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Itell HL, Humes D, Overbaugh J. Several cell-intrinsic effectors drive type I interferon-mediated restriction of HIV-1 in primary CD4 + T cells. Cell Rep 2023; 42:112556. [PMID: 37227817 PMCID: PMC10592456 DOI: 10.1016/j.celrep.2023.112556] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/30/2023] [Accepted: 05/05/2023] [Indexed: 05/27/2023] Open
Abstract
Type I interferon (IFN) upregulates proteins that inhibit HIV within infected cells. Prior studies have identified IFN-stimulated genes (ISGs) that impede lab-adapted HIV in cell lines, yet the ISG(s) that mediate IFN restriction in HIV target cells, primary CD4+ T cells, are unknown. Here, we interrogate ISG restriction of primary HIV in CD4+ T cells by performing CRISPR-knockout screens with a custom library that specifically targets ISGs expressed in CD4+ T cells. Our investigation identifies previously undescribed HIV-restricting ISGs (HM13, IGFBP2, LAP3) and finds that two factors characterized in other HIV infection models (IFI16 and UBE2L6) mediate IFN restriction in T cells. Inactivation of these five ISGs in combination further diminishes IFN's protective effect against diverse HIV strains. This work demonstrates that IFN restriction of HIV is multifaceted, resulting from several effectors functioning collectively, and establishes a primary cell ISG screening model to identify both single and combinations of HIV-restricting ISGs.
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Affiliation(s)
- Hannah L Itell
- Molecular and Cellular Biology PhD Program, University of Washington, Seattle, WA 98195, USA; Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Daryl Humes
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Julie Overbaugh
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
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2
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Itell HL, Humes D, Overbaugh J. Several cell-intrinsic effectors drive type I interferon-mediated restriction of HIV-1 in primary CD4 + T cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.07.527545. [PMID: 36798236 PMCID: PMC9934674 DOI: 10.1101/2023.02.07.527545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Type I interferon (IFN) upregulates proteins that inhibit HIV within infected cells. Prior studies have identified IFN-stimulated genes (ISGs) that impede lab-adapted HIV in cell lines, yet the ISG(s) that mediate IFN restriction in HIV target cells, primary CD4 + T cells, are unknown. Here, we interrogate ISG restriction of primary HIV in CD4 + T cells. We performed CRISPR-knockout screens using a custom library that specifically targets ISGs expressed in CD4 + T cells and validated top hits. Our investigation identified new HIV-restricting ISGs (HM13, IGFBP2, LAP3) and found that two previously studied factors (IFI16, UBE2L6) are IFN effectors in T cells. Inactivation of these five ISGs in combination further diminished IFN’s protective effect against six diverse HIV strains. This work demonstrates that IFN restriction of HIV is multifaceted, resulting from several effectors functioning collectively, and establishes a primary cell ISG screening model to identify both single and combinations of HIV-restricting ISGs.
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Affiliation(s)
- Hannah L. Itell
- Molecular and Cellular Biology PhD Program, University of Washington, Seattle, WA, 98109, USA
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Daryl Humes
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
- Present address: Tr1X Inc, La Jolla, CA, 92037, USA
| | - Julie Overbaugh
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
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3
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Jurczyszak D, Manganaro L, Buta S, Gruber C, Martin-Fernandez M, Taft J, Patel RS, Cipolla M, Alshammary H, Mulder LCF, Sachidanandam R, Bogunovic D, Simon V. ISG15 deficiency restricts HIV-1 infection. PLoS Pathog 2022; 18:e1010405. [PMID: 35333911 PMCID: PMC8986114 DOI: 10.1371/journal.ppat.1010405] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 04/06/2022] [Accepted: 02/28/2022] [Indexed: 01/01/2023] Open
Abstract
Type I interferons (IFN-Is) are a group of potent inflammatory and antiviral cytokines. They induce IFN stimulated genes (ISGs), which act as proinflammatory mediators, antiviral effectors, and negative regulators of the IFN-I signaling cascade itself. One such regulator is interferon stimulated gene 15 (ISG15). Humans with complete ISG15 deficiency express persistently elevated levels of ISGs, and consequently, exhibit broad spectrum resistance to viral infection. Here, we demonstrate that IFN-I primed fibroblasts derived from ISG15-deficient individuals are more resistant to infection with single-cycle HIV-1 compared to healthy control fibroblasts. Complementation with both wild-type (WT) ISG15 and ISG15ΔGG (incapable of ISGylation while retaining negative regulation activity) was sufficient to reverse this phenotype, restoring susceptibility to infection to levels comparable to WT cells. Furthermore, CRISPR-edited ISG15ko primary CD4+ T cells were less susceptible to HIV-1 infection compared to cells treated with non-targeting controls. Transcriptome analysis of these CRISPR-edited ISG15ko primary CD4+ T cells recapitulated the ISG signatures of ISG15 deficient patients. Taken together, we document that the increased broad-spectrum viral resistance in ISG15-deficiency also extends to HIV-1 and is driven by a combination of T-cell-specific ISGs, with both known and unknown functions, predicted to target HIV-1 replication at multiple steps. Type I interferons (IFN-Is) are a group of potent inflammatory and antiviral agents. They induce IFN stimulated genes (ISGs), which perform downstream functions to resolve viral infection, mediate the inflammatory response, as well as negatively regulate the IFN-I signaling cascade to prevent hyperinflammation. One such negative regulator is interferon stimulated gene 15 (ISG15). Humans that lack ISG15 have chronic, low levels of antiviral ISGs, and ensuing broad-spectrum resistance to viral infection. We demonstrate that IFN-I priming of ISG15-deficient cells leads to superior resistance to human immunodeficiency virus 1 (HIV-1) infection compared to IFN-I primed healthy control cells. This is true for fibroblast cell lines, as well as primary CD4+ T cells, the main target of HIV-1. Analysis of the gene expression profiles show that ISG15-knockout CD4+ T cells express similar inflammatory markers as ISG15-deficient patients. Overall, we show that the broad-spectrum viral resistance in ISG15-deficiency extends to HIV-1.
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Affiliation(s)
- Denise Jurczyszak
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
- Center for Inborn Errors of Immunity, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
| | - Lara Manganaro
- INGM-Istituto Nazionale di Genetica Molecolare, Virology, Milan, Italy
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), University of MIlan, Milan, Italy
| | - Sofija Buta
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
- Center for Inborn Errors of Immunity, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
| | - Conor Gruber
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
- Center for Inborn Errors of Immunity, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
| | - Marta Martin-Fernandez
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
- Center for Inborn Errors of Immunity, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
| | - Justin Taft
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
- Center for Inborn Errors of Immunity, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
| | - Roosheel S. Patel
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
- Center for Inborn Errors of Immunity, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
| | - Melissa Cipolla
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
- Center for Inborn Errors of Immunity, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
| | - Hala Alshammary
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
| | - Lubbertus C. F. Mulder
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
| | - Ravi Sachidanandam
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
| | - Dusan Bogunovic
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
- Center for Inborn Errors of Immunity, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
- * E-mail: (DB); (VS)
| | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York City, New York, United States of America
- * E-mail: (DB); (VS)
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4
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Concurrent administration of IFNα14 and cART in TKO-BLT mice enhances suppression of HIV-1 viremia but does not eliminate the latent reservoir. Sci Rep 2019; 9:18089. [PMID: 31792317 PMCID: PMC6889145 DOI: 10.1038/s41598-019-54650-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 11/15/2019] [Indexed: 01/31/2023] Open
Abstract
Combination antiretroviral therapy (cART) prevents HIV-1 replication but does not eliminate the latent reservoir and cure the infection. Type I interferons (IFN) mediate antiviral effects through different mechanisms than cART. We previously showed that IFNα14 is the most potent IFNα subtype against HIV-1 and that it can significantly reduce the HIV-1 proviral reservoir. This study sought to determine whether combining cART with IFNα14 therapy would produce greater reductions in HIV-1 viral and proviral loads than ART alone. Immunodeficient Rag2-/-γc-/-CD47-/- C57BL/6 mice were humanized by the BLT method, infected with HIV-1JR-CSF and the in vivo efficacy of cART was compared with combined cART/IFNα14 therapy. Infection was allowed to establish for 6 weeks prior to 4 weeks of treatment with oral cART either with or without IFNα14. Plasma viral RNA and splenic CD4+ T cell viral DNA levels were measured immediately after treatment and after 2 weeks of therapy interruption. Augmentation of cART with IFNα14 resulted in significantly enhanced suppression of HIV-1 plasma viremia. However, no significant reduction in total viral DNA was detectable. Furthermore, virus rebounded after treatment interruption to similar levels in both groups. Thus, augmentation of cART with IFNα14 resulted in a more pronounced reduction of HIV viremia levels over cART alone, but the effect was not potent enough to be detected at the viral DNA level or to prevent virus rebound following therapy interruption in immune system-humanized mice.
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5
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Dickow J, Francois S, Kaiserling RL, Malyshkina A, Drexler I, Westendorf AM, Lang KS, Santiago ML, Dittmer U, Sutter K. Diverse Immunomodulatory Effects of Individual IFNα Subtypes on Virus-Specific CD8 + T Cell Responses. Front Immunol 2019; 10:2255. [PMID: 31608062 PMCID: PMC6771563 DOI: 10.3389/fimmu.2019.02255] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 09/06/2019] [Indexed: 12/21/2022] Open
Abstract
Clinical administration of Interferon α (IFNα) resulted in limited therapeutic success against some viral infections. Immune modulation of CD8+ T cell responses during IFNα therapy is believed to play a pivotal role in promoting viral clearance. However, these clinical studies primarily focused on IFNα subtype 2. To date, the immunomodulatory roles of the remaining 10-13 IFNα subtypes remains poorly understood, thereby precluding assessments of their potential for more effective treatments. Here, we report that virus-specific CD8+ T cell responses were influenced to various extents by individual IFNα subtypes. IFNα4, 6, and 9 had the strongest effects on CD8+ T cells, including antiproliferative effects, improved cytokine production and cytotoxicity. Interestingly, augmented cytokine responses were dependent on IFNα subtype stimulation of dendritic cells (DCs), while antiproliferative effects and cytotoxicity were mediated by IFNAR signaling in either CD8+ T cells or DCs. Thus, precise modulation of virus-specific CD8+ T cell responses may be feasible for specific antiviral immunotherapies through careful selection and administration of individual IFNα subtypes.
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Affiliation(s)
- Julia Dickow
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Sandra Francois
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Rouven-Luca Kaiserling
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Anna Malyshkina
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Ingo Drexler
- Institute of Virology, University Hospital Duesseldorf, Heinrich Heine University Duesseldorf, Düsseldorf, Germany
| | - Astrid Maria Westendorf
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Karl Sebastian Lang
- Institute for Immunology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Mario L. Santiago
- Department of Medicine, University of Colorado Denver, Aurora, CO, United States
| | - Ulf Dittmer
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Kathrin Sutter
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
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6
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He B, Tran JT, Sanchez DJ. Manipulation of Type I Interferon Signaling by HIV and AIDS-Associated Viruses. J Immunol Res 2019; 2019:8685312. [PMID: 31089479 PMCID: PMC6476103 DOI: 10.1155/2019/8685312] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 02/14/2019] [Indexed: 12/20/2022] Open
Abstract
Type I Interferons were first described for their profound antiviral abilities in cell culture and animal models, and later, they were translated into potent antiviral therapeutics. However, as additional studies into the function of Type I Interferons progressed, it was also seen that pathogenic viruses have coevolved to encode potent mechanisms allowing them to evade or suppress the impact of Type I Interferons on their replication. For chronic viral infections, such as HIV and many of the AIDS-associated viruses, including HTLV, HCV, KSHV, and EBV, the clinical efficacy of Type I Interferons is limited by these mechanisms. Here, we review some of the ways that HIV and AIDS-associated viruses thrive in Type I Interferon-rich environments via mechanisms that block the function of this important antiviral cytokine. Overall, a better understanding of these mechanisms creates avenues to better understand the innate immune response to these viruses as well as plan the development of antivirals that would allow the natural antiviral effect of Type I Interferons to manifest during these infections.
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Affiliation(s)
- Buyuan He
- Pharmaceutical Sciences Department, College of Pharmacy, Western University of Health Sciences, Pomona 91766, California, USA
| | - James T. Tran
- Pharmaceutical Sciences Department, College of Pharmacy, Western University of Health Sciences, Pomona 91766, California, USA
| | - David Jesse Sanchez
- Pharmaceutical Sciences Department, College of Pharmacy, Western University of Health Sciences, Pomona 91766, California, USA
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7
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SAMHD1 Phosphorylation Coordinates the Anti-HIV-1 Response by Diverse Interferons and Tyrosine Kinase Inhibition. mBio 2018; 9:mBio.00819-18. [PMID: 29764952 PMCID: PMC5954222 DOI: 10.1128/mbio.00819-18] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Macrophages are susceptible to human immunodeficiency virus type 1 (HIV-1) infection despite abundant expression of antiviral proteins. Perhaps the most important antiviral protein is the restriction factor sterile alpha motif domain and histidine/aspartic acid domain-containing protein 1 (SAMHD1). We investigated the role of SAMHD1 and its phospho-dependent regulation in the context of HIV-1 infection in primary human monocyte-derived macrophages and the ability of various interferons (IFNs) and pharmacologic agents to modulate SAMHD1. Here we show that stimulation by type I, type II, and to a lesser degree, type III interferons share activation of SAMHD1 via dephosphorylation at threonine-592 as a consequence of signaling. Cyclin-dependent kinase 1 (CDK1), a known effector kinase for SAMHD1, was downregulated at the protein level by all IFN types tested. Pharmacologic inhibition or small interfering RNA (siRNA)-mediated knockdown of CDK1 phenocopied the effects of IFN on SAMHD1. A panel of FDA-approved tyrosine kinase inhibitors potently induced activation of SAMHD1 and subsequent HIV-1 inhibition. The viral restriction imposed via IFNs or dasatinib could be overcome through depletion of SAMHD1, indicating that their effects are exerted primarily through this pathway. Our results demonstrate that SAMHD1 activation, but not transcriptional upregulation or protein induction, is the predominant mechanism of HIV-1 restriction induced by type I, type II, and type III IFN signaling in macrophages. Furthermore, SAMHD1 activation presents a pharmacologically actionable target through which HIV-1 infection can be subverted. Our experimental results demonstrate that SAMHD1 dephosphorylation at threonine-592 represents a central mechanism of HIV-1 restriction that is common to the three known families of IFNs. While IFN types I and II were potent inhibitors of HIV-1, type III IFN showed modest to undetectable activity. Regulation of SAMHD1 by IFNs involved changes in phosphorylation status but not in protein levels. Phosphorylation of SAMHD1 in macrophages occurred at least in part via CDK1. Tyrosine kinase inhibitors similarly induced SAMHD1 dephosphorylation, which protects macrophages from HIV-1 in a SAMHD1-dependent manner. SAMHD1 is a critical restriction factor regulating HIV-1 infection of macrophages.
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8
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Knuschke T, Rotan O, Bayer W, Kollenda S, Dickow J, Sutter K, Hansen W, Dittmer U, Lang KS, Epple M, Buer J, Westendorf AM. Induction of Type I Interferons by Therapeutic Nanoparticle-Based Vaccination Is Indispensable to Reinforce Cytotoxic CD8 + T Cell Responses During Chronic Retroviral Infection. Front Immunol 2018; 9:614. [PMID: 29740425 PMCID: PMC5924795 DOI: 10.3389/fimmu.2018.00614] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 03/12/2018] [Indexed: 11/29/2022] Open
Abstract
T cell dysfunction and immunosuppression are characteristic for chronic viral infections and contribute to viral persistence. Overcoming these burdens is the goal of new therapeutic strategies to cure chronic infectious diseases. We recently described that therapeutic vaccination of chronic retrovirus infected mice with a calcium phosphate (CaP) nanoparticle (NP)-based vaccine carrier, functionalized with CpG and viral peptides is able to efficiently reactivate the CD8+ T cell response and improve the eradication of virus infected cells. However, the mechanisms underlying this effect were largely unclear. While type I interferons (IFNs I) are considered to drive T cell exhaustion by persistent immune activation during chronic viral infection, we here describe an indispensable role of IFN I induced by therapeutic vaccination to efficiently reinforce cytotoxic CD8+ T cells (CTL) and improve control of chronic retroviral infection. The induction of IFN I is CpG dependent and leads to significant IFN signaling indicated by upregulation of IFN stimulated genes. By vaccinating chronically retrovirus-infected mice lacking the IFN I receptor (IFNAR−/−) or by blocking IFN I signaling in vivo during therapeutic vaccination, we demonstrate that IFN I signaling is necessary to drive full reactivation of CTLs. Surprisingly, we also identified an impaired suppressive capability of regulatory T cells in the presence of IFNα, which implicates an important role for vaccine-induced IFNα in the regulation of the T cell response during chronic retroviral infection. Our data suggest that inducing IFN I signaling in conjunction with the presentation of viral antigens can reactivate immune functions and reduce viral loads in chronic infections. Therefore, we propose CaP NPs as potential therapeutic tool to treat chronic infections.
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Affiliation(s)
- Torben Knuschke
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Olga Rotan
- Institute of Inorganic Chemistry, Center for Nanointegration Duisburg-Essen (CeNIDE), University of Duisburg-Essen, Essen, Germany
| | - Wibke Bayer
- Institute of Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Sebastian Kollenda
- Institute of Inorganic Chemistry, Center for Nanointegration Duisburg-Essen (CeNIDE), University of Duisburg-Essen, Essen, Germany
| | - Julia Dickow
- Institute of Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Kathrin Sutter
- Institute of Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Wiebke Hansen
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Ulf Dittmer
- Institute of Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Karl S Lang
- Institute for Immunology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Matthias Epple
- Institute of Inorganic Chemistry, Center for Nanointegration Duisburg-Essen (CeNIDE), University of Duisburg-Essen, Essen, Germany
| | - Jan Buer
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Astrid M Westendorf
- Institute of Medical Microbiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
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9
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Echebli N, Tchitchek N, Dupuy S, Bruel T, Peireira Bittencourt Passaes C, Bosquet N, Le Grand R, Bourgeois C, Favier B, Cheynier R, Lambotte O, Vaslin B. Stage-specific IFN-induced and IFN gene expression reveal convergence of type I and type II IFN and highlight their role in both acute and chronic stage of pathogenic SIV infection. PLoS One 2018; 13:e0190334. [PMID: 29324751 PMCID: PMC5764266 DOI: 10.1371/journal.pone.0190334] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 12/12/2017] [Indexed: 02/07/2023] Open
Abstract
Interferons (IFNs) play a major role in controlling viral infections including HIV/SIV infections. Persistent up-regulation of interferon stimulated genes (ISGs) is associated with chronic immune activation and progression in SIV/HIV infections, but the respective contribution of different IFNs is unclear. We analyzed the expression of IFN genes and ISGs in tissues of SIV infected macaques to understand the respective roles of type I and type II IFNs. Both IFN types were induced in lymph nodes during early stage of primary infection and to some extent in rectal biopsies but not in PBMCs. Induction of Type II IFN expression persisted during the chronic phase, in contrast to undetectable induction of type I IFN expression. Global gene expression analysis with a major focus on ISGs revealed that at both acute and chronic infection phases most differentially expressed ISGs were inducible by both type I and type II IFNs and displayed the highest increases, indicating strong convergence and synergy between type I and type II IFNs. The analysis of functional signatures of ISG expression revealed temporal changes in IFN expression patterns identifying phase-specific ISGs. These results suggest that IFN-γ strongly contribute to shape ISG upregulation in addition to type I IFN.
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Affiliation(s)
- Nadia Echebli
- CEA, Université Paris Sud, INSERM U1184, Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department / IBFJ, Fontenay-aux-Roses, France
| | - Nicolas Tchitchek
- CEA, Université Paris Sud, INSERM U1184, Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department / IBFJ, Fontenay-aux-Roses, France
| | - Stéphanie Dupuy
- CEA, Université Paris Sud, INSERM U1184, Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department / IBFJ, Fontenay-aux-Roses, France
| | - Timothée Bruel
- CEA, Université Paris Sud, INSERM U1184, Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department / IBFJ, Fontenay-aux-Roses, France
| | - Caroline Peireira Bittencourt Passaes
- CEA, Université Paris Sud, INSERM U1184, Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department / IBFJ, Fontenay-aux-Roses, France
| | - Nathalie Bosquet
- CEA, Université Paris Sud, INSERM U1184, Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department / IBFJ, Fontenay-aux-Roses, France
| | - Roger Le Grand
- CEA, Université Paris Sud, INSERM U1184, Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department / IBFJ, Fontenay-aux-Roses, France
| | - Christine Bourgeois
- CEA, Université Paris Sud, INSERM U1184, Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department / IBFJ, Fontenay-aux-Roses, France
| | - Benoit Favier
- CEA, Université Paris Sud, INSERM U1184, Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department / IBFJ, Fontenay-aux-Roses, France
| | - Rémi Cheynier
- Cytokines and Viral Infections, Immunology Infection and Inflammation Department, Institut Cochin, INSERM U1016, Paris, France
- CNRS, UMR8104, Paris, France
- Université Paris Descartes, Paris, France
| | - Olivier Lambotte
- CEA, Université Paris Sud, INSERM U1184, Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department / IBFJ, Fontenay-aux-Roses, France
- APHP, Service de Médecine Interne–Immunologie Clinique, Hôpitaux Universitaires Paris Sud, Le Kremlin-Bicêtre, France
| | - Bruno Vaslin
- CEA, Université Paris Sud, INSERM U1184, Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department / IBFJ, Fontenay-aux-Roses, France
- * E-mail:
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10
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Sandstrom TS, Ranganath N, Angel JB. Impairment of the type I interferon response by HIV-1: Potential targets for HIV eradication. Cytokine Growth Factor Rev 2017; 37:1-16. [PMID: 28455216 DOI: 10.1016/j.cytogfr.2017.04.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 04/20/2017] [Accepted: 04/21/2017] [Indexed: 12/11/2022]
Abstract
By interfering with the type I interferon (IFN1) response, human immunodeficiency virus 1 (HIV-1) can circumvent host antiviral signalling and establish persistent viral reservoirs. HIV-1-mediated defects in the IFN pathway are numerous, and include the impairment of protein receptors involved in pathogen detection, downstream signalling cascades required for IFN1 upregulation, and expression or function of key IFN1-inducible, antiviral proteins. Despite this, the activation of IFN1-inducible, antiviral proteins has been shown to facilitate the killing of latently HIV-infected cells in vitro. Understanding how IFN1 signalling is blocked in physiologically-relevant models of HIV-1 infection, and whether these defects can be reversed, is therefore of great importance for the development of novel therapeutic strategies aimed at eradicating the HIV-1 reservoir.
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Affiliation(s)
- Teslin S Sandstrom
- Ottawa Hospital Research Institute, ORCC Room C4445, 501 Smyth Road, Ottawa, ON, K1H 8L6, Canada; Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, K1H 8M5, Canada.
| | - Nischal Ranganath
- Ottawa Hospital Research Institute, ORCC Room C4445, 501 Smyth Road, Ottawa, ON, K1H 8L6, Canada; Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, K1H 8M5, Canada.
| | - Jonathan B Angel
- Ottawa Hospital Research Institute, ORCC Room C4445, 501 Smyth Road, Ottawa, ON, K1H 8L6, Canada; Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, K1H 8M5, Canada; Division of Infectious Diseases, Ottawa Hospital-General Campus, 501 Smyth Road, Ottawa, ON, K1H 8L6, Canada.
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11
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Vanwalscappel B, Rato S, Perez-Olmeda M, Díez Fuertes F, Casartelli N, Alcami J, Mammano F. Genetic and phenotypic analyses of sequential vpu alleles from HIV-infected IFN-treated patients. Virology 2016; 500:247-258. [PMID: 27855354 DOI: 10.1016/j.virol.2016.10.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 10/24/2016] [Accepted: 10/25/2016] [Indexed: 02/06/2023]
Abstract
Treatment of HIV-infected patients with IFN-α results in significant, but clinically insufficient, reductions of viremia. IFN induces the expression of several antiviral proteins including BST-2, which inhibits HIV by multiple mechanisms. The viral protein Vpu counteracts different effects of BST-2. We thus asked if Vpu proteins from IFN-treated patients displayed improved anti-BST-2 activities as compared to Vpu from baseline. Deep-sequencing analyses revealed that in five of seven patients treated by IFN-α for a concomitant HCV infection in the absence of antiretroviral drugs, the dominant Vpu sequences differed before and during treatment. In three patients, vpu alleles that emerged during treatment improved virus replication in the presence of IFN-α, and two of them conferred improved virus budding from cells expressing BST-2. Differences were observed for the ability to down-regulate CD4, while all Vpu variants potently down-modulated BST-2 from the cell surface. This report discloses relevant consequences of IFN-treatment on HIV properties.
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Affiliation(s)
- Bénédicte Vanwalscappel
- INSERM, U941, Paris F-75010, France; Univ Paris Diderot, Sorbonne Paris Cité, F-75475 Paris, France
| | | | - Mayte Perez-Olmeda
- AIDS Immunopathogenesis Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Francisco Díez Fuertes
- AIDS Immunopathogenesis Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | | | - José Alcami
- AIDS Immunopathogenesis Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain.
| | - Fabrizio Mammano
- INSERM, U941, Paris F-75010, France; Univ Paris Diderot, Sorbonne Paris Cité, F-75475 Paris, France.
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12
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Teijaro JR. Type I interferons in viral control and immune regulation. Curr Opin Virol 2016; 16:31-40. [PMID: 26812607 PMCID: PMC4821698 DOI: 10.1016/j.coviro.2016.01.001] [Citation(s) in RCA: 156] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 12/24/2015] [Accepted: 01/05/2016] [Indexed: 02/07/2023]
Abstract
Type 1 interferons (IFN-I) exert pleiotropic biological effects during viral infections, all which contribute to balancing virus control and immune pathology. Despite extensive antiviral functions that subdue virus replication, recent studies demonstrate pathogenic and pro-viral roles for IFN-I signaling during acute and persistent virus infection. IFN-I signaling can promote morbidity and mortality through induction of aberrant inflammatory responses during acute viral infection. In contrast, IFN-I signaling during persistent viral infection supports immune suppression, lymphoid tissue disorganization and CD4 T cell dysfunction. Systematic characterization of the cellular populations and intricacies of IFN-I signaling that promote pathology or immune suppression during acute and persistent viral infections, respectively, should inform the development of treatments and modalities to control viral associated pathologies.
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Affiliation(s)
- John R Teijaro
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, United States; Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, United States.
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13
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Asmuth DM, Utay NS, Pollard RB. Peginterferon α-2a for the treatment of HIV infection. Expert Opin Investig Drugs 2016; 25:249-57. [PMID: 26667398 DOI: 10.1517/13543784.2016.1132699] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
INTRODUCTION Novel approaches are urgently needed to achieve the next level of control of HIV infection beyond antiretroviral medications that will lead to the ultimate goal of curing HIV infection. Exploiting the innate immune system control of HIV is one possible component of that strategy with pegylated interferon α representing a well-characterized agent that is being applied to this effort. AREAS COVERED In this review, the authors summarize the history of interferon α treatment in the setting of HIV infection with a focus on clinical trials that examined the downstream effects on innate immune responses. More recently, clinical trials that administered pegylated interferon α-2a have demonstrated which interferon-stimulated genes are associated with its antiviral effects and which of these host-restriction factors may play a role in limiting the magnitude of the HIV reservoir. EXPERT OPINION The potential to exploit interferon α as part of a cure strategy is provocative. Whether key interferon-induced antiviral factors can be upregulated sufficiently to affect the reservoir is unknown. Additional research employing pegylated interferon α-2a is needed to identify which innate immune pathways are candidate targets for novel biological therapies for the potential cure of HIV infection.
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Affiliation(s)
- David M Asmuth
- a Department of Internal Medicine , University of California Davis Medical Center , Sacramento , CA , USA
| | - Netanya S Utay
- b Department of Internal Medicine , University of Texas Medical Branch , Galveston , TX , USA
| | - Richard B Pollard
- a Department of Internal Medicine , University of California Davis Medical Center , Sacramento , CA , USA
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14
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Abstract
Since Isaac's and Lindenmann's seminal experiments over 50 years ago demonstrating a soluble factor generated from heat killed virus-stimulated chicken embryos could inhibit live influenza virus replication, the term interferon has been synonymous with inhibition of virus replication. While the antiviral properties of type 1 interferon (IFN-I) are undeniable, recent studies have reported expanding and somewhat unexpected roles of IFN-I signaling during both acute and persistent viral infections. IFN-I signaling can promote morbidity and mortality through induction of aberrant inflammatory responses and recruitment of inflammatory innate immune cell populations during acute respiratory viral infections. During persistent viral infection, IFN-I signaling promotes containment of early viral replication/dissemination, however, also initiates and maintains immune suppression, lymphoid tissue disorganization, and CD4 T cell dysfunction through modulation of multiple immune cell populations. Finally, new data are emerging illuminating how specific IFN-I species regulate immune pathology and suppression during acute and persistent viral infections, respectively. Systematic characterization of the cellular populations that produce IFN-I, how the timing of IFN-I induction and intricacies of subtype specific IFN-I signaling promote pathology or immune suppression during acute and persistent viral infections should inform the development of treatments and modalities to control viral associated pathologies.
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15
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Katsounas A, Frank AC, Lempicki RA, Polis MA, Asmuth DM, Kottilil S. Differential Specificity of Interferon-alpha Inducible Gene Expression in Association with Human Immunodeficiency Virus and Hepatitis C Virus Levels and Declines in vivo. JOURNAL OF AIDS & CLINICAL RESEARCH 2015; 6:1000410. [PMID: 26052470 PMCID: PMC4456029 DOI: 10.4172/2155-6113.1000410] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
OBJECTIVE This study was aimed to correlate in vivo interferon (IFN) inducible gene (IFIG) expression and IFIG induction with viral-load (VL) and VL-kinetics of Human-Immunodeficiency-Virus (HIV) or Hepatitis-C-Virus (HCV) in HIV-positive patients treated with pegylated IFN-alpha-2a (PegIFNα). METHODS HIV mono-infected patients (N=8) and HIV/HCV co-infected patients (N=23, without HIV-viremia) were treated with PegIFNα (180 μg/week) for 12 and 48 weeks, respectively. Blood sampling for monitoring IFIG expression occurred at day_0 and week_3, _6 and _12 for HIV mono-infected patients vs. only at day_0 and week_48 for HIV/HCV co-infected subjects. IFIG expression (N=20) was measured in peripheral blood mononuclear cells by bDNA-assay. VL levels/changes in plasma were analyzed for correlation with IFIG expression/induction at/between selected time points. Overall, P<0.05 was considered significant. RESULTS None of the 20 IFIG expression profiles at day_0 correlated significantly with HIV-VL at day_0. Expression at day_0 of 3 IFIG (APOBEC3G/OAS1/OAS2) correlated significantly (r>+0.42/P<0.05) with HCV-VL at day_0. The strongest antiviral effect [measured as median viral decline per week: ΔVL/week (log10)] occurred in common against HIV and HCV between day_0 and week_3 during 12 weeks of continuous PegIFNα treatment in both cohorts. Expression at day_0 of 1 IFIG (APOBEC3A) correlated significantly (r<-0.71/P<0.05) with HIV-ΔVL/week (log10) from day_0 to week_3. No significance was reached in correlations between expression values of 20 IFIG at day_0 and HCV-ΔVL/week (log10) from day_0 to week_3. No significant correlation was detected between IFIG expression changes (ΔIFIG=induction) from day_0 to week_3 and HIV-ΔVL/week (log10) from day_0 to week_3. Interestingly, induction of 1 IFIG (ΔISG20) from day_0 to week_48 was significantly associated (P<0.05) with permanent HCV clearance. CONCLUSION This study demonstrates the differential specificity of PegIFNα mediated molecular actions by dissecting the kinetics of IFIG expression and induction, suggesting multiple, possibly non-overlapping mechanisms for antiviral effects against HCV and HIV.
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Affiliation(s)
- Antonios Katsounas
- Department of Gastroenterology and Hepatology, University Hospital Essen, Hufelandstrasse 55, 45147 Essen, Germany
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 10 Center Dr., Bethesda, MD 20892, USA
| | - Astrid C Frank
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 10 Center Dr., Bethesda, MD 20892, USA
| | - Richard A Lempicki
- Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Michael A Polis
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 10 Center Dr., Bethesda, MD 20892, USA
| | - David M Asmuth
- Division of Infectious and Immunologic Diseases, UC Davis, Medical Center 4150 V Street, PSSB G500 Sacramento, CA 95817, USA
| | - Shyam Kottilil
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 10 Center Dr., Bethesda, MD 20892, USA
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16
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Doyle T, Goujon C, Malim MH. HIV-1 and interferons: who's interfering with whom? Nat Rev Microbiol 2015; 13:403-13. [PMID: 25915633 DOI: 10.1038/nrmicro3449] [Citation(s) in RCA: 224] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The ability of interferons (IFNs) to inhibit HIV-1 replication in cell culture models has long been recognized, and the therapeutic administration of IFNα to HIV-1-infected patients who are not receiving antiretroviral therapy produces a clear but transient decrease in plasma viral load. Conversely, studies of chronic HIV-1 infection in humans and SIV-infected animal models of AIDS show positive correlations between elevated plasma levels of IFNs, increased expression of IFN-stimulated genes (ISGs), biomarkers of inflammation and disease progression. In this Review, we discuss the evidence that IFNs can control HIV-1 replication in vivo and debate the controversial role of IFNs in promoting the pathological sequelae of chronic HIV-1 infection.
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Affiliation(s)
- Tomas Doyle
- Department of Infectious Diseases, King's College London, 2nd Floor, Borough Wing, Guy's Hospital, London Bridge, London SE1 9RT, UK
| | - Caroline Goujon
- Department of Infectious Diseases, King's College London, 2nd Floor, Borough Wing, Guy's Hospital, London Bridge, London SE1 9RT, UK
| | - Michael H Malim
- Department of Infectious Diseases, King's College London, 2nd Floor, Borough Wing, Guy's Hospital, London Bridge, London SE1 9RT, UK
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17
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Abdel-Mohsen M, Deng X, Danesh A, Liegler T, Jacobs ES, Rauch A, Ledergerber B, Norris PJ, Günthard HF, Wong JK, Pillai SK. Role of microRNA modulation in the interferon-α/ribavirin suppression of HIV-1 in vivo. PLoS One 2014; 9:e109220. [PMID: 25275557 PMCID: PMC4183579 DOI: 10.1371/journal.pone.0109220] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 08/29/2014] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Interferon-α (IFN-α) treatment suppresses HIV-1 viremia and reduces the size of the HIV-1 latent reservoir. Therefore, investigation of the molecular and immunologic effects of IFN-α may provide insights that contribute to the development of novel prophylactic, therapeutic and curative strategies for HIV-1 infection. In this study, we hypothesized that microRNAs (miRNAs) contribute to the IFN-α-mediated suppression of HIV-1. To inform the development of novel miRNA-based antiretroviral strategies, we investigated the effects of exogenous IFN-α treatment on global miRNA expression profile, HIV-1 viremia, and potential regulatory networks between miRNAs and cell-intrinsic anti-HIV-1 host factors in vivo. METHODS Global miRNA expression was examined in longitudinal PBMC samples obtained from seven HIV/HCV-coinfected, antiretroviral therapy-naïve individuals before, during, and after pegylated interferon-α/ribavirin therapy (IFN-α/RBV). We implemented novel hybrid computational-empirical approaches to characterize regulatory networks between miRNAs and anti-HIV-1 host restriction factors. RESULTS miR-422a was the only miRNA significantly modulated by IFN-α/RBV in vivo (p<0.0001, paired t test; FDR<0.037). Our interactome mapping revealed extensive regulatory involvement of miR-422a in p53-dependent apoptotic and pyroptotic pathways. Based on sequence homology and inverse expression relationships, 29 unique miRNAs may regulate anti-HIV-1 restriction factor expression in vivo. CONCLUSIONS The specific reduction of miR-422a is associated with exogenous IFN-α treatment, and likely contributes to the IFN-α suppression of HIV-1 through the enhancement of anti-HIV-1 restriction factor expression and regulation of genes involved in programmed cell death. Moreover, our regulatory network analysis presents additional candidate miRNAs that may be targeted to enhance anti-HIV-1 restriction factor expression in vivo.
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Affiliation(s)
- Mohamed Abdel-Mohsen
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
- Blood Systems Research Institute, San Francisco, California, United States of America
| | - Xutao Deng
- Blood Systems Research Institute, San Francisco, California, United States of America
| | - Ali Danesh
- Blood Systems Research Institute, San Francisco, California, United States of America
| | - Teri Liegler
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Evan S. Jacobs
- Blood Systems Research Institute, San Francisco, California, United States of America
| | - Andri Rauch
- Department of Infectious Diseases, Bern University Hospital and University of Bern, Bern, Switzerland
| | - Bruno Ledergerber
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Philip J. Norris
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
- Blood Systems Research Institute, San Francisco, California, United States of America
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Huldrych F. Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Joseph K. Wong
- Department of Medicine, San Francisco Veterans Affairs Medical Center, San Francisco, California, United States of America
| | - Satish K. Pillai
- Blood Systems Research Institute, San Francisco, California, United States of America
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America
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18
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Abdel-Mohsen M, Deng X, Liegler T, Guatelli JC, Salama MS, Ghanem HEDA, Rauch A, Ledergerber B, Deeks SG, Günthard HF, Wong JK, Pillai SK. Effects of alpha interferon treatment on intrinsic anti-HIV-1 immunity in vivo. J Virol 2014; 88:763-7. [PMID: 24155399 PMCID: PMC3911728 DOI: 10.1128/jvi.02687-13] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 10/17/2013] [Indexed: 12/29/2022] Open
Abstract
Alpha interferon (IFN-α) suppresses human immunodeficiency virus type 1 (HIV-1) replication in vitro by inducing cell-intrinsic retroviral restriction mechanisms. We investigated the effects of IFN-α/ribavirin (IFN-α/riba) treatment on 34 anti-HIV-1 restriction factors in vivo. Expression of several anti-HIV-1 restriction factors was significantly induced by IFN-α/riba in HIV/hepatitis C virus (HCV)-coinfected individuals. Fold induction of cumulative restriction factor expression in CD4(+) T cells was significantly correlated with viral load reduction during IFN-α/riba treatment (r(2) = 0.649; P < 0.016). Exogenous IFN-α induces supraphysiologic restriction factor expression associated with a pronounced decrease in HIV-1 viremia.
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Affiliation(s)
- Mohamed Abdel-Mohsen
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
- Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Xutao Deng
- Blood Systems Research Institute, San Francisco, California, USA
| | - Teri Liegler
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - John C. Guatelli
- University of California, San Diego, La Jolla, California, and VA San Diego Healthcare System, San Diego, California, USA
| | | | | | - Andri Rauch
- Department of Infectious Diseases, Bern University Hospital and University of Bern, Bern, Switzerland
| | - Bruno Ledergerber
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Steven G. Deeks
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Huldrych F. Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Joseph K. Wong
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
- Department of Medicine, San Francisco VA Medical Center, San Francisco, California, USA
| | - Satish K. Pillai
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
- Blood Systems Research Institute, San Francisco, California, USA
- Department of Medicine, San Francisco VA Medical Center, San Francisco, California, USA
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