MERS-CoV and H5N1 influenza virus antagonize antigen presentation by altering the epigenetic landscape

Menachery, Vineet D.; Schäfer, Alexandra; Burnum-Johnson, Kristin E.; Mitchell, Hugh D.; Eisfeld, Amie J.; Walters, Kevin B.; Nicora, Carrie D.; Purvine, Samuel O.; Casey, Cameron P.; Monroe, Matthew E.; Weitz, Karl K.; Stratton, Kelly G.; Webb-Robertson, Bobbie-Jo M.; Gralinski, Lisa E.; Metz, Thomas O.; Smith, Richard D.; Waters, Katrina M.; Sims, Amy C.; Kawaoka, Yoshihiro; Baric, Ralph S.

Having previously identified type I IFN-dependent genes specific to the human airway epithelial cell line Calu3 cells (6) , the same approach was applied to define genes responsive to IFN-γ. While some reports have indicated production by epithelial cells (9), RNA expression data indicated no IFN-γ signal following infection of Calu3 cells. However, responses to IFN-γ have been shown to be critical in the innate and adaptive immune response to respiratory infection, and epithelial cell IFN-γ responses may play a key role during infection (10) (11) (12) (13) (14) . Calu3 cells, treated with recombinant IFN-γ, induced differential expression (DE) of 426 genes [logtwofold change (FC) of >1.5, adjusted P value < 0.05]. Using these data, we developed a consensus IFN-γ-responsive list from the 136 genes induced at more than one time point (Table S1 ). While significant overlap was observed with type I IFN-responsive genes (42 of 136, 31%) (6), consensus IFN-γ genes also induced transcription factors, apoptosis/cell survival genes, ubiquitination machinery, and genes within other functional categories ( Table 1 ). The consensus IFN-γ gene list was then used to examine expression changes following infection with successful respiratory viruses. Despite the absence of IFN-γ signal in these cultures, infection with influenza H1N1-09, H5N1-VN1203, SARS-CoV, and MERS-CoV induced expression of IFN-γ-responsive genes by other factors; however, these IFN-γ-responsive gene expressions varied across viral infections, despite similar kinetics of replication (Fig. 1) . For H1N1-09 and SARS-CoV, the majority of IFN-γ-responsive genes were strongly up-regulated, with only ∼10% exhibiting downregulation. In contrast, >40% of these same genes were downregulated by H5N1-VN1203 and MERS-CoV. Examining the IFN-γ-responsive genes by functional subsets revealed multiple gene groups targeted for down-regulation (Table 1 ). Most notable for both H5N1-VN1203 and MERS-CoV infection were genes associated with antigen presentation, including several MHC molecules; 80% or more of the IFN-γ-responsive genes associated with antigen presentation were down-regulated following H5N1-VN1203 or MERS-CoV infection ( Table 1 ). In contrast, <10% of these genes were down-regulated following either H1N1-09 or SARS-CoV infection. Together, the results suggest strong down-regulation of antigen-presentation genes following both H5N1-VN1203 and MERS-CoV infection.