Specific mutations in H5N1 mainly impact the magnitude and velocity of the host response in mice

Tchitchek, Nicolas; Eisfeld, Amie J; Tisoncik-Go, Jennifer; Josset, Laurence; Gralinski, Lisa E; Bécavin, Christophe; Tilton, Susan C; Webb-Robertson, Bobbie-Jo; Ferris, Martin T; Totura, Allison L; Li, Chengjun; Neumann, Gabriele; Metz, Thomas O; Smith, Richard D; Waters, Katrina M; Baric, Ralph; Kawaoka, Yoshihiro; Katze, Michael G

For each set of transcripts and proteins, we identified over-represented biological functions, canonical pathways, and upstream regulators (Tables 1 and 2) . Eigentranscript #2 profile was enriched for transcripts associated with Death Receptor Signaling, Role of Pattern Recognition Receptors in Recognition of Bacteria and Viruses, and Apoptosis Signaling, as well as the Protein Ubiquitination Pathway, which has previously been observed in mouse lung responses following pandemic 1918 influenza virus infection [25] . There was representation of transcripts encoding immuno proteasome components (e.g., PSMB9 and PSMB10), ubiquitin-protein conjugates (e.g., USP18 and USP3), and heat shock proteins (e.g., HSPA5 and HSPB7) accompanying the Protein Ubiquitination Pathway. Eigentranscript #1 profile was comprised of transcripts predominantly associated with metabolic cellular processes including Glutathionemediated Detoxification (e.g., GSTK1 and GSTA3) and Xenobiotic Metabolism Signaling (e.g., AHR and CAT). Respiratory System Development and Function was an enriched biological function for eigentranscript #1 that included RARG and RARB transcripts, two ligand-dependent nuclear receptors that modulate an array of cellular responses related to cellular growth. Eigentranscript #3 profile was enriched for transcripts associated with T cell responses, CD3G, ZAP70, and ICOS, related to T Cell Receptor Signaling, iCOS-iCOSL Signaling in T Helper Cells, and Regulation of IL-2 Expression in Activated and Anergic T Lymphocytes. Activated CD8 T cells in the lungs of mice infected with H5N1 virus are impaired in their ability to control viral replication linked to high pathogenicity [26] . Eigenprotein #2 profile had strong representation of proteins associated with Acute Phase Response Signaling (e.g., SAA2 and SERPINA1), LXR/RXR Activation (e.g., APOA1 and APOA2), Complement System (e.g., CFB and C4B) and Coagulation System (e.g., F2 and FGG), cellular responses that are critical to host antiviral defenses. Examination of proteins associated with eigenprotein #1 profile showed enrichment of proteins related to modification of reactive oxygen species. For example, there was enrichment of PRDX1, PTPLAD1, and ERP29, suggesting heightened oxidative stress responses in the lungs of VN1203-infected mice. H5N1 infection causes acute lung injury and mice inoculated with inactivated H5N1 virus have compromised lung function, including altered lung elastance and increased For each eigentranscript identified in the kinetics of the host response to H5N1 VN1203 wild-type, the number of correlating transcripts is indicated. For each set of transcript the top 5 associated over-represented biological functions, canonical pathways, and upstream regulators are indicated. Ingenuity pathway analysis was used to determine the top 5 bio function categories, canonical pathways, and upstream regulators. The functions annotation p-value range represents the range of p-values for the functions annotations associated with each bio function category. The p-value of overlap associated for each upstream regulator indicates the significance of the overlap between the genes targeted by the upstream regulator in the IPKB database and the experimental dataset. *Upstream regulators with an apteryx signify a chemical reagent or chemical drug.