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Gassen NC, Papies J, Bajaj T, Emanuel J, Dethloff F, Chua RL, Trimpert J, Heinemann N, Niemeyer C, Weege F, Hönzke K, Aschman T, Heinz DE, Weckmann K, Ebert T, Zellner A, Lennarz M, Wyler E, Schroeder S, Richter A, Niemeyer D, Hoffmann K, Meyer TF, Heppner FL, Corman VM, Landthaler M, Hocke AC, Morkel M, Osterrieder N, Conrad C, Eils R, Radbruch H, Giavalisco P, Drosten C, Müller MA. SARS-CoV-2-mediated dysregulation of metabolism and autophagy uncovers host-targeting antivirals. Nat Commun 2021; 12:3818. [PMID: 34155207 PMCID: PMC8217552 DOI: 10.1038/s41467-021-24007-w] [Citation(s) in RCA: 145] [Impact Index Per Article: 48.3] [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: 03/12/2021] [Accepted: 05/29/2021] [Indexed: 02/07/2023] Open
Abstract
Viruses manipulate cellular metabolism and macromolecule recycling processes like autophagy. Dysregulated metabolism might lead to excessive inflammatory and autoimmune responses as observed in severe and long COVID-19 patients. Here we show that SARS-CoV-2 modulates cellular metabolism and reduces autophagy. Accordingly, compound-driven induction of autophagy limits SARS-CoV-2 propagation. In detail, SARS-CoV-2-infected cells show accumulation of key metabolites, activation of autophagy inhibitors (AKT1, SKP2) and reduction of proteins responsible for autophagy initiation (AMPK, TSC2, ULK1), membrane nucleation, and phagophore formation (BECN1, VPS34, ATG14), as well as autophagosome-lysosome fusion (BECN1, ATG14 oligomers). Consequently, phagophore-incorporated autophagy markers LC3B-II and P62 accumulate, which we confirm in a hamster model and lung samples of COVID-19 patients. Single-nucleus and single-cell sequencing of patient-derived lung and mucosal samples show differential transcriptional regulation of autophagy and immune genes depending on cell type, disease duration, and SARS-CoV-2 replication levels. Targeting of autophagic pathways by exogenous administration of the polyamines spermidine and spermine, the selective AKT1 inhibitor MK-2206, and the BECN1-stabilizing anthelmintic drug niclosamide inhibit SARS-CoV-2 propagation in vitro with IC50 values of 136.7, 7.67, 0.11, and 0.13 μM, respectively. Autophagy-inducing compounds reduce SARS-CoV-2 propagation in primary human lung cells and intestinal organoids emphasizing their potential as treatment options against COVID-19.
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Affiliation(s)
- Nils C Gassen
- Department of Psychiatry and Psychotherapy, University of Bonn, Medical Faculty, Bonn, Germany.
| | - Jan Papies
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- German Center for Infection Research (DZIF), partner site Charité, Berlin, Germany
| | - Thomas Bajaj
- Department of Psychiatry and Psychotherapy, University of Bonn, Medical Faculty, Bonn, Germany
| | - Jackson Emanuel
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- German Center for Infection Research (DZIF), partner site Charité, Berlin, Germany
| | | | - Robert Lorenz Chua
- Center for Digital Health, Berlin Institute of Health (BIH) and Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jakob Trimpert
- Institute of Virology, Freie Universität Berlin, Berlin, Germany
| | - Nicolas Heinemann
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- German Center for Infection Research (DZIF), partner site Charité, Berlin, Germany
| | - Christine Niemeyer
- Department of Psychiatry and Psychotherapy, University of Bonn, Medical Faculty, Bonn, Germany
| | - Friderike Weege
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- German Center for Infection Research (DZIF), partner site Charité, Berlin, Germany
| | - Katja Hönzke
- Molecular Imaging of Immunoregulation, Medizinische Klinik m.S. Infektiologie & Pneumologie, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Tom Aschman
- Department of Neuropathology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Daniel E Heinz
- Department of Psychiatry and Psychotherapy, University of Bonn, Medical Faculty, Bonn, Germany
| | - Katja Weckmann
- Department of Psychiatry and Psychotherapy, University of Bonn, Medical Faculty, Bonn, Germany
| | - Tim Ebert
- Department of Psychiatry and Psychotherapy, University of Bonn, Medical Faculty, Bonn, Germany
| | - Andreas Zellner
- Department of Psychiatry and Psychotherapy, University of Bonn, Medical Faculty, Bonn, Germany
| | - Martina Lennarz
- Department of Psychiatry and Psychotherapy, University of Bonn, Medical Faculty, Bonn, Germany
| | - Emanuel Wyler
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Simon Schroeder
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- German Center for Infection Research (DZIF), partner site Charité, Berlin, Germany
| | - Anja Richter
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- German Center for Infection Research (DZIF), partner site Charité, Berlin, Germany
| | - Daniela Niemeyer
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- German Center for Infection Research (DZIF), partner site Charité, Berlin, Germany
| | - Karen Hoffmann
- Molecular Imaging of Immunoregulation, Medizinische Klinik m.S. Infektiologie & Pneumologie, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Thomas F Meyer
- Laboratory of Infection Oncology, Institute of Clinical Molecular Biology, UKSH, Christian Albrechts University of Kiel, Kiel, Germany
| | - Frank L Heppner
- Department of Neuropathology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Cluster of Excellence, NeuroCure, Berlin, Germany
| | - Victor M Corman
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- German Center for Infection Research (DZIF), partner site Charité, Berlin, Germany
| | - Markus Landthaler
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- IRI Life Sciences, Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Andreas C Hocke
- Molecular Imaging of Immunoregulation, Medizinische Klinik m.S. Infektiologie & Pneumologie, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Markus Morkel
- Institute for Pathology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium (DKTK) Partner Site Berlin, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Nikolaus Osterrieder
- Institute of Virology, Freie Universität Berlin, Berlin, Germany
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong
| | - Christian Conrad
- Center for Digital Health, Berlin Institute of Health (BIH) and Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Roland Eils
- Center for Digital Health, Berlin Institute of Health (BIH) and Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- German Center for Lung Research (DZL), Berlin, Germany
- Data Science Unit, Heidelberg University Hospital and BioQuant, Heidelberg, Germany
| | - Helena Radbruch
- Department of Neuropathology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Christian Drosten
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- German Center for Infection Research (DZIF), partner site Charité, Berlin, Germany
| | - Marcel A Müller
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany.
- German Center for Infection Research (DZIF), partner site Charité, Berlin, Germany.
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, Moscow, Russia.
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