Overview of data analysis on COPD cohort.

<p>Overview of data analysis on COPD cohort.</p

Correlation network illustrating functional co-clustering of analytes associated with FEV₁, FEV₁/FVC and DLCO.

<p>Analytes are plotted in a network using Cytoscape <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038629#pone.0038629-Shannon1" target="_blank">[83]</a> where nodes represent analytes and edges represent significant correlations (<i>r</i> >0.4, <i>p</i><0.05, corrected for multiple testing). Analytes are colored according to whether they were associated with FEV₁ related parameters (green), DLCO (red) or both DLCO and FEV₁ related parameters (orange) in univariate regression. Node size is proportional to the number of lung function parameters that showed significant association with a given analyte. Clusters of co-expressed analytes with similar function are highlighted by dotted regions in the graph as neutrophil function (orange), systemic inflammation (blue) and growth factor pathways (grey).</p

Multivariate analysis of protein analyte data for COPD subjects.

<p>Spearman correlation and adjusted R squared values were computed using test set samples, in a 5-fold nested cross-validation scheme, averaged over 10 random seeds. R squared values were adjusted for the number of predictor terms in the model.</p

Univariate regression analysis of protein analytes versus lung function parameters in COPD subjects with and without metabolic syndrome.

<p>Significance (<i>p</i> values) and effect sizes (spearman correlation) are listed for biomarker associations with lung function parameters. Interaction <i>p</i> values indicate significance of differences in biomarker associations with lung function parameters, between metabolic syndrome and non- metabolic syndrome groups.</p

Association of MPO with FEV₁/FVC and Fibrinogen with DLCO in COPD patients with and without metabolic syndrome.

<p>Log2-transformed levels of MPO (A, C) and Fibrinogen (B, D) (ng/ml for MPO and mg/dl for Fibrinogen) are plotted against covariate adjusted values for FEV₁/FVC and DLCO, respectively in COPD patients with (A, B) and without (C, D) metabolic syndrome (<i>r</i> values indicate spearman correlation, covariates include age, sex, BMI, pack years and smoking status).</p

Protein analyte differences between COPD and control disease severity groups.

<p>Data are expressed as median (interquartile range) in ng/ml for individual analytes, except for Fibrinogen which is in mg/dl.</p><p>All analyte data shown are from profiling on the RBM Luminex platform, except for Fibrinogen which was tested at Hospital Grosshansdorf. COPD subjects were grouped as GOLD I/II (mild/moderate) and GOLD III/IV (severe/very severe). ANOVA was used for group-wise comparisons, except for analytes noted with *, which did not follow a normal distribution and a non-parametric Kruskal Wallis test was used.</p

Bleomycin induces inflammatory and fibrotic changes in the lungs of mice.

<p>The numbers of BALF inflammatory cells increased after either a single (<b>A</b>) or repetitive (<b>D</b> bleomycin (black bars) instillation compared to the saline treated controls (white bars). Both a single (<b>B</b>) and repetitive (<b>E</b>) instillation of bleomycin led to increased fibrotic tissue in the lung. Changes in work of inflation (WoI), a measure of lung mechanics, were minimal in both the single (<b>C</b>) and repetitive (<b>F</b>) systems. Data are expressed as mean ± SEM of n = 7–8 mice. Significance (relative to the time-matched control at each time point) was determined using a Student’s t-test and is denoted as follows: *p<0.05; **p<0.01; and ***p<0.001.</p

Unsupervised hierarchical clustering of genes differentially expressed between bleomycin and saline treated mice across time points.

<p>A union of 730 genes differentially expressed between bleomycin and saline treatments (fold-difference >2, false discovery rate (FDR) <0.05) were clustered across all mouse samples. Three distinct clusters of genes were revealed corresponding to phases of the bleomycin response, with most up-regulated genes being specific to the 7–14 days post-bleomycin treatment clusters. Inflammation phase (1–2 days) samples also clustered together and showed up-regulation of a subset of genes, while late fibrosis phase (21–35 days) samples also showed moderate up-regulation of a subset of genes.</p

The ALK-5 inhibitor, SB525334, attenuates bleomycin-induced lung fibrosis.

<p>SB525334 was administered prophylactically (<b>A</b>) or therapeutically (<b>B</b>) at a dose of 60 mg/kg in chow beginning 1 day prior or 5 days after bleomycin instillation, respectively. SB525334 inhibited the lung fibrosis under both dosing conditions. Data are expressed as a percentage of the total collagen I stained area in the bleomycin vehicle control group ± SEM of n = 10–12 bleomycin treated mice in the prophylactic study and n = 6–9 in the therapeutic study. Saline treated control groups consisted of n = 5–7 mice. Significance (relative to the bleomycin vehicle control) was determined using a 2-tailed t-testand is denoted as **p<0.01 or ***p<0.001.</p

Heatmap of gene set enrichment of mouse bleomycin-induced signatures in clinical IPF datasets.

<p>GSEA was performed for gene sets comprised of up-regulated genes in response to bleomycin at each time point from the mouse model. Enrichment of each gene set (denoted in rows) was determined against ranked lists of genes from clinical datasets comparing IPF vs. non-IPF conditions as well as IPF with acute exacerbation vs. stable IPF from two datasets (GSE2052, GSE10667, denoted in columns). Enrichment scores were plotted in a heatmap where gene sets enriched in IPF samples (nominal p<0.05, FDR <0.25) were denoted in red with intensity based on enrichment score (calculated in GSEA).</p