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

We found a total of 5,660 transcripts that correlated with 3 main eigentranscripts (eigentranscript #1 contained 2,706 transcripts, eigentranscript #2 contained 2,826 transcripts, and eigentranscript #3 contained 128 transcripts). There were a total of 162 proteins that correlated with 3 main eigenproteins (eigenprotein #1 contained 59 proteins, eigenprotein #2 contained 86 proteins, and eigenprotein #3 contained 17 proteins). Additional file 3: Table S1 and Additional file 4: Table S2 provide the lists of transcripts and proteins associated with each eigentranscript and eigenprotein, respectively. The patterns of the eigentranscripts and eigenproteins identified in the VN1203-WT host response are represented in Figure 3A and B. Eigentranscript #2 was increasing over time, whereas eigentranscript #1 was decreasing over time. Eigentranscript #3 showed a distinct pattern with a transient decrease at 2 and 4 dpi, followed by an increase at 7 dpi. Eigenprotein #1 was increased in abundance over time. In brief, the dynamics of the transcriptomic and proteomic host response were captured by 3 sets of co-expressed transcripts and 3 sets of co-expressed proteins with different patterns of variations.