1
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Wang S, Lee K, Gray S, Zhang Y, Tang C, Morrish RB, Tosti E, van Oers J, Amin MR, Cohen PE, MacCarthy T, Roa S, Scharff MD, Edelmann W, Chahwan R. Role of EXO1 nuclease activity in genome maintenance, the immune response and tumor suppression in Exo1D173A mice. Nucleic Acids Res 2022; 50:8093-8106. [PMID: 35849338 PMCID: PMC9371890 DOI: 10.1093/nar/gkac616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 05/30/2022] [Accepted: 06/30/2022] [Indexed: 11/14/2022] Open
Abstract
DNA damage response pathways rely extensively on nuclease activity to process DNA intermediates. Exonuclease 1 (EXO1) is a pleiotropic evolutionary conserved DNA exonuclease involved in various DNA repair pathways, replication, antibody diversification, and meiosis. But, whether EXO1 facilitates these DNA metabolic processes through its enzymatic or scaffolding functions remains unclear. Here, we dissect the contribution of EXO1 enzymatic versus scaffolding activity by comparing Exo1DA/DA mice expressing a proven nuclease-dead mutant form of EXO1 to entirely EXO1-deficient Exo1−/− and EXO1 wild type Exo1+/+ mice. We show that Exo1DA/DA and Exo1–/– mice are compromised in canonical DNA repair processing, suggesting that the EXO1 enzymatic role is important for error-free DNA mismatch and double-strand break repair pathways. However, in non-canonical repair pathways, EXO1 appears to have a more nuanced function. Next-generation sequencing of heavy chain V region in B cells showed the mutation spectra of Exo1DA/DA mice to be intermediate between Exo1+/+ and Exo1–/– mice, suggesting that both catalytic and scaffolding roles of EXO1 are important for somatic hypermutation. Similarly, while overall class switch recombination in Exo1DA/DA and Exo1–/– mice was comparably defective, switch junction analysis suggests that EXO1 might fulfill an additional scaffolding function downstream of class switching. In contrast to Exo1−/− mice that are infertile, meiosis progressed normally in Exo1DA/DA and Exo1+/+ cohorts, indicating that a structural but not the nuclease function of EXO1 is critical for meiosis. However, both Exo1DA/DA and Exo1–/– mice displayed similar mortality and cancer predisposition profiles. Taken together, these data demonstrate that EXO1 has both scaffolding and enzymatic functions in distinct DNA repair processes and suggest a more composite and intricate role for EXO1 in DNA metabolic processes and disease.
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Affiliation(s)
- Shanzhi Wang
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, NY 10461, USA.,Current position: Department of Chemistry, University of Arkansas at Little Rock, Little Rock, AR 72204, USA
| | - Kyeryoung Lee
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, NY 10461, USA
| | - Stephen Gray
- Department of Biomedical Sciences, Cornell University, NY 14853, USA.,Current position: School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK
| | - Yongwei Zhang
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, NY 10461, USA
| | - Catherine Tang
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA
| | - Rikke B Morrish
- Current position: School of Physics and Astronomy, University of Exeter, Exeter EX4 4QD, UK
| | - Elena Tosti
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, NY 10461, USA
| | - Johanna van Oers
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, NY 10461, USA
| | - Mohammad Ruhul Amin
- Department of Computer and Information Science, Fordham University, Bronx, NY, USA
| | - Paula E Cohen
- Department of Biomedical Sciences, Cornell University, NY 14853, USA
| | - Thomas MacCarthy
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA
| | - Sergio Roa
- Department of Biochemistry and Genetics, University of Navarra, 31008Pamplona, Spain.,Centro de Investigacion Biomedica en Red de Cancer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain.,Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
| | - Matthew D Scharff
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, NY 10461, USA
| | - Winfried Edelmann
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, NY 10461, USA
| | - Richard Chahwan
- Institute of Experimental Immunology, University of Zurich, Zurich 8057, Switzerland
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2
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Hargreaves CE, Salatino S, Sasson SC, Charlesworth JEG, Bateman E, Patel AM, Anzilotti C, Broxholme J, Knight JC, Patel SY. Decreased ATM Function Causes Delayed DNA Repair and Apoptosis in Common Variable Immunodeficiency Disorders. J Clin Immunol 2021; 41:1315-1330. [PMID: 34009545 PMCID: PMC8310859 DOI: 10.1007/s10875-021-01050-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 04/20/2021] [Indexed: 12/14/2022]
Abstract
PURPOSE Common variable immunodeficiency disorders (CVID) is characterized by low/absent serum immunoglobulins and susceptibility to bacterial infection. Patients can develop an infections-only phenotype or a complex disease course with inflammatory, autoimmune, and/or malignant complications. We hypothesized that deficient DNA repair mechanisms may be responsible for the antibody deficiency and susceptibility to inflammation and cancer in some patients. METHODS Germline variants were identified following targeted sequencing of n = 252 genes related to DNA repair in n = 38 patients. NanoString nCounter PlexSet assay measured gene expression in n = 20 CVID patients and n = 7 controls. DNA damage and apoptosis were assessed by flow cytometry in n = 34 CVID patients and n = 11 controls. RESULTS Targeted sequencing supported enrichment of rare genetic variants in genes related to DNA repair pathways with novel and rare likely pathogenic variants identified and an altered gene expression signature that distinguished patients from controls and complex patients from those with an infections-only phenotype. Consistent with this, flow cytometric analyses of lymphocytes following DNA damage revealed a subset of CVID patients whose immune cells have downregulated ATM, impairing the recruitment of other repair factors, delaying repair and promoting apoptosis. CONCLUSION These data suggest that germline genetics and altered gene expression predispose a subset of CVID patients to increased sensitivity to DNA damage and reduced DNA repair capacity.
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Affiliation(s)
- Chantal E Hargreaves
- Nuffield Department of Medicine and Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, OX3 9DU, UK.
| | - Silvia Salatino
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Sarah C Sasson
- Nuffield Department of Medicine and Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, OX3 9DU, UK
| | - James E G Charlesworth
- Oxford University Clinical Academic Graduate School, Medical Sciences Office, John Radcliffe Hospital, University of Oxford, OX3 9DU, Oxford, UK
| | - Elizabeth Bateman
- Department of Immunology, Churchill Hospital, Oxford University Hospitals NHS Trust, Oxford, OX3 7LE, UK
| | - Arzoo M Patel
- Nuffield Department of Medicine and Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, OX3 9DU, UK
| | - Consuelo Anzilotti
- Clinical Immunology Department, Oxford University Hospitals Trust, Oxford, OX3 9DU, UK
| | - John Broxholme
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Julian C Knight
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Smita Y Patel
- Nuffield Department of Medicine and Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, OX3 9DU, UK
- Clinical Immunology Department, Oxford University Hospitals Trust, Oxford, OX3 9DU, UK
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3
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Safavi S, Larouche A, Zahn A, Patenaude AM, Domanska D, Dionne K, Rognes T, Dingler F, Kang SK, Liu Y, Johnson N, Hébert J, Verdun RE, Rada CA, Vega F, Nilsen H, Di Noia JM. The uracil-DNA glycosylase UNG protects the fitness of normal and cancer B cells expressing AID. NAR Cancer 2021; 2:zcaa019. [PMID: 33554121 PMCID: PMC7848951 DOI: 10.1093/narcan/zcaa019] [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: 06/30/2020] [Revised: 08/09/2020] [Accepted: 08/13/2020] [Indexed: 12/14/2022] Open
Abstract
In B lymphocytes, the uracil N-glycosylase (UNG) excises genomic uracils made by activation-induced deaminase (AID), thus underpinning antibody gene diversification and oncogenic chromosomal translocations, but also initiating faithful DNA repair. Ung−/− mice develop B-cell lymphoma (BCL). However, since UNG has anti- and pro-oncogenic activities, its tumor suppressor relevance is unclear. Moreover, how the constant DNA damage and repair caused by the AID and UNG interplay affects B-cell fitness and thereby the dynamics of cell populations in vivo is unknown. Here, we show that UNG specifically protects the fitness of germinal center B cells, which express AID, and not of any other B-cell subset, coincident with AID-induced telomere damage activating p53-dependent checkpoints. Consistent with AID expression being detrimental in UNG-deficient B cells, Ung−/− mice develop BCL originating from activated B cells but lose AID expression in the established tumor. Accordingly, we find that UNG is rarely lost in human BCL. The fitness preservation activity of UNG contingent to AID expression was confirmed in a B-cell leukemia model. Hence, UNG, typically considered a tumor suppressor, acquires tumor-enabling activity in cancer cell populations that express AID by protecting cell fitness.
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Affiliation(s)
- Shiva Safavi
- Institut de Recherches Cliniques de Montréal, 110 Av des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Ariane Larouche
- Institut de Recherches Cliniques de Montréal, 110 Av des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Astrid Zahn
- Institut de Recherches Cliniques de Montréal, 110 Av des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Anne-Marie Patenaude
- Institut de Recherches Cliniques de Montréal, 110 Av des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Diana Domanska
- Department of Informatics, University of Oslo, PO Box 1080, Blindern, 0316 Oslo, Norway
| | - Kiersten Dionne
- Institut de Recherches Cliniques de Montréal, 110 Av des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Torbjørn Rognes
- Department of Informatics, University of Oslo, PO Box 1080, Blindern, 0316 Oslo, Norway
| | - Felix Dingler
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Seong-Kwi Kang
- ITR Laboratories Canada, Inc., 19601 Clark Graham Ave, Baie-D'Urfe, QC H9X 3T1, Canada
| | - Yan Liu
- Section for Clinical Molecular Biology, Akershus University Hospital, PO 1000, 1478 Lørenskog, Norway
| | - Nathalie Johnson
- Division of Experimental Medicine, Department of Medicine, McGill University, Montréal, QC H4A 3J1, Canada
| | - Josée Hébert
- Department of Medicine, Université de Montréal, C.P. 6128, Montreal, QC H3C 3J7, Canada
| | - Ramiro E Verdun
- Division of Hematology, Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33136, USA
| | | | - Francisco Vega
- Division of Hematology, Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33136, USA
| | - Hilde Nilsen
- Section for Clinical Molecular Biology, Akershus University Hospital, PO 1000, 1478 Lørenskog, Norway
| | - Javier M Di Noia
- Institut de Recherches Cliniques de Montréal, 110 Av des Pins Ouest, Montréal, QC H2W 1R7, Canada
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4
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Bai L, Hirose T, Assi W, Wada S, Takeshima SN, Aida Y. Bovine Leukemia Virus Infection Affects Host Gene Expression Associated with DNA Mismatch Repair. Pathogens 2020; 9:pathogens9110909. [PMID: 33143351 PMCID: PMC7694100 DOI: 10.3390/pathogens9110909] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 01/17/2023] Open
Abstract
Bovine leukemia virus (BLV) causes enzootic bovine leukosis, a malignant form of B-cell lymphoma, and is closely related to human T-cell leukemia viruses. We investigated whether BLV infection affects host genes associated with DNA mismatch repair (MMR). Next-generation sequencing of blood samples from five calves experimentally infected with BLV revealed the highest expression levels of seven MMR genes (EXO1, UNG, PCNA, MSH2, MSH3, MSH6, and PMS2) at the point of peak proviral loads (PVLs). Furthermore, MMR gene expression was only upregulated in cattle with higher PVLs. In particular, the expression levels of MSH2, MSH3, and UNG positively correlated with PVL in vivo. The expression levels of all seven MMR genes in pig kidney-15 cells and the levels of PMS2 and EXO1 in HeLa cells also increased tendencies after transient transfection with a BLV infectious clone. Moreover, MMR gene expression levels were significantly higher in BLV-expressing cell lines compared with those in the respective parental cell lines. Expression levels of MSH2 and EXO1 in BLV-infected cattle with lymphoma were significantly lower and higher, respectively, compared with those in infected cattle in vivo. These results reveal that BLV infection affects MMR gene expression, offering new candidate markers for lymphoma diagnosis.
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Affiliation(s)
- Lanlan Bai
- Photonics Control Technology Team, RIKEN Center for Advanced Photonics, Wako 351-0198, Japan; (L.B.); (W.A.); (S.W.); (S.-n.T.)
- Viral Infectious Diseases Unit, RIKEN, Wako 351-0198, Japan;
| | - Tomoya Hirose
- Viral Infectious Diseases Unit, RIKEN, Wako 351-0198, Japan;
- Laboratory of Viral Infectious Diseases, Department of Medical Genome Sciences, Graduate School of Frontier Science, The University of Tokyo, Tokyo 113-8657, Japan
| | - Wlaa Assi
- Photonics Control Technology Team, RIKEN Center for Advanced Photonics, Wako 351-0198, Japan; (L.B.); (W.A.); (S.W.); (S.-n.T.)
- Viral Infectious Diseases Unit, RIKEN, Wako 351-0198, Japan;
- Laboratory of Viral Infectious Diseases, Department of Medical Genome Sciences, Graduate School of Frontier Science, The University of Tokyo, Tokyo 113-8657, Japan
| | - Satoshi Wada
- Photonics Control Technology Team, RIKEN Center for Advanced Photonics, Wako 351-0198, Japan; (L.B.); (W.A.); (S.W.); (S.-n.T.)
| | - Shin-nosuke Takeshima
- Photonics Control Technology Team, RIKEN Center for Advanced Photonics, Wako 351-0198, Japan; (L.B.); (W.A.); (S.W.); (S.-n.T.)
- Viral Infectious Diseases Unit, RIKEN, Wako 351-0198, Japan;
- Department of Food and Nutrition, Faculty of Human Life, Jumonji University, Niiza 352-0017, Japan
| | - Yoko Aida
- Viral Infectious Diseases Unit, RIKEN, Wako 351-0198, Japan;
- Laboratory of Viral Infectious Diseases, Department of Medical Genome Sciences, Graduate School of Frontier Science, The University of Tokyo, Tokyo 113-8657, Japan
- Nakamura Laboratory, Baton Zone Program, RIKEN Cluster for Science, Technology and Innovation Hub, Wako 351-0198, Japan
- Correspondence: ; Tel.: +81-48-462-4418
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5
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Choi JE, Matthews AJ, Michel G, Vuong BQ. AID Phosphorylation Regulates Mismatch Repair-Dependent Class Switch Recombination and Affinity Maturation. THE JOURNAL OF IMMUNOLOGY 2020; 204:13-22. [PMID: 31757865 DOI: 10.4049/jimmunol.1900809] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 10/25/2019] [Indexed: 01/01/2023]
Abstract
Activation-induced cytidine deaminase (AID) generates U:G mismatches in Ig genes that can be converted into untemplated mutations during somatic hypermutation or DNA double-strand breaks during class switch recombination (CSR). Null mutations in UNG and MSH2 demonstrate the complementary roles of the base excision repair (BER) and mismatch repair pathways, respectively, in CSR. Phosphorylation of AID at serine 38 was previously hypothesized to regulate BER during CSR, as the AID phosphorylation mutant, AID(S38A), cannot interact with APE1, a BER protein. Consistent with these findings, we observe a complete block in CSR in AIDS38A/S38AMSH2-/- mouse B cells that correlates with an impaired mutation frequency at 5'Sμ. Similarly, somatic hypermutation is almost negligible at the JH4 intron in AIDS38A/S38AMSH2-/- mouse B cells, and, consistent with this, NP-specific affinity maturation in AIDS38A/S38AMSH2-/- mice is not significantly elevated in response to NP-CGG immunization. Surprisingly, AIDS38A/S38AUNG-/- mouse B cells also cannot complete CSR or affinity maturation despite accumulating significant mutations in 5'Sμ as well as the JH4 intron. These data identify a novel role for phosphorylation of AID at serine 38 in mismatch repair-dependent CSR and affinity maturation.
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Affiliation(s)
- Jee Eun Choi
- The City College of New York, The City University of New York, New York, NY 10031; and
| | - Allysia J Matthews
- The City College of New York, The City University of New York, New York, NY 10031; and
| | - Genesis Michel
- The City College of New York, The City University of New York, New York, NY 10031; and
| | - Bao Q Vuong
- The Graduate Center, The City University of New York, New York, NY 10016
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6
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Li H, Wang X, Zhao H, Wang F, Bao Y, Guo J, Chang S, Wu L, Cheng H, Chen S, Zou J, Cui X, Niswander L, Finnell RH, Wang H, Zhang T. Low folate concentration impacts mismatch repair deficiency in neural tube defects. Epigenomics 2019; 12:5-18. [PMID: 31769301 DOI: 10.2217/epi-2019-0279] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Aim: To know the cause of sequence variants in neural tube defect (NTD). Materials & methods: We sequenced genes implicated in neural tube closure (NTC) in a Chinese cohort and elucidated the molecular mechanism-driving mutations. Results: In NTD cases, an increase in specific variants was identified, potentially deleterious rare variants harbored in H3K36me3 occupancy regions that recruits mismatch repair (MMR) machinery. Lower folate concentrations in local brain tissues were also observed. In neuroectoderm cells, folic acid insufficiency attenuated association of Msh6 to H3K36me3, and reduced bindings to NTC genes. Rare variants in human NTDs were featured by MMR deficiency and more severe microsatellite instability. Conclusion: Our work suggests a mechanistic link between folate insufficiency and MMR deficiency that correlates with an increase of rare variants in NTC genes.
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Affiliation(s)
- Huili Li
- Beijing Municipal Key Laboratory of Child Development & Nutriomics, Capital Institute of Pediatrics, Beijing 100020, China.,Department of Molecular, Cellular & Developmental Biology, University of Colorado at Boulder, Boulder, CO 80309, USA
| | - Xiaolei Wang
- Beijing Municipal Key Laboratory of Child Development & Nutriomics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Huizhi Zhao
- Beijing Municipal Key Laboratory of Child Development & Nutriomics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Fang Wang
- Beijing Municipal Key Laboratory of Child Development & Nutriomics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Yihua Bao
- Beijing Municipal Key Laboratory of Child Development & Nutriomics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Jin Guo
- Beijing Municipal Key Laboratory of Child Development & Nutriomics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Shaoyan Chang
- Beijing Municipal Key Laboratory of Child Development & Nutriomics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Lihua Wu
- Beijing Municipal Key Laboratory of Child Development & Nutriomics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Haiqin Cheng
- Beijing Municipal Key Laboratory of Child Development & Nutriomics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Shuyuan Chen
- Beijing Municipal Key Laboratory of Child Development & Nutriomics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Jizhen Zou
- Beijing Municipal Key Laboratory of Child Development & Nutriomics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Xiaodai Cui
- Beijing Municipal Key Laboratory of Child Development & Nutriomics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Lee Niswander
- Department of Molecular, Cellular & Developmental Biology, University of Colorado at Boulder, Boulder, CO 80309, USA
| | - Richard H Finnell
- Obstetrics & Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Institute of Reproduction & Development, Fudan University, Shanghai 200011, China.,Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hongyan Wang
- Obstetrics & Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Institute of Reproduction & Development, Fudan University, Shanghai 200011, China.,Key Laboratory of Reproduction Regulation of NPFPC, Collaborative Innovation Center of Genetics & Development, Fudan University, Shanghai 200032, China.,Children's Hospital, Fudan University, Shanghai 201102, China
| | - Ting Zhang
- Beijing Municipal Key Laboratory of Child Development & Nutriomics, Capital Institute of Pediatrics, Beijing 100020, China
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7
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Abstract
PURPOSE OF REVIEW Recent lymphoma genome sequencing projects have shed light on the genomic landscape of indolent and aggressive lymphomas, as well as some of the molecular mechanisms underlying recurrent mutations and translocations in these entities. Here, we review these recent genomic discoveries, focusing on acquired DNA repair defects in lymphoma. In addition, we highlight recently identified actionable molecular vulnerabilities associated with recurrent mutations in chronic lymphocytic leukemia (CLL), which serves as a model entity. RECENT FINDINGS The results of several large lymphoma genome sequencing projects have recently been reported, including CLL, T-PLL and DLBCL. We align these discoveries with proposed mechanisms of mutation acquisition in B-cell lymphomas. Moreover, novel autochthonous mouse models of CLL have recently been generated and we discuss how these models serve as preclinical tools to drive the development of novel targeted therapeutic interventions. Lastly, we highlight the results of early clinical data on novel compounds targeting defects in the DNA damage response of CLL with a particular focus on deleterious ATM mutations. SUMMARY Defects in DNA repair pathways are selected events in cancer, including lymphomas. Specifically, ATM deficiency is associated with PARP1- and DNA-PKcs inhibitor sensitivity in vitro and in vivo.
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8
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Zanotti KJ, Maul RW, Yang W, Gearhart PJ. DNA Breaks in Ig V Regions Are Predominantly Single Stranded and Are Generated by UNG and MSH6 DNA Repair Pathways. THE JOURNAL OF IMMUNOLOGY 2019; 202:1573-1581. [PMID: 30665938 DOI: 10.4049/jimmunol.1801183] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 12/16/2018] [Indexed: 11/19/2022]
Abstract
Antibody diversity is initiated by activation-induced deaminase (AID), which deaminates cytosine to uracil in DNA. Uracils in the Ig gene loci can be recognized by uracil DNA glycosylase (UNG) or mutS homologs 2 and 6 (MSH2-MSH6) proteins, and then processed into DNA breaks. Breaks in switch regions of the H chain locus cause isotype switching and have been extensively characterized as staggered and blunt double-strand breaks. However, breaks in V regions that arise during somatic hypermutation are poorly understood. In this study, we characterize AID-dependent break formation in JH introns from mouse germinal center B cells. We used a ligation-mediated PCR assay to detect single-strand breaks and double-strand breaks that were either staggered or blunt. In contrast to switch regions, V regions contained predominantly single-strand breaks, which peaked 10 d after immunization. We then examined the pathways used to generate these breaks in UNG- and MSH6-deficient mice. Surprisingly, both DNA repair pathways contributed substantially to break formation, and in the absence of both UNG and MSH6, the frequency of breaks was severely reduced. When the breaks were sequenced and mapped, they were widely distributed over a 1000-bp intron region downstream of JH3 and JH4 exons and were unexpectedly located at all 4 nt. These data suggest that during DNA repair, nicks are generated at distal sites from the original deaminated cytosine, and these repair intermediates could generate both faithful and mutagenic repair. During mutagenesis, single-strand breaks would allow entry for low-fidelity DNA polymerases to generate somatic hypermutation.
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Affiliation(s)
- Kimberly J Zanotti
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224
| | - Robert W Maul
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224
| | - William Yang
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224
| | - Patricia J Gearhart
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224
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9
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Bahjat M, Guikema JEJ. The Complex Interplay between DNA Injury and Repair in Enzymatically Induced Mutagenesis and DNA Damage in B Lymphocytes. Int J Mol Sci 2017; 18:ijms18091876. [PMID: 28867784 PMCID: PMC5618525 DOI: 10.3390/ijms18091876] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 08/24/2017] [Accepted: 08/29/2017] [Indexed: 11/25/2022] Open
Abstract
Lymphocytes are endowed with unique and specialized enzymatic mutagenic properties that allow them to diversify their antigen receptors, which are crucial sensors for pathogens and mediators of adaptive immunity. During lymphocyte development, the antigen receptors expressed by B and T lymphocytes are assembled in an antigen-independent fashion by ordered variable gene segment recombinations (V(D)J recombination), which is a highly ordered and regulated process that requires the recombination activating gene products 1 & 2 (RAG1, RAG2). Upon activation by antigen, B lymphocytes undergo additional diversifications of their immunoglobulin B-cell receptors. Enzymatically induced somatic hypermutation (SHM) and immunoglobulin class switch recombination (CSR) improves the affinity for antigen and shape the effector function of the humoral immune response, respectively. The activation-induced cytidine deaminase (AID) enzyme is crucial for both SHM and CSR. These processes have evolved to both utilize as well as evade different DNA repair and DNA damage response pathways. The delicate balance between enzymatic mutagenesis and DNA repair is crucial for effective immune responses and the maintenance of genomic integrity. Not surprisingly, disturbances in this balance are at the basis of lymphoid malignancies by provoking the formation of oncogenic mutations and chromosomal aberrations. In this review, we discuss recent mechanistic insight into the regulation of RAG1/2 and AID expression and activity in lymphocytes and the complex interplay between these mutagenic enzymes and DNA repair and DNA damage response pathways, focusing on the base excision repair and mismatch repair pathways. We discuss how disturbances of this interplay induce genomic instability and contribute to oncogenesis.
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Affiliation(s)
- Mahnoush Bahjat
- Department of Pathology, Academic Medical Center, University of Amsterdam; Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam 1105 AZ, The Netherlands.
| | - Jeroen E J Guikema
- Department of Pathology, Academic Medical Center, University of Amsterdam; Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam 1105 AZ, The Netherlands.
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10
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Eid MMA, Shimoda M, Singh SK, Almofty SA, Pham P, Goodman MF, Maeda K, Sakaguchi N. Integrity of immunoglobulin variable regions is supported by GANP during AID-induced somatic hypermutation in germinal center B cells. Int Immunol 2017; 29:211-220. [PMID: 28541550 PMCID: PMC5890899 DOI: 10.1093/intimm/dxx032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 05/22/2017] [Indexed: 11/13/2022] Open
Abstract
Immunoglobulin affinity maturation depends on somatic hypermutation (SHM) in immunoglobulin variable (IgV) regions initiated by activation-induced cytidine deaminase (AID). AID induces transition mutations by C→U deamination on both strands, causing C:G→T:A. Error-prone repairs of U by base excision and mismatch repairs (MMRs) create transversion mutations at C/G and mutations at A/T sites. In Neuberger’s model, it remained to be clarified how transition/transversion repair is regulated. We investigate the role of AID-interacting GANP (germinal center-associated nuclear protein) in the IgV SHM profile. GANP enhances transition mutation of the non-transcribed strand G and reduces mutation at A, restricted to GYW of the AID hotspot motif. It reduces DNA polymerase η hotspot mutations associated with MMRs followed by uracil-DNA glycosylase. Mutation comparison between IgV complementary and framework regions (FWRs) by Bayesian statistical estimation demonstrates that GANP supports the preservation of IgV FWR genomic sequences. GANP works to maintain antibody structure by reducing drastic changes in the IgV FWR in affinity maturation.
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Affiliation(s)
| | - Mayuko Shimoda
- Department of Immunology, Graduate School of Medical Sciences, Kumamoto University, 1-1-1 Honjo, Kumamoto 860-8556, Japan.,Laboratory of Host Defense, World Premier International Research Center Initiative (WPI) Immunology Frontier Research Center (IFReC).,Department of Host Defense, Research Institute for Microbial Diseases (RIMD), Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Shailendra Kumar Singh
- Laboratory of Host Defense, World Premier International Research Center Initiative (WPI) Immunology Frontier Research Center (IFReC)
| | - Sarah Ameen Almofty
- Laboratory of Immunology, Institute for Research and Medical Consultations (IRMC), University Of Dammam (UOD), PO Box 1982, Dammam 31441, Saudi Arabia
| | - Phuong Pham
- Departments of Biological Sciences and Chemistry, University of Southern California, 1050 Childs Way, University Park, Los Angeles, CA 90089-2910, USA
| | - Myron F Goodman
- Departments of Biological Sciences and Chemistry, University of Southern California, 1050 Childs Way, University Park, Los Angeles, CA 90089-2910, USA
| | - Kazuhiko Maeda
- Laboratory of Host Defense, World Premier International Research Center Initiative (WPI) Immunology Frontier Research Center (IFReC).,Department of Host Defense, Research Institute for Microbial Diseases (RIMD), Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Nobuo Sakaguchi
- World Premier International Research Center Initiative (WPI) Immunology Frontier Research Center, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan.,Tokyo Metropolitan Institute of Medical Science, 2-1-6, Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
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11
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Novel Implications in Molecular Diagnosis of Lynch Syndrome. Gastroenterol Res Pract 2017; 2017:2595098. [PMID: 28250766 PMCID: PMC5303590 DOI: 10.1155/2017/2595098] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 01/05/2017] [Indexed: 02/07/2023] Open
Abstract
About 10% of total colorectal cancers are associated with known Mendelian inheritance, as Familial Adenomatous Polyposis (FAP) and Lynch syndrome (LS). In these cancer types the clinical manifestations of disease are due to mutations in high-risk alleles, with a penetrance at least of 70%. The LS is associated with germline mutations in the DNA mismatch repair (MMR) genes. However, the mutation detection analysis of these genes does not always provide informative results for genetic counseling of LS patients. Very often, the molecular analysis reveals the presence of variants of unknown significance (VUSs) whose interpretation is not easy and requires the combination of different analytical strategies to get a proper assessment of their pathogenicity. In some cases, these VUSs may make a more substantial overall contribution to cancer risk than the well-assessed severe Mendelian variants. Moreover, it could also be possible that the simultaneous presence of these genetic variants in several MMR genes that behave as low risk alleles might contribute in a cooperative manner to increase the risk of hereditary cancer. In this paper, through a review of the recent literature, we have speculated a novel inheritance model in the Lynch syndrome; this could pave the way toward new diagnostic perspectives.
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12
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Methot S, Di Noia J. Molecular Mechanisms of Somatic Hypermutation and Class Switch Recombination. Adv Immunol 2017; 133:37-87. [DOI: 10.1016/bs.ai.2016.11.002] [Citation(s) in RCA: 165] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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13
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Yue X, Lukowski JK, Weaver EM, Skube SB, Hummon AB. Quantitative Proteomic and Phosphoproteomic Comparison of 2D and 3D Colon Cancer Cell Culture Models. J Proteome Res 2016; 15:4265-4276. [PMID: 27696853 DOI: 10.1021/acs.jproteome.6b00342] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cell cultures are widely used model systems. Some immortalized cell lines can be grown in either two-dimensional (2D) adherent monolayers or in three-dimensional (3D) multicellular aggregates, or spheroids. Here, the quantitative proteome and phosphoproteome of colon carcinoma HT29 cells cultures in 2D monolayers and 3D spheroids were compared with a stable isotope labeling of amino acids (SILAC) labeling strategy. Two biological replicates from each sample were examined, and notable differences in both the proteome and the phosphoproteome were determined by nanoliquid chromatography tandem mass spectrometry (LC-MS/MS) to assess how growth configuration affects molecular expression. A total of 5867 protein groups, including 2523 phosphoprotein groups and 8733 phosphopeptides were identified in the samples. The Gene Ontology analysis revealed enriched GO terms in the 3D samples for RNA binding, nucleic acid binding, enzyme binding, cytoskeletal protein binding, and histone binding for their molecular functions (MF) and in the process of cell cycle, cytoskeleton organization, and DNA metabolic process for the biological process (BP). The KEGG pathway analysis indicated that 3D cultures are enriched for oxidative phosphorylation pathways, metabolic pathways, peroxisome pathways, and biosynthesis of amino acids. In contrast, analysis of the phosphoproteomes indicated that 3D cultures have decreased phosphorylation correlating with slower growth rates and lower cell-to-extracellular matrix interactions. In sum, these results provide quantitative assessments of the effects on the proteome and phosphoproteome of culturing cells in 2D versus 3D cell culture configurations.
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Affiliation(s)
- Xiaoshan Yue
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame , 251 Nieuwland Science Hall, Notre Dame, Indiana 46556, United States
| | - Jessica K Lukowski
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame , 251 Nieuwland Science Hall, Notre Dame, Indiana 46556, United States
| | - Eric M Weaver
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame , 251 Nieuwland Science Hall, Notre Dame, Indiana 46556, United States
| | - Susan B Skube
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame , 251 Nieuwland Science Hall, Notre Dame, Indiana 46556, United States
| | - Amanda B Hummon
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame , 251 Nieuwland Science Hall, Notre Dame, Indiana 46556, United States
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14
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Zanotti KJ, Gearhart PJ. Antibody diversification caused by disrupted mismatch repair and promiscuous DNA polymerases. DNA Repair (Amst) 2016; 38:110-116. [PMID: 26719140 PMCID: PMC4740194 DOI: 10.1016/j.dnarep.2015.11.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 11/30/2015] [Indexed: 10/25/2022]
Abstract
The enzyme activation-induced deaminase (AID) targets the immunoglobulin loci in activated B cells and creates DNA mutations in the antigen-binding variable region and DNA breaks in the switch region through processes known, respectively, as somatic hypermutation and class switch recombination. AID deaminates cytosine to uracil in DNA to create a U:G mismatch. During somatic hypermutation, the MutSα complex binds to the mismatch, and the error-prone DNA polymerase η generates mutations at A and T bases. During class switch recombination, both MutSα and MutLα complexes bind to the mismatch, resulting in double-strand break formation and end-joining. This review is centered on the mechanisms of how the MMR pathway is commandeered by B cells to generate antibody diversity.
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Affiliation(s)
- Kimberly J Zanotti
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Patricia J Gearhart
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA.
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15
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Bak ST, Sakellariou D, Pena-Diaz J. The dual nature of mismatch repair as antimutator and mutator: for better or for worse. Front Genet 2014; 5:287. [PMID: 25191341 PMCID: PMC4139959 DOI: 10.3389/fgene.2014.00287] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 08/04/2014] [Indexed: 01/19/2023] Open
Abstract
DNA is constantly under attack by a number of both exogenous and endogenous agents that challenge its integrity. Among the mechanisms that have evolved to counteract this deleterious action, mismatch repair (MMR) has specialized in removing DNA biosynthetic errors that occur when replicating the genome. Malfunction or inactivation of this system results in an increase in spontaneous mutability and a strong predisposition to tumor development. Besides this key corrective role, MMR proteins are involved in other pathways of DNA metabolism such as mitotic and meiotic recombination and processing of oxidative damage. Surprisingly, MMR is also required for certain mutagenic processes. The mutagenic MMR has beneficial consequences contributing to the generation of a vast repertoire of antibodies through class switch recombination and somatic hypermutation processes. However, this non-canonical mutagenic MMR also has detrimental effects; it promotes repeat expansions associated with neuromuscular and neurodegenerative diseases and may contribute to cancer/disease-related aberrant mutations and translocations. The reaction responsible for replication error correction has been the most thoroughly studied and it is the subject to numerous reviews. This review describes briefly the biochemistry of MMR and focuses primarily on the non-canonical MMR activities described in mammals as well as emerging research implicating interplay of MMR and chromatin.
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Affiliation(s)
- Sara Thornby Bak
- Department of Neuroscience and Pharmacology and Center for Healthy Aging, University of Copenhagen Copenhagen, Denmark
| | - Despoina Sakellariou
- Department of Neuroscience and Pharmacology and Center for Healthy Aging, University of Copenhagen Copenhagen, Denmark
| | - Javier Pena-Diaz
- Department of Neuroscience and Pharmacology and Center for Healthy Aging, University of Copenhagen Copenhagen, Denmark
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16
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Differential expression of APE1 and APE2 in germinal centers promotes error-prone repair and A:T mutations during somatic hypermutation. Proc Natl Acad Sci U S A 2014; 111:9217-22. [PMID: 24927551 DOI: 10.1073/pnas.1405590111] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Somatic hypermutation (SHM) of antibody variable region genes is initiated in germinal center B cells during an immune response by activation-induced cytidine deaminase (AID), which converts cytosines to uracils. During accurate repair in nonmutating cells, uracil is excised by uracil DNA glycosylase (UNG), leaving abasic sites that are incised by AP endonuclease (APE) to create single-strand breaks, and the correct nucleotide is reinserted by DNA polymerase β. During SHM, for unknown reasons, repair is error prone. There are two APE homologs in mammals and, surprisingly, APE1, in contrast to its high expression in both resting and in vitro-activated splenic B cells, is expressed at very low levels in mouse germinal center B cells where SHM occurs, and APE1 haploinsufficiency has very little effect on SHM. In contrast, the less efficient homolog, APE2, is highly expressed and contributes not only to the frequency of mutations, but also to the generation of mutations at A:T base pair (bp), insertions, and deletions. In the absence of both UNG and APE2, mutations at A:T bp are dramatically reduced. Single-strand breaks generated by APE2 could provide entry points for exonuclease recruited by the mismatch repair proteins Msh2-Msh6, and the known association of APE2 with proliferating cell nuclear antigen could recruit translesion polymerases to create mutations at AID-induced lesions and also at A:T bp. Our data provide new insight into error-prone repair of AID-induced lesions, which we propose is facilitated by down-regulation of APE1 and up-regulation of APE2 expression in germinal center B cells.
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17
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Wyatt MD. Advances in understanding the coupling of DNA base modifying enzymes to processes involving base excision repair. Adv Cancer Res 2014; 119:63-106. [PMID: 23870509 DOI: 10.1016/b978-0-12-407190-2.00002-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
This chapter describes some of the recent, exciting developments that have characterized and connected processes that modify DNA bases with DNA repair pathways. It begins with AID/APOBEC or TET family members that covalently modify bases within DNA. The modified bases, such as uracil or 5-formylcytosine, are then excised by DNA glycosylases including UNG or TDG to initiate base excision repair (BER). BER is known to preserve genome integrity by removing damaged bases. The newer studies underscore the necessity of BER following enzymes that deliberately damage DNA. This includes the role of BER in antibody diversification and more recently, its requirement for demethylation of 5-methylcytosine in mammalian cells. The recent advances have shed light on mechanisms of DNA demethylation, and have raised many more questions. The potential hazards of these processes have also been revealed. Dysregulation of the activity of base modifying enzymes, and resolution by unfaithful or corrupt means can be a driver of genome instability and tumorigenesis. The understanding of both DNA and histone methylation and demethylation is now revealing the true extent to which epigenetics influence normal development and cancer, an abnormal development.
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Affiliation(s)
- Michael D Wyatt
- Department of Drug Discovery and Biomedical Sciences, South Carolina College of Pharmacy, University of South Carolina, Columbia, South Carolina, USA.
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18
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Matthews AJ, Zheng S, DiMenna LJ, Chaudhuri J. Regulation of immunoglobulin class-switch recombination: choreography of noncoding transcription, targeted DNA deamination, and long-range DNA repair. Adv Immunol 2014; 122:1-57. [PMID: 24507154 PMCID: PMC4150736 DOI: 10.1016/b978-0-12-800267-4.00001-8] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Upon encountering antigens, mature IgM-positive B lymphocytes undergo class-switch recombination (CSR) wherein exons encoding the default Cμ constant coding gene segment of the immunoglobulin (Ig) heavy-chain (Igh) locus are excised and replaced with a new constant gene segment (referred to as "Ch genes", e.g., Cγ, Cɛ, or Cα). The B cell thereby changes from expressing IgM to one producing IgG, IgE, or IgA, with each antibody isotype having a different effector function during an immune reaction. CSR is a DNA deletional-recombination reaction that proceeds through the generation of DNA double-strand breaks (DSBs) in repetitive switch (S) sequences preceding each Ch gene and is completed by end-joining between donor Sμ and acceptor S regions. CSR is a multistep reaction requiring transcription through S regions, the DNA cytidine deaminase AID, and the participation of several general DNA repair pathways including base excision repair, mismatch repair, and classical nonhomologous end-joining. In this review, we discuss our current understanding of how transcription through S regions generates substrates for AID-mediated deamination and how AID participates not only in the initiation of CSR but also in the conversion of deaminated residues into DSBs. Additionally, we review the multiple processes that regulate AID expression and facilitate its recruitment specifically to the Ig loci, and how deregulation of AID specificity leads to oncogenic translocations. Finally, we summarize recent data on the potential role of AID in the maintenance of the pluripotent stem cell state during epigenetic reprogramming.
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Affiliation(s)
- Allysia J Matthews
- Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, New York, USA
| | - Simin Zheng
- Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, New York, USA
| | - Lauren J DiMenna
- Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, New York, USA
| | - Jayanta Chaudhuri
- Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, New York, USA.
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19
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Mammalian Exo1 encodes both structural and catalytic functions that play distinct roles in essential biological processes. Proc Natl Acad Sci U S A 2013; 110:E2470-9. [PMID: 23754438 DOI: 10.1073/pnas.1308512110] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Mammalian Exonuclease 1 (EXO1) is an evolutionarily conserved, multifunctional exonuclease involved in DNA damage repair, replication, immunoglobulin diversity, meiosis, and telomere maintenance. It has been assumed that EXO1 participates in these processes primarily through its exonuclease activity, but recent studies also suggest that EXO1 has a structural function in the assembly of higher-order protein complexes. To dissect the enzymatic and nonenzymatic roles of EXO1 in the different biological processes in vivo, we generated an EXO1-E109K knockin (Exo1(EK)) mouse expressing a stable exonuclease-deficient protein and, for comparison, a fully EXO1-deficient (Exo1(null)) mouse. In contrast to Exo1(null/null) mice, Exo1(EK/EK) mice retained mismatch repair activity and displayed normal class switch recombination and meiosis. However, both Exo1-mutant lines showed defects in DNA damage response including DNA double-strand break repair (DSBR) through DNA end resection, chromosomal stability, and tumor suppression, indicating that the enzymatic function is required for those processes. On a transformation-related protein 53 (Trp53)-null background, the DSBR defect caused by the E109K mutation altered the tumor spectrum but did not affect the overall survival as compared with p53-Exo1(null) mice, whose defects in both DSBR and mismatch repair also compromised survival. The separation of these functions demonstrates the differential requirement for the structural function and nuclease activity of mammalian EXO1 in distinct DNA repair processes and tumorigenesis in vivo.
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20
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Campo VA, Patenaude AM, Kaden S, Horb L, Firka D, Jiricny J, Di Noia JM. MSH6- or PMS2-deficiency causes re-replication in DT40 B cells, but it has little effect on immunoglobulin gene conversion or on repair of AID-generated uracils. Nucleic Acids Res 2013; 41:3032-46. [PMID: 23314153 PMCID: PMC3597665 DOI: 10.1093/nar/gks1470] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The mammalian antibody repertoire is shaped by somatic hypermutation (SHM) and class switch recombination (CSR) of the immunoglobulin (Ig) loci of B lymphocytes. SHM and CSR are triggered by non-canonical, error-prone processing of G/U mismatches generated by activation-induced deaminase (AID). In birds, AID does not trigger SHM, but it triggers Ig gene conversion (GC), a ‘homeologous’ recombination process involving the Ig variable region and proximal pseudogenes. Because recombination fidelity is controlled by the mismatch repair (MMR) system, we investigated whether MMR affects GC in the chicken B cell line DT40. We show here that Msh6−/− and Pms2−/− DT40 cells display cell cycle defects, including genomic re-replication. However, although IgVλ GC tracts in MMR-deficient cells were slightly longer than in normal cells, Ig GC frequency, donor choice or the number of mutations per sequence remained unaltered. The finding that the avian MMR system, unlike that of mammals, does not seem to contribute towards the processing of G/U mismatches in vitro could explain why MMR is unable to initiate Ig GC in this species, despite initiating SHM and CSR in mammalian cells. Moreover, as MMR does not counteract or govern Ig GC, we report a rare example of ‘homeologous’ recombination insensitive to MMR.
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Affiliation(s)
- Vanina A Campo
- Institut de Recherches Cliniques de Montréal, Division of Immunity and Viral Infections, Montréal, H2W 1R7 Québec, Canada
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21
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Couronné L, Ruminy P, Waultier-Rascalou A, Rainville V, Cornic M, Picquenot JM, Figeac M, Bastard C, Tilly H, Jardin F. Mutation mismatch repair gene deletions in diffuse large B-cell lymphoma. Leuk Lymphoma 2012; 54:1079-86. [DOI: 10.3109/10428194.2012.739687] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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22
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Saribasak H, Gearhart PJ. Does DNA repair occur during somatic hypermutation? Semin Immunol 2012; 24:287-92. [PMID: 22728014 DOI: 10.1016/j.smim.2012.05.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Accepted: 05/18/2012] [Indexed: 11/25/2022]
Abstract
Activation-induced deaminase (AID) initiates a flood of DNA damage in the immunoglobulin loci, leading to abasic sites, single-strand breaks and mismatches. It is compelling that some proteins in the canonical base excision and mismatch repair pathways have been hijacked to increase mutagenesis during somatic hypermutation. Thus, the AID-induced mutagenic pathways involve a mix of DNA repair proteins and low fidelity DNA polymerases to create antibody diversity. In this review, we analyze the roles of base excision repair, mismatch repair, and mutagenesis during somatic hypermutation of rearranged variable genes. The emerging view is that faithful base excision repair occurs simultaneously with mutagenesis, whereas faithful mismatch repair is mostly absent.
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Affiliation(s)
- Huseyin Saribasak
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, United States
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23
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AIDing antibody diversity by error-prone mismatch repair. Semin Immunol 2012; 24:293-300. [PMID: 22703640 DOI: 10.1016/j.smim.2012.05.005] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Accepted: 05/18/2012] [Indexed: 11/20/2022]
Abstract
The creation of a highly diverse antibody repertoire requires the synergistic activity of a DNA mutator, known as activation-induced deaminase (AID), coupled with an error-prone repair process that recognizes the DNA mismatch catalyzed by AID. Instead of facilitating the canonical error-free response, which generally occurs throughout the genome, DNA mismatch repair (MMR) participates in an error-prone repair mode that promotes A:T mutagenesis and double-strand breaks at the immunoglobulin (Ig) genes. As such, MMR is capable of compounding the mutation frequency of AID activity as well as broadening the spectrum of base mutations; thereby increasing the efficiency of antibody maturation. We here review the current understanding of this MMR-mediated process and describe how the MMR signaling cascade downstream of AID diverges in a locus dependent manner and even within the Ig locus itself to differentially promote somatic hypermutation (SHM) and class switch recombination (CSR) in B cells.
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24
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Peña-Diaz J, Jiricny J. Mammalian mismatch repair: error-free or error-prone? Trends Biochem Sci 2012; 37:206-14. [PMID: 22475811 DOI: 10.1016/j.tibs.2012.03.001] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Revised: 02/15/2012] [Accepted: 03/01/2012] [Indexed: 01/13/2023]
Abstract
A considerable surge of interest in the mismatch repair (MMR) system has been brought about by the discovery of a link between Lynch syndrome, an inherited predisposition to cancer of the colon and other organs, and malfunction of this key DNA metabolic pathway. This review focuses on recent advances in our understanding of the molecular mechanisms of canonical MMR, which improves replication fidelity by removing misincorporated nucleotides from the nascent DNA strand. We also discuss the involvement of MMR proteins in two other processes: trinucleotide repeat expansion and antibody maturation, in which MMR proteins are required for mutagenesis rather than for its prevention.
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Affiliation(s)
- Javier Peña-Diaz
- Institute of Molecular Cancer Research of the University of Zurich, Switzerland
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25
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Chahwan R, van Oers JMM, Avdievich E, Zhao C, Edelmann W, Scharff MD, Roa S. The ATPase activity of MLH1 is required to orchestrate DNA double-strand breaks and end processing during class switch recombination. ACTA ACUST UNITED AC 2012; 209:671-8. [PMID: 22451719 PMCID: PMC3328365 DOI: 10.1084/jem.20111531] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
MLH1 ATPase activity is essential for class switch recombination but not for somatic hypermutation. Antibody diversification through somatic hypermutation (SHM) and class switch recombination (CSR) are similarly initiated in B cells with the generation of U:G mismatches by activation-induced cytidine deaminase but differ in their subsequent mutagenic consequences. Although SHM relies on the generation of nondeleterious point mutations, CSR depends on the production of DNA double-strand breaks (DSBs) and their adequate recombination through nonhomologous end joining (NHEJ). MLH1, an ATPase member of the mismatch repair (MMR) machinery, is emerging as a likely regulator of whether a U:G mismatch progresses toward mutation or DSB formation. We conducted experiments on cancer modeled ATPase-deficient MLH1G67R knockin mice to determine the function that the ATPase domain of MLH1 mediates in SHM and CSR. Mlh1GR/GR mice displayed a significant decrease in CSR, mainly attributed to a reduction in the generation of DSBs and diminished accumulation of 53BP1 at the immunoglobulin switch regions. However, SHM was normal in these mice, which distinguishes MLH1 from upstream members of the MMR pathway and suggests a very specific role of its ATPase-dependent functions during CSR. In addition, we show that the residual switching events still taking place in Mlh1GR/GR mice display unique features, suggesting a role for the ATPase activity of MLH1 beyond the activation of the endonuclease functions of its MMR partner PMS2. A preference for switch junctions with longer microhomologies in Mlh1GR/GR mice suggests that through its ATPase activity, MLH1 also has an impact in DNA end processing, favoring canonical NHEJ downstream of the DSB. Collectively, our study shows that the ATPase domain of MLH1 is important to transmit the CSR signaling cascade both upstream and downstream of the generation of DSBs.
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Affiliation(s)
- Richard Chahwan
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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Chahwan R, Edelmann W, Scharff MD, Roa S. Mismatch-mediated error prone repair at the immunoglobulin genes. Biomed Pharmacother 2011; 65:529-36. [PMID: 22100214 DOI: 10.1016/j.biopha.2011.09.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022] Open
Abstract
The generation of effective antibodies depends upon somatic hypermutation (SHM) and class-switch recombination (CSR) of antibody genes by activation induced cytidine deaminase (AID) and the subsequent recruitment of error prone base excision and mismatch repair. While AID initiates and is required for SHM, more than half of the base changes that accumulate in V regions are not due to the direct deamination of dC to dU by AID, but rather arise through the recruitment of the mismatch repair complex (MMR) to the U:G mismatch created by AID and the subsequent perversion of mismatch repair from a high fidelity process to one that is very error prone. In addition, the generation of double-strand breaks (DSBs) is essential during CSR, and the resolution of AID-generated mismatches by MMR to promote such DSBs is critical for the efficiency of the process. While a great deal has been learned about how AID and MMR cause hypermutations and DSBs, it is still unclear how the error prone aspect of these processes is largely restricted to antibody genes. The use of knockout models and mice expressing mismatch repair proteins with separation-of-function point mutations have been decisive in gaining a better understanding of the roles of each of the major MMR proteins and providing further insight into how mutation and repair are coordinated. Here, we review the cascade of MMR factors and repair signals that are diverted from their canonical error free role and hijacked by B cells to promote genetic diversification of the Ig locus. This error prone process involves AID as the inducer of enzymatically-mediated DNA mismatches, and a plethora of downstream MMR factors acting as sensors, adaptors and effectors of a complex and tightly regulated process from much of which is not yet well understood.
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Affiliation(s)
- Richard Chahwan
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave-Chanin 404, Bronx, NY 10461, United States
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Saribasak H, Maul RW, Cao Z, McClure RL, Yang W, McNeill DR, Wilson DM, Gearhart PJ. XRCC1 suppresses somatic hypermutation and promotes alternative nonhomologous end joining in Igh genes. ACTA ACUST UNITED AC 2011; 208:2209-16. [PMID: 21967769 PMCID: PMC3201205 DOI: 10.1084/jem.20111135] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
As revealed using mice heterozygous for the base excision repair (BER) protein XRCC1, BER and mutagenic repair pathways can simultaneously compete for access to single-strand breaks induced by activation-induced deaminase. Activation-induced deaminase (AID) deaminates cytosine to uracil in immunoglobulin genes. Uracils in DNA can be recognized by uracil DNA glycosylase and abasic endonuclease to produce single-strand breaks. The breaks are repaired either faithfully by DNA base excision repair (BER) or mutagenically to produce somatic hypermutation (SHM) and class switch recombination (CSR). To unravel the interplay between repair and mutagenesis, we decreased the level of x-ray cross-complementing 1 (XRCC1), a scaffold protein involved in BER. Mice heterozygous for XRCC1 showed a significant increase in the frequencies of SHM in Igh variable regions in Peyer’s patch cells, and of double-strand breaks in the switch regions during CSR. Although the frequency of CSR was normal in Xrcc1+/− splenic B cells, the length of microhomology at the switch junctions decreased, suggesting that XRCC1 also participates in alternative nonhomologous end joining. Furthermore, Xrcc1+/− B cells had reduced Igh/c-myc translocations during CSR, supporting a role for XRCC1 in microhomology-mediated joining. Our results imply that AID-induced single-strand breaks in Igh variable and switch regions become substrates simultaneously for BER and mutagenesis pathways.
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Affiliation(s)
- Huseyin Saribasak
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
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Barreto VM, Magor BG. Activation-induced cytidine deaminase structure and functions: a species comparative view. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2011; 35:991-1007. [PMID: 21349283 DOI: 10.1016/j.dci.2011.02.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Revised: 02/09/2011] [Accepted: 02/16/2011] [Indexed: 05/30/2023]
Abstract
In the ten years since the discovery of activation-induced cytidine deaminase (AID) there has been considerable effort to understand the mechanisms behind this enzyme's ability to target and modify immunoglobulin genes leading to somatic hypermutation and class switch recombination. While the majority of research has focused on mouse and human models of AID function, work on other species, from lamprey to rabbit and sheep, has taught us much about the scope of functions of the AID mutator. This review takes a species-comparative approach to what has been learned about the AID mutator enzyme and its role in humoral immunity.
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Ranjit S, Khair L, Linehan EK, Ucher AJ, Chakrabarti M, Schrader CE, Stavnezer J. AID recruits UNG and Msh2 to Ig switch regions dependent upon the AID C terminus [corrected]. THE JOURNAL OF IMMUNOLOGY 2011; 187:2464-75. [PMID: 21804017 DOI: 10.4049/jimmunol.1101406] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Activation-induced cytidine deaminase (AID) is induced in B cells during an immune response and is essential for both class-switch recombination (CSR) and somatic hypermutation of Ab genes. The C-terminal 10 aa of AID are required for CSR but not for somatic hypermutation, although their role in CSR is unknown. Using retroviral transduction into mouse splenic B cells, we show that the C terminus is not required for switch (S) region double-strand breaks (DSBs) and therefore functions downstream of DSBs. Using chromatin immunoprecipitation, we show that AID binds cooperatively with UNG and the mismatch repair proteins Msh2-Msh6 to Ig Sμ and Sγ3 regions, and this depends on the C terminus and the deaminase activity of AID. We also show that mismatch repair does not contribute to the efficiency of CSR in the absence of the AID C terminus. Although it has been demonstrated that both UNG and Msh2-Msh6 are important for introduction of S region DSBs, our data suggest that the ability of AID to recruit these proteins is important for DSB resolution, perhaps by directing the S region DSBs toward accurate and efficient CSR via nonhomologous end joining.
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Affiliation(s)
- Sanjay Ranjit
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01655, USA
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Clark AB, Lujan SA, Kissling GE, Kunkel TA. Mismatch repair-independent tandem repeat sequence instability resulting from ribonucleotide incorporation by DNA polymerase ε. DNA Repair (Amst) 2011; 10:476-82. [PMID: 21414850 DOI: 10.1016/j.dnarep.2011.02.001] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Revised: 01/27/2011] [Accepted: 02/11/2011] [Indexed: 01/11/2023]
Abstract
During DNA synthesis in vitro using dNTP and rNTP concentrations present in vivo, yeast replicative DNA polymerases α, δ and ɛ (Pols α, δ and ɛ) stably incorporate rNTPs into DNA. rNTPs are also incorporated during replication in vivo, and they are repaired in an RNase H2-dependent manner. In strains encoding a mutator allele of Pol ɛ (pol2-M644G), failure to remove rNMPs from DNA due to deletion of the RNH201 gene encoding the catalytic subunit of RNase H2, results in deletion of 2-5 base pairs in short repetitive sequences. Deletion rates depend on the orientation of the reporter gene relative to a nearby replication origin, suggesting that mutations result from rNMPs incorporated during replication. Here we demonstrate that 2-5 base pair deletion mutagenesis also strongly increases in rnh201Δ strains encoding wild type DNA polymerases. As in the pol2-M644G strains, the deletions occur at repetitive sequences and are orientation-dependent, suggesting that mismatches involving misaligned strands arise that could be subject to mismatch repair. Unexpectedly however, 2-5 base pair deletion rates resulting from loss of RNH201 in the pol2-M644G strain are unaffected by concomitant loss of MSH3, MSH6, or both. It could be that the mismatch repair machinery is unable to repair mismatches resulting from unrepaired rNMPs incorporated into DNA by M644G Pol ɛ, but this possibility is belied by the observation that Msh2-Msh6 can bind to a ribonucleotide-containing mismatch. Alternatively, following incorporation of rNMPs by M644G Pol ɛ during replication, the conversion of unrepaired rNMPs into mutations may occur outside the context of replication, e.g., during the repair of nicks resulting from rNMPs in DNA. The results make interesting predictions that can be tested.
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Affiliation(s)
- Alan B Clark
- Laboratory of Molecular Genetics and Laboratory of Structural Biology, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, United States
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