberg, Austria.
| | - Peter Bettelheim
- Division of Hematology/Oncology, Elisabethinen Hospital Linz, Fadingerstraße 1, 4020 Linz, Austria.
| | - Christian Gabriel
- Red Cross Transfusion Service for Upper Austria, Krankenhausstraße 7, 4020 Linz, Austria.
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144
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Lomakin YA, Zakharova MY, Stepanov AV, Dronina MA, Smirnov IV, Bobik TV, Pyrkov AY, Tikunova NV, Sharanova SN, Boitsov VM, Vyazmin SY, Kabilov MR, Tupikin AE, Krasnov AN, Bykova NA, Medvedeva YA, Fridman MV, Favorov AV, Ponomarenko NA, Dubina MV, Boyko AN, Vlassov VV, Belogurov AA, Gabibov AG. Heavy-light chain interrelations of MS-associated immunoglobulins probed by deep sequencing and rational variation. Mol Immunol 2014; 62:305-14. [PMID: 24534716 DOI: 10.1016/j.molimm.2014.01.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 01/17/2014] [Accepted: 01/22/2014] [Indexed: 01/21/2023]
Abstract
The mechanisms triggering most of autoimmune diseases are still obscure. Autoreactive B cells play a crucial role in the development of such pathologies and, in particular, production of autoantibodies of different specificities. The combination of deep-sequencing technology with functional studies of antibodies selected from highly representative immunoglobulin combinatorial libraries may provide unique information on specific features in the repertoires of autoreactive B cells. Here, we have analyzed cross-combinations of the variable regions of human immunoglobulins against the myelin basic protein (MBP) previously selected from a multiple sclerosis (MS)-related scFv phage-display library. On the other hand, we have performed deep sequencing of the sublibraries of scFvs against MBP, Epstein-Barr virus (EBV) latent membrane protein 1 (LMP1), and myelin oligodendrocyte glycoprotein (MOG). Bioinformatics analysis of sequencing data and surface plasmon resonance (SPR) studies have shown that it is the variable fragments of antibody heavy chains that mainly determine both the affinity of antibodies to the parent autoantigen and their cross-reactivity. It is suggested that LMP1-cross-reactive anti-myelin autoantibodies contain heavy chains encoded by certain germline gene segments, which may be a hallmark of the EBV-specific B cell subpopulation involved in MS triggering.
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Affiliation(s)
- Yakov A Lomakin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Maria Yu Zakharova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexey V Stepanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Maria A Dronina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Ivan V Smirnov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia; Faculty of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Tatyana V Bobik
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Andrey Yu Pyrkov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Nina V Tikunova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Svetlana N Sharanova
- Russian State Medical University, Department of Neurology & Neurosurgery, Moscow Multiple Sclerosis Center at the City Hospital #11, Moscow, Russia
| | - Vitali M Boitsov
- St. Petersburg Academic University, Nanotechnology Research and Education Centre, Russian Academy of Sciences, St. Petersburg, Russia
| | - Sergey Yu Vyazmin
- St. Petersburg Academic University, Nanotechnology Research and Education Centre, Russian Academy of Sciences, St. Petersburg, Russia
| | - Marsel R Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia; Genomics Core Facility, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Alexey E Tupikin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia; Genomics Core Facility, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia; Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexey N Krasnov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Nadezda A Bykova
- Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Yulia A Medvedeva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia; Institut de Medicina Predictiva I Personalitzada del Càncer, Badalona (Barcelona), Spain
| | - Marina V Fridman
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Alexander V Favorov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia; Department of Oncology, Division of Biostatistics and Bioinformatics, Johns Hopkins University School of Medicine, Baltimore, MD, USA; State Research Institute of Genetics and Selection of Industrial Microorganisms GosNIIGenetika, Moscow, Russia
| | - Natalia A Ponomarenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Michael V Dubina
- St. Petersburg Academic University, Nanotechnology Research and Education Centre, Russian Academy of Sciences, St. Petersburg, Russia
| | - Alexey N Boyko
- Russian State Medical University, Department of Neurology & Neurosurgery, Moscow Multiple Sclerosis Center at the City Hospital #11, Moscow, Russia
| | - Valentin V Vlassov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia; Novosibirsk State University, Novosibirsk, Russia
| | - Alexey A Belogurov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia; Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexander G Gabibov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia; Faculty of Chemistry, Lomonosov Moscow State University, Moscow, Russia; Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.
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145
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The promise and challenge of high-throughput sequencing of the antibody repertoire. Nat Biotechnol 2014; 32:158-68. [PMID: 24441474 PMCID: PMC4113560 DOI: 10.1038/nbt.2782] [Citation(s) in RCA: 471] [Impact Index Per Article: 47.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Accepted: 12/04/2013] [Indexed: 12/16/2022]
Abstract
Georgiou and colleagues discuss rapidly evolving methods for high-throughput sequencing of the antibody repertoire, and how the resulting data may be applied to answer basic and translational research questions. Efforts to determine the antibody repertoire encoded by B cells in the blood or lymphoid organs using high-throughput DNA sequencing technologies have been advancing at an extremely rapid pace and are transforming our understanding of humoral immune responses. Information gained from high-throughput DNA sequencing of immunoglobulin genes (Ig-seq) can be applied to detect B-cell malignancies with high sensitivity, to discover antibodies specific for antigens of interest, to guide vaccine development and to understand autoimmunity. Rapid progress in the development of experimental protocols and informatics analysis tools is helping to reduce sequencing artifacts, to achieve more precise quantification of clonal diversity and to extract the most pertinent biological information. That said, broader application of Ig-seq, especially in clinical settings, will require the development of a standardized experimental design framework that will enable the sharing and meta-analysis of sequencing data generated by different laboratories.
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146
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Parameswaran P, Liu Y, Roskin KM, Jackson KKL, Dixit VP, Lee JY, Artiles KL, Zompi S, Vargas MJ, Simen BB, Hanczaruk B, McGowan KR, Tariq MA, Pourmand N, Koller D, Balmaseda A, Boyd SD, Harris E, Fire AZ. Convergent antibody signatures in human dengue. Cell Host Microbe 2013; 13:691-700. [PMID: 23768493 DOI: 10.1016/j.chom.2013.05.008] [Citation(s) in RCA: 192] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 04/03/2013] [Accepted: 04/30/2013] [Indexed: 01/05/2023]
Abstract
Dengue is the most prevalent mosquito-borne viral disease in humans, and the lack of early prognostics, vaccines, and therapeutics contributes to immense disease burden. To identify patterns that could be used for sequence-based monitoring of the antibody response to dengue, we examined antibody heavy-chain gene rearrangements in longitudinal peripheral blood samples from 60 dengue patients. Comparing signatures between acute dengue, postrecovery, and healthy samples, we found increased expansion of B cell clones in acute dengue patients, with higher overall clonality in secondary infection. Additionally, we observed consistent antibody sequence features in acute dengue in the highly variable major antigen-binding determinant, complementarity-determining region 3 (CDR3), with specific CDR3 sequences highly enriched in acute samples compared to postrecovery, healthy, or non-dengue samples. Dengue thus provides a striking example of a human viral infection where convergent immune signatures can be identified in multiple individuals. Such signatures could facilitate surveillance of immunological memory in communities.
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Affiliation(s)
- Poornima Parameswaran
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA 94720-3370, USA
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147
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Mori A, Deola S, Xumerle L, Mijatovic V, Malerba G, Monsurrò V. Next generation sequencing: new tools in immunology and hematology. Blood Res 2013; 48:242-9. [PMID: 24466547 PMCID: PMC3894381 DOI: 10.5045/br.2013.48.4.242] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Revised: 11/21/2013] [Accepted: 12/11/2013] [Indexed: 11/17/2022] Open
Abstract
One of the hallmarks of the adaptive immune system is the specificity of B and T cell receptors. Thanks to somatic recombination, a large repertoire of receptors can be generated within an individual that guarantee the recognition of a vast number of antigens. Monoclonal antibodies have limited applicability, given the high degree of diversity among these receptors, in BCR and TCR monitoring. Furthermore, with regard to cancer, better characterization of complex genomes and the ability to monitor tumor-specific cryptic mutations or translocations are needed to develop better tailored therapies. Novel technologies, by enhancing the ability of BCR and TCR monitoring, can help in the search for minimal residual disease during hematological malignancy diagnosis and follow-up, and can aid in improving bone marrow transplantation techniques. Recently, a novel technology known as next generation sequencing has been developed; this allows the recognition of unique sequences and provides depth of coverage, heterogeneity, and accuracy of sequencing. This provides a powerful tool that, along with microarray analysis for gene expression, may become integral in resolving the remaining key problems in hematology. This review describes the state of the art of this novel technology, its application in the immunological and hematological fields, and the possible benefits it will provide for the hematology and immunology community.
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Affiliation(s)
- Antonio Mori
- Department of Life and Reproduction Science, University of Verona, Verona, Italy
| | - Sara Deola
- Hematology Unit, Bolzano Central Hospital, Bolzano, Italy
| | - Luciano Xumerle
- Department of Life and Reproduction Science, University of Verona, Verona, Italy
| | - Vladan Mijatovic
- Department of Life and Reproduction Science, University of Verona, Verona, Italy
| | - Giovanni Malerba
- Department of Life and Reproduction Science, University of Verona, Verona, Italy
| | - Vladia Monsurrò
- Department of Pathology and Diagnostics, University of Verona, Verona, Italy
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148
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Wang C, Liu Y, Xu LT, Jackson KJL, Roskin KM, Pham TD, Laserson J, Marshall EL, Seo K, Lee JY, Furman D, Koller D, Dekker CL, Davis MM, Fire AZ, Boyd SD. Effects of aging, cytomegalovirus infection, and EBV infection on human B cell repertoires. THE JOURNAL OF IMMUNOLOGY 2013; 192:603-11. [PMID: 24337376 DOI: 10.4049/jimmunol.1301384] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Elderly humans show decreased humoral immunity to pathogens and vaccines, yet the effects of aging on B cells are not fully known. Chronic viral infection by CMV is implicated as a driver of clonal T cell proliferations in some aging humans, but whether CMV or EBV infection contributes to alterations in the B cell repertoire with age is unclear. We have used high-throughput DNA sequencing of IGH gene rearrangements to study the BCR repertoires over two successive years in 27 individuals ranging in age from 20 to 89 y. Some features of the B cell repertoire remain stable with age, but elderly subjects show increased numbers of B cells with long CDR3 regions, a trend toward accumulation of more highly mutated IgM and IgG Ig genes, and persistent clonal B cell populations in the blood. Seropositivity for CMV or EBV infection alters B cell repertoires, regardless of the individual's age: EBV infection correlates with the presence of persistent clonal B cell expansions, whereas CMV infection correlates with the proportion of highly mutated Ab genes. These findings isolate effects of aging from those of chronic viral infection on B cell repertoires and provide a baseline for understanding human B cell responses to vaccination or infectious stimuli.
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Affiliation(s)
- Chen Wang
- Department of Pathology, Stanford University, Stanford, CA 94305
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149
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Gadermaier E, Levin M, Flicker S, Ohlin M. The human IgE repertoire. Int Arch Allergy Immunol 2013; 163:77-91. [PMID: 24296690 DOI: 10.1159/000355947] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
IgE is a key mediator in allergic diseases. However, in strong contrast to other antibody isotypes, many details of the composition of the human IgE repertoire are poorly defined. The low levels of human IgE in the circulation and the rarity of IgE-producing B cells are important reasons for this lack of knowledge. In this review, we summarize the current knowledge on these repertoires both in terms of their complexity and activity, i.e. knowledge which despite the difficulties encountered when studying the molecular details of human IgE has been acquired in recent years. We also take a look at likely future developments, for instance through improvements in sequencing technology and methodology that allow the isolation of additional allergen-specific human antibodies mimicking IgE, as this certainly will support our understanding of human IgE in the context of human disease in the years to come.
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Affiliation(s)
- Elisabeth Gadermaier
- Division of Immunopathology, Department of Pathophysiology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
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150
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Genomic and systems approaches to translational biomarker discovery in immunological diseases. Drug Discov Today 2013; 19:133-9. [PMID: 24126144 DOI: 10.1016/j.drudis.2013.10.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Revised: 09/13/2013] [Accepted: 10/04/2013] [Indexed: 02/07/2023]
Abstract
The high failure rate of new therapeutic mechanisms tested in clinical development has spurred an upsurge in research dedicated to discovering biomarker readouts that can improve decision-making. Increasingly, systems biology and genomic technologies, such as transcriptional profiling, are being leveraged to aid in the discovery of biomarker readouts. For inflammatory and immunological diseases, such as rheumatoid arthritis (RA) and asthma, progress has been made in developing biomarkers to monitor disease activity, prediction of response to therapy, and pharmacodynamic (PD) measurements. In this review, we discuss recent successes and challenges in these endeavors, highlighting the importance of human clinical studies of standard-of-care treatments in control subjects and patients with disease as the most direct path toward identifying useful translational biomarkers for clinical development.
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