Fig. 3: Global proteomic profiling highlights 13 modulated kinases in IAV infection.

A Experimental design workflow for global proteomic profiling of protein abundance (AB) and phosphorylation (PH) changes in NHBE and PMA-differentiated THP-1 cells infected in biological duplicate with pH1N1, H3N2 or H5N1 IAV (MOI 2, four time points post-infection with time-matched mocks). B–D AB data are not available (N/A) for pH1N1 and H3N2 IAV at the 12-hour time point in THP-1 cells, as these samples did not pass MS quality control. Bar chart plotting the total number of (B) proteins from the AB dataset and (C) phosphorylation sites from the PH dataset quantified at each time point (light red=significantly increased; light blue=significantly decreased; dark red=only detected in IAV infection; dark blue=only detected in mock infection; grey=no significant change). D Log2 intensity of IAV NP AB detected over the time course of pH1N1, H3N2 and H5N1 IAV infection in NHBE and THP-1 cells. E–G All represented data corresponds to 18 hours (pH1N1, H3N2) and 12 hours (H5N1) post-IAV infection. E Correlation of the PH and AB data for all peptides where significant changes in both protein PH and AB could be measured (green=PH-AB change in the same direction; yellow=PH-AB change in the opposite direction; grey=no significant AB changes). Correlation data is represented as a total across all virus strains and cell types. F Heatmap of predicted kinase activity (kinase Z score) with FDR < 0.05 from IAV-infected NHBE and THP-1 cells (red=increased activity; blue=decreased activity; grey=not detected). G IAV-human PPI map of 10 IAV proteins (grey diamonds) interacting with 45 human proteins (small white circles) that possess significantly changing phosphorylation sites (adjusted p-value < 0.05; two-sided t-test). Significantly changing phosphorylation sites (emanating large circular nodes) are stratified by IAV strain (pie sections) and colored by the maximum log2 fold change (log2FC) (IAV/mock; red=increase, blue=decrease, grey=not detected). Phosphorylation sites detected across multiple cell lines are represented by the maximum absolute value, non-infinite fold change.