1
|
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.
Collapse
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
| |
Collapse
|
2
|
Senigl F, Maman Y, Dinesh RK, Alinikula J, Seth RB, Pecnova L, Omer AD, Rao SSP, Weisz D, Buerstedde JM, Aiden EL, Casellas R, Hejnar J, Schatz DG. Topologically Associated Domains Delineate Susceptibility to Somatic Hypermutation. Cell Rep 2020; 29:3902-3915.e8. [PMID: 31851922 PMCID: PMC6980758 DOI: 10.1016/j.celrep.2019.11.039] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 06/26/2019] [Accepted: 11/08/2019] [Indexed: 12/26/2022] Open
Abstract
Somatic hypermutation (SHM) introduces point mutations into immunoglobulin (Ig) genes but also causes mutations in other parts of the genome. We have used lentiviral SHM reporter vectors to identify regions of the genome that are susceptible (“hot”) and resistant (“cold”) to SHM, revealing that SHM susceptibility and resistance are often properties of entire topologically associated domains (TADs). Comparison of hot and cold TADs reveals that while levels of transcription are equivalent, hot TADs are enriched for the cohesin loader NIPBL, super-enhancers, markers of paused/stalled RNA polymerase 2, and multiple important B cell transcription factors. We demonstrate that at least some hot TADs contain enhancers that possess SHM targeting activity and that insertion of a strong Ig SHM-targeting element into a cold TAD renders it hot. Our findings lead to a model for SHM susceptibility involving the cooperative action of cis-acting SHM targeting elements and the dynamic and architectural properties of TADs. Senigl et al. show that genome susceptibility to somatic hypermutation (SHM) is confined within topologically associated domains (TADs) and is linked to markers of strong enhancers and stalled transcription and high levels of the cohesin loader NIPBL. Insertion of an ectopic SHM targeting element renders an entire TAD susceptible to SHM.
Collapse
Affiliation(s)
- Filip Senigl
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 14220 Prague 4, Czech Republic.
| | - Yaakov Maman
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Ravi K Dinesh
- Department of Immunobiology, Yale School of Medicine, 300 Cedar Street, Box 208011, New Haven, CT 06520-8011, USA
| | - Jukka Alinikula
- Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, 20520 Turku, Finland
| | - Rashu B Seth
- Department of Immunobiology, Yale School of Medicine, 300 Cedar Street, Box 208011, New Haven, CT 06520-8011, USA
| | - Lubomira Pecnova
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 14220 Prague 4, Czech Republic
| | - Arina D Omer
- Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - Suhas S P Rao
- Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - David Weisz
- Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Erez Lieberman Aiden
- Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
| | - Rafael Casellas
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA; Center of Cancer Research, NCI, NIH, Bethesda, MD 20892, USA
| | - Jiri Hejnar
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 14220 Prague 4, Czech Republic
| | - David G Schatz
- Department of Immunobiology, Yale School of Medicine, 300 Cedar Street, Box 208011, New Haven, CT 06520-8011, USA.
| |
Collapse
|
3
|
Tepper S, Mortusewicz O, Członka E, Bello A, Schmidt A, Jeschke J, Fischbach A, Pfeil I, Petersen-Mahrt SK, Mangerich A, Helleday T, Leonhardt H, Jungnickel B. Restriction of AID activity and somatic hypermutation by PARP-1. Nucleic Acids Res 2019; 47:7418-7429. [PMID: 31127309 PMCID: PMC6698665 DOI: 10.1093/nar/gkz466] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/13/2019] [Accepted: 05/16/2019] [Indexed: 12/20/2022] Open
Abstract
Affinity maturation of the humoral immune response depends on somatic hypermutation (SHM) of immunoglobulin (Ig) genes, which is initiated by targeted lesion introduction by activation-induced deaminase (AID), followed by error-prone DNA repair. Stringent regulation of this process is essential to prevent genetic instability, but no negative feedback control has been identified to date. Here we show that poly(ADP-ribose) polymerase-1 (PARP-1) is a key factor restricting AID activity during somatic hypermutation. Poly(ADP-ribose) (PAR) chains formed at DNA breaks trigger AID-PAR association, thus preventing excessive DNA damage induction at sites of AID action. Accordingly, AID activity and somatic hypermutation at the Ig variable region is decreased by PARP-1 activity. In addition, PARP-1 regulates DNA lesion processing by affecting strand biased A:T mutagenesis. Our study establishes a novel function of the ancestral genome maintenance factor PARP-1 as a critical local feedback regulator of both AID activity and DNA repair during Ig gene diversification.
Collapse
Affiliation(s)
- Sandra Tepper
- Department of Cell Biology, Institute of Biochemistry and Biophysics, School of Biology and Pharmacy, Friedrich Schiller University, 07745 Jena, Germany
| | - Oliver Mortusewicz
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Ludwig Maximilians University Munich, 82152 Planegg-Martinsried, Germany.,Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Ewelina Członka
- Department of Cell Biology, Institute of Biochemistry and Biophysics, School of Biology and Pharmacy, Friedrich Schiller University, 07745 Jena, Germany
| | - Amanda Bello
- Department of Cell Biology, Institute of Biochemistry and Biophysics, School of Biology and Pharmacy, Friedrich Schiller University, 07745 Jena, Germany
| | - Angelika Schmidt
- Department of Cell Biology, Institute of Biochemistry and Biophysics, School of Biology and Pharmacy, Friedrich Schiller University, 07745 Jena, Germany
| | - Julia Jeschke
- Department of Cell Biology, Institute of Biochemistry and Biophysics, School of Biology and Pharmacy, Friedrich Schiller University, 07745 Jena, Germany
| | - Arthur Fischbach
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Ines Pfeil
- Institute of Clinical Molecular Biology, Helmholtz Center Munich, German Research Center for Environmental Health, 81377 Munich, Germany
| | - Svend K Petersen-Mahrt
- DNA Editing in Immunity and Epigenetics, IFOM-Fondazione Instituto FIRC di Oncologia Molecolare, Milano, Italy
| | - Aswin Mangerich
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Thomas Helleday
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Heinrich Leonhardt
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Ludwig Maximilians University Munich, 82152 Planegg-Martinsried, Germany
| | - Berit Jungnickel
- Department of Cell Biology, Institute of Biochemistry and Biophysics, School of Biology and Pharmacy, Friedrich Schiller University, 07745 Jena, Germany.,Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| |
Collapse
|
4
|
Activation-induced deaminase (AID) localizes to the nucleus in brief pulses. PLoS Genet 2019; 15:e1007968. [PMID: 30811383 PMCID: PMC6411215 DOI: 10.1371/journal.pgen.1007968] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 03/11/2019] [Accepted: 01/16/2019] [Indexed: 11/19/2022] Open
Abstract
Activation-induced deaminase (AID) converts C to U and 5-methyl-C to T. These mutagenic activities are critical to immunoglobulin (Ig) gene diversification and epigenetic reprogramming, but they must be tightly controlled to prevent compromising cell fitness. AID acts in the nucleus but localizes predominately to the cytoplasm. To address this apparent paradox, we have carried out time-lapse imaging of AID in single living B cells and fibroblasts. We demonstrate that AID enters the nucleus in brief (30 min) pulses, evident in about 10% of cells in the course of a single cell cycle (24 hr imaging). Pulses do not depend on AID catalytic activity, but they are coordinated with nuclear accumulation of P53. Pulsing may protect cells from pathologic consequences of excess exposure to AID, or enable AID to synchronize its activity with transcription of genes that are AID targets or with nuclear entry of factors that act at sites of AID-catalyzed DNA deamination to promote Ig gene diversification or epigenetic reprogramming.
Collapse
|
5
|
Abstract
Class switch recombination (CSR) generates isotype-switched antibodies with distinct effector functions essential for mediating effective humoral immunity. CSR is catalyzed by activation-induced deaminase (AID) that initiates DNA lesions in the evolutionarily conserved switch (S) regions at the immunoglobulin heavy chain (Igh) locus. AID-initiated DNA lesions are subsequently converted into DNA double stranded breaks (DSBs) in the S regions of Igh locus, repaired by non-homologous end-joining to effect CSR in mammalian B lymphocytes. While molecular mechanisms of CSR are well characterized, it remains less well understood how upstream signaling pathways regulate AID expression and CSR. B lymphocytes express multiple receptors including the B cell antigen receptor (BCR) and co-receptors (e.g., CD40). These receptors may share common signaling pathways or may use distinct signaling elements to regulate CSR. Here, we discuss how signals emanating from different receptors positively or negatively regulate AID expression and CSR.
Collapse
Affiliation(s)
- Zhangguo Chen
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States.
| | - Jing H Wang
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States.
| |
Collapse
|
6
|
A licensing step links AID to transcription elongation for mutagenesis in B cells. Nat Commun 2018; 9:1248. [PMID: 29593215 PMCID: PMC5871760 DOI: 10.1038/s41467-018-03387-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 02/08/2018] [Indexed: 01/01/2023] Open
Abstract
Activation-induced deaminase (AID) mutates the immunoglobulin (Ig) genes to initiate somatic hypermutation (SHM) and class switch recombination (CSR) in B cells, thus underpinning antibody responses. AID mutates a few hundred other loci, but most AID-occupied genes are spared. The mechanisms underlying productive deamination versus non-productive AID targeting are unclear. Here we show that three clustered arginine residues define a functional AID domain required for SHM, CSR, and off-target activity in B cells without affecting AID deaminase activity or Escherichia coli mutagenesis. Both wt AID and mutants with single amino acid replacements in this domain broadly associate with Spt5 and chromatin and occupy the promoter of AID target genes. However, mutant AID fails to occupy the corresponding gene bodies and loses association with transcription elongation factors. Thus AID mutagenic activity is determined not by locus occupancy but by a licensing mechanism, which couples AID to transcription elongation. Activation-induced deaminase (AID) is important for inducing desirable mutations at the B cell receptor genes for effective antibody responses. Here the authors show that three key arginine residues of AID link AID-chromatin association with transcription elongation to license AID for specific mutagenesis in B cells.
Collapse
|
7
|
Abstract
In this issue of JEM, Álvarez-Prado et al. designed a DNA capture library allowing them to identify 275 genes targeted by AID in mouse germinal center B cells. Using the molecular features of these genes to feed a machine-learning algorithm, they determined that high-density RNA PolII and Spt5 binding—found in 2.3% of the genes—are the best predictors of AID specificity. In this issue of JEM, Álvarez-Prado et al. (https://doi.org/10.1084/jem.20171738) designed a DNA capture library allowing them to identify 275 genes targeted by AID in mouse germinal center B cells. Using the molecular features of these genes to feed a machine-learning algorithm, they determined that high-density RNA PolII and Spt5 binding—found in 2.3% of the genes—are the best predictors of AID specificity.
Collapse
Affiliation(s)
- Claude-Agnès Reynaud
- Institut Necker-Enfants Malades, INSERM U1151-CNRS UMR 8253, Faculté de Médecine Paris Descartes, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Jean-Claude Weill
- Institut Necker-Enfants Malades, INSERM U1151-CNRS UMR 8253, Faculté de Médecine Paris Descartes, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| |
Collapse
|
8
|
Tepper S, Jeschke J, Böttcher K, Schmidt A, Davari K, Müller P, Kremmer E, Hemmerich P, Pfeil I, Jungnickel B. PARP activation promotes nuclear AID accumulation in lymphoma cells. Oncotarget 2017; 7:13197-208. [PMID: 26921193 PMCID: PMC4914351 DOI: 10.18632/oncotarget.7603] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 01/12/2016] [Indexed: 12/20/2022] Open
Abstract
Activation-induced cytidine deaminase (AID) initiates immunoglobulin diversification in germinal center B cells by targeted introduction of DNA damage. As aberrant nuclear AID action contributes to the generation of B cell lymphoma, the protein's activity is tightly regulated, e.g. by nuclear/cytoplasmic shuttling and nuclear degradation. In the present study, we asked whether DNA damage may affect regulation of the AID protein. We show that exogenous DNA damage that mainly activates base excision repair leads to prevention of proteasomal degradation of AID and hence its nuclear accumulation. Inhibitor as well as knockout studies indicate that activation of poly (ADP-ribose) polymerase (PARP) by DNA damaging agents promotes both phenomena. These findings suggest that PARP inhibitors influence DNA damage dependent AID regulation, with interesting implications for the regulation of AID function and chemotherapy of lymphoma.
Collapse
Affiliation(s)
- Sandra Tepper
- Department of Cell Biology, Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine, Friedrich-Schiller University, 07745 Jena, Germany
| | - Julia Jeschke
- Department of Cell Biology, Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine, Friedrich-Schiller University, 07745 Jena, Germany.,Institute of Clinical and Molecular Biology, Helmholtz Center Munich, 81377 Munich, Germany
| | - Katrin Böttcher
- Department of Cell Biology, Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine, Friedrich-Schiller University, 07745 Jena, Germany
| | - Angelika Schmidt
- Department of Cell Biology, Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine, Friedrich-Schiller University, 07745 Jena, Germany
| | - Kathrin Davari
- Department of Cell Biology, Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine, Friedrich-Schiller University, 07745 Jena, Germany
| | - Peter Müller
- Department of Cell Biology, Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine, Friedrich-Schiller University, 07745 Jena, Germany
| | - Elisabeth Kremmer
- Institute of Molecular Immunology, Helmholtz Center Munich, 81377 Munich, Germany
| | - Peter Hemmerich
- Imaging Facility, Leibniz- Institute on Aging - Fritz Lipmann Institute, 07745 Jena, Germany
| | - Ines Pfeil
- Institute of Clinical and Molecular Biology, Helmholtz Center Munich, 81377 Munich, Germany
| | - Berit Jungnickel
- Department of Cell Biology, Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine, Friedrich-Schiller University, 07745 Jena, Germany.,Institute of Clinical and Molecular Biology, Helmholtz Center Munich, 81377 Munich, Germany
| |
Collapse
|
9
|
Gelmez MY, Coskunpinar E, Saracoglu B, Deniz G, Aktan M. Investigation of AID, Dicer, and Drosha Expressions in Patients with Chronic Lymphocytic Leukemia. Immunol Invest 2017; 46:433-446. [PMID: 28388279 DOI: 10.1080/08820139.2017.1288241] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Chronic lymphocytic leukemia (CLL) is the most common leukemia in Western countries. Cytogenetic lesions such as del13q14, del11q22.3, and del17p13 are identified in 50-60% of patients. Activation-induced cytidine deaminase (AID) plays a central role in somatic hyper mutation (SHM) and class switch recombination (CSR) and functions on Ig genes, but also target non-Ig genes, and over-expression of AID can lead to point mutations or translocations in non-Ig genes such as IgH/Myc translocation. Dicer and Drosha, which have a role in activation process of miRNA, also act in a double-strand DNA break (DSB) repair mechanism. In this study, whether the changes of AID, Dicer and Drosha expressions may be associated with both deletions and clinical outcomes in patients with CLL were investigated. AID expressions were increased in patients with CLL. However, cell lysate AID protein levels were only increased in patients with del17p or del11q who have poor prognosis. Decreased Dicer expressions were found in patients with deletion, whereas increased Drosha expressions were found in patients without deletion and with del13q. According to Rai and Binet staging systems, advanced-stage patients showed increased AID protein levels, decreased Dicer and Drosha expressions. Our findings may suggest that high AID expression and lower Dicer expression were observed in patients with CLL especially del17p and del11q and might associated with deletions such as del17p and del11q. AID, Dicer, and Drosha expressions might be used as an indicator of prognosis for CLL.
Collapse
Affiliation(s)
- Metin Yusuf Gelmez
- a Department of Immunology, Institute of Experimental Medicine (DETAE) , Istanbul University , Istanbul , Turkey
| | - Ender Coskunpinar
- b Division of Medical Genetic, Istanbul Faculty of Medicine , Istanbul University , Istanbul , Turkey
| | - Basak Saracoglu
- c Division of Hematology, Istanbul Faculty of Medicine , Istanbul University , Istanbul , Turkey
| | - Gunnur Deniz
- a Department of Immunology, Institute of Experimental Medicine (DETAE) , Istanbul University , Istanbul , Turkey
| | - Melih Aktan
- c Division of Hematology, Istanbul Faculty of Medicine , Istanbul University , Istanbul , Turkey
| |
Collapse
|
10
|
Chen J, MacCarthy T. The preferred nucleotide contexts of the AID/APOBEC cytidine deaminases have differential effects when mutating retrotransposon and virus sequences compared to host genes. PLoS Comput Biol 2017; 13:e1005471. [PMID: 28362825 PMCID: PMC5391955 DOI: 10.1371/journal.pcbi.1005471] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 04/14/2017] [Accepted: 03/21/2017] [Indexed: 12/22/2022] Open
Abstract
The AID / APOBEC genes are a family of cytidine deaminases that have evolved in vertebrates, and particularly mammals, to mutate RNA and DNA at distinct preferred nucleotide contexts (or “hotspots”) on foreign genomes such as viruses and retrotransposons. These enzymes play a pivotal role in intrinsic immunity defense mechanisms, often deleteriously mutating invading retroviruses or retrotransposons and, in the case of AID, changing antibody sequences to drive affinity maturation. We investigate the strength of various hotspots on their known biological targets by evaluating the potential impact of mutations on the DNA coding sequences of these targets, and compare these results to hypothetical hotspots that did not evolve. We find that the existing AID / APOBEC hotspots have a large impact on retrotransposons and non-mammalian viruses while having a much smaller effect on vital mammalian genes, suggesting co-evolution with AID / APOBECs may have had an impact on the genomes of the viruses we analyzed. We determine that GC content appears to be a significant, but not sole, factor in resistance to deaminase activity. We discuss possible mechanisms AID and APOBEC viral targets have adopted to escape the impacts of deamination activity, including changing the GC content of the genome. The APOBEC family of cytidine deaminases are important enzymes in most vertebrates. The ancestral member of this gene family is activation induced deaminase (AID), which mutates the Immunoglobulin loci in B Cells during antibody affinity maturation in jawed vertebrates. The APOBEC family has expanded particularly in the mammals and in primates, where they have evolved roles in restriction of viruses and retrotransposons. Biochemical studies have established that AID preferentially targets “hotspots” such as AGC and avoids “coldspots” such as CCC. Other APOBECs have evolved distinct hotspots. For example, APOBEC3G, which targets retroviruses including HIV, has evolved to target the motif CCC as a hotspot, but it is unclear why. Here we ask why the AID/APOBEC cytidine deaminases evolved their particular mutational hotspots. Our results show that a wide range of unrelated genes including mammalian LINE1 ORFs and non- mammalian (ancestral-like) viruses are highly susceptible to mutations in APOBEC hotspots and less susceptible to the hypothetical non-APOBEC hotspots. On the other hand, mammalian viruses tend to exhibit low susceptibility to the same APOBEC hotspots, suggesting these viruses have co-evolved to minimize potential damaging mutations, and that the native GC content plays a large role in this behavior.
Collapse
Affiliation(s)
- Jeffrey Chen
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Book, New York, United States of America
| | - Thomas MacCarthy
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Book, New York, United States of America
- * E-mail:
| |
Collapse
|
11
|
The metabolomic signature of hematologic malignancies. Leuk Res 2016; 49:22-35. [PMID: 27526405 DOI: 10.1016/j.leukres.2016.08.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Revised: 08/04/2016] [Accepted: 08/08/2016] [Indexed: 12/17/2022]
Abstract
The ongoing accumulation of knowledge raises hopes that understanding tumor metabolism will provide new ways for predicting, diagnosing, and even treating cancers. Some metabolic biomarkers are at present routinely utilized to diagnose cancer and metabolic alterations of tumors are being confirmed as therapeutic targets. The growing utilization of metabolomics in clinical research may rapidly turn it into one of the most potent instruments used to detect and fight tumor. In fact, while the current state and trends of high throughput metabolomics profiling focus on the purpose of discovering biomarkers and hunting for metabolic mechanism, a prospective direction, namely reprogramming metabolomics, highlights the way to use metabolomics approach for the aim of treatment of disease by way of reconstruction of disturbed metabolic pathways. In this review, we present an ample summary of the current clinical appliances of metabolomics in hematological malignancies.
Collapse
|
12
|
Abstract
Epstein-Barr virus (EBV) infection is a common feature of B cell lymphoproliferative disorders (LPDs), including diffuse large B cell lymphoma. Approximately 10 % of DLBCLs are EBV-positive, with the highest incidence in immunocompromised and elderly patients. Here, we review the clinical, genetic, and pathologic characteristics of DLBCL and discuss the molecular role of EBV in lymphoma tumorigenesis. Using EBV-positive DLBCL of the elderly as a model, we describe the key features of EBV-positive DLBCL. Studies of EBV-positive DLBCL of the elderly demonstrate that EBV-positive DLBCL has a distinct biology, related to both viral and host factors. The pathogenic mechanisms noted in EBV-positive DLBCL of the elderly, including enhanced NFκB activity, are likely to be a generalizable feature of EBV-positive DLBCL. Therefore, we review how this information might be used to target the EBV or its host response for the development of novel treatment strategies.
Collapse
|
13
|
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.
Collapse
|
14
|
Affiliation(s)
- Cristina Rada
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
- * E-mail:
| |
Collapse
|
15
|
Le Q, Maizels N. Cell Cycle Regulates Nuclear Stability of AID and Determines the Cellular Response to AID. PLoS Genet 2015; 11:e1005411. [PMID: 26355458 PMCID: PMC4565580 DOI: 10.1371/journal.pgen.1005411] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 07/02/2015] [Indexed: 12/12/2022] Open
Abstract
AID (Activation Induced Deaminase) deaminates cytosines in DNA to initiate immunoglobulin gene diversification and to reprogram CpG methylation in early development. AID is potentially highly mutagenic, and it causes genomic instability evident as translocations in B cell malignancies. Here we show that AID is cell cycle regulated. By high content screening microscopy, we demonstrate that AID undergoes nuclear degradation more slowly in G1 phase than in S or G2-M phase, and that mutations that affect regulatory phosphorylation or catalytic activity can alter AID stability and abundance. We directly test the role of cell cycle regulation by fusing AID to tags that destabilize nuclear protein outside of G1 or S-G2/M phases. We show that enforced nuclear localization of AID in G1 phase accelerates somatic hypermutation and class switch recombination, and is well-tolerated; while nuclear AID compromises viability in S-G2/M phase cells. We identify AID derivatives that accelerate somatic hypermutation with minimal impact on viability, which will be useful tools for engineering genes and proteins by iterative mutagenesis and selection. Our results further suggest that use of cell cycle tags to regulate nuclear stability may be generally applicable to studying DNA repair and to engineering the genome.
Collapse
Affiliation(s)
- Quy Le
- Molecular and Cellular Biology Graduate Program, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Nancy Maizels
- Molecular and Cellular Biology Graduate Program, University of Washington School of Medicine, Seattle, Washington, United States of America
- Departments of Immunology, Biochemistry and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
- * E-mail:
| |
Collapse
|
16
|
Montamat-Sicotte D, Liztler LC, Abreu C, Safavi S, Zahn A, Orthwein A, Muschen M, Oppezzo P, Muñoz DP, Di Noia JM. HSP90 inhibitors decrease AID levels and activity in mice and in human cells. Eur J Immunol 2015; 45:2365-76. [PMID: 25912253 PMCID: PMC4536124 DOI: 10.1002/eji.201545462] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 03/26/2015] [Accepted: 04/25/2015] [Indexed: 01/25/2023]
Abstract
Activation induced deaminase (AID) initiates somatic hypermutation and class switch recombination of the Ig genes in antigen-activated B cells, underpinning antibody affinity maturation and isotype switching. AID can also be pathogenic by contributing to autoimmune diseases and oncogenic mutations. Moreover, AID can exert noncanonical functions when aberrantly expressed in epithelial cells. The lack of specific inhibitors prevents therapeutic applications to modulate AID functions. Here, we have exploited our previous finding that the HSP90 molecular chaperoning pathway stabilizes AID in B cells, to test whether HSP90 inhibitors could target AID in vivo. We demonstrate that chronic administration of HSP90 inhibitors decreases AID protein levels and isotype switching in immunized mice. HSP90 inhibitors also reduce disease severity in a mouse model of acute B-cell lymphoblastic leukemia in which AID accelerates disease progression. We further show that human AID protein levels are sensitive to HSP90 inhibition in normal and leukemic B cells, and that HSP90 inhibition prevents AID-dependent epithelial to mesenchymal transition in a human breast cancer cell line in vitro. Thus, we provide proof-of-concept that HSP90 inhibitors indirectly target AID in vivo and that endogenous human AID is widely sensitive to them, which could have therapeutic applications.
Collapse
Affiliation(s)
| | - Ludivine C Liztler
- Institut de Recherches Cliniques de Montréal, Montréal, Canada
- Department of Biochemistry, Université de Montréal, Montréal, QC, Canada
| | - Cecilia Abreu
- Research Laboratory on Chronic Lymphocytic Leukemia, Instituto Pasteur de Montevideo, Montevideo, Uruguay
| | - Shiva Safavi
- Institut de Recherches Cliniques de Montréal, Montréal, Canada
- Department of Medicine, McGill University, Montréal, QC, Canada
| | - Astrid Zahn
- Institut de Recherches Cliniques de Montréal, Montréal, Canada
| | | | - Markus Muschen
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco,USA
| | - Pablo Oppezzo
- Research Laboratory on Chronic Lymphocytic Leukemia, Instituto Pasteur de Montevideo, Montevideo, Uruguay
| | - Denise P Muñoz
- UCSF Benioff Children’s Hospital and Research Institute at Oakland, Oakland, USA
| | - Javier M Di Noia
- Institut de Recherches Cliniques de Montréal, Montréal, Canada
- Department of Biochemistry, Université de Montréal, Montréal, QC, Canada
- Department of Medicine, McGill University, Montréal, QC, Canada
- Department of Medicine, Université de Montréal, Montréal, Canada
| |
Collapse
|
17
|
Saier MH, Zhang Z. Control of Transposon-Mediated Directed Mutation by the Escherichia coli Phosphoenolpyruvate:Sugar Phosphotransferase System. J Mol Microbiol Biotechnol 2015; 25:226-33. [PMID: 26159081 DOI: 10.1159/000375375] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The phosphoenolpyruvate:sugar phosphotransferase system (PTS) has been shown to control transport, cell metabolism and gene expression. We here present results supporting the novel suggestion that in certain instances it also regulates the mutation rate. Directed mutations are defined as mutations that occur at higher frequencies when beneficial than when neutral or detrimental. To date, the occurrence of directed point mutations has not been documented and confirmed, but a few examples of transposon-mediated directed mutations have been reported. Here we focus on the first and best-studied example of directed mutation, which involves the regulation of insertion sequence-5 hopping into a specific site upstream of the glpFK glycerol utilization operon in Escherichia coli. This insertional event specifically activates expression of the glpFK operon, allowing the growth of wild-type cells with glycerol as a carbon source in the presence of nonmetabolizable glucose analogues which normally block glycerol utilization. The sugar-transporting PTS controls this process by regulating levels of cytoplasmic glycerol-3-phosphate and cyclic (c)AMP as established in previous publications. Direct involvement of the glycerol repressor, GlpR, and the cAMP receptor protein, Crp, in the regulation of transposon-mediated directed mutation has been demonstrated.
Collapse
Affiliation(s)
- Milton H Saier
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, Calif., USA
| | | |
Collapse
|
18
|
Parp3 negatively regulates immunoglobulin class switch recombination. PLoS Genet 2015; 11:e1005240. [PMID: 26000965 PMCID: PMC4441492 DOI: 10.1371/journal.pgen.1005240] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 04/26/2015] [Indexed: 12/11/2022] Open
Abstract
To generate highly specific and adapted immune responses, B cells diversify their antibody repertoire through mechanisms involving the generation of programmed DNA damage. Somatic hypermutation (SHM) and class switch recombination (CSR) are initiated by the recruitment of activation-induced cytidine deaminase (AID) to immunoglobulin loci and by the subsequent generation of DNA lesions, which are differentially processed to mutations during SHM or to double-stranded DNA break intermediates during CSR. The latter activate the DNA damage response and mobilize multiple DNA repair factors, including Parp1 and Parp2, to promote DNA repair and long-range recombination. We examined the contribution of Parp3 in CSR and SHM. We find that deficiency in Parp3 results in enhanced CSR, while SHM remains unaffected. Mechanistically, this is due to increased occupancy of AID at the donor (Sμ) switch region. We also find evidence of increased levels of DNA damage at switch region junctions and a bias towards alternative end joining in the absence of Parp3. We propose that Parp3 plays a CSR-specific role by controlling AID levels at switch regions during CSR. During infections, B cells diversify the antibodies they produce by two mechanisms: somatic hypermutation (SHM) and class switch recombination (CSR). SHM mutates the regions encoding the antigen-binding site, generating high-affinity antibodies. CSR allows B cells to switch the class of antibody they produce (from IgM to IgA, IgG or IgE), providing novel effector functions. Together, SHM and CSR establish highly specific and pathogen-adapted antibody responses. SHM and CSR are initiated by the recruitment of the activation-induced cytidine deaminase (AID) enzyme to antibody genes. Once recruited, AID induces DNA lesions that are processed into mutations during SHM or chromosomal DNA breaks during CSR. These breaks activate multiple DNA repair proteins and are resolved by replacing the IgM gene segments by those encoding IgA, IgG or IgE. AID carries a significant oncogenic potential that needs to be controlled to preserve genome integrity. Nevertheless, the underlying mechanisms remain poorly understood. Here we show that Poly(ADP)ribose polymerase 3 (Parp3), an enzyme recently implicated in DNA repair, contributes to antibody diversification by negatively regulating CSR without affecting SHM. We show that Parp3 facilitates the repair of AID-induced DNA damage and controls AID levels on chromatin. We propose that Parp3 protects antibody genes from sustained AID-dependent DNA damage.
Collapse
|
19
|
Methot SP, Litzler LC, Trajtenberg F, Zahn A, Robert F, Pelletier J, Buschiazzo A, Magor BG, Di Noia JM. Consecutive interactions with HSP90 and eEF1A underlie a functional maturation and storage pathway of AID in the cytoplasm. ACTA ACUST UNITED AC 2015; 212:581-96. [PMID: 25824822 PMCID: PMC4387293 DOI: 10.1084/jem.20141157] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 03/03/2015] [Indexed: 11/13/2022]
Abstract
Methot et al. identify a mechanism for cytoplasmic retention of activation-induced deaminase (AID) in cells. Interactions of AID with Hsp90 and eEF1A proteins, both of which stabilize AID, promote sequential folding and retention of functional AID in the cytoplasm. Inhibition of the translation elongation factor eEF1A blocks its interaction with AID, which then accumulates in the nucleus, increasing class switch recombination and the generation of chromosomal translocation byproducts. Activation-induced deaminase (AID) initiates mutagenic pathways to diversify the antibody genes during immune responses. The access of AID to the nucleus is limited by CRM1-mediated nuclear export and by an uncharacterized mechanism of cytoplasmic retention. Here, we define a conformational motif in AID that dictates its cytoplasmic retention and demonstrate that the translation elongation factor eukaryotic elongation factor 1 α (eEF1A) is necessary for AID cytoplasmic sequestering. The mechanism is independent of protein synthesis but dependent on a tRNA-free form of eEF1A. Inhibiting eEF1A prevents the interaction with AID, which accumulates in the nucleus and increases class switch recombination as well as chromosomal translocation byproducts. Most AID is associated to unspecified cytoplasmic complexes. We find that the interactions of AID with eEF1A and heat-shock protein 90 kD (HSP90) are inversely correlated. Despite both interactions stabilizing AID, the nature of the AID fractions associated with HSP90 or eEF1A are different, defining two complexes that sequentially produce and store functional AID in the cytoplasm. In addition, nuclear export and cytoplasmic retention cooperate to exclude AID from the nucleus but might not be functionally equivalent. Our results elucidate the molecular basis of AID cytoplasmic retention, define its functional relevance and distinguish it from other mechanisms regulating AID.
Collapse
Affiliation(s)
- Stephen P Methot
- Institut de Recherches Cliniques de Montréal, Montréal, Québec H2W 1R7, Canada Department of Medicine, Department of Biochemistry, The Rosalind and Morris Goodman Cancer Research Center, and Department of Oncology, McGill University, Montréal, Québec H3A 0G4, Canada
| | - Ludivine C Litzler
- Institut de Recherches Cliniques de Montréal, Montréal, Québec H2W 1R7, Canada Department of Biochemistry and Department of Medicine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Felipe Trajtenberg
- Unit of Protein Crystallography, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
| | - Astrid Zahn
- Institut de Recherches Cliniques de Montréal, Montréal, Québec H2W 1R7, Canada
| | - Francis Robert
- Department of Medicine, Department of Biochemistry, The Rosalind and Morris Goodman Cancer Research Center, and Department of Oncology, McGill University, Montréal, Québec H3A 0G4, Canada
| | - Jerry Pelletier
- Department of Medicine, Department of Biochemistry, The Rosalind and Morris Goodman Cancer Research Center, and Department of Oncology, McGill University, Montréal, Québec H3A 0G4, Canada Department of Medicine, Department of Biochemistry, The Rosalind and Morris Goodman Cancer Research Center, and Department of Oncology, McGill University, Montréal, Québec H3A 0G4, Canada Department of Medicine, Department of Biochemistry, The Rosalind and Morris Goodman Cancer Research Center, and Department of Oncology, McGill University, Montréal, Québec H3A 0G4, Canada
| | - Alejandro Buschiazzo
- Unit of Protein Crystallography, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay Department of Structural Biology and Chemistry, Institut Pasteur, 75015 Paris, France
| | - Brad G Magor
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Javier M Di Noia
- Institut de Recherches Cliniques de Montréal, Montréal, Québec H2W 1R7, Canada Department of Medicine, Department of Biochemistry, The Rosalind and Morris Goodman Cancer Research Center, and Department of Oncology, McGill University, Montréal, Québec H3A 0G4, Canada Department of Biochemistry and Department of Medicine, Université de Montréal, Montréal, Québec H3T 1J4, Canada Department of Biochemistry and Department of Medicine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| |
Collapse
|
20
|
Overlapping hotspots in CDRs are critical sites for V region diversification. Proc Natl Acad Sci U S A 2015; 112:E728-37. [PMID: 25646473 DOI: 10.1073/pnas.1500788112] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Activation-induced deaminase (AID) mediates the somatic hypermutation (SHM) of Ig variable (V) regions that is required for the affinity maturation of the antibody response. An intensive analysis of a published database of somatic hypermutations that arose in the IGHV3-23*01 human V region expressed in vivo by human memory B cells revealed that the focus of mutations in complementary determining region (CDR)1 and CDR2 coincided with a combination of overlapping AGCT hotspots, the absence of AID cold spots, and an abundance of polymerase eta hotspots. If the overlapping hotspots in the CDR1 or CDR2 did not undergo mutation, the frequency of mutations throughout the V region was reduced. To model this result, we examined the mutation of the human IGHV3-23*01 biochemically and in the endogenous heavy chain locus of Ramos B cells. Deep sequencing revealed that IGHV3-23*01 in Ramos cells accumulates AID-induced mutations primarily in the AGCT in CDR2, which was also the most frequent site of mutation in vivo. Replacing the overlapping hotspots in CDR1 and CDR2 with neutral or cold motifs resulted in a reduction in mutations within the modified motifs and, to some degree, throughout the V region. In addition, some of the overlapping hotspots in the CDRs were at sites in which replacement mutations could change the structure of the CDR loops. Our analysis suggests that the local sequence environment of the V region, and especially of the CDR1 and CDR2, is highly evolved to recruit mutations to key residues in the CDRs of the IgV region.
Collapse
|
21
|
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.
Collapse
|
22
|
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.
Collapse
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
| |
Collapse
|
23
|
Villota-Herdoiza D, Pila EA, Quiniou S, Waldbieser GC, Magor BG. Transcriptional regulation of teleost Aicda genes. Part 1 - suppressors of promiscuous promoters. FISH & SHELLFISH IMMUNOLOGY 2013; 35:1981-1987. [PMID: 24161771 DOI: 10.1016/j.fsi.2013.09.035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 09/30/2013] [Accepted: 09/30/2013] [Indexed: 06/02/2023]
Abstract
In order to better understand antibody affinity maturation in fishes we sought to identify gene regulatory elements that could drive expression of activated B-cell specific fluorescent reporter transgenes in zebrafish. Specifically the promoter and several non-coding regions of the channel catfish (Ictalurus punctatus) and zebrafish (Danio rerio) were tested for transcriptional activity using a dual luciferase reporter system in transfected fish leukocytes and two mammalian cell lines that constitutively express Aicda (activation-induced cytidine deaminase). The promoters of both fish Aicda genes were as transcriptionally active as an SV40 promoter control in all cell lines tested, regardless of the cells ability to express Aicda. Coupling of a putative intron 1 enhancer or a region 10 kb upstream of the zebrafish promoter effectively silenced transcription from the fish Aicda promoter. Paradoxically these suppressor elements enhanced transcription when they were coupled to the mouse Aicda intron 1 enhancer. The results are considered in context of similar observations for Aicda transcriptional regulation in mice and in light of recent evidence that Aicda is utilized for epigenetic reprogramming of several non-lymphoid cell types.
Collapse
Affiliation(s)
- Daniela Villota-Herdoiza
- Dept. of Biological Sciences, University of Alberta, CW405 BioSci Bldg., Edmonton, AB T6G-2E5, Canada.
| | | | | | | | | |
Collapse
|
24
|
Shivarov V, Dimitrova P, Vassilev T. Complex downstream effects of nuclear export inhibition in B-cell lymphomas: a possible role for activation-induced cytidine deaminase (AID). Haematologica 2013; 98:e111-3. [PMID: 24006409 DOI: 10.3324/haematol.2013.094540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
|
25
|
Activation-induced cytidine deaminase (AID) is necessary for the epithelial-mesenchymal transition in mammary epithelial cells. Proc Natl Acad Sci U S A 2013; 110:E2977-86. [PMID: 23882083 DOI: 10.1073/pnas.1301021110] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Activation-induced cytidine deaminase (AID), which functions in antibody diversification, is also expressed in a variety of germ and somatic cells. Evidence that AID promotes DNA demethylation in epigenetic reprogramming phenomena, and that it is induced by inflammatory signals, led us to investigate its role in the epithelial-mesenchymal transition (EMT), a critical process in normal morphogenesis and tumor metastasis. We find that expression of AID is induced by inflammatory signals that induce the EMT in nontransformed mammary epithelial cells and in ZR75.1 breast cancer cells. shRNA-mediated knockdown of AID blocks induction of the EMT and prevents cells from acquiring invasive properties. Knockdown of AID suppresses expression of several key EMT transcriptional regulators and is associated with increased methylation of CpG islands proximal to the promoters of these genes; furthermore, the DNA demethylating agent 5 aza-2'deoxycytidine (5-Aza-dC) antagonizes the effects of AID knockdown on the expression of EMT factors. We conclude that AID is necessary for the EMT in this breast cancer cell model and in nontransformed mammary epithelial cells. Our results suggest that AID may act near the apex of a hierarchy of regulatory steps that drive the EMT, and are consistent with this effect being mediated by cytosine demethylation. This evidence links our findings to other reports of a role for AID in epigenetic reprogramming and control of gene expression.
Collapse
|
26
|
Abstract
Chemical modifications to the DNA and histone protein components of chromatin can modulate gene expression and genome stability. Understanding the physiological impact of changes in chromatin structure remains an important question in biology. As one example, in order to generate antibody diversity with somatic hypermutation and class switch recombination, chromatin must be made accessible for activation-induced cytidine deaminase (AID)-mediated deamination of cytosines in DNA. These lesions are recognized and removed by various DNA repair pathways but, if not handled properly, can lead to formation of oncogenic chromosomal translocations. In this review, we focus the discussion on how chromatin-modifying activities and -binding proteins contribute to the native chromatin environment in which AID-induced DNA damage is targeted and repaired. Outstanding questions remain regarding the direct roles of histone posttranslational modifications and the significance of AID function outside of antibody diversity.
Collapse
Affiliation(s)
- Jeremy A. Daniel
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, 2200 Copenhagen N, Denmark
| | | |
Collapse
|
27
|
Sun J, Rothschild G, Pefanis E, Basu U. Transcriptional stalling in B-lymphocytes: a mechanism for antibody diversification and maintenance of genomic integrity. Transcription 2013; 4:127-35. [PMID: 23584095 PMCID: PMC4042586 DOI: 10.4161/trns.24556] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
B cells utilize three DNA alteration strategies-V(D)J recombination, somatic hypermutation (SHM) and class switch recombination (CSR)-to somatically mutate their genome, thereby expressing a plethora of antibodies tailor-made against the innumerable antigens they encounter while in circulation. Of these three events, the single-strand DNA cytidine deaminase, Activation Induced cytidine Deaminase (AID), is responsible for SHM and CSR. Recent advances, discussed in this review article, point toward various components of RNA polymerase II "stalling" machinery as regulators of AID activity during antibody diversification and maintenance of B cell genome integrity.
Collapse
Affiliation(s)
- Jianbo Sun
- Department of Microbiology and Immunology; College of Physicians and Surgeons; Columbia University; New York, NY USA
| | | | | | | |
Collapse
|
28
|
Incorvaia E, Sicouri L, Petersen-Mahrt SK, Schmitz KM. Hormones and AID: Balancing immunity and autoimmunity. Autoimmunity 2013. [DOI: 10.3109/08916934.2012.748752] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
|
29
|
Abstract
The mechanisms by which B cells somatically engineer their genomes to generate the vast diversity of antibodies required to challenge the nearly infinite number of antigens that immune systems encounter are of tremendous clinical and academic interest. The DNA cytidine deaminase activation-induced deaminase (AID) catalyzes two of these mechanisms: class switch recombination (CSR) and somatic hypermutation (SHM). Recent discoveries indicate a significant promiscuous targeting of this B-cell mutator enzyme genome-wide. Here we discuss the various regulatory elements that control AID activity and prevent AID from inducing genomic instability and thereby initiating oncogenesis.
Collapse
Affiliation(s)
- Celia Keim
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, New York 10032, USA
| | - David Kazadi
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, New York 10032, USA
| | - Gerson Rothschild
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, New York 10032, USA
| | - Uttiya Basu
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, New York 10032, USA
| |
Collapse
|