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

Abstract

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.

Type-I interferon signatures in SARS-CoV-2 infected Huh7 cells

“…This indicates that IFIT1 might be an important antiviral-factor that needs further attention. Also, the differences observed among the two cell lines underscores the drawback of studying a single cell line (Huh7 in this case) as it may not be reflective of other cell populations where there could be differential regulation of IFN-response 44 .…”

“…One limitation of our study is that the analysis is restricted to only one cell line that may not provide a comprehensive picture since we have observed cell-type specific differences in susceptibility to SARS-CoV-2 and interferon response 44 . Furthermore, Huh7 is an immortalized cancer cell line, which may not be physiologically representative of the human tissue.…”

Air-liquid interphase culture confers SARS-CoV-2 susceptibility to A549 alveolar epithelial cells

“…This cell line showed limited endogenous ACE2 expression level and was non-permissive to SARS-CoV-2 infection under submerged culture conditions ( Fig. 1 F–H) [ 7 ]. Our study and other studies demonstrated that exogenous expression of human ACE2 mediates SARS-CoV-2 entry and renders A549 cells permissive for SARS-CoV-2 infection [ [24] , [25] , [26] ].…”

“…In particular, the interaction between ACE2 and S protein has attracted attention, because emerging SARS-CoV-2 variants possess amino acid substitutions in the receptor binding domain of S protein which can increase the binding affinity to human ACE2 [ 5 ]. In addition, the exogenous expression of ACE2 confers SARS-CoV-2 susceptibility to cells which are normally resistant to infection [ 6 , 7 ]; therefore, ACE2 is a major determinant of SARS-CoV-2 susceptibility. On the other hand, certain host proteases proteolytically activate (or prime) S protein for membrane fusion.…”

“…A549 and Calu-3 cells are human lung-derived epithelial cells and widely used for studies of virus infection. In contrast to Calu-3 cells, only limited entry and growth of SARS-CoV-2 occurs in A549 cells [ 7 ]. The decreased susceptibility of A549 cells to SARS-CoV-2 infection was attributed to the low expression level of ACE2 and the retinoic acid-inducible gene-I (RIG-I)-mediated antiviral response [ 1 , 16 ].…”