1
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Lauring MC, Basu U. Somatic hypermutation mechanisms during lymphomagenesis and transformation. Curr Opin Genet Dev 2024; 85:102165. [PMID: 38428317 DOI: 10.1016/j.gde.2024.102165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 01/31/2024] [Accepted: 02/02/2024] [Indexed: 03/03/2024]
Abstract
B cells undergoing physiologically programmed or aberrant genomic alterations provide an opportune system to study the causes and consequences of genome mutagenesis. Activated B cells in germinal centers express activation-induced cytidine deaminase (AID) to accomplish physiological somatic hypermutation (SHM) of their antibody-encoding genes. In attempting to diversify their immunoglobulin (Ig) heavy- and light-chain genes, several B-cell clones successfully optimize their antigen-binding affinities. However, SHM can sometimes occur at non-Ig loci, causing genetic alternations that lay the foundation for lymphomagenesis, particularly diffuse large B-cell lymphoma. Thus, SHM acts as a double-edged sword, bestowing superb humoral immunity at the potential risk of initiating disease. We refer to off-target, non-Ig AID mutations - that are often but not always associated with disease - as aberrant SHM (aSHM). A key challenge in understanding SHM and aSHM is determining how AID targets and mutates specific DNA sequences in the Ig loci to generate antibody diversity and non-Ig genes to initiate lymphomagenesis. Herein, we discuss some current advances regarding the regulation of AID's DNA mutagenesis activity in B cells.
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Affiliation(s)
- Max C Lauring
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York 10032, USA.
| | - Uttiya Basu
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York 10032, USA.
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2
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Leeman-Neill RJ, Bhagat G, Basu U. AID in non-Hodgkin B-cell lymphomas: The consequences of on- and off-target activity. Adv Immunol 2024; 161:127-164. [PMID: 38763700 DOI: 10.1016/bs.ai.2024.03.005] [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] [Indexed: 05/21/2024]
Abstract
Activation induced cytidine deaminase (AID) is a key element of the adaptive immune system, required for immunoglobulin isotype switching and affinity maturation of B-cells as they undergo the germinal center (GC) reaction in peripheral lymphoid tissue. The inherent DNA damaging activity of this enzyme can also have off-target effects in B-cells, producing lymphomagenic chromosomal translocations that are characteristic features of various classes of non-Hodgkin B-cell lymphoma (B-NHL), and generating oncogenic mutations, so-called aberrant somatic hypermutation (aSHM). Additionally, AID has been found to affect gene expression through demethylation as well as altered interactions between gene regulatory elements. These changes have been most thoroughly studied in B-NHL arising from GC B-cells. Here, we describe the most common classes of GC-derived B-NHL and explore the consequences of on- and off-target AID activity in B and plasma cell neoplasms. The relationships between AID expression, including effects of infection and other exposures/agents, mutagenic activity and lymphoma biology are also discussed.
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Affiliation(s)
- Rebecca J Leeman-Neill
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States; Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States.
| | - Govind Bhagat
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States
| | - Uttiya Basu
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States
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3
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Kligfeld H, Han I, Abraham A, Shukla V. Alternative DNA structures in hematopoiesis and adaptive immunity. Adv Immunol 2024; 161:109-126. [PMID: 38763699 DOI: 10.1016/bs.ai.2024.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2024]
Abstract
Besides the canonical B-form, DNA also adopts alternative non-B form conformations which are highly conserved in all domains of life. While extensive research over decades has centered on the genomic functions of B-form DNA, understanding how non-B-form conformations influence functional genomic states remains a fundamental and open question. Recent studies have ascribed alternative DNA conformations such as G-quadruplexes and R-loops as important functional features in eukaryotic genomes. This review delves into the biological importance of alternative DNA structures, with a specific focus on hematopoiesis and adaptive immunity. We discuss the emerging roles of G-quadruplex and R-loop structures, the two most well-studied alternative DNA conformations, in the hematopoietic compartment and present evidence for their functional roles in normal cellular physiology and associated pathologies.
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Affiliation(s)
- Heather Kligfeld
- Department of Cell and Developmental Biology, Northwestern University, Chicago, IL, United States; Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, United States
| | - Isabella Han
- Department of Cell and Developmental Biology, Northwestern University, Chicago, IL, United States
| | - Ajay Abraham
- Department of Cell and Developmental Biology, Northwestern University, Chicago, IL, United States; Center for Human Immunobiology, Northwestern University, Chicago, IL, United States
| | - Vipul Shukla
- Department of Cell and Developmental Biology, Northwestern University, Chicago, IL, United States; Center for Human Immunobiology, Northwestern University, Chicago, IL, United States; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, United States.
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4
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Berríos KN, Barka A, Gill J, Serrano JC, Bailer PF, Parker JB, Evitt NH, Gajula KS, Shi J, Kohli RM. Cooperativity between Cas9 and hyperactive AID establishes broad and diversifying mutational footprints in base editors. Nucleic Acids Res 2024; 52:2078-2090. [PMID: 38261989 PMCID: PMC10899762 DOI: 10.1093/nar/gkae024] [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: 04/09/2023] [Revised: 12/20/2023] [Accepted: 01/04/2024] [Indexed: 01/25/2024] Open
Abstract
The partnership of DNA deaminase enzymes with CRISPR-Cas nucleases is now a well-established method to enable targeted genomic base editing. However, an understanding of how Cas9 and DNA deaminases collaborate to shape base editor (BE) outcomes has been lacking. Here, we support a novel mechanistic model of base editing by deriving a range of hyperactive activation-induced deaminase (AID) base editors (hBEs) and exploiting their characteristic diversifying activity. Our model involves multiple layers of previously underappreciated cooperativity in BE steps including: (i) Cas9 binding can potentially expose both DNA strands for 'capture' by the deaminase, a feature that is enhanced by guide RNA mismatches; (ii) after strand capture, the intrinsic activity of the DNA deaminase can tune window size and base editing efficiency; (iii) Cas9 defines the boundaries of editing on each strand, with deamination blocked by Cas9 binding to either the PAM or the protospacer and (iv) non-canonical edits on the guide RNA bound strand can be further elicited by changing which strand is nicked by Cas9. Leveraging insights from our mechanistic model, we create novel hBEs that can remarkably generate simultaneous C > T and G > A transitions over >65 bp with significant potential for targeted gene diversification.
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Affiliation(s)
- Kiara N Berríos
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Aleksia Barka
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jasleen Gill
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Juan C Serrano
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Peter F Bailer
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jared B Parker
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Niklaus H Evitt
- Graduate Group in Cell and Molecular Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kiran S Gajula
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Junwei Shi
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rahul M Kohli
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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5
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Weischedel J, Higgins L, Rogers S, Gramalla-Schmitz A, Wyrzykowska P, Borgoni S, MacCarthy T, Chahwan R. Modular cytosine base editing promotes epigenomic and genomic modifications. Nucleic Acids Res 2024; 52:e8. [PMID: 37994786 PMCID: PMC10810192 DOI: 10.1093/nar/gkad1118] [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: 12/08/2022] [Revised: 10/06/2023] [Accepted: 11/06/2023] [Indexed: 11/24/2023] Open
Abstract
Prokaryotic and eukaryotic adaptive immunity differ considerably. Yet, their fundamental mechanisms of gene editing via Cas9 and activation-induced deaminase (AID), respectively, can be conveniently complimentary. Cas9 is an RNA targeted dual nuclease expressed in several bacterial species. AID is a cytosine deaminase expressed in germinal centre B cells to mediate genomic antibody diversification. AID can also mediate epigenomic reprogramming via active DNA demethylation. It is known that sequence motifs, nucleic acid structures, and associated co-factors affect AID activity. But despite repeated attempts, deciphering AID's intrinsic catalytic activities and harnessing its targeted recruitment to DNA is still intractable. Even recent cytosine base editors are unable to fully recapitulate AID's genomic and epigenomic editing properties. Here, we describe the first instance of a modular AID-based editor that recapitulates the full spectrum of genomic and epigenomic editing activity. Our 'Swiss army knife' toolbox will help better understand AID biology per se as well as improve targeted genomic and epigenomic editing.
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Affiliation(s)
- Julian Weischedel
- Institute of Experimental Immunology, University of Zurich, Zurich 8057, Switzerland
| | - Laurence Higgins
- Living Systems Institute, University of Exeter, Exeter EX4 4QD, UK
| | - Sally Rogers
- Living Systems Institute, University of Exeter, Exeter EX4 4QD, UK
| | - Anna Gramalla-Schmitz
- Institute of Experimental Immunology, University of Zurich, Zurich 8057, Switzerland
| | - Paulina Wyrzykowska
- Institute of Experimental Immunology, University of Zurich, Zurich 8057, Switzerland
| | - Simone Borgoni
- Institute of Experimental Immunology, University of Zurich, Zurich 8057, Switzerland
| | - Thomas MacCarthy
- Department of Applied Mathematics & Statistics, Stony Brook University, NY 11794-3600, USA
| | - Richard Chahwan
- Institute of Experimental Immunology, University of Zurich, Zurich 8057, Switzerland
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6
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Wang Y, Zhang S, Zheng X, Yeap LS, Meng FL. A high-throughput protocol for deamination of long single-stranded DNA and oligo pools containing complex sequences. STAR Protoc 2023; 4:102602. [PMID: 37742176 PMCID: PMC10522977 DOI: 10.1016/j.xpro.2023.102602] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/08/2023] [Accepted: 09/05/2023] [Indexed: 09/26/2023] Open
Abstract
Cytidine deaminases as DNA mutators play important roles in immunity and genome stability. Here, we present a high-throughput protocol for deamination of long single-stranded (ss) DNA or oligo pools containing complex sequences. We describe steps for the preparation of both enzyme (activation-induced deaminase, AID) and ssDNA substrates, the deamination reaction, uracil-friendly amplification, and data analysis. This assay can be used to determine the intrinsic mutation profile of a single antibody gene or a pool of selected regions on genomic DNA. For complete details on the use and execution of this protocol, please refer to Wang et al. (2023).1.
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Affiliation(s)
- Yanyan Wang
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| | - Senxin Zhang
- Department of Mathematics, Shanghai Normal University, Shanghai 200234, China
| | - Xiaoqi Zheng
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Leng-Siew Yeap
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Center for Immune-Related Diseases at Shanghai Institute of Immunology, Department of Endocrinology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| | - Fei-Long Meng
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China.
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7
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Skrekas C, Limeta A, Siewers V, David F. Targeted In Vivo Mutagenesis in Yeast Using CRISPR/Cas9 and Hyperactive Cytidine and Adenine Deaminases. ACS Synth Biol 2023; 12:2278-2289. [PMID: 37486333 PMCID: PMC10443040 DOI: 10.1021/acssynbio.2c00690] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Indexed: 07/25/2023]
Abstract
Directed evolution is a preferred strategy to improve the function of proteins such as enzymes that act as bottlenecks in metabolic pathways. Common directed evolution approaches rely on error-prone PCR-based libraries where the number of possible variants is usually limited by cellular transformation efficiencies. Targeted in vivo mutagenesis can advance directed evolution approaches and help to overcome limitations in library generation. In the current study, we aimed to develop a high-efficiency time-controllable targeted mutagenesis toolkit in the yeast Saccharomyces cerevisiae by employing the CRISPR/Cas9 technology. To that end, we fused the dCas9 protein with hyperactive variants of adenine and cytidine deaminases aiming to create an inducible CRISPR-based mutagenesis tool targeting a specific DNA sequence in vivo with extended editing windows and high mutagenesis efficiency. We also investigated the effect of guide RNA multiplexing on the mutagenesis efficiency both phenotypically and on the DNA level.
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Affiliation(s)
- Christos Skrekas
- Department
of Life Sciences, Chalmers University of
Technology, Gothenburg SE-41296, Sweden
| | - Angelo Limeta
- Department
of Life Sciences, Chalmers University of
Technology, Gothenburg SE-41296, Sweden
| | - Verena Siewers
- Department
of Life Sciences, Chalmers University of
Technology, Gothenburg SE-41296, Sweden
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Florian David
- Department
of Life Sciences, Chalmers University of
Technology, Gothenburg SE-41296, Sweden
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8
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Li J, Dai HQ. Mesoscale sequence feature modulates AID activity in antibody diversification. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1515-1517. [PMID: 37537958 PMCID: PMC10520465 DOI: 10.3724/abbs.2023145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 07/17/2023] [Indexed: 08/05/2023] Open
Affiliation(s)
- Jiayang Li
- />State Key Laboratory of Molecular BiologyShanghai Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell ScienceChinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghai200031China
| | - Hai-Qiang Dai
- />State Key Laboratory of Molecular BiologyShanghai Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell ScienceChinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghai200031China
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9
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Wang Y, Zhang S, Yang X, Hwang JK, Zhan C, Lian C, Wang C, Gui T, Wang B, Xie X, Dai P, Zhang L, Tian Y, Zhang H, Han C, Cai Y, Hao Q, Ye X, Liu X, Liu J, Cao Z, Huang S, Song J, Pan-Hammarström Q, Zhao Y, Alt FW, Zheng X, Da LT, Yeap LS, Meng FL. Mesoscale DNA feature in antibody-coding sequence facilitates somatic hypermutation. Cell 2023; 186:2193-2207.e19. [PMID: 37098343 DOI: 10.1016/j.cell.2023.03.030] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 03/06/2023] [Accepted: 03/24/2023] [Indexed: 04/27/2023]
Abstract
Somatic hypermutation (SHM), initiated by activation-induced cytidine deaminase (AID), generates mutations in the antibody-coding sequence to allow affinity maturation. Why these mutations intrinsically focus on the three nonconsecutive complementarity-determining regions (CDRs) remains enigmatic. Here, we found that predisposition mutagenesis depends on the single-strand (ss) DNA substrate flexibility determined by the mesoscale sequence surrounding AID deaminase motifs. Mesoscale DNA sequences containing flexible pyrimidine-pyrimidine bases bind effectively to the positively charged surface patches of AID, resulting in preferential deamination activities. The CDR hypermutability is mimicable in in vitro deaminase assays and is evolutionarily conserved among species using SHM as a major diversification strategy. We demonstrated that mesoscale sequence alterations tune the in vivo mutability and promote mutations in an otherwise cold region in mice. Our results show a non-coding role of antibody-coding sequence in directing hypermutation, paving the way for the synthetic design of humanized animal models for optimal antibody discovery and explaining the AID mutagenesis pattern in lymphoma.
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Affiliation(s)
- Yanyan Wang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, 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, Shanghai 200025, China
| | - Senxin Zhang
- Department of Mathematics, Shanghai Normal University, Shanghai 200234, China
| | - Xinrui Yang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Joyce K Hwang
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Chuanzong Zhan
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, 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, Shanghai 200025, China
| | - Chong Wang
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - 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, 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, Shanghai 200025, China
| | - Xia Xie
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Pengfei Dai
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Lu Zhang
- School of Life Sciences, Fudan University, Shanghai 200438, 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, Shanghai 200025, China
| | - Huizhi Zhang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Chong Han
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Yanni Cai
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Qian Hao
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xiaofei Ye
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, 141-83 Stockholm, Sweden; Kindstar Global Precision Medicine Institute, Wuhan 430000, China
| | - Xiaojing Liu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Jiaquan Liu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhiwei Cao
- School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Shaohui Huang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; School of Biosciences, University of Chinese Academy of Sciences, Beijing 101499, China
| | - Jie Song
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Qiang Pan-Hammarström
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, 141-83 Stockholm, Sweden; Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Yaofeng Zhao
- State Key Laboratory of Farm Animal Biotech Breeding, China Agricultural University, Beijing 100193, China
| | - Frederick W Alt
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Xiaoqi Zheng
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lin-Tai Da
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Leng-Siew Yeap
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; 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.
| | - Fei-Long Meng
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China; Shanghai Huashen Institute of Microbes and Infections, Shanghai 200052, China.
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10
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Abstract
Activation-induced cytidine deaminase (AID) initiates somatic hypermutation of immunoglobulin (Ig) gene variable regions and class switch recombination (CSR) of Ig heavy chain constant regions. Two decades of intensive research has greatly expanded our knowledge of how AID functions in peripheral B cells to optimize antibody responses against infections, while maintaining tight regulation of AID to restrain its activity to protect B cell genomic integrity. The many exciting recent advances in the field include: 1) the first description of AID's molecular structure, 2) remarkable advances in high throughput approaches that precisely track AID targeting genome-wide, and 3) the discovery that the cohesion-mediate loop extrusion mechanism [initially discovered in V(D)J recombination studies] also governs AID-medicated CSR. These advances have significantly advanced our understanding of AID's biochemical properties in vitro and AID's function and regulation in vivo. This mini review will discuss these recent discoveries and outline the challenges and questions that remain to be addressed.
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11
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Contribution of rare mutational outcomes to broadly neutralizing antibodies. Acta Biochim Biophys Sin (Shanghai) 2022; 54:820-827. [PMID: 35713319 PMCID: PMC9828561 DOI: 10.3724/abbs.2022065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Antibodies are important immune molecules that are elicited by B cells to protect our bodies during viral infections or vaccinations. In humans, the antibody repertoire is diversified by programmed DNA lesion processes to ensure specific and high affinity binding to various antigens. Broadly neutralizing antibodies (bnAbs) are antibodies that have strong neutralizing activities against different variants of a virus. bnAbs such as anti-HIV bnAbs often have special characteristics including insertions and deletions, long complementarity determining region 3 (CDR3), and high frequencies of mutations, often at improbable sites of the variable regions. These unique features are rare mutational outcomes that are acquired during antibody diversification processes. In this review, we will discuss possible mechanisms that generate these rare antibody mutational outcomes. The understanding of the mechanisms that generate these rare mutational outcomes during antibody diversification will have implications in vaccine design strategies to elicit bnAbs.
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12
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Summerauer AM, Jäggi V, Ogwang R, Traxel S, Colombo L, Amundsen E, Eyer T, Subramanian B, Fehr J, Mantel P, Idro R, Bürgler S. Epstein-Barr virus and malaria upregulate AID and APOBEC3 enzymes, but only AID seems to play a major mutagenic role in Burkitt lymphoma. Eur J Immunol 2022; 52:1273-1284. [PMID: 35503749 PMCID: PMC7613445 DOI: 10.1002/eji.202249820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 04/01/2022] [Accepted: 04/27/2022] [Indexed: 11/26/2022]
Abstract
Endemic Burkitt lymphoma (eBL) is characterized by an oncogenic IGH/c‐MYC translocation and Epstein–Barr virus (EBV) positivity, and is epidemiologically linked to Plasmodium falciparum malaria. Both EBV and malaria are thought to contribute to eBL by inducing the expression of activation‐induced cytidine deaminase (AID), an enzyme involved in the IGH/c‐MYC translocation. AID/apolipoprotein B mRNA editing catalytic polypeptide‐like (AID/APOBEC) family enzymes have recently emerged as potent mutagenic sources in a variety of cancers, but apart from AID, their involvement in eBL and their regulation by EBV and P. falciparum is unknown. Here, we show that upon inoculation with EBV, human B cells strongly upregulate the expression of enzymatically active APOBEC3B and APOBEC3G. In addition, we found significantly increased levels of APOBEC3A in B cells of malaria patients, which correlated with parasite load. Interestingly, despite the fact that APOBEC3A, APOBEC3B, and APOBEC3G caused c‐MYC mutations when overexpressed in HEK293T cells, a mutational enrichment in eBL tumors was only detected in AID motifs. This suggests that even though the EBV‐ and P. falciparum‐directed immune response triggers the expression and activity of several AID/APOBEC members, only the upregulation of AID has oncogenic consequences, while the induction of the APOBEC3 subfamily may primarily have immunoprotective functions.
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Affiliation(s)
- Andrea M. Summerauer
- Experimental Infectious Diseases and Cancer Research, Children's Research CenterUniversity Children's Hospital ZurichZurichSwitzerland
- Department of Infectious Diseases and Hospital EpidemiologyUniversity Hospital ZurichZurichSwitzerland
| | - Vera Jäggi
- Experimental Infectious Diseases and Cancer Research, Children's Research CenterUniversity Children's Hospital ZurichZurichSwitzerland
| | - Rodney Ogwang
- College of Health SciencesMakerere UniversityKampalaUganda
- Centre of Tropical NeuroscienceKitgum SiteKampalaUganda
- KEMRI‐Wellcome Trust Research ProgrammeCentre for Geographic Medicine CoastKilifiKenya
| | - Sabrina Traxel
- Experimental Infectious Diseases and Cancer Research, Children's Research CenterUniversity Children's Hospital ZurichZurichSwitzerland
| | - Lorenzo Colombo
- Experimental Infectious Diseases and Cancer Research, Children's Research CenterUniversity Children's Hospital ZurichZurichSwitzerland
| | - Eivind Amundsen
- KG Jebsen Centre for B Cell Malignancies, Institute of Clinical MedicineUniversity of OsloOsloNorway
| | - Tatjana Eyer
- Experimental Infectious Diseases and Cancer Research, Children's Research CenterUniversity Children's Hospital ZurichZurichSwitzerland
| | - Bibin Subramanian
- Department of Oncology, Microbiology, and Immunology, Faculty of Science and MedicineUniversity of FribourgFribourgSwitzerland
| | - Jan Fehr
- Department of Infectious Diseases and Hospital EpidemiologyUniversity Hospital ZurichZurichSwitzerland
| | - Pierre‐Yves Mantel
- Department of Oncology, Microbiology, and Immunology, Faculty of Science and MedicineUniversity of FribourgFribourgSwitzerland
| | - Richard Idro
- College of Health SciencesMakerere UniversityKampalaUganda
- Centre of Tropical NeuroscienceKitgum SiteKampalaUganda
| | - Simone Bürgler
- Experimental Infectious Diseases and Cancer Research, Children's Research CenterUniversity Children's Hospital ZurichZurichSwitzerland
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13
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López C, Schleussner N, Bernhart SH, Kleinheinz K, Sungalee S, Sczakiel HL, Kretzmer H, Toprak UH, Glaser S, Wagener R, Ammerpohl O, Bens S, Giefing M, González Sánchez JC, Apic G, Hübschmann D, Janz M, Kreuz M, Mottok A, Müller JM, Seufert J, Hoffmann S, Korbel JO, Russell RB, Schüle R, Trümper L, Klapper W, Radlwimmer B, Lichter P, Küppers R, Schlesner M, Mathas S, Siebert R. Focal structural variants revealed by whole genome sequencing disrupt the histone demethylase KDM4C in B-cell lymphomas. Haematologica 2022; 108:543-554. [PMID: 35522148 PMCID: PMC9890021 DOI: 10.3324/haematol.2021.280005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Indexed: 02/03/2023] Open
Abstract
Histone methylation-modifiers, such as EZH2 and KMT2D, are recurrently altered in B-cell lymphomas. To comprehensively describe the landscape of alterations affecting genes encoding histone methylation-modifiers in lymphomagenesis we investigated whole genome and transcriptome data of 186 mature B-cell lymphomas sequenced in the ICGC MMML-Seq project. Besides confirming common alterations of KMT2D (47% of cases), EZH2 (17%), SETD1B (5%), PRDM9 (4%), KMT2C (4%), and SETD2 (4%), also identified by prior exome or RNA-sequencing studies, we here found recurrent alterations to KDM4C in chromosome 9p24, encoding a histone demethylase. Focal structural variation was the main mechanism of KDM4C alterations, and was independent from 9p24 amplification. We also identified KDM4C alterations in lymphoma cell lines including a focal homozygous deletion in a classical Hodgkin lymphoma cell line. By integrating RNA-sequencing and genome sequencing data we predict that KDM4C structural variants result in loss-offunction. By functional reconstitution studies in cell lines, we provide evidence that KDM4C can act as a tumor suppressor. Thus, we show that identification of structural variants in whole genome sequencing data adds to the comprehensive description of the mutational landscape of lymphomas and, moreover, establish KDM4C as a putative tumor suppressive gene recurrently altered in subsets of B-cell derived lymphomas.
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Affiliation(s)
- Cristina López
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany,Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany,*CL and NS contributed equally as co-first authors
| | - Nikolai Schleussner
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany,Hematology, Oncology and Tumor Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany, and Experimental and Clinical Research Center, a joint cooperation between the MDC and the Charité, Berlin, Germany,*CL and NS contributed equally as co-first authors
| | - Stephan H. Bernhart
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany,Bioinformatics Group, Department of Computer, University of Leipzig, Leipzig, Germany,Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Kortine Kleinheinz
- Department for Bioinformatics and Functional Genomics, Institute of Pharmacy and Molecular Biotechnology and Bioquant, University of Heidelberg, Heidelberg, Germany
| | | | - Henrike L. Sczakiel
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany,Hematology, Oncology and Tumor Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany, and Experimental and Clinical Research Center, a joint cooperation between the MDC and the Charité, Berlin, Germany
| | - Helene Kretzmer
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany,Bioinformatics Group, Department of Computer, University of Leipzig, Leipzig, Germany,Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany,Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Umut H. Toprak
- Bioinformatics and Omics Data Analytics (B240), German Cancer Research Center (DKFZ), Heidelberg, Germany,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany,Hopp-Children’s Cancer Center at the NCT Heidelberg (KiTZ), Division of Neuroblastoma Genomics (B087), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Selina Glaser
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Rabea Wagener
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany,Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Ole Ammerpohl
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany,Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Susanne Bens
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany,Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany
| | - Maciej Giefing
- Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany,Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | | | - Gordana Apic
- BioQuant and Biochemie Zentrum Heidelberg (BZH), Heidelberg University, Heidelberg, Germany
| | - Daniel Hübschmann
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany,Department for Bioinformatics and Functional Genomics, Institute of Pharmacy and Molecular Biotechnology and Bioquant, University of Heidelberg, Heidelberg, Germany,German Cancer Consortium (DKTK), Heidelberg, Germany,Heidelberg Institute of Stem Cell Technology and Experimental Medicine (HI-STEM), Heidelberg, Germany
| | - Martin Janz
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany,Hematology, Oncology and Tumor Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany, and Experimental and Clinical Research Center, a joint cooperation between the MDC and the Charité, Berlin, Germany
| | - Markus Kreuz
- Institute for Medical Informatics Statistics and Epidemiology, Leipzig, Germany
| | - Anja Mottok
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Judith M. Müller
- Klinik fur Urologie und Zentrale Klinische Forschung, Klinikum der Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Julian Seufert
- Bioinformatics and Omics Data Analytics (B240), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Steve Hoffmann
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany,Bioinformatics Group, Department of Computer, University of Leipzig, Leipzig, Germany,Transcriptome Bioinformatics, LIFE Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany,Leibniz Institute on Ageing-Fritz Lipmann Institute (FLI), Computational Biology, Jena, Germany
| | - Jan O. Korbel
- EMBL Heidelberg, Genome Biology Unit, Heidelberg,, Germany
| | - Robert B. Russell
- BioQuant and Biochemie Zentrum Heidelberg (BZH), Heidelberg University, Heidelberg, Germany
| | - Roland Schüle
- Klinik fur Urologie und Zentrale Klinische Forschung, Klinikum der Albert-Ludwigs-Universität Freiburg, Freiburg, Germany,BIOSS Centre of Biological Signalling Studies, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Lorenz Trümper
- Department of Hematology and Oncology, Georg-August-University of Göttingen, Göttingen, Germany
| | - Wolfram Klapper
- Hematopathology Section, Christian-Albrechts-University, Kiel, Germany
| | - Bernhard Radlwimmer
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Peter Lichter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ralf Küppers
- Institute of Cell Biology (Cancer Research), University of Duisburg-Essen, Essen, Germany, and German Cancer Consortium (DKTK)
| | - Matthias Schlesner
- Bioinformatics and Omics Data Analytics (B240), German Cancer Research Center (DKFZ), Heidelberg, Germany,Biomedical Informatics, Data Mining and Data Analytics, Augsburg University, Augsburg, Germany
| | - Stephan Mathas
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany,Hematology, Oncology and Tumor Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany, and Experimental and Clinical Research Center, a joint cooperation between the MDC and the Charité, Berlin, Germany,SM and RS contributed equally as co-senior authors
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany,Institute of Human Genetics, Christian-Albrechts-University, Kiel, Germany,SM and RS contributed equally as co-senior authors
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14
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Liu D, Goodman MF, Pham P, Yu K, Hsieh CL, Lieber MR. The mRNA tether model for activation-induced deaminase and its relevance for Ig somatic hypermutation and class switch recombination. DNA Repair (Amst) 2022; 110:103271. [PMID: 34990960 PMCID: PMC8816865 DOI: 10.1016/j.dnarep.2021.103271] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/19/2021] [Accepted: 12/28/2021] [Indexed: 02/03/2023]
Abstract
Activation-induced deaminase (AID) only deaminates cytosine within single-stranded DNA. Transcription is known to increase AID deamination on duplex DNA substrates during transcription. Using a purified T7 RNA polymerase transcription system, we recently found that AID deamination of a duplex DNA substrate is reduced if RNase A is added during transcription. This finding prompted us to consider that the mRNA tail may contribute to AID action at the nearby transcribed strand (TS) or non-transcribed strand (NTS) of DNA, which are transiently single-stranded in the wake of RNA polymerase movement. Here, we used a purified system to test whether a single-stranded oligonucleotide (oligo) consisting of RNA in the 5' portion and DNA in the 3' portion (i.e., 5'RNA-DNA3', also termed an RNA-DNA fusion substrate) could be deaminated equally efficiently as the same sequence when it is entirely DNA. We found that AID acts on the RNA-DNA fusion substrate and the DNA-only substrate with similar efficiency. Based on this finding and our recent observation on the importance of the mRNA tail, we propose a model in which the proximity and length of the mRNA tail provide a critical site for AID loading to permit a high local collision frequency with the NTS and TS in the transient wake of the RNA polymerase. When the mRNA tail is not present, we know that AID action drops to levels equivalent to when there is no transcription at all. This mRNA tether model explains several local and global features of Ig somatic hypermutation and Ig class switch recombination, while integrating structural and functional features of AID.
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Affiliation(s)
- Di Liu
- Departments of Pathology, Biochemistry & Molecular Biology, and Molecular Microbiology & Immunology, and the Section of Molecular & Computational Biology in the Department of Biological Sciences, Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, CA 90033
| | - Myron F. Goodman
- Department of Biological Sciences (Section of Molecular & Computational Biology), University of Southern California, Los Angeles, CA 90089
| | - Phuong Pham
- Department of Biological Sciences (Section of Molecular & Computational Biology), University of Southern California, Los Angeles, CA 90089
| | - Kefei Yu
- Microbiology and Molecular Genetics, Michigan State University, 5175 Biomedical Physical Sciences, East Lansing, MI 48824
| | - Chih-Lin Hsieh
- USC Norris Comprehensive Cancer Center, Department of Urology, University of Southern California and USC Keck School of Medicine, Los Angeles, CA 90033
| | - Michael R. Lieber
- Departments of Pathology, Biochemistry & Molecular Biology, and Molecular Microbiology & Immunology, and the Section of Molecular & Computational Biology in the Department of Biological Sciences, Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, CA 90033,Corresponding author: M. Lieber, , ph. 323 865 0568
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15
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Tang C, Krantsevich A, MacCarthy T. Deep learning model of somatic hypermutation reveals importance of sequence context beyond hotspot targeting. iScience 2022; 25:103668. [PMID: 35036866 PMCID: PMC8749460 DOI: 10.1016/j.isci.2021.103668] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 11/08/2021] [Accepted: 12/16/2021] [Indexed: 11/23/2022] Open
Abstract
B cells undergo somatic hypermutation (SHM) of the Immunoglobulin (Ig) variable region to generate high-affinity antibodies. SHM relies on the activity of activation-induced deaminase (AID), which mutates C>U preferentially targeting WRC (W=A/T, R=A/G) hotspots. Downstream mutations at WA Polymerase η hotspots contribute further mutations. Computational models of SHM can describe the probability of mutations essential for vaccine responses. Previous studies using short subsequences (k-mers) failed to explain divergent mutability for the same k-mer. We developed the DeepSHM (Deep learning on SHM) model using k-mers of size 5-21, improving accuracy over previous models. Interpretation of DeepSHM identified an extended WWRCT motif with particularly high mutability. Increased mutability was further associated with lower surrounding G content. Our model also discovered a conserved AGYCTGGGGG (Y=C/T) motif within FW1 of IGHV3 family genes with unusually high T>G substitution rates. Thus, a wider sequence context increases predictive power and identifies features that drive mutational targeting.
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Affiliation(s)
- Catherine Tang
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Artem Krantsevich
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Thomas MacCarthy
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
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16
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Masuda H, Sawada A, Hashimoto SI, Tamai K, Lin KY, Harigai N, Kurosawa K, Ohta K, Seo H, Itou H. Fast-tracking antibody maturation using a B cell-based display system. MAbs 2022; 14:2122275. [PMID: 36202784 PMCID: PMC9542628 DOI: 10.1080/19420862.2022.2122275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Affinity maturation, an essential component of antibody engineering, is crucial for developing therapeutic antibodies. Cell display system coupled with somatic hypermutation (SHM) initiated by activation-induced cytidine deaminase (AID) is a commonly used technique for affinity maturation. AID introduces targeted DNA lesions into hotspots of immunoglobulin (Ig) gene loci followed by erroneous DNA repair, leading to biased mutations in the complementary determining regions. However, systems that use an in vivo mimicking mechanism often require several rounds of selection to enrich clones possessing accumulated mutations. We previously described the human ADLib® system, which features autonomous, AID-mediated diversification in Ig gene loci of a chicken B cell line DT40 and streamlines human antibody generation and optimization in one integrated platform. In this study, we further engineered DT40 capable of receiving exogenous antibody genes and examined whether the antibody could be affinity matured. The Ig genes of three representative anti-hVEGF-A antibodies originating from the human ADLib® were introduced; the resulting human IgG1 antibodies had up to 76.4-fold improvement in binding affinities (sub-picomolar KD) within just one round of optimization, owing to efficient accumulation of functional mutations. Moreover, we successfully improved the affinity of a mouse hybridoma-derived anti-hCDCP1 antibody using the engineered DT40, and the observed mutations remained effective in the post-humanized antibody as exhibited by an 8.2-fold increase of in vitro cytotoxicity without compromised physical stability. These results demonstrated the versatility of the novel B cell-based affinity maturation system as an easy-to-use antibody optimization tool regardless of the species of origin.Abbreviations: ADLib®: Autonomously diversifying library, ADLib® KI-AMP: ADLib® knock-in affinity maturation platform, AID: activation-induced cytidine deaminase, CDRs: complementary-determining regions, DIVAC: diversification activator, ECD: extracellular domain, FACS: fluorescence-activated cell sorting, FCM: flow cytometry, HC: heavy chainIg: immunoglobulin, LC: light chain, NGS: next-generation sequencing, PBD: pyrrolobenzodiazepine, SHM: somatic hypermutation, SPR: surface plasmon resonance.
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Affiliation(s)
- Hitomi Masuda
- Research Laboratories, Chiome Bioscience Inc, Tokyo, Japan,CONTACT Hitomi Masuda Research Laboratories, Chiome Bioscience Inc, Sumitomo-Fudosan Nishi-shinjuku bldg. No. 6, 3-12-1 Honmachi, Shibuya-ku, Tokyo151-0071, Japan
| | - Atsushi Sawada
- Research Laboratories, Chiome Bioscience Inc, Tokyo, Japan
| | | | - Kanako Tamai
- Research Laboratories, Chiome Bioscience Inc, Tokyo, Japan
| | - Ke-Yi Lin
- Research Laboratories, Chiome Bioscience Inc, Tokyo, Japan
| | - Naoto Harigai
- Research Laboratories, Chiome Bioscience Inc, Tokyo, Japan
| | - Kohei Kurosawa
- Research Laboratories, Chiome Bioscience Inc, Tokyo, Japan
| | - Kunihiro Ohta
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Hidetaka Seo
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Hiroshi Itou
- Research Laboratories, Chiome Bioscience Inc, Tokyo, Japan,Hiroshi Itou Research Laboratories, Chiome Bioscience Inc, Sumitomo-Fudosan Nishi-shinjuku bldg. No. 6, 3-12-1, Honmachi, Shibuya-ku, Tokyo 151-0071 Japan
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17
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Liu D, Lieber MR. The mechanisms of human lymphoid chromosomal translocations and their medical relevance. Crit Rev Biochem Mol Biol 2021; 57:227-243. [PMID: 34875186 DOI: 10.1080/10409238.2021.2004576] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The most common human lymphoid chromosomal translocations involve concurrent failures of the recombination activating gene (RAG) complex and Activation-Induced Deaminase (AID). These are two enzymes that are normally expressed for purposes of the two site-specific DNA recombination processes: V(D)J recombination and class switch recombination (CSR). First, though it is rare, a low level of expression of AID can introduce long-lived T:G mismatch lesions at 20-600 bp fragile zones. Second, the V(D)J recombination process can occasionally fail to rejoin coding ends, and this failure may permit an opportunity for Artemis:DNA-dependent kinase catalytic subunit (DNA-PKcs) to convert the T:G mismatch sites at the fragile zones into double-strand breaks. The 20-600 bp fragile zones must be, at least transiently, in a single-stranded DNA (ssDNA) state for the first step to occur, because AID only acts on ssDNA. Here we discuss the key DNA sequence features that lead to AID action at a fragile zone, which are (a) the proximity and density of strings of cytosine nucleotides (C-strings) that cause a B/A-intermediate DNA conformation; (b) overlapping AID hotspots that contain a methyl CpG (WRCG), which AID converts to a long-lived T:G mismatch; and (c) transcription, which, though not essential, favors increased ssDNA in the fragile zone. We also summarize chromosomal features of the focal fragile zones in lymphoid malignancies and discuss the clinical relevance of understanding the translocation mechanisms. Many of the key principles covered here are also relevant to chromosomal translocations in non-lymphoid somatic cells as well.
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Affiliation(s)
- Di Liu
- Department of Pathology & Laboratory Medicine, Department of Biochemistry & Molecular Biology, Department of Molecular Microbiology and Immunology, and Section of Computational Biology in the Department of Biological Sciences, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Michael R Lieber
- Department of Pathology & Laboratory Medicine, Department of Biochemistry & Molecular Biology, Department of Molecular Microbiology and Immunology, and Section of Computational Biology in the Department of Biological Sciences, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
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18
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The optimal pH of AID is skewed from that of its catalytic pocket by DNA-binding residues and surface charge. Biochem J 2021; 479:39-55. [PMID: 34870314 DOI: 10.1042/bcj20210529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 12/02/2021] [Accepted: 12/06/2021] [Indexed: 11/17/2022]
Abstract
Activation-induced cytidine deaminase (AID) is a member of the apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like (APOBEC) family of cytidine deaminases. AID mutates immunoglobulin loci to initiate secondary antibody diversification. The APOBEC3 (A3) sub-branch mutates viral pathogens in the cytosol and acidic endosomal compartments. Accordingly, AID functions optimally near neutral pH, while most A3s are acid-adapted (optimal pH 5.5-6.5). To gain a structural understanding for this pH disparity, we constructed high-resolution maps of AID catalytic activity vs pH. We found AID's optimal pH was 7.3 but it retained most (>70%) of the activity at pH 8. Probing of ssDNA-binding residues near the catalytic pocket, key for bending ssDNA into the pocket (e.g R25) yielded mutants with altered pH preference, corroborating previous findings that the equivalent residue in APOBEC3G (H216) underlies its acidic pH preference. AID from bony fish exhibited more basic optimal pH (pH 7.5-8.1) and several R25-equivalent mutants altered pH preference. Comparison of pH optima across the AID/APOBEC3 family revealed an inverse correlation between positive surface charge and overall catalysis. The paralogue with the most robust catalytic activity (APOBEC3A) has the lowest surface charge, most acidic pH preference, while the paralogue with the most lethargic catalytic rate (AID) has the most positive surface charge and highest optimal pH. We suggest one possible mechanism is through surface charge dictating an overall optimal pH that is different from the optimal pH of the catalytic pocket microenvironment. These findings illuminate an additional structural mechanism that regulates AID/APOBEC3 mutagenesis.
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19
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Liu D, Loh YHE, Hsieh CL, Lieber MR. Mechanistic basis for chromosomal translocations at the E2A gene and its broader relevance to human B cell malignancies. Cell Rep 2021; 36:109387. [PMID: 34260910 PMCID: PMC8327686 DOI: 10.1016/j.celrep.2021.109387] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 03/31/2021] [Accepted: 06/21/2021] [Indexed: 11/22/2022] Open
Abstract
Analysis of translocation breakpoints in human B cell malignancies reveals that DNA double-strand breaks at oncogenes most frequently occur at CpG sites located within 20-600 bp fragile zones and depend on activation-induced deaminase (AID). AID requires single-stranded DNA (ssDNA) to act, but it has been unclear why or how this region transiently acquires a ssDNA state. Here, we demonstrate the ssDNA state in the 23 bp E2A fragile zone using several methods, including native bisulfite DNA structural analysis in live human pre-B cells. AID deamination within the E2A fragile zone does not require but is increased upon transcription. High C-string density, nascent RNA tails, and direct DNA sequence repeats prolong the ssDNA state of the E2A fragile zone and increase AID deamination at overlapping AID hotspots that contain the CpG sites at which breaks occur in patients. These features provide key insights into lymphoid fragile zones generally.
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Affiliation(s)
- Di Liu
- Departments of Pathology, Biochemistry & Molecular Biology, and Molecular Microbiology & Immunology, and Section of Molecular & Computational Biology (Department of Biological Sciences), USC Norris Comprehensive Cancer Center, University of Southern California and USC Keck School of Medicine, Los Angeles, CA, USA
| | - Yong-Hwee Eddie Loh
- USC Libraries Bioinformatics Services, University of Southern California and USC Keck School of Medicine, Los Angeles, CA, USA
| | - Chih-Lin Hsieh
- Department of Urology, USC Norris Comprehensive Cancer Center, University of Southern California and USC Keck School of Medicine, Los Angeles, CA, USA
| | - Michael R Lieber
- Departments of Pathology, Biochemistry & Molecular Biology, and Molecular Microbiology & Immunology, and Section of Molecular & Computational Biology (Department of Biological Sciences), USC Norris Comprehensive Cancer Center, University of Southern California and USC Keck School of Medicine, Los Angeles, CA, USA.
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20
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Oppezzo P, Navarrete M, Chiorazzi N. AID in Chronic Lymphocytic Leukemia: Induction and Action During Disease Progression. Front Oncol 2021; 11:634383. [PMID: 34041018 PMCID: PMC8141630 DOI: 10.3389/fonc.2021.634383] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 02/23/2021] [Indexed: 12/12/2022] Open
Abstract
The enzyme activation-induced cytidine deaminase (AID) initiates somatic hypermutation (SHM) and class switch recombination (CSR) of immunoglobulin (Ig) genes, critical actions for an effective adaptive immune response. However, in addition to the benefits generated by its physiological roles, AID is an etiological factor for the development of human and murine leukemias and lymphomas. This review highlights the pathological role of AID and the consequences of its actions on the development, progression, and therapeutic refractoriness of chronic lymphocytic leukemia (CLL) as a model disease for mature lymphoid malignancies. First, we summarize pertinent aspects of the expression and function of AID in normal B lymphocytes. Then, we assess putative causes for AID expression in leukemic cells emphasizing the role of an activated microenvironment. Thirdly, we discuss the role of AID in lymphomagenesis, in light of recent data obtained by NGS analyses on the genomic landscape of leukemia and lymphomas, concentrating on the frequency of AID signatures in these cancers and correlating previously described tumor-gene drivers with the presence of AID off-target mutations. Finally, we discuss how these changes could affect tumor suppressor and proto-oncogene targets and how they could be associated with disease progression. Collectively, we hope that these sections will help to better understand the complex paradox between the physiological role of AID in adaptive immunity and its potential causative activity in B-cell malignancies.
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Affiliation(s)
- Pablo Oppezzo
- Research Laboratory on Chronic Lymphocytic Leukemia, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | | | - Nicholas Chiorazzi
- The Karches Center for Oncology Research, The Feinstein Institutes for Medical Research, New York, NY, United States
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21
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Alvarez-Gonzalez J, Yasgar A, Maul RW, Rieffer AE, Crawford DJ, Salamango DJ, Dorjsuren D, Zakharov AV, Jansen DJ, Rai G, Marugan J, Simeonov A, Harris RS, Kohli RM, Gearhart PJ. Small Molecule Inhibitors of Activation-Induced Deaminase Decrease Class Switch Recombination in B Cells. ACS Pharmacol Transl Sci 2021; 4:1214-1226. [PMID: 34151211 DOI: 10.1021/acsptsci.1c00064] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Indexed: 11/30/2022]
Abstract
Activation-induced deaminase (AID) not only mutates DNA within the immunoglobulin loci to generate antibody diversity, but it also promotes development of B cell lymphomas. To tame this mutagen, we performed a quantitative high-throughput screen of over 90 000 compounds to see if AID activity could be mitigated. The enzymatic activity was assessed in biochemical assays to detect cytosine deamination and in cellular assays to measure class switch recombination. Three compounds showed promise via inhibition of switching in a transformed B cell line and in murine splenic B cells. These compounds have similar chemical structures, which suggests a shared mechanism of action. Importantly, the inhibitors blocked AID, but not a related cytosine DNA deaminase, APOBEC3B. We further determined that AID was continually expressed for several days after B cell activation to induce switching. This first report of small molecules that inhibit AID can be used to gain regulatory control over base editors.
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Affiliation(s)
- Juan Alvarez-Gonzalez
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224, United States
| | - Adam Yasgar
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20816, United States
| | - Robert W Maul
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224, United States
| | - Amanda E Rieffer
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States.,Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States.,Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Daniel J Crawford
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Daniel J Salamango
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States.,Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States.,Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Dorjbal Dorjsuren
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20816, United States
| | - Alexey V Zakharov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20816, United States
| | - Daniel J Jansen
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20816, United States
| | - Ganesha Rai
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20816, United States
| | - Juan Marugan
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20816, United States
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20816, United States
| | - Reuben S Harris
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States.,Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States.,Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota 55455, United States.,Howard Hughes Medical Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Rahul M Kohli
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Patricia J Gearhart
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224, United States
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22
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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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23
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The Role of APOBECs in Viral Replication. Microorganisms 2020; 8:microorganisms8121899. [PMID: 33266042 PMCID: PMC7760323 DOI: 10.3390/microorganisms8121899] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/25/2020] [Accepted: 11/26/2020] [Indexed: 12/14/2022] Open
Abstract
Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like (APOBEC) proteins are a diverse and evolutionarily conserved family of cytidine deaminases that provide a variety of functions from tissue-specific gene expression and immunoglobulin diversity to control of viruses and retrotransposons. APOBEC family expansion has been documented among mammalian species, suggesting a powerful selection for their activity. Enzymes with a duplicated zinc-binding domain often have catalytically active and inactive domains, yet both have antiviral function. Although APOBEC antiviral function was discovered through hypermutation of HIV-1 genomes lacking an active Vif protein, much evidence indicates that APOBECs also inhibit virus replication through mechanisms other than mutagenesis. Multiple steps of the viral replication cycle may be affected, although nucleic acid replication is a primary target. Packaging of APOBECs into virions was first noted with HIV-1, yet is not a prerequisite for viral inhibition. APOBEC antagonism may occur in viral producer and recipient cells. Signatures of APOBEC activity include G-to-A and C-to-T mutations in a particular sequence context. The importance of APOBEC activity for viral inhibition is reflected in the identification of numerous viral factors, including HIV-1 Vif, which are dedicated to antagonism of these deaminases. Such viral antagonists often are only partially successful, leading to APOBEC selection for viral variants that enhance replication or avoid immune elimination.
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24
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Activation-induced cytidine deaminase: in sickness and in health. J Cancer Res Clin Oncol 2020; 146:2721-2730. [PMID: 32772231 DOI: 10.1007/s00432-020-03348-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 08/04/2020] [Indexed: 12/17/2022]
Abstract
Activation Induced cytidine Deaminase (AID) is an essential enzyme of the adaptive immune system. Its canonical activity is restricted to B lymphocytes, playing an essential role in the diversification of antibodies by enhancing specificity and changing affinity. This is possible through its DNA deaminase function, leading to mutations in DNA. In the last decade, AID has been assigned an additional function: that of a powerful DNA demethylator. Adverse cellular conditions such as chronic inflammation can lead to its deregulation and overexpression. It is an important driver of B-cell lymphoma due to its natural ability to modify DNA through deamination, leading to mutations and epigenetic changes. However, the deregulation of AID is not restricted to lymphoid cells. Recent findings have provided new insights into the role that this protein plays in the development of non-lymphoid cancers, with some research shedding light on novel AID-driven mechanisms of cellular transformation. In this review, we provide an updated narrative of the normal physiological functions of AID. Additionally, we review and discuss the recent research studies that have implicated AID in carcinogenesis in varying tissue types including lymphoid and non-lymphoid cancers. We review the mechanisms, whereby AID promotes carcinogenesis and highlight important areas of future research.
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25
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Immunoglobulin Class Switch Recombination Is Initiated by Rare Cytosine Deamination Events at Switch Regions. Mol Cell Biol 2020; 40:MCB.00125-20. [PMID: 32513818 DOI: 10.1128/mcb.00125-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 06/01/2020] [Indexed: 11/20/2022] Open
Abstract
Activation-induced cytidine deaminase (AID) initiates immunoglobulin (Ig) class switch recombination (CSR), somatic hypermutation (SHM), and gene conversion by converting DNA cytosines to uracils at specific genomic regions. In this study, we examined AID footprints across the entire length of an engineered switch region in cells ablated for uracil repair. We found that AID deamination occurs predominantly at WRC hot spots (where W is A or T and R is A or G) and that the deamination frequency remains constant across the entire switch region. Importantly, we analyzed monoallelic AID deamination footprints on both DNA strands occurring within a single cell cycle. We found that AID generates few and mostly isolated uracils in the switch region, although processive AID deaminations are evident in some molecules. The frequency of molecules containing deamination on both DNA strands at the acceptor switch region correlates with the class switch efficiency, raising the possibility that the minimal requirement for DNA double-strand break (DSB) formation is as low as even one AID deamination event on both DNA strands.
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26
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Tang C, Bagnara D, Chiorazzi N, Scharff MD, MacCarthy T. AID Overlapping and Polη Hotspots Are Key Features of Evolutionary Variation Within the Human Antibody Heavy Chain (IGHV) Genes. Front Immunol 2020; 11:788. [PMID: 32425948 PMCID: PMC7204545 DOI: 10.3389/fimmu.2020.00788] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 04/07/2020] [Indexed: 01/09/2023] Open
Abstract
Somatic hypermutation (SHM) of the immunoglobulin variable (IgV) loci is a key process in antibody affinity maturation. The enzyme activation-induced deaminase (AID), initiates SHM by creating C → U mismatches on single-stranded DNA (ssDNA). AID has preferential hotspot motif targets in the context of WRC/GYW (W = A/T, R = A/G, Y = C/T) and particularly at WGCW overlapping hotspots where hotspots appear opposite each other on both strands. Subsequent recruitment of the low-fidelity DNA repair enzyme, Polymerase eta (Polη), during mismatch repair, creates additional mutations at WA/TW sites. Although there are more than 50 functional immunoglobulin heavy chain variable (IGHV) segments in humans, the fundamental differences between these genes and their ability to respond to all possible foreign antigens is still poorly understood. To better understand this, we generated profiles of WGCW hotspots in each of the human IGHV genes and found the expected high frequency in complementarity determining regions (CDRs) that encode the antigen binding sites but also an unexpectedly high frequency of WGCW in certain framework (FW) sub-regions. Principal Components Analysis (PCA) of these overlapping AID hotspot profiles revealed that one major difference between IGHV families is the presence or absence of WGCW in a sub-region of FW3 sometimes referred to as “CDR4.” Further differences between members of each family (e.g., IGHV1) are primarily determined by their WGCW densities in CDR1. We previously suggested that the co-localization of AID overlapping and Polη hotspots was associated with high mutability of certain IGHV sub-regions, such as the CDRs. To evaluate the importance of this feature, we extended the WGCW profiles, combining them with local densities of Polη (WA) hotspots, thus describing the co-localization of both types of hotspots across all IGHV genes. We also verified that co-localization is associated with higher mutability. PCA of the co-localization profiles showed CDR1 and CDR2 as being the main contributors to variance among IGHV genes, consistent with the importance of these sub-regions in antigen binding. Our results suggest that AID overlapping (WGCW) hotspots alone or in conjunction with Polη (WA/TW) hotspots are key features of evolutionary variation between IGHV genes.
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Affiliation(s)
- Catherine Tang
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, United States
| | - Davide Bagnara
- Karches Center for Oncology Research, The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, United States.,Department of Experimental Medicine, University of Genoa, Genoa, Italy
| | - Nicholas Chiorazzi
- Karches Center for Oncology Research, The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, United States
| | - Matthew D Scharff
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Thomas MacCarthy
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, United States
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27
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Weiser BP, Rodriguez G, Cole PA, Stivers JT. N-terminal domain of human uracil DNA glycosylase (hUNG2) promotes targeting to uracil sites adjacent to ssDNA-dsDNA junctions. Nucleic Acids Res 2019; 46:7169-7178. [PMID: 29917162 PMCID: PMC6101581 DOI: 10.1093/nar/gky525] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 05/24/2018] [Indexed: 01/29/2023] Open
Abstract
The N-terminal domain (NTD) of nuclear human uracil DNA glycosylase (hUNG2) assists in targeting hUNG2 to replication forks through specific interactions with replication protein A (RPA). Here, we explored hUNG2 activity in the presence and absence of RPA using substrates with ssDNA–dsDNA junctions that mimic structural features of the replication fork and transcriptional R-loops. We find that when RPA is tightly bound to the ssDNA overhang of junction DNA substrates, base excision by hUNG2 is strongly biased toward uracils located 21 bp or less from the ssDNA–dsDNA junction. In the absence of RPA, hUNG2 still showed an 8-fold excision bias for uracil located <10 bp from the junction, but only when the overhang had a 5′ end. Biased targeting required the NTD and was not observed with the hUNG2 catalytic domain alone. Consistent with this requirement, the isolated NTD was found to bind weakly to ssDNA. These findings indicate that the NTD of hUNG2 targets the enzyme to ssDNA–dsDNA junctions using RPA-dependent and RPA-independent mechanisms. This structure-based specificity may promote efficient removal of uracils that arise from dUTP incorporation during DNA replication, or additionally, uracils that arise from DNA cytidine deamination at transcriptional R-loops during immunoglobulin class-switch recombination.
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Affiliation(s)
- Brian P Weiser
- Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084, USA
| | - Gaddiel Rodriguez
- Department of Pharmacology & Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Philip A Cole
- Division of Genetics, Department of Medicine and Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - James T Stivers
- Department of Pharmacology & Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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28
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Singh GB, Byun H, Ali AF, Medina F, Wylie D, Shivram H, Nash AK, Lozano MM, Dudley JP. A Protein Antagonist of Activation-Induced Cytidine Deaminase Encoded by a Complex Mouse Retrovirus. mBio 2019; 10:e01678-19. [PMID: 31409681 PMCID: PMC6692512 DOI: 10.1128/mbio.01678-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 07/08/2019] [Indexed: 01/27/2023] Open
Abstract
Complex human-pathogenic retroviruses cause high morbidity and mortality worldwide, but resist antiviral drugs and vaccine development due to evasion of the immune response. A complex retrovirus, mouse mammary tumor virus (MMTV), requires replication in B and T lymphocytes for mammary gland transmission and is antagonized by the innate immune restriction factor murine Apobec3 (mA3). To determine whether the regulatory/accessory protein Rem affects innate responses to MMTV, a splice-donor mutant (MMTV-SD) lacking Rem expression was injected into BALB/c mice. Mammary tumors induced by MMTV-SD had a lower proviral load, lower incidence, and longer latency than mammary tumors induced by wild-type MMTV (MMTV-WT). MMTV-SD proviruses had many G-to-A mutations on the proviral plus strand, but also C-to-T transitions within WRC motifs. Similarly, a lymphomagenic MMTV variant lacking Rem expression showed decreased proviral loads and increased WRC motif mutations relative to those in wild-type-virus-induced tumors, consistent with activation-induced cytidine deaminase (AID) mutagenesis in lymphoid cells. These mutations are typical of the Apobec family member AID, a B-cell-specific mutagenic protein involved in antibody variable region hypermutation. In contrast, mutations in WRC motifs and proviral loads were similar in MMTV-WT and MMTV-SD proviruses from tumors in AID-insufficient mice. AID was not packaged in MMTV virions. Rem coexpression in transfection experiments led to AID proteasomal degradation. Our data suggest that rem specifies a human-pathogenic immunodeficiency virus type 1 (HIV-1) Vif-like protein that inhibits AID and antagonizes innate immunity during MMTV replication in lymphocytes.IMPORTANCE Complex retroviruses, such as human-pathogenic immunodeficiency virus type 1 (HIV-1), cause many human deaths. These retroviruses produce lifelong infections through viral proteins that interfere with host immunity. The complex retrovirus mouse mammary tumor virus (MMTV) allows for studies of host-pathogen interactions not possible in humans. A mutation preventing expression of the MMTV Rem protein in two different MMTV strains decreased proviral loads in tumors and increased viral genome mutations typical of an evolutionarily ancient enzyme, AID. Although the presence of AID generally improves antibody-based immunity, it may contribute to human cancer progression. We observed that coexpression of MMTV Rem and AID led to AID destruction. Our results suggest that Rem is the first known protein inhibitor of AID and that further experiments could lead to new disease treatments.
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Affiliation(s)
- Gurvani B Singh
- Dept. of Molecular Biosciences, LaMontagne Center for Infectious Disease, and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Hyewon Byun
- Dept. of Molecular Biosciences, LaMontagne Center for Infectious Disease, and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Almas F Ali
- Dept. of Molecular Biosciences, LaMontagne Center for Infectious Disease, and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Frank Medina
- Dept. of Molecular Biosciences, LaMontagne Center for Infectious Disease, and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Dennis Wylie
- Computational Biology and Bioinformatics and Center for Biomedical Research Support, The University of Texas at Austin, Austin, Texas, USA
| | - Haridha Shivram
- Dept. of Molecular Biosciences, LaMontagne Center for Infectious Disease, and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Andrea K Nash
- Dept. of Molecular Biosciences, LaMontagne Center for Infectious Disease, and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Mary M Lozano
- Dept. of Molecular Biosciences, LaMontagne Center for Infectious Disease, and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Jaquelin P Dudley
- Dept. of Molecular Biosciences, LaMontagne Center for Infectious Disease, and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA
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29
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AID, APOBEC3A and APOBEC3B efficiently deaminate deoxycytidines neighboring DNA damage induced by oxidation or alkylation. Biochim Biophys Acta Gen Subj 2019; 1863:129415. [PMID: 31404619 DOI: 10.1016/j.bbagen.2019.129415] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 07/26/2019] [Accepted: 08/07/2019] [Indexed: 12/29/2022]
Abstract
BACKGROUND AID/APOBEC3 (A3) enzymes instigate genomic mutations that are involved in immunity and cancer. Although they can deaminate any deoxycytidine (dC) to deoxyuridine (dU), each family member has a signature preference determined by nucleotides surrounding the target dC. This WRC (W = A/T, R = A/G) and YC (Y = T/C) hotspot preference is established for AID and A3A/A3B, respectively. Base alkylation and oxidation are two of the most common types of DNA damage induced environmentally or by chemotherapy. Here we examined the activity of AID, A3A and A3B on dCs neighboring such damaged bases. METHODS Substrates were designed to contain target dCs either in normal WRC/YC hotspots, or in oxidized/alkylated DNA motifs. AID, A3A and A3B were purified and deamination kinetics of each were compared between substrates containing damaged vs. normal motifs. RESULTS All three enzymes efficiently deaminated dC when common damaged bases were present in the -2 or -1 positions. Strikingly, some damaged motifs supported comparable or higher catalytic efficiencies by AID, A3A and A3B than the WRC/YC motifs which are their most favored normal sequences. Based on the resolved interactions of AID, A3A and A3B with DNA, we modeled interactions with alkylated or oxidized bases. Corroborating the enzyme assay data, the surface regions that recognize normal bases are predicted to also interact robustly with oxidized and alkylated bases. CONCLUSIONS AID, A3A and A3B can efficiently recognize and deaminate dC whose neighbouring nucleotides are damaged. GENERAL SIGNIFICANCE Beyond AID/A3s initiating DNA damage, some forms of pre-existing damaged DNA can constitute favored targets of AID/A3s if encountered.
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30
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Yu K, Lieber MR. Current insights into the mechanism of mammalian immunoglobulin class switch recombination. Crit Rev Biochem Mol Biol 2019; 54:333-351. [PMID: 31509023 PMCID: PMC6856442 DOI: 10.1080/10409238.2019.1659227] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/13/2019] [Accepted: 08/20/2019] [Indexed: 12/12/2022]
Abstract
Immunoglobulin (Ig) class switch recombination (CSR) is the gene rearrangement process by which B lymphocytes change the Ig heavy chain constant region to permit a switch of Ig isotype from IgM to IgG, IgA, or IgE. At the DNA level, CSR occurs via generation and joining of DNA double strand breaks (DSBs) at intronic switch regions located just upstream of each of the heavy chain constant regions. Activation-induced deaminase (AID), a B cell specific enzyme, catalyzes cytosine deaminations (converting cytosines to uracils) as the initial DNA lesions that eventually lead to DSBs and CSR. Progress on AID structure integrates very well with knowledge about Ig class switch region nucleic acid structures that are supported by functional studies. It is an ideal time to review what is known about the mechanism of Ig CSR and its relation to somatic hypermutation. There have been many comprehensive reviews on various aspects of the CSR reaction and regulation of AID expression and activity. This review is focused on the relation between AID and switch region nucleic acid structures, with a particular emphasis on R-loops.
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Affiliation(s)
- Kefei Yu
- Michigan State University, Department of Microbiology & Molecular Genetics, 5175 Biomedical Physical Sciences, East Lansing, MI 48824
| | - Michael R. Lieber
- USC Norris Comprehensive Cancer Ctr., Departments of Pathology, of Molecular Microbiology & Immunology, of Biochemistry & Molecular Biology, and of the Section of Molecular & Computational Biology within the Department of Biological Sciences, 1441 Eastlake Ave., NTT5428, Los Angeles, CA 90089-9176
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31
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Zanotti KJ, Maul RW, Yang W, Gearhart PJ. DNA Breaks in Ig V Regions Are Predominantly Single Stranded and Are Generated by UNG and MSH6 DNA Repair Pathways. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2019; 202:1573-1581. [PMID: 30665938 PMCID: PMC6382588 DOI: 10.4049/jimmunol.1801183] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 12/16/2018] [Indexed: 11/19/2022]
Abstract
Antibody diversity is initiated by activation-induced deaminase (AID), which deaminates cytosine to uracil in DNA. Uracils in the Ig gene loci can be recognized by uracil DNA glycosylase (UNG) or mutS homologs 2 and 6 (MSH2-MSH6) proteins, and then processed into DNA breaks. Breaks in switch regions of the H chain locus cause isotype switching and have been extensively characterized as staggered and blunt double-strand breaks. However, breaks in V regions that arise during somatic hypermutation are poorly understood. In this study, we characterize AID-dependent break formation in JH introns from mouse germinal center B cells. We used a ligation-mediated PCR assay to detect single-strand breaks and double-strand breaks that were either staggered or blunt. In contrast to switch regions, V regions contained predominantly single-strand breaks, which peaked 10 d after immunization. We then examined the pathways used to generate these breaks in UNG- and MSH6-deficient mice. Surprisingly, both DNA repair pathways contributed substantially to break formation, and in the absence of both UNG and MSH6, the frequency of breaks was severely reduced. When the breaks were sequenced and mapped, they were widely distributed over a 1000-bp intron region downstream of JH3 and JH4 exons and were unexpectedly located at all 4 nt. These data suggest that during DNA repair, nicks are generated at distal sites from the original deaminated cytosine, and these repair intermediates could generate both faithful and mutagenic repair. During mutagenesis, single-strand breaks would allow entry for low-fidelity DNA polymerases to generate somatic hypermutation.
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Affiliation(s)
- Kimberly J Zanotti
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224
| | - Robert W Maul
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224
| | - William Yang
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224
| | - Patricia J Gearhart
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224
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32
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Yeap LS, Meng FL. Cis- and trans-factors affecting AID targeting and mutagenic outcomes in antibody diversification. Adv Immunol 2019; 141:51-103. [PMID: 30904133 DOI: 10.1016/bs.ai.2019.01.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Antigen receptor diversification is a hallmark of adaptive immunity which allows specificity of the receptor to particular antigen. B cell receptor (BCR) or its secreted form, antibody, is diversified through antigen-independent and antigen-dependent mechanisms. During B cell development in bone marrow, BCR is diversified via V(D)J recombination mediated by RAG endonuclease. Upon stimulation by antigen, B cell undergo somatic hypermutation (SHM) to allow affinity maturation and class switch recombination (CSR) to change the effector function of the antibody. Both SHM and CSR are initiated by activation-induced cytidine deaminase (AID). Repair of AID-initiated lesions through different DNA repair pathways results in diverse mutagenic outcomes. Here, we focus on discussing cis- and trans-factors that target AID to its substrates and factors that affect different outcomes of AID-initiated lesions. The knowledge of mechanisms that govern AID targeting and outcomes could be harnessed to elicit rare functional antibodies and develop ex vivo antibody diversification approaches with diversifying base editors.
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Affiliation(s)
- Leng-Siew Yeap
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Fei-Long Meng
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.
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33
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Jacobsen JT, Mesin L, Markoulaki S, Schiepers A, Cavazzoni CB, Bousbaine D, Jaenisch R, Victora GD. One-step generation of monoclonal B cell receptor mice capable of isotype switching and somatic hypermutation. J Exp Med 2018; 215:2686-2695. [PMID: 30181412 PMCID: PMC6170169 DOI: 10.1084/jem.20172064] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 07/05/2018] [Accepted: 08/16/2018] [Indexed: 12/11/2022] Open
Abstract
Jacobsen et al. describe a method to quickly generate mice carrying monoclonal immunoglobulins using CRISPR–Cas9-based genome editing in zygotes. Both chains are targeted in tandem into the Igh locus, allowing for isotype switching, somatic hypermutation, and affinity maturation. We developed a method for rapid generation of B cell receptor (BCR) monoclonal mice expressing prerearranged Igh and Igk chains monoallelically from the Igh locus by CRISPR-Cas9 injection into fertilized oocytes. B cells from these mice undergo somatic hypermutation (SHM), class switch recombination (CSR), and affinity-based selection in germinal centers. This method combines the practicality of BCR transgenes with the ability to study Ig SHM, CSR, and affinity maturation.
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Affiliation(s)
- Johanne T Jacobsen
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY .,Center for Immune Regulation, Oslo University Hospital, University of Oslo, Oslo, Norway
| | - Luka Mesin
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY
| | | | - Ariën Schiepers
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY
| | - Cecília B Cavazzoni
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY.,Carlos Chagas Filho Biophysics Institute, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | - Gabriel D Victora
- Laboratory of Lymphocyte Dynamics, The Rockefeller University, New York, NY
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34
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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: 33] [Impact Index Per Article: 5.5] [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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Pannunzio NR, Lieber MR. Concept of DNA Lesion Longevity and Chromosomal Translocations. Trends Biochem Sci 2018; 43:490-498. [PMID: 29735400 DOI: 10.1016/j.tibs.2018.04.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 04/07/2018] [Accepted: 04/08/2018] [Indexed: 01/11/2023]
Abstract
A subset of chromosomal translocations related to B cell malignancy in human patients arises due to DNA breaks occurring within defined 20-600 base pair (bp) zones. Several factors influence the breakage rate at these sites including transcription, DNA sequence, and topological tension. These factors favor non-B DNA structures that permit formation of transient single-stranded DNA (ssDNA), making the DNA more vulnerable to agents such as the enzyme activation-induced cytidine deaminase (AID) and reactive oxygen species (ROS). Certain DNA lesions created during the ssDNA state persist after the DNA resumes its normal duplex structure. We propose that factors favoring both formation of transient ssDNA and persistent DNA lesions are key in determining the DNA breakage mechanism.
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Affiliation(s)
- Nicholas R Pannunzio
- University of Southern California Keck School of Medicine, Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA
| | - Michael R Lieber
- University of Southern California Keck School of Medicine, Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA; Department of Pathology, Keck School of Medicine of USC, Los Angeles, CA 90033, USA; Department of Molecular Microbiology and Immunology, Keck School of Medicine of USC, Los Angeles, CA 90033, USA; Department of Biochemistry and Molecular Biology, Keck School of Medicine of USC, Los Angeles, CA 90033, USA; Section of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.
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36
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Ziegler SJ, Liu C, Landau M, Buzovetsky O, Desimmie BA, Zhao Q, Sasaki T, Burdick RC, Pathak VK, Anderson KS, Xiong Y. Insights into DNA substrate selection by APOBEC3G from structural, biochemical, and functional studies. PLoS One 2018; 13:e0195048. [PMID: 29596531 PMCID: PMC5875850 DOI: 10.1371/journal.pone.0195048] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 03/15/2018] [Indexed: 01/27/2023] Open
Abstract
Human apolipoprotein B mRNA-editing enzyme-catalytic polypeptide-like 3 (A3) proteins are a family of cytidine deaminases that catalyze the conversion of deoxycytidine (dC) to deoxyuridine (dU) in single-stranded DNA (ssDNA). A3 proteins act in the innate immune response to viral infection by mutating the viral ssDNA. One of the most well-studied human A3 family members is A3G, which is a potent inhibitor of HIV-1. Each A3 protein prefers a specific substrate sequence for catalysis-for example, A3G deaminates the third dC in the CCCA sequence motif. However, the interaction between A3G and ssDNA is difficult to characterize due to poor solution behavior of the full-length protein and loss of DNA affinity of the truncated protein. Here, we present a novel DNA-anchoring fusion strategy using the protection of telomeres protein 1 (Pot1) which has nanomolar affinity for ssDNA, with which we captured an A3G-ssDNA interaction. We crystallized a non-preferred adenine in the -1 nucleotide-binding pocket of A3G. The structure reveals a unique conformation of the catalytic site loops that sheds light onto how the enzyme scans substrate in the -1 pocket. Furthermore, our biochemistry and virology studies provide evidence that the nucleotide-binding pockets on A3G influence each other in selecting the preferred DNA substrate. Together, the results provide insights into the mechanism by which A3G selects and deaminates its preferred substrates and help define how A3 proteins are tailored to recognize specific DNA sequences. This knowledge contributes to a better understanding of the mechanism of DNA substrate selection by A3G, as well as A3G antiviral activity against HIV-1.
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Affiliation(s)
- Samantha J. Ziegler
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Chang Liu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Mark Landau
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Olga Buzovetsky
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Belete A. Desimmie
- Viral Mutation Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Qi Zhao
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Tomoaki Sasaki
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Ryan C. Burdick
- Viral Mutation Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Vinay K. Pathak
- Viral Mutation Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Karen S. Anderson
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
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Pannunzio NR, Lieber MR. AID and Reactive Oxygen Species Can Induce DNA Breaks within Human Chromosomal Translocation Fragile Zones. Mol Cell 2017; 68:901-912.e3. [PMID: 29220655 DOI: 10.1016/j.molcel.2017.11.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 10/02/2017] [Accepted: 11/10/2017] [Indexed: 01/07/2023]
Abstract
DNA double-strand breaks (DSBs) occurring within fragile zones of less than 200 base pairs account for the formation of the most common human chromosomal translocations in lymphoid malignancies, yet the mechanism of how breaks occur remains unknown. Here, we have transferred human fragile zones into S. cerevisiae in the context of a genetic assay to understand the mechanism leading to DSBs at these sites. Our findings indicate that a combination of factors is required to sensitize these regions. Foremost, DNA strand separation by transcription or increased torsional stress can expose these DNA regions to damage from either the expression of human AID or increased oxidative stress. This damage causes DNA lesions that, if not repaired quickly, are prone to nuclease cleavage, resulting in DSBs. Our results provide mechanistic insight into why human neoplastic translocation fragile DNA sequences are more prone to enzymes or agents that cause longer-lived DNA lesions.
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Affiliation(s)
- Nicholas R Pannunzio
- USC Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, 1441 Eastlake Avenue, Rm. 5428, Los Angeles, CA 90089, USA
| | - Michael R Lieber
- USC Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, 1441 Eastlake Avenue, Rm. 5428, Los Angeles, CA 90089, USA.
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Abdouni HS, King JJ, Ghorbani A, Fifield H, Berghuis L, Larijani M. DNA/RNA hybrid substrates modulate the catalytic activity of purified AID. Mol Immunol 2017; 93:94-106. [PMID: 29161581 DOI: 10.1016/j.molimm.2017.11.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 11/10/2017] [Accepted: 11/11/2017] [Indexed: 11/28/2022]
Abstract
Activation-induced cytidine deaminase (AID) converts cytidine to uridine at Immunoglobulin (Ig) loci, initiating somatic hypermutation and class switching of antibodies. In vitro, AID acts on single stranded DNA (ssDNA), but neither double-stranded DNA (dsDNA) oligonucleotides nor RNA, and it is believed that transcription is the in vivo generator of ssDNA targeted by AID. It is also known that the Ig loci, particularly the switch (S) regions targeted by AID are rich in transcription-generated DNA/RNA hybrids. Here, we examined the binding and catalytic behavior of purified AID on DNA/RNA hybrid substrates bearing either random sequences or GC-rich sequences simulating Ig S regions. If substrates were made up of a random sequence, AID preferred substrates composed entirely of DNA over DNA/RNA hybrids. In contrast, if substrates were composed of S region sequences, AID preferred to mutate DNA/RNA hybrids over substrates composed entirely of DNA. Accordingly, AID exhibited a significantly higher affinity for binding DNA/RNA hybrid substrates composed specifically of S region sequences, than any other substrates composed of DNA. Thus, in the absence of any other cellular processes or factors, AID itself favors binding and mutating DNA/RNA hybrids composed of S region sequences. AID:DNA/RNA complex formation and supporting mutational analyses suggest that recognition of DNA/RNA hybrids is an inherent structural property of AID.
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Affiliation(s)
- Hala S Abdouni
- Program in immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, A1 B 3V6, Canada
| | - Justin J King
- Program in immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, A1 B 3V6, Canada
| | - Atefeh Ghorbani
- Program in immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, A1 B 3V6, Canada
| | - Heather Fifield
- Program in immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, A1 B 3V6, Canada
| | - Lesley Berghuis
- Program in immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, A1 B 3V6, Canada
| | - Mani Larijani
- Program in immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, A1 B 3V6, Canada.
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Chan SK, Rahumatullah A, Lai JY, Lim TS. Naïve Human Antibody Libraries for Infectious Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1053:35-59. [PMID: 29549634 PMCID: PMC7120739 DOI: 10.1007/978-3-319-72077-7_3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Many countries are facing an uphill battle in combating the spread of infectious diseases. The constant evolution of microorganisms magnifies the problem as it facilitates the re-emergence of old infectious diseases as well as promote the introduction of new and more deadly variants. Evidently, infectious diseases have contributed to an alarming rate of mortality worldwide making it a growing concern. Historically, antibodies have been used successfully to prevent and treat infectious diseases since the nineteenth century using antisera collected from immunized animals. The inherent ability of antibodies to trigger effector mechanisms aids the immune system to fight off pathogens that invades the host. Immune libraries have always been an important source of antibodies for infectious diseases due to the skewed repertoire generated post infection. Even so, the role and ability of naïve antibody libraries should not be underestimated. The naïve repertoire has its own unique advantages in generating antibodies against target antigens. This chapter will highlight the concept, advantages and application of human naïve libraries as a source to isolate antibodies against infectious disease target antigens.
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Affiliation(s)
- Soo Khim Chan
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Minden, Penang, Malaysia
| | - Anizah Rahumatullah
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Minden, Penang, Malaysia
| | - Jing Yi Lai
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Minden, Penang, Malaysia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Minden, Penang, Malaysia.
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Minden, 11800, Penang, Malaysia.
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40
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Hess GT, Frésard L, Han K, Lee CH, Li A, Cimprich KA, Montgomery SB, Bassik MC. Directed evolution using dCas9-targeted somatic hypermutation in mammalian cells. Nat Methods 2016; 13:1036-1042. [PMID: 27798611 PMCID: PMC5557288 DOI: 10.1038/nmeth.4038] [Citation(s) in RCA: 328] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 09/27/2016] [Indexed: 12/23/2022]
Abstract
Engineering and study of protein function by directed evolution has been limited by the technical requirement to use global mutagenesis or introduce DNA libraries. Here, we develop CRISPR-X, a strategy to repurpose the somatic hypermutation machinery for protein engineering in situ. Using catalytically inactive dCas9 to recruit variants of cytidine deaminase (AID) with MS2-modified sgRNAs, we can specifically mutagenize endogenous targets with limited off-target damage. This generates diverse libraries of localized point mutations and can target multiple genomic locations simultaneously. We mutagenize GFP and select for spectrum-shifted variants, including EGFP. Additionally, we mutate the target of the cancer therapeutic bortezomib, PSMB5, and identify known and novel mutations that confer bortezomib resistance. Finally, using a hyperactive AID variant, we mutagenize loci both upstream and downstream of transcriptional start sites. These experiments illustrate a powerful approach to create complex libraries of genetic variants in native context, which is broadly applicable to investigate and improve protein function.
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Affiliation(s)
- Gaelen T Hess
- Department of Genetics, Stanford University, Stanford, California, USA
| | - Laure Frésard
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Kyuho Han
- Department of Genetics, Stanford University, Stanford, California, USA
| | - Cameron H Lee
- Department of Genetics, Stanford University, Stanford, California, USA
| | - Amy Li
- Department of Genetics, Stanford University, Stanford, California, USA
| | - Karlene A Cimprich
- Department of Chemical and Systems Biology, Stanford University, Stanford, California, USA
| | - Stephen B Montgomery
- Department of Genetics, Stanford University, Stanford, California, USA
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Michael C Bassik
- Department of Genetics, Stanford University, Stanford, California, USA
- Stanford University Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford, California, USA
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41
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Kim A, Han L, Santiago GE, Verdun RE, Yu K. Class-Switch Recombination in the Absence of the IgH 3' Regulatory Region. THE JOURNAL OF IMMUNOLOGY 2016; 197:2930-5. [PMID: 27559052 DOI: 10.4049/jimmunol.1600530] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 07/25/2016] [Indexed: 01/09/2023]
Abstract
The ∼28-kb 3' regulatory region (3'RR), which is located at the most distal 3' region of the Ig H chain locus, has multiple regulatory functions that control IgH expression, class-switch recombination (CSR), and somatic hypermutation. In this article, we report that deletion of the entire 3'RR in a mouse B cell line that is capable of robust cytokine-dependent CSR to IgA results in reduced, but not abolished, CSR. These data suggest that 3'RR is not absolutely required for CSR and, thus, is not essential for targeting activation-induced cytidine deaminase to S regions, as was suggested. Moreover, replacing 3'RR with a DNA fragment including only its four DNase I hypersensitive sites (lacking the large spacer regions) restores CSR to a level equivalent to or even higher than in wild-type cells, suggesting that the four hypersensitive sites contain most of the CSR-promoting functions of 3'RR. Stimulated cells express abundant germline transcripts, with the presence or absence of 3'RR, providing evidence that 3'RR has a role in promoting CSR that is unique from enhancing S region transcription.
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Affiliation(s)
- Ahrom Kim
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824
| | - Li Han
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824
| | - Gabriel E Santiago
- Department of Medicine, Division of Hematology-Oncology, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33136; and
| | - Ramiro E Verdun
- Department of Medicine, Division of Hematology-Oncology, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33136; and Geriatric Research, Education, and Clinical Center, Miami Veterans Affairs Healthcare System, Miami, FL 33125
| | - Kefei Yu
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824;
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Abstract
Analysis of chromosomal translocation sequence locations in human lymphomas has provided valuable clues about the mechanism of the translocations and when they occur. Biochemical analyses on the mechanisms of DNA breakage and rejoining permit formulation of detailed models of the human chromosomal translocation process in lymphoid neoplasms. Most human lymphomas are derived from B cells in which a DNA break at an oncogene is initiated by activation-induced deaminase (AID). The partner locus in many cases is located at one of the antigen receptor loci, and this break is generated by the recombination activating gene (RAG) complex or by AID. After breakage, the joining process typically occurs by non-homologous DNA end-joining (NHEJ). Some of the insights into this mechanism also apply to translocations that occur in non-lymphoid neoplasms.
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Affiliation(s)
- Michael R Lieber
- USC Norris Comprehensive Cancer Center, Room 5428, University of Southern California Keck School of Medicine, 1441 Eastlake Avenue, MC9176, Los Angeles, California 90089-9176, USA
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43
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Nonaka T, Toda Y, Hiai H, Uemura M, Nakamura M, Yamamoto N, Asato R, Hattori Y, Bessho K, Minato N, Kinoshita K. Involvement of activation-induced cytidine deaminase in skin cancer development. J Clin Invest 2016; 126:1367-82. [PMID: 26974156 DOI: 10.1172/jci81522] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 02/04/2016] [Indexed: 01/30/2023] Open
Abstract
Most skin cancers develop as the result of UV light-induced DNA damage; however, a substantial number of cases appear to occur independently of UV damage. A causal link between UV-independent skin cancers and chronic inflammation has been suspected, although the precise mechanism underlying this association is unclear. Here, we have proposed that activation-induced cytidine deaminase (AID, encoded by AICDA) links chronic inflammation and skin cancer. We demonstrated that Tg mice expressing AID in the skin spontaneously developed skin squamous cell carcinoma with Hras and Trp53 mutations. Furthermore, genetic deletion of Aicda reduced tumor incidence in a murine model of chemical-induced skin carcinogenesis. AID was expressed in human primary keratinocytes in an inflammatory stimulus-dependent manner and was detectable in human skin cancers. Together, the results of this study indicate that inflammation-induced AID expression promotes skin cancer development independently of UV damage and suggest AID as a potential target for skin cancer therapeutics.
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Lu Z, Lieber MR, Tsai AG, Pardo CE, Müschen M, Kladde MP, Hsieh CL. Human lymphoid translocation fragile zones are hypomethylated and have accessible chromatin. Mol Cell Biol 2015; 35:1209-22. [PMID: 25624348 PMCID: PMC4355534 DOI: 10.1128/mcb.01085-14] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Revised: 11/26/2014] [Accepted: 01/16/2015] [Indexed: 12/19/2022] Open
Abstract
Chromosomal translocations are a hallmark of hematopoietic malignancies. CG motifs within translocation fragile zones (typically 20 to 600 bp in size) are prone to chromosomal translocation in lymphomas. Here we demonstrate that the CG motifs in human translocation fragile zones are hypomethylated relative to the adjacent DNA. Using a methyltransferase footprinting assay on isolated nuclei (in vitro), we find that the chromatin at these fragile zones is accessible. We also examined in vivo accessibility using cellular expression of a prokaryotic methylase. Based on this assay, which measures accessibility over a much longer time interval than is possible with in vitro methods, these fragile zones were found to be more accessible than the adjacent DNA. Because DNA within the fragile zones can be methylated by both cellular and exogenous methyltransferases, the fragile zones are predominantly in a duplex DNA conformation. These observations permit more-refined models for why these zones are 100- to 1,000-fold more prone to undergo chromosomal translocation than the adjacent regions.
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Affiliation(s)
- Zhengfei Lu
- USC Norris Comprehensive Cancer Ctr., Los Angeles, California, USA
| | - Michael R Lieber
- USC Norris Comprehensive Cancer Ctr., Los Angeles, California, USA
| | - Albert G Tsai
- USC Norris Comprehensive Cancer Ctr., Los Angeles, California, USA
| | - Carolina E Pardo
- Department of Biochemistry & Molecular Biology, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Markus Müschen
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Michael P Kladde
- Department of Biochemistry & Molecular Biology, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Chih-Lin Hsieh
- USC Norris Comprehensive Cancer Ctr., Los Angeles, California, USA
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Long-term arsenite exposure induces premature senescence in B cell lymphoma A20 cells. Arch Toxicol 2015; 90:793-803. [PMID: 25787150 DOI: 10.1007/s00204-015-1500-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2014] [Accepted: 03/05/2015] [Indexed: 12/29/2022]
Abstract
Chronic arsenite exposure induces immunosuppression, but the precise mechanisms remain elusive. Our previous studies demonstrated that arsenite exposure for 24 h induces G0/G1 arrest in mouse B lymphoma A20 cells and the arrest is caused through induction of cyclin-dependent kinase inhibitor p16(INK4a) followed by accumulation of an Rb family protein, p130. In this study, we further investigated the consequences of long-term arsenite exposure of A20 cells. The results demonstrated that exposure to 10 μM sodium arsenite up to 14 days induces a great increase in G0/G1 arrest, irreversible cell growth suppression, cellular morphological changes and positive staining for senescence-associated β-galactosidase. The long-term arsenite exposure also induced up-regulation of p16(INK4a) followed by robust accumulation of p130 and activation of the p53 pathway. Knockdown experiments with siRNA showed that p130 accumulation is essential for cell cycle arrest by long-term arsenite exposure. Since p16(INK4a) and the p53 pathway are known to be activated by DNA damage, we investigated the involvement of DNA damage formation by long-term arsenite exposure. We found that a variety of DNA repair-related genes were significantly down-regulated from 24 h of arsenite exposure and activation-induced cytidine deaminase was greatly up-regulated after long-term arsenite exposure. Consistent with these findings, long-term arsenite exposure increased a DNA double-strand break marker, γ-H2AX and increased mutation frequency in a Bcl6 gene region. These results revealed that long-term arsenite exposure induces premature senescence through DNA damage increase and p130 accumulation in lymphoid cells.
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46
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Overlapping hotspots in CDRs are critical sites for V region diversification. Proc Natl Acad Sci U S A 2015; 112:E728-37. [PMID: 25646473 DOI: 10.1073/pnas.1500788112] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Activation-induced deaminase (AID) mediates the somatic hypermutation (SHM) of Ig variable (V) regions that is required for the affinity maturation of the antibody response. An intensive analysis of a published database of somatic hypermutations that arose in the IGHV3-23*01 human V region expressed in vivo by human memory B cells revealed that the focus of mutations in complementary determining region (CDR)1 and CDR2 coincided with a combination of overlapping AGCT hotspots, the absence of AID cold spots, and an abundance of polymerase eta hotspots. If the overlapping hotspots in the CDR1 or CDR2 did not undergo mutation, the frequency of mutations throughout the V region was reduced. To model this result, we examined the mutation of the human IGHV3-23*01 biochemically and in the endogenous heavy chain locus of Ramos B cells. Deep sequencing revealed that IGHV3-23*01 in Ramos cells accumulates AID-induced mutations primarily in the AGCT in CDR2, which was also the most frequent site of mutation in vivo. Replacing the overlapping hotspots in CDR1 and CDR2 with neutral or cold motifs resulted in a reduction in mutations within the modified motifs and, to some degree, throughout the V region. In addition, some of the overlapping hotspots in the CDRs were at sites in which replacement mutations could change the structure of the CDR loops. Our analysis suggests that the local sequence environment of the V region, and especially of the CDR1 and CDR2, is highly evolved to recruit mutations to key residues in the CDRs of the IgV region.
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47
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Zhang ZZ, Pannunzio NR, Han L, Hsieh CL, Yu K, Lieber MR. The strength of an Ig switch region is determined by its ability to drive R loop formation and its number of WGCW sites. Cell Rep 2014; 8:557-69. [PMID: 25017067 DOI: 10.1016/j.celrep.2014.06.021] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Revised: 05/20/2014] [Accepted: 06/12/2014] [Indexed: 12/22/2022] Open
Abstract
R loops exist at the murine IgH switch regions and possibly other locations, but their functional importance is unclear. In biochemical systems, R loop initiation requires DNA sequence regions containing clusters of G nucleotides, but cellular studies have not been done. Here, we vary the G-clustering, total switch region length, and the number of target sites (WGCW sites for the activation-induced deaminase) at synthetic switch regions in a murine B cell line to determine the effect on class switch recombination (CSR). G-clusters increase CSR regardless of their immediate proximity to the WGCW sites. This increase is accompanied by an increase in R loop formation. CSR efficiency correlates better with the absolute number of WGCW sites in the switch region rather than the total switch region length or density of WGCW sites. Thus, the overall strength of the switch region depends on G-clusters, which initiate R loop formation, and on the number of WGCW sites.
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Affiliation(s)
- Zheng Z Zhang
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA; Molecular and Computational Biology Section, Department of Biological Sciences, USC Dornsife, University of Southern California, Los Angeles, CA 90033, USA; Departments of Pathology, Biochemistry & Molecular Biology, Molecular Microbiology & Immunology, and Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Nicholas R Pannunzio
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA; Molecular and Computational Biology Section, Department of Biological Sciences, USC Dornsife, University of Southern California, Los Angeles, CA 90033, USA; Departments of Pathology, Biochemistry & Molecular Biology, Molecular Microbiology & Immunology, and Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Li Han
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Chih-Lin Hsieh
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA; Molecular and Computational Biology Section, Department of Biological Sciences, USC Dornsife, University of Southern California, Los Angeles, CA 90033, USA; Departments of Pathology, Biochemistry & Molecular Biology, Molecular Microbiology & Immunology, and Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Kefei Yu
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA.
| | - Michael R Lieber
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA; Molecular and Computational Biology Section, Department of Biological Sciences, USC Dornsife, University of Southern California, Los Angeles, CA 90033, USA; Departments of Pathology, Biochemistry & Molecular Biology, Molecular Microbiology & Immunology, and Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.
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Liljavirta J, Ekman A, Knight JS, Pernthaner A, Iivanainen A, Niku M. Activation-induced cytidine deaminase (AID) is strongly expressed in the fetal bovine ileal Peyer's patch and spleen and is associated with expansion of the primary antibody repertoire in the absence of exogenous antigens. Mucosal Immunol 2013; 6:942-9. [PMID: 23299615 DOI: 10.1038/mi.2012.132] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Accepted: 11/27/2012] [Indexed: 02/04/2023]
Abstract
Due to a limited range of immunoglobulin (Ig) genes, cattle and several other domestic animals rely on postrecombinatorial amplification of the primary repertoire. We report that activation-induced cytidine deaminase (AID) is strongly expressed in the fetal bovine ileal Peyer's patch and spleen but not in fetal bone marrow. The numbers of IGHV (immunoglobulin heavy chain variable) mutations correlate with AID expression. The mutational profile in the fetuses is similar to postnatal and immunized calves, with targeting of complementarity-determining region (CDR) over framework region (FR), preference of replacement over silent mutations in CDRs but not in FRs, and targeting of the AID hotspot motif RGYW/WRCY. Statistical analysis indicates negative selection on FRs and positive selection on CDRs. Our results suggest that AID-mediated somatic hypermutation and selection take place in bovine fetuses, implying a role for AID in the diversification of the primary antibody repertoire in the absence of exogenous antigens.
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Affiliation(s)
- J Liljavirta
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
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49
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Abdouni H, King JJ, Suliman M, Quinlan M, Fifield H, Larijani M. Zebrafish AID is capable of deaminating methylated deoxycytidines. Nucleic Acids Res 2013; 41:5457-68. [PMID: 23585279 PMCID: PMC3664802 DOI: 10.1093/nar/gkt212] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Activation-induced cytidine deaminase (AID) deaminates deoxycytidine (dC) to deoxyuracil (dU) at immunoglobulin loci in B lymphocytes to mediate secondary antibody diversification. Recently, AID has been proposed to also mediate epigenetic reprogramming by demethylating methylated cytidines (mC) possibly through deamination. AID overexpression in zebrafish embryos was shown to promote genome demethylation through G:T lesions, implicating a deamination-dependent mechanism. We and others have previously shown that mC is a poor substrate for human AID. Here, we examined the ability of bony fish AID to deaminate mC. We report that zebrafish AID was unique among all orthologs in that it efficiently deaminates mC. Analysis of domain-swapped and mutant AID revealed that mC specificity is independent of the overall high-catalytic efficiency of zebrafish AID. Structural modeling with or without bound DNA suggests that efficient deamination of mC by zebrafish AID is likely not due to a larger catalytic pocket allowing for better fit of mC, but rather because of subtle differences in the flexibility of its structure.
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Affiliation(s)
- Hala Abdouni
- Program in Immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St John's, Newfoundland A1B 3V6, Canada
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50
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BCL6 breaks occur at different AID sequence motifs in Ig-BCL6 and non-Ig-BCL6 rearrangements. Blood 2013; 121:4551-4. [PMID: 23476051 DOI: 10.1182/blood-2012-10-464958] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
BCL6 translocations are common in B-cell lymphomas and frequently have chromosomal breaks in immunoglobulin heavy chain (IgH) switch regions, suggesting that they occur during class-switch recombination. We analyze 120 BCL6 translocation breakpoints clustered in a 2156-bp segment of BCL6 intron 1, including 62 breakpoints (52%) joined to IgH, 12 (10%) joined to Ig light chains, and 46 (38%) joined to non-Ig partners. The BCL6 breaks in Ig-BCL6 translocations prefer known activation-induced cytosine deaminase (AID) hotspots such as WGCW and WRC (W = A/T, R = A/G), whereas BCL6 breaks in non-Ig rearrangements occur at CpG/CGC sites in addition to WGCW. Unlike previously identified CpG breaks in pro-B/pre-B-cell translocations, the BCL6 breaks do not show evidence of recombination activating gene or terminal deoxynucleotidyl transferase activity. Both WGCW/WRC and CpG/CGC breaks at BCL6 are most likely initiated by AID in germinal center B-cells, and their differential use suggests subtle mechanistic differences between Ig-BCL6 and non-Ig-BCL6 rearrangements.
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