TMPRSS2-mediated SARS-CoV-2 uptake boosts innate immune activation, enhances cytopathology, and drives convergent virus evolution

Proc Natl Acad Sci U S A. 2024 Jun 4;121(23):e2407437121. doi: 10.1073/pnas.2407437121.

Bingqian Qu ¹ ², Csaba Miskey ³, André Gömer ⁴, Robin D V Kleinert ¹, Sara Calvo Ibanez ⁵, Regina Eberle ⁵, Aileen Ebenig ¹, Dylan Postmus ⁶ ⁷, Maximilian K Nocke ⁴, Maike Herrmann ¹, Tabitha K Itotia ¹ ⁸, Simon T Herrmann ⁴, Natalie Heinen ⁴, Sebastian Höck ¹, Florian D Hastert ⁹, Christine von Rhein ⁹, Christoph Schürmann ¹, Xue Li ¹⁰, Ger van Zandbergen ¹¹ ¹² ¹³, Marek Widera ¹⁴, Sandra Ciesek ¹⁴ ¹⁵ ¹⁶, Barbara S Schnierle ⁹, Alexander W Tarr ¹⁷ ¹⁸, Eike Steinmann ⁴, Christine Goffinet ⁶ ⁷, Stephanie Pfaender ⁴ ¹⁹ ²⁰, Jacomina Krijnse Locker ⁵ ²¹, Michael D Mühlebach ¹ ²², Daniel Todt ² ⁴, Richard J P Brown ¹ ⁴

Affiliations

1 Division of Veterinary Medicine, Paul-Ehrlich-Institut, 63225 Langen, Germany.
2 European Virus Bioinformatics Center, 07743 Jena, Germany.
3 Division of Medical Biotechnology, Paul-Ehrlich-Institut, 63225 Langen, Germany.
4 Department of Molecular and Medical Virology, Ruhr University Bochum, 44801 Bochum, Germany.
5 Electron Microscopy of Pathogens, Paul-Ehrlich-Institut, 63225 Langen, Germany.
6 Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, United Kingdom.
7 Institute of Virology, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany.
8 Department of Physical Sciences, Chuka University, 60400 Chuka, Kenya.
9 Division of Virology, Paul-Ehrlich-Institut, 63225 Langen, Germany.
10 Department of Cardiology, Medical University Hospital, 69120 Heidelberg, Germany.
11 Division of Immunology, Paul-Ehrlich-Institut, 63225 Langen, Germany.
12 Institute for Immunology, University Medical Center of the Johannes Gutenberg University of Mainz, 55131 Mainz, Germany.
13 Research Center for Immunotherapy, University Medical Center, Johannes Gutenberg-University Mainz, 55131 Mainz, Germany.
14 Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, 60596 Frankfurt am Main, Germany.
15 Fraunhofer Institute for Translational Medicine and Pharmacology, 60596 Frankfurt am Main, Germany.
16 German Center for Infection Research, 38124 Braunschweig, Germany.
17 School of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham NG7 2UH, United Kingdom.
18 School of Life Sciences and National Institute for Health and Care Research, Nottingham Biomedical Research Centre, University of Nottingham, Nottingham NG7 2UH, United Kingdom.
19 Research Unit Emerging Viruses, Leibniz Institute of Virology, 20251 Hamburg, Germany.
20 University of Lübeck, 23562 Lübeck, Germany.
21 Justus Liebig University Geissen, 35390 Giessen, Germany.
22 German Center for Infection Research, 63225 Giessen-Marburg-Langen, Germany.

PMID: 38814864 DOI: 10.1073/pnas.2407437121

Abstract

The accessory Protease transmembrane Protease serine 2 (TMPRSS2) enhances severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) uptake into ACE2-expressing cells, although how increased entry impacts downstream viral and host processes remains unclear. To investigate this in more detail, we performed Infection assays in engineered cells promoting ACE2-mediated entry with and without TMPRSS2 coexpression. Electron microscopy and inhibitor experiments indicated TMPRSS2-mediated cell entry was associated with increased virion internalization into endosomes, and partially dependent upon clathrin-mediated endocytosis. TMPRSS2 increased panvariant uptake efficiency and enhanced early rates of virus replication, transcription, and secretion, with variant-specific profiles observed. On the host side, transcriptional profiling confirmed the magnitude of infection-induced Antiviral and proinflammatory responses were linked to uptake efficiency, with TMPRSS2-assisted entry boosting early Antiviral responses. In addition, TMPRSS2-enhanced infections increased rates of cytopathology, Apoptosis, and necrosis and modulated virus secretion kinetics in a variant-specific manner. On the virus side, convergent signatures of cell-uptake-dependent innate immune induction were recorded in viral genomes, manifesting as switches in dominant coupled Nsp3 residues whose frequencies were correlated to the magnitude of the cellular response to Infection. Experimentally, we demonstrated that selected Nsp3 mutations conferred enhanced interferon antagonism. More broadly, we show that TMPRSS2 orthologues from evolutionarily diverse mammals facilitate panvariant enhancement of cell uptake. In summary, our study uncovers previously unreported associations, linking cell entry efficiency to innate immune activation kinetics, cell death rates, virus secretion dynamics, and convergent selection of viral mutations. These data expand our understanding of TMPRSS2's role in the SARS-CoV-2 life cycle and confirm its broader significance in zoonotic reservoirs and animal models.

Keywords

SARS-CoV-2 entry; cytolytic responses; host-species range; innate immunity; viral evolution.

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Cat. No.

Product Name

Description

Target

Research Area
HY-128140

Z-FY-CHO

CTSL Inhibitor

Cathepsin

Neurological Disease; Metabolic Disease

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