1
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Lauring MC, Basu U. Somatic hypermutation mechanisms during lymphomagenesis and transformation. Curr Opin Genet Dev 2024; 85:102165. [PMID: 38428317 DOI: 10.1016/j.gde.2024.102165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 01/31/2024] [Accepted: 02/02/2024] [Indexed: 03/03/2024]
Abstract
B cells undergoing physiologically programmed or aberrant genomic alterations provide an opportune system to study the causes and consequences of genome mutagenesis. Activated B cells in germinal centers express activation-induced cytidine deaminase (AID) to accomplish physiological somatic hypermutation (SHM) of their antibody-encoding genes. In attempting to diversify their immunoglobulin (Ig) heavy- and light-chain genes, several B-cell clones successfully optimize their antigen-binding affinities. However, SHM can sometimes occur at non-Ig loci, causing genetic alternations that lay the foundation for lymphomagenesis, particularly diffuse large B-cell lymphoma. Thus, SHM acts as a double-edged sword, bestowing superb humoral immunity at the potential risk of initiating disease. We refer to off-target, non-Ig AID mutations - that are often but not always associated with disease - as aberrant SHM (aSHM). A key challenge in understanding SHM and aSHM is determining how AID targets and mutates specific DNA sequences in the Ig loci to generate antibody diversity and non-Ig genes to initiate lymphomagenesis. Herein, we discuss some current advances regarding the regulation of AID's DNA mutagenesis activity in B cells.
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Affiliation(s)
- Max C Lauring
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York 10032, USA.
| | - Uttiya Basu
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York 10032, USA.
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2
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Liu D, Goodman MF, Pham P, Yu K, Hsieh CL, Lieber MR. The mRNA tether model for activation-induced deaminase and its relevance for Ig somatic hypermutation and class switch recombination. DNA Repair (Amst) 2022; 110:103271. [PMID: 34990960 PMCID: PMC8816865 DOI: 10.1016/j.dnarep.2021.103271] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/19/2021] [Accepted: 12/28/2021] [Indexed: 02/03/2023]
Abstract
Activation-induced deaminase (AID) only deaminates cytosine within single-stranded DNA. Transcription is known to increase AID deamination on duplex DNA substrates during transcription. Using a purified T7 RNA polymerase transcription system, we recently found that AID deamination of a duplex DNA substrate is reduced if RNase A is added during transcription. This finding prompted us to consider that the mRNA tail may contribute to AID action at the nearby transcribed strand (TS) or non-transcribed strand (NTS) of DNA, which are transiently single-stranded in the wake of RNA polymerase movement. Here, we used a purified system to test whether a single-stranded oligonucleotide (oligo) consisting of RNA in the 5' portion and DNA in the 3' portion (i.e., 5'RNA-DNA3', also termed an RNA-DNA fusion substrate) could be deaminated equally efficiently as the same sequence when it is entirely DNA. We found that AID acts on the RNA-DNA fusion substrate and the DNA-only substrate with similar efficiency. Based on this finding and our recent observation on the importance of the mRNA tail, we propose a model in which the proximity and length of the mRNA tail provide a critical site for AID loading to permit a high local collision frequency with the NTS and TS in the transient wake of the RNA polymerase. When the mRNA tail is not present, we know that AID action drops to levels equivalent to when there is no transcription at all. This mRNA tether model explains several local and global features of Ig somatic hypermutation and Ig class switch recombination, while integrating structural and functional features of AID.
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Affiliation(s)
- Di Liu
- Departments of Pathology, Biochemistry & Molecular Biology, and Molecular Microbiology & Immunology, and the Section of Molecular & Computational Biology in the Department of Biological Sciences, Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, CA 90033
| | - Myron F. Goodman
- Department of Biological Sciences (Section of Molecular & Computational Biology), University of Southern California, Los Angeles, CA 90089
| | - Phuong Pham
- Department of Biological Sciences (Section of Molecular & Computational Biology), University of Southern California, Los Angeles, CA 90089
| | - Kefei Yu
- Microbiology and Molecular Genetics, Michigan State University, 5175 Biomedical Physical Sciences, East Lansing, MI 48824
| | - Chih-Lin Hsieh
- USC Norris Comprehensive Cancer Center, Department of Urology, University of Southern California and USC Keck School of Medicine, Los Angeles, CA 90033
| | - Michael R. Lieber
- Departments of Pathology, Biochemistry & Molecular Biology, and Molecular Microbiology & Immunology, and the Section of Molecular & Computational Biology in the Department of Biological Sciences, Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, CA 90033,Corresponding author: M. Lieber, , ph. 323 865 0568
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3
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A Bayesian model based computational analysis of the relationship between bisulfite accessible single-stranded DNA in chromatin and somatic hypermutation of immunoglobulin genes. PLoS Comput Biol 2021; 17:e1009323. [PMID: 34491985 PMCID: PMC8462741 DOI: 10.1371/journal.pcbi.1009323] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 09/24/2021] [Accepted: 08/04/2021] [Indexed: 11/19/2022] Open
Abstract
The B cells in our body generate protective antibodies by introducing somatic hypermutations (SHM) into the variable region of immunoglobulin genes (IgVs). The mutations are generated by activation induced deaminase (AID) that converts cytosine to uracil in single stranded DNA (ssDNA) generated during transcription. Attempts have been made to correlate SHM with ssDNA using bisulfite to chemically convert cytosines that are accessible in the intact chromatin of mutating B cells. These studies have been complicated by using different definitions of "bisulfite accessible regions" (BARs). Recently, deep-sequencing has provided much larger datasets of such regions but computational methods are needed to enable this analysis. Here we leveraged the deep-sequencing approach with unique molecular identifiers and developed a novel Hidden Markov Model based Bayesian Segmentation algorithm to characterize the ssDNA regions in the IGHV4-34 gene of the human Ramos B cell line. Combining hierarchical clustering and our new Bayesian model, we identified recurrent BARs in certain subregions of both top and bottom strands of this gene. Using this new system, the average size of BARs is about 15 bp. We also identified potential G-quadruplex DNA structures in this gene and found that the BARs co-locate with G-quadruplex structures in the opposite strand. Using various correlation analyses, there is not a direct site-to-site relationship between the bisulfite accessible ssDNA and all sites of SHM but most of the highly AID mutated sites are within 15 bp of a BAR. In summary, we developed a novel platform to study single stranded DNA in chromatin at a base pair resolution that reveals potential relationships among BARs, SHM and G-quadruplexes. This platform could be applied to genome wide studies in the future.
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Role of Dot1L and H3K79 methylation in regulating somatic hypermutation of immunoglobulin genes. Proc Natl Acad Sci U S A 2021; 118:2104013118. [PMID: 34253616 DOI: 10.1073/pnas.2104013118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Somatic hypermutation (SHM) and class-switch recombination (CSR) of the immunoglobulin (Ig) genes allow B cells to make antibodies that protect us against a wide variety of pathogens. SHM is mediated by activation-induced deaminase (AID), occurs at a million times higher frequency than other mutations in the mammalian genome, and is largely restricted to the variable (V) and switch (S) regions of Ig genes. Using the Ramos human Burkitt's lymphoma cell line, we find that H3K79me2/3 and its methyltransferase Dot1L are more abundant on the V region than on the constant (C) region, which does not undergo mutation. In primary naïve mouse B cells examined ex vivo, the H3K79me2/3 modification appears constitutively in the donor Sμ and is inducible in the recipient Sγ1 upon CSR stimulation. Knockout and inhibition of Dot1L in Ramos cells significantly reduces V region mutation and the abundance of H3K79me2/3 on the V region and is associated with a decrease of polymerase II (Pol II) and its S2 phosphorylated form at the IgH locus. Knockout of Dot1L also decreases the abundance of BRD4 and CDK9 (a subunit of the P-TEFb complex) on the V region, and this is accompanied by decreased nascent transcripts throughout the IgH gene. Treatment with JQ1 (inhibitor of BRD4) or DRB (inhibitor of CDK9) decreases SHM and the abundance of Pol II S2P at the IgH locus. Since all these factors play a role in transcription elongation, our studies reinforce the idea that the chromatin context and dynamics of transcription are critical for SHM.
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Kasprzyk ME, Sura W, Dzikiewicz-Krawczyk A. Enhancing B-Cell Malignancies-On Repurposing Enhancer Activity towards Cancer. Cancers (Basel) 2021; 13:3270. [PMID: 34210001 PMCID: PMC8269369 DOI: 10.3390/cancers13133270] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/24/2021] [Accepted: 06/28/2021] [Indexed: 01/19/2023] Open
Abstract
B-cell lymphomas and leukemias derive from B cells at various stages of maturation and are the 6th most common cancer-related cause of death. While the role of several oncogenes and tumor suppressors in the pathogenesis of B-cell neoplasms was established, recent research indicated the involvement of non-coding, regulatory sequences. Enhancers are DNA elements controlling gene expression in a cell type- and developmental stage-specific manner. They ensure proper differentiation and maturation of B cells, resulting in production of high affinity antibodies. However, the activity of enhancers can be redirected, setting B cells on the path towards cancer. In this review we discuss different mechanisms through which enhancers are exploited in malignant B cells, from the well-studied translocations juxtaposing oncogenes to immunoglobulin loci, through enhancer dysregulation by sequence variants and mutations, to enhancer hijacking by viruses. We also highlight the potential of therapeutic targeting of enhancers as a direction for future investigation.
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6
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Català-Moll F, Ferreté-Bonastre AG, Li T, Weichenhan D, Lutsik P, Ciudad L, Álvarez-Prado ÁF, Rodríguez-Ubreva J, Klemann C, Speckmann C, Vilas-Zornoza A, Abolhassani H, Martínez-Gallo M, Dieli-Crimi R, Rivière JG, Martín-Nalda A, Colobran R, Soler-Palacín P, Kracker S, Hammarström L, Prosper F, Durandy A, Grimbacher B, Plass C, Ballestar E. Activation-induced deaminase is critical for the establishment of DNA methylation patterns prior to the germinal center reaction. Nucleic Acids Res 2021; 49:5057-5073. [PMID: 33950194 PMCID: PMC8136777 DOI: 10.1093/nar/gkab322] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 04/15/2021] [Accepted: 04/19/2021] [Indexed: 12/31/2022] Open
Abstract
Activation-induced deaminase (AID) initiates antibody diversification in germinal center B cells by deaminating cytosines, leading to somatic hypermutation and class-switch recombination. Loss-of-function mutations in AID lead to hyper-IgM syndrome type 2 (HIGM2), a rare human primary antibody deficiency. AID-mediated deamination has been proposed as leading to active demethylation of 5-methycytosines in the DNA, although evidence both supports and casts doubt on such a role. In this study, using whole-genome bisulfite sequencing of HIGM2 B cells, we investigated direct AID involvement in active DNA demethylation. HIGM2 naïve and memory B cells both display widespread DNA methylation alterations, of which ∼25% are attributable to active DNA demethylation. For genes that undergo active demethylation that is impaired in HIGM2 individuals, our analysis indicates that AID is not directly involved. We demonstrate that the widespread alterations in the DNA methylation and expression profiles of HIGM2 naïve B cells result from premature overstimulation of the B-cell receptor prior to the germinal center reaction. Our data support a role for AID in B cell central tolerance in preventing the expansion of autoreactive cell clones, affecting the correct establishment of DNA methylation patterns.
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Affiliation(s)
- Francesc Català-Moll
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Barcelona, Spain
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L’Hospitalet de Llobregat, Barcelona, Spain
| | - Anna G Ferreté-Bonastre
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Barcelona, Spain
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L’Hospitalet de Llobregat, Barcelona, Spain
| | - Tianlu Li
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Barcelona, Spain
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L’Hospitalet de Llobregat, Barcelona, Spain
| | - Dieter Weichenhan
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Pavlo Lutsik
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Laura Ciudad
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Barcelona, Spain
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L’Hospitalet de Llobregat, Barcelona, Spain
| | - Ángel F Álvarez-Prado
- B Cell Biology Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Javier Rodríguez-Ubreva
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Barcelona, Spain
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L’Hospitalet de Llobregat, Barcelona, Spain
| | - Christian Klemann
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center, Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
| | - Carsten Speckmann
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center, Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
- Faculty of Medicine, Center for Pediatrics and Adolescent Medicine, Medical Center, University of Freiburg, Germany
| | - Amaya Vilas-Zornoza
- Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain
| | - Hassan Abolhassani
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, SE 14186 Stockholm , Sweden
| | - Mónica Martínez-Gallo
- Immunology Division, Hospital Universitari Vall d’Hebron and Diagnostic Immunology Research Group, Vall d’Hebron Research Institute (VHIR), Barcelona, Spain
| | - Romina Dieli-Crimi
- Immunology Division, Hospital Universitari Vall d’Hebron and Diagnostic Immunology Research Group, Vall d’Hebron Research Institute (VHIR), Barcelona, Spain
| | - Jacques G Rivière
- Pediatric Infectious Diseases & Immunodeficiencies Unit, Hospital Universitari Vall d’Hebron, Vall d’Hebron Research Institute (VHIR), Autonomous University of Barcelona, Barcelona, Spain
- Infection in Immunocompromised Pediatric Patients Research Group, Vall d’Hebron Institut de Recerca (VHIR), Hospital Universitari Vall d’Hebron, 08035 Barcelona, Spain
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Spain
| | - Andrea Martín-Nalda
- Pediatric Infectious Diseases & Immunodeficiencies Unit, Hospital Universitari Vall d’Hebron, Vall d’Hebron Research Institute (VHIR), Autonomous University of Barcelona, Barcelona, Spain
- Infection in Immunocompromised Pediatric Patients Research Group, Vall d’Hebron Institut de Recerca (VHIR), Hospital Universitari Vall d’Hebron, 08035 Barcelona, Spain
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Spain
| | - Roger Colobran
- Immunology Division, Hospital Universitari Vall d’Hebron and Diagnostic Immunology Research Group, Vall d’Hebron Research Institute (VHIR), Barcelona, Spain
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Spain
- Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona (UAB), Bellaterra, Catalonia, Spain
| | - Pere Soler-Palacín
- Pediatric Infectious Diseases & Immunodeficiencies Unit, Hospital Universitari Vall d’Hebron, Vall d’Hebron Research Institute (VHIR), Autonomous University of Barcelona, Barcelona, Spain
- Infection in Immunocompromised Pediatric Patients Research Group, Vall d’Hebron Institut de Recerca (VHIR), Hospital Universitari Vall d’Hebron, 08035 Barcelona, Spain
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Spain
| | - Sven Kracker
- Laboratory of Human Lymphohematopoiesis, Imagine Institute, INSERM UMR 1163, Université de Paris, Paris, France
| | - Lennart Hammarström
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, SE 14186 Stockholm , Sweden
| | - Felipe Prosper
- Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain
| | - Anne Durandy
- Laboratory of Human Lymphohematopoiesis, Imagine Institute, INSERM UMR 1163, Université de Paris, Paris, France
| | - Bodo Grimbacher
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center, Faculty of Medicine, University of Freiburg, 79110 Freiburg, Germany
- German Center for Infection Research (DZIF), Satellite Center Freiburg, Germany
- Centre for Integrative Biological Signalling Studies (CIBSS), Albert-Ludwigs University, Freiburg, Germany
- RESIST, Cluster of Excellence 2155 to Hanover Medical School, Satellite Center Freiburg, Germany
- Institute of Immunity & Transplantation, Royal Free Hospital, University College London, UK
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Barcelona, Spain
- Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L’Hospitalet de Llobregat, Barcelona, Spain
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7
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Kennedy DE, Clark MR. Compartments and Connections Within the Germinal Center. Front Immunol 2021; 12:659151. [PMID: 33868306 PMCID: PMC8045557 DOI: 10.3389/fimmu.2021.659151] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/15/2021] [Indexed: 11/13/2022] Open
Abstract
Protective high affinity antibody responses emerge through an orchestrated developmental process that occurs in germinal centers (GCs). While GCs have been appreciated since 1930, a wealth of recent progress provides new insights into the molecular and cellular dynamics governing humoral immunity. In this review, we highlight advances that demonstrate that fundamental GC B cell function, selection, proliferation and SHM occur within distinct cell states. The resulting new model provides new opportunities to understand the evolution of immunity in infectious, autoimmune and neoplastic diseases.
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Affiliation(s)
| | - Marcus R. Clark
- Gwen Knapp Center for Lupus and Immunology Research, Section of Rheumatology, Department of Medicine, University of Chicago, Chicago, IL, United States
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8
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Support of BCP-ALL-cells by autologous bone marrow Th-cells involves induction of AID expression but not widespread AID off-target mutagenesis. Cancer Immunol Immunother 2021; 70:2275-2289. [PMID: 33507341 PMCID: PMC8289808 DOI: 10.1007/s00262-020-02835-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 12/17/2020] [Indexed: 12/22/2022]
Abstract
B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is the most common childhood malignancy. The two-step BCP-ALL pathogenesis requires in utero-induced chromosomal aberrations and additional mutagenic events for overt leukemia. In mouse models, activation-induced cytidine deaminase (AID/AICDA) was suggested to contribute to BCP-ALL pathogenesis by off-target mutagenic activity. The role of AID in patients, however, remains unclear. Moreover, AID is usually not expressed in precursor B-cells but in germinal center B-cells, where it is induced upon T-helper (Th) cell stimulation. We have previously demonstrated that autologous Th-cells supportively interacted with BCP-ALL-cells. Here, we hypothesize that this interaction additionally induces AID expression in BCP-ALL-cells, leading to off-target mutagenic activity. We show that co-culture with autologous bone marrow Th-cells induced high AICDA expression in primary BCP-ALL-cells. This induction was mediated by a mechanism similar to the induction in mature B-cells involving IL-13/Stat6, CD40L/NF-κB and TGFβ/Smad2/3 signaling. Even though Th-cell-induced AID seemed to be active in vitro in a BCP-ALL reporter cell line, extensive mutational signature analysis revealed no major contribution of AID activity to the mutational landscape in BCP-ALL patients. AID activity was neither detected in mutation clusters nor in known AID targets. Moreover, no recurrently mutated gene showed a relevant enrichment of mutations in the AID motif. Together, the lack of AID-induced mutational consequences argues towards a Th-cell-promoted yet AID-independent BCP-ALL pathogenesis and favors therapeutic research focusing on Th-cell-derived support of BCP-ALL-cells rather than AID-induced effects.
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9
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King JJ, Larijani M. Structural plasticity of substrate selection by activation-induced cytidine deaminase as a regulator of its genome-wide mutagenic activity. FEBS Lett 2020; 595:3-13. [PMID: 33089497 DOI: 10.1002/1873-3468.13962] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 09/28/2020] [Accepted: 10/08/2020] [Indexed: 01/25/2023]
Abstract
Activation-induced cytidine deaminase (AID) mediates somatic hypermutation and class-switch recombination of antibodies. Computational-biochemical and crystallography analyses of AID have identified three surface grooves for binding single-stranded DNA (ssDNA). Functional studies have also found evidence for RNA-binding motifs on AID. Although AID and the related apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like (APOBEC) enzymes share a conserved core, AID uniquely features multiple substrate-binding motifs on its surface. Here we suggest that combinatorial deployment of AID's multiple ssDNA- or RNA-binding motifs yields many substrate-binding modes that can accommodate ssDNA, RNA, or DNA/RNA substrates of diverse structures. We also suggest that AID oligomerization generates yet additional novel substrate-binding modes. We propose that this plasticity in substrate choice is an evolved aspect of AID's structure that contributes to the regulation of its differential mutagenic activity at various loci.
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Affiliation(s)
- Justin J King
- Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Canada
| | - Mani Larijani
- Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, Canada
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10
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Branton SA, Ghorbani A, Bolt BN, Fifield H, Berghuis LM, Larijani M. Activation-induced cytidine deaminase can target multiple topologies of double-stranded DNA in a transcription-independent manner. FASEB J 2020; 34:9245-9268. [PMID: 32437054 DOI: 10.1096/fj.201903036rr] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 04/20/2020] [Accepted: 04/24/2020] [Indexed: 12/30/2022]
Abstract
Activation-induced cytidine deaminase (AID) mutates immunoglobulin genes and acts genome-wide. AID targets robustly transcribed genes, and purified AID acts on single-stranded (ss) but not double-stranded (ds) DNA oligonucleotides. Thus, it is believed that transcription is the generator of ssDNA for AID. Previous cell-free studies examining the relationship between transcription and AID targeting have employed a bacterial colony count assay wherein AID reverts an antibiotic resistance stop codon in plasmid substrates, leading to colony formation. Here, we established a novel assay where kb-long dsDNA of varying topologies is incubated with AID, with or without transcription, followed by direct sequencing. This assay allows for an unselected and in-depth comparison of mutation frequency and pattern of AID targeting in the absence of transcription or across a range of transcription dynamics. We found that without transcription, AID targets breathing ssDNA in supercoiled and, to a lesser extent, in relaxed dsDNA. The most optimal transcription only modestly enhanced AID action on supercoiled dsDNA in a manner dependent on RNA polymerase speed. These data suggest that the correlation between transcription and AID targeting may reflect transcription leading to AID-accessible breathing ssDNA patches naturally occurring in de-chromatinized dsDNA, as much as being due to transcription directly generating ssDNA.
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Affiliation(s)
- Sarah A Branton
- Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Atefeh Ghorbani
- Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Brittany N Bolt
- Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Heather Fifield
- Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Lesley M Berghuis
- Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Mani Larijani
- Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada.,Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, BC, Canada
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11
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Novel specialized cell state and spatial compartments within the germinal center. Nat Immunol 2020; 21:660-670. [PMID: 32341509 PMCID: PMC7255947 DOI: 10.1038/s41590-020-0660-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 03/11/2020] [Indexed: 01/08/2023]
Abstract
Within germinal centers (GCs), complex and highly orchestrated molecular programs must balance proliferation, somatic hypermutation (SHM) and selection to both provide effective humoral immunity and to protect against genomic instability and neoplastic transformation. In contrast to this complexity, GC B cells are canonically divided into two principal populations, dark zone (DZ) and light zone (LZ) cells. We now demonstrate that following selection in the LZ, B cells migrated to specialized sites within the canonical DZ that contained tingible body macrophages (TBMs) and were sites of ongoing cell division. Proliferating DZ (DZp) cells then transited into the larger DZ to become differentiating DZ (DZd) cells before re-entering the LZ. Multidimensional analysis revealed distinct molecular programs in each population commensurate with observed compartmentization of non-compatable functions. These data provide a new three-cell population model that both orders critical GC functions and reveals essential molecular programs of humoral adaptive immunity.
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12
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Current insights into the mechanism of mammalian immunoglobulin class switch recombination. Crit Rev Biochem Mol Biol 2019; 54:333-351. [PMID: 31509023 DOI: 10.1080/10409238.2019.1659227] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Immunoglobulin (Ig) class switch recombination (CSR) is the gene rearrangement process by which B lymphocytes change the Ig heavy chain constant region to permit a switch of Ig isotype from IgM to IgG, IgA, or IgE. At the DNA level, CSR occurs via generation and joining of DNA double strand breaks (DSBs) at intronic switch regions located just upstream of each of the heavy chain constant regions. Activation-induced deaminase (AID), a B cell specific enzyme, catalyzes cytosine deaminations (converting cytosines to uracils) as the initial DNA lesions that eventually lead to DSBs and CSR. Progress on AID structure integrates very well with knowledge about Ig class switch region nucleic acid structures that are supported by functional studies. It is an ideal time to review what is known about the mechanism of Ig CSR and its relation to somatic hypermutation. There have been many comprehensive reviews on various aspects of the CSR reaction and regulation of AID expression and activity. This review is focused on the relation between AID and switch region nucleic acid structures, with a particular emphasis on R-loops.
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13
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AID, APOBEC3A and APOBEC3B efficiently deaminate deoxycytidines neighboring DNA damage induced by oxidation or alkylation. Biochim Biophys Acta Gen Subj 2019; 1863:129415. [PMID: 31404619 DOI: 10.1016/j.bbagen.2019.129415] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 07/26/2019] [Accepted: 08/07/2019] [Indexed: 12/29/2022]
Abstract
BACKGROUND AID/APOBEC3 (A3) enzymes instigate genomic mutations that are involved in immunity and cancer. Although they can deaminate any deoxycytidine (dC) to deoxyuridine (dU), each family member has a signature preference determined by nucleotides surrounding the target dC. This WRC (W = A/T, R = A/G) and YC (Y = T/C) hotspot preference is established for AID and A3A/A3B, respectively. Base alkylation and oxidation are two of the most common types of DNA damage induced environmentally or by chemotherapy. Here we examined the activity of AID, A3A and A3B on dCs neighboring such damaged bases. METHODS Substrates were designed to contain target dCs either in normal WRC/YC hotspots, or in oxidized/alkylated DNA motifs. AID, A3A and A3B were purified and deamination kinetics of each were compared between substrates containing damaged vs. normal motifs. RESULTS All three enzymes efficiently deaminated dC when common damaged bases were present in the -2 or -1 positions. Strikingly, some damaged motifs supported comparable or higher catalytic efficiencies by AID, A3A and A3B than the WRC/YC motifs which are their most favored normal sequences. Based on the resolved interactions of AID, A3A and A3B with DNA, we modeled interactions with alkylated or oxidized bases. Corroborating the enzyme assay data, the surface regions that recognize normal bases are predicted to also interact robustly with oxidized and alkylated bases. CONCLUSIONS AID, A3A and A3B can efficiently recognize and deaminate dC whose neighbouring nucleotides are damaged. GENERAL SIGNIFICANCE Beyond AID/A3s initiating DNA damage, some forms of pre-existing damaged DNA can constitute favored targets of AID/A3s if encountered.
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14
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Singh AK, Jaiswal A, Kodgire P. AID preferentially targets the top strand in nucleosome sequences. Mol Immunol 2019; 112:198-205. [DOI: 10.1016/j.molimm.2019.05.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Revised: 04/29/2019] [Accepted: 05/31/2019] [Indexed: 02/06/2023]
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15
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Yeap LS, Meng FL. Cis- and trans-factors affecting AID targeting and mutagenic outcomes in antibody diversification. Adv Immunol 2019; 141:51-103. [PMID: 30904133 DOI: 10.1016/bs.ai.2019.01.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Antigen receptor diversification is a hallmark of adaptive immunity which allows specificity of the receptor to particular antigen. B cell receptor (BCR) or its secreted form, antibody, is diversified through antigen-independent and antigen-dependent mechanisms. During B cell development in bone marrow, BCR is diversified via V(D)J recombination mediated by RAG endonuclease. Upon stimulation by antigen, B cell undergo somatic hypermutation (SHM) to allow affinity maturation and class switch recombination (CSR) to change the effector function of the antibody. Both SHM and CSR are initiated by activation-induced cytidine deaminase (AID). Repair of AID-initiated lesions through different DNA repair pathways results in diverse mutagenic outcomes. Here, we focus on discussing cis- and trans-factors that target AID to its substrates and factors that affect different outcomes of AID-initiated lesions. The knowledge of mechanisms that govern AID targeting and outcomes could be harnessed to elicit rare functional antibodies and develop ex vivo antibody diversification approaches with diversifying base editors.
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Affiliation(s)
- Leng-Siew Yeap
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - 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.
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16
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Salter JD, Smith HC. Modeling the Embrace of a Mutator: APOBEC Selection of Nucleic Acid Ligands. Trends Biochem Sci 2018; 43:606-622. [PMID: 29803538 PMCID: PMC6073885 DOI: 10.1016/j.tibs.2018.04.013] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 04/25/2018] [Accepted: 04/30/2018] [Indexed: 12/17/2022]
Abstract
The 11-member APOBEC (apolipoprotein B mRNA editing catalytic polypeptide-like) family of zinc-dependent cytidine deaminases bind to RNA and single-stranded DNA (ssDNA) and, in specific contexts, modify select (deoxy)cytidines to (deoxy)uridines. In this review, we describe advances made through high-resolution co-crystal structures of APOBECs bound to mono- or oligonucleotides that reveal potential substrate-specific binding sites at the active site and non-sequence-specific nucleic acid binding sites distal to the active site. We also discuss the effect of APOBEC oligomerization on functionality. Future structural studies will need to address how ssDNA binding away from the active site may enhance catalysis and the mechanism by which RNA binding may modulate catalytic activity on ssDNA. APOBEC proteins catalyze deamination of cytidine or deoxycytidine in either a sequence-specific or semi-specific manner on either DNA or RNA. APOBECs each possess the cytidine deaminase core fold, but sequence and structural differences among loops surrounding the zinc-dependent active site impart differences in sequence-dependent target preferences, binding affinity, catalytic rate, and regulation of substrate access to the active site among the 11 family members. APOBECs also regulate the deamination reaction through additional nucleic acid substrate binding sites located within surface grooves or patches of positive electrostatic potential that are distal to the active site but may do so nonspecifically. Binding of nonsubstrate RNA and RNA-mediated oligomerization by APOBECs that deaminate ssDNA downregulates catalytic activity but also controls APOBEC subcellular or virion localization. The presence of a second, though noncatalytic, cytidine deaminase domain for some APOBECs and the ability of some APOBECs to oligomerize add additional molecular surfaces for positive or negative regulation of catalysis through nucleic acid binding.
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Affiliation(s)
- Jason D Salter
- OyaGen, Inc., 77 Ridgeland Road, Rochester, NY 14623, USA.
| | - Harold C Smith
- OyaGen, Inc., 77 Ridgeland Road, Rochester, NY 14623, USA; University of Rochester, School of Medicine and Dentistry, Department of Biochemistry and Biophysics, 601 Elmwood Avenue, Rochester, NY 14642, USA.
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17
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Abstract
Long-term survivors of human immunodeficiency virus (HIV) infection have been shown to have a greatly increased incidence of B cell lymphomas. This increased lymphomagenesis suggests some link between HIV infection and the destabilization of the host B cell genome, a phenomenon also suggested by the extraordinary high frequency of mutation, insertion, and deletion in the broadly neutralizing HIV antibodies. Since HIV does not infect B cells, the molecular mechanisms of this genomic instability remain to be fully defined. Here, we demonstrate that the cell membrane-permeable HIV Tat proteins enhance activation-induced deaminase (AID)-mediated somatic hypermutation (SHM) of antibody V regions through their modulation of the endogenous polymerase II (Pol II) transcriptional process. Extremely small amounts of Tat that could come from bystander HIV-infected cells were sufficient to promote SHM. Our data suggest HIV Tat is one missing link between HIV infection and the overall B cell genomic instability in AIDS patients. Although the introduction of antiretroviral therapy (ART) has successfully controlled primary effects of human immunodeficiency virus (HIV) infection, such as HIV proliferation and HIV-induced immune deficiency, it did not eliminate the increased susceptibility of HIV-infected patients to B cell lymphomas. We find that a secreted HIV protein, Tat, enhances the intrinsic antibody diversification mechanism by increasing the AID-induced somatic mutations at the heavy-chain variable (VH) regions in human B cells. This could contribute to the high rate of mutation in the variable regions of broadly neutralizing anti-HIV antibodies and the genomewide mutations leading to B cell malignancies in HIV carriers.
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18
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Álvarez-Prado ÁF, Pérez-Durán P, Pérez-García A, Benguria A, Torroja C, de Yébenes VG, Ramiro AR. A broad atlas of somatic hypermutation allows prediction of activation-induced deaminase targets. J Exp Med 2018; 215:761-771. [PMID: 29374026 PMCID: PMC5839764 DOI: 10.1084/jem.20171738] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 11/22/2017] [Accepted: 12/21/2017] [Indexed: 12/18/2022] Open
Abstract
Activation-induced deaminase (AID) initiates antibody diversification in germinal center (GC) B cells through the deamination of cytosines on immunoglobulin genes. AID can also target other regions in the genome, triggering mutations or chromosome translocations, with major implications for oncogenic transformation. However, understanding the specificity of AID has proved extremely challenging. We have sequenced at very high depth >1,500 genomic regions from GC B cells and identified 275 genes targeted by AID, including 30 of the previously known 35 AID targets. We have also identified the most highly mutated hotspot for AID activity described to date. Furthermore, integrative analysis of the molecular features of mutated genes coupled to machine learning has produced a powerful predictive tool for AID targets. We also have found that base excision repair and mismatch repair back up each other to faithfully repair AID-induced lesions. Finally, our data establish a novel link between AID mutagenic activity and lymphomagenesis.
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Affiliation(s)
- Ángel F Álvarez-Prado
- B Cell Biology Lab, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
| | - Pablo Pérez-Durán
- B Cell Biology Lab, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
| | - Arantxa Pérez-García
- B Cell Biology Lab, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
| | - Alberto Benguria
- Genomics Unit, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
| | - Carlos Torroja
- Bioinformatics Unit, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
| | - Virginia G de Yébenes
- B Cell Biology Lab, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
| | - Almudena R Ramiro
- B Cell Biology Lab, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
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19
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Abdouni HS, King JJ, Ghorbani A, Fifield H, Berghuis L, Larijani M. DNA/RNA hybrid substrates modulate the catalytic activity of purified AID. Mol Immunol 2017; 93:94-106. [PMID: 29161581 DOI: 10.1016/j.molimm.2017.11.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 11/10/2017] [Accepted: 11/11/2017] [Indexed: 11/28/2022]
Abstract
Activation-induced cytidine deaminase (AID) converts cytidine to uridine at Immunoglobulin (Ig) loci, initiating somatic hypermutation and class switching of antibodies. In vitro, AID acts on single stranded DNA (ssDNA), but neither double-stranded DNA (dsDNA) oligonucleotides nor RNA, and it is believed that transcription is the in vivo generator of ssDNA targeted by AID. It is also known that the Ig loci, particularly the switch (S) regions targeted by AID are rich in transcription-generated DNA/RNA hybrids. Here, we examined the binding and catalytic behavior of purified AID on DNA/RNA hybrid substrates bearing either random sequences or GC-rich sequences simulating Ig S regions. If substrates were made up of a random sequence, AID preferred substrates composed entirely of DNA over DNA/RNA hybrids. In contrast, if substrates were composed of S region sequences, AID preferred to mutate DNA/RNA hybrids over substrates composed entirely of DNA. Accordingly, AID exhibited a significantly higher affinity for binding DNA/RNA hybrid substrates composed specifically of S region sequences, than any other substrates composed of DNA. Thus, in the absence of any other cellular processes or factors, AID itself favors binding and mutating DNA/RNA hybrids composed of S region sequences. AID:DNA/RNA complex formation and supporting mutational analyses suggest that recognition of DNA/RNA hybrids is an inherent structural property of AID.
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Affiliation(s)
- Hala S Abdouni
- Program in immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, A1 B 3V6, Canada
| | - Justin J King
- Program in immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, A1 B 3V6, Canada
| | - Atefeh Ghorbani
- Program in immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, A1 B 3V6, Canada
| | - Heather Fifield
- Program in immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, A1 B 3V6, Canada
| | - Lesley Berghuis
- Program in immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, A1 B 3V6, Canada
| | - Mani Larijani
- Program in immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, A1 B 3V6, Canada.
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20
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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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21
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Cortizas EM, Zahn A, Safavi S, Reed JA, Vega F, Di Noia JM, Verdun RE. UNG protects B cells from AID-induced telomere loss. J Exp Med 2016; 213:2459-2472. [PMID: 27697833 PMCID: PMC5068241 DOI: 10.1084/jem.20160635] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 08/16/2016] [Indexed: 02/05/2023] Open
Abstract
Verdun and colleagues find that the uracil-DNA glycosylase UNG, which promotes DNA breaks in the immunoglobulin genes during class switch recombination and is required for AID-induced chromosomal translocations, protects telomeres from AID-induced DNA damage and subsequent dysfunction. Activation-induced deaminase (AID) initiates antibody gene diversification by creating G:U mismatches in the immunoglobulin loci. However, AID also deaminates nonimmunoglobulin genes, and failure to faithfully repair these off-target lesions can cause B cell lymphoma. In this study, we identify a mechanism by which processing of G:U produced by AID at the telomeres can eliminate B cells at risk of genomic instability. We show that telomeres are off-target substrates of AID and that B cell proliferation depends on protective repair by uracil-DNA glycosylase (UNG). In contrast, in the absence of UNG activity, deleterious processing by mismatch repair leads to telomere loss and defective cell proliferation. Indeed, we show that UNG deficiency reduces B cell clonal expansion in the germinal center in mice and blocks the proliferation of tumor B cells expressing AID. We propose that AID-induced damage at telomeres acts as a fail-safe mechanism to limit the tumor promoting activity of AID when it overwhelms uracil excision repair.
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Affiliation(s)
- Elena M Cortizas
- Department of Medicine, Division of Hematology-Oncology, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33136
| | - Astrid Zahn
- Institut de Recherches Cliniques de Montréal, Montréal, Québec H2W 1R7, Canada
| | - Shiva Safavi
- Institut de Recherches Cliniques de Montréal, Montréal, Québec H2W 1R7, Canada.,Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec H3A 0G4, Canada
| | - Joseph A Reed
- Department of Medicine, Division of Hematology-Oncology, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33136
| | - Francisco Vega
- Department of Pathology and Laboratory Medicine, Division of Hematopathology, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33146
| | - Javier M Di Noia
- Institut de Recherches Cliniques de Montréal, Montréal, Québec H2W 1R7, Canada .,Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec H3A 0G4, Canada.,Department of Medicine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Ramiro E Verdun
- Department of Medicine, Division of Hematology-Oncology, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33136 .,Geriatric Research, Education, and Clinical Center, Miami VA Healthcare System, FL 33125
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22
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Somatic hypermutation in immunity and cancer: Critical analysis of strand-biased and codon-context mutation signatures. DNA Repair (Amst) 2016; 45:1-24. [DOI: 10.1016/j.dnarep.2016.07.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 07/01/2016] [Indexed: 01/01/2023]
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23
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Abstract
Transcription termination is a fundamental process in which RNA polymerase ceases RNA chain extension and dissociates from the chromatin template, thereby defining the end of the transcription unit. Our understanding of the biological role and functional importance of termination by RNA polymerase II and the range of processes in which it is involved has grown significantly in recent years. A large set of nucleic acid-binding proteins and enzymes have been identified as part of the termination machinery. A greater appreciation for the coupling of termination to RNA processing and metabolism has been recognized. In addition to serving as an essential step at the end of the transcription cycle, termination is involved in the regulation of a broad range of cellular processes. More recently, a role for termination in pervasive transcription, non-coding RNA regulation, genetic stability, chromatin remodeling, the immune response, and disease has come to the fore. Interesting mechanistic questions remain, but the last several years have resulted in significant insights into termination and an increasing recognition of its biological importance.
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Affiliation(s)
- Travis J Loya
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Daniel Reines
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, 30322, USA
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24
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Pefanis E, Wang J, Rothschild G, Lim J, Kazadi D, Sun J, Federation A, Chao J, Elliott O, Liu ZP, Economides AN, Bradner JE, Rabadan R, Basu U. RNA exosome-regulated long non-coding RNA transcription controls super-enhancer activity. Cell 2016; 161:774-89. [PMID: 25957685 DOI: 10.1016/j.cell.2015.04.034] [Citation(s) in RCA: 325] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Revised: 03/11/2015] [Accepted: 04/20/2015] [Indexed: 01/19/2023]
Abstract
We have ablated the cellular RNA degradation machinery in differentiated B cells and pluripotent embryonic stem cells (ESCs) by conditional mutagenesis of core (Exosc3) and nuclear RNase (Exosc10) components of RNA exosome and identified a vast number of long non-coding RNAs (lncRNAs) and enhancer RNAs (eRNAs) with emergent functionality. Unexpectedly, eRNA-expressing regions accumulate R-loop structures upon RNA exosome ablation, thus demonstrating the role of RNA exosome in resolving deleterious DNA/RNA hybrids arising from active enhancers. We have uncovered a distal divergent eRNA-expressing element (lncRNA-CSR) engaged in long-range DNA interactions and regulating IgH 3' regulatory region super-enhancer function. CRISPR-Cas9-mediated ablation of lncRNA-CSR transcription decreases its chromosomal looping-mediated association with the IgH 3' regulatory region super-enhancer and leads to decreased class switch recombination efficiency. We propose that the RNA exosome protects divergently transcribed lncRNA expressing enhancers by resolving deleterious transcription-coupled secondary DNA structures, while also regulating long-range super-enhancer chromosomal interactions important for cellular function.
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Affiliation(s)
- Evangelos Pefanis
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA; Regeneron Pharmaceuticals and Regeneron Genetics Center, Tarrytown, NY 10591, USA
| | - Jiguang Wang
- Department of Biomedical Informatics and Department of Systems Biology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Gerson Rothschild
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Junghyun Lim
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - David Kazadi
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Jianbo Sun
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | | | - Jaime Chao
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Oliver Elliott
- Department of Biomedical Informatics and Department of Systems Biology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Zhi-Ping Liu
- Department of Biomedical Engineering, School of Control Science and Engineering, Shandong University, Jinan, Shandong 250061, China
| | - Aris N Economides
- Regeneron Pharmaceuticals and Regeneron Genetics Center, Tarrytown, NY 10591, USA
| | - James E Bradner
- Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02115, USA
| | - Raul Rabadan
- Department of Biomedical Informatics and Department of Systems Biology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.
| | - Uttiya Basu
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.
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25
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Related Mechanisms of Antibody Somatic Hypermutation and Class Switch Recombination. Microbiol Spectr 2016; 3:MDNA3-0037-2014. [PMID: 26104555 DOI: 10.1128/microbiolspec.mdna3-0037-2014] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The primary antibody repertoire is generated by mechanisms involving the assembly of the exons that encode the antigen-binding variable regions of immunoglobulin heavy (IgH) and light (IgL) chains during the early development of B lymphocytes. After antigen-dependent activation, mature B lymphocytes can further alter their IgH and IgL variable region exons by the process of somatic hypermutation (SHM), which allows the selection of B cells in which SHMs resulted in the production of antibodies with increased antigen affinity. In addition, during antigen-dependent activation, B cells can also change the constant region of their IgH chain through a DNA double-strand-break (DSB) dependent process referred to as IgH class switch recombination (CSR), which generates B cell progeny that produce antibodies with different IgH constant region effector functions that are best suited for a elimination of a particular pathogen or in a particular setting. Both the mutations that underlie SHM and the DSBs that underlie CSR are initiated in target genes by activation-induced cytidine deaminase (AID). This review describes in depth the processes of SHM and CSR with a focus on mechanisms that direct AID cytidine deamination in activated B cells and mechanisms that promote the differential outcomes of such cytidine deamination.
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26
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Huang ZQ, Raska M, Stewart TJ, Reily C, King RG, Crossman DK, Crowley MR, Hargett A, Zhang Z, Suzuki H, Hall S, Wyatt RJ, Julian BA, Renfrow MB, Gharavi AG, Novak J. Somatic Mutations Modulate Autoantibodies against Galactose-Deficient IgA1 in IgA Nephropathy. J Am Soc Nephrol 2016; 27:3278-3284. [PMID: 26966014 DOI: 10.1681/asn.2014101044] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 02/04/2016] [Indexed: 12/22/2022] Open
Abstract
Autoantibodies against galactose-deficient IgA1 drive formation of pathogenic immune complexes in IgA nephropathy. IgG autoantibodies against galactose-deficient IgA1 in patients with IgA nephropathy have a specific amino-acid sequence, Y1CS3, in the complementarity-determining region 3 of the heavy chain variable region compared with a Y1CA3 sequence in similar isotype-matched IgG from healthy controls. We previously found that the S3 residue is critical for binding galactose-deficient IgA1. To determine whether this difference is due to a rare germline sequence, we amplified and sequenced the corresponding germline variable region genes from peripheral blood mononuclear cells of seven patients with IgA nephropathy and six healthy controls from whom we had cloned single-cell lines secreting monoclonal IgG specific for galactose-deficient IgA1. Sanger DNA sequencing revealed that complementarity-determining region 3 in the variable region of the germline genes encoded the Y1C(A/V)3 amino-acid sequence. Thus, the A/V>S substitution in the complementarity-determining region 3 of anti-galactose-deficient-IgA1 autoantibodies of the patients with IgA nephropathy is not a rare germline gene variant. Modeling analyses indicated that the S3 hydroxyl group spans the complementarity-determining region 3 loop stem, stabilizing the adjacent β-sheet and stem structure, important features for effective binding to galactose-deficient IgA1. Understanding processes leading to production of the autoantibodies may offer new approaches to treat IgA nephropathy.
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Affiliation(s)
| | - Milan Raska
- University of Alabama at Birmingham, Birmingham, Alabama.,Palacky University and University Hospital Olomouc, Olomouc, Czech Republic
| | | | - Colin Reily
- University of Alabama at Birmingham, Birmingham, Alabama
| | - R Glenn King
- University of Alabama at Birmingham, Birmingham, Alabama
| | | | | | - Audra Hargett
- University of Alabama at Birmingham, Birmingham, Alabama
| | - Zhixin Zhang
- University of Nebraska Medical Center, Omaha, Nebraska.,West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
| | - Hitoshi Suzuki
- University of Alabama at Birmingham, Birmingham, Alabama.,Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Stacy Hall
- University of Alabama at Birmingham, Birmingham, Alabama
| | - Robert J Wyatt
- University of Tennessee Health Science Center, Memphis, Tennessee; and
| | - Bruce A Julian
- University of Alabama at Birmingham, Birmingham, Alabama
| | | | | | - Jan Novak
- University of Alabama at Birmingham, Birmingham, Alabama;
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27
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AID hits the jackpot when missing the target. Curr Opin Immunol 2016; 39:96-102. [PMID: 26845615 DOI: 10.1016/j.coi.2016.01.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 01/12/2016] [Accepted: 01/14/2016] [Indexed: 01/07/2023]
Abstract
Activation induced deaminase is the single B cell specific factor mediating class switch recombination and somatic hypermutation. Numerous studies have shown that AID preferentially targets Ig substrates and also attacks non-Ig substrates to create DNA damage that contributes to lymphomagenesis. AID targeting to Ig loci is linked to transcription but the mechanism governing this process has been obscure. Here we discuss research that illustrates the connection between AID targeting to DNA substrates and transcription processes to reveal rules governing the specificity of AID attack. These observations are woven together to provide a integrated view of AID function and a surprising linkage with global regulation of gene expression.
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28
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Senavirathne G, Bertram JG, Jaszczur M, Chaurasiya KR, Pham P, Mak CH, Goodman MF, Rueda D. Activation-induced deoxycytidine deaminase (AID) co-transcriptional scanning at single-molecule resolution. Nat Commun 2015; 6:10209. [PMID: 26681117 PMCID: PMC4703863 DOI: 10.1038/ncomms10209] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 11/13/2015] [Indexed: 12/20/2022] Open
Abstract
Activation-induced deoxycytidine deaminase (AID) generates antibody diversity in B cells by initiating somatic hypermutation (SHM) and class-switch recombination (CSR) during transcription of immunoglobulin variable (IgV) and switch region (IgS) DNA. Using single-molecule FRET, we show that AID binds to transcribed dsDNA and translocates unidirectionally in concert with RNA polymerase (RNAP) on moving transcription bubbles, while increasing the fraction of stalled bubbles. AID scans randomly when constrained in an 8 nt model bubble. When unconstrained on single-stranded (ss) DNA, AID moves in random bidirectional short slides/hops over the entire molecule while remaining bound for ∼5 min. Our analysis distinguishes dynamic scanning from static ssDNA creasing. That AID alone can track along with RNAP during transcription and scan within stalled transcription bubbles suggests a mechanism by which AID can initiate SHM and CSR when properly regulated, yet when unregulated can access non-Ig genes and cause cancer. Activation-induced deoxycytidine deaminase (AID) induces somatic hypermutation and class-switch recombination during transcription of immunoglobulin genes. Here the authors use single-molecule FRET to show that AID translocates together with RNA polymerase and scans within stalled transcription bubbles.
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Affiliation(s)
- Gayan Senavirathne
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, USA
| | - Jeffrey G Bertram
- Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
| | - Malgorzata Jaszczur
- Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
| | - Kathy R Chaurasiya
- Department of Medicine, Section of Virology, Imperial College London, Du Cane Road, London W12 0NN, UK.,Single Molecule Imaging Group, MRC Clinical Sciences Center, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Phuong Pham
- Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
| | - Chi H Mak
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA.,Center for Applied Mathematical Science, University of Southern California, Los Angeles, California 90089, USA
| | - Myron F Goodman
- Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA.,Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - David Rueda
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, USA.,Department of Medicine, Section of Virology, Imperial College London, Du Cane Road, London W12 0NN, UK.,Single Molecule Imaging Group, MRC Clinical Sciences Center, Imperial College London, Du Cane Road, London W12 0NN, UK
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29
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Yeap LS, Hwang JK, Du Z, Meyers RM, Meng FL, Jakubauskaitė A, Liu M, Mani V, Neuberg D, Kepler TB, Wang JH, Alt FW. Sequence-Intrinsic Mechanisms that Target AID Mutational Outcomes on Antibody Genes. Cell 2015; 163:1124-1137. [PMID: 26582132 DOI: 10.1016/j.cell.2015.10.042] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 09/01/2015] [Accepted: 10/13/2015] [Indexed: 12/27/2022]
Abstract
In activated B lymphocytes, AID initiates antibody variable (V) exon somatic hypermutation (SHM) for affinity maturation in germinal centers (GCs) and IgH switch (S) region DNA breaks (DSBs) for class-switch recombination (CSR). To resolve long-standing questions, we have developed an in vivo assay to study AID targeting of passenger sequences replacing a V exon. First, we find AID targets SHM hotspots within V exon and S region passengers at similar frequencies and that the normal SHM process frequently generates deletions, indicating that SHM and CSR employ the same mechanism. Second, AID mutates targets in diverse non-Ig passengers in GC B cells at levels similar to those of V exons, definitively establishing the V exon location as "privileged" for SHM. Finally, Peyer's patch GC B cells generate a reservoir of V exons that are highly mutated before selection for affinity maturation. We discuss the implications of these findings for harnessing antibody diversification mechanisms.
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Affiliation(s)
- Leng-Siew Yeap
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine at Boston Children's Hospital, and Department of Genetics, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Joyce K Hwang
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine at Boston Children's Hospital, and Department of Genetics, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Zhou Du
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine at Boston Children's Hospital, and Department of Genetics, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Robin M Meyers
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine at Boston Children's Hospital, and Department of Genetics, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Fei-Long Meng
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine at Boston Children's Hospital, and Department of Genetics, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Agnė Jakubauskaitė
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine at Boston Children's Hospital, and Department of Genetics, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Mengyuan Liu
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine at Boston Children's Hospital, and Department of Genetics, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Vinidhra Mani
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine at Boston Children's Hospital, and Department of Genetics, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Donna Neuberg
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Thomas B Kepler
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02215, USA
| | - Jing H Wang
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine at Boston Children's Hospital, and Department of Genetics, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Frederick W Alt
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine at Boston Children's Hospital, and Department of Genetics, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA.
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30
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Abstract
The immunoglobulin diversification processes of somatic hypermutation and class switch recombination critically rely on transcription-coupled targeting of activation-induced cytidine deaminase (AID) to Ig loci in activated B lymphocytes. AID catalyzes deamination of cytidine deoxynucleotides on exposed single-stranded DNA. In addition to driving immunoglobulin diversity, promiscuous targeting of AID mutagenic activity poses a deleterious threat to genomic stability. Recent genome-wide studies have uncovered pervasive AID activity throughout the B cell genome. It is increasingly apparent that AID activity is frequently targeted to genomic loci undergoing early transcription termination where RNA exosome promotes the resolution of stalled transcription complexes via cotranscriptional RNA degradation mechanisms. Here, we review aspects and consequences of eukaryotic transcription that lead to early termination, RNA exosome recruitment, and ultimately targeting of AID mutagenic activity.
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Affiliation(s)
- Evangelos Pefanis
- Department of Microbiology & Immunology, College of Physicians and Surgeons, Columbia University, New York, USA.
| | - Uttiya Basu
- Department of Microbiology & Immunology, College of Physicians and Surgeons, Columbia University, New York, USA.
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31
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Abstract
AID mis-targeting is poorly understood but contributes significantly to B cell genome instability. Two new papers in Cell reveal that AID mistargeting occurs primarily in gene bodies within a nuclear microenvironment characterized by high levels of transcriptional activity, interconnected transcriptional regulatory elements, and overlapping sense and antisense (convergent) transcription.
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Affiliation(s)
- Jukka Alinikula
- Department of Immunobiology, Yale University School of Medicine and Howard Hughes Medical Institute, 300 Cedar Street, Box 208011, New Haven, CT 06520-8011, USA
| | - David G Schatz
- Department of Immunobiology, Yale University School of Medicine and Howard Hughes Medical Institute, 300 Cedar Street, Box 208011, New Haven, CT 06520-8011, USA.
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32
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Meng FL, Du Z, Federation A, Hu J, Wang Q, Kieffer-Kwon KR, Meyers RM, Amor C, Wasserman CR, Neuberg D, Casellas R, Nussenzweig MC, Bradner JE, Liu XS, Alt FW. Convergent transcription at intragenic super-enhancers targets AID-initiated genomic instability. Cell 2014; 159:1538-48. [PMID: 25483776 PMCID: PMC4322776 DOI: 10.1016/j.cell.2014.11.014] [Citation(s) in RCA: 188] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 10/01/2014] [Accepted: 10/27/2014] [Indexed: 01/08/2023]
Abstract
Activation-induced cytidine deaminase (AID) initiates both somatic hypermutation (SHM) for antibody affinity maturation and DNA breakage for antibody class switch recombination (CSR) via transcription-dependent cytidine deamination of single-stranded DNA targets. Though largely specific for immunoglobulin genes, AID also acts on a limited set of off-targets, generating oncogenic translocations and mutations that contribute to B cell lymphoma. How AID is recruited to off-targets has been a long-standing mystery. Based on deep GRO-seq studies of mouse and human B lineage cells activated for CSR or SHM, we report that most robust AID off-target translocations occur within highly focal regions of target genes in which sense and antisense transcription converge. Moreover, we found that such AID-targeting "convergent" transcription arises from antisense transcription that emanates from super-enhancers within sense transcribed gene bodies. Our findings provide an explanation for AID off-targeting to a small subset of mostly lineage-specific genes in activated B cells.
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Affiliation(s)
- Fei-Long Meng
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Zhou Du
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Department of Bioinformatics, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Alexander Federation
- Department of Medical Oncology, Dana-Farber Cancer Institute, and Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Jiazhi Hu
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Qiao Wang
- Howard Hughes Medical Institute, Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Kyong-Rim Kieffer-Kwon
- Genomics and Immunity, NIAMS, and Center of Cancer Research, NCI, National Institutes of Health, Bethesda, MD 20892, USA
| | - Robin M Meyers
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Corina Amor
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Caitlyn R Wasserman
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Donna Neuberg
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA 02115, USA
| | - Rafael Casellas
- Genomics and Immunity, NIAMS, and Center of Cancer Research, NCI, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michel C Nussenzweig
- Howard Hughes Medical Institute, Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, and Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.
| | - X Shirley Liu
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA 02115, USA
| | - Frederick W Alt
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
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33
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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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34
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Abstract
Transcription requires unwinding complementary DNA strands, generating torsional stress, and sensitizing the exposed single strands to chemical reactions and endogenous damaging agents. In addition, transcription can occur concomitantly with the other major DNA metabolic processes (replication, repair, and recombination), creating opportunities for either cooperation or conflict. Genetic modifications associated with transcription are a global issue in the small genomes of microorganisms in which noncoding sequences are rare. Transcription likewise becomes significant when one considers that most of the human genome is transcriptionally active. In this review, we focus specifically on the mutagenic consequences of transcription. Mechanisms of transcription-associated mutagenesis in microorganisms are discussed, as is the role of transcription in somatic instability of the vertebrate immune system.
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Affiliation(s)
- Sue Jinks-Robertson
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710;
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35
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Tepsuporn S, Hu J, Gostissa M, Alt FW. Mechanisms that can promote peripheral B-cell lymphoma in ATM-deficient mice. Cancer Immunol Res 2014; 2:857-66. [PMID: 24913718 PMCID: PMC4156541 DOI: 10.1158/2326-6066.cir-14-0090] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The Ataxia Telangiectasia-mutated (ATM) kinase senses DNA double-strand breaks (DSB) and facilitates their repair. In humans, ATM deficiency predisposes to B- and T-cell lymphomas, but in mice it leads only to thymic lymphomas. We tested the hypothesis that increased DSB frequency at a cellular oncogene could promote B-cell lymphoma by generating ATM-deficient mice with a V(D)J recombination target (DJβ cassette) within c-myc intron 1 ("DA" mice). We also generated ATM-deficient mice carrying an Eμ-Bcl-2 transgene (AB mice) to test whether enhanced cellular survival could promote B-cell lymphomas. About 30% of DA or AB mice and nearly 100% of mice harboring the combined genotypes (DAB mice) developed mature B-cell lymphomas. In all genotypes, B-cell tumors harbored oncogenic c-myc amplification generated by breakage-fusion-bridge (BFB) from dicentric chromosomes formed through fusion of IgH V(D)J recombination-associated DSBs on chromosome 12 to sequences downstream of c-myc on chromosome 15. AB tumors demonstrate that B lineage cells harboring spontaneous DSBs leading to IgH/c-myc dicentrics are blocked from progressing to B-cell lymphomas by cellular apoptotic responses. DA and DAB tumor translocations were strictly linked to the cassette, but occurred downstream, frequently in a 6-kb region adjacent to c-myc that harbors multiple cryptic V(D)J recombination targets, suggesting that bona fide V(D)J target sequences may activate linked cryptic targets. Our findings indicate that ATM deficiency allows IgH V(D)J recombination DSBs in developing B cells to generate dicentric translocations that, via BFB cycles, lead to c-myc-activating oncogenic translocations and amplifications in mature B cells.
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Affiliation(s)
- Suprawee Tepsuporn
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital; and Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Jiazhi Hu
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital; and Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Monica Gostissa
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital; and Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Frederick W Alt
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital; and Department of Genetics, Harvard Medical School, Boston, Massachusetts
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36
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Genomic uracil homeostasis during normal B cell maturation and loss of this balance during B cell cancer development. Mol Cell Biol 2014; 34:4019-32. [PMID: 25154417 DOI: 10.1128/mcb.00589-14] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Activation-induced deaminase (AID) converts DNA cytosines to uracils in immunoglobulin genes, creating antibody diversification. It also causes mutations and translocations that promote cancer. We examined the interplay between uracil creation by AID and its removal by UNG2 glycosylase in splenocytes undergoing maturation and in B cell cancers. The genomic uracil levels remain unchanged in normal stimulated B cells, demonstrating a balance between uracil generation and removal. In stimulated UNG(-/-) cells, uracil levels increase by 11- to 60-fold during the first 3 days. In wild-type B cells, UNG2 gene expression and enzymatic activity rise and fall with AID levels, suggesting that UNG2 expression is coordinated with uracil creation by AID. Remarkably, a murine lymphoma cell line, several human B cell cancer lines, and human B cell tumors expressing AID at high levels have genomic uracils comparable to those seen with stimulated UNG(-/-)splenocytes. However, cancer cells express UNG2 gene at levels similar to or higher than those seen with peripheral B cells and have nuclear uracil excision activity comparable to that seen with stimulated wild-type B cells. We propose that more uracils are created during B cell cancer development than are removed from the genome but that the uracil creation/excision balance is restored during establishment of cell lines, fixing the genomic uracil load at high levels.
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37
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Noncoding RNA transcription targets AID to divergently transcribed loci in B cells. Nature 2014; 514:389-93. [PMID: 25119026 DOI: 10.1038/nature13580] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 06/12/2014] [Indexed: 12/21/2022]
Abstract
The vast majority of the mammalian genome has the potential to express noncoding RNA (ncRNA). The 11-subunit RNA exosome complex is the main source of cellular 3'-5' exoribonucleolytic activity and potentially regulates the mammalian noncoding transcriptome. Here we generated a mouse model in which the essential subunit Exosc3 of the RNA exosome complex can be conditionally deleted. Exosc3-deficient B cells lack the ability to undergo normal levels of class switch recombination and somatic hypermutation, two mutagenic DNA processes used to generate antibody diversity via the B-cell mutator protein activation-induced cytidine deaminase (AID). The transcriptome of Exosc3-deficient B cells has revealed the presence of many novel RNA exosome substrate ncRNAs. RNA exosome substrate RNAs include xTSS-RNAs, transcription start site (TSS)-associated antisense transcripts that can exceed 500 base pairs in length and are transcribed divergently from cognate coding gene transcripts. xTSS-RNAs are most strongly expressed at genes that accumulate AID-mediated somatic mutations and/or are frequent translocation partners of DNA double-strand breaks generated at Igh in B cells. Strikingly, translocations near TSSs or within gene bodies occur over regions of RNA exosome substrate ncRNA expression. These RNA exosome-regulated, antisense-transcribed regions of the B-cell genome recruit AID and accumulate single-strand DNA structures containing RNA-DNA hybrids. We propose that RNA exosome regulation of ncRNA recruits AID to single-strand DNA-forming sites of antisense and divergent transcription in the B-cell genome, thereby creating a link between ncRNA transcription and overall maintenance of B-cell genomic integrity.
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