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Collins AM, Ohlin M, Corcoran M, Heather JM, Ralph D, Law M, Martínez-Barnetche J, Ye J, Richardson E, Gibson WS, Rodriguez OL, Peres A, Yaari G, Watson CT, Lees WD. AIRR-C IG Reference Sets: curated sets of immunoglobulin heavy and light chain germline genes. Front Immunol 2024; 14:1330153. [PMID: 38406579 PMCID: PMC10884231 DOI: 10.3389/fimmu.2023.1330153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 12/27/2023] [Indexed: 02/27/2024] Open
Abstract
Introduction Analysis of an individual's immunoglobulin (IG) gene repertoire requires the use of high-quality germline gene reference sets. When sets only contain alleles supported by strong evidence, AIRR sequencing (AIRR-seq) data analysis is more accurate and studies of the evolution of IG genes, their allelic variants and the expressed immune repertoire is therefore facilitated. Methods The Adaptive Immune Receptor Repertoire Community (AIRR-C) IG Reference Sets have been developed by including only human IG heavy and light chain alleles that have been confirmed by evidence from multiple high-quality sources. To further improve AIRR-seq analysis, some alleles have been extended to deal with short 3' or 5' truncations that can lead them to be overlooked by alignment utilities. To avoid other challenges for analysis programs, exact paralogs (e.g. IGHV1-69*01 and IGHV1-69D*01) are only represented once in each set, though alternative sequence names are noted in accompanying metadata. Results and discussion The Reference Sets include less than half the previously recognised IG alleles (e.g. just 198 IGHV sequences), and also include a number of novel alleles: 8 IGHV alleles, 2 IGKV alleles and 5 IGLV alleles. Despite their smaller sizes, erroneous calls were eliminated, and excellent coverage was achieved when a set of repertoires comprising over 4 million V(D)J rearrangements from 99 individuals were analyzed using the Sets. The version-tracked AIRR-C IG Reference Sets are freely available at the OGRDB website (https://ogrdb.airr-community.org/germline_sets/Human) and will be regularly updated to include newly observed and previously reported sequences that can be confirmed by new high-quality data.
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Affiliation(s)
- Andrew M. Collins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Mats Ohlin
- Department of Immunotechnology, and SciLifeLab, Lund University, Lund, Sweden
| | - Martin Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - James M. Heather
- Mass General Cancer Center, Massachusetts General Hospital, Charlestown, MA, United States
- Department of Medicine, Harvard Medical School, Boston, MA, United States
| | - Duncan Ralph
- Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Mansun Law
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
| | - Jesus Martínez-Barnetche
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, Mexico
| | - Jian Ye
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States
| | - Eve Richardson
- La Jolla Institute for Immunology, San Diego, CA, United States
| | - William S. Gibson
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, Louisville, KY, United States
| | - Oscar L. Rodriguez
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, Louisville, KY, United States
| | - Ayelet Peres
- Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan, Israel
| | - Gur Yaari
- Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan, Israel
| | - Corey T. Watson
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, Louisville, KY, United States
| | - William D. Lees
- Institute of Structural and Molecular Biology, Birkbeck College, London, United Kingdom
- Human-Centered Computing and Information Science, Institute for Systems and Computer Engineering, Technology and Science, Porto, Portugal
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2
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Roberts AD, Davenport TM, Dickey AM, Ahn R, Sochacki KA, Taraska JW. Structurally distinct endocytic pathways for B cell receptors in B lymphocytes. Mol Biol Cell 2020; 31:2826-2840. [PMID: 33085561 PMCID: PMC7851864 DOI: 10.1091/mbc.e20-08-0532] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
B lymphocytes play a critical role in adaptive immunity. On antigen binding, B cell receptors (BCR) cluster on the plasma membrane and are internalized by endocytosis. In this process, B cells capture diverse antigens in various contexts and concentrations. However, it is unclear whether the mechanism of BCR endocytosis changes in response to these factors. Here, we studied the mechanism of soluble antigen-induced BCR clustering and internalization in a cultured human B cell line using correlative superresolution fluorescence and platinum replica electron microscopy. First, by visualizing nanoscale BCR clusters, we provide direct evidence that BCR cluster size increases with F(ab’)2 concentration. Next, we show that the physical mechanism of internalization switches in response to BCR cluster size. At low concentrations of antigen, B cells internalize small BCR clusters by classical clathrin-mediated endocytosis. At high antigen concentrations, when cluster size increases beyond the size of a single clathrin-coated pit, B cells retrieve receptor clusters using large invaginations of the plasma membrane capped with clathrin. At these sites, we observed early and sustained recruitment of actin and an actin polymerizing protein FCHSD2. We further show that actin recruitment is required for the efficient generation of these novel endocytic carriers and for their capture into the cytosol. We propose that in B cells, the mechanism of endocytosis switches to accommodate large receptor clusters formed when cells encounter high concentrations of soluble antigen. This mechanism is regulated by the organization and dynamics of the cortical actin cytoskeleton.
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Affiliation(s)
- Aleah D Roberts
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - Thaddeus M Davenport
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - Andrea M Dickey
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - Regina Ahn
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - Kem A Sochacki
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - Justin W Taraska
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
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3
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Lefranc MP, Lefranc G. Immunoglobulins or Antibodies: IMGT ® Bridging Genes, Structures and Functions. Biomedicines 2020; 8:E319. [PMID: 32878258 PMCID: PMC7555362 DOI: 10.3390/biomedicines8090319] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 08/23/2020] [Accepted: 08/25/2020] [Indexed: 12/18/2022] Open
Abstract
IMGT®, the international ImMunoGeneTics® information system founded in 1989 by Marie-Paule Lefranc (Université de Montpellier and CNRS), marked the advent of immunoinformatics, a new science at the interface between immunogenetics and bioinformatics. For the first time, the immunoglobulin (IG) or antibody and T cell receptor (TR) genes were officially recognized as 'genes' as well as were conventional genes. This major breakthrough has allowed the entry, in genomic databases, of the IG and TR variable (V), diversity (D) and joining (J) genes and alleles of Homo sapiens and of other jawed vertebrate species, based on the CLASSIFICATION axiom. The second major breakthrough has been the IMGT unique numbering and the IMGT Collier de Perles for the V and constant (C) domains of the IG and TR and other proteins of the IG superfamily (IgSF), based on the NUMEROTATION axiom. IMGT-ONTOLOGY axioms and concepts bridge genes, sequences, structures and functions, between biological and computational spheres in the IMGT® system (Web resources, databases and tools). They provide the IMGT Scientific chart rules to identify, to describe and to analyse the IG complex molecular data, the huge diversity of repertoires, the genetic (alleles, allotypes, CNV) polymorphisms, the IG dual function (paratope/epitope, effector properties), the antibody humanization and engineering.
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Affiliation(s)
- Marie-Paule Lefranc
- IMGT, The International ImMunoGeneTics Information System, Laboratoire d’ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, Université de Montpellier UM, Centre National de la Recherche Scientifique CNRS, UMR 9002 CNRS-UM, 141 Rue de la Cardonille, CEDEX 5, 34396 Montpellier, France
| | - Gérard Lefranc
- IMGT, The International ImMunoGeneTics Information System, Laboratoire d’ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, Université de Montpellier UM, Centre National de la Recherche Scientifique CNRS, UMR 9002 CNRS-UM, 141 Rue de la Cardonille, CEDEX 5, 34396 Montpellier, France
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4
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Neumann L, Moos V, Giesecke-Thiel C, Dörner T, Allers K, Aebischer T, Schneider T. T Cell-Dependent Maturation of Pathogen-Specific Igs in the Antrum of Chronically Helicobacter pylori-Infected Patients. THE JOURNAL OF IMMUNOLOGY 2019; 203:208-215. [PMID: 31101665 DOI: 10.4049/jimmunol.1900074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 04/20/2019] [Indexed: 11/19/2022]
Abstract
Mucosal plasma cells (PC) and Ig production are essential to fend pathogens and to maintain mucosal homeostasis. In human Helicobacter pylori infection, mucosal PC express inducible NO synthase (iNOS), which positively correlates with clearance of experimental human infection. To characterize Ig genes and specificities of antral mucosal iNOS+ and iNOS- PC in H. pylori infection, we sequenced rearranged Ig genes from single cell-sorted PC from biopsy specimens of chronically infected patients and analyzed them with respect to their molecular features. The binding specificity of individual PC's Ig was determined following recombinant expression. We identified high rates of somatic hypermutations, especially targeting RGYW/WRCY hotspot motifs in the individual Ig genes, indicating T cell-dependent maturation. For seven of 14 recombinantly expressed Ig, Ag specificity could be determined. Two clones reacted to H. pylori proteins, and five were found to be polyreactive against LPSs, dsDNA, and ssDNA. All specific Ig originated from iNOS+ PC. H. pylori-specific Ig are encoded by V and J family genes previously shown to be also used in rearranged Ig loci of MALT B cell lymphomas. In summary, mucosal iNOS+ PC producing H. pylori-specific Ig accumulate in infection and appear to be a product of T cell-dependent B cell maturation. Moreover, the Ig's molecular features partly resembled that of MALT B cell lymphoma Ig genes, suggestive of a mechanism in which a progressive molecular evolution of pathogen-specific B cells to MALT B cell lymphoma occurs.
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Affiliation(s)
- Laura Neumann
- Medizinische Klinik für Gastroenterologie, Infektiologie und Rheumatologie, Charité - Universitätsmedizin Berlin, 12203 Berlin, Germany
| | - Verena Moos
- Medizinische Klinik für Gastroenterologie, Infektiologie und Rheumatologie, Charité - Universitätsmedizin Berlin, 12203 Berlin, Germany;
| | - Claudia Giesecke-Thiel
- Abteilung für Medizin, Rheumatologie und Klinische Immunology, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany; and
| | - Thomas Dörner
- Abteilung für Medizin, Rheumatologie und Klinische Immunology, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany; and
| | - Kristina Allers
- Medizinische Klinik für Gastroenterologie, Infektiologie und Rheumatologie, Charité - Universitätsmedizin Berlin, 12203 Berlin, Germany
| | | | - Thomas Schneider
- Medizinische Klinik für Gastroenterologie, Infektiologie und Rheumatologie, Charité - Universitätsmedizin Berlin, 12203 Berlin, Germany
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5
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Morabito F, Shanafelt TD, Gentile M, Reda G, Mauro FR, Rossi D, Di Renzo N, Molica S, Angrilli F, Chiarenza A, Cutrona G, Chaffee KG, Parikh SA, Tripepi G, D'Arrigo G, Vigna E, Recchia AG, Cortelezzi A, Gaidano G, Di Raimondo F, Fais F, Foà R, Neri A, Ferrarini M. Immunoglobulin heavy chain variable region gene and prediction of time to first treatment in patients with chronic lymphocytic leukemia: Mutational load or mutational status? Analysis of 1003 cases. Am J Hematol 2018; 93:E216-E219. [PMID: 29984867 DOI: 10.1002/ajh.25206] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Accepted: 06/28/2018] [Indexed: 01/04/2023]
Affiliation(s)
- Fortunato Morabito
- Biotechnology Research Unit, Azienda Sanitaria Provinciale di Cosenza Aprigliano (CS) Italy
| | - Tait D Shanafelt
- Department of Medicine, Division of Hematology Stanford University California
| | - Massimo Gentile
- Hematology Unit, Department of Onco‐hematology A.O. of Cosenza Cosenza Italy
| | - Gianluigi Reda
- Hematology Unit, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico Milan Italy
| | - Francesca Romana Mauro
- Hematology, Department of Cellular Biotechnologies and Hematology ‘Sapienza’ University Rome Italy
| | - Davide Rossi
- Oncology Institute of Southern Switzerland and Institute of Oncology Research Bellinzona Switzerland
| | | | - Stefano Molica
- Department of Oncology and Haematology Pugliese‐Ciaccio Hospital Catanzaro Italy
| | | | - Annalisa Chiarenza
- Division of Hematology AOU Policlinico‐OVE, University of Catania Catania Italy
| | - Giovanna Cutrona
- UO Molecular Pathology, IRCCS Ospedale Policlinico San Martino, Genoa Italy
| | - Kari G. Chaffee
- Division of Biomedical Statistics and Informatics Mayo Clinic Rochester Minnesota
| | - Sameer A. Parikh
- Department of Internal Medicine, Division of Hematology Mayo Clinic Rochester Minnesota
| | - Giovanni Tripepi
- Consiglio Nazionale delle Ricerche, Istituto di Biomedicina ed Immunologia Molecolare Reggio Calabria Italy
| | - Graziella D'Arrigo
- Consiglio Nazionale delle Ricerche, Istituto di Biomedicina ed Immunologia Molecolare Reggio Calabria Italy
| | - Ernesto Vigna
- Hematology Unit, Department of Onco‐hematology A.O. of Cosenza Cosenza Italy
| | - Anna Grazia Recchia
- Biotechnology Research Unit, Azienda Sanitaria Provinciale di Cosenza Aprigliano (CS) Italy
| | - Agostino Cortelezzi
- Hematology Unit, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico Milan Italy
| | - Gianluca Gaidano
- Division of Haematology, Department of Translational Medicine Università del Piemonte Orientale Novara Italy
| | | | - Franco Fais
- UO Molecular Pathology, IRCCS Ospedale Policlinico San Martino, Genoa Italy
- Department of Experimental Medicine University of Genova Genoa Italy
| | - Robin Foà
- Hematology, Department of Cellular Biotechnologies and Hematology ‘Sapienza’ University Rome Italy
| | - Antonino Neri
- Hematology Unit, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico Milan Italy
| | - Manlio Ferrarini
- Department of Experimental Medicine University of Genova Genoa Italy
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6
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Thörnqvist L, Ohlin M. The functional 3'-end of immunoglobulin heavy chain variable (IGHV) genes. Mol Immunol 2018; 96:61-68. [PMID: 29499482 DOI: 10.1016/j.molimm.2018.02.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 02/01/2018] [Accepted: 02/18/2018] [Indexed: 12/15/2022]
Abstract
Inference of antibody gene repertoires using transcriptome data has emerged as an alternative approach to the complex process of sequencing of adaptive immune receptor germline gene loci. The diversity introduced during rearrangement of immunoglobulin heavy chain variable (IGHV), diversity, and joining genes has however been identified as potentially affecting inference specificity. In this study, we have addressed this issue by analysing the nucleotide composition of unmutated human immunoglobulin heavy chains-encoding transcripts, focusing on the 3ö most bases of 47 IGHV germline genes. Although transcripts derived from some of the germline genes predominately incorporated the germline encoded base even at position 320, the last base of most IGHV genes, transcripts originating in other genes presented other nucleotides to the same extent at this position. In transcripts derived from two of the germline genes, IGHV3-13*01 and IGHV4-30-2*01, the predominating nucleotide (G) was in fact not that of the gene (A). Hence, we suggest that inference of IGHV genes should be limited to bases preceding nucleotide 320, as inference beyond this would jeopardize the specificity of the inference process. The different degree of incorporation of the final base of the IGHV gene directly influences the distribution of amino acids of the ascending strand of the third complementarity determining region of the heavy chain. Thereby it influences the nature of this specificity-determining part of the antibody population. In addition, we also present data that indicate the existence of a common so far un-recognized allelic variant of IGHV3-7 that carries an A318G difference in relation to IGHV3-7*02.
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Affiliation(s)
| | - Mats Ohlin
- Department of Immunotechnology, Lund University, Lund, Sweden.
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7
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Jain P, Nogueras González GM, Kanagal-Shamanna R, Rozovski U, Sarwari N, Tam C, Wierda WG, A. Thompson P, Jain N, Luthra R, Quesada A, Sanchez-Petitto G, Ferrajoli A, Burger J, Kantarjian H, Cortes J, O’Brien S, Keating MJ, Estrov Z. The absolute percent deviation of IGHV mutation rather than a 98% cut-off predicts survival of chronic lymphocytic leukaemia patients treated with fludarabine, cyclophosphamide and rituximab. Br J Haematol 2018; 180:33-40. [PMID: 29164608 PMCID: PMC5745295 DOI: 10.1111/bjh.15018] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 09/19/2017] [Indexed: 01/03/2023]
Abstract
The degree of somatic hypermutation, determined as percent deviation of immunoglobulin heavy chain gene variable region sequence from the germline (IGHV%), is an important prognostic factor in chronic lymphocytic leukaemia (CLL). Currently, a cut-off of 2% deviation or 98% sequence identity to germline in IGHV sequence is routinely used to dichotomize CLL patients into mutated and unmutated groups. Because dissimilar IGHV% cut-offs of 1-5% were identified in different studies, we wondered whether no cut-off should be applied and IGHV% treated as a continuous variable. We analysed the significance of IGHV% in 203 CLL patients enrolled on the original frontline fludarabine, cyclophosphamide and rituximab (FCR) trial with a median of 10 years follow-up. Using the Cox Proportional Hazard model, IGHV% was identified as a continuous variable that is significantly associated with progression-free (PFS) and overall survival (OS) (P < 0·001). Furthermore, we validated this finding in 323 patients treated with FCR off-protocol and in the total cohort (n = 535). Multivariate analysis revealed a continuous trend. Higher IGHV% levels were incrementally associated with favorable PFS and OS in both FCR-treated cohorts (P < 0·001, both cohorts). Taken together, our data suggest that IGHV% is a continuous variable in CLL patients treated with FCR.
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MESH Headings
- Adolescent
- Adult
- Aged
- Aged, 80 and over
- Antineoplastic Combined Chemotherapy Protocols/adverse effects
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- Biomarkers
- Cyclophosphamide/administration & dosage
- Female
- Humans
- Immunoglobulin Heavy Chains/genetics
- Immunoglobulin Variable Region/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/diagnosis
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/mortality
- Male
- Middle Aged
- Mutation
- Neoplasm Staging
- Prognosis
- Proportional Hazards Models
- Rituximab/administration & dosage
- Treatment Outcome
- Vidarabine/administration & dosage
- Vidarabine/analogs & derivatives
- Young Adult
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Affiliation(s)
- Preetesh Jain
- Department of Leukemia, and, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Rashmi Kanagal-Shamanna
- Department of Hematopathology, and, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Uri Rozovski
- Davidoff Cancer Center, Beilinson Campus, Tel-Aviv University, Tel-Aviv, Israel
| | - Nawid Sarwari
- Department of Leukemia, and, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - William G. Wierda
- Department of Leukemia, and, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Philip A. Thompson
- Department of Leukemia, and, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Nitin Jain
- Department of Leukemia, and, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Rajyalakshmi Luthra
- Department of Hematopathology, and, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Andres Quesada
- Department of Hematopathology, and, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Gabriela Sanchez-Petitto
- Department of Leukemia, and, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Alessandra Ferrajoli
- Department of Leukemia, and, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jan Burger
- Department of Leukemia, and, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Hagop Kantarjian
- Department of Leukemia, and, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jorge Cortes
- Department of Leukemia, and, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Susan O’Brien
- Department of Leukemia, and, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Chao Family Comprehensive Cancer Center, University of Irvine, Irvine, California, USA
| | - Michael J. Keating
- Department of Leukemia, and, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Zeev Estrov
- Department of Leukemia, and, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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8
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Ghraichy M, Galson JD, Kelly DF, Trück J. B-cell receptor repertoire sequencing in patients with primary immunodeficiency: a review. Immunology 2017; 153:145-160. [PMID: 29140551 DOI: 10.1111/imm.12865] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 10/25/2017] [Accepted: 11/07/2017] [Indexed: 12/17/2022] Open
Abstract
The advent of next-generation sequencing (NGS) now allows a detailed assessment of the adaptive immune system in health and disease. In particular, high-throughput B-cell receptor (BCR) repertoire sequencing provides detailed information about the functionality and abnormalities of the B-cell system. However, it is mostly unknown how the BCR repertoire is altered in the context of primary immunodeficiencies (PID) and whether findings are consistent throughout phenotypes and genotypes. We have performed an extensive literature search of the published work on BCR repertoire sequencing in PID patients, including several forms of predominantly antibody disorders and combined immunodeficiencies. It is somewhat surprising that BCR repertoires, even from severe clinical phenotypes, often show only mild abnormalities and that diversity or immunoglobulin gene segment usage is generally preserved to some extent. Despite the great variety of wet laboratory and analytical methods that were used in the different studies, several findings are common to most investigated PIDs, such as the increased usage of gene segments that are associated with self-reactivity. These findings suggest that BCR repertoire characteristics may be used to assess the functionality of the B-cell compartment irrespective of the underlying defect. With the use of NGS approaches, there is now the opportunity to apply BCR repertoire sequencing to multiple patients and explore the PID BCR repertoire in more detail. Ultimately, using BCR repertoire sequencing in translational research could aid the management of PID patients by improving diagnosis, estimating functionality of the immune system and improving assessment of prognosis.
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Affiliation(s)
- Marie Ghraichy
- Division of Immunology, University Children's Hospital Zurich, Zurich, Switzerland.,Children's Research Center, University Children's Hospital, University of Zurich, Zurich, Switzerland
| | - Jacob D Galson
- Children's Research Center, University Children's Hospital, University of Zurich, Zurich, Switzerland.,University of Zurich, Zurich, Switzerland
| | - Dominic F Kelly
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Johannes Trück
- Division of Immunology, University Children's Hospital Zurich, Zurich, Switzerland.,Children's Research Center, University Children's Hospital, University of Zurich, Zurich, Switzerland.,University of Zurich, Zurich, Switzerland
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9
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Parks T, Mirabel MM, Kado J, Auckland K, Nowak J, Rautanen A, Mentzer AJ, Marijon E, Jouven X, Perman ML, Cua T, Kauwe JK, Allen JB, Taylor H, Robson KJ, Deane CM, Steer AC, Hill AVS. Association between a common immunoglobulin heavy chain allele and rheumatic heart disease risk in Oceania. Nat Commun 2017; 8:14946. [PMID: 28492228 PMCID: PMC5437274 DOI: 10.1038/ncomms14946] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 02/15/2017] [Indexed: 12/19/2022] Open
Abstract
The indigenous populations of the South Pacific experience a high burden of rheumatic heart disease (RHD). Here we report a genome-wide association study (GWAS) of RHD susceptibility in 2,852 individuals recruited in eight Oceanian countries. Stratifying by ancestry, we analysed genotyped and imputed variants in Melanesians (607 cases and 1,229 controls) before follow-up of suggestive loci in three further ancestral groups: Polynesians, South Asians and Mixed or other populations (totalling 399 cases and 617 controls). We identify a novel susceptibility signal in the immunoglobulin heavy chain (IGH) locus centring on a haplotype of nonsynonymous variants in the IGHV4-61 gene segment corresponding to the IGHV4-61*02 allele. We show each copy of IGHV4-61*02 is associated with a 1.4-fold increase in the risk of RHD (odds ratio 1.43, 95% confidence intervals 1.27–1.61, P=4.1 × 10−9). These findings provide new insight into the role of germline variation in the IGH locus in disease susceptibility. Rheumatic heart disease (RHD) is a chronic auto-inflammatory reaction to group A streptococcal infection, and frequently occurs in individuals from the South Pacific. This study finds a novel association between an immunoglobulin heavy chain allele and risk of RHD in Pacific Islanders and South Asians.
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Affiliation(s)
- Tom Parks
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Mariana M Mirabel
- Paris Centre de Recherche Cardiovasculaire, Institut National de la Santé et de la Recherche Médicale, Hôpital Européen Georges Pompidou, 56, rue Leblanc, 75908 Paris, France
| | - Joseph Kado
- Department of Paediatrics, Ministry of Health and Medical Services, Colonial War Memorial Hospital, Brown Street, Suva, Fiji.,College of Medicine, Nursing &Health Sciences, Fiji National University, Brown Street, Suva, Fiji
| | - Kathryn Auckland
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Jaroslaw Nowak
- Department of Statistics, University of Oxford, Peter Medawar Building for Pathogen Research, Oxford OX1 3S, UK
| | - Anna Rautanen
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Alexander J Mentzer
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Eloi Marijon
- Paris Centre de Recherche Cardiovasculaire, Institut National de la Santé et de la Recherche Médicale, Hôpital Européen Georges Pompidou, 56, rue Leblanc, 75908 Paris, France.,Faculté de Médecine Paris Descartes, Université Paris Descartes, 15, rue de l'école de medicine, 75006 Paris, France
| | - Xavier Jouven
- Paris Centre de Recherche Cardiovasculaire, Institut National de la Santé et de la Recherche Médicale, Hôpital Européen Georges Pompidou, 56, rue Leblanc, 75908 Paris, France.,Faculté de Médecine Paris Descartes, Université Paris Descartes, 15, rue de l'école de medicine, 75006 Paris, France
| | - Mai Ling Perman
- College of Medicine, Nursing &Health Sciences, Fiji National University, Brown Street, Suva, Fiji
| | - Tuliana Cua
- Rheumatic Heart Disease Control Programme, Ministry of Health and Medical Services, Colonial War Memorial Hospital, Brown Street, Suva, Fiji
| | - John K Kauwe
- College of Life Sciences, Brigham Young University, 4146 Life Sciences Building, Provo, Utah 84602, USA
| | - John B Allen
- College of Life Sciences, Brigham Young University, 4146 Life Sciences Building, Provo, Utah 84602, USA
| | - Henry Taylor
- Rheumatic Heart Disease Control Programme, Samoa Ministry of Health, Moto'otua, Ifiifi Street, Apia, Samoa
| | - Kathryn J Robson
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK
| | - Charlotte M Deane
- Department of Statistics, University of Oxford, Peter Medawar Building for Pathogen Research, Oxford OX1 3S, UK
| | - Andrew C Steer
- Centre for International Child Health, University of Melbourne, 50 Flemington Road, Parkville, Melbourne Victoria 3052, Australia.,Murdoch Children's Research Institute, 50 Flemington Road, Parkville, Melbourne, Victoria 3052, Australia
| | - Adrian V S Hill
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
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10
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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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11
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Tabibian-Keissar H, Hazanov L, Schiby G, Rosenthal N, Rakovsky A, Michaeli M, Shahaf GL, Pickman Y, Rosenblatt K, Melamed D, Dunn-Walters D, Mehr R, Barshack I. Aging affects B-cell antigen receptor repertoire diversity in primary and secondary lymphoid tissues. Eur J Immunol 2015; 46:480-92. [PMID: 26614343 DOI: 10.1002/eji.201545586] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Revised: 09/17/2015] [Accepted: 11/23/2015] [Indexed: 01/10/2023]
Abstract
The elderly immune system is characterized by reduced responses to infections and vaccines, and an increase in the incidence of autoimmune diseases and cancer. Age-related deficits in the immune system may be caused by peripheral homeostatic pressures that limit bone marrow B-cell production or migration to the peripheral lymphoid tissues. Studies of peripheral blood B-cell receptor spectratypes have shown that those of the elderly are characterized by reduced diversity, which is correlated with poor health status. In the present study, we performed for the first time high-throughput sequencing of immunoglobulin genes from archived biopsy samples of primary and secondary lymphoid tissues in old (74 ± 7 years old, range 61-89) versus young (24 ± 5 years old, range 18-45) individuals, analyzed repertoire diversities and compared these to results in peripheral blood. We found reduced repertoire diversity in peripheral blood and lymph node repertoires from old people, while in the old spleen samples the diversity was larger than in the young. There were no differences in somatic hypermutation characteristics between age groups. These results support the hypothesis that age-related immune frailty stems from altered B-cell homeostasis leading to narrower memory B-cell repertoires, rather than changes in somatic hypermutation mechanisms.
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Affiliation(s)
- Hilla Tabibian-Keissar
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel.,Department of Pathology, Sheba Medical Center, Ramat Gan, Israel
| | - Lena Hazanov
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Ginette Schiby
- Department of Pathology, Sheba Medical Center, Ramat Gan, Israel.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Noemie Rosenthal
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Aviya Rakovsky
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Miri Michaeli
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Gitit Lavy Shahaf
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Yishai Pickman
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | | | - Doron Melamed
- Department of Immunology, Technion Faculty of Medicine, Haifa, Israel
| | - Deborah Dunn-Walters
- Division of Immunology, Infection, and Inflammatory Diseases, King's College London, Faculty of Life Sciences & Medicine, London, United Kingdom
| | - Ramit Mehr
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Iris Barshack
- Department of Pathology, Sheba Medical Center, Ramat Gan, Israel.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
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12
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Brüggemann M, Osborn MJ, Ma B, Hayre J, Avis S, Lundstrom B, Buelow R. Human antibody production in transgenic animals. Arch Immunol Ther Exp (Warsz) 2014; 63:101-8. [PMID: 25467949 PMCID: PMC4359279 DOI: 10.1007/s00005-014-0322-x] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 11/19/2014] [Indexed: 11/26/2022]
Abstract
Fully human antibodies from transgenic animals account for an increasing number of new therapeutics. After immunization, diverse human monoclonal antibodies of high affinity can be obtained from transgenic rodents, while large animals, such as transchromosomic cattle, have produced respectable amounts of specific human immunoglobulin (Ig) in serum. Several strategies to derive animals expressing human antibody repertoires have been successful. In rodents, gene loci on bacterial artificial chromosomes or yeast artificial chromosomes were integrated by oocyte microinjection or transfection of embryonic stem (ES) cells, while ruminants were derived from manipulated fibroblasts with integrated human chromosome fragments or human artificial chromosomes. In all strains, the endogenous Ig loci have been silenced by gene targeting, either in ES or fibroblast cells, or by zinc finger technology via DNA microinjection; this was essential for optimal production. However, comparisons showed that fully human antibodies were not as efficiently produced as wild-type Ig. This suboptimal performance, with respect to immune response and antibody yield, was attributed to imperfect interaction of the human constant region with endogenous signaling components such as the Igα/β in mouse, rat or cattle. Significant improvements were obtained when the human V-region genes were linked to the endogenous CH-region, either on large constructs or, separately, by site-specific integration, which could also silence the endogenous Ig locus by gene replacement or inversion. In animals with knocked-out endogenous Ig loci and integrated large IgH loci, containing many human Vs, all D and all J segments linked to endogenous C genes, highly diverse human antibody production similar to normal animals was obtained.
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Affiliation(s)
- Marianne Brüggemann
- Recombinant Antibody Technology Ltd., Babraham Research Campus, Babraham, Cambridge CB22 3AT UK
- Open Monoclonal Technology, Inc., Palo Alto, CA 94303 USA
| | - Michael J. Osborn
- Recombinant Antibody Technology Ltd., Babraham Research Campus, Babraham, Cambridge CB22 3AT UK
| | - Biao Ma
- Recombinant Antibody Technology Ltd., Babraham Research Campus, Babraham, Cambridge CB22 3AT UK
| | - Jasvinder Hayre
- Recombinant Antibody Technology Ltd., Babraham Research Campus, Babraham, Cambridge CB22 3AT UK
| | - Suzanne Avis
- Recombinant Antibody Technology Ltd., Babraham Research Campus, Babraham, Cambridge CB22 3AT UK
| | | | - Roland Buelow
- Open Monoclonal Technology, Inc., Palo Alto, CA 94303 USA
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13
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Clonotypic analysis of immunoglobulin heavy chain sequences in patients with Waldenström's macroglobulinemia: correlation with MYD88 L265P somatic mutation status, clinical features, and outcome. BIOMED RESEARCH INTERNATIONAL 2014; 2014:809103. [PMID: 25197661 PMCID: PMC4147361 DOI: 10.1155/2014/809103] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 07/12/2014] [Indexed: 01/09/2023]
Abstract
We performed IGH clonotypic sequence analysis in WM in order to determine whether a preferential IGH gene rearrangement was observed and to assess IGHV mutational status in blood and/or bone marrow samples from 36 WM patients. In addition we investigated the presence of MYD88 L265P somatic mutation. After IGH VDJ locus amplification, monoclonal VDJ rearranged fragments were sequenced and analyzed. MYD88 L265P mutation was detected by AS-PCR. The most frequent family usage was IGHV3 (74%); IGHV3-23 and IGHV3-74 segments were used in 26% and 17%, respectively. Somatic hypermutation was seen in 91% of cases. MYD88 L265P mutation was found in 65,5% of patients and absent in the 3 unmutated. These findings did not correlate with clinical findings and outcome. Conclusion. IGH genes' repertoire differed in WM from those observed in other B-cell disorders with a recurrent IGHV3-23 and IGHV3-74 usage; monoclonal IGHV was mutated in most cases, and a high but not omnipresent prevalence of MYD88 L265P mutation was observed. In addition, the identification of 3 patients with unmutated IGHV gene segments, negative for the MYD88 L265P mutation, could support the hypothesis that an extra-germinal B-cell may represent the originating malignant cell in this minority of WM patients.
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14
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Michaeli M, Tabibian-Keissar H, Schiby G, Shahaf G, Pickman Y, Hazanov L, Rosenblatt K, Dunn-Walters DK, Barshack I, Mehr R. Immunoglobulin gene repertoire diversification and selection in the stomach - from gastritis to gastric lymphomas. Front Immunol 2014; 5:264. [PMID: 24917868 PMCID: PMC4042156 DOI: 10.3389/fimmu.2014.00264] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 05/20/2014] [Indexed: 01/06/2023] Open
Abstract
Chronic gastritis is characterized by gastric mucosal inflammation due to autoimmune responses or infection, frequently with Helicobacter pylori. Gastritis with H. pylori background can cause gastric mucosa-associated lymphoid tissue lymphoma (MALT-L), which sometimes further transforms into diffuse large B-cell lymphoma (DLBCL). However, gastric DLBCL can also be initiated de novo. The mechanisms underlying transformation into DLBCL are not completely understood. We analyzed immunoglobulin repertoires and clonal trees to investigate whether and how immunoglobulin gene repertoires, clonal diversification, and selection in gastritis, gastric MALT-L, and DLBCL differ from each other and from normal responses. The two gastritis types (positive or negative for H. pylori) had similarly diverse repertoires. MALT-L dominant clones (defined as the largest clones in each sample) presented higher diversification and longer mutational histories compared with all other conditions. DLBCL dominant clones displayed lower clonal diversification, suggesting the transforming events are triggered by similar responses in different patients. These results are surprising, as we expected to find similarities between the dominant clones of gastritis and MALT-L and between those of MALT-L and DLBCL.
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Affiliation(s)
- Miri Michaeli
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Hilla Tabibian-Keissar
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
- Department of Pathology, Sheba Medical Center, Ramat Gan, Israel
| | - Ginette Schiby
- Department of Pathology, Sheba Medical Center, Ramat Gan, Israel
| | - Gitit Shahaf
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Yishai Pickman
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Lena Hazanov
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | | | - Deborah K. Dunn-Walters
- Division of Immunology, Infection, and Inflammatory Diseases, King’s College London School of Medicine, London, UK
| | - Iris Barshack
- Department of Pathology, Sheba Medical Center, Ramat Gan, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ramit Mehr
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
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15
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Butler J, Wertz N, Sun X. Antibody repertoire development in fetal and neonatal piglets. XIV. Highly restricted IGKV gene usage parallels the pattern seen with IGLV and IGHV. Mol Immunol 2013; 55:329-36. [DOI: 10.1016/j.molimm.2013.03.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 03/04/2013] [Accepted: 03/13/2013] [Indexed: 01/17/2023]
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16
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Wertz N, Vazquez J, Wells K, Sun J, Butler JE. Antibody repertoire development in fetal and neonatal piglets. XII. Three IGLV genes comprise 70% of the pre-immune repertoire and there is little junctional diversity. Mol Immunol 2013; 55:319-28. [PMID: 23570908 DOI: 10.1016/j.molimm.2013.03.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 03/04/2013] [Accepted: 03/13/2013] [Indexed: 01/17/2023]
Abstract
We characterized 239 lambda rearrangements from fetal and germfree (GF) piglets to: (1) determine if transcripts recovered from the earliest sites of B cell lymphogenesis were unique (2) determine what proportion of the genome is used to form the pre-immune repertoire (3) estimate the degree of somatic hypermutation and junctional diversity during ontogeny and (4) test whether piglets maintained germfree in isolators (GF piglets) have a more diversified repertoire than fetal piglets. We show that all expressed lambda genes belong to the IGLV3 and IGLV8 families and only IGLJ2 and IGLJ3 were expressed and used equally throughout fetal and neonatal life. Only genes of the IGLV8 family were used in yolk sac and fetal liver and in these tissues, IGLV8-10 comprised >50%. However, the IGLV8 genes recovered at these early sites of B cell lymphogenesis were recovered at all stages of development. Thus, no unique lambda rearrangement was recovered at the first sites of B cell development. The frequency of somatic hypermutation (SHM) in fetal piglets was ~5.9 per Kb equivalent, mutation were concentrated in CDR regions and did not increase in GF piglets. The average CDR3 length was 30 nt ± 2.7 and did not change in GF piglets. Similar to the heavy chain pre-immune repertoire in this species, three IGLV genes account for ~70% of the repertoire. Unlike the heavy chain repertoire, junctional diversity was very limited.
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Affiliation(s)
- Nancy Wertz
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
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17
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Hamblin TJ. Searching for surrogates for IGHV mutations in chronic lymphocytic leukemia. Leuk Res 2011; 35:1432-5. [DOI: 10.1016/j.leukres.2011.07.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Revised: 07/11/2011] [Accepted: 07/16/2011] [Indexed: 10/17/2022]
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18
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Butler JE, Sun X, Wertz N, Lager KM, Chaloner K, Urban J, Francis DL, Nara PL, Tobin GJ. Antibody repertoire development in fetal and neonatal piglets XXI. Usage of most VH genes remains constant during fetal and postnatal development. Mol Immunol 2011; 49:483-94. [PMID: 22018637 DOI: 10.1016/j.molimm.2011.09.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Revised: 09/22/2011] [Accepted: 09/24/2011] [Indexed: 01/15/2023]
Abstract
Usage of variable region gene segments during development of the antibody repertoire in mammals is unresolved in part because of the complexity of the locus in mice and humans and the difficulty of distinguishing intrinsic from extrinsic influences in these species. We present the first vertical studies on VH usage that spans the fetal and neonatal period using the piglet model. We tracked VH usage in DNA rearrangements and in VDJ transcripts throughout 75 days of gestation (DG) in outbred fetuses, thereafter in outbred germfree and colonized isolator piglets, isolator piglets infected with swine influenza and in conventionally reared nematode-infected adults. Seven VH genes account for >90% of the pre-immune repertoire which is the same among tissues and in both transcripts and DNA rearrangements. Statistical modeling supports the view that proportional usage of the major genes remains constant during fetal life and that postnatal usage ranking is similar to that during fetal life. Changes in usage ranking are developmental not antigen dependent. In this species exposure to environmental antigens results in diversification of the repertoire by somatic hypermutation of the same small number of VH genes that comprise the pre-immune repertoire, not by using other VH gene available in the germline. Therefore in swine a small number of VH genes shape the antibody repertoire throughout life questioning the need for extensive VH polygeny.
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Affiliation(s)
- John E Butler
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.
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19
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Andris-Widhopf J, Steinberger P, Fuller R, Rader C, Barbas CF. Generation of human Fab antibody libraries: PCR amplification and assembly of light- and heavy-chain coding sequences. Cold Spring Harb Protoc 2011; 2011:2011/9/pdb.prot065565. [PMID: 21880817 DOI: 10.1101/pdb.prot065565] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The development of therapeutic antibodies for use in the treatment of human diseases has long been a goal for many researchers in the antibody field. One way to obtain these antibodies is through phage-display libraries constructed from human lymphocytes. This protocol describes the construction of human Fab (fragment antigen binding) antibody libraries. In this method, the individual rearranged heavy- and light-chain variable regions are amplified separately and are linked through a series of overlap polymerase chain reaction (PCR) steps to give the final Fab products that are used for cloning.
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20
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Gaudet RG, Breden F, Plummer F, Berry JD. Molecular characterization of the cervical and systemic B-cell repertoire: Unique, yet overlapping, immune compartments of an HIV-1 resistant individual. MAbs 2011; 3:181-91. [PMID: 21293180 DOI: 10.4161/mabs.3.2.14858] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The cervical mucosa of women who are highly exposed to HIV-1, yet remain persistently seronegative (HEPS), presents a unique opportunity to study the dynamics of an immune compartment potentially capable of preventing HIV-1 infection. Herein, we provide a detailed characterization of the immunoglobulin repertoire of cervical and systemic B cells from one such HEPS individual from Nairobi, Kenya. Analysis was done on 512 VH sequences that were RT-PCR amplified from B cells in a paired sample from the cervix and peripheral blood. The VH3 and DH repertoire of class switched cervical B cells differs significantly from that of systemic B cells indicating that the cervical environment affects local B cell populations and hence VH gene expression. Six networks of clonally related, heavily mutated B cells were identified that spanned the systemic and cervical B cell compartments. Analysis of somatic mutations suggests this is likely the result of systemic, class switched B cells homing to the cervical mucosa. Multiple networks of somatically mutated V-gene sequences, unique to the cervical mucosa, were also identified. This supports the notion that site specific responses occur and have unique regulation of tolerance and recruitment into local memory or blast B cell compartments. We conclude that while the nature of the cervical environment shapes the local B cell repertoire, the infusion of post germinal center B cells to the human cervix is a common occurrence, and represents a means by which systemic immunization could provide the local antibodies necessary to prevent HIV-1 at the site of initial contact.
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Affiliation(s)
- Ryan G Gaudet
- Department of Medical Microbiology, University of Manitoba, Winnipeg, MB, Canada
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21
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Prinz N, Häuser F, Lorenz M, Lackner KJ, von Landenberg P. Structural and functional characterization of a human IgG monoclonal antiphospholipid antibody. Immunobiology 2011; 216:145-51. [DOI: 10.1016/j.imbio.2010.05.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2009] [Revised: 04/22/2010] [Accepted: 05/02/2010] [Indexed: 10/19/2022]
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22
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Perez M, Pacchiarotti A, Frontani M, Pescarmona E, Caprini E, Lombardo G, Russo G, Faraggiana T. Primary cutaneous B-cell lymphoma is associated with somatically hypermutated immunoglobulin variable genes and frequent use of VH1-69 and VH4-59 segments. Br J Dermatol 2009; 162:611-8. [DOI: 10.1111/j.1365-2133.2009.09576.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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23
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Exploration of factors affecting the onset and maturation course of follicular lymphoma through simulations of the germinal center. Bull Math Biol 2009; 71:1432-62. [PMID: 19412639 DOI: 10.1007/s11538-009-9408-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2007] [Accepted: 02/10/2009] [Indexed: 10/20/2022]
Abstract
Genetic mutations frequently observed in human follicular lymphoma (FL) B-cells result in aberrant expression of the anti-apoptotic protein bcl-2 and surface immunoglobulins (Igs) which display one or more novel variable (V) region N-glycosylation motifs. In the present study, we develop a simulation model of the germinal center (GC) to explore how these mutations might influence the emergence and clonal expansion of key mutants which provoke FL development. The simulations employ a stochastic method for calculating the cellular dynamics, which incorporates actual IgV region sequences and a simplified hypermutation scheme. We first bring our simulations into agreement with experimental data for well-characterized normal and bcl-2(+) anti-hapten GC responses in mice to provide a model for understanding how bcl-2 expression leads to permissive selection and memory cell differentiation of weakly competitive B-cells. However, as bcl-2 expression in the GC alone is thought to be insufficient for FL development, we next monitor simulated IgV region mutations to determine the emergence times of key mutants displaying aberrant N-glycosylation motifs recurrently observed in human FL IgV regions. Simulations of 26 germline V(H) gene segments indicate that particular IgV regions have a dynamical selective advantage by virtue of the speed with which one or more of their key sites can generate N-glycosylation motifs upon hypermutation. Separate calculations attribute the high occurrence frequency of such IgV regions in FL to an ability to produce key mutants at a fast enough rate to overcome stochastic processes in the GC that hinder clonal expansion. Altogether, these simulations characterize three pathways for FL maturation through positively selected N-glycosylations, namely, via one of two key sites within germline V(H) region gene segments, or via a site in the third heavy chain complementarity-determining region (CDR-H3) that is generated from VDJ recombination.
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25
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Abstract
The human immunoglobulins (Ig) are the products of three unlinked sets of genes: the immunoglobulin heavy (IGH), the immunoglobulin kappa (IGK), and the immunoglobulin lambda (IGL) genes, localized on chromosome 14 (14q32.33), 2 (2p12), and 22 (22q11.2), respectively. This appendix presents tabulated lists of the human immunoglobulin heavy, kappa, and lambda genes named in accordance with the International ImMunoGeneTics database (IMGT) and approved by the Human Genome Organization (HUGO) Nomenclature Committee in 1999. Three additional tables list corresponding nomenclatures for these genes.
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Affiliation(s)
- M P Lefranc
- Université Montpellier II, CNRS, Montpellier, France
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26
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Volpe JM, Kepler TB. Large-scale analysis of human heavy chain V(D)J recombination patterns. Immunome Res 2008; 4:3. [PMID: 18304322 PMCID: PMC2275228 DOI: 10.1186/1745-7580-4-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2007] [Accepted: 02/27/2008] [Indexed: 12/24/2022] Open
Abstract
Background The processes involved in the somatic assembly of antigen receptor genes are unique to the immune system and are driven largely by random events. Subtle biases, however, may exist and provide clues to the molecular mechanisms involved in their assembly and selection. Large-scale efforts to provide baseline data about the genetic characteristics of immunoglobulin (Ig) genes and the mechanisms involved in their assembly have recently become possible due to the rapid growth of genetic databases. Results We gathered and analyzed nearly 6,500 productive human Ig heavy chain genes and compared them with 325 non-productive Ig genes that were originally rearranged out of frame and therefore incapable of being biased by selection. We found evidence for differences in n-nucleotide tract length distributions which have interesting interpretations for the mechanisms involved in n-nucleotide polymerization. Additionally, we found striking statistical evidence for pairing preferences among D and J segments. We present a statistical model to support our hypothesis that these pairing biases are due to multiple sequential D-to-J rearrangements. Conclusion We present here the most precise estimates of gene segment usage frequencies currently available along with analyses regarding n-nucleotide distributions and D-J segment pair preferences. Additionally, we provide the first statistical evidence that sequential D-J recombinations occur at the human heavy chain locus during B-cell ontogeny with an approximate frequency of 20%.
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Affiliation(s)
- Joseph M Volpe
- Center for Computational Immunology, Duke University, Durham, NC, USA.
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27
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Hamblin TJ, Davis ZA, Oscier DG. Determination of how many immunoglobulin variable region heavy chain mutations are allowable in unmutated chronic lymphocytic leukaemia - long-term follow up of patients with different percentages of mutations. Br J Haematol 2007; 140:320-3. [PMID: 18053068 DOI: 10.1111/j.1365-2141.2007.06928.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The choice of 98% sequence homology for immunoglobulin heavy chains to distinguish between mutated and unmutated versions of chronic lymphocytic leukaemia (CLL) was arbitrary and was chosen to account for supposed polymorphisms. Some authors chose 97% or even 95%. This study examined survival curves for cohorts of patients with varying degrees of sequence homology. All patients with <97% homology behaved as if mutated. Those with 97-98% homology were more aggressive than the mutated cases, but less aggressive than those with >98% homology.
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Affiliation(s)
- Terry J Hamblin
- Department of Haematology, Royal Bournemouth Hospital, Bournemouth, UK.
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28
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Martín-Jiménez P, García-Sanz R, González D, Balanzategui A, Pérez JJ, Caballero MD, Sarasquete ME, Galende J, Orfao A, López-Berges MC, San Miguel JF, González M. Molecular Characterization of Complete and Incomplete Immunoglobulin Heavy Chain Gene Rearrangements in Hairy Cell Leukemia. ACTA ACUST UNITED AC 2007; 7:573-9. [DOI: 10.3816/clm.2007.n.043] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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29
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Nikitin EA, Malakho SG, Biderman BV, Baranova AV, Lorie YY, Shevelev AY, Peklo MM, Vlasik TN, Moskalev EA, Zingerman BV, Vorob'ev IA, Poltaraus AB, Sudarikov AB, Vorobjev AI. Expression level of lipoprotein lipase and dystrophin genes predict survival in B-cell chronic lymphocytic leukemia. Leuk Lymphoma 2007; 48:912-22. [PMID: 17487735 DOI: 10.1080/10428190701245112] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Mutational status of immunoglobulin variable region genes (VH-genes) is known as the strongest predictor of long term prognosis in B-CLL. However, applications in the routine clinical practice are time consuming, and therefore some other predictions are required. In this study, we have compared prognostic values of real time PCR quantification of the expression levels of four genes previously shown to be differentially expressed in V(H)-unmutated and mutated B-CLL subtypes: ZAP-70, ZBTB20, DMD and LPL. The study included 134 B-CLL patients. Expression levels of LPL and DMD genes were significantly correlated to mutational status, while expression levels of of ZAP-70 gene correlated only in CD19+ selected cases (N = 40). No correlation was observed for ZBTB20 gene. Expression levels of LPL and DMD predicted overall survival in the entire cohort of patients. Prognostic values of LPL gene expression levels were significant even for CLL patients with stage A. Quantitative RT-PCR assays for measuring LPL gene expression are robust enough to be introduced into routine clinical practice.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Dystrophin/biosynthesis
- Female
- Gene Expression Regulation, Neoplastic
- Humans
- Leukemia, B-Cell/metabolism
- Leukemia, B-Cell/mortality
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Leukemia, Lymphocytic, Chronic, B-Cell/mortality
- Leukocytes, Mononuclear/metabolism
- Lipoprotein Lipase/biosynthesis
- Male
- Middle Aged
- Prognosis
- Treatment Outcome
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Affiliation(s)
- E A Nikitin
- Hematology Research Center of Russia, Moscow, Russia.
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30
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Lee CEH, Jackson KJL, Sewell WA, Collins AM. Use of IGHJ and IGHD gene mutations in analysis of immunoglobulin sequences for the prognosis of chronic lymphocytic leukemia. Leuk Res 2006; 31:1247-52. [PMID: 17169423 DOI: 10.1016/j.leukres.2006.10.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2006] [Revised: 09/21/2006] [Accepted: 10/19/2006] [Indexed: 11/28/2022]
Abstract
The level of somatic point mutation in immunoglobulin genes is an important prognostic indicator for patients with chronic lymphocytic leukemia (CLL). Mutation analysis presently focuses solely upon the heavy chain IGHV gene, however mutation is a stochastic process that also targets IGHD and IGHJ genes. Here, we evaluate the completeness and reliability of the reported IGHJ gene repertoire, and demonstrate the likely consequences of the inclusion of IGHD and IGHJ mutations in CLL analysis, using a dataset of 607 sequences. Inclusion of these mutations would lead to the re-classification of many sequences, which should significantly improve the prognostic value of mutation analysis.
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Affiliation(s)
- Cindy E H Lee
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, Sydney, NSW 2052, Australia
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31
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Chang H, Cerny J. Molecular Characterization of Chronic Lymphocytic Leukemia With Two Distinct Cell Populations. Am J Clin Pathol 2006. [DOI: 10.1309/0yyf17gfkfjfnp5g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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32
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Babbage G, Ottensmeier CH, Blaydes J, Stevenson FK, Sahota SS. Immunoglobulin heavy chain locus events and expression of activation-induced cytidine deaminase in epithelial breast cancer cell lines. Cancer Res 2006; 66:3996-4000. [PMID: 16618718 DOI: 10.1158/0008-5472.can-05-3704] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
When cells transform, phenotypic and genetic profiles can be dramatically altered. Nevertheless, a recent report identifying IgG in breast cancer cells was unexpected, revealing differentiation features normally associated with B lymphocytes. To extend these findings, we focused on immunoglobulin variable (V) region gene analysis using well-defined breast cancer cell lines expressing the epithelial marker, epithelial cell adhesion molecule (EpCAM). V(H) gene transcripts were identifiable by nested reverse transcription-PCR either as single or dual V, diversity (D), and joining (J) rearrangements in four of six lines, most being potentially functional. V(D)J transcripts were observed in sequential cultures, indicating stable expression. To exclude coexisting lymphocytes, each cell line was shown to be EBV negative, with CD19/CD20 and cytoplasmic/surface immunoglobulin also absent by flow cytometry. Identified V(H) transcripts were then sought in individual tumor cells, isolated as EpCAM+ single cells by flow cytometry. Importantly, in three of three selected cell lines, V(H) genes were identifiable in a significant fraction (approximately 32%) of single cells. In five of six identified V(H) genes, somatic mutations were apparent with no intraclonal variation, indicating cessation of mutational activity. V(H) transcripts were pre- and post-isotype switch, with activation of switch events evident from expressed germ-line switch transcripts in two of six lines. Strikingly, six of six cell lines expressed activation-induced cytidine deaminase (AID) essential for mutational and switch activity. These data suggest either a de novo rearrangement and modification of V(H) genes in epithelial tumor cells or assimilation of lymphocyte-derived chromatin. Constitutive AID activation in malignant epithelial cells further raises a potential for inducing aberrant mutational activity.
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Affiliation(s)
- Gavin Babbage
- Genetic Vaccine Group and Cancer Sciences Division, School of Medicine, University of Southampton, Southampton, United Kingdom
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33
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Cheng CA, John JAC, Wu MS, Lee CY, Lin CH, Lin CH, Chang CY. Characterization of serum immunoglobulin M of grouper and cDNA cloning of its heavy chain. Vet Immunol Immunopathol 2006; 109:255-65. [PMID: 16199094 DOI: 10.1016/j.vetimm.2005.08.029] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2005] [Revised: 07/15/2005] [Accepted: 08/15/2005] [Indexed: 11/24/2022]
Abstract
Immunoglobulin M (IgM) from the whole serum of grouper fish, Epinephelus coioides was purified by affinity chromatography using protein A-Sepharose column. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) under reducing conditions revealed that the relative molecular masses (Mr) of the equimolar heavy and light chains of IgM were 78,000 and 27,000, respectively. The cDNAs encoding IgM heavy chain comprising its variable (VH) and constant (CH) regions have been cloned and sequenced from a grouper kidney cDNA library by antibody screening method. Five VH (130-142 amino acids) and four CH (450-454 amino acids) families were identified. The variable and constant regions were conserved with their putative domains. All the four constant region domains (CH1-CH2-CH3-CH4) contained each three conserved cysteine residues, which are considered to form the inter- and intra-chain disulfide bridges. There were three carbohydrate acceptor sites in the constant region. In general, the pattern of IgM gene organization seems to resemble that of other teleosts. Moreover, the CH genes in grouper IgM occur as multifamily as reported in Atlantic salmon and common carp.
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Affiliation(s)
- Chao-An Cheng
- Department of Food Science, National Kinmen Institute of Technology, Kinmen, Taiwan
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34
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Tobin G, Rosenquist R. Prognostic usage of V(H) gene mutation status and its surrogate markers and the role of antigen selection in chronic lymphocytic leukemia. Med Oncol 2006; 22:217-28. [PMID: 16110132 DOI: 10.1385/mo:22:3:217] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2005] [Accepted: 02/22/2005] [Indexed: 11/11/2022]
Abstract
B-cell chronic lymphocytic leukemia (CLL) is a clinically heterogeneous disease with many patients surviving for decades with minimal or no treatment, whereas others succumb rapidly to their disease despite therapy. In recent years, new molecular prognostic factors have emerged in CLL that have significantly improved the subgrouping of the disease. One of the most important molecular predictors, the immunoglobulin V(H) gene mutation status, divides CLL into two prognostic groups, depending on the presence or absence of somatic hypermutation, where unmutated V(H) genes are associated with considerably worse prognosis than mutated V(H) genes. An exception to this appears to be CLL patients utilizing the V(H)3-21 gene as they have poor outcome irrespective of mutation status. Surrogate markers for the VH gene mutation status have been suggested, such as CD38 and ZAP-70 expression. However, the CD38 level was later shown to display poor correlation to the mutation status, although it may still serve as an independent prognostic factor. More promising is the expression levels of ZAP-70, which appears to be both a strong surrogate marker for V(H) gene mutation status, although discrepancies have been reported, as well as an independent prognostic marker. Immunoglobulin gene analysis has also indicated the possibility of antigen selection in CLL considering the significant bias in V(H) gene usage. Intriguingly, the V(H)3-21+ group and several other CLL subsets using certain V(H) genes was recently reported to display strikingly restricted immunoglobulin gene features, in both their heavy and light chain gene rearrangements, thus further high-lighting the possible role of antigen involvement in CLL development.
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Affiliation(s)
- Gerard Tobin
- Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden.
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35
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Souza TA, Stollar BD, Sullivan JL, Luzuriaga K, Thorley-Lawson DA. Peripheral B cells latently infected with Epstein-Barr virus display molecular hallmarks of classical antigen-selected memory B cells. Proc Natl Acad Sci U S A 2005; 102:18093-8. [PMID: 16330748 PMCID: PMC1306799 DOI: 10.1073/pnas.0509311102] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2005] [Indexed: 11/18/2022] Open
Abstract
Epstein-Barr virus (EBV) establishes a lifelong persistent infection within peripheral blood B cells with the surface phenotype of memory cells. To date there is no proof that these cells have the genotype of true germinal-center-derived memory B cells. It is critical to understand the relative contribution of viral mimicry versus antigen signaling to the production of these cells because EBV encodes proteins that can affect the surface phenotype of infected cells and provide both T cell help and B cell receptor signals in the absence of cognate antigen. To address these questions we have developed a technique to identify single EBV-infected cells in the peripheral blood and examine their expressed Ig genes. The genes were all isotype-switched and somatically mutated. Furthermore, the mutations do not cause stop codons and display the pattern expected for antigen-selected memory cells based on their frequency, type, and location within the Ig gene. We conclude that latently infected peripheral blood B cells display the molecular hallmarks of classical antigen-selected memory B cells. Therefore, EBV does not disrupt the normal processing of latently infected cells into memory, and deviations from normal B cell biology are not tolerated in the infected cells. This article provides definitive evidence that EBV in the peripheral blood persists in true memory B cells.
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Affiliation(s)
- Tatyana A Souza
- Department of Pathology, Tufts University School of Medicine, Boston, MA 02111, USA
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36
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Abstract
Charles Darwin proposed that evolution occurs primarily by natural selection, but this view has been controversial from the beginning. Two of the major opposing views have been mutationism and neutralism. Early molecular studies suggested that most amino acid substitutions in proteins are neutral or nearly neutral and the functional change of proteins occurs by a few key amino acid substitutions. This suggestion generated an intense controversy over selectionism and neutralism. This controversy is partially caused by Kimura's definition of neutrality, which was too strict (|2Ns|< or =1). If we define neutral mutations as the mutations that do not change the function of gene products appreciably, many controversies disappear because slightly deleterious and slightly advantageous mutations are engulfed by neutral mutations. The ratio of the rate of nonsynonymous nucleotide substitution to that of synonymous substitution is a useful quantity to study positive Darwinian selection operating at highly variable genetic loci, but it does not necessarily detect adaptively important codons. Previously, multigene families were thought to evolve following the model of concerted evolution, but new evidence indicates that most of them evolve by a birth-and-death process of duplicate genes. It is now clear that most phenotypic characters or genetic systems such as the adaptive immune system in vertebrates are controlled by the interaction of a number of multigene families, which are often evolutionarily related and are subject to birth-and-death evolution. Therefore, it is important to study the mechanisms of gene family interaction for understanding phenotypic evolution. Because gene duplication occurs more or less at random, phenotypic evolution contains some fortuitous elements, though the environmental factors also play an important role. The randomness of phenotypic evolution is qualitatively different from allele frequency changes by random genetic drift. However, there is some similarity between phenotypic and molecular evolution with respect to functional or environmental constraints and evolutionary rate. It appears that mutation (including gene duplication and other DNA changes) is the driving force of evolution at both the genic and the phenotypic levels.
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Affiliation(s)
- Masatoshi Nei
- Department of Biology, Institute of Molecular Evolutionary Genetics, , Pennsylvania State University, USA.
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37
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Marasca R, Maffei R, Morselli M, Zucchini P, Castelli I, Martinelli S, Fontana M, Ravanetti S, Curotti M, Leonardi G, Cagossi K, Partesotti G, Torelli G. Immunoglobulin mutational status detected through single-round amplification of partial V(H) region represents a good prognostic marker for clinical outcome in chronic lymphocytic leukemia. J Mol Diagn 2005; 7:566-74. [PMID: 16258154 PMCID: PMC1867549 DOI: 10.1016/s1525-1578(10)60589-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/18/2005] [Indexed: 11/27/2022] Open
Abstract
The immunoglobulin (Ig) mutational status in B-cell chronic lymphocytic leukemia (CLL) distinguishes two subsets of patients with different prognosis. Ig status detection is commonly performed with a panel of V(H) family-specific primers. Although this method detects clonal VDJ rearrangement in virtually all cases, it is technically cumbersome and therefore not widely used clinically. Here, we describe a simple and rapid method to establish the mutational status of IgV(H) in CLL. The method is based on a consensus V(H) FR2 primer, used in both polymerase chain reaction (PCR) and sequencing reactions. Overall, monoclonal B-cell populations were detected in 163 of 189 CLL patients (86%). The prognostic value of IgV(H) mutational status was then evaluated by analyzing survival in 146 CLL cases using different V(H) homology cutoffs. CLL prognostic groups were best separated by the classical 98% cutoff: median survival was 127 and 206 months in unmutated and mutated CLL cases, respectively (P = 0.0023). V(H) FR2 consensus and V(H) family PCR were compared in 41 cases, correctly assigning all cases by both methods. Therefore, we suggest a sequential strategy to detect immunoglobulin mutational status in CLL patients by first using the approach described in this study followed by alternative V(H) family-specific PCRs for negative cases.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Base Sequence
- Biomarkers
- Complementarity Determining Regions/genetics
- DNA Mutational Analysis
- Female
- Genes, Immunoglobulin/genetics
- Humans
- Immunoglobulin Variable Region/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Male
- Middle Aged
- Molecular Sequence Data
- Mutation/genetics
- Polymerase Chain Reaction
- Prognosis
- Sequence Alignment
- Survival Analysis
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Affiliation(s)
- Roberto Marasca
- Department of Oncology and Hematology, University of Modena and Reggio Emilia, Via Del Pozzo 71, 41100 Modena, Italy.
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38
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Chimge NO, Pramanik S, Hu G, Lin Y, Gao R, Shen L, Li H. Determination of gene organization in the human IGHV region on single chromosomes. Genes Immun 2005; 6:186-93. [PMID: 15744329 DOI: 10.1038/sj.gene.6364176] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Organization of the IGHV genes (n=108) on single human chromosomes has been determined by detecting these sequences in single sperm using multiplex PCR amplification followed by microarray detection. A total of 374 single sperm samples from five Caucasian males were studied. Three deletion/insertion polymorphisms (Del I-Del III) with deletion allele frequencies ranging from 0.1 to 0.3 were identified. Del I is a previously reported polymorphism affecting three IGHV genes (IGHV1-8, IGHV3-9, and IGHV2-10). Del II affects a region 2-18 kb containing two pseudogenes IGHV(II)-28.1 and IGHV3-29, and Del III spans approximately 21-53 kb involving genes IGHV4-39, IGHV7-40, IGHV(II)-40-1, and IGHV3-41. Deletion alleles of both Dels II and III were found in a heterozygous state, and therefore, could not be easily detected if haploid samples were not used in the study. Results of the present study indicate that deletions/insertions together with other possible chromosomal rearrangements may play an important role in forming the genetic structure of the IGHV region, and may significantly contribute to antibody diversity. Since these three polymorphisms are located within or next to the 3' half of the IGHV region, they may have an important role in the expressed IGHV gene repertoire during immune response.
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Affiliation(s)
- N-O Chimge
- Department of Molecular Genetics, Microbiology and Immunology, University of Medicine and Dentistry of New Jersey Robert Wood Johnson Medical School, New Brunswick, NJ, USA
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39
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Grabowski P, Hultdin M, Karlsson K, Tobin G, Aleskog A, Thunberg U, Laurell A, Sundström C, Rosenquist R, Roos G. Telomere length as a prognostic parameter in chronic lymphocytic leukemia with special reference to VH gene mutation status. Blood 2005; 105:4807-12. [PMID: 15746080 DOI: 10.1182/blood-2004-11-4394] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
B-cell chronic lymphocytic leukemia (CLL) consists of 2 prognostic entities where cases with mutated immunoglobulin V(H) genes have better outcome than unmutated cases. V(H)-mutated CLLs display longer telomeres compared with unmutated cases and telomere length has been indicated to predict outcome, although the prognostic value of telomere length has not been fully established in CLL. We analyzed telomere length, V(H) gene mutation status, and clinical parameters in a large series of CLL. Telomere length was assessed by quantitative polymerase chain reaction (PCR), giving a very good correlation to telomere length estimated by Southern blotting (P < .001). The prognostic information given by mutation status (n = 282) and telomere length (n = 246) was significant (P < .001, respectively). Telomere length was a prognostic factor for stage A (P = .021) and stage B/C (P = .018) patients, whereas mutation status predicted outcome only in stage A patients (P < .001). Furthermore, mutated CLLs were subdivided by telomere length into 2 groups with different prognoses (P = .003), a subdivision not seen for unmutated cases (P = .232). Interestingly, the V(H)-mutated group with short telomeres had an overall survival close to that of the unmutated cases. Thus, by combining V(H) mutation status and telomere length, an improved subclassification of CLL was achieved identifying previously unrecognized patient groups with different outcomes.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Blotting, Southern
- Female
- Genes, Immunoglobulin
- Humans
- Immunoglobulin Heavy Chains/genetics
- Immunophenotyping
- In Situ Hybridization, Fluorescence
- Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Lymph Nodes/pathology
- Male
- Middle Aged
- Models, Statistical
- Mutation
- Polymerase Chain Reaction
- Prognosis
- Reverse Transcriptase Polymerase Chain Reaction
- Telomere/ultrastructure
- Time Factors
- Treatment Outcome
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Affiliation(s)
- Pawel Grabowski
- Department of Medical Biosciences, Pathology, Umeå University, SE-90187 Umeå, Sweden
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40
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Ek S, Ortega E, Borrebaeck CAK. Transcriptional profiling and assessment of cell lines as in vitro models for mantle cell lymphoma. Leuk Res 2005; 29:205-13. [PMID: 15607370 DOI: 10.1016/j.leukres.2004.06.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2004] [Accepted: 06/29/2004] [Indexed: 10/26/2022]
Abstract
Mantle cell lymphoma (MCL) is an aggressive malignancy and new treatment modalities must be established to increase patient survival time. In the search for new therapeutic targets, reliable and well-characterised in vitro models are essential. In this study, we have characterised three MCL cell lines (SP53, Granta 519 and NCEB1) in comparison with primary tumours from MCL, follicular lymphomas (FL), a FL cell line (RL), a Burkitt lymphoma cell line (RAJI) and five different B cell populations from healthy individuals. Expression profiling was used to determine the relative expression of >12000 transcripts in these samples, and flow cytometry analysis was performed to establish a phenotypic signature for each of the cell lines. In addition, the cell lines were sequenced, and the frequency of somatic mutations and immunoglobulin (Ig) variable heavy chain (VH) usage were determined. We show by hierarchical clustering that the cell lines retain a genetic signature similar to primary MCL, which readily separated the MCL samples from the other lymphoma cell lines and the FL tumours. Furthermore, the MCL cell lines showed differences in the frequency of VH somatic mutations (0-2.1%). The increased number of mutations in NCEB1, compared to the other MCL cell lines, was in agreement with a decreased expression of CD31, CD44, CXCR5, CCR7 and CCR6. Taken together, our data show that the cell lines are clearly derived from MCL tumours and expressed similar genetic and phenotypic signatures compared to primary tumours, which confirmed their usefulness as in vitro models.
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Affiliation(s)
- Sara Ek
- Department of Immunotechnology, Lund University, P.O. Box 7031, SE-22007 Lund, Sweden.
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41
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Bando Y, Shimizu A, Ra C. Characterization of VHepsilon gene expressed in PBL from children with atopic diseases: detection of homologous VH1-69 derived transcripts from three unrelated patients. Immunol Lett 2005; 94:99-106. [PMID: 15234541 DOI: 10.1016/j.imlet.2004.04.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2004] [Revised: 03/31/2004] [Accepted: 04/16/2004] [Indexed: 11/28/2022]
Abstract
To elucidate the molecular background of IgE production in early infancy, we analyzed the nucleotide sequences of 36 VH-Cepsilon transcripts expressed in PBL from three infants with allergic diseases. We detected transcripts derived from VH1, VH3, VH4 gene family members, and no bias was observed in the usage of particular VH gene family. However, some VH members, VH1; 1-46, 1-69, VH3; 3-11, 3-21, VH4; 4-39, 4-59 were frequently seen and thus notable. VH4 gene was dominant in one patient with severe atopic dermatitis and food allergy, suggesting the involvement of this gene in pathogenesis of the disease. Even a limited number of clones were analyzed, we also found highly homologous VH1-69 derived sequences from all the three patients, which share the same somatic mutations or polymorphic variations in complementarity-determining region (CDR) 1, and 2 with the same CDR3 (D-JH) sequences including the junctions. These findings might suggest that a rather limited VH gene might be rearranged for specific IgE in early life.
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Affiliation(s)
- Yuki Bando
- Department of Pediatrics, Kitasato University School of Medicine, Kanagawa 228-8555, Japan.
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42
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Romo-González T, Vargas-Madrazo E. Structural analysis of substitution patterns in alleles of human immunoglobulin VH genes. Mol Immunol 2004; 42:1085-97. [PMID: 15829298 DOI: 10.1016/j.molimm.2004.11.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2004] [Indexed: 10/26/2022]
Abstract
The diversity in repertoires of antibodies (Abs) needed in response to the antigen challenge is produced by evolutionary and somatic processes. The mechanisms operating at a somatic level have been studied in great detail. In contrast, neither the mechanisms nor the strategies of diversification at an evolutionary level have yet been understood in similar detail. Particularly, the substitution patterns in alleles of immunoglobulin genes (Igs) have not been systematically studied. Furthermore, there is a scarcity of studies which link the analysis at a genetic level of the diversification of repertoires with the structural consequences at the protein level of the changes in DNA information. For the purpose of systematically characterizing the strategies of evolutionary diversification through sequence variation at alleles, in this work, we built a database for all the alleles of the IGHV locus in humans reported until now. Based on these data, we performed diverse analyses of substitution patterns and linked these results with studies at the protein level. We found that the sequence diversification in different alleles does not operate with equal intensity for all V genes. Our studies, both of the number of substitutions and of the type of amino acid change per sub-segment of the V-REGION evidenced differences in the selective pressure to which these regions are exposed. The implications of these results for understanding the evolutionary diversification strategies, as well as for the somatic generation of antibody repertoires are discussed.
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Affiliation(s)
- Tania Romo-González
- Departamento Biología Sistémica, Instituto de Investigaciones Biológicas, Universidad Veracruzana, Morelos 9 La Pitaya, Zoncuantla, 91500 Coatepec, Xalapa, Veracruz, Mexico
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43
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de Bono B, Madera M, Chothia C. VH gene segments in the mouse and human genomes. J Mol Biol 2004; 342:131-43. [PMID: 15313612 DOI: 10.1016/j.jmb.2004.06.055] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2004] [Revised: 06/18/2004] [Accepted: 06/18/2004] [Indexed: 10/26/2022]
Abstract
We have examined the mouse genome sequence to determine its VH gene segment repertoire. In all, 141 segments are mapped to a 3 Mb region of chromosome 12. There is evidence that 92 of these are functional in the mouse strain used for the genome sequence, C57BL/6J; 12 are functional in other mouse strains, and 37 are pseudogenes. The mouse VH gene segment repertoire is therefore twice the size of that in humans. The mouse and human loci bear no large-scale similarity to each other. The 104 functional segments belong to one of the 15 known sequence subgroups, which have been further clustered into eight sets here. Seven of these sets, comprising 101 sequences, are related to five of the human VH families and have the same canonical structures in their hypervariable regions. Duplication of members of one set in the distal half of the locus is mainly responsible for the larger size of the mouse repertoire. Phylogenetic analysis of the VH segments indicates that most of the sequences in the human and mouse VH loci have arisen subsequent to the divergence of the two organisms from their common ancestor.
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Affiliation(s)
- Bernard de Bono
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.
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Cerny J, Slavickova A, Krepelova A, Trneny M, Karban J, Klener P. Biallelic IgH rearrangements in patients with indolent lymphoproliferative disorders: Molecular and practical implications. J Cell Physiol 2004; 199:217-26. [PMID: 15040004 DOI: 10.1002/jcp.10459] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
We report a group of patients (pts) with indolent lymphoproliferative disorder who had both alleles for the immunoglobulin heavy chain genes rearranged (biIgH). This group of 17 pts consisted of 9 small lymphocytic lymphomas (SLL) and 8 chronic lymphocytic leukemia (CLL). The polymerase chain reaction (PCR) amplification of clonal immunoglobulin heavy (IgH) rearrangement using the complementarity determining region III (CDRIII) constantly retrieved two distinct bands in all PCR informative samples of those pts. To rule out biclonality, we evaluated samples by fluorescein activated cell sorting (FACS) analysis and sequenced the PCR products. We were able to obtain both IgH sequences from 12 patients. FACS suggested biclonality in one case, which also correlated with sequencing results as both IgH rearrangements were in-frame. Recently, we reported a patient who sustained transformation into an aggressive disease after biIgH was detected in the setting of monoclonal disease (Cerny et al., 2003b, Haematologica 88(05):ECR15 B.). We decided to compare clinical characteristics and prognosis of 17 pts with biIgH and 37 pts with monoIgH rearrangements. Although we found some minor differences in disease characteristics between both groups, these did not translate into a significantly different overall survival. Our findings suggest that true biclonal cases of CLL are rare.
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Affiliation(s)
- Jan Cerny
- 1st Department of Internal Medicine, Charles University General Hospital, Prague, Czech Republic.
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Davis ZA, Orchard JA, Corcoran MM, Oscier DG. Divergence from the germ-line sequence in unmutated chronic lymphocytic leukemia is due to somatic mutation rather than polymorphisms. Blood 2003; 102:3075. [PMID: 14527893 DOI: 10.1182/blood-2003-08-2696] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Hultdin M, Rosenquist R, Thunberg U, Tobin G, Norrback KF, Johnson A, Sundström C, Roos G. Association between telomere length and V(H) gene mutation status in chronic lymphocytic leukaemia: clinical and biological implications. Br J Cancer 2003; 88:593-8. [PMID: 12592375 PMCID: PMC2377180 DOI: 10.1038/sj.bjc.6600763] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The immunoglobulin V(H) gene mutation status can divide B-cell chronic lymphocytic leukaemia (CLL) into two entities with a different clinical course. Cases with unmutated V(H) genes, considered to evolve from pregerminal centre (GC) cells, have a worse outcome compared to cases showing mutated V(H) genes, that is, post-GC derived. Also, telomere length has been reported to be of prognostic significance in CLL. Interestingly, telomerase becomes activated during the GC reaction and an elongation of the telomeres occurs in GC B cells. We performed telomere length and V(H) gene analysis in a series of 61 CLL cases, in order to investigate if the unique telomere lengthening shown in GC B cells could reflect the telomere status in the two subsets of mutated and unmutated CLL. A novel association was found between V(H) gene mutation status and telomere length, since significantly shorter telomeres were demonstrated in the unmutated group compared to the mutated group (mean length 4.3 vs 6.3 kbp). Shorter telomeres also constituted a subgroup with a worse prognosis than cases with longer telomeres (median survival 59 vs 159 months). Furthermore, the Ig gene sequence data revealed that samples with high mutations frequency (>6%) had long telomeres ( approximately 8 kbp). Thus, both the telomere and V(H) gene mutation status in CLL appear linked, which may reflect the proliferative history of the clonal cells with regard to the GC reaction.
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Affiliation(s)
- M Hultdin
- Department of Medical Biosciences, Pathology, Umeå University, SE-90185 Umeå, Sweden
| | - R Rosenquist
- Departments of Genetics and Pathology, Uppsala University, SE-751 85 Uppsala, Sweden
| | - U Thunberg
- Department of Oncology, Radiology and Clinical Immunology, Uppsala University, SE-751 85 Uppsala, Sweden
| | - G Tobin
- Departments of Genetics and Pathology, Uppsala University, SE-751 85 Uppsala, Sweden
| | - K-F Norrback
- Department of Medical Biosciences, Pathology, Umeå University, SE-90185 Umeå, Sweden
| | - A Johnson
- Department of Oncology, Radiology and Clinical Immunology, Uppsala University, SE-751 85 Uppsala, Sweden
| | - C Sundström
- Departments of Genetics and Pathology, Uppsala University, SE-751 85 Uppsala, Sweden
| | - G Roos
- Department of Medical Biosciences, Pathology, Umeå University, SE-90185 Umeå, Sweden
- Department of Medical Biosciences, Pathology, Umeå University, SE-90185 Umeå, Sweden. E-mail:
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Giles IP, Haley JD, Nagl S, Isenberg DA, Latchman DS, Rahman A. A systematic analysis of sequences of human antiphospholipid and anti-beta2-glycoprotein I antibodies: the importance of somatic mutations and certain sequence motifs. Semin Arthritis Rheum 2003; 32:246-65. [PMID: 12621590 DOI: 10.1053/sarh.2003.49994] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
OBJECTIVE Previous studies have suggested the importance of somatic mutations and certain residues in the complementarity determining regions (CDRs) of antiphospholipid antibodies (aPL) implicated in the pathogenesis of antiphospholipid antibody syndrome (APS). The authors tested this hypothesis by carrying out a systematic analysis of all published aPL sequences. METHODS Each aPL variable region sequence was aligned to the closest germline counterpart in the VBASE Sequence Directory by using DNAPLOT software, allowing analysis of nucleotide homology and distribution of somatic mutations. The probability that this distribution arose as a result of antigen-driven accumulation of replacement mutations in the CDRs was tested statistically. RESULTS There was no preferential gene or family use in the 36 aPL sequences identified. Immunoglobulin (Ig) M aPL had few somatic mutations compared with IgG. Of the IgG aPL, 9 of 14 showed evidence of antigen-driven accumulation of replacement mutations in the CDRs. Multinomial analysis allowed a clearer statistical identification of sequences that had been subject to antigen drive. The more specific IgM aPL and some IgG aPL displayed an accumulation of arginine, asparagine, and lysine residues in CDRs. CONCLUSIONS High-specificity binding in IgG aPL, but not in more specific IgM aPL, is conferred by antigen-driven somatic mutation. This may in part be caused by an accumulation of arginine, asparagine, and lysine residues in the CDRs, which are germlines encoded in the more specific IgM aPL, but often arise because of somatic mutation in IgG aPL. RELEVANCE An understanding of the role of arginine, asparagine, and lysine residues in the binding of pathogenic aPL to phospholipids, and to beta(2)-glycoprotein I, may eventually help in the development of drugs to interfere with those interactions, and thereby improve the treatment of antiphospholipid antibody syndrome.
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Affiliation(s)
- Ian P Giles
- Department of Medicine, Centre for Rheumatology, University College London, London, England
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Riboldi P, Ikematsu W, Brambilla B, Caprani C, Gerosa M, Casali P. Diversity and somatic hypermutation of the Ig VHDJH, V kappa J kappa, and V lambda J lambda gene segments in lymphoma B cells: relevance to the origin of the neoplastic B cell clone. Hum Immunol 2003; 64:69-81. [PMID: 12507816 DOI: 10.1016/s0198-8859(02)00740-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Burkitt's lymphoma (BL) is a malignancy of B cells characterized by chromosomal translocations involving the immunoglobulin (Ig) and c-MYC gene loci. To address the putative role of antigen in the clonal expansion of these neoplastic B cells, we analyzed the VHDJH and VLJL gene segments expressed by the established cell lines derived from six endemic BL and six sporadic BL. Eight BL cell lines used genes of the VH3 family, two of the VH4, and two of the VH1. Eight VL chains were kappa (four members of the V kappa3, two of the V kappa1, and two of the V kappa2 subgroups) and four lambda (three members of the V lambda1 and one of the Vl ambda3 subgroup). The VH gene utilization was stochastic (i.e., it reflected the relative representation of the different VH gene family members in the human haploid genome). In contrast, the VL gene utilization was skewed toward the overutilization of the V kappa3 and V lambda1 gene subgroups. When compared with those of the respective germline genes, the sequences of the expressed Ig VDJ genes displayed nucleotide differences that resulted from somatic hypermutation. In three endemic and three sporadic BL cells, nucleotide changes yielding amino acid substitutions segregated within the complementarity determining region, indicating the application of a positive pressure for replacement mutations and suggesting that these neoplastic lymphocytes underwent a process of clonal selection driven by antigen, perhaps emerging from or transitioning through germinal centers.
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Pichurin PN, Guo J, Estienne V, Carayon P, Ruf J, Rapoport B, McLachlan SM. Evidence that the complement control protein-epidermal growth factor-like domain of thyroid peroxidase lies on the fringe of the immunodominant region recognized by autoantibodies. Thyroid 2002; 12:1085-95. [PMID: 12593722 DOI: 10.1089/105072502321085180] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
There is no consensus regarding the location of the immunodominant region (IDR) on thyroid peroxidase (TPO) recognized by the majority of autoantibodies. Strong evidence indicates that it lies upstream of amino acid 741. However, an epitope has been localized to downstream residues 742-848 encompassing a disulfide-rich complement control protein (CCP)-like and epidermal growth factor (EGF)-like domain. To determine whether these domains comprise part of the IDR, we used a recombinant CCP/EGF-like polypeptide to screen a thyroid B-cell-derived immunoglobulin gene phage display library. Two unusual TPO autoantibodies were isolated. Neither was among the 83 clones previously obtained by panning the same library on native or denatured TPO, or TPO with the IDR masked. Fab from these clones bound native TPO, one with high affinity (Kd 6 x 10(-10) M), and both recognized TPO expressed on the surface of mammalian cells. Phage-expressing multiple copies of the antibody (multivalent), but not monovalent Fab from these clones, bound to the CCP/EGF polypeptide. Most important, inhibition of TPO binding by autoantibodies to the IDR indicated that the epitopes of the two new autoantibodies overlap with this region. The value of these two rare clones lies in the insight they provide into the location of the TPO IDR. From their binding characteristics, we deduce that the CCP/EGF-like domain lies on the fringe of the TPO immunodominant region.
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Affiliation(s)
- Pavel N Pichurin
- Autoimmune Disease Unit, Cedars-Sinai Research Institute, Los Angeles, California, USA
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Abstract
The human immunoglobulin heavy chain VH region is one of the most complex regions in the human genome. The high level of diversity of this region has been shown by a number of studies. However, because of the limitations of the conventional experimental methods, it has been difficult to learn the extent of the diversity and the underlying mechanisms. This review describes a number of new genetic approaches developed in the authors' laboratory. By using these approaches, significant progress has been made in assigning different VH sequences to their respective loci, in learning the diversity of gene segment number and composition among the VH haplotypes, and in learning VH gene segment organization in individual haplotypes. Information obtained toward this direction could help in understanding the mechanisms underlying VH region diversity and the biological impact of the VH region diversity.
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Affiliation(s)
- Honghua Li
- Department of Molecular Genetics, Microbiology & Immunology/The Cancer Institute of New Jersey, University of Medicine and Dentistry of New Jersey Robert Wood Johnson Medical School, New Brunswick, NJ 08903, USA.
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