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Smith NJ, Reddin I, Policelli P, Oh S, Zainal N, Howes E, Jenkins B, Tracy I, Edmond M, Sharpe B, Amendra D, Zheng K, Egawa N, Doorbar J, Rao A, Mahadevan S, Carpenter MA, Harris RS, Ali S, Hanley C, Buisson R, King E, Thomas GJ, Fenton TR. Differentiation signals induce APOBEC3A expression via GRHL3 in squamous epithelia and squamous cell carcinoma. RESEARCH SQUARE 2024:rs.3.rs-3997426. [PMID: 38496447 PMCID: PMC10942551 DOI: 10.21203/rs.3.rs-3997426/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Two APOBEC (apolipoprotein-B mRNA editing enzyme catalytic polypeptide-like) DNA cytosine deaminase enzymes (APOBEC3A and APOBEC3B) generate somatic mutations in cancer, driving tumour development and drug resistance. Here we used single cell RNA sequencing to study APOBEC3A and APOBEC3B expression in healthy and malignant mucosal epithelia, validating key observations with immunohistochemistry, spatial transcriptomics and functional experiments. Whereas APOBEC3B is expressed in keratinocytes entering mitosis, we show that APOBEC3A expression is confined largely to terminally differentiating cells and requires Grainyhead-like transcription factor 3 (GRHL3). Thus, in normal tissue, neither deaminase appears to be expressed at high levels during DNA replication, the cell cycle stage associated with APOBEC-mediated mutagenesis. In contrast, we show that in squamous cell carcinoma tissues, there is expansion of GRHL3 expression and activity to a subset of cells undergoing DNA replication and concomitant extension of APOBEC3A expression to proliferating cells. These findings indicate a mechanism for acquisition of APOBEC3A mutagenic activity in tumours.
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Affiliation(s)
- Nicola J. Smith
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
- School of Biosciences, University of Kent, UK
| | - Ian Reddin
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
- Bio-R Bioinformatics Research Facility, Faculty of Medicine, University of Southampton, UK
| | - Paige Policelli
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Sunwoo Oh
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
| | - Nur Zainal
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Emma Howes
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Benjamin Jenkins
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Ian Tracy
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Mark Edmond
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Benjamin Sharpe
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Damian Amendra
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Ke Zheng
- Department of Pathology, University of Cambridge, UK
| | | | - John Doorbar
- Department of Pathology, University of Cambridge, UK
| | - Anjali Rao
- Gilead Sciences, Research Department, 324 Lakeside Dr. Foster City, CA 94404, USA
| | - Sangeetha Mahadevan
- Gilead Sciences, Research Department, 324 Lakeside Dr. Foster City, CA 94404, USA
| | - Michael A. Carpenter
- 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
| | - 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
| | - Simak Ali
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London, UK
| | - Christopher Hanley
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Rémi Buisson
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
| | - Emma King
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Gareth J. Thomas
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
- Institute for Life Sciences, University of Southampton, UK
| | - Tim R. Fenton
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
- Institute for Life Sciences, University of Southampton, UK
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2
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Fu Q, Yi B, Su Q, Huang Y, Wang L, Zhang Z. A prognostic risk model for programmed cell death and revealing TRIB3 as a promising apoptosis suppressor in renal cell carcinoma. Aging (Albany NY) 2023; 15:13213-13238. [PMID: 38006403 DOI: 10.18632/aging.205237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/19/2023] [Indexed: 11/27/2023]
Abstract
Programmed cell death (PCD), a common modality of cell death, affects tumor development and acts as a target for tumor therapeutics. Many modalities of PCD regulate genesis, progression and metastasis of cancers, thus affecting the patients' prognosis, but the comprehensive molecular mechanisms of PCD in tumors are lacking, especially in renal cancer. Here, seventeen PRPCDGs were identified from 1257 genes associated with thirteen PCD modalities, which were highly differentially expressed and significantly affected patients' prognosis. Then, LASSO regression analysis of these PRPCDGs screened the 9-gene PRPCDGs risk signature in TCGA-KIRC database. The PRPCDGs risk signature was closely associated with the patients' prognosis and presented stable prediction efficacy for 5- and 7-year overall survival (OS) in three different cohorts of renal cancer. Immune cell infiltration, immune checkpoint expression and pathway enrichment (including GO, KEGG pathway, tumor-associated pathways and metabolism-associated pathways) were significantly different in the high- or low-PRPCDGs-risk group. Finally, we illustrated that TRIB3 might be a protumor factor responsible for the elevated proliferation and invasion capacities of renal cell carcinoma (RCC) cells. In summary, the PRPCDGs risk signature was developed and showed stable prediction efficacy for the prognosis of patients and that (such as TRIB3) could be a potential target for RCC management.
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Affiliation(s)
- Qingfeng Fu
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin 300211, China
| | - Bocun Yi
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin 300211, China
| | - Qiang Su
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin 300211, China
| | - Yue Huang
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin 300211, China
| | - Lin Wang
- Department of Urology, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai 264000, Shandong, China
| | - Zhihong Zhang
- Department of Urology, Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin 300211, China
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3
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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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4
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The functions and molecular mechanisms of Tribbles homolog 3 (TRIB3) implicated in the pathophysiology of cancer. Int Immunopharmacol 2023; 114:109581. [PMID: 36527874 DOI: 10.1016/j.intimp.2022.109581] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/21/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022]
Abstract
Currently, cancer ranks as the second leading cause of death worldwide, and at the same time, the burden of cancer continues to increase. The underlying molecular pathways involved in the initiation and development of cancer are the subject of considerable research worldwide. Further understanding of these pathways may lead to new cancer treatments. Growing data suggest that Tribble's homolog 3 (TRIB3) is essential in oncogenesis in many types of cancer. The mammalian tribbles family's proteins regulate various cellular and physiological functions, such as the cell cycle, stress response, signal transduction, propagation, development, differentiation, immunity, inflammatory processes, and metabolism. To exert their activities, Tribbles proteins must alter key signaling pathways, including the mitogen-activated protein kinase (MAPK) and phosphatidylinositol 3 kinase (PI3K)/AKT pathways. Recent evidence supports that TRIB3 dysregulation has been linked to various diseases, including tumor development and chemoresistance. It has been speculated that TRIB3 may either promote or inhibit the onset and development of cancer. However, it is still unclear how TRIB3 performs this dual function in cancer. In this review, we present and discuss the most recent data on the role of TRIB3 in cancer pathophysiology and chemoresistance. Furthermore, we describe in detail the molecular mechanism TRIB3 regulates in cancer.
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5
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Sang J, Zhang T, Kim J, Li M, Pesatori AC, Consonni D, Song L, Liu J, Zhao W, Hoang PH, Campbell DS, Feng J, D'Arcy ME, Synnott N, Chen Y, Wu Z, Zhu B, Yang XR, Brown KM, Choi J, Shi J, Landi MT. Rare germline deleterious variants increase susceptibility for lung cancer. Hum Mol Genet 2022; 31:3558-3565. [PMID: 35717579 PMCID: PMC9558843 DOI: 10.1093/hmg/ddac123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/16/2022] [Accepted: 05/23/2022] [Indexed: 01/10/2023] Open
Abstract
Although multiple common susceptibility loci for lung cancer (LC) have been identified by genome-wide association studies, they can explain only a small portion of heritability. The etiological contribution of rare deleterious variants (RDVs) to LC risk is not fully characterized and may account for part of the missing heritability. Here, we sequenced the whole exomes of 2777 participants from the Environment and Genetics in Lung cancer Etiology study, a homogenous population including 1461 LC cases and 1316 controls. In single-variant analyses, we identified a new RDV, rs77187983 [EHBP1, odds ratio (OR) = 3.13, 95% confidence interval (CI) = 1.34-7.30, P = 0.008] and replicated two previously reported RDVs, rs11571833 (BRCA2, OR = 2.18; 95% CI = 1.25-3.81, P = 0.006) and rs752672077 (MPZL2, OR = 3.70, 95% CI = 1.04-13.15, P = 0.044). In gene-based analyses, we confirmed BRCA2 (P = 0.007) and ATM (P = 0.014) associations with LC risk and identified TRIB3 (P = 0.009), involved in maintaining genome stability and DNA repair, as a new candidate susceptibility gene. Furthermore, cases were enriched with RDVs in homologous recombination repair [carrier frequency (CF) = 22.9% versus 19.5%, P = 0.017] and Fanconi anemia (CF = 12.5% versus 10.2%, P = 0.036) pathways. Our results were not significant after multiple testing corrections but were enriched in cases versus controls from large scale public biobank resources, including The Cancer Genome Atlas, FinnGen and UK Biobank. Our study identifies novel candidate genes and highlights the importance of RDVs in DNA repair-related genes for LC susceptibility. These findings improve our understanding of LC heritability and may contribute to the development of risk stratification and prevention strategies.
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Affiliation(s)
- Jian Sang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jung Kim
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mengying Li
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Angela C Pesatori
- Department of Clinical Sciences and Community Health, University of Milan, Milan 20122, Italy
| | - Dario Consonni
- Epidemiology Unit, Fondazione IRCCS Ca' Granda-Ospedale Maggiore Policlinico, Milan 20122, Italy
| | - Lei Song
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Jia Liu
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Wei Zhao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Phuc H Hoang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - James Feng
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Monica E D'Arcy
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Naoise Synnott
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yingxi Chen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zeni Wu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xiaohong R Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kevin M Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jiyeon Choi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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6
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Berry N, Suspène R, Caval V, Khalfi P, Beauclair G, Rigaud S, Blanc H, Vignuzzi M, Wain-Hobson S, Vartanian JP. Herpes Simplex Virus Type 1 Infection Disturbs the Mitochondrial Network, Leading to Type I Interferon Production through the RNA Polymerase III/RIG-I Pathway. mBio 2021; 12:e0255721. [PMID: 34809467 PMCID: PMC8609356 DOI: 10.1128/mbio.02557-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 10/19/2021] [Indexed: 11/20/2022] Open
Abstract
Viruses have evolved a plethora of mechanisms to impair host innate immune responses. Herpes simplex virus type 1 (HSV-1), a double-stranded linear DNA virus, impairs the mitochondrial network and dynamics predominantly through the UL12.5 gene. We demonstrated that HSV-1 infection induced a remodeling of mitochondrial shape, resulting in a fragmentation of the mitochondria associated with a decrease in their volume and an increase in their sphericity. This damage leads to the release of mitochondrial DNA (mtDNA) to the cytosol. By generating a stable THP-1 cell line expressing the DNase I-mCherry fusion protein and a THP-1 cell line specifically depleted of mtDNA upon ethidium bromide treatment, we showed that cytosolic mtDNA contributes to type I interferon and APOBEC3A upregulation. This was confirmed by using an HSV-1 strain (KOS37 UL98-SPA) with a deletion of the UL12.5 gene that impaired its ability to induce mtDNA stress. Furthermore, by using an inhibitor of RNA polymerase III, we demonstrated that upon HSV-1 infection, cytosolic mtDNA enhanced type I interferon induction through the RNA polymerase III/RIG-I pathway. APOBEC3A was in turn induced by interferon. Deep sequencing analyses of cytosolic mtDNA mutations revealed an APOBEC3A signature predominantly in the 5'TpCpG context. These data demonstrate that upon HSV-1 infection, the mitochondrial network is disrupted, leading to the release of mtDNA and ultimately to its catabolism through APOBEC3-induced mutations. IMPORTANCE Herpes simplex virus 1 (HSV-1) impairs the mitochondrial network through the viral protein UL12.5. This leads to the fusion of mitochondria and simultaneous release of mitochondrial DNA (mtDNA) in a mouse model. We have shown that released mtDNA is recognized as a danger signal, capable of stimulating signaling pathways and inducing the production of proinflammatory cytokines. The expression of the human cytidine deaminase APOBEC3A is highly upregulated by interferon responses. This enzyme catalyzes the deamination of cytidine to uridine in single-stranded DNA substrates, resulting in the catabolism of edited DNA. Using human cell lines deprived of mtDNA and viral strains deficient in UL12, we demonstrated the implication of mtDNA in the production of interferon and APOBEC3A expression during viral infection. We have shown that HSV-1 induces mitochondrial network fragmentation in a human model and confirmed the implication of RNA polymerase III/RIG-I signaling in the capture of cytosolic mtDNA.
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Affiliation(s)
- Noémie Berry
- Molecular Retrovirology Unit, Institut Pasteur, Paris, France
- Sorbonne Université, Complexité du Vivant, Paris, France
| | | | - Vincent Caval
- Molecular Retrovirology Unit, Institut Pasteur, Paris, France
| | - Pierre Khalfi
- Molecular Retrovirology Unit, Institut Pasteur, Paris, France
- Sorbonne Université, Complexité du Vivant, Paris, France
| | | | | | - Hervé Blanc
- Viral Populations and Pathogenesis Unit, Institut Pasteur, CNRS UMR 3569, Paris, France
| | - Marco Vignuzzi
- Viral Populations and Pathogenesis Unit, Institut Pasteur, CNRS UMR 3569, Paris, France
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The Pseudokinase TRIB3 Negatively Regulates the HER2 Receptor Pathway and Is a Biomarker of Good Prognosis in Luminal Breast Cancer. Cancers (Basel) 2021; 13:cancers13215307. [PMID: 34771470 PMCID: PMC8582533 DOI: 10.3390/cancers13215307] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/15/2021] [Accepted: 10/19/2021] [Indexed: 02/05/2023] Open
Abstract
Simple Summary Breast cancer is the most frequent type of cancer in women. More than 70% of these tumors belong to the so-called luminal subtype which has, in general, a good prognosis. However, a fraction of patients with luminal breast cancer progress to an advanced or metastatic disease, which remains a major clinical and social problem. Therefore, it is crucial to identify novel biomarkers that help to predict the progression of the disease and to develop more efficacious therapeutic approaches to fight advanced luminal breast cancer. In this work we found that the increased expression of the protein tribbles pseudokinase 3 (TRIB3) is associated with a good prognosis and a better response to therapy in luminal breast cancer patients. We also found that this effect is at least in part due to the ability of TRIB3 to inhibit the activity of the oncogene HER2. Abstract Background: Tribbles pseudokinase 3 (TRIB3) has been proposed to both promote and restrict cancer generation and progression. However, the precise mechanisms that determine this dual role of TRIB3 in cancer remain to be understood. In this study we aimed to investigate the role of TRIB3 in luminal breast cancer, the most frequent subtype of this malignancy. Methods: We genetically manipulated TRIB3 expression in a panel of luminal breast cancer cell lines and analyzed its impact on cell proliferation, and the phosphorylation, levels, or subcellular localization of TRIB3 and other protein regulators of key signaling pathways in luminal breast cancer. We also analyzed TRIB3 protein expression in samples from luminal breast cancer patients and performed bioinformatic analyses in public datasets. Results: TRIB3 enhanced the proliferation and AKT phosphorylation in luminal A (HER2-) but decreased them in luminal B (HER2+) breast cancer cell lines. TRIB3 negatively regulated the stability of HER2 in luminal B breast cancer cell lines. TRIB3 expression was associated with increased disease-free survival and a better response to therapy in luminal breast cancer patients. Conclusions: Our findings support the exploration of TRIB3 as a potential biomarker and therapeutic target in luminal breast cancer.
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8
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Constantin D, Dubuis G, Conde-Rubio MDC, Widmann C. APOBEC3C, a nucleolar protein induced by genotoxins, is excluded from DNA damage sites. FEBS J 2021; 289:808-831. [PMID: 34528388 PMCID: PMC9292673 DOI: 10.1111/febs.16202] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 08/22/2021] [Accepted: 09/14/2021] [Indexed: 01/23/2023]
Abstract
The human genome contains 11 APOBEC (apolipoprotein B mRNA editing catalytic polypeptide‐like) cytidine deaminases classified into four families. These proteins function mainly in innate antiviral immunity and can also restrict endogenous retrotransposable element multiplication. The present study focuses on APOBEC3C (A3C), a member of the APOBEC3 subfamily. Some APOBEC3 proteins use their enzymatic activity on genomic DNA, inducing mutations and DNA damage, while other members facilitate DNA repair. Our results show that A3C is highly expressed in cells treated with DNA‐damaging agents. Its expression is regulated by p53. Depletion of A3C slightly decreases proliferation and does not affect DNA repair via homologous recombination or nonhomologous end joining. The A3C interactomes obtained from control cells and cells exposed to the genotoxin etoposide indicated that A3C is a nucleolar protein. This was confirmed by the detection of either endogenous or ectopic A3C in nucleoli. Interestingly, we show that A3C is excluded from areas of DNA breaks in live cells. Our data also indicate that the C‐terminal part of A3C is responsible for its nucleolar localization and exclusion from DNA damage sites.
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Affiliation(s)
- Daniel Constantin
- Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Switzerland
| | - Gilles Dubuis
- Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Switzerland
| | | | - Christian Widmann
- Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Switzerland
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9
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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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10
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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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11
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Links between the unfolded protein response and the DNA damage response in hypoxia: a systematic review. Biochem Soc Trans 2021; 49:1251-1263. [PMID: 34003246 PMCID: PMC8286837 DOI: 10.1042/bst20200861] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 02/06/2023]
Abstract
Hypoxia is a feature of most solid tumours and predicts for poor prognosis. In radiobiological hypoxia (<0.1% O2) cells become up to three times more resistant to radiation. The biological response to radiobiological hypoxia is one of few physiologically relevant stresses that activates both the unfolded protein and DNA damage responses (UPR and DDR). Links between these pathways have been identified in studies carried out in normoxia. Based in part on these previous studies and recent work from our laboratory, we hypothesised that the biological response to hypoxia likely includes overlap between the DDR and UPR. While inhibition of the DDR is a recognised strategy for improving radiation response, the possibility of achieving this through targeting the UPR has not been realised. We carried out a systematic review to identify links between the DDR and UPR, in human cell lines exposed to <2% O2. Following PRISMA guidance, literature from January 2010 to October 2020 were retrieved via Ovid MEDLINE and evaluated. A total of 202 studies were included. LAMP3, ULK1, TRIB3, CHOP, NOXA, NORAD, SIAH1/2, DYRK2, HIPK2, CREB, NUPR1, JMJD2B, NRF2, GSK-3B, GADD45a, GADD45b, STAU1, C-SRC, HK2, CAV1, CypB, CLU, IGFBP-3 and SP1 were highlighted as potential links between the hypoxic DDR and UPR. Overall, we identified very few studies which demonstrate a molecular link between the DDR and UPR in hypoxia, however, it is clear that many of the molecules highlighted warrant further investigation under radiobiological hypoxia as these may include novel therapeutic targets to improve radiotherapy response.
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12
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Stefanovska B, André F, Fromigué O. Tribbles Pseudokinase 3 Regulation and Contribution to Cancer. Cancers (Basel) 2021; 13:cancers13081822. [PMID: 33920424 PMCID: PMC8070086 DOI: 10.3390/cancers13081822] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/08/2021] [Accepted: 04/08/2021] [Indexed: 12/11/2022] Open
Abstract
Simple Summary Accumulating evidence supports a key function for Tribbles proteins in oncogenesis, both in leukemia and solid tumors. However, the exact role of these proteins is hard to define since in a context-dependent manner they can function as both oncogenes and tumor suppressors. Their complex role arises from the capacity to interact with a wide range of target molecules thereby acting as molecular scaffolds and signaling regulators of multiple pathways. This review focuses on one particular Tribbles family member, namely, TRIB3, addressing its gene and protein expression, as well as its role in cancer development and progression. Abstract The first Tribbles protein was identified as critical for the coordination of morphogenesis in Drosophila melanogaster. Three mammalian homologs were subsequently identified, with a structure similar to classic serine/threonine kinases, but lacking crucial amino acids for the catalytic activity. Thereby, the very weak ATP affinity classifies TRIB proteins as pseudokinases. In this review, we provide an overview of the regulation of TRIB3 gene expression at both transcriptional and post-translational levels. Despite the absence of kinase activity, TRIB3 interferes with a broad range of cellular processes through protein–protein interactions. In fact, TRIB3 acts as an adaptor/scaffold protein for many other proteins such as kinase-dependent proteins, transcription factors, ubiquitin ligases, or even components of the spliceosome machinery. We then state the contribution of TRIB3 to cancer development, progression, and metastasis. TRIB3 dysregulation can be associated with good or bad prognosis. Indeed, as TRIB3 interacts with and regulates the activity of many key signaling components, it can act as a tumor-suppressor or oncogene in a context-dependent manner.
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Affiliation(s)
- Bojana Stefanovska
- Inserm, UMR981, F-94805 Villejuif, France; (B.S.); (F.A.)
- Gustave Roussy, F-94805 Villejuif, France
- Orsay, Université Paris Saclay, F-91400 Gif-sur-Yvette, France
| | - Fabrice André
- Inserm, UMR981, F-94805 Villejuif, France; (B.S.); (F.A.)
- Gustave Roussy, F-94805 Villejuif, France
- Orsay, Université Paris Saclay, F-91400 Gif-sur-Yvette, France
- Department of Medical Oncology, Gustave Roussy, F-94805 Villejuif, France
| | - Olivia Fromigué
- Inserm, UMR981, F-94805 Villejuif, France; (B.S.); (F.A.)
- Gustave Roussy, F-94805 Villejuif, France
- Orsay, Université Paris Saclay, F-91400 Gif-sur-Yvette, France
- Correspondence: ; Tel.: +33-142114211
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13
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Rouf Banday A, Onabajo OO, Lin SHY, Obajemu A, Vargas JM, Delviks-Frankenberry KA, Lamy P, Bayanjargal A, Zettelmeyer C, Florez-Vargas O, Pathak VK, Dyrskjøt L, Prokunina-Olsson L. Targeting natural splicing plasticity of APOBEC3B restricts its expression and mutagenic activity. Commun Biol 2021; 4:386. [PMID: 33753867 PMCID: PMC7985488 DOI: 10.1038/s42003-021-01844-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 02/11/2021] [Indexed: 12/14/2022] Open
Abstract
APOBEC3A (A3A) and APOBEC3B (A3B) enzymes drive APOBEC-mediated mutagenesis. Identification of factors affecting the activity of these enzymes could help modulate mutagenesis and associated clinical outcomes. Here, we show that canonical and alternatively spliced A3A and A3B isoforms produce corresponding mutagenic and non-mutagenic enzymes. Increased expression of the mutagenic A3B isoform predicted shorter progression-free survival in bladder cancer. We demonstrate that the production of mutagenic vs. non-mutagenic A3B protein isoforms was considerably affected by inclusion/skipping of exon 5 in A3B. Furthermore, exon 5 skipping, resulting in lower levels of mutagenic A3B enzyme, could be increased in vitro. Specifically, we showed the effects of treatment with an SF3B1 inhibitor affecting spliceosome interaction with a branch point site in intron 4, or with splice-switching oligonucleotides targeting exon 5 of A3B. Our results underscore the clinical role of A3B and implicate alternative splicing of A3B as a mechanism that could be targeted to restrict APOBEC-mediated mutagenesis.
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Affiliation(s)
- A Rouf Banday
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Olusegun O Onabajo
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Seraph Han-Yin Lin
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Adeola Obajemu
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Joselin M Vargas
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Krista A Delviks-Frankenberry
- Viral Mutation Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Philippe Lamy
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Ariunaa Bayanjargal
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Clara Zettelmeyer
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Oscar Florez-Vargas
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Vinay K Pathak
- Viral Mutation Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Ludmila Prokunina-Olsson
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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14
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Transcriptomic Changes Associated with Loss of Cell Viability Induced by Oxysterol Treatment of a Retinal Photoreceptor-Derived Cell Line: An In Vitro Model of Smith-Lemli-Opitz Syndrome. Int J Mol Sci 2021; 22:ijms22052339. [PMID: 33652836 PMCID: PMC7956713 DOI: 10.3390/ijms22052339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/19/2021] [Accepted: 02/21/2021] [Indexed: 11/17/2022] Open
Abstract
Smith–Lemli–Opitz Syndrome (SLOS) results from mutations in the gene encoding the enzyme DHCR7, which catalyzes conversion of 7-dehydrocholesterol (7DHC) to cholesterol (CHOL). Rats treated with a DHCR7 inhibitor serve as a SLOS animal model, and exhibit progressive photoreceptor-specific cell death, with accumulation of 7DHC and oxidized sterols. To understand the basis of this cell type specificity, we performed transcriptomic analyses on a photoreceptor-derived cell line (661W), treating cells with two 7DHC-derived oxysterols, which accumulate in tissues and bodily fluids of SLOS patients and in the rat SLOS model, as well as with CHOL (negative control), and evaluated differentially expressed genes (DEGs) for each treatment. Gene enrichment analysis and compilation of DEG sets indicated that endoplasmic reticulum stress, oxidative stress, DNA damage and repair, and autophagy were all highly up-regulated pathways in oxysterol-treated cells. Detailed analysis indicated that the two oxysterols exert their effects via different molecular mechanisms. Changes in expression of key genes in highlighted pathways (Hmox1, Ddit3, Trib3, and Herpud1) were validated by immunofluorescence confocal microscopy. The results extend our understanding of the pathobiology of retinal degeneration and SLOS, identifying potential new druggable targets for therapeutic intervention into these and other related orphan diseases.
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15
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Petljak M, Maciejowski J. Molecular origins of APOBEC-associated mutations in cancer. DNA Repair (Amst) 2020; 94:102905. [PMID: 32818816 PMCID: PMC7494591 DOI: 10.1016/j.dnarep.2020.102905] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/26/2020] [Accepted: 06/27/2020] [Indexed: 01/03/2023]
Abstract
The APOBEC family of cytidine deaminases has been proposed to represent a major enzymatic source of mutations in cancer. Here, we summarize available evidence that links APOBEC deaminases to cancer mutagenesis. We also highlight newly identified human cell models of APOBEC mutagenesis, including cancer cell lines with suspected endogenous APOBEC activity and a cell system of telomere crisis-associated mutations. Finally, we draw on recent data to propose potential causes of APOBEC misregulation in cancer, including the instigating factors, the relevant mutator(s), and the mechanisms underlying generation of the genome-dispersed and clustered APOBEC-induced mutations.
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Affiliation(s)
- Mia Petljak
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142 , USA.
| | - John Maciejowski
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
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16
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Franaszczyk M, Truszkowska G, Chmielewski P, Rydzanicz M, Kosinska J, Rywik T, Biernacka A, Spiewak M, Kostrzewa G, Stepien-Wojno M, Stawinski P, Bilinska M, Krajewski P, Zielinski T, Lutynska A, Bilinska ZT, Ploski R. Analysis of De Novo Mutations in Sporadic Cardiomyopathies Emphasizes Their Clinical Relevance and Points to Novel Candidate Genes. J Clin Med 2020; 9:jcm9020370. [PMID: 32013205 PMCID: PMC7073782 DOI: 10.3390/jcm9020370] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/22/2020] [Accepted: 01/24/2020] [Indexed: 02/06/2023] Open
Abstract
The vast majority of cardiomyopathies have an autosomal dominant inheritance; hence, genetic testing is typically offered to patients with a positive family history. A de novo mutation is a new germline mutation not inherited from either parent. The purpose of our study was to search for de novo mutations in patients with cardiomyopathy and no evidence of the disease in the family. Using next-generation sequencing, we analyzed cardiomyopathy genes in 12 probands. In 8 (66.7%), we found de novo variants in known cardiomyopathy genes (TTN, DSP, SCN5A, TNNC1, TPM1, CRYAB, MYH7). In the remaining probands, the analysis was extended to whole exome sequencing in a trio (proband and parents). We found de novo variants in genes that, so far, were not associated with any disease (TRIB3, SLC2A6), a possible disease-causing biallelic genotype (APOBEC gene family), and a de novo mosaic variant without strong evidence of pathogenicity (UNC45A). The high prevalence of de novo mutations emphasizes that genetic screening is also indicated in cases of sporadic cardiomyopathy. Moreover, we have identified novel cardiomyopathy candidate genes that are likely to affect immunological function and/or reaction to stress that could be especially relevant in patients with disease onset associated with infection/infestation.
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Affiliation(s)
- Maria Franaszczyk
- Molecular Biology Laboratory, Department of Medical Biology, Institute of Cardiology, 04-628 Warsaw, Poland; (M.F.)
| | - Grazyna Truszkowska
- Molecular Biology Laboratory, Department of Medical Biology, Institute of Cardiology, 04-628 Warsaw, Poland; (M.F.)
| | - Przemyslaw Chmielewski
- Unit for Screening Studies in Inherited Cardiovascular Diseases, Institute of Cardiology, 04-628 Warsaw, Poland
| | - Malgorzata Rydzanicz
- Department of Medical Genetics, Medical University of Warsaw, 02-106 Warsaw, Poland
| | - Joanna Kosinska
- Department of Medical Genetics, Medical University of Warsaw, 02-106 Warsaw, Poland
| | - Tomasz Rywik
- Department of Heart Failure and Transplantology, Institute of Cardiology, 04-628 Warsaw, Poland
| | - Anna Biernacka
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland
| | - Mateusz Spiewak
- Magnetic Resonance Unit, Department of Radiology, Institute of Cardiology, 04-628 Warsaw, Poland
| | - Grazyna Kostrzewa
- Department of Forensic Medicine, Medical University of Warsaw, 02-007 Warsaw, Poland
| | - Malgorzata Stepien-Wojno
- Unit for Screening Studies in Inherited Cardiovascular Diseases, Institute of Cardiology, 04-628 Warsaw, Poland
| | - Piotr Stawinski
- Department of Medical Genetics, Medical University of Warsaw, 02-106 Warsaw, Poland
| | - Maria Bilinska
- Department of Arrhythmia, Institute of Cardiology, 04-628 Warsaw, Poland
| | - Pawel Krajewski
- Department of Forensic Medicine, Medical University of Warsaw, 02-007 Warsaw, Poland
| | - Tomasz Zielinski
- Department of Heart Failure and Transplantology, Institute of Cardiology, 04-628 Warsaw, Poland
| | - Anna Lutynska
- Department of Medical Biology, Institute of Cardiology, 04-628 Warsaw, Poland
| | - Zofia T. Bilinska
- Unit for Screening Studies in Inherited Cardiovascular Diseases, Institute of Cardiology, 04-628 Warsaw, Poland
- Correspondence: (Z.T.B.); (R.P.); Tel.: +48-223434710 (Z.T.B.); +48-225720695 (R.P.)
| | - Rafal Ploski
- Department of Medical Genetics, Medical University of Warsaw, 02-106 Warsaw, Poland
- Correspondence: (Z.T.B.); (R.P.); Tel.: +48-223434710 (Z.T.B.); +48-225720695 (R.P.)
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17
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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: 68] [Impact Index Per Article: 13.6] [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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18
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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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19
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Hypoxia-induced human deoxyribonuclease I is a cellular restriction factor of hepatitis B virus. Nat Microbiol 2019; 4:1196-1207. [PMID: 30936483 DOI: 10.1038/s41564-019-0405-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 02/11/2019] [Indexed: 12/17/2022]
Abstract
Numerous human APOBEC3 cytidine deaminases have proven to be, inter alia, host cell restriction factors for retroviruses and hepadnaviruses. Although they can bind to genomic RNA and become encapsidated, they are only catalytically active on single-stranded DNA. As there are many cellular deoxyribonucleases (DNases), we hypothesized that a parallel could be struck between APOBEC3 and DNases. For human hepatitis B virus (HBV), we show that DNase I can considerably reduce the virion genome copy number from a variety of transfected or infected cells. DNASE1 is overexpressed and encapsidated in HBV particles in vitro in hypoxic environments and in vivo in cirrhotic patient livers as well as in the serum of infected patients. The use of CoCl2 and dimethyloxalylglycine, mimetic agents used to induce hypoxia by inhibiting prolyl hydroxylase enzymes that stabilize hypoxia-inducible factor (HIF)-1α, showed that the formation of HIF-1α/HIF-1β heterodimers results in the induction of DNASE1. Indeed, transfection with HIF-1α and HIF-1β expression constructs upregulated DNASE1. These findings suggest that human DNase I can impact HBV replication through the catabolism of the DNA genome within the capsid. The activity of DNases in general may explain in part the high frequency of empty or 'light' hepatitis B virions observed in vivo.
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20
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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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21
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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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22
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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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23
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Nicolas E, Demidova EV, Iqbal W, Serebriiskii IG, Vlasenkova R, Ghatalia P, Zhou Y, Rainey K, Forman AF, Dunbrack RL, Golemis EA, Hall MJ, Daly MB, Arora S. Interaction of germline variants in a family with a history of early-onset clear cell renal cell carcinoma. Mol Genet Genomic Med 2019; 7:e556. [PMID: 30680959 PMCID: PMC6418363 DOI: 10.1002/mgg3.556] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 12/06/2018] [Accepted: 12/11/2018] [Indexed: 12/31/2022] Open
Abstract
Background Identification of genetic factors causing predisposition to renal cell carcinoma has helped improve screening, early detection, and patient survival. Methods We report the characterization of a proband with renal and thyroid cancers and a family history of renal and other cancers by whole‐exome sequencing (WES), coupled with WES analysis of germline DNA from additional affected and unaffected family members. Results This work identified multiple predicted protein‐damaging variants relevant to the pattern of inherited cancer risk. Among these, the proband and an affected brother each had a heterozygous Ala45Thr variant in SDHA, a component of the succinate dehydrogenase (SDH) complex. SDH defects are associated with mitochondrial disorders and risk for various cancers; immunochemical analysis indicated loss of SDHB protein expression in the patient’s tumor, compatible with SDH deficiency. Integrated analysis of public databases and structural predictions indicated that the two affected individuals also had additional variants in genes including TGFB2, TRAP1, PARP1, and EGF, each potentially relevant to cancer risk alone or in conjunction with the SDHA variant. In addition, allelic imbalances of PARP1 and TGFB2 were detected in the tumor of the proband. Conclusion Together, these data suggest the possibility of risk associated with interaction of two or more variants.
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Affiliation(s)
- Emmanuelle Nicolas
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Elena V Demidova
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania.,Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania.,Kazan Federal University, Kazan, Russia
| | - Waleed Iqbal
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Ilya G Serebriiskii
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania.,Kazan Federal University, Kazan, Russia
| | | | - Pooja Ghatalia
- Department of Hematology/Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Yan Zhou
- Biostatistics and Bioinformatics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Kim Rainey
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Andrea F Forman
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Roland L Dunbrack
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Erica A Golemis
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Michael J Hall
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania.,Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Mary B Daly
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania.,Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Sanjeevani Arora
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
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24
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Lerner T, Papavasiliou FN, Pecori R. RNA Editors, Cofactors, and mRNA Targets: An Overview of the C-to-U RNA Editing Machinery and Its Implication in Human Disease. Genes (Basel) 2018; 10:E13. [PMID: 30591678 PMCID: PMC6356216 DOI: 10.3390/genes10010013] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 12/10/2018] [Accepted: 12/20/2018] [Indexed: 12/22/2022] Open
Abstract
One of the most prevalent epitranscriptomic modifications is RNA editing. In higher eukaryotes, RNA editing is catalyzed by one of two classes of deaminases: ADAR family enzymes that catalyze A-to-I (read as G) editing, and AID/APOBEC family enzymes that catalyze C-to-U. ADAR-catalyzed deamination has been studied extensively. Here we focus on AID/APOBEC-catalyzed editing, and review the emergent knowledge regarding C-to-U editing consequences in the context of human disease.
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Affiliation(s)
- Taga Lerner
- Division of Immune Diversity, Program in Cancer Immunology, German Cancer Research Centre, 69120 Heidelberg, Germany.
- Division of Biosciences, Uni Heidelberg, 69120 Heidelberg, Germany.
| | - F Nina Papavasiliou
- Division of Immune Diversity, Program in Cancer Immunology, German Cancer Research Centre, 69120 Heidelberg, Germany.
| | - Riccardo Pecori
- Division of Immune Diversity, Program in Cancer Immunology, German Cancer Research Centre, 69120 Heidelberg, Germany.
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25
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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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26
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APOBEC3H Subcellular Localization Determinants Define Zipcode for Targeting HIV-1 for Restriction. Mol Cell Biol 2018; 38:MCB.00356-18. [PMID: 30224517 DOI: 10.1128/mcb.00356-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 09/11/2018] [Indexed: 12/22/2022] Open
Abstract
APOBEC enzymes are DNA cytosine deaminases that normally serve as virus restriction factors, but several members, including APOBEC3H, also contribute to cancer mutagenesis. Despite their importance in multiple fields, little is known about cellular processes that regulate these DNA mutating enzymes. We show that APOBEC3H exists in two distinct subcellular compartments, cytoplasm and nucleolus, and that the structural determinants for each mechanism are genetically separable. First, native and fluorescently tagged APOBEC3Hs localize to these two compartments in multiple cell types. Second, a series of genetic, pharmacologic, and cell biological studies demonstrate active cytoplasmic and nucleolar retention mechanisms, whereas nuclear import and export occur through passive diffusion. Third, APOBEC3H cytoplasmic retention determinants relocalize APOBEC3A from a passive cell-wide state to the cytosol and, additionally, endow potent HIV-1 restriction activity. These results indicate that APOBEC3H has a structural zipcode for subcellular localization and selecting viral substrates for restriction.
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27
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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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28
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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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29
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Balachandran A, Wong R, Stoilov P, Pan S, Blencowe B, Cheung P, Harrigan PR, Cochrane A. Identification of small molecule modulators of HIV-1 Tat and Rev protein accumulation. Retrovirology 2017; 14:7. [PMID: 28122580 PMCID: PMC5267425 DOI: 10.1186/s12977-017-0330-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 01/04/2017] [Indexed: 11/10/2022] Open
Abstract
Background HIV-1 replication is critically dependent upon controlled processing of its RNA and the activities provided by its encoded regulatory factors Tat and Rev. A screen of small molecule modulators of RNA processing identified several which inhibited virus gene expression, affecting both relative abundance of specific HIV-1 RNAs and the levels of Tat and Rev proteins. Results The screen for small molecules modulators of HIV-1 gene expression at the post-transcriptional level identified three (a pyrimidin-7-amine, biphenylcarboxamide, and benzohydrazide, designated 791, 833, and 892, respectively) that not only reduce expression of HIV-1 Gag and Env and alter the accumulation of viral RNAs, but also dramatically decrease Tat and Rev levels. Analyses of viral RNA levels by qRTPCR and RTPCR indicated that the loss of either protein could not be attributed to changes in abundance of the mRNAs encoding these factors. However, addition of the proteasome inhibitor MG132 did result in significant restoration of Tat expression, indicating that the compounds are affecting Tat synthesis and/or degradation. Tests in the context of replicating HIV-1 in PBMCs confirmed that 791 significantly reduced virus replication. Parallel analyses of the effect of the compounds on host gene expression revealed only minor changes in either mRNA abundance or alternative splicing. Subsequent tests suggest that 791 may function by reducing levels of the Tat/Rev chaperone Nap1. Conclusions The three compounds examined (791, 833, 892), despite their lack of structural similarity, all suppressed HIV-1 gene expression by preventing accumulation of two key HIV-1 regulatory factors, Tat and Rev. These findings demonstrate that selective disruption of HIV-1 gene expression can be achieved. Electronic supplementary material The online version of this article (doi:10.1186/s12977-017-0330-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ahalya Balachandran
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON, M5S1A8, Canada
| | - Raymond Wong
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Peter Stoilov
- Department of Biochemistry, University of West Virginia, Morgantown, WV, USA
| | - Sandy Pan
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Benjamin Blencowe
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON, M5S1A8, Canada.,Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Peter Cheung
- British Columbia Centre for Excellence in HIV/AIDS, 608-1081 Burrard St., Vancouver, BC, Canada
| | - P Richard Harrigan
- British Columbia Centre for Excellence in HIV/AIDS, 608-1081 Burrard St., Vancouver, BC, Canada.,Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Alan Cochrane
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON, M5S1A8, Canada.
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30
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Long noncoding RNA #32 contributes to antiviral responses by controlling interferon-stimulated gene expression. Proc Natl Acad Sci U S A 2016; 113:10388-93. [PMID: 27582466 DOI: 10.1073/pnas.1525022113] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Despite the breadth of knowledge that exists regarding the function of long noncoding RNAs (lncRNAs) in biological phenomena, the role of lncRNAs in host antiviral responses is poorly understood. Here, we report that lncRNA#32 is associated with type I IFN signaling. The silencing of lncRNA#32 dramatically reduced the level of IFN-stimulated gene (ISG) expression, resulting in sensitivity to encephalomyocarditis virus (EMCV) infection. In contrast, the ectopic expression of lncRNA#32 significantly suppressed EMCV replication, suggesting that lncRNA#32 positively regulates the host antiviral response. We further demonstrated the suppressive function of lncRNA#32 in hepatitis B virus and hepatitis C virus infection. lncRNA#32 bound to activating transcription factor 2 (ATF2) and regulated ISG expression. Our results reveal a role for lncRNA#32 in host antiviral responses.
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31
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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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32
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Akre MK, Starrett GJ, Quist JS, Temiz NA, Carpenter MA, Tutt ANJ, Grigoriadis A, Harris RS. Mutation Processes in 293-Based Clones Overexpressing the DNA Cytosine Deaminase APOBEC3B. PLoS One 2016; 11:e0155391. [PMID: 27163364 PMCID: PMC4862684 DOI: 10.1371/journal.pone.0155391] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 04/05/2016] [Indexed: 11/18/2022] Open
Abstract
Molecular, cellular, and clinical studies have combined to demonstrate a contribution from the DNA cytosine deaminase APOBEC3B (A3B) to the overall mutation load in breast, head/neck, lung, bladder, cervical, ovarian, and other cancer types. However, the complete landscape of mutations attributable to this enzyme has yet to be determined in a controlled human cell system. We report a conditional and isogenic system for A3B induction, genomic DNA deamination, and mutagenesis. Human 293-derived cells were engineered to express doxycycline-inducible A3B-eGFP or eGFP constructs. Cells were subjected to 10 rounds of A3B-eGFP exposure that each caused 80–90% cell death. Control pools were subjected to parallel rounds of non-toxic eGFP exposure, and dilutions were done each round to mimic A3B-eGFP induced population fluctuations. Targeted sequencing of portions of TP53 and MYC demonstrated greater mutation accumulation in the A3B-eGFP exposed pools. Clones were generated and microarray analyses were used to identify those with the greatest number of SNP alterations for whole genome sequencing. A3B-eGFP exposed clones showed global increases in C-to-T transition mutations, enrichments for cytosine mutations within A3B-preferred trinucleotide motifs, and more copy number aberrations. Surprisingly, both control and A3B-eGFP clones also elicited strong mutator phenotypes characteristic of defective mismatch repair. Despite this additional mutational process, the 293-based system characterized here still yielded a genome-wide view of A3B-catalyzed mutagenesis in human cells and a system for additional studies on the compounded effects of simultaneous mutation mechanisms in cancer cells.
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Affiliation(s)
- Monica K. Akre
- Department of Biochemistry, Molecular Biology, and Biophysics, Institute for Molecular Virology, Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States of America
| | - Gabriel J. Starrett
- Department of Biochemistry, Molecular Biology, and Biophysics, Institute for Molecular Virology, Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States of America
| | - Jelmar S. Quist
- Breast Cancer Now Research Unit, Research Oncology, Guy’s Hospital, King’s College London, London, United Kingdom
| | - Nuri A. Temiz
- Department of Biochemistry, Molecular Biology, and Biophysics, Institute for Molecular Virology, Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States of America
| | - Michael A. Carpenter
- Department of Biochemistry, Molecular Biology, and Biophysics, Institute for Molecular Virology, Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States of America
| | - Andrew N. J. Tutt
- Breast Cancer Now Research Unit, Research Oncology, Guy’s Hospital, King’s College London, London, United Kingdom
| | - Anita Grigoriadis
- Breast Cancer Now Research Unit, Research Oncology, Guy’s Hospital, King’s College London, London, United Kingdom
| | - Reuben S. Harris
- Department of Biochemistry, Molecular Biology, and Biophysics, Institute for Molecular Virology, Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States of America
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN, United States of America
- * E-mail:
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33
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Mondal D, Mathur A, Chandra PK. Tripping on TRIB3 at the junction of health, metabolic dysfunction and cancer. Biochimie 2016; 124:34-52. [DOI: 10.1016/j.biochi.2016.02.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 02/04/2016] [Indexed: 12/16/2022]
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34
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Hirz T, Dumontet C. Neutrophil Isolation and Analysis to Determine their Role in Lymphoma Cell Sensitivity to Therapeutic Agents. J Vis Exp 2016:e53846. [PMID: 27078837 DOI: 10.3791/53846] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Neutrophils are the most abundant (40% to 75%) type of white blood cells and among the first inflammatory cells to migrate towards the site of inflammation. They are key players in the innate immune system and play major roles in cancer biology. Neutrophils have been proposed as key mediators of malignant transformation, tumor progression, angiogenesis and in the modulation of the antitumor immunity; through their release of soluble factors or their interaction with tumor cells. To characterize the specific functions of neutrophils, a fast and reliable method is coveted for in vitro isolation of neutrophils from human blood. Here, a density gradient separation method is demonstrated to isolate neutrophils as well as mononuclear cells from the blood. The procedure consists of layering the density gradient solution such as Ficoll carefully above the diluted blood obtained from patients diagnosed with chronic lymphocytic leukemia (CLL), followed by centrifugation, isolation of mononuclear layer, separation of neutrophils from RBCsby dextran then lysis of residual erythrocytes. This method has been shown to isolate neutrophils ≥ 90 % pure. To mimic the tumor microenvironment, 3-dimensional (3D) experiments were performed using basement membrane matrix such as Matrigel. Given the short half-life of neutrophils in vitro, 3D experiments with fresh human neutrophils cannot be performed. For this reason promyelocytic HL60 cells are differentiated along the granulocytic pathway using the differentiation inducers dimethyl sulfoxide (DMSO) and retinoic acid (RA). The aim of our experiments is to study the role of neutrophils on the sensitivity of lymphoma cells to anti-lymphoma agents. However these methods can be generalized to study the interactions of neutrophils or neutrophil-like cells with a large range of cell types in different situations.
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Affiliation(s)
- Taghreed Hirz
- Immunity, Microenvironment, Virus, Cancer Research Center in Lyon
| | - Charles Dumontet
- Immunity, Microenvironment, Virus, Cancer Research Center in Lyon;
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Wang Y, Schmitt K, Guo K, Santiago ML, Stephens EB. Role of the single deaminase domain APOBEC3A in virus restriction, retrotransposition, DNA damage and cancer. J Gen Virol 2015; 97:1-17. [PMID: 26489798 DOI: 10.1099/jgv.0.000320] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The apolipoprotein mRNA editing enzyme catalytic polypeptide-like 3 (APOBEC3; A3) proteins are a family of seven cytidine deaminases (A3A, A3B, A3C, A3D, A3F, A3G and A3H) that restrict certain viral infections. These innate defence factors are best known for their ability to restrict the replication of human immunodeficiency virus type 1 (HIV-1) lacking a functional Vif protein (HIV-1Δvif) through the deamination of cytidine residues to uridines during reverse transcription, ultimately leading to lethal G → A changes in the viral genome. The best studied of the A3 proteins has been APOBEC3G because of its potent activity against HIV-1Δvif. However, one member of this family, A3A, has biological properties that make it unique among the A3 proteins. In this review, we will focus on the structural and phylogenetic features of the human and non-human primate A3A proteins, their role in the restriction of retroviruses and other viruses, and current findings on other biological properties affected by this protein.
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Affiliation(s)
- Yaqiong Wang
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS 66160, USA
| | - Kimberly Schmitt
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS 66160, USA
| | - Kejun Guo
- Departments of Medicine, Microbiology and Immunology, University of Colorado Denver Medical School, Aurora, CO 80045, USA
| | - Mario L Santiago
- Departments of Medicine, Microbiology and Immunology, University of Colorado Denver Medical School, Aurora, CO 80045, USA
| | - Edward B Stephens
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS 66160, USA
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Abstract
UNLABELLED Parkinson's disease (PD) is characterized by the progressive loss of select neuronal populations, but the prodeath genes mediating the neurodegenerative processes remain to be fully elucidated. Trib3 (tribbles pseudokinase 3) is a stress-induced gene with proapoptotic activity that was previously described as highly activated at the transcriptional level in a 6-hydroxydopamine (6-OHDA) cellular model of PD. Here, we report that Trib3 immunostaining is elevated in dopaminergic neurons of the substantia nigra pars compacta (SNpc) of human PD patients. Trib3 protein is also upregulated in cellular models of PD, including neuronal PC12 cells and rat dopaminergic ventral midbrain neurons treated with 6-OHDA, 1-methyl-4-phenylpyridinium (MPP+), or α-synuclein fibrils (αSYN). In the toxin models, Trib3 induction is substantially mediated by the transcription factors CHOP and ATF4. Trib3 overexpression is sufficient to promote neuronal death; conversely, Trib3 knockdown protects neuronal PC12 cells as well as ventral midbrain dopaminergic neurons from 6-OHDA, MPP+, or αSYN. Mechanism studies revealed that Trib3 physically interacts with Parkin, a prosurvival protein whose loss of function is associated with PD. Elevated Trib3 reduces Parkin expression in cultured cells; and in the SNpc of PD patients, Parkin levels are reduced in a subset of dopaminergic neurons expressing high levels of Trib3. Loss of Parkin at least partially mediates the prodeath actions of Trib3 in that Parkin knockdown in cellular PD models abolishes the protective effect of Trib3 downregulation. Together, these findings identify Trib3 and its regulatory pathways as potential targets to suppress the progression of neuron death and degeneration in PD. SIGNIFICANCE STATEMENT Parkinson's disease (PD) is the most common neurodegenerative movement disorder. Current treatments ameliorate symptoms, but not the underlying neuronal death. Understanding the core neurodegenerative processes in PD is a prerequisite for identifying new therapeutic targets and, ultimately, curing this disease. Here, we describe a novel pathway involving the proapoptotic protein Trib3 in neuronal death associated with PD. These findings are supported by data from multiple cellular models of PD and by immunostaining of postmortem PD brains. Upstream, Trib3 is induced by the transcription factors ATF4 and CHOP; and downstream, Trib3 interferes with the PD-associated prosurvival protein Parkin to mediate death. These findings establish this new pathway as a potential and promising therapeutic target for treatment of PD.
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Caval V, Bouzidi MS, Suspène R, Laude H, Dumargne MC, Bashamboo A, Krey T, Vartanian JP, Wain-Hobson S. Molecular basis of the attenuated phenotype of human APOBEC3B DNA mutator enzyme. Nucleic Acids Res 2015; 43:9340-9. [PMID: 26384561 PMCID: PMC4627089 DOI: 10.1093/nar/gkv935] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 09/08/2015] [Indexed: 12/22/2022] Open
Abstract
The human APOBEC3A and APOBEC3B genes (A3A and A3B) encode DNA mutator enzymes that deaminate cytidine and 5-methylcytidine residues in single-stranded DNA (ssDNA). They are important sources of mutations in many cancer genomes which show a preponderance of CG->TA transitions. Although both enzymes can hypermutate chromosomal DNA in an experimental setting, only A3A can induce double strand DNA breaks, even though the catalytic domains of A3B and A3A differ by only 9% at the protein level. Accordingly we sought the molecular basis underlying A3B attenuation through the generation of A3A-A3B chimeras and mutants. It transpires that the N-terminal domain facilitates A3B activity while a handful of substitutions in the catalytic C-terminal domain impacting ssDNA binding serve to attenuate A3B compared to A3A. Interestingly, functional attenuation is also observed for the rhesus monkey rhA3B enzyme compared to rhA3A indicating that this genotoxic dichotomy has been selected for and maintained for some 38 million years. Expression of all human ssDNA cytidine deaminase genes is absent in mature sperm indicating they contribute to somatic mutation and cancer but not human diversity.
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Affiliation(s)
- Vincent Caval
- Molecular Retrovirology Unit, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris cedex 15, France
| | - Mohamed S Bouzidi
- Molecular Retrovirology Unit, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris cedex 15, France
| | - Rodolphe Suspène
- Molecular Retrovirology Unit, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris cedex 15, France
| | - Hélène Laude
- Molecular Retrovirology Unit, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris cedex 15, France
| | - Marie-Charlotte Dumargne
- Human Developmental Genetics Unit, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris cedex 15, France
| | - Anu Bashamboo
- Human Developmental Genetics Unit, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris cedex 15, France
| | - Thomas Krey
- Structural Virology Unit, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris cedex 15, France
| | - Jean-Pierre Vartanian
- Molecular Retrovirology Unit, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris cedex 15, France
| | - Simon Wain-Hobson
- Molecular Retrovirology Unit, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris cedex 15, France
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38
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Willems L, Gillet NA. APOBEC3 Interference during Replication of Viral Genomes. Viruses 2015; 7:2999-3018. [PMID: 26110583 PMCID: PMC4488724 DOI: 10.3390/v7062757] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 05/26/2015] [Accepted: 06/04/2015] [Indexed: 01/05/2023] Open
Abstract
Co-evolution of viruses and their hosts has reached a fragile and dynamic equilibrium that allows viral persistence, replication and transmission. In response, infected hosts have developed strategies of defense that counteract the deleterious effects of viral infections. In particular, single-strand DNA editing by Apolipoprotein B Editing Catalytic subunits proteins 3 (APOBEC3s) is a well-conserved mechanism of mammalian innate immunity that mutates and inactivates viral genomes. In this review, we describe the mechanisms of APOBEC3 editing during viral replication, the viral strategies that prevent APOBEC3 activity and the consequences of APOBEC3 modulation on viral fitness and host genome integrity. Understanding the mechanisms involved reveals new prospects for therapeutic intervention.
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Affiliation(s)
- Luc Willems
- Molecular and Cellular Epigenetics, Interdisciplinary Cluster for Applied Genoproteomics (GIGA) of University of Liège (ULg), B34, 1 avenue de L'Hôpital, Sart-Tilman Liège 4000, Belgium.
- Molecular and Cellular Biology, Gembloux Agro-Bio Tech, University of Liège (ULg), 13 avenue Maréchal Juin, Gembloux 5030, Belgium.
| | - Nicolas Albert Gillet
- Molecular and Cellular Epigenetics, Interdisciplinary Cluster for Applied Genoproteomics (GIGA) of University of Liège (ULg), B34, 1 avenue de L'Hôpital, Sart-Tilman Liège 4000, Belgium.
- Molecular and Cellular Biology, Gembloux Agro-Bio Tech, University of Liège (ULg), 13 avenue Maréchal Juin, Gembloux 5030, Belgium.
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Abstract
Cancer genomic DNA sequences enable identification of all mutations and suggest targets for precision medicine. The identities and patterns of the mutations themselves also provide critical information for deducing the originating DNA damaging agents, causal molecular mechanisms, and thus additional therapeutic targets. A classic example is ultraviolet light, which crosslinks adjacent pyrimidines and leads to C-to-T transitions. A new example is the DNA cytosine deaminase APOBEC3B, which was identified recently as a source of DNA damage and mutagenesis in breast, head/neck, cervix, bladder, lung, ovary, and to lesser extents additional cancer types. This enzyme is normally an effector protein in the innate immune response to virus infection but upregulation in these cancer types causes elevated levels of genomic C-to-U deamination events, which manifest as C-to-T transitions and C-to-G transversions within distinct DNA trinucleotide contexts (preferentially 5’-TCA and 5’-TCG). Genomic C-to-U deamination events within the same trinucleotide contexts also lead to cytosine mutation clusters (kataegis), and may precipitate visible chromosomal aberrations such as translocations. Clinical studies indicate that APOBEC3B upregulation correlates with poorer outcomes for estrogen receptor-positive breast cancer patients, including shorter durations of disease-free survival and overall survival after surgery. APOBEC3B may therefore have both diagnostic and prognostic potential. APOBEC3B may also be a candidate for therapeutic targeting because inhibition of this non-essential enzyme is predicted to decrease tumor mutation rates and diminish the likelihood of undesirable mutation-dependent outcomes such as recurrence, metastasis, and the development of therapy resistant tumors.
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40
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Shandilya SMD, Bohn MF, Schiffer CA. A computational analysis of the structural determinants of APOBEC3's catalytic activity and vulnerability to HIV-1 Vif. Virology 2014; 471-473:105-16. [PMID: 25461536 PMCID: PMC4857191 DOI: 10.1016/j.virol.2014.09.023] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 09/29/2014] [Accepted: 09/30/2014] [Indexed: 11/23/2022]
Abstract
APOBEC3s (A3) are Zn(2+) dependent cytidine deaminases with diverse biological functions and implications for cancer and immunity. Four of the seven human A3s restrict HIV by 'hypermutating' the reverse-transcribed viral genomic DNA. HIV Virion Infectivity Factor (Vif) counters this restriction by targeting A3s to proteasomal degradation. However, there is no apparent correlation between catalytic activity, Vif binding, and sequence similarity between A3 domains. Our comparative structural analysis reveals features required for binding Vif and features influencing polynucleotide deaminase activity in A3 proteins. All Vif-binding A3s share a negatively charged surface region that includes residues previously implicated in binding the highly-positively charged Vif. Additionally, catalytically active A3s share a positively charged groove near the Zn(2+) coordinating active site, which may accommodate the negatively charged polynucleotide substrate. Our findings suggest surface electrostatics, as well as the spatial extent of substrate accommodating region, are critical determinants of substrate and Vif binding across A3 proteins with implications for anti-retroviral and anti-cancer therapeutic design.
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Affiliation(s)
- Shivender M D Shandilya
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Markus-Frederik Bohn
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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41
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Kostrzak A, Henry M, Demoyen PL, Wain-Hobson S, Vartanian JP. APOBEC3A catabolism of electroporated plasmid DNA in mouse muscle. Gene Ther 2014; 22:96-103. [PMID: 25298040 DOI: 10.1038/gt.2014.88] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 07/25/2014] [Accepted: 08/26/2014] [Indexed: 11/09/2022]
Abstract
The mouse is widely used as a model for DNA therapy and vaccination even though the efficiency of DNA delivery in higher mammals and humans is much less. The human APOBEC3 (A3) enzymes impact viral genomes by cytidine deamination, which introduces multiple uridine residues into single-stranded DNA, a process known as genetic editing. This initiates rapid DNA catabolism via a uracil DNA glycosylase dependent pathway. In tissue culture, A3A, A3C and A3B can hyperedit transfected plasmid DNA. We explored plasmid catabolism in vivo initiated by A3A, the most efficient of the human enzymes and one that is functionally conserved across most mammals. As rodents do not encode an A3A enzyme, it was possible to explore DNA degradation in the mouse model. Human A3A genetically edits co-electroporated luciferase plasmid DNA in mouse skeletal muscle that initiates DNA degradation resulting in approximately fourfold decrease in bioluminescence. Part of the degradation occurs in the nucleus as indicated by complex hyperedited DNA molecules. As human A3A is strongly upregulated by interferon α and DNA sensing pathways, it is a strong candidate enzyme for restricting plasmid DNA in higher mammals.
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Affiliation(s)
- A Kostrzak
- Invectys, Pasteur BioTop, Institut Pasteur, CNRS URA 3015, France
| | - M Henry
- Molecular Retrovirology Unit, Institut Pasteur, CNRS URA 3015, France
| | - P L Demoyen
- Invectys, Pasteur BioTop, Institut Pasteur, CNRS URA 3015, France
| | - S Wain-Hobson
- 1] Invectys, Pasteur BioTop, Institut Pasteur, CNRS URA 3015, France [2] Molecular Retrovirology Unit, Institut Pasteur, CNRS URA 3015, France
| | - J-P Vartanian
- Molecular Retrovirology Unit, Institut Pasteur, CNRS URA 3015, France
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42
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Suspène R, Caval V, Henry M, Bouzidi MS, Wain-Hobson S, Vartanian JP. Erroneous identification of APOBEC3-edited chromosomal DNA in cancer genomics. Br J Cancer 2014; 110:2615-22. [PMID: 24691422 PMCID: PMC4021520 DOI: 10.1038/bjc.2014.176] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 02/26/2014] [Accepted: 03/10/2014] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND The revolution in cancer genomics shows that the dominant mutations are CG->TA transitions. The sources of these mutations are probably two host cell cytidine deaminases APOBEC3A and APOBEC3B. The former in particular can access nuclear DNA and monotonously introduce phenomenal numbers of C->T mutations in the signature 5'TpC context. These can be copied as G->A transitions in the 5'GpA context. METHODS DNA hypermutated by an APOBEC3 enzyme can be recovered by a technique called 3DPCR, which stands for differential DNA denaturation PCR. This method exploits the fact that APOBEC3-edited DNA is richer in A+T compared with the reference. We explore explicitly 3DPCR error using cloned DNA. RESULTS Here we show that the technique has a higher error rate compared with standard PCR and can generate DNA strands containing both C->T and G->A mutations in a 5'GpCpR context. Sequences with similar traits have been recovered from human tumour DNA using 3DPCR. CONCLUSIONS Differential DNA denaturation PCR cannot be used to identify fixed C->T transitions in cancer genomes. Presently, the overall mutation frequency is ∼10(4)-10(5) base substitutions per cancer genome, or 0.003-0.03 kb(-1). By contrast, the 3DPCR error rate is of the order of 4-20 kb(-1) owing to constant selection for AT DNA and PCR-mediated recombination. Accordingly, sequences recovered by 3DPCR harbouring mixed C->T and G->A mutations associated with the 5'GpC represent artefacts.
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Affiliation(s)
- R Suspène
- Molecular Retrovirology Unit, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris, France
| | - V Caval
- Molecular Retrovirology Unit, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris, France
| | - M Henry
- Molecular Retrovirology Unit, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris, France
| | - M S Bouzidi
- Molecular Retrovirology Unit, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris, France
| | - S Wain-Hobson
- Molecular Retrovirology Unit, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris, France
| | - J-P Vartanian
- Molecular Retrovirology Unit, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris, France
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43
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Li J, Chen Y, Li M, Carpenter MA, McDougle RM, Luengas EM, Macdonald PJ, Harris RS, Mueller JD. APOBEC3 multimerization correlates with HIV-1 packaging and restriction activity in living cells. J Mol Biol 2014; 426:1296-307. [PMID: 24361275 PMCID: PMC3977201 DOI: 10.1016/j.jmb.2013.12.014] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 12/10/2013] [Accepted: 12/10/2013] [Indexed: 12/30/2022]
Abstract
APOBEC3G belongs to a family of DNA cytosine deaminases that are involved in the restriction of a broad number of retroviruses including human immunodeficiency virus type 1 (HIV-1). Prior studies have identified two distinct mechanistic steps in Vif-deficient HIV-1 restriction: packaging into virions and deaminating viral cDNA. APOBEC3A, for example, although highly active, is not packaged and is therefore not restrictive. APOBEC3G, on the other hand, although having weaker enzymatic activity, is packaged into virions and is strongly restrictive. Although a number of studies have described the propensity for APOBEC3 oligomerization, its relevance to HIV-1 restriction remains unclear. Here, we address this problem by examining APOBEC3 oligomerization in living cells using molecular brightness analysis. We find that APOBEC3G forms high-order multimers as a function of protein concentration. In contrast, APOBEC3A, APOBEC3C and APOBEC2 are monomers at all tested concentrations. Among other members of the APOBEC3 family, we show that the multimerization propensities of APOBEC3B, APOBEC3D, APOBEC3F and APOBEC3H (haplotype II) bear more resemblance to APOBEC3G than to APOBEC3A/3C/2. Prior studies have shown that all of these multimerizing APOBEC3 proteins, but not the monomeric family members, have the capacity to package into HIV-1 particles and restrict viral infectivity. This correlation between oligomerization and restriction is further evidenced by two different APOBEC3G mutants, which are each compromised for multimerization, packaging and HIV-1 restriction. Overall, our results imply that multimerization of APOBEC3 proteins may be related to the packaging mechanism and ultimately to virus restriction.
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Affiliation(s)
- Jinhui Li
- School of Physics and Astronomy, University of Minnesota, 116 Church Street Southeast, Minneapolis, MN 55455, USA; Institute for Molecular Virology, University of Minnesota, 515 Delaware Street Southeast, Minneapolis, MN 55455, USA
| | - Yan Chen
- School of Physics and Astronomy, University of Minnesota, 116 Church Street Southeast, Minneapolis, MN 55455, USA; Institute for Molecular Virology, University of Minnesota, 515 Delaware Street Southeast, Minneapolis, MN 55455, USA
| | - Ming Li
- Institute for Molecular Virology, University of Minnesota, 515 Delaware Street Southeast, Minneapolis, MN 55455, USA; Department of Biochemistry, Molecular Biology and Biophysics, 321 Church Street Southeast, Minneapolis, MN 55455, USA
| | - Michael A Carpenter
- Institute for Molecular Virology, University of Minnesota, 515 Delaware Street Southeast, Minneapolis, MN 55455, USA; Department of Biochemistry, Molecular Biology and Biophysics, 321 Church Street Southeast, Minneapolis, MN 55455, USA
| | - Rebecca M McDougle
- Institute for Molecular Virology, University of Minnesota, 515 Delaware Street Southeast, Minneapolis, MN 55455, USA; Department of Biochemistry, Molecular Biology and Biophysics, 321 Church Street Southeast, Minneapolis, MN 55455, USA
| | - Elizabeth M Luengas
- Institute for Molecular Virology, University of Minnesota, 515 Delaware Street Southeast, Minneapolis, MN 55455, USA; Department of Biochemistry, Molecular Biology and Biophysics, 321 Church Street Southeast, Minneapolis, MN 55455, USA
| | - Patrick J Macdonald
- Department of Biomedical Engineering, University of Minnesota, 312 Church Street Southeast, Minneapolis, MN 55455, USA
| | - Reuben S Harris
- Institute for Molecular Virology, University of Minnesota, 515 Delaware Street Southeast, Minneapolis, MN 55455, USA; Department of Biochemistry, Molecular Biology and Biophysics, 321 Church Street Southeast, Minneapolis, MN 55455, USA
| | - Joachim D Mueller
- School of Physics and Astronomy, University of Minnesota, 116 Church Street Southeast, Minneapolis, MN 55455, USA; Institute for Molecular Virology, University of Minnesota, 515 Delaware Street Southeast, Minneapolis, MN 55455, USA; Department of Biomedical Engineering, University of Minnesota, 312 Church Street Southeast, Minneapolis, MN 55455, USA.
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44
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Roberts SA, Gordenin DA. Clustered and genome-wide transient mutagenesis in human cancers: Hypermutation without permanent mutators or loss of fitness. Bioessays 2014; 36:382-393. [PMID: 24615916 DOI: 10.1002/bies.201300140] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The gain of a selective advantage in cancer as well as the establishment of complex traits during evolution require multiple genetic alterations, but how these mutations accumulate over time is currently unclear. There is increasing evidence that a mutator phenotype perpetuates the development of many human cancers. While in some cases the increased mutation rate is the result of a genetic disruption of DNA repair and replication or environmental exposures, other evidence suggests that endogenous DNA damage induced by AID/APOBEC cytidine deaminases can result in transient localized hypermutation generating simultaneous, closely spaced (i.e. "clustered") multiple mutations. Here, we discuss mechanisms that lead to mutation cluster formation, the biological consequences of their formation in cancer and evidence suggesting that APOBEC mutagenesis can also occur genome-wide. This raises the possibility that dysregulation of these enzymes may enable rapid malignant transformation by increasing mutation rates without the loss of fitness associated with permanent mutators.
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Affiliation(s)
- Steven A Roberts
- Chromosome Stability Group, Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Durham, NC, USA
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45
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Lucifora J, Xia Y, Reisinger F, Zhang K, Stadler D, Cheng X, Sprinzl MF, Koppensteiner H, Makowska Z, Volz T, Remouchamps C, Chou WM, Thasler WE, Hüser N, Durantel D, Liang TJ, Münk C, Heim MH, Browning JL, Dejardin E, Dandri M, Schindler M, Heikenwalder M, Protzer U. Specific and nonhepatotoxic degradation of nuclear hepatitis B virus cccDNA. Science 2014; 343:1221-8. [PMID: 24557838 DOI: 10.1126/science.1243462] [Citation(s) in RCA: 698] [Impact Index Per Article: 69.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Current antiviral agents can control but not eliminate hepatitis B virus (HBV), because HBV establishes a stable nuclear covalently closed circular DNA (cccDNA). Interferon-α treatment can clear HBV but is limited by systemic side effects. We describe how interferon-α can induce specific degradation of the nuclear viral DNA without hepatotoxicity and propose lymphotoxin-β receptor activation as a therapeutic alternative. Interferon-α and lymphotoxin-β receptor activation up-regulated APOBEC3A and APOBEC3B cytidine deaminases, respectively, in HBV-infected cells, primary hepatocytes, and human liver needle biopsies. HBV core protein mediated the interaction with nuclear cccDNA, resulting in cytidine deamination, apurinic/apyrimidinic site formation, and finally cccDNA degradation that prevented HBV reactivation. Genomic DNA was not affected. Thus, inducing nuclear deaminases-for example, by lymphotoxin-β receptor activation-allows the development of new therapeutics that, in combination with existing antivirals, may cure hepatitis B.
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Affiliation(s)
- Julie Lucifora
- Institute of Virology, Technische Universität München-Helmholtz Zentrum München, 81675 Munich, Germany
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46
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NMR structure of human restriction factor APOBEC3A reveals substrate binding and enzyme specificity. Nat Commun 2013; 4:1890. [PMID: 23695684 PMCID: PMC3674325 DOI: 10.1038/ncomms2883] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 04/12/2013] [Indexed: 02/07/2023] Open
Abstract
Human APOBEC3A (A3A) is a single-stranded DNA (ssDNA) cytidine deaminase that restricts viral pathogens and endogenous retrotransposons and plays a role in the innate immune response. Furthermore, its potential to act as a genomic DNA mutator has implications for a role in carcinogenesis. A deeper understanding of A3A’s deaminase and nucleic acid binding properties, which is central to its biological activities, has been limited by the lack of structural information. Here, we report the NMR solution structure of A3A and show that the critical interface for interaction with ssDNA substrates includes residues extending beyond the catalytic center. Importantly, by monitoring deaminase activity in real time, we find that A3A displays similar catalytic activity on A3A-specific TTCA- or A3G-specific CCCA-containing substrates, involving key determinants immediately 5′ of the reactive C. Our results afford novel mechanistic insights into A3A-mediated deamination and provide the structural basis for further molecular studies.
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47
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Caval V, Suspène R, Vartanian JP, Wain-Hobson S. Orthologous mammalian APOBEC3A cytidine deaminases hypermutate nuclear DNA. Mol Biol Evol 2013; 31:330-40. [PMID: 24162735 DOI: 10.1093/molbev/mst195] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The human APOBEC3 gene cluster locus encodes polynucleotide cytidine deaminases. Although many act as viral restriction factors through mutation of single-stranded DNA, recent reports have shown that human APOBEC3A was capable of efficiently hypermutating nuclear DNA and inducing DNA breaks in genomic DNA. In addition, the enzyme was unique in efficiently deaminating 5-methylcytidine in single-stranded DNA. To appreciate the evolutionary relevance of these activities, we analyzed A3A-related enzymes from the rhesus and tamarin monkey, horse, sheep, dog, and panda. All proved to be orthologous to the human enzyme in all these activities revealing strong conservation more than 148 My. Hence, their singular role in DNA catabolism is a well-established mechanism probably outweighing any deleterious or pathological roles such as genomic instability and cancer formation.
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Affiliation(s)
- Vincent Caval
- Molecular Retrovirology Unit, Institut Pasteur, Paris, France
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Mitra M, Hercík K, Byeon IJL, Ahn J, Hill S, Hinchee-Rodriguez K, Singer D, Byeon CH, Charlton LM, Nam G, Heidecker G, Gronenborn AM, Levin JG. Structural determinants of human APOBEC3A enzymatic and nucleic acid binding properties. Nucleic Acids Res 2013; 42:1095-110. [PMID: 24163103 PMCID: PMC3902935 DOI: 10.1093/nar/gkt945] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Human APOBEC3A (A3A) is a single-domain cytidine deaminase that converts deoxycytidine residues to deoxyuridine in single-stranded DNA (ssDNA). It inhibits a wide range of viruses and endogenous retroelements such as LINE-1, but it can also edit genomic DNA, which may play a role in carcinogenesis. Here, we extend our recent findings on the NMR structure of A3A and report structural, biochemical and cell-based mutagenesis studies to further characterize A3A’s deaminase and nucleic acid binding activities. We find that A3A binds ssRNA, but the RNA and DNA binding interfaces differ and no deamination of ssRNA is detected. Surprisingly, with only one exception (G105A), alanine substitution mutants with changes in residues affected by specific ssDNA binding retain deaminase activity. Furthermore, A3A binds and deaminates ssDNA in a length-dependent manner. Using catalytically active and inactive A3A mutants, we show that the determinants of A3A deaminase activity and anti-LINE-1 activity are not the same. Finally, we demonstrate A3A’s potential to mutate genomic DNA during transient strand separation and show that this process could be counteracted by ssDNA binding proteins. Taken together, our studies provide new insights into the molecular properties of A3A and its role in multiple cellular and antiviral functions.
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Affiliation(s)
- Mithun Mitra
- Section on Viral Gene Regulation, Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-2780, USA, Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA, Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA and HIV Drug Resistance Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
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Pham P, Landolph A, Mendez C, Li N, Goodman MF. A biochemical analysis linking APOBEC3A to disparate HIV-1 restriction and skin cancer. J Biol Chem 2013; 288:29294-304. [PMID: 23979356 DOI: 10.1074/jbc.m113.504175] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Human deoxycytidine deaminase APOBEC3A (Apo3A) acts as an HIV-1 restriction factor in cells of myeloid lineage yet functions separately as a potent mutator for genomic DNA. Apo3A activity and C motif deamination specificity exhibit a striking dependence on pH that reflects these two distinct biological processes. Upon infection of macrophages, HIV-1 induces the formation of autophagosomes, and requires autophagosomes for replication, whereas inhibiting lysosomal fusion indicative of late stage autophagy. Here we show that Apo3A has optimal activity and a strict 5'-YYCR motif specificity in the pH 5.8-6.1 range, characteristic of enclosed autophagosomal membrane compartments, and reflective of the mutation pattern of HIV-1. In contrast to the high activity and narrow specificity of Apo3A at acid pH, a 13-30-fold reduction in specific activity is accompanied by relaxed C deamination specificity at pH 7.4-8. Notably, Apo3A is also expressed in keratinocytes, and is up-regulated in skin lesions. At pH 7.9, we show that Apo3A generates transcription-dependent CC → TT tandem mutations on the non-transcribed strand, a hallmark signature of skin cancer. The biochemical data taken in conjunction with the biological up-regulation of Apo3A in skin lesions suggests that enzyme-catalyzed deaminations at adjacent C sites followed by normal replication generating CC → TT mutations provides an alternative molecular basis for the initiation events in skin cancer in contrast to well established pathways in which CC dimers formed in response to UV radiation either undergo nonenzymatic spontaneous deaminations or aberrant replication.
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Affiliation(s)
- Phuong Pham
- From the Departments of Biological Sciences and Chemistry, Molecular and Computational Biology Section, University of Southern California, Los Angeles, California 90089-2910
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Mussil B, Suspène R, Aynaud MM, Gauvrit A, Vartanian JP, Wain-Hobson S. Human APOBEC3A isoforms translocate to the nucleus and induce DNA double strand breaks leading to cell stress and death. PLoS One 2013; 8:e73641. [PMID: 23977391 PMCID: PMC3748023 DOI: 10.1371/journal.pone.0073641] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 07/21/2013] [Indexed: 01/14/2023] Open
Abstract
Human APOBEC3 enzymes deaminate single stranded DNA. At least five can deaminate mitochondrial DNA in the cytoplasm, while three can deaminate viral DNA in the nucleus. However, only one, APOBEC3A, can hypermutate genomic DNA. We analysed the distribution and function of the two APOBEC3A isoforms p1 and p2 in transfected cell lines. Both can translocate to the nucleus and hypermutate CMYC DNA and induce DNA double strand breaks as visualized by the detection of ©H2AX or Chk2. APOBEC3A induced G1 phase cell cycle arrest and triggered several members of the intrinsic apoptosis pathway. Activation of purified human CD4+ T lymphocytes with PHA, IL2 and interferon α resulted in C->T hypermutation of genomic DNA and double stranded breaks suggesting a role for APOBEC3A in pro-inflammatory conditions. As chronic inflammation underlies many diseases including numerous cancers, it is possible that APOBEC3A induction may generate many of the lesions typical of a cancer genome.
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Affiliation(s)
- Bianka Mussil
- Molecular Retrovirology Unit, Institut Pasteur, Paris, France
| | | | | | - Anne Gauvrit
- Molecular Retrovirology Unit, Institut Pasteur, Paris, France
| | | | - Simon Wain-Hobson
- Molecular Retrovirology Unit, Institut Pasteur, Paris, France
- * E-mail:
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