Dissecting childhood asthma with nasal transcriptomics distinguishes subphenotypes of disease Alex Poole, MS, Cydney Urbanek, BS, Celeste Eng, BS, Jeoffrey.

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Presentation transcript:

Dissecting childhood asthma with nasal transcriptomics distinguishes subphenotypes of disease Alex Poole, MS, Cydney Urbanek, BS, Celeste Eng, BS, Jeoffrey Schageman, BS, Sean Jacobson, MS, Brian P. O'Connor, PhD, Joshua M. Galanter, MD, Christopher R. Gignoux, PhD, Lindsey A. Roth, MA, Rajesh Kumar, MD, Sharon Lutz, PhD, Andrew H. Liu, MD, Tasha E. Fingerlin, PhD, Robert A. Setterquist, PhD, Esteban G. Burchard, MD, Jose Rodriguez-Santana, MD, Max A. Seibold, PhD Journal of Allergy and Clinical Immunology Volume 133, Issue 3, Pages 670-678.e12 (March 2014) DOI: 10.1016/j.jaci.2013.11.025 Copyright © 2014 American Academy of Allergy, Asthma & Immunology Terms and Conditions

Fig 1 Comparison of nonubiquitous gene expression between airway tissues. A-D, Overlap of expressed genes between nasal-bronchial (Fig 1, A), nasal-SAE (Fig 1, B), and bronchial-SAE (Fig 1, C) tissues and between all tissues (Fig 1, D). E-G, Scatter plot of mean expression levels for genes commonly expressed between nasal-bronchial (Fig 1, E), nasal-SAE (Fig 1, F), and bronchial-SAE (Fig 1, G) tissues. H, Correspondence-at-top plot for the top 500 genes ranked by expression level from highest to lowest for each tissue. Journal of Allergy and Clinical Immunology 2014 133, 670-678.e12DOI: (10.1016/j.jaci.2013.11.025) Copyright © 2014 American Academy of Allergy, Asthma & Immunology Terms and Conditions

Fig 2 Unsupervised clustering of subjects with atopic asthma and healthy control subjects by using nasal transcriptome expression levels. FPKM expression levels for all genes in the nasal whole-transcriptome sequencing data were used for clustering. Journal of Allergy and Clinical Immunology 2014 133, 670-678.e12DOI: (10.1016/j.jaci.2013.11.025) Copyright © 2014 American Academy of Allergy, Asthma & Immunology Terms and Conditions

Fig 3 Comparison of gene expression fold changes in asthmatic subjects between bronchial and nasal airway expression data for bronchial airway biomarker genes. Scatter plot of previously reported bronchial airway gene expression log2 fold changes in asthmatic subjects for the top 20 upregulated and downregulated genes versus fold changes in asthma for these genes in the nasal airway transcriptome data. The linear regression best-fit line is shown. WTS, Whole-transcriptome sequencing. Journal of Allergy and Clinical Immunology 2014 133, 670-678.e12DOI: (10.1016/j.jaci.2013.11.025) Copyright © 2014 American Academy of Allergy, Asthma & Immunology Terms and Conditions

Fig 4 Correlation between AmpliSeq nasal gene expression of IL13 and the other 47 genes differentially expressed in asthmatic subjects. Genes are ranked from top to bottom by decreasing Spearman correlation coefficient (ρ) values. Purple and pink regions correspond to levels of high positive (ρ > 0.5) and negative (ρ < −0.5) correlation, respectively. Open bars, Significant IL13 correlations; solid bars, nonsignificant IL13 correlations. Journal of Allergy and Clinical Immunology 2014 133, 670-678.e12DOI: (10.1016/j.jaci.2013.11.025) Copyright © 2014 American Academy of Allergy, Asthma & Immunology Terms and Conditions

Fig 5 Clustering of AmpliSeq nasal gene expression levels in study subjects. Clustering was generated by using relative nasal expression levels for the 70 genes differentially expressed in the setting of atopy (n = 99). The heat map represents normalized expression counts (red, low; green, high) for each gene. The presence (blue) or absence (red) of atopy, asthma, eosinophil levels, and rhinitis is displayed directly below the heat map. Open squares, Missing data. Journal of Allergy and Clinical Immunology 2014 133, 670-678.e12DOI: (10.1016/j.jaci.2013.11.025) Copyright © 2014 American Academy of Allergy, Asthma & Immunology Terms and Conditions

Fig 6 Box plots of genes differentially expressed in asthmatic but not atopic subjects in the nasal airway. AmpliSeq-normalized expression counts for 3 of the 6 genes (MUC5B, OSM, and KRT5) differentially expressed in the setting of asthma but not atopy (+1 pseudocount and log10 scale) are plotted according to the subject's asthma and atopy status. Journal of Allergy and Clinical Immunology 2014 133, 670-678.e12DOI: (10.1016/j.jaci.2013.11.025) Copyright © 2014 American Academy of Allergy, Asthma & Immunology Terms and Conditions

Fig E1 Representative nasal brush smear staining. A Wright-stained nasal brush cell smear showing nasal airway epithelial cells. Journal of Allergy and Clinical Immunology 2014 133, 670-678.e12DOI: (10.1016/j.jaci.2013.11.025) Copyright © 2014 American Academy of Allergy, Asthma & Immunology Terms and Conditions

Fig E2 Nasal airway epithelial whole-transcriptome gene expression in healthy subjects. Expressed genes are categorized as having low (0.125-1 FPKM), medium (1-10 FPKM), and high (>10 FPKM) expression. The expression distribution for all genes is shown in red and the non-ubiquitously expressed genes is shown in blue (determined per Ramskold et al method).E10 Journal of Allergy and Clinical Immunology 2014 133, 670-678.e12DOI: (10.1016/j.jaci.2013.11.025) Copyright © 2014 American Academy of Allergy, Asthma & Immunology Terms and Conditions

Fig E3 Scatter plot of AmpliSeq gene expression versus nasal whole-transcriptome gene expression data. Data are shown for the 20 overlapping subjects and genes between the 2 expression methods. The FPKM cutoff was 0.125. Spearman correlation coefficient is shown. WTS, Whole-transcriptome sequencing. Journal of Allergy and Clinical Immunology 2014 133, 670-678.e12DOI: (10.1016/j.jaci.2013.11.025) Copyright © 2014 American Academy of Allergy, Asthma & Immunology Terms and Conditions

Fig E4 IL13 AmpliSeq nasal gene expression levels categorized by asthmatic exacerbations. Box plots display normalized IL13 expression count data for subjects requiring an asthma-related emergency department (ER) visit in the past year (n = 30) compared with those who did not (n = 19). A 1-read pseudocount was added to each sample to allow log transformation of genes with expression values of zero. The P value for differential expression between the groups was calculated by using a nonparametric Wilcoxon Mann-Whitney test. Journal of Allergy and Clinical Immunology 2014 133, 670-678.e12DOI: (10.1016/j.jaci.2013.11.025) Copyright © 2014 American Academy of Allergy, Asthma & Immunology Terms and Conditions