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Hirschenberger M, Hayn M, Laliberté A, Koepke L, Kirchhoff F, Sparrer KMJ. Luciferase reporter assays to monitor interferon signaling modulation by SARS-CoV-2 proteins. STAR Protoc 2021; 2:100781. [PMID: 34405154 PMCID: PMC8361205 DOI: 10.1016/j.xpro.2021.100781] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
We present a protocol for analyzing the impact of SARS-CoV-2 proteins in interferon signaling using luciferase reporter assays. Here, the induction of defined promoters can be quantitatively assessed with high sensitivity and broad linear range. The results are similar to those obtained using qPCR to measure endogenous mRNA induction. The assay requires stringent normalization and confirmation of the results in more physiological settings. The protocol is adaptable for other viruses and other innate immune stimuli. For complete details on the use and execution of this protocol, please refer to Hayn et al. (2021).
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Affiliation(s)
- Maximilian Hirschenberger
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Baden-Württemberg, Germany
| | - Manuel Hayn
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Baden-Württemberg, Germany
| | - Alexandre Laliberté
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Baden-Württemberg, Germany
| | - Lennart Koepke
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Baden-Württemberg, Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Baden-Württemberg, Germany
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Tripathi U, Nchioua R, Prata LGPL, Zhu Y, Gerdes EOW, Giorgadze N, Pirtskhalava T, Parker E, Xue A, Espindola-Netto JM, Stenger S, Robbins PD, Niedernhofer LJ, Dickinson SL, Allison DB, Kirchhoff F, Sparrer KMJ, Tchkonia T, Kirkland JL. SARS-CoV-2 causes senescence in human cells and exacerbates the senescence-associated secretory phenotype through TLR-3. Aging (Albany NY) 2021; 13:21838-21854. [PMID: 34531331 PMCID: PMC8507266 DOI: 10.18632/aging.203560] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [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: 08/20/2021] [Accepted: 09/14/2021] [Indexed: 12/15/2022]
Abstract
Senescent cells, which arise due to damage-associated signals, are apoptosis-resistant and can express a pro-inflammatory, tissue-destructive senescence-associated secretory phenotype (SASP). We recently reported that a component of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) surface protein, S1, can amplify the SASP of senescent cultured human cells and that a related mouse β-coronavirus, mouse hepatitis virus (MHV), increases SASP factors and senescent cell burden in infected mice. Here, we show that SARS-CoV-2 induces senescence in human non-senescent cells and exacerbates the SASP in human senescent cells through Toll-like receptor-3 (TLR-3). TLR-3, which senses viral RNA, was increased in human senescent compared to non-senescent cells. Notably, genetically or pharmacologically inhibiting TLR-3 prevented senescence induction and SASP amplification by SARS-CoV-2 or Spike pseudotyped virus. While an artificial TLR-3 agonist alone was not sufficient to induce senescence, it amplified the SASP in senescent human cells. Consistent with these findings, lung p16INK4a+ senescent cell burden was higher in patients who died from acute SARS-CoV-2 infection than other causes. Our results suggest that induction of cellular senescence and SASP amplification through TLR-3 contribute to SARS-CoV-2 morbidity, indicating that clinical trials of senolytics and/or SASP/TLR-3 inhibitors for alleviating acute and long-term SARS-CoV-2 sequelae are warranted.
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Affiliation(s)
- Utkarsh Tripathi
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN 55905, USA
| | - Rayhane Nchioua
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
| | | | - Yi Zhu
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN 55905, USA
- Department of Physiology and Bioengineering, Mayo Clinic, Rochester, MN 55905, USA
| | | | - Nino Giorgadze
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN 55905, USA
| | - Tamar Pirtskhalava
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN 55905, USA
| | - Erik Parker
- Department of Epidemiology and Biostatistics, School of Public Health, Indiana University-Bloomington, Bloomington, IN 47405, USA
| | - Ailing Xue
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN 55905, USA
| | | | - Steffen Stenger
- Institute for Medical Microbiology and Hygiene, Ulm University Medical Center, Ulm 89081, Germany
| | - Paul D. Robbins
- Institute on the Biology of Aging and Metabolism, Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Laura J. Niedernhofer
- Institute on the Biology of Aging and Metabolism, Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Stephanie L. Dickinson
- Department of Epidemiology and Biostatistics, School of Public Health, Indiana University-Bloomington, Bloomington, IN 47405, USA
| | - David B. Allison
- Department of Epidemiology and Biostatistics, School of Public Health, Indiana University-Bloomington, Bloomington, IN 47405, USA
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
| | | | - Tamar Tchkonia
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN 55905, USA
- Department of Physiology and Bioengineering, Mayo Clinic, Rochester, MN 55905, USA
| | - James L. Kirkland
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN 55905, USA
- Department of Physiology and Bioengineering, Mayo Clinic, Rochester, MN 55905, USA
- Division of General Internal Medicine, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
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Hirschenberger M, Hunszinger V, Sparrer KMJ. Implications of Innate Immunity in Post-Acute Sequelae of Non-Persistent Viral Infections. Cells 2021; 10:2134. [PMID: 34440903 PMCID: PMC8391718 DOI: 10.3390/cells10082134] [Citation(s) in RCA: 20] [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: 07/21/2021] [Revised: 08/12/2021] [Accepted: 08/18/2021] [Indexed: 02/06/2023] Open
Abstract
Non-persistent viruses classically cause transient, acute infections triggering immune responses aimed at the elimination of the pathogen. Successful viruses evolved strategies to manipulate and evade these anti-viral defenses. Symptoms during the acute phase are often linked to dysregulated immune responses that disappear once the patient recovers. In some patients, however, symptoms persist or new symptoms emerge beyond the acute phase. Conditions resulting from previous transient infection are termed post-acute sequelae (PAS) and were reported for a wide range of non-persistent viruses such as rota-, influenza- or polioviruses. Here we provide an overview of non-persistent viral pathogens reported to be associated with diverse PAS, among them chronic fatigue, auto-immune disorders, or neurological complications and highlight known mechanistic details. Recently, the emergence of post-acute sequelae of COVID-19 (PASC) or long COVID highlighted the impact of PAS. Notably, PAS of non-persistent infections often resemble symptoms of persistent viral infections, defined by chronic inflammation. Inflammation maintained after the acute phase may be a key driver of PAS of non-persistent viruses. Therefore, we explore current insights into aberrant activation of innate immune signaling pathways in the post-acute phase of non-persistent viruses. Finally, conclusions are drawn and future perspectives for treatment and prevention of PAS are discussed.
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Hayn M, Hirschenberger M, Koepke L, Nchioua R, Straub JH, Klute S, Hunszinger V, Zech F, Prelli Bozzo C, Aftab W, Christensen MH, Conzelmann C, Müller JA, Srinivasachar Badarinarayan S, Stürzel CM, Forne I, Stenger S, Conzelmann KK, Münch J, Schmidt FI, Sauter D, Imhof A, Kirchhoff F, Sparrer KMJ. Systematic functional analysis of SARS-CoV-2 proteins uncovers viral innate immune antagonists and remaining vulnerabilities. Cell Rep 2021; 35:109126. [PMID: 33974846 PMCID: PMC8078906 DOI: 10.1016/j.celrep.2021.109126] [Citation(s) in RCA: 147] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 03/03/2021] [Accepted: 04/22/2021] [Indexed: 12/23/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evades most innate immune responses but may still be vulnerable to some. Here, we systematically analyze the impact of SARS-CoV-2 proteins on interferon (IFN) responses and autophagy. We show that SARS-CoV-2 proteins synergize to counteract anti-viral immune responses. For example, Nsp14 targets the type I IFN receptor for lysosomal degradation, ORF3a prevents fusion of autophagosomes and lysosomes, and ORF7a interferes with autophagosome acidification. Most activities are evolutionarily conserved. However, SARS-CoV-2 Nsp15 antagonizes IFN signaling less efficiently than the orthologs of closely related RaTG13-CoV and SARS-CoV-1. Overall, SARS-CoV-2 proteins counteract autophagy and type I IFN more efficiently than type II or III IFN signaling, and infection experiments confirm potent inhibition by IFN-γ and -λ1. Our results define the repertoire and selected mechanisms of SARS-CoV-2 innate immune antagonists but also reveal vulnerability to type II and III IFN that may help to develop safe and effective anti-viral approaches.
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Affiliation(s)
- Manuel Hayn
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | | | - Lennart Koepke
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Rayhane Nchioua
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Jan Hendrik Straub
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Susanne Klute
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Victoria Hunszinger
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Fabian Zech
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | | | - Wasim Aftab
- Biomedical Center, Zentrallabor für Proteinanalytik (Protein Analysis Unit), Medical Faculty, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany; Graduate School for Quantitative Biosciences (QBM), Ludwig-Maximilians-University of Munich, 81377 Munich, Germany
| | | | - Carina Conzelmann
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | | | - Smitha Srinivasachar Badarinarayan
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany; Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, 72076 Tübingen, Germany
| | | | - Ignasi Forne
- Biomedical Center, Zentrallabor für Proteinanalytik (Protein Analysis Unit), Medical Faculty, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Steffen Stenger
- Institute for Medical Microbiology and Hygiene, Ulm University Medical Center, 89081 Ulm, Germany
| | - Karl-Klaus Conzelmann
- Max von Pettenkofer-Institute of Virology, Medical Faculty, and Gene Center, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Florian Ingo Schmidt
- Institute of Innate Immunity, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - Daniel Sauter
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany; Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Axel Imhof
- Biomedical Center, Zentrallabor für Proteinanalytik (Protein Analysis Unit), Medical Faculty, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
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