Cell type resolved quantitative proteomics map of interferon response against SARS-CoV-2

Saccon, Elisa; Chen, Xi; Mikaeloff, Flora; Rodriguez, Jimmy Esneider; Szekely, Laszlo; Vinhas, Beatriz Sá; Krishnan, Shuba; Byrareddy, Siddappa N.; Frisan, Teresa; Végvári, Ákos; Mirazimi, Ali; Neogi, Ujjwal; Gupta, Soham

The commonly used laboratory cell lines are the first line of experimental models to study the pathogenicity and performing antiviral assays for emerging viruses. Here, we assessed the tropism and cytopathogenicity of the first Swedish isolate of SARS-CoV-2 in six different human cell lines, compared their growth characteristics and performed quantitative proteomics for the susceptible cell lines. Overall, Calu-3, Caco2, Huh7, and 293FT cell lines showed a high to moderate level of susceptibility to SARS-CoV-2. In Caco2 cells the virus can achieve high titers in the absence of any prominent cytopathic effect. The protein abundance profile during SARS-CoV-2 infection revealed cell-type-specific regulation of cellular pathways. Type-I interferon signaling was identified as the common dysregulated cellular response in Caco2, Calu-3 and Huh7 cells. Together, our data shows cell-type specific variability for cytopathogenicity, susceptibility and cellular response to SARS-CoV-2 and provide important clues to guide future studies.