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Mu Y, Chen Z, Plummer JB, Zelazowska MA, Dong Q, Krug LT, McBride KM. UNG-RPA interaction governs the choice between high-fidelity and mutagenic uracil repair. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.30.591927. [PMID: 38746347 PMCID: PMC11092621 DOI: 10.1101/2024.04.30.591927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Mammalian Uracil DNA glycosylase (UNG) removes uracils and initiates high-fidelity base excision repair to maintain genomic stability. During B cell development, activation-induced cytidine deaminase (AID) creates uracils that UNG processes in an error-prone fashion to accomplish immunoglobulin (Ig) somatic hypermutation (SHM) or class switch recombination (CSR). The mechanism that governs high-fidelity versus mutagenic uracil repair is not understood. The B cell tropic gammaherpesvirus (GHV) encodes a functional homolog of UNG that can process AID induced genomic uracils. GHVUNG does not support hypermutation, suggesting intrinsic properties of UNG influence repair outcome. Noting the structural divergence between the UNGs, we define the RPA interacting motif as the determinant of mutation outcome. UNG or RPA mutants unable to interact with each other, only support high-fidelity repair. In B cells, transversions at the Ig variable region are abated while CSR is supported. Thus UNG-RPA governs the generation of mutations and has implications for locus specific mutagenesis in B cells and deamination associated mutational signatures in cancer.
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Sánchez-Ramón S, Fuentes-Antrás J, Rider NL, Pérez-Segura P, de la Fuente-Muñoz E, Fernández-Arquero M, Neves E, Pérez de Diego R, Ocaña A, Guevara-Hoyer K. Exploring gastric cancer genetics: A turning point in common variable immunodeficiency. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. GLOBAL 2024; 3:100203. [PMID: 38283086 PMCID: PMC10818086 DOI: 10.1016/j.jacig.2023.100203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 10/11/2023] [Accepted: 10/31/2023] [Indexed: 01/30/2024]
Abstract
Background Gastric cancer (GC) stands as a prominent cause of cancer-related mortality and ranks second among the most frequently diagnosed malignancies in individuals with common variable immunodeficiency (CVID). Objective We sought to conduct a comprehensive, large-scale genetic analysis to explore the CVID-associated germline variant landscape within gastric adenocarcinoma samples and to seek to delineate the transcriptomic similarities between GC and CVID. Methods We investigated the presence of CVID-associated germline variants in 1591 GC samples and assessed their impact on tumor mutational load. The progression of GC was evaluated in patients with and without these variants. Transcriptomic similarities were explored by matching differentially expressed genes in GC to healthy gastric tissue with a CVID transcriptomic signature. Results CVID-associated germline variants were found in 60% of GC samples. Our analysis revealed a significant association between the presence of CVID-related genetic variants and higher tumor mutational load in GC (P < .0001); high GC mutational load seems to be linked to immunotherapy response and worse prognosis. Transcriptomic similarities unveiled key genes and pathways implicated in innate immune responses and tumorigenesis. We identified upregulated genes related to oncogene drivers, inflammation, tumor suppression, DNA repair, and downregulated immunomodulatory genes shared between GC and CVID. Conclusions Our findings contribute to a deeper understanding of potential molecular modulators of GC and shed light on the intricate interplay between immunodeficiency and cancer. This study underscores the clinical relevance of CVID-related variants in influencing GC progression and opens avenues for further exploration into novel therapeutic approaches.
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Affiliation(s)
- Silvia Sánchez-Ramón
- Cancer Immunomonitoring and Immune-Mediated Diseases Research Unit, San Carlos Health Research Institute (IdSSC), Department of Clinical Immunology, San Carlos University Hospital, Madrid, Spain
- Department of Clinical Immunology, Instituto de médicina de laboratorio (IML) and IdSSC, San Carlos University Hospital, Madrid, Spain
- Department of Immunology, Ophthalmology and ENT, School of Medicine, Universidad Complutense, Madrid, Spain
| | - Jesús Fuentes-Antrás
- Department of Medical Oncology, IdSSC, San Carlos University Hospital, Madrid, Spain
- Experimental Therapeutics and Translational Oncology Unit, Department of Medical Oncology, IdSSC, San Carlos University Hospital, and CIBERONC, Madrid, Spain
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Nicholas L. Rider
- Division of Clinical Informatics, Pediatrics, Allergy and Immunology, Liberty University College of Osteopathic Medicine and Collaborative Health Partners, Lynchburg, Va
| | - Pedro Pérez-Segura
- Department of Medical Oncology, IdSSC, San Carlos University Hospital, Madrid, Spain
| | - Eduardo de la Fuente-Muñoz
- Cancer Immunomonitoring and Immune-Mediated Diseases Research Unit, San Carlos Health Research Institute (IdSSC), Department of Clinical Immunology, San Carlos University Hospital, Madrid, Spain
- Department of Clinical Immunology, Instituto de médicina de laboratorio (IML) and IdSSC, San Carlos University Hospital, Madrid, Spain
- Department of Immunology, Ophthalmology and ENT, School of Medicine, Universidad Complutense, Madrid, Spain
| | - Miguel Fernández-Arquero
- Cancer Immunomonitoring and Immune-Mediated Diseases Research Unit, San Carlos Health Research Institute (IdSSC), Department of Clinical Immunology, San Carlos University Hospital, Madrid, Spain
- Department of Clinical Immunology, Instituto de médicina de laboratorio (IML) and IdSSC, San Carlos University Hospital, Madrid, Spain
- Department of Immunology, Ophthalmology and ENT, School of Medicine, Universidad Complutense, Madrid, Spain
| | - Esmeralda Neves
- Department of Immunology, Centro Hospitalar e Universitário de Santo António, Porto, Portugal
| | - Rebeca Pérez de Diego
- Department of Immunology, Ophthalmology and ENT, School of Medicine, Universidad Complutense, Madrid, Spain
- Laboratory of Immunogenetics of Human Diseases, IdiPAZ Institute for Health Research, Madrid, Spain
| | - Alberto Ocaña
- Department of Medical Oncology, IdSSC, San Carlos University Hospital, Madrid, Spain
- Experimental Therapeutics and Translational Oncology Unit, Department of Medical Oncology, IdSSC, San Carlos University Hospital, and CIBERONC, Madrid, Spain
| | - Kissy Guevara-Hoyer
- Cancer Immunomonitoring and Immune-Mediated Diseases Research Unit, San Carlos Health Research Institute (IdSSC), Department of Clinical Immunology, San Carlos University Hospital, Madrid, Spain
- Department of Clinical Immunology, Instituto de médicina de laboratorio (IML) and IdSSC, San Carlos University Hospital, Madrid, Spain
- Department of Immunology, Ophthalmology and ENT, School of Medicine, Universidad Complutense, Madrid, Spain
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3
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Rieffer AE, Chen Y, Salamango DJ, Moraes SN, Harris RS. APOBEC Reporter Systems for Evaluating diNucleotide Editing Levels. CRISPR J 2023; 6:430-446. [PMID: 37672599 PMCID: PMC10611974 DOI: 10.1089/crispr.2023.0027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 08/14/2023] [Indexed: 09/08/2023] Open
Abstract
Precision genome editing has become a reality with the discovery of base editors. Cytosine base editor (CBE) technologies are improving rapidly but are mostly optimized for TC dinucleotide targets. Here, we report the development and implementation of APOBEC Reporter Systems for Evaluating diNucleotide Editing Levels (ARSENEL) in living cells. The ARSENEL panel is comprised of four constructs that quantitatively report editing of each of the four dinucleotide motifs (AC/CC/GC/TC) through real-time accumulation of eGFP fluorescence. Editing rates of APOBEC3Bctd and AIDΔC CBEs reflect established mechanistic preferences with intrinsic biases to TC and GC, respectively. Twelve different (new and established) base editors are tested here using this system with a full-length APOBEC3B CBE showing the greatest on-target TC specificity and an APOBEC3A construct showing the highest editing efficiency. In addition, ARSENEL enables real-time assessment of natural and synthetic APOBEC inhibitors with the most potent to-date being the large subunit of the Epstein-Barr virus ribonucleotide reductase. These reporters have the potential to play important roles in research and development as precision genome engineering technologies progress toward achieving maximal specificity and efficiency.
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Affiliation(s)
- Amanda E. Rieffer
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota—Twin Cities, Minneapolis, Minnesota, USA; University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Yanjun Chen
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA; and University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Daniel J. Salamango
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota—Twin Cities, Minneapolis, Minnesota, USA; University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Sofia N. Moraes
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota—Twin Cities, Minneapolis, Minnesota, USA; University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Reuben S. Harris
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota—Twin Cities, Minneapolis, Minnesota, USA; University of Texas Health San Antonio, San Antonio, Texas, USA
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA; and University of Texas Health San Antonio, San Antonio, Texas, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, Texas, USA
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4
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Bello A, Hirth G, Voigt S, Tepper S, Jungnickel B. Mechanism and regulation of secondary immunoglobulin diversification. Cell Cycle 2023; 22:2070-2087. [PMID: 37909747 PMCID: PMC10761156 DOI: 10.1080/15384101.2023.2275397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 10/20/2023] [Indexed: 11/03/2023] Open
Abstract
Secondary immunoglobulin diversification by somatic hypermutation and class switch recombination in B cells is instrumental for an adequate adaptive humoral immune response. These genetic events may, however, also introduce aberrations into other cellular genes and thereby cause B cell malignancies. While the basic mechanism of somatic hypermutation and class switch recombination is now well understood, their regulation and in particular the mechanism of their specific targeting to immunoglobulin genes is still rather mysterious. In this review, we summarize the current knowledge on the mechanism and regulation of secondary immunoglobulin diversification and discuss known mechanisms of physiological targeting to immunoglobulin genes and mistargeting to other cellular genes. We summarize open questions in the field and provide an outlook on future research.
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Affiliation(s)
- Amanda Bello
- Institute of Biochemistry and Biophysics, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
| | - Gianna Hirth
- Institute of Biochemistry and Biophysics, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
| | - Stefanie Voigt
- Institute of Biochemistry and Biophysics, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
| | - Sandra Tepper
- Institute of Biochemistry and Biophysics, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
| | - Berit Jungnickel
- Institute of Biochemistry and Biophysics, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
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5
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Schrader CE, Williams T, Pechhold K, Linehan EK, Tsuchimoto D, Nakabeppu Y. APE2 Promotes AID-Dependent Somatic Hypermutation in Primary B Cell Cultures That Is Suppressed by APE1. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 210:1804-1814. [PMID: 37074207 PMCID: PMC10234595 DOI: 10.4049/jimmunol.2100946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 03/29/2023] [Indexed: 04/20/2023]
Abstract
Somatic hypermutation (SHM) is necessary for Ab diversification and involves error-prone DNA repair of activation-induced cytidine deaminase-induced lesions in germinal center (GC) B cells but can also cause genomic instability. GC B cells express low levels of the DNA repair protein apurinic/apyrimidinic (AP) endonuclease (APE)1 and high levels of its homolog APE2. Reduced SHM in APE2-deficient mice suggests that APE2 promotes SHM, but these GC B cells also exhibit reduced proliferation that could impact mutation frequency. In this study, we test the hypothesis that APE2 promotes and APE1 suppresses SHM. We show how APE1/APE2 expression changes in primary murine spleen B cells during activation, impacting both SHM and class-switch recombination (CSR). High levels of both APE1 and APE2 early after activation promote CSR. However, after 2 d, APE1 levels decrease steadily with each cell division, even with repeated stimulation, whereas APE2 levels increase with each stimulation. When GC-level APE1/APE2 expression was engineered by reducing APE1 genetically (apex1+/-) and overexpressing APE2, bona fide activation-induced cytidine deaminase-dependent VDJH4 intron SHM became detectable in primary B cell cultures. The C terminus of APE2 that interacts with proliferating cell nuclear Ag promotes SHM and CSR, although its ATR-Chk1-interacting Zf-GRF domain is not required. However, APE2 does not increase mutations unless APE1 is reduced. Although APE1 promotes CSR, it suppresses SHM, suggesting that downregulation of APE1 in the GC is required for SHM. Genome-wide expression data compare GC and cultured B cells and new models depict how APE1 and APE2 expression and protein interactions change during B cell activation and affect the balance between accurate and error-prone repair during CSR and SHM.
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Affiliation(s)
- Carol E. Schrader
- Department of Microbiology and Physiological Systems, Program in Immunology and Microbiology, UMassChan Medical School, Worcester, MA 01655
| | - Travis Williams
- Department of Microbiology and Physiological Systems, Program in Immunology and Microbiology, UMassChan Medical School, Worcester, MA 01655
| | - Klaus Pechhold
- Department of Microbiology and Physiological Systems, Program in Immunology and Microbiology, UMassChan Medical School, Worcester, MA 01655
| | - Erin K. Linehan
- Department of Microbiology and Physiological Systems, Program in Immunology and Microbiology, UMassChan Medical School, Worcester, MA 01655
| | - Daisuke Tsuchimoto
- Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yusaku Nakabeppu
- Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
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6
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Hao Q, Zhan C, Lian C, Luo S, Cao W, Wang B, Xie X, Ye X, Gui T, Voena C, Pighi C, Wang Y, Tian Y, Wang X, Dai P, Cai Y, Liu X, Ouyang S, Sun S, Hu Q, Liu J, Ye Y, Zhao J, Lu A, Wang JY, Huang C, Su B, Meng FL, Chiarle R, Pan-Hammarström Q, Yeap LS. DNA repair mechanisms that promote insertion-deletion events during immunoglobulin gene diversification. Sci Immunol 2023; 8:eade1167. [PMID: 36961908 PMCID: PMC10351598 DOI: 10.1126/sciimmunol.ade1167] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 03/01/2023] [Indexed: 03/26/2023]
Abstract
Insertions and deletions (indels) are low-frequency deleterious genomic DNA alterations. Despite their rarity, indels are common, and insertions leading to long complementarity-determining region 3 (CDR3) are vital for antigen-binding functions in broadly neutralizing and polyreactive antibodies targeting viruses. Because of challenges in detecting indels, the mechanism that generates indels during immunoglobulin diversification processes remains poorly understood. We carried out ultra-deep profiling of indels and systematically dissected the underlying mechanisms using passenger-immunoglobulin mouse models. We found that activation-induced cytidine deaminase-dependent ±1-base pair (bp) indels are the most prevalent indel events, biasing deleterious outcomes, whereas longer in-frame indels, especially insertions that can extend the CDR3 length, are rare outcomes. The ±1-bp indels are channeled by base excision repair, but longer indels require additional DNA-processing factors. Ectopic expression of a DNA exonuclease or perturbation of the balance of DNA polymerases can increase the frequency of longer indels, thus paving the way for models that can generate antibodies with long CDR3. Our study reveals the mechanisms that generate beneficial and deleterious indels during the process of antibody somatic hypermutation and has implications in understanding the detrimental genomic alterations in various conditions, including tumorigenesis.
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Affiliation(s)
- Qian Hao
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Department of Endocrinology and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Chuanzong Zhan
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Department of Endocrinology and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Chaoyang Lian
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Simin Luo
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Wenyi Cao
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Binbin Wang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Xia Xie
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences; 320 Yueyang Road, Shanghai 200031, China
| | - Xiaofei Ye
- Department of Biosciences and Nutrition, Karolinska Institutet; SE141-83, Huddinge, Stockholm, Sweden
- Present address: Kindstar Global Precision Medicine Institute, Wuhan, China and Kindstar Biotech, Wuhan, China
| | - Tuantuan Gui
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Claudia Voena
- Department of Molecular Biotechnology and Health Sciences, University of Torino; 10126 Torino, Italy
| | - Chiara Pighi
- Department of Molecular Biotechnology and Health Sciences, University of Torino; 10126 Torino, Italy
- Department of Pathology, Boston Children’s Hospital, and Harvard Medical School; Boston, MA 02115, USA
| | - Yanyan Wang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences; 320 Yueyang Road, Shanghai 200031, China
| | - Ying Tian
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Xin Wang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Pengfei Dai
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences; 320 Yueyang Road, Shanghai 200031, China
| | - Yanni Cai
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences; 320 Yueyang Road, Shanghai 200031, China
| | - Xiaojing Liu
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences; 320 Yueyang Road, Shanghai 200031, China
| | - Shengqun Ouyang
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Department of Endocrinology and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Shiqi Sun
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Qianwen Hu
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Jun Liu
- Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Youqiong Ye
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Jingkun Zhao
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Aiguo Lu
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Ji-Yang Wang
- Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
- Department of Microbiology and Immunology, College of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Chuanxin Huang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Bing Su
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Departments of Endocrinology and Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Jiao Tong University School of Medicine-Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai 200025
| | - Fei-Long Meng
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences; 320 Yueyang Road, Shanghai 200031, China
| | - Roberto Chiarle
- Department of Molecular Biotechnology and Health Sciences, University of Torino; 10126 Torino, Italy
- Department of Pathology, Boston Children’s Hospital, and Harvard Medical School; Boston, MA 02115, USA
| | - Qiang Pan-Hammarström
- Department of Biosciences and Nutrition, Karolinska Institutet; SE141-83, Huddinge, Stockholm, Sweden
| | - Leng-Siew Yeap
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Department of Endocrinology and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
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7
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Çakan E, Gunaydin G. Activation induced cytidine deaminase: An old friend with new faces. Front Immunol 2022; 13:965312. [PMID: 36405752 PMCID: PMC9670734 DOI: 10.3389/fimmu.2022.965312] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 10/10/2022] [Indexed: 11/25/2022] Open
Abstract
Activation induced cytidine deaminase (AID) protein is a member of APOBEC family. AID converts cytidine to uracil, which is a key step for somatic hypermutation (SHM) and class switch recombination (CSR). AID also plays critical roles in B cell precursor stages, removing polyreactive B cells from immune repertoire. Since the main function of AID is inducing point mutations, dysregulation can lead to increased mutation load, translocations, disturbed genomic integrity, and lymphomagenesis. As such, expression of AID as well as its function is controlled strictly at various molecular steps. Other members of the APOBEC family also play crucial roles during carcinogenesis. Considering all these functions, AID represents a bridge, linking chronic inflammation to carcinogenesis and immune deficiencies to autoimmune manifestations.
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Affiliation(s)
- Elif Çakan
- Hacettepe University School of Medicine, Sihhiye, Ankara, Turkey
| | - Gurcan Gunaydin
- Department of Basic Oncology, Hacettepe University Cancer Institute, Sihhiye, Ankara, Turkey
- *Correspondence: Gurcan Gunaydin,
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8
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Guevara-Hoyer K, Fuentes-Antrás J, de la Fuente-Muñoz E, Fernández-Arquero M, Solano F, Pérez-Segura P, Neves E, Ocaña A, Pérez de Diego R, Sánchez-Ramón S. Genomic crossroads between non-Hodgkin’s lymphoma and common variable immunodeficiency. Front Immunol 2022; 13:937872. [PMID: 35990641 PMCID: PMC9390007 DOI: 10.3389/fimmu.2022.937872] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/07/2022] [Indexed: 12/03/2022] Open
Abstract
Common variable immunodeficiency (CVID) represents the largest group of primary immunodeficiencies that may manifest with infections, inflammation, autoimmunity, and cancer, mainly B-cell non-Hodgkin’s lymphoma (NHL). Indeed, NHL may result from chronic or recurrent infections and has, therefore, been recognized as a clinical phenotype of CVID, although rare. The more one delves into the mechanisms involved in CVID and cancer, the stronger the idea that both pathologies can be a reflection of the same primer events observed from different angles. The potential effects of germline variants on specific somatic modifications in malignancies suggest that it might be possible to anticipate critical events during tumor development. In the same way, a somatic alteration in NHL could be conditioning a similar response at the transcriptional level in the shared signaling pathways with genetic germline alterations in CVID. We aimed to explore the genomic substrate shared between these entities to better characterize the CVID phenotype immunodeficiency in NHL. By means of an in-silico approach, we interrogated the large, publicly available datasets contained in cBioPortal for the presence of genes associated with genetic pathogenic variants in a panel of 50 genes recurrently altered in CVID and previously described as causative or disease-modifying. We found that 323 (25%) of the 1,309 NHL samples available for analysis harbored variants of the CVID spectrum, with the most recurrent alteration presented in NHL occurring in PIK3CD (6%) and STAT3 (4%). Pathway analysis of common gene alterations showed enrichment in inflammatory, immune surveillance, and defective DNA repair mechanisms similar to those affected in CVID, with PIK3R1 appearing as a central node in the protein interaction network. The co-occurrence of gene alterations was a frequent phenomenon. This study represents an attempt to identify common genomic grounds between CVID and NHL. Further prospective studies are required to better know the role of genetic variants associated with CVID and their reflection on the somatic pathogenic variants responsible for cancer, as well as to characterize the CVID-like phenotype in NHL, with the potential to influence early CVID detection and therapeutic management.
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Affiliation(s)
- Kissy Guevara-Hoyer
- Cancer Immunomonitoring and Immuno-Mediated Pathologies Support Unit, IdSSC, Department of Clinical Immunology, San Carlos Clinical Hospital, Madrid, Spain
- Department of Clinical Immunology, IML and IdSSC, San Carlos Clinical Hospital, Madrid, Spain
- Department of Immunology, Ophthalmology and ENT, School of Medicine, Complutense University, Madrid, Spain
- *Correspondence: Kissy Guevara-Hoyer,
| | - Jesús Fuentes-Antrás
- Oncology Department, San Carlos Clinical Hospital, Madrid, Spain
- Experimental Therapeutics and Translational Oncology Unit, Medical Oncology Department, San Carlos University Hospital, Madrid, Spain
| | - Eduardo de la Fuente-Muñoz
- Cancer Immunomonitoring and Immuno-Mediated Pathologies Support Unit, IdSSC, Department of Clinical Immunology, San Carlos Clinical Hospital, Madrid, Spain
- Department of Clinical Immunology, IML and IdSSC, San Carlos Clinical Hospital, Madrid, Spain
- Department of Immunology, Ophthalmology and ENT, School of Medicine, Complutense University, Madrid, Spain
| | - Miguel Fernández-Arquero
- Cancer Immunomonitoring and Immuno-Mediated Pathologies Support Unit, IdSSC, Department of Clinical Immunology, San Carlos Clinical Hospital, Madrid, Spain
- Department of Clinical Immunology, IML and IdSSC, San Carlos Clinical Hospital, Madrid, Spain
- Department of Immunology, Ophthalmology and ENT, School of Medicine, Complutense University, Madrid, Spain
| | - Fernando Solano
- Department of Hematology, General University Hospital Nuestra Señora del Prado, Talavera de la Reina, Spain
| | | | - Esmeralda Neves
- Department of Immunology, Centro Hospitalar e Universitário do Porto, Porto, Portugal
- Unit for Multidisciplinary Research in Biomedicine (UMIB), Hospital and University Center of Porto, Porto, Portugal
| | - Alberto Ocaña
- Oncology Department, San Carlos Clinical Hospital, Madrid, Spain
- Experimental Therapeutics and Translational Oncology Unit, Medical Oncology Department, San Carlos University Hospital, Madrid, Spain
| | - Rebeca Pérez de Diego
- Department of Immunology, Ophthalmology and ENT, School of Medicine, Complutense University, Madrid, Spain
- Laboratory of Immunogenetics of Human Diseases, IdiPAZ Institute for Health Research, Madrid, Spain
| | - Silvia Sánchez-Ramón
- Cancer Immunomonitoring and Immuno-Mediated Pathologies Support Unit, IdSSC, Department of Clinical Immunology, San Carlos Clinical Hospital, Madrid, Spain
- Department of Clinical Immunology, IML and IdSSC, San Carlos Clinical Hospital, Madrid, Spain
- Department of Immunology, Ophthalmology and ENT, School of Medicine, Complutense University, Madrid, Spain
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9
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Li CC, Zhang G, Du J, Liu D, Li Z, Ni Y, Zhou J, Li Y, Hou S, Zheng X, Lan Y, Liu B, He A. Pre-configuring chromatin architecture with histone modifications guides hematopoietic stem cell formation in mouse embryos. Nat Commun 2022; 13:346. [PMID: 35039499 PMCID: PMC8764075 DOI: 10.1038/s41467-022-28018-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 01/03/2022] [Indexed: 11/09/2022] Open
Abstract
The gene activity underlying cell differentiation is regulated by a diverse set of transcription factors (TFs), histone modifications, chromatin structures and more. Although definitive hematopoietic stem cells (HSCs) are known to emerge via endothelial-to-hematopoietic transition (EHT), how the multi-layered epigenome is sequentially unfolded in a small portion of endothelial cells (ECs) transitioning into the hematopoietic fate remains elusive. With optimized low-input itChIP-seq and Hi-C assays, we performed multi-omics dissection of the HSC ontogeny trajectory across early arterial ECs (eAECs), hemogenic endothelial cells (HECs), pre-HSCs and long-term HSCs (LT-HSCs) in mouse embryos. Interestingly, HSC regulatory regions are already pre-configurated with active histone modifications as early as eAECs, preceding chromatin looping dynamics within topologically associating domains. Chromatin looping structures between enhancers and promoters only become gradually strengthened over time. Notably, RUNX1, a master TF for hematopoiesis, enriched at half of these loops is observed early from eAECs through pre-HSCs but its enrichment further increases in HSCs. RUNX1 and co-TFs together constitute a central, progressively intensified enhancer-promoter interactions. Thus, our study provides a framework to decipher how temporal epigenomic configurations fulfill cell lineage specification during development.
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Affiliation(s)
- Chen C Li
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China
| | - Guangyu Zhang
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, 100850, Beijing, China
| | - Junjie Du
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, 100850, Beijing, China
| | - Di Liu
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China
| | - Zongcheng Li
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Fifth Medical Center of Chinese PLA General Hospital, 100850, Beijing, China
| | - Yanli Ni
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Fifth Medical Center of Chinese PLA General Hospital, 100850, Beijing, China
| | - Jie Zhou
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Fifth Medical Center of Chinese PLA General Hospital, 100850, Beijing, China
| | - Yunqiao Li
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, 100850, Beijing, China
| | - Siyuan Hou
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, China
| | - Xiaona Zheng
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, 100850, Beijing, China
| | - Yu Lan
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, China.
| | - Bing Liu
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, 100850, Beijing, China.
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Fifth Medical Center of Chinese PLA General Hospital, 100850, Beijing, China.
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou, China.
| | - Aibin He
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China.
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10
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Nucleotide Pool Imbalance and Antibody Gene Diversification. Vaccines (Basel) 2021; 9:vaccines9101050. [PMID: 34696158 PMCID: PMC8538681 DOI: 10.3390/vaccines9101050] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/13/2021] [Accepted: 09/17/2021] [Indexed: 01/10/2023] Open
Abstract
The availability and adequate balance of deoxyribonucleoside triphosphate (dNTP) is an important determinant of both the fidelity and the processivity of DNA polymerases. Therefore, maintaining an optimal balance of the dNTP pool is critical for genomic stability in replicating and quiescent cells. Since DNA synthesis is required not only in genomic replication but also in DNA damage repair and recombination, the abnormalities in the dNTP pool affect a wide range of chromosomal activities. The generation of antibody diversity relies on antigen-independent V(D)J recombination, as well as antigen-dependent somatic hypermutation and class switch recombination. These processes involve diverse sets of DNA polymerases, which are affected by the dNTP pool imbalances. This review discusses the role of the optimal dNTP pool balance in the diversification of antibody encoding genes.
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11
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Repair of programmed DNA lesions in antibody class switch recombination: common and unique features. ACTA ACUST UNITED AC 2021; 2:115-125. [PMID: 33817557 PMCID: PMC7996122 DOI: 10.1007/s42764-021-00035-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 02/22/2021] [Accepted: 03/04/2021] [Indexed: 01/31/2023]
Abstract
The adaptive immune system can diversify the antigen receptors to eliminate various pathogens through programmed DNA lesions at antigen receptor genes. In immune diversification, general DNA repair machineries are applied to transform the programmed DNA lesions into gene mutation or recombination events with common and unique features. Here we focus on antibody class switch recombination (CSR), and review the initiation of base damages, the conversion of damaged base to DNA double-strand break, and the ligation of broken ends. With an emphasis on the unique features in CSR, we discuss recent advances in the understanding of DNA repair/replication coordination, and ERCC6L2-mediated deletional recombination. We further elaborate the application of CSR in end-joining, resection and translesion synthesis assays. In the time of the COVID-19 pandemic, we hope it help to understand the generation of therapeutic antibodies.
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12
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Oreste U, Ametrano A, Coscia MR. On Origin and Evolution of the Antibody Molecule. BIOLOGY 2021; 10:biology10020140. [PMID: 33578914 PMCID: PMC7916673 DOI: 10.3390/biology10020140] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/05/2021] [Accepted: 02/07/2021] [Indexed: 12/29/2022]
Abstract
Simple Summary Like many other molecules playing vital functions in animals, the antibody molecule possesses a complex structure with distinctive features. The structure of the basic unit, i.e., the immunoglobulin domain of very ancient origin is substantially simple. However, high complexity resides in the types and numbers of the domains composing the whole molecule. The emergence of the antibody molecule during evolution overturned the effectiveness of the organisms’ defense system. The particular organization of the coding genes, the mechanisms generating antibody diversity, and the plasticity of the overall protein structure, attest to an extraordinary successful evolutionary history. Here, we attempt to trace, across the evolutionary scale, the very early origins of the most significant features characterizing the structure of the antibody molecule and of the molecular mechanisms underlying its major role in recognizing an almost unlimited number of pathogens. Abstract The vertebrate immune system provides a powerful defense because of the ability to potentially recognize an unlimited number of pathogens. The antibody molecule, also termed immunoglobulin (Ig) is one of the major mediators of the immune response. It is built up from two types of Ig domains: the variable domain, which provides the capability to recognize and bind a potentially infinite range of foreign substances, and the constant domains, which exert the effector functions. In the last 20 years, advances in our understanding of the molecular mechanisms and structural features of antibody in mammals and in a variety of other organisms have uncovered the underlying principles and complexity of this fundamental molecule. One notable evolutionary topic is the origin and evolution of antibody. Many aspects have been clearly stated, but some others remain limited or obscure. By considering a wide range of prokaryotic and eukaryotic organisms through a literature survey about the topic, we have provided an integrated view of the emergence of antibodies in evolution and underlined the very ancient origins.
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Affiliation(s)
- Umberto Oreste
- Institute of Biochemistry and Cell Biology, National Research Council of Italy, Via P. Castellino, 111, 80131 Naples, Italy; (U.O.); (A.A.)
| | - Alessia Ametrano
- Institute of Biochemistry and Cell Biology, National Research Council of Italy, Via P. Castellino, 111, 80131 Naples, Italy; (U.O.); (A.A.)
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania Luigi Vanvitelli, 81100 Caserta, Italy
| | - Maria Rosaria Coscia
- Institute of Biochemistry and Cell Biology, National Research Council of Italy, Via P. Castellino, 111, 80131 Naples, Italy; (U.O.); (A.A.)
- Correspondence: ; Tel.: +39-081-6132556
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13
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Yoshioka KI, Matsuno Y. Genomic destabilization and its associated mutagenesis increase with senescence-associated phenotype expression. Cancer Sci 2020; 112:515-522. [PMID: 33222327 PMCID: PMC7893996 DOI: 10.1111/cas.14746] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 11/10/2020] [Accepted: 11/19/2020] [Indexed: 12/20/2022] Open
Abstract
Cancer develops through multiple rounds of clonal evolution of cells with abrogated defense systems. Such clonal evolution is triggered by genomic destabilization with associated mutagenesis. However, what increases the risk of genomic destabilization remains unclear. Genomic instability is usually the result of erroneous repair of DNA double‐strand breaks (DSB); paradoxically, however, most cancers develop with genomic instability but lack mutations in DNA repair systems. In this manuscript, we review current knowledge regarding a cellular state that increases the risk of genomic destabilization, in which cells exhibit phenotypes often observed during senescence. In addition, we explore the pathways that lead to genomic destabilization and its associated mutagenesis, which ultimately result in cancer.
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Affiliation(s)
- Ken-Ichi Yoshioka
- Laboratory of Genome Stability Maintenance, National Cancer Center Research Institute, Tokyo, Japan
| | - Yusuke Matsuno
- Laboratory of Genome Stability Maintenance, National Cancer Center Research Institute, Tokyo, Japan.,Department of Applied Chemistry, Tokyo University of Science, Tokyo, Japan
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14
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Delgado P, Álvarez-Prado ÁF, Marina-Zárate E, Sernandez IV, Mur SM, de la Barrera J, Sanchez-Cabo F, Cañamero M, de Molina A, Belver L, de Yébenes VG, Ramiro AR. Interplay between UNG and AID governs intratumoral heterogeneity in mature B cell lymphoma. PLoS Genet 2020; 16:e1008960. [PMID: 33362210 PMCID: PMC7790409 DOI: 10.1371/journal.pgen.1008960] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 01/07/2021] [Accepted: 11/08/2020] [Indexed: 12/11/2022] Open
Abstract
Most B cell lymphomas originate from B cells that have germinal center (GC) experience and bear chromosome translocations and numerous point mutations. GC B cells remodel their immunoglobulin (Ig) genes by somatic hypermutation (SHM) and class switch recombination (CSR) in their Ig genes. Activation Induced Deaminase (AID) initiates CSR and SHM by generating U:G mismatches on Ig DNA that can then be processed by Uracyl-N-glycosylase (UNG). AID promotes collateral damage in the form of chromosome translocations and off-target SHM, however, the exact contribution of AID activity to lymphoma generation and progression is not completely understood. Here we show using a conditional knock-in strategy that AID supra-activity alone is not sufficient to generate B cell transformation. In contrast, in the absence of UNG, AID supra-expression increases SHM and promotes lymphoma. Whole exome sequencing revealed that AID heavily contributes to lymphoma SHM, promoting subclonal variability and a wider range of oncogenic variants. Thus, our data provide direct evidence that UNG is a brake to AID-induced intratumoral heterogeneity and evolution of B cell lymphoma.
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Affiliation(s)
- Pilar Delgado
- B Lymphocyte Biology Lab. Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Ángel F. Álvarez-Prado
- B Lymphocyte Biology Lab. Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Ester Marina-Zárate
- B Lymphocyte Biology Lab. Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Isora V. Sernandez
- B Lymphocyte Biology Lab. Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Sonia M. Mur
- B Lymphocyte Biology Lab. Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Jorge de la Barrera
- Bioinformatics Unit. Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Fátima Sanchez-Cabo
- Bioinformatics Unit. Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | | | - Antonio de Molina
- Comparative Medicine Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Laura Belver
- B Lymphocyte Biology Lab. Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Virginia G. de Yébenes
- B Lymphocyte Biology Lab. Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Almudena R. Ramiro
- B Lymphocyte Biology Lab. Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
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15
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Zhou JQ, Kleinstein SH. Position-Dependent Differential Targeting of Somatic Hypermutation. THE JOURNAL OF IMMUNOLOGY 2020; 205:3468-3479. [PMID: 33188076 DOI: 10.4049/jimmunol.2000496] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 10/04/2020] [Indexed: 01/28/2023]
Abstract
Somatic hypermutation (SHM) generates much of the Ab diversity necessary for affinity maturation and effective humoral immunity. The activation-induced cytidine deaminase-induced DNA lesions and error-prone repair that underlie SHM are known to exhibit intrinsic biases when targeting the Ig sequences. Computational models for SHM targeting often model the targeting probability of a nucleotide in a motif-based fashion, assuming that the same DNA motif is equally likely to be targeted regardless of its position along the Ig sequence. The validity of this assumption, however, has not been rigorously studied in vivo. In this study, by analyzing a large collection of 956,157 human Ig sequences while controlling for the confounding influence of selection, we show that the likelihood of a DNA 5-mer motif being targeted by SHM is not the same at different positions in the same Ig sequence. We found position-dependent differential SHM targeting for about three quarters of the 38 and 269 unique motifs from more than half of the 292 and 1912 motif-allele pairs analyzed using productive and nonproductive Ig sequences, respectively. The direction of the differential SHM targeting was largely conserved across individuals with no allele-specific effect within an IgH variable gene family, but was not consistent with general decay of SHM targeting with increasing distance from the transcription start site. However, SHM targeting did correlate positively with the mutability of the wider sequence neighborhood surrounding the motif. These findings provide insights and future directions for computational efforts toward modeling SHM.
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Affiliation(s)
- Julian Q Zhou
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511; and
| | - Steven H Kleinstein
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511; and .,Department of Pathology and Department of Immunobiology, Yale School of Medicine, New Haven, CT 06511
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16
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Feng Y, Seija N, Di Noia JM, Martin A. AID in Antibody Diversification: There and Back Again. Trends Immunol 2020; 41:586-600. [PMID: 32434680 PMCID: PMC7183997 DOI: 10.1016/j.it.2020.04.009] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/16/2020] [Accepted: 04/20/2020] [Indexed: 01/01/2023]
Abstract
Activation-Induced cytidine Deaminase (AID) initiates affinity maturation and isotype switching by deaminating deoxycytidines within immunoglobulin genes, leading to somatic hypermutation (SHM) and class switch recombination (CSR). AID thus potentiates the humoral response to clear pathogens. Marking the 20th anniversary of the discovery of AID, we review the current understanding of AID function. We discuss AID biochemistry and how error-free forms of DNA repair are co-opted to prioritize mutagenesis over accuracy during antibody diversification. We discuss the regulation of DNA double-strand break (DSB) repair pathways during CSR. We describe genomic targeting of AID as a multilayered process involving chromatin architecture, cis- and trans-acting factors, and determining mutagenesis – distinct from AID occupancy at loci that are spared from mutation. Subverted base excision repair (BER) and mismatch repair (MMR) pathways act concertedly to generate antibody sequence diversity during SHM. In CSR, DNA DSBs are repaired by the nonhomologous end-joining pathway involving the 53BP1–Rif1–Shieldin axis, and by an alternative end-joining pathway involving HMCES (5-Hydroxymethylcytosine binding, ES-cell-specific) that binds and protects resected DSB ends. Genomic targeting of AID appears to be multilayered, with inbuilt redundancy, but robust enough to ensure that most of the genome is spared from AID activity. Cis elements and genome topology act together with trans-acting factors involved in transcription and RNA processing to determine AID activity at specific Ig regions. Other loci sharing genomic and transcriptional features with the Ig are collaterally targeted during SHM and CSR.
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Affiliation(s)
- Yuqing Feng
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Noé Seija
- Institute de Recherches Cliniques de Montréal, Montréal, QC, Canada; Molecular Biology Programs, Department of Medicine, University of Montreal, Montréal, QC, Canada
| | - Javier M Di Noia
- Institute de Recherches Cliniques de Montréal, Montréal, QC, Canada; Molecular Biology Programs, Department of Medicine, University of Montreal, Montréal, QC, Canada.
| | - Alberto Martin
- Department of Immunology, University of Toronto, Toronto, ON, Canada.
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17
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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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18
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IJspeert H, van Schouwenburg PA, Pico-Knijnenburg I, Loeffen J, Brugieres L, Driessen GJ, Blattmann C, Suerink M, Januszkiewicz-Lewandowska D, Azizi AA, Seidel MG, Jacobs H, van der Burg M. Repertoire Sequencing of B Cells Elucidates the Role of UNG and Mismatch Repair Proteins in Somatic Hypermutation in Humans. Front Immunol 2019; 10:1913. [PMID: 31507588 PMCID: PMC6718458 DOI: 10.3389/fimmu.2019.01913] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 07/29/2019] [Indexed: 01/12/2023] Open
Abstract
The generation of high-affinity antibodies depends on somatic hypermutation (SHM). SHM is initiated by the activation-induced cytidine deaminase (AID), which generates uracil (U) lesions in the B-cell receptor (BCR) encoding genes. Error-prone processing of U lesions creates a typical spectrum of point mutations during SHM. The aim of this study was to determine the molecular mechanism of SHM in humans; currently available knowledge is limited by the number of mutations analyzed per patient. We collected a unique cohort of 10 well-defined patients with bi-allelic mutations in genes involved in base excision repair (BER) (UNG) or mismatch repair (MMR) (MSH2, MSH6, or PMS2) and are the first to present next-generation sequencing (NGS) data of the BCR, allowing us to study SHM extensively in humans. Analysis using ARGalaxy revealed selective skewing of SHM mutation patterns specific for each genetic defect, which are in line with the five-pathway model of SHM that was recently proposed based on mice data. However, trans-species comparison revealed differences in the role of PMS2 and MSH2 in strand targeting between mice and man. In conclusion, our results indicate a role for UNG, MSH2, MSH6, and PMS2 in the generation of SHM in humans comparable to their function in mice. However, we observed differences in strand targeting between humans and mice, emphasizing the importance of studying molecular mechanisms in a human setting. The here developed method combining NGS and ARGalaxy analysis of BCR mutation data forms the basis for efficient SHM analyses of other immune deficiencies.
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Affiliation(s)
- Hanna IJspeert
- Department of Immunology, Erasmus Medical Center, University Medical Center Rotterdam, Rotterdam, Netherlands.,Laboratory for Immunology, Department of Pediatrics, Leiden University Medical Center, Leiden, Netherlands
| | - Pauline A van Schouwenburg
- Department of Immunology, Erasmus Medical Center, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Ingrid Pico-Knijnenburg
- Laboratory for Immunology, Department of Pediatrics, Leiden University Medical Center, Leiden, Netherlands
| | - Jan Loeffen
- Department of Pediatric Oncology and Hematology, Erasmus Medical Centre, Sophia Children's Hospital, Rotterdam, Netherlands
| | - Laurence Brugieres
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Campus, Villejuif, France
| | - Gertjan J Driessen
- Department of Paediatrics, Juliana Children's Hospital, Haga Teaching Hospital, The Hague, Netherlands
| | - Claudia Blattmann
- Department of Pediatric Hematology and Oncology, Palliative Care, Olgahospital Klinikum Stuttgart, Stuttgart, Germany
| | - Manon Suerink
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, Netherlands
| | | | - Amedeo A Azizi
- Department of Pediatrics and Adolescent Medicine, Medical University Vienna, Vienna, Austria
| | - Marcus G Seidel
- Research Unit Pediatric Hematology and Immunology, Division of Pediatric Hematology-Oncology, Department of Pediatrics and Adolescent Medicine, Medical University Graz, Graz, Austria
| | - Heinz Jacobs
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Mirjam van der Burg
- Laboratory for Immunology, Department of Pediatrics, Leiden University Medical Center, Leiden, Netherlands
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19
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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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20
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van Schouwenburg PA, IJspeert H, Pico-Knijnenburg I, Dalm VASH, van Hagen PM, van Zessen D, Stubbs AP, Patel SY, van der Burg M. Identification of CVID Patients With Defects in Immune Repertoire Formation or Specification. Front Immunol 2018; 9:2545. [PMID: 30532750 PMCID: PMC6265514 DOI: 10.3389/fimmu.2018.02545] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 10/16/2018] [Indexed: 01/08/2023] Open
Abstract
Common variable immune deficiency disorder (CVID) is the most clinically relevant cause of antibody failure. It is a highly heterogeneous disease with different underlying etiologies. CVID has been associated with a quantitative B cell defect, however, little is known about the quality of B cells present. Here, we studied the naïve and antigen selected B-cell receptor (BCR) repertoire in 33 CVID patients using next generation sequencing, to investigate B cells quality. Analysis for each individual patient revealed whether they have a defect in immune repertoire formation [V(D)J recombination] or specification (somatic hypermutation, subclass distribution, or selection). The naïve BCR repertoire was normal in most of the patients, although alterations in repertoire diversity and the junctions were found in a limited number of patients indicating possible defects in early B-cell development or V(D)J recombination in these patients. In contrast, major differences were found in the antigen selected BCR repertoire. Here, most patients (15/17) showed a reduced frequency of somatic hypermutation (SHM), changes in subclass distribution and/or minor alterations in antigen selection. Together these data show that in our CVID cohort only a small number of patients have a defect in formation of the naïve BCR repertoire, whereas the clear majority of patients have disturbances in their antigen selected repertoire, suggesting a defect in repertoire specification in the germinal centers of these patients. This highlights that CVID patients not only have a quantitative B cell defect, but that also the quality of, especially post germinal center B cells, is impaired.
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Affiliation(s)
| | - Hanna IJspeert
- Department of Immunology, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | | | - Virgil A S H Dalm
- Department of Immunology, Erasmus MC University Medical Center, Rotterdam, Netherlands.,Division of Clinical Immunology, Department of Internal Medicine, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - P Martin van Hagen
- Department of Immunology, Erasmus MC University Medical Center, Rotterdam, Netherlands.,Division of Clinical Immunology, Department of Internal Medicine, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - David van Zessen
- Clinical Bioinformatics Unit, Department of Pathology, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Andrew P Stubbs
- Clinical Bioinformatics Unit, Department of Pathology, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Smita Y Patel
- Nuffield Department of Clinical Medicine and Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Mirjam van der Burg
- Department of Immunology, Erasmus MC University Medical Center, Rotterdam, Netherlands
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21
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Schramm CA, Douek DC. Beyond Hot Spots: Biases in Antibody Somatic Hypermutation and Implications for Vaccine Design. Front Immunol 2018; 9:1876. [PMID: 30154794 PMCID: PMC6102386 DOI: 10.3389/fimmu.2018.01876] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 07/30/2018] [Indexed: 11/15/2022] Open
Abstract
The evolution of antibodies in an individual during an immune response by somatic hypermutation (SHM) is essential for the ability of the immune system to recognize and remove the diverse spectrum of antigens that may be encountered. These mutations are not produced at random; nucleotide motifs that result in increased or decreased rates of mutation were first reported in 1992. Newer models that estimate the propensity for mutation for every possible 5- or 7-nucleotide motif have emphasized the complexity of SHM targeting and suggested possible new hot spot motifs. Even with these fine-grained approaches, however, non-local context matters, and the mutations observed at a specific nucleotide motif varies between species and even by locus, gene segment, and position along the gene segment within a single species. An alternative method has been provided to further abstract away the molecular mechanisms underpinning SHM, prompted by evidence that certain stereotypical amino acid substitutions are favored at each position of a particular V gene. These "substitution profiles," whether obtained from a single B cell lineage or an entire repertoire, offer a simplified approach to predict which substitutions will be well-tolerated and which will be disfavored, without the need to consider path-dependent effects from neighboring positions. However, this comes at the cost of merging the effects of two distinct biological processes, the generation of mutations, and the selection acting on those mutations. Since selection is contingent on the particular antigens an individual has been exposed to, this suggests that SHM may have evolved to prefer mutations that are most likely to be useful against pathogens that have co-evolved with us. Alternatively, the ability to select favorable mutations may be strongly limited by the biases of SHM targeting. In either scenario, the sequence space explored by SHM is significantly limited and this consequently has profound implications for the rational design of vaccine strategies.
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Affiliation(s)
- Chaim A. Schramm
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, United States
| | - Daniel C. Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, United States
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22
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SAMHD1 enhances immunoglobulin hypermutation by promoting transversion mutation. Proc Natl Acad Sci U S A 2018; 115:4921-4926. [PMID: 29669924 DOI: 10.1073/pnas.1719771115] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Activation-induced deaminase (AID) initiates hypermutation of Ig genes in activated B cells by converting C:G into U:G base pairs. G1-phase variants of uracil base excision repair (BER) and mismatch repair (MMR) then deploy translesion polymerases including REV1 and Pol η, which exacerbates mutation. dNTP paucity may contribute to hypermutation, because dNTP levels are reduced in G1 phase to inhibit viral replication. To derestrict G1-phase dNTP supply, we CRISPR-inactivated SAMHD1 (which degrades dNTPs) in germinal center B cells. Samhd1 inactivation increased B cell virus susceptibility, increased transition mutations at C:G base pairs, and substantially decreased transversion mutations at A:T and C:G base pairs in both strands. We conclude that SAMHD1's restriction of dNTP supply enhances AID's mutagenicity and that the evolution of Ig hypermutation included the repurposing of antiviral mechanisms based on dNTP starvation.
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23
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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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24
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Steele EJ. Reverse Transcriptase Mechanism of Somatic Hypermutation: 60 Years of Clonal Selection Theory. Front Immunol 2017; 8:1611. [PMID: 29218047 PMCID: PMC5704389 DOI: 10.3389/fimmu.2017.01611] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 11/07/2017] [Indexed: 01/24/2023] Open
Abstract
The evidence for the reverse transcriptase mechanism of somatic hypermutation is substantial and multifactorial. In this 60th anniversary year of the publication of Sir MacFarlane Burnet's Clonal Selection Theory, the evidence is briefly reviewed and updated.
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Affiliation(s)
- Edward J. Steele
- CYO’Connor ERADE Village Foundation Inc., Piara Waters, WA, Australia
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25
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Abstract
Bloom's syndrome (BS) is an autosomal recessive disease, caused by mutations in the BLM gene. This gene codes for BLM protein, which is a helicase involved in DNA repair. DNA repair is especially important for the development and maturation of the T and B cells. Since BLM is involved in DNA repair, we aimed to study if BLM deficiency affects T and B cell development and especially somatic hypermutation (SHM) and class switch recombination (CSR) processes. Clinical data of six BS patients was collected, and immunoglobulin serum levels were measured at different time points. In addition, we performed immune phenotyping of the B and T cells and analyzed the SHM and CSR in detail by analyzing IGHA and IGHG transcripts using next-generation sequencing. The serum immunoglobulin levels were relatively low, and patients had an increased number of infections. The absolute number of T, B, and NK cells were low but still in the normal range. Remarkably, all BS patients studied had a high percentage (20-80%) of CD4+ and CD8+ effector memory T cells. The process of SHM seems normal; however, the Ig subclass distribution was not normal, since the BS patients had more IGHG1 and IGHG3 transcripts. In conclusion, BS patients have low number of lymphocytes, but the immunodeficiency seems relatively mild since they have no severe or opportunistic infections. Most changes in the B cell development were seen in the CSR process; however, further studies are necessary to elucidate the exact role of BLM in CSR.
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26
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Thientosapol ES, Sharbeen G, Lau KKE, Bosnjak D, Durack T, Stevanovski I, Weninger W, Jolly CJ. Proximity to AGCT sequences dictates MMR-independent versus MMR-dependent mechanisms for AID-induced mutation via UNG2. Nucleic Acids Res 2017; 45:3146-3157. [PMID: 28039326 PMCID: PMC5389528 DOI: 10.1093/nar/gkw1300] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 12/16/2016] [Indexed: 11/30/2022] Open
Abstract
AID deaminates C to U in either strand of Ig genes, exclusively producing C:G/G:C to T:A/A:T transition mutations if U is left unrepaired. Error-prone processing by UNG2 or mismatch repair diversifies mutation, predominantly at C:G or A:T base pairs, respectively. Here, we show that transversions at C:G base pairs occur by two distinct processing pathways that are dictated by sequence context. Within and near AGCT mutation hotspots, transversion mutation at C:G was driven by UNG2 without requirement for mismatch repair. Deaminations in AGCT were refractive both to processing by UNG2 and to high-fidelity base excision repair (BER) downstream of UNG2, regardless of mismatch repair activity. We propose that AGCT sequences resist faithful BER because they bind BER-inhibitory protein(s) and/or because hemi-deaminated AGCT motifs innately form a BER-resistant DNA structure. Distal to AGCT sequences, transversions at G were largely co-dependent on UNG2 and mismatch repair. We propose that AGCT-distal transversions are produced when apyrimidinic sites are exposed in mismatch excision patches, because completion of mismatch repair would require bypass of these sites.
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Affiliation(s)
- Eddy Sanchai Thientosapol
- Centenary Institute, Royal Prince Alfred Hospital, Camperdown NSW 2050, and Sydney Medical School, The University of Sydney, Sydney NSW 2006, Australia
| | - George Sharbeen
- Centenary Institute, Royal Prince Alfred Hospital, Camperdown NSW 2050, and Sydney Medical School, The University of Sydney, Sydney NSW 2006, Australia
| | - K K Edwin Lau
- Centenary Institute, Royal Prince Alfred Hospital, Camperdown NSW 2050, and Sydney Medical School, The University of Sydney, Sydney NSW 2006, Australia
| | - Daniel Bosnjak
- Centenary Institute, Royal Prince Alfred Hospital, Camperdown NSW 2050, and Sydney Medical School, The University of Sydney, Sydney NSW 2006, Australia
| | - Timothy Durack
- Centenary Institute, Royal Prince Alfred Hospital, Camperdown NSW 2050, and Sydney Medical School, The University of Sydney, Sydney NSW 2006, Australia
| | - Igor Stevanovski
- Centenary Institute, Royal Prince Alfred Hospital, Camperdown NSW 2050, and Sydney Medical School, The University of Sydney, Sydney NSW 2006, Australia
| | - Wolfgang Weninger
- Centenary Institute, Royal Prince Alfred Hospital, Camperdown NSW 2050, and Sydney Medical School, The University of Sydney, Sydney NSW 2006, Australia
| | - Christopher J Jolly
- Centenary Institute, Royal Prince Alfred Hospital, Camperdown NSW 2050, and Sydney Medical School, The University of Sydney, Sydney NSW 2006, Australia
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27
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Girelli Zubani G, Zivojnovic M, De Smet A, Albagli-Curiel O, Huetz F, Weill JC, Reynaud CA, Storck S. Pms2 and uracil-DNA glycosylases act jointly in the mismatch repair pathway to generate Ig gene mutations at A-T base pairs. J Exp Med 2017; 214:1169-1180. [PMID: 28283534 PMCID: PMC5379981 DOI: 10.1084/jem.20161576] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 12/19/2016] [Accepted: 01/26/2017] [Indexed: 11/06/2022] Open
Abstract
Girelli Zubani et al. show that the Pms2 component of the mismatch repair complex and multiple uracil glycosylases contribute, each with a distinct strand bias, to enlarge the Ig gene mutation spectrum from G-C to A-T bases. During somatic hypermutation (SHM) of immunoglobulin genes, uracils introduced by activation-induced cytidine deaminase are processed by uracil-DNA glycosylase (UNG) and mismatch repair (MMR) pathways to generate mutations at G-C and A-T base pairs, respectively. Paradoxically, the MMR-nicking complex Pms2/Mlh1 is apparently dispensable for A-T mutagenesis. Thus, how detection of U:G mismatches is translated into the single-strand nick required for error-prone synthesis is an open question. One model proposed that UNG could cooperate with MMR by excising a second uracil in the vicinity of the U:G mismatch, but it failed to explain the low impact of UNG inactivation on A-T mutagenesis. In this study, we show that uracils generated in the G1 phase in B cells can generate equal proportions of A-T and G-C mutations, which suggests that UNG and MMR can operate within the same time frame during SHM. Furthermore, we show that Ung−/−Pms2−/− mice display a 50% reduction in mutations at A-T base pairs and that most remaining mutations at A-T bases depend on two additional uracil glycosylases, thymine-DNA glycosylase and SMUG1. These results demonstrate that Pms2/Mlh1 and multiple uracil glycosylases act jointly, each one with a distinct strand bias, to enlarge the immunoglobulin gene mutation spectrum from G-C to A-T bases.
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Affiliation(s)
- Giulia Girelli Zubani
- Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151, Centre National de la Recherche Scientifique UMR 8253, Faculté de Médecine-Site Broussais, Université Paris Descartes, Sorbonne Paris Cité, 75014 Paris, France
| | - Marija Zivojnovic
- Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151, Centre National de la Recherche Scientifique UMR 8253, Faculté de Médecine-Site Broussais, Université Paris Descartes, Sorbonne Paris Cité, 75014 Paris, France
| | - Annie De Smet
- Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151, Centre National de la Recherche Scientifique UMR 8253, Faculté de Médecine-Site Broussais, Université Paris Descartes, Sorbonne Paris Cité, 75014 Paris, France
| | - Olivier Albagli-Curiel
- Institut Cochin, Institut National de la Santé et de la Recherche Médicale U1016, Centre National de la Recherche Scientifique UMR8104, Faculté de Médecine-Site Cochin, Université Paris Descartes, Sorbonne Paris Cité, 75006 Paris, France
| | - François Huetz
- Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151, Centre National de la Recherche Scientifique UMR 8253, Faculté de Médecine-Site Broussais, Université Paris Descartes, Sorbonne Paris Cité, 75014 Paris, France.,Département d'Immunologie, Institut Pasteur, 75015 Paris, France
| | - Jean-Claude Weill
- Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151, Centre National de la Recherche Scientifique UMR 8253, Faculté de Médecine-Site Broussais, Université Paris Descartes, Sorbonne Paris Cité, 75014 Paris, France
| | - Claude-Agnès Reynaud
- Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151, Centre National de la Recherche Scientifique UMR 8253, Faculté de Médecine-Site Broussais, Université Paris Descartes, Sorbonne Paris Cité, 75014 Paris, France
| | - Sébastien Storck
- Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale U1151, Centre National de la Recherche Scientifique UMR 8253, Faculté de Médecine-Site Broussais, Université Paris Descartes, Sorbonne Paris Cité, 75014 Paris, France
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28
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Lee DW, Khavrutskii IV, Wallqvist A, Bavari S, Cooper CL, Chaudhury S. BRILIA: Integrated Tool for High-Throughput Annotation and Lineage Tree Assembly of B-Cell Repertoires. Front Immunol 2017; 7:681. [PMID: 28144239 PMCID: PMC5239784 DOI: 10.3389/fimmu.2016.00681] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 12/21/2016] [Indexed: 11/13/2022] Open
Abstract
The somatic diversity of antigen-recognizing B-cell receptors (BCRs) arises from Variable (V), Diversity (D), and Joining (J) (VDJ) recombination and somatic hypermutation (SHM) during B-cell development and affinity maturation. The VDJ junction of the BCR heavy chain forms the highly variable complementarity determining region 3 (CDR3), which plays a critical role in antigen specificity and binding affinity. Tracking the selection and mutation of the CDR3 can be useful in characterizing humoral responses to infection and vaccination. Although tens to hundreds of thousands of unique BCR genes within an expressed B-cell repertoire can now be resolved with high-throughput sequencing, tracking SHMs is still challenging because existing annotation methods are often limited by poor annotation coverage, inconsistent SHM identification across the VDJ junction, or lack of B-cell lineage data. Here, we present B-cell repertoire inductive lineage and immunosequence annotator (BRILIA), an algorithm that leverages repertoire-wide sequencing data to globally improve the VDJ annotation coverage, lineage tree assembly, and SHM identification. On benchmark tests against simulated human and mouse BCR repertoires, BRILIA correctly annotated germline and clonally expanded sequences with 94 and 70% accuracy, respectively, and it has a 90% SHM-positive prediction rate in the CDR3 of heavily mutated sequences; these are substantial improvements over existing methods. We used BRILIA to process BCR sequences obtained from splenic germinal center B cells extracted from C57BL/6 mice. BRILIA returned robust B-cell lineage trees and yielded SHM patterns that are consistent across the VDJ junction and agree with known biological mechanisms of SHM. By contrast, existing BCR annotation tools, which do not account for repertoire-wide clonal relationships, systematically underestimated both the size of clonally related B-cell clusters and yielded inconsistent SHM frequencies. We demonstrate BRILIA’s utility in B-cell repertoire studies related to VDJ gene usage, mechanisms for adenosine mutations, and SHM hot spot motifs. Furthermore, we show that the complete gene usage annotation and SHM identification across the entire CDR3 are essential for studying the B-cell affinity maturation process through immunosequencing methods.
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Affiliation(s)
- Donald W Lee
- Biotechnology HPC Software Applications Institute (BHSAI), Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command , Fort Detrick, MD , USA
| | - Ilja V Khavrutskii
- Biotechnology HPC Software Applications Institute (BHSAI), Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command , Fort Detrick, MD , USA
| | - Anders Wallqvist
- Biotechnology HPC Software Applications Institute (BHSAI), Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command , Fort Detrick, MD , USA
| | - Sina Bavari
- Molecular and Translational Sciences, U.S. Army Medical Research Institute of Infectious Diseases , Frederick, MD , USA
| | - Christopher L Cooper
- Molecular and Translational Sciences, U.S. Army Medical Research Institute of Infectious Diseases , Frederick, MD , USA
| | - Sidhartha Chaudhury
- Biotechnology HPC Software Applications Institute (BHSAI), Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command , Fort Detrick, MD , USA
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29
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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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30
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IJspeert H, van Schouwenburg PA, van Zessen D, Pico-Knijnenburg I, Driessen GJ, Stubbs AP, van der Burg M. Evaluation of the Antigen-Experienced B-Cell Receptor Repertoire in Healthy Children and Adults. Front Immunol 2016; 7:410. [PMID: 27799928 PMCID: PMC5066086 DOI: 10.3389/fimmu.2016.00410] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 09/22/2016] [Indexed: 12/03/2022] Open
Abstract
Upon antigen recognition via their B cell receptor (BR), B cells migrate to the germinal center where they undergo somatic hypermutation (SHM) to increase their affinity for the antigen, and class switch recombination (CSR) to change the effector function of the secreted antibodies. These steps are essential to create an antigen-experienced BR repertoire that efficiently protects the body against pathogens. At the same time, the BR repertoire should be selected to protect against responses to self-antigen or harmless antigens. Insights into the processes of SHM, selection, and CSR can be obtained by studying the antigen-experienced BR repertoire. Currently, a large reference data set of healthy children and adults, which ranges from neonates to the elderly, is not available. In this study, we analyzed the antigen-experienced repertoire of 38 healthy donors (HD), ranging from cord blood to 74 years old, by sequencing IGA and IGG transcripts using next generation sequencing. This resulted in a large, freely available reference data set containing 412,890 IGA and IGG transcripts. We used this data set to study mutation levels, SHM patterns, antigenic selection, and CSR from birth to elderly HD. Only small differences were observed in SHM patterns, while the mutation levels increase in early childhood and stabilize at 6 years of age at around 7%. Furthermore, comparison of the antigen-experienced repertoire with sequences from the naive immune repertoire showed that features associated with autoimmunity such as long CDR3 length and IGHV4-34 usage are reduced in the antigen-experienced repertoire. Moreover, IGA2 and IGG2 usage was increased in HD in higher age categories, while IGG1 usage was decreased. In addition, we studied clonal relationship in the different samples. Clonally related sequences were found with different subclasses. Interestingly, we found transcripts with the same CDR1–CDR3 sequence, but different subclasses. Together, these data suggest that a single antigen can provoke a B-cell response with BR of different subclasses and that, during the course of an immune response, some B cells change their isotype without acquiring additional SHM or can directly switch to different isotypes.
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Affiliation(s)
- Hanna IJspeert
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam , Rotterdam , Netherlands
| | | | - David van Zessen
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands; Department of Bioinformatics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Ingrid Pico-Knijnenburg
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam , Rotterdam , Netherlands
| | - Gertjan J Driessen
- Department of Pediatrics, Erasmus MC-Sophia Children's Hospital, University Medical Center Rotterdam , Rotterdam , Netherlands
| | - Andrew P Stubbs
- Department of Bioinformatics, Erasmus MC, University Medical Center Rotterdam , Rotterdam , Netherlands
| | - Mirjam van der Burg
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam , Rotterdam , Netherlands
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31
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Prasad R, Poltoratsky V, Hou EW, Wilson SH. Rev1 is a base excision repair enzyme with 5'-deoxyribose phosphate lyase activity. Nucleic Acids Res 2016; 44:10824-10833. [PMID: 27683219 PMCID: PMC5159550 DOI: 10.1093/nar/gkw869] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 09/16/2016] [Accepted: 09/21/2016] [Indexed: 12/28/2022] Open
Abstract
Rev1 is a member of the Y-family of DNA polymerases and is known for its deoxycytidyl transferase activity that incorporates dCMP into DNA and its ability to function as a scaffold factor for other Y-family polymerases in translesion bypass events. Rev1 also is involved in mutagenic processes during somatic hypermutation of immunoglobulin genes. In light of the mutation pattern consistent with dCMP insertion observed earlier in mouse fibroblast cells treated with a base excision repair-inducing agent, we questioned whether Rev1 could also be involved in base excision repair (BER). Here, we uncovered a weak 5′-deoxyribose phosphate (5′-dRP) lyase activity in mouse Rev1 and demonstrated the enzyme can mediate BER in vitro. The full-length Rev1 protein and its catalytic core domain are similar in their ability to support BER in vitro. The dRP lyase activity in both of these proteins was confirmed by NaBH4 reduction of the Schiff base intermediate and kinetics studies. Limited proteolysis, mass spectrometry and deletion analysis localized the dRP lyase active site to the C-terminal segment of Rev1's catalytic core domain. These results suggest that Rev1 could serve as a backup polymerase in BER and could potentially contribute to AID-initiated antibody diversification through this activity.
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Affiliation(s)
- Rajendra Prasad
- Genome Integrity and Structural Biology Laboratory, National Institutes of Health, NIEHS, 111 T.W. Alexander Drive, PO Box 12233, MD F3-01, Research Triangle Park, NC 27709, USA
| | - Vladimir Poltoratsky
- Genome Integrity and Structural Biology Laboratory, National Institutes of Health, NIEHS, 111 T.W. Alexander Drive, PO Box 12233, MD F3-01, Research Triangle Park, NC 27709, USA
| | - Esther W Hou
- Genome Integrity and Structural Biology Laboratory, National Institutes of Health, NIEHS, 111 T.W. Alexander Drive, PO Box 12233, MD F3-01, Research Triangle Park, NC 27709, USA
| | - Samuel H Wilson
- Genome Integrity and Structural Biology Laboratory, National Institutes of Health, NIEHS, 111 T.W. Alexander Drive, PO Box 12233, MD F3-01, Research Triangle Park, NC 27709, USA
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32
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Somatic hypermutation in immunity and cancer: Critical analysis of strand-biased and codon-context mutation signatures. DNA Repair (Amst) 2016; 45:1-24. [DOI: 10.1016/j.dnarep.2016.07.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 07/01/2016] [Indexed: 01/01/2023]
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33
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Yamamoto N, Kerfoot SM, Hutchinson AT, Dela Cruz CS, Nakazawa N, Szczepanik M, Majewska-Szczepanik M, Nazimek K, Ohana N, Bryniarski K, Mori T, Muramatsu M, Kanemitsu K, Askenase PW. Expression of activation-induced cytidine deaminase enhances the clearance of pneumococcal pneumonia: evidence of a subpopulation of protective anti-pneumococcal B1a cells. Immunology 2016; 147:97-113. [PMID: 26456931 DOI: 10.1111/imm.12544] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 09/28/2015] [Accepted: 10/05/2015] [Indexed: 12/28/2022] Open
Abstract
We describe a protective early acquired immune response to pneumococcal pneumonia that is mediated by a subset of B1a cells. Mice deficient in B1 cells (xid), or activation-induced cytidine deaminase (AID(-/-) ), or invariant natural killer T (iNKT) cells (Jα18(-/-) ), or interleukin-13 (IL-13(-/-) ) had impaired early clearance of pneumococci in the lung, compared with wild-type mice. In contrast, AID(-/-) mice adoptively transferred with AID(+/+) B1a cells, significantly cleared bacteria from the lungs as early as 3 days post infection. We show that this early bacterial clearance corresponds to an allergic contact sensitivity-like cutaneous response, probably due to a subpopulation of initiating B1a cells. In the pneumonia model, these B1a cells were found to secrete higher affinity antigen-specific IgM. In addition, as in contact sensitivity, iNKT cells were required for the anti-pneumococcal B1a cell initiating response, probably through early production of IL-13, given that IL-13(-/-) mice also failed to clear infection. Our study is the first to demonstrate the importance of AID in generating an appropriate B1a cell response to pathogenic bacteria. Given the antibody affinity and pneumonia resistance data, natural IgM produced by conventional B1a cells are not responsible for pneumonia clearance compared with the AID-dependent subset.
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Affiliation(s)
- Natsuo Yamamoto
- Section of Allergy and Clinical Immunology, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA.,Department of Infection Control, Fukushima Medical University, Hikarigaoka, Japan
| | - Steven M Kerfoot
- Section of Allergy and Clinical Immunology, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Andrew T Hutchinson
- Section of Allergy and Clinical Immunology, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Charles S Dela Cruz
- Section of Allergy and Clinical Immunology, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Naomi Nakazawa
- Department of Infection Control, Fukushima Medical University, Hikarigaoka, Japan
| | - Marian Szczepanik
- Section of Allergy and Clinical Immunology, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA.,Department of Medical Biology, Jagiellonian University Medical College, Krakow, Poland
| | - Monika Majewska-Szczepanik
- Section of Allergy and Clinical Immunology, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA.,Department of Medical Biology, Jagiellonian University Medical College, Krakow, Poland
| | - Katarzyna Nazimek
- Section of Allergy and Clinical Immunology, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA.,Department of Immunology, Jagiellonian University Medical College, Krakow, Poland
| | - Noboru Ohana
- Department of Infection Control, Fukushima Medical University, Hikarigaoka, Japan
| | - Krzysztof Bryniarski
- Section of Allergy and Clinical Immunology, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA.,Department of Immunology, Jagiellonian University Medical College, Krakow, Poland
| | - Tsutomu Mori
- Department of Infection Control, Fukushima Medical University, Hikarigaoka, Japan
| | - Masamichi Muramatsu
- Department of Molecular Genetics, Graduate School of Medical Science, Kanazawa University, Kanazawa, Japan
| | - Keiji Kanemitsu
- Department of Infection Control, Fukushima Medical University, Hikarigaoka, Japan
| | - Philip W Askenase
- Section of Allergy and Clinical Immunology, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
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34
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Chen Z, Eder MD, Elos MT, Viboolsittiseri SS, Chen X, Wang JH. Interplay between Target Sequences and Repair Pathways Determines Distinct Outcomes of AID-Initiated Lesions. THE JOURNAL OF IMMUNOLOGY 2016; 196:2335-47. [PMID: 26810227 DOI: 10.4049/jimmunol.1502184] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 12/22/2015] [Indexed: 11/19/2022]
Abstract
Activation-induced deaminase (AID) functions by deaminating cytosines and causing U:G mismatches, a rate-limiting step of Ab gene diversification. However, precise mechanisms regulating AID deamination frequency remain incompletely understood. Moreover, it is not known whether different sequence contexts influence the preferential access of mismatch repair or uracil glycosylase (UNG) to AID-initiated U:G mismatches. In this study, we employed two knock-in models to directly compare the mutability of core Sμ and VDJ exon sequences and their ability to regulate AID deamination and subsequent repair process. We find that the switch (S) region is a much more efficient AID deamination target than the V region. Igh locus AID-initiated lesions are processed by error-free and error-prone repair. S region U:G mismatches are preferentially accessed by UNG, leading to more UNG-dependent deletions, enhanced by mismatch repair deficiency. V region mutation hotspots are largely determined by AID deamination. Recurrent and conserved S region motifs potentially function as spacers between AID deamination hotspots. We conclude that the pattern of mutation hotspots and DNA break generation is influenced by sequence-intrinsic properties, which regulate AID deamination and affect the preferential access of downstream repair. Our studies reveal an evolutionarily conserved role for substrate sequences in regulating Ab gene diversity and AID targeting specificity.
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Affiliation(s)
- Zhangguo Chen
- Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045; and Department of Biomedical Research, National Jewish Health, Denver, CO 80206
| | - Maxwell D Eder
- Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045; and
| | - Mihret T Elos
- Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045; and
| | - Sawanee S Viboolsittiseri
- Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045; and
| | - Xiaomi Chen
- Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045; and
| | - Jing H Wang
- Department of Immunology and Microbiology, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045; and Department of Biomedical Research, National Jewish Health, Denver, CO 80206
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35
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Crouse GF. Non-canonical actions of mismatch repair. DNA Repair (Amst) 2016; 38:102-109. [PMID: 26698648 PMCID: PMC4740236 DOI: 10.1016/j.dnarep.2015.11.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Revised: 09/06/2015] [Accepted: 11/30/2015] [Indexed: 12/13/2022]
Abstract
At the heart of the mismatch repair (MMR) system are proteins that recognize mismatches in DNA. Such mismatches can be mispairs involving normal or damaged bases or insertion/deletion loops due to strand misalignment. When such mispairs are generated during replication or recombination, MMR will direct removal of an incorrectly paired base or block recombination between nonidentical sequences. However, when mispairs are recognized outside the context of replication, proper strand discrimination between old and new DNA is lost, and MMR can act randomly and mutagenically on mispaired DNA. Such non-canonical actions of MMR are important in somatic hypermutation and class switch recombination, expansion of triplet repeats, and potentially in mutations arising in nondividing cells. MMR involvement in damage recognition and signaling is complex, with the end result likely dependent on the amount of DNA damage in a cell.
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Affiliation(s)
- Gray F Crouse
- Department of Biology, Emory University, Atlanta, GA 30322, USA.
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36
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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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37
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Bregenhorn S, Kallenberger L, Artola-Borán M, Peña-Diaz J, Jiricny J. Non-canonical uracil processing in DNA gives rise to double-strand breaks and deletions: relevance to class switch recombination. Nucleic Acids Res 2016; 44:2691-705. [PMID: 26743004 PMCID: PMC4824095 DOI: 10.1093/nar/gkv1535] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 12/23/2015] [Indexed: 12/24/2022] Open
Abstract
During class switch recombination (CSR), antigen-stimulated B-cells rearrange their immunoglobulin constant heavy chain (CH) loci to generate antibodies with different effector functions. CSR is initiated by activation-induced deaminase (AID), which converts cytosines in switch (S) regions, repetitive sequences flanking the CH loci, to uracils. Although U/G mispairs arising in this way are generally efficiently repaired to C/Gs by uracil DNA glycosylase (UNG)-initiated base excision repair (BER), uracil processing in S-regions of activated B-cells occasionally gives rise to double strand breaks (DSBs), which trigger CSR. Surprisingly, genetic experiments revealed that CSR is dependent not only on AID and UNG, but also on mismatch repair (MMR). To elucidate the role of MMR in CSR, we studied the processing of uracil-containing DNA substrates in extracts of MMR-proficient and –deficient human cells, as well as in a system reconstituted from recombinant BER and MMR proteins. Here, we show that the interplay of these repair systems gives rise to DSBs in vitro and to genomic deletions and mutations in vivo, particularly in an S-region sequence. Our findings further suggest that MMR affects pathway choice in DSB repair. Given its amenability to manipulation, our system represents a powerful tool for the molecular dissection of CSR.
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Affiliation(s)
- Stephanie Bregenhorn
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland Department of Biology, Swiss Federal Institute of Technology (ETH) Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Lia Kallenberger
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Mariela Artola-Borán
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Javier Peña-Diaz
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland University of Copenhagen, Faculty of Health Sciences Center for Healthy Aging, Department of Neuroscience and Pharmacology, Blegdamsvej 3b, DK-2200 Copenhagen N, Denmark
| | - Josef Jiricny
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland Department of Biology, Swiss Federal Institute of Technology (ETH) Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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38
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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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39
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Rajewsky K. The DNA deamination model of somatic antibody diversification. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2015; 194:2041-2042. [PMID: 25710956 DOI: 10.4049/jimmunol.1403252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Affiliation(s)
- Klaus Rajewsky
- Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
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40
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Chen Z, Ranganath S, Viboolsittiseri SS, Eder MD, Chen X, Elos MT, Yuan S, Yuan S, Hansen E, Wang JH. AID-initiated DNA lesions are differentially processed in distinct B cell populations. THE JOURNAL OF IMMUNOLOGY 2014; 193:5545-56. [PMID: 25339658 DOI: 10.4049/jimmunol.1401549] [Citation(s) in RCA: 13] [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) initiates U:G mismatches, causing point mutations or DNA double-stranded breaks at Ig loci. How AID-initiated lesions are prevented from inducing genome-wide damage remains elusive. A differential DNA repair mechanism might protect certain non-Ig loci such as c-myc from AID attack. However, determinants regulating such protective mechanisms are largely unknown. To test whether target DNA sequences modulate protective mechanisms via altering the processing manner of AID-initiated lesions, we established a knock-in model by inserting an Sγ2b region, a bona fide AID target, into the first intron of c-myc. Unexpectedly, we found that the inserted S region did not mutate or enhance c-myc genomic instability, due to error-free repair of AID-initiated lesions, in Ag-stimulated germinal center B cells. In contrast, in vitro cytokine-activated B cells display a much higher level of c-myc genomic instability in an AID- and S region-dependent manner. Furthermore, we observe a comparable frequency of AID deamination events between the c-myc intronic sequence and inserted S region in different B cell populations, demonstrating a similar frequency of AID targeting. Thus, our study reveals a clear difference between germinal center and cytokine-activated B cells in their ability to develop genomic instability, attributable to a differential processing of AID-initiated lesions in distinct B cell populations. We propose that locus-specific regulatory mechanisms (e.g., transcription) appear to not only override the effects of S region sequence on AID targeting frequency but also influence the repair manner of AID-initiated lesions.
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Affiliation(s)
- Zhangguo Chen
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045; Department of Biomedical Research, National Jewish Health, Denver, CO 80206; and
| | - Sheila Ranganath
- Boston Children's Hospital, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115
| | - Sawanee S Viboolsittiseri
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045
| | - Maxwell D Eder
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045
| | - Xiaomi Chen
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045; Department of Biomedical Research, National Jewish Health, Denver, CO 80206; and
| | - Mihret T Elos
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045
| | - Shunzong Yuan
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045
| | | | - Erica Hansen
- Boston Children's Hospital, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115
| | - Jing H Wang
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045; Department of Biomedical Research, National Jewish Health, Denver, CO 80206; and
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41
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Franchini DM, Petersen-Mahrt SK. AID and APOBEC deaminases: balancing DNA damage in epigenetics and immunity. Epigenomics 2014; 6:427-43. [DOI: 10.2217/epi.14.35] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
DNA mutations and genomic recombinations are the origin of oncogenesis, yet parts of developmental programs as well as immunity are intimately linked to, or even depend on, such DNA damages. Therefore, the balance between deleterious DNA damages and organismal survival utilizing DNA editing (modification and repair) is in continuous flux. The cytosine deaminases AID/APOBEC are a DNA editing family and actively participate in various biological processes. In conjunction with altered DNA repair, the mutagenic potential of the family allows for APOBEC3 proteins to restrict viral infection and transposons propagation, while AID can induce somatic hypermutation and class switch recombination in antibody genes. On the other hand, the synergy between effective DNA repair and the nonmutagenic potential of the DNA deaminases can induce local DNA demethylation to support epigenetic cellular identity. Here, we review the current state of knowledge on the mechanisms of action of the AID/APOBEC family in immunity and epigenetics.
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Affiliation(s)
- Don-Marc Franchini
- DNA Editing in Immunity and Epigenetics, IFOM-Fondazione Instituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139 Milano, Italy
| | - Svend K Petersen-Mahrt
- DNA Editing in Immunity and Epigenetics, IFOM-Fondazione Instituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139 Milano, Italy
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42
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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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43
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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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44
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Dingler FA, Kemmerich K, Neuberger MS, Rada C. Uracil excision by endogenous SMUG1 glycosylase promotes efficient Ig class switching and impacts on A:T substitutions during somatic mutation. Eur J Immunol 2014; 44:1925-35. [PMID: 24771041 PMCID: PMC4158878 DOI: 10.1002/eji.201444482] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 03/06/2014] [Accepted: 04/15/2014] [Indexed: 12/23/2022]
Abstract
Excision of uracil introduced into the immunoglobulin loci by AID is central to antibody diversification. While predominantly carried out by the UNG uracil‐DNA glycosylase as reflected by deficiency in immunoglobulin class switching in Ung−/− mice, the deficiency is incomplete, as evidenced by the emergence of switched IgG in the serum of Ung−/− mice. Lack of switching in mice deficient in both UNG and MSH2 suggested that mismatch repair initiated a backup pathway. We now show that most of the residual class switching in Ung−/− mice depends upon the endogenous SMUG1 uracil‐DNA glycosylase, with in vitro switching to IgG1 as well as serum IgG3, IgG2b, and IgA greatly diminished in Ung−/−Smug1−/− mice, and that Smug1 partially compensates for Ung deficiency over time. Nonetheless, using a highly MSH2‐dependent mechanism, Ung−/−Smug1−/− mice can still produce detectable levels of switched isotypes, especially IgG1. While not affecting the pattern of base substitutions, SMUG1 deficiency in an Ung−/− background further reduces somatic hypermutation at A:T base pairs. Our data reveal an essential requirement for uracil excision in class switching and in facilitating noncanonical mismatch repair for the A:T phase of hypermutation presumably by creating nicks near the U:G lesion recognized by MSH2.
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45
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Differential regulation of S-region hypermutation and class-switch recombination by noncanonical functions of uracil DNA glycosylase. Proc Natl Acad Sci U S A 2014; 111:E1016-24. [PMID: 24591630 DOI: 10.1073/pnas.1402391111] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Activation-induced cytidine deaminase (AID) is essential to class-switch recombination (CSR) and somatic hypermutation (SHM) in both V region SHM and S region SHM (s-SHM). Uracil DNA glycosylase (UNG), a member of the base excision repair (BER) complex, is required for CSR. Strikingly, however, UNG deficiency causes augmentation of SHM, suggesting involvement of distinct functions of UNG in SHM and CSR. Here, we show that noncanonical scaffold functions of UNG regulate s-SHM negatively and CSR positively. The s-SHM suppressive function of UNG is attributed to the recruitment of faithful BER components at the cleaved DNA locus, with competition against error-prone polymerases. By contrast, the CSR-promoting function of UNG enhances AID-dependent S-S synapse formation by recruiting p53-binding protein 1 and DNA-dependent protein kinase, catalytic subunit. Several loss-of-catalysis mutants of UNG discriminated CSR-promoting activity from s-SHM suppressive activity. Taken together, the noncanonical function of UNG regulates the steps after AID-induced DNA cleavage: error-prone repair suppression in s-SHM and end-joining promotion in CSR.
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46
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Franchini DM, Incorvaia E, Rangam G, Coker HA, Petersen-Mahrt SK. Simultaneous in vitro characterisation of DNA deaminase function and associated DNA repair pathways. PLoS One 2013; 8:e82097. [PMID: 24349193 PMCID: PMC3857227 DOI: 10.1371/journal.pone.0082097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 10/25/2013] [Indexed: 02/02/2023] Open
Abstract
During immunoglobulin (Ig) diversification, activation-induced deaminase (AID) initiates somatic hypermutation and class switch recombination by catalysing the conversion of cytosine to uracil. The synergy between AID and DNA repair pathways is fundamental for the introduction of mutations, however the molecular and biochemical mechanisms underlying this process are not fully elucidated. We describe a novel method to efficiently decipher the composition and activity of DNA repair pathways that are activated by AID-induced lesions. The in vitro resolution (IVR) assay combines AID based deamination and DNA repair activities from a cellular milieu in a single assay, thus avoiding synthetically created DNA-lesions or genetic-based readouts. Recombinant GAL4-AID fusion protein is targeted to a plasmid containing GAL4 binding sites, allowing for controlled cytosine deamination within a substrate plasmid. Subsequently, the Xenopus laevis egg extract provides a source of DNA repair proteins and functional repair pathways. Our results demonstrated that DNA repair pathways which are in vitro activated by AID-induced lesions are reminiscent of those found during AID-induced in vivo Ig diversification. The comparative ease of manipulation of this in vitro systems provides a new approach to dissect the complex DNA repair pathways acting on defined physiologically lesions, can be adapted to use with other DNA damaging proteins (e.g. APOBECs), and provide a means to develop and characterise pharmacological agents to inhibit these potentially oncogenic processes.
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Affiliation(s)
- Don-Marc Franchini
- DNA Editing in Immunity and Epigenetics, IFOM-Fondazione Instituto FIRC di Oncologia Molecolare, Milano, Italy
- DNA Editing Lab, Clare Hall Laboratories, London Research Institute, South Mimms, United Kingdom
| | - Elisabetta Incorvaia
- DNA Editing in Immunity and Epigenetics, IFOM-Fondazione Instituto FIRC di Oncologia Molecolare, Milano, Italy
| | - Gopinath Rangam
- DNA Editing in Immunity and Epigenetics, IFOM-Fondazione Instituto FIRC di Oncologia Molecolare, Milano, Italy
- DNA Editing Lab, Clare Hall Laboratories, London Research Institute, South Mimms, United Kingdom
| | - Heather A. Coker
- DNA Editing Lab, Clare Hall Laboratories, London Research Institute, South Mimms, United Kingdom
| | - Svend K. Petersen-Mahrt
- DNA Editing in Immunity and Epigenetics, IFOM-Fondazione Instituto FIRC di Oncologia Molecolare, Milano, Italy
- DNA Editing Lab, Clare Hall Laboratories, London Research Institute, South Mimms, United Kingdom
- * E-mail:
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47
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Winter G. Michael Neuberger (1953-2013). Eur J Immunol 2013. [DOI: 10.1002/eji.201370126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Krijger PHL, Tsaalbi-Shtylik A, Wit N, van den Berk PCM, de Wind N, Jacobs H. Rev1 is essential in generating G to C transversions downstream of the Ung2 pathway but not the Msh2+Ung2 hybrid pathway. Eur J Immunol 2013; 43:2765-70. [PMID: 23857323 DOI: 10.1002/eji.201243191] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Revised: 05/06/2013] [Accepted: 07/12/2013] [Indexed: 11/07/2022]
Abstract
Somatic hypermutation (SHM) and class switch recombination (CSR) of immunoglobulin (Ig) genes are initiated by the enzymatic deamination of cytosine (C) to uracil (U). Uracil-DNA-glycosylase (Ung2) converts uracils into apyrimidinic (AP) sites, which is essential for the generation of transversions (TVs) at G/C basepairs during SHM and for efficient DNA break formation during CSR. Besides Ung2, the mismatch repair protein Msh2 and the translesion synthesis (TLS) DNA polymerase (Pol) Rev1 are implicated in SHM and CSR. To further unravel the role of Rev1, we studied WT, Rev1-deficient, Msh2-deficient, and Rev1, Msh2 double-deficient B cells. Loss of Rev1 only slightly reduced CSR. During SHM G/C to C/G TVs are generated in both Ung2- and Ung+Msh2-dependent fashions. We found that Rev1 is essential for the Msh2-independent generation of these TVs downstream of Ung2-induced AP sites. In the Ung+Msh2 hybrid pathway, Rev1 is not essential and can be substituted by an alternative TLS Pol, especially when Rev1 is lacking.
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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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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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