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Han Z, Benlagha K, Lee P, Park CS, Filatov A, Byazrova MG, Miller H, Yang L, Liu C. The function of serine/threonine-specific protein kinases in B cells. Front Immunol 2024; 15:1459527. [PMID: 39445011 PMCID: PMC11496051 DOI: 10.3389/fimmu.2024.1459527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Accepted: 09/06/2024] [Indexed: 10/25/2024] Open
Abstract
The serine/threonine-specific protein kinases (STKs) are important for cell survival, proliferation, differentiation, and apoptosis. In B cells, these kinases play indispensable roles in regulating important cellular functions. Multiple studies on human and other animal cells have shown that multiple STKs are involved in different stages of B cell development and antibody production. However, how STKs affect B cell development and function is still not completely understood. Considering that B cells are clinically important in immunity and diseases, our understanding of STKs' roles in B cells is in great need of investigation with current technologies. Investigating serine/threonine kinases will not only deepen our insight into B cell-related disorders but also facilitate the identification of more effective drug targets for conditions like lymphoma and systemic lupus erythematosus.
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Affiliation(s)
- Zhennan Han
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Kamel Benlagha
- Université de Paris, Institut de Recherche Saint-Louis, EMiLy, Paris, France
| | - Pamela Lee
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Chan-Sik Park
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Alexander Filatov
- Laboratory of Immunochemistry, National Research Center Institute of Immunology, Federal Medical Biological Agency of Russia, Moscow, Russia
| | - Maria G. Byazrova
- Laboratory of Immunochemistry, National Research Center Institute of Immunology, Federal Medical Biological Agency of Russia, Moscow, Russia
| | - Heather Miller
- Cytek Biosciences, R&D Clinical Reagents, Fremont, CA, United States
| | - Lu Yang
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Chaohong Liu
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan, Hubei, China
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2
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Hayran AB, Liabakk NB, Aas PA, Kusnierczyk A, Vågbø CB, Sarno A, Iveland TS, Chawla K, Zahn A, Di Noia JM, Slupphaug G, Kavli B. RPA guides UNG to uracil in ssDNA to facilitate antibody class switching and repair of mutagenic uracil at the replication fork. Nucleic Acids Res 2024; 52:784-800. [PMID: 38000394 PMCID: PMC10810282 DOI: 10.1093/nar/gkad1115] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 10/27/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
Activation-induced cytidine deaminase (AID) interacts with replication protein A (RPA), the major ssDNA-binding protein, to promote deamination of cytosine to uracil in transcribed immunoglobulin (Ig) genes. Uracil-DNA glycosylase (UNG) acts in concert with AID during Ig diversification. In addition, UNG preserves genome integrity by base-excision repair (BER) in the overall genome. How UNG is regulated to support both mutagenic processing and error-free repair remains unknown. UNG is expressed as two isoforms, UNG1 and UNG2, which both contain an RPA-binding helix that facilitates uracil excision from RPA-coated ssDNA. However, the impact of this interaction in antibody diversification and genome maintenance has not been investigated. Here, we generated B-cell clones with targeted mutations in the UNG RPA-binding motif, and analysed class switch recombination (CSR), mutation frequency (5' Ig Sμ), and genomic uracil in clones representing seven Ung genotypes. We show that the UNG:RPA interaction plays a crucial role in both CSR and repair of AID-induced uracil at the Ig loci. By contrast, the interaction had no significant impact on total genomic uracil levels. Thus, RPA coordinates UNG during CSR and pre-replicative repair of mutagenic uracil in ssDNA but is not essential in post-replicative and canonical BER of uracil in dsDNA.
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Affiliation(s)
- Abdul B Hayran
- Department of Clinical and Molecular Medicine, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Nina B Liabakk
- Department of Clinical and Molecular Medicine, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Per A Aas
- Department of Clinical and Molecular Medicine, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Anna Kusnierczyk
- Department of Clinical and Molecular Medicine, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
- PROMEC - Proteomics and Modomics Experimental Core Facility at NTNU and the Central Norway Regional Health Authority, NO-7491 Trondheim, Norway
| | - Cathrine B Vågbø
- Department of Clinical and Molecular Medicine, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
- PROMEC - Proteomics and Modomics Experimental Core Facility at NTNU and the Central Norway Regional Health Authority, NO-7491 Trondheim, Norway
| | - Antonio Sarno
- Department of Clinical and Molecular Medicine, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Tobias S Iveland
- Department of Clinical and Molecular Medicine, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
- Cancer Clinic, St. Olav's Hospital, Trondheim University Hospital, NO-7006 Trondheim, Norway
| | - Konika Chawla
- Department of Clinical and Molecular Medicine, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
- BioCore - Bioinformatics Core Facility at NTNU and the Central Norway Regional Health Authority, NO-7491 Trondheim, Norway
| | - Astrid Zahn
- Institut de Recherches Cliniques de Montréal, 110 Av des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Javier M Di Noia
- Institut de Recherches Cliniques de Montréal, 110 Av des Pins Ouest, Montréal, QC H2W 1R7, Canada
- Département of Médicine, Université de Montréal H3C 3J7 Montréal, Québec, Canada
| | - Geir Slupphaug
- Department of Clinical and Molecular Medicine, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
- PROMEC - Proteomics and Modomics Experimental Core Facility at NTNU and the Central Norway Regional Health Authority, NO-7491 Trondheim, Norway
- Clinic of Laboratory Medicine, St. Olav's Hospital, Trondheim University Hospital, NO-7006 Trondheim, Norway
| | - Bodil Kavli
- Department of Clinical and Molecular Medicine, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
- Clinic of Laboratory Medicine, St. Olav's Hospital, Trondheim University Hospital, NO-7006 Trondheim, Norway
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3
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Bello A, Hirth G, Voigt S, Tepper S, Jungnickel B. Mechanism and regulation of secondary immunoglobulin diversification. Cell Cycle 2023; 22:2070-2087. [PMID: 37909747 PMCID: PMC10761156 DOI: 10.1080/15384101.2023.2275397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 10/20/2023] [Indexed: 11/03/2023] Open
Abstract
Secondary immunoglobulin diversification by somatic hypermutation and class switch recombination in B cells is instrumental for an adequate adaptive humoral immune response. These genetic events may, however, also introduce aberrations into other cellular genes and thereby cause B cell malignancies. While the basic mechanism of somatic hypermutation and class switch recombination is now well understood, their regulation and in particular the mechanism of their specific targeting to immunoglobulin genes is still rather mysterious. In this review, we summarize the current knowledge on the mechanism and regulation of secondary immunoglobulin diversification and discuss known mechanisms of physiological targeting to immunoglobulin genes and mistargeting to other cellular genes. We summarize open questions in the field and provide an outlook on future research.
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Affiliation(s)
- Amanda Bello
- Institute of Biochemistry and Biophysics, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
| | - Gianna Hirth
- Institute of Biochemistry and Biophysics, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
| | - Stefanie Voigt
- Institute of Biochemistry and Biophysics, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
| | - Sandra Tepper
- Institute of Biochemistry and Biophysics, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
| | - Berit Jungnickel
- Institute of Biochemistry and Biophysics, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
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4
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Heterologous expression of hAID in E. coli leads to the production of a splice isoform of AID: hAIDδC, a mystery to be explored. Protein Expr Purif 2022; 199:106149. [PMID: 35952962 DOI: 10.1016/j.pep.2022.106149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/20/2022] [Accepted: 07/25/2022] [Indexed: 11/21/2022]
Abstract
Activation-induced cytidine deaminase (AID) is a key player that initiates antibody diversification in activated B-cell. AID mediates somatic hypermutation (SHM) and class switch recombination (CSR) via the deamination of cytosine to uracil at the Ig locus, resulting in the production of high-affinity antibodies. AID is predominantly restricted to Ig genes, whereas off-targeting of AID leads to lymphocyte-related malignancies. Interestingly, apart from FL-AID other splice isoforms of AID are highly expressed in the lymphocyte malignancies. In our study, we found that the heterologous expression of hAID-FL in E. coli cells produced two induced bands of hAID as demonstrated by SDS-PAGE and western blotting. Remarkably, peptide mapping data predicted that one band is hAID-FL and the other is its splice isoform, hAIDδE4a. To get an insight into why E. coli cells expressed hAID-FL and hAID variant, we mutated the 5' and 3' splice site of a putative intron of hAID, but it failed to produce only hAID-FL. Incidentally, hAID expressed with fusion partners also displayed two bands, and peptide mapping data strongly suggest that besides hAID-FL, the lower band showed a significant number of amino acids missing towards the C-terminal domain (named as hAIDδC). Our results are the first report to show that expression of recombinant hAID alone or irrespective of solubilization tags in E. coli cells produced hAID-FL and hAIDδC. It will be fascinating to explore the potential mechanism underlying the expression of hAIDδC from recombinant hAID plasmid in E. coli cells.
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5
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Çakan E, Gunaydin G. Activation induced cytidine deaminase: An old friend with new faces. Front Immunol 2022; 13:965312. [PMID: 36405752 PMCID: PMC9670734 DOI: 10.3389/fimmu.2022.965312] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 10/10/2022] [Indexed: 11/25/2022] Open
Abstract
Activation induced cytidine deaminase (AID) protein is a member of APOBEC family. AID converts cytidine to uracil, which is a key step for somatic hypermutation (SHM) and class switch recombination (CSR). AID also plays critical roles in B cell precursor stages, removing polyreactive B cells from immune repertoire. Since the main function of AID is inducing point mutations, dysregulation can lead to increased mutation load, translocations, disturbed genomic integrity, and lymphomagenesis. As such, expression of AID as well as its function is controlled strictly at various molecular steps. Other members of the APOBEC family also play crucial roles during carcinogenesis. Considering all these functions, AID represents a bridge, linking chronic inflammation to carcinogenesis and immune deficiencies to autoimmune manifestations.
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Affiliation(s)
- Elif Çakan
- Hacettepe University School of Medicine, Sihhiye, Ankara, Turkey
| | - Gurcan Gunaydin
- Department of Basic Oncology, Hacettepe University Cancer Institute, Sihhiye, Ankara, Turkey
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6
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Pietrobon AJ, Andrejew R, Custódio RWA, Oliveira LDM, Scholl JN, Teixeira FME, de Brito CA, Glaser T, Kazmierski J, Goffinet C, Turdo AC, Yendo T, Aoki V, Figueiró F, Battastini AM, Ulrich H, Benard G, Duarte AJDS, Sato MN. Dysfunctional purinergic signaling correlates with disease severity in COVID-19 patients. Front Immunol 2022; 13:1012027. [PMID: 36248842 PMCID: PMC9562777 DOI: 10.3389/fimmu.2022.1012027] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 09/14/2022] [Indexed: 11/30/2022] Open
Abstract
Ectonucleotidases modulate inflammatory responses by balancing extracellular ATP and adenosine (ADO) and might be involved in COVID-19 immunopathogenesis. Here, we explored the contribution of extracellular nucleotide metabolism to COVID-19 severity in mild and severe cases of the disease. We verified that the gene expression of ectonucleotidases is reduced in the whole blood of patients with COVID-19 and is negatively correlated to levels of CRP, an inflammatory marker of disease severity. In line with these findings, COVID-19 patients present higher ATP levels in plasma and reduced levels of ADO when compared to healthy controls. Cell type-specific analysis revealed higher frequencies of CD39+ T cells in severely ill patients, while CD4+ and CD8+ expressing CD73 are reduced in this same group. The frequency of B cells CD39+CD73+ is also decreased during acute COVID-19. Interestingly, B cells from COVID-19 patients showed a reduced capacity to hydrolyze ATP into ADP and ADO. Furthermore, impaired expression of ADO receptors and a compromised activation of its signaling pathway is observed in COVID-19 patients. The presence of ADO in vitro, however, suppressed inflammatory responses triggered in patients’ cells. In summary, our findings support the idea that alterations in the metabolism of extracellular purines contribute to immune dysregulation during COVID-19, possibly favoring disease severity, and suggest that ADO may be a therapeutic approach for the disease.
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Affiliation(s)
- Anna Julia Pietrobon
- Laboratory of Dermatology and Immunodeficiencies, LIM-56, Department of Dermatology, Tropical Medicine Institute of São Paulo, University of São Paulo Medical School, São Paulo, Brazil
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Roberta Andrejew
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Ricardo Wesley Alberca Custódio
- Laboratory of Dermatology and Immunodeficiencies, LIM-56, Department of Dermatology, Tropical Medicine Institute of São Paulo, University of São Paulo Medical School, São Paulo, Brazil
| | - Luana de Mendonça Oliveira
- Laboratory of Dermatology and Immunodeficiencies, LIM-56, Department of Dermatology, Tropical Medicine Institute of São Paulo, University of São Paulo Medical School, São Paulo, Brazil
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Juliete Nathali Scholl
- Department of Biochemistry, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Franciane Mouradian Emidio Teixeira
- Laboratory of Dermatology and Immunodeficiencies, LIM-56, Department of Dermatology, Tropical Medicine Institute of São Paulo, University of São Paulo Medical School, São Paulo, Brazil
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Cyro Alves de Brito
- Technical Division of Medical Biology, Immunology Center, Adolfo Lutz Institute, São Paulo, Brazil
| | - Talita Glaser
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Julia Kazmierski
- Institute of Virology, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Department and Division of Infectious and Parasitic Diseases, Berlin Institute of Health, Berlin, Germany
| | - Christine Goffinet
- Institute of Virology, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Department and Division of Infectious and Parasitic Diseases, Berlin Institute of Health, Berlin, Germany
| | - Anna Claudia Turdo
- Department and Division of Infectious and Parasitic Diseases, Hospital das Clinicas, University of São Paulo Medical School, São Paulo, Brazil
| | - Tatiana Yendo
- Laboratory of Dermatology and Immunodeficiencies, LIM-56, Department of Dermatology, Tropical Medicine Institute of São Paulo, University of São Paulo Medical School, São Paulo, Brazil
| | - Valeria Aoki
- Laboratory of Dermatology and Immunodeficiencies, LIM-56, Department of Dermatology, Tropical Medicine Institute of São Paulo, University of São Paulo Medical School, São Paulo, Brazil
| | - Fabricio Figueiró
- Department of Biochemistry, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Ana Maria Battastini
- Department of Biochemistry, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Henning Ulrich
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Gill Benard
- Laboratory of Dermatology and Immunodeficiencies, LIM-56, Department of Dermatology, Tropical Medicine Institute of São Paulo, University of São Paulo Medical School, São Paulo, Brazil
| | - Alberto Jose da Silva Duarte
- Laboratory of Dermatology and Immunodeficiencies, LIM-56, Department of Dermatology, Tropical Medicine Institute of São Paulo, University of São Paulo Medical School, São Paulo, Brazil
| | - Maria Notomi Sato
- Laboratory of Dermatology and Immunodeficiencies, LIM-56, Department of Dermatology, Tropical Medicine Institute of São Paulo, University of São Paulo Medical School, São Paulo, Brazil
- *Correspondence: Maria Notomi Sato,
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7
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Abstract
The AID/APOBEC polynucleotide cytidine deaminases have historically been classified as either DNA mutators or RNA editors based on their first identified nucleic acid substrate preference. DNA mutators can generate functional diversity at antibody genes but also cause genomic instability in cancer. RNA editors can generate informational diversity in the transcriptome of innate immune cells, and of cancer cells. Members of both classes can act as antiviral restriction factors. Recent structural work has illuminated differences and similarities between AID/APOBEC enzymes that can catalyse DNA mutation, RNA editing or both, suggesting that the strict functional classification of members of this family should be reconsidered. As many of these enzymes have been employed for targeted genome (or transcriptome) editing, a more holistic understanding will help improve the design of therapeutically relevant programmable base editors. In this Perspective, Pecori et al. provide an overview of the AID/APOBEC cytidine deaminase family, discussing key structural features, how they contribute to viral and tumour evolution and how they can be harnessed for (potentially therapeutic) base-editing purposes.
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8
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Shilova ON, Tsyba DL, Shilov ES. Mutagenic Activity of AID/APOBEC Deaminases in Antiviral Defense and Carcinogenesis. Mol Biol 2022; 56:46-58. [PMID: 35194245 PMCID: PMC8852905 DOI: 10.1134/s002689332201006x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 04/23/2021] [Accepted: 06/01/2021] [Indexed: 01/02/2023]
Abstract
Proteins of the AID/APOBEC family are capable of cytidine deamination in nucleic acids forming uracil. These enzymes are involved in mRNA editing, protection against viruses, the introduction of point mutations into DNA during somatic hypermutation, and antibody isotype switching. Since these deaminases, especially AID, are potent mutagens, their expression, activity, and specificity are regulated by several intracellular mechanisms. In this review, we discuss the mechanisms of impaired expression and activation of AID/APOBEC proteins in human tumors and their role in carcinogenesis and tumor progression. Also, the diagnostic and potential therapeutic value of increased expression of AID/APOBEC in different types of tumors is analyzed. We assume that in the case of solid tumors, increased expression of endogenous deaminases can serve as a marker of response to immunotherapy since multiple point mutations in host DNA could lead to amino acid substitutions in tumor proteins and thereby increase the frequency of neoepitopes.
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Affiliation(s)
- O. N. Shilova
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - D. L. Tsyba
- Pavlov First State Medical University, 197022 St. Petersburg, Russia
- Sirius University of Science and Technology, 354340 Sochi, Russia
| | - E. S. Shilov
- Faculty of Biology, Moscow State University, 119234 Moscow, Russia
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9
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APOBECs orchestrate genomic and epigenomic editing across health and disease. Trends Genet 2021; 37:1028-1043. [PMID: 34353635 DOI: 10.1016/j.tig.2021.07.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 07/03/2021] [Accepted: 07/05/2021] [Indexed: 12/17/2022]
Abstract
APOBEC proteins can deaminate cytosine residues in DNA and RNA. This can lead to somatic mutations, DNA breaks, RNA modifications, or DNA demethylation in a selective manner. APOBECs function in various cellular compartments and recognize different nucleic acid motifs and structures. They orchestrate a wide array of genomic and epigenomic modifications, thereby affecting various cellular functions positively or negatively, including immune editing, viral and retroelement restriction, DNA damage responses, DNA demethylation, gene expression, and tissue homeostasis. Furthermore, the cumulative increase in genomic and epigenomic editing with aging could also, at least in part, be attributed to APOBEC function. We synthesize our cumulative understanding of APOBEC activity in a unifying overview and discuss their genomic and epigenomic impact in physiological, pathological, and technological contexts.
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10
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Ghorbani A, Quinlan EM, Larijani M. Evolutionary Comparative Analyses of DNA-Editing Enzymes of the Immune System: From 5-Dimensional Description of Protein Structures to Immunological Insights and Applications to Protein Engineering. Front Immunol 2021; 12:642343. [PMID: 34135887 PMCID: PMC8201067 DOI: 10.3389/fimmu.2021.642343] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 04/06/2021] [Indexed: 01/02/2023] Open
Abstract
The immune system is unique among all biological sub-systems in its usage of DNA-editing enzymes to introduce targeted gene mutations and double-strand DNA breaks to diversify antigen receptor genes and combat viral infections. These processes, initiated by specific DNA-editing enzymes, often result in mistargeted induction of genome lesions that initiate and drive cancers. Like other molecules involved in human health and disease, the DNA-editing enzymes of the immune system have been intensively studied in humans and mice, with little attention paid (< 1% of published studies) to the same enzymes in evolutionarily distant species. Here, we present a systematic review of the literature on the characterization of one such DNA-editing enzyme, activation-induced cytidine deaminase (AID), from an evolutionary comparative perspective. The central thesis of this review is that although the evolutionary comparative approach represents a minuscule fraction of published works on this and other DNA-editing enzymes, this approach has made significant impacts across the fields of structural biology, immunology, and cancer research. Using AID as an example, we highlight the value of the evolutionary comparative approach in discoveries already made, and in the context of emerging directions in immunology and protein engineering. We introduce the concept of 5-dimensional (5D) description of protein structures, a more nuanced view of a structure that is made possible by evolutionary comparative studies. In this higher dimensional view of a protein's structure, the classical 3-dimensional (3D) structure is integrated in the context of real-time conformations and evolutionary time shifts (4th dimension) and the relevance of these dynamics to its biological function (5th dimension).
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Affiliation(s)
- Atefeh Ghorbani
- Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL, Canada
- Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, BC, Canada
| | - Emma M. Quinlan
- Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL, Canada
| | - Mani Larijani
- Program in Immunology and Infectious Diseases, Department of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL, Canada
- Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, BC, Canada
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11
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Kuhny M, Forbes LR, Çakan E, Vega-Loza A, Kostiuk V, Dinesh RK, Glauzy S, Stray-Pedersen A, Pezzi AE, Hanson IC, Vargas-Hernandez A, Xu ML, Coban-Akdemir ZH, Jhangiani SN, Muzny DM, Gibbs RA, Lupski JR, Chinn IK, Schatz DG, Orange JS, Meffre E. Disease-associated CTNNBL1 mutation impairs somatic hypermutation by decreasing nuclear AID. J Clin Invest 2021; 130:4411-4422. [PMID: 32484799 DOI: 10.1172/jci131297] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 05/13/2020] [Indexed: 01/02/2023] Open
Abstract
Patients with common variable immunodeficiency associated with autoimmune cytopenia (CVID+AIC) generate few isotype-switched B cells with severely decreased frequencies of somatic hypermutations (SHMs), but their underlying molecular defects remain poorly characterized. We identified a CVID+AIC patient who displays a rare homozygous missense M466V mutation in β-catenin-like protein 1 (CTNNBL1). Because CTNNBL1 binds activation-induced cytidine deaminase (AID) that catalyzes SHM, we tested AID interactions with the CTNNBL1 M466V variant. We found that the M466V mutation interfered with the association of CTNNBL1 with AID, resulting in decreased AID in the nuclei of patient EBV-transformed B cell lines and of CTNNBL1 466V/V Ramos B cells engineered to express only CTNNBL1 M466V using CRISPR/Cas9 technology. As a consequence, the scarce IgG+ memory B cells from the CTNNBL1 466V/V patient showed a low SHM frequency that averaged 6.7 mutations compared with about 18 mutations per clone in healthy-donor counterparts. In addition, CTNNBL1 466V/V Ramos B cells displayed a decreased incidence of SHM that was reduced by half compared with parental WT Ramos B cells, demonstrating that the CTNNBL1 M466V mutation is responsible for defective SHM induction. We conclude that CTNNBL1 plays an important role in regulating AID-dependent antibody diversification in humans.
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Affiliation(s)
- Marcel Kuhny
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Lisa R Forbes
- Section of Pediatric Allergy, Immunology, and Rheumatology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA.,William T. Shearer Texas Children's Hospital Center for Human Immunobiology, Houston, Texas, USA
| | - Elif Çakan
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Andrea Vega-Loza
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Valentyna Kostiuk
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Ravi K Dinesh
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Salomé Glauzy
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Asbjorg Stray-Pedersen
- Baylor-Hopkins Center for Mendelian Genomics, Houston, Texas, USA.,Institute of Clinical Medicine and.,Norwegian National Unit for Newborn Screening, Department of Pediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | - Ashley E Pezzi
- Department of Dermatology, Baylor College of Medicine, Houston, Texas, USA
| | - I Celine Hanson
- Section of Pediatric Allergy, Immunology, and Rheumatology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Alexander Vargas-Hernandez
- Section of Pediatric Allergy, Immunology, and Rheumatology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA.,William T. Shearer Texas Children's Hospital Center for Human Immunobiology, Houston, Texas, USA
| | - Mina LuQuing Xu
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Zeynep H Coban-Akdemir
- Baylor-Hopkins Center for Mendelian Genomics, Houston, Texas, USA.,Department of Molecular and Human Genetics and
| | - Shalini N Jhangiani
- Department of Molecular and Human Genetics and.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Donna M Muzny
- Department of Molecular and Human Genetics and.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Richard A Gibbs
- Baylor-Hopkins Center for Mendelian Genomics, Houston, Texas, USA.,Department of Molecular and Human Genetics and.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - James R Lupski
- Baylor-Hopkins Center for Mendelian Genomics, Houston, Texas, USA.,Department of Molecular and Human Genetics and.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Ivan K Chinn
- Section of Pediatric Allergy, Immunology, and Rheumatology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA.,William T. Shearer Texas Children's Hospital Center for Human Immunobiology, Houston, Texas, USA.,Baylor-Hopkins Center for Mendelian Genomics, Houston, Texas, USA
| | - David G Schatz
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Jordan S Orange
- Department of Pediatrics, College of Physicians and Surgeons of Columbia University, New York-Presbyterian Morgan Stanley Children's Hospital, New York, New York, USA
| | - Eric Meffre
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA.,Section of Rheumatology, Allergy, and Clinical Immunology, Yale University School of Medicine, New Haven, Connecticut, USA
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12
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Jaiswal A, Singh AK, Tamrakar A, Kodgire P. Unfolding the Role of Splicing Factors and RNA Debranching in AID Mediated Antibody Diversification. Int Rev Immunol 2020; 40:289-306. [PMID: 32924658 DOI: 10.1080/08830185.2020.1815725] [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] [Indexed: 10/23/2022]
Abstract
Activated B-cells diversify their antibody repertoire via somatic hypermutation (SHM) and class switch recombination (CSR). SHM is restricted to the variable region, whereas, CSR is confined to the constant region of immunoglobulin (Ig) genes. Activation-induced cytidine deaminase (AID) is a crucial player in the diversification of antibodies in the activated B-cell. AID catalyzes the deamination of cytidine (C) into uracil (U) at Ig genes. Subsequently, low fidelity repair of U:G mismatches may lead to mutations. Transcription is essential for the AID action, as it provides a transient single-strand DNA substrate. Since splicing is a co-transcriptional event, various splicing factors or regulators influence the transcription. Numerous splicing factors are known to regulate the AID targeting, function, Ig transcription, and AID splicing, which eventually influence antibody diversification processes. Splicing regulator SRSF1-3, a splicing isoform of serine arginine-rich splicing factor (SRSF1), and CTNNBL1, a spliceosome interacting factor, interact with AID and play a critical role in SHM. Likewise, a splicing regulator polypyrimidine tract binding protein-2 (PTBP2) and the debranching enzyme (DBR1) debranches primary switch transcripts which later forms G-quadruplex structures, and the S region guide RNAs direct AID to S region DNA. Moreover, AID shows several alternate splicing isoforms, like AID devoid of exon-4 (AIDΔE4) that is expressed in various pathological conditions. Interestingly, RBM5, a splicing regulator, is responsible for the skipping of AID exon 4. In this review, we discuss the role and significance of splicing factors in the AID mediated antibody diversification.
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Affiliation(s)
- Ankit Jaiswal
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| | - Amit Kumar Singh
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| | - Anubhav Tamrakar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| | - Prashant Kodgire
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
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13
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Arbab M, Shen MW, Mok B, Wilson C, Matuszek Ż, Cassa CA, Liu DR. Determinants of Base Editing Outcomes from Target Library Analysis and Machine Learning. Cell 2020; 182:463-480.e30. [PMID: 32533916 PMCID: PMC7384975 DOI: 10.1016/j.cell.2020.05.037] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 04/09/2020] [Accepted: 05/19/2020] [Indexed: 12/26/2022]
Abstract
Although base editors are widely used to install targeted point mutations, the factors that determine base editing outcomes are not well understood. We characterized sequence-activity relationships of 11 cytosine and adenine base editors (CBEs and ABEs) on 38,538 genomically integrated targets in mammalian cells and used the resulting outcomes to train BE-Hive, a machine learning model that accurately predicts base editing genotypic outcomes (R ≈ 0.9) and efficiency (R ≈ 0.7). We corrected 3,388 disease-associated SNVs with ≥90% precision, including 675 alleles with bystander nucleotides that BE-Hive correctly predicted would not be edited. We discovered determinants of previously unpredictable C-to-G, or C-to-A editing and used these discoveries to correct coding sequences of 174 pathogenic transversion SNVs with ≥90% precision. Finally, we used insights from BE-Hive to engineer novel CBE variants that modulate editing outcomes. These discoveries illuminate base editing, enable editing at previously intractable targets, and provide new base editors with improved editing capabilities.
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Affiliation(s)
- Mandana Arbab
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Max W Shen
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA; Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Beverly Mok
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Christopher Wilson
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Żaneta Matuszek
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Christopher A Cassa
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA.
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14
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Feng Y, Seija N, Di Noia JM, Martin A. AID in Antibody Diversification: There and Back Again. Trends Immunol 2020; 41:586-600. [PMID: 32434680 PMCID: PMC7183997 DOI: 10.1016/j.it.2020.04.009] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/16/2020] [Accepted: 04/20/2020] [Indexed: 01/01/2023]
Abstract
Activation-Induced cytidine Deaminase (AID) initiates affinity maturation and isotype switching by deaminating deoxycytidines within immunoglobulin genes, leading to somatic hypermutation (SHM) and class switch recombination (CSR). AID thus potentiates the humoral response to clear pathogens. Marking the 20th anniversary of the discovery of AID, we review the current understanding of AID function. We discuss AID biochemistry and how error-free forms of DNA repair are co-opted to prioritize mutagenesis over accuracy during antibody diversification. We discuss the regulation of DNA double-strand break (DSB) repair pathways during CSR. We describe genomic targeting of AID as a multilayered process involving chromatin architecture, cis- and trans-acting factors, and determining mutagenesis – distinct from AID occupancy at loci that are spared from mutation. Subverted base excision repair (BER) and mismatch repair (MMR) pathways act concertedly to generate antibody sequence diversity during SHM. In CSR, DNA DSBs are repaired by the nonhomologous end-joining pathway involving the 53BP1–Rif1–Shieldin axis, and by an alternative end-joining pathway involving HMCES (5-Hydroxymethylcytosine binding, ES-cell-specific) that binds and protects resected DSB ends. Genomic targeting of AID appears to be multilayered, with inbuilt redundancy, but robust enough to ensure that most of the genome is spared from AID activity. Cis elements and genome topology act together with trans-acting factors involved in transcription and RNA processing to determine AID activity at specific Ig regions. Other loci sharing genomic and transcriptional features with the Ig are collaterally targeted during SHM and CSR.
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Affiliation(s)
- Yuqing Feng
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Noé Seija
- Institute de Recherches Cliniques de Montréal, Montréal, QC, Canada; Molecular Biology Programs, Department of Medicine, University of Montreal, Montréal, QC, Canada
| | - Javier M Di Noia
- Institute de Recherches Cliniques de Montréal, Montréal, QC, Canada; Molecular Biology Programs, Department of Medicine, University of Montreal, Montréal, QC, Canada.
| | - Alberto Martin
- Department of Immunology, University of Toronto, Toronto, ON, Canada.
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15
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Singh AK, Tamrakar A, Jaiswal A, Kanayama N, Kodgire P. SRSF1-3, a splicing and somatic hypermutation regulator, controls transcription of IgV genes via chromatin regulators SATB2, UBN1 and histone variant H3.3. Mol Immunol 2020; 119:69-82. [DOI: 10.1016/j.molimm.2020.01.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/01/2020] [Accepted: 01/11/2020] [Indexed: 12/21/2022]
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16
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Chi X, Li Y, Qiu X. V(D)J recombination, somatic hypermutation and class switch recombination of immunoglobulins: mechanism and regulation. Immunology 2020; 160:233-247. [PMID: 32031242 DOI: 10.1111/imm.13176] [Citation(s) in RCA: 116] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 12/30/2019] [Accepted: 01/08/2020] [Indexed: 02/06/2023] Open
Abstract
Immunoglobulins emerging from B lymphocytes and capable of recognizing almost all kinds of antigens owing to the extreme diversity of their antigen-binding portions, known as variable (V) regions, play an important role in immune responses. The exons encoding the V regions are known as V (variable), D (diversity), or J (joining) genes. V, D, J segments exist as multiple copy arrays on the chromosome. The recombination of the V(D)J gene is the key mechanism to produce antibody diversity. The recombinational process, including randomly choosing a pair of V, D, J segments, introducing double-strand breaks adjacent to each segment, deleting (or inverting in some cases) the intervening DNA and ligating the segments together, is defined as V(D)J recombination, which contributes to surprising immunoglobulin diversity in vertebrate immune systems. To enhance both the ability of immunoglobulins to recognize and bind to foreign antigens and the effector capacities of the expressed antibodies, naive B cells will undergo class switching recombination (CSR) and somatic hypermutation (SHM). However, the genetics mechanisms of V(D)J recombination, CSR and SHM are not clear. In this review, we summarize the major progress in mechanism studies of immunoglobulin V(D)J gene recombination and CSR as well as SHM, and their regulatory mechanisms.
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Affiliation(s)
- Xiying Chi
- Department of Immunology, School of Basic Medical Sciences, Peking University, Beijing, China.,NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Yue Li
- Department of Immunology, School of Basic Medical Sciences, Peking University, Beijing, China.,NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Xiaoyan Qiu
- Department of Immunology, School of Basic Medical Sciences, Peking University, Beijing, China.,NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China
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17
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Choi JE, Matthews AJ, Michel G, Vuong BQ. AID Phosphorylation Regulates Mismatch Repair-Dependent Class Switch Recombination and Affinity Maturation. THE JOURNAL OF IMMUNOLOGY 2020; 204:13-22. [PMID: 31757865 DOI: 10.4049/jimmunol.1900809] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 10/25/2019] [Indexed: 01/01/2023]
Abstract
Activation-induced cytidine deaminase (AID) generates U:G mismatches in Ig genes that can be converted into untemplated mutations during somatic hypermutation or DNA double-strand breaks during class switch recombination (CSR). Null mutations in UNG and MSH2 demonstrate the complementary roles of the base excision repair (BER) and mismatch repair pathways, respectively, in CSR. Phosphorylation of AID at serine 38 was previously hypothesized to regulate BER during CSR, as the AID phosphorylation mutant, AID(S38A), cannot interact with APE1, a BER protein. Consistent with these findings, we observe a complete block in CSR in AIDS38A/S38AMSH2-/- mouse B cells that correlates with an impaired mutation frequency at 5'Sμ. Similarly, somatic hypermutation is almost negligible at the JH4 intron in AIDS38A/S38AMSH2-/- mouse B cells, and, consistent with this, NP-specific affinity maturation in AIDS38A/S38AMSH2-/- mice is not significantly elevated in response to NP-CGG immunization. Surprisingly, AIDS38A/S38AUNG-/- mouse B cells also cannot complete CSR or affinity maturation despite accumulating significant mutations in 5'Sμ as well as the JH4 intron. These data identify a novel role for phosphorylation of AID at serine 38 in mismatch repair-dependent CSR and affinity maturation.
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Affiliation(s)
- Jee Eun Choi
- The City College of New York, The City University of New York, New York, NY 10031; and
| | - Allysia J Matthews
- The City College of New York, The City University of New York, New York, NY 10031; and
| | - Genesis Michel
- The City College of New York, The City University of New York, New York, NY 10031; and
| | - Bao Q Vuong
- The Graduate Center, The City University of New York, New York, NY 10016
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18
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Protein kinase A inhibits tumor mutator APOBEC3B through phosphorylation. Sci Rep 2019; 9:8307. [PMID: 31165764 PMCID: PMC6549188 DOI: 10.1038/s41598-019-44407-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 05/14/2019] [Indexed: 12/26/2022] Open
Abstract
APOBEC3B cytidine deaminase (A3B) catalyzes cytosine into uracil in single-strand DNA and induces C-to-T mutations in genomic DNA of various types of tumors. Accumulation of APOBEC signature mutations is correlated with a worse prognosis for patients with breast cancer or multiple myeloma, suggesting that A3B activity might be a cause of the unfavorable DNA mutations and clonal evolution in these tumors. Phosphorylation of conserved threonine residues of other cytidine deaminases, activation induced deaminase (AID) and APOBEC3G, inhibits their activity. Here we show that protein kinase A (PKA) physically binds to A3B and phosphorylates Thr214. In vitro deaminase assays and foreign DNA editing assays in cells confirm that phosphomimetic A3B mutants, T214D and T214E, completely lose deaminase activity. Molecular dynamics simulation of A3B phosphorylation reveals that Thr214 phosphorylation disrupts binding between the phospho-A3B catalytic core and ssDNA. These mutants still inhibit retroviral infectivity at least partially, and also retain full anti-retrotransposition activity. These results imply that PKA-mediated phosphorylation inhibits A3B mutagenic activity without destructing its innate immune functions. Therefore, PKA activation could reduce further accumulation of mutations in A3B overexpressing tumors.
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19
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Li H, Li Q, Ma Z, Zhou Z, Fan J, Jin Y, Wu Y, Cheng F, Liang P. AID modulates carcinogenesis network via DNA demethylation in bladder urothelial cell carcinoma. Cell Death Dis 2019; 10:251. [PMID: 30874539 PMCID: PMC6420503 DOI: 10.1038/s41419-019-1472-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 11/12/2018] [Accepted: 02/18/2019] [Indexed: 12/25/2022]
Abstract
Bladder cancer is one of the most common malignant diseases in the urinary system, with poor survival after metastasis. Activation-induced cytidine deaminase (AID), a versatile enzyme involved in antibody diversification, is an oncogenic gene that induces somatic hypermutation and class-switch recombination (CSR). However, the contribution of AID-mediated DNA demethylation to bladder urothelial cell carcinoma (BUCC) remains unclear. Herein, we evaluated the impact on BUCC caused by AID and explored the gene network downstream of AID by using a proteomic approach. Lentiviral vector containing AID-specific shRNA significantly reduced AID expression in T24 and 5637 cells. Silencing AID expression remarkably inhibited tumour malignancies, including cell proliferation, invasion and migration. We used Isobaric tags for relative and absolute quantitation (iTRAQ)-based proteomics analysis technology to study the underpinning mechanism in monoclonal T24 cells, with or without AID knockdown. Among the 6452 proteins identified, 99 and 142 proteins in shAICDA-T24 cells were significantly up- or downregulated, respectively (1.2-fold change) compared with the NC-T24 control. After a pipeline of bioinformatics analyses, we identified three tumour-associated factors, namely, matrix metallopeptidase 14 (MMP14), C–X–C motif chemokine ligand 12 and wntless Wnt ligand secretion mediator, which were further confirmed in human BUCC tissues. Nonetheless, only MMP14 was sensitive to the DNA demethylation molecule 5-aza-2’-deoxycytidine (5-azadC; 5 μM), which reversed the inhibition of carcinogenesis by AID silence in T24 and 5637 cells. Overall, AID is an oncogene that mediates tumourigenesis via DNA demethylation. Our findings provide novel insights into the clinical treatment for BUCC.
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Affiliation(s)
- Haoyong Li
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, Hubei Province, China
| | - Qi Li
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, Hubei Province, China.,Department of Urology, the First Affiliated Hospital of Hainan Medical College, Haikou, Hainan Province, China
| | - Zhe Ma
- Department of Urology, the First Affiliated Hospital of Hainan Medical College, Haikou, Hainan Province, China
| | - Zhiyan Zhou
- Department of Urology, the First Affiliated Hospital of Hainan Medical College, Haikou, Hainan Province, China
| | - Jinfeng Fan
- Department of Urology, the First Affiliated Hospital of Hainan Medical College, Haikou, Hainan Province, China
| | - Yingxia Jin
- Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, Hubei Province, China
| | - Yaoxi Wu
- Department of Urology, the First Affiliated Hospital of Hainan Medical College, Haikou, Hainan Province, China
| | - Fan Cheng
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, Hubei Province, China.
| | - Peiyu Liang
- Department of Urology, the First Affiliated Hospital of Hainan Medical College, Haikou, Hainan Province, China.
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20
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Abstract
Class switch recombination (CSR) generates isotype-switched antibodies with distinct effector functions essential for mediating effective humoral immunity. CSR is catalyzed by activation-induced deaminase (AID) that initiates DNA lesions in the evolutionarily conserved switch (S) regions at the immunoglobulin heavy chain (Igh) locus. AID-initiated DNA lesions are subsequently converted into DNA double stranded breaks (DSBs) in the S regions of Igh locus, repaired by non-homologous end-joining to effect CSR in mammalian B lymphocytes. While molecular mechanisms of CSR are well characterized, it remains less well understood how upstream signaling pathways regulate AID expression and CSR. B lymphocytes express multiple receptors including the B cell antigen receptor (BCR) and co-receptors (e.g., CD40). These receptors may share common signaling pathways or may use distinct signaling elements to regulate CSR. Here, we discuss how signals emanating from different receptors positively or negatively regulate AID expression and CSR.
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Affiliation(s)
- Zhangguo Chen
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States.
| | - Jing H Wang
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States.
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21
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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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22
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Patel B, Banerjee R, Samanta M, Das S. Diversity of Immunoglobulin (Ig) Isotypes and the Role of Activation-Induced Cytidine Deaminase (AID) in Fish. Mol Biotechnol 2018; 60:435-453. [PMID: 29704159 DOI: 10.1007/s12033-018-0081-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The disparate diversity in immunoglobulin (Ig) repertoire has been a subject of fascination since the emergence of prototypic adaptive immune system in vertebrates. The carboxy terminus region of activation-induced cytidine deaminase (AID) has been well established in tetrapod lineage and is crucial for its function in class switch recombination (CSR) event of Ig diversification. The absence of CSR in the paraphyletic group of fish is probably due to changes in catalytic domain of AID and lack of cis-elements in IgH locus. Therefore, understanding the arrangement of Ig genes in IgH locus and functional facets of fish AID opens up new realms of unravelling the alternative mechanisms of isotype switching and antibody diversity. Further, the teleost AID has been recently reported to have potential of catalyzing CSR in mammalian B cells by complementing AID deficiency in them. In that context, the present review focuses on the recent advances regarding the generation of diversity in Ig repertoire in the absence of AID-regulated class switching in teleosts and the possible role of T cell-independent pathway involving B cell activating factor and a proliferation-inducing ligand in activation of CSR machinery.
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Affiliation(s)
- Bhakti Patel
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769 008, India
| | - Rajanya Banerjee
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769 008, India
| | - Mrinal Samanta
- Immunology Laboratory, Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, Odisha, 751 002, India
| | - Surajit Das
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769 008, India.
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23
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Mu Y, McBride KM. Targeting mutagenesis in B cells: Phosphorylation goes beyond AID association. Mol Cell Oncol 2018; 5:e1432259. [PMID: 30263937 PMCID: PMC6154841 DOI: 10.1080/23723556.2018.1432259] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 12/27/2017] [Accepted: 12/27/2017] [Indexed: 10/29/2022]
Abstract
The mutations induced by activation-induced cytidine deaminase (AID) trigger antibody diversification but can cause genome instability. We find that AID phosphorylation is an important determinant of "off-target" mutagenesis and identify a drug that increases this activity. These studies demonstrate how dysregulating AID phosphorylation can promote oncogenesis.
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Affiliation(s)
- Yunxiang Mu
- Department of Epigenetics and Molecular Carcinogenesis, Science Park, The University of Texas MD Anderson Cancer Center, Smithville, Texas
| | - Kevin M McBride
- Department of Epigenetics and Molecular Carcinogenesis, Science Park, The University of Texas MD Anderson Cancer Center, Smithville, Texas
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24
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Haakenson JK, Huang R, Smider VV. Diversity in the Cow Ultralong CDR H3 Antibody Repertoire. Front Immunol 2018; 9:1262. [PMID: 29915599 PMCID: PMC5994613 DOI: 10.3389/fimmu.2018.01262] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 05/18/2018] [Indexed: 01/26/2023] Open
Abstract
Typical antibodies found in humans and mice usually have short CDR H3s and generally flat binding surfaces. However, cows possess a subset of antibodies with ultralong CDR H3s that can range up to 70 amino acids and form a unique “stalk and knob” structure, with the knob protruding far out of the antibody surface, where it has the potential to bind antigens with concave epitopes. Activation-induced cytidine deaminase (AID) has a proven role in diversifying antibody repertoires in humoral immunity, and it has been found to induce somatic hypermutation in bovine immunoglobulin genes both before and after contact with antigen. Due to limited use of variable and diversity genes in the V(D)J recombination events that produce ultralong CDR H3 antibodies in cows, the diversity in the bovine ultralong antibody repertoire has been proposed to rely on AID-induced mutations targeted to the IGHD8-2 gene that encodes the entire knob region. In this review, we discuss the genetics, structures, and diversity of bovine ultralong antibodies, as well as the role of AID in creating a diverse antibody repertoire.
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Affiliation(s)
- Jeremy K Haakenson
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States
| | - Ruiqi Huang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States
| | - Vaughn V Smider
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States
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25
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Nicolas L, Cols M, Choi JE, Chaudhuri J, Vuong B. Generating and repairing genetically programmed DNA breaks during immunoglobulin class switch recombination. F1000Res 2018; 7:458. [PMID: 29744038 PMCID: PMC5904731 DOI: 10.12688/f1000research.13247.1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/09/2018] [Indexed: 01/03/2023] Open
Abstract
Adaptive immune responses require the generation of a diverse repertoire of immunoglobulins (Igs) that can recognize and neutralize a seemingly infinite number of antigens. V(D)J recombination creates the primary Ig repertoire, which subsequently is modified by somatic hypermutation (SHM) and class switch recombination (CSR). SHM promotes Ig affinity maturation whereas CSR alters the effector function of the Ig. Both SHM and CSR require activation-induced cytidine deaminase (AID) to produce dU:dG mismatches in the Ig locus that are transformed into untemplated mutations in variable coding segments during SHM or DNA double-strand breaks (DSBs) in switch regions during CSR. Within the Ig locus, DNA repair pathways are diverted from their canonical role in maintaining genomic integrity to permit AID-directed mutation and deletion of gene coding segments. Recently identified proteins, genes, and regulatory networks have provided new insights into the temporally and spatially coordinated molecular interactions that control the formation and repair of DSBs within the Ig locus. Unravelling the genetic program that allows B cells to selectively alter the Ig coding regions while protecting non-Ig genes from DNA damage advances our understanding of the molecular processes that maintain genomic integrity as well as humoral immunity.
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Affiliation(s)
- Laura Nicolas
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Montserrat Cols
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jee Eun Choi
- Department of Biology, The City College of New York and The Graduate Center of The City University of New York, New York, NY, USA
| | - Jayanta Chaudhuri
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bao Vuong
- Department of Biology, The City College of New York and The Graduate Center of The City University of New York, New York, NY, USA
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Liu X, Meng FL. Generation of Genomic Alteration from Cytidine Deamination. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1044:49-64. [DOI: 10.1007/978-981-13-0593-1_5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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27
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Tepper S, Jeschke J, Böttcher K, Schmidt A, Davari K, Müller P, Kremmer E, Hemmerich P, Pfeil I, Jungnickel B. PARP activation promotes nuclear AID accumulation in lymphoma cells. Oncotarget 2017; 7:13197-208. [PMID: 26921193 PMCID: PMC4914351 DOI: 10.18632/oncotarget.7603] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 01/12/2016] [Indexed: 12/20/2022] Open
Abstract
Activation-induced cytidine deaminase (AID) initiates immunoglobulin diversification in germinal center B cells by targeted introduction of DNA damage. As aberrant nuclear AID action contributes to the generation of B cell lymphoma, the protein's activity is tightly regulated, e.g. by nuclear/cytoplasmic shuttling and nuclear degradation. In the present study, we asked whether DNA damage may affect regulation of the AID protein. We show that exogenous DNA damage that mainly activates base excision repair leads to prevention of proteasomal degradation of AID and hence its nuclear accumulation. Inhibitor as well as knockout studies indicate that activation of poly (ADP-ribose) polymerase (PARP) by DNA damaging agents promotes both phenomena. These findings suggest that PARP inhibitors influence DNA damage dependent AID regulation, with interesting implications for the regulation of AID function and chemotherapy of lymphoma.
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Affiliation(s)
- Sandra Tepper
- Department of Cell Biology, Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine, Friedrich-Schiller University, 07745 Jena, Germany
| | - Julia Jeschke
- Department of Cell Biology, Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine, Friedrich-Schiller University, 07745 Jena, Germany.,Institute of Clinical and Molecular Biology, Helmholtz Center Munich, 81377 Munich, Germany
| | - Katrin Böttcher
- Department of Cell Biology, Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine, Friedrich-Schiller University, 07745 Jena, Germany
| | - Angelika Schmidt
- Department of Cell Biology, Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine, Friedrich-Schiller University, 07745 Jena, Germany
| | - Kathrin Davari
- Department of Cell Biology, Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine, Friedrich-Schiller University, 07745 Jena, Germany
| | - Peter Müller
- Department of Cell Biology, Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine, Friedrich-Schiller University, 07745 Jena, Germany
| | - Elisabeth Kremmer
- Institute of Molecular Immunology, Helmholtz Center Munich, 81377 Munich, Germany
| | - Peter Hemmerich
- Imaging Facility, Leibniz- Institute on Aging - Fritz Lipmann Institute, 07745 Jena, Germany
| | - Ines Pfeil
- Institute of Clinical and Molecular Biology, Helmholtz Center Munich, 81377 Munich, Germany
| | - Berit Jungnickel
- Department of Cell Biology, Institute of Biochemistry and Biophysics, Center for Molecular Biomedicine, Friedrich-Schiller University, 07745 Jena, Germany.,Institute of Clinical and Molecular Biology, Helmholtz Center Munich, 81377 Munich, Germany
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28
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Mu Y, Zelazowska MA, McBride KM. Phosphorylation promotes activation-induced cytidine deaminase activity at the Myc oncogene. J Exp Med 2017; 214:3543-3552. [PMID: 29122947 PMCID: PMC5716038 DOI: 10.1084/jem.20170468] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 08/16/2017] [Accepted: 09/26/2017] [Indexed: 12/31/2022] Open
Abstract
The molecular mechanisms that regulate AID mutator activity at off-target genes are not well characterized. Mu et al. show AID phosphorylation dynamically controls activity at Myc and other sites. Pharmacological induction of AID phosphorylation leads to increased mutations, double strand breakss and translocations. Activation-induced cytidine deaminase (AID) is a mutator enzyme that targets immunoglobulin (Ig) genes to initiate antibody somatic hypermutation (SHM) and class switch recombination (CSR). Off-target AID association also occurs, which causes oncogenic mutations and chromosome rearrangements. However, AID occupancy does not directly correlate with DNA damage, suggesting that factors beyond AID association contribute to mutation targeting. CSR and SHM are regulated by phosphorylation on AID serine38 (pS38), but the role of pS38 in off-target activity has not been evaluated. We determined that lithium, a clinically used therapeutic, induced high AID pS38 levels. Using lithium and an AID-S38 phospho mutant, we compared the role of pS38 in AID activity at the Ig switch region and off-target Myc gene. We found that deficient pS38 abated AID chromatin association and CSR but not mutation at Myc. Enhanced pS38 elevated Myc translocation and mutation frequency but not CSR or Ig switch region mutation. Thus, AID activity can be differentially targeted by phosphorylation to induce oncogenic lesions.
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Affiliation(s)
- Yunxiang Mu
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX
| | - Monika A Zelazowska
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX
| | - Kevin M McBride
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX
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29
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Choudhary M, Tamrakar A, Singh AK, Jain M, Jaiswal A, Kodgire P. AID Biology: A pathological and clinical perspective. Int Rev Immunol 2017; 37:37-56. [PMID: 28933967 DOI: 10.1080/08830185.2017.1369980] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Activation-induced cytidine deaminase (AID), primarily expressed in activated mature B lymphocytes in germinal centers, is the key factor in adaptive immune response against foreign antigens. AID is responsible for producing high-affinity and high-specificity antibodies against an infectious agent, through the physiological DNA alteration processes of antibody genes by somatic hypermutation (SHM) and class-switch recombination (CSR) and functions by deaminating deoxycytidines (dC) to deoxyuridines (dU), thereby introducing point mutations and double-stranded chromosomal breaks (DSBs). The beneficial physiological role of AID in antibody diversification is outweighed by its detrimental role in the genesis of several chronic immune diseases, under non-physiological conditions. This review offers a comprehensive and better understanding of AID biology and its pathological aspects, as well as addresses the challenges involved in AID-related cancer therapeutics, based on various recent advances and evidence available in the literature till date. In this article, we discuss ways through which our interpretation of AID biology may reflect upon novel clinical insights, which could be successfully translated into designing clinical trials and improving patient prognosis and disease management.
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Affiliation(s)
- Meenal Choudhary
- a Centre for Biosciences and Biomedical Engineering , Indian Institute of Technology Indore , Simrol , Indore , Madhya Pradesh , India
| | - Anubhav Tamrakar
- a Centre for Biosciences and Biomedical Engineering , Indian Institute of Technology Indore , Simrol , Indore , Madhya Pradesh , India
| | - Amit Kumar Singh
- a Centre for Biosciences and Biomedical Engineering , Indian Institute of Technology Indore , Simrol , Indore , Madhya Pradesh , India
| | - Monika Jain
- a Centre for Biosciences and Biomedical Engineering , Indian Institute of Technology Indore , Simrol , Indore , Madhya Pradesh , India
| | - Ankit Jaiswal
- a Centre for Biosciences and Biomedical Engineering , Indian Institute of Technology Indore , Simrol , Indore , Madhya Pradesh , India
| | - Prashant Kodgire
- a Centre for Biosciences and Biomedical Engineering , Indian Institute of Technology Indore , Simrol , Indore , Madhya Pradesh , India
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30
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Bahjat M, Guikema JEJ. The Complex Interplay between DNA Injury and Repair in Enzymatically Induced Mutagenesis and DNA Damage in B Lymphocytes. Int J Mol Sci 2017; 18:ijms18091876. [PMID: 28867784 PMCID: PMC5618525 DOI: 10.3390/ijms18091876] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 08/24/2017] [Accepted: 08/29/2017] [Indexed: 11/25/2022] Open
Abstract
Lymphocytes are endowed with unique and specialized enzymatic mutagenic properties that allow them to diversify their antigen receptors, which are crucial sensors for pathogens and mediators of adaptive immunity. During lymphocyte development, the antigen receptors expressed by B and T lymphocytes are assembled in an antigen-independent fashion by ordered variable gene segment recombinations (V(D)J recombination), which is a highly ordered and regulated process that requires the recombination activating gene products 1 & 2 (RAG1, RAG2). Upon activation by antigen, B lymphocytes undergo additional diversifications of their immunoglobulin B-cell receptors. Enzymatically induced somatic hypermutation (SHM) and immunoglobulin class switch recombination (CSR) improves the affinity for antigen and shape the effector function of the humoral immune response, respectively. The activation-induced cytidine deaminase (AID) enzyme is crucial for both SHM and CSR. These processes have evolved to both utilize as well as evade different DNA repair and DNA damage response pathways. The delicate balance between enzymatic mutagenesis and DNA repair is crucial for effective immune responses and the maintenance of genomic integrity. Not surprisingly, disturbances in this balance are at the basis of lymphoid malignancies by provoking the formation of oncogenic mutations and chromosomal aberrations. In this review, we discuss recent mechanistic insight into the regulation of RAG1/2 and AID expression and activity in lymphocytes and the complex interplay between these mutagenic enzymes and DNA repair and DNA damage response pathways, focusing on the base excision repair and mismatch repair pathways. We discuss how disturbances of this interplay induce genomic instability and contribute to oncogenesis.
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Affiliation(s)
- Mahnoush Bahjat
- Department of Pathology, Academic Medical Center, University of Amsterdam; Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam 1105 AZ, The Netherlands.
| | - Jeroen E J Guikema
- Department of Pathology, Academic Medical Center, University of Amsterdam; Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam 1105 AZ, The Netherlands.
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31
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Qiao Q, Wang L, Meng FL, Hwang JK, Alt FW, Wu H. AID Recognizes Structured DNA for Class Switch Recombination. Mol Cell 2017; 67:361-373.e4. [PMID: 28757211 PMCID: PMC5771415 DOI: 10.1016/j.molcel.2017.06.034] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 05/03/2017] [Accepted: 06/27/2017] [Indexed: 12/27/2022]
Abstract
Activation-induced cytidine deaminase (AID) initiates both class switch recombination (CSR) and somatic hypermutation (SHM) in antibody diversification. Mechanisms of AID targeting and catalysis remain elusive despite its critical immunological roles and off-target effects in tumorigenesis. Here, we produced active human AID and revealed its preferred recognition and deamination of structured substrates. G-quadruplex (G4)-containing substrates mimicking the mammalian immunoglobulin switch regions are particularly good AID substrates in vitro. By solving crystal structures of maltose binding protein (MBP)-fused AID alone and in complex with deoxycytidine monophosphate, we surprisingly identify a bifurcated substrate-binding surface that explains structured substrate recognition by capturing two adjacent single-stranded overhangs simultaneously. Moreover, G4 substrates induce cooperative AID oligomerization. Structure-based mutations that disrupt bifurcated substrate recognition or oligomerization both compromise CSR in splenic B cells. Collectively, our data implicate intrinsic preference of AID for structured substrates and uncover the importance of G4 recognition and oligomerization of AID in CSR.
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Affiliation(s)
- Qi Qiao
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Li Wang
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Fei-Long Meng
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Joyce K Hwang
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Frederick W Alt
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Hao Wu
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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32
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Budzko L, Jackowiak P, Kamel K, Sarzynska J, Bujnicki JM, Figlerowicz M. Mutations in human AID differentially affect its ability to deaminate cytidine and 5-methylcytidine in ssDNA substrates in vitro. Sci Rep 2017. [PMID: 28634398 PMCID: PMC5478644 DOI: 10.1038/s41598-017-03936-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Activation-induced cytidine deaminase (AID) is known for its established role in antibody production. AID induces the diversification of antibodies by deaminating deoxycytidine (C) within immunoglobulin genes. The capacity of AID to deaminate 5-methyldeoxycytidine (5 mC) and/or 5-hydroxymethyldeoxycytidine (5 hmC), and consequently AID involvement in active DNA demethylation, is not fully resolved. For instance, structural determinants of AID activity on different substrates remain to be identified. To better understand the latter issue, we tested how mutations in human AID (hAID) influence its ability to deaminate C, 5 mC, and 5 hmC in vitro. We showed that each of the selected mutations differentially affects hAID’s ability to deaminate C and 5 mC. At the same time, we did not observe hAID activity on 5 hmC. Surprisingly, we found that the N51A hAID mutant, with no detectable activity on C, efficiently deaminated 5 mC, which may suggest different requirements for C and 5 mC deamination. Homology modeling and molecular dynamics simulations revealed that the pattern of enzyme-substrate recognition is one of the important factors determining enzyme activity on C and 5 mC. Consequently, we have proposed mechanisms that explain why wild type hAID more efficiently deaminates C than 5 mC in vitro and why 5 hmC is not deaminated.
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Affiliation(s)
- Lucyna Budzko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Paulina Jackowiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Karol Kamel
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Joanna Sarzynska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Trojdena 4, 02-109, Warsaw, Poland.,Laboratory of Bioinformatics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland. .,Institute of Computing Science, Poznan University of Technology, Piotrowo 3A, 60-965, Poznan, Poland.
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33
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Budzyńska PM, Kyläniemi MK, Kallonen T, Soikkeli AI, Nera KP, Lassila O, Alinikula J. Bach2 regulates AID-mediated immunoglobulin gene conversion and somatic hypermutation in DT40 B cells. Eur J Immunol 2017; 47:993-1001. [DOI: 10.1002/eji.201646895] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 02/09/2017] [Accepted: 03/13/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Paulina M Budzyńska
- Department of Medical Microbiology and Immunology; University of Turku; Turku Finland
- Turku Doctoral Programme of Biomedical Sciences and Turku Doctoral Programme of Molecular Medicine; University of Turku; Turku Finland
| | - Minna K Kyläniemi
- Department of Medical Microbiology and Immunology; University of Turku; Turku Finland
| | - Teemu Kallonen
- Department of Medical Microbiology and Immunology; University of Turku; Turku Finland
| | - Anni I Soikkeli
- Department of Medical Microbiology and Immunology; University of Turku; Turku Finland
| | - Kalle-Pekka Nera
- Department of Medical Microbiology and Immunology; University of Turku; Turku Finland
| | - Olli Lassila
- Department of Medical Microbiology and Immunology; University of Turku; Turku Finland
- Departament of Medical Microbiology and Immunology; Turku University Hospital; Turku Finland
| | - Jukka Alinikula
- Department of Medical Microbiology and Immunology; University of Turku; Turku Finland
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34
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King JJ, Larijani M. A Novel Regulator of Activation-Induced Cytidine Deaminase/APOBECs in Immunity and Cancer: Schrödinger's CATalytic Pocket. Front Immunol 2017; 8:351. [PMID: 28439266 PMCID: PMC5382155 DOI: 10.3389/fimmu.2017.00351] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 03/10/2017] [Indexed: 12/20/2022] Open
Abstract
Activation-induced cytidine deaminase (AID) and its relative APOBEC3 cytidine deaminases boost immune response by mutating immune or viral genes. Because of their genome-mutating activities, AID/APOBECs are also drivers of tumorigenesis. Due to highly charged surfaces, extensive non-specific protein-protein/nucleic acid interactions, formation of polydisperse oligomers, and general insolubility, structure elucidation of these proteins by X-ray crystallography and NMR has been challenging. Hence, almost all available AID/APOBEC structures are of mutated and/or truncated versions. In 2015, we reported a functional structure for AID using a combined computational-biochemical approach. In so doing, we described a new regulatory mechanism that is a first for human DNA/RNA-editing enzymes. This mechanism involves dynamic closure of the catalytic pocket. Subsequent X-ray and NMR studies confirmed our discovery by showing that other APOBEC3s also close their catalytic pockets. Here, we highlight catalytic pocket closure as an emerging and important regulatory mechanism of AID/APOBEC3s. We focus on three sub-topics: first, we propose that variable pocket closure rates across AID/APOBEC3s underlie differential activity in immunity and cancer and review supporting evidence. Second, we discuss dynamic pocket closure as an ever-present internal regulator, in contrast to other proposed regulatory mechanisms that involve extrinsic binding partners. Third, we compare the merits of classical approaches of X-ray and NMR, with that of emerging computational-biochemical approaches, for structural elucidation specifically for AID/APOBEC3s.
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Affiliation(s)
- Justin J. King
- Immunology and Infectious Diseases Program, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL, Canada
| | - Mani Larijani
- Immunology and Infectious Diseases Program, Division of Biomedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL, Canada
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35
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Methot S, Di Noia J. Molecular Mechanisms of Somatic Hypermutation and Class Switch Recombination. Adv Immunol 2017; 133:37-87. [DOI: 10.1016/bs.ai.2016.11.002] [Citation(s) in RCA: 165] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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36
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Abstract
Apolipoprotein B mRNA Editing Catalytic Polypeptide-like 1 or APOBEC1 was discovered in 1993 as the zinc-dependent cytidine deaminase responsible for the production of an in frame stop codon in apoB mRNA through modification of cytidine at nucleotide position 6666 to uridine. At the time of this discovery there was much speculation concerning the mechanism of base modification RNA editing which has been rekindled by the discovery of multiple C to U RNA editing events in the 3′ UTRs of mRNAs and the finding that other members of the APOBEC family while able to bind RNA, have the biological function of being DNA mutating enzymes. Current research is addressing the mechanism for these nucleotide modification events that appear not to adhere to the mooring sequence-dependent model for APOBEC1 involving the assembly of a multi protein containing editosome. This review will summarize our current understanding of the structure and function of APOBEC proteins and examine how RNA binding to them may be a regulatory mechanism.
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Affiliation(s)
- Harold C Smith
- a University of Rochester, School of Medicine and Dentistry , Department of Biochemistry and Biophysics , Rochester , NY , USA
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37
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Abbott RK, Thayer M, Labuda J, Silva M, Philbrook P, Cain DW, Kojima H, Hatfield S, Sethumadhavan S, Ohta A, Reinherz EL, Kelsoe G, Sitkovsky M. Germinal Center Hypoxia Potentiates Immunoglobulin Class Switch Recombination. THE JOURNAL OF IMMUNOLOGY 2016; 197:4014-4020. [PMID: 27798169 DOI: 10.4049/jimmunol.1601401] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 09/16/2016] [Indexed: 11/19/2022]
Abstract
Germinal centers (GCs) are anatomic sites where B cells undergo secondary diversification to produce high-affinity, class-switched Abs. We hypothesized that proliferating B cells in GCs create a hypoxic microenvironment that governs their further differentiation. Using molecular markers, we found GCs to be predominantly hypoxic. Compared to normoxia (21% O2), hypoxic culture conditions (1% O2) in vitro accelerated class switching and plasma cell formation and enhanced expression of GL-7 on B and CD4+ T cells. Reversal of GC hypoxia in vivo by breathing 60% O2 during immunization resulted in reduced frequencies of GC B cells, T follicular helper cells, and plasmacytes, as well as lower expression of ICOS on T follicular helper cells. Importantly, this reversal of GC hypoxia decreased Ag-specific serum IgG1 and reduced the frequency of IgG1+ B cells within the Ag-specific GC. Taken together, these observations reveal a critical role for hypoxia in GC B cell differentiation.
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Affiliation(s)
- Robert K Abbott
- New England Inflammation and Tissue Protection Institute, Northeastern University, Boston, MA 02115;
| | - Molly Thayer
- New England Inflammation and Tissue Protection Institute, Northeastern University, Boston, MA 02115
| | - Jasmine Labuda
- New England Inflammation and Tissue Protection Institute, Northeastern University, Boston, MA 02115
| | - Murillo Silva
- New England Inflammation and Tissue Protection Institute, Northeastern University, Boston, MA 02115
| | - Phaethon Philbrook
- New England Inflammation and Tissue Protection Institute, Northeastern University, Boston, MA 02115
| | - Derek W Cain
- Department of Immunology and Human Vaccine Institute, Duke University, Durham, NC 27710
| | - Hidefumi Kojima
- Department of Immunology, Dokkyo Medical University School of Medicine, Tochigi 321-0293, Japan; and
| | - Stephen Hatfield
- New England Inflammation and Tissue Protection Institute, Northeastern University, Boston, MA 02115
| | - Shalini Sethumadhavan
- New England Inflammation and Tissue Protection Institute, Northeastern University, Boston, MA 02115
| | - Akio Ohta
- New England Inflammation and Tissue Protection Institute, Northeastern University, Boston, MA 02115
| | - Ellis L Reinherz
- Laboratory of Immunobiology, Department of Medical Oncology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA 02115
| | - Garnett Kelsoe
- Department of Immunology and Human Vaccine Institute, Duke University, Durham, NC 27710
| | - Michail Sitkovsky
- New England Inflammation and Tissue Protection Institute, Northeastern University, Boston, MA 02115
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38
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Related Mechanisms of Antibody Somatic Hypermutation and Class Switch Recombination. Microbiol Spectr 2016; 3:MDNA3-0037-2014. [PMID: 26104555 DOI: 10.1128/microbiolspec.mdna3-0037-2014] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The primary antibody repertoire is generated by mechanisms involving the assembly of the exons that encode the antigen-binding variable regions of immunoglobulin heavy (IgH) and light (IgL) chains during the early development of B lymphocytes. After antigen-dependent activation, mature B lymphocytes can further alter their IgH and IgL variable region exons by the process of somatic hypermutation (SHM), which allows the selection of B cells in which SHMs resulted in the production of antibodies with increased antigen affinity. In addition, during antigen-dependent activation, B cells can also change the constant region of their IgH chain through a DNA double-strand-break (DSB) dependent process referred to as IgH class switch recombination (CSR), which generates B cell progeny that produce antibodies with different IgH constant region effector functions that are best suited for a elimination of a particular pathogen or in a particular setting. Both the mutations that underlie SHM and the DSBs that underlie CSR are initiated in target genes by activation-induced cytidine deaminase (AID). This review describes in depth the processes of SHM and CSR with a focus on mechanisms that direct AID cytidine deamination in activated B cells and mechanisms that promote the differential outcomes of such cytidine deamination.
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39
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Mutations, kataegis and translocations in B cells: understanding AID promiscuous activity. Nat Rev Immunol 2016; 16:164-76. [PMID: 26898111 DOI: 10.1038/nri.2016.2] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
As B cells engage in the immune response, they express activation-induced cytidine deaminase (AID) to initiate the hypermutation and recombination of immunoglobulin genes, which are crucial processes for the efficient recognition and disposal of pathogens. However, AID must be tightly controlled in B cells to minimize off-target mutations, which can drive chromosomal translocations and the development of B cell malignancies, such as lymphomas. Recent genomic and biochemical analyses have begun to unravel the mechanisms of how AID-mediated deamination is targeted outside immunoglobulin genes. Here, we discuss the transcriptional and topological features that are emerging as key drivers of AID promiscuous activity.
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Hara Y, Tashiro Y, Murakami A, Nishimura M, Shimizu T, Kubo M, Burrows PD, Azuma T. High affinity IgM(+) memory B cells are generated through a germinal center-dependent pathway. Mol Immunol 2015; 68:617-27. [PMID: 26514429 DOI: 10.1016/j.molimm.2015.10.003] [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: 07/09/2015] [Revised: 09/30/2015] [Accepted: 10/08/2015] [Indexed: 12/19/2022]
Abstract
During a T cell-dependent immune response, B cells undergo clonal expansion and selection and the induction of isotype switching and somatic hypermutation (SHM). Although somatically mutated IgM(+) memory B cells have been reported, it has not been established whether they are really high affinity B cells. We tracked (4-hydroxy-3-nitrophenyl) acetyl hapten-specific GC B cells from normal immunized mice based on affinity of their B cell receptor (BCR) and performed BCR sequence analysis. SHM was evident by day 7 postimmunization and increased with time, such that high affinity IgM(+) as well as IgG(+) memory B cells continued to be generated up to day 42. In contrast, class-switch recombination (CSR) was almost completed by day 7 and then the ratio of IgG1(+)/IgM(+) GC B cells remained unchanged. Together these findings suggest that IgM(+) B cells undergo SHM in the GC to generate high affinity IgM(+) memory cells and that this process continues even after CSR is accomplished.
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Affiliation(s)
- Yasushi Hara
- Laboratory for Structural Immunology, Research Institute for Biomedical Sciences, Tokyo University of Science, 2669 Yamazaki, Noda, Chiba 278-0022, Japan
| | - Yasuyuki Tashiro
- Laboratory for Structural Immunology, Research Institute for Biomedical Sciences, Tokyo University of Science, 2669 Yamazaki, Noda, Chiba 278-0022, Japan; Division of Development and Aging, Research Institute for Biomedical Sciences, Tokyo University of Science, 2669 Yamazaki, Noda, Chiba 278-0022, Japan
| | - Akikazu Murakami
- Laboratory for Structural Immunology, Research Institute for Biomedical Sciences, Tokyo University of Science, 2669 Yamazaki, Noda, Chiba 278-0022, Japan
| | - Miyuki Nishimura
- Laboratory for Structural Immunology, Research Institute for Biomedical Sciences, Tokyo University of Science, 2669 Yamazaki, Noda, Chiba 278-0022, Japan
| | - Takeyuki Shimizu
- Department of Immunology, Kochi Medical School, Kochi University, Oko-cho Kohasu, Nankoku, Kochi 783-8505, Japan
| | - Masato Kubo
- Division of Molecular Pathology, Research Institute for Biomedical Sciences, Tokyo University of Science, 2669 Yamazaki, Noda, Chiba 278-0022, Japan; Laboratory for Cytokine Regulation, Riken Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Peter D Burrows
- Department of Microbiology, University of Alabama at Birmingham, UAB 406 SHEL, 1530 Third Avenue South, Birmingham, AL 35294, USA; Department of Genetics, University of Alabama at Birmingham, UAB 406 SHEL, 1530 Third Avenue South, Birmingham, AL 35294, USA
| | - Takachika Azuma
- Laboratory for Structural Immunology, Research Institute for Biomedical Sciences, Tokyo University of Science, 2669 Yamazaki, Noda, Chiba 278-0022, Japan; Antibody Technology Research Center, Co., Ltd., 2361-1-S401 Yamazaki, Noda, Chiba 278-0022, Japan.
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Le Q, Maizels N. Cell Cycle Regulates Nuclear Stability of AID and Determines the Cellular Response to AID. PLoS Genet 2015; 11:e1005411. [PMID: 26355458 PMCID: PMC4565580 DOI: 10.1371/journal.pgen.1005411] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 07/02/2015] [Indexed: 12/12/2022] Open
Abstract
AID (Activation Induced Deaminase) deaminates cytosines in DNA to initiate immunoglobulin gene diversification and to reprogram CpG methylation in early development. AID is potentially highly mutagenic, and it causes genomic instability evident as translocations in B cell malignancies. Here we show that AID is cell cycle regulated. By high content screening microscopy, we demonstrate that AID undergoes nuclear degradation more slowly in G1 phase than in S or G2-M phase, and that mutations that affect regulatory phosphorylation or catalytic activity can alter AID stability and abundance. We directly test the role of cell cycle regulation by fusing AID to tags that destabilize nuclear protein outside of G1 or S-G2/M phases. We show that enforced nuclear localization of AID in G1 phase accelerates somatic hypermutation and class switch recombination, and is well-tolerated; while nuclear AID compromises viability in S-G2/M phase cells. We identify AID derivatives that accelerate somatic hypermutation with minimal impact on viability, which will be useful tools for engineering genes and proteins by iterative mutagenesis and selection. Our results further suggest that use of cell cycle tags to regulate nuclear stability may be generally applicable to studying DNA repair and to engineering the genome.
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Affiliation(s)
- Quy Le
- Molecular and Cellular Biology Graduate Program, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Nancy Maizels
- Molecular and Cellular Biology Graduate Program, University of Washington School of Medicine, Seattle, Washington, United States of America
- Departments of Immunology, Biochemistry and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
- * E-mail:
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Frasca D, Diaz A, Romero M, Ferracci F, Blomberg BB. MicroRNAs miR-155 and miR-16 Decrease AID and E47 in B Cells from Elderly Individuals. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2015; 195. [PMID: 26223652 PMCID: PMC4546853 DOI: 10.4049/jimmunol.1500520] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Our research in the past few years has identified B cell-specific biomarkers able to predict optimal Ab responses in both young and elderly individuals. These biomarkers are activation-induced cytidine deaminase (AID), the enzyme of class switch recombination and somatic hypermutation; the transcription factor E47, crucial for AID expression; and the ability to generate optimal memory B cells. Moreover, we have found that the increased proinflammatory status of the elderly, both in sera and intrinsic to B cells, negatively impacts B cell function. We have now investigated whether particular inflammatory microRNAs (miRs) contribute to decreased E47 and AID in aged B cells. Our data indicate that E47 and AID mRNA stability is lower in stimulated B cells from elderly individuals. We measured the expression of two miRs crucial for class switch recombination, miR-155 and miR-16, in human unstimulated B cells from young and elderly individuals with the rationale that increases in these before stimulation would decrease E47/AID upon cell activation. We found these miRs and B cell-intrinsic inflammation upregulated in aged unstimulated B cells and negatively associated with AID in the same B cells after stimulation with CpG. We propose that the downregulation of AID in aged human B cells may occur through binding of miR-155 to the 3'-untranslated regions of AID mRNA and/or binding of miR-16 to the 3'-untranslated regions of E47 mRNA, as well as at the transcriptional level of less E47 for AID. Our results indicate novel molecular pathways leading to reduced B cell function with aging.
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Affiliation(s)
- Daniela Frasca
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL 33101
| | - Alain Diaz
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL 33101
| | - Maria Romero
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL 33101
| | - Franco Ferracci
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL 33101
| | - Bonnie B Blomberg
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL 33101
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Expression of activation-induced cytidine deaminase is associated with a poor prognosis of diffuse large B cell lymphoma patients treated with CHOP-based chemotherapy. J Cancer Res Clin Oncol 2015; 142:27-36. [PMID: 26077666 DOI: 10.1007/s00432-015-2001-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 06/10/2015] [Indexed: 01/22/2023]
Abstract
PURPOSE Activation-induced cytidine deaminase (AID) is involved in somatic hypermutation and class switch recombination processes in the antibody formation. The AID activity induces gene mutations and could be associated with transformation processes of B cells. Nevertheless, the relation between AID expression and the prognosis of B cell lymphoma patients remains uncharacterized. METHODS We examined expression levels of the AID gene in 89 lymph node specimens from lymphoma and non-lymphoma patients with Northern blot analysis and investigated an association with their survival. RESULTS The AID gene was preferentially expressed in B cell lymphoma in particular in diffuse large B cell lymphoma and follicular lymphoma. We confirmed AID protein expression in the mRNA-positive but not in the negative specimens with Western blot analysis and immunohistochemical staining. Survival of the patients treated with cyclophosphamide-/doxorubicin-/vincristine-/prednisone-based chemotherapy demonstrated that the prognosis of diffuse large B cell patients was unfavorable in the mRNA-positive group compared with the negative group, and that AID expression levels were correlated with the poor prognosis. In contrast, AID expression was not linked with the prognosis of follicular lymphoma patients. CONCLUSIONS AID expression is a predictive marker for an unfavorable outcome in DLBCL patients treated with the chemotherapy.
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Parp3 negatively regulates immunoglobulin class switch recombination. PLoS Genet 2015; 11:e1005240. [PMID: 26000965 PMCID: PMC4441492 DOI: 10.1371/journal.pgen.1005240] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 04/26/2015] [Indexed: 12/11/2022] Open
Abstract
To generate highly specific and adapted immune responses, B cells diversify their antibody repertoire through mechanisms involving the generation of programmed DNA damage. Somatic hypermutation (SHM) and class switch recombination (CSR) are initiated by the recruitment of activation-induced cytidine deaminase (AID) to immunoglobulin loci and by the subsequent generation of DNA lesions, which are differentially processed to mutations during SHM or to double-stranded DNA break intermediates during CSR. The latter activate the DNA damage response and mobilize multiple DNA repair factors, including Parp1 and Parp2, to promote DNA repair and long-range recombination. We examined the contribution of Parp3 in CSR and SHM. We find that deficiency in Parp3 results in enhanced CSR, while SHM remains unaffected. Mechanistically, this is due to increased occupancy of AID at the donor (Sμ) switch region. We also find evidence of increased levels of DNA damage at switch region junctions and a bias towards alternative end joining in the absence of Parp3. We propose that Parp3 plays a CSR-specific role by controlling AID levels at switch regions during CSR. During infections, B cells diversify the antibodies they produce by two mechanisms: somatic hypermutation (SHM) and class switch recombination (CSR). SHM mutates the regions encoding the antigen-binding site, generating high-affinity antibodies. CSR allows B cells to switch the class of antibody they produce (from IgM to IgA, IgG or IgE), providing novel effector functions. Together, SHM and CSR establish highly specific and pathogen-adapted antibody responses. SHM and CSR are initiated by the recruitment of the activation-induced cytidine deaminase (AID) enzyme to antibody genes. Once recruited, AID induces DNA lesions that are processed into mutations during SHM or chromosomal DNA breaks during CSR. These breaks activate multiple DNA repair proteins and are resolved by replacing the IgM gene segments by those encoding IgA, IgG or IgE. AID carries a significant oncogenic potential that needs to be controlled to preserve genome integrity. Nevertheless, the underlying mechanisms remain poorly understood. Here we show that Poly(ADP)ribose polymerase 3 (Parp3), an enzyme recently implicated in DNA repair, contributes to antibody diversification by negatively regulating CSR without affecting SHM. We show that Parp3 facilitates the repair of AID-induced DNA damage and controls AID levels on chromatin. We propose that Parp3 protects antibody genes from sustained AID-dependent DNA damage.
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Rebhandl S, Huemer M, Greil R, Geisberger R. AID/APOBEC deaminases and cancer. Oncoscience 2015; 2:320-33. [PMID: 26097867 PMCID: PMC4468319 DOI: 10.18632/oncoscience.155] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 04/01/2015] [Indexed: 02/06/2023] Open
Abstract
Mutations are the basis for evolution and the development of genetic diseases. Especially in cancer, somatic mutations in oncogenes and tumor suppressor genes alongside the occurrence of passenger mutations have been observed by recent deep-sequencing approaches. While mutations have long been considered random events induced by DNA-replication errors or by DNA damaging agents, genome sequencing led to the discovery of non-random mutation signatures in many human cancer. Common non-random mutations comprise DNA strand-biased mutation showers and mutations restricted to certain DNA motifs, which recently have become attributed to the activity of the AID/APOBEC family of DNA deaminases. Hence, APOBEC enzymes, which have evolved as key players in natural and adaptive immunity, have been proposed to contribute to cancer development and clonal evolution of cancer by inducing collateral genomic damage due to their DNA deaminating activity. This review focuses on how mutagenic events through AID/APOBEC deaminases may contribute to cancer development.
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Affiliation(s)
- Stefan Rebhandl
- Department of internal Medicine III with Hematology, Medical Oncology, Hemostaseology, Infectious Diseases, Rheumatology, Oncologic Center, Laboratory for Immunological and Molecular Cancer Research, Paracelsus Medical University Salzburg, Austria ; Salzburg Cancer Research Institute, Salzburg, Austria
| | - Michael Huemer
- Department of internal Medicine III with Hematology, Medical Oncology, Hemostaseology, Infectious Diseases, Rheumatology, Oncologic Center, Laboratory for Immunological and Molecular Cancer Research, Paracelsus Medical University Salzburg, Austria ; Salzburg Cancer Research Institute, Salzburg, Austria
| | - Richard Greil
- Department of internal Medicine III with Hematology, Medical Oncology, Hemostaseology, Infectious Diseases, Rheumatology, Oncologic Center, Laboratory for Immunological and Molecular Cancer Research, Paracelsus Medical University Salzburg, Austria ; Salzburg Cancer Research Institute, Salzburg, Austria
| | - Roland Geisberger
- Department of internal Medicine III with Hematology, Medical Oncology, Hemostaseology, Infectious Diseases, Rheumatology, Oncologic Center, Laboratory for Immunological and Molecular Cancer Research, Paracelsus Medical University Salzburg, Austria ; Salzburg Cancer Research Institute, Salzburg, Austria
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AID expression increased by TNF-α is associated with class switch recombination of Igα gene in cancers. Cell Mol Immunol 2015; 13:484-91. [PMID: 25849121 DOI: 10.1038/cmi.2015.26] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 02/28/2015] [Accepted: 02/28/2015] [Indexed: 12/25/2022] Open
Abstract
Recently, immunoglobulins (Igs) were unexpectedly found to be expressed in epithelial cancers. Immunoglobulin class switching or class switch recombination (CSR) is a natural biological process that alters a B cell's production of antibodies (immunoglobulins) from one class to another. However, the mechanism of CSR of Ig genes in cancer is still unknown. Here, we confirmed by detecting the hallmark of CSR that the Igα gene in cancer underwent CSR. Then we focused on activation-induced cytidine deaminase (AID), a crucial factor for initiating CSR. Further studies using tumor necrosis factor (TNF)-α stimulation and specific inhibitor of NF-κB revealed that TNF-α could increase AID expression through NF-κB signaling. Finally, we demonstrated that AID could co-localize with protein kinase A and bind to the switching (Sα) region of the Igα gene. Overexpression of AID obviously enhanced Igα heavy chain expression and its binding ability to the Sα region. These findings indicated that TNF-α-induced AID expression is involved with CSR in cancer.
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Sala C, Mattiuz G, Pietrobono S, Chicca A, Conticello SG. Splice variants of activation induced deaminase (AID) do not affect the efficiency of class switch recombination in murine CH12F3 cells. PLoS One 2015; 10:e0121719. [PMID: 25803053 PMCID: PMC4372541 DOI: 10.1371/journal.pone.0121719] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 02/18/2015] [Indexed: 12/11/2022] Open
Abstract
Activation Induced Deaminase (AID) triggers the antigen-driven antibody diversification processes through its ability to edit DNA. AID dependent DNA damage is also the cause of genetic alterations often found in mature B cell tumors. A number of splice variants of AID have been identified, for which a role in the modulation of its activity has been hypothesized. We have thus tested two of these splice variants, which we find catalytically inactive, for their ability to modulate the activity of endogenous AID in CH12F3 cells, a murine lymphoma cell line in which Class Switch Recombination (CSR) can be induced. In contrast to full-length AID, neither these splice variants or a catalytically impaired AID mutant affect the efficiency of Class Switch Recombination. Thus, while a role for these splice variants at the RNA level remains possible, it is unlikely that they exert any regulatory effect on the function of AID.
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Affiliation(s)
- Cesare Sala
- Core Research Laboratory—Istituto Toscano Tumori, Firenze, Italy
| | - Giorgio Mattiuz
- Core Research Laboratory—Istituto Toscano Tumori, Firenze, Italy
| | - Silvia Pietrobono
- Core Research Laboratory—Istituto Toscano Tumori, Firenze, Italy
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Andrea Chicca
- Core Research Laboratory—Istituto Toscano Tumori, Firenze, Italy
| | - Silvestro G. Conticello
- Core Research Laboratory—Istituto Toscano Tumori, Firenze, Italy
- Department of Oncology—Azienda Ospedaliero-Universitaria Careggi, Firenze, Italy
- * E-mail:
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He M, Cortizas EM, Verdun RE, Severinson E. Cyclin-dependent kinases regulate Ig class switching by controlling access of AID to the switch region. THE JOURNAL OF IMMUNOLOGY 2015; 194:4231-9. [PMID: 25795757 DOI: 10.4049/jimmunol.1402146] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 02/05/2015] [Indexed: 01/08/2023]
Abstract
Ig class switching requires cell proliferation and is division linked, but the detailed mechanism is unknown. By analyzing the first switching cells early in the kinetics, our analysis suggested that proliferating B cells had a very short G1 phase (<3.5 h), a total cell cycle time of ∼ 11 h, and that Ig class switching preferentially occurred in the late G1 or early S phase. Inhibition of cyclin-dependent kinases (CDKs) caused dramatic reduction of switching rate within 6 h. This was associated with less targeting of activation-induced cytidine deaminase (AID) to the Igh locus. Interestingly, ectopically expressed nuclear AID in HeLa cells was preferentially found in the early S phase. Furthermore, in CDK2 hypomorphic cells there was reduced nuclear AID accumulation. Thus, our data are compatible with the idea that division-linked Ig class switching is in part due to CDK2-regulated AID nuclear access at the G1/S border.
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Affiliation(s)
- Minghui He
- Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Elena M Cortizas
- Division of Gerontology and Geriatric Medicine, Department of Medicine, Miller School of Medicine, University of Miami, Miami, FL 33136
| | - Ramiro E Verdun
- Division of Gerontology and Geriatric Medicine, Department of Medicine, Miller School of Medicine, University of Miami, Miami, FL 33136; 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
| | - Eva Severinson
- Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden;
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Senger K, Hackney J, Payandeh J, Zarrin AA. Antibody Isotype Switching in Vertebrates. Results Probl Cell Differ 2015; 57:295-324. [PMID: 26537387 DOI: 10.1007/978-3-319-20819-0_13] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The humoral or antibody-mediated immune response in vertebrates has evolved to respond to diverse antigenic challenges in various anatomical locations. Diversification of the immunoglobulin heavy chain (IgH) constant region via isotype switching allows for remarkable plasticity in the immune response, including versatile tissue distribution, Fc receptor binding, and complement fixation. This enables antibody molecules to exert various biological functions while maintaining antigen-binding specificity. Different immunoglobulin (Ig) classes include IgM, IgD, IgG, IgE, and IgA, which exist as surface-bound and secreted forms. High-affinity autoantibodies are associated with various autoimmune diseases such as lupus and arthritis, while defects in components of isotype switching are associated with infections. A major route of infection used by a large number of pathogens is invasion of mucosal surfaces within the respiratory, digestive, or urinary tract. Most infections of this nature are initially limited by effector mechanisms such as secretory IgA antibodies. Mucosal surfaces have been proposed as a major site for the genesis of adaptive immune responses, not just in fighting infections but also in tolerating commensals and constant dietary antigens. We will discuss the evolution of isotype switching in various species and provide an overview of the function of various isotypes with a focus on IgA, which is universally important in gut homeostasis as well as pathogen clearance. Finally, we will discuss the utility of antibodies as therapeutic modalities.
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Affiliation(s)
- Kate Senger
- Department of Immunology, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Jason Hackney
- Department of Bioinformatics, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Jian Payandeh
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Ali A Zarrin
- Department of Immunology, Genentech Inc., South San Francisco, CA, 94080, USA.
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Fairfax KA, Gantier MP, Mackay F, Williams BRG, McCoy CE. IL-10 regulates Aicda expression through miR-155. J Leukoc Biol 2014; 97:71-8. [PMID: 25381386 DOI: 10.1189/jlb.2a0314-178r] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Aicda is a critical component of antibody class-switching in B cells. In this work, we study the impact of TLR4 activation and IL-10 stimulation on Aicda expression in B cells. Through the global analysis of miRNAs in response to TLR4 activation, in combination with IL-10 stimulation, we identified that IL-10 can suppress TLR4-induced miR-155 expression, an effect that resulted in enhanced Aicda expression. Furthermore, when preventing miR-155 control of Aicda expression, by genetic mutation of its target site in the Aicda mRNA, IL-10 could further potentiate Aicda expression. Given that miR-155 expression is lost, and expression levels of both Aicda and IL-10 are high in diseases, such as Burkitt's lymphoma, our results suggest a stringent and sophisticated control of Aicda by a novel IL-10/miR-155 axis, where the imbalance of IL-10 and/or miR-155 may contribute to disease pathogenesis.
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Affiliation(s)
- Kirsten A Fairfax
- *Faculty of Medicine, Department of Immunology, Monash University, Prahran, and Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia; The Department of Experimental Medicine, University of Melbourne, Parkville, Victoria, Australia; Division of Molecular Medicine, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia; Centre for Cancer Research, Monash Institute of Medical Research-Prince Henry's Institute of Medical Research, Clayton, Victoria, Australia; and School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Ireland
| | - Michael P Gantier
- *Faculty of Medicine, Department of Immunology, Monash University, Prahran, and Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia; The Department of Experimental Medicine, University of Melbourne, Parkville, Victoria, Australia; Division of Molecular Medicine, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia; Centre for Cancer Research, Monash Institute of Medical Research-Prince Henry's Institute of Medical Research, Clayton, Victoria, Australia; and School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Ireland
| | - Fabienne Mackay
- *Faculty of Medicine, Department of Immunology, Monash University, Prahran, and Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia; The Department of Experimental Medicine, University of Melbourne, Parkville, Victoria, Australia; Division of Molecular Medicine, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia; Centre for Cancer Research, Monash Institute of Medical Research-Prince Henry's Institute of Medical Research, Clayton, Victoria, Australia; and School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Ireland
| | - Bryan R G Williams
- *Faculty of Medicine, Department of Immunology, Monash University, Prahran, and Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia; The Department of Experimental Medicine, University of Melbourne, Parkville, Victoria, Australia; Division of Molecular Medicine, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia; Centre for Cancer Research, Monash Institute of Medical Research-Prince Henry's Institute of Medical Research, Clayton, Victoria, Australia; and School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Ireland
| | - Claire E McCoy
- *Faculty of Medicine, Department of Immunology, Monash University, Prahran, and Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia; The Department of Experimental Medicine, University of Melbourne, Parkville, Victoria, Australia; Division of Molecular Medicine, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia; Centre for Cancer Research, Monash Institute of Medical Research-Prince Henry's Institute of Medical Research, Clayton, Victoria, Australia; and School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Ireland
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