Supplementary Material
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Supplementary materials and methods. ERJ-00437-2018_Supplement
Table E1. Subject characteristics (n=39). ERJ-00437-2018_Table_E1
Table E2. Comparison of nasal and bronchial cells within groups (n=39). ERJ-00437-2018_Table_E2
Table E3. Comparison between included (n=26) and excluded (n=13) subject characteristics. ERJ-00437-2018_Table_E3
Table E4. 63 most-regulated genes between nasal and bronchial cells in healthy subjects (C). ERJ-00437-2018_Table_E4
Figure E1. Flow chart of the study. ERJ-00437-2018_Figure_E1
Figure E2. Differential gene expression between nasal and bronchial tissues (323 transcripts). Unsupervised hierarchical clustering of the RNAseq data based on a set of the 323 most differentially expressed genes (adjusted p-value <0.05 and an abs(log2 FC)>2). Each square represents the expression level of a given gene in a given sample relative to the average expression level in all samples. A red-to-blue color scale indicates gene expression levels above (red) or below (blue) the average level of expression for this same gene. ERJ-00437-2018_Figure_E2
Figure E3. Biological theme analysis of nose/bronchus signature. Physiological system development and functional categories found to be significantly affected in an Ingenuity Pathway Analysis® downstream effect analysis of a selection of 323 genes differentially expressed between nasal and bronchial samples (adjusted p-value <0.05 and an abs(log2 FC)>2). Bars represent the strength of the statistical significance. ERJ-00437-2018_Figure_E3
Figure E4. Boxplots showing the expression in AR, R and C samples from the nose and bronchi for the 28 transcripts defining the initial Th2 gene signature, defined from GSE19190, GSE110799, GSE37693 and GSE4804. Distribution of expression levels (log2) in each experimental group for the 28-gene set of our Th2 signature. Footnotes: B: bronchus; N: nose; AR: allergic rhinitis and asthma group; R: isolated allergic rhinitis group; C: healthy controls. ERJ-00437-2018_Figure_E4
Figure E5. Hierarchical clustering based on initial Th2 gene signature. Unsupervised hierarchical clustering of the RNAseq data based the initial 28 genes Th2 signature. Each square represents the expression level of a given gene in a given sample relative to the gene average expression level in all samples. A red-to-blue color scale indicates gene expression levels above (red) or below (blue) the average level of expression for the same transcript. Footnotes: B: bronchus; N: nose; AR: allergic rhinitis and asthma group; R: isolated allergic rhinitis group; C: healthy controls. ERJ-00437-2018_Figure_E5
Figure E6. Heatmap of Pearson correlation between Th2 markers. Unsupervised hierarchical clustering of the pairwise correlations between Th2 markers. Each square represents the Pearson correlation coefficient between 2 genes. A red-to-blue color scale indicates positive (red) or negative (blue) correlation. ERJ-00437-2018_Figure_E6
Figure E7. Hierarchical clustering based Th2, Th17 and IFN gene signature. Unsupervised hierarchical clustering of the RNAseq data based on the (A) initial 4-genes Th2 signature (B) Th17 signature, (C) IFN signature. Each square represents the expression level of a given gene in a given sample relative to the gene average expression level in all samples. A red-to-blue color scale indicates gene expression levels above (red) or below (blue) the average level of expression for the same transcript. Footnotes: B: bronchus; N: nose; AR: allergic rhinitis and asthma group; R: isolated allergic rhinitis group; C: healthy controls. ERJ-00437-2018_Figure_E7
Figure E8. Th2 score of bronchial samples in the R group as a function of asthma history. Boxplots of Th2 score in the bronchial samples from the patients belonging to the R group according to clinical history. *: p-value <0.05. Footnotes: A: asthma history; EW: isolated wheeze on exertion history; N: no asthma or wheeze on exertion history. ERJ-00437-2018_Figure_E8
Figure E9. Hierarchical clustering based on an enlarged IFN gene signature. Unsupervised hierarchical clustering of the RNAseq data based on an extended 33-gene IFN signature. Each square represents the expression level of a given gene in a given sample relative to the gene average expression level in all samples. A red-to-blue color scale indicates gene expression levels above (red) or below (blue) the average level of expression for the same transcript. Footnotes: B: bronchus; N: nose; AR: allergic rhinitis and asthma group; R: isolated allergic rhinitis group; C: healthy controls. ERJ-00437-2018_Figure_E9
Figure E10. IFN score in nasal and bronchial samples. Boxplots of IFN score in the nasal and bronchial samples (score based on the 33 genes signature), in the (A) whole dataset and (B) removing the four samples with the highest scores. ERJ-00437-2018_Figure_E10