1
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Bello A, Hirth G, Voigt S, Tepper S, Jungnickel B. Mechanism and regulation of secondary immunoglobulin diversification. Cell Cycle 2023; 22:2070-2087. [PMID: 37909747 PMCID: PMC10761156 DOI: 10.1080/15384101.2023.2275397] [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] [Received: 05/04/2023] [Accepted: 10/20/2023] [Indexed: 11/03/2023] Open
Abstract
Secondary immunoglobulin diversification by somatic hypermutation and class switch recombination in B cells is instrumental for an adequate adaptive humoral immune response. These genetic events may, however, also introduce aberrations into other cellular genes and thereby cause B cell malignancies. While the basic mechanism of somatic hypermutation and class switch recombination is now well understood, their regulation and in particular the mechanism of their specific targeting to immunoglobulin genes is still rather mysterious. In this review, we summarize the current knowledge on the mechanism and regulation of secondary immunoglobulin diversification and discuss known mechanisms of physiological targeting to immunoglobulin genes and mistargeting to other cellular genes. We summarize open questions in the field and provide an outlook on future research.
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Affiliation(s)
- Amanda Bello
- Institute of Biochemistry and Biophysics, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
| | - Gianna Hirth
- Institute of Biochemistry and Biophysics, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
| | - Stefanie Voigt
- Institute of Biochemistry and Biophysics, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
| | - Sandra Tepper
- Institute of Biochemistry and Biophysics, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
| | - Berit Jungnickel
- Institute of Biochemistry and Biophysics, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
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2
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Ghorbani A, Khataeipour SJ, Solbakken MH, Huebert DNG, Khoddami M, Eslamloo K, Collins C, Hori T, Jentoft S, Rise ML, Larijani M. Ancestral reconstruction reveals catalytic inactivation of activation-induced cytidine deaminase concomitant with cold water adaption in the Gadiformes bony fish. BMC Biol 2022; 20:293. [PMID: 36575514 PMCID: PMC9795746 DOI: 10.1186/s12915-022-01489-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 11/30/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Antibody affinity maturation in vertebrates requires the enzyme activation-induced cytidine deaminase (AID) which initiates secondary antibody diversification by mutating the immunoglobulin loci. AID-driven antibody diversification is conserved across jawed vertebrates since bony and cartilaginous fish. Two exceptions have recently been reported, the Pipefish and Anglerfish, in which the AID-encoding aicda gene has been lost. Both cases are associated with unusual reproductive behavior, including male pregnancy and sexual parasitism. Several cold water fish in the Atlantic cod (Gadinae) family carry an aicda gene that encodes for a full-length enzyme but lack affinity-matured antibodies and rely on antibodies of broad antigenic specificity. Hence, we examined the functionality of their AID. RESULTS By combining genomics, transcriptomics, immune responsiveness, and functional enzymology of AID from 36 extant species, we demonstrate that AID of that Atlantic cod and related fish have extremely lethargic or no catalytic activity. Through ancestral reconstruction and functional enzymology of 71 AID enzymes, we show that this enzymatic inactivation likely took place relatively recently at the emergence of the true cod family (Gadidae) from their ancestral Gadiformes order. We show that this AID inactivation is not only concordant with the previously shown loss of key adaptive immune genes and expansion of innate and cell-based immune genes in the Gadiformes but is further reflected in the genomes of these fish in the form of loss of AID-favored sequence motifs in their immunoglobulin variable region genes. CONCLUSIONS Recent demonstrations of the loss of the aicda gene in two fish species challenge the paradigm that AID-driven secondary antibody diversification is absolutely conserved in jawed vertebrates. These species have unusual reproductive behaviors forming an evolutionary pressure for a certain loss of immunity to avoid tissue rejection. We report here an instance of catalytic inactivation and functional loss of AID rather than gene loss in a conventionally reproducing vertebrate. Our data suggest that an expanded innate immunity, in addition to lower pathogenic pressures in a cold environment relieved the pressure to maintain robust secondary antibody diversification. We suggest that in this unique scenario, the AID-mediated collateral genome-wide damage would form an evolutionary pressure to lose AID function.
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Affiliation(s)
- Atefeh Ghorbani
- grid.61971.380000 0004 1936 7494Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada ,grid.25055.370000 0000 9130 6822Program in Immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Canada
| | - S. Javad Khataeipour
- grid.25055.370000 0000 9130 6822Department of Computer Science, Faculty of Science, Memorial University of Newfoundland, St. John’s, Canada
| | - Monica H. Solbakken
- grid.5510.10000 0004 1936 8921Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - David N. G. Huebert
- grid.61971.380000 0004 1936 7494Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada ,grid.25055.370000 0000 9130 6822Program in Immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Canada
| | - Minasadat Khoddami
- grid.61971.380000 0004 1936 7494Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Khalil Eslamloo
- grid.25055.370000 0000 9130 6822Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, Canada
| | - Cassandra Collins
- grid.61971.380000 0004 1936 7494Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Tiago Hori
- grid.25055.370000 0000 9130 6822Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, Canada
| | - Sissel Jentoft
- grid.5510.10000 0004 1936 8921Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Matthew L. Rise
- grid.25055.370000 0000 9130 6822Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, Canada
| | - Mani Larijani
- grid.61971.380000 0004 1936 7494Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada ,grid.25055.370000 0000 9130 6822Program in Immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Canada
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3
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Xie X, Gan T, Rao B, Zhang W, Panchakshari RA, Yang D, Ji X, Cao Y, Alt FW, Meng FL, Hu J. C-terminal deletion-induced condensation sequesters AID from IgH targets in immunodeficiency. EMBO J 2022; 41:e109324. [PMID: 35471583 PMCID: PMC9156971 DOI: 10.15252/embj.2021109324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 04/07/2022] [Accepted: 04/08/2022] [Indexed: 11/09/2022] Open
Abstract
In activated B cells, activation-induced cytidine deaminase (AID) generates programmed DNA lesions required for antibody class switch recombination (CSR), which may also threaten genome integrity. AID dynamically shuttles between cytoplasm and nucleus, and the majority stays in the cytoplasm due to active nuclear export mediated by its C-terminal peptide. In immunodeficient-patient cells expressing mutant AID lacking its C-terminus, a catalytically active AID-delC protein accumulates in the nucleus but nevertheless fails to support CSR. To resolve this apparent paradox, we dissected the function of AID-delC proteins in the CSR process and found that they cannot efficiently target antibody genes. We demonstrate that AID-delC proteins form condensates both in vivo and in vitro, dependent on its N-terminus and on a surface arginine-rich patch. Co-expression of AID-delC and wild-type AID leads to an unbalanced nuclear AID-delC/AID ratio, with AID-delC proteins able to trap wild-type AID in condensates, resulting in a dominant-negative phenotype that could contribute to immunodeficiency. The co-condensation model of mutant and wild-type proteins could be an alternative explanation for the dominant-negative effect in genetic disorders.
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Affiliation(s)
- Xia Xie
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Tingting Gan
- The MOE Key Laboratory of Cell Proliferation and Differentiation, Genome Editing Research Center, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Bing Rao
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Weiwei Zhang
- The MOE Key Laboratory of Cell Proliferation and Differentiation, Genome Editing Research Center, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Rohit A Panchakshari
- Program in Cellular and Molecular Medicine, Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Dingpeng Yang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Xiong Ji
- The MOE Key Laboratory of Cell Proliferation and Differentiation, Genome Editing Research Center, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Yu Cao
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Frederick W Alt
- Program in Cellular and Molecular Medicine, Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Fei-Long Meng
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Jiazhi Hu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, Genome Editing Research Center, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
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4
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Ramirez NJ, Posadas-Cantera S, Caballero-Oteyza A, Camacho-Ordonez N, Grimbacher B. There is no gene for CVID - novel monogenetic causes for primary antibody deficiency. Curr Opin Immunol 2021; 72:176-185. [PMID: 34153571 DOI: 10.1016/j.coi.2021.05.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 12/25/2022]
Abstract
'There is no gene for fate' (citation from the movie 'GATTACA') - and there is no gene for CVID. Common Variable ImmunoDeficiency (CVID) is the most prevalent primary immunodeficiency in humans. CVID is characterized by an increased susceptibility to infections, hypogammaglobulinemia, reduced switched memory B cell numbers in peripheral blood and a defective response to vaccination, often complicated by autoimmune and autoinflammatory conditions. However, as soon as a genetic diagnosis has been made in a patient with CVID, the diagnosis must be changed to the respective genetic cause (www.esid.org). Therefore, there are genetic causes for primary antibody deficiencies, but not for CVID. Primary antibody deficiencies (PADs) are a heterogeneous group of disorders. Several attempts have been made to gain further insights into the pathogenesis of PAD, using unbiased approaches such as whole exome or genome sequencing. Today, in just about 35% of cases with PAD, monogenic mutations (including those in the gene TNFRSF13B) can be identified in a set of 68 genes [1•]. These mutations occur either sporadically or are inherited and do explain an often complex phenotype. In our review, we not only discuss gene defects identified in PAD patients previously diagnosed with CVID and/or CVID-like disorders such as IKZF1, CTNNBL1, TNFSF13 and BACH2, but also genetic defects which were initially described in non-CVID patients but have later also been observed in patients with PAD such as PLCG2, PIK3CG, PMS2, RNF31, KMT2D, STAT3. We also included interesting genetic defects in which the pathophysiology suggests a close relation to other known defects of the adaptive immune response, such as DEF6, SAMD9 and SAMD9L, and hence a CVID-like phenotype may be observed in the future. However, alternative mechanisms most likely add to the development of an antibody-deficient phenotype, such as polygenic origins, epigenetic changes, and/or environmental factors.
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Affiliation(s)
- Neftali J Ramirez
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Freiburg, Germany; Integrated Research Training Group (IRTG) Medical Epigenetics, Collaborative Research Centre 992, Freiburg, Germany; Faculty of Biology, Albert-Ludwigs-University of Freiburg, Germany
| | - Sara Posadas-Cantera
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Andrés Caballero-Oteyza
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Freiburg, Germany; RESIST - Cluster of Excellence 2155 to Hanover Medical School, Satellite Center Freiburg, Freiburg, Germany
| | - Nadezhda Camacho-Ordonez
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Freiburg, Germany; Faculty of Biology, Albert-Ludwigs-University of Freiburg, Germany
| | - Bodo Grimbacher
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Freiburg, Germany; DZIF - German Center for Infection Research, Satellite Center Freiburg, Freiburg, Germany; CIBSS - Centre for Integrative Biological Signalling Studies, Albert-Ludwigs University, Freiburg, Germany; RESIST - Cluster of Excellence 2155 to Hanover Medical School, Satellite Center Freiburg, Freiburg, Germany.
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5
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Oppezzo P, Navarrete M, Chiorazzi N. AID in Chronic Lymphocytic Leukemia: Induction and Action During Disease Progression. Front Oncol 2021; 11:634383. [PMID: 34041018 PMCID: PMC8141630 DOI: 10.3389/fonc.2021.634383] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 02/23/2021] [Indexed: 12/12/2022] Open
Abstract
The enzyme activation-induced cytidine deaminase (AID) initiates somatic hypermutation (SHM) and class switch recombination (CSR) of immunoglobulin (Ig) genes, critical actions for an effective adaptive immune response. However, in addition to the benefits generated by its physiological roles, AID is an etiological factor for the development of human and murine leukemias and lymphomas. This review highlights the pathological role of AID and the consequences of its actions on the development, progression, and therapeutic refractoriness of chronic lymphocytic leukemia (CLL) as a model disease for mature lymphoid malignancies. First, we summarize pertinent aspects of the expression and function of AID in normal B lymphocytes. Then, we assess putative causes for AID expression in leukemic cells emphasizing the role of an activated microenvironment. Thirdly, we discuss the role of AID in lymphomagenesis, in light of recent data obtained by NGS analyses on the genomic landscape of leukemia and lymphomas, concentrating on the frequency of AID signatures in these cancers and correlating previously described tumor-gene drivers with the presence of AID off-target mutations. Finally, we discuss how these changes could affect tumor suppressor and proto-oncogene targets and how they could be associated with disease progression. Collectively, we hope that these sections will help to better understand the complex paradox between the physiological role of AID in adaptive immunity and its potential causative activity in B-cell malignancies.
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Affiliation(s)
- Pablo Oppezzo
- Research Laboratory on Chronic Lymphocytic Leukemia, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | | | - Nicholas Chiorazzi
- The Karches Center for Oncology Research, The Feinstein Institutes for Medical Research, New York, NY, United States
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6
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Kuhny M, Forbes LR, Çakan E, Vega-Loza A, Kostiuk V, Dinesh RK, Glauzy S, Stray-Pedersen A, Pezzi AE, Hanson IC, Vargas-Hernandez A, Xu ML, Coban-Akdemir ZH, Jhangiani SN, Muzny DM, Gibbs RA, Lupski JR, Chinn IK, Schatz DG, Orange JS, Meffre E. Disease-associated CTNNBL1 mutation impairs somatic hypermutation by decreasing nuclear AID. J Clin Invest 2021; 130:4411-4422. [PMID: 32484799 DOI: 10.1172/jci131297] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 05/13/2020] [Indexed: 01/02/2023] Open
Abstract
Patients with common variable immunodeficiency associated with autoimmune cytopenia (CVID+AIC) generate few isotype-switched B cells with severely decreased frequencies of somatic hypermutations (SHMs), but their underlying molecular defects remain poorly characterized. We identified a CVID+AIC patient who displays a rare homozygous missense M466V mutation in β-catenin-like protein 1 (CTNNBL1). Because CTNNBL1 binds activation-induced cytidine deaminase (AID) that catalyzes SHM, we tested AID interactions with the CTNNBL1 M466V variant. We found that the M466V mutation interfered with the association of CTNNBL1 with AID, resulting in decreased AID in the nuclei of patient EBV-transformed B cell lines and of CTNNBL1 466V/V Ramos B cells engineered to express only CTNNBL1 M466V using CRISPR/Cas9 technology. As a consequence, the scarce IgG+ memory B cells from the CTNNBL1 466V/V patient showed a low SHM frequency that averaged 6.7 mutations compared with about 18 mutations per clone in healthy-donor counterparts. In addition, CTNNBL1 466V/V Ramos B cells displayed a decreased incidence of SHM that was reduced by half compared with parental WT Ramos B cells, demonstrating that the CTNNBL1 M466V mutation is responsible for defective SHM induction. We conclude that CTNNBL1 plays an important role in regulating AID-dependent antibody diversification in humans.
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Affiliation(s)
- Marcel Kuhny
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Lisa R Forbes
- Section of Pediatric Allergy, Immunology, and Rheumatology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA.,William T. Shearer Texas Children's Hospital Center for Human Immunobiology, Houston, Texas, USA
| | - Elif Çakan
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Andrea Vega-Loza
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Valentyna Kostiuk
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Ravi K Dinesh
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Salomé Glauzy
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Asbjorg Stray-Pedersen
- Baylor-Hopkins Center for Mendelian Genomics, Houston, Texas, USA.,Institute of Clinical Medicine and.,Norwegian National Unit for Newborn Screening, Department of Pediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | - Ashley E Pezzi
- Department of Dermatology, Baylor College of Medicine, Houston, Texas, USA
| | - I Celine Hanson
- Section of Pediatric Allergy, Immunology, and Rheumatology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Alexander Vargas-Hernandez
- Section of Pediatric Allergy, Immunology, and Rheumatology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA.,William T. Shearer Texas Children's Hospital Center for Human Immunobiology, Houston, Texas, USA
| | - Mina LuQuing Xu
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Zeynep H Coban-Akdemir
- Baylor-Hopkins Center for Mendelian Genomics, Houston, Texas, USA.,Department of Molecular and Human Genetics and
| | - Shalini N Jhangiani
- Department of Molecular and Human Genetics and.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Donna M Muzny
- Department of Molecular and Human Genetics and.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Richard A Gibbs
- Baylor-Hopkins Center for Mendelian Genomics, Houston, Texas, USA.,Department of Molecular and Human Genetics and.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - James R Lupski
- Baylor-Hopkins Center for Mendelian Genomics, Houston, Texas, USA.,Department of Molecular and Human Genetics and.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Ivan K Chinn
- Section of Pediatric Allergy, Immunology, and Rheumatology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA.,William T. Shearer Texas Children's Hospital Center for Human Immunobiology, Houston, Texas, USA.,Baylor-Hopkins Center for Mendelian Genomics, Houston, Texas, USA
| | - David G Schatz
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Jordan S Orange
- Department of Pediatrics, College of Physicians and Surgeons of Columbia University, New York-Presbyterian Morgan Stanley Children's Hospital, New York, New York, USA
| | - Eric Meffre
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA.,Section of Rheumatology, Allergy, and Clinical Immunology, Yale University School of Medicine, New Haven, Connecticut, USA
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7
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Feng Y, Seija N, Di Noia JM, Martin A. AID in Antibody Diversification: There and Back Again. Trends Immunol 2020; 41:586-600. [PMID: 32434680 PMCID: PMC7183997 DOI: 10.1016/j.it.2020.04.009] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/16/2020] [Accepted: 04/20/2020] [Indexed: 01/01/2023]
Abstract
Activation-Induced cytidine Deaminase (AID) initiates affinity maturation and isotype switching by deaminating deoxycytidines within immunoglobulin genes, leading to somatic hypermutation (SHM) and class switch recombination (CSR). AID thus potentiates the humoral response to clear pathogens. Marking the 20th anniversary of the discovery of AID, we review the current understanding of AID function. We discuss AID biochemistry and how error-free forms of DNA repair are co-opted to prioritize mutagenesis over accuracy during antibody diversification. We discuss the regulation of DNA double-strand break (DSB) repair pathways during CSR. We describe genomic targeting of AID as a multilayered process involving chromatin architecture, cis- and trans-acting factors, and determining mutagenesis – distinct from AID occupancy at loci that are spared from mutation. Subverted base excision repair (BER) and mismatch repair (MMR) pathways act concertedly to generate antibody sequence diversity during SHM. In CSR, DNA DSBs are repaired by the nonhomologous end-joining pathway involving the 53BP1–Rif1–Shieldin axis, and by an alternative end-joining pathway involving HMCES (5-Hydroxymethylcytosine binding, ES-cell-specific) that binds and protects resected DSB ends. Genomic targeting of AID appears to be multilayered, with inbuilt redundancy, but robust enough to ensure that most of the genome is spared from AID activity. Cis elements and genome topology act together with trans-acting factors involved in transcription and RNA processing to determine AID activity at specific Ig regions. Other loci sharing genomic and transcriptional features with the Ig are collaterally targeted during SHM and CSR.
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Affiliation(s)
- Yuqing Feng
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Noé Seija
- Institute de Recherches Cliniques de Montréal, Montréal, QC, Canada; Molecular Biology Programs, Department of Medicine, University of Montreal, Montréal, QC, Canada
| | - Javier M Di Noia
- Institute de Recherches Cliniques de Montréal, Montréal, QC, Canada; Molecular Biology Programs, Department of Medicine, University of Montreal, Montréal, QC, Canada.
| | - Alberto Martin
- Department of Immunology, University of Toronto, Toronto, ON, Canada.
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8
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Pichugin A, Iarovaia OV, Gavrilov A, Sklyar I, Barinova N, Barinov A, Ivashkin E, Caron G, Aoufouchi S, Razin SV, Fest T, Lipinski M, Vassetzky YS. The IGH locus relocalizes to a "recombination compartment" in the perinucleolar region of differentiating B-lymphocytes. Oncotarget 2018; 8:40079-40089. [PMID: 28445143 PMCID: PMC5522243 DOI: 10.18632/oncotarget.16941] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 03/29/2017] [Indexed: 12/22/2022] Open
Abstract
The immunoglobulin heavy chain (IGH) gene loci are subject to specific recombination events during B-cell differentiation including somatic hypermutation and class switch recombination which mark the end of immunoglobulin gene maturation in germinal centers of secondary lymph nodes. These two events rely on the activity of activation-induced cytidine deaminase (AID) which requires DNA double strand breaks be created, a potential danger to the cell. Applying 3D-fluorescence in situ hybridization coupled with immunofluorescence staining to a previously described experimental system recapitulating normal B-cell differentiation ex vivo, we have kinetically analyzed the radial positioning of the two IGH gene loci as well as their proximity with the nucleolus, heterochromatin and γH2AX foci. Our observations are consistent with the proposal that these IGH gene rearrangements take place in a specific perinucleolar “recombination compartment” where AID could be sequestered thus limiting the extent of its potentially deleterious off-target effects.
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Affiliation(s)
- Andrey Pichugin
- UMR8126, CNRS, Université Paris Sud Paris Saclay, Institut Gustave Roussy, Villejuif, France.,LIA 1066, Laboratoire Franco-Russe de Recherche en Oncologie, Villejuif, France.,Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
| | - Olga V Iarovaia
- UMR8126, CNRS, Université Paris Sud Paris Saclay, Institut Gustave Roussy, Villejuif, France.,Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.,LIA 1066, Laboratoire Franco-Russe de Recherche en Oncologie, Villejuif, France
| | - Alexey Gavrilov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.,LIA 1066, Laboratoire Franco-Russe de Recherche en Oncologie, Villejuif, France
| | - Ilya Sklyar
- UMR8126, CNRS, Université Paris Sud Paris Saclay, Institut Gustave Roussy, Villejuif, France.,Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.,LIA 1066, Laboratoire Franco-Russe de Recherche en Oncologie, Villejuif, France
| | - Natalja Barinova
- UMR8126, CNRS, Université Paris Sud Paris Saclay, Institut Gustave Roussy, Villejuif, France.,LIA 1066, Laboratoire Franco-Russe de Recherche en Oncologie, Villejuif, France
| | - Aleksandr Barinov
- LIA 1066, Laboratoire Franco-Russe de Recherche en Oncologie, Villejuif, France
| | - Evgeny Ivashkin
- UMR8126, CNRS, Université Paris Sud Paris Saclay, Institut Gustave Roussy, Villejuif, France.,LIA 1066, Laboratoire Franco-Russe de Recherche en Oncologie, Villejuif, France.,Department of Experimental Neurocytology, Research Center of Neurology, Branch of Brain Research, Moscow, Russia
| | - Gersende Caron
- INSERM U1236, CHU de Rennes, Université Rennes 1, Rennes, France
| | - Said Aoufouchi
- UMR8200 CNRS, Université Paris-Sud, Institut de Cancérologie Gustave Roussy, Villejuif, France
| | - Sergey V Razin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.,LIA 1066, Laboratoire Franco-Russe de Recherche en Oncologie, Villejuif, France.,Moscow State University, Moscow, Russia
| | - Thierry Fest
- INSERM U1236, CHU de Rennes, Université Rennes 1, Rennes, France
| | - Marc Lipinski
- UMR8126, CNRS, Université Paris Sud Paris Saclay, Institut Gustave Roussy, Villejuif, France.,LIA 1066, Laboratoire Franco-Russe de Recherche en Oncologie, Villejuif, France
| | - Yegor S Vassetzky
- UMR8126, CNRS, Université Paris Sud Paris Saclay, Institut Gustave Roussy, Villejuif, France.,LIA 1066, Laboratoire Franco-Russe de Recherche en Oncologie, Villejuif, France.,Moscow State University, Moscow, Russia
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9
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Iarovaia OV, Ioudinkova ES, Razin SV, Vassetzky YS. Role of the Nucleolus in Rearrangements of the IGH Locus. Mol Biol 2018. [DOI: 10.1134/s0026893317050211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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10
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Methot S, Di Noia J. Molecular Mechanisms of Somatic Hypermutation and Class Switch Recombination. Adv Immunol 2017; 133:37-87. [DOI: 10.1016/bs.ai.2016.11.002] [Citation(s) in RCA: 165] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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11
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Activation induced cytidine deaminase mutant (AID-His130Pro) from Hyper IgM 2 patient retained mutagenic activity on SHM artificial substrate. Mol Immunol 2016; 79:77-82. [PMID: 27716525 DOI: 10.1016/j.molimm.2016.09.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 09/27/2016] [Accepted: 09/29/2016] [Indexed: 01/01/2023]
Abstract
Activation induced cytidine deaminase (AID) is an essential enzyme for class switch recombination (CSR) and somatic hypermutation (SHM) during secondary immune response. Mutations in the AICDA gene are responsible for Hyper IgM 2 syndrome where both CSR and SHM or only CSR are affected. Indeed, triggering either of the two mechanisms requires the DNA deamination activity of AID. Besides, different domains of AID may be differentially involved in CSR and SHM through their interaction with specific cofactors. Herein, we studied the AID-induced SHM activity of the AID-His130Pro mutant identified in a patient with Hyper IgM 2 syndrome. AID mutagenic activity was monitored by the reversion of nonsense mutations of the EGFP gene assessed by flow cytometry. We found that the His130Pro mutation, which affects CSR, preserves AID mutagenic activity. Indeed, the His130 residue is located in a putative specific CSR region in the APOBEC-like domain, known to involve CSR specific cofactors that probably play a major role in AID physiological activities.
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12
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Sklyar I, Iarovaia OV, Gavrilov AA, Pichugin A, Germini D, Tsfasman T, Caron G, Fest T, Lipinski M, Razin SV, Vassetzky YS. Distinct Patterns of Colocalization of theCCND1andCMYCGenes With Their Potential Translocation PartnerIGHat Successive Stages of B-Cell Differentiation. J Cell Biochem 2016; 117:1506-10. [DOI: 10.1002/jcb.25516] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 02/10/2016] [Indexed: 01/22/2023]
Affiliation(s)
- Ilya Sklyar
- UMR8126, CNRS; Université Paris-Sud, Institut de Cancérologie Gustave Roussy; Villejuif France
- LIA1066; Laboratoire Franco-Russe de Recherche en Oncologie; Villejuif France
- Institute of Gene Biology; Russian Academy of Sciences; Moscow Russia
| | - Olga V. Iarovaia
- UMR8126, CNRS; Université Paris-Sud, Institut de Cancérologie Gustave Roussy; Villejuif France
- LIA1066; Laboratoire Franco-Russe de Recherche en Oncologie; Villejuif France
- Institute of Gene Biology; Russian Academy of Sciences; Moscow Russia
| | - Alexey A. Gavrilov
- LIA1066; Laboratoire Franco-Russe de Recherche en Oncologie; Villejuif France
- Institute of Gene Biology; Russian Academy of Sciences; Moscow Russia
| | - Andrey Pichugin
- UMR8126, CNRS; Université Paris-Sud, Institut de Cancérologie Gustave Roussy; Villejuif France
- LIA1066; Laboratoire Franco-Russe de Recherche en Oncologie; Villejuif France
- Peter the Great St. Petersburg Polytechnic University; St. Petersburg Russia
| | - Diego Germini
- UMR8126, CNRS; Université Paris-Sud, Institut de Cancérologie Gustave Roussy; Villejuif France
- LIA1066; Laboratoire Franco-Russe de Recherche en Oncologie; Villejuif France
- Peter the Great St. Petersburg Polytechnic University; St. Petersburg Russia
| | - Tatiana Tsfasman
- UMR8126, CNRS; Université Paris-Sud, Institut de Cancérologie Gustave Roussy; Villejuif France
- LIA1066; Laboratoire Franco-Russe de Recherche en Oncologie; Villejuif France
| | | | - Thierry Fest
- INSERM U917; Université de Rennes; Rennes France
| | - Marc Lipinski
- UMR8126, CNRS; Université Paris-Sud, Institut de Cancérologie Gustave Roussy; Villejuif France
- LIA1066; Laboratoire Franco-Russe de Recherche en Oncologie; Villejuif France
| | - Sergey V. Razin
- LIA1066; Laboratoire Franco-Russe de Recherche en Oncologie; Villejuif France
- Institute of Gene Biology; Russian Academy of Sciences; Moscow Russia
- Faculty of Biology; M.V. Lomonosov Moscow State University; 119992 Moscow Russia
| | - Yegor S. Vassetzky
- UMR8126, CNRS; Université Paris-Sud, Institut de Cancérologie Gustave Roussy; Villejuif France
- LIA1066; Laboratoire Franco-Russe de Recherche en Oncologie; Villejuif France
- Faculty of Biology; M.V. Lomonosov Moscow State University; 119992 Moscow Russia
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13
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Mutations, kataegis and translocations in B cells: understanding AID promiscuous activity. Nat Rev Immunol 2016; 16:164-76. [PMID: 26898111 DOI: 10.1038/nri.2016.2] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
As B cells engage in the immune response, they express activation-induced cytidine deaminase (AID) to initiate the hypermutation and recombination of immunoglobulin genes, which are crucial processes for the efficient recognition and disposal of pathogens. However, AID must be tightly controlled in B cells to minimize off-target mutations, which can drive chromosomal translocations and the development of B cell malignancies, such as lymphomas. Recent genomic and biochemical analyses have begun to unravel the mechanisms of how AID-mediated deamination is targeted outside immunoglobulin genes. Here, we discuss the transcriptional and topological features that are emerging as key drivers of AID promiscuous activity.
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14
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Ouadani H, Ben-Mustapha I, Ben-ali M, Ben-khemis L, Larguèche B, Boussoffara R, Maalej S, Fetni I, Hassayoun S, Mahfoudh A, Mellouli F, Yalaoui S, Masmoudi H, Bejaoui M, Barbouche MR. Novel and recurrent AID mutations underlie prevalent autosomal recessive form of HIGM in consanguineous patients. Immunogenetics 2015; 68:19-28. [PMID: 26545377 DOI: 10.1007/s00251-015-0878-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 10/12/2015] [Indexed: 10/22/2022]
Abstract
Immunoglobulin class switch recombination deficiencies (Ig-CSR-D) are characterized by normal or elevated serum IgM level and absence of IgG, IgA, and IgE. Most reported cases are due to X-linked CD40L deficiency. Activation-induced cytidine deaminase deficiency is the most frequent autosomal recessive form, whereas CD40 deficiency is more rare. Herein, we present the first North African study on hyper IgM (HIGM) syndrome including 16 Tunisian patients. Phenotypic and genetic studies allowed us to determine their molecular basis. Three CD40LG mutations have been identified including two novels (c.348_351dup and c.782_*2del) and one already reported mutation (g.6182G>A). No mutation has been found in another patient despite the lack of CD40L expression. Interestingly, three AICDA mutations have been identified in 11 patients. Two mutations were novel (c.91T>C and c.389A>C found in one and five patients respectively), and one previously reported splicing mutation (c.156+1T>G) was found in five patients. Only one CD40-deficient patient, bearing a novel mutation (c.109T>G), has been identified. Thus, unlike previous reports, AID deficiency is the most frequent underlying molecular basis (68%) of Ig-CSR-D in Tunisian patients. This finding and the presence of specific recurrent mutations are probably due to the critical role played by inbreeding in North African populations.
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Affiliation(s)
- Hanen Ouadani
- Laboratory of Transmission, Control and Immunobiology of Infection (LR11IPT02), Institut Pasteur de Tunis and University Tunis El Manar, Tunis, Tunisia
| | - Imen Ben-Mustapha
- Laboratory of Transmission, Control and Immunobiology of Infection (LR11IPT02), Institut Pasteur de Tunis and University Tunis El Manar, Tunis, Tunisia
| | - Meriem Ben-ali
- Laboratory of Transmission, Control and Immunobiology of Infection (LR11IPT02), Institut Pasteur de Tunis and University Tunis El Manar, Tunis, Tunisia
| | - Leila Ben-khemis
- Laboratory of Transmission, Control and Immunobiology of Infection (LR11IPT02), Institut Pasteur de Tunis and University Tunis El Manar, Tunis, Tunisia
| | - Beya Larguèche
- Laboratory of Transmission, Control and Immunobiology of Infection (LR11IPT02), Institut Pasteur de Tunis and University Tunis El Manar, Tunis, Tunisia
| | | | - Sonia Maalej
- Department of Pneumology "D", Abderahman Mami Hospital, Ariana, Tunisia
| | - Ilhem Fetni
- Department of Pediatrics, Mongi Slim Hospital, Marsa, Tunisia
| | | | | | - Fethi Mellouli
- Department of Pediatrics, Bone Marrow Transplantation Center, Tunis, Tunisia
| | - Sadok Yalaoui
- Laboratory of Biology, Abderahman Mami Hospital, Ariana, Tunisia
| | - Hatem Masmoudi
- Laboratory of Immunology, Habib Bourguiba Hospital, Sfax, Tunisia
| | - Mohamed Bejaoui
- Department of Pediatrics, Bone Marrow Transplantation Center, Tunis, Tunisia
| | - Mohamed-Ridha Barbouche
- Laboratory of Transmission, Control and Immunobiology of Infection (LR11IPT02), Institut Pasteur de Tunis and University Tunis El Manar, Tunis, Tunisia.
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15
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Strongin DE, Groudine M, Politz JCR. Nucleolar tethering mediates pairing between the IgH and Myc loci. Nucleus 2015; 5:474-81. [PMID: 25482199 PMCID: PMC4164489 DOI: 10.4161/nucl.36233] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Gene loci on different chromosomes can preferentially colocalize in the cell nucleus. However, many of the mechanisms mediating this spatial proximity remain to be elucidated. The IgH locus on Chromosome 12 and the Myc locus on Chromosome 15 are a well-studied model for gene colocalization in murine B cells, where the two loci are positioned in close proximity at a higher than expected frequency. These gene loci are also partners in the chromosomal translocation that causes murine plasmacytoma and Burkitt’s lymphoma. Because both Chromosome 12 and Chromosome 15 carry nucleolar organizer regions (NORs) in the most commonly studied mouse strains, we hypothesized that NOR-mediated tethering of the IgH and Myc loci to shared nucleoli could serve as a mechanism to drive IgH:Myc colocalization. Using mouse strains that naturally carry nucleolar organizer regions (NORs) on different sets of chromosomes, we establish that IgH and Myc are positioned proximal to nucleoli in a NOR dependent manner and show that their joint association with nucleoli significantly increases the frequency of IgH and Myc pairing. Thus we demonstrate that simple nucleolar tethering can increase the colocalization frequency of genes on NOR-bearing chromosomes.
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Affiliation(s)
- Daniel E Strongin
- a Division of Basic Sciences; Fred Hutchinson Cancer Research Center; Seattle, WA USA
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16
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He M, Cortizas EM, Verdun RE, Severinson E. Cyclin-dependent kinases regulate Ig class switching by controlling access of AID to the switch region. THE JOURNAL OF IMMUNOLOGY 2015; 194:4231-9. [PMID: 25795757 DOI: 10.4049/jimmunol.1402146] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 02/05/2015] [Indexed: 01/08/2023]
Abstract
Ig class switching requires cell proliferation and is division linked, but the detailed mechanism is unknown. By analyzing the first switching cells early in the kinetics, our analysis suggested that proliferating B cells had a very short G1 phase (<3.5 h), a total cell cycle time of ∼ 11 h, and that Ig class switching preferentially occurred in the late G1 or early S phase. Inhibition of cyclin-dependent kinases (CDKs) caused dramatic reduction of switching rate within 6 h. This was associated with less targeting of activation-induced cytidine deaminase (AID) to the Igh locus. Interestingly, ectopically expressed nuclear AID in HeLa cells was preferentially found in the early S phase. Furthermore, in CDK2 hypomorphic cells there was reduced nuclear AID accumulation. Thus, our data are compatible with the idea that division-linked Ig class switching is in part due to CDK2-regulated AID nuclear access at the G1/S border.
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Affiliation(s)
- Minghui He
- Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Elena M Cortizas
- Division of Gerontology and Geriatric Medicine, Department of Medicine, Miller School of Medicine, University of Miami, Miami, FL 33136
| | - Ramiro E Verdun
- Division of Gerontology and Geriatric Medicine, Department of Medicine, Miller School of Medicine, University of Miami, Miami, FL 33136; Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33136; and Geriatric Research, Education, and Clinical Center, Miami Veterans Affairs Healthcare System, Miami, FL 33125
| | - Eva Severinson
- Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden;
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17
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AID expression in B-cell lymphomas causes accumulation of genomic uracil and a distinct AID mutational signature. DNA Repair (Amst) 2014; 25:60-71. [PMID: 25486549 DOI: 10.1016/j.dnarep.2014.11.006] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 11/06/2014] [Accepted: 11/17/2014] [Indexed: 11/23/2022]
Abstract
The most common mutations in cancer are C to T transitions, but their origin has remained elusive. Recently, mutational signatures of APOBEC-family cytosine deaminases were identified in many common cancers, suggesting off-target deamination of cytosine to uracil as a common mutagenic mechanism. Here we present evidence from mass spectrometric quantitation of deoxyuridine in DNA that shows significantly higher genomic uracil content in B-cell lymphoma cell lines compared to non-lymphoma cancer cell lines and normal circulating lymphocytes. The genomic uracil levels were highly correlated with AID mRNA and protein expression, but not with expression of other APOBECs. Accordingly, AID knockdown significantly reduced genomic uracil content. B-cells stimulated to express endogenous AID and undergo class switch recombination displayed a several-fold increase in total genomic uracil, indicating that B cells may undergo widespread cytosine deamination after stimulation. In line with this, we found that clustered mutations (kataegis) in lymphoma and chronic lymphocytic leukemia predominantly carry AID-hotspot mutational signatures. Moreover, we observed an inverse correlation of genomic uracil with uracil excision activity and expression of the uracil-DNA glycosylases UNG and SMUG1. In conclusion, AID-induced mutagenic U:G mismatches in DNA may be a fundamental and common cause of mutations in B-cell malignancies.
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18
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Dahlberg CIM, He M, Visnes T, Torres ML, Cortizas EM, Verdun RE, Westerberg LS, Severinson E, Ström L. A novel mouse model for the hyper-IgM syndrome: a spontaneous activation-induced cytidine deaminase mutation leading to complete loss of Ig class switching and reduced somatic hypermutation. THE JOURNAL OF IMMUNOLOGY 2014; 193:4732-8. [PMID: 25252954 DOI: 10.4049/jimmunol.1401242] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We describe a spontaneously derived mouse line that completely failed to induce Ig class switching in vitro and in vivo. The mice inherited abolished IgG serum titers in a recessive manner caused by a spontaneous G → A transition mutation in codon 112 of the aicda gene, leading to an arginine to histidine replacement (AID(R112H)). Ig class switching was completely reconstituted by expressing wild-type AID. Mice homozygous for AID(R112H) had peripheral B cell hyperplasia and large germinal centers in the absence of Ag challenge. Immunization with SRBCs elicited an Ag-specific IgG1 response in wild-type mice, whereas AID(R112H) mice failed to produce IgG1 and had reduced somatic hypermutation. The phenotype recapitulates the human hyper-IgM (HIGM) syndrome that is caused by point mutations in the orthologous gene in humans, and the AID(R112H) mutation is frequently found in HIGM patients. The AID(R112H) mouse model for HIGM provides a powerful and more precise tool than conventional knockout strategies.
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Affiliation(s)
- Carin I M Dahlberg
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Minghui He
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Torkild Visnes
- Department of Cell and Molecular Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden; and
| | - Magda Liz Torres
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Elena M Cortizas
- Division of Gerontology and Geriatric Medicine, Department of Medicine, Miller School of Medicine, University of Miami, Miami, FL 33136
| | - Ramiro E Verdun
- Division of Gerontology and Geriatric Medicine, Department of Medicine, Miller School of Medicine, University of Miami, Miami, FL 33136
| | - Lisa S Westerberg
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden;
| | - Eva Severinson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden;
| | - Lena Ström
- Department of Cell and Molecular Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden; and
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19
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Taylor BJM, Wu YL, Rada C. Active RNAP pre-initiation sites are highly mutated by cytidine deaminases in yeast, with AID targeting small RNA genes. eLife 2014; 3:e03553. [PMID: 25237741 PMCID: PMC4359381 DOI: 10.7554/elife.03553] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 09/17/2014] [Indexed: 12/21/2022] Open
Abstract
Cytidine deaminases are single stranded DNA mutators diversifying antibodies and restricting viral infection. Improper access to the genome leads to translocations and mutations in B cells and contributes to the mutation landscape in cancer, such as kataegis. It remains unclear how deaminases access double stranded genomes and whether off-target mutations favor certain loci, although transcription and opportunistic access during DNA repair are thought to play a role. In yeast, AID and the catalytic domain of APOBEC3G preferentially mutate transcriptionally active genes within narrow regions, 110 base pairs in width, fixed at RNA polymerase initiation sites. Unlike APOBEC3G, AID shows enhanced mutational preference for small RNA genes (tRNAs, snoRNAs and snRNAs) suggesting a putative role for RNA in its recruitment. We uncover the high affinity of the deaminases for the single stranded DNA exposed by initiating RNA polymerases (a DNA configuration reproduced at stalled polymerases) without a requirement for specific cofactors.
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Affiliation(s)
- Benjamin J M Taylor
- Protein and Nucleic Acid Chemistry Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Yee Ling Wu
- Protein and Nucleic Acid Chemistry Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Cristina Rada
- Protein and Nucleic Acid Chemistry Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
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20
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Krokan HE, Sætrom P, Aas PA, Pettersen HS, Kavli B, Slupphaug G. Error-free versus mutagenic processing of genomic uracil—Relevance to cancer. DNA Repair (Amst) 2014; 19:38-47. [DOI: 10.1016/j.dnarep.2014.03.028] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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21
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Vaidyanathan B, Yen WF, Pucella JN, Chaudhuri J. AIDing Chromatin and Transcription-Coupled Orchestration of Immunoglobulin Class-Switch Recombination. Front Immunol 2014; 5:120. [PMID: 24734031 PMCID: PMC3975107 DOI: 10.3389/fimmu.2014.00120] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 03/07/2014] [Indexed: 12/29/2022] Open
Abstract
Secondary diversification of the antibody repertoire upon antigenic challenge, in the form of immunoglobulin heavy chain (IgH) class-switch recombination (CSR) endows mature, naïve B cells in peripheral lymphoid organs with a limitless ability to mount an optimal humoral immune response, thus expediting pathogen elimination. CSR replaces the default constant (CH) region exons (Cμ) of IgH with any of the downstream CH exons (Cγ, Cε, or Cα), thereby altering effector functions of the antibody molecule. This process depends on, and is orchestrated by, activation-induced deaminase (AID), a DNA cytidine deaminase that acts on single-stranded DNA exposed during transcription of switch (S) region sequences at the IgH locus. DNA lesions thus generated are processed by components of several general DNA repair pathways to drive CSR. Given that AID can instigate DNA lesions and genomic instability, stringent checks are imposed that constrain and restrict its mutagenic potential. In this review, we will discuss how AID expression and substrate specificity and activity is rigorously enforced at the transcriptional, post-transcriptional, post-translational, and epigenetic levels, and how the DNA-damage response is choreographed with precision to permit targeted activity while limiting bystander catastrophe.
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Affiliation(s)
- Bharat Vaidyanathan
- Weill Cornell Graduate School of Medical Sciences , New York, NY , USA ; Immunology Program, Memorial Sloan Kettering Cancer Center, Gerstner Sloan Kettering Graduate School , New York, NY , USA
| | - Wei-Feng Yen
- Weill Cornell Graduate School of Medical Sciences , New York, NY , USA ; Immunology Program, Memorial Sloan Kettering Cancer Center, Gerstner Sloan Kettering Graduate School , New York, NY , USA
| | - Joseph N Pucella
- Immunology Program, Memorial Sloan Kettering Cancer Center, Gerstner Sloan Kettering Graduate School , New York, NY , USA
| | - Jayanta Chaudhuri
- Weill Cornell Graduate School of Medical Sciences , New York, NY , USA ; Immunology Program, Memorial Sloan Kettering Cancer Center, Gerstner Sloan Kettering Graduate School , New York, NY , USA
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22
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Hu Y, Ericsson I, Doseth B, Liabakk NB, Krokan HE, Kavli B. Activation-induced cytidine deaminase (AID) is localized to subnuclear domains enriched in splicing factors. Exp Cell Res 2014; 322:178-92. [DOI: 10.1016/j.yexcr.2014.01.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 01/02/2014] [Accepted: 01/06/2014] [Indexed: 10/25/2022]
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23
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Ahn JW, Kim S, Kim EJ, Kim YJ, Kim KJ. Structural insights into the novel ARM-repeat protein CTNNBL1 and its association with the hPrp19-CDC5L complex. ACTA ACUST UNITED AC 2014; 70:780-8. [PMID: 24598747 DOI: 10.1107/s139900471303318x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 12/08/2013] [Indexed: 11/10/2022]
Abstract
The hPrp19-CDC5L complex plays a crucial role during human pre-mRNA splicing by catalytic activation of the spliceosome. In order to elucidate the molecular architecture of the hPrp19-CDC5L complex, the crystal structure of CTNNBL1, one of the major components of this complex, was determined. Unlike canonical ARM-repeat proteins such as β-catenin and importin-α, CTNNBL1 was found to contain a twisted and extended ARM-repeat structure at the C-terminal domain and, more importantly, the protein formed a stable dimer. A highly negatively charged patch formed in the N-terminal ARM-repeat domain of CTNNBL1 provides a binding site for CDC5L, a binding partner of the protein in the hPrp19-CDC5L complex, and these two proteins form a complex with a stoichiometry of 2:2. These findings not only present the crystal structure of a novel ARM-repeat protein, CTNNBL1, but also provide insights into the detailed molecular architecture of the hPrp19-CDC5L complex.
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Affiliation(s)
- Jae-Woo Ahn
- Structural and Molecular Biology Laboratory, School of Life Sciences and Biotechnology, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu 702-701, Republic of Korea
| | - Sangwoo Kim
- School of Nano-Bioscience and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Eun-Jung Kim
- Structural and Molecular Biology Laboratory, School of Life Sciences and Biotechnology, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu 702-701, Republic of Korea
| | - Yeo-Jin Kim
- Structural and Molecular Biology Laboratory, School of Life Sciences and Biotechnology, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu 702-701, Republic of Korea
| | - Kyung-Jin Kim
- Structural and Molecular Biology Laboratory, School of Life Sciences and Biotechnology, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu 702-701, Republic of Korea
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24
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Matthews AJ, Zheng S, DiMenna LJ, Chaudhuri J. Regulation of immunoglobulin class-switch recombination: choreography of noncoding transcription, targeted DNA deamination, and long-range DNA repair. Adv Immunol 2014; 122:1-57. [PMID: 24507154 PMCID: PMC4150736 DOI: 10.1016/b978-0-12-800267-4.00001-8] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Upon encountering antigens, mature IgM-positive B lymphocytes undergo class-switch recombination (CSR) wherein exons encoding the default Cμ constant coding gene segment of the immunoglobulin (Ig) heavy-chain (Igh) locus are excised and replaced with a new constant gene segment (referred to as "Ch genes", e.g., Cγ, Cɛ, or Cα). The B cell thereby changes from expressing IgM to one producing IgG, IgE, or IgA, with each antibody isotype having a different effector function during an immune reaction. CSR is a DNA deletional-recombination reaction that proceeds through the generation of DNA double-strand breaks (DSBs) in repetitive switch (S) sequences preceding each Ch gene and is completed by end-joining between donor Sμ and acceptor S regions. CSR is a multistep reaction requiring transcription through S regions, the DNA cytidine deaminase AID, and the participation of several general DNA repair pathways including base excision repair, mismatch repair, and classical nonhomologous end-joining. In this review, we discuss our current understanding of how transcription through S regions generates substrates for AID-mediated deamination and how AID participates not only in the initiation of CSR but also in the conversion of deaminated residues into DSBs. Additionally, we review the multiple processes that regulate AID expression and facilitate its recruitment specifically to the Ig loci, and how deregulation of AID specificity leads to oncogenic translocations. Finally, we summarize recent data on the potential role of AID in the maintenance of the pluripotent stem cell state during epigenetic reprogramming.
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Affiliation(s)
- Allysia J Matthews
- Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, New York, USA
| | - Simin Zheng
- Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, New York, USA
| | - Lauren J DiMenna
- Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, New York, USA
| | - Jayanta Chaudhuri
- Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, New York, USA.
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Huang X, Wang G, Wu Y, Du Z. The structure of full-length human CTNNBL1 reveals a distinct member of the armadillo-repeat protein family. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1598-608. [DOI: 10.1107/s0907444913011360] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 04/25/2013] [Indexed: 12/20/2022]
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Park SR. Activation-induced Cytidine Deaminase in B Cell Immunity and Cancers. Immune Netw 2012; 12:230-9. [PMID: 23396757 PMCID: PMC3566417 DOI: 10.4110/in.2012.12.6.230] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Revised: 11/09/2012] [Accepted: 11/13/2012] [Indexed: 01/26/2023] Open
Abstract
Activation-induced cytidine deaminase (AID) is an enzyme that is predominantly expressed in germinal center B cells and plays a pivotal role in immunoglobulin class switch recombination and somatic hypermutation for antibody (Ab) maturation. These two genetic processes endow Abs with protective functions against a multitude of antigens (pathogens) during humoral immune responses. In B cells, AID expression is regulated at the level of either transcriptional activation on AID gene loci or post-transcriptional suppression of AID mRNA. Furthermore, AID stabilization and targeting are determined by post-translational modifications and interactions with other cellular/nuclear factors. On the other hand, aberrant expression of AID causes B cell leukemias and lymphomas, including Burkitt's lymphoma caused by c-myc/IgH translocation. AID is also ectopically expressed in T cells and non-immune cells, and triggers point mutations in relevant DNA loci, resulting in tumorigenesis. Here, I review the recent literatures on the function of AID, regulation of AID expression, stability and targeting in B cells, and AID-related tumor formation.
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Affiliation(s)
- Seok-Rae Park
- Department of Microbiology, College of Medicine, Konyang University, Daejeon 302-718, Korea
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