Figure 2: Transcriptomic analyses of the host response to influenza virus infection and CF disease progression in ferrets.

(a) Heat map visualization shows distinct gene expression changes in lung and trachea samples from ferrets infected with either the 2009 pandemic H1N1 influenza A/CA/04/2009 virus (CA04) or the 1918 pandemic H1N1 influenza A/Brevig Mission/1/1918 virus (1918). Each row shows the log₂ (fold-change) for three infected animals relative to corresponding tissue from three mock-infected ferrets. The heat map is organized by the specificity of the changes with respect to tissue or virus. From left to right black bars at the top of the panel indicate four groups of genes: specific to trachea; distinct profiles in trachea and lung; similar profiles in trachea and lung; specific to lung (for additional details see Supplementary Fig. 18). Within each group orange subsections differ between the virus strains; green subsections do not. (b) Multidimensional scaling (MDS) representation of the distances among samples based on the indicated cluster of 2,592 genes from a that distinguish viruses in trachea but not in lung. Points show individual animals as indicated on the far right. The x and y axes represent a conceptual 2-dimensional space to which the MDS algorithm projected individual lung and trachea samples of high-dimensionality; that is, the number of genes in the block associated with each sample, while preserving the distances/dissimilarities between samples as closely as possible. Double arrow illustrates that the gene signature distinguishes the two virus infections in trachea at 1 dpi, while lung samples show no separation (dotted rectangle). (c) As in b, for the indicated cluster of 152 genes that is differentially regulated in lung but not trachea tissues and separates the two virus strains on 1 dpi. (d,e) Differential transcriptional responses in an experiment comparing lung samples from 15-day-old CF ferrets (n = 3) vs. non-CF ferrets (n = 5). (d) Similar pathways enriched in genes differentially expressed in 15-day-old CF ferret lung samples and CF human bronchial brushings, derived from Ingenuity Pathway Analysis. The values in parentheses are the enrichment P values for the corresponding pathways in the genes differentially expressed in CF human bronchial brushing¹⁹. In brackets are genes that were differentially expressed in both ferret and human CF/non-CF comparisons. (e) Network illustration of 32 genes of the function “inflammatory response”, which were differentially expressed in the same direction in ferret and human CF data sets (for additional details see Supplementary Fig. 20). Red and blue shading reflects the extent of increased or decreased expression, respectively, in CF relative to non-CF individuals. A solid line between two genes indicates direct interaction(s) among them and a dotted line for indirect interaction(s), as documented in the literature.