Project description:To better understand the molecular determinants of lung disease variability among patients with cystic fibrosis (CF), we carried out an epigenome-wide association study (EWAS) in sputum samples from patients with CF. Sputum samples were collected from 50 patients with CF at four time points (visit 1, 2, 3 and 4) over an 18-month follow-up period. We profiled 64 sputum samples collected at visit 1 and 2, using human methylation BeadChips (EPIC). Selected CpG sites were reassessed in independent sputum samples collected at visit 3 and 4, by pyrosequencing. Overall, we provide the first longitudinal assessment of genome-wide DNA methylation in a cohort of patients with CF and identify CpG sites that predict clinical traits of key importance for lung disease. Specifically, we identified (i) differentially methylated CpG sites that correlate with lung function (FEV1pp), (ii) a DNA methylation signature that predicts patients with a pulmonary exacerbation and (iii) CpG sites that split patients with declining lung function from those whose lung function either improved or remained stable.
Project description:Little is known about the lung microbiome dynamics and host-microbiome interactions in relation to chronic obstructive pulmonary disease (COPD) exacerbations and in patient subgroups based on smoking status and disease severity. Here we performed a 16S ribosomal RNA survey on sputum microbiome from 16 healthy and 43 COPD subjects. For COPD subjects, a longitudinal sampling was performed from stable state to exacerbations, at two and six weeks post-exacerbations and at six months from first stable visit. Host sputum transcriptome were characterized for a subset of COPD patient samples.
2021-03-21 | GSE112165 | GEO
Project description:Sputum microbiota of patients with bronchiectasis
Project description:This study evaluates the peripheral blood mononuclear cell transcriptomes of cornea transplant (CT) recipients from a prospective multi-center clinical study. 244 CT patients were recruited in 5 European clinical centers and biological samples were collected before and 6- and 12-months after the CT. Two groups of patients were recruited: 102 CT patients with a high risk of rejection and 142 with a low risk of rejection. The risk of rejection was defined according to consensus clinical features associated with higher or lower risk of rejection. The gene expression profiles from a total of 572 samples (277 high-risk and 296 low-risk) were generated using Affymetrix transcriptome-wide gene-level expression profiling microarray.
