Virus- and Interferon Alpha-Induced Transcriptomes of Cells from the Microbat Myotis daubentonii

Hölzer, Martin; Schoen, Andreas; Wulle, Julia; Müller, Marcel A.; Drosten, Christian; Marz, Manja; Weber, Friedemann

To our knowledge, a kinetic and side-by-side comparison of virus-driven versus IFN-driven host cell transcriptomes was not reported for any mammalian species so far. Therefore, beyond the bat-specific aspects this study was initiated for, we took advantage of our database to filter out genes that are uniquely regulated by either treatment. To address this issue, we compared gene expression at the 6-and 24-h time points of Clone 13 infection and IFN treatment with each other. Overall, running the two transcriptomes next to each other showed once more that at 6 h Clone 13 infection stimulated less genes (denominated as being ''downregulated'') than 6-h IFN treatment ( Figures 4A and 4B ). We could identify some genes that are upregulated exclusively by Clone 13, most prominently the prototypical, IRF3-driven virus-response gene IFNB1. When restricting ourselves to genes that were not at all regulated by IFN but upregulated by a log2 of more than 3 by virus (i.e., stricter than the log2-fold change of 2 filter we had set for the heatmaps), a similar virus-only response behavior was exhibited by other cytokines such as, e.g., CCL2, CCL4, IFNL3 (IFN-l3), and CSF2, and also by more untypical genes such as CH25H, ICAM1, and STEAP4. Figure 4C shows RNA-seq data as expression box plots to illustrate the exclusive virus-response behavior in M. daubentonii cells.