1
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Song JH, Dávalos LM, MacCarthy T, Damaghi M. Evolvability of cancer-associated genes under APOBEC3A/B selection. iScience 2024; 27:109433. [PMID: 38550998 PMCID: PMC10972820 DOI: 10.1016/j.isci.2024.109433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 12/08/2023] [Accepted: 03/04/2024] [Indexed: 04/04/2024] Open
Abstract
Evolvability is an emergent hallmark of cancer that depends on intra-tumor heterogeneity and genetic variation. Mutations generated by APOBEC3 contribute to genetic variation and tumor evolvability. However, the influence of APOBEC3 on the evolvability of the genome and its differential impact on cancer genes versus non-cancer genes remains unclear. Analyzing over 40,000 human protein-coding transcripts, we identified distinct distribution patterns of APOBEC3A/B TC motifs between cancer and non-cancer genes, suggesting unique associations with cancer. Studying a bat species with numerous APOBEC3 genes, we found distinct motif patterns in orthologs of cancer genes compared to non-cancer genes, as in humans, suggesting APOBEC3 evolution to reduce impacts on the genome rather than the converse. Simulations confirmed that APOBEC3-induced heterogeneity enhances cancer evolution through bimodal patterns of mutations in certain classes of genes. Our results suggest the bimodal distribution of APOBEC-induced mutations can significantly increase cancer heterogeneity.
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Affiliation(s)
- Joon-Hyun Song
- Stony Brook Cancer Center, Stony Brook Medicine, Stony Brook University, Stony Brook, NY, USA
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA
| | - Liliana M Dávalos
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794, USA
- Consortium for Inter-Disciplinary Environmental Research, Stony Brook University, Stony Brook, NY 11794, USA
| | - Thomas MacCarthy
- Stony Brook Cancer Center, Stony Brook Medicine, Stony Brook University, Stony Brook, NY, USA
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA
| | - Mehdi Damaghi
- Stony Brook Cancer Center, Stony Brook Medicine, Stony Brook University, Stony Brook, NY, USA
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA
- Department of Pathology, Stony Brook Medicine, Stony Brook University, Stony Brook, NY, USA
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2
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Song JH, Dávalos LM, MacCarthy T, Damaghi M. Evolvability of cancer-associated genes under APOBEC3A/B selection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.27.554991. [PMID: 38106028 PMCID: PMC10723265 DOI: 10.1101/2023.08.27.554991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Evolvability is an emergent hallmark of cancer that depends on intra-tumor heterogeneity and, ultimately, genetic variation. Mutations generated by APOBEC3 cytidine deaminases can contribute to genetic variation and the consequences of APOBEC activation differ depending on the stage of cancer, with the most significant impact observed during the early stages. However, how APOBEC activity shapes evolutionary patterns of genes in the host genome and differential impacts on cancer-associated and non-cancer genes remain unclear. Analyzing over 40,000 human protein-coding transcripts, we identified distinct distribution patterns of APOBEC3A/B TC motifs between cancer-related genes and controls, suggesting unique associations with cancer. Studying a bat species with many more APOBEC3 genes, we found diverse motif patterns in orthologs of cancer genes compared to controls, similar to humans and suggesting APOBEC evolution to reduce impacts on the genome rather than the converse. Simulations confirmed that APOBEC-induced heterogeneity enhances cancer evolution, shaping clonal dynamics through bimodal introduction of mutations in certain classes of genes. Our results suggest that a major consequence of the bimodal distribution of APOBEC affects greater cancer heterogeneity.
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Affiliation(s)
- Joon-Hyun Song
- Stony Brook Cancer Center, Stony Brook Medicine, Stony Brook University, Stony Brook, NY, USA
- Department of Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA
| | - Liliana M. Dávalos
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, 11794, USA
- Consortium for Inter-Disciplinary Environmental Research, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Thomas MacCarthy
- Stony Brook Cancer Center, Stony Brook Medicine, Stony Brook University, Stony Brook, NY, USA
- Department of Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA
| | - Mehdi Damaghi
- Stony Brook Cancer Center, Stony Brook Medicine, Stony Brook University, Stony Brook, NY, USA
- Department of Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA
- Department of Pathology, Stony Brook Medicine, Stony Brook University, Stony Brook, NY, USA
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3
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Coxon M, Dennis MA, Dananberg A, Collins C, Wilson H, Meekma J, Savenkova M, Ng D, Osbron C, Mertz T, Goodman A, Duttke S, Maciejowski J, Roberts S. An impaired ubiquitin-proteasome system increases APOBEC3A abundance. NAR Cancer 2023; 5:zcad058. [PMID: 38155930 PMCID: PMC10753533 DOI: 10.1093/narcan/zcad058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 11/21/2023] [Accepted: 12/08/2023] [Indexed: 12/30/2023] Open
Abstract
Apolipoprotein B messenger RNA (mRNA) editing enzyme, catalytic polypeptide-like (APOBEC) cytidine deaminases cause genetic instability during cancer development. Elevated APOBEC3A (A3A) levels result in APOBEC signature mutations; however, mechanisms regulating A3A abundance in breast cancer are unknown. Here, we show that dysregulating the ubiquitin-proteasome system with proteasome inhibitors, including Food and Drug Administration-approved anticancer drugs, increased A3A abundance in breast cancer and multiple myeloma cell lines. Unexpectedly, elevated A3A occurs via an ∼100-fold increase in A3A mRNA levels, indicating that proteasome inhibition triggers a transcriptional response as opposed to or in addition to blocking A3A degradation. This transcriptional regulation is mediated in part through FBXO22, a protein that functions in SKP1-cullin-F-box ubiquitin ligase complexes and becomes dysregulated during carcinogenesis. Proteasome inhibitors increased cellular cytidine deaminase activity, decreased cellular proliferation and increased genomic DNA damage in an A3A-dependent manner. Our findings suggest that proteasome dysfunction, either acquired during cancer development or induced therapeutically, could increase A3A-induced genetic heterogeneity and thereby influence therapeutic responses in patients.
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Affiliation(s)
- Margo Coxon
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
| | - Madeline A Dennis
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
| | - Alexandra Dananberg
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Christopher D Collins
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
| | - Hannah E Wilson
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
| | - Jordyn Meekma
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
| | - Marina I Savenkova
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
| | - Daniel Ng
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
| | - Chelsea A Osbron
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
| | - Tony M Mertz
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
- Department of Microbiology and Molecular Genetics, University of Vermont Cancer Center, University of Vermont, Burlington, VT 05405, USA
| | - Alan G Goodman
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
| | - Sascha H Duttke
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
| | - John Maciejowski
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Steven A Roberts
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
- Department of Microbiology and Molecular Genetics, University of Vermont Cancer Center, University of Vermont, Burlington, VT 05405, USA
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4
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Alonso de la Vega A, Temiz NA, Tasakis R, Somogyi K, Salgueiro L, Zimmer E, Ramos M, Diaz-Jimenez A, Chocarro S, Fernández-Vaquero M, Stefanovska B, Reuveni E, Ben-David U, Stenzinger A, Poth T, Heikenwälder M, Papavasiliou N, Harris RS, Sotillo R. Acute expression of human APOBEC3B in mice results in RNA editing and lethality. Genome Biol 2023; 24:267. [PMID: 38001542 PMCID: PMC10668425 DOI: 10.1186/s13059-023-03115-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 11/20/2023] [Indexed: 11/26/2023] Open
Abstract
BACKGROUND RNA editing has been described as promoting genetic heterogeneity, leading to the development of multiple disorders, including cancer. The cytosine deaminase APOBEC3B is implicated in tumor evolution through DNA mutation, but whether it also functions as an RNA editing enzyme has not been studied. RESULTS Here, we engineer a novel doxycycline-inducible mouse model of human APOBEC3B-overexpression to understand the impact of this enzyme in tissue homeostasis and address a potential role in C-to-U RNA editing. Elevated and sustained levels of APOBEC3B lead to rapid alteration of cellular fitness, major organ dysfunction, and ultimately lethality in mice. Importantly, RNA-sequencing of mouse tissues expressing high levels of APOBEC3B identifies frequent UCC-to-UUC RNA editing events that are not evident in the corresponding genomic DNA. CONCLUSIONS This work identifies, for the first time, a new deaminase-dependent function for APOBEC3B in RNA editing and presents a preclinical tool to help understand the emerging role of APOBEC3B as a driver of carcinogenesis.
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Affiliation(s)
- Alicia Alonso de la Vega
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Ruprecht Karl University of Heidelberg, 69120, Heidelberg, Germany
| | - Nuri Alpay Temiz
- Health Informatics Institute, University of Minnesota, Minneapolis, 55455, USA
| | - Rafail Tasakis
- Division of Immune Diversity, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Kalman Somogyi
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Lorena Salgueiro
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Eleni Zimmer
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Ruprecht Karl University of Heidelberg, 69120, Heidelberg, Germany
| | - Maria Ramos
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Ruprecht Karl University of Heidelberg, 69120, Heidelberg, Germany
| | - Alberto Diaz-Jimenez
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Ruprecht Karl University of Heidelberg, 69120, Heidelberg, Germany
| | - Sara Chocarro
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Ruprecht Karl University of Heidelberg, 69120, Heidelberg, Germany
| | - Mirian Fernández-Vaquero
- Ruprecht Karl University of Heidelberg, 69120, Heidelberg, Germany
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bojana Stefanovska
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Eli Reuveni
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Uri Ben-David
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Albrecht Stenzinger
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TRLC), German Center for Lung Research (DZL), Heidelberg, Germany
| | - Tanja Poth
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Mathias Heikenwälder
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Nina Papavasiliou
- Division of Immune Diversity, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Reuben S Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Rocio Sotillo
- Division of Molecular Thoracic Oncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.
- Translational Lung Research Center Heidelberg (TRLC), German Center for Lung Research (DZL), Heidelberg, Germany.
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5
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Granadillo Rodríguez M, Wong L, Chelico L. Similar deamination activities but different phenotypic outcomes induced by APOBEC3 enzymes in breast epithelial cells. Front Genome Ed 2023; 5:1196697. [PMID: 37324648 PMCID: PMC10267419 DOI: 10.3389/fgeed.2023.1196697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/22/2023] [Indexed: 06/17/2023] Open
Abstract
APOBEC3 (A3) enzymes deaminate cytosine to uracil in viral single-stranded DNA as a mutagenic barrier for some viruses. A3-induced deaminations can also occur in human genomes resulting in an endogenous source of somatic mutations in multiple cancers. However, the roles of each A3 are unclear since few studies have assessed these enzymes in parallel. Thus, we developed stable cell lines expressing A3A, A3B, or A3H Hap I using non-tumorigenic MCF10A and tumorigenic MCF7 breast epithelial cells to assess their mutagenic potential and cancer phenotypes in breast cells. The activity of these enzymes was characterized by γH2AX foci formation and in vitro deamination. Cell migration and soft agar colony formation assays assessed cellular transformation potential. We found that all three A3 enzymes had similar γH2AX foci formation, despite different deamination activities in vitro. Notably, in nuclear lysates, the in vitro deaminase activity of A3A, A3B, and A3H did not require digestion of cellular RNA, in contrast to that of A3B and A3H in whole-cell lysates. Their similar activities in cells, nonetheless, resulted in distinct phenotypes where A3A decreased colony formation in soft agar, A3B decreased colony formation in soft agar after hydroxyurea treatment, and A3H Hap I promoted cell migration. Overall, we show that in vitro deamination data do not always reflect cell DNA damage, all three A3s induce DNA damage, and the impact of each is different.
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6
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Wong L, Sami A, Chelico L. Competition for DNA binding between the genome protector replication protein A and the genome modifying APOBEC3 single-stranded DNA deaminases. Nucleic Acids Res 2022; 50:12039-12057. [PMID: 36444883 PMCID: PMC9757055 DOI: 10.1093/nar/gkac1121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/21/2022] [Accepted: 11/08/2022] [Indexed: 11/30/2022] Open
Abstract
The human APOBEC family of eleven cytosine deaminases use RNA and single-stranded DNA (ssDNA) as substrates to deaminate cytosine to uracil. This deamination event has roles in lipid metabolism by altering mRNA coding, adaptive immunity by causing evolution of antibody genes, and innate immunity through inactivation of viral genomes. These benefits come at a cost where some family members, primarily from the APOBEC3 subfamily (APOBEC3A-H, excluding E), can cause off-target deaminations of cytosine to form uracil on transiently single-stranded genomic DNA, which induces mutations that are associated with cancer evolution. Since uracil is only promutagenic, the mutations observed in cancer genomes originate only when uracil is not removed by uracil DNA glycosylase (UNG) or when the UNG-induced abasic site is erroneously repaired. However, when ssDNA is present, replication protein A (RPA) binds and protects the DNA from nucleases or recruits DNA repair proteins, such as UNG. Thus, APOBEC enzymes must compete with RPA to access their substrate. Certain APOBEC enzymes can displace RPA, bind and scan ssDNA efficiently to search for cytosines, and can become highly overexpressed in tumor cells. Depending on the DNA replication conditions and DNA structure, RPA can either be in excess or deficient. Here we discuss the interplay between these factors and how despite RPA, multiple cancer genomes have a mutation bias at cytosines indicative of APOBEC activity.
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Affiliation(s)
- Lai Wong
- University of Saskatchewan, College of Medicine, Department of Biochemistry, Microbiology, and Immunology, Saskatoon, Saskatchewan, S7N 5E5, Canada
| | - Alina Sami
- University of Saskatchewan, College of Medicine, Department of Biochemistry, Microbiology, and Immunology, Saskatoon, Saskatchewan, S7N 5E5, Canada
| | - Linda Chelico
- To whom correspondence should be addressed. Tel: +1 306 966 4318; Fax: +1 306 966 4298;
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7
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Dananberg A, Maciejowski J. Monitoring APOBEC3A protein levels in human cancer cells. Methods Cell Biol 2022; 182:313-327. [PMID: 38359985 PMCID: PMC10869936 DOI: 10.1016/bs.mcb.2022.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The APOBEC3 family of cytosine deaminases, which target single-stranded DNA and RNA of viruses and retroelements as part of the innate immune defense, generate mutations in many human cancers. Although the APOBEC3A paralog is a major endogenous source of these mutations, low APOBEC3A mRNA levels and protein abundance have hampered functional characterization. Extensive homology across APOBEC3 paralogs have further challenged the development of specific detection reagents. Here, we describe the isolation and use of monoclonal antibodies with specificity for APOBEC3A and the APOBEC3A/APOBEC3B/APOBEC3G proteins. We provide protocols and technical advice for detection and measurement of APOBEC3A protein across human cancer cell lines using standard immunoblotting and immunofluorescence protocols.
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Affiliation(s)
- Alexandra Dananberg
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - John Maciejowski
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, United States.
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8
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Yang X, Dai J, Yao S, An J, Wen G, Jin H, Zhang L, Zheng L, Chen X, Yi Z, Tuo B. APOBEC3B: Future direction of liver cancer research. Front Oncol 2022; 12:996115. [PMID: 36203448 PMCID: PMC9530283 DOI: 10.3389/fonc.2022.996115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 08/22/2022] [Indexed: 12/03/2022] Open
Abstract
Liver cancer is one of the most common cancers in the world, and the rate of liver cancer is high due to the of its illness. The main risk factor for liver cancer is infection with the hepatitis B virus (HBV), but a considerable number of genetic and epigenetic factors are also directly or indirectly involved in the underlying pathogenesis of liver cancer. In particular, the apolipoprotein B mRNA editing enzyme, catalytic peptide-like protein (APOBEC) family (DNA or mRNA editor family), which has been the focus of virology research for more than a decade, has been found to play a significant role in the occurrence and development of various cancers, providing a new direction for the research of liver cancer. APOBEC3B is a cytosine deaminase that controls a variety of biological processes, such as protein expression, innate immunity, and embryonic development, by participating in the process of cytidine deamination to uridine in DNA and RNA. In humans, APOBEC3B has long been known as a DNA editor for limiting viral replication and transcription. APOBEC3B is widely expressed at low levels in a variety of normal tissues and organs, but it is significantly upregulated in different types of tumor tissues and tumor lines. Thus, APOBEC3B has received increasing attention in various cancers, but the role of APOBEC3B in the occurrence and development of liver cancer due to infection with HBV remains unclear. This review provides a brief introduction to the pathogenesis of hepatocellular carcinoma induced by HBV, and it further explores the latest results of APOBEC3B research in the development of HBV and liver cancer, thereby providing new directions and strategies for the treatment and prevention of liver cancer.
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Affiliation(s)
- Xingyue Yang
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Jing Dai
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Shun Yao
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Jiaxing An
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Guorong Wen
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Hai Jin
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Li Zhang
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Liming Zheng
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Xingyue Chen
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Zhiqiang Yi
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Biguang Tuo
- Department of Gastroenterology, Digestive Disease Hospital, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- The Collaborative Innovation Center of Tissue Damage Repair and Regenerative Medicine of Zunyi Medical University, Zunyi, China
- *Correspondence: Biguang Tuo,
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9
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Unifying Different Cancer Theories in a Unique Tumour Model: Chronic Inflammation and Deaminases as Meeting Points. Int J Mol Sci 2022; 23:ijms23158720. [PMID: 35955853 PMCID: PMC9368936 DOI: 10.3390/ijms23158720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 07/29/2022] [Accepted: 08/02/2022] [Indexed: 12/24/2022] Open
Abstract
The increase in cancer incidences shows that there is a need to better understand tumour heterogeneity to achieve efficient treatments. Interestingly, there are several common features among almost all types of cancers, with chronic inflammation induction and deaminase dysfunctions singled out. Deaminases are a family of enzymes with nucleotide-editing capacity, which are classified into two main groups: DNA-based and RNA-based. Remarkably, a close relationship between inflammation and the dysregulation of these molecules has been widely documented, which may explain the characteristic intratumor heterogeneity, both at DNA and transcriptional levels. Indeed, heterogeneity in cancer makes it difficult to establish a unique tumour progression model. Currently, there are three main cancer models—stochastic, hierarchic, and dynamic—although there is no consensus on which one better resembles cancer biology because they are usually overly simplified. Here, to accurately explain tumour progression, we propose interactions among chronic inflammation, deaminases dysregulation, intratumor genetic heterogeneity, cancer phenotypic plasticity, and even the previously proposed appearance of cancer stem-like cell populations in the edges of advanced solid tumour masses (instead of being the cells of origin of primary malignancies). The new tumour development model proposed in this study does not contradict previously accepted models and it may open up a window to interesting therapeutic approaches.
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10
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DeWeerd RA, Németh E, Póti Á, Petryk N, Chen CL, Hyrien O, Szüts D, Green AM. Prospectively defined patterns of APOBEC3A mutagenesis are prevalent in human cancers. Cell Rep 2022; 38:110555. [PMID: 35320711 PMCID: PMC9283007 DOI: 10.1016/j.celrep.2022.110555] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 12/15/2021] [Accepted: 03/02/2022] [Indexed: 12/14/2022] Open
Abstract
Mutational signatures defined by single base substitution (SBS) patterns in cancer have elucidated potential mutagenic processes that contribute to malignancy. Two prevalent mutational patterns in human cancers are attributed to the APOBEC3 cytidine deaminase enzymes. Among the seven human APOBEC3 proteins, APOBEC3A is a potent deaminase and proposed driver of cancer mutagenesis. In this study, we prospectively examine genome-wide aberrations by expressing human APOBEC3A in avian DT40 cells. From whole-genome sequencing, we detect hundreds to thousands of base substitutions per genome. The APOBEC3A signature includes widespread cytidine mutations and a unique insertion-deletion (indel) signature consisting largely of cytidine deletions. This multi-dimensional APOBEC3A signature is prevalent in human cancer genomes. Our data further reveal replication-associated mutations, the rate of stem-loop and clustered mutations, and deamination of methylated cytidines. This comprehensive signature of APOBEC3A mutagenesis is a tool for future studies and a potential biomarker for APOBEC3 activity in cancer.
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Affiliation(s)
- Rachel A DeWeerd
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Eszter Németh
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Ádám Póti
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Nataliya Petryk
- Epigenetics & Cell Fate UMR7216, CNRS, University of Paris, 35 rue Hélène Brion, 75013 Paris, France
| | - Chun-Long Chen
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3244, Dynamics of Genetic Information, Paris, France
| | - Olivier Hyrien
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 46 rue d'Ulm, 75005 Paris, France
| | - Dávid Szüts
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary.
| | - Abby M Green
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA; Center for Genome Integrity, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA.
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11
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Impact of the APOBEC3A/B deletion polymorphism on risk of ovarian cancer. Sci Rep 2021; 11:23463. [PMID: 34873230 PMCID: PMC8648731 DOI: 10.1038/s41598-021-02820-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 11/16/2021] [Indexed: 12/24/2022] Open
Abstract
A germline 29.5-kb deletion variant removes the 3’ end of the APOBEC3A gene and a large part of APOBEC3B, creating a hybrid gene that has been linked to increased APOBEC3 activity and DNA damage in human cancers. We genotyped the APOBEC3A/B deletion in hospital-based samples of 1398 Norwegian epithelial ovarian cancer patients without detected BRCA1/2 germline mutations and compared to 1,918 healthy female controls, to assess the potential cancer risk associated with the deletion. We observed an association between APOBEC3A/B status and reduced risk for ovarian cancer (OR = 0.75; CI = 0.61–0.91; p = 0.003) applying the dominant model. Similar results were found in other models. The association was observed both in non-serous and serous cases (dominant model: OR = 0.69; CI = 0.50–0.95; p = 0.018 and OR = 0.77; CI = 0.62–0.96; p = 0.019, respectively) as well as within high-grade serous cases (dominant model: OR = 0.79; CI = 0.59–1.05). For validation purposes, we mined an available large multinational GWAS-based data set of > 18,000 cases and > 26,000 controls for SNP rs12628403, known to be in linkage disequilibrium with the APOBEC3A/B deletion. We found a non-significant trend for SNP rs12628403 being linked to reduced risk of ovarian cancer in general and similar trends for all subtypes. For clear cell cancers, the risk reduction reached significance (OR = 0.85; CI = 0.69–1.00).
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12
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Li MM, Mroz EA, Faquin WC, Lott-Limbach A, Rocco JW. ERα: A biomarker and treatment target for oropharyngeal cancer? Oral Oncol 2021; 124:105637. [PMID: 34857487 DOI: 10.1016/j.oraloncology.2021.105637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/16/2021] [Accepted: 11/18/2021] [Indexed: 11/16/2022]
Affiliation(s)
- Michael M Li
- Department of Otolaryngology - Head and Neck Surgery, Ohio State University Wexner Medical Center, Columbus, OH 43201, USA
| | - Edmund A Mroz
- Department of Otolaryngology - Head and Neck Surgery, Ohio State University Wexner Medical Center, Columbus, OH 43201, USA; The Ohio State University Comprehensive Cancer Center - James, 818 BRT, 460 West 12th Avenue, Columbus, OH 43210, USA
| | - William C Faquin
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Abberly Lott-Limbach
- Department of Pathology, Ohio State University Wexner Medical Center, Columbus, OH 43201, USA
| | - James W Rocco
- Department of Otolaryngology - Head and Neck Surgery, Ohio State University Wexner Medical Center, Columbus, OH 43201, USA; The Ohio State University Comprehensive Cancer Center - James, 818 BRT, 460 West 12th Avenue, Columbus, OH 43210, USA.
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13
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Caval V, Suspène R, Khalfi P, Gaillard J, Caignard G, Vitour D, Roingeard P, Vartanian JP, Wain-Hobson S. Frame-shifted APOBEC3A encodes two alternative proapoptotic proteins that target the mitochondrial network. J Biol Chem 2021; 297:101081. [PMID: 34403699 PMCID: PMC8424220 DOI: 10.1016/j.jbc.2021.101081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 08/04/2021] [Accepted: 08/12/2021] [Indexed: 12/02/2022] Open
Abstract
The human APOBEC3A (A3A) cytidine deaminase is a powerful DNA mutator enzyme recognized as a major source of somatic mutations in tumor cell genomes. However, there is a discrepancy between APOBEC3A mRNA levels after interferon stimulation in myeloid cells and A3A detection at the protein level. To understand this difference, we investigated the expression of two novel alternative “A3Alt” proteins encoded in the +1-shifted reading frame of the APOBEC3A gene. A3Alt-L and its shorter isoform A3Alt-S appear to be transmembrane proteins targeted to the mitochondrial compartment that induce membrane depolarization and apoptosis. Thus, the APOBEC3A gene represents a new example wherein a single gene encodes two proapoptotic proteins, A3A cytidine deaminases that target the genome and A3Alt proteins that target mitochondria.
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Affiliation(s)
- Vincent Caval
- Molecular Retrovirology Unit, Institut Pasteur, Paris, France.
| | | | - Pierre Khalfi
- Molecular Retrovirology Unit, Institut Pasteur, Paris, France; Sorbonne Université, Complexité du Vivant, ED515, Paris, France
| | - Julien Gaillard
- Morphogenèse et Antigénicité du VIH et des Virus des Hépatites, Inserm-U1259 MAVIVH, Université de Tours and CHRU de Tours, Tours, France; Plate-Forme IBiSA des Microscopies, PPF ASB, Université de Tours and CHRU de Tours, Tours, France
| | - Grégory Caignard
- UMR Virologie, INRAE, Ecole Nationale Vétérinaire d'Alfort, Laboratoire de santé animale d'Alfort, Anses, Université Paris-Est, Maisons-Alfort, France
| | - Damien Vitour
- UMR Virologie, INRAE, Ecole Nationale Vétérinaire d'Alfort, Laboratoire de santé animale d'Alfort, Anses, Université Paris-Est, Maisons-Alfort, France
| | - Philippe Roingeard
- Morphogenèse et Antigénicité du VIH et des Virus des Hépatites, Inserm-U1259 MAVIVH, Université de Tours and CHRU de Tours, Tours, France; Plate-Forme IBiSA des Microscopies, PPF ASB, Université de Tours and CHRU de Tours, Tours, France
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14
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Green AM, DeWeerd RA, O'Leary DR, Hansen AR, Hayer KE, Kulej K, Dineen AS, Szeto JH, Garcia BA, Weitzman MD. Interaction with the CCT chaperonin complex limits APOBEC3A cytidine deaminase cytotoxicity. EMBO Rep 2021; 22:e52145. [PMID: 34347354 DOI: 10.15252/embr.202052145] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 07/02/2021] [Accepted: 07/05/2021] [Indexed: 11/09/2022] Open
Abstract
The APOBEC3 cytidine deaminases are implicated as the cause of a prevalent somatic mutation pattern found in cancer genomes. The APOBEC3 enzymes act as viral restriction factors by mutating viral genomes. Mutation of the cellular genome is presumed to be an off-target activity of the enzymes, although the regulatory measures for APOBEC3 expression and activity remain undefined. It is therefore difficult to predict circumstances that enable APOBEC3 interaction with cellular DNA that leads to mutagenesis. The APOBEC3A (A3A) enzyme is the most potent deaminase of the family. Using proteomics, we evaluate protein interactors of A3A to identify potential regulators. We find that A3A interacts with the chaperonin-containing TCP-1 (CCT) complex, a cellular machine that assists in protein folding and function. Importantly, depletion of CCT results in A3A-induced DNA damage and cytotoxicity. Evaluation of cancer genomes demonstrates an enrichment of A3A mutational signatures in cancers with silencing mutations in CCT subunit genes. Together, these data suggest that the CCT complex interacts with A3A, and that disruption of CCT function results in increased A3A mutational activity.
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Affiliation(s)
- Abby M Green
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA.,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Rachel A DeWeerd
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - David R O'Leary
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Ava R Hansen
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Katharina E Hayer
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Katarzyna Kulej
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ariel S Dineen
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Julia H Szeto
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Perelman School of Medicine, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew D Weitzman
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Perelman School of Medicine, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA.,Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
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15
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Pan JW, Zabidi MMA, Chong BK, Meng MY, Ng PS, Hasan SN, Sandey B, Bahnu S, Rajadurai P, Yip CH, Rueda OM, Caldas C, Chin SF, Teo SH. Germline APOBEC3B deletion increases somatic hypermutation in Asian breast cancer that is associated with Her2 subtype, PIK3CA mutations and immune activation. Int J Cancer 2021; 148:2489-2501. [PMID: 33423300 DOI: 10.1002/ijc.33463] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 12/03/2020] [Accepted: 12/04/2020] [Indexed: 12/11/2022]
Abstract
A 30-kb deletion that eliminates the coding region of APOBEC3B (A3B) is >5 times more common in women of Asian descent compared to European descent. This polymorphism creates a chimera with the APOBEC3A (A3A) coding region and A3B 3'UTR, and it is associated with an increased risk for breast cancer in Asian women. Here, we explored the relationship between the A3B deletion polymorphism with tumour characteristics in Asian women. Using whole exome and whole transcriptome sequencing data of 527 breast tumours, we report that germline A3B deletion polymorphism leads to expression of the A3A-B hybrid isoform and increased APOBEC-associated somatic hypermutation. Hypermutated tumours, regardless of A3B germline status, were associated with the Her2 molecular subtype and PIK3CA mutations. Compared to nonhypermutated tumours, hypermutated tumours also had higher neoantigen burden, tumour heterogeneity and immune activation. Taken together, our results suggest that the germline A3B deletion polymorphism, via the A3A-B hybrid isoform, contributes to APOBEC mutagenesis in a significant proportion of Asian breast cancers. In addition, APOBEC somatic hypermutation, regardless of A3B background, may be an important clinical biomarker for Asian breast cancers.
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Affiliation(s)
- Jia-Wern Pan
- Genomics and Bioinformatics Research Unit, Cancer Research Malaysia, Subang Jaya, Malaysia
| | | | - Boon-Keat Chong
- Genomics and Bioinformatics Research Unit, Cancer Research Malaysia, Subang Jaya, Malaysia
| | - Mei-Yee Meng
- Genomics and Bioinformatics Research Unit, Cancer Research Malaysia, Subang Jaya, Malaysia
| | - Pei-Sze Ng
- Genomics and Bioinformatics Research Unit, Cancer Research Malaysia, Subang Jaya, Malaysia
- University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - Siti Norhidayu Hasan
- Genomics and Bioinformatics Research Unit, Cancer Research Malaysia, Subang Jaya, Malaysia
| | - Bethan Sandey
- Cancer Research UK, Cambridge Institute & Department of Oncology, Li Ka Shing Centre, Cambridge, UK
| | - Saira Bahnu
- Subang Jaya Medical Centre, Subang Jaya, Malaysia
| | | | - Cheng-Har Yip
- University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
- Subang Jaya Medical Centre, Subang Jaya, Malaysia
| | - Oscar M Rueda
- Cancer Research UK, Cambridge Institute & Department of Oncology, Li Ka Shing Centre, Cambridge, UK
| | - Carlos Caldas
- Cancer Research UK, Cambridge Institute & Department of Oncology, Li Ka Shing Centre, Cambridge, UK
- Cambridge Breast Cancer Research Unit, CRUK Cambridge Cancer Centre, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre and Cambridge Experimental Cancer Medicine Centre, Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
| | - Suet-Feung Chin
- Cancer Research UK, Cambridge Institute & Department of Oncology, Li Ka Shing Centre, Cambridge, UK
| | - Soo-Hwang Teo
- Genomics and Bioinformatics Research Unit, Cancer Research Malaysia, Subang Jaya, Malaysia
- University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
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16
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Perez-Bercoff D, Laude H, Lemaire M, Hunewald O, Thiers V, Vignuzzi M, Blanc H, Poli A, Amoura Z, Caval V, Suspène R, Hafezi F, Mathian A, Vartanian JP, Wain-Hobson S. Sustained high expression of multiple APOBEC3 cytidine deaminases in systemic lupus erythematosus. Sci Rep 2021; 11:7893. [PMID: 33846459 PMCID: PMC8041901 DOI: 10.1038/s41598-021-87024-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 03/23/2021] [Indexed: 12/13/2022] Open
Abstract
APOBEC3 (A3) enzymes are best known for their role as antiviral restriction factors and as mutagens in cancer. Although four of them, A3A, A3B, A3F and A3G, are induced by type-1-interferon (IFN-I), their role in inflammatory conditions is unknown. We thus investigated the expression of A3, and particularly A3A and A3B because of their ability to edit cellular DNA, in Systemic Lupus Erythematosus (SLE), a chronic inflammatory disease characterized by high IFN-α serum levels. In a cohort of 57 SLE patients, A3A and A3B, but also A3C and A3G, were upregulated ~ 10 to 15-fold (> 1000-fold for A3B) compared to healthy controls, particularly in patients with flares and elevated serum IFN-α levels. Hydroxychloroquine, corticosteroids and immunosuppressive treatment did not reverse A3 levels. The A3AΔ3B polymorphism, which potentiates A3A, was detected in 14.9% of patients and in 10% of controls, and was associated with higher A3A mRNA expression. A3A and A3B mRNA levels, but not A3C or A3G, were correlated positively with dsDNA breaks and negatively with lymphopenia. Exposure of SLE PBMCs to IFN-α in culture induced massive and sustained A3A levels by 4 h and led to massive cell death. Furthermore, the rs2853669 A > G polymorphism in the telomerase reverse transcriptase (TERT) promoter, which disrupts an Ets-TCF-binding site and influences certain cancers, was highly prevalent in SLE patients, possibly contributing to lymphopenia. Taken together, these findings suggest that high baseline A3A and A3B levels may contribute to cell frailty, lymphopenia and to the generation of neoantigens in SLE patients. Targeting A3 expression could be a strategy to reverse cell death and the generation of neoantigens.
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Affiliation(s)
- Danielle Perez-Bercoff
- Department of Infection and Immunity, Luxembourg Institute of Health, 29 rue Henri Koch, 4354, Esch-sur-Alzette, Luxembourg.
| | - Hélène Laude
- ICAReB Platform, 28 rue du Docteur Roux, 75724, Paris Cedex 15, France
- Viral Populations and Pathogenesis Unit, UMR 3569, CNRS, Institut Pasteur, 28 rue du Dr. Roux, 75724, Paris Cedex 15, France
| | - Morgane Lemaire
- Department of Infection and Immunity, Luxembourg Institute of Health, 29 rue Henri Koch, 4354, Esch-sur-Alzette, Luxembourg
| | - Oliver Hunewald
- Department of Infection and Immunity, Luxembourg Institute of Health, 29 rue Henri Koch, 4354, Esch-sur-Alzette, Luxembourg
| | - Valérie Thiers
- Molecular Retrovirology Unit, UMR 3569, Institut Pasteur, CNRS, 28 rue du Dr. Roux, 75724, Paris cedex 15, France
| | - Marco Vignuzzi
- Viral Populations and Pathogenesis Unit, UMR 3569, CNRS, Institut Pasteur, 28 rue du Dr. Roux, 75724, Paris Cedex 15, France
| | - Hervé Blanc
- Viral Populations and Pathogenesis Unit, UMR 3569, CNRS, Institut Pasteur, 28 rue du Dr. Roux, 75724, Paris Cedex 15, France
| | - Aurélie Poli
- Department of Infection and Immunity, Luxembourg Institute of Health, 29 rue Henri Koch, 4354, Esch-sur-Alzette, Luxembourg
| | - Zahir Amoura
- Sorbonne Université, Assistance Publique-Hôpitaux de Paris, Groupement Hospitalier Pitié-Salpêtrière, French National Referral Center for Systemic Lupus Erythematosus, Antiphospholipid Antibody Syndrome and Other Autoimmune Disorders, Service de Médecine Interne 2, Institut E3M, Inserm UMRS, Centre D'Immunologie Et Des Maladies Infectieuses (CIMI-Paris), Paris, France
| | - Vincent Caval
- Departement de Virologie, Institut Pasteur, 28 rue du Dr. Roux, 75724, Paris Cedex 15, France
| | - Rodolphe Suspène
- Departement de Virologie, Institut Pasteur, 28 rue du Dr. Roux, 75724, Paris Cedex 15, France
| | - François Hafezi
- Department of Infection and Immunity, Luxembourg Institute of Health, 29 rue Henri Koch, 4354, Esch-sur-Alzette, Luxembourg
| | - Alexis Mathian
- Sorbonne Université, Assistance Publique-Hôpitaux de Paris, Groupement Hospitalier Pitié-Salpêtrière, French National Referral Center for Systemic Lupus Erythematosus, Antiphospholipid Antibody Syndrome and Other Autoimmune Disorders, Service de Médecine Interne 2, Institut E3M, Inserm UMRS, Centre D'Immunologie Et Des Maladies Infectieuses (CIMI-Paris), Paris, France
| | - Jean-Pierre Vartanian
- Molecular Retrovirology Unit, UMR 3569, Institut Pasteur, CNRS, 28 rue du Dr. Roux, 75724, Paris cedex 15, France
- Departement de Virologie, Institut Pasteur, 28 rue du Dr. Roux, 75724, Paris Cedex 15, France
| | - Simon Wain-Hobson
- Molecular Retrovirology Unit, UMR 3569, Institut Pasteur, CNRS, 28 rue du Dr. Roux, 75724, Paris cedex 15, France
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17
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Ben X, Tian D, Liang J, Wu M, Xie F, Zheng J, Chen J, Fei Q, Guo X, Weng X, Liu S, Xie X, Ying Y, Qiao G, Jing C. APOBEC3B deletion polymorphism and lung cancer risk in the southern Chinese population. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:656. [PMID: 33987354 PMCID: PMC8105993 DOI: 10.21037/atm-21-989] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Background Approximately 80–85% of lung cancer is the non-small cell lung cancer (NSCLC) subtype, which ranks as the leading cause of cancer deaths worldwide. APOBEC3B (A3B) was reported to be a key source of mutations in NSCLC. However, the role of the A3B deletion polymorphism in the etiology of NSCLC has not been well-documented. Methods A case-control study with 317 NSCLC patients and 334 healthy controls was conducted to explore the association between the A3B deletion polymorphism and the risk of NSCLC. The unconditional logistic regression model was performed to calculate the odds ratio (OR) and the 95% confidence interval (CI), and the confounding factors were adjusted, including age, gender, and smoking status, to estimate the risk. An analysis of gene-environment interactions was performed using multifactor dimensionality reduction (MDR) software. Results We found that the del/del genotype of A3B deletion significantly increased NSCLC risk. Compared with individuals carrying the ins/ins genotype of A3B deletion, individuals with the del/del genotype had a 2.36 times increased risk of developing NSCLC after adjusting for confounding factors (OR =2.71, 95% CI: 1.67–4.42, P<0.001). A 3-factor gene-environment (A3B deletion, gender, and smoking) interaction model was found for NSCLC (OR =4.407, 95% CI: 1.174–16.549, P=0.028). Conclusions We propose that the A3B deletion polymorphism can increase the risk of developing NSCLC, and their interactions with gender and smoking may contribute to the risk of NSCLC in the southern Chinese population.
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Affiliation(s)
- Xiaosong Ben
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Dan Tian
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Jiayu Liang
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China
| | - Min Wu
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China
| | - Fan Xie
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China
| | - Jinlong Zheng
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China
| | - Jingmin Chen
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China
| | - Qiaoyuan Fei
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China
| | - Xinrong Guo
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China
| | - Xueqiong Weng
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China
| | - Shan Liu
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China
| | - Xin Xie
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China
| | - Yuting Ying
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China
| | - Guibin Qiao
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Chunxia Jing
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China.,Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou, China
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18
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Riva G, Albano C, Gugliesi F, Pasquero S, Pacheco SFC, Pecorari G, Landolfo S, Biolatti M, Dell’Oste V. HPV Meets APOBEC: New Players in Head and Neck Cancer. Int J Mol Sci 2021; 22:1402. [PMID: 33573337 PMCID: PMC7866819 DOI: 10.3390/ijms22031402] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/28/2021] [Accepted: 01/28/2021] [Indexed: 12/13/2022] Open
Abstract
Besides smoking and alcohol, human papillomavirus (HPV) is a factor promoting head and neck squamous cell carcinoma (HNSCC). In some human tumors, including HNSCC, a number of mutations are caused by aberrantly activated DNA-modifying enzymes, such as the apolipoprotein B mRNA editing enzyme catalytic polypeptide-like (APOBEC) family of cytidine deaminases. As the enzymatic activity of APOBEC proteins contributes to the innate immune response to viruses, including HPV, the role of APOBEC proteins in HPV-driven head and neck carcinogenesis has recently gained increasing attention. Ongoing research efforts take the cue from two key observations: (1) APOBEC expression depends on HPV infection status in HNSCC; and (2) APOBEC activity plays a major role in HPV-positive HNSCC mutagenesis. This review focuses on recent advances on the role of APOBEC proteins in HPV-positive vs. HPV-negative HNSCC.
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Affiliation(s)
- Giuseppe Riva
- Otorhinolaryngology Division, Department of Surgical Sciences, University of Turin, 10126 Turin, Italy; (G.R.); (G.P.)
| | - Camilla Albano
- Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy; (C.A.); (F.G.); (S.P.); (S.F.C.P.); (S.L.)
| | - Francesca Gugliesi
- Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy; (C.A.); (F.G.); (S.P.); (S.F.C.P.); (S.L.)
| | - Selina Pasquero
- Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy; (C.A.); (F.G.); (S.P.); (S.F.C.P.); (S.L.)
| | - Sergio Fernando Castillo Pacheco
- Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy; (C.A.); (F.G.); (S.P.); (S.F.C.P.); (S.L.)
| | - Giancarlo Pecorari
- Otorhinolaryngology Division, Department of Surgical Sciences, University of Turin, 10126 Turin, Italy; (G.R.); (G.P.)
| | - Santo Landolfo
- Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy; (C.A.); (F.G.); (S.P.); (S.F.C.P.); (S.L.)
| | - Matteo Biolatti
- Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy; (C.A.); (F.G.); (S.P.); (S.F.C.P.); (S.L.)
| | - Valentina Dell’Oste
- Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy; (C.A.); (F.G.); (S.P.); (S.F.C.P.); (S.L.)
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19
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Granadillo Rodríguez M, Flath B, Chelico L. The interesting relationship between APOBEC3 deoxycytidine deaminases and cancer: a long road ahead. Open Biol 2020; 10:200188. [PMID: 33292100 PMCID: PMC7776566 DOI: 10.1098/rsob.200188] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/26/2020] [Indexed: 12/24/2022] Open
Abstract
Cancer is considered a group of diseases characterized by uncontrolled growth and spread of abnormal cells and is propelled by somatic mutations. Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3) family of enzymes are endogenous sources of somatic mutations found in multiple human cancers. While these enzymes normally act as an intrinsic immune defence against viruses, they can also catalyse 'off-target' cytidine deamination in genomic single-stranded DNA intermediates. The deamination of cytosine forms uracil, which is promutagenic in DNA. Key factors to trigger the APOBEC 'off-target' activity are overexpression in a non-normal cell type, nuclear localization and replication stress. The resulting uracil-induced mutations contribute to genomic variation, which may result in neutral, beneficial or harmful consequences for the cancer. This review summarizes the functional and biochemical basis of the APOBEC3 enzyme activity and highlights their relationship with the most well-studied cancers in this particular context such as breast, lung, bladder, and human papillomavirus-associated cancers. We focus on APOBEC3A, APOBEC3B and APOBEC3H haplotype I because they are the leading candidates as sources of somatic mutations in these and other cancers. Also, we discuss the prognostic value of the APOBEC3 expression in drug resistance and response to therapies.
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Affiliation(s)
| | | | - Linda Chelico
- Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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20
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Kajihara D, Hon CC, Abdullah AN, Wosniak J, Moretti AIS, Poloni JF, Bonatto D, Hashimoto K, Carninci P, Laurindo FRM. Analysis of splice variants of the human protein disulfide isomerase (P4HB) gene. BMC Genomics 2020; 21:766. [PMID: 33148170 PMCID: PMC7640458 DOI: 10.1186/s12864-020-07164-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 10/20/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Protein Disulfide Isomerases are thiol oxidoreductase chaperones from thioredoxin superfamily with crucial roles in endoplasmic reticulum proteostasis, implicated in many diseases. The family prototype PDIA1 is also involved in vascular redox cell signaling. PDIA1 is coded by the P4HB gene. While forced changes in P4HB gene expression promote physiological effects, little is known about endogenous P4HB gene regulation and, in particular, gene modulation by alternative splicing. This study addressed the P4HB splice variant landscape. RESULTS Ten protein coding sequences (Ensembl) of the P4HB gene originating from alternative splicing were characterized. Structural features suggest that except for P4HB-021, other splice variants are unlikely to exert thiol isomerase activity at the endoplasmic reticulum. Extensive analyses using FANTOM5, ENCODE Consortium and GTEx project databases as RNA-seq data sources were performed. These indicated widespread expression but significant variability in the degree of isoform expression among distinct tissues and even among distinct locations of the same cell, e.g., vascular smooth muscle cells from different origins. P4HB-02, P4HB-027 and P4HB-021 were relatively more expressed across each database, the latter particularly in vascular smooth muscle. Expression of such variants was validated by qRT-PCR in some cell types. The most consistently expressed splice variant was P4HB-021 in human mammary artery vascular smooth muscle which, together with canonical P4HB gene, had its expression enhanced by serum starvation. CONCLUSIONS Our study details the splice variant landscape of the P4HB gene, indicating their potential role to diversify the functional reach of this crucial gene. P4HB-021 splice variant deserves further investigation in vascular smooth muscle cells.
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Affiliation(s)
- Daniela Kajihara
- Vascular Biology Laboratory, LIM-64, Heart Institute (InCor), University of Sao Paulo School of Medicine, Av. Eneas Carvalho Aguiar, 44, Annex 2, 9th floor, Sao Paulo, CEP 05403-000, Brazil.,Laboratory for Transcriptome Technology, Division of Genomic Medicine, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Chung-Chau Hon
- Laboratory for Genome Information Analysis, Division of Genomic Medicine, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Aimi Naim Abdullah
- Laboratory for Transcriptome Technology, Division of Genomic Medicine, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - João Wosniak
- Vascular Biology Laboratory, LIM-64, Heart Institute (InCor), University of Sao Paulo School of Medicine, Av. Eneas Carvalho Aguiar, 44, Annex 2, 9th floor, Sao Paulo, CEP 05403-000, Brazil
| | - Ana Iochabel S Moretti
- Vascular Biology Laboratory, LIM-64, Heart Institute (InCor), University of Sao Paulo School of Medicine, Av. Eneas Carvalho Aguiar, 44, Annex 2, 9th floor, Sao Paulo, CEP 05403-000, Brazil
| | - Joice F Poloni
- Department of Molecular Biology and Biotechnology, Biotechnology Center of the Federal University of Rio Grande do Sul, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Diego Bonatto
- Department of Molecular Biology and Biotechnology, Biotechnology Center of the Federal University of Rio Grande do Sul, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Kosuke Hashimoto
- Laboratory for Transcriptome Technology, Division of Genomic Medicine, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Laboratory of Computational Biology, Institute for Protein Research, Osaka University, Osaka, 565-0871, Japan
| | - Piero Carninci
- Laboratory for Transcriptome Technology, Division of Genomic Medicine, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Francisco R M Laurindo
- Vascular Biology Laboratory, LIM-64, Heart Institute (InCor), University of Sao Paulo School of Medicine, Av. Eneas Carvalho Aguiar, 44, Annex 2, 9th floor, Sao Paulo, CEP 05403-000, Brazil.
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21
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Sui S, Jiao Z, Chen H, Niyazi M, Wang L. Association between APOBEC3s and HPV16 E2 gene hypermutation in Uygur females with cervical cancer. Oncol Lett 2020; 20:1752-1760. [PMID: 32724418 PMCID: PMC7377173 DOI: 10.3892/ol.2020.11697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 01/15/2020] [Indexed: 11/05/2022] Open
Abstract
The present study aimed to investigate whether apolipoprotein B mRNA-editing enzyme catalytic polypeptides (A3) are involved in the regulation of cervical cancer development and human papilloma virus (HPV)16 sustained infection in Uighur females. Cervical tissues of Uygur patients with HPV16 with cervical lesions were collected. Expression levels of A3C, A3F and A3G were detected using reverse transcription-quantitative PCR and western blotting. A model of SiHa cells with high expression levels of A3C, A3F and A3G was constructed. Hypermutation was detected using the differential DNA denaturation PCR and positive samples were amplified and sequenced. There were significant differences in A3 expression levels in cervical lesions of different grades. A3C and A3F mRNA and protein expression in cervical cancer tissues were significantly lower, whereas the A3G mRNA and protein expression levels were significantly higher compared with the cervicitis and cervical intraepithelial neoplasia (CIN) I–III groups. Hypermutation rates were increased with cervical lesion development. C>T and G>A base substitutions were detected in all hypermutation samples and numbers of C>T and G>A base substitutions in single samples in the cervical cancer group were significantly higher compared with those in the CIN I–III and cervicitis groups. Following transfection of A3F and A3G, HPV E2 mRNA and protein expression levels were significantly decreased in SiHa cells. Numerous C>T and G>A base substitutions were detected in the HPV E2 gene in A3G and A3C overexpressing SiHa cells. A3 family proteins inhibit viral replication during HPV16 infection and regulate the HPV16 integration by inducing C>T and G>A hypermutations in the HPV16 E2 gene, thus affecting the cervical cancer pathogenesis and development.
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Affiliation(s)
- Shuang Sui
- Department of Obstetrics and Gynecology, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang Uygur Autonomous Region 830001, P.R. China
| | - Zhen Jiao
- Department of Obstetrics and Gynecology, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang Uygur Autonomous Region 830001, P.R. China
| | - Hongxiang Chen
- Department of Obstetrics and Gynecology, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang Uygur Autonomous Region 830001, P.R. China
| | - Mayinuer Niyazi
- Department of Obstetrics and Gynecology, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang Uygur Autonomous Region 830001, P.R. China
| | - Lin Wang
- Department of Obstetrics and Gynecology, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang Uygur Autonomous Region 830001, P.R. China
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22
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Association between APOBEC3H-Mediated Demethylation and Immune Landscape in Head and Neck Squamous Carcinoma. BIOMED RESEARCH INTERNATIONAL 2020; 2020:4612375. [PMID: 32775421 PMCID: PMC7397441 DOI: 10.1155/2020/4612375] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/31/2020] [Accepted: 06/25/2020] [Indexed: 12/18/2022]
Abstract
Immunotherapy has been demonstrated as a promising strategy in controlling head and neck squamous cell carcinoma (HNSC). The AID/APOBEC family is well characterized as DNA mutator and considered to play critical roles in immune responses in HNSC. However, the expression pattern and deamination-dependent demethylation roles of AID/APOBECs in HNSC are unclear. In this study, the RNA-seq and DNA methylation profiles of HNSC from TCGA database and cell-based experiments were applied to analyze the relationships between AID/APOBEC expression levels, patients' clinical outcomes, methylation alterations, and immune responses. Here, we found that APOBEC3H was abnormally upregulated in HNSC patients. HPV+ patients tended to have higher APOBEC3H levels than HPV- patients. Remarkably, patients with high APOBEC3H levels showed a favorable overall survival. Furthermore, tumors with high APOBEC3H levels exhibited a genome-wide DNA hypomethylation pattern. APOBEC3H was identified to demethylate and upregulate CXCL10 and improve CD8+ T cell tumor infiltration in the tumor microenvironment. Collectively, APOBEC3H plays critical roles in CD8+ T cell immune infiltration and activation in HNSC, which may be a potential biomarker for oncoimmunotherapy in HNSC.
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23
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Germline APOBEC3B deletion influences clinicopathological parameters in luminal-A breast cancer: evidences from a southern Brazilian cohort. J Cancer Res Clin Oncol 2020; 146:1523-1532. [PMID: 32285256 DOI: 10.1007/s00432-020-03208-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 04/02/2020] [Indexed: 12/18/2022]
Abstract
PURPOSE APOBEC3A and APOBEC3B cytidine deaminases have been implicated in the pathogenesis of multiple cancers, including breast cancer (BC). A germline deletion linking APOBEC3A and APOBEC3B loci (A3A/B) has been associated with higher APOBEC-mediated mutational burden, but its association with BC risk have been controversial. Therefore, this study investigated the association between A3A/B and BC susceptibility and clinical presentation in a Brazilian cohort. METHODS A3A/B deletion was evaluated through allele-specific PCR in 341 BC patients and 397 women without familial or personal history of neoplasia from Brazil and associations with susceptibility to BC subtypes were tested through age-adjusted logistic models while correlations with clinicopathological parameters were tested using Kendall's tests. RESULTS No association was found between A3A/B and BC susceptibility; however, in Luminal-A BCs, it was positively correlated with tumor size (Tau-c = 0.125) and Ki67 (Tau-c = 0.116) and negatively correlated with lymph node metastasis (LNM) (Tau-c = - 0.162). The negative association between A3A/B with LNM in Luminal-A BCs remained significant even after adjusting for tumor size and Ki67 in logistic models (OR = 0.22; p = 0.008). CONCLUSION These results show that although A3A/B may not modify BC susceptibility in Brazilian population, it may affect clinicopathological features in BC subtypes, promoting tumor cell proliferation while being negatively associated with LNM in Luminal-A BCs.
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24
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Cortez LM, Brown AL, Dennis MA, Collins CD, Brown AJ, Mitchell D, Mertz TM, Roberts SA. APOBEC3A is a prominent cytidine deaminase in breast cancer. PLoS Genet 2019; 15:e1008545. [PMID: 31841499 PMCID: PMC6936861 DOI: 10.1371/journal.pgen.1008545] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 12/30/2019] [Accepted: 12/01/2019] [Indexed: 11/19/2022] Open
Abstract
APOBEC cytidine deaminases are the second-most prominent source of mutagenesis in sequenced tumors. Previous studies have proposed that APOBEC3B (A3B) is the major source of mutagenesis in breast cancer (BRCA). We show that APOBEC3A (A3A) is the only APOBEC whose expression correlates with APOBEC-induced mutation load and that A3A expression is responsible for cytidine deamination in multiple BRCA cell lines. Comparative analysis of A3A and A3B expression by qRT-PCR, RSEM-normalized RNA-seq, and unambiguous RNA-seq validated the use of RNA-seq to measure APOBEC expression, which indicates that A3A is the primary correlate with APOBEC-mutation load in primary BRCA tumors. We also demonstrate that A3A has >100-fold more cytidine deamination activity than A3B in the presence of cellular RNA, likely explaining why higher levels of A3B expression contributes less to mutagenesis in BRCA. Our findings identify A3A as a major source of cytidine deaminase activity in breast cancer cells and possibly a prominent contributor to the APOBEC mutation signature.
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Affiliation(s)
- Luis M. Cortez
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, WA, United States of America
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, United States of America
| | - Amber L. Brown
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, WA, United States of America
| | - Madeline A. Dennis
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, WA, United States of America
| | - Christopher D. Collins
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, WA, United States of America
| | - Alexander J. Brown
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, WA, United States of America
- School of Molecular Biosciences, Washington State University-Vancouver, Vancouver, WA, United States of America
| | - Debra Mitchell
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, WA, United States of America
| | - Tony M. Mertz
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, WA, United States of America
| | - Steven A. Roberts
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, WA, United States of America
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25
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Caval V, Jiao W, Berry N, Khalfi P, Pitré E, Thiers V, Vartanian JP, Wain-Hobson S, Suspène R. Mouse APOBEC1 cytidine deaminase can induce somatic mutations in chromosomal DNA. BMC Genomics 2019; 20:858. [PMID: 31726973 PMCID: PMC6854741 DOI: 10.1186/s12864-019-6216-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 10/22/2019] [Indexed: 02/06/2023] Open
Abstract
Background APOBEC1 (A1) enzymes are cytidine deaminases involved in RNA editing. In addition to this activity, a few A1 enzymes have been shown to be active on single stranded DNA. As two human ssDNA cytidine deaminases APOBEC3A (A3A), APOBEC3B (A3B) and related enzymes across the spectrum of placental mammals have been shown to introduce somatic mutations into nuclear DNA of cancer genomes, we explored the mutagenic threat of A1 cytidine deaminases to chromosomal DNA. Results Molecular cloning and expression of various A1 enzymes reveal that the cow, pig, dog, rabbit and mouse A1 have an intracellular ssDNA substrate specificity. However, among all the enzymes studied, mouse A1 appears to be singular, being able to introduce somatic mutations into nuclear DNA with a clear 5’TpC editing context, and to deaminate 5-methylcytidine substituted DNA which are characteristic features of the cancer related mammalian A3A and A3B enzymes. However, mouse A1 activity fails to elicit formation of double stranded DNA breaks, suggesting that mouse A1 possess an attenuated nuclear DNA mutator phenotype reminiscent of human A3B. Conclusions At an experimental level mouse APOBEC1 is remarkable among 12 mammalian A1 enzymes in that it represents a source of somatic mutations in mouse genome, potentially fueling oncogenesis. While the order Rodentia is bereft of A3A and A3B like enzymes it seems that APOBEC1 may well substitute for it, albeit remaining much less active. This modifies the paradigm that APOBEC3 and AID enzymes are the sole endogenous mutator enzymes giving rise to off-target editing of mammalian genomes.
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Affiliation(s)
- Vincent Caval
- Molecular Retrovirology Unit, Institut Pasteur, CNRS UMR 3569, 28 rue du Dr. Roux, 75724, Paris cedex 15, France.
| | - Wenjuan Jiao
- Molecular Retrovirology Unit, Institut Pasteur, CNRS UMR 3569, 28 rue du Dr. Roux, 75724, Paris cedex 15, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Noémie Berry
- Molecular Retrovirology Unit, Institut Pasteur, CNRS UMR 3569, 28 rue du Dr. Roux, 75724, Paris cedex 15, France.,Sorbonne Université, Complexité du Vivant, ED515, 75005, Paris, France
| | - Pierre Khalfi
- Molecular Retrovirology Unit, Institut Pasteur, CNRS UMR 3569, 28 rue du Dr. Roux, 75724, Paris cedex 15, France.,Sorbonne Université, Complexité du Vivant, ED515, 75005, Paris, France
| | - Emmanuelle Pitré
- Molecular Retrovirology Unit, Institut Pasteur, CNRS UMR 3569, 28 rue du Dr. Roux, 75724, Paris cedex 15, France.,Sorbonne Université, Complexité du Vivant, ED515, 75005, Paris, France
| | - Valérie Thiers
- Molecular Retrovirology Unit, Institut Pasteur, CNRS UMR 3569, 28 rue du Dr. Roux, 75724, Paris cedex 15, France
| | - Jean-Pierre Vartanian
- Molecular Retrovirology Unit, Institut Pasteur, CNRS UMR 3569, 28 rue du Dr. Roux, 75724, Paris cedex 15, France
| | - Simon Wain-Hobson
- Molecular Retrovirology Unit, Institut Pasteur, CNRS UMR 3569, 28 rue du Dr. Roux, 75724, Paris cedex 15, France
| | - Rodolphe Suspène
- Molecular Retrovirology Unit, Institut Pasteur, CNRS UMR 3569, 28 rue du Dr. Roux, 75724, Paris cedex 15, France
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26
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Stewart JA, Holland TC, Bhagwat AS. Human Herpes Simplex Virus-1 depletes APOBEC3A from nuclei. Virology 2019; 537:104-109. [PMID: 31493648 DOI: 10.1016/j.virol.2019.08.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 08/01/2019] [Accepted: 08/12/2019] [Indexed: 02/07/2023]
Abstract
APOBEC3 family of DNA-cytosine deaminases inactivate and mutate several human viruses. We constructed a human cell line that is inducible for EGFP-tagged APOBEC3A and found A3A predominantly in the nuclei. When these cells were infected with Herpes Simplex Virus-1, virus titer was unaffected by A3A expression despite nuclear virus replication. When A3A expression and virus infection were monitored, A3A was found predominantly to be nuclear in infected cells up to 3 h post-infection, but was predominantly cytoplasmic by 12 h. This effect did not require the whole virus, and could be reproduced using the UL39 gene of the virus which codes for a subunit of the viral ribonucleotide reductase. These results are similar to the reported exclusion of APOBEC3B by Epstein Barr virus ortholog of UL39, BORF2, but HSV1 UL39 gene product appears better at excluding A3A than A3B from nuclei.
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Affiliation(s)
- Jessica A Stewart
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - Thomas C Holland
- Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Ashok S Bhagwat
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA; Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, Detroit, MI, 48201, USA.
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27
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Kano M, Kondo S, Wakisaka N, Wakae K, Aga M, Moriyama-Kita M, Ishikawa K, Ueno T, Nakanishi Y, Hatano M, Endo K, Sugimoto H, Kitamura K, Muramatsu M, Yoshizaki T. Expression of estrogen receptor alpha is associated with pathogenesis and prognosis of human papillomavirus-positive oropharyngeal cancer. Int J Cancer 2019; 145:1547-1557. [PMID: 31228270 DOI: 10.1002/ijc.32500] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 05/29/2019] [Indexed: 12/13/2022]
Abstract
Human papillomavirus (HPV) has been identified as a causative agent of cervical cancer and oropharyngeal cancer (OPC). Intriguingly, estrogen and HPV were shown to play synergistic roles in cervical carcinogenesis. We recently demonstrated that the apolipoprotein B mRNA-editing catalytic polypeptide 3 (APOBEC3, A3) family, which is inducible by estrogen, could lead to HPV DNA hypermutation and cause viral DNA integration. In the present study, we examined the relationships between estrogen-estrogen receptor α (ERα) and A3s in HPV-positive OPC. ERα expression was associated with HPV positivity in OPC biopsy samples using immunohistochemical analysis and reverse-transcription quantitative polymerase chain reaction. In addition, ERα was significantly associated with improved overall survival in HPV-positive OPC (hazard ratio, 0.26; p = 0.029). APOBEC3A (A3A) mRNA was induced by estrogen in HPV and ERα-positive OPC cells. Furthermore, A3A mRNA and protein expression were significantly higher in ERα-positive cases than in ERα-negative ones, among HPV-positive biopsy samples (p = 0.037 and 0.047). These findings suggest that A3A is associated with a good prognosis in ERα-positive OPC, and indicate the prognostic significance of ERα in HPV-positive OPC. This is the first study to demonstrate the prognostic role of ERα in HPV-positive OPC.
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Affiliation(s)
- Makoto Kano
- Division of Otolaryngology-Head and Neck Surgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa, Japan.,Department of Otolaryngology, National Hospital Organization Kanazawa Medical Center, Kanazawa, Ishikawa, Japan
| | - Satoru Kondo
- Division of Otolaryngology-Head and Neck Surgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Naohiro Wakisaka
- Division of Otolaryngology-Head and Neck Surgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Kosho Wakae
- Department of Molecular Genetics, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa, Japan.,Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Mituharu Aga
- Division of Otolaryngology-Head and Neck Surgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Makiko Moriyama-Kita
- Division of Otolaryngology-Head and Neck Surgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Kazuya Ishikawa
- Division of Otolaryngology-Head and Neck Surgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Takayoshi Ueno
- Division of Otolaryngology-Head and Neck Surgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Yosuke Nakanishi
- Division of Otolaryngology-Head and Neck Surgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Miyako Hatano
- Division of Otolaryngology-Head and Neck Surgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Kazuhira Endo
- Division of Otolaryngology-Head and Neck Surgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Hisashi Sugimoto
- Division of Otolaryngology-Head and Neck Surgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Kouichi Kitamura
- Department of Molecular Genetics, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Masamichi Muramatsu
- Department of Molecular Genetics, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa, Japan.,Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tomokazu Yoshizaki
- Division of Otolaryngology-Head and Neck Surgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa, Japan
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28
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Smith NJ, Fenton TR. The APOBEC3 genes and their role in cancer: insights from human papillomavirus. J Mol Endocrinol 2019; 62:R269-R287. [PMID: 30870810 DOI: 10.1530/jme-19-0011] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 03/14/2019] [Indexed: 12/14/2022]
Abstract
The interaction between human papillomaviruses (HPV) and the apolipoprotein-B mRNA-editing catalytic polypeptide-like (APOBEC)3 (A3) genes has garnered increasing attention in recent years, with considerable efforts focused on understanding their apparent roles in both viral editing and in HPV-driven carcinogenesis. Here, we review these developments and highlight several outstanding questions in the field. We consider whether editing of the virus and mutagenesis of the host are linked or whether both are essentially separate events, coincidentally mediated by a common or distinct A3 enzymes. We discuss the viral mechanisms and cellular signalling pathways implicated in A3 induction in virally infected cells and examine which of the A3 enzymes might play the major role in HPV-associated carcinogenesis and in the development of therapeutic resistance. We consider the parallels between A3 induction in HPV-infected cells and what might be causing aberrant A3 activity in HPV-independent cancers such as those arising in the bladder, lung and breast. Finally, we discuss the implications of ongoing A3 activity in tumours under treatment and the therapeutic opportunities that this may present.
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Affiliation(s)
- Nicola J Smith
- School of Biosciences, University of Kent, Canterbury, Kent, UK
| | - Tim R Fenton
- School of Biosciences, University of Kent, Canterbury, Kent, UK
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29
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Zhou Y, Qiao H, Yin N, Chen L, Xie Y, Wu J, Du J, Lin X, Wang Y, Liu Y, Yi S, Zhang G, Sun M, He Z, Li H. Immune and cytokine/chemokine responses of PBMCs in rotavirus‐infected rhesus infants and their significance in viral pathogenesis. J Med Virol 2019; 91:1448-1469. [DOI: 10.1002/jmv.25460] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 01/17/2019] [Accepted: 02/01/2019] [Indexed: 12/23/2022]
Affiliation(s)
- Yan Zhou
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on severe Infectious Disease Kunming China
| | - Hongtu Qiao
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on severe Infectious Disease Kunming China
| | - Na Yin
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on severe Infectious Disease Kunming China
| | - Linlin Chen
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on severe Infectious Disease Kunming China
| | - Yuping Xie
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on severe Infectious Disease Kunming China
| | - Jinyuan Wu
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on severe Infectious Disease Kunming China
| | - Jing Du
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on severe Infectious Disease Kunming China
| | - Xiaochen Lin
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on severe Infectious Disease Kunming China
| | - Yi Wang
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on severe Infectious Disease Kunming China
| | - Yang Liu
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on severe Infectious Disease Kunming China
| | - Shan Yi
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on severe Infectious Disease Kunming China
| | - Guangming Zhang
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on severe Infectious Disease Kunming China
| | - Maosheng Sun
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on severe Infectious Disease Kunming China
| | - Zhanlong He
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on severe Infectious Disease Kunming China
| | - Hongjun Li
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on severe Infectious Disease Kunming China
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30
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The DNA damage induced by the Cytosine Deaminase APOBEC3A Leads to the production of ROS. Sci Rep 2019; 9:4714. [PMID: 30886206 PMCID: PMC6423136 DOI: 10.1038/s41598-019-40941-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 02/25/2019] [Indexed: 01/26/2023] Open
Abstract
Human apolipoprotein B mRNA-editing catalytic polypeptide-like 3 proteins (APOBEC3s or A3s) are cytosine deaminases that protect cells by introducing promutagenic uraciles in invading retro-elements. However as a drawback of this protective activity, A3s can also target cellular DNA, leading to DNA damage and to the accumulation of somatic mutations that may contribute to tumorigenesis. Among A3s, A3A has been shown to be particularly proficient at mutagenizing cellular DNA, but whether this enzyme exerts additional effects on the cellular physiology remains unclear. Here, we show that A3A editing of cellular DNA leads to reactive oxygen species (ROS) production through Nox-enzymes. ROS production occurs in two distinct model cell lines and it is contingent upon DNA replication and intact enzymatic properties of A3A. For the first time, our results indicate that the editing activity of A3A results in the induction of a pro-inflammatory state that may possibly contribute to the constitution of a tumorigenic-prone environment.
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31
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Mussil B, Suspène R, Caval V, Durandy A, Wain-Hobson S, Vartanian JP. Genotoxic stress increases cytoplasmic mitochondrial DNA editing by human APOBEC3 mutator enzymes at a single cell level. Sci Rep 2019; 9:3109. [PMID: 30816165 PMCID: PMC6395610 DOI: 10.1038/s41598-019-39245-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 11/23/2018] [Indexed: 01/23/2023] Open
Abstract
Human cells are stressed by numerous mechanisms that can lead to leakage of mitochondrial DNA (mtDNA) to the cytoplasm and ultimately apoptosis. This agonist DNA constitutes a danger to the cell and is counteracted by cytoplasmic DNases and APOBEC3 cytidine deamination of DNA. To investigate APOBEC3 editing of leaked mtDNA to the cytoplasm, we performed a PCR analysis of APOBEC3 edited cytoplasmic mtDNA (cymtDNA) at the single cell level for primary CD4+ T cells and the established P2 EBV blast cell line. Up to 17% of primary CD4+ T cells showed signs of APOBEC3 edited cymtDNA with ~50% of all mtDNA sequences showing signs of APOBEC3 editing - between 1500-5000 molecules. Although the P2 cell line showed a much lower frequency of stressed cells, the number of edited mtDNA molecules in such cells was of the same order. Addition of the genotoxic molecules, etoposide or actinomycin D increased the number of cells showing APOBEC3 edited cymtDNA to around 40%. These findings reveal a very dynamic image of the mitochondrial network, which changes considerably under stress. APOBEC3 deaminases are involved in the catabolism of mitochondrial DNA to circumvent chronic immune stimulation triggered by released mitochondrial DNA from damaged cells.
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Affiliation(s)
- Bianka Mussil
- Molecular Retrovirology Unit, Institut Pasteur, CNRS, UMR 3569, 28 rue du Dr. Roux, F-75724, Paris cedex 15, France
- Unit of Infection Models, German Primate Centre, Kellnerweg 4, D-37077, Goettingen, Germany
| | - Rodolphe Suspène
- Molecular Retrovirology Unit, Institut Pasteur, CNRS, UMR 3569, 28 rue du Dr. Roux, F-75724, Paris cedex 15, France
| | - Vincent Caval
- Molecular Retrovirology Unit, Institut Pasteur, CNRS, UMR 3569, 28 rue du Dr. Roux, F-75724, Paris cedex 15, France
| | - Anne Durandy
- INSERM UMR 1163, The Human Lymphohematopoiesis Laboratory, Institut Imagine, 24 boulevard du Montparnasse, F-75015, Paris, France
| | - Simon Wain-Hobson
- Molecular Retrovirology Unit, Institut Pasteur, CNRS, UMR 3569, 28 rue du Dr. Roux, F-75724, Paris cedex 15, France
| | - Jean-Pierre Vartanian
- Molecular Retrovirology Unit, Institut Pasteur, CNRS, UMR 3569, 28 rue du Dr. Roux, F-75724, Paris cedex 15, France.
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32
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Li X, Caval V, Wain-Hobson S, Vartanian JP. Elephant APOBEC3A cytidine deaminase induces massive double-stranded DNA breaks and apoptosis. Sci Rep 2019; 9:728. [PMID: 30679716 PMCID: PMC6345769 DOI: 10.1038/s41598-018-37305-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 12/06/2018] [Indexed: 01/24/2023] Open
Abstract
The incidence of developing cancer should increase with the body mass, yet is not the case, a conundrum referred to as Peto’s paradox. Elephants have a lower incidence of cancer suggesting that these animals have probably evolved different ways to protect themselves against the disease. The paradox is worth revisiting with the realization that most mammals encode an endogenous APOBEC3 cytidine deaminase capable of mutating single stranded DNA. Indeed, the mutagenic activity of some APOBEC3 enzymes has been shown to introduce somatic mutations into genomic DNA. These enzymes are now recognized as causal agent responsible for the accumulation of CG- > TA transitions and DNA breaks leading to chromosomal rearrangements in human cancer genomes. Here, we identified an elephant A3Z1 gene, related to human APOBEC3A and showed that it could efficiently deaminate cytidine, 5-methylcytidine and produce DNA breaks leading to massive apoptosis, similar to other mammalian APOBEC3A enzymes where body mass varies by up to four orders of magnitude. Consequently, it could be considered that eAZ1 might contribute to cancer in elephants in a manner similar to their proposed role in humans. If so, eAZ1 might be particularly well regulated to counter Peto’s paradox.
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Affiliation(s)
- Xiongxiong Li
- Molecular Retrovirology Unit, Institut Pasteur, CNRS-URA 3015, 28 rue du Docteur Roux, 75724, Paris, France.,Lanzhou Institute of Biological Products Co., Ltd (LIBP), subsidiary company of China National Biotec Group Company Limited (CNBG), 730046, Lanzhou, China
| | - Vincent Caval
- Molecular Retrovirology Unit, Institut Pasteur, CNRS-URA 3015, 28 rue du Docteur Roux, 75724, Paris, France
| | - Simon Wain-Hobson
- Molecular Retrovirology Unit, Institut Pasteur, CNRS-URA 3015, 28 rue du Docteur Roux, 75724, Paris, France
| | - Jean-Pierre Vartanian
- Molecular Retrovirology Unit, Institut Pasteur, CNRS-URA 3015, 28 rue du Docteur Roux, 75724, Paris, France.
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A Tumor-Promoting Phorbol Ester Causes a Large Increase in APOBEC3A Expression and a Moderate Increase in APOBEC3B Expression in a Normal Human Keratinocyte Cell Line without Increasing Genomic Uracils. Mol Cell Biol 2018; 39:MCB.00238-18. [PMID: 30348839 DOI: 10.1128/mcb.00238-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 10/07/2018] [Indexed: 12/14/2022] Open
Abstract
Phorbol 12-myristate 13-acetate (PMA) promotes skin cancer in rodents. The mutations found in murine tumors are similar to those found in human skin cancers, and PMA promotes proliferation of human skin cells. PMA treatment of human keratinocytes increases the synthesis of APOBEC3A, an enzyme that converts cytosines in single-stranded DNA to uracil, and mutations in a variety of human cancers are attributed to APOBEC3A or APOBEC3B expression. We tested here the possibility that induction of APOBEC3A by PMA causes genomic accumulation of uracils that may lead to such mutations. When a human keratinocyte cell line was treated with PMA, both APOBEC3A and APOBEC3B gene expression increased, anti-APOBEC3A/APOBEC3B antibody bound a protein(s) in the nucleus, and nuclear extracts displayed cytosine deamination activity. Surprisingly, there was little increase in genomic uracils in PMA-treated wild-type or uracil repair-defective cells. In contrast, cells transfected with a plasmid expressing APOBEC3A acquired more genomic uracils. Unexpectedly, PMA treatment, but not APOBEC3A plasmid transfection, caused a cessation in cell growth. Hence, a reduction in single-stranded DNA at replication forks may explain the inability of PMA-induced APOBEC3A/APOBEC3B to increase genomic uracils. These results suggest that the proinflammatory PMA is unlikely to promote extensive APOBEC3A/APOBEC3B-mediated cytosine deaminations in human keratinocytes.
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Keratinocyte differentiation induces APOBEC3A, 3B, and mitochondrial DNA hypermutation. Sci Rep 2018; 8:9745. [PMID: 29950685 PMCID: PMC6021414 DOI: 10.1038/s41598-018-27930-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 06/13/2018] [Indexed: 12/12/2022] Open
Abstract
Mitochondrial DNA (mtDNA) mutations are found in many types of cancers and suspected to be involved in carcinogenesis, although the mechanism has not been elucidated. In this study, we report that consecutive C-to-T mutations (hypermutations), a unique feature of mutations induced by APOBECs, are found in mtDNA from cervical dysplasia and oropharyngeal cancers. In vitro, we found that APOBEC3A (A3A) and 3B (A3B) expression, as well as mtDNA hypermutation, were induced in a cervical dysplastic cell line W12 when cultured in a differentiating condition. The ectopic expression of A3A or A3B was sufficient to hypermutate mtDNA. Fractionation of W12 cell lysates and immunocytochemical analysis revealed that A3A and A3B could be contained in mitochondrion. These results suggest that mtDNA hypermutation is induced upon keratinocyte differentiation, and shed light on its molecular mechanism, which involves A3s. The possible involvement of mtDNA hypermutations in carcinogenesis is also discussed.
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35
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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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36
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Westrich JA, Warren CJ, Klausner MJ, Guo K, Liu CW, Santiago ML, Pyeon D. Human Papillomavirus 16 E7 Stabilizes APOBEC3A Protein by Inhibiting Cullin 2-Dependent Protein Degradation. J Virol 2018; 92:e01318-17. [PMID: 29367246 PMCID: PMC5972886 DOI: 10.1128/jvi.01318-17] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 01/15/2018] [Indexed: 12/21/2022] Open
Abstract
APOBEC3 (A3) mutation signatures have been observed in a variety of human cancer genomes, including those of cervical and head and neck cancers caused by human papillomavirus (HPV) infection. However, the driving forces that promote off-target A3 activity remain mostly unclear. Here, we report a mechanism for the dramatic increase of A3A protein levels in HPV-positive keratinocytes. We show that expression of the viral protein E7 from high-risk HPVs, but not E7 from low-risk HPVs, significantly prolongs the cellular half-life of A3A protein in human keratinocytes and HPV-positive cancer cell lines. We have mapped several residues within the cullin 2 (CUL2) binding motif of HPV16 E7 as being important for mediating A3A protein stabilization. Furthermore, we provide direct evidence that both A3A and HPV16 E7 interact with CUL2, suggesting that the E7-CUL2 complex formed during HPV infection may regulate A3A protein levels in the cell. Using an in vitro cytidine deaminase assay, we show that E7-stabilized A3A remains catalytically active. Taken together, our findings suggest that the HPV oncoprotein E7 dysregulates endogenous A3A protein levels and thus provides novel mechanistic insight into cellular triggers of A3 mutations in HPV-positive cancers.IMPORTANCE Human papillomavirus (HPV) is causally associated with over 5% of all human malignancies. Several recent studies have shown that a subset of cancers, including HPV-positive head and neck and cervical cancers, have distinct mutational signatures potentially caused by members of the APOBEC3 cytidine deaminase family. However, the mechanism that induces APOBEC3 activity in cancer cells is poorly understood. Here, we report that the HPV oncoprotein E7 stabilizes the APOBEC3A (A3A) protein in human keratinocytes by inhibiting ubiquitin-dependent protein degradation in a cullin-dependent manner. Interestingly, the HPV E7-stabilized A3A protein maintains its deaminase activity. These findings provide a new insight into cancer mutagenesis enhanced by virus-induced A3A protein stabilization.
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Affiliation(s)
- Joseph A Westrich
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Cody J Warren
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Michael J Klausner
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Kejun Guo
- Division of Infectious Diseases, Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Chang-Wei Liu
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Mario L Santiago
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
- Division of Infectious Diseases, Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Dohun Pyeon
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
- Division of Infectious Diseases, Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
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37
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Adolph MB, Love RP, Chelico L. Biochemical Basis of APOBEC3 Deoxycytidine Deaminase Activity on Diverse DNA Substrates. ACS Infect Dis 2018; 4:224-238. [PMID: 29347817 DOI: 10.1021/acsinfecdis.7b00221] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The Apolipoprotein B mRNA editing complex (APOBEC) family of enzymes contains single-stranded polynucleotide cytidine deaminases. These enzymes catalyze the deamination of cytidine in RNA or single-stranded DNA, which forms uracil. From this 11 member enzyme family in humans, the deamination of single-stranded DNA by the seven APOBEC3 family members is considered here. The APOBEC3 family has many roles, such as restricting endogenous and exogenous retrovirus replication and retrotransposon insertion events and reducing DNA-induced inflammation. Similar to other APOBEC family members, the APOBEC3 enzymes are a double-edged sword that can catalyze deamination of cytosine in genomic DNA, which results in potential genomic instability due to the many mutagenic fates of uracil in DNA. Here, we discuss how these enzymes find their single-stranded DNA substrate in different biological contexts such as during human immunodeficiency virus (HIV) proviral DNA synthesis, retrotransposition of the LINE-1 element, and the "off-target" genomic DNA substrate. The enzymes must be able to efficiently deaminate transiently available single-stranded DNA during reverse transcription, replication, or transcription. Specific biochemical characteristics promote deamination in each situation to increase enzyme efficiency through processivity, rapid enzyme cycling between substrates, or oligomerization state. The use of biochemical data to clarify biological functions and alignment with cellular data is discussed. Models to bridge knowledge from biochemical, structural, and single molecule experiments are presented.
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Affiliation(s)
- Madison B Adolph
- Department of Microbiology and Immunology, College of Medicine , University of Saskatchewan , 107 Wiggins Road , Saskatoon , Saskatchewan S7N 5E5 , Canada
| | - Robin P Love
- Department of Microbiology and Immunology, College of Medicine , University of Saskatchewan , 107 Wiggins Road , Saskatoon , Saskatchewan S7N 5E5 , Canada
| | - Linda Chelico
- Department of Microbiology and Immunology, College of Medicine , University of Saskatchewan , 107 Wiggins Road , Saskatoon , Saskatchewan S7N 5E5 , Canada
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38
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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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39
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Glaser AP, Fantini D, Wang Y, Yu Y, Rimar KJ, Podojil JR, Miller SD, Meeks JJ. APOBEC-mediated mutagenesis in urothelial carcinoma is associated with improved survival, mutations in DNA damage response genes, and immune response. Oncotarget 2017; 9:4537-4548. [PMID: 29435122 PMCID: PMC5796993 DOI: 10.18632/oncotarget.23344] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 11/26/2017] [Indexed: 12/20/2022] Open
Abstract
APOBEC enzymes are responsible for a mutation signature (TCW>T/G) implicated in a wide variety of tumors. We explore the APOBEC mutational signature in bladder cancer and the relationship with specific mutations, molecular subtype, gene expression, and survival using sequencing data from The Cancer Genome Atlas (n = 395), Beijing Genomics Institute (n = 99), and Cancer Cell Line Encyclopedia. Tumors were split into “APOBEC-high” and “APOBEC-low” based on APOBEC enrichment. Patients with APOBEC-high tumors have better overall survival compared to those with APOBEC-low tumors (38.2 vs. 18.5 months, p = 0.005). APOBEC-high tumors are more likely to have mutations in DNA damage response genes (TP53, ATR, BRCA2) and chromatin regulatory genes (ARID1A, MLL, MLL3), while APOBEC-low tumors are more likely to have mutations in FGFR3 and KRAS. APOBEC3A and APOBEC3B expression correlates with mutation burden, regardless of bladder tumor molecular subtype. APOBEC mutagenesis is associated with increased expression of immune signatures, including interferon signaling, and expression of APOBEC3B is increased after stimulation of APOBEC-high bladder cancer cell lines with IFNγ. In summary, APOBEC-high tumors are more likely to have mutations in DNA damage response and chromatin regulatory genes, potentially providing more substrate for APOBEC enzymes, leading to a hypermutational phenotype and the subsequent enhanced immune response.
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Affiliation(s)
- Alexander P Glaser
- Department of Urology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA
| | - Damiano Fantini
- Department of Urology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA
| | - Yiduo Wang
- Department of Urology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA
| | - Yanni Yu
- Department of Urology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA
| | - Kalen J Rimar
- Department of Urology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA
| | - Joseph R Podojil
- Interdepartmental Immunobiology Center, Department of Microbiology-Immunology, Northwestern University, Chicago, IL, USA
| | - Stephen D Miller
- Interdepartmental Immunobiology Center, Department of Microbiology-Immunology, Northwestern University, Chicago, IL, USA
| | - Joshua J Meeks
- Department of Urology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA
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40
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Boulianne B, Feldhahn N. Transcribing malignancy: transcription-associated genomic instability in cancer. Oncogene 2017; 37:971-981. [DOI: 10.1038/onc.2017.402] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 09/12/2017] [Accepted: 09/12/2017] [Indexed: 12/17/2022]
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41
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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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42
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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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43
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Zou J, Wang C, Ma X, Wang E, Peng G. APOBEC3B, a molecular driver of mutagenesis in human cancers. Cell Biosci 2017; 7:29. [PMID: 28572915 PMCID: PMC5450379 DOI: 10.1186/s13578-017-0156-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 05/23/2017] [Indexed: 02/07/2023] Open
Abstract
Human cancers results in large part from the accumulation of multiple mutations. The progression of premalignant cells is an evolutionary process in which mutations provide the fundamental driving force for genetic diversity. The increased mutation rate in premalignant cells allows selection for increased proliferation and survival and ultimately leads to invasion, metastasis, recurrence, and therapeutic resistance. Therefore, it is important to understand the molecular determinants of the mutational processes. Recent genome-wide sequencing data showed that apolipoprotein B mRNA editing catalytic polypeptide-like 3B (APOBEC3B) is a key molecular driver inducing mutations in multiple human cancers. APOBEC3B, a DNA cytosine deaminase, is overexpressed in a wide spectrum of human cancers. Its overexpression and aberrant activation lead to unexpected clusters of mutations in the majority of cancers. This phenomenon of clustered mutations, termed kataegis (from the Greek word for showers), forms unique mutation signatures. In this review, we will discuss the biological function of APOBEC3B, its tumorigenic role in promoting mutational processes in cancer development and the clinical potential to develop novel therapeutics by targeting APOBEC3B.
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Affiliation(s)
- Jun Zou
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 China
| | - Chen Wang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 China
| | - Xiangyi Ma
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 China
| | - Edward Wang
- OncoMed Pharmaceuticals, 800 Chesapeake Dr., Redwood City, CA 94063 USA
| | - Guang Peng
- Department of Clinical Cancer Prevention, MD Anderson Cancer Center, The University of Texas, Houston, TX 77030 USA
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44
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Harjes S, Jameson GB, Filichev VV, Edwards P, Harjes E. NMR-based method of small changes reveals how DNA mutator APOBEC3A interacts with its single-stranded DNA substrate. Nucleic Acids Res 2017; 45:5602-5613. [PMID: 28369637 PMCID: PMC5435981 DOI: 10.1093/nar/gkx196] [Citation(s) in RCA: 11] [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: 12/23/2016] [Revised: 02/21/2017] [Accepted: 03/14/2017] [Indexed: 12/14/2022] Open
Abstract
APOBEC3 proteins are double-edged swords. They deaminate cytosine to uracil in single-stranded DNA and provide protection, as part of our innate immune system, against viruses and retrotransposons, but they are also involved in cancer evolution and development of drug resistance. We report a solution-state model of APOBEC3A interaction with its single-stranded DNA substrate obtained with the 'method of small changes'. This method compares pairwise the 2D 15N-1H NMR spectra of APOBEC3A bearing a deactivating mutation E72A in the presence of 36 slightly different DNA substrates. From changes in chemical shifts of peptide N-H moieties, the positions of each nucleotide relative to the protein can be identified. This provided distance restraints for molecular-dynamic simulations to derive a 3-D molecular model of the APOBEC3A-ssDNA complex. The model reveals that loops 1 and 7 of APOBEC3A move to accommodate substrate binding, indicating an important role for protein-DNA dynamics. Overall, our method may prove useful to study other DNA-protein complexes where crystallographic techniques or full NMR structure calculations are hindered by weak binding or other problems. Subsequent to submission, an APOBEC3A structure with a bound DNA oligomer was published and coordinates released, which has provided an unbiased validation of the 'method of small changes'.
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Affiliation(s)
- Stefan Harjes
- Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Geoffrey B. Jameson
- Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Vyacheslav V. Filichev
- Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Patrick J. B. Edwards
- Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Elena Harjes
- Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
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45
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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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46
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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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47
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APOBEC3A associates with human papillomavirus genome integration in oropharyngeal cancers. Oncogene 2016; 36:1687-1697. [PMID: 27694899 DOI: 10.1038/onc.2016.335] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2015] [Revised: 07/27/2016] [Accepted: 08/02/2016] [Indexed: 12/27/2022]
Abstract
The prevalence of human papillomavirus (HPV)-related oropharyngeal cancers has been increasing in developed countries. We recently demonstrated that members of the apolipoprotein B mRNA-editing catalytic polypeptide 3 (APOBEC3, A3) family, which are antiviral factors, can induce hypermutation of HPV DNA in vitro. In the present study, we found numerous C-to-T and G-to-A hypermutations in the HPV16 genome in oropharyngeal cancer (OPC) biopsy samples using differential DNA denaturation PCR and next-generation sequencing. A3s were more abundantly expressed in HPV16-positive OPCs than in HPV-negative, as assessed using immunohistochemistry and reverse transcription quantitative PCR. In addition, interferons upregulated A3s in an HPV16-positive OPC cell line. Furthermore, quantitative PCR analysis of HPV DNA suggests that APOBEC3A (A3A) expression is strongly correlated with the integration of HPV DNA. These results suggest that HPV16 infection may upregulate A3A expression, thereby increasing the chance of viral DNA integration. The role of A3A in HPV-induced carcinogenesis is discussed.
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48
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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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49
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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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50
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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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