IL-17 expression in the submucosa of bronchial biopsies of 4 groups of studied population.

<p>atopic inhaled corticosteroid (ICS) user (frame A), nonatopic ICS user (frame B), atopic non-ICS user (frame C), nonatopic non-ICS user (frame D). Single staining for IL-17 (frame E; blue) and MPO (frame F; red) and double staining for IL-17 and MPO (frame G; purple) in adjacent sections of a nonatopic non-ICS user asthmatic patient. Single staining for IL-17 (frame H; blue) and EPX (frame I; red) and double staining for IL-17 and EPX (frame J; purple) in adjacent sections of an atopic non-ICS user asthmatic patient.</p

Number of IL-17⁺ cells in submucosa in bronchial biopsies from atopic and nonatopic asthmatics who are inhaled corticosteroid (ICS) users or non-ICS users.

<p>Number of IL-17⁺ cells in submucosa in bronchial biopsies from atopic and nonatopic asthmatics who are inhaled corticosteroid (ICS) users or non-ICS users.</p

Patient characteristics.

<p>Patient characteristics.</p

Inflammation in atopic and nonatopic asthmatics.

<p>Inflammation in atopic and nonatopic asthmatics.</p

Positive correlation between the number of IL-17⁺ cells and neutrophils in the submucosa of bronchial biopsies from atopic (r_s = 0.44; p<0.001) and nonatopic (r_s = 0.45, p = 0.009) asthmatics (A), or from asthmatics who are inhaled corticosteroid (ICS) (r_s = 0.35; p = 0.01) and non-ICS (r_s = 0.48; p<0.0001) users (B).

<p>Positive correlation between the number of IL-17⁺ cells and neutrophils in the submucosa of bronchial biopsies from atopic (r_s = 0.44; p<0.001) and nonatopic (r_s = 0.45, p = 0.009) asthmatics (A), or from asthmatics who are inhaled corticosteroid (ICS) (r_s = 0.35; p = 0.01) and non-ICS (r_s = 0.48; p<0.0001) users (B).</p

Negative correlation between the number of IL-17⁺ cells in the submucosa of bronchial biopsies and serum specific IgE (Phadiatop) from asthmatics (rs = -0.37; P<0.001).

<p>Negative correlation between the number of IL-17⁺ cells in the submucosa of bronchial biopsies and serum specific IgE (Phadiatop) from asthmatics (rs = -0.37; P<0.001).</p

Additional file 3: of Altered DNA methylation is associated with aberrant gene expression in parenchymal but not airway fibroblasts isolated from individuals with COPD

Figure S1. (.EPS): CpG methylation variation in parenchymal fibroblasts in COPD samples. A) Plot of the difference in methylation standard deviation of samples from donors with COPD and donors without COPD at the 359 CpGs differentially variably methylated between samples from donors with COPD and donors without COPD. B) Representation of the CpG type with which DVPs were associated versus CpG types of all CpGs included in the analysis. (EPS 1922 kb

Additional file 4: of Altered DNA methylation is associated with aberrant gene expression in parenchymal but not airway fibroblasts isolated from individuals with COPD

Figure S2. (.EPS): GRIK2 methylation and expression do not correlate with smoking pack-years or smoking status. A) Correlation plot of GRIK2 cg16006558 methylation with smoking pack years. B) Correlation plot of GRIK2 expression with smoking pack-years. Neither CpG methylation nor gene expression correlates with smoking pack-years. C) GRIK2 expression separated by smoking status. D) GRIK2 CpG methylation separated by smoking status. Smoking status does not drive alterations to GRIK2 DNA methylation or gene expression. (EPS 2269 kb

Differentially expressed miRNAs after TGF-β1 stimulation in control lung fibroblasts in the discovery group.

<p>(A) The miRNA expression in primary parenchymal lung fibroblasts of control subjects with and without TGF-β1 stimulation was determined by microarray. Unsupervised hierarchical clustering was used to generate the heatmap and pearson correlation was used as the distance metric. Twenty-nine miRNAs were differentially expressed after TGF-β1 stimulation (FDR<0.05). The heatmap shows the median-centered expression of the 29 miRNAs of which 8 miRNAs were downregulated and 21 miRNAs were upregulated after TGF-β1 stimulation. (B) Validation of differentially expressed miRNAs after TGF-β1 stimulation in the discovery group using qRT-PCR. Data are presented as relative expression (2^-ΔCp) normalized to RNU48. *p<0.05, **p<0.01.</p

Upregulation of ECM genes and α-SMA after TGF-β1 stimulation in primary parenchymal lung fibroblasts.

<p>(A) Effective TGF-β1 stimulation of control fibroblasts in the discovery group was confirmed by the upregulation of <i>FN1</i> (fibronectin 1), <i>COL1A1</i> (collagen type I alpha I) and <i>α-SMA</i> (alpha-smooth muscle actin), genes that are well-known to be affected by TGF-β. (B) These genes were also upregulated in the control and COPD fibroblasts in the replication group after 2.5 ng/ml TGF-β1 and (C) after 7.5 ng/ml TGF-β1 stimulation. Data are presented as relative expression (2^-ΔCp). **p<0.01, ***p<0.001, ****p<0.0001.</p