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Begum MM, Bokani A, Rajib SA, Soleimanpour M, Maeda Y, Yoshimura K, Satou Y, Ebrahimi D, Ikeda T. Potential Role of APOBEC3 Family Proteins in SARS-CoV-2 Replication. Viruses 2024; 16:1141. [PMID: 39066304 DOI: 10.3390/v16071141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 07/12/2024] [Accepted: 07/13/2024] [Indexed: 07/28/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has acquired multiple mutations since its emergence. Analyses of the SARS-CoV-2 genomes from infected patients exhibit a bias toward C-to-U mutations, which are suggested to be caused by the apolipoprotein B mRNA editing enzyme polypeptide-like 3 (APOBEC3, A3) cytosine deaminase proteins. However, the role of A3 enzymes in SARS-CoV-2 replication remains unclear. To address this question, we investigated the effect of A3 family proteins on SARS-CoV-2 replication in the myeloid leukemia cell line THP-1 lacking A3A to A3G genes. The Wuhan, BA.1, and BA.5 variants had comparable viral replication in parent and A3A-to-A3G-null THP-1 cells stably expressing angiotensin-converting enzyme 2 (ACE2) protein. On the other hand, the replication and infectivity of these variants were abolished in A3A-to-A3G-null THP-1-ACE2 cells in a series of passage experiments over 20 days. In contrast to previous reports, we observed no evidence of A3-induced SARS-CoV-2 mutagenesis in the passage experiments. Furthermore, our analysis of a large number of publicly available SARS-CoV-2 genomes did not reveal conclusive evidence for A3-induced mutagenesis. Our studies suggest that A3 family proteins can positively contribute to SARS-CoV-2 replication; however, this effect is deaminase-independent.
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Affiliation(s)
- Mst Monira Begum
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 860-0811, Japan
| | - Ayub Bokani
- School of Engineering and Technology, CQ University, Sydney, NSW 2000, Australia
| | - Samiul Alam Rajib
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 860-0811, Japan
| | | | - Yosuke Maeda
- Department of Microbiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
- Department of Nursing, Kibi International University, Takahashi 716-8508, Japan
| | | | - Yorifumi Satou
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 860-0811, Japan
| | - Diako Ebrahimi
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Terumasa Ikeda
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 860-0811, Japan
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2
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Robinson JF, Das S, Khan W, Khanam R, Price JT, Rahman A, Ahmed S, Ali SM, Deb S, Deveale B, Dutta A, Gormley M, Hall SC, Hasan ASMT, Hotwani A, Juma MH, Kasaro MP, Khalid J, Kshetrapal P, McMaster MT, Mehmood U, Nisar I, Pervin J, Rahman S, Raqib R, San A, Sarker P, Tuomivaara ST, Zhang G, Zhou Y, Aktar S, Baqui AH, Jehan F, Sazawal S, Stringer JSA, Fisher SJ. High rates of placental inflammation among samples collected by the Multi-Omics for Mothers and Infants consortium. Am J Obstet Gynecol 2024:S0002-9378(24)00560-X. [PMID: 38697337 DOI: 10.1016/j.ajog.2024.04.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 04/18/2024] [Accepted: 04/24/2024] [Indexed: 05/04/2024]
Abstract
BACKGROUND The Multi-Omics for Mothers and Infants consortium aims to improve birth outcomes. Preterm birth is a major obstetrical complication globally and causes significant infant and childhood morbidity and mortality. OBJECTIVE We analyzed placental samples (basal plate, placenta or chorionic villi, and the chorionic plate) collected by the 5 Multi-Omics for Mothers and Infants sites, namely The Alliance for Maternal and Newborn Health Improvement Bangladesh, The Alliance for Maternal and Newborn Health Improvement Pakistan, The Alliance for Maternal and Newborn Health Improvement Tanzania, The Global Alliance to Prevent Prematurity and Stillbirth Bangladesh, and The Global Alliance to Prevent Prematurity and Stillbirth Zambia. The goal was to analyze the morphology and gene expression of samples collected from preterm and uncomplicated term births. STUDY DESIGN The teams provided biopsies from 166 singleton preterm (<37 weeks' gestation) and 175 term (≥37 weeks' gestation) deliveries. The samples were fixed in formalin and paraffin embedded. Tissue sections from these samples were stained with hematoxylin and eosin and subjected to morphologic analyses. Other placental biopsies (n=35 preterm, 21 term) were flash frozen, which enabled RNA purification for bulk transcriptomics. RESULTS The morphologic analyses revealed a surprisingly high rate of inflammation that involved the basal plate, placenta or chorionic villi, and the chorionic plate. The rate of inflammation in chorionic villus samples, likely attributable to chronic villitis, ranged from 25% (Pakistan site) to 60% (Zambia site) of cases. Leukocyte infiltration in this location vs in the basal plate or chorionic plate correlated with preterm birth. Our transcriptomic analyses identified 267 genes that were differentially expressed between placentas from preterm vs those from term births (123 upregulated, 144 downregulated). Mapping the differentially expressed genes onto single-cell RNA sequencing data from human placentas suggested that all the component cell types, either singly or in subsets, contributed to the observed dysregulation. Consistent with the histopathologic findings, gene ontology analyses highlighted the presence of leukocyte infiltration or activation and inflammatory responses in both the fetal and maternal compartments. CONCLUSION The relationship between placental inflammation and preterm birth is appreciated in developed countries. In this study, we showed that this link also exists in developing geographies. In addition, among the participating sites, we found geographic- and population-based differences in placental inflammation and preterm birth, suggesting the importance of local factors.
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Affiliation(s)
- Joshua F Robinson
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Center for Reproductive Sciences, University of California, San Francisco, CA
| | - Sayan Das
- Public Health Laboratory Ivo de Carneri, Wawi, Chake, Pemba, Zanzibar, Tanzania
| | - Waqasuddin Khan
- Biorepository and Omics Research Group, Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Stadium Road, Karachi, Pakistan; Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Stadium Road, Karachi, Pakistan
| | - Rasheda Khanam
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Joan T Price
- UNC Global Projects - Zambia, Lusaka, Zambia; Department of Obstetrics and Gynecology, University of North Carolina School of Medicine, Chapel Hill, NC
| | - Anisur Rahman
- Maternal and Child Health Division, International Centre for Diarrhoeal Disease Research Bangladesh, Dhaka, Bangladesh
| | | | - Said Mohammed Ali
- Public Health Laboratory Ivo de Carneri, Wawi, Chake, Pemba, Zanzibar, Tanzania
| | - Saikat Deb
- Public Health Laboratory Ivo de Carneri, Wawi, Chake, Pemba, Zanzibar, Tanzania; Center for Public Health Kinetics, Vinoba Puri, Lajpatnagar II, New Delhi, India
| | - Brian Deveale
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Center for Reproductive Sciences, University of California, San Francisco, CA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA; Department of Urology, University of California, San Francisco, San Francisco, CA
| | - Arup Dutta
- Center for Public Health Kinetics, Vinoba Puri, Lajpatnagar II, New Delhi, India
| | - Matthew Gormley
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Center for Reproductive Sciences, University of California, San Francisco, CA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA; Sandler-Moore Mass Spectrometry Core Facility, University of California, San Francisco, San Francisco, CA
| | - Steven C Hall
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Center for Reproductive Sciences, University of California, San Francisco, CA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA; Sandler-Moore Mass Spectrometry Core Facility, University of California, San Francisco, San Francisco, CA
| | - A S M Tarik Hasan
- Maternal and Child Health Division, International Centre for Diarrhoeal Disease Research Bangladesh, Dhaka, Bangladesh
| | - Aneeta Hotwani
- Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Stadium Road, Karachi, Pakistan
| | - Mohamed Hamid Juma
- Public Health Laboratory Ivo de Carneri, Wawi, Chake, Pemba, Zanzibar, Tanzania
| | - Margaret P Kasaro
- UNC Global Projects - Zambia, Lusaka, Zambia; Department of Obstetrics and Gynecology, University of North Carolina School of Medicine, Chapel Hill, NC; Department of Gynaecology and Obstetrics, University of Zambia School of Medicine, Lusaka, Zambia
| | - Javairia Khalid
- Biorepository and Omics Research Group, Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Stadium Road, Karachi, Pakistan; Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Stadium Road, Karachi, Pakistan
| | - Pallavi Kshetrapal
- Maternal and Child Health, Translational Health Science and Technology Institute, Faridabad, India
| | - Michael T McMaster
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Center for Reproductive Sciences, University of California, San Francisco, CA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA; Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA
| | - Usma Mehmood
- Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Stadium Road, Karachi, Pakistan
| | - Imran Nisar
- Biorepository and Omics Research Group, Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Stadium Road, Karachi, Pakistan; Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Stadium Road, Karachi, Pakistan
| | - Jesmin Pervin
- Maternal and Child Health Division, International Centre for Diarrhoeal Disease Research Bangladesh, Dhaka, Bangladesh
| | - Sayedur Rahman
- Maternal and Child Health Division, International Centre for Diarrhoeal Disease Research Bangladesh, Dhaka, Bangladesh; Projahnmo Research Foundation, Dhaka, Bangladesh
| | - Rubhana Raqib
- International Centre for Diarrhoeal Disease Research Bangladesh, Dhaka, Bangladesh
| | - Ali San
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Center for Reproductive Sciences, University of California, San Francisco, CA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA
| | - Protim Sarker
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research Bangladesh, Dhaka, Bangladesh
| | - Sami T Tuomivaara
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Center for Reproductive Sciences, University of California, San Francisco, CA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA; Sandler-Moore Mass Spectrometry Core Facility, University of California, San Francisco, San Francisco, CA
| | - Ge Zhang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH; Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Yan Zhou
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Center for Reproductive Sciences, University of California, San Francisco, CA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA
| | - Shaki Aktar
- Maternal and Child Health Division, International Centre for Diarrhoeal Disease Research Bangladesh, Dhaka, Bangladesh
| | - Abdullah H Baqui
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Fyezah Jehan
- Biorepository and Omics Research Group, Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Stadium Road, Karachi, Pakistan; Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Stadium Road, Karachi, Pakistan
| | - Sunil Sazawal
- Center for Public Health Kinetics, Vinoba Puri, Lajpatnagar II, New Delhi, India
| | - Jeffrey S A Stringer
- Department of Obstetrics and Gynecology, University of North Carolina School of Medicine, Chapel Hill, NC
| | - Susan J Fisher
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Center for Reproductive Sciences, University of California, San Francisco, CA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA; Sandler-Moore Mass Spectrometry Core Facility, University of California, San Francisco, San Francisco, CA.
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3
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Zhang T, Sang J, Hoang PH, Zhao W, Rosenbaum J, Johnson KE, Klimczak LJ, McElderry J, Klein A, Wirth C, Bergstrom EN, Díaz-Gay M, Vangara R, Colon-Matos F, Hutchinson A, Lawrence SM, Cole N, Zhu B, Przytycka TM, Shi J, Caporaso NE, Homer R, Pesatori AC, Consonni D, Imielinski M, Chanock SJ, Wedge DC, Gordenin DA, Alexandrov LB, Harris RS, Landi MT. APOBEC shapes tumor evolution and age at onset of lung cancer in smokers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.02.587805. [PMID: 38617360 PMCID: PMC11014539 DOI: 10.1101/2024.04.02.587805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
APOBEC enzymes are part of the innate immunity and are responsible for restricting viruses and retroelements by deaminating cytosine residues1,2. Most solid tumors harbor different levels of somatic mutations attributed to the off-target activities of APOBEC3A (A3A) and/or APOBEC3B (A3B)3-6. However, how APOBEC3A/B enzymes shape the tumor evolution in the presence of exogenous mutagenic processes is largely unknown. Here, by combining deep whole-genome sequencing with multi-omics profiling of 309 lung cancers from smokers with detailed tobacco smoking information, we identify two subtypes defined by low (LAS) and high (HAS) APOBEC mutagenesis. LAS are enriched for A3B-like mutagenesis and KRAS mutations, whereas HAS for A3A-like mutagenesis and TP53 mutations. Unlike APOBEC3A, APOBEC3B expression is strongly associated with an upregulation of the base excision repair pathway. Hypermutation by unrepaired A3A and tobacco smoking mutagenesis combined with TP53-induced genomic instability can trigger senescence7, apoptosis8, and cell regeneration9, as indicated by high expression of pulmonary healing signaling pathway, stemness markers and distal cell-of-origin in HAS. The expected association of tobacco smoking variables (e.g., time to first cigarette) with genomic/epigenomic changes are not observed in HAS, a plausible consequence of frequent cell senescence or apoptosis. HAS have more neoantigens, slower clonal expansion, and older age at onset compared to LAS, particularly in heavy smokers, consistent with high proportions of newly generated, unmutated cells and frequent immuno-editing. These findings show how heterogeneity in mutational burden across co-occurring mutational processes and cell types contributes to tumor development, with important clinical implications.
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Affiliation(s)
- Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jian Sang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Phuc H. Hoang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Wei Zhao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | | | | | - Leszek J. Klimczak
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - John McElderry
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Alyssa Klein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Christopher Wirth
- Manchester Cancer Research Centre, The University of Manchester, Manchester, UK
| | - Erik N. Bergstrom
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Marcos Díaz-Gay
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Raviteja Vangara
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Frank Colon-Matos
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Scott M. Lawrence
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Nathan Cole
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Teresa M. Przytycka
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Neil E. Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Robert Homer
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Angela C. Pesatori
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Dario Consonni
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - David C. Wedge
- Manchester Cancer Research Centre, The University of Manchester, Manchester, UK
| | - Dmitry A. Gordenin
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Ludmil B. Alexandrov
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Reuben S. Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
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4
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Butt Y, Sakhtemani R, Mohamad-Ramshan R, Lawrence MS, Bhagwat AS. Distinguishing preferences of human APOBEC3A and APOBEC3B for cytosines in hairpin loops, and reflection of these preferences in APOBEC-signature cancer genome mutations. Nat Commun 2024; 15:2369. [PMID: 38499553 PMCID: PMC10948833 DOI: 10.1038/s41467-024-46231-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 02/19/2024] [Indexed: 03/20/2024] Open
Abstract
The APOBEC3 enzymes convert cytosines in single-stranded DNA to uracils to protect against viruses and retrotransposons but can contribute to mutations that diversify tumors. To understand the mechanism of mutagenesis, we map the uracils resulting from expression of APOBEC3B or its catalytic carboxy-terminal domain (CTD) in Escherichia coli. Like APOBEC3A, the uracilomes of A3B and A3B-CTD show a preference to deaminate cytosines near transcription start sites and the lagging-strand replication templates and in hairpin loops. Both biochemical activities of the enzymes and genomic uracil distribution show that A3A prefers 3 nt loops the best, while A3B prefers 4 nt loops. Reanalysis of hairpin loop mutations in human tumors finds intrinsic characteristics of both the enzymes, with a much stronger contribution from A3A. We apply Hairpin Signatures 1 and 2, which define A3A and A3B preferences respectively and are orthogonal to published methods, to evaluate their contribution to human tumor mutations.
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Affiliation(s)
- Yasha Butt
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | - Ramin Sakhtemani
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Michael S Lawrence
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ashok S Bhagwat
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA.
- Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, Detroit, MI, 48201, USA.
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5
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Duval C, Bourreau E, Warrick E, Bastien P, Nouveau S, Bernerd F. A chronic pro-inflammatory environment contributes to the physiopathology of actinic lentigines. Sci Rep 2024; 14:5256. [PMID: 38438410 PMCID: PMC10912228 DOI: 10.1038/s41598-024-53990-5] [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: 10/20/2023] [Accepted: 02/07/2024] [Indexed: 03/06/2024] Open
Abstract
Actinic lentigines (AL) or age spots, are skin hyperpigmented lesions associated with age and chronic sun exposure. To better understand the physiopathology of AL, we have characterized the inflammation response in AL of European and Japanese volunteers. Gene expression profile showed that in both populations, 10% of the modulated genes in AL versus adjacent non lesional skin (NL), i.e. 31 genes, are associated with inflammation/immune process. A pro-inflammatory environment in AL is strongly suggested by the activation of the arachidonic acid cascade and the plasmin pathway leading to prostaglandin production, along with the decrease of anti-inflammatory cytokines and the identification of inflammatory upstream regulators. Furthermore, in line with the over-expression of genes associated with the recruitment and activation of immune cells, immunostaining on skin sections revealed a significant infiltration of CD68+ macrophages and CD4+ T-cells in the dermis of AL. Strikingly, investigation of infiltrated macrophage subsets evidenced a significant increase of pro-inflammatory CD80+/CD68+ M1 macrophages in AL compared to NL. In conclusion, a chronic inflammation, sustained by pro-inflammatory mediators and infiltration of immune cells, particularly pro-inflammatory M1 macrophages, takes place in AL. This pro-inflammatory loop should be thus broken to normalize skin and improve the efficacy of age spot treatment.
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Affiliation(s)
| | | | - Emilie Warrick
- L'Oréal Research and Innovation, Aulnay Sous Bois, France
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6
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Sievers BL, Cheng MTK, Csiba K, Meng B, Gupta RK. SARS-CoV-2 and innate immunity: the good, the bad, and the "goldilocks". Cell Mol Immunol 2024; 21:171-183. [PMID: 37985854 PMCID: PMC10805730 DOI: 10.1038/s41423-023-01104-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 11/01/2023] [Indexed: 11/22/2023] Open
Abstract
An ancient conflict between hosts and pathogens has driven the innate and adaptive arms of immunity. Knowledge about this interplay can not only help us identify biological mechanisms but also reveal pathogen vulnerabilities that can be leveraged therapeutically. The humoral response to SARS-CoV-2 infection has been the focus of intense research, and the role of the innate immune system has received significantly less attention. Here, we review current knowledge of the innate immune response to SARS-CoV-2 infection and the various means SARS-CoV-2 employs to evade innate defense systems. We also consider the role of innate immunity in SARS-CoV-2 vaccines and in the phenomenon of long COVID.
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Affiliation(s)
| | - Mark T K Cheng
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Kata Csiba
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Bo Meng
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK.
| | - Ravindra K Gupta
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK.
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7
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Caswell DR, Gui P, Mayekar MK, Law EK, Pich O, Bailey C, Boumelha J, Kerr DL, Blakely CM, Manabe T, Martinez-Ruiz C, Bakker B, De Dios Palomino Villcas J, I Vokes N, Dietzen M, Angelova M, Gini B, Tamaki W, Allegakoen P, Wu W, Humpton TJ, Hill W, Tomaschko M, Lu WT, Haderk F, Al Bakir M, Nagano A, Gimeno-Valiente F, de Carné Trécesson S, Vendramin R, Barbè V, Mugabo M, Weeden CE, Rowan A, McCoach CE, Almeida B, Green M, Gomez C, Nanjo S, Barbosa D, Moore C, Przewrocka J, Black JRM, Grönroos E, Suarez-Bonnet A, Priestnall SL, Zverev C, Lighterness S, Cormack J, Olivas V, Cech L, Andrews T, Rule B, Jiao Y, Zhang X, Ashford P, Durfee C, Venkatesan S, Temiz NA, Tan L, Larson LK, Argyris PP, Brown WL, Yu EA, Rotow JK, Guha U, Roper N, Yu J, Vogel RI, Thomas NJ, Marra A, Selenica P, Yu H, Bakhoum SF, Chew SK, Reis-Filho JS, Jamal-Hanjani M, Vousden KH, McGranahan N, Van Allen EM, Kanu N, Harris RS, Downward J, Bivona TG, Swanton C. The role of APOBEC3B in lung tumor evolution and targeted cancer therapy resistance. Nat Genet 2024; 56:60-73. [PMID: 38049664 PMCID: PMC10786726 DOI: 10.1038/s41588-023-01592-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 10/25/2023] [Indexed: 12/06/2023]
Abstract
In this study, the impact of the apolipoprotein B mRNA-editing catalytic subunit-like (APOBEC) enzyme APOBEC3B (A3B) on epidermal growth factor receptor (EGFR)-driven lung cancer was assessed. A3B expression in EGFR mutant (EGFRmut) non-small-cell lung cancer (NSCLC) mouse models constrained tumorigenesis, while A3B expression in tumors treated with EGFR-targeted cancer therapy was associated with treatment resistance. Analyses of human NSCLC models treated with EGFR-targeted therapy showed upregulation of A3B and revealed therapy-induced activation of nuclear factor kappa B (NF-κB) as an inducer of A3B expression. Significantly reduced viability was observed with A3B deficiency, and A3B was required for the enrichment of APOBEC mutation signatures, in targeted therapy-treated human NSCLC preclinical models. Upregulation of A3B was confirmed in patients with NSCLC treated with EGFR-targeted therapy. This study uncovers the multifaceted roles of A3B in NSCLC and identifies A3B as a potential target for more durable responses to targeted cancer therapy.
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Affiliation(s)
- Deborah R Caswell
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
| | - Philippe Gui
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Manasi K Mayekar
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Emily K Law
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Oriol Pich
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Chris Bailey
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Jesse Boumelha
- Oncogene Biology Laboratory, The Francis Crick Institute, London, UK
| | - D Lucas Kerr
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Collin M Blakely
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Tadashi Manabe
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Carlos Martinez-Ruiz
- Cancer Genome Evolution Research Group, University College London, Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, UK
| | - Bjorn Bakker
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | | | - Natalie I Vokes
- Department of Thoracic and Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michelle Dietzen
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Genome Evolution Research Group, University College London, Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, UK
| | - Mihaela Angelova
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Beatrice Gini
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Whitney Tamaki
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Paul Allegakoen
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Wei Wu
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Timothy J Humpton
- p53 and Metabolism Laboratory, The Francis Crick Institute, London, UK
- CRUK Beatson Institute, Glasgow, UK
- Glasgow Caledonian University, Glasgow, UK
| | - William Hill
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Mona Tomaschko
- Oncogene Biology Laboratory, The Francis Crick Institute, London, UK
| | - Wei-Ting Lu
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Franziska Haderk
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Maise Al Bakir
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Ai Nagano
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | | | | | - Roberto Vendramin
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Vittorio Barbè
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Miriam Mugabo
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, UK
| | - Clare E Weeden
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Andrew Rowan
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | | | - Bruna Almeida
- The Roger Williams Institute of Hepatology, Foundation for Liver Research, London, UK
- Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Mary Green
- Experimental Histopathology, The Francis Crick Institute, London, UK
| | - Carlos Gomez
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Shigeki Nanjo
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Dora Barbosa
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Chris Moore
- Oncogene Biology Laboratory, The Francis Crick Institute, London, UK
| | - Joanna Przewrocka
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - James R M Black
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Genome Evolution Research Group, University College London, Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, UK
| | - Eva Grönroos
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Alejandro Suarez-Bonnet
- Experimental Histopathology, The Francis Crick Institute, London, UK
- Department of Pathobiology & Population Sciences, The Royal Veterinary College, London, UK
| | - Simon L Priestnall
- Experimental Histopathology, The Francis Crick Institute, London, UK
- Department of Pathobiology & Population Sciences, The Royal Veterinary College, London, UK
| | - Caroline Zverev
- Biological Research Facility, The Francis Crick Institute, London, UK
| | - Scott Lighterness
- Biological Research Facility, The Francis Crick Institute, London, UK
| | - James Cormack
- Biological Research Facility, The Francis Crick Institute, London, UK
| | - Victor Olivas
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Lauren Cech
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Trisha Andrews
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | | | | | | | - Paul Ashford
- Institute of Structural and Molecular Biology, University College London, London, UK
| | - Cameron Durfee
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Subramanian Venkatesan
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Nuri Alpay Temiz
- Institute for Health Informatics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Lisa Tan
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Lindsay K Larson
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Prokopios P Argyris
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
- School of Dentistry, University of Minnesota, Minneapolis, MN, USA
- College of Dentistry, Ohio State University, Columbus, OH, USA
| | - William L Brown
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Elizabeth A Yu
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Sutter Health Palo Alto Medical Foundation, Department of Pulmonary and Critical Care, Mountain View, CA, USA
| | - Julia K Rotow
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Udayan Guha
- Thoracic and GI Malignancies Branch, NCI, NIH, Bethesda, MD, USA
- NextCure Inc., Beltsville, MD, USA
| | - Nitin Roper
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Johnny Yu
- Biomedical Sciences Program, University of California, San Francisco, San Francisco, CA, USA
| | - Rachel I Vogel
- Department of Obstetrics, Gynecology and Women's Health, University of Minnesota, Minneapolis, MN, USA
| | - Nicholas J Thomas
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Antonio Marra
- Division of Early Drug Development for Innovative Therapy, European Institute of Oncology IRCCS, Milan, Italy
| | - Pier Selenica
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
| | - Helena Yu
- Memorial Sloan Kettering Cancer Center, New York City, NY, USA
- Department of Medicine, Weill Cornell College of Medicine, New York City, NY, USA
| | - Samuel F Bakhoum
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
| | - Su Kit Chew
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | | | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
- Department of Medical Oncology, University College London Hospitals, London, UK
| | - Karen H Vousden
- p53 and Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Nicholas McGranahan
- Cancer Genome Evolution Research Group, University College London, Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, UK
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nnennaya Kanu
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, UK
| | - Reuben S Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Julian Downward
- Oncogene Biology Laboratory, The Francis Crick Institute, London, UK
| | - Trever G Bivona
- Departments of Medicine and Cellular and Molecular Pharmacology, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, UK
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8
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Song JH, Dávalos LM, MacCarthy T, Damaghi M. Evolvability of cancer-associated genes under APOBEC3A/B selection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.27.554991. [PMID: 38106028 PMCID: PMC10723265 DOI: 10.1101/2023.08.27.554991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Evolvability is an emergent hallmark of cancer that depends on intra-tumor heterogeneity and, ultimately, genetic variation. Mutations generated by APOBEC3 cytidine deaminases can contribute to genetic variation and the consequences of APOBEC activation differ depending on the stage of cancer, with the most significant impact observed during the early stages. However, how APOBEC activity shapes evolutionary patterns of genes in the host genome and differential impacts on cancer-associated and non-cancer genes remain unclear. Analyzing over 40,000 human protein-coding transcripts, we identified distinct distribution patterns of APOBEC3A/B TC motifs between cancer-related genes and controls, suggesting unique associations with cancer. Studying a bat species with many more APOBEC3 genes, we found diverse motif patterns in orthologs of cancer genes compared to controls, similar to humans and suggesting APOBEC evolution to reduce impacts on the genome rather than the converse. Simulations confirmed that APOBEC-induced heterogeneity enhances cancer evolution, shaping clonal dynamics through bimodal introduction of mutations in certain classes of genes. Our results suggest that a major consequence of the bimodal distribution of APOBEC affects greater cancer heterogeneity.
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Affiliation(s)
- Joon-Hyun Song
- Stony Brook Cancer Center, Stony Brook Medicine, Stony Brook University, Stony Brook, NY, USA
- Department of Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA
| | - Liliana M. Dávalos
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, 11794, USA
- Consortium for Inter-Disciplinary Environmental Research, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Thomas MacCarthy
- Stony Brook Cancer Center, Stony Brook Medicine, Stony Brook University, Stony Brook, NY, USA
- Department of Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA
| | - Mehdi Damaghi
- Stony Brook Cancer Center, Stony Brook Medicine, Stony Brook University, Stony Brook, NY, USA
- Department of Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA
- Department of Pathology, Stony Brook Medicine, Stony Brook University, Stony Brook, NY, USA
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9
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Smith KR, Paul S, Dong Q, Anannya O, Oldenburg DG, Forrest JC, McBride KM, Krug LT. Uracil-DNA glycosylase of murine gammaherpesvirus 68 binds cognate viral replication factors independently of its catalytic residues. mSphere 2023; 8:e0027823. [PMID: 37747202 PMCID: PMC10597349 DOI: 10.1128/msphere.00278-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 08/03/2023] [Indexed: 09/26/2023] Open
Abstract
Herpesviruses are large double-stranded DNA viruses that encode core replication proteins and accessory factors involved in nucleotide metabolism and DNA repair. Mammalian uracil-DNA glycosylases (UNG) excise deleterious uracil residues from their genomic DNA. Each herpesvirus UNG studied to date has demonstrated conservation of the enzymatic function to excise uracil residues from DNA. We previously reported that a murine gammaherpesvirus (MHV68) with a stop codon in ORF46 (ORF46.stop) that encodes for vUNG was defective in lytic replication and latency in vivo. However, a mutant virus that expressed a catalytically inactive vUNG (ORF46.CM) had no replication defect unless coupled with additional mutations in the catalytic motif of the viral dUTPase (ORF54.CM). The disparate phenotypes observed in the vUNG mutants led us to explore the non-enzymatic properties of vUNG. Immunoprecipitation of vUNG followed by mass spectrometry in MHV68-infected fibroblasts identified a complex comprising the cognate viral DNA polymerase, vPOL, encoded by ORF9, and the viral DNA polymerase processivity factor, vPPF, encoded by ORF59. MHV68 vUNG co-localized with vPOL and vPPF in subnuclear structures consistent with viral replication compartments. In reciprocal co-immunoprecipitations, the vUNG formed a complex with the vPOL and vPPF upon transfection with either factor alone or in combination. Lastly, we determined that key catalytic residues of vUNG are not required for interactions with vPOL and vPPF upon transfection or in the context of infection. We conclude that the vUNG of MHV68 associates with vPOL and vPPF independently of its catalytic activity. IMPORTANCE Gammaherpesviruses encode a uracil-DNA glycosylase (vUNG) that is presumed to excise uracil residues from viral genomes. We previously identified the vUNG enzymatic activity, but not the protein itself, as dispensable for gammaherpesvirus replication in vivo. In this study, we report a non-enzymatic role for the viral UNG of a murine gammaherpesvirus in forming a complex with two key components of the viral DNA replication machinery. Understanding the role of the vUNG in this viral DNA replication complex may inform the development of antiviral drugs that combat gammaherpesvirus-associated cancers.
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Affiliation(s)
- Kyle R. Smith
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, Maryland, USA
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
| | - Somnath Paul
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Qiwen Dong
- Molecular and Cellular Biology Program, Stony Brook University, Stony Brook, New York, USA
| | - Orchi Anannya
- Department of Physiology and Biophysics, Molecular and Cellular Biology Program, Stony Brook University, Stony Brook, New York, USA
| | - Darby G. Oldenburg
- Gundersen Medical Foundation, Gunderson Health System, La Crosse, Wisconsin, USA
| | - J. Craig Forrest
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Kevin M. McBride
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Laurie T. Krug
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, Maryland, USA
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
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10
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Rieffer AE, Chen Y, Salamango DJ, Moraes SN, Harris RS. APOBEC Reporter Systems for Evaluating diNucleotide Editing Levels. CRISPR J 2023; 6:430-446. [PMID: 37672599 PMCID: PMC10611974 DOI: 10.1089/crispr.2023.0027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 08/14/2023] [Indexed: 09/08/2023] Open
Abstract
Precision genome editing has become a reality with the discovery of base editors. Cytosine base editor (CBE) technologies are improving rapidly but are mostly optimized for TC dinucleotide targets. Here, we report the development and implementation of APOBEC Reporter Systems for Evaluating diNucleotide Editing Levels (ARSENEL) in living cells. The ARSENEL panel is comprised of four constructs that quantitatively report editing of each of the four dinucleotide motifs (AC/CC/GC/TC) through real-time accumulation of eGFP fluorescence. Editing rates of APOBEC3Bctd and AIDΔC CBEs reflect established mechanistic preferences with intrinsic biases to TC and GC, respectively. Twelve different (new and established) base editors are tested here using this system with a full-length APOBEC3B CBE showing the greatest on-target TC specificity and an APOBEC3A construct showing the highest editing efficiency. In addition, ARSENEL enables real-time assessment of natural and synthetic APOBEC inhibitors with the most potent to-date being the large subunit of the Epstein-Barr virus ribonucleotide reductase. These reporters have the potential to play important roles in research and development as precision genome engineering technologies progress toward achieving maximal specificity and efficiency.
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Affiliation(s)
- Amanda E. Rieffer
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota—Twin Cities, Minneapolis, Minnesota, USA; University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Yanjun Chen
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA; and University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Daniel J. Salamango
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota—Twin Cities, Minneapolis, Minnesota, USA; University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Sofia N. Moraes
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota—Twin Cities, Minneapolis, Minnesota, USA; University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Reuben S. Harris
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota—Twin Cities, Minneapolis, Minnesota, USA; University of Texas Health San Antonio, San Antonio, Texas, USA
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA; and University of Texas Health San Antonio, San Antonio, Texas, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, Texas, USA
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11
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Ivanišević V, Žilić L, Čunko M, Fadiga H, Munitić I, Jurak I. RNA Editing-Dependent and -Independent Roles of Adenosine Deaminases Acting on RNA Proteins in Herpesvirus Infection-Hints on Another Layer of Complexity. Viruses 2023; 15:2007. [PMID: 37896783 PMCID: PMC10611208 DOI: 10.3390/v15102007] [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: 09/11/2023] [Revised: 09/24/2023] [Accepted: 09/25/2023] [Indexed: 10/29/2023] Open
Abstract
The Adenosine Deaminases Acting on RNA (ADAR) catalyze the posttranscriptional deamination of adenosine residues to inosine in double-stranded RNAs (dsRNAs, A-to-I editing), preventing the overactivation of dsRNA sensor molecules and interferons. RNA editing is the cornerstone of innate immunity that distinguishes between self and non-self (virus), and it is essential for normal regulation of cellular homeostasis. Although much is already known about the role of ADAR proteins in RNA virus infection, the role of ADAR proteins in herpesvirus infection remains largely unexplored. In this review, we provide several lines of evidence from studies of different herpesviruses for another level of complexity in regulating the already intricate biphasic life cycle of herpesviruses.
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Affiliation(s)
| | | | | | | | | | - Igor Jurak
- Department of Biotechnology, University of Rijeka, 51000 Rijeka, Croatia (L.Ž.)
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12
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Fanunza E, Cheng AZ, Auerbach AA, Stefanovska B, Moraes SN, Lokensgard JR, Biolatti M, Dell'Oste V, Bierle CJ, Bresnahan WA, Harris RS. Human cytomegalovirus mediates APOBEC3B relocalization early during infection through a ribonucleotide reductase-independent mechanism. J Virol 2023; 97:e0078123. [PMID: 37565748 PMCID: PMC10506462 DOI: 10.1128/jvi.00781-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 06/21/2023] [Indexed: 08/12/2023] Open
Abstract
The APOBEC3 family of DNA cytosine deaminases comprises an important arm of the innate antiviral defense system. The gamma-herpesviruses Epstein-Barr virus and Kaposi's sarcoma-associated herpesvirus and the alpha-herpesviruses herpes simplex virus (HSV)-1 and HSV-2 have evolved an efficient mechanism to avoid APOBEC3 restriction by directly binding to APOBEC3B and facilitating its exclusion from the nuclear compartment. The only viral protein required for APOBEC3B relocalization is the large subunit of the ribonucleotide reductase (RNR). Here, we ask whether this APOBEC3B relocalization mechanism is conserved with the beta-herpesvirus human cytomegalovirus (HCMV). Although HCMV infection causes APOBEC3B relocalization from the nucleus to the cytoplasm in multiple cell types, the viral RNR (UL45) is not required. APOBEC3B relocalization occurs rapidly following infection suggesting the involvement of an immediate early or early (IE/E) viral protein. In support of this possibility, genetic (IE1 mutant) and pharmacologic (cycloheximide) strategies that prevent the expression of IE/E viral proteins also block APOBEC3B relocalization. In comparison, the treatment of infected cells with phosphonoacetic acid, which interferes with viral late protein expression, still permits A3B relocalization. These results combine to indicate that the beta-herpesvirus HCMV uses an RNR-independent, yet phenotypically similar, molecular mechanism to antagonize APOBEC3B. IMPORTANCE Human cytomegalovirus (HCMV) infections can range from asymptomatic to severe, particularly in neonates and immunocompromised patients. HCMV has evolved strategies to overcome host-encoded antiviral defenses to achieve lytic viral DNA replication and dissemination and, under some conditions, latency and long-term persistence. Here, we show that HCMV infection causes the antiviral factor, APOBEC3B, to relocalize from the nuclear compartment to the cytoplasm. This overall strategy resembles that used by related herpesviruses. However, the HCMV relocalization mechanism utilizes a different viral factor(s) and available evidence suggests the involvement of at least one protein expressed at the early stages of infection. This knowledge is important because a greater understanding of this mechanism could lead to novel antiviral strategies that enable APOBEC3B to naturally restrict HCMV infection.
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Affiliation(s)
- Elisa Fanunza
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, Cagilari, Italy
| | - Adam Z. Cheng
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Ashley A. Auerbach
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Bojana Stefanovska
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Sofia N. Moraes
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - James R. Lokensgard
- Department of Medicine, University of Minnesota, Minneapolis, Minnesota, USA
| | - Matteo Biolatti
- Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy
| | - Valentina Dell'Oste
- Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy
| | - Craig J. Bierle
- Department of Pediatrics, Division of Pediatric Infectious Diseases and Immunology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Wade A. Bresnahan
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Reuben S. Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, Texas, USA
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13
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Ikeda T, Shimizu R, Nasser H, Carpenter MA, Cheng AZ, Brown WL, Sauter D, Harris RS. APOBEC3 degradation is the primary function of HIV-1 Vif determining virion infectivity in the myeloid cell line THP-1. mBio 2023; 14:e0078223. [PMID: 37555667 PMCID: PMC10470580 DOI: 10.1128/mbio.00782-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 06/22/2023] [Indexed: 08/10/2023] Open
Abstract
HIV-1 must overcome multiple innate antiviral mechanisms to replicate in CD4+ T lymphocytes and macrophages. Previous studies have demonstrated that the apolipoprotein B mRNA editing enzyme polypeptide-like 3 (APOBEC3, A3) family of proteins (at least A3D, A3F, A3G, and stable A3H haplotypes) contribute to HIV-1 restriction in CD4+ T lymphocytes. Virus-encoded virion infectivity factor (Vif) counteracts this antiviral activity by degrading A3 enzymes allowing HIV-1 replication in infected cells. In addition to A3 proteins, Vif also targets other cellular proteins in CD4+ T lymphocytes, including PPP2R5 proteins. However, whether Vif primarily degrades only A3 proteins during viral replication is currently unknown. Herein, we describe the development and characterization of A3F-, A3F/A3G-, and A3A-to-A3G-null THP-1 cells. In comparison to Vif-proficient HIV-1, Vif-deficient viruses have substantially reduced infectivity in parental and A3F-null THP-1 cells, and a more modest decrease in infectivity in A3F/A3G-null cells. Remarkably, disruption of A3A-A3G protein expression completely restores the infectivity of Vif-deficient viruses in THP-1 cells. These results indicate that the primary function of Vif during infectious HIV-1 production from THP-1 cells is the targeting and degradation of A3 enzymes. IMPORTANCE HIV-1 Vif neutralizes the HIV-1 restriction activity of A3 proteins. However, it is currently unclear whether Vif has additional essential cellular targets. To address this question, we disrupted A3A to A3G genes in the THP-1 myeloid cell line using CRISPR and compared the infectivity of wild-type HIV-1 and Vif mutants with the selective A3 neutralization activities. Our results demonstrate that the infectivity of Vif-deficient HIV-1 and the other Vif mutants is fully restored by ablating the expression of cellular A3A to A3G proteins. These results indicate that A3 proteins are the only essential target of Vif that is required for fully infectious HIV-1 production from THP-1 cells.
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Affiliation(s)
- Terumasa Ikeda
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Ryo Shimizu
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
- Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Hesham Nasser
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
- Department of Clinical Pathology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Michael A. Carpenter
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Adam Z. Cheng
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA
| | - William L. Brown
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Daniel Sauter
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Reuben S. Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, Texas, USA
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14
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Butt Y, Sakhtemani R, Mohamad-Ramshan R, Lawrence MS, Bhagwat AS. Distinguishing preferences of human APOBEC3A and APOBEC3B for cytosines in hairpin loops, and reflection of these preferences in APOBEC-signature cancer genome mutations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.01.551518. [PMID: 37577595 PMCID: PMC10418155 DOI: 10.1101/2023.08.01.551518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
The APOBEC3 family of enzymes convert cytosines in single-stranded DNA to uracils thereby causing mutations. These enzymes protect human cells against viruses and retrotransposons, but in many cancers they contribute to mutations that diversify the tumors and help them escape anticancer drug treatments. To understand the mechanism of mutagenesis by APOBEC3B, we expressed the complete enzyme or its catalytic carboxy-terminal domain (CTD) in repair-deficient Eschericia coli and mapped the resulting uracils using uracil pull-down and sequencing technology. The uracilomes of A3B-full and A3B-CTD showed peaks in many of the same regions where APOBEC3A also created uracilation peaks. Like A3A, the two A3B enzymes also preferred to deaminate cytosines near transcription start sites and in the lagging-strand template at replication forks. In contrast to an earlier report that A3B does not favor hairpin loops over linear DNA, we found that both A3B-full and A3B-CTD showed a strong preference for cytosines in hairpin loops. The major difference between A3A and A3B was that while the former enzyme prefers 3 nt loops the best, A3B prefers loops of 4 nt over those of other lengths. Furthermore, within 5 nt loops, A3A prefers cytosine to be in the penultimate position, while A3B prefers it to be at the 3' end of the loop. We confirmed these loop size and sequence preferences experimentally using purified A3A and A3B-CTD proteins. Reanalysis of hairpin loop mutations in human tumors using the size, sequence and position preferences of the two enzymes found that the tumors displayed mutations with intrinsic characteristics of both the enzymes with a stronger contribution from A3A.
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Wang XF, Zhang X, Ma W, Li J, Wang X. Host cell restriction factors of equine infectious anemia virus. Virol Sin 2023; 38:485-496. [PMID: 37419416 PMCID: PMC10436108 DOI: 10.1016/j.virs.2023.07.001] [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: 04/13/2023] [Accepted: 07/03/2023] [Indexed: 07/09/2023] Open
Abstract
Equine infectious anemia virus (EIAV) is a member of the lentivirus genus in the Retroviridae family and is considered an animal model for HIV/AIDS research. An attenuated EIAV vaccine, which was successfully developed in the 1970s by classical serial passage techniques, is the first and only lentivirus vaccine that has been widely used to date. Restriction factors are cellular proteins that provide an early line of defense against viral replication and spread by interfering with various critical steps in the viral replication cycle. However, viruses have evolved specific mechanisms to overcome these host barriers through adaptation. The battle between the viruses and restriction factors is actually a natural part of the viral replication process, which has been well studied in human immunodeficiency virus type 1 (HIV-1). EIAV has the simplest genome composition of all lentiviruses, making it an intriguing subject for understanding how the virus employs its limited viral proteins to overcome restriction factors. In this review, we summarize the current literature on the interactions between equine restriction factors and EIAV. The features of equine restriction factors and the mechanisms by which the EIAV counteract the restriction suggest that lentiviruses employ diverse strategies to counteract innate immune restrictions. In addition, we present our insights on whether restriction factors induce alterations in the phenotype of the attenuated EIAV vaccine.
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Affiliation(s)
- Xue-Feng Wang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Xiangmin Zhang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Weiwei Ma
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Jiwei Li
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Xiaojun Wang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin 150069, China.
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16
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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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Smith KR, Paul S, Dong Q, Anannya O, Oldenburg DG, Forrest JC, McBride KM, Krug LT. Uracil-DNA Glycosylase of Murine Gammaherpesvirus 68 Binds Cognate Viral Replication Factors Independently of its Catalytic Residues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.19.541466. [PMID: 37398059 PMCID: PMC10312458 DOI: 10.1101/2023.05.19.541466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Herpesviruses are large double-stranded DNA viruses that encode core replication proteins and accessory factors involved in nucleotide metabolism and DNA repair. Mammalian Uracil-DNA glycosylases (UNG) excise deleterious uracil residues from their genomic DNA. Each herpesvirus UNG studied to date has demonstrated conservation of the enzymatic function to excise uracil residues from DNA. We previously reported that a murine gammaherpesvirus (MHV68) with a stop codon in ORF46 (ORF46.stop) that encodes for vUNG was defective in lytic replication and latency in vivo. However, a mutant virus that expressed a catalytically inactive vUNG (ORF46.CM) had no replication defect, unless coupled with additional mutations in the catalytic motif of the viral dUTPase (ORF54.CM). The disparate phenotypes observed in the vUNG mutants led us to explore the non-enzymatic properties of vUNG. Immunoprecipitation of vUNG followed by mass spectrometry in MHV68-infected fibroblasts identified a complex comprised of the cognate viral DNA polymerase, vPOL encoded by ORF9 , and the viral DNA polymerase processivity factor, vPPF encoded by ORF59 . MHV68 vUNG colocalized with vPOL and vPPF in subnuclear structures consistent with viral replication compartments. In reciprocal co-immunoprecipitations, the vUNG formed a complex with the vPOL and vPPF upon transfection with either factor alone, or in combination. Last, we determined that key catalytic residues of vUNG are not required for interactions with vPOL and vPPF upon transfection or in the context of infection. We conclude that the vUNG of MHV68 associates with vPOL and vPPF independently of its catalytic activity. IMPORTANCE Gammaherpesviruses encode a uracil-DNA glycosylase (vUNG) that is presumed to excise uracil residues from viral genomes. We previously identified the vUNG enzymatic activity, but not the protein itself, as dispensable for gammaherpesvirus replication in vivo . In this study, we report a non-enzymatic role for the viral UNG of a murine gammaherpesvirus to form a complex with two key components of the viral DNA replication machinery. Understanding the role of the vUNG in this viral DNA replication complex may inform the development of antiviral drugs that combat gammaherpesvirus associated cancers.
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Affiliation(s)
- Kyle R. Smith
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, MD, USA
- Department of Microbiology & Immunology, Stony Brook University, Stony Brook, NY, USA
| | - Somnath Paul
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Qiwen Dong
- Molecular and Cellular Biology Program, Stony Brook University, Stony Brook, NY, USA
| | - Orchi Anannya
- Department of Physiology and Biophysics, Molecular and Cellular Biology Program, Stony Brook University, Stony Brook, NY, USA
| | - Darby G. Oldenburg
- Gundersen Medical Foundation, Gunderson Health System, LaCrosse, Wisconsin, USA
| | - J. Craig Forrest
- Department of Microbiology & Immunology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Kevin M. McBride
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Laurie T. Krug
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, MD, USA
- Department of Microbiology & Immunology, Stony Brook University, Stony Brook, NY, USA
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18
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Ikeda T, Shimizu R, Nasser H, Carpenter MA, Cheng AZ, Brown WL, Sauter D, Harris RS. APOBEC3 degradation is the primary function of HIV-1 Vif for virus replication in the myeloid cell line THP-1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.28.534666. [PMID: 37034786 PMCID: PMC10081227 DOI: 10.1101/2023.03.28.534666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
HIV-1 must overcome multiple innate antiviral mechanisms to replicate in CD4 + T lymphocytes and macrophages. Previous studies have demonstrated that the APOBEC3 (A3) family of proteins (at least A3D, A3F, A3G, and stable A3H haplotypes) contribute to HIV-1 restriction in CD4 + T lymphocytes. Virus-encoded virion infectivity factor (Vif) counteracts this antiviral activity by degrading A3 enzymes allowing HIV-1 replication in infected cells. In addition to A3 proteins, Vif also targets other cellular proteins in CD4 + T lymphocytes, including PPP2R5 proteins. However, whether Vif primarily degrades only A3 proteins or has additional essential targets during viral replication is currently unknown. Herein, we describe the development and characterization of A3F -, A3F/A3G -, and A3A -to- A3G -null THP-1 cells. In comparison to Vif-proficient HIV-1, Vif-deficient viruses have substantially reduced infectivity in parental and A3F -null THP-1 cells, and a more modest decrease in infectivity in A3F/A3G -null cells. Remarkably, disruption of A3Aâ€"A3G protein expression completely restores the infectivity of Vif-deficient viruses in THP-1 cells. These results indicate that the primary function of Vif during HIV-1 replication in THP-1 cells is the targeting and degradation of A3 enzymes. Importance HIV-1 Vif neutralizes the HIV-1 restriction activity of A3 proteins. However, it is currently unclear whether Vif has additional essential cellular targets. To address this question, we disrupted A3A to A3G genes in the THP-1 myeloid cell line using CRISPR and compared the infectivity of wildtype HIV-1 and Vif mutants with the selective A3 neutralization activities. Our results demonstrate that the infectivity of Vif-deficient HIV-1 and the other Vif mutants is fully restored by ablating the expression of cellular A3A to A3G proteins. These results indicate that A3 proteins are the only essential target of Vif that is required for HIV-1 replication in THP-1 cells.
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Affiliation(s)
- Terumasa Ikeda
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan
| | - Ryo Shimizu
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan
- Graduate School of Medical Sciences, Kumamoto University, Kumamoto 8600811, Japan
| | - Hesham Nasser
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan
- Department of Clinical Pathology, Faculty of Medicine, Suez Canal University, Ismailia 41511, Egypt
| | - Michael A. Carpenter
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas 78229, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, Texas 78229, USA
| | - Adam Z. Cheng
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - William L. Brown
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Daniel Sauter
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen 72076, Germany
| | - Reuben S. Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas 78229, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, Texas 78229, USA
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19
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Argyris PP, Naumann J, Jarvis MC, Wilkinson PE, Ho DP, Islam MN, Bhattacharyya I, Gopalakrishnan R, Li F, Koutlas IG, Giubellino A, Harris RS. Primary mucosal melanomas of the head and neck are characterised by overexpression of the DNA mutating enzyme APOBEC3B. Histopathology 2023; 82:608-621. [PMID: 36416305 PMCID: PMC10107945 DOI: 10.1111/his.14843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 09/12/2022] [Accepted: 09/23/2022] [Indexed: 11/24/2022]
Abstract
AIMS Primary head/neck mucosal melanomas (MMs) are rare and exhibit aggressive biologic behaviour and elevated mutational loads. The molecular mechanisms responsible for high genomic instability observed in head/neck MMs remain elusive. The DNA cytosine deaminase APOBEC3B (A3B) constitutes a major endogenous source of mutation in human cancer. A3B-related mutations are identified through C-to-T/-G base substitutions in 5'-TCA/T motifs. Herein, we present immunohistochemical and genomic data supportive of a role for A3B in head/neck MMs. METHODS AND RESULTS A3B protein levels were assessed in oral (n = 13) and sinonasal (n = 13) melanomas, and oral melanocytic nevi (n = 13) by immunohistochemistry using a custom rabbit α-A3B mAb (5210-87-13). Heterogeneous, selective-to-diffuse, nuclear only, A3B immunopositivity was observed in 12 of 13 (92.3%) oral melanomas (H-score range = 9-72, median = 40) and 8 of 13 (62%) sinonasal melanomas (H-score range = 1-110, median = 24). Two cases negative for A3B showed prominent cytoplasmic staining consistent with A3G. A3B protein levels were significantly higher in oral and sinonasal MMs than intraoral melanocytic nevi (P < 0.0001 and P = 0.0022, respectively), which were A3B-negative (H-score range = 1-8, median = 4). A3B levels, however, did not differ significantly between oral and sinonasal tumours (P > 0.99). NGS performed in 10 sinonasal MMs revealed missense NRAS mutations in 50% of the studied cases and one each KIT and HRAS mutations. Publicly available whole-genome sequencing (WGS) data disclosed that the number of C-to-T mutations and APOBEC3 enrichment score were markedly elevated in head/neck MMs (n = 2). CONCLUSION The above data strongly indicate a possible role for the mutagenic enzyme A3B in head/neck melanomagenesis, but not benign melanocytic neoplasms.
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Affiliation(s)
- Prokopios P Argyris
- Department of Biochemistry, Molecular Biology and BiophysicsUniversity of MinnesotaMinneapolisMNUSA
- Masonic Cancer CenterUniversity of MinnesotaMinneapolisMNUSA
- Institute for Molecular VirologyUniversity of MinnesotaMinneapolisMNUSA
- Center for Genome EngineeringUniversity of MinnesotaMinneapolisMNUSA
- Howard Hughes Medical InstituteUniversity of MinnesotaMinneapolisMNUSA
- Division of Oral and Maxillofacial PathologySchool of Dentistry, University of MinnesotaMinneapolisMNUSA
| | - Jordan Naumann
- Department of Biochemistry, Molecular Biology and BiophysicsUniversity of MinnesotaMinneapolisMNUSA
- Masonic Cancer CenterUniversity of MinnesotaMinneapolisMNUSA
- Institute for Molecular VirologyUniversity of MinnesotaMinneapolisMNUSA
- Center for Genome EngineeringUniversity of MinnesotaMinneapolisMNUSA
| | - Matthew C Jarvis
- Department of Biochemistry, Molecular Biology and BiophysicsUniversity of MinnesotaMinneapolisMNUSA
- Masonic Cancer CenterUniversity of MinnesotaMinneapolisMNUSA
- Institute for Molecular VirologyUniversity of MinnesotaMinneapolisMNUSA
- Center for Genome EngineeringUniversity of MinnesotaMinneapolisMNUSA
| | - Peter E Wilkinson
- Department of Diagnostic and Biological SciencesSchool of Dentistry, University of MinnesotaMinneapolisMNUSA
| | - Dan P Ho
- Department of Diagnostic and Biological SciencesSchool of Dentistry, University of MinnesotaMinneapolisMNUSA
| | - Mohammed N Islam
- Department of Oral and Maxillofacial Diagnostic SciencesUniversity of Florida College of DentistryGainesvilleFLUSA
| | - Indraneel Bhattacharyya
- Department of Oral and Maxillofacial Diagnostic SciencesUniversity of Florida College of DentistryGainesvilleFLUSA
| | - Rajaram Gopalakrishnan
- Division of Oral and Maxillofacial PathologySchool of Dentistry, University of MinnesotaMinneapolisMNUSA
| | - Faqian Li
- Department of Laboratory Medicine and PathologyMedical School, University of MinnesotaMinneapolisMNUSA
| | - Ioannis G Koutlas
- Division of Oral and Maxillofacial PathologySchool of Dentistry, University of MinnesotaMinneapolisMNUSA
| | - Alessio Giubellino
- Department of Laboratory Medicine and PathologyMedical School, University of MinnesotaMinneapolisMNUSA
| | - Reuben S Harris
- Department of Biochemistry, Molecular Biology and BiophysicsUniversity of MinnesotaMinneapolisMNUSA
- Masonic Cancer CenterUniversity of MinnesotaMinneapolisMNUSA
- Institute for Molecular VirologyUniversity of MinnesotaMinneapolisMNUSA
- Center for Genome EngineeringUniversity of MinnesotaMinneapolisMNUSA
- Howard Hughes Medical InstituteUniversity of MinnesotaMinneapolisMNUSA
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20
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Li YL, Langley CA, Azumaya CM, Echeverria I, Chesarino NM, Emerman M, Cheng Y, Gross JD. The structural basis for HIV-1 Vif antagonism of human APOBEC3G. Nature 2023; 615:728-733. [PMID: 36754086 PMCID: PMC10033410 DOI: 10.1038/s41586-023-05779-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 02/02/2023] [Indexed: 02/10/2023]
Abstract
The APOBEC3 (A3) proteins are host antiviral cellular proteins that hypermutate the viral genome of diverse viral families. In retroviruses, this process requires A3 packaging into viral particles1-4. The lentiviruses encode a protein, Vif, that antagonizes A3 family members by targeting them for degradation. Diversification of A3 allows host escape from Vif whereas adaptations in Vif enable cross-species transmission of primate lentiviruses. How this 'molecular arms race' plays out at the structural level is unknown. Here, we report the cryogenic electron microscopy structure of human APOBEC3G (A3G) bound to HIV-1 Vif, and the hijacked cellular proteins that promote ubiquitin-mediated proteolysis. A small surface explains the molecular arms race, including a cross-species transmission event that led to the birth of HIV-1. Unexpectedly, we find that RNA is a molecular glue for the Vif-A3G interaction, enabling Vif to repress A3G by ubiquitin-dependent and -independent mechanisms. Our results suggest a model in which Vif antagonizes A3G by intercepting it in its most dangerous form for the virus-when bound to RNA and on the pathway to packaging-to prevent viral restriction. By engaging essential surfaces required for restriction, Vif exploits a vulnerability in A3G, suggesting a general mechanism by which RNA binding helps to position key residues necessary for viral antagonism of a host antiviral gene.
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Affiliation(s)
- Yen-Li Li
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - Caroline A Langley
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, USA
| | - Caleigh M Azumaya
- Fred Hutchinson Cancer Center, Electron Microscopy Shared Resource, Seattle, WA, USA
| | - Ignacia Echeverria
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
- Quantitative Bioscience Institute, University of California, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - Nicholas M Chesarino
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Michael Emerman
- Divisions of Human Biology and Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Yifan Cheng
- Quantitative Bioscience Institute, University of California, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, CA, USA
| | - John D Gross
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA.
- Quantitative Bioscience Institute, University of California, San Francisco, CA, USA.
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21
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Stability of APOBEC3F in the Presence of the APOBEC3 Antagonist HIV-1 Vif Increases at the Expense of Co-Expressed APOBEC3H Haplotype I. Viruses 2023; 15:v15020463. [PMID: 36851677 PMCID: PMC9960753 DOI: 10.3390/v15020463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/03/2023] [Accepted: 02/04/2023] [Indexed: 02/10/2023] Open
Abstract
The seven human APOBEC3 enzymes (APOBEC3A through H, excluding E) are host restriction factors. Most of the APOBEC3 enzymes can restrict HIV-1 replication with different efficiencies. The HIV-1 Vif protein combats APOBEC3-mediated restriction by inducing ubiquitination and degradation in the proteasome. APOBEC3F and APOBEC3G can hetero-oligomerize, which increases their restriction capacity and resistance to Vif. Here we determined if APOBEC3C, APOBEC3F, or APOBEC3G could hetero-oligomerize with APOBEC3H haplotype I. APOBEC3H haplotype I has a short half-life in cells due to ubiquitination and degradation by host proteins, but is also resistant to Vif. We hypothesized that hetero-oligomerization with APOBEC3H haplotype I may result in less Vif-mediated degradation of the interacting APOBEC3 and stabilize APOBEC3H haplotype I, resulting in more efficient HIV-1 restriction. Although we found that all three APOBEC3s could interact with APOBEC3H haplotype I, only APOBEC3F affected APOBEC3H haplotype I by surprisingly accelerating its proteasomal degradation. However, this increased APOBEC3F levels in cells and virions in the absence or presence of Vif and enabled APOBEC3F-mediated restriction of HIV-1 in the presence of Vif. Altogether, the data suggest that APOBEC3 enzymes can co-regulate each other at the protein level and that they cooperate to ensure HIV-1 inactivation rather than evolution.
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22
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Fanunza E, Cheng AZ, Auerbach AA, Stefanovska B, Moraes SN, Lokensgard JR, Biolatti M, Dell’Oste V, Bierle CJ, Bresnahan WA, Harris RS. Human cytomegalovirus mediates APOBEC3B relocalization early during infection through a ribonucleotide reductase-independent mechanism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.30.526383. [PMID: 36778493 PMCID: PMC9915650 DOI: 10.1101/2023.01.30.526383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The APOBEC3 family of DNA cytosine deaminases comprises an important arm of the innate antiviral defense system. The gamma-herpesviruses EBV and KSHV and the alpha-herpesviruses HSV-1 and HSV-2 have evolved an efficient mechanism to avoid APOBEC3 restriction by directly binding to APOBEC3B and facilitating its exclusion from the nuclear compartment. The only viral protein required for APOBEC3B relocalization is the large subunit of the ribonucleotide reductase (RNR). Here, we ask whether this APOBEC3B relocalization mechanism is conserved with the beta-herpesvirus human cytomegalovirus (HCMV). Although HCMV infection causes APOBEC3B relocalization from the nucleus to the cytoplasm in multiple cell types, the viral RNR (UL45) is not required. APOBEC3B relocalization occurs rapidly following infection suggesting involvement of an immediate early or early (IE-E) viral protein. In support of this mechanism, cycloheximide treatment of HCMV-infected cells prevents the expression of viral proteins and simultaneously blocks APOBEC3B relocalization. In comparison, the treatment of infected cells with phosphonoacetic acid, which is a viral DNA synthesis inhibitor affecting late protein expression, still permits A3B relocalization. These results combine to show that the beta-herpesvirus HCMV uses a fundamentally different, RNR-independent molecular mechanism to antagonize APOBEC3B. Importance Human cytomegalovirus (HCMV) infections can range from asymptomatic to severe, particularly in neonates and immunocompromised patients. HCMV has evolved strategies to overcome host-encoded antiviral defenses in order to achieve lytic viral DNA replication and dissemination and, under some conditions, latency and long-term persistence. Here, we show that HCMV infection causes the antiviral factor, APOBEC3B, to relocalize from the nuclear compartment to the cytoplasm. This overall strategy resembles that used by related herpesviruses. However, the HCMV relocalization mechanism utilizes a different viral factor(s) and available evidence suggests the involvement of at least one protein expressed at the early stages of infection. This knowledge is important because a greater understanding of this mechanism could lead to novel antiviral strategies that enable APOBEC3B to naturally restrict HCMV infection.
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Affiliation(s)
- Elisa Fanunza
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Adam Z. Cheng
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ashley A. Auerbach
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Bojana Stefanovska
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Sofia N. Moraes
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - James R. Lokensgard
- Department of Medicine, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Matteo Biolatti
- Department of Public Health and Pediatric Sciences, University of Turin, Turin, 10126, Italy
| | - Valentina Dell’Oste
- Department of Public Health and Pediatric Sciences, University of Turin, Turin, 10126, Italy
| | - Craig J. Bierle
- Department of Pediatrics, Division of Pediatric Infectious Diseases and Immunology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Wade A. Bresnahan
- Department of Microbiology and Immunology, University of Minnesota, MN 55455, 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
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23
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Auerbach AA, Becker JT, Moraes SN, Moghadasi SA, Duda JM, Salamango DJ, Harris RS. Ancestral APOBEC3B Nuclear Localization Is Maintained in Humans and Apes and Altered in Most Other Old World Primate Species. mSphere 2022; 7:e0045122. [PMID: 36374108 PMCID: PMC9769932 DOI: 10.1128/msphere.00451-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 10/24/2022] [Indexed: 11/16/2022] Open
Abstract
APOBEC3B is an innate immune effector enzyme capable of introducing mutations in viral genomes through DNA cytosine-to-uracil editing. Recent studies have shown that gamma-herpesviruses, such as Epstein-Barr virus (EBV), have evolved a potent APOBEC3B neutralization mechanism to protect lytic viral DNA replication intermediates in the nuclear compartment. APOBEC3B is additionally unique as the only human DNA deaminase family member that is constitutively nuclear. Nuclear localization has therefore been inferred to be essential for innate antiviral function. Here, we combine evolutionary, molecular, and cell biology approaches to address whether nuclear localization is a conserved feature of APOBEC3B in primates. Despite the relatively recent emergence of APOBEC3B approximately 30 to 40 million years ago (MYA) in Old World primates by genetic recombination (after the split from the New World monkey lineage 40 to 50 MYA), we find that the hallmark nuclear localization of APOBEC3B shows variability. For instance, although human and several nonhuman primate APOBEC3B enzymes are predominantly nuclear, rhesus macaque and other Old World primate APOBEC3B proteins are clearly cytoplasmic or cell wide. A series of human/rhesus macaque chimeras and mutants combined to map localization determinants to the N-terminal half of the protein with residues 15, 19, and 24 proving critical. Ancestral APOBEC3B reconstructed from present-day primate species also shows strong nuclear localization. Together, these results indicate that the ancestral nuclear localization of APOBEC3B is maintained in present-day human and ape proteins, but nuclear localization is not conserved in all Old World monkey species despite a need for antiviral functions in the nuclear compartment. IMPORTANCE APOBEC3 enzymes are single-stranded DNA cytosine-to-uracil deaminases with beneficial roles in antiviral immunity and detrimental roles in cancer mutagenesis. Regarding viral infection, all seven human APOBEC3 enzymes have overlapping roles in restricting virus types that require DNA for replication, including EBV, HIV, human papillomavirus (HPV), and human T-cell leukemia virus (HTLV). Regarding cancer, at least two APOBEC3 enzymes, APOBEC3B and APOBEC3A, are prominent sources of mutation capable of influencing clinical outcomes. Here, we combine evolutionary, molecular, and cell biology approaches to characterize primate APOBEC3B enzymes. We show that nuclear localization is an ancestral property of APOBEC3B that is maintained in present-day human and ape enzymes, but not conserved in other nonhuman primates. This partial mechanistic conservation indicates that APOBEC3B is important for limiting the replication of DNA-based viruses in the nuclear compartment. Understanding these pathogen-host interactions may contribute to the development of future antiviral and antitumor therapies.
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Affiliation(s)
- Ashley A Auerbach
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA
- Institute for Molecular Virology, University of Minnesotagrid.17635.36 - Twin Cities, Minneapolis, Minnesota, USA
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesotagrid.17635.36 - Twin Cities, Minneapolis, Minnesota, USA
| | - Jordan T Becker
- Institute for Molecular Virology, University of Minnesotagrid.17635.36 - Twin Cities, Minneapolis, Minnesota, USA
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesotagrid.17635.36 - Twin Cities, Minneapolis, Minnesota, USA
- Department of Microbiology and Immunology, University of Minnesotagrid.17635.36 - Twin Cities, Minneapolis, Minnesota, USA
| | - Sofia N Moraes
- Institute for Molecular Virology, University of Minnesotagrid.17635.36 - Twin Cities, Minneapolis, Minnesota, USA
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesotagrid.17635.36 - Twin Cities, Minneapolis, Minnesota, USA
| | - Seyed Arad Moghadasi
- Institute for Molecular Virology, University of Minnesotagrid.17635.36 - Twin Cities, Minneapolis, Minnesota, USA
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesotagrid.17635.36 - Twin Cities, Minneapolis, Minnesota, USA
| | - Jolene M Duda
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesotagrid.17635.36 - Twin Cities, Minneapolis, Minnesota, USA
| | - Daniel J Salamango
- Institute for Molecular Virology, University of Minnesotagrid.17635.36 - Twin Cities, Minneapolis, Minnesota, USA
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesotagrid.17635.36 - Twin Cities, Minneapolis, Minnesota, USA
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
| | - Reuben S Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, Texas, USA
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Moraes SN, Becker JT, Moghadasi SA, Shaban NM, Auerbach AA, Cheng AZ, Harris RS. Evidence linking APOBEC3B genesis and evolution of innate immune antagonism by gamma-herpesvirus ribonucleotide reductases. eLife 2022; 11:83893. [PMID: 36458685 DOI: 10.7554/elife.83893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 10/12/2022] [Indexed: 12/04/2022] Open
Abstract
Viruses have evolved diverse mechanisms to antagonize host immunity such as direct inhibition and relocalization of cellular APOBEC3B (A3B) by the ribonucleotide reductase (RNR) of Epstein-Barr virus. Here, we investigate the mechanistic conservation and evolutionary origin of this innate immune counteraction strategy. First, we find that human gamma-herpesvirus RNRs engage A3B via largely distinct surfaces. Second, we show that RNR-mediated enzymatic inhibition and relocalization of A3B depend upon binding to different regions of the catalytic domain. Third, we show that the capability of viral RNRs to antagonize A3B is conserved among gamma-herpesviruses that infect humans and Old World monkeys that encode this enzyme but absent in homologous viruses that infect New World monkeys that naturally lack the A3B gene. Finally, we reconstruct the ancestral primate A3B protein and demonstrate that it is active and similarly engaged by the RNRs from viruses that infect humans and Old World monkeys but not by the RNRs from viruses that infect New World monkeys. These results combine to indicate that the birth of A3B at a critical branchpoint in primate evolution may have been a driving force in selecting for an ancestral gamma-herpesvirus with an expanded RNR functionality through counteraction of this antiviral enzyme.
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Affiliation(s)
- Sofia N Moraes
- Department of Biochemistry, Molecular Biology, and Biophysics, Institute for Molecular Virology, Masonic Cancer Center, University of Minnesota, Minneapolis, United States
| | - Jordan T Becker
- Department of Biochemistry, Molecular Biology, and Biophysics, Institute for Molecular Virology, Masonic Cancer Center, University of Minnesota, Minneapolis, United States
| | - Seyed Arad Moghadasi
- Department of Biochemistry, Molecular Biology, and Biophysics, Institute for Molecular Virology, Masonic Cancer Center, University of Minnesota, Minneapolis, United States
| | - Nadine M Shaban
- Department of Biochemistry, Molecular Biology, and Biophysics, Institute for Molecular Virology, Masonic Cancer Center, University of Minnesota, Minneapolis, United States
| | - Ashley A Auerbach
- Department of Biochemistry, Molecular Biology, and Biophysics, Institute for Molecular Virology, Masonic Cancer Center, University of Minnesota, Minneapolis, United States.,Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, United States
| | - Adam Z Cheng
- Department of Biochemistry, Molecular Biology, and Biophysics, Institute for Molecular Virology, Masonic Cancer Center, University of Minnesota, Minneapolis, United States
| | - Reuben S Harris
- Department of Biochemistry, Molecular Biology, and Biophysics, Institute for Molecular Virology, Masonic Cancer Center, University of Minnesota, Minneapolis, United States.,Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, United States.,Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, United States
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Wong L, Sami A, Chelico L. Competition for DNA binding between the genome protector replication protein A and the genome modifying APOBEC3 single-stranded DNA deaminases. Nucleic Acids Res 2022; 50:12039-12057. [PMID: 36444883 PMCID: PMC9757055 DOI: 10.1093/nar/gkac1121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/21/2022] [Accepted: 11/08/2022] [Indexed: 11/30/2022] Open
Abstract
The human APOBEC family of eleven cytosine deaminases use RNA and single-stranded DNA (ssDNA) as substrates to deaminate cytosine to uracil. This deamination event has roles in lipid metabolism by altering mRNA coding, adaptive immunity by causing evolution of antibody genes, and innate immunity through inactivation of viral genomes. These benefits come at a cost where some family members, primarily from the APOBEC3 subfamily (APOBEC3A-H, excluding E), can cause off-target deaminations of cytosine to form uracil on transiently single-stranded genomic DNA, which induces mutations that are associated with cancer evolution. Since uracil is only promutagenic, the mutations observed in cancer genomes originate only when uracil is not removed by uracil DNA glycosylase (UNG) or when the UNG-induced abasic site is erroneously repaired. However, when ssDNA is present, replication protein A (RPA) binds and protects the DNA from nucleases or recruits DNA repair proteins, such as UNG. Thus, APOBEC enzymes must compete with RPA to access their substrate. Certain APOBEC enzymes can displace RPA, bind and scan ssDNA efficiently to search for cytosines, and can become highly overexpressed in tumor cells. Depending on the DNA replication conditions and DNA structure, RPA can either be in excess or deficient. Here we discuss the interplay between these factors and how despite RPA, multiple cancer genomes have a mutation bias at cytosines indicative of APOBEC activity.
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Affiliation(s)
- Lai Wong
- University of Saskatchewan, College of Medicine, Department of Biochemistry, Microbiology, and Immunology, Saskatoon, Saskatchewan, S7N 5E5, Canada
| | - Alina Sami
- University of Saskatchewan, College of Medicine, Department of Biochemistry, Microbiology, and Immunology, Saskatoon, Saskatchewan, S7N 5E5, Canada
| | - Linda Chelico
- To whom correspondence should be addressed. Tel: +1 306 966 4318; Fax: +1 306 966 4298;
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26
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Shaban NM, Yan R, Shi K, Moraes SN, Cheng AZ, Carpenter MA, McLellan JS, Yu Z, Harris RS. Cryo-EM structure of the EBV ribonucleotide reductase BORF2 and mechanism of APOBEC3B inhibition. SCIENCE ADVANCES 2022; 8:eabm2827. [PMID: 35476445 PMCID: PMC9045721 DOI: 10.1126/sciadv.abm2827] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 02/23/2022] [Indexed: 05/26/2023]
Abstract
Viruses use a plethora of mechanisms to evade immune responses. A recent example is neutralization of the nuclear DNA cytosine deaminase APOBEC3B by the Epstein-Barr virus (EBV) ribonucleotide reductase subunit BORF2. Cryo-EM studies of APOBEC3B-BORF2 complexes reveal a large >1000-Å2 binding surface composed of multiple structural elements from each protein, which effectively blocks the APOBEC3B active site from accessing single-stranded DNA substrates. Evolutionary optimization is suggested by unique insertions in BORF2 absent from other ribonucleotide reductases and preferential binding to APOBEC3B relative to the highly related APOBEC3A and APOBEC3G enzymes. A molecular understanding of this pathogen-host interaction has potential to inform the development of drugs that block the interaction and liberate the natural antiviral activity of APOBEC3B. In addition, given a role for APOBEC3B in cancer mutagenesis, it may also be possible for information from the interaction to be used to develop DNA deaminase inhibitors.
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Affiliation(s)
- Nadine M. Shaban
- Department of Biochemistry, Molecular Biology, and Biophysics, Institute for Molecular Virology, Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Rui Yan
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 55416, USA
| | - Ke Shi
- Department of Biochemistry, Molecular Biology, and Biophysics, Institute for Molecular Virology, Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Sofia N. Moraes
- Department of Biochemistry, Molecular Biology, and Biophysics, Institute for Molecular Virology, Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Adam Z. Cheng
- Department of Biochemistry, Molecular Biology, and Biophysics, Institute for Molecular Virology, Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Michael A. Carpenter
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN 55416, USA
| | - Jason S. McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Zhiheng Yu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 55416, USA
| | - Reuben S. Harris
- Department of Biochemistry, Molecular Biology, and Biophysics, Institute for Molecular Virology, Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN 55416, USA
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Barka A, Berríos KN, Bailer P, Schutsky EK, Wang T, Kohli RM. The Base-Editing Enzyme APOBEC3A Catalyzes Cytosine Deamination in RNA with Low Proficiency and High Selectivity. ACS Chem Biol 2022; 17:629-636. [PMID: 35262324 PMCID: PMC9949940 DOI: 10.1021/acschembio.1c00919] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Human APOBEC3A (A3A) is a nucleic acid-modifying enzyme that belongs to the cytidine deaminase family. Canonically, A3A catalyzes the deamination of cytosine into uracil in single-stranded DNA, an activity that makes A3A both a critical antiviral defense factor and a useful tool for targeted genome editing. However, mutagenesis by A3A has also been readily detected in both cellular DNA and RNA, activities that have been implicated in cancer. Given the importance of substrate discrimination for the physiological, pathological, and biotechnological activities of A3A, here we explore the mechanistic basis for its preferential targeting of DNA over RNA. Using a chimeric substrate containing a target ribocytidine within an otherwise DNA backbone, we demonstrate that a single hydroxyl at the sugar of the target base acts as a major selectivity determinant for deamination. To assess the contribution of bases neighboring the target cytosine, we show that overall RNA deamination is greatly reduced relative to that of DNA but can be observed when ideal features are present, such as preferred sequence context and secondary structure. A strong dependence on idealized substrate features can also be observed with a mutant of A3A (eA3A, N57G), which has been employed for genome editing due to altered selectivity for DNA over RNA. Altogether, our work reveals a relationship between the overall decreased reactivity of A3A and increased substrate selectivity, and our results hold implications both for characterizing off-target mutagenesis and for engineering optimized DNA deaminases for base-editing technologies.
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Affiliation(s)
- Aleksia Barka
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Kiara N Berríos
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Peter Bailer
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Emily K Schutsky
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Tong Wang
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Rahul M Kohli
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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Chen Y, Luo L, Deng L, Tian X, Chen S, Xu A, Yuan S. New Insights Into the Lineage-Specific Expansion and Functional Diversification of Lamprey AID/APOBEC Family. Front Immunol 2022; 13:822616. [PMID: 35359986 PMCID: PMC8962628 DOI: 10.3389/fimmu.2022.822616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 02/15/2022] [Indexed: 11/13/2022] Open
Abstract
The AID/APOBEC family which converts cytidine to uridine on RNA or DNA experienced dynamic expansion in primates in order to resist exogenous viruses and endogenous retrotransposons. Recently, expansion of AID/APOBEC-like homologs has also been observed in the extant jawless vertebrate lamprey. To reveal what causes such expansion and leads to the functional diversification of lamprey cytosine deaminases (CDAs), we reassessed the CDA genes in Lethenteron japonicum (Lj). We first confirmed the expansion of LjCDA1L1 (CDA1-like 1) genes and found the expression correlation of LjCDA2 and LjCDA1L2 with LjVLRs (variable lymphocyte receptors). Among up to 14 LjCDA1L1 proteins, LjCDA1L1_4a has an extremely high deamination activity on ssDNA and buDNA and, unexpectedly, on dsDNA. LjCDA1L1s can also restrict the infection of HSV-1 particles. Thus, the arms race between the host and pathogens along with the recruitment by VLR assembly may participate together to form a driving force in the expansion and diversification of the lamprey AID/APOBEC family.
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Affiliation(s)
- Yan Chen
- Guangdong Key Laboratory of Pharmaceutical Functional Genes, Southern Laboratory of Ocean Science and Engineering (Zhuhai), State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Lingjie Luo
- Guangdong Key Laboratory of Pharmaceutical Functional Genes, Southern Laboratory of Ocean Science and Engineering (Zhuhai), State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Lisi Deng
- Guangdong Key Laboratory of Pharmaceutical Functional Genes, Southern Laboratory of Ocean Science and Engineering (Zhuhai), State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xiaoxue Tian
- Guangdong Key Laboratory of Pharmaceutical Functional Genes, Southern Laboratory of Ocean Science and Engineering (Zhuhai), State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shangwu Chen
- Guangdong Key Laboratory of Pharmaceutical Functional Genes, Southern Laboratory of Ocean Science and Engineering (Zhuhai), State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Anlong Xu
- Guangdong Key Laboratory of Pharmaceutical Functional Genes, Southern Laboratory of Ocean Science and Engineering (Zhuhai), State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
- *Correspondence: Shaochun Yuan, ; Anlong Xu,
| | - Shaochun Yuan
- Guangdong Key Laboratory of Pharmaceutical Functional Genes, Southern Laboratory of Ocean Science and Engineering (Zhuhai), State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- *Correspondence: Shaochun Yuan, ; Anlong Xu,
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The current toolbox for APOBEC drug discovery. Trends Pharmacol Sci 2022; 43:362-377. [PMID: 35272863 PMCID: PMC9018551 DOI: 10.1016/j.tips.2022.02.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 02/03/2022] [Accepted: 02/09/2022] [Indexed: 12/14/2022]
Abstract
Mutational processes driving genome evolution and heterogeneity contribute to immune evasion and therapy resistance in viral infections and cancer. APOBEC3 (A3) enzymes promote such mutations by catalyzing the deamination of cytosines to uracils in single-stranded DNA. Chemical inhibition of A3 enzymes may yield an antimutation therapeutic strategy to improve the durability of current drug therapies that are prone to resistance mutations. A3 small-molecule drug discovery efforts to date have been restricted to a single high-throughput biochemical activity assay; however, the arsenal of discovery assays has significantly expanded in recent years. The assays used to study A3 enzymes are reviewed here with an eye towards their potential for small-molecule discovery efforts.
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Moens U, Prezioso C, Pietropaolo V. Functional Domains of the Early Proteins and Experimental and Epidemiological Studies Suggest a Role for the Novel Human Polyomaviruses in Cancer. Front Microbiol 2022; 13:834368. [PMID: 35250950 PMCID: PMC8894888 DOI: 10.3389/fmicb.2022.834368] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 01/31/2022] [Indexed: 11/13/2022] Open
Abstract
As their name indicates, polyomaviruses (PyVs) can induce tumors. Mouse PyV, hamster PyV and raccoon PyV have been shown to cause tumors in their natural host. During the last 30 years, 15 PyVs have been isolated from humans. From these, Merkel cell PyV is classified as a Group 2A carcinogenic pathogen (probably carcinogenic to humans), whereas BKPyV and JCPyV are class 2B (possibly carcinogenic to humans) by the International Agency for Research on Cancer. Although the other PyVs recently detected in humans (referred to here as novel HPyV; nHPyV) share many common features with PyVs, including the viral oncoproteins large tumor antigen and small tumor antigen, as their role in cancer is questioned. This review discusses whether the nHPyVs may play a role in cancer based on predicted and experimentally proven functions of their early proteins in oncogenic processes. The functional domains that mediate the oncogenic properties of early proteins of known PyVs, that can cause cancer in their natural host or animal models, have been well characterized and we examined whether these functional domains are conserved in the early proteins of the nHPyVs and presented experimental evidence that these conserved domains are functional. Furthermore, we reviewed the literature describing the detection of nHPyV in human tumors.
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Affiliation(s)
- Ugo Moens
- Faculty of Health Sciences, Department of Medical Biology, University of Tromsø – The Arctic University of Norway, Tromsø, Norway
- *Correspondence: Ugo Moens,
| | - Carla Prezioso
- Microbiology of Chronic Neuro-Degenerative Pathologies, IRCSS San Raffaele Roma, Rome, Italy
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Valeria Pietropaolo
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
- Valeria Pietropaolo,
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Demchenko V, Kobylinskyi S, Iurzhenko M, Riabov S, Vashchuk A, Rybalchenko N, Zahorodnia S, Naumenko K, Demchenko O, Adamus G, Kowalczuk M. Nanocomposites based on polylactide and silver nanoparticles and their antimicrobial and antiviral applications. REACT FUNCT POLYM 2022. [DOI: 10.1016/j.reactfunctpolym.2021.105096] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Sakhtemani R, Perera MLW, Hübschmann D, Siebert R, Lawrence M, Bhagwat A. OUP accepted manuscript. Nucleic Acids Res 2022; 50:5145-5157. [PMID: 35524550 PMCID: PMC9122604 DOI: 10.1093/nar/gkac296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 04/08/2022] [Accepted: 04/29/2022] [Indexed: 12/04/2022] Open
Abstract
Activation-induced deaminase (AID) is a DNA-cytosine deaminase that mediates maturation of antibodies through somatic hypermutation and class-switch recombination. While it causes mutations in immunoglobulin heavy and light chain genes and strand breaks in the switch regions of the immunoglobulin heavy chain gene, it largely avoids causing such damage in the rest of the genome. To help understand targeting by human AID, we expressed it in repair-deficient Escherichia coli and mapped the created uracils in the genomic DNA using uracil pull-down and sequencing, UPD-seq. We found that both AID and the human APOBEC3A preferentially target tRNA genes and transcription start sites, but do not show preference for highly transcribed genes. Unlike A3A, AID did not show a strong replicative strand bias or a preference for hairpin loops. Overlapping uracilation peaks between these enzymes contained binding sites for a protein, FIS, that helps create topological domains in the E. coli genome. To confirm whether these findings were relevant to B cells, we examined mutations from lymphoma and leukemia genomes within AID-preferred sequences. These mutations also lacked replicative strand bias or a hairpin loop preference. We propose here a model for how AID avoids causing mutations in the single-stranded DNA found within replication forks.
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Affiliation(s)
- Ramin Sakhtemani
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | | | - Daniel Hübschmann
- Molecular Precision Oncology Program, National Center for Tumor Diseases, Heidelberg and German Cancer Research Center, Heidelberg, Germany
- Heidelberg Institute for Stem cell Technology and Experimental Medicine, Heidelberg, Germany
- German Cancer Consortium, Heidelberg, Germany
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Michael S Lawrence
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Ashok S Bhagwat
- To whom correspondence should be addressed. Tel: +1 734 425 1749; Fax: +1 313 577 8822, 443;
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INMI1 Zika Virus NS4B Antagonizes the Interferon Signaling by Suppressing STAT1 Phosphorylation. Viruses 2021; 13:v13122448. [PMID: 34960717 PMCID: PMC8705506 DOI: 10.3390/v13122448] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/22/2021] [Accepted: 12/02/2021] [Indexed: 12/17/2022] Open
Abstract
The evasion of the Interferon response has important implications in Zika virus (ZIKV) disease. Mutations in ZIKV viral protein NS4B, associated with modulation of the interferon (IFN) system, have been linked to increased pathogenicity in animal models. In this study, we unravel ZIKV NS4B as antagonist of the IFN signaling cascade. Firstly, we reported the genomic characterization of NS4B isolated from a strain of the 2016 outbreak, ZIKV Brazil/2016/INMI1, and we predicted its membrane topology. Secondly, we analyzed its phylogenetic correlation with other flaviviruses, finding a high similarity with dengue virus 2 (DEN2) strains; in particular, the highest conservation was found when NS4B was aligned with the IFN inhibitory domain of DEN2 NS4B. Hence, we asked whether ZIKV NS4B was also able to inhibit the IFN signaling cascade, as reported for DEN2 NS4B. Our results showed that ZIKV NS4B was able to strongly inhibit the IFN stimulated response element and the IFN-γ-activated site transcription, blocking IFN-I/-II responses. mRNA expression levels of the IFN stimulated genes ISG15 and OAS1 were also strongly reduced in presence of NS4B. We found that the viral protein was acting by suppressing the STAT1 phosphorylation and consequently blocking the nuclear transport of both STAT1 and STAT2.
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Gaba A, Hix MA, Suhail S, Flath B, Boysan B, Williams DR, Pelletier T, Emerman M, Morcos F, Cisneros GA, Chelico L. Divergence in Dimerization and Activity of Primate APOBEC3C. J Mol Biol 2021; 433:167306. [PMID: 34666043 PMCID: PMC9202443 DOI: 10.1016/j.jmb.2021.167306] [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: 08/22/2021] [Revised: 10/08/2021] [Accepted: 10/08/2021] [Indexed: 11/21/2022]
Abstract
The APOBEC3 (A3) family of single-stranded DNA cytidine deaminases are host restriction factors that inhibit lentiviruses, such as HIV-1, in the absence of the Vif protein that causes their degradation. Deamination of cytidine in HIV-1 (−)DNA forms uracil that causes inactivating mutations when uracil is used as a template for (+)DNA synthesis. For APOBEC3C (A3C), the chimpanzee and gorilla orthologues are more active than human A3C, and we determined that Old World Monkey A3C from rhesus macaque (rh) is not active against HIV-1. Biochemical, virological, and coevolutionary analyses combined with molecular dynamics simulations showed that the key amino acids needed to promote rhA3C antiviral activity, 44, 45, and 144, also promoted dimerization and changes to the dynamics of loop 1, near the enzyme active site. Although forced evolution of rhA3C resulted in a similar dimer interface with hominid A3C, the key amino acid contacts were different. Overall, our results determine the basis for why rhA3C is less active than human A3C and establish the amino acid network for dimerization and increased activity. Based on identification of the key amino acids determining Old World Monkey antiviral activity we predict that other Old World Monkey A3Cs did not impart anti-lentiviral activity, despite fixation of a key residue needed for hominid A3C activity. Overall, the coevolutionary analysis of the A3C dimerization interface presented also provides a basis from which to analyze dimerization interfaces of other A3 family members.
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Affiliation(s)
- Amit Gaba
- Department of Biochemistry, Microbiology, and Immunology, College of Medicine, University of Saskatchewan, Saskatoon, Canada. https://twitter.com/optimist1023
| | - Mark A Hix
- Department of Chemistry, University of North Texas, Denton, TX, USA. https://twitter.com/markahix
| | - Sana Suhail
- Department of Biological Sciences, Center for Systems Biology, University of Texas at Dallas, Richardson, TX, USA. https://twitter.com/sakuraa_329
| | - Ben Flath
- Department of Biochemistry, Microbiology, and Immunology, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Brock Boysan
- Department of Chemistry, University of North Texas, Denton, TX, USA
| | - Danielle R Williams
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA. https://twitter.com/dani_renee_
| | - Tomas Pelletier
- Department of Biochemistry, Microbiology, and Immunology, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Michael Emerman
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA. https://twitter.com/memerman
| | - Faruck Morcos
- Department of Biological Sciences, Center for Systems Biology, University of Texas at Dallas, Richardson, TX, USA; Department of Bioengineering, University of Texas at Dallas, Dallas, TX, USA. https://twitter.com/MorcosLab
| | - G Andrés Cisneros
- Department of Chemistry, University of North Texas, Denton, TX, USA. https://twitter.com/CisnerosRes
| | - Linda Chelico
- Department of Biochemistry, Microbiology, and Immunology, College of Medicine, University of Saskatchewan, Saskatoon, Canada.
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Giongo V, Falanga A, De Melo CPP, da Silva GB, Bellavita R, De-Simone SG, Paixão IC, Galdiero S. Antiviral Potential of Naphthoquinones Derivatives Encapsulated within Liposomes. Molecules 2021; 26:molecules26216440. [PMID: 34770849 PMCID: PMC8586984 DOI: 10.3390/molecules26216440] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/13/2021] [Accepted: 10/22/2021] [Indexed: 11/16/2022] Open
Abstract
HSV infections, both type 1 and type 2, are among the most widespread viral diseases affecting people of all ages. Their symptoms could be mild, with cold sores up to 10 days of infection, blindness and encephalitis caused by HSV-1 affecting immunocompetent and immunosuppressed individuals. The severe effects derive from co-evolution with the host, resulting in immune evasion mechanisms, including latency and growing resistance to acyclovir and derivatives. An efficient alternative to controlling the spreading of HSV mutations is the exploitation of new drugs, and the possibility of enhancing their delivery through the encapsulation of drugs into nanoparticles, such as liposomes. In this work, liposomes were loaded with a series of 2-aminomethyl- 3-hydroxy-1,4-naphthoquinones derivatives with n-butyl (compound 1), benzyl (compound 2) and nitrobenzene (compound 3) substituents in the primary amine of naphthoquinone. They were previously identified to have significant inhibitory activity against HSV-1. All of the aminomethylnaphthoquinones derivatives encapsulated in the phosphatidylcholine liposomes were able to control the early and late phases of HSV-1 replication, especially those substituted with the benzyl (compound 2) and nitrobenzene (compound 3), which yields selective index values that are almost nine times more efficient than acyclovir. The growing interest of the industry in topical administration against HSV supports our choice of liposome as a drug carrier of aminomethylnaphthoquinones derivatives for formulations of in vivo pre-clinical assays.
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Affiliation(s)
- Viveca Giongo
- Programa de Pós-Graduação em Ciências e Biotecnologia, Department of Cellular and Molecular Biology, Biology Institute, Federal Fluminense University, Niterói 24020-141, Brazil; (C.P.P.D.M.); (S.G.D.-S.); (I.C.P.)
- Correspondence: (V.G.); (S.G.); Tel.: +552-130-829-025 (V.G.); +390-812-534-503 (S.G.)
| | - Annarita Falanga
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy;
| | - Camilly P. Pires De Melo
- Programa de Pós-Graduação em Ciências e Biotecnologia, Department of Cellular and Molecular Biology, Biology Institute, Federal Fluminense University, Niterói 24020-141, Brazil; (C.P.P.D.M.); (S.G.D.-S.); (I.C.P.)
| | - Gustavo B. da Silva
- Department of of Fundamental Chemistry, Federal Rural University of Rio de Janeiro, Seropédica 23897-000, Brazil;
| | - Rosa Bellavita
- Department of Pharmacy, University of Naples Federico II, 34102 Naples, Italy;
| | - Salvatore G. De-Simone
- Programa de Pós-Graduação em Ciências e Biotecnologia, Department of Cellular and Molecular Biology, Biology Institute, Federal Fluminense University, Niterói 24020-141, Brazil; (C.P.P.D.M.); (S.G.D.-S.); (I.C.P.)
- FIOCRUZ, Center for Technological Development in Health(CDTS)/National Institute of Science and Technology for Innovation in Neglected Diseases Populations (INCT-IDNP), Rio de Janeiro 21040-900, Brazil
| | - Izabel C. Paixão
- Programa de Pós-Graduação em Ciências e Biotecnologia, Department of Cellular and Molecular Biology, Biology Institute, Federal Fluminense University, Niterói 24020-141, Brazil; (C.P.P.D.M.); (S.G.D.-S.); (I.C.P.)
| | - Stefania Galdiero
- Department of Pharmacy, University of Naples Federico II, 34102 Naples, Italy;
- Correspondence: (V.G.); (S.G.); Tel.: +552-130-829-025 (V.G.); +390-812-534-503 (S.G.)
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Chelico L. Special Issue "APOBECs and Virus Restriction". Viruses 2021; 13:v13081613. [PMID: 34452478 PMCID: PMC8402836 DOI: 10.3390/v13081613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 08/10/2021] [Indexed: 11/28/2022] Open
Affiliation(s)
- Linda Chelico
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SA S7H 0E5, Canada
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APOBECs orchestrate genomic and epigenomic editing across health and disease. Trends Genet 2021; 37:1028-1043. [PMID: 34353635 DOI: 10.1016/j.tig.2021.07.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 07/03/2021] [Accepted: 07/05/2021] [Indexed: 12/17/2022]
Abstract
APOBEC proteins can deaminate cytosine residues in DNA and RNA. This can lead to somatic mutations, DNA breaks, RNA modifications, or DNA demethylation in a selective manner. APOBECs function in various cellular compartments and recognize different nucleic acid motifs and structures. They orchestrate a wide array of genomic and epigenomic modifications, thereby affecting various cellular functions positively or negatively, including immune editing, viral and retroelement restriction, DNA damage responses, DNA demethylation, gene expression, and tissue homeostasis. Furthermore, the cumulative increase in genomic and epigenomic editing with aging could also, at least in part, be attributed to APOBEC function. We synthesize our cumulative understanding of APOBEC activity in a unifying overview and discuss their genomic and epigenomic impact in physiological, pathological, and technological contexts.
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Sadeghpour S, Khodaee S, Rahnama M, Rahimi H, Ebrahimi D. Human APOBEC3 Variations and Viral Infection. Viruses 2021; 13:1366. [PMID: 34372572 PMCID: PMC8310219 DOI: 10.3390/v13071366] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/07/2021] [Accepted: 07/08/2021] [Indexed: 12/13/2022] Open
Abstract
Human APOBEC3 (apolipoprotein B mRNA-editing catalytic polypeptide-like 3) enzymes are capable of inhibiting a wide range of endogenous and exogenous viruses using deaminase and deaminase-independent mechanisms. These enzymes are essential components of our innate immune system, as evidenced by (a) their strong positive selection and expansion in primates, (b) the evolution of viral counter-defense mechanisms, such as proteasomal degradation mediated by HIV Vif, and (c) hypermutation and inactivation of a large number of integrated HIV-1 proviruses. Numerous APOBEC3 single nucleotide polymorphisms, haplotypes, and splice variants have been identified in humans. Several of these variants have been reported to be associated with differential antiviral immunity. This review focuses on the current knowledge in the field about these natural variations and their roles in infectious diseases.
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Affiliation(s)
- Shiva Sadeghpour
- Department of Biological Science, University of California Irvine, Irvine, CA 92697, USA;
| | - Saeideh Khodaee
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran 1417614335, Iran;
| | - Mostafa Rahnama
- Department of Plant Pathology, University of Kentucky, Lexington, KY 40546, USA;
| | - Hamzeh Rahimi
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran;
| | - Diako Ebrahimi
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA
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Degradation-Independent Inhibition of APOBEC3G by the HIV-1 Vif Protein. Viruses 2021; 13:v13040617. [PMID: 33916704 PMCID: PMC8066197 DOI: 10.3390/v13040617] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/30/2021] [Accepted: 04/01/2021] [Indexed: 12/20/2022] Open
Abstract
The ubiquitin–proteasome system plays an important role in the cell under normal physiological conditions but also during viral infections. Indeed, many auxiliary proteins from the (HIV-1) divert this system to its own advantage, notably to induce the degradation of cellular restriction factors. For instance, the HIV-1 viral infectivity factor (Vif) has been shown to specifically counteract several cellular deaminases belonging to the apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like (APOBEC3 or A3) family (A3A to A3H) by recruiting an E3-ubiquitin ligase complex and inducing their polyubiquitination and degradation through the proteasome. Although this pathway has been extensively characterized so far, Vif has also been shown to impede A3s through degradation-independent processes, but research on this matter remains limited. In this review, we describe our current knowledge regarding the degradation-independent inhibition of A3s, and A3G in particular, by the HIV-1 Vif protein, the molecular mechanisms involved, and highlight important properties of this small viral protein.
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