key: cord-1006016-9i0q1gdm
authors: Grossegesse, Marica; Bourquain, Daniel; Neumann, Markus; Schaade, Lars; Nitsche, Andreas; Doellinger, Joerg
title: Deep time course proteomics of SARS-CoV- and SARS-CoV-2-infected human lung epithelial cells (Calu-3) reveals strong induction of interferon-stimulated gene (ISG) expression by SARS-CoV-2 in contrast to SARS-CoV
date: 2021-04-21
journal: bioRxiv
DOI: 10.1101/2021.04.21.440783
sha: 2d97c20d84a991362474765a14c699c747a4d993
doc_id: 1006016
cord_uid: 9i0q1gdm

SARS-CoV and SARS-CoV-2 infections are characterized by remarkable differences, including contagiosity and case fatality rate. The underlying mechanisms are not well understood, illustrating major knowledge gaps of coronavirus biology. In this study, protein expression of SARS-CoV- and SARS-CoV-2-infected human lung epithelial cell line Calu-3 was analysed using data-independent acquisition mass spectrometry (DIA-MS). This resulted in the so far most comprehensive map of infection-related proteome-wide expression changes in human cells covering the quantification of 7478 proteins across 4 time points. Most notably, the activation of interferon type-I response was observed, which surprisingly is absent in other recent proteome studies, but is known to occur in SARS-CoV-2-infected patients. The data reveal that SARS-CoV-2 triggers interferon-stimulated gene (ISG) expression much stronger than SARS-CoV, which reflects the already described differences in interferon sensitivity. Potentially, this may be caused by the enhanced expression of viral M protein of SARS-CoV in comparison to SARS-CoV-2, which is a known inhibitor of type I interferon expression. This study expands the knowledge on the host response to SARS-CoV-2 infections on a global scale using an infection model, which seems to be well suited to analyse innate immunity.

In late 2019, first cases of severe pneumonia of unknown origin were reported in 42 Wuhan, China. Shortly afterwards a new coronavirus was discovered as the causative 43 agent and named SARS-CoV-2 and the related disease COVID-19. The virus turned 44 out to be highly contagious and caused a world-wide pandemic, which is still ongoing 45 and has already led to the death of > 2,900,000 humans worldwide. Already in 2002, 46 another coronavirus, SARS-CoV, was discovered in China which was related to a 47 severe acute respiratory syndrome (SARS) and caused an outbreak with about 780 48 deaths (1). However, at this time the outbreak could be controlled probably due to the 49 lower contagiosity of SARS-CoV compared to SARS-CoV-2 (2). SARS-CoV and 50 SARS-CoV-2 share about 80 % of their genome sequence and protein homology 51 ranges between 40 and 94% (3, 4). Although both viruses mainly lead to respiratory 52 tract infections and can cause severe pneumonia, they are characterized by remarkable 53 differences, including contagiosity and case fatality rate (5). As the respiratory tract is 54 the first and main target of SARS-CoV and SARS-CoV-2 infections, it seems 55 conclusive to use airway epithelia cells to study differences of these two viruses. 56 However, no comparative proteomics study has been published using Calu-3 cells L-Gln and non-essential amino acids. A total of 5x10 5 cells per well were seeded in 6-72 well plates and incubated overnight at 37°C and 5% CO2 in a humified atmosphere. 

Input files for library prediction were generated using EncyclopeDIA (Version 0.9.5) 145 (14). The in-silico library was corrected using the data of the gas-phase fractionated 146 pooled sample in DIA-NN (Version 1.7.10) (15). Mass tolerances were set to 10 ppm 147 for MS1 and 20 ppm for MS² spectra, and the "unrelated run" option was enabled with 148 the false discovery rate being set to 0.01. The single-run data were analysed using the 149 corrected library with fixed mass tolerances of 10 ppm for MS1 and 20 ppm for MS² 150 spectra with enabled "RT profiling" using the "robust LC (high accuracy)" 

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The authors would like to thank Clemens Bodenstein, Bianca Hube, Melanie

Hoffmeister and Stefanie Schürer for supporting the infection experiments and qPCR