1
|
Olson RM, Gornalusse G, Whitmore LS, Newhouse D, Tisoncik-Go J, Smith E, Ochsenbauer C, Hladik F, Gale M. Innate immune regulation in HIV latency models. Retrovirology 2022; 19:15. [PMID: 35804422 PMCID: PMC9270781 DOI: 10.1186/s12977-022-00599-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/25/2022] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Innate immunity and type 1 interferon (IFN) defenses are critical for early control of HIV infection within CD4 + T cells. Despite these defenses, some acutely infected cells silence viral transcription to become latently infected and form the HIV reservoir in vivo. Latently infected cells persist through antiretroviral therapy (ART) and are a major barrier to HIV cure. Here, we evaluated innate immunity and IFN responses in multiple T cell models of HIV latency, including established latent cell lines, Jurkat cells latently infected with a reporter virus, and a primary CD4 + T cell model of virologic suppression. RESULTS We found that while latently infected T cell lines have functional RNA sensing and IFN signaling pathways, they fail to induce specific interferon-stimulated genes (ISGs) in response to innate immune activation or type 1 IFN treatment. Jurkat cells latently infected with a fluorescent reporter HIV similarly demonstrate attenuated responses to type 1 IFN. Using bulk and single-cell RNA sequencing we applied a functional genomics approach and define ISG expression dynamics in latent HIV infection, including HIV-infected ART-suppressed primary CD4 + T cells. CONCLUSIONS Our observations indicate that HIV latency and viral suppression each link with cell-intrinsic defects in specific ISG induction. We identify a set of ISGs for consideration as latency restriction factors whose expression and function could possibly mitigate establishing latent HIV infection.
Collapse
Affiliation(s)
- Rebecca M. Olson
- grid.34477.330000000122986657Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington School of Medicine, Seattle, WA USA
| | - Germán Gornalusse
- grid.270240.30000 0001 2180 1622Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA USA ,grid.34477.330000000122986657Department of Obstetrics & Gynecology, University of Washington, Seattle, WA USA
| | - Leanne S. Whitmore
- grid.34477.330000000122986657Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington School of Medicine, Seattle, WA USA
| | - Dan Newhouse
- grid.34477.330000000122986657Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington School of Medicine, Seattle, WA USA
| | - Jennifer Tisoncik-Go
- grid.34477.330000000122986657Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington School of Medicine, Seattle, WA USA
| | - Elise Smith
- grid.34477.330000000122986657Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington School of Medicine, Seattle, WA USA
| | - Christina Ochsenbauer
- grid.270240.30000 0001 2180 1622Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA USA
| | - Florian Hladik
- grid.270240.30000 0001 2180 1622Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA USA ,grid.34477.330000000122986657Department of Obstetrics & Gynecology, University of Washington, Seattle, WA USA ,grid.34477.330000000122986657Department of Medicine, University of Washington, Seattle, WA USA
| | - Michael Gale
- grid.34477.330000000122986657Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington School of Medicine, Seattle, WA USA
| |
Collapse
|
2
|
Beachboard DC, Park M, Vijayan M, Snider DL, Fernando DJ, Williams GD, Stanley S, McFadden MJ, Horner SM. The small GTPase RAB1B promotes antiviral innate immunity by interacting with TNF receptor-associated factor 3 (TRAF3). J Biol Chem 2019; 294:14231-14240. [PMID: 31375559 PMCID: PMC6768648 DOI: 10.1074/jbc.ra119.007917] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 07/25/2019] [Indexed: 12/24/2022] Open
Abstract
Innate immune detection of viral nucleic acids during viral infection activates a signaling cascade that induces type I and type III IFNs as well as other cytokines, to generate an antiviral response. This signaling is initiated by pattern recognition receptors, such as the RNA helicase retinoic acid-inducible gene I (RIG-I), that sense viral RNA. These sensors then interact with the adaptor protein mitochondrial antiviral signaling protein (MAVS), which recruits additional signaling proteins, including TNF receptor-associated factor 3 (TRAF3) and TANK-binding kinase 1 (TBK1), to form a signaling complex that activates IFN regulatory factor 3 (IRF3) for transcriptional induction of type I IFNs. Here, using several immunological and biochemical approaches in multiple human cell types, we show that the GTPase-trafficking protein RAB1B up-regulates RIG-I pathway signaling and thereby promotes IFN-β induction and the antiviral response. We observed that RAB1B overexpression increases RIG-I-mediated signaling to IFN-β and that RAB1B deletion reduces signaling of this pathway. Additionally, loss of RAB1B dampened the antiviral response, indicated by enhanced Zika virus infection of cells depleted of RAB1B. Importantly, we identified the mechanism of RAB1B action in the antiviral response, finding that it forms a protein complex with TRAF3 to facilitate the interaction of TRAF3 with mitochondrial antiviral signaling protein. We conclude that RAB1B regulates TRAF3 and promotes the formation of innate immune signaling complexes in response to nucleic acid sensing during RNA virus infection.
Collapse
Affiliation(s)
- Dia C Beachboard
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710
| | - Moonhee Park
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710
| | - Madhuvanthi Vijayan
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710
| | - Daltry L Snider
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710
| | - Dillon J Fernando
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710
| | - Graham D Williams
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710
| | - Sydney Stanley
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710
| | - Michael J McFadden
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710
| | - Stacy M Horner
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710
- Department of Medicine, Duke University Medical Center, Durham, North Carolina 27710
| |
Collapse
|
3
|
Esser-Nobis K, Aarreberg LD, Roby JA, Fairgrieve MR, Green R, Gale M. Comparative Analysis of African and Asian Lineage-Derived Zika Virus Strains Reveals Differences in Activation of and Sensitivity to Antiviral Innate Immunity. J Virol 2019; 93:e00640-19. [PMID: 31019057 PMCID: PMC6580957 DOI: 10.1128/jvi.00640-19] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 04/18/2019] [Indexed: 12/24/2022] Open
Abstract
In recent years, Asian lineage Zika virus (ZIKV) strains emerged to cause pandemic outbreaks associated with a high rate of congenital ZIKV syndrome (CZVS). The reasons for the enhanced spread and severe disease caused by newly emerging strains are not fully understood. Here we compared viral sequences, viral replication, and innate immune signaling induction of three different ZIKV strains derived from African and Asian lineages and West Nile virus, another flavivirus. We found pronounced differences in activation of innate immune signaling and inhibition of viral replication across ZIKV strains. The newly emerged Asian ZIKV strain Brazil Fortaleza 2015, which is associated with a higher rate of neurodevelopmental disorders like microcephaly, induced much weaker and delayed innate immune signaling in infected cells. However, superinfection studies to assess control of innate immune signaling induced by Sendai virus argue against an active block of IRF3 activation by the Brazilian strain of ZIKV and rather suggest an evasion of detection by host cell pattern recognition receptors. Compared to the Asian strain FSS13025 isolated in Cambodia, both ZIKV Uganda MR766 and ZIKV Brazil Fortaleza appear less sensitive to the interferon-induced antiviral response. ZIKV infection studies of cells lacking the different RIG-I-like receptors identified RIG-I as the major cytosolic pattern recognition receptor for detection of ZIKV.IMPORTANCE Zika Virus (ZIKV), discovered in 1947, is divided into African and Asian lineages. Pandemic outbreaks caused by currently emerging Asian lineage strains are accompanied by high rates of neurological disorders and exemplify the global health burden associated with this virus. Here we compared virological and innate immunological aspects of two ZIKV strains from the Asian lineage, an emerging Brazilian strain and a less-pathogenic Cambodian strain, and the prototypic African lineage ZIKV strain from Uganda. Compared to the replication of other ZIKV strains, the replication of ZIKV Brazil was less sensitive to the antiviral actions of interferon (IFN), while infection with this strain induced weaker and delayed innate immune responses in vitro Our data suggest that ZIKV Brazil directs a passive strategy of innate immune evasion that is reminiscent of a stealth virus. Such strain-specific properties likely contribute to differential pathogenesis and should be taken into consideration when choosing virus strains for future molecular studies.
Collapse
Affiliation(s)
- Katharina Esser-Nobis
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Lauren D Aarreberg
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Justin A Roby
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Marian R Fairgrieve
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Richard Green
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Michael Gale
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington School of Medicine, Seattle, Washington, USA
| |
Collapse
|
4
|
Aarreberg LD, Esser-Nobis K, Driscoll C, Shuvarikov A, Roby JA, Gale M. Interleukin-1β Induces mtDNA Release to Activate Innate Immune Signaling via cGAS-STING. Mol Cell 2019; 74:801-815.e6. [PMID: 30952515 DOI: 10.1016/j.molcel.2019.02.038] [Citation(s) in RCA: 201] [Impact Index Per Article: 40.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 01/11/2019] [Accepted: 02/27/2019] [Indexed: 12/11/2022]
Abstract
Interleukin-1 beta (IL-1β) is a pleiotropic mediator of inflammation and is produced in response to a wide range of stimuli. During infection, IL-1β production occurs in parallel with the onset of innate antimicrobial defenses, but the contribution of IL-1β signaling to cell-intrinsic immunity is not defined. Here, we report that exogenous IL-1β induces interferon regulatory factor 3 (IRF3) activation in human myeloid, fibroblast, and epithelial cells. IRF3 activation by IL-1β is dependent upon the DNA-sensing pathway adaptor, stimulator of interferon genes (STING), through the recognition of cytosolic mtDNA by cyclic guanosine monophosphate (GMP)-AMP synthase (cGAS). IL-1β treatment results in interferon (IFN) production and activation of IFN signaling to direct a potent innate immune response that restricts dengue virus infection. This study identifies a new function for IL-1β in the onset or enhancement of cell-intrinsic immunity, with important implications for cGAS-STING in integrating inflammatory and microbial cues for host defense.
Collapse
Affiliation(s)
- Lauren D Aarreberg
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Katharina Esser-Nobis
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Connor Driscoll
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Andrey Shuvarikov
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Justin A Roby
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Michael Gale
- Center for Innate Immunity and Immune Disease, Department of Immunology, University of Washington School of Medicine, Seattle, WA 98109, USA.
| |
Collapse
|
5
|
Chow KT, Wilkins C, Narita M, Green R, Knoll M, Loo YM, Gale M. Differential and Overlapping Immune Programs Regulated by IRF3 and IRF5 in Plasmacytoid Dendritic Cells. THE JOURNAL OF IMMUNOLOGY 2018; 201:3036-3050. [PMID: 30297339 DOI: 10.4049/jimmunol.1800221] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 09/13/2018] [Indexed: 01/20/2023]
Abstract
We examined the signaling pathways and cell type-specific responses of IFN regulatory factor (IRF) 5, an immune-regulatory transcription factor. We show that the protein kinases IKKα, IKKβ, IKKε, and TANK-binding kinase 1 each confer IRF5 phosphorylation/dimerization, thus extending the family of IRF5 activator kinases. Among primary human immune cell subsets, we found that IRF5 is most abundant in plasmacytoid dendritic cells (pDCs). Flow cytometric cell imaging revealed that IRF5 is specifically activated by endosomal TLR signaling. Comparative analyses revealed that IRF3 is activated in pDCs uniquely through RIG-I-like receptor (RLR) signaling. Transcriptomic analyses of pDCs show that the partitioning of TLR7/IRF5 and RLR/IRF3 pathways confers differential gene expression and immune cytokine production in pDCs, linking IRF5 with immune regulatory and proinflammatory gene expression. Thus, TLR7/IRF5 and RLR-IRF3 partitioning serves to polarize pDC response outcome. Strategies to differentially engage IRF signaling pathways should be considered in the design of immunotherapeutic approaches to modulate or polarize the immune response for specific outcome.
Collapse
Affiliation(s)
- Kwan T Chow
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA 98109.,Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong Special Administrative Region; and
| | - Courtney Wilkins
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA 98109
| | - Miwako Narita
- Laboratory of Hematology and Oncology, Graduate School of Health Sciences, Niigata University, Niigata, Niigata Prefecture 950-2181, Japan
| | - Richard Green
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA 98109
| | - Megan Knoll
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA 98109
| | - Yueh-Ming Loo
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA 98109;
| | - Michael Gale
- Department of Immunology, Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA 98109;
| |
Collapse
|
6
|
Ahlers LRH, Bastos RG, Hiroyasu A, Goodman AG. Invertebrate Iridescent Virus 6, a DNA Virus, Stimulates a Mammalian Innate Immune Response through RIG-I-Like Receptors. PLoS One 2016; 11:e0166088. [PMID: 27824940 PMCID: PMC5100955 DOI: 10.1371/journal.pone.0166088] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 10/22/2016] [Indexed: 12/21/2022] Open
Abstract
Insects are not only major vectors of mammalian viruses, but are also host to insect-restricted viruses that can potentially be transmitted to mammals. While mammalian innate immune responses to arboviruses are well studied, less is known about how mammalian cells respond to viruses that are restricted to infect only invertebrates. Here we demonstrate that IIV-6, a DNA virus of the family Iridoviridae, is able to induce a type I interferon-dependent antiviral immune response in mammalian cells. Although IIV-6 is a DNA virus, we demonstrate that the immune response activated during IIV-6 infection is mediated by the RIG-I-like receptor (RLR) pathway, and not the canonical DNA sensing pathway via cGAS/STING. We further show that RNA polymerase III is required for maximal IFN-β secretion, suggesting that viral DNA is transcribed by this enzyme into an RNA species capable of activating the RLR pathway. Finally, we demonstrate that the RLR-driven mammalian innate immune response to IIV-6 is functionally capable of protecting cells from subsequent infection with the arboviruses Vesicular Stomatitis virus and Kunjin virus. These results represent a novel example of an invertebrate DNA virus activating a canonically RNA sensing pathway in the mammalian innate immune response, which reduces viral load of ensuing arboviral infection.
Collapse
Affiliation(s)
- Laura R. H. Ahlers
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
- NIH Protein Biotechnology Graduate Training Program, Washington State University, Pullman, Washington, United States of America
| | - Reginaldo G. Bastos
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
| | - Aoi Hiroyasu
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
| | - Alan G. Goodman
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
- * E-mail:
| |
Collapse
|
7
|
Targeting cell division cycle 25 homolog B to regulate influenza virus replication. J Virol 2013; 87:13775-84. [PMID: 24109234 DOI: 10.1128/jvi.01509-13] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Influenza virus is a worldwide global health concern causing seasonal morbidity mortality and economic burden. Chemotherapeutics is available; however, rapid emergence of drug-resistant influenza virus strains has reduced its efficacy. Thus, there is a need to discover novel antiviral agents. In this study, RNA interference (RNAi) was used to screen host genes required for influenza virus replication. One pro-influenza virus host gene identified was dual-specificity phosphatase cell division cycle 25 B (CDC25B). RNAi screening of CDC25B resulted in reduced influenza A virus replication, and a CDC25B small-molecule inhibitor (NSC95397) inhibited influenza A virus replication in a dose-dependent fashion. Viral RNA synthesis was reduced by NSC95397 in favor of increased beta interferon (IFN-β) expression, and NSC95397 was found to interfere with nuclear localization and chromatin association of NS1, an influenza virus protein. As NS1 has been shown to be chromatin associated and to suppress host transcription, it is likely that CDC25B supports NS1 nuclear function to hijack host transcription machinery in favor of viral RNA synthesis, a process that is blocked by NSC95397. Importantly, NSC95397 treatment protects mice against lethal influenza virus challenge. The findings establish CDC25B as a pro-influenza A virus host factor that may be targeted as a novel influenza A therapeutic strategy.
Collapse
|
8
|
Semler BL, Whelan SP. Methods to study RNA virus molecular biology. Methods 2013; 59:165-6. [DOI: 10.1016/j.ymeth.2013.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
|