Quantitative proteomic analysis of SARS-CoV-2 infection of primary human airway ciliated cells and lung epithelial cells demonstrates the effectiveness of SARS-CoV-2 innate immune evasion

• Published in: Wellcome open research Vol. 7; p. 224
• Main Authors: Crozier, Thomas W.M., Greenwood, Edward J.D., Williamson, James C., Guo, Wenrui, Porter, Linsey M., Gabaev, Ildar, Teixeira-Silva, Ana, Grice, Guinevere L., Wickenhagen, Arthur, Stanton, Richard J., Wang, Eddie C. Y., Wilson, Sam J., Matheson, Nicholas J., Nathan, James A., McCaughan, Frank, Lehner, Paul J.
• Format: Journal Article
• Language: English
• Published: England F1000 Research Limited 2022; Wellcome
• Subjects: Coronavirus; COVID-19; eng; proteomics; SARS-CoV-2; COVID-19; SARS-CoV-2; Coronavirus; proteomics
• ISSN: 2398-502X; 2398-502X
• DOI: 10.12688/wellcomeopenres.17946.1

Background: Quantitative proteomics is able to provide a comprehensive, unbiased description of changes to cells caused by viral infection, but interpretation may be complicated by differential changes in infected and uninfected ‘bystander’ cells, or the use of non-physiological cellular models. Methods: In this paper, we use fluorescence-activated cell sorting (FACS) and quantitative proteomics to analyse cell-autonomous changes caused by authentic SARS-CoV-2 infection of respiratory epithelial cells, the main target of viral infection in vivo . First, we determine the relative abundance of proteins in primary human airway epithelial cells differentiated at the air-liquid interface (basal, secretory and ciliated cells). Next, we specifically characterise changes caused by SARS-CoV-2 infection of ciliated cells. Finally, we compare temporal proteomic changes in infected and uninfected ‘bystander’ Calu-3 lung epithelial cells and compare infection with B.29 and B.1.1.7 (Alpha) variants. Results: Amongst 5,709 quantified proteins in primary human airway ciliated cells, the abundance of 226 changed significantly in the presence of SARS-CoV-2 infection (q <0.05 and >1.5-fold). Notably, viral replication proceeded without inducing a type-I interferon response. Amongst 6,996 quantified proteins in Calu-3 cells, the abundance of 645 proteins changed significantly in the presence of SARS-CoV-2 infection (q < 0.05 and > 1.5-fold). In contrast to the primary cell model, a clear type I interferon (IFN) response was observed. Nonetheless, induction of IFN-inducible proteins was markedly attenuated in infected cells, compared with uninfected ‘bystander’ cells. Infection with B.29 and B.1.1.7 (Alpha) variants gave similar results. Conclusions: Taken together, our data provide a detailed proteomic map of changes in SARS-CoV-2-infected respiratory epithelial cells in two widely used, physiologically relevant models of infection. As well as identifying dysregulated cellular proteins and processes, the effectiveness of strategies employed by SARS-CoV-2 to avoid the type I IFN response is illustrated in both models.