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Stamatopoulos K, Bruford E, Campo E, Lefranc MP. Immunogenetics in hematopathology and hematology: why a common language is important. Leukemia 2024; 38:1474-1476. [PMID: 38664547 PMCID: PMC11216993 DOI: 10.1038/s41375-024-02260-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 07/03/2024]
Affiliation(s)
- Kostas Stamatopoulos
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece.
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden.
| | - Elspeth Bruford
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - Elias Campo
- Hematopathology Section, Pathology Department, Hospital Clínic, University of Barcelona, Barcelona, Spain
- Molecular Pathology of Lymphoid Neoplasms Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Marie-Paule Lefranc
- IMGT®, the international ImMunoGeneTics information system®, Laboratoire d'ImmunoGénétique Moléculaire (LIGM), Institut de Génétique Humaine (IGH), Centre National de la Recherche Scientifique (CNRS), Université de Montpellier, Montpellier, France.
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2
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Leeman-Neill RJ, Bhagat G, Basu U. AID in non-Hodgkin B-cell lymphomas: The consequences of on- and off-target activity. Adv Immunol 2024; 161:127-164. [PMID: 38763700 DOI: 10.1016/bs.ai.2024.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2024]
Abstract
Activation induced cytidine deaminase (AID) is a key element of the adaptive immune system, required for immunoglobulin isotype switching and affinity maturation of B-cells as they undergo the germinal center (GC) reaction in peripheral lymphoid tissue. The inherent DNA damaging activity of this enzyme can also have off-target effects in B-cells, producing lymphomagenic chromosomal translocations that are characteristic features of various classes of non-Hodgkin B-cell lymphoma (B-NHL), and generating oncogenic mutations, so-called aberrant somatic hypermutation (aSHM). Additionally, AID has been found to affect gene expression through demethylation as well as altered interactions between gene regulatory elements. These changes have been most thoroughly studied in B-NHL arising from GC B-cells. Here, we describe the most common classes of GC-derived B-NHL and explore the consequences of on- and off-target AID activity in B and plasma cell neoplasms. The relationships between AID expression, including effects of infection and other exposures/agents, mutagenic activity and lymphoma biology are also discussed.
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Affiliation(s)
- Rebecca J Leeman-Neill
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States; Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States.
| | - Govind Bhagat
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States
| | - Uttiya Basu
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States
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3
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Dalloul I, Laffleur B, Dalloul Z, Wehbi B, Jouan F, Brauge B, Derouault P, Moreau J, Kracker S, Fischer A, Durandy A, Le Noir S, Cogné M. UnAIDed Class Switching in Activated B-Cells Reveals Intrinsic Features of a Self-Cleaving IgH Locus. Front Immunol 2021; 12:737427. [PMID: 34777346 PMCID: PMC8581400 DOI: 10.3389/fimmu.2021.737427] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 10/11/2021] [Indexed: 11/13/2022] Open
Abstract
Activation-induced deaminase (AID) is the major actor of immunoglobulin (Ig) gene diversification in germinal center B-cells. From its first description, it was considered as mandatory for class switch recombination (CSR), and this discovery initiated a long quest for all of the AID-interacting factors controlling its activity. The mechanisms focusing AID-mediated DNA lesions to given target sequences remain incompletely understood with regards the detailed characterization of optimal substrates in which cytidine deamination will lead to double strand breaks (DSBs) and chromosomal cleavage. In an effort to reconsider whether such CSR breaks absolutely require AID, we herein provide evidence, based on deep-sequencing approaches, showing that this dogma is not absolute in both human and mouse B lymphocytes. In activated B-cells from either AID-deficient mice or human AID-deficient patients, we report an intrinsic ability of the IgH locus to undergo "on-target" cleavage and subsequent synapsis of broken regions in conditions able to yield low-level CSR. DNA breaks occur in such conditions within the same repetitive S regions usually targeted by AID, but their repair follows a specific pathway with increased usage of microhomology-mediated repair. These data further demonstrate the role of AID machinery as not initiating de novo chromosomal cleavage but rather catalyzing a process which spontaneously initiates at low levels in an appropriately conformed IgH locus.
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Affiliation(s)
- Iman Dalloul
- Institut National de la Santé et de la Recherche Médicale (INSERM) U1262, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 7276, Limoges University, Limoges, France
| | - Brice Laffleur
- Institut National de la Santé et de la Recherche Médicale (INSERM) U 1236, Rennes1 University, Rennes, France
| | - Zeinab Dalloul
- Institut National de la Santé et de la Recherche Médicale (INSERM) U1262, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 7276, Limoges University, Limoges, France
| | - Batoul Wehbi
- Institut National de la Santé et de la Recherche Médicale (INSERM) U1262, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 7276, Limoges University, Limoges, France
| | - Florence Jouan
- Institut National de la Santé et de la Recherche Médicale (INSERM) U 1236, Rennes1 University, Rennes, France
| | - Baptiste Brauge
- Institut National de la Santé et de la Recherche Médicale (INSERM) U 1236, Rennes1 University, Rennes, France
| | - Paco Derouault
- Centre Hospitalier Universitaire (CHU) Dupuytren, Limoges, France
| | - Jeanne Moreau
- Institut National de la Santé et de la Recherche Médicale (INSERM) U1262, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 7276, Limoges University, Limoges, France
| | - Sven Kracker
- Institut National de la Santé et de la Recherche Médicale (INSERM) Unité Mixte de Recherche (UMR) 1163, Laboratory of Human Lympho-hematopoiesis, Imagine Institute, Université de Paris, Paris, France
| | - Alain Fischer
- Institut National de la Santé et de la Recherche Médicale (INSERM) Unité Mixte de Recherche (UMR) 1163, Laboratory of Human Lympho-hematopoiesis, Imagine Institute, Université de Paris, Paris, France
| | - Anne Durandy
- Institut National de la Santé et de la Recherche Médicale (INSERM) Unité Mixte de Recherche (UMR) 1163, Laboratory of Human Lympho-hematopoiesis, Imagine Institute, Université de Paris, Paris, France
| | - Sandrine Le Noir
- Institut National de la Santé et de la Recherche Médicale (INSERM) U1262, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 7276, Limoges University, Limoges, France
| | - Michel Cogné
- Institut National de la Santé et de la Recherche Médicale (INSERM) U1262, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 7276, Limoges University, Limoges, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) U 1236, Rennes1 University, Rennes, France
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4
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Savage P. Chemotherapy Curability in Leukemia, Lymphoma, Germ Cell Tumors and Gestational Malignancies: A Reflection of the Unique Physiology of Their Cells of Origin. Front Genet 2020; 11:426. [PMID: 32582272 PMCID: PMC7295948 DOI: 10.3389/fgene.2020.00426] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 04/06/2020] [Indexed: 11/21/2022] Open
Abstract
Cytotoxic DNA damaging chemotherapy brings clinical benefits in the treatment of many metastatic malignancies. However routine curative treatment remains restricted to a small number of malignancies including acute leukemia, high grade lymphoma, germ cell tumors, gestational malignancies and some of the rare childhood cancers. The detailed explanation for this dramatic divergence in outcomes remains to be elucidated. However, we have previously argued that there is a strong correlation between presence of the unique genetic events of immunoglobulin gene variable/diversity/joining (VDJ) recombination, somatic hypermutation (SHM), meiosis, nuclear fusion and gastrulation occurring in cells of origin of these malignancies and their high sensitivity to DNA damaging chemotherapy. In this study we have reviewed some of the basic physiological information relating to the specialized activity and sensitivity to DNA damage mediated apoptosis of normal cells undergoing these processes. In each of unique genetic events there are dramatic changes in apoptotic sensitivity. In VDJ recombination and somatic hypermutation over 95% of the cells involved undergo apoptosis, whilst in meiosis and nuclear fusion there are dramatic short term increases in the apoptotic sensitivity to DNA damage. It is apparent that each of the malignancies arising during these processes retains some of the unique phenotype associated with it. The impact of the physiological differences is most clearly seen in the two non-mutational malignancies. Gestational choriocarcinoma which arises shortly after nuclear fusion is routinely curable with chemotherapy whilst CIMP-positive ependymomas which is not linked to any of the unique genetic events is highly resistant. A similar pattern is found in a pair of malignancies driven by a single driver mutation. Infantile acute lymphoblastic leukemia (ALL) arises in a cell undergoing the early stages of VDJ recombination and has a 40% cure rate in contrast pediatric rhabdoid malignancy which is not linked to a unique genetic event responds very poorly to chemotherapy treatment. The physiological changes occurring in cancer cells at the time of the malignant transformation appear to have a major impact on the subsequent sensitivity to chemotherapy and curability. New therapies that impact on these pathways may be of therapeutic value.
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Affiliation(s)
- Philip Savage
- Department of Oncology, Brighton and Sussex University Hospitals, Brighton, United Kingdom
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5
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Gemenetzi K, Agathangelidis A, Zaragoza-Infante L, Sofou E, Papaioannou M, Chatzidimitriou A, Stamatopoulos K. B Cell Receptor Immunogenetics in B Cell Lymphomas: Immunoglobulin Genes as Key to Ontogeny and Clinical Decision Making. Front Oncol 2020; 10:67. [PMID: 32083012 PMCID: PMC7006488 DOI: 10.3389/fonc.2020.00067] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 01/15/2020] [Indexed: 12/21/2022] Open
Abstract
The clonotypic B cell receptor immunoglobulin (BcR IG) plays a seminal role in B cell lymphoma development and evolution. From a clinical perspective, this view is supported by the remarkable therapeutic efficacy of BcR signaling inhibitors, even among heavily pre-treated, relapsed/refractory patients. This clinical development complements immunogenetic evidence for antigen drive in the natural history of these tumors. Indeed, BcR IG gene repertoire biases have been documented in different B cell lymphoma subtypes, alluding to selection of B cell progenitors that express particular BcR IG. Moreover, distinct entities display imprints of somatic hypermutation within the clonotypic BcR IG gene following patterns that strengthen the argument for antigen selection. Of note, at least in certain B cell lymphomas, the BcR IG genes are intraclonally diversified, likely in a context of ongoing interactions with antigen(s). Moreover, BcR IG gene repertoire profiling suggests that unique immune pathways lead to distinct B cell lymphomas through targeting cells at different stages in the B cell differentiation trajectory (e.g., germinal center B cells in follicular lymphoma, FL). Regarding the implicated antigens, although their precise nature remains to be fully elucidated, immunogenetic analysis has offered important hints by revealing similarities between the BcR IG of particular lymphomas and B cell clones with known antigenic specificity: this has paved the way to functional studies that identified relevant antigenic determinants of classes of structurally similar epitopes. Finally, in certain tumors, most notably chronic lymphocytic leukemia (CLL), immunogenetic analysis has also proven instrumental in accurate patient risk stratification since cases with differing BcR IG gene sequence features follow distinct disease courses and respond differently to particular treatment modalities. Overall, delving into the BcR IG gene sequences emerges as key to understanding B cell lymphoma pathophysiology, refining prognostication and assisting in making educated treatment choices.
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Affiliation(s)
- Katerina Gemenetzi
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Andreas Agathangelidis
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Laura Zaragoza-Infante
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Electra Sofou
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Maria Papaioannou
- Hematology Department, University General Hospital of Thessaloniki AHEPA, Thessaloniki, Greece
| | | | - Kostas Stamatopoulos
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
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6
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McBride KM, Kil H, Mu Y, Plummer JB, Lee J, Zelazowski MJ, Sebastian M, Abba MC, Aldaz CM. Wwox Deletion in Mouse B Cells Leads to Genomic Instability, Neoplastic Transformation, and Monoclonal Gammopathies. Front Oncol 2019; 9:517. [PMID: 31275852 PMCID: PMC6593956 DOI: 10.3389/fonc.2019.00517] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 05/29/2019] [Indexed: 01/18/2023] Open
Abstract
WWOX (WW domain containing oxidoreductase) expression loss is common in various cancers and characteristic of poor prognosis. Deletions, translocations, and loss of expression affecting the WWOX gene are a common feature of various B cell neoplasms such as certain B cell lymphomas and multiple myeloma. However, the role of this common abnormality in B cell tumor initiation and/or progression has not been defined. In this study, we conditionally deleted Wwox early in B cell development by means of breeding Cd19-Cre transgenic mice crossed to Wwox floxed mice (Cd19 Wwox KO). We observed a significant reduced survival in Cd19 Wwox KO mice and the development of B cell neoplasms including B cell lymphomas, plasma cell neoplasias characterized by increased numbers of CD138+ populations as well as monoclonal gammopathies detected by serum protein electrophoresis. To investigate whether Wwox loss could play a role in genomic instability, we analyzed DNA repair functions during immunoglobulin class switch joining between DNA segments in antibody genes. While class switch recombination (CSR) was only slightly impaired, Wwox deficiency resulted in a dramatic shift of double strand break (DSB) repair from normal classical-NHEJ toward the microhomology-mediated alternative-NHEJ pathway, a pathway associated with chromosome translocations and genome instability. Consistent with this, Wwox deficiency resulted in a marked increase of spontaneous translocations during CSR. This work defines for the first time a role for Wwox for maintaining B cell genome stability during a process that can promote neoplastic transformation and monoclonal gammopathies.
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Affiliation(s)
- Kevin M McBride
- Department of Epigenetics and Molecular Carcinogenesis, Science Park, The University of Texas MD Anderson Cancer Center, Smithville, TX, United States
| | - Hyunsuk Kil
- Department of Epigenetics and Molecular Carcinogenesis, Science Park, The University of Texas MD Anderson Cancer Center, Smithville, TX, United States
| | - Yunxiang Mu
- Department of Epigenetics and Molecular Carcinogenesis, Science Park, The University of Texas MD Anderson Cancer Center, Smithville, TX, United States
| | - Joshua B Plummer
- Department of Epigenetics and Molecular Carcinogenesis, Science Park, The University of Texas MD Anderson Cancer Center, Smithville, TX, United States
| | - Jaeho Lee
- Department of Epigenetics and Molecular Carcinogenesis, Science Park, The University of Texas MD Anderson Cancer Center, Smithville, TX, United States
| | - Maciej J Zelazowski
- Department of Epigenetics and Molecular Carcinogenesis, Science Park, The University of Texas MD Anderson Cancer Center, Smithville, TX, United States
| | - Manu Sebastian
- Department of Epigenetics and Molecular Carcinogenesis, Science Park, The University of Texas MD Anderson Cancer Center, Smithville, TX, United States
| | - Martin C Abba
- School of Medicine, Center for Immunological Basic and Applied Research (CINIBA), National University of La Plata (UNLP), La Plata, Argentina
| | - C Marcelo Aldaz
- Department of Epigenetics and Molecular Carcinogenesis, Science Park, The University of Texas MD Anderson Cancer Center, Smithville, TX, United States
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7
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Wiley SR, Raman VS. Molecular Methods and Bioinformatic Tools for Adjuvant Characterization by High-Throughput Sequencing. Methods Mol Biol 2018; 1494:353-368. [PMID: 27718207 DOI: 10.1007/978-1-4939-6445-1_26] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Adjuvants in vaccine formulations are designed to enhance immune responses against a target antigen or pathogen. The ability of these vaccines to induce activation and differentiation of mature naïve B cells to produce pathogen-specific antibodies (immunoglobulins; Ig) helps guarantee long-lived humoral immunity. This process involves clonal expansion of antigen-specific B cells, genomic rearrangement of Ig heavy (IgH) and light (IgL) loci, somatic hypermutation (SHM), and clonal selection for affinity-matured antibody, resulting in a vast but directed repertoire of B cells expressing highly specific antibody proteins. High-throughput sequencing of the IgH and IgL complementary determining regions (CDRs) derived from various B cell populations provides an unprecedented way to observe dynamic responses of the humoral immune repertoire in response to vaccination. However, applying high-throughput sequencing (HTS) methodologies to multi-armed in vivo experiments requires careful coordination of sample preparation with downstream bioinformatics, particularly with regard to issues of quantitation, sequence fidelity, bar-coding, and multiplexing strategies. Here, we overview strategies of high-throughput sequencing and analysis of the adaptive immune complex loci applied to multi-armed, multiplexed experiments.
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Affiliation(s)
- Steven R Wiley
- Imdaptive Inc., 3010 NW 56th Street, Seattle, WA, 98107, USA.
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8
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Lee DW, Khavrutskii IV, Wallqvist A, Bavari S, Cooper CL, Chaudhury S. BRILIA: Integrated Tool for High-Throughput Annotation and Lineage Tree Assembly of B-Cell Repertoires. Front Immunol 2017; 7:681. [PMID: 28144239 PMCID: PMC5239784 DOI: 10.3389/fimmu.2016.00681] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 12/21/2016] [Indexed: 11/13/2022] Open
Abstract
The somatic diversity of antigen-recognizing B-cell receptors (BCRs) arises from Variable (V), Diversity (D), and Joining (J) (VDJ) recombination and somatic hypermutation (SHM) during B-cell development and affinity maturation. The VDJ junction of the BCR heavy chain forms the highly variable complementarity determining region 3 (CDR3), which plays a critical role in antigen specificity and binding affinity. Tracking the selection and mutation of the CDR3 can be useful in characterizing humoral responses to infection and vaccination. Although tens to hundreds of thousands of unique BCR genes within an expressed B-cell repertoire can now be resolved with high-throughput sequencing, tracking SHMs is still challenging because existing annotation methods are often limited by poor annotation coverage, inconsistent SHM identification across the VDJ junction, or lack of B-cell lineage data. Here, we present B-cell repertoire inductive lineage and immunosequence annotator (BRILIA), an algorithm that leverages repertoire-wide sequencing data to globally improve the VDJ annotation coverage, lineage tree assembly, and SHM identification. On benchmark tests against simulated human and mouse BCR repertoires, BRILIA correctly annotated germline and clonally expanded sequences with 94 and 70% accuracy, respectively, and it has a 90% SHM-positive prediction rate in the CDR3 of heavily mutated sequences; these are substantial improvements over existing methods. We used BRILIA to process BCR sequences obtained from splenic germinal center B cells extracted from C57BL/6 mice. BRILIA returned robust B-cell lineage trees and yielded SHM patterns that are consistent across the VDJ junction and agree with known biological mechanisms of SHM. By contrast, existing BCR annotation tools, which do not account for repertoire-wide clonal relationships, systematically underestimated both the size of clonally related B-cell clusters and yielded inconsistent SHM frequencies. We demonstrate BRILIA’s utility in B-cell repertoire studies related to VDJ gene usage, mechanisms for adenosine mutations, and SHM hot spot motifs. Furthermore, we show that the complete gene usage annotation and SHM identification across the entire CDR3 are essential for studying the B-cell affinity maturation process through immunosequencing methods.
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Affiliation(s)
- Donald W Lee
- Biotechnology HPC Software Applications Institute (BHSAI), Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command , Fort Detrick, MD , USA
| | - Ilja V Khavrutskii
- Biotechnology HPC Software Applications Institute (BHSAI), Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command , Fort Detrick, MD , USA
| | - Anders Wallqvist
- Biotechnology HPC Software Applications Institute (BHSAI), Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command , Fort Detrick, MD , USA
| | - Sina Bavari
- Molecular and Translational Sciences, U.S. Army Medical Research Institute of Infectious Diseases , Frederick, MD , USA
| | - Christopher L Cooper
- Molecular and Translational Sciences, U.S. Army Medical Research Institute of Infectious Diseases , Frederick, MD , USA
| | - Sidhartha Chaudhury
- Biotechnology HPC Software Applications Institute (BHSAI), Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command , Fort Detrick, MD , USA
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9
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Kavakiotis I, Xochelli A, Agathangelidis A, Tsoumakas G, Maglaveras N, Stamatopoulos K, Hadzidimitriou A, Vlahavas I, Chouvarda I. Integrating multiple immunogenetic data sources for feature extraction and mining somatic hypermutation patterns: the case of "towards analysis" in chronic lymphocytic leukaemia. BMC Bioinformatics 2016; 17 Suppl 5:173. [PMID: 27295298 PMCID: PMC4905615 DOI: 10.1186/s12859-016-1044-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023] Open
Abstract
BACKGROUND Somatic Hypermutation (SHM) refers to the introduction of mutations within rearranged V(D)J genes, a process that increases the diversity of Immunoglobulins (IGs). The analysis of SHM has offered critical insight into the physiology and pathology of B cells, leading to strong prognostication markers for clinical outcome in chronic lymphocytic leukaemia (CLL), the most frequent adult B-cell malignancy. In this paper we present a methodology for integrating multiple immunogenetic and clinocobiological data sources in order to extract features and create high quality datasets for SHM analysis in IG receptors of CLL patients. This dataset is used as the basis for a higher level integration procedure, inspired form social choice theory. This is applied in the Towards Analysis, our attempt to investigate the potential ontogenetic transformation of genes belonging to specific stereotyped CLL subsets towards other genes or gene families, through SHM. RESULTS The data integration process, followed by feature extraction, resulted in the generation of a dataset containing information about mutations occurring through SHM. The Towards analysis performed on the integrated dataset applying voting techniques, revealed the distinct behaviour of subset #201 compared to other subsets, as regards SHM related movements among gene clans, both in allele-conserved and non-conserved gene areas. With respect to movement between genes, a high percentage movement towards pseudo genes was found in all CLL subsets. CONCLUSIONS This data integration and feature extraction process can set the basis for exploratory analysis or a fully automated computational data mining approach on many as yet unanswered, clinically relevant biological questions.
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Affiliation(s)
- Ioannis Kavakiotis
- Department of Informatics, Aristotle University of Thessaloniki, Thessaloniki, Greece.
| | - Aliki Xochelli
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece.,Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Andreas Agathangelidis
- Division of Molecular Oncology and Department of Onco-Hematology, San Raffaele Scientific Institute, Milan, Italy
| | - Grigorios Tsoumakas
- Department of Informatics, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Nicos Maglaveras
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece.,Lab of Computing and Medical Informatics, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece.,Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anastasia Hadzidimitriou
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece.,Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ioannis Vlahavas
- Department of Informatics, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Ioanna Chouvarda
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece.,Lab of Computing and Medical Informatics, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
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10
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Godoy-Lozano EE, Téllez-Sosa J, Sánchez-González G, Sámano-Sánchez H, Aguilar-Salgado A, Salinas-Rodríguez A, Cortina-Ceballos B, Vivanco-Cid H, Hernández-Flores K, Pfaff JM, Kahle KM, Doranz BJ, Gómez-Barreto RE, Valdovinos-Torres H, López-Martínez I, Rodriguez MH, Martínez-Barnetche J. Lower IgG somatic hypermutation rates during acute dengue virus infection is compatible with a germinal center-independent B cell response. Genome Med 2016; 8:23. [PMID: 26917418 PMCID: PMC4766701 DOI: 10.1186/s13073-016-0276-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Accepted: 02/03/2016] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The study of human B cell response to dengue virus (DENV) infection is critical to understand serotype-specific protection and the cross-reactive sub-neutralizing response. Whereas the first is beneficial and thus represents the ultimate goal of vaccination, the latter has been implicated in the development of severe disease, which occurs in a small, albeit significant, fraction of secondary DENV infections. Both primary and secondary infections are associated with the production of poly-reactive and cross-reactive IgG antibodies. METHODS To gain insight into the effect of DENV infection on the B cell repertoire, we used VH region high-throughput cDNA sequencing of the peripheral blood IgG B cell compartment of 19 individuals during the acute phase of infection. For 11 individuals, a second sample obtained 6 months later was analyzed for comparison. Probabilities of sequencing antibody secreting cells or memory B cells were estimated using second-order Monte Carlo simulation. RESULTS We found that in acute disease there is an increase in IgG B cell diversity and changes in the relative use of segments IGHV1-2, IGHV1-18, and IGHV1-69. Somewhat unexpectedly, an overall low proportion of somatic hypermutated antibody genes was observed during the acute phase plasmablasts, particularly in secondary infections and those cases with more severe disease. CONCLUSIONS Our data are consistent with an innate-like antiviral recognition system mediated by B cells using defined germ-line coded B cell receptors, which could provide a rapid germinal center-independent antibody response during the early phase of infection. A model describing concurrent T-dependent and T-independent B cell responses in the context of DENV infection is proposed, which incorporates the selection of B cells using hypomutated IGHV segments and their potential role in poly/cross-reactivity. Its formal demonstration could lead to a definition of its potential implication in antibody-dependent enhancement, and may contribute to rational vaccine development efforts.
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Affiliation(s)
| | - Juan Téllez-Sosa
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | - Gilberto Sánchez-González
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | - Hugo Sámano-Sánchez
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | - Andrés Aguilar-Salgado
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | - Aarón Salinas-Rodríguez
- Centro de Investigación en Evaluación y Encuestas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | - Bernardo Cortina-Ceballos
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | - Héctor Vivanco-Cid
- Instituto de Investigaciones Médico-Biológicas, Universidad Veracruzana, Veracruz, Veracruz, México
| | - Karina Hernández-Flores
- Instituto de Investigaciones Médico-Biológicas, Universidad Veracruzana, Veracruz, Veracruz, México
| | | | | | | | - Rosa Elena Gómez-Barreto
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | - Humberto Valdovinos-Torres
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | | | - Mario H Rodriguez
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | - Jesús Martínez-Barnetche
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México.
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11
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Zanotti KJ, Gearhart PJ. Antibody diversification caused by disrupted mismatch repair and promiscuous DNA polymerases. DNA Repair (Amst) 2016; 38:110-116. [PMID: 26719140 PMCID: PMC4740194 DOI: 10.1016/j.dnarep.2015.11.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 11/30/2015] [Indexed: 10/25/2022]
Abstract
The enzyme activation-induced deaminase (AID) targets the immunoglobulin loci in activated B cells and creates DNA mutations in the antigen-binding variable region and DNA breaks in the switch region through processes known, respectively, as somatic hypermutation and class switch recombination. AID deaminates cytosine to uracil in DNA to create a U:G mismatch. During somatic hypermutation, the MutSα complex binds to the mismatch, and the error-prone DNA polymerase η generates mutations at A and T bases. During class switch recombination, both MutSα and MutLα complexes bind to the mismatch, resulting in double-strand break formation and end-joining. This review is centered on the mechanisms of how the MMR pathway is commandeered by B cells to generate antibody diversity.
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Affiliation(s)
- Kimberly J Zanotti
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Patricia J Gearhart
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA.
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12
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Yeap LS, Hwang JK, Du Z, Meyers RM, Meng FL, Jakubauskaitė A, Liu M, Mani V, Neuberg D, Kepler TB, Wang JH, Alt FW. Sequence-Intrinsic Mechanisms that Target AID Mutational Outcomes on Antibody Genes. Cell 2015; 163:1124-1137. [PMID: 26582132 DOI: 10.1016/j.cell.2015.10.042] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 09/01/2015] [Accepted: 10/13/2015] [Indexed: 12/27/2022]
Abstract
In activated B lymphocytes, AID initiates antibody variable (V) exon somatic hypermutation (SHM) for affinity maturation in germinal centers (GCs) and IgH switch (S) region DNA breaks (DSBs) for class-switch recombination (CSR). To resolve long-standing questions, we have developed an in vivo assay to study AID targeting of passenger sequences replacing a V exon. First, we find AID targets SHM hotspots within V exon and S region passengers at similar frequencies and that the normal SHM process frequently generates deletions, indicating that SHM and CSR employ the same mechanism. Second, AID mutates targets in diverse non-Ig passengers in GC B cells at levels similar to those of V exons, definitively establishing the V exon location as "privileged" for SHM. Finally, Peyer's patch GC B cells generate a reservoir of V exons that are highly mutated before selection for affinity maturation. We discuss the implications of these findings for harnessing antibody diversification mechanisms.
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Affiliation(s)
- Leng-Siew Yeap
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine at Boston Children's Hospital, and Department of Genetics, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Joyce K Hwang
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine at Boston Children's Hospital, and Department of Genetics, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Zhou Du
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine at Boston Children's Hospital, and Department of Genetics, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Robin M Meyers
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine at Boston Children's Hospital, and Department of Genetics, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Fei-Long Meng
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine at Boston Children's Hospital, and Department of Genetics, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Agnė Jakubauskaitė
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine at Boston Children's Hospital, and Department of Genetics, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Mengyuan Liu
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine at Boston Children's Hospital, and Department of Genetics, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Vinidhra Mani
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine at Boston Children's Hospital, and Department of Genetics, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Donna Neuberg
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Thomas B Kepler
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02215, USA
| | - Jing H Wang
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine at Boston Children's Hospital, and Department of Genetics, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Frederick W Alt
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine at Boston Children's Hospital, and Department of Genetics, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA.
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13
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Iglesia MD, Vincent BG, Parker JS, Hoadley KA, Carey LA, Perou CM, Serody JS. Prognostic B-cell signatures using mRNA-seq in patients with subtype-specific breast and ovarian cancer. Clin Cancer Res 2014; 20:3818-29. [PMID: 24916698 DOI: 10.1158/1078-0432.ccr-13-3368] [Citation(s) in RCA: 193] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
PURPOSE Lymphocytic infiltration of tumors predicts improved survival in patients with breast cancer. Previous studies have suggested that this survival benefit is confined predominantly to the basal-like subtype. Immune infiltration in ovarian tumors is also associated with improved prognosis. Currently, it is unclear what aspects of the immune response mediate this improved outcome. EXPERIMENTAL DESIGN Using The Cancer Genome Atlas mRNA-seq data and a large microarray dataset, we evaluated adaptive immune gene expression by genomic subtype in breast and ovarian cancer. To investigate B-cells observed to be prognostic within specific subtypes, we developed methods to analyze B-cell population diversity and degree of somatic hypermutation (SHM) from B-cell receptor (BCR) sequences in mRNA-seq data. RESULTS Improved metastasis-free/progression-free survival was correlated with B-cell gene expression signatures, which were restricted mainly to the basal-like and HER2-enriched breast cancer subtypes and the immunoreactive ovarian cancer subtype. Consistent with a restricted epitope-driven response, a subset of basal-like and HER2-enriched breast tumors and immunoreactive ovarian tumors showed high expression of a low-diversity population of BCR gene segments. More BCR segments showed improved prognosis with increased expression in basal-like breast tumors and immunoreactive ovarian tumors compared with other subtypes. Basal-like and HER2-enriched tumors exhibited more BCR sequence variants in regions consistent with SHM. CONCLUSION Taken together, these data suggest the presence of a productive and potentially restricted antitumor B-cell response in basal-like breast and immunoreactive ovarian cancers. Immunomodulatory therapies that support B-cell responses may be a promising therapeutic approach to targeting these B-cell infiltrated tumors.
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MESH Headings
- B-Lymphocytes/metabolism
- Breast Neoplasms/genetics
- Breast Neoplasms/immunology
- Breast Neoplasms/metabolism
- Breast Neoplasms/mortality
- Disease-Free Survival
- Female
- Humans
- Mutation
- Neoplasms, Basal Cell/genetics
- Neoplasms, Basal Cell/immunology
- Neoplasms, Basal Cell/metabolism
- Neoplasms, Basal Cell/secondary
- Ovarian Neoplasms/genetics
- Ovarian Neoplasms/immunology
- Ovarian Neoplasms/metabolism
- Ovarian Neoplasms/mortality
- Prognosis
- Proportional Hazards Models
- RNA, Messenger/genetics
- Receptors, Antigen, B-Cell/genetics
- Receptors, Antigen, B-Cell/metabolism
- Sequence Analysis, RNA
- Transcriptome
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Affiliation(s)
- Michael D Iglesia
- Authors' Affiliations: Lineberger Comprehensive Cancer Center; Curriculum in Genetics and Molecular Biology; Departments of
| | | | - Joel S Parker
- Authors' Affiliations: Lineberger Comprehensive Cancer Center; Genetics
| | | | - Lisa A Carey
- Authors' Affiliations: Lineberger Comprehensive Cancer Center; Medicine
| | - Charles M Perou
- Authors' Affiliations: Lineberger Comprehensive Cancer Center; Genetics; Pathology and Laboratory Medicine; and
| | - Jonathan S Serody
- Authors' Affiliations: Lineberger Comprehensive Cancer Center; Medicine; Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina
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14
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Müller-Sienerth N, Crosnier C, Wright GJ, Staudt N. Cloning of recombinant monoclonal antibodies from hybridomas in a single mammalian expression plasmid. Methods Mol Biol 2014; 1131:229-240. [PMID: 24515469 DOI: 10.1007/978-1-62703-992-5_14] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Antibodies are an integral part of biological and medical research. In addition, immunoglobulins are used in many diagnostic tests and are becoming increasingly important in the therapy of diseases. To express antibodies recombinantly, the immunoglobulin heavy and light chains are usually cloned into two different expression plasmids. Here, we describe a method for recombinant antibody expression from a single plasmid.
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Affiliation(s)
- Nicole Müller-Sienerth
- Cell Surface Signalling Laboratory, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
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15
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Antigen selection in B-cell lymphomas—Tracing the evidence. Semin Cancer Biol 2013; 23:399-409. [DOI: 10.1016/j.semcancer.2013.07.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 07/26/2013] [Indexed: 12/22/2022]
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16
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Erratum to: The role of activation-induced deaminase in antibody diversification and genomic instability. Immunol Res 2013. [DOI: 10.1007/s12026-013-8432-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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17
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Rouaud P, Vincent-Fabert C, Saintamand A, Fiancette R, Marquet M, Robert I, Reina-San-Martin B, Pinaud E, Cogné M, Denizot Y. The IgH 3' regulatory region controls somatic hypermutation in germinal center B cells. ACTA ACUST UNITED AC 2013; 210:1501-7. [PMID: 23825188 PMCID: PMC3727322 DOI: 10.1084/jem.20130072] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Somatic hypermutation in variable heavy chain rearranged regions is abrogated in the absence of the 3′ regulatory region enhancer, whereas transcription rate in the Ig heavy chain is only partially reduced. Interactions with cognate antigens recruit activated B cells into germinal centers where they undergo somatic hypermutation (SHM) in V(D)J exons for the generation of high-affinity antibodies. The contribution of IgH transcriptional enhancers in SHM is unclear. The Eμ enhancer upstream of Cμ has a marginal role, whereas the influence of the IgH 3′ regulatory region (3′RR) enhancers (hs3a, hs1,2, hs3b, and hs4) is controversial. To clarify the latter issue, we analyzed mice lacking the whole 30-kb extent of the IgH 3′RR. We show that SHM in VH rearranged regions is almost totally abrogated in 3′RR-deficient mice, whereas the simultaneous Ig heavy chain transcription rate is only partially reduced. In contrast, SHM in κ light chain genes remains unaltered, acquitting for any global SHM defect in our model. Beyond class switch recombination, the IgH 3′RR is a central element that controls heavy chain accessibility to activation-induced deaminase modifications including SHM.
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Affiliation(s)
- Pauline Rouaud
- Centre National de la Recherche Scientifique (CNRS) UMR 7276, Université de Limoges, 87025 Limoges, France
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18
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Wang JH. The role of activation-induced deaminase in antibody diversification and genomic instability. Immunol Res 2013; 55:287-97. [PMID: 22956489 DOI: 10.1007/s12026-012-8369-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
More than a decade ago, activation-induced deaminase (AID) was identified as the initiator for somatic hypermutation (SHM) and class switch recombination (CSR). Since then, tremendous progress has been achieved toward elucidating how AID functions. AID targets the highly repetitive switch regions of the immunoglobulin heavy chain (IgH) locus to induce DNA double-strand breaks (DSBs), which can be rejoined, leading to switch of constant regions of antibody. When targeting to variable region exons of IgH and IgL loci, AID predominantly induces point mutations, termed SHM, resulting in increased affinity of antibody for antigen. While SHM and CSR enhance antibody diversity, AID-initiated DSBs and mutations may predispose B cells to carcinogenesis. This review focuses on the mechanisms that provide the specificity of AID targeting to Ig loci and the role of AID in genomic instability.
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Affiliation(s)
- Jing H Wang
- Integrated Department of Immunology, University of Colorado School of Medicine and National Jewish Health, Denver, CO 80206, USA.
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19
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Abstract
Base excision repair (BER) corrects DNA damage from oxidation, deamination and alkylation. Such base lesions cause little distortion to the DNA helix structure. BER is initiated by a DNA glycosylase that recognizes and removes the damaged base, leaving an abasic site that is further processed by short-patch repair or long-patch repair that largely uses different proteins to complete BER. At least 11 distinct mammalian DNA glycosylases are known, each recognizing a few related lesions, frequently with some overlap in specificities. Impressively, the damaged bases are rapidly identified in a vast excess of normal bases, without a supply of energy. BER protects against cancer, aging, and neurodegeneration and takes place both in nuclei and mitochondria. More recently, an important role of uracil-DNA glycosylase UNG2 in adaptive immunity was revealed. Furthermore, other DNA glycosylases may have important roles in epigenetics, thus expanding the repertoire of BER proteins.
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Affiliation(s)
- Hans E Krokan
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, N-7489 Trondheim, Norway.
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20
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Zan H, White CA, Thomas LM, Mai T, Li G, Xu Z, Zhang J, Casali P. Rev1 recruits ung to switch regions and enhances du glycosylation for immunoglobulin class switch DNA recombination. Cell Rep 2012; 2:1220-32. [PMID: 23140944 DOI: 10.1016/j.celrep.2012.09.029] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Revised: 06/29/2012] [Accepted: 09/24/2012] [Indexed: 02/03/2023] Open
Abstract
By diversifying the biological effector functions of antibodies, class switch DNA recombination (CSR) plays a critical role in the maturation of the immune response. It is initiated by activation-induced cytidine deaminase (AID)-mediated deoxycytosine deamination, yielding deoxyuridine (dU), and dU glycosylation by uracil DNA glycosylase (Ung) in antibody switch (S) region DNA. Here we showed that the translesion DNA synthesis polymerase Rev1 directly interacted with Ung and targeted in an AID-dependent and Ung-independent fashion the S regions undergoing CSR. Rev1(-/-)Ung(+/+) B cells reduced Ung recruitment to S regions, DNA-dU glycosylation, and CSR. Together with an S region spectrum of mutations similar to that of Rev1(+/+)Ung(-/-) B cells, this suggests that Rev1 operates in the same pathway as Ung, as emphasized by further decreased CSR in Rev1(-/-)Msh2(-/-) B cells. Rescue of CSR in Rev1(-/-) B cells by a catalytically inactive Rev1 mutant shows that the important role of Rev1 in CSR is mediated by Rev1's scaffolding function, not its enzymatic function.
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Affiliation(s)
- Hong Zan
- Institute for Immunology and School of Medicine, University of California, 3028 Hewitt Hall, Irvine, CA 92697-4120, USA
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21
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Xiong H, Dolpady J, Wabl M, Curotto de Lafaille MA, Lafaille JJ. Sequential class switching is required for the generation of high affinity IgE antibodies. ACTA ACUST UNITED AC 2012; 209:353-64. [PMID: 22249450 PMCID: PMC3280879 DOI: 10.1084/jem.20111941] [Citation(s) in RCA: 188] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Generation of anaphylaxis-inducing high affinity IgE requires sequential class switching. IgE antibodies with high affinity for their antigens can be stably cross-linked at low concentrations by trace amounts of antigen, whereas IgE antibodies with low affinity bind their antigens weakly. In this study, we find that there are two distinct pathways to generate high and low affinity IgE. High affinity IgE is generated through sequential class switching (μ→γ→ε) in which an intermediary IgG phase is necessary for the affinity maturation of the IgE response, where the IgE inherits somatic hypermutations and high affinity from the IgG1 phase. In contrast, low affinity IgE is generated through direct class switching (μ→ε) and is much less mutated. Mice deficient in IgG1 production cannot produce high affinity IgE, even after repeated immunizations. We demonstrate that a small amount of high affinity IgE can cause anaphylaxis and is pathogenic. Low affinity IgE competes with high affinity IgE for binding to Fcε receptors and prevents anaphylaxis and is thus beneficial.
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Affiliation(s)
- Huizhong Xiong
- Skirball Institute of Biomolecular Medicine, The Sackler Institute of Graduate Biomedical Sciences, New York University School of Medicine, New York, NY 10016, USA
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22
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da Silva TA, Fontes FL, Coutinho LG, de Souza FRS, de Melo JTA, de Souto JT, Leib SL, Agnez-Lima LF. SNPs in DNA repair genes associated to meningitis and host immune response. Mutat Res 2011; 713:39-47. [PMID: 21651918 DOI: 10.1016/j.mrfmmm.2011.05.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2011] [Revised: 05/11/2011] [Accepted: 05/20/2011] [Indexed: 05/30/2023]
Abstract
In vitro and in animal models, APE1, OGG1, and PARP-1 have been proposed as being involved with inflammatory response. In this work, we have investigated if the SNPs APE1 Asn148Glu, OGG1 Ser326Cys, and PARP-1 Val762Ala are associated to meningitis. The patient genotypes were investigated by PIRA-PCR or PCR-RFLP. DNA damages were detected in genomic DNA by Fpg treatment. IgG and IgA were measured from plasma and the cytokines and chemokines were measured from cerebrospinal fluid samples using Bio-Plex assays. A higher frequency (P<0.05) of APE1 Glu allele in bacterial meningitis (BM) and aseptic meningitis (AM) patients was observed. The genotypes Asn/Asn in control group and Asn/Glu in BM group was also higher. For the SNP OGG1 Ser326Cys, the genotype Cys/Cys was more frequent (P<0.05) in BM group. The frequency of PARP-1 Val/Val genotype was higher in control group (P<0.05). The occurrence of combined SNPs is significantly higher in BM patients, indicating that these SNPs may be associated to the disease. Increasing in sensitive sites to Fpg was observed in carriers of APE1 Glu allele or OGG1 Cys allele, suggesting that SNPs affect DNA repair activity. Alterations in IgG production were observed in the presence of SNPs APE1 Asn148Glu, OGG1 Ser326Cys or PARP-1 Val762Ala. Moreover, reduction in the levels of IL-6, IL-1Ra, MCP-1/CCL2 and IL-8/CXCL8 was observed in the presence of APE1 Glu allele in BM patients. In conclusion, we obtained indications of an effect of SNPs in DNA repair genes on the regulation of immune response in meningitis.
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Affiliation(s)
- Thayse Azevedo da Silva
- Departamento de Biologia Celular e Genética, Universidade Federal do Rio Grande do Norte (UFRN), Av. Salgado Filho s/n, 59072-970 Natal, RN, Brazil
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23
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Braoudaki M, Katsibardi K, Giudicelli V, Karamolegou K, Papathanassiou C, Lefranc MP, Tzortzatou-Stathopoulou F. Analysis of somatic hypermutations of immunoglobulin gene rearrangements in childhood acute lymphoblastic leukemia. Cancer Invest 2011; 29:360-4. [PMID: 21599512 DOI: 10.3109/07357907.2011.584587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The current study investigated the presence, frequency, and status of somatic hypermutations as well as their role in children with B lineage ALL. The obtained sequences were analyzed using IMGT/V-QUEST. Totally, 150 IGH sequences were evaluated; 139 from the 111 patients at the time of diagnosis and 11 from 8/111 patients at the time of relapse. The findings of the current report revealed the presence of somatically mutated V genes in childhood B lineage ALL. A higher frequency of somatic hypermutations was noted in unproductive rearrangements and was generally attributed to nucleotide mutation type, region, and IGHV gene subgroup biases.
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Affiliation(s)
- M Braoudaki
- University Research Institute for the Study and Treatment of Childhood Genetic and Malignant Diseases, Hematology/Oncology Unit, First Department of Pediatrics, Aghia Sophia Children's Hospital, University of Athens, Athens, Greece.
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24
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Li F, Yan Y, Pieretti J, Feldman DA, Eckhardt LA. Comparison of identical and functional Igh alleles reveals a nonessential role for Eμ in somatic hypermutation and class-switch recombination. THE JOURNAL OF IMMUNOLOGY 2010; 185:6049-57. [PMID: 20937850 DOI: 10.4049/jimmunol.0902992] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Somatic hypermutation (SHM), coupled with Ag selection, provides a mechanism for generating Abs with high affinity for invading pathogens. Class-switch recombination (CSR) ensures that these Abs attain pathogen-appropriate effector functions. Although the enzyme critical to both processes, activation-induced cytidine deaminase, has been identified, it remains unclear which cis-elements within the Ig loci are responsible for recruiting activation-induced cytidine deaminase and promoting its activity. Studies showed that Ig gene-transcription levels are positively correlated with the frequency of SHM and CSR, making the intronic, transcriptional enhancer Eμ a likely contributor to both processes. Tests of this hypothesis yielded mixed results arising, in part, from the difficulty in studying B cell function in mice devoid of Eμ. In Eμ's absence, V(H) gene assembly is dramatically impaired, arresting B cell development. The current study circumvented this problem by modifying the murine Igh locus through simultaneous insertion of a fully assembled V(H) gene and deletion of Eμ. The behavior of this allele was compared with that of a matched allele carrying the same V(H) gene but with Eμ intact. Although IgH transcription was as great or greater on the Eμ-deficient allele, CSR and SHM were consistently, but modestly, reduced relative to the allele in which Eμ remained intact. We conclude that Eμ contributes to, but is not essential for, these complex processes and that its contribution is not as a transcriptional enhancer but, rather, is at the level of recruitment and/or activation of the SHM/CSR machinery.
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Affiliation(s)
- Fubin Li
- Department of Biological Sciences, Hunter College and Graduate Center, City University of New York, New York, NY 10065, USA
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