Additional file 2: of Activation and polarization of circulating monocytes in severe chronic obstructive pulmonary disease

Figure S2. Analysis of CCR2 and CCR5 expression by classical and non-classical monocytes. Classical (a, c, e) and non-classical (b, d, f) monocytes were stained for CCR2 and CCR5 expression. The data are presented for the percentage of CCR2-positive (a, b), CCR5-positive (c, d), and CCR2- and CCR5-double positive (e, f) monocytes. The data are presented as the percentage of total classical or non-classical monocytes for each group. (PDF 13 kb

Additional file 3: of Activation and polarization of circulating monocytes in severe chronic obstructive pulmonary disease

Figure S3. Altered surface expression density of monocytes in COPD patients. Classical (a-c) and non-classical monocytes (panels d-f) were stained for CCR2 (a, d), CCR5 (b, e), and CD14 (c, f) expression. The degree of expression is reported as the mean fluorescence intensity (MFI). * = p < 0.05 and ** = p < 0.01 relative to the normal. (PDF 13 kb

Additional file 1: of Activation and polarization of circulating monocytes in severe chronic obstructive pulmonary disease

Figure S1. Flow cytometry gating strategy to identify and characterize monocyte subpopulations. PMBCs were stained as described in the Methods section and at least 250,000 events per sample were collected. Singlets (red rectangle, panel a) were gated using the forward side-scatter area (FSC-A) vs height (FSC-H). From the singlets gate, monocytes (red oval, panel b) were gated using the FSC-A vs side-scatter area (SSC-A). The monocytes were further gated using CD14 vs CD16 and are indicated by the red boxes (panel c). The classical monocytes are CD14 + CD16-; the intermediate monocytes are CD14 + CD16+; and the non-classical monocytes are CD14DIMCD16+. From the classical gate, cells stained for CCR2, CCR5, CD163, CD206, and IL-13Ra1 are shown (panels i-m), and from the non-classical gate, the staining for CCR2, CCR5, CD163, CD206, and IL-13Ra1 are shown in panels d-h. The red histograms indicate the isotype control for each marker. The black histograms indicated the expression of each marker. (PDF 311 kb

Additional file 4: of Activation and polarization of circulating monocytes in severe chronic obstructive pulmonary disease

Figure S4. Increased CX3CR1 expression density in CD206 + CCR5+ non-classical monocytes in severe COPD patients. CD206 + CCR5+ co-expressing cells were stained for CX3CR1, and the mean fluorescence intensity (MFI) for each patient population was determined. Results represent the mean MFI ± SEM of all subjects in each subject group. * = p < 0.05. (PDF 4 kb

Additional file 5: of Activation and polarization of circulating monocytes in severe chronic obstructive pulmonary disease

Figure S5. Reduced numbers of CD206 + CCR5+ monocytes in severe COPD. CD206 + CCR5+ classical (a) and CD206 + CCR5+ non-classical (b) monocytes data were expressed as the number of cells per μl. * = p < 0.05; ** = p < 0.01; and *** = p < 0.001 relative to the normal. (PDF 11 kb

Additional file 1: of Ensemble genomic analysis in human lung tissue identifies novel genes for chronic obstructive pulmonary disease

Supplemental Data. Supplemental supporting figures (Figures S1–S10) and tables (Tables S1-S8). (PDF 4193 kb

Additional file 2: of Ensemble genomic analysis in human lung tissue identifies novel genes for chronic obstructive pulmonary disease

Supplemental Table S5. Table containing Sherlock results. (PDF 68 kb

DNA methylation profiling in human lung tissue identifies genes associated with COPD

<p>Chronic obstructive pulmonary disease (COPD) is a smoking-related disease characterized by genetic and phenotypic heterogeneity. Although association studies have identified multiple genomic regions with replicated associations to COPD, genetic variation only partially explains the susceptibility to lung disease, and suggests the relevance of epigenetic investigations. We performed genome-wide DNA methylation profiling in homogenized lung tissue samples from 46 control subjects with normal lung function and 114 subjects with COPD, all former smokers. The differentially methylated loci were integrated with previous genome-wide association study results. The top 535 differentially methylated sites, filtered for a minimum mean methylation difference of 5% between cases and controls, were enriched for CpG shelves and shores. Pathway analysis revealed enrichment for transcription factors. The top differentially methylated sites from the intersection with previous GWAS were in <i>CHRM1, GLT1D1</i>, and <i>C10orf11</i>; sorted by GWAS <i>P</i>-value, the top sites included <i>FRMD4A, THSD4</i>, and <i>C10orf11</i>. Epigenetic association studies complement genetic association studies to identify genes potentially involved in COPD pathogenesis. Enrichment for genes implicated in asthma and lung function and for transcription factors suggests the potential pathogenic relevance of genes identified through differential methylation and the intersection with a broader range of GWAS associations.</p

Additional file 2: Table S2. of Serum IgG subclass levels and risk of exacerbations and hospitalizations in patients with COPD

Median and interquartile range related to each IgG subclass according to the presence or absence of corresponding IgG subclass deficiency in MACRO and STATCOPE cohorts. (DOCX 15 kb

Additional file 6: Table S4. of Serum IgG subclass levels and risk of exacerbations and hospitalizations in patients with COPD

Interactions between IgG subclass levels and inhaled steroid use at enrollment and use of systemic steroids in previous 12 months for both outcomes of interest (time to first exacerbation and time to first hospitalization). (DOCX 15 kb