Virus-induced senescence is a driver and therapeutic target in COVID-19.
Soyoung Lee, Yong Yu, Jakob Trimpert, Fahad Benthani, Mario Mairhofer, Paulina Richter-Pechanska, Emanuel Wyler, Dimitri Belenki, Sabine Kaltenbrunner, Maria Pammer, Lea Kausche, Theresa C Firsching, Kristina Dietert, Michael Schotsaert, Carles Martínez-Romero, Gagandeep Singh, Séverine Kunz, Daniela Niemeyer, Riad Ghanem, Helmut J F Salzer, Christian Paar, Michael Mülleder, Melissa Uccellini, Edward G Michaelis, Amjad Khan, Andrea Lau, Martin Schönlein, Anna Habringer, Josef Tomasits, Julia M Adler, Susanne Kimeswenger, Achim D Gruber, Wolfram Hoetzenecker, Herta Steinkellner, Bettina Purfürst, Reinhard Motz, Francesco Di Pierro, Bernd Lamprecht, Nikolaus Osterrieder, Markus Landthaler, Christian Drosten, Adolfo García-Sastre, Rupert Langer, Markus Ralser, Roland Eils, Maurice Reimann, Dorothy N Y Fan, Clemens A Schmitt
Author Information
Soyoung Lee: Medical Department of Hematology, Oncology and Tumor Immunology, Molekulares Krebsforschungszentrum (MKFZ), Charité - Universitätsmedizin, Berlin, Germany. ORCID
Yong Yu: Medical Faculty, Johannes Kepler University, Linz, Austria.
Jakob Trimpert: Institute of Virology, Freie Universität Berlin, Berlin, Germany. ORCID
Fahad Benthani: Medical Faculty, Johannes Kepler University, Linz, Austria. ORCID
Mario Mairhofer: Medical Faculty, Johannes Kepler University, Linz, Austria.
Paulina Richter-Pechanska: Medical Department of Hematology, Oncology and Tumor Immunology, Molekulares Krebsforschungszentrum (MKFZ), Charité - Universitätsmedizin, Berlin, Germany.
Emanuel Wyler: Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany. ORCID
Dimitri Belenki: Medical Department of Hematology, Oncology and Tumor Immunology, Molekulares Krebsforschungszentrum (MKFZ), Charité - Universitätsmedizin, Berlin, Germany. ORCID
Sabine Kaltenbrunner: Medical Faculty, Johannes Kepler University, Linz, Austria.
Maria Pammer: Medical Faculty, Johannes Kepler University, Linz, Austria.
Lea Kausche: Medical Department of Hematology, Oncology and Tumor Immunology, Molekulares Krebsforschungszentrum (MKFZ), Charité - Universitätsmedizin, Berlin, Germany.
Theresa C Firsching: Institute of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany. ORCID
Kristina Dietert: Institute of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany.
Michael Schotsaert: Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. ORCID
Carles Martínez-Romero: Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. ORCID
Gagandeep Singh: Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. ORCID
Séverine Kunz: Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany. ORCID
Daniela Niemeyer: Institute of Virology, German Center for Infection Research (DZIF), Charité-Universitätsmedizin,, Berlin, Germany. ORCID
Riad Ghanem: Department of Hematology and Oncology, Kepler University Hospital, Linz, Austria.
Helmut J F Salzer: Department of Pulmonology, Kepler University Hospital, Linz, Austria.
Christian Paar: Laboratory Medicine, Kepler University Hospital, Linz, Austria.
Michael Mülleder: Core Facility - High-Throughput Mass Spectrometry and Department of Biochemistry, Charité - Universitätsmedizin, Berlin, Germany.
Melissa Uccellini: Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Edward G Michaelis: Institute of Pathology, Charité - Universitätsmedizin, Berlin, Germany.
Amjad Khan: Department of Chemistry, University of Oxford, Oxford, UK.
Andrea Lau: Medical Department of Hematology, Oncology and Tumor Immunology, Molekulares Krebsforschungszentrum (MKFZ), Charité - Universitätsmedizin, Berlin, Germany.
Martin Schönlein: Medical Department of Hematology, Oncology and Tumor Immunology, Molekulares Krebsforschungszentrum (MKFZ), Charité - Universitätsmedizin, Berlin, Germany.
Anna Habringer: Laboratory Medicine, Kepler University Hospital, Linz, Austria.
Josef Tomasits: Laboratory Medicine, Kepler University Hospital, Linz, Austria.
Julia M Adler: Institute of Virology, Freie Universität Berlin, Berlin, Germany.
Susanne Kimeswenger: Medical Faculty, Johannes Kepler University, Linz, Austria. ORCID
Achim D Gruber: Institute of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany. ORCID
Wolfram Hoetzenecker: Medical Faculty, Johannes Kepler University, Linz, Austria.
Herta Steinkellner: Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria.
Bettina Purfürst: Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
Reinhard Motz: Institute of Pathology, Kepler University Hospital, Linz, Austria.
Francesco Di Pierro: Scientific and Research Department, Velleja Research, Milan, Italy.
Bernd Lamprecht: Medical Faculty, Johannes Kepler University, Linz, Austria. ORCID
Nikolaus Osterrieder: Institute of Virology, Freie Universität Berlin, Berlin, Germany.
Markus Landthaler: Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany. ORCID
Christian Drosten: Institute of Virology, German Center for Infection Research (DZIF), Charité-Universitätsmedizin,, Berlin, Germany. ORCID
Adolfo García-Sastre: Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. ORCID
Rupert Langer: Medical Faculty, Johannes Kepler University, Linz, Austria.
Markus Ralser: Core Facility - High-Throughput Mass Spectrometry and Department of Biochemistry, Charité - Universitätsmedizin, Berlin, Germany.
Roland Eils: Center for Digital Health, Charité - Universitätsmedizin and Berlin Institute of Health (BIH), Berlin, Germany. ORCID
Maurice Reimann: Medical Department of Hematology, Oncology and Tumor Immunology, Molekulares Krebsforschungszentrum (MKFZ), Charité - Universitätsmedizin, Berlin, Germany.
Dorothy N Y Fan: Medical Department of Hematology, Oncology and Tumor Immunology, Molekulares Krebsforschungszentrum (MKFZ), Charité - Universitätsmedizin, Berlin, Germany.
Clemens A Schmitt: Medical Department of Hematology, Oncology and Tumor Immunology, Molekulares Krebsforschungszentrum (MKFZ), Charité - Universitätsmedizin, Berlin, Germany. clemens.schmitt@charite.de. ORCID
Derailed cytokine and immune cell networks account for the organ damage and the clinical severity of COVID-19 (refs. ). Here we show that SARS-CoV-2, like other viruses, evokes cellular senescence as a primary stress response in infected cells. Virus-induced senescence (VIS) is indistinguishable from other forms of cellular senescence and is accompanied by a senescence-associated secretory phenotype (SASP), which comprises pro-inflammatory cytokines, extracellular-matrix-active factors and pro-coagulatory mediators. Patients with COVID-19 displayed markers of senescence in their airway mucosa in situ and increased serum levels of SASP factors. In vitro assays demonstrated macrophage activation with SASP-reminiscent secretion, complement lysis and SASP-amplifying secondary senescence of endothelial cells, which mirrored hallmark features of COVID-19 such as macrophage and neutrophil infiltration, endothelial damage and widespread thrombosis in affected lung tissue. Moreover, supernatant from VIS cells, including SARS-CoV-2-induced senescence, induced neutrophil extracellular trap formation and activation of platelets and the clotting cascade. Senolytics such as navitoclax and a combination of dasatinib plus quercetin selectively eliminated VIS cells, mitigated COVID-19-reminiscent lung disease and reduced inflammation in SARS-CoV-2-infected hamsters and mice. Our findings mark VIS as a pathogenic trigger of COVID-19-related cytokine escalation and organ damage, and suggest that senolytic targeting of virus-infected cells is a treatment option against SARS-CoV-2 and perhaps other viral infections.
References
Zhang, X. et al. Viral and host factors related to the clinical outcome of COVID-19. Nature 583, 437–440 (2020).
[PMID: 32434211]
Mehta, P. et al. COVID-19: consider cytokine storm syndromes and immunosuppression. Lancet 395, 1033–1034 (2020).
[PMID: 32192578]
Merad, M. & Martin, J. C. Pathological inflammation in patients with COVID-19: a key role for monocytes and macrophages. Nat. Rev. Immunol. 20, 355–362 (2020).
[PMID: 32376901]
Blanco-Melo, D. et al. Imbalanced host response to SARS-CoV-2 drives development of COVID-19. Cell 181, 1036–1045.e9 (2020).
[PMID: 32416070]
Coppe, J. P., Desprez, P. Y., Krtolica, A. & Campisi, J. The senescence-associated secretory phenotype: the dark side of tumor suppression. Annu. Rev. Pathol. 5, 99–118 (2010).
[PMID: 20078217]
Lee, S. & Schmitt, C. A. The dynamic nature of senescence in cancer. Nat. Cell Biol. 21, 94–101 (2019).
[PMID: 30602768]
Wiley, C. D. et al. SILAC analysis reveals increased secretion of hemostasis-related factors by senescent cells. Cell Rep. 28, 3329–3337.e5 (2019).
[PMID: 31553904]
Ackermann, M. et al. Pulmonary vascular endothelialitis, thrombosis, and angiogenesis in Covid-19. N. Engl. J. Med. 383, 120–128 (2020).
[PMID: 32437596]
Middleton, E. A. et al. Neutrophil extracellular traps contribute to immunothrombosis in COVID-19 acute respiratory distress syndrome. Blood 136, 1169–1179 (2020).
[PMID: 32597954]
Berlin, D. A., Gulick, R. M. & Martinez, F. J. Severe Covid-19. N. Engl. J. Med. 383, 2451–2460 (2020).
[PMID: 32412710]
Wolfel, R. et al. Virological assessment of hospitalized patients with COVID-2019. Nature 581, 465–469 (2020).
[PMID: 32235945]
Hoffmann, M. et al. SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor. Cell 181, 271–280.e8 (2020).
[PMID: 32142651]
Ju, B. et al. Human neutralizing antibodies elicited by SARS-CoV-2 infection. Nature 584, 115–119 (2020).
[PMID: 32454513]
Horby, P. et al. Dexamethasone in hospitalized patients with Covid-19. N. Engl. J. Med. 384, 693–704 (2021).
[PMID: 32678530]
Xu, X. et al. Effective treatment of severe COVID-19 patients with tocilizumab. Proc. Natl Acad. Sci. USA 117, 10970–10975 (2020).
[PMID: 32350134]
Chuprin, A. et al. Cell fusion induced by ERVWE1 or measles virus causes cellular senescence. Genes Dev. 27, 2356–2366 (2013).
[PMID: 24186980]
Martínez, I. et al. Induction of DNA double-strand breaks and cellular senescence by human respiratory syncytial virus. Virulence 7, 427–442 (2016).
[PMID: 26809688]
Baz-Martinez, M. et al. Cell senescence is an antiviral defense mechanism. Sci. Rep. 6, 37007 (2016).
[PMID: 27849057]
Hsieh, T. H. et al. Senescence in monocytes facilitates dengue virus infection by increasing infectivity. Front. Cell. Infect. Microbiol. 10, 375 (2020).
[PMID: 32850477]
Dimri, G. P. et al. A biomarker that identifies senescent human cells in culture and in aging skin in vivo. Proc. Natl Acad. Sci. USA 92, 9363–9367 (1995).
[PMID: 7568133]
Narita, M. et al. Rb-mediated heterochromatin formation and silencing of E2F target genes during cellular senescence. Cell 113, 703–716 (2003).
[PMID: 12809602]
Yu, Y. et al. Targeting the senescence-overriding cooperative activity of structurally unrelated H3K9 demethylases in melanoma. Cancer Cell 33, 322–336 (2018).
[PMID: 29438700]
Kuilman, T. et al. Oncogene-induced senescence relayed by an interleukin-dependent inflammatory network. Cell 133, 1019–1031 (2008).
[PMID: 18555778]
Jing, H. et al. Opposing roles of NF-κB in anti-cancer treatment outcome unveiled by cross-species investigations. Genes Dev. 25, 2137–2146 (2011).
[PMID: 21979374]
Serrano, M., Lin, A. W., McCurrach, M. E., Beach, D. & Lowe, S. W. Oncogenic ras provokes premature cell senescence associated with accumulation of p53 and p16INK4a. Cell 88, 593–602 (1997).
[PMID: 9054499]
Dou, Z. et al. Cytoplasmic chromatin triggers inflammation in senescence and cancer. Nature 550, 402–406 (2017).
[PMID: 28976970]
Liu, S. et al. Phosphorylation of innate immune adaptor proteins MAVS, STING, and TRIF induces IRF3 activation. Science 347, aaa2630 (2015).
[PMID: 25636800]
Buss, H. et al. Constitutive and interleukin-1-inducible phosphorylation of p65 NF-kB at serine 536 is mediated by multiple protein kinases including IkB kinase (IKK)-α, IKKβ, IKKε, TRAF family member-associated (TANK)-binding kinase 1 (TBK1), and an unknown kinase and couples p65 to TATA-binding protein-associated factor II31-mediated interleukin-8 transcription. J. Biol. Chem. 279, 55633–55643 (2004).
[PMID: 15489227]
Wang, P. et al. Expression cloning of functional receptor used by SARS coronavirus. Biochem. Biophys. Res. Commun. 315, 439–444 (2004).
[PMID: 14766227]
Chua, R. L. et al. COVID-19 severity correlates with airway epithelium–immune cell interactions identified by single-cell analysis. Nat. Biotechnol. 38, 970–979 (2020).
[PMID: 32591762]
Acosta, J. C. et al. A complex secretory program orchestrated by the inflammasome controls paracrine senescence. Nat. Cell Biol. 15, 978–990 (2013).
[PMID: 23770676]
Roussel, M. et al. Mass cytometry deep phenotyping of human mononuclear phagocytes and myeloid-derived suppressor cells from human blood and bone marrow. J. Leukoc. Biol. 102, 437–447 (2017).
[PMID: 28400539]
Li, X. et al. The flavonoid quercetin ameliorates liver inflammation and fibrosis by regulating hepatic macrophages activation and polarization in mice. Front. Pharmacol. 9, 72 (2018).
[PMID: 29497376]
Messner, C. B. et al. Ultra-high-throughput clinical proteomics reveals classifiers of COVID-19 infection. Cell Syst. 11, 11–24.e4 (2020).
[PMID: 32619549]
Demichev, V. et al. A time-resolved proteomic and prognostic map of COVID-19. Cell Syst. 12, 780–794.e7 (2021).
[PMID: 34139154]
Kang, S. et al. IL-6 trans-signaling induces plasminogen activator inhibitor-1 from vascular endothelial cells in cytokine release syndrome. Proc. Natl Acad. Sci. USA 117, 22351–22356 (2020).
[PMID: 32826331]
Beigi, R., Kobatake, E., Aizawa, M. & Dubyak, G. R. Detection of local ATP release from activated platelets using cell surface-attached firefly luciferase. Am. J. Physiol. 276, C267–C278 (1999).
[PMID: 9886943]
Zhu, Y. et al. The Achilles’ heel of senescent cells: from transcriptome to senolytic drugs. Aging Cell 14, 644–658 (2015).
[PMID: 25754370]
Xu, M. et al. Senolytics improve physical function and increase lifespan in old age. Nat. Med. 24, 1246–1256 (2018).
[PMID: 29988130]
Dorr, J. R. et al. Synthetic lethal metabolic targeting of cellular senescence in cancer therapy. Nature 501, 421–425 (2013).
[PMID: 23945590]
Chang, J. et al. Clearance of senescent cells by ABT263 rejuvenates aged hematopoietic stem cells in mice. Nat. Med. 22, 78–83 (2016).
[PMID: 26657143]
Kirkland, J. L. & Tchkonia, T. Senolytic drugs: from discovery to translation. J. Intern. Med. 288, 518–536 (2020).
[PMID: 32686219]
Freund, A., Patil, C. K. & Campisi, J. p38MAPK is a novel DNA damage response-independent regulator of the senescence-associated secretory phenotype. EMBO J. 30, 1536–1548 (2011).
[PMID: 21399611]
Bent, E. H., Gilbert, L. A. & Hemann, M. T. A senescence secretory switch mediated by PI3K/AKT/mTOR activation controls chemoprotective endothelial secretory responses. Genes Dev. 30, 1811–1821 (2016).
[PMID: 27566778]
Jung, S. H. et al. Integrin α6β4–Src–AKT signaling induces cellular senescence by counteracting apoptosis in irradiated tumor cells and tissues. Cell Death Differ. 26, 245–259 (2019).
[PMID: 29786073]
Kreye, J. et al. A therapeutic non-self-reactive SARS-CoV-2 antibody protects from lung pathology in a COVID-19 hamster model. Cell 183, 1058–1069.e19 (2020).
[PMID: 33058755]
Osterrieder, N. et al. Age-dependent progression of SARS-CoV-2 infection in Syrian hamsters. Viruses 12, 779 (2020).
[>PMCID: ]
Trimpert, J. et al. The Roborovski dwarf hamster is a highly susceptible model for a rapid and fatal course of SARS-CoV-2 infection. Cell Rep. 33, 108488 (2020).
[PMID: 33271063]
Winkler, E. S. et al. SARS-CoV-2 infection of human ACE2-transgenic mice causes severe lung inflammation and impaired function. Nat. Immunol. 21, 1327–1335 (2020).
[PMID: 32839612]
White, K. M. et al. Plitidepsin has potent preclinical efficacy against SARS-CoV-2 by targeting the host protein eEF1A. Science 371, 926–931 (2021).
[PMID: 33495306]
Di Pierro, F. et al. Possible therapeutic effects of adjuvant quercetin supplementation against early-stage COVID-19 infection: a prospective, randomized, controlled, and open-label study. Int. J. Gen. Med. 14, 2359–2366 (2021).
[PMID: 34135619]
Di Pierro, F. et al. Potential clinical benefits of quercetin in the early stage of COVID-19: results of a second, pilot, randomized, controlled and open-label clinical trial. Int. J. Gen. Med. 14, 2807–2816 (2021).
[PMID: 34194240]
Camell, C. D. et al. Senolytics reduce coronavirus-related mortality in old mice. Science 373, eabe4832 (2021).
[PMID: 34103349]
Nalbandian, A. et al. Post-acute COVID-19 syndrome. Nat. Med. 27, 601–615 (2021).
[PMID: 33753937]
Milanovic, M. et al. Senescence-associated reprogramming promotes cancer stemness. Nature 553, 96–100 (2018).
[PMID: 29258294]
Schmitt, C. A., Rosenthal, C. T. & Lowe, S. W. Genetic analysis of chemoresistance in primary murine lymphomas. Nat. Med. 6, 1029–1035 (2000).
[PMID: 10973324]
Corman, V. M. et al. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT–PCR. Euro Surveill. 25, 2000045 (2020).
[>PMCID: ]
Schmitt, C. A., McCurrach, M. E., de Stanchina, E., Wallace-Brodeur, R. R. & Lowe, S. W. INK4a/ARF mutations accelerate lymphomagenesis and promote chemoresistance by disabling p53. Genes Dev. 13, 2670–2677 (1999).
[PMID: 10541553]
Nouailles, G. et al. Longitudinal omics in Syrian hamsters integrated with human data unravel complexity of moderate immune responses to SARS-CoV-2. Preprint at https://doi.org/10.1101/2020.12.18.423524 (2020).
Reimann, M. et al. Tumor stroma-derived TGF-β limits Myc-driven lymphomagenesis via Suv39h1-dependent senescence. Cancer Cell 17, 262–272 (2010).
[PMID: 20227040]
Veras, F. P. et al. SARS-CoV-2-triggered neutrophil extracellular traps mediate COVID-19 pathology. J. Exp. Med. 217, e20201129 (2020).
[PMID: 32926098]
Rathnasinghe, R. et al. Comparison of transgenic and adenovirus hACE2 mouse models for SARS-CoV-2 infection. Emerg. Microbes Infect. 9, 2433–2445 (2020).
[PMID: 33073694]
Gruber, A. D. et al. Standardization of reporting criteria for lung pathology in SARS-CoV-2-infected hamsters: what matters? Am. J. Respir. Cell Mol. Biol. 63, 856–859 (2020).
[PMID: 32897757]
Hochberg, Y. & Benjamini, Y. More powerful procedures for multiple significance testing. Stat. Med. 9, 811–818 (1990).
[PMID: 2218183]
Schneider, C. A., Rasband, W. S. & Eliceiri, K. W. NIH Image to ImageJ: 25 years of image analysis. Nat. Methods 9, 671–675 (2012).
[PMID: 22930834]
Fridman, A. L. & Tainsky, M. A. Critical pathways in cellular senescence and immortalization revealed by gene expression profiling. Oncogene 27, 5975–5987 (2008).
[PMID: 18711403]
Hari, P. et al. The innate immune sensor Toll-like receptor 2 controls the senescence-associated secretory phenotype. Sci. Adv. 5, eaaw0254 (2019).
[PMID: 31183403]
Schleich, K. et al. H3K9me3-mediated epigenetic regulation of senescence in mice predicts outcome of lymphoma patients. Nat. Commun. 11, 3651 (2020).
[PMID: 32686676]