Project description:Pseudomonas aeruginosa airway infection is the primary cause of death in Cystic Fibrosis (CF). During early infection P. aeruginosa produces multiple virulence factors, which cause acute pulmonary disease and are largely regulated by quorum sensing (QS) intercellular signalling networks. Longitudinal clinical studies have observed the loss, through adaptive mutation, of QS and QS-related virulence in late chronic infection. Although the mechanisms are not understood, infection with QS mutants has been linked to a worse outcome for CF patients. By comparing QS-active and QS-inactive P. aeruginosa CF isolates, we have identified novel virulence factors and pathways associated with QS disruption. In particular, we noted factors implicating increased intra-phagocyte survival. Our data present novel targets as candidates for future CF therapies. Some of these targets are already the subject of drug development programmes for the treatment of other bacterial pathogens and may provide cross-over benefit to the CF population. Refer to individual Series. This SuperSeries is composed of the following subset Series: GSE25128: Gene expression data from Pseudomonas aeruginosa strains isolated from cystic fibrosis lung infections GSE25129: Comparative genomic hybridisation data from Pseudomonas aeruginosa strains isolated from cystic fibrosis lung infections
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:In this study, we investigated whether miRNA deregulation might underlie the functional abnormalities of cystic fibrosis (CF) macrophages. To this aim we performed miRNA profiling in macrophages from CF and non-CF macrophages. This led to the identification of a panel of differentially expressed miRNAs in CF macrophages compared to non-CF cells.
Project description:Pseudomonas aeruginosa airway infection is the primary cause of death in Cystic Fibrosis (CF). During early infection P. aeruginosa produces multiple virulence factors, which cause acute pulmonary disease and are largely regulated by quorum sensing (QS) intercellular signalling networks. Longitudinal clinical studies have observed the loss, through adaptive mutation, of QS and QS-related virulence in late chronic infection. Although the mechanisms are not understood, infection with QS mutants has been linked to a worse outcome for CF patients. By comparing QS-active and QS-inactive P. aeruginosa CF isolates, we have identified novel virulence factors and pathways associated with QS disruption. In particular, we noted factors implicating increased intra-phagocyte survival. Our data present novel targets as candidates for future CF therapies. Some of these targets are already the subject of drug development programmes for the treatment of other bacterial pathogens and may provide cross-over benefit to the CF population. This SuperSeries is composed of the SubSeries listed below.
Project description:Chronic Pseudomonas aeruginosa infections evades antibiotic therapy and are associated with mortality in cystic fibrosis (CF) patients. We find that in vitro resistance evolution of P.aeruginosa towards clinically relevant antibiotics leads to phenotypic convergence towards distinct states. These states are associated with collateral sensitivity towards several antibiotic classes and encoded by mutations in antibiotic resistance genes, including transcriptional regulator nfxB. Longitudinal analysis of isolates from CF patients reveals similar and defined phenotypic states, which are associated with extinction of specific sub-lineages in patients. In depth investigation of chronic P.aeruginosa populations in a CF patient during antibiotic therapy revealed dramatic genotypic and phenotypic convergence. Notably, fluoroquinolone-resistant subpopulations harboring nfxB mutations were eradicated by antibiotic therapy as predicted by our in vitro data. This study supports the hypothesis that antibiotic treatment of chronic infections can be optimized by targeting phenotypic states associated with specific mutations to improve treatment success in chronic infections.
Project description:A small-scale whole genome microarray study of gene expression in human native nasal epithelial cells from F508del-CFTR homozygous CF patients and non-CF controls. We used the custom designed Affymetrix HsAirwaya520108F Arrays to compare gene expression in 5 CF and 5 non CF nasal epithelial cell samples.