51
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Laude HC, Caval V, Bouzidi MS, Li X, Jamet F, Henry M, Suspène R, Wain-Hobson S, Vartanian JP. The rabbit as an orthologous small animal model for APOBEC3A oncogenesis. Oncotarget 2018; 9:27809-27822. [PMID: 29963239 PMCID: PMC6021247 DOI: 10.18632/oncotarget.25593] [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: 03/15/2018] [Accepted: 05/24/2018] [Indexed: 11/25/2022] Open
Abstract
APOBEC3 are cytidine deaminases that convert cytidine to uridine residues. APOBEC3A and APOBEC3B enzymes able to target genomic DNA are involved in oncogenesis of a sizeable proportion of human cancers. While the APOBEC3 locus is conserved in mammals, it encodes from 1–7 genes. APOBEC3A is conserved in most mammals, although absent in pigs, cats and throughout Rodentia whereas APOBEC3B is restricted to the Primate order. Here we show that the rabbit APOBEC3 locus encodes two genes of which APOBEC3A enzyme is strictly orthologous to human APOBEC3A. The rabbit enzyme is expressed in the nucleus and the cytoplasm, it can deaminate cytidine, 5-methcytidine residues, nuclear DNA and induce double-strand DNA breaks. The rabbit APOBEC3A enzyme is negatively regulated by the rabbit TRIB3 pseudokinase protein which is guardian of genome integrity, just like its human counterpart. This indicates that the APOBEC3A/TRIB3 pair is conserved over approximately 100 million years. The rabbit APOBEC3A gene is widely expressed in rabbit tissues, unlike human APOBEC3A. These data demonstrate that rabbit could be used as a small animal model for studying APOBEC3 driven oncogenesis.
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Affiliation(s)
- Hélène C Laude
- Molecular Retrovirology Unit, Institut Pasteur, CNRS UMR 3569, France
| | - Vincent Caval
- Molecular Retrovirology Unit, Institut Pasteur, CNRS UMR 3569, France
| | - Mohamed S Bouzidi
- Molecular Retrovirology Unit, Institut Pasteur, CNRS UMR 3569, France
| | - Xiongxiong Li
- Molecular Retrovirology Unit, Institut Pasteur, CNRS UMR 3569, France.,Lanzhou Institute of Biological Products Co., Ltd (LIBP), subsidiary company of China National Biotec Group Company Limited (CNBG), Lanzhou 730046, China
| | - Florence Jamet
- Molecular Retrovirology Unit, Institut Pasteur, CNRS UMR 3569, France
| | - Michel Henry
- Molecular Retrovirology Unit, Institut Pasteur, CNRS UMR 3569, France
| | - Rodolphe Suspène
- Molecular Retrovirology Unit, Institut Pasteur, CNRS UMR 3569, France
| | - Simon Wain-Hobson
- Molecular Retrovirology Unit, Institut Pasteur, CNRS UMR 3569, France
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52
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Venkatesan S, Rosenthal R, Kanu N, McGranahan N, Bartek J, Quezada SA, Hare J, Harris RS, Swanton C. Perspective: APOBEC mutagenesis in drug resistance and immune escape in HIV and cancer evolution. Ann Oncol 2018; 29:563-572. [PMID: 29324969 PMCID: PMC5888943 DOI: 10.1093/annonc/mdy003] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like (APOBEC) mutational signature has only recently been detected in a multitude of cancers through next-generation sequencing. In contrast, APOBEC has been a focus of virology research for over a decade. Many lessons learnt regarding APOBEC within virology are likely to be applicable to cancer. In this review, we explore the parallels between the role of APOBEC enzymes in HIV and cancer evolution. We discuss data supporting the role of APOBEC mutagenesis in creating HIV genome heterogeneity, drug resistance, and immune escape variants. We hypothesize similar functions of APOBEC will also hold true in cancer.
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Affiliation(s)
- S Venkatesan
- CRUK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, UK; Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, London, UK
| | - R Rosenthal
- CRUK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, UK
| | - N Kanu
- CRUK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, UK
| | - N McGranahan
- CRUK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, UK
| | - J Bartek
- Danish Cancer Society Research Center, Copenhagen, Denmark, UK; Science for Life Laboratory, Stockholm, Sweden; Division of Genome Biology, Department of Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - S A Quezada
- CRUK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, UK; Cancer Immunology Unit, UCL Cancer Institute, London, UK
| | - J Hare
- International AIDS Vaccine Initiative (IAVI), New York, USA
| | - R S Harris
- Masonic Cancer Center, Minneapolis, USA; Institute for Molecular Virology, Minneapolis, USA; Center for Genome Engineering, Minneapolis, USA; Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, USA; Howard Hughes Medical Institute, University of Minnesota, Minneapolis, USA.
| | - C Swanton
- CRUK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, UK; Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, London, UK.
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53
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Guo X, Shi J, Cai Q, Shu XO, He J, Wen W, Allen J, Pharoah P, Dunning A, Hunter DJ, Kraft P, Easton DF, Zheng W, Long J. Use of deep whole-genome sequencing data to identify structure risk variants in breast cancer susceptibility genes. Hum Mol Genet 2018; 27:853-859. [PMID: 29325031 PMCID: PMC6454518 DOI: 10.1093/hmg/ddy005] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 12/01/2017] [Accepted: 12/29/2017] [Indexed: 12/30/2022] Open
Abstract
Functional disruptions of susceptibility genes by large genomic structure variant (SV) deletions in germlines are known to be associated with cancer risk. However, few studies have been conducted to systematically search for SV deletions in breast cancer susceptibility genes. We analysed deep (> 30x) whole-genome sequencing (WGS) data generated in blood samples from 128 breast cancer patients of Asian and European descent with either a strong family history of breast cancer or early cancer onset disease. To identify SV deletions in known or suspected breast cancer susceptibility genes, we used multiple SV calling tools including Genome STRiP, Delly, Manta, BreakDancer and Pindel. SV deletions were detected by at least three of these bioinformatics tools in five genes. Specifically, we identified heterozygous deletions covering a fraction of the coding regions of BRCA1 (with approximately 80kb in two patients), and TP53 genes (with ∼1.6 kb in two patients), and of intronic regions (∼1 kb) of the PALB2 (one patient), PTEN (three patients) and RAD51C genes (one patient). We confirmed the presence of these deletions using real-time quantitative PCR (qPCR). Our study identified novel SV deletions in breast cancer susceptibility genes and the identification of such SV deletions may improve clinical testing.
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Affiliation(s)
- Xingyi Guo
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37203, USA
| | - Jiajun Shi
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37203, USA
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37203, USA
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37203, USA
| | - Jing He
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37203, USA
| | - Wanqing Wen
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37203, USA
| | - Jamie Allen
- Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Paul Pharoah
- Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Alison Dunning
- Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - David J Hunter
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Peter Kraft
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Douglas F Easton
- Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37203, USA
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37203, USA
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54
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Gansmo LB, Romundstad P, Hveem K, Vatten L, Nik-Zainal S, Lønning PE, Knappskog S. APOBEC3A/B deletion polymorphism and cancer risk. Carcinogenesis 2018; 39:118-124. [PMID: 29140415 PMCID: PMC5862322 DOI: 10.1093/carcin/bgx131] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Activity of the apolipoprotein B mRNA editing enzyme, catalytic-polypeptide-like (APOBEC) enzymes has been linked to specific mutational processes in human cancer genomes. A germline APOBEC3A/B deletion polymorphism is associated with APOBEC-dependent mutational signatures, and the deletion allele has been reported to confer an elevated risk of some cancers in Asian populations, while the results in European populations, so far, have been conflicting. We genotyped the APOBEC3A/B deletion polymorphism in a large population-based sample consisting of 11 106 Caucasian (Norwegian) individuals, including 7279 incident cancer cases (1769 breast, 1360 lung, 1585 colon, and 2565 prostate cancer) and a control group of 3827 matched individuals without cancer (1918 females and 1909 males) from the same population. Overall, the APOBEC3A/B deletion polymorphism was not associated with risk of any of the four cancer types. However, in subgroup analyses stratified by age, we found that the deletion allele was associated with increased risk for lung cancer among individuals <50 years of age (OR 2.17, CI 1.19-3.97), and that the association was gradually reduced with increasing age (P = 0.01). A similar but weaker pattern was observed for prostate cancer. In support of these findings, the APOBEC3A/B deletion was associated with young age at diagnosis among the cancer cases for both cancer forms (lung cancer: P = 0.02; dominant model and prostate cancer: P = 0.03; recessive model). No such associations were observed for breast or colon cancer.
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Affiliation(s)
- Liv B Gansmo
- Section of Oncology, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Oncology, Haukeland University Hospital, Bergen, Norway
| | - Paal Romundstad
- Department of Public Health, Faculty of Medicine, Trondheim, Norway
| | - Kristian Hveem
- Department of Public Health, Faculty of Medicine, K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Lars Vatten
- Department of Public Health, Faculty of Medicine, Trondheim, Norway
| | - Serena Nik-Zainal
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
- Department of Medical Genetics, Addenbrooke’s Hospital National Health Service (NHS) Trust, Cambridge, UK
| | - Per Eystein Lønning
- Section of Oncology, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Oncology, Haukeland University Hospital, Bergen, Norway
| | - Stian Knappskog
- Section of Oncology, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Oncology, Haukeland University Hospital, Bergen, Norway
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55
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Jaguva Vasudevan AA, Goering W, Häussinger D, Münk C. Detection of APOBEC3 Proteins and Catalytic Activity in Urothelial Carcinoma. Methods Mol Biol 2018; 1655:97-107. [PMID: 28889380 DOI: 10.1007/978-1-4939-7234-0_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Members of the APOBEC3 (A3) family of enzymes were shown to act in an oncogenic manner in several cancer types. Immunodetection of APOBEC3A (A3A), APOBEC3B (A3B), and APOBEC3G (A3G) proteins is particularly challenging due to the large sequence homology of these proteins and limited availability of antibodies. Here we combine independent immunoblotting with an in vitro activity assay technique, to detect and categorize specific A3s expressed in urothelial bladder cancer and other cancer cells.
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Affiliation(s)
- Ananda Ayyappan Jaguva Vasudevan
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany
- Department of Urology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Wolfgang Goering
- Department of Urology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute of Pathology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Dieter Häussinger
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Carsten Münk
- Clinic for Gastroenterology, Hepatology, and Infectiology, Medical Faculty, Heinrich Heine University Düsseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany.
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56
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Cao W, Wu W. Apolipoprotein B mRNA Editing Enzyme, Catalytic Polypeptide-Like Gene Expression, RNA Editing, and MicroRNAs Regulation. Methods Mol Biol 2018; 1699:75-81. [PMID: 29086369 DOI: 10.1007/978-1-4939-7435-1_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like (APOBEC) protein family is encoded by eleven genes located in human genome. APOBECs are a family of evolutionarily conserved cytidine deaminases in vertebrates, and particularly in mammals. APOBECs play key roles in innate immunity against viral infection and retrotransposons. Subtypes of APOBEC3 can cause specific mutations in RNA and DNA at distinct preferred nucleotide contexts in human cancer. The pervasive APOBEC3s activation in the host genome converts cytosine to uracile on single-stranded DNA, which has been suggested to depend on ATR/chk1 pathways. In this chapter, we review the expression profiling of APOBEC expression in normal and disease states, discuss how microRNAs interact with APOBEC gene family, and post-transcriptionally regulate APOBEC gene expression in the APOBECA-B fusion allele and APOBEC-mediated RNA editing. It is reasonable to speculate targeting specific microRNAs may reduce host genome mutagenesis via inactivation of APOBEC deaminases.
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Affiliation(s)
- Wei Cao
- Translational Medical Center, Zhengzhou Central Hospital, Affiliated to Zhengzhou University, 195 Tongbai Road, Zhengzhou, 450007, People's Republic of China.
| | - Wei Wu
- Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California in San Francisco, 600 16th Street Mission Bay/Genentech Hall, Room N212, San Francisco, CA, 94143, USA
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57
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Xiao X, Yang H, Arutiunian V, Fang Y, Besse G, Morimoto C, Zirkle B, Chen XS. Structural determinants of APOBEC3B non-catalytic domain for molecular assembly and catalytic regulation. Nucleic Acids Res 2017; 45:7494-7506. [PMID: 28575276 PMCID: PMC5499559 DOI: 10.1093/nar/gkx362] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 05/27/2017] [Indexed: 12/26/2022] Open
Abstract
The catalytic activity of human cytidine deaminase APOBEC3B (A3B) has been correlated with kataegic mutational patterns within multiple cancer types. The molecular basis of how the N-terminal non-catalytic CD1 regulates the catalytic activity and consequently, biological function of A3B remains relatively unknown. Here, we report the crystal structure of a soluble human A3B-CD1 variant and delineate several structural elements of CD1 involved in molecular assembly, nucleic acid interactions and catalytic regulation of A3B. We show that (i) A3B expressed in human cells exists in hypoactive high-molecular-weight (HMW) complexes, which can be activated without apparent dissociation into low-molecular-weight (LMW) species after RNase A treatment. (ii) Multiple surface hydrophobic residues of CD1 mediate the HMW complex assembly and affect the catalytic activity, including one tryptophan residue W127 that likely acts through regulating nucleic acid binding. (iii) One of the highly positively charged surfaces on CD1 is involved in RNA-dependent attenuation of A3B catalysis. (iv) Surface hydrophobic residues of CD1 are involved in heterogeneous nuclear ribonucleoproteins (hnRNPs) binding to A3B. The structural and biochemical insights described here suggest that unique structural features on CD1 regulate the molecular assembly and catalytic activity of A3B through distinct mechanisms.
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Affiliation(s)
- Xiao Xiao
- Genetic, Molecular and Cellular Biology Program, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
- Molecular and Computational Biology, Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA 90089, USA
- These authors contributed equally to this work as first authors
| | - Hanjing Yang
- Molecular and Computational Biology, Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA 90089, USA
- These authors contributed equally to this work as first authors
| | - Vagan Arutiunian
- Molecular and Computational Biology, Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Yao Fang
- Molecular and Computational Biology, Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA 90089, USA
- Department of Clinical Microbiology and Immunology of Southwest Hospital, Third Military Medical University, Chongqing 400038, China
- 161 Hospital, Wuhan 430012, China
| | - Guillaume Besse
- Molecular and Computational Biology, Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA 90089, USA
- Polytech' Clermont-Ferrand, Université Blaise Pascal, Clermont-Ferrand, France
| | - Cherie Morimoto
- Molecular and Computational Biology, Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Brett Zirkle
- Genetic, Molecular and Cellular Biology Program, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
- Molecular and Computational Biology, Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Xiaojiang S. Chen
- Genetic, Molecular and Cellular Biology Program, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
- Molecular and Computational Biology, Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, CA 90089, USA
- Center of Excellence in NanoBiophysics, University of Southern California, Los Angeles, CA 90089, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA
- To whom correspondence should be addressed. Tel: +1 213 740 5487; Fax: +1 213 740 4340;
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58
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Chen TW, Lee CC, Liu H, Wu CS, Pickering CR, Huang PJ, Wang J, Chang IYF, Yeh YM, Chen CD, Li HP, Luo JD, Tan BCM, Chan TEH, Hsueh C, Chu LJ, Chen YT, Zhang B, Yang CY, Wu CC, Hsu CW, See LC, Tang P, Yu JS, Liao WC, Chiang WF, Rodriguez H, Myers JN, Chang KP, Chang YS. APOBEC3A is an oral cancer prognostic biomarker in Taiwanese carriers of an APOBEC deletion polymorphism. Nat Commun 2017; 8:465. [PMID: 28878238 PMCID: PMC5587710 DOI: 10.1038/s41467-017-00493-9] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 07/04/2017] [Indexed: 12/29/2022] Open
Abstract
Oral squamous cell carcinoma is a prominent cancer worldwide, particularly in Taiwan. By integrating omics analyses in 50 matched samples, we uncover in Taiwanese patients a predominant mutation signature associated with cytidine deaminase APOBEC, which correlates with the upregulation of APOBEC3A expression in the APOBEC3 gene cluster at 22q13. APOBEC3A expression is significantly higher in tumors carrying APOBEC3B-deletion allele(s). High-level APOBEC3A expression is associated with better overall survival, especially among patients carrying APOBEC3B-deletion alleles, as examined in a second cohort (n = 188; p = 0.004). The frequency of APOBEC3B-deletion alleles is ~50% in 143 genotyped oral squamous cell carcinoma -Taiwan samples (27A3B−/−:89A3B+/−:27A3B+/+), compared to the 5.8% found in 314 OSCC-TCGA samples. We thus report a frequent APOBEC mutational profile, which relates to a APOBEC3B-deletion germline polymorphism in Taiwanese oral squamous cell carcinoma that impacts expression of APOBEC3A, and is shown to be of clinical prognostic relevance. Our finding might be recapitulated by genomic studies in other cancer types. Oral squamous cell carcinoma is a prevalent malignancy in Taiwan. Here, the authors show that OSCC in Taiwanese show a frequent deletion polymorphism in the cytidine deaminases gene cluster APOBEC3 resulting in increased expression of A3A, which is shown to be of clinical prognostic relevance.
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Affiliation(s)
- Ting-Wen Chen
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Bioinformatics Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan
| | - Chi-Ching Lee
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Bioinformatics Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Department and Graduate Institute of Computer Science and Information Engineering, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan
| | - Hsuan Liu
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Graduate Institute of Biomedical Sciences, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Department of Biochemistry, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Division of Colon and Rectal Surgery, Chang Gung Memorial Hospital, Linkou, Gueishan, Taoyuan, 33305, Taiwan
| | - Chi-Sheng Wu
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Department of Otolaryngology-Head & Neck Surgery, Chang Gung Memorial Hospital at Linkou, Gueishan, Taoyuan, 33305, Taiwan
| | - Curtis R Pickering
- Departments of Head and Neck Surgery, the University of Texas MD Anderson Cancer Center, Houston, Texas, 77030, USA
| | - Po-Jung Huang
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Bioinformatics Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Department of Biomedical Sciences, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital at Linkou, Gueishan, Taoyuan, 33305, Taiwan
| | - Jing Wang
- Departments of Biostatistics, the University of Texas MD Anderson Cancer Center, Houston, Texas, 77030, USA
| | - Ian Yi-Feng Chang
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Bioinformatics Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan
| | - Yuan-Ming Yeh
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Bioinformatics Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan
| | - Chih-De Chen
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan
| | - Hsin-Pai Li
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Graduate Institute of Biomedical Sciences, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Department of Microbiology and Immunology, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Division of Hematology-Oncology, Chang Gung Memorial Hospital at Linkou, Gueishan, Taoyuan, 33305, Taiwan
| | - Ji-Dung Luo
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Bioinformatics Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan
| | - Bertrand Chin-Ming Tan
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Graduate Institute of Biomedical Sciences, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Department of Biomedical Sciences, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Department of Neurosurgery, Chang Gung Memorial Hospital at Linkou, Gueishan, Taoyuan, 33305, Taiwan
| | - Timothy En Haw Chan
- Graduate Institute of Biomedical Sciences, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan
| | - Chuen Hsueh
- Pathology Core of the Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Department of Pathology, Chang Gung Memorial Hospital at Linkou, Gueishan, Taoyuan, 33305, Taiwan
| | - Lichieh Julie Chu
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Liver Research Center, Chang Gung Memorial Hospital at Linkou, Gueishan, Taoyuan, 33305, Taiwan
| | - Yi-Ting Chen
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Graduate Institute of Biomedical Sciences, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Department of Biomedical Sciences, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan
| | - Bing Zhang
- Department of Molecular and Human Genetics Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Chia-Yu Yang
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Division of Colon and Rectal Surgery, Chang Gung Memorial Hospital, Linkou, Gueishan, Taoyuan, 33305, Taiwan.,Department of Microbiology and Immunology, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan
| | - Chih-Ching Wu
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Department of Otolaryngology-Head & Neck Surgery, Chang Gung Memorial Hospital at Linkou, Gueishan, Taoyuan, 33305, Taiwan.,Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan
| | - Chia-Wei Hsu
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan
| | - Lai-Chu See
- Department of Public Health, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Biostatistics Core Laboratory, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan
| | - Petrus Tang
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Bioinformatics Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Molecular Regulation and Bioinformatics Laboratory, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Molecular Infectious Diseases Research Center, Chang Gung Memorial Hospital at Linkou, Gueishan, Taoyuan, 33305, Taiwan
| | - Jau-Song Yu
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Liver Research Center, Chang Gung Memorial Hospital at Linkou, Gueishan, Taoyuan, 33305, Taiwan.,Department of Cell and Molecular Biology, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan
| | - Wei-Chao Liao
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.,Department of Otolaryngology-Head & Neck Surgery, Chang Gung Memorial Hospital at Linkou, Gueishan, Taoyuan, 33305, Taiwan
| | - Wei-Fan Chiang
- Department of Oral & Maxillofacial Surgery, Chi-Mei Medical Center, Liouying, 736, Taiwan.,School of Dentistry, National Yang Ming University, Taipei, 112, Taiwan
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, US National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Jeffrey N Myers
- Department of Otolaryngology-Head & Neck Surgery, Chang Gung Memorial Hospital at Linkou, Gueishan, Taoyuan, 33305, Taiwan
| | - Kai-Ping Chang
- Department of Otolaryngology-Head & Neck Surgery, Chang Gung Memorial Hospital at Linkou, Gueishan, Taoyuan, 33305, Taiwan. .,College of Medicine, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan.
| | - Yu-Sun Chang
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan. .,Graduate Institute of Biomedical Sciences, Chang Gung University, Guishan, Taoyuan, 33302, Taiwan. .,Department of Otolaryngology-Head & Neck Surgery, Chang Gung Memorial Hospital at Linkou, Gueishan, Taoyuan, 33305, Taiwan.
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59
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Green AM, Budagyan K, Hayer KE, Reed MA, Savani MR, Wertheim GB, Weitzman MD. Cytosine Deaminase APOBEC3A Sensitizes Leukemia Cells to Inhibition of the DNA Replication Checkpoint. Cancer Res 2017; 77:4579-4588. [PMID: 28655787 PMCID: PMC5581702 DOI: 10.1158/0008-5472.can-16-3394] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 03/18/2017] [Accepted: 06/22/2017] [Indexed: 12/27/2022]
Abstract
Mutational signatures in cancer genomes have implicated the APOBEC3 cytosine deaminases in oncogenesis, possibly offering a therapeutic vulnerability. Elevated APOBEC3B expression has been detected in solid tumors, but expression of APOBEC3A (A3A) in cancer has not been described to date. Here, we report that A3A is highly expressed in subsets of pediatric and adult acute myelogenous leukemia (AML). We modeled A3A expression in the THP1 AML cell line by introducing an inducible A3A gene. A3A expression caused ATR-dependent phosphorylation of Chk1 and cell-cycle arrest, consistent with replication checkpoint activation. Further, replication checkpoint blockade via small-molecule inhibition of ATR kinase in cells expressing A3A led to apoptosis and cell death. Although DNA damage checkpoints are broadly activated in response to A3A activity, synthetic lethality was specific to ATR signaling via Chk1 and did not occur with ATM inhibition. Our findings identify elevation of A3A expression in AML cells, enabling apoptotic sensitivity to inhibitors of the DNA replication checkpoint and suggesting it as a candidate biomarker for ATR inhibitor therapy. Cancer Res; 77(17); 4579-88. ©2017 AACR.
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Affiliation(s)
- Abby M Green
- Department of Pediatrics, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Konstantin Budagyan
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Katharina E Hayer
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Morgann A Reed
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Milan R Savani
- University of Pennsylvania College of Arts and Sciences, Philadelphia, Pennsylvania
| | - Gerald B Wertheim
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Matthew D Weitzman
- Department of Pediatrics, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.
- Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
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60
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Kakushadze Z, Yu W. *K-means and cluster models for cancer signatures. BIOMOLECULAR DETECTION AND QUANTIFICATION 2017; 13:7-31. [PMID: 29021969 PMCID: PMC5634820 DOI: 10.1016/j.bdq.2017.07.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 07/18/2017] [Accepted: 07/18/2017] [Indexed: 01/03/2023]
Abstract
We present *K-means clustering algorithm and source code by expanding statistical clustering methods applied in https://ssrn.com/abstract=2802753 to quantitative finance. *K-means is statistically deterministic without specifying initial centers, etc. We apply *K-means to extracting cancer signatures from genome data without using nonnegative matrix factorization (NMF). *K-means' computational cost is a fraction of NMF's. Using 1389 published samples for 14 cancer types, we find that 3 cancers (liver cancer, lung cancer and renal cell carcinoma) stand out and do not have cluster-like structures. Two clusters have especially high within-cluster correlations with 11 other cancers indicating common underlying structures. Our approach opens a novel avenue for studying such structures. *K-means is universal and can be applied in other fields. We discuss some potential applications in quantitative finance.
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Affiliation(s)
- Zura Kakushadze
- Quantigic® Solutions LLC, 1127 High Ridge Road #135, Stamford, CT 06905, United States
- Free University of Tbilisi, Business School & School of Physics, 240, David Agmashenebeli Alley, Tbilisi 0159, Georgia
| | - Willie Yu
- Centre for Computational Biology, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
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61
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Roles of APOBEC3A and APOBEC3B in Human Papillomavirus Infection and Disease Progression. Viruses 2017; 9:v9080233. [PMID: 28825669 PMCID: PMC5580490 DOI: 10.3390/v9080233] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 08/16/2017] [Accepted: 08/16/2017] [Indexed: 02/06/2023] Open
Abstract
The apolipoprotein B messenger RNA-editing, enzyme-catalytic, polypeptide-like 3 (APOBEC3) family of cytidine deaminases plays an important role in the innate immune response to viral infections by editing viral genomes. However, the cytidine deaminase activity of APOBEC3 enzymes also induces somatic mutations in host genomes, which may drive cancer progression. Recent studies of human papillomavirus (HPV) infection and disease outcome highlight this duality. HPV infection is potently inhibited by one family member, APOBEC3A. Expression of APOBEC3A and APOBEC3B is highly elevated by the HPV oncoproteins E6 and E7 during persistent virus infection and disease progression. Furthermore, there is a high prevalence of APOBEC3A and APOBEC3B mutation signatures in HPV-associated cancers. These findings suggest that induction of an APOBEC3-mediated antiviral response during HPV infection may inadvertently contribute to cancer mutagenesis and virus evolution. Here, we discuss current understanding of APOBEC3A and APOBEC3B biology in HPV restriction, evolution, and associated cancer mutagenesis.
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62
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Yang B, Li X, Lei L, Chen J. APOBEC: From mutator to editor. J Genet Genomics 2017; 44:423-437. [PMID: 28964683 DOI: 10.1016/j.jgg.2017.04.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 04/04/2017] [Accepted: 04/10/2017] [Indexed: 12/21/2022]
Abstract
APOBECs (apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like) are a family of cytidine deaminases that prefer single-stranded nucleic acids as substrates. Besides their physiological functions, APOBEC family members have been found to cause hypermutations of cancer genomes, which could be correlated with cancer development and poor prognosis. Recently, APOBEC family members have been combined with the versatile CRISPR/Cas9 system to perform targeted base editing or induce hypermutagenesis. This combination improved the CRISPR/Cas9-mediated gene editing at single-base precision, greatly enhancing its usefulness. Here, we review the physiological functions and structural characteristics of APOBEC family members and their roles as endogenous mutators that contribute to hypermutations during carcinogenesis. We also review the various iterations of the APOBEC-CRISPR/Cas9 gene-editing tools, pointing out their features and limitations as well as the possibilities for future developments.
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Affiliation(s)
- Bei Yang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China.
| | - Xiaosa Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Liqun Lei
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jia Chen
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
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63
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Klonowska K, Kluzniak W, Rusak B, Jakubowska A, Ratajska M, Krawczynska N, Vasilevska D, Czubak K, Wojciechowska M, Cybulski C, Lubinski J, Kozlowski P. The 30 kb deletion in the APOBEC3 cluster decreases APOBEC3A and APOBEC3B expression and creates a transcriptionally active hybrid gene but does not associate with breast cancer in the European population. Oncotarget 2017; 8:76357-76374. [PMID: 29100317 PMCID: PMC5652711 DOI: 10.18632/oncotarget.19400] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 06/10/2017] [Indexed: 02/06/2023] Open
Abstract
APOBEC3B, in addition to other members of the APOBEC3 gene family, has recently been intensively studied due to its identification as a gene whose activation in cancer is responsible for a specific pattern of massively occurring somatic mutations. It was recently shown that a common large deletion in the APOBEC3 cluster (the APOBEC3B deletion) may increase the risk of breast cancer. However, conflicting evidence regarding this association was also reported. In the first step of our study, using different approaches, including an in-house designed multiplex ligation-dependent probe amplification assay, we analyzed the structure of the deletion and showed that although the breakpoints are located in highly homologous regions, which may generate recurrent occurrence of similar but not identical deletions, there is no sign of deletion heterogeneity. This knowledge allowed us to distinguish transcripts of all affected genes, including the highly homologous canonical APOBEC3A and APOBEC3B, and the hybrid APOBEC3A/APOBEC3B gene. We unambiguously confirmed the presence of the hybrid transcript and showed that the APOBEC3B deletion negatively correlates with APOBEC3A and APOBEC3B expression and positively correlates with APOBEC3A/APOBEC3B expression, whose mRNA level is >10-fold and >1500-fold lower than the level of APOBEC3A and APOBEC3B, respectively. In the next step, we performed a large-scale association study in three different cohorts (2972 cases and 3682 controls) and showed no association of the deletion with breast cancer, familial breast cancer or ovarian cancer. Further, we conducted a meta-analysis that confirmed the lack of the association of the deletion with breast cancer in non-Asian populations.
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Affiliation(s)
- Katarzyna Klonowska
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Wojciech Kluzniak
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Bogna Rusak
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Anna Jakubowska
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Magdalena Ratajska
- Department of Biology and Medical Genetics, Medical University of Gdansk, Gdansk, Poland
| | - Natalia Krawczynska
- Department of Biology and Medical Genetics, Medical University of Gdansk, Gdansk, Poland
| | - Danuta Vasilevska
- Department of Gynecology, Centre of Obstetrics and Gynecology, Vilnius University Hospital Santariskiu Klinikos, Vilnius, Lithuania
| | - Karol Czubak
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Marzena Wojciechowska
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Cezary Cybulski
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Jan Lubinski
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Piotr Kozlowski
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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64
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Buisson R, Lawrence MS, Benes CH, Zou L. APOBEC3A and APOBEC3B Activities Render Cancer Cells Susceptible to ATR Inhibition. Cancer Res 2017; 77:4567-4578. [PMID: 28698210 DOI: 10.1158/0008-5472.can-16-3389] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 03/15/2017] [Accepted: 05/02/2017] [Indexed: 12/24/2022]
Abstract
The apolipoprotein B mRNA editing enzyme catalytic polypeptide-like APOBEC3A and APOBEC3B have emerged as key mutation drivers in cancer. Here, we show that APOBEC3A and APOBEC3B activities impose a unique type of replication stress by inducing abasic sites at replication forks. In contrast to cells under other types of replication stress, APOBEC3A-expressing cells were selectively sensitive to ATR inhibitors (ATRi), but not to a variety of DNA replication inhibitors and DNA-damaging drugs. In proliferating cells, APOBEC3A modestly elicited ATR but not ATM. ATR inhibition in APOBEC3A-expressing cells resulted in a surge of abasic sites at replication forks, revealing an ATR-mediated negative feedback loop during replication. The surge of abasic sites upon ATR inhibition associated with increased accumulation of single-stranded DNA, a substrate of APOBEC3A, triggering an APOBEC3A-driven feed-forward loop that ultimately drove cells into replication catastrophe. In a panel of cancer cell lines, ATRi selectively induced replication catastrophe in those harboring high APOBEC3A and/or APOBEC3B activities, showing that APOBEC3A and APOBEC3B activities conferred susceptibility to ATRi. Our results define an APOBEC-driven replication stress in cancer cells that may offer an opportunity for ATR-targeted therapy. Cancer Res; 77(17); 4567-78. ©2017 AACR.
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Affiliation(s)
- Rémi Buisson
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Michael S Lawrence
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Cyril H Benes
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts. .,Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
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65
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Chen Z, Eggerman TL, Bocharov AV, Baranova IN, Vishnyakova TG, Kurlander R, Patterson AP. Heat shock proteins stimulate APOBEC-3-mediated cytidine deamination in the hepatitis B virus. J Biol Chem 2017. [PMID: 28637869 DOI: 10.1074/jbc.m116.760637] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Apolipoprotein B mRNA-editing enzyme catalytic subunit 3 (APOBEC-3) enzymes are cytidine deaminases that are broadly and constitutively expressed. They are often up-regulated during carcinogenesis and candidate genes for causing the major single-base substitution in cancer-associated DNA mutations. Moreover, APOBEC-3s are involved in host innate immunity against many viruses. However, how APOBEC-3 mutational activity is regulated in normal and pathological conditions remains largely unknown. Heat shock protein levels are often elevated in both carcinogenesis and viral infection and are associated with DNA mutations. Here, using mutational analyses of hepatitis B virus (HBV), we found that Hsp90 stimulates deamination activity of APOBEC-3G (A3G), A3B, and A3C during co-expression in human liver HepG2 cells. Hsp90 directly stimulated A3G deamination activity when the purified proteins were used in in vitro reactions. Hsp40, -60, and -70 also had variable stimulatory effects in the cellular assay, but not in vitro Sequencing analyses further demonstrated that Hsp90 increased both A3G cytosine mutation efficiency on HBV DNA and total HBV mutation frequency. In addition, Hsp90 shifted A3G's cytosine region selection in HBV DNA and increased A3G's 5' nucleoside preference for deoxycytidine (5'-CC). Furthermore, the Hsp90 inhibitor 17-N-allylamino-17-demethoxygeldanamycin dose dependently inhibited A3G and A3B mutational activity on HBV viral DNA. Hsp90 knockdown by siRNA or by Hsp90 active-site mutation also decreased A3G activity. These results indicate that heat shock proteins, in particular Hsp90, stimulate APOBEC-3-mediated DNA deamination activity, suggesting a potential physiological role in carcinogenesis and viral innate immunity.
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Affiliation(s)
- Zhigang Chen
- From the Department of Laboratory Medicine, Clinical Center
| | - Thomas L Eggerman
- From the Department of Laboratory Medicine, Clinical Center.,the Division of Diabetes, Endocrinology, and Metabolic Diseases, NIDDK, and
| | | | | | | | | | - Amy P Patterson
- From the Department of Laboratory Medicine, Clinical Center, .,NHLBI, National Institutes of Health, Bethesda, Maryland 20892
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66
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Ito F, Fu Y, Kao SCA, Yang H, Chen XS. Family-Wide Comparative Analysis of Cytidine and Methylcytidine Deamination by Eleven Human APOBEC Proteins. J Mol Biol 2017; 429:1787-1799. [PMID: 28479091 DOI: 10.1016/j.jmb.2017.04.021] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Revised: 04/28/2017] [Accepted: 04/29/2017] [Indexed: 01/17/2023]
Abstract
Apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like (APOBEC) proteins are a family of cytidine deaminases involved in various important biological processes such as antibody diversification/maturation, restriction of viral infection, and generation of somatic mutations. Catalytically active APOBEC proteins execute their biological functions mostly through deaminating cytosine (C) to uracil on single-stranded DNA/RNA. Activation-induced cytidine deaminase, one of the APOBEC members, was reported to deaminate methylated cytosine (mC) on DNA, and this mC deamination was proposed to be involved in the demethylation of mC for epigenetic regulation. The mC deamination activity is later demonstrated for APOBEC3A (A3A) and more recently for APOBEC3B and APOBEC3H (A3H). Despite extensive studies on APOBEC proteins, questions regarding whether the rest of APOBEC members have any mC deaminase activity and what are the relative deaminase activities for each APOBEC member remain unclear. Here, we performed a family-wide analysis of deaminase activities on C and mC by using purified recombinant proteins for 11 known human APOBEC proteins under similar conditions. Our comprehensive analyses revealed that each APOBEC has unique deaminase activity and selectivity for mC. A3A and A3H showed distinctively high deaminase activities on C and mC with relatively high selectivity for mC, whereas six other APOBEC members showed relatively low deaminase activity and selectivity for mC. Our mutational analysis showed that loop-1 of A3A is responsible for its high deaminase activity and selectivity for mC. These findings extend our understanding of APOBEC family proteins that have important roles in diverse biological functions and in genetic mutations.
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Affiliation(s)
- Fumiaki Ito
- Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Yang Fu
- Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Shen-Chi A Kao
- Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Hanjing Yang
- Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Xiaojiang S Chen
- Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA; Department of Chemistry, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA; Center of Excellence in NanoBiophysics, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA.
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67
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Suspène R, Mussil B, Laude H, Caval V, Berry N, Bouzidi MS, Thiers V, Wain-Hobson S, Vartanian JP. Self-cytoplasmic DNA upregulates the mutator enzyme APOBEC3A leading to chromosomal DNA damage. Nucleic Acids Res 2017; 45:3231-3241. [PMID: 28100701 PMCID: PMC5389686 DOI: 10.1093/nar/gkx001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Revised: 12/29/2016] [Accepted: 01/02/2017] [Indexed: 12/23/2022] Open
Abstract
Foreign and self-cytoplasmic DNA are recognized by numerous DNA sensor molecules leading to the production of type I interferons. Such DNA agonists should be degraded otherwise cells would be chronically stressed. Most human APOBEC3 cytidine deaminases can initiate catabolism of cytoplasmic mitochondrial DNA. Using the human myeloid cell line THP-1 with an interferon inducible APOBEC3A gene, we show that cytoplasmic DNA triggers interferon α and β production through the RNA polymerase III transcription/RIG-I pathway leading to massive upregulation of APOBEC3A. By catalyzing C→U editing in single stranded DNA fragments, the enzyme prevents them from re-annealing so attenuating the danger signal. The price to pay is chromosomal DNA damage in the form of CG→TA mutations and double stranded DNA breaks which, in the context of chronic inflammation, could drive cells down the path toward cancer.
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Affiliation(s)
- Rodolphe Suspène
- Molecular Retrovirology Unit, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris cedex 15, France
| | - Bianka Mussil
- Molecular Retrovirology Unit, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris cedex 15, France
- Unit of Infection Models, German Primate Centre, Kellnerweg 4, 37077 Goettingen, Germany
| | - Hélène Laude
- Molecular Retrovirology Unit, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris cedex 15, France
| | - Vincent Caval
- Molecular Retrovirology Unit, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris cedex 15, France
| | - Noémie Berry
- Molecular Retrovirology Unit, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris cedex 15, France
| | - Mohamed S. Bouzidi
- Molecular Retrovirology Unit, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris cedex 15, France
| | - Valérie Thiers
- Molecular Retrovirology Unit, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris cedex 15, France
| | - Simon Wain-Hobson
- Molecular Retrovirology Unit, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris cedex 15, France
| | - Jean-Pierre Vartanian
- Molecular Retrovirology Unit, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris cedex 15, France
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68
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B-Myb Induces APOBEC3B Expression Leading to Somatic Mutation in Multiple Cancers. Sci Rep 2017; 7:44089. [PMID: 28276478 PMCID: PMC5343453 DOI: 10.1038/srep44089] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 02/01/2017] [Indexed: 01/09/2023] Open
Abstract
The key signature of cancer genomes is the accumulation of DNA mutations, the most abundant of which is the cytosine-to-thymine (C-to-T) transition that results from cytosine deamination. Analysis of The Cancer Genome Atlas (TCGA) database has demonstrated that this transition is caused mainly by upregulation of the cytosine deaminase APOBEC3B (A3B), but the mechanism has not been completely characterized. We found that B-Myb (encoded by MYBL2) binds the A3B promoter, causing transactivation, and this is responsible for the C-to-T transitions and DNA hypermutation in breast cancer cells. Analysis of TCGA database yielded similar results, supporting that MYBL2 and A3B are upregulated and putatively promote C-to-T transitions in multiple cancer types. Moreover, blockade of EGF receptor with afatinib attenuated B-Myb-A3B signaling, suggesting a clinically relevant means of suppressing mutagenesis. Our results suggest that B-Myb-A3B contributes to DNA damage and could be targeted by inhibiting EGF receptor.
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69
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Shi K, Carpenter M, Banerjee S, Shaban N, Kurahashi K, Salamango D, McCann J, Starrett G, Duffy J, Demir Ö, Amaro R, Harki D, Harris R, Aihara H. Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B. Nat Struct Mol Biol 2017; 24:131-139. [PMID: 27991903 PMCID: PMC5296220 DOI: 10.1038/nsmb.3344] [Citation(s) in RCA: 176] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 11/16/2016] [Indexed: 12/17/2022]
Abstract
APOBEC-catalyzed cytosine-to-uracil deamination of single-stranded DNA (ssDNA) has beneficial functions in immunity and detrimental effects in cancer. APOBEC enzymes have intrinsic dinucleotide specificities that impart hallmark mutation signatures. Although numerous structures have been solved, mechanisms for global ssDNA recognition and local target-sequence selection remain unclear. Here we report crystal structures of human APOBEC3A and a chimera of human APOBEC3B and APOBEC3A bound to ssDNA at 3.1-Å and 1.7-Å resolution, respectively. These structures reveal a U-shaped DNA conformation, with the specificity-conferring -1 thymine flipped out and the target cytosine inserted deep into the zinc-coordinating active site pocket. The -1 thymine base fits into a groove between flexible loops and makes direct hydrogen bonds with the protein, accounting for the strong 5'-TC preference. These findings explain both conserved and unique properties among APOBEC family members, and they provide a basis for the rational design of inhibitors to impede the evolvability of viruses and tumors.
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Affiliation(s)
- K. Shi
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA, 55455
| | - M.A. Carpenter
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, Minnesota, USA, 55455
| | - S. Banerjee
- Northeastern Collaborative Access Team, Cornell University, Advanced Photon Source, Lemont, Illinois, USA, 60439
| | - N.M. Shaban
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA, 55455
| | - K. Kurahashi
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA, 55455
| | - D.J. Salamango
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA, 55455
| | - J.L. McCann
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA, 55455
| | - G.J. Starrett
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA, 55455
| | - J.V. Duffy
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA, 55455
| | - Ö. Demir
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093
| | - R.E. Amaro
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093
| | - D.A. Harki
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota, USA, 55455
| | - R.S. Harris
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, Minnesota, USA, 55455
| | - H. Aihara
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA, 55455
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA, 55455
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70
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Risks at the DNA Replication Fork: Effects upon Carcinogenesis and Tumor Heterogeneity. Genes (Basel) 2017; 8:genes8010046. [PMID: 28117753 PMCID: PMC5295039 DOI: 10.3390/genes8010046] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 01/09/2017] [Accepted: 01/17/2017] [Indexed: 12/27/2022] Open
Abstract
The ability of all organisms to copy their genetic information via DNA replication is a prerequisite for cell division and a biological imperative of life. In multicellular organisms, however, mutations arising from DNA replication errors in the germline and somatic cells are the basis of genetic diseases and cancer, respectively. Within human tumors, replication errors additionally contribute to mutator phenotypes and tumor heterogeneity, which are major confounding factors for cancer therapeutics. Successful DNA replication involves the coordination of many large-scale, complex cellular processes. In this review, we focus on the roles that defects in enzymes that normally act at the replication fork and dysregulation of enzymes that inappropriately damage single-stranded DNA at the fork play in causing mutations that contribute to carcinogenesis. We focus on tumor data and experimental evidence that error-prone variants of replicative polymerases promote carcinogenesis and on research indicating that the primary target mutated by APOBEC (apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like) cytidine deaminases is ssDNA present at the replication fork. Furthermore, we discuss evidence from model systems that indicate replication stress and other cancer-associated metabolic changes may modulate mutagenic enzymatic activities at the replication fork.
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71
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Radmanesh H, Spethmann T, Enßen J, Schürmann P, Bhuju S, Geffers R, Antonenkova N, Khusnutdinova E, Sadr-Nabavi A, Shandiz FH, Park-Simon TW, Hillemanns P, Christiansen H, Bogdanova N, Dörk T. Assessment of an APOBEC3B truncating mutation, c.783delG, in patients with breast cancer. Breast Cancer Res Treat 2017; 162:31-37. [PMID: 28062980 DOI: 10.1007/s10549-016-4100-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 12/30/2016] [Indexed: 12/30/2022]
Abstract
PURPOSE APOBEC3B belongs to the family of DNA-editing enzymes. A copy number variant targeting the genomic APOBEC3A-APOBEC3B locus has a significant impact on breast cancer risk, but the relative contribution of APOBEC3B is uncertain. In this study, we investigate a loss-of-function mutation that selectively targets APOBEC3B, for its association with breast cancer risk. METHODS We performed exome sequencing on genomic DNA samples of 6 Byelorussian patients with familial breast cancer. We then studied through mutation-specific genotyping four hospital-based breast cancer case-control series from Belarus, Russia, Germany, and Iran, respectively, comprising a total of 3070 breast cancer patients and 2878 healthy females. Results were evaluated using fixed-effects meta-analyses. RESULTS Exome sequencing uncovered a frameshift mutation, APOBEC3B*c.783delG, that was recurrent in the study populations. Subsequent genotyping identified this mutation in 23 additional breast cancer cases and 9 healthy female controls, with an adjusted Odds Ratio 2.29 (95% CI 1.04; 5.03, P = 0.04) in the combined analysis. There was an enrichment of the c.783delG mutation in patients with breast cancer diagnosed below 50 years of age (OR 3.22, 95% CI 1.37; 7.56, P = 0.007). CONCLUSIONS APOBEC3B*c.783delG showed evidence of modest association with breast cancer and seemed to contribute to earlier onset of the disease. These results may need to be reconciled with proposals to consider APOBEC3B as a possible therapeutic target in breast cancer.
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Affiliation(s)
- Hoda Radmanesh
- Gynaecology Research Unit, Clinics of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany
| | - Tessa Spethmann
- Gynaecology Research Unit, Clinics of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany.,Radiation Oncology Research Unit, Hannover Medical School, Hannover, Germany
| | - Julia Enßen
- Gynaecology Research Unit, Clinics of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany
| | - Peter Schürmann
- Gynaecology Research Unit, Clinics of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany
| | - Sabin Bhuju
- Genome Analytics Unit, Helmholtz Center for Infection Research, Brunswick, Germany
| | - Robert Geffers
- Genome Analytics Unit, Helmholtz Center for Infection Research, Brunswick, Germany
| | - Natalia Antonenkova
- N.N. Alexandrov Research Institute of Oncology and Medical Radiology, Minsk, Belarus
| | - Elza Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Science Center, Ufa, Russia.,Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia
| | - Ariane Sadr-Nabavi
- Medical Genetic Research Center (MGRC), School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Molecular Medicine Research Group, Academic Centers for EducationCulture and Research (ACECR), Khorasan Basavi Branch, Mashhad, Iran.,Department of Medical Genetics, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Fatemeh Homaei Shandiz
- Radiation Oncology Cancer Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Tjoung-Won Park-Simon
- Gynaecology Research Unit, Clinics of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany
| | - Peter Hillemanns
- Gynaecology Research Unit, Clinics of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany
| | - Hans Christiansen
- Radiation Oncology Research Unit, Hannover Medical School, Hannover, Germany
| | - Natalia Bogdanova
- Gynaecology Research Unit, Clinics of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany.,Radiation Oncology Research Unit, Hannover Medical School, Hannover, Germany
| | - Thilo Dörk
- Gynaecology Research Unit, Clinics of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany.
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72
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Kostrzak A, Caval V, Escande M, Pliquet E, Thalmensi J, Bestetti T, Julithe M, Fiette L, Huet T, Wain-Hobson S, Langlade-Demoyen P. APOBEC3A intratumoral DNA electroporation in mice. Gene Ther 2016; 24:74-83. [PMID: 27858943 DOI: 10.1038/gt.2016.77] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 10/26/2016] [Accepted: 11/11/2016] [Indexed: 12/21/2022]
Abstract
Human APOBEC3A (A3A) cytidine deaminase shows pro-apoptotic properties resulting from hypermutation of genomic DNA, induction of double-stranded DNA breaks (DSBs) and G1 cell cycle arrest. Given this, we evaluated the antitumor efficacy of A3A by intratumoral electroporation of an A3A expression plasmid. DNA was repeatedly electroporated into B16OVA, B16Luc tumors of C57BL/6J mice as well as the aggressive fibrosarcoma Sarc2 tumor of HLA-A*0201/DRB1*0101 transgenic mice using noninvasive plate electrodes. Intratumoral electroporation of A3A plasmid DNA resulted in regression of ~50% of small B16OVA melanoma tumors that did not rebound in the following 2 months without treatment. Larger or more aggressive tumors escaped regression when so treated. As APOBEC3A was much less efficient in provoking hypermutation and DSBs in B16OVA cells compared with human or quail cells, it is likely that APOBEC3A would be more efficient in a human setting than in a mouse model.
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Affiliation(s)
- A Kostrzak
- Invectys, Pepinière Paris Biotech Santé Cochin, Paris, France
| | - V Caval
- Molecular Retrovirology Unit, Institut Pasteur, Paris, France
| | - M Escande
- Invectys, Pepinière Paris Biotech Santé Cochin, Paris, France
| | - E Pliquet
- Invectys, Pepinière Paris Biotech Santé Cochin, Paris, France
| | - J Thalmensi
- Invectys, Pepinière Paris Biotech Santé Cochin, Paris, France
| | - T Bestetti
- Invectys, Pepinière Paris Biotech Santé Cochin, Paris, France
| | - M Julithe
- Invectys, Pepinière Paris Biotech Santé Cochin, Paris, France
| | - L Fiette
- Human Histopathology and Animal Models, Infection & Epidemiology Department, Institut Pasteur, Paris, France.,Université Paris Descartes, Sorbonne Paris-Cité, Paris, France
| | - T Huet
- Invectys, Pepinière Paris Biotech Santé Cochin, Paris, France
| | - S Wain-Hobson
- Invectys, Pepinière Paris Biotech Santé Cochin, Paris, France.,Molecular Retrovirology Unit, Institut Pasteur, Paris, France
| | - P Langlade-Demoyen
- Invectys, Pepinière Paris Biotech Santé Cochin, Paris, France.,Molecular Retrovirology Unit, Institut Pasteur, Paris, France
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73
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Middlebrooks CD, Banday AR, Matsuda K, Udquim KI, Onabajo OO, Paquin A, Figueroa JD, Zhu B, Koutros S, Kubo M, Shuin T, Freedman ND, Kogevinas M, Malats N, Chanock SJ, Garcia-Closas M, Silverman DT, Rothman N, Prokunina-Olsson L. Association of germline variants in the APOBEC3 region with cancer risk and enrichment with APOBEC-signature mutations in tumors. Nat Genet 2016; 48:1330-1338. [PMID: 27643540 PMCID: PMC6583788 DOI: 10.1038/ng.3670] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Accepted: 08/18/2016] [Indexed: 12/14/2022]
Abstract
High rates of APOBEC-signature mutations are found in many tumors, but factors affecting this mutation pattern are not well understood. Here we explored the contribution of two common germline variants in the APOBEC3 region. SNP rs1014971 was associated with bladder cancer risk, increased APOBEC3B expression, and enrichment with APOBEC-signature mutations in bladder tumors. In contrast, a 30-kb deletion that eliminates APOBEC3B and creates an APOBEC3A-APOBEC3B chimera was not important in bladder cancer, whereas it was associated with breast cancer risk and enrichment with APOBEC-signature mutations in breast tumors. In vitro, APOBEC3B expression was predominantly induced by treatment with a DNA-damaging drug in bladder cancer cell lines, and APOBEC3A expression was induced as part of the antiviral interferon-stimulated response in breast cancer cell lines. These findings suggest a tissue-specific role of environmental oncogenic triggers, particularly in individuals with germline APOBEC3 risk variants.
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Affiliation(s)
- Candace D. Middlebrooks
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, USA
| | - A. Rouf Banday
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, USA
| | - Koichi Matsuda
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Krizia-Ivana Udquim
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, USA
| | - Olusegun O. Onabajo
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, USA
| | - Ashley Paquin
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, USA
| | - Jonine D. Figueroa
- Usher Institute of Population Health Sciences and Informatics, Medical School, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, UK
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, USA
| | - Stella Koutros
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, USA
| | - Michiaki Kubo
- Center for Integrative Medical Science, The Institute of Physical and Chemical Research (RIKEN), Kanagawa, Japan
| | - Taro Shuin
- Department of Urology, School of Medicine, Kochi University, Koichi, Japan
| | - Neal D. Freedman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, USA
| | - Manolis Kogevinas
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
- Epidemiologia y Salud Pública (CIBERESP), Centro de Investigación Biomédica en Red (CIBER), Madrid, Spain
| | - Nuria Malats
- Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, USA
| | | | - Debra T. Silverman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, USA
| | - Ludmila Prokunina-Olsson
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, USA
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74
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Law EK, Sieuwerts AM, LaPara K, Leonard B, Starrett GJ, Molan AM, Temiz NA, Vogel RI, Meijer-van Gelder ME, Sweep FCGJ, Span PN, Foekens JA, Martens JWM, Yee D, Harris RS. The DNA cytosine deaminase APOBEC3B promotes tamoxifen resistance in ER-positive breast cancer. SCIENCE ADVANCES 2016; 2:e1601737. [PMID: 27730215 PMCID: PMC5055383 DOI: 10.1126/sciadv.1601737] [Citation(s) in RCA: 150] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 08/31/2016] [Indexed: 05/27/2023]
Abstract
Breast tumors often display extreme genetic heterogeneity characterized by hundreds of gross chromosomal aberrations and tens of thousands of somatic mutations. Tumor evolution is thought to be ongoing and driven by multiple mutagenic processes. A major outstanding question is whether primary tumors have preexisting mutations for therapy resistance or whether additional DNA damage and mutagenesis are necessary. Drug resistance is a key measure of tumor evolvability. If a resistance mutation preexists at the time of primary tumor presentation, then the intended therapy is likely to fail. However, if resistance does not preexist, then ongoing mutational processes still have the potential to undermine therapeutic efficacy. The antiviral enzyme APOBEC3B (apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3B) preferentially deaminates DNA C-to-U, which results in signature C-to-T and C-to-G mutations commonly observed in breast tumors. We use clinical data and xenograft experiments to ask whether APOBEC3B contributes to ongoing breast tumor evolution and resistance to the selective estrogen receptor modulator, tamoxifen. First, APOBEC3B levels in primary estrogen receptor-positive (ER+) breast tumors inversely correlate with the clinical benefit of tamoxifen in the treatment of metastatic ER+ disease. Second, APOBEC3B depletion in an ER+ breast cancer cell line results in prolonged tamoxifen responses in murine xenograft experiments. Third, APOBEC3B overexpression accelerates the development of tamoxifen resistance in murine xenograft experiments by a mechanism that requires the enzyme's catalytic activity. These studies combine to indicate that APOBEC3B promotes drug resistance in breast cancer and that inhibiting APOBEC3B-dependent tumor evolvability may be an effective strategy to improve efficacies of targeted cancer therapies.
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Affiliation(s)
- Emily K. Law
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN 55455, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Anieta M. Sieuwerts
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, 3015 GE Rotterdam, Netherlands
| | - Kelly LaPara
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Brandon Leonard
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Gabriel J. Starrett
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Amy M. Molan
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Nuri A. Temiz
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Rachel Isaksson Vogel
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology and Women’s Health, University of Minnesota, Minneapolis, MN 55455, USA
| | - Marion E. Meijer-van Gelder
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, 3015 GE Rotterdam, Netherlands
| | - Fred C. G. J. Sweep
- Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - Paul N. Span
- Department of Radiation Oncology, Radboud University Medical Center, Nijmegen, Netherlands
| | - John A. Foekens
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, 3015 GE Rotterdam, Netherlands
| | - John W. M. Martens
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, 3015 GE Rotterdam, Netherlands
| | - Douglas Yee
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Reuben S. Harris
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN 55455, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
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75
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Starrett GJ, Luengas EM, McCann JL, Ebrahimi D, Temiz NA, Love RP, Feng Y, Adolph MB, Chelico L, Law EK, Carpenter MA, Harris RS. The DNA cytosine deaminase APOBEC3H haplotype I likely contributes to breast and lung cancer mutagenesis. Nat Commun 2016; 7:12918. [PMID: 27650891 PMCID: PMC5036005 DOI: 10.1038/ncomms12918] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 08/16/2016] [Indexed: 12/17/2022] Open
Abstract
Cytosine mutations within TCA/T motifs are common in cancer. A likely cause is the DNA cytosine deaminase APOBEC3B (A3B). However, A3B-null breast tumours still have this mutational bias. Here we show that APOBEC3H haplotype I (A3H-I) provides a likely solution to this paradox. A3B-null tumours with this mutational bias have at least one copy of A3H-I despite little genetic linkage between these genes. Although deemed inactive previously, A3H-I has robust activity in biochemical and cellular assays, similar to A3H-II after compensation for lower protein expression levels. Gly105 in A3H-I (versus Arg105 in A3H-II) results in lower protein expression levels and increased nuclear localization, providing a mechanism for accessing genomic DNA. A3H-I also associates with clonal TCA/T-biased mutations in lung adenocarcinoma suggesting this enzyme makes broader contributions to cancer mutagenesis. These studies combine to suggest that A3B and A3H-I, together, explain the bulk of ‘APOBEC signature' mutations in cancer. The APOBEC family of enzymes are cytidine deaminases with APOBEC3A and APOBEC3B thought to contribute to DNA damage signatures detected in cancer genomes. Here, the authors demonstrate an unappreciated role for APOBEC3H haplotype I in the generation of DNA damage in breast cancer.
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Affiliation(s)
- Gabriel J Starrett
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Elizabeth M Luengas
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Jennifer L McCann
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Diako Ebrahimi
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Nuri A Temiz
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Robin P Love
- Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 5E5
| | - Yuqing Feng
- Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 5E5
| | - Madison B Adolph
- Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 5E5
| | - Linda Chelico
- Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 5E5
| | - Emily K Law
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Howard Hughes Medical Institute, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Michael A Carpenter
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Howard Hughes Medical Institute, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Reuben S Harris
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Howard Hughes Medical Institute, University of Minnesota, Minneapolis, Minnesota 55455, USA
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76
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Abstract
It has been long understood that mutation distribution is not completely random across genomic space and in time. Indeed, recent surprising discoveries identified multiple simultaneous mutations occurring in tiny regions within chromosomes while the rest of the genome remains relatively mutation-free. Mechanistic elucidation of these phenomena, called mutation showers, mutation clusters, or kataegis, in parallel with findings of abundant clustered mutagenesis in cancer genomes, is ongoing. So far, the combination of factors most important for clustered mutagenesis is the induction of DNA lesions within unusually long and persistent single-strand DNA intermediates. In addition to being a fascinating phenomenon, clustered mutagenesis also became an indispensable tool for identifying a previously unrecognized major source of mutation in cancer, APOBEC cytidine deaminases. Future research on clustered mutagenesis may shed light onto important mechanistic details of genome maintenance, with potentially profound implications for human health.
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Affiliation(s)
- Kin Chan
- Mechanisms of Genome Dynamics Group, National Institute of Environmental Health Sciences, Department of Health and Human Services, National Institutes of Health, Durham, North Carolina 27709; ,
| | - Dmitry A Gordenin
- Mechanisms of Genome Dynamics Group, National Institute of Environmental Health Sciences, Department of Health and Human Services, National Institutes of Health, Durham, North Carolina 27709; ,
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77
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Abstract
Prevention is an essential component of cancer eradication. Next-generation sequencing of cancer genomes and epigenomes has defined large numbers of driver mutations and molecular subgroups, leading to therapeutic advances. By comparison, there is a relative paucity of such knowledge in premalignant neoplasia, which inherently limits the potential to develop precision prevention strategies. Studies on the interplay between germ-line and somatic events have elucidated genetic processes underlying premalignant progression and preventive targets. Emerging data hint at the immune system's ability to intercept premalignancy and prevent cancer. Genetically engineered mouse models have identified mechanisms by which genetic drivers and other somatic alterations recruit inflammatory cells and induce changes in normal cells to create and interact with the premalignant tumor microenvironment to promote oncogenesis and immune evasion. These studies are currently limited to only a few lesion types and patients. In this Perspective, we advocate a large-scale collaborative effort to systematically map the biology of premalignancy and the surrounding cellular response. By bringing together scientists from diverse disciplines (e.g., biochemistry, omics, and computational biology; microbiology, immunology, and medical genetics; engineering, imaging, and synthetic chemistry; and implementation science), we can drive a concerted effort focused on cancer vaccines to reprogram the immune response to prevent, detect, and reject premalignancy. Lynch syndrome, clonal hematopoiesis, and cervical intraepithelial neoplasia which also serve as models for inherited syndromes, blood, and viral premalignancies, are ideal scenarios in which to launch this initiative.
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78
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Liu J, Sieuwerts AM, Look MP, van der Vlugt-Daane M, Meijer-van Gelder ME, Foekens JA, Hollestelle A, Martens JWM. The 29.5 kb APOBEC3B Deletion Polymorphism Is Not Associated with Clinical Outcome of Breast Cancer. PLoS One 2016; 11:e0161731. [PMID: 27552096 PMCID: PMC4995039 DOI: 10.1371/journal.pone.0161731] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 08/10/2016] [Indexed: 12/25/2022] Open
Abstract
Increased APOBEC3B mRNA levels are associated with a hypermutator phenotype and poor prognosis in ER-positive breast cancer patients. In addition, a 29.5 kb deletion polymorphism of APOBEC3B, resulting in an APOBEC3A-B hybrid transcript, has been associated with an increased breast cancer risk and the hypermutator phenotype. Here we evaluated whether the APOBEC3B deletion polymorphism also associates with clinical outcome of breast cancer. Copy number analysis was performed by quantitative PCR (qPCR) in primary tumors of 1,756 Dutch breast cancer patients. The APOBEC3B deletion was found in 187 patients of whom 16 carried a two-copy deletion and 171 carried a one-copy deletion. The prognostic value of the APOBEC3B deletion for the natural course of the disease was evaluated among 1,076 lymph-node negative (LNN) patients who did not receive adjuvant systemic treatment. No association was found between APOBEC3B copy number values and the length of metastasis-free survival (MFS; hazard ratio (HR) = 1.00, 95% confidence interval (CI) = 0.90–1.11, P = 0.96). Subgroup analysis by ER status also did not reveal an association between APOBEC3B copy number values and the length of MFS. The predictive value of the APOBEC3B deletion was assessed among 329 ER-positive breast cancer patients who received tamoxifen as the first-line therapy for recurrent disease and 226 breast cancer patients who received first-line chemotherapy for recurrent disease. No association between APOBEC3B copy number values and the overall response rate (ORR) to either tamoxifen (odds ratio (OR) = 0.88, 95% CI = 0.69–1.13, P = 0.31) or chemotherapy (OR = 0.97, 95% CI = 0.71–1.33, P = 0.87) was found. Thus, in contrast to APOBEC3B mRNA levels, the APOBEC3B deletion polymorphism has neither a prognostic nor a predictive value for breast cancer patients. Although a correlation exists between APOBEC3B copy number and mRNA expression, it is relatively weak. This suggests that other mechanisms exist that may affect and therefore determine the prognostic value of APOBEC3B mRNA levels.
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Affiliation(s)
- Jingjing Liu
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Anieta M. Sieuwerts
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
- Cancer Genomics Netherlands, Utrecht, the Netherlands
| | - Maxime P. Look
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Michelle van der Vlugt-Daane
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Marion E. Meijer-van Gelder
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - John A. Foekens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Antoinette Hollestelle
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
- * E-mail:
| | - John W. M. Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
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79
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Abstract
Cancer classification based on site of origin is very significant research issue for prediction and treatment of cancer. This paper is addressing the problem of cancer classification for Homo Sapiens genes composed of amino acid chain. Cancer gene network is realized by equivalent electrical circuits based on hydrophilic/ hydrophobic property of amino acid and a classifier is modeled to determine the cancer origin. The phase value, peak gain value and shape of Nyquist curve of network model are investigated to characterize different types of cancer gene origins. The model achieves 81.09% of classification accuracy and proves to be more sensitive and simple, since it shows 69% better performance compare to the existing nucleotide based method. The proposed classifier successfully predicts the site of origin of 93 cancer gene samples.
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80
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Bouzidi MS, Caval V, Suspène R, Hallez C, Pineau P, Wain-Hobson S, Vartanian JP. APOBEC3DE Antagonizes Hepatitis B Virus Restriction Factors APOBEC3F and APOBEC3G. J Mol Biol 2016; 428:3514-28. [PMID: 27289067 DOI: 10.1016/j.jmb.2016.05.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 05/10/2016] [Accepted: 05/12/2016] [Indexed: 01/05/2023]
Abstract
The APOBEC3 locus consists of seven genes (A3A-A3C, A3DE, A3F-A3H) that encode DNA cytidine deaminases. These enzymes deaminate single-stranded DNA, the result being DNA peppered with CG →TA mutations preferentially in the context of 5'TpC with the exception of APOBEC3G (A3G), which prefers 5'CpC dinucleotides. Hepatitis B virus (HBV) DNA is vulnerable to genetic editing by APOBEC3 cytidine deaminases, A3G being a major restriction factor. APOBEC3DE (A3DE) stands out in that it is catalytically inactive due to a fixed Tyr320Cys substitution in the C-terminal domain. As A3DE is closely related to A3F and A3G, which can form homo- and heterodimers and multimers, the impact of A3DE on HBV replication via modulation of other APOBEC3 restriction factors was investigated. A3DE binds to itself, A3F, and A3G and antagonizes A3F and, to a lesser extent, A3G restriction of HBV replication. A3DE suppresses A3F and A3G from HBV particles, leading to enhanced HBV replication. Ironically, while being part of a cluster of innate restriction factors, the A3DE phenotype is proviral. As the gorilla genome encodes the same Tyr320Cys substitution, this proviral phenotype seems to have been selected for.
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Affiliation(s)
- Mohamed S Bouzidi
- Molecular Retrovirology Unit, Institut Pasteur, CNRS URA 3015, 28 rue du Dr. Roux, 75724 Paris CEDEX 15, France
| | - Vincent Caval
- Molecular Retrovirology Unit, Institut Pasteur, CNRS URA 3015, 28 rue du Dr. Roux, 75724 Paris CEDEX 15, France
| | - Rodolphe Suspène
- Molecular Retrovirology Unit, Institut Pasteur, CNRS URA 3015, 28 rue du Dr. Roux, 75724 Paris CEDEX 15, France
| | - Camille Hallez
- Molecular Retrovirology Unit, Institut Pasteur, CNRS URA 3015, 28 rue du Dr. Roux, 75724 Paris CEDEX 15, France
| | - Pascal Pineau
- Nuclear Organization and Oncogenesis Unit, Institut Pasteur, INSERM U579, 28 rue du Dr. Roux, 75724 Paris CEDEX 15, France
| | - Simon Wain-Hobson
- Molecular Retrovirology Unit, Institut Pasteur, CNRS URA 3015, 28 rue du Dr. Roux, 75724 Paris CEDEX 15, France
| | - Jean-Pierre Vartanian
- Molecular Retrovirology Unit, Institut Pasteur, CNRS URA 3015, 28 rue du Dr. Roux, 75724 Paris CEDEX 15, France.
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81
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The APOBEC Protein Family: United by Structure, Divergent in Function. Trends Biochem Sci 2016; 41:578-594. [PMID: 27283515 DOI: 10.1016/j.tibs.2016.05.001] [Citation(s) in RCA: 235] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Revised: 04/28/2016] [Accepted: 05/03/2016] [Indexed: 12/13/2022]
Abstract
The APOBEC (apolipoprotein B mRNA editing catalytic polypeptide-like) family of proteins have diverse and important functions in human health and disease. These proteins have an intrinsic ability to bind to both RNA and single-stranded (ss) DNA. Both function and tissue-specific expression varies widely for each APOBEC protein. We are beginning to understand that the activity of APOBEC proteins is regulated through genetic alterations, changes in their transcription and mRNA processing, and through their interactions with other macromolecules in the cell. Loss of cellular control of APOBEC activities leads to DNA hypermutation and promiscuous RNA editing associated with the development of cancer or viral drug resistance, underscoring the importance of understanding how APOBEC proteins are regulated.
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82
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Wen WX, Soo JSS, Kwan PY, Hong E, Khang TF, Mariapun S, Lee CSM, Hasan SN, Rajadurai P, Yip CH, Mohd Taib NA, Teo SH. Germline APOBEC3B deletion is associated with breast cancer risk in an Asian multi-ethnic cohort and with immune cell presentation. Breast Cancer Res 2016; 18:56. [PMID: 27233495 PMCID: PMC4884363 DOI: 10.1186/s13058-016-0717-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 05/08/2016] [Indexed: 01/05/2023] Open
Abstract
Background APOBEC3B is a cytosine deaminase implicated in immune response to viral infection, cancer predisposition and carcinogenesis. Germline APOBEC3B deletion is more common in East Asian women and confers a modest risk to breast cancer in both East Asian and Caucasian women. Analysis of tumour samples from women of European descent has shown that germline APOBEC3B deletion is associated with an increased propensity to develop somatic mutations and with an enrichment for immune response-related gene sets. However, this has not been examined in Asian tumour samples, where population differences in genetic and dietary factors may have an impact on the immune system. Methods In this study, we determined the prevalence of germline APOBEC3B deletion and its association with breast cancer risk in a cross-sectional hospital-based Asian multi-ethnic cohort of 1451 cases and 1442 controls from Malaysia. We compared gene expression profiles of breast cancers arising from APOBEC3B deletion carriers and non-carriers using microarray analyses. Finally, we characterised the overall abundance of tumour-infiltrating immune cells in breast cancers from TCGA and METABRIC using ESTIMATE and relative frequency of 22 immune cell subsets in breast cancers from METABRIC using CIBERSORT. Results The minor allelic frequency of APOBEC3B deletion was estimated to be 0.35, 0.42 and 0.16 in female populations of Chinese, Malay and Indian descent, respectively, and that germline APOBEC3B deletion was associated with breast cancer risk with odds ratios of 1.23 (95 % CI: [1.05, 1.44]) for one-copy deletion and 1.38 (95 % CI: [1.10, 1.74]) for two-copy deletion compared to women with no deletion. Germline APOBEC3B deletion was not associated with any clinicopathologic features or the expression of any APOBEC family members but was associated with immune response-related gene sets (FDR q values < 0.05). Analysis of breast cancers from METABRIC revealed breast cancers from APOBEC3B deletion carriers to have significantly higher abundance of tumour-infiltrating immune cells (P < 0.001). Conclusions Taken together, our data suggests that tumour-infiltrating immune cells may be an important feature of breast cancers arising in women with APOBEC3B germline deletion, and that this may be of particular interest in Asian women where the germline deletion is more common. Electronic supplementary material The online version of this article (doi:10.1186/s13058-016-0717-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wei Xiong Wen
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia.,Breast Cancer Research Unit, University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - Jaslyn Sian-Siu Soo
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia.,Breast Cancer Research Unit, University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - Pui Yoke Kwan
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
| | - Elaine Hong
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia
| | - Tsung Fei Khang
- Institute of Mathematical Sciences, Faculty of Science, University Malaya, Kuala Lumpur, Malaysia
| | | | | | | | | | - Cheng Har Yip
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia.,Sime Darby Medical Centre, Subang Jaya, Selangor, Malaysia
| | - Nur Aishah Mohd Taib
- Breast Cancer Research Unit, University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia.,Department of Surgery, Faculty of Medicine, University Malaya Medical Centre, Kuala Lumpur, Malaysia
| | - Soo Hwang Teo
- Cancer Research Malaysia, Subang Jaya, Selangor, Malaysia. .,Breast Cancer Research Unit, University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia. .,Department of Surgery, Faculty of Medicine, University Malaya Medical Centre, Kuala Lumpur, Malaysia.
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83
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Byeon IJL, Byeon CH, Wu T, Mitra M, Singer D, Levin JG, Gronenborn AM. Nuclear Magnetic Resonance Structure of the APOBEC3B Catalytic Domain: Structural Basis for Substrate Binding and DNA Deaminase Activity. Biochemistry 2016; 55:2944-59. [PMID: 27163633 DOI: 10.1021/acs.biochem.6b00382] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Human APOBEC3B (A3B) is a member of the APOBEC3 (A3) family of cytidine deaminases, which function as DNA mutators and restrict viral pathogens and endogenous retrotransposons. Recently, A3B was identified as a major source of genetic heterogeneity in several human cancers. Here, we determined the solution nuclear magnetic resonance structure of the catalytically active C-terminal domain (CTD) of A3B and performed detailed analyses of its deaminase activity. The core of the structure comprises a central five-stranded β-sheet with six surrounding helices, common to all A3 proteins. The structural fold is most similar to that of A3A and A3G-CTD, with the most prominent difference being found in loop 1. The catalytic activity of A3B-CTD is ∼15-fold lower than that of A3A, although both exhibit a similar pH dependence. Interestingly, A3B-CTD with an A3A loop 1 substitution had significantly increased deaminase activity, while a single-residue change (H29R) in A3A loop 1 reduced A3A activity to the level seen with A3B-CTD. This establishes that loop 1 plays an important role in A3-catalyzed deamination by precisely positioning the deamination-targeted C into the active site. Overall, our data provide important insights into the determinants of the activities of individual A3 proteins and facilitate understanding of their biological function.
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Affiliation(s)
| | | | - Tiyun Wu
- Section on Viral Gene Regulation, Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Mithun Mitra
- Section on Viral Gene Regulation, Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Dustin Singer
- Section on Viral Gene Regulation, Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Judith G Levin
- Section on Viral Gene Regulation, Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health , Bethesda, Maryland 20892, United States
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84
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Akre MK, Starrett GJ, Quist JS, Temiz NA, Carpenter MA, Tutt ANJ, Grigoriadis A, Harris RS. Mutation Processes in 293-Based Clones Overexpressing the DNA Cytosine Deaminase APOBEC3B. PLoS One 2016; 11:e0155391. [PMID: 27163364 PMCID: PMC4862684 DOI: 10.1371/journal.pone.0155391] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 04/05/2016] [Indexed: 11/18/2022] Open
Abstract
Molecular, cellular, and clinical studies have combined to demonstrate a contribution from the DNA cytosine deaminase APOBEC3B (A3B) to the overall mutation load in breast, head/neck, lung, bladder, cervical, ovarian, and other cancer types. However, the complete landscape of mutations attributable to this enzyme has yet to be determined in a controlled human cell system. We report a conditional and isogenic system for A3B induction, genomic DNA deamination, and mutagenesis. Human 293-derived cells were engineered to express doxycycline-inducible A3B-eGFP or eGFP constructs. Cells were subjected to 10 rounds of A3B-eGFP exposure that each caused 80–90% cell death. Control pools were subjected to parallel rounds of non-toxic eGFP exposure, and dilutions were done each round to mimic A3B-eGFP induced population fluctuations. Targeted sequencing of portions of TP53 and MYC demonstrated greater mutation accumulation in the A3B-eGFP exposed pools. Clones were generated and microarray analyses were used to identify those with the greatest number of SNP alterations for whole genome sequencing. A3B-eGFP exposed clones showed global increases in C-to-T transition mutations, enrichments for cytosine mutations within A3B-preferred trinucleotide motifs, and more copy number aberrations. Surprisingly, both control and A3B-eGFP clones also elicited strong mutator phenotypes characteristic of defective mismatch repair. Despite this additional mutational process, the 293-based system characterized here still yielded a genome-wide view of A3B-catalyzed mutagenesis in human cells and a system for additional studies on the compounded effects of simultaneous mutation mechanisms in cancer cells.
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Affiliation(s)
- Monica K. Akre
- Department of Biochemistry, Molecular Biology, and Biophysics, Institute for Molecular Virology, Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States of America
| | - Gabriel J. Starrett
- Department of Biochemistry, Molecular Biology, and Biophysics, Institute for Molecular Virology, Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States of America
| | - Jelmar S. Quist
- Breast Cancer Now Research Unit, Research Oncology, Guy’s Hospital, King’s College London, London, United Kingdom
| | - Nuri A. Temiz
- Department of Biochemistry, Molecular Biology, and Biophysics, Institute for Molecular Virology, Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States of America
| | - Michael A. Carpenter
- Department of Biochemistry, Molecular Biology, and Biophysics, Institute for Molecular Virology, Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States of America
| | - Andrew N. J. Tutt
- Breast Cancer Now Research Unit, Research Oncology, Guy’s Hospital, King’s College London, London, United Kingdom
| | - Anita Grigoriadis
- Breast Cancer Now Research Unit, Research Oncology, Guy’s Hospital, King’s College London, London, United Kingdom
| | - Reuben S. Harris
- Department of Biochemistry, Molecular Biology, and Biophysics, Institute for Molecular Virology, Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States of America
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN, United States of America
- * E-mail:
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85
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Revathidevi S, Manikandan M, Rao AKDM, Vinothkumar V, Arunkumar G, Rajkumar KS, Ramani R, Rajaraman R, Ajay C, Munirajan AK. Analysis of APOBEC3A/3B germline deletion polymorphism in breast, cervical and oral cancers from South India and its impact on miRNA regulation. Tumour Biol 2016; 37:11983-11990. [PMID: 27155849 DOI: 10.1007/s13277-016-5064-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 05/01/2016] [Indexed: 12/19/2022] Open
Abstract
Breast cancer and cervical cancer are the leading causes of death in women worldwide as well as in India, whilst oral cancer is the top most common cancer among Asian especially in Indian men in terms of both incidence and mortality rate. Genetic factors determining the predisposition to cancer are being explored to identify the signature genetic variations associated with these cancers. Recently, a germline deletion polymorphism in APOBEC3 gene cluster which completely deletes APOBEC3B coding region has been studied for its association with cancer risk. We screened the germline deletion polymorphism in 409 cancer patients (224 breast cancer, 88 cervical cancer and 97 oral cancer samples), 478 controls and 239 cervical cancer tissue DNAs of South Indian origin. The results suggest that the APOBEC3A/3B deletion polymorphism is not significantly associated with cancer risk in our study population (OR 0.739, 95 % CI, p value 0.91457). Considering the viral restriction property of APOBEC3s, we also screened cervical cancer tissue DNAs for the human papilloma virus infection. We observed a gradual increase in the frequency of HPV16 infection from AA/BB cases (66.86 %) to AA/-- cases (71.43) which signifies the impact of this deletion polymorphism in HPV infection. In addition, we performed in silico analysis to understand the effect of this polymorphism on miRNA regulation of the APOBEC3A/3B fusion transcript. Only 8 APOBEC3B targeting miRNAs were observed to regulate the fusion transcript of which miR-34b-3p and miR-138-5p were found to be frequently downregulated in cancers suggesting miRNA-mediated deregulation of APOBEC3A expression in cancer patients harbouring this particular deletion polymorphism.
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Affiliation(s)
- Sundaramoorthy Revathidevi
- Department of Genetics, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Taramani, Chennai, 600113, Tamil Nadu, India
| | - Mayakannan Manikandan
- Department of Genetics, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Taramani, Chennai, 600113, Tamil Nadu, India
| | - Arunagiri Kuha Deva Magendhra Rao
- Department of Genetics, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Taramani, Chennai, 600113, Tamil Nadu, India
| | - Vilvanathan Vinothkumar
- Department of Genetics, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Taramani, Chennai, 600113, Tamil Nadu, India
| | - Ganesan Arunkumar
- Department of Genetics, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Taramani, Chennai, 600113, Tamil Nadu, India
| | | | - Rajendran Ramani
- Institute of Social Obstetrics and Government Kasturba Gandhi Hospital for Women and Children, Chennai, Tamil Nadu, India
| | - Ramamurthy Rajaraman
- Centre for Oncology, Government Royapettah Hospital & Kilpauk Medical College, Chennai, Tamil Nadu, India
| | - Chandrasekar Ajay
- Centre for Oncology, Government Royapettah Hospital & Kilpauk Medical College, Chennai, Tamil Nadu, India
| | - Arasambattu Kannan Munirajan
- Department of Genetics, Dr. ALM PG Institute of Basic Medical Sciences, University of Madras, Taramani, Chennai, 600113, Tamil Nadu, India.
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86
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Leonard B, Starrett GJ, Maurer MJ, Oberg AL, Van Bockstal M, Van Dorpe J, De Wever O, Helleman J, Sieuwerts AM, Berns EMJJ, Martens JWM, Anderson BD, Brown WL, Kalli KR, Kaufmann SH, Harris RS. APOBEC3G Expression Correlates with T-Cell Infiltration and Improved Clinical Outcomes in High-grade Serous Ovarian Carcinoma. Clin Cancer Res 2016; 22:4746-55. [PMID: 27016308 PMCID: PMC5026552 DOI: 10.1158/1078-0432.ccr-15-2910] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 03/09/2016] [Indexed: 01/05/2023]
Abstract
PURPOSE APOBEC3 DNA cytosine deaminase family members normally defend against viruses and transposons. However, deregulated APOBEC3 activity causes mutations in cancer. Because of broad expression profiles and varying mixtures of normal and cancer cells in tumors, including immune cell infiltration, it is difficult to determine where different APOBEC3s are expressed. Here, we ask whether correlations exist between APOBEC3 expression and T-cell infiltration in high-grade serous ovarian cancer (HGSOC), and assess whether these correlations have prognostic value. EXPERIMENTAL DESIGN Transcripts for APOBEC3G, APOBEC3B, and the T-cell markers, CD3D, CD4, CD8A, GZMB, PRF1, and RNF128 were quantified by RT-qPCR for a cohort of 354 HGSOC patients. Expression values were correlated with each other and clinical parameters. Two additional cohorts were used to extend HGSOC clinical results. Immunoimaging was used to colocalize APOBEC3G and the T-cell marker CD3. TCGA data extended expression analyses to additional cancer types. RESULTS A surprising positive correlation was found for expression of APOBEC3G and several T cell genes in HGSOC. Immunohistochemistry and immunofluorescent imaging showed protein colocalization in tumor-infiltrating T lymphocytes. High APOBEC3G expression correlated with improved outcomes in multiple HGSOC cohorts. TCGA data analyses revealed that expression of APOBEC3D and APOBEC3H also correlates with CD3D across multiple cancer types. CONCLUSIONS Our results identify APOBEC3G as a new candidate biomarker for tumor-infiltrating T lymphocytes and favorable prognoses for HGSOC. Our data also highlight the complexity of the tumor environment with respect to differential APOBEC family gene expression in both tumor and surrounding normal cell types. Clin Cancer Res; 22(18); 4746-55. ©2016 AACR.
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Affiliation(s)
- Brandon Leonard
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota. Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Gabriel J Starrett
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota. Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Matthew J Maurer
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Ann L Oberg
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | | | - Jo Van Dorpe
- Department of Pathology, Ghent University Hospital, Ghent, Belgium
| | - Olivier De Wever
- Department of Radiation Oncology and Experimental Cancer Research, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Jozien Helleman
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Anieta M Sieuwerts
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Els M J J Berns
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Brett D Anderson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota. Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - William L Brown
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota. Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Kimberly R Kalli
- Women's Cancer Program, Mayo Clinic Cancer Center, Rochester, Minnesota
| | - Scott H Kaufmann
- Division of Oncology Research, Department of Oncology, Mayo Clinic, Rochester, Minnesota. Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota
| | - Reuben S Harris
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota. Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota. Howard Hughes Medical Institute, University of Minnesota, Minneapolis, Minnesota.
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87
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Onguru O, Yalcin S, Rosemblit C, Zhang PJ, Kilic S, Gunduz U. APOBEC3B expression in drug resistant MCF-7 breast cancer cell lines. Biomed Pharmacother 2016; 79:87-92. [PMID: 27044816 DOI: 10.1016/j.biopha.2016.02.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 02/03/2016] [Accepted: 02/06/2016] [Indexed: 10/22/2022] Open
Abstract
APOBEC3B belongs to a protein family of cytidine deaminases that can insert mutations in DNA and RNA as a result of their ability to deaminate cytidine to uridine. It has been shown that APOBEC3B-catalysed deamination provides a chronic source of DNA damage in breast cancers. We investigated APOBEC3B expression in four drug resistant breast cancer cell lines (Doxorubicin, Etoposide, Paclitaxel and Docetaxel resistant MCF-7 cell lines) using a novel RNA in situ hybridization technology (RNAscope) and compared expression levels with drug sensitive MCF-7 cell line. After RNAscope staining, slides were scanned and saved as digital images using Aperio scanner and software. Quantitative scoring utilizing the number of punctate dots present within each cell boundary was performed for the parameters including positive cell percentage and signal intensity per positive cell. In Doxorubicin and Etoposide resistant MCF-7 cell lines, APOBEC3B expression was approximately five-fold increased (23% and 24% respectively) with higher signal intensity (1.92 and 1.44 signal/cell, respectively) compared to drug sensitive MCF-7 cell line (5%, 1.00 signal/cell) with statistical significance. The increase of APOBEC3B expression in Docataxel resitant and Paclitaxel resistant MCF-7 cell lines was not very high. In conclusion, APOBEC3B expression was increased in some population of tumor cells of drug resistant cell lines. At least for some drugs, APOBEC3B expression may be related to drug resistance, subjecting to some tumor cells to frequent mutation.
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Affiliation(s)
- Onder Onguru
- Department of Pathology, GATA, Ankara, Turkey; Department of Pathology and Laboratory Medicine, University of Pennsylvania Medical Center, Philadelphia, PA, United States.
| | - Serap Yalcin
- Department of Food Engineering, Ahi Evran University, Kırsehir, Turkey
| | - Cinthia Rosemblit
- Department of Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States
| | - Paul J Zhang
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Medical Center, Philadelphia, PA, United States
| | - Selim Kilic
- Department of Public Health, GATA, Ankara, Turkey
| | - Ufuk Gunduz
- Department of Biology, Middle East Technical University, Ankara, Turkey
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88
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Hoopes JI, Cortez LM, Mertz TM, Malc EP, Mieczkowski PA, Roberts SA. APOBEC3A and APOBEC3B Preferentially Deaminate the Lagging Strand Template during DNA Replication. Cell Rep 2016; 14:1273-1282. [PMID: 26832400 DOI: 10.1016/j.celrep.2016.01.021] [Citation(s) in RCA: 142] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 01/07/2016] [Accepted: 01/11/2016] [Indexed: 11/19/2022] Open
Abstract
APOBEC family cytidine deaminases have recently been implicated as powerful mutators of cancer genomes. How APOBECs, which are ssDNA-specific enzymes, gain access to chromosomal DNA is unclear. To ascertain the chromosomal ssDNA substrates of the APOBECs, we expressed APOBEC3A and APOBEC3B, the two most probable APOBECs mediating cancer mutagenesis, in a yeast model system. We demonstrate, using mutation reporters and whole genome sequencing, that APOBEC3A- and APOBEC3B-induced mutagenesis primarily results from the deamination of the lagging strand template during DNA replication. Moreover, our results indicate that both genetic deficiencies in replication fork-stabilizing proteins and chemical induction of replication stress greatly augment the mutagenesis of APOBEC3A and APOBEC3B. Taken together, these results strongly indicate that ssDNA formed during DNA lagging strand synthesis is a major substrate for APOBECs and may be the principal substrate in human cancers experiencing replication stress.
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Affiliation(s)
- James I Hoopes
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
| | - Luis M Cortez
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
| | - Tony M Mertz
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
| | - Ewa P Malc
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Piotr A Mieczkowski
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Steven A Roberts
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA.
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89
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Seplyarskiy VB, Soldatov RA, Popadin KY, Antonarakis SE, Bazykin GA, Nikolaev SI. APOBEC-induced mutations in human cancers are strongly enriched on the lagging DNA strand during replication. Genome Res 2016; 26:174-82. [PMID: 26755635 PMCID: PMC4728370 DOI: 10.1101/gr.197046.115] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 12/10/2015] [Indexed: 12/31/2022]
Abstract
APOBEC3A and APOBEC3B, cytidine deaminases of the APOBEC family, are among the main factors causing mutations in human cancers. APOBEC deaminates cytosines in single-stranded DNA (ssDNA). A fraction of the APOBEC-induced mutations occur as clusters ("kataegis") in single-stranded DNA produced during repair of double-stranded breaks (DSBs). However, the properties of the remaining 87% of nonclustered APOBEC-induced mutations, the source and the genomic distribution of the ssDNA where they occur, are largely unknown. By analyzing genomic and exomic cancer databases, we show that >33% of dispersed APOBEC-induced mutations occur on the lagging strand during DNA replication, thus unraveling the major source of ssDNA targeted by APOBEC in cancer. Although methylated cytosine is generally more mutation-prone than nonmethylated cytosine, we report that methylation reduces the rate of APOBEC-induced mutations by a factor of roughly two. Finally, we show that in cancers with extensive APOBEC-induced mutagenesis, there is almost no increase in mutation rates in late replicating regions (contrary to other cancers). Because late-replicating regions are depleted in exons, this results in a 1.3-fold higher fraction of mutations residing within exons in such cancers. This study provides novel insight into the APOBEC-induced mutagenesis and describes the peculiarity of the mutational processes in cancers with the signature of APOBEC-induced mutations.
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Affiliation(s)
- Vladimir B Seplyarskiy
- Institute of Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia, 127051; Lomonosov Moscow State University, Moscow, Russia, 119991; Pirogov Russian National Research Medical University, Moscow, Russia, 117997
| | - Ruslan A Soldatov
- Institute of Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia, 127051; Lomonosov Moscow State University, Moscow, Russia, 119991
| | - Konstantin Y Popadin
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland; Institute of Genetics and Genomics in Geneva, 1211 Geneva, Switzerland
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland; Institute of Genetics and Genomics in Geneva, 1211 Geneva, Switzerland
| | - Georgii A Bazykin
- Institute of Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia, 127051; Lomonosov Moscow State University, Moscow, Russia, 119991; Pirogov Russian National Research Medical University, Moscow, Russia, 117997
| | - Sergey I Nikolaev
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland; Institute of Genetics and Genomics in Geneva, 1211 Geneva, Switzerland; Service of Genetic Medicine, University Hospitals of Geneva, 1211 Geneva, Switzerland
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90
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Knisbacher BA, Gerber D, Levanon EY. DNA Editing by APOBECs: A Genomic Preserver and Transformer. Trends Genet 2016; 32:16-28. [PMID: 26608778 DOI: 10.1016/j.tig.2015.10.005] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Revised: 10/18/2015] [Accepted: 10/22/2015] [Indexed: 10/22/2022]
Abstract
Information warfare is not limited to the cyber world because it is waged within our cells as well. The unique AID (activation-induced cytidine deaminase)/APOBEC (apolipoprotein B mRNA editing enzyme, catalytic polypeptide) family comprises proteins that alter DNA sequences by converting deoxycytidines to deoxyuridines through deamination. This C-to-U DNA editing enables them to inhibit parasitic viruses and retrotransposons by disrupting their genomic content. In addition to attacking genomic invaders, APOBECs can target their host genome, which can be beneficial by initiating processes that create antibody diversity needed for the immune system or by accelerating the rate of evolution. AID can also alter gene regulation by removing epigenetic modifications from genomic DNA. However, when uncontrolled, these powerful agents of change can threaten genome stability and eventually lead to cancer.
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Affiliation(s)
- Binyamin A Knisbacher
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 52900 Israel
| | - Doron Gerber
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 52900 Israel
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 52900 Israel.
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91
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Wang Y, Schmitt K, Guo K, Santiago ML, Stephens EB. Role of the single deaminase domain APOBEC3A in virus restriction, retrotransposition, DNA damage and cancer. J Gen Virol 2015; 97:1-17. [PMID: 26489798 DOI: 10.1099/jgv.0.000320] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The apolipoprotein mRNA editing enzyme catalytic polypeptide-like 3 (APOBEC3; A3) proteins are a family of seven cytidine deaminases (A3A, A3B, A3C, A3D, A3F, A3G and A3H) that restrict certain viral infections. These innate defence factors are best known for their ability to restrict the replication of human immunodeficiency virus type 1 (HIV-1) lacking a functional Vif protein (HIV-1Δvif) through the deamination of cytidine residues to uridines during reverse transcription, ultimately leading to lethal G → A changes in the viral genome. The best studied of the A3 proteins has been APOBEC3G because of its potent activity against HIV-1Δvif. However, one member of this family, A3A, has biological properties that make it unique among the A3 proteins. In this review, we will focus on the structural and phylogenetic features of the human and non-human primate A3A proteins, their role in the restriction of retroviruses and other viruses, and current findings on other biological properties affected by this protein.
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Affiliation(s)
- Yaqiong Wang
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS 66160, USA
| | - Kimberly Schmitt
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS 66160, USA
| | - Kejun Guo
- Departments of Medicine, Microbiology and Immunology, University of Colorado Denver Medical School, Aurora, CO 80045, USA
| | - Mario L Santiago
- Departments of Medicine, Microbiology and Immunology, University of Colorado Denver Medical School, Aurora, CO 80045, USA
| | - Edward B Stephens
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS 66160, USA
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92
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APOBEC3B high expression status is associated with aggressive phenotype in Japanese breast cancers. Breast Cancer 2015; 23:780-8. [PMID: 26476745 DOI: 10.1007/s12282-015-0641-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 09/18/2015] [Indexed: 12/29/2022]
Abstract
BACKGROUND The members of AID/APOBEC protein family possess cytidine deaminase activity that converts cytidine residue to uridine on DNA and RNA. Recent studies have shown the possible influence of APOBEC3B (A3B) as DNA mutators of breast cancer genome. However, the clinical significance of A3B expression in Japanese breast cancer has not been studied in detail. METHODS Ninety-three primary breast cancer tissues (74 estrogen-receptor (ER) positive, 3 ER and HER2 positive, 6 HER2 positive, and 10 triple negative) including 37 tumor-normal pairs were assessed for A3B mRNA expression using quantitative real-time RT-PCR. We analyzed the relation between A3B expression, mutation analysis of TP53 and PIK3CA by direct sequencing, polymorphic A3B deletion allele and human papillomavirus (HPV) infection in tumors. RESULTS A3B mRNA was overexpressed in tumors compared with normal tissue. Patients with high A3B expression were associated with subtype and progression of lymph node metastasis and pathological nuclear grade. However, the expression was not related to any other clinicopathological factors, including mutation of TP53 and PIK3CA, polymorphic A3B deletion allele, HPV infection and survival time. CONCLUSION The expression of A3B in breast cancer was higher than in non-cancerous tissues and was related to the lymph node metastasis and nuclear grade, which are reliable aggressive phenotype markers in breast cancer. Evaluation of A3B expression in tumor may be a marker for breast cancer with malignant potential.
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93
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Caval V, Bouzidi MS, Suspène R, Laude H, Dumargne MC, Bashamboo A, Krey T, Vartanian JP, Wain-Hobson S. Molecular basis of the attenuated phenotype of human APOBEC3B DNA mutator enzyme. Nucleic Acids Res 2015; 43:9340-9. [PMID: 26384561 PMCID: PMC4627089 DOI: 10.1093/nar/gkv935] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 09/08/2015] [Indexed: 12/22/2022] Open
Abstract
The human APOBEC3A and APOBEC3B genes (A3A and A3B) encode DNA mutator enzymes that deaminate cytidine and 5-methylcytidine residues in single-stranded DNA (ssDNA). They are important sources of mutations in many cancer genomes which show a preponderance of CG->TA transitions. Although both enzymes can hypermutate chromosomal DNA in an experimental setting, only A3A can induce double strand DNA breaks, even though the catalytic domains of A3B and A3A differ by only 9% at the protein level. Accordingly we sought the molecular basis underlying A3B attenuation through the generation of A3A-A3B chimeras and mutants. It transpires that the N-terminal domain facilitates A3B activity while a handful of substitutions in the catalytic C-terminal domain impacting ssDNA binding serve to attenuate A3B compared to A3A. Interestingly, functional attenuation is also observed for the rhesus monkey rhA3B enzyme compared to rhA3A indicating that this genotoxic dichotomy has been selected for and maintained for some 38 million years. Expression of all human ssDNA cytidine deaminase genes is absent in mature sperm indicating they contribute to somatic mutation and cancer but not human diversity.
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Affiliation(s)
- Vincent Caval
- Molecular Retrovirology Unit, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris cedex 15, France
| | - Mohamed S Bouzidi
- Molecular Retrovirology Unit, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris cedex 15, France
| | - Rodolphe Suspène
- Molecular Retrovirology Unit, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris cedex 15, France
| | - Hélène Laude
- Molecular Retrovirology Unit, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris cedex 15, France
| | - Marie-Charlotte Dumargne
- Human Developmental Genetics Unit, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris cedex 15, France
| | - Anu Bashamboo
- Human Developmental Genetics Unit, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris cedex 15, France
| | - Thomas Krey
- Structural Virology Unit, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris cedex 15, France
| | - Jean-Pierre Vartanian
- Molecular Retrovirology Unit, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris cedex 15, France
| | - Simon Wain-Hobson
- Molecular Retrovirology Unit, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris cedex 15, France
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94
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An APOBEC3A hypermutation signature is distinguishable from the signature of background mutagenesis by APOBEC3B in human cancers. Nat Genet 2015; 47:1067-72. [PMID: 26258849 PMCID: PMC4594173 DOI: 10.1038/ng.3378] [Citation(s) in RCA: 295] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 07/13/2015] [Indexed: 02/07/2023]
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95
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Swanton C, McGranahan N, Starrett GJ, Harris RS. APOBEC Enzymes: Mutagenic Fuel for Cancer Evolution and Heterogeneity. Cancer Discov 2015; 5:704-12. [PMID: 26091828 PMCID: PMC4497973 DOI: 10.1158/2159-8290.cd-15-0344] [Citation(s) in RCA: 344] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 05/14/2015] [Indexed: 12/16/2022]
Abstract
UNLABELLED Deep sequencing technologies are revealing the complexities of cancer evolution, casting light on mutational processes fueling tumor adaptation, immune escape, and treatment resistance. Understanding mechanisms driving cancer diversity is a critical step toward developing strategies to attenuate tumor evolution and adaptation. One emerging mechanism fueling tumor diversity and subclonal evolution is genomic DNA cytosine deamination catalyzed by APOBEC3B and at least one other APOBEC family member. Deregulation of APOBEC3 enzymes causes a general mutator phenotype that manifests as diverse and heterogeneous tumor subclones. Here, we summarize knowledge of the APOBEC DNA deaminase family in cancer, and their role as driving forces for intratumor heterogeneity and a therapeutic target to limit tumor adaptation. SIGNIFICANCE APOBEC mutational signatures may be enriched in tumor subclones, suggesting APOBEC cytosine deaminases fuel subclonal expansions and intratumor heterogeneity. APOBEC family members might represent a new class of drug target aimed at limiting tumor evolution, adaptation, and drug resistance.
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Affiliation(s)
- Charles Swanton
- The Francis Crick Institute, London, United Kingdom. UCL Cancer Institute, CRUK Lung Cancer Centre of Excellence, London, United Kingdom.
| | - Nicholas McGranahan
- The Francis Crick Institute, London, United Kingdom. Centre for Mathematics & Physics in the Life Sciences & Experimental Biology (CoMPLEX), University College London, London, United Kingdom
| | - Gabriel J Starrett
- Department of Biochemistry, Molecular Biology and Biophysics, Institute for Molecular Virology, and Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Reuben S Harris
- Department of Biochemistry, Molecular Biology and Biophysics, Institute for Molecular Virology, and Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota.
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96
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Bohn MF, Shandilya SMD, Silvas TV, Nalivaika EA, Kouno T, Kelch BA, Ryder SP, Kurt-Yilmaz N, Somasundaran M, Schiffer CA. The ssDNA Mutator APOBEC3A Is Regulated by Cooperative Dimerization. Structure 2015; 23:903-911. [PMID: 25914058 DOI: 10.1016/j.str.2015.03.016] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Revised: 03/11/2015] [Accepted: 03/19/2015] [Indexed: 01/27/2023]
Abstract
Deaminase activity mediated by the human APOBEC3 family of proteins contributes to genomic instability and cancer. APOBEC3A is by far the most active in this family and can cause rapid cell death when overexpressed, but in general how the activity of APOBEC3s is regulated on a molecular level is unclear. In this study, the biochemical and structural basis of APOBEC3A substrate binding and specificity is elucidated. We find that specific binding of single-stranded DNA is regulated by the cooperative dimerization of APOBEC3A. The crystal structure elucidates this homodimer as a symmetric domain swap of the N-terminal residues. This dimer interface provides insights into how cooperative protein-protein interactions may affect function in the APOBEC3 enzymes and provides a potential scaffold for strategies aimed at reducing their mutation load.
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Affiliation(s)
- Markus-Frederik Bohn
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School Worcester, 364 Plantation Street, MA 01605, USA
| | - Shivender M D Shandilya
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School Worcester, 364 Plantation Street, MA 01605, USA
| | - Tania V Silvas
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School Worcester, 364 Plantation Street, MA 01605, USA
| | - Ellen A Nalivaika
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School Worcester, 364 Plantation Street, MA 01605, USA
| | - Takahide Kouno
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School Worcester, 364 Plantation Street, MA 01605, USA; Department of Biochemistry, Molecular Biology and Biophysics, Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Brian A Kelch
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School Worcester, 364 Plantation Street, MA 01605, USA
| | - Sean P Ryder
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School Worcester, 364 Plantation Street, MA 01605, USA
| | - Nese Kurt-Yilmaz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School Worcester, 364 Plantation Street, MA 01605, USA
| | - Mohan Somasundaran
- Department of Pediatrics and Program in Molecular Medicine, University of Massachusetts Medical School Worcester, MA 01605, USA
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School Worcester, 364 Plantation Street, MA 01605, USA.
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97
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Henderson S, Fenton T. APOBEC3 genes: retroviral restriction factors to cancer drivers. Trends Mol Med 2015; 21:274-84. [PMID: 25820175 DOI: 10.1016/j.molmed.2015.02.007] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 02/09/2015] [Accepted: 02/19/2015] [Indexed: 12/31/2022]
Abstract
The APOBEC3 cytosine deaminases play key roles in innate immunity through their ability to mutagenize viral DNA and restrict viral replication. Recent advances in cancer genomics, together with biochemical characterization of the APOBEC3 enzymes, have now implicated at least two family members in somatic mutagenesis during tumor development. We review the evidence linking these enzymes to carcinogenesis and highlight key questions, including the potential mechanisms that misdirect APOBEC3 activity to the host genome, the links to viral infection, and the association between a common APOBEC3 polymorphism and cancer risk.
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Affiliation(s)
- Stephen Henderson
- Bill Lyons Informatics Centre, University College London Cancer Institute, London, UK
| | - Tim Fenton
- Department of Oncology, University College London Cancer Institute, London, UK.
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98
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APOBEC3B expression in breast cancer reflects cellular proliferation, while a deletion polymorphism is associated with immune activation. Proc Natl Acad Sci U S A 2015; 112:2841-6. [PMID: 25730878 DOI: 10.1073/pnas.1424869112] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Genomic sequencing studies of breast and other cancers have identified patterns of mutations that have been attributed to the endogenous mutator activity of APOBEC3B (A3B), a member of the AID/APOBEC family of cytidine deaminases. A3B gene expression is increased in many cancers, but its upstream drivers remain undefined. Furthermore, there exists a common germ-line deletion polymorphism (A3B(del)), which has been associated with a paradoxical increase in breast cancer risk. To examine causes and consequences of A3B expression and its constitutive absence in breast cancer, we analyzed two large clinically annotated genomic datasets [The Cancer Genome Atlas (TCGA) and the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC)]. We confirmed that A3B expression is associated with aggressive clinicopathologic characteristics and adverse outcomes and show that A3B expression is highly correlated with proliferative features (mitosis and cell cycle-related gene expression) in breast and 15 of 16 other solid tumor types. However, breast cancers arising in homozygous A3B(del) individuals with A3B absent did not differ in these features, indicating that A3B expression is a reflection rather than a direct cause of increased proliferation. Using gene set enrichment analysis (GSEA), we detected a pattern of immune activation in A3B(del) breast cancers, which seems to be related to hypermutation arising in A3B(del) carriers. Together, these results provide an explanation for A3B overexpression and its prognostic effect, giving context to additional study of this mutator as a cancer biomarker or putative drug target. In addition, although immune features of A3B(del) require additional study, these findings nominate the A3B(del) polymorphism as a potential predictor for cancer immunotherapy.
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99
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Abstract
Cancer genomic DNA sequences enable identification of all mutations and suggest targets for precision medicine. The identities and patterns of the mutations themselves also provide critical information for deducing the originating DNA damaging agents, causal molecular mechanisms, and thus additional therapeutic targets. A classic example is ultraviolet light, which crosslinks adjacent pyrimidines and leads to C-to-T transitions. A new example is the DNA cytosine deaminase APOBEC3B, which was identified recently as a source of DNA damage and mutagenesis in breast, head/neck, cervix, bladder, lung, ovary, and to lesser extents additional cancer types. This enzyme is normally an effector protein in the innate immune response to virus infection but upregulation in these cancer types causes elevated levels of genomic C-to-U deamination events, which manifest as C-to-T transitions and C-to-G transversions within distinct DNA trinucleotide contexts (preferentially 5’-TCA and 5’-TCG). Genomic C-to-U deamination events within the same trinucleotide contexts also lead to cytosine mutation clusters (kataegis), and may precipitate visible chromosomal aberrations such as translocations. Clinical studies indicate that APOBEC3B upregulation correlates with poorer outcomes for estrogen receptor-positive breast cancer patients, including shorter durations of disease-free survival and overall survival after surgery. APOBEC3B may therefore have both diagnostic and prognostic potential. APOBEC3B may also be a candidate for therapeutic targeting because inhibition of this non-essential enzyme is predicted to decrease tumor mutation rates and diminish the likelihood of undesirable mutation-dependent outcomes such as recurrence, metastasis, and the development of therapy resistant tumors.
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