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Shaw TM, Dettle ST, Mejia A, Hayes JM, Simmons HA, Basu P, Kuhn JH, Ramuta MD, Warren CJ, Jahrling PB, O'Connor DH, Huang L, Zaeem M, Seo J, Slukvin II, Brown ME, Bailey AL. Isolation of Diverse Simian Arteriviruses Causing Hemorrhagic Disease. Emerg Infect Dis 2024; 30:721-731. [PMID: 38526136 PMCID: PMC10977827 DOI: 10.3201/eid3004.231457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024] Open
Abstract
Genetically diverse simian arteriviruses (simarteriviruses) naturally infect geographically and phylogenetically diverse monkeys, and cross-species transmission and emergence are of considerable concern. Characterization of most simarteriviruses beyond sequence analysis has not been possible because the viruses fail to propagate in the laboratory. We attempted to isolate 4 simarteriviruses, Kibale red colobus virus 1, Pebjah virus, simian hemorrhagic fever virus, and Southwest baboon virus 1, by inoculating an immortalized grivet cell line (known to replicate simian hemorrhagic fever virus), primary macaque cells, macrophages derived from macaque induced pluripotent stem cells, and mice engrafted with macaque CD34+-enriched hematopoietic stem cells. The combined effort resulted in successful virus isolation; however, no single approach was successful for all 4 simarteriviruses. We describe several approaches that might be used to isolate additional simarteriviruses for phenotypic characterization. Our results will expedite laboratory studies of simarteriviruses to elucidate virus-host interactions, assess zoonotic risk, and develop medical countermeasures.
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Warren CJ, Barbachano-Guerrero A, Bauer VL, Stabell AC, Dirasantha O, Yang Q, Sawyer SL. Adaptation of CD4 in gorillas and chimpanzees conveyed resistance to simian immunodeficiency viruses. bioRxiv 2024:2023.11.13.566830. [PMID: 38014262 PMCID: PMC10680607 DOI: 10.1101/2023.11.13.566830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Simian immunodeficiency viruses (SIVs) comprise a large group of primate lentiviruses that endemically infect African monkeys. HIV-1 spilled over to humans from this viral reservoir, but the spillover did not occur directly from monkeys to humans. Instead, a key event was the introduction of SIVs into great apes, which then set the stage for infection of humans. Here, we investigate the role of the lentiviral entry receptor, CD4, in this key and fateful event in the history of SIV/HIV emergence. First, we reconstructed and tested ancient forms of CD4 at two important nodes in ape speciation, both prior to the infection of chimpanzees and gorillas with these viruses. These ancestral CD4s fully supported entry of diverse SIV isolates related to the viruses that made this initial jump to apes. In stark contrast, modern chimpanzee and gorilla CD4 orthologs are more resistant to these viruses. To investigate how this resistance in CD4 was gained, we acquired CD4 gene sequences from 32 gorilla individuals of two species, and identified alleles that encode 8 unique CD4 protein variants. Functional testing of these identified variant-specific differences in susceptibility to virus entry. By engineering single point mutations from resistant gorilla CD4 variants into the permissive human CD4 receptor, we demonstrate that acquired substitutions in gorilla CD4 did convey resistance to virus entry. We provide a population genetic analysis to support the theory that selection is acting in favor of more and more resistant CD4 alleles in ape species harboring SIV endemically (gorillas and chimpanzees), but not in other ape species that lack SIV infections (bonobos and orangutans). Taken together, our results show that SIV has placed intense selective pressure on ape CD4, acting to propagate SIV-resistant alleles in chimpanzee and gorilla populations.
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Affiliation(s)
- Cody J. Warren
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, USA
| | - Arturo Barbachano-Guerrero
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, USA
| | - Vanessa L. Bauer
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, USA
| | - Alex C. Stabell
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, USA
| | - Obaiah Dirasantha
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, USA
| | - Qing Yang
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, USA
| | - Sara L. Sawyer
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, USA
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3
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Yang Q, Barbachano-Guerrero A, Fairchild LM, Rowland TJ, Dowell RD, Allen MA, Warren CJ, Sawyer SL. Macrophages derived from human induced pluripotent stem cells (iPSCs) serve as a high-fidelity cellular model for investigating HIV-1, dengue, and influenza viruses. J Virol 2024; 98:e0156323. [PMID: 38323811 PMCID: PMC10949493 DOI: 10.1128/jvi.01563-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 01/08/2024] [Indexed: 02/08/2024] Open
Abstract
Macrophages are important target cells for diverse viruses and thus represent a valuable system for studying virus biology. Isolation of primary human macrophages is done by culture of dissociated tissues or from differentiated blood monocytes, but these methods are both time consuming and result in low numbers of recovered macrophages. Here, we explore whether macrophages derived from human induced pluripotent stem cells (iPSCs)-which proliferate indefinitely and potentially provide unlimited starting material-could serve as a faithful model system for studying virus biology. Human iPSC-derived monocytes were differentiated into macrophages and then infected with HIV-1, dengue virus, or influenza virus as model human viruses. We show that iPSC-derived macrophages support the replication of these viruses with kinetics and phenotypes similar to human blood monocyte-derived macrophages. These iPSC-derived macrophages were virtually indistinguishable from human blood monocyte-derived macrophages based on surface marker expression (flow cytometry), transcriptomics (RNA sequencing), and chromatin accessibility profiling. iPSC lines were additionally generated from non-human primate (chimpanzee) fibroblasts. When challenged with dengue virus, human and chimpanzee iPSC-derived macrophages show differential susceptibility to infection, thus providing a valuable resource for studying the species-tropism of viruses. We also show that blood- and iPSC-derived macrophages both restrict influenza virus at a late stage of the virus lifecycle. Collectively, our results substantiate iPSC-derived macrophages as an alternative to blood monocyte-derived macrophages for the study of virus biology. IMPORTANCE Macrophages have complex relationships with viruses: while macrophages aid in the removal of pathogenic viruses from the body, macrophages are also manipulated by some viruses to serve as vessels for viral replication, dissemination, and long-term persistence. Here, we show that iPSC-derived macrophages are an excellent model that can be exploited in virology.
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Affiliation(s)
- Qing Yang
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, USA
| | | | - Laurence M. Fairchild
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, USA
| | - Teisha J. Rowland
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, USA
| | - Robin D. Dowell
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, USA
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Linda Crnic Institute for Down Syndrome Boulder Branch, BioFrontiers Institute, Boulder, Colorado, USA
- Department of Computer Science, University of Colorado Boulder, Boulder, Colorado, USA
| | - Mary A. Allen
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, USA
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Linda Crnic Institute for Down Syndrome Boulder Branch, BioFrontiers Institute, Boulder, Colorado, USA
| | - Cody J. Warren
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, USA
- Center for Retrovirus Research, The Ohio State University, Columbus, Ohio, USA
- Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
- Viruses and Emerging Pathogens Program, Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
| | - Sara L. Sawyer
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, USA
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Shaw TM, Maloney SM, Nennig K, Ramuta MD, Norton A, Ibarra R, Kuehnert P, Brinton M, Faaberg K, Kuhn JH, O'Connor DH, Warren CJ, Bailey AL. Ectopic expression of murine CD163 enables cell-culture isolation of lactate dehydrogenase-elevating virus 63 years after its discovery. J Virol 2023; 97:e0093023. [PMID: 37792000 PMCID: PMC10617578 DOI: 10.1128/jvi.00930-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 08/08/2023] [Indexed: 10/05/2023] Open
Abstract
IMPORTANCE Mouse models of viral infection play an especially large role in virology. In 1960, a mouse virus, lactate dehydrogenase-elevating virus (LDV), was discovered and found to have the peculiar ability to evade clearance by the immune system, enabling it to persistently infect an individual mouse for its entire lifespan without causing overt disease. However, researchers were unable to grow LDV in culture, ultimately resulting in the demise of this system as a model of failed immunity. We solve this problem by identifying the cell-surface molecule CD163 as the critical missing component in cell-culture systems, enabling the growth of LDV in immortalized cell lines for the first time. This advance creates abundant opportunities for further characterizing LDV in order to study both failed immunity and the family of viruses to which LDV belongs, Arteriviridae (aka, arteriviruses).
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Affiliation(s)
- Teressa M Shaw
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison School of Medicine and Public Health , Madison, Wisconsin, USA
| | - Sara M Maloney
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison School of Medicine and Public Health , Madison, Wisconsin, USA
| | - Kylie Nennig
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison School of Medicine and Public Health , Madison, Wisconsin, USA
| | - Mitchell D Ramuta
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison School of Medicine and Public Health , Madison, Wisconsin, USA
| | - Andrew Norton
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison School of Medicine and Public Health , Madison, Wisconsin, USA
| | - Rodrigo Ibarra
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison School of Medicine and Public Health , Madison, Wisconsin, USA
| | - Paul Kuehnert
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison School of Medicine and Public Health , Madison, Wisconsin, USA
| | - Margo Brinton
- Department of Biology, Georgia State University , Atlanta, Georgia, USA
| | - Kay Faaberg
- Virus and Prion Research Unit, USA Department of Agriculture, National Animal Disease Center , Ames, Iowa, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick , Frederick, Maryland, USA
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison School of Medicine and Public Health , Madison, Wisconsin, USA
| | - Cody J Warren
- Department of Veterinary Biosciences, The Ohio State University , Columbus, Ohio, USA
| | - Adam L Bailey
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison School of Medicine and Public Health , Madison, Wisconsin, USA
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Pasquesi GIM, Allen H, Ivancevic A, Barbachano-Guerrero A, Joyner O, Guo K, Simpson DM, Gapin K, Horton I, Nguyen L, Yang Q, Warren CJ, Florea LD, Bitler BG, Santiago ML, Sawyer SL, Chuong EB. Regulation of human interferon signaling by transposon exonization. bioRxiv 2023:2023.09.11.557241. [PMID: 37745311 PMCID: PMC10515820 DOI: 10.1101/2023.09.11.557241] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Innate immune signaling is essential for clearing pathogens and damaged cells, and must be tightly regulated to avoid excessive inflammation or autoimmunity. Here, we found that the alternative splicing of exons derived from transposable elements is a key mechanism controlling immune signaling in human cells. By analyzing long-read transcriptome datasets, we identified numerous transposon exonization events predicted to generate functional protein variants of immune genes, including the type I interferon receptor IFNAR2. We demonstrated that the transposon-derived isoform of IFNAR2 is more highly expressed than the canonical isoform in almost all tissues, and functions as a decoy receptor that potently inhibits interferon signaling including in cells infected with SARS-CoV-2. Our findings uncover a primate-specific axis controlling interferon signaling and show how a transposon exonization event can be co-opted for immune regulation.
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Affiliation(s)
- Giulia Irene Maria Pasquesi
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309
- Crnic Institute Boulder Branch, BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, 80303
| | - Holly Allen
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309
| | - Atma Ivancevic
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309
| | - Arturo Barbachano-Guerrero
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309
| | - Olivia Joyner
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309
| | - Kejun Guo
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045
| | - David M. Simpson
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309
| | - Keala Gapin
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309
| | - Isabella Horton
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309
| | - Lily Nguyen
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045
| | - Qing Yang
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309
- Fred Hutchinson Cancer Research Center, Seattle, WA, 98109
| | - Cody J. Warren
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309
- The Ohio State University College of Veterinary Medicine, Columbus, OH, 43210
| | - Liliana D. Florea
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205
| | - Benjamin G. Bitler
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045
| | - Mario L. Santiago
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045
| | - Sara L. Sawyer
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309
| | - Edward B. Chuong
- BioFrontiers Institute and Department of Molecular, Cellular & Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309
- Crnic Institute Boulder Branch, BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, 80303
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Warren CJ, Barbachano-Guerrero A, Huey D, Yang Q, Worden-Sapper ER, Kuhn JH, Sawyer SL. Quantification of virus-infected cells using RNA FISH-Flow. STAR Protoc 2023; 4:102291. [PMID: 37209094 PMCID: PMC10209735 DOI: 10.1016/j.xpro.2023.102291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/13/2023] [Accepted: 04/17/2023] [Indexed: 05/22/2023] Open
Abstract
We present a protocol to detect cells that have been infected by RNA viruses. The method, RNA fluorescence in situ hybridization flow cytometry (RNA FISH-Flow), uses 48 fluorescently labeled DNA probes that hybridize in tandem to viral RNA. RNA FISH-Flow probes can be synthesized to match any RNA virus genome, in either sense or anti-sense, enabling detection of genomes or replication intermediates within cells. Flow cytometry enables high-throughput analysis of infection dynamics within a population at the single cell level. For complete details on the use and execution of this protocol, please refer to Warren et al. (2022).1.
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Affiliation(s)
- Cody J Warren
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA.
| | - Arturo Barbachano-Guerrero
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80303, USA
| | - Devra Huey
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA
| | - Qing Yang
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80303, USA
| | - Emma R Worden-Sapper
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80303, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA
| | - Sara L Sawyer
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80303, USA.
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Warren CJ, Sawyer SL. Identifying animal viruses in humans. Science 2023; 379:982-983. [PMID: 36893227 DOI: 10.1126/science.ade6985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Experimental virology can inform strategic monitoring for new viruses in humans.
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Affiliation(s)
- Cody J Warren
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, USA
| | - Sara L Sawyer
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA
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8
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Warren CJ, Yu S, Peters DK, Barbachano-Guerrero A, Yang Q, Burris BL, Worwa G, Huang IC, Wilkerson GK, Goldberg TL, Kuhn JH, Sawyer SL. Primate hemorrhagic fever-causing arteriviruses are poised for spillover to humans. Cell 2022; 185:3980-3991.e18. [PMID: 36182704 PMCID: PMC9588614 DOI: 10.1016/j.cell.2022.09.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 06/22/2022] [Accepted: 09/12/2022] [Indexed: 01/26/2023]
Abstract
Simian arteriviruses are endemic in some African primates and can cause fatal hemorrhagic fevers when they cross into primate hosts of new species. We find that CD163 acts as an intracellular receptor for simian hemorrhagic fever virus (SHFV; a simian arterivirus), a rare mode of virus entry that is shared with other hemorrhagic fever-causing viruses (e.g., Ebola and Lassa viruses). Further, SHFV enters and replicates in human monocytes, indicating full functionality of all of the human cellular proteins required for viral replication. Thus, simian arteriviruses in nature may not require major adaptations to the human host. Given that at least three distinct simian arteriviruses have caused fatal infections in captive macaques after host-switching, and that humans are immunologically naive to this family of viruses, development of serology tests for human surveillance should be a priority.
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Affiliation(s)
- Cody J Warren
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80303, USA
| | - Shuiqing Yu
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA
| | - Douglas K Peters
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80303, USA
| | - Arturo Barbachano-Guerrero
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80303, USA
| | - Qing Yang
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80303, USA
| | - Bridget L Burris
- Department of Comparative Medicine, Michale E. Keeling Center for Comparative Medicine and Research, The University of Texas MD Anderson Cancer Center, Bastrop, TX 78602, USA
| | - Gabriella Worwa
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA
| | - I-Chueh Huang
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA
| | - Gregory K Wilkerson
- Department of Comparative Medicine, Michale E. Keeling Center for Comparative Medicine and Research, The University of Texas MD Anderson Cancer Center, Bastrop, TX 78602, USA
| | - Tony L Goldberg
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA.
| | - Sara L Sawyer
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80303, USA.
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Warren CJ, Santiago ML, Pyeon D. APOBEC3: Friend or Foe in Human Papillomavirus Infection and Oncogenesis? Annu Rev Virol 2022; 9:375-395. [PMID: 35671565 PMCID: PMC9637027 DOI: 10.1146/annurev-virology-092920-030354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Human papillomavirus (HPV) infection is a causative agent of multiple human cancers, including cervical and head and neck cancers. In these HPV-positive tumors, somatic mutations are caused by aberrant activation of DNA mutators such as members of the apolipoprotein B messenger RNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3) family of cytidine deaminases. APOBEC3 proteins are most notable for their restriction of various viruses, including anti-HPV activity. However, the potential role of APOBEC3 proteins in HPV-induced cancer progression has recently garnered significant attention. Ongoing research stems from the observations that elevated APOBEC3 expression is driven by HPV oncogene expression and that APOBEC3 activity is likely a significant contributor to somatic mutagenesis in HPV-positive cancers. This review focuses on recent advances in the study of APOBEC3 proteins and their roles in HPV infection and HPV-driven oncogenesis. Further, we discuss critical gaps and unanswered questions in our understanding of APOBEC3 in virus-associated cancers.
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Affiliation(s)
- Cody J Warren
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA
| | - Mario L Santiago
- Division of Infectious Diseases, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA;
| | - Dohun Pyeon
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA;
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10
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Seekings AH, Warren CJ, Thomas SS, Mahmood S, James J, Byrne AMP, Watson S, Bianco C, Nunez A, Brown IH, Brookes SM, Slomka MJ. Highly pathogenic avian influenza virus H5N6 (clade 2.3.4.4b) has a preferable host tropism for waterfowl reflected in its inefficient transmission to terrestrial poultry. Virology 2021; 559:74-85. [PMID: 33839461 DOI: 10.1016/j.virol.2021.03.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 03/12/2021] [Accepted: 03/14/2021] [Indexed: 10/21/2022]
Abstract
Highly-pathogenic avian influenza virus (HPAIV) H5N6 (clade 2.3.4.4b) incurred into Europe in late 2017 and was predominantly detected in wild birds, with very few terrestrial poultry cases. Pekin ducks directly-infected with a UK virus (H5N6-2017) were donors of infection to investigate contact transmission to three recipient species: Ducks, chickens and turkeys. H5N6-2017 transmission to ducks was 100% efficient, but transmission to in-contact galliforme species was infrequent and unpredictable, thereby reflecting the European 2017-2018 H5N6 epidemiology. Although only two of 28 (7%) infected ducks died, the six turkeys and one chicken which became infected all died and displayed systemic H5N6-2017 dissemination, while pathogenesis in ducks was generally milder. Analysis of H5N6-2017 progeny in the contacts revealed no emergent polymorphisms in an infected duck, but the galliforme species included changes in the polymerase (PB2 A199T, PA D347A), matrix (M1 T218A) and neuraminidase genes (T88I). H5N6-2017 environmental contamination was associated with duck shedding.
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Affiliation(s)
- A H Seekings
- Avian Virology and Mammalian Influenza Research, Virology Department, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey, KT15 3NB, UK
| | - C J Warren
- Avian Virology and Mammalian Influenza Research, Virology Department, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey, KT15 3NB, UK
| | - S S Thomas
- Avian Virology and Mammalian Influenza Research, Virology Department, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey, KT15 3NB, UK
| | - S Mahmood
- Avian Virology and Mammalian Influenza Research, Virology Department, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey, KT15 3NB, UK
| | - J James
- Avian Virology and Mammalian Influenza Research, Virology Department, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey, KT15 3NB, UK
| | - A M P Byrne
- Avian Virology and Mammalian Influenza Research, Virology Department, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey, KT15 3NB, UK
| | - S Watson
- Animal Sciences Unit, APHA-Weybridge, Addlestone, Surrey, KT15 3NB, UK
| | - C Bianco
- Pathology Department, APHA-Weybridge, Addlestone, Surrey, KT15 3NB, UK
| | - A Nunez
- Pathology Department, APHA-Weybridge, Addlestone, Surrey, KT15 3NB, UK
| | - I H Brown
- Avian Virology and Mammalian Influenza Research, Virology Department, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey, KT15 3NB, UK
| | - S M Brookes
- Avian Virology and Mammalian Influenza Research, Virology Department, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey, KT15 3NB, UK
| | - M J Slomka
- Avian Virology and Mammalian Influenza Research, Virology Department, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey, KT15 3NB, UK.
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Behbahani S, Malerba S, Karanfilian KM, Warren CJ, Alhatem A, Samie FH. Demographics and outcomes of eccrine porocarcinoma: results from the National Cancer Database. Br J Dermatol 2020; 183:161-163. [PMID: 31954060 DOI: 10.1111/bjd.18874] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- S Behbahani
- Rutgers New Jersey Medical School, Newark, NJ, U.S.A
| | - S Malerba
- Rutgers New Jersey Medical School, Newark, NJ, U.S.A
| | | | - C J Warren
- Rutgers New Jersey Medical School, Newark, NJ, U.S.A
| | - A Alhatem
- Department of Pathology and Laboratory, Rutgers New Jersey Medical School, Newark, NJ, U.S.A
| | - F H Samie
- Department of Dermatology, Columbia University Irving Medical Centre, New York, NY, U.S.A
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Warren CJ, Meyerson NR, Dirasantha O, Feldman ER, Wilkerson GK, Sawyer SL. Selective use of primate CD4 receptors by HIV-1. PLoS Biol 2019; 17:e3000304. [PMID: 31181085 PMCID: PMC6586362 DOI: 10.1371/journal.pbio.3000304] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 06/20/2019] [Accepted: 05/15/2019] [Indexed: 12/15/2022] Open
Abstract
Individuals chronically infected with HIV-1 harbor complex viral populations within their bloodstreams. Recently, it has come to light that when these people infect others, the new infection is typically established by only one or a small number of virions from within this complex viral swarm. An important goal is to characterize the biological properties of HIV-1 virions that seed and exist early in new human infections because these are potentially the only viruses against which a prophylactic HIV-1 vaccine would need to elicit protection. This includes understanding how the Envelope (Env) protein of these virions interacts with the T-cell receptor CD4, which supports attachment and entry of HIV-1 into target cells. We examined early HIV-1 isolates for their ability to infect cells via the CD4 receptor of 15 different primate species. Primates were the original source of HIV-1 and now serve as valuable animal models for studying HIV-1. We find that most primary isolates of HIV-1 from the blood, including early isolates, are highly selective and enter cells through some primate CD4 receptor orthologs but not others. This phenotype is remarkably consistent, regardless of route of transmission, viral subtype, or time of isolation post infection. We show that the weak CD4 binding affinity of blood-derived HIV-1 isolates is what makes them sensitive to the small sequence differences in CD4 from one primate species to the next. To substantiate this, we engineered an early HIV-1 Env to have high, medium, or low binding affinity to CD4, and we show that it loses the ability to enter cells via the CD4 receptor of many primate species as the binding affinity gets weaker. Based on the phenotype of selective use of primate CD4, we find that weak CD4 binding appears to be a nearly universal property of HIV-1 circulating in the bloodstream. Therefore, weak binding to CD4 must be a selected and important property in the biology of HIV-1 in the body. We identify six primate species that encode CD4 receptors that fully support the entry of early HIV-1 isolates despite their low binding affinity for CD4. These findings will help inform long-standing efforts to model HIV-1 transmission and early disease in primates. The current animal model for HIV, the macaque, encodes a CD4 receptor that is non-permissive for HIV entry. This paper reveals that six primate species encode CD4 receptors compatible with HIV infection, potentially making them powerful tools for the study of HIV biology. Furthermore, weak CD4 binding is a nearly constant, and apparently selected, property of HIV circulating in the human bloodstream.
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Affiliation(s)
- Cody J. Warren
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, United States of America
| | - Nicholas R. Meyerson
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, United States of America
| | - Obaiah Dirasantha
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, United States of America
| | - Emily R. Feldman
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, United States of America
| | - Gregory K. Wilkerson
- Department of Comparative Medicine, Michale E. Keeling Center for Comparative Medicine and Research, The University of Texas MD Anderson Cancer Center, Bastrop, Texas, United States of America
| | - Sara L. Sawyer
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, United States of America
- * E-mail:
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13
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Abstract
Viruses of wild and domestic animals can infect humans in a process called zoonosis, and these events can give rise to explosive epidemics such as those caused by the HIV and Ebola viruses. While humans are constantly exposed to animal viruses, those that can successfully infect and transmit between humans are exceedingly rare. The key event in zoonosis is when an animal virus begins to replicate (one virion making many) in the first human subject. Only at this point will the animal virus first experience the selective environment of the human body, rendering possible viral adaptation and refinement for humans. In addition, appreciable viral titers in this first human may enable infection of a second, thus initiating selection for viral variants with increased capacity for spread. We assert that host genetics plays a critical role in defining which animal viruses in nature will achieve this key event of replication in a first human host. This is because animal viruses that pose the greatest risk to humans will have few (or no) genetic barriers to replicating themselves in human cells, thus requiring minimal mutations to make this jump. Only experimental virology provides a path to identifying animal viruses with the potential to replicate themselves in humans because this information will not be evident from viral sequencing data alone.
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Affiliation(s)
- Cody J. Warren
- BioFrontiers Institute and Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Sara L. Sawyer
- BioFrontiers Institute and Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, United States of America
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14
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Meyerson NR, Warren CJ, Vieira DASA, Diaz-Griffero F, Sawyer SL. Correction: Species-specific vulnerability of RanBP2 shaped the evolution of SIV as it transmitted in African apes. PLoS Pathog 2018; 14:e1006983. [PMID: 29614111 PMCID: PMC5882152 DOI: 10.1371/journal.ppat.1006983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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15
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Westrich JA, Warren CJ, Klausner MJ, Guo K, Liu CW, Santiago ML, Pyeon D. Human Papillomavirus 16 E7 Stabilizes APOBEC3A Protein by Inhibiting Cullin 2-Dependent Protein Degradation. J Virol 2018; 92:e01318-17. [PMID: 29367246 PMCID: PMC5972886 DOI: 10.1128/jvi.01318-17] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 01/15/2018] [Indexed: 12/21/2022] Open
Abstract
APOBEC3 (A3) mutation signatures have been observed in a variety of human cancer genomes, including those of cervical and head and neck cancers caused by human papillomavirus (HPV) infection. However, the driving forces that promote off-target A3 activity remain mostly unclear. Here, we report a mechanism for the dramatic increase of A3A protein levels in HPV-positive keratinocytes. We show that expression of the viral protein E7 from high-risk HPVs, but not E7 from low-risk HPVs, significantly prolongs the cellular half-life of A3A protein in human keratinocytes and HPV-positive cancer cell lines. We have mapped several residues within the cullin 2 (CUL2) binding motif of HPV16 E7 as being important for mediating A3A protein stabilization. Furthermore, we provide direct evidence that both A3A and HPV16 E7 interact with CUL2, suggesting that the E7-CUL2 complex formed during HPV infection may regulate A3A protein levels in the cell. Using an in vitro cytidine deaminase assay, we show that E7-stabilized A3A remains catalytically active. Taken together, our findings suggest that the HPV oncoprotein E7 dysregulates endogenous A3A protein levels and thus provides novel mechanistic insight into cellular triggers of A3 mutations in HPV-positive cancers.IMPORTANCE Human papillomavirus (HPV) is causally associated with over 5% of all human malignancies. Several recent studies have shown that a subset of cancers, including HPV-positive head and neck and cervical cancers, have distinct mutational signatures potentially caused by members of the APOBEC3 cytidine deaminase family. However, the mechanism that induces APOBEC3 activity in cancer cells is poorly understood. Here, we report that the HPV oncoprotein E7 stabilizes the APOBEC3A (A3A) protein in human keratinocytes by inhibiting ubiquitin-dependent protein degradation in a cullin-dependent manner. Interestingly, the HPV E7-stabilized A3A protein maintains its deaminase activity. These findings provide a new insight into cancer mutagenesis enhanced by virus-induced A3A protein stabilization.
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Affiliation(s)
- Joseph A Westrich
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Cody J Warren
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Michael J Klausner
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Kejun Guo
- Division of Infectious Diseases, Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Chang-Wei Liu
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Mario L Santiago
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
- Division of Infectious Diseases, Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Dohun Pyeon
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
- Division of Infectious Diseases, Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
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16
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Abstract
HIV-1 arose as the result of spillover of simian immunodeficiency viruses (SIVs) from great apes in Africa, namely from chimpanzees and gorillas. Chimpanzees and gorillas were, themselves, infected with SIV after virus spillover from African monkeys. During spillover events, SIV is thought to require adaptation to the new host species. The host barriers that drive viral adaptation have predominantly been attributed to restriction factors, rather than cofactors (host proteins exploited to promote viral replication). Here, we consider the role of one cofactor, RanBP2, in providing a barrier that drove viral genome evolution during SIV spillover events. RanBP2 (also known as Nup358) is a component of the nuclear pore complex known to facilitate nuclear entry of HIV-1. Our data suggest that transmission of SIV from monkeys to chimpanzees, and then from chimpanzees to gorillas, both coincided with changes in the viral capsid that allowed interaction with RanBP2 of the new host species. However, human RanBP2 subsequently provided no barrier to the zoonotic transmission of SIV from chimpanzees or gorillas, indicating that chimpanzee- and gorilla-adapted SIVs are pre-adapted to humans in this regard. Our observations are in agreement with RanBP2 driving virus evolution during cross-species transmissions of SIV, particularly in the transmissions to and between great ape species. Multiple times, HIV-1 has entered the human population after emerging from a viral reservoir that exists in African primates. First, simian immunodeficiency virus (SIV) made the jump from monkeys into African great apes, and then from apes (namely, chimpanzees and gorillas) into humans. It is well appreciated that restriction factors, which are specialized proteins of the innate immune system, acted as host-specific barriers that drove virus adaptation during these spillover events. Here, we present data showing that a major constituent of the nuclear pore complex, RanBP2, was also a barrier to the spillover of SIVs, particularly in great ape species. Spillover of SIV into chimpanzee and gorilla populations required that the SIV capsid mutate to establish interaction with RanBP2 in the new host species. Our study highlights how essential housekeeping proteins, despite being generally more evolutionarily conserved than restriction factors, can also drive virus evolution during spillover events.
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Affiliation(s)
- Nicholas R. Meyerson
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO, United States of America
| | - Cody J. Warren
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO, United States of America
| | - Daniel A. S. A. Vieira
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, United States of America
| | - Felipe Diaz-Griferro
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, United States of America
| | - Sara L. Sawyer
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO, United States of America
- * E-mail:
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17
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Cicchini L, Blumhagen RZ, Westrich JA, Myers ME, Warren CJ, Siska C, Raben D, Kechris KJ, Pyeon D. High-Risk Human Papillomavirus E7 Alters Host DNA Methylome and Represses HLA-E Expression in Human Keratinocytes. Sci Rep 2017; 7:3633. [PMID: 28623356 PMCID: PMC5473897 DOI: 10.1038/s41598-017-03295-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 04/26/2017] [Indexed: 02/06/2023] Open
Abstract
Human papillomavirus (HPV) infection distinctly alters methylation patterns in HPV-associated cancer. We have recently reported that HPV E7-dependent promoter hypermethylation leads to downregulation of the chemokine CXCL14 and suppression of antitumor immune responses. To investigate the extent of gene expression dysregulated by HPV E7-induced DNA methylation, we analyzed parallel global gene expression and DNA methylation using normal immortalized keratinocyte lines, NIKS, NIKS-16, NIKS-18, and NIKS-16∆E7. We show that expression of the MHC class I genes is downregulated in HPV-positive keratinocytes in an E7-dependent manner. Methylome analysis revealed hypermethylation at a distal CpG island (CGI) near the HLA-E gene in NIKS-16 cells compared to either NIKS cells or NIKS-16∆E7 cells, which lack E7 expression. The HLA-E CGI functions as an active promoter element which is dramatically repressed by DNA methylation. HLA-E protein expression on cell surface is downregulated by high-risk HPV16 and HPV18 E7 expression, but not by low-risk HPV6 and HPV11 E7 expression. Conversely, demethylation at the HLA-E CGI restores HLA-E protein expression in HPV-positive keratinocytes. Because HLA-E plays an important role in antiviral immunity by regulating natural killer and CD8+ T cells, epigenetic downregulation of HLA-E by high-risk HPV E7 may contribute to virus-induced immune evasion during HPV persistence.
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Affiliation(s)
- Louis Cicchini
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Rachel Z Blumhagen
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, Colorado, USA
| | - Joseph A Westrich
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Mallory E Myers
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Cody J Warren
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Charlotte Siska
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, Colorado, USA
| | - David Raben
- Department of Radiation Oncology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Katerina J Kechris
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, Colorado, USA
| | - Dohun Pyeon
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA.
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA.
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18
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Abstract
A majority of human papillomavirus (HPV) infections are asymptomatic and self-resolving in the absence of medical interventions. Various innate and adaptive immune responses, as well as physical barriers, have been implicated in controlling early HPV infections. However, if HPV overcomes these host immune defenses and establishes persistence in basal keratinocytes, it becomes very difficult for the host to eliminate the infection. The HPV oncoproteins E5, E6, and E7 are important in regulating host immune responses. These oncoproteins dysregulate gene expression, protein-protein interactions, posttranslational modifications, and cellular trafficking of critical host immune modulators. In addition to the HPV oncoproteins, sequence variation and dinucleotide depletion in papillomavirus genomes has been suggested as an alternative strategy for evasion of host immune defenses. Since anti-HPV host immune responses are also considered to be important for antitumor immunity, immune dysregulation by HPV during virus persistence may contribute to immune suppression essential for HPV-associated cancer progression. Here, we discuss cellular pathways dysregulated by HPV that allow the virus to evade various host immune defenses.
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Affiliation(s)
- Joseph A Westrich
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Cody J Warren
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA; Current address: BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Dohun Pyeon
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA; Department of Medicine, University of Colorado School of Medicine, Aurora, CO 80045, USA.
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19
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Affiliation(s)
- Cody J Warren
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Dohun Pyeon
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
- Division of Infectious Diseases, Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
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20
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Abstract
More than 270 different types of papillomaviruses have been discovered in a wide array of animal species. Despite the great diversity of papillomaviruses, little is known about the evolutionary processes that drive host tropism and the emergence of oncogenic genotypes. Although host defense mechanisms have evolved to interfere with various aspects of a virus life cycle, viruses have also coevolved copious strategies to avoid host antiviral restriction. Our and other studies have shown that the cytidine deaminase APOBEC3 family members edit HPV genomes and restrict virus infectivity. Thus, we hypothesized that host restriction by APOBEC3 served as selective pressure during papillomavirus evolution. To test this hypothesis, we analyzed the relative abundance of all dinucleotide sequences in full-length genomes of 274 papillomavirus types documented in the Papillomavirus Episteme database (PaVE). Here, we report that TC dinucleotides, the preferred target sequence of several human APOBEC3 proteins (hA3A, hA3B, hA3F, and hA3H), are highly depleted in papillomavirus genomes. Given that HPV infection is highly tissue-specific, the expression levels of APOBEC3 family members were analyzed. The basal expression levels of all APOBEC3 isoforms, excluding hA3B, are significantly higher in mucosal skin compared with cutaneous skin. Interestingly, we reveal that Alphapapillomaviruses (alpha-PVs), a majority of which infects anogenital mucosa, display the most dramatic reduction in TC dinucleotide content. Computer modeling and reconstruction of ancestral alpha-PV genomes suggest that TC depletion occurred after the alpha-PVs diverged from their most recent common ancestor. In addition, we found that TC depletion in alpha-PVs is greatly affected by protein coding potential. Taken together, our results suggest that PVs replicating in tissues with high APOBEC3 levels may have evolved to evade restriction by selecting for variants that contain reduced APOBEC3 target sites in their genomes.
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Affiliation(s)
- Cody J Warren
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Koenraad Van Doorslaer
- DNA Tumor Virus Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ahwan Pandey
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA; Linda Crnic Institute for Down Syndrome, University of Colorado School of Medicine, Aurora, CO, USA
| | - Joaquin M Espinosa
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA; Linda Crnic Institute for Down Syndrome, University of Colorado School of Medicine, Aurora, CO, USA
| | - Dohun Pyeon
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, USA; Division of Infectious Diseases, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA
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21
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Warren CJ, Griffin LM, Little AS, Huang IC, Farzan M, Pyeon D. The antiviral restriction factors IFITM1, 2 and 3 do not inhibit infection of human papillomavirus, cytomegalovirus and adenovirus. PLoS One 2014; 9:e96579. [PMID: 24827144 PMCID: PMC4020762 DOI: 10.1371/journal.pone.0096579] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 04/07/2014] [Indexed: 11/18/2022] Open
Abstract
Type I interferons (IFN-α and β) induce dynamic host defense mechanisms to inhibit viral infections. It has been recently recognized that the interferon-inducible transmembrane proteins (IFITM) 1, 2 and 3 can block entry of a broad spectrum of RNA viruses. However, no study to date has focused on the role of IFITM proteins in DNA virus restriction. Here, we demonstrate that IFN-α or -β treatment of keratinocytes substantially decreases human papillomavirus 16 (HPV16) infection while robustly inducing IFITM1, 2 and 3 expression. However, IFITM1, 2 and 3 overexpression did not inhibit HPV16 infection; rather, IFITM1 and IFITM3 modestly enhanced HPV16 infection in various cell types including primary keratinocytes. Moreover, IFITM1, 2 and 3 did not inhibit infection by two other DNA viruses, human cytomegalovirus (HCMV) and adenovirus type 5 (Ad5). Taken together, we reveal that the entry of several DNA viruses, including HPV, HCMV, and Ad5 is not affected by IFITM1, 2 and 3 expression. These results imply that HPV, and other DNA viruses, may bypass IFITM restriction during intracellular trafficking.
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Affiliation(s)
- Cody J. Warren
- Department of Microbiology, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Laura M. Griffin
- Department of Microbiology, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Alexander S. Little
- Department of Microbiology, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - I-Chueh Huang
- Department of Cell Biology and Neuroscience, University of California Riverside, Riverside, California, United States of America
| | - Michael Farzan
- Department of Infectious Diseases, The Scripps Research Institute, Jupiter, Florida, United States of America
| | - Dohun Pyeon
- Department of Microbiology, University of Colorado School of Medicine, Aurora, Colorado, United States of America
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, United States of America
- * E-mail:
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22
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Warren CJ. What is homocysteine? Am J Nurs 1999; 99:39-41. [PMID: 10542847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Affiliation(s)
- C J Warren
- Kent State University, New Philadelphia, OH, USA
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23
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Warren CJ. Tarasoff: Duty to warn? Duty to protect? Med Health R I 1998; 81:377-8. [PMID: 15580798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Affiliation(s)
- C J Warren
- Brown, Rudnick, Freed & Gessmer, Providence, RI 02903, USA
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Abstract
This study used a simulator to determine the effectiveness of two file-handle sleeves that are claimed to improve tactile discrimination and the ease of manipulation of endodontic hand instruments. Thirty final-year dental undergraduates inserted files into instrument setting rods until a putty resistance was felt, following which depth of penetration into the material was measured with a microscope. Results were analysed statistically. Despite favourable comments from participants in the trial, the devices failed to deliver enhanced tactile discrimination.
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Affiliation(s)
- C J Warren
- Department of Oral Rehabilitation, School of Dentistry, University of Otago, Dunedin, New Zealand
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25
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Abstract
One hundred ninety cardiac patients were prospectively enrolled in an amiodarone protocol. Over a 10-year period, 16 patients developed new or progressive respiratory symptoms while taking amiodarone. These symptoms included dyspnea associated with abnormal chest radiographs or new or worsening abnormalities on pulmonary function testing. Specimens for microscopic examination were obtained by fiberoptic bronchoscopy with transbronchial lung biopsy (TBB), bronchoalveolar lavage (BAL), open lung biopsy (OLB), or autopsy. Large foamy macrophages with characteristic lamellated cytoplasmic inclusions were noted in all specimens, regardless of other evidence of pulmonary toxicity, suggesting that foamy macrophages represent a routine drug effect. Foamy macrophages were not present in BAL specimens from 53 normal controls and were rarely seen in specimens from 27 patients who had other interstitial lung diseases. When present, the foamy macrophages were less prominent than those seen in specimens from patients receiving amiodarone. Fibrosis was noted in 11 of 16 histological specimens, whereas type II-cell-hyperplasia was observed in 7 of the 16 specimens. Four of the 16 patients with respiratory symptoms died, and their autopsy revealed a combination of foamy macrophages with fibrosis and type II cell hyperplasia reflective of amiodarone pulmonary toxicity. Hyperplastic type II cells were not found in the absence of fibrosis. Immunocytochemistry allowed differentiation between foamy macrophages and type II cells and represents a useful tool for future investigations of the pathogenesis of amiodarone-induced pulmonary disease.
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Affiliation(s)
- C W Bedrossian
- Department of Pathology, Northwestern University, Chicago, IL, USA
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26
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Thorburn DN, Warren CJ. Sleep apnoea. N Z Dent J 1997; 93:95-7. [PMID: 9323899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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27
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Abstract
The purpose of this study was to determine what coping resources are used by women who suffer from premenstrual syndrome (PMS), and to compare the coping resources used with those of a normative population. Two hundred forty-four women volunteered to be in the study. After screening and a 3-month lapse time required for diary completion, 54 subjects remained in the study. A history developed by the researchers, menstrual diaries, and the Coping Resources Inventory (CRIS) were used in data collection. The findings indicate a statistically significant relationship between the dependent variable, severity of PMS, and the independent variables, self-disclosure, stress monitoring, social support, and structure. There was a positive relationship between self-disclosure and stress monitoring with severity of PMS, and an inverse relationship between social support and structuring and severity of PMS.
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Affiliation(s)
- C J Warren
- School of Nursing, College of Health Sciences, Georgia State University, Atlanta 30302-4019
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28
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Howell WM, Warren CJ, Cook NJ, Cawley MI, Smith JL. Detection of IL-2 at mRNA and protein levels in synovial infiltrates from inflammatory arthropathies using biotinylated oligonucleotide probes in situ. Clin Exp Immunol 1991; 86:393-8. [PMID: 1747947 PMCID: PMC1554195 DOI: 10.1111/j.1365-2249.1991.tb02943.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
A non-radioactive in situ hybridization method for IL-2 mRNA detection based on the use of four biotinylated oligonucleotide probes, plus appropriate positive and negative control probes was developed and applied to synovial surgical and needle biopsies from rheumatoid arthritis (RA), spondyloarthropathy (SpA), psoriatic arthritis (PsA) and juvenile chronic arthritis (JCA) patients. In eight surgical biopsies (six RA, one SpA, one PsA) this non-radioactive system showed similar sensitivity to that of a previously described 32P-labelled probe system, and in addition detected IL-2 mRNA in five out of seven biopsies from SpA and PsA patients and in two out of two JCA needle biopsies. IL-2 mRNA was found in the absence of IL-2 protein in RA biopsies (six surgical, 12 needle), but variable amounts of IL-2 protein were detected in six out of seven needle biopsies from SpA, PsA and JCA patients, where CD3+ lymphoid infiltrates were present. These data suggest differences in IL-2 regulation and expression in RA and non-RA inflammatory arthropathies.
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Affiliation(s)
- W M Howell
- Molecular Immunology Group, Tenovus Research Laboratory, Southampton, UK
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Warren CJ, Howell WM, Bhambhani M, Cawley MI, Smith JL. An investigation of T-cell subset phenotype and function in the rheumatoid synovium using in situ hybridization for IL-2 mRNA. Immunol Suppl 1991; 72:250-5. [PMID: 2016122 PMCID: PMC1384492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Cryostat sections of synovial biopsy tissue from patients with active rheumatoid arthritis (RA), spondyloarthritis (SpA) and osteoarthritis (OA) have been investigated for interleukin-2 (IL-2) mRNA and protein production. In situ hybridization using 32P-labelled oligonucleotide probes based on IL-2 gene sequences coded by exon 1 and exon 3 of the IL-2 gene revealed IL-2 mRNA over lymphoid aggregates in RA and SpA tissue. No IL-2 mRNA was detected in OA tissue and reflected the absence of lymphoid infiltrates in these tissues. Total mRNA, as detected by a 32P oligo dT probe, was found in all tissue examined. IL-2 protein product was detected by monoclonal antibody staining in SpA but not in RA or OA tissue. This is the first report of in situ studies of lymphoid function in the microenvironment of the RA synovium. Whether these data reflect the function of normal CD3+ CD4+ CD45RO+ T-cell subsets in the diseased joint remains to be resolved.
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Affiliation(s)
- C J Warren
- Regional Immunology Service, Southampton General Hospital, U.K
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Warren CJ, Yorker BC. Coping with cutbacks in psychiatric nursing education programs. J Child Adolesc Psychiatr Ment Health Nurs 1989; 2:163-5. [PMID: 2585256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Abstract
Although adenoid cystic carcinomas are occasionally manifested in atypical ways, metastatic disease preceding detection of the primary tumor has not been previously reported. We have described a patient in whom multiple pulmonary metastatic nodules were found one year before identification of primary adenoid cystic carcinoma of the maxilla. This case illustrates the need to include adenoid cystic carcinoma in the differential diagnosis of patients with metastatic disease and an unknown primary lesion. The use of special stains and electron microscopy can be helpful in confirming a diagnosis of adenoid cystic carcinoma.
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Affiliation(s)
- C J Warren
- Department of Pathology, St. Louis University School of Medicine, Mo
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Gulesserian B, Warren CJ. Coping resources of depressed patients. Arch Psychiatr Nurs 1987; 1:392-8. [PMID: 3426249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Goetz IE, Moklebust R, Warren CJ. Effects of some antibiotics on the growth of human diploid skin fibroblasts in cell culture. In Vitro 1979; 15:114-9. [PMID: 457178 DOI: 10.1007/bf02618107] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
During serial subcultures 50 micrograms per ml gentamicin and penicillin (100 U per ml)-streptomycin (100 micrograms per ml) depressed cell growth signficantly 2 weeks after the addition of the antibiotics; gentamicin, but not penicillin-streptomycin, stimulated cell growth before it became inhibitory. Removal of the antibiotics resulted in the cell yield returning to normal. The results show that these antibiotics can be harmful to cells even at concentrations thought to be safe.
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