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 biological condition, differentially expressed transcripts (DET) and proteins (DEP) compared to the mock-infected samples were identified and the overlap between the lists of DET or DEP of each virus were compared. Figure 2A and B provide visual representations of the intersections between the lists of DET and DEP for the strain conditions using proportional Euler-diagrams [23] . There were large degrees of overlap (defined here as the percentage of DET or DEP also found in another condition) between the strain conditions, between 69.41% -99.62% and 85.94% -96.98%, DET and DEP, respectively. The VN1203-PB1F2del strain condition had the smallest degree of overlap at the transcriptomic (69.41%) level, and a relatively small degree at the proteomic (87.95%) levels. Notably, at 7 dpi, only one transcriptomic profile was available for the VN1203-PB1F2del strain condition inoculated at the 10 4 PFU concentration. Hence, with only one sample available, the statistical identification of DET lead to the identification of a fraction of false-positive, explaining this lowest degree of overlap observed for this strain condition at the transcriptomic level. The VN1203-WT strain condition also showed a relatively small degree of overlap at the transcriptomic (85.55%) level; and the VN1203-NS1trunc strain condition showed the smallest degree of overlap at the proteomic (85.94%) level compared to the other strain conditions. It should be noted that the strain conditions with the lowest degrees of overlap corresponded to the same strain conditions that triggered the largest amount of DET and DEP. Similar large amounts of overlap have been identified between the dosage conditions, with degrees of overlap ranging from 68% to 98.81% for the transcriptome and from 89.87% to 99.89% for the proteome. Despite differences in clinical manifestation of the disease, these results suggest that the specific mutations in VN1203 examined herein resulted in the induction of similar groups of transcripts and proteins compared to VN1203-WT, implying that magnitude and/or the kinetics of dysregulation of these overlapping genes might differentiate the viruses. Figure 2C is a heatmap of the transcript expression values, ratioed to the mock-infected samples, of each infected sample of our dataset. This heatmap has been restricted to the lists of transcripts specific to each strain condition (i.e. transcripts found as differentially expressed within one viral strain but not in the others). We cannot distinguish any particular patterns or sets of transcript specific to any viral strain based on these transcript expression values. The transcript or protein subsets specific to each viral strain are the consequences of small variations in the host response, detected by the statistical procedures, that have no specific biological meaning.