Transcriptomic Characterization of the Novel Avian-Origin Influenza A (H7N9) Virus: Specific Host Response and Responses Intermediate between Avian (H5N1 and H7N7) and Human (H3N2) Viruses and Implications for Treatment Options

Josset, Laurence; Zeng, Hui; Kelly, Sara M.; Tumpey, Terrence M.; Katze, Michael G.

Functional characterization of host responses specific to H7N9 and to human and avian IAVs. To further study specificities in the host response to each IAV, we identified genes differentially expressed (DE) between IAV-infected samples and mockinfected samples for each time point using the following criteria: a q value of Ͻ0.01, as determined by Limma's empirical Bayes moderated t test, and a log 2 fold change (log 2 FC) value of Ͼ1.5 (Fig. 3) . Consistent with transcriptomic distance analysis, IAVs induced few transcriptomic changes at 3 and 7 hpi (Fig. 3A) . At 12 hpi, the response to H3N2 infection was quite robust, with 1,631 DE genes, while there were only 824 DE genes after H7N9 infection Similarities in transcriptomic responses are depicted using nonparametric multidimensional scaling (MDS). Each RNA sample is represented as a single point colored by viral treatment and with a different shape according to the time point. Euclidian distance was calculated using the whole normalized transcriptomic data, such that proximity indicates similarity, whereas distance indicates dissimilarity, of gene expression profiles. Kruskal's stress quantifies the quality of the representations as a fraction of the information lost during the dimensionality reduction procedure. (B) Average distances between Anhui01-infected samples and time-matched infected or mock samples quantifying whole-transcriptome diversity after infection. Pearson correlation distance (Pearson cor distance) is defined as 1 Ϫ Pearson correlation coefficient calculated using normalized transcriptomic data. Error bars indicate SD. Similar results were obtained with Euclidian, Manhattan, or Spearman correlation distance (data not shown). (C) Hierarchical clustering by average linkage of IAV-and mock-infected samples at each time hpi based on their gene expression profiles. Distances were calculated using Pearson correlation distance, but similar clustering was observed with other distance metrics. and 580 and 331 for H7N7 and H5N1, respectively. At 24 hpi, all IAVs induced a drastic host response, with the number of DE genes ranging from 5,187 genes for H3N2 to 10,637 genes for H5N1 and 11,413 genes for H7N7. With 6,618 DE genes for H7N9 at 24 hpi, the amplitude of the host response to H7N9 at 24 hpi was closer to that for human than that for avian IAV (Fig. 3A) . Therefore, we observed a more progressive host response to human H3N2 infection, whereas avian IAVs delayed the host response until 24 hpi, when a massive dysregulation of the host response was observed. The response to H7N9 was characterized by a number of DE genes intermediate between those of avian and human IAVs.