1
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Benitez-Cantos MS, Cano C, Cuadros M, Medina PP. Activation-induced cytidine deaminase causes recurrent splicing mutations in diffuse large B-cell lymphoma. Mol Cancer 2024; 23:42. [PMID: 38402205 PMCID: PMC10893679 DOI: 10.1186/s12943-024-01960-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/16/2024] [Indexed: 02/26/2024] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) is the most common lymphoma. A major mutagenic process in DLBCL is aberrant somatic hypermutation (aSHM) by activation-induced cytidine deaminase (AID), which occurs preferentially at RCH/TW sequence motifs proximal to transcription start sites. Splice sequences are highly conserved, rich in RCH/TW motifs, and recurrently mutated in DLBCL. Therefore, we hypothesized that aSHM may cause recurrent splicing mutations in DLBCL. In a meta-cohort of > 1,800 DLBCLs, we found that 77.5% of splicing mutations in 29 recurrently mutated genes followed aSHM patterns. In addition, in whole-genome sequencing (WGS) data from 153 DLBCLs, proximal mutations in splice sequences, especially in donors, were significantly enriched in RCH/TW motifs (p < 0.01). We validated this enrichment in two additional DLBCL cohorts (N > 2,000; p < 0.0001) and confirmed its absence in 12 cancer types without aSHM (N > 6,300). Comparing sequencing data from mouse models with and without AID activity showed that the splice donor sequences were the top genomic feature enriched in AID-induced mutations (p < 0.0001). Finally, we observed that most AID-related splice site mutations are clonal within a sample, indicating that aSHM may cause early loss-of-function events in lymphomagenesis. Overall, these findings support that AID causes an overrepresentation of clonal splicing mutations in DLBCL.
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Affiliation(s)
- Maria S Benitez-Cantos
- GENYO. Centre for Genomics and Oncological Research: Pfizer / University of Granada / Andalusian Regional Government, PTS Granada - Avenida de la Ilustración 114, Granada, 18016, Spain
- Health Research Institute of Granada (Ibs.Granada), Avenida de Madrid 15, Granada, 18012, Spain
- Department of Biochemistry and Molecular Biology III and Immunology, Faculty of Medicine, University of Granada, Avenida de la Investigación 11, Granada, 18016, Spain
| | - Carlos Cano
- Department of Computer Science and Artificial Intelligence, School of Computer and Telecommunication Engineering, University of Granada, Calle Periodista Daniel Saucedo Aranda s/n, Granada, 18014, Spain
| | - Marta Cuadros
- GENYO. Centre for Genomics and Oncological Research: Pfizer / University of Granada / Andalusian Regional Government, PTS Granada - Avenida de la Ilustración 114, Granada, 18016, Spain
- Health Research Institute of Granada (Ibs.Granada), Avenida de Madrid 15, Granada, 18012, Spain
- Department of Biochemistry and Molecular Biology III and Immunology, Faculty of Medicine, University of Granada, Avenida de la Investigación 11, Granada, 18016, Spain
| | - Pedro P Medina
- GENYO. Centre for Genomics and Oncological Research: Pfizer / University of Granada / Andalusian Regional Government, PTS Granada - Avenida de la Ilustración 114, Granada, 18016, Spain.
- Health Research Institute of Granada (Ibs.Granada), Avenida de Madrid 15, Granada, 18012, Spain.
- Department of Biochemistry and Molecular Biology I, Faculty of Sciences, University of Granada, Avenida de Fuentenueva s/n, Granada, 18071, Spain.
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2
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Shimkus G, Nonaka T. Molecular classification and therapeutics in diffuse large B-cell lymphoma. Front Mol Biosci 2023; 10:1124360. [PMID: 36818048 PMCID: PMC9936827 DOI: 10.3389/fmolb.2023.1124360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 01/09/2023] [Indexed: 02/05/2023] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) encompasses a wide variety of disease states that have to date been subgrouped and characterized based on immunohistochemical methods, which provide limited prognostic value to clinicians and no alteration in treatment regimen. The addition of rituximab to CHOP therapy was the last leap forward in terms of treatment, but regimens currently follow a standardized course when disease becomes refractory with no individualization based on genotype. Research groups are tentatively proposing new strategies for categorizing DLBCL based on genetic abnormalities that are frequently found together to better predict disease course following dysregulation of specific pathways and to deliver targeted treatment. Novel algorithms in combination with next-generation sequencing techniques have identified between 4 and 7 subgroups of DLBCL, depending on the research team, with potentially significant and actionable genetic alterations. Various drugs aimed at pathways including BCR signaling, NF-κB dysfunction, and epigenetic regulation have shown promise in their respective groups and may show initial utility as second or third line therapies to patients with recurrent DLBCL. Implementation of subgroups will allow collection of necessary data to determine which groups are significant, which treatments may be indicated, and will provide better insight to clinicians and patients on specific disease course.
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Affiliation(s)
- Gaelen Shimkus
- School of Medicine, Louisiana State University Health Shreveport, Shreveport, LA, United States
| | - Taichiro Nonaka
- Department of Cellular Biology and Anatomy, Louisiana State University Health Sciences Center, Shreveport, LA, United States,Feist-Weiller Cancer Center, Louisiana State University Health Shreveport, Shreveport, LA, United States,*Correspondence: Taichiro Nonaka,
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3
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Wang Y, Yang Y, Zhao Z, Sun H, Luo D, Huttad L, Zhang B, Han B. A new nomogram model for prognosis of hepatocellular carcinoma based on novel gene signature that regulates cross-talk between immune and tumor cells. BMC Cancer 2022; 22:379. [PMID: 35397536 PMCID: PMC8994280 DOI: 10.1186/s12885-022-09465-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 03/25/2022] [Indexed: 02/07/2023] Open
Abstract
Background The combined application of immune cells and specific biomarkers related to the tumor immune microenvironment has a better predictive value for the prognosis of HCC. The purpose of this study is to construct a new prognostic model based on immune-related genes that regulate cross-talk between immune and tumor cells to assess the prognosis and explore possible mechanisms. Method The immune cell abundance ratio of 424 cases in the TCGA-LIHC database is obtained through the CIBERSORT algorithm. The differential gene analysis and cox regression analysis is used to screen IRGs. In addition, the function of IRGs was preliminarily explored through the co-culture of M2 macrophages and HCC cell lines. The clinical validation, nomogram establishment and performing tumor microenvironment score were validated. Results We identified 4 immune cells and 9 hub genes related to the prognosis. Further, we identified S100A9, CD79B, TNFRSF11B as an IRGs signature, which is verified in the ICGC and GSE76427 database. Importantly, IRGs signature is closely related to the prognosis, tumor microenvironment score, clinical characteristics and immunotherapy, and nomogram combined with clinical characteristics is more conducive to clinical promotion. In addition, after co-culture with M2 macrophages, the migration capacity and cell pseudopod of MHCC97H increased significantly. And CD79B and TNFRSF11B were significantly down-regulated in MHCC97H, Huh7 and LM3, while S100A9 was up-regulated. Conclusion We constructed an IRGs signature and discussed possible mechanisms. The nomogram established based on IRGs can accurately predict the prognosis of HCC patients. These findings may provide a suitable therapeutic target for HCC. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09465-9.
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4
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King JJ, Borzooee F, Im J, Asgharpour M, Ghorbani A, Diamond CP, Fifield H, Berghuis L, Larijani M. Structure-Based Design of First-Generation Small Molecule Inhibitors Targeting the Catalytic Pockets of AID, APOBEC3A, and APOBEC3B. ACS Pharmacol Transl Sci 2021; 4:1390-1407. [PMID: 34423273 PMCID: PMC8369683 DOI: 10.1021/acsptsci.1c00091] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Indexed: 12/12/2022]
Abstract
![]()
Activation-induced
cytidine deaminase (AID) initiates antibody
diversification by mutating immunoglobulin loci in B lymphocytes.
AID and related APOBEC3 (A3) enzymes also induce genome-wide mutations
and lesions implicated in tumorigenesis and tumor progression. The
most prevalent mutation signatures across diverse tumor genomes are
attributable to the mistargeted mutagenic activities of AID/A3s. Thus,
inhibiting AID/A3s has been suggested to be of therapeutic benefit.
We previously used a computational-biochemical approach to gain insight
into the structure of AID’s catalytic pocket, which resulted
in the discovery of a novel type of regulatory catalytic pocket closure
that regulates AID/A3s that we termed the “Schrodinger’s
CATalytic pocket”. Our findings were subsequently confirmed
by direct structural studies. Here, we describe our search for small
molecules that target the catalytic pocket of AID. We identified small
molecules that inhibit purified AID, AID in cell extracts, and endogenous
AID of lymphoma cells. Analogue expansion yielded derivatives with
improved potencies. These were found to also inhibit A3A and A3B,
the two most tumorigenic siblings of AID. Two compounds exhibit low
micromolar IC50 inhibition of AID and A3A, exhibiting the
strongest potency for A3A. Docking suggests key interactions between
their warheads and residues lining the catalytic pockets of AID, A3A,
and A3B and between the tails and DNA-interacting residues on the
surface proximal to the catalytic pocket opening. Accordingly, mutants
of these residues decreased inhibition potency. The chemistry and
abundance of key stabilizing interactions between the small molecules
and residues within and immediately outside the catalytic pockets
are promising for therapeutic development.
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Affiliation(s)
- Justin J King
- Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.,Program in immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland A1B 3 V6, Canada
| | - Faezeh Borzooee
- Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.,Program in immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland A1B 3 V6, Canada
| | - Junbum Im
- Program in immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland A1B 3 V6, Canada.,BC Cancer Research/Terry Fox Labs, University of British Columbia, Vancouver, British Columbia BC V5Z 1L3, Canada
| | - Mahdi Asgharpour
- Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.,Program in immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland A1B 3 V6, Canada
| | - Atefeh Ghorbani
- Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.,Program in immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland A1B 3 V6, Canada
| | - Cody P Diamond
- Program in immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland A1B 3 V6, Canada
| | - Heather Fifield
- Program in immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland A1B 3 V6, Canada
| | - Lesley Berghuis
- Program in immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland A1B 3 V6, Canada
| | - Mani Larijani
- Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.,Program in immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland A1B 3 V6, Canada
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5
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Thurner L, Hartmann S, Bewarder M, Fadle N, Regitz E, Schormann C, Quiroga N, Kemele M, Klapper W, Rosenwald A, Trümper L, Bohle RM, Nimmesgern A, Körbel C, Lascke MW, Menger MD, Barth S, Kubuschok B, Mottok A, Kaddu-Mulindwa D, Hansmann ML, Pöschel V, Held G, Murawski N, Stilgenbauer S, Neumann F, Preuss KD, Pfreundschuh M. Identification of the atypically modified autoantigen Ars2 as the target of B-cell receptors from activated B-cell-type diffuse large B-cell lymphoma. Haematologica 2021; 106:2224-2232. [PMID: 32675228 PMCID: PMC8327713 DOI: 10.3324/haematol.2019.241653] [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: 10/28/2019] [Indexed: 12/14/2022] Open
Abstract
It has been suggested that stimulation of B-cell receptors (BCR) by specific antigens plays a pathogenic role in diffuse large B-cell lymphoma (DLBCL). Here, it was the aim to screen for specific reactivities of DLBCL-BCR in the spectrum of autoantigens and antigens of infectious origin. Arsenite resistance protein 2 (Ars2) was identified as the BCR target of three of five activated B-cell type DLBCL cell lines and two of 11 primary DLBCL cases. Compared to controls, Ars2 was hypophosphorylated exclusively in cases and cell lines with Ars2-specific BCR. In a validation cohort, hypophosphorylated Ars2 was found in eight of 31 activated B-cell type DLBCL, but in only one of 20 germinal center B-cell like type DLBCL. Incubation with Ars2 induced BCR-pathway activation and increased proliferation, while an Ars2/ETA’ toxin conjugate induced killing of cell lines with Ars2-reactive BCR. Ars2 appears to play a role in a subgroup of activated B-cell-type DLBCL. Moreover, transformed DLBCL lines with Ars2-reactive BCR still showed growth advantage after incubation with Ars2. These results provide knowledge about the pathogenic role of a specific antigen stimulating the BCR pathway in DLCBL.
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Affiliation(s)
- Lorenz Thurner
- Saarland Medical School, Internal Medicine I, Homburg/Saar, Germany
| | | | - Moritz Bewarder
- Saarland Medical School, Internal Medicine I, Homburg/Saar, Germany
| | - Natalie Fadle
- Saarland Medical School, Internal Medicine I, Homburg/Saar, Germany
| | - Evi Regitz
- Saarland Medical School, Internal Medicine I, Homburg/Saar, Germany
| | | | - Natalia Quiroga
- Saarland Medical School, Internal Medicine I, Homburg/Saar, Germany
| | - Maria Kemele
- Saarland Medical School, Internal Medicine I, Homburg/Saar, Germany
| | | | - Andreas Rosenwald
- Institute of Pathology, University of Würzburg and CCC Mainfranken, Würzburg, Germany
| | - Lorenz Trümper
- Department of Hematology and Medical Oncology, University Hospital Göttingen, Germany
| | - Rainer Maria Bohle
- Saarland University Medical School, Institute of Pathology, Homburg/Saar, Germany
| | - Anna Nimmesgern
- Institute of Medical Microbiology and Hygiene, University of Saarland, Homburg, Germany
| | - Christina Körbel
- Institute for Clinical and Experimental Surgery, University of Saarland, Homburg/Saar, Germany
| | - Matthias W Lascke
- Institute for Clinical and Experimental Surgery, University of Saarland, Homburg/Saar, Germany
| | - Michael D Menger
- Institute for Clinical and Experimental Surgery, University of Saarland, Homburg/Saar, Germany
| | - Stefan Barth
- Institute for Infectious disease and Molecular Medicine, University of Cape Town, South Africa
| | - Boris Kubuschok
- Department of Internal Medicine II, Augsburg University Medical Center, Augsburg, Germany
| | - Anja Mottok
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Germany
| | | | | | - Viola Pöschel
- Saarland Medical School, Internal Medicine I, Homburg/Saar, Germany
| | - Gerhard Held
- Department of Hematology/Oncology, Westpfalzklinikum Kaiserslautern, Germany
| | - Niels Murawski
- Saarland Medical School, Internal Medicine I, Homburg/Saar, Germany
| | | | - Frank Neumann
- Saarland Medical School, Internal Medicine I, Homburg/Saar, Germany
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6
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Wang Y, Xue P, Cao M, Yu T, Lane ST, Zhao H. Directed Evolution: Methodologies and Applications. Chem Rev 2021; 121:12384-12444. [PMID: 34297541 DOI: 10.1021/acs.chemrev.1c00260] [Citation(s) in RCA: 196] [Impact Index Per Article: 65.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Directed evolution aims to expedite the natural evolution process of biological molecules and systems in a test tube through iterative rounds of gene diversifications and library screening/selection. It has become one of the most powerful and widespread tools for engineering improved or novel functions in proteins, metabolic pathways, and even whole genomes. This review describes the commonly used gene diversification strategies, screening/selection methods, and recently developed continuous evolution strategies for directed evolution. Moreover, we highlight some representative applications of directed evolution in engineering nucleic acids, proteins, pathways, genetic circuits, viruses, and whole cells. Finally, we discuss the challenges and future perspectives in directed evolution.
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Affiliation(s)
- Yajie Wang
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Pu Xue
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Mingfeng Cao
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Tianhao Yu
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Stephan T Lane
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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7
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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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8
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Miao Y, Medeiros LJ, Li Y, Li J, Young KH. Genetic alterations and their clinical implications in DLBCL. Nat Rev Clin Oncol 2019; 16:634-652. [PMID: 31127191 DOI: 10.1038/s41571-019-0225-1] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Diffuse large B cell lymphoma (DLBCL) is a highly heterogeneous lymphoid neoplasm with variations in gene expression profiles and genetic alterations, which lead to substantial variations in clinical course and response to therapy. The advent of high-throughput genome sequencing platforms, and especially whole-exome sequencing, has helped to define the genetic landscape of DLBCL. In the past 10 years, these studies have identified many genetic alterations in DLBCL, some of which are specific to B cell lymphomas, whereas others can also be observed in other types of cancer. These aberrations result in altered activation of a wide range of signalling pathways and other cellular processes, including those involved in B cell differentiation, B cell receptor signalling, activation of the NF-κB pathway, apoptosis and epigenetic regulation. Further elaboration of the genetics of DLBCL will not only improve our understanding of disease pathogenesis but also provide further insight into disease classification, prognostication and therapeutic targets. In this Review, we describe the current understanding of the prevalence and causes of specific genetic alterations in DLBCL and their role in disease development and progression. We also summarize the available clinical data on therapies designed to target the aberrant pathways driven by these alterations.
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Affiliation(s)
- Yi Miao
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - L Jeffrey Medeiros
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yong Li
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Jianyong Li
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing, China
| | - Ken H Young
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. .,Graduate School of Biomedical Sciences, University of Texas Health Science Center, Houston, TX, USA.
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9
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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.
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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.
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10
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Ricci JE, Chiche J. Metabolic Reprogramming of Non-Hodgkin's B-Cell Lymphomas and Potential Therapeutic Strategies. Front Oncol 2018; 8:556. [PMID: 30564554 PMCID: PMC6288288 DOI: 10.3389/fonc.2018.00556] [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: 09/26/2018] [Accepted: 11/09/2018] [Indexed: 11/13/2022] Open
Abstract
Metabolism is a wide and general term that refers to any intracellular pathways the cell utilizes in order to satisfy its energetic demand and to support cell viability and/or division. Along with phenotypic changes, all mammalian cells including immune cells modulate their metabolic program in order to reach their effector functions. Exacerbated metabolism and metabolic flexibility are also hallmarks of tumor initiation and of tumor cell progression in a complex tumor microenvironment. Metabolic reprogramming is mainly directed by the serine/threonine kinase mTOR (mammalian target of rapamycin). mTOR exists in two structurally and functionally distinct complexes, mTORC1 and mTORC2 that coordinate environmental signals and metabolic/anabolic pathways to provide macromolecules and energy needed for survival and growth. Activation of mTORC1 is required during development, differentiation and activation of immune cells. Aberrant and persistent activation of mTORC1 is often observed in malignant B cells such as Non-Hodgkin's (NH) B-cell lymphomas. Here, we review recent insights on cell metabolism and on basic mechanisms of mTORC1 regulation and metabolic functions. We highlight the distinct mechanisms driving mTORC1 activation in the three most-common types of NH B-cell lymphomas (Diffuse Large B Cell Lymphomas, Follicular Lymphomas, and Mantle Cell Lymphomas), for which the first generation of mTORC1 inhibitors (rapalogs) have been extensively evaluated in preclinical and clinical settings. Finally, we discuss the reasons for limited clinical success of this therapy and focus on potential therapeutic strategies targeting metabolic pathways, upstream and downstream of mTORC1, that can be combined to rapalogs in order to improve patient's outcome.
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Affiliation(s)
- Jean-Ehrland Ricci
- INSERM U1065, C3M, Team Metabolism, Cancer and Immune Responses, Universiteé Côte d'Azur, Nice, France
| | - Johanna Chiche
- INSERM U1065, C3M, Team Metabolism, Cancer and Immune Responses, Universiteé Côte d'Azur, Nice, France
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11
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De novo gene mutations in normal human memory B cells. Leukemia 2018; 33:1219-1230. [PMID: 30353030 DOI: 10.1038/s41375-018-0289-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 08/20/2018] [Accepted: 08/31/2018] [Indexed: 12/12/2022]
Abstract
In the past years, the genomes of thousands of tumors have been elucidated. To date however, our knowledge on somatic gene alterations in normal cells is very limited. In this study, we demonstrate that tetanus-specific human memory B lymphocytes carry a substantial number of somatic mutations in the coding regions of the genome. Interestingly, we observed a statistically significant correlation between the number of exome mutations and those present in the immunoglobulin heavy variable regions. Our findings indicate that the majority of these genomic mutations arise in an antigen-dependent fashion, most likely during clonal expansion in germinal centers. The knowledge that normal B cells accumulate genomic alterations outside the immunoglobulin loci during development is relevant for our understanding of the process of lymphomagenesis.
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12
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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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13
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Liu X, Meng FL. Generation of Genomic Alteration from Cytidine Deamination. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1044:49-64. [DOI: 10.1007/978-981-13-0593-1_5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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14
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Boulianne B, Feldhahn N. Transcribing malignancy: transcription-associated genomic instability in cancer. Oncogene 2017; 37:971-981. [DOI: 10.1038/onc.2017.402] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 09/12/2017] [Accepted: 09/12/2017] [Indexed: 12/17/2022]
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15
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Juskevicius D, Müller A, Hashwah H, Lundberg P, Tzankov A, Menter T. Characterization of the mutational profile of 11 diffuse large B-cell lymphoma cell lines. Leuk Lymphoma 2017; 59:1710-1716. [DOI: 10.1080/10428194.2017.1387903] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Darius Juskevicius
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Anne Müller
- Institute of Molecular Cancer Research, University of Zürich, Zürich, Switzerland
| | - Hind Hashwah
- Institute of Molecular Cancer Research, University of Zürich, Zürich, Switzerland
| | - Pontus Lundberg
- Department of Hematology, University Hospital Basel, Basel, Switzerland
| | - Alexandar Tzankov
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Thomas Menter
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
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16
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Choudhary M, Tamrakar A, Singh AK, Jain M, Jaiswal A, Kodgire P. AID Biology: A pathological and clinical perspective. Int Rev Immunol 2017; 37:37-56. [PMID: 28933967 DOI: 10.1080/08830185.2017.1369980] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Activation-induced cytidine deaminase (AID), primarily expressed in activated mature B lymphocytes in germinal centers, is the key factor in adaptive immune response against foreign antigens. AID is responsible for producing high-affinity and high-specificity antibodies against an infectious agent, through the physiological DNA alteration processes of antibody genes by somatic hypermutation (SHM) and class-switch recombination (CSR) and functions by deaminating deoxycytidines (dC) to deoxyuridines (dU), thereby introducing point mutations and double-stranded chromosomal breaks (DSBs). The beneficial physiological role of AID in antibody diversification is outweighed by its detrimental role in the genesis of several chronic immune diseases, under non-physiological conditions. This review offers a comprehensive and better understanding of AID biology and its pathological aspects, as well as addresses the challenges involved in AID-related cancer therapeutics, based on various recent advances and evidence available in the literature till date. In this article, we discuss ways through which our interpretation of AID biology may reflect upon novel clinical insights, which could be successfully translated into designing clinical trials and improving patient prognosis and disease management.
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Affiliation(s)
- Meenal Choudhary
- a Centre for Biosciences and Biomedical Engineering , Indian Institute of Technology Indore , Simrol , Indore , Madhya Pradesh , India
| | - Anubhav Tamrakar
- a Centre for Biosciences and Biomedical Engineering , Indian Institute of Technology Indore , Simrol , Indore , Madhya Pradesh , India
| | - Amit Kumar Singh
- a Centre for Biosciences and Biomedical Engineering , Indian Institute of Technology Indore , Simrol , Indore , Madhya Pradesh , India
| | - Monika Jain
- a Centre for Biosciences and Biomedical Engineering , Indian Institute of Technology Indore , Simrol , Indore , Madhya Pradesh , India
| | - Ankit Jaiswal
- a Centre for Biosciences and Biomedical Engineering , Indian Institute of Technology Indore , Simrol , Indore , Madhya Pradesh , India
| | - Prashant Kodgire
- a Centre for Biosciences and Biomedical Engineering , Indian Institute of Technology Indore , Simrol , Indore , Madhya Pradesh , India
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17
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Activation-induced cytidine deaminase targets SUV4-20-mediated histone H4K20 trimethylation to class-switch recombination sites. Sci Rep 2017; 7:7594. [PMID: 28790320 PMCID: PMC5548798 DOI: 10.1038/s41598-017-07380-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 06/28/2017] [Indexed: 11/22/2022] Open
Abstract
Activation-induced cytidine deaminase (AID) triggers antibody diversification in B cells by catalysing deamination and subsequently mutating immunoglobulin (Ig) genes. Association of AID with RNA Pol II and occurrence of epigenetic changes during Ig gene diversification suggest participation of AID in epigenetic regulation. AID is mutated in hyper-IgM type 2 (HIGM2) syndrome. Here, we investigated the potential role of AID in the acquisition of epigenetic changes. We discovered that AID binding to the IgH locus promotes an increase in H4K20me3. In 293F cells, we demonstrate interaction between co-transfected AID and the three SUV4-20 histone H4K20 methyltransferases, and that SUV4-20H1.2, bound to the IgH switch (S) mu site, is replaced by SUV4-20H2 upon AID binding. Analysis of HIGM2 mutants shows that the AID truncated form W68X is impaired to interact with SUV4-20H1.2 and SUV4-20H2 and is unable to bind and target H4K20me3 to the Smu site. We finally show in mouse primary B cells undergoing class-switch recombination (CSR) that AID deficiency associates with decreased H4K20me3 levels at the Smu site. Our results provide a novel link between SUV4-20 enzymes and CSR and offer a new aspect of the interplay between AID and histone modifications in setting the epigenetic status of CSR sites.
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18
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Ezell SA, Wang S, Bihani T, Lai Z, Grosskurth SE, Tepsuporn S, Davies BR, Huszar D, Byth KF. Differential regulation of mTOR signaling determines sensitivity to AKT inhibition in diffuse large B cell lymphoma. Oncotarget 2016; 7:9163-74. [PMID: 26824321 PMCID: PMC4891033 DOI: 10.18632/oncotarget.7036] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 01/19/2016] [Indexed: 12/04/2022] Open
Abstract
Agents that target components of the PI3K/AKT/mTOR pathway are under investigation for the treatment of diffuse large B cell lymphoma (DLBCL). Given the highly heterogeneous nature of DLBCL, it is not clear whether all subtypes of DLBCL will be susceptible to PI3K pathway inhibition, or which kinase within this pathway is the most favorable target. Pharmacological profiling of a panel of DLBCL cell lines revealed a subset of DLBCL that was resistant to AKT inhibition. Strikingly, sensitivity to AKT inhibitors correlated with the ability of these inhibitors to block phosphorylation of S6K1 and ribosomal protein S6. Cell lines resistant to AKT inhibition activated S6K1 independent of AKT either through upregulation of PIM2 or through activation by B cell receptor (BCR) signaling components. Finally, combined inhibition of AKT and BTK, PIM2, or S6K1 proved to be an effective strategy to overcome resistance to AKT inhibition in DLBCL.
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Affiliation(s)
- Scott A Ezell
- AstraZeneca Oncology, Waltham, Massachusetts, MA, USA
| | - Suping Wang
- AstraZeneca Oncology, Waltham, Massachusetts, MA, USA
| | - Teeru Bihani
- AstraZeneca Oncology, Waltham, Massachusetts, MA, USA
| | - Zhongwu Lai
- AstraZeneca Oncology, Waltham, Massachusetts, MA, USA
| | | | | | | | - Dennis Huszar
- AstraZeneca Oncology, Waltham, Massachusetts, MA, USA
| | - Kate F Byth
- AstraZeneca Oncology, Waltham, Massachusetts, MA, USA
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19
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Kim JH, Kim WS, Ryu K, Kim SJ, Park C. CD79B limits response of diffuse large B cell lymphoma to ibrutinib. Leuk Lymphoma 2015; 57:1413-22. [PMID: 26699656 DOI: 10.3109/10428194.2015.1113276] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Blockage of B cell receptor signaling with ibrutinib presents a promising clinical approach for treatment of B-cell malignancies. However, many patients show primary resistance to the drug or develop secondary resistance. In the current study, cDNA microarray and Western blot analyses revealed CD79B upregulation in the activated B cell-like diffuse large B-cell lymphoma (ABC-DLBCL) that display differential resistance to ibrutinib. CD79B overexpression was sufficient to induce resistance to ibrutinib and enhanced AKT and MAPK activation, indicative of an alternative mechanism underlying resistance. Conversely, depletion of CD79B sensitized primary refractory cells to ibrutinib and led to reduced phosphorylation of AKT or MAPK. Combination of the AKT inhibitor or the MAPK inhibitor with ibrutinib resulted in circumvention of both primary and acquired resistance in ABC-DLBCL. Our data collectively indicate that CD79B overexpression leading to activation of AKT/MAPK is a potential mechanism underlying primary ibrutinib resistance in ABC-DLBCL, and support its utility as an effective biomarker to predict therapeutic response to ibrutinib.
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Affiliation(s)
- Joo Hyun Kim
- a Research Institute for Future Medicine, Samsung Medical Center , Sungkyunkwan University School of Medicine , Seoul , Korea
| | - Won Seog Kim
- a Research Institute for Future Medicine, Samsung Medical Center , Sungkyunkwan University School of Medicine , Seoul , Korea ;,b Division of Hematology and Oncology, Department of Medicine, Samsung Medical Center , Sungkyunkwan University School of Medicine , Seoul , Korea
| | - Kyungju Ryu
- a Research Institute for Future Medicine, Samsung Medical Center , Sungkyunkwan University School of Medicine , Seoul , Korea
| | - Seok Jin Kim
- a Research Institute for Future Medicine, Samsung Medical Center , Sungkyunkwan University School of Medicine , Seoul , Korea ;,b Division of Hematology and Oncology, Department of Medicine, Samsung Medical Center , Sungkyunkwan University School of Medicine , Seoul , Korea
| | - Chaehwa Park
- a Research Institute for Future Medicine, Samsung Medical Center , Sungkyunkwan University School of Medicine , Seoul , Korea
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20
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Chandra V, Bortnick A, Murre C. AID targeting: old mysteries and new challenges. Trends Immunol 2015; 36:527-35. [PMID: 26254147 DOI: 10.1016/j.it.2015.07.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 07/14/2015] [Accepted: 07/14/2015] [Indexed: 01/09/2023]
Abstract
Activation-induced cytidine deaminase (AID) mediates cytosine deamination and underlies two central processes in antibody diversification: somatic hypermutation and class-switch recombination. AID deamination is not exclusive to immunoglobulin loci; it can instigate DNA lesions in non-immunoglobulin genes and thus stringent checks are in place to constrain and restrict its activity. Recent findings have provided new insights into the mechanisms that target AID activity to specific genomic regions, revealing an involvement for noncoding RNAs associated with polymerase pausing and with enhancer transcription as well as genomic architecture. We review these findings and integrate them into a model for multilevel regulation of AID expression and targeting in immunoglobulin and non-immunoglobulin loci. Within this framework we discuss gaps in understanding, and outline important areas of further research.
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Affiliation(s)
- Vivek Chandra
- Department of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0377, USA
| | - Alexandra Bortnick
- Department of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0377, USA
| | - Cornelis Murre
- Department of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0377, USA.
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21
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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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22
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Rebhandl S, Huemer M, Greil R, Geisberger R. AID/APOBEC deaminases and cancer. Oncoscience 2015; 2:320-33. [PMID: 26097867 PMCID: PMC4468319 DOI: 10.18632/oncoscience.155] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 04/01/2015] [Indexed: 02/06/2023] Open
Abstract
Mutations are the basis for evolution and the development of genetic diseases. Especially in cancer, somatic mutations in oncogenes and tumor suppressor genes alongside the occurrence of passenger mutations have been observed by recent deep-sequencing approaches. While mutations have long been considered random events induced by DNA-replication errors or by DNA damaging agents, genome sequencing led to the discovery of non-random mutation signatures in many human cancer. Common non-random mutations comprise DNA strand-biased mutation showers and mutations restricted to certain DNA motifs, which recently have become attributed to the activity of the AID/APOBEC family of DNA deaminases. Hence, APOBEC enzymes, which have evolved as key players in natural and adaptive immunity, have been proposed to contribute to cancer development and clonal evolution of cancer by inducing collateral genomic damage due to their DNA deaminating activity. This review focuses on how mutagenic events through AID/APOBEC deaminases may contribute to cancer development.
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Affiliation(s)
- Stefan Rebhandl
- Department of internal Medicine III with Hematology, Medical Oncology, Hemostaseology, Infectious Diseases, Rheumatology, Oncologic Center, Laboratory for Immunological and Molecular Cancer Research, Paracelsus Medical University Salzburg, Austria ; Salzburg Cancer Research Institute, Salzburg, Austria
| | - Michael Huemer
- Department of internal Medicine III with Hematology, Medical Oncology, Hemostaseology, Infectious Diseases, Rheumatology, Oncologic Center, Laboratory for Immunological and Molecular Cancer Research, Paracelsus Medical University Salzburg, Austria ; Salzburg Cancer Research Institute, Salzburg, Austria
| | - Richard Greil
- Department of internal Medicine III with Hematology, Medical Oncology, Hemostaseology, Infectious Diseases, Rheumatology, Oncologic Center, Laboratory for Immunological and Molecular Cancer Research, Paracelsus Medical University Salzburg, Austria ; Salzburg Cancer Research Institute, Salzburg, Austria
| | - Roland Geisberger
- Department of internal Medicine III with Hematology, Medical Oncology, Hemostaseology, Infectious Diseases, Rheumatology, Oncologic Center, Laboratory for Immunological and Molecular Cancer Research, Paracelsus Medical University Salzburg, Austria ; Salzburg Cancer Research Institute, Salzburg, Austria
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23
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Dominguez PM, Shaknovich R. Epigenetic function of activation-induced cytidine deaminase and its link to lymphomagenesis. Front Immunol 2014; 5:642. [PMID: 25566255 PMCID: PMC4270259 DOI: 10.3389/fimmu.2014.00642] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 12/02/2014] [Indexed: 01/16/2023] Open
Abstract
Activation-induced cytidine deaminase (AID) is essential for somatic hypermutation and class switch recombination of immunoglobulin (Ig) genes during B cell maturation and immune response. Expression of AID is tightly regulated due to its mutagenic and recombinogenic potential, which is known to target not only Ig genes, but also non-Ig genes, contributing to lymphomagenesis. In recent years, a new epigenetic function of AID and its link to DNA demethylation came to light in several developmental systems. In this review, we summarize existing evidence linking deamination of unmodified and modified cytidine by AID to base-excision repair and mismatch repair machinery resulting in passive or active removal of DNA methylation mark, with the focus on B cell biology. We also discuss potential contribution of AID-dependent DNA hypomethylation to lymphomagenesis.
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Affiliation(s)
- Pilar M Dominguez
- Division of Hematology and Oncology, Weill Cornell Medical College , New York, NY , USA
| | - Rita Shaknovich
- Division of Hematology and Oncology, Weill Cornell Medical College , New York, NY , USA ; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College , New York, NY , USA
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24
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Shaknovich R, De S, Michor F. Epigenetic diversity in hematopoietic neoplasms. Biochim Biophys Acta Rev Cancer 2014; 1846:477-84. [PMID: 25240947 DOI: 10.1016/j.bbcan.2014.09.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 09/09/2014] [Accepted: 09/11/2014] [Indexed: 12/31/2022]
Abstract
Tumor cell populations display a remarkable extent of variability in non-genetic characteristics such as DNA methylation, histone modification patterns, and differentiation levels of individual cells. It remains to be elucidated whether non-genetic heterogeneity is simply a byproduct of tumor evolution or instead a manifestation of a higher-order tissue organization that is maintained within the neoplasm to establish a differentiation hierarchy, a favorable microenvironment, or a buffer against changing selection pressures during tumorigenesis. Here, we review recent findings on epigenetic diversity, particularly heterogeneity in DNA methylation patterns in hematologic malignancies. We also address the implications of epigenetic heterogeneity for the clonal evolution of tumors and discuss its effects on gene expression and other genome functions in cancer.
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Affiliation(s)
- Rita Shaknovich
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medical College, New York, NY 10021, USA; Division of Immunopathology, Department of Pathology, Weill Cornell Medical College, New York, NY 10021, USA
| | - Subhajyoti De
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO 80045, USA; University of Colorado Cancer Center, Aurora, CO 80045, USA
| | - Franziska Michor
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, MA 02215, USA; Department of Biostatistics, Harvard School of Public Health, Boston, MA 02215, USA.
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25
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Della Valle L, Dohmen SE, Verhagen OJHM, Berkowska MA, Vidarsson G, Ellen van der Schoot C. The majority of human memory B cells recognizing RhD and tetanus resides in IgM+ B cells. THE JOURNAL OF IMMUNOLOGY 2014; 193:1071-9. [PMID: 24965774 DOI: 10.4049/jimmunol.1400706] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
B cell memory to T cell-dependent (TD) Ags are considered to largely reside in class-switched CD27(+) cells. However, we previously observed that anti-RhD (D) Igs cloned from two donors, hyperimmunized with D(+) erythrocytes, were predominantly of the IgM isotype. We therefore analyzed in this study the phenotype and frequency of D- and tetanus toxoid-specific B cells by culturing B cells in limiting dilution upon irradiated CD40L-expressing EL4.B5 cells and testing the culture supernatant. Most Ag-specific B cells for both TD Ags were found to reside in the IgM-expressing B cells, including CD27(-) B cells, in both hyperimmunized donors and nonhyperimmunized volunteers. Only shortly after immunization a sharp increase in Ag-specific CD27(+)IgG(+) B cells was observed. Next, B cells were enriched with D(+) erythrocyte ghosts and sorted as single cells. Sequencing of IGHV, IGLV, IGKV, and BCL6 genes from these D-specific B cell clones demonstrated that both CD27(-)IgM(+) and CD27(+)IgM(+) B cells harbored somatic mutations, documenting their Ag-selected nature. Furthermore, sequencing revealed a clonal relationship between the CD27(-)IgM(+), CD27(+)IgM(+), and CD27(+)IgG(+) B cell subsets. These data strongly support the recently described multiple layers of memory B cells to TD Ags in mice, where IgM(+) B cells represent a memory reservoir which can re-enter the germinal center and ensure replenishment of class-switched memory CD27(+) B cells from Ag-experienced precursors.
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Affiliation(s)
- Luciana Della Valle
- Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, 1066 CX Amsterdam, the Netherlands; and
| | - Serge E Dohmen
- Department of Internal Medicine, BovenIJ Hospital, 1034 CS Amsterdam, the Netherlands
| | - Onno J H M Verhagen
- Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, 1066 CX Amsterdam, the Netherlands; and
| | - Magdalena A Berkowska
- Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, 1066 CX Amsterdam, the Netherlands; and
| | - Gestur Vidarsson
- Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, 1066 CX Amsterdam, the Netherlands; and
| | - C Ellen van der Schoot
- Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory, Academic Medical Center, University of Amsterdam, 1066 CX Amsterdam, the Netherlands; and
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26
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Chen Z, Wang JH. Generation and repair of AID-initiated DNA lesions in B lymphocytes. Front Med 2014; 8:201-16. [PMID: 24748462 PMCID: PMC4039616 DOI: 10.1007/s11684-014-0324-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 12/30/2013] [Indexed: 01/12/2023]
Abstract
Activation-induced deaminase (AID) initiates the secondary antibody diversification process in B lymphocytes. In mammalian B cells, this process includes somatic hypermutation (SHM) and class switch recombination (CSR), both of which require AID. AID induces U:G mismatch lesions in DNA that are subsequently converted into point mutations or DNA double stranded breaks during SHM/CSR. In a physiological context, AID targets immunoglobulin (Ig) loci to mediate SHM/CSR. However, recent studies reveal genome-wide access of AID to numerous non-Ig loci. Thus, AID poses a threat to the genome of B cells if AID-initiated DNA lesions cannot be properly repaired. In this review, we focus on the molecular mechanisms that regulate the specificity of AID targeting and the repair pathways responsible for processing AID-initiated DNA lesions.
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Affiliation(s)
- Zhangguo Chen
- Integrated Department of Immunology, University of Colorado Anschutz Medical Campus and National Jewish Health, Denver, CO 80206
| | - Jing H. Wang
- Integrated Department of Immunology, University of Colorado Anschutz Medical Campus and National Jewish Health, Denver, CO 80206
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27
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Erratum to: The role of activation-induced deaminase in antibody diversification and genomic instability. Immunol Res 2013. [DOI: 10.1007/s12026-013-8432-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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28
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Wang JH. The role of activation-induced deaminase in antibody diversification and genomic instability. Immunol Res 2013; 55:287-97. [PMID: 22956489 DOI: 10.1007/s12026-012-8369-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
More than a decade ago, activation-induced deaminase (AID) was identified as the initiator for somatic hypermutation (SHM) and class switch recombination (CSR). Since then, tremendous progress has been achieved toward elucidating how AID functions. AID targets the highly repetitive switch regions of the immunoglobulin heavy chain (IgH) locus to induce DNA double-strand breaks (DSBs), which can be rejoined, leading to switch of constant regions of antibody. When targeting to variable region exons of IgH and IgL loci, AID predominantly induces point mutations, termed SHM, resulting in increased affinity of antibody for antigen. While SHM and CSR enhance antibody diversity, AID-initiated DSBs and mutations may predispose B cells to carcinogenesis. This review focuses on the mechanisms that provide the specificity of AID targeting to Ig loci and the role of AID in genomic instability.
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Affiliation(s)
- Jing H Wang
- Integrated Department of Immunology, University of Colorado School of Medicine and National Jewish Health, Denver, CO 80206, USA.
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29
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Ponce RA, Gelzleichter T, Haggerty HG, Heidel S, Holdren MS, Lebrec H, Mellon RD, Pallardy M. Immunomodulation and lymphoma in humans. J Immunotoxicol 2013; 11:1-12. [DOI: 10.3109/1547691x.2013.798388] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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30
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Yoo EJ, Cooke NE, Liebhaber SA. Identification of a secondary promoter within the human B cell receptor component gene hCD79b. J Biol Chem 2013; 288:18353-65. [PMID: 23649625 DOI: 10.1074/jbc.m113.461988] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The human B cell-specific protein, CD79b (also known as Igβ and B29) constitutes an essential signal transduction component of the B cell receptor. Although its function is central to the triggering of B cell terminal differentiation in response to antigen stimulation, the transcriptional determinants that control CD79b gene expression remain poorly defined. In the present study, we explored these determinants using a series of hCD79b transgenic mouse models. Remarkably, we observed that the previously described hCD79b promoter along with its associated enhancer elements and first exon could be deleted without appreciable loss of hCD79b transcriptional activity or tissue specificity. In this deletion setting, a secondary promoter located within exon 2 maintained full levels and specificity of hCD79b transcription. Of note, this secondary promoter was also active, albeit at lower levels, in the wild-type hCD79b locus. The activity of the secondary promoter was dependent on the action(s) of a conserved sequence element mapping to a chromatin DNase I hypersensitive site located within intron 1. mRNA generated from this secondary promoter is predicted to encode an Igβ protein lacking a signal sequence and thus unable to serve normal B cell receptor function. Although the physiologic role of the hCD79b secondary promoter and its encoded protein remain unclear, the current data suggest that it has the capacity to play a role in normal as well as pathologic states in B cell proliferation and function.
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Affiliation(s)
- Eung Jae Yoo
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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Jaszczur M, Bertram JG, Pham P, Scharff MD, Goodman MF. AID and Apobec3G haphazard deamination and mutational diversity. Cell Mol Life Sci 2012. [PMID: 23178850 DOI: 10.1007/s00018-012-1212-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Activation-induced deoxycytidine deaminase (AID) and Apobec 3G (Apo3G) cause mutational diversity by initiating mutations on regions of single-stranded (ss) DNA. Expressed in B cells, AID deaminates C → U in actively transcribed immunoglobulin (Ig) variable and switch regions to initiate the somatic hypermutation (SHM) and class switch recombination (CSR) that are essential for antibody diversity. Apo3G expressed in T cells catalyzes C deaminations on reverse transcribed cDNA causing HIV-1 retroviral inactivation. When operating properly, AID- and Apo3G-initiated mutations boost human fitness. Yet, both enzymes are potentially powerful somatic cell "mutators". Loss of regulated expression and proper genome targeting can cause human cancer. Here, we review well-established biological roles of AID and Apo3G. We provide a synopsis of AID partnering proteins during SHM and CSR, and describe how an Apo2 crystal structure provides "surrogate" insight for AID and Apo3G biochemical behavior. However, large gaps remain in our understanding of how dC deaminases search ssDNA to identify trinucleotide motifs to deaminate. We discuss two recent methods to analyze ssDNA scanning and deamination. Apo3G scanning and deamination is visualized in real-time using single-molecule FRET, and AID deamination efficiencies are determined with a random walk analysis. AID and Apo3G encounter many candidate deamination sites while scanning ssDNA. Generating mutational diversity is a principal aim of AID and an important ancillary property of Apo3G. Success seems likely to involve hit and miss deamination motif targeting, biased strongly toward miss.
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Affiliation(s)
- Malgorzata Jaszczur
- Departments of Biological Sciences and Chemistry, Molecular and Computational Biology Section, University of Southern California, Los Angeles, CA 90089-2910, USA
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Chen Z, Viboolsittiseri SS, O'Connor BP, Wang JH. Target DNA sequence directly regulates the frequency of activation-induced deaminase-dependent mutations. THE JOURNAL OF IMMUNOLOGY 2012; 189:3970-82. [PMID: 22962683 DOI: 10.4049/jimmunol.1200416] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Activation-induced deaminase (AID) catalyses class switch recombination (CSR) and somatic hypermutation (SHM) in B lymphocytes to enhance Ab diversity. CSR involves breaking and rejoining highly repetitive switch (S) regions in the IgH (Igh) locus. S regions appear to be preferential targets of AID. To determine whether S region sequence per se, independent of Igh cis regulatory elements, can influence AID targeting efficiency and mutation frequency, we established a knock-in mouse model by inserting a core Sγ1 region into the first intron of proto-oncogene Bcl6, which is a non-Ig target of SHM. We found that the mutation frequency of the inserted Sγ1 region was dramatically higher than that of the adjacent Bcl6 endogenous sequence. Mechanistically, S region-enhanced SHM was associated with increased recruitment of AID and RNA polymerase II, together with Spt5, albeit to a lesser extent. Our studies demonstrate that target DNA sequences influence mutation frequency via regulating AID recruitment. We propose that the nucleotide sequence preference may serve as an additional layer of AID regulation by restricting its mutagenic activity to specific sequences despite the observation that AID has the potential to access the genome widely.
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Affiliation(s)
- Zhangguo Chen
- Integrated Department of Immunology, University of Colorado School of Medicine and National Jewish Health, Denver, CO 80206, USA
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Gramlich HS, Reisbig T, Schatz DG. AID-targeting and hypermutation of non-immunoglobulin genes does not correlate with proximity to immunoglobulin genes in germinal center B cells. PLoS One 2012; 7:e39601. [PMID: 22768095 PMCID: PMC3387148 DOI: 10.1371/journal.pone.0039601] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Accepted: 05/25/2012] [Indexed: 12/21/2022] Open
Abstract
Upon activation, B cells divide, form a germinal center, and express the activation induced deaminase (AID), an enzyme that triggers somatic hypermutation of the variable regions of immunoglobulin (Ig) loci. Recent evidence indicates that at least 25% of expressed genes in germinal center B cells are mutated or deaminated by AID. One of the most deaminated genes, c-Myc, frequently appears as a translocation partner with the Ig heavy chain gene (Igh) in mouse plasmacytomas and human Burkitt's lymphomas. This indicates that the two genes or their double-strand break ends come into close proximity at a biologically relevant frequency. However, the proximity of c-Myc and Igh has never been measured in germinal center B cells, where many such translocations are thought to occur. We hypothesized that in germinal center B cells, not only is c-Myc near Igh, but other mutating non-Ig genes are deaminated by AID because they are near Ig genes, the primary targets of AID. We tested this "collateral damage" model using 3D-fluorescence in situ hybridization (3D-FISH) to measure the distance from non-Ig genes to Ig genes in germinal center B cells. We also made mice transgenic for human MYC and measured expression and mutation of the transgenes. We found that there is no correlation between proximity to Ig genes and levels of AID targeting or gene mutation, and that c-Myc was not closer to Igh than were other non-Ig genes. In addition, the human MYC transgenes did not accumulate mutations and were not deaminated by AID. We conclude that proximity to Ig loci is unlikely to be a major determinant of AID targeting or mutation of non-Ig genes, and that the MYC transgenes are either missing important regulatory elements that allow mutation or are unable to mutate because their new nuclear position is not conducive to AID deamination.
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Affiliation(s)
- Hillary Selle Gramlich
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Tara Reisbig
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - David G. Schatz
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
- * E-mail:
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Honjo T, Kobayashi M, Begum N, Kotani A, Sabouri S, Nagaoka H. The AID dilemma: infection, or cancer? Adv Cancer Res 2012; 113:1-44. [PMID: 22429851 DOI: 10.1016/b978-0-12-394280-7.00001-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Activation-induced cytidine deaminase (AID), which is both essential and sufficient for forming antibody memory, is also linked to tumorigenesis. AID is found in many B lymphomas, in myeloid leukemia, and in pathogen-induced tumors such as adult T cell leukemia. Although there is no solid evidence that AID causes human tumors, AID-transgenic and AID-deficient mouse models indicate that AID is both sufficient and required for tumorigenesis. Recently, AID's ability to cleave DNA has been shown to depend on topoisomerase 1 (Top1) and a histone H3K4 epigenetic mark. When the level of Top1 protein is decreased by AID activation, it induces irreversible cleavage in highly transcribed targets. This finding and others led to the idea that there is an evolutionary link between meiotic recombination and class switch recombination, which share H3K4 trimethyl, topoisomerase, the MRN complex, mismatch repair family proteins, and exonuclease 3. As Top1 has recently been shown to be involved in many transcription-associated genome instabilities, it is likely that AID took advantage of basic genome instability or diversification to evolve its mechanism for immune diversity. AID targets are therefore not highly specific to immunoglobulin genes and are relatively abundant, although they have strict requirements for transcription-induced H3K4 trimethyl modification and repetitive sequences prone to forming non-B structures. Inevitably, AID-dependent cleavage takes place in nonimmunoglobulin targets and eventually causes tumors. However, battles against infection are waged in the context of acute emergencies, while tumorigenesis is rather a chronic, long-term process. In the interest of survival, vertebrates must have evolved AID to prevent infection despite its long-term risk of causing tumorigenesis.
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Gazumyan A, Bothmer A, Klein IA, Nussenzweig MC, McBride KM. Activation-induced cytidine deaminase in antibody diversification and chromosome translocation. Adv Cancer Res 2012; 113:167-90. [PMID: 22429855 PMCID: PMC4353630 DOI: 10.1016/b978-0-12-394280-7.00005-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DNA damage, rearrangement, and mutation of the human genome are the basis of carcinogenesis and thought to be avoided at all costs. An exception is the adaptive immune system where lymphocytes utilize programmed DNA damage to effect antigen receptor diversification. Both B and T lymphocytes diversify their antigen receptors through RAG1/2 mediated recombination, but B cells undergo two additional processes--somatic hypermutation (SHM) and class-switch recombination (CSR), both initiated by activation-induced cytidine deaminase (AID). AID deaminates cytidines in DNA resulting in U:G mismatches that are processed into point mutations in SHM or double-strand breaks in CSR. Although AID activity is focused at Immunoglobulin (Ig) gene loci, it also targets a wide array of non-Ig genes including oncogenes associated with lymphomas. Here, we review the molecular basis of AID regulation, targeting, and initiation of CSR and SHM, as well as AID's role in generating chromosome translocations that contribute to lymphomagenesis.
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Affiliation(s)
- Anna Gazumyan
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, USA
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Klein IA, Resch W, Jankovic M, Oliveira T, Yamane A, Nakahashi H, Di Virgilio M, Bothmer A, Nussenzweig A, Robbiani DF, Casellas R, Nussenzweig MC. Translocation-capture sequencing reveals the extent and nature of chromosomal rearrangements in B lymphocytes. Cell 2011; 147:95-106. [PMID: 21962510 DOI: 10.1016/j.cell.2011.07.048] [Citation(s) in RCA: 286] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Revised: 07/14/2011] [Accepted: 07/27/2011] [Indexed: 02/06/2023]
Abstract
Chromosomal rearrangements, including translocations, require formation and joining of DNA double strand breaks (DSBs). These events disrupt the integrity of the genome and are frequently involved in producing leukemias, lymphomas and sarcomas. Despite the importance of these events, current understanding of their genesis is limited. To examine the origins of chromosomal rearrangements we developed Translocation Capture Sequencing (TC-Seq), a method to document chromosomal rearrangements genome-wide, in primary cells. We examined over 180,000 rearrangements obtained from 400 million B lymphocytes, revealing that proximity between DSBs, transcriptional activity and chromosome territories are key determinants of genome rearrangement. Specifically, rearrangements tend to occur in cis and to transcribed genes. Finally, we find that activation-induced cytidine deaminase (AID) induces the rearrangement of many genes found as translocation partners in mature B cell lymphoma.
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Affiliation(s)
- Isaac A Klein
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
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Abstract
Antibody maturation requires class switch recombination (CSR) and somatic hypermutation (SHM), both of which are initiated by activation-induced cytidine deaminase (AID). AID deaminates cytosine residues resulting in mismatches that are differentially processed to produce double-strand breaks in Ig switch (S) regions that lead to CSR, or to point mutations in variable (V) exons resulting in SHM. Although AID was first thought to be Ig-specific, recent work indicates that it also targets a diverse group of non-Ig loci, including genes such as Bcl6 and c-myc, whose modification by AID results in lymphoma-associated mutations and translocations. Here, we review the recent literature on AID targeting and the role for transcriptional stalling in recruitment of this enzyme to Ig and non-Ig loci. We propose a model for AID recruitment based on transcriptional stalling, which reconciles several of the key features of SHM, CSR, and lymphoma-associated translocation.
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Affiliation(s)
- Rushad Pavri
- Laboratory of Molecular Immunology, The Rockefeller University, New York, USA
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Oliveira TY, Resch W, Jankovic M, Casellas R, Nussenzweig MC, Klein IA. Translocation capture sequencing: a method for high throughput mapping of chromosomal rearrangements. J Immunol Methods 2011; 375:176-81. [PMID: 22033343 DOI: 10.1016/j.jim.2011.10.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Accepted: 10/11/2011] [Indexed: 10/16/2022]
Abstract
Chromosomal translocations require formation and joining of DNA double strand breaks (DSBs). These events disrupt the integrity of the genome and are involved in producing leukemias, lymphomas and sarcomas. Translocations are frequent, clonal and recurrent in mature B cell lymphomas, which bear a particularly high DNA damage burden by virtue of activation-induced cytidine deaminase (AID) expression. Despite the ubiquity of genomic rearrangements, the forces that underlie their genesis are not well understood. Here, we provide a detailed description of a new method for studying these events, translocation capture sequencing (TC-Seq). TC-Seq provides the means to document chromosomal rearrangements genome-wide in primary cells, and to discover recombination hotspots. Demonstrating its effectiveness, we successfully estimate the frequency of c-myc/IgH translocations in primary B cells, and identify hotspots of AID-mediated recombination. Furthermore, TC-Seq can be adapted to generate genome-wide rearrangement maps in any cell type and under any condition.
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Affiliation(s)
- Thiago Y Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
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39
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Abstract
The immunoglobulin (Ig) genes of B cells are diversified at high rate by point mutations whereas the non-Ig genes of B cells accumulate no or significantly fewer mutations. Ig hypermutations are critical for the affinity maturation of antibodies for most of jawed vertebrates and also contribute to the primary Ig diversity repertoire formation in some species. How the hypermutation activity is specifically targeted to the Ig loci is a long-standing debate. Here we describe a new experimental approach to investigate the locus specificity of Ig hypermutation using the chicken B-cell line DT40. One feature is the use of a green fluorescent protein (GFP) gene as a mutation reporter. Some nucleotide changes produced by somatic hypermutation can cripple the GFP gene which leads to a decrease or loss of the green fluorescence. Therefore such changes can be easily quantified by fluorescence-activated cell sorting (FACS). Another advantage of this approach is the targeted integration of the mutation reporter into a defined chromosomal position. This system allowed us to identify a 10 kb sequence within the Ig light chain (IgL) locus, which is both necessary and sufficient to activate hypermutation in the neighboring reporter gene. We have called this sequence Diversification Activator (DIVAC) and postulated that similar cis-acting sequences exist in the heavy and light chain Ig loci of all jawed vertebrate species. Our experimental system promises further insight into the molecular mechanism of Ig hypermutation. For example, it may be possible to identify smaller functional motifs within DIVAC and address the role of putative transacting binding factors by gene knock-outs.
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Kracker S, Durandy A. Insights into the B cell specific process of immunoglobulin class switch recombination. Immunol Lett 2011; 138:97-103. [DOI: 10.1016/j.imlet.2011.02.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Revised: 01/31/2011] [Accepted: 02/03/2011] [Indexed: 10/18/2022]
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Stavnezer J. Complex regulation and function of activation-induced cytidine deaminase. Trends Immunol 2011; 32:194-201. [PMID: 21493144 DOI: 10.1016/j.it.2011.03.003] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Revised: 03/05/2011] [Accepted: 03/08/2011] [Indexed: 01/10/2023]
Abstract
Activation-induced cytidine deaminase (AID) instigates mutations and DNA breaks in Ig genes that undergo somatic hypermutation and class switch recombination during B cell activation in response to immunization and infection. This review discusses how AID expression and activity are regulated, including recent discoveries of AID-interacting proteins that might recruit AID to Ig genes, and allow it to target both DNA strands. Also discussed is the accumulating evidence that AID binds to, mutates, and creates breaks at numerous non-Ig sites in the genome, which initiates cell transformation and malignancies.
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Affiliation(s)
- Janet Stavnezer
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01655, USA.
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Huang X, Takata K, Sato Y, Tanaka T, Ichimura K, Tamura M, Oka T, Yoshino T. Downregulation of the B-cell receptor signaling component CD79b in plasma cell myeloma: a possible post transcriptional regulation. Pathol Int 2011; 61:122-9. [PMID: 21355953 DOI: 10.1111/j.1440-1827.2010.02634.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The CD79 molecule, encoded by the CD79a and CD79b genes, is a signaling unit of the B-cell receptor complex, which transmits signals of B-cell activation, growth, and differentiation. They are B-cell-specific and expressed at most stages of B-cell development. Although plasma cells have been believed to lack these gene products, the regulation of CD79 expression in plasma cells is still controversial. In particular, the regulation of CD79b expression remains unclear. We sought to examine CD79b expression in normal and neoplastic plasma cells by immunohistochemical analysis. Out of the 23 clinical samples and 11 cell lines of plasma cell myeloma (PCM), none of the clinical samples and only 1 of 11 cell lines expressed CD79b immunohistologically, whereas non-neoplastic plasma cells in reactive hyperplastic lymph nodes exhibited loss of CD79b protein expression. This finding is quite different from our previous report on CD79a. Not only immunocytochemistry, but also RT-PCR and Western blot analysis of PCM cell lines gave identical results. Interestingly, we detected mRNA transcripts of CD79b in PCM cell lines, although protein translation was lacking. These findings suggest that expression of CD79b is downregulated in both plasma cells and plasma cell myeloma, and this process is possibly under post transcriptional regulation.
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Affiliation(s)
- Xingang Huang
- Department of Pathology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
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Deep-sequencing identification of the genomic targets of the cytidine deaminase AID and its cofactor RPA in B lymphocytes. Nat Immunol 2010; 12:62-9. [PMID: 21113164 DOI: 10.1038/ni.1964] [Citation(s) in RCA: 221] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2010] [Accepted: 11/02/2010] [Indexed: 12/13/2022]
Abstract
The cytidine deaminase AID hypermutates immunoglobulin genes but can also target oncogenes, leading to tumorigenesis. The extent of AID's promiscuity and its predilection for immunoglobulin genes are unknown. We report here that AID interacted broadly with promoter-proximal sequences associated with stalled polymerases and chromatin-activating marks. In contrast, genomic occupancy of replication protein A (RPA), an AID cofactor, was restricted to immunoglobulin genes. The recruitment of RPA to the immunoglobulin loci was facilitated by phosphorylation of AID at Ser38 and Thr140. We propose that stalled polymerases recruit AID, thereby resulting in low frequencies of hypermutation across the B cell genome. Efficient hypermutation and switch recombination required AID phosphorylation and correlated with recruitment of RPA. Our findings provide a rationale for the oncogenic role of AID in B cell malignancy.
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Li F, Yan Y, Pieretti J, Feldman DA, Eckhardt LA. Comparison of identical and functional Igh alleles reveals a nonessential role for Eμ in somatic hypermutation and class-switch recombination. THE JOURNAL OF IMMUNOLOGY 2010; 185:6049-57. [PMID: 20937850 DOI: 10.4049/jimmunol.0902992] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Somatic hypermutation (SHM), coupled with Ag selection, provides a mechanism for generating Abs with high affinity for invading pathogens. Class-switch recombination (CSR) ensures that these Abs attain pathogen-appropriate effector functions. Although the enzyme critical to both processes, activation-induced cytidine deaminase, has been identified, it remains unclear which cis-elements within the Ig loci are responsible for recruiting activation-induced cytidine deaminase and promoting its activity. Studies showed that Ig gene-transcription levels are positively correlated with the frequency of SHM and CSR, making the intronic, transcriptional enhancer Eμ a likely contributor to both processes. Tests of this hypothesis yielded mixed results arising, in part, from the difficulty in studying B cell function in mice devoid of Eμ. In Eμ's absence, V(H) gene assembly is dramatically impaired, arresting B cell development. The current study circumvented this problem by modifying the murine Igh locus through simultaneous insertion of a fully assembled V(H) gene and deletion of Eμ. The behavior of this allele was compared with that of a matched allele carrying the same V(H) gene but with Eμ intact. Although IgH transcription was as great or greater on the Eμ-deficient allele, CSR and SHM were consistently, but modestly, reduced relative to the allele in which Eμ remained intact. We conclude that Eμ contributes to, but is not essential for, these complex processes and that its contribution is not as a transcriptional enhancer but, rather, is at the level of recruitment and/or activation of the SHM/CSR machinery.
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Affiliation(s)
- Fubin Li
- Department of Biological Sciences, Hunter College and Graduate Center, City University of New York, New York, NY 10065, USA
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45
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Peled JU, Sellers RS, Iglesias-Ussel MD, Shin DM, Montagna C, Zhao C, Li Z, Edelmann W, Morse HC, Scharff MD. Msh6 protects mature B cells from lymphoma by preserving genomic stability. THE AMERICAN JOURNAL OF PATHOLOGY 2010; 177:2597-608. [PMID: 20934970 DOI: 10.2353/ajpath.2010.100234] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Most human B-cell non-Hodgkin's lymphomas arise from germinal centers. Within these sites, the mismatch repair factor MSH6 participates in antibody diversification. Reminiscent of the neoplasms arising in patients with Lynch syndrome III, mice deficient in MSH6 die prematurely of lymphoma. In this study, we characterized the B-cell tumors in MSH6-deficient mice and describe their histological, immunohistochemical, and molecular features, which include moderate microsatellite instability. Based on histological markers and gene expression, the tumor cells seem to be at or beyond the germinal center stage. The simultaneous loss of MSH6 and of activation-induced cytidine deaminase did not appreciably affect the survival of these animals, suggesting that these germinal center-like tumors arose by an activation-induced cytidine deaminase-independent pathway. We conclude that MSH6 protects B cells from neoplastic transformation by preserving genomic stability.
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Affiliation(s)
- Jonathan U Peled
- Cell Biology Department, Chanin 403, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
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46
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Nussenzweig A, Nussenzweig MC. Origin of chromosomal translocations in lymphoid cancer. Cell 2010; 141:27-38. [PMID: 20371343 DOI: 10.1016/j.cell.2010.03.016] [Citation(s) in RCA: 227] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2009] [Revised: 01/13/2010] [Accepted: 03/16/2010] [Indexed: 11/26/2022]
Abstract
Aberrant fusions between heterologous chromosomes are among the most prevalent cytogenetic abnormalities found in cancer cells. Oncogenic chromosomal translocations provide cells with a proliferative or survival advantage. They may either initiate transformation or be acquired secondarily as a result of genomic instability. Here, we highlight recent advances toward understanding the origin of chromosomal translocations in incipient lymphoid cancers and how tumor-suppressive pathways normally limit the frequency of these aberrant recombination events. Deciphering the mechanisms that mediate chromosomal fusions will open new avenues for developing therapeutic strategies aimed at eliminating lesions that lead to the initiation, maintenance, and progression of cancer.
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Affiliation(s)
- André Nussenzweig
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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47
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Davis RE, Ngo VN, Lenz G, Tolar P, Young RM, Romesser PB, Kohlhammer H, Lamy L, Zhao H, Yang Y, Xu W, Shaffer AL, Wright G, Xiao W, Powell J, Jiang JK, Thomas CJ, Rosenwald A, Ott G, Muller-Hermelink HK, Gascoyne RD, Connors JM, Johnson NA, Rimsza LM, Campo E, Jaffe ES, Wilson WH, Delabie J, Smeland EB, Fisher RI, Braziel RM, Tubbs RR, Cook JR, Weisenburger DD, Chan WC, Pierce SK, Staudt LM. Chronic active B-cell-receptor signalling in diffuse large B-cell lymphoma. Nature 2010; 463:88-92. [PMID: 20054396 DOI: 10.1038/nature08638] [Citation(s) in RCA: 1221] [Impact Index Per Article: 87.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2009] [Accepted: 11/04/2009] [Indexed: 12/15/2022]
Abstract
A role for B-cell-receptor (BCR) signalling in lymphomagenesis has been inferred by studying immunoglobulin genes in human lymphomas and by engineering mouse models, but genetic and functional evidence for its oncogenic role in human lymphomas is needed. Here we describe a form of 'chronic active' BCR signalling that is required for cell survival in the activated B-cell-like (ABC) subtype of diffuse large B-cell lymphoma (DLBCL). The signalling adaptor CARD11 is required for constitutive NF-kappaB pathway activity and survival in ABC DLBCL. Roughly 10% of ABC DLBCLs have mutant CARD11 isoforms that activate NF-kappaB, but the mechanism that engages wild-type CARD11 in other ABC DLBCLs was unknown. An RNA interference genetic screen revealed that a BCR signalling component, Bruton's tyrosine kinase, is essential for the survival of ABC DLBCLs with wild-type CARD11. In addition, knockdown of proximal BCR subunits (IgM, Ig-kappa, CD79A and CD79B) killed ABC DLBCLs with wild-type CARD11 but not other lymphomas. The BCRs in these ABC DLBCLs formed prominent clusters in the plasma membrane with low diffusion, similarly to BCRs in antigen-stimulated normal B cells. Somatic mutations affecting the immunoreceptor tyrosine-based activation motif (ITAM) signalling modules of CD79B and CD79A were detected frequently in ABC DLBCL biopsy samples but rarely in other DLBCLs and never in Burkitt's lymphoma or mucosa-associated lymphoid tissue lymphoma. In 18% of ABC DLBCLs, one functionally critical residue of CD79B, the first ITAM tyrosine, was mutated. These mutations increased surface BCR expression and attenuated Lyn kinase, a feedback inhibitor of BCR signalling. These findings establish chronic active BCR signalling as a new pathogenetic mechanism in ABC DLBCL, suggesting several therapeutic strategies.
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Affiliation(s)
- R Eric Davis
- Metabolism Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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Tanaka A, Shen HM, Ratnam S, Kodgire P, Storb U. Attracting AID to targets of somatic hypermutation. ACTA ACUST UNITED AC 2010; 207:405-15. [PMID: 20100870 PMCID: PMC2822603 DOI: 10.1084/jem.20090821] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The process of somatic hypermutation (SHM) of immunoglobulin (Ig) genes requires activation-induced cytidine deaminase (AID). Although mistargeting of AID is detrimental to genome integrity, the mechanism and the cis-elements responsible for targeting of AID are largely unknown. We show that three CAGGTG cis-elements in the context of Ig enhancers are sufficient to target SHM to a nearby transcribed gene. The CAGGTG motif binds E47 in nuclear extracts of the mutating cells. Replacing CAGGTG with AAGGTG in the construct without any other E47 binding site eliminates SHM. The CA versus AA effect requires AID. CAGGTG does not enhance transcription, chromatin acetylation, or overall target gene activity. The other cis-elements of Ig enhancers alone cannot attract the SHM machinery. Collectively with other recent findings, we postulate that AID targets all genes expressed in mutating B cells that are associated with CAGGTG motifs in the appropriate context. Ig genes are the most highly mutated genes, presumably because of multiple CAGGTG motifs within the Ig genes, high transcription activity, and the presence of other cooperating elements in Ig enhancers.
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Affiliation(s)
- Atsushi Tanaka
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
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Role of the translocation partner in protection against AID-dependent chromosomal translocations. Proc Natl Acad Sci U S A 2009; 107:187-92. [PMID: 19966290 DOI: 10.1073/pnas.0908946107] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chromosome translocations between Ig (Ig) and non-Ig genes are frequently associated with B-cell lymphomas in humans and mice. The best characterized of these is c-myc/IgH translocation, which is associated with Burkitt's lymphoma. These translocations are caused by activation-induced cytidine deaminase (AID), which produces double-strand DNA breaks in both genes. c-myc/IgH translocations are rare events, in part because ATM, p53, and p19 actively suppress them. To further define the mechanism of protection against the accumulation of cells that bear c-myc/IgH translocation, we assayed B cells from mice that carry mutations in cell-cycle and apoptosis regulator proteins that act downstream of p53. We find that PUMA, Bim, and PKCdelta are required for protection against c-myc/IgH translocation, whereas Bcl-XL and BAFF enhance c-myc/IgH translocation. Whether these effects are general or specific to c-myc/IgH translocation and whether AID produces dsDNA breaks in genes other than c-myc and Ig is not known. To examine these questions, we developed an assay for translocation between IgH and Igbeta, both of which are somatically mutated by AID. Igbeta/IgH, like c-myc/IgH translocations, are AID-dependent, and AID is responsible for lesions on IgH and the non-IgH translocation partners. However, ATM, p53, and p19 do not protect against Igbeta/IgH translocations. Instead, B cells are protected against Igbeta/IgH translocations by a BAFF- and PKCdelta-dependent pathway. We conclude that AID-induced double-strand breaks in non-Ig genes other than c-myc lead to their translocation, and that at least two nonoverlapping pathways protect against translocations in primary B cells.
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Wang X, Gotoh O. Accurate molecular classification of cancer using simple rules. BMC Med Genomics 2009; 2:64. [PMID: 19874631 PMCID: PMC2777919 DOI: 10.1186/1755-8794-2-64] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2009] [Accepted: 10/30/2009] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND One intractable problem with using microarray data analysis for cancer classification is how to reduce the extremely high-dimensionality gene feature data to remove the effects of noise. Feature selection is often used to address this problem by selecting informative genes from among thousands or tens of thousands of genes. However, most of the existing methods of microarray-based cancer classification utilize too many genes to achieve accurate classification, which often hampers the interpretability of the models. For a better understanding of the classification results, it is desirable to develop simpler rule-based models with as few marker genes as possible. METHODS We screened a small number of informative single genes and gene pairs on the basis of their depended degrees proposed in rough sets. Applying the decision rules induced by the selected genes or gene pairs, we constructed cancer classifiers. We tested the efficacy of the classifiers by leave-one-out cross-validation (LOOCV) of training sets and classification of independent test sets. RESULTS We applied our methods to five cancerous gene expression datasets: leukemia (acute lymphoblastic leukemia [ALL] vs. acute myeloid leukemia [AML]), lung cancer, prostate cancer, breast cancer, and leukemia (ALL vs. mixed-lineage leukemia [MLL] vs. AML). Accurate classification outcomes were obtained by utilizing just one or two genes. Some genes that correlated closely with the pathogenesis of relevant cancers were identified. In terms of both classification performance and algorithm simplicity, our approach outperformed or at least matched existing methods. CONCLUSION In cancerous gene expression datasets, a small number of genes, even one or two if selected correctly, is capable of achieving an ideal cancer classification effect. This finding also means that very simple rules may perform well for cancerous class prediction.
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Affiliation(s)
- Xiaosheng Wang
- Department of Intelligence Science and Technology, Graduate School of Informatics, Kyoto University, Kyoto 606-8501, Japan.
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