Ontology highlight
ABSTRACT:
PROVIDER: PRJNA495633 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Lung macrophages are major participants in the pulmonary innate immune response. In the cystic fibrosis (CF) lung, the inability of lung macrophages to successfully regulate the exaggerated inflammatory response suggests dysfunctional innate immune cell function. In this study, we aim to gain insight into innate immune cell dysfunction in CF by investigating alterations in DNA methylation in bronchoalveolar lavage (BAL) cells, composed primarily of lung macrophages of CF subjects compared with healthy controls. All analyses were performed using primary alveolar macrophages from human subjects collected via bronchoalveolar lavage. Epigenome-wide DNA methylation was examined via Illumina MethylationEPIC (850 K) array. Targeted next-generation bisulfite sequencing was used to validate selected differentially methylated CpGs. Methylation-based sample classification was performed using the recursively partitioned mixture model (RPMM) and was tested against sample case-control status. Differentially methylated loci were identified by fitting linear models with adjustment of age, sex, estimated cell type proportions, and repeat measurement.
2019-02-15 | GSE126646 | GEO
Project description:Airway microbiota composition correlates with cystic fibrosis (CF) progression, however, microbial drivers of disease remain unclear. MS-based metaproteomics of bronchoalveolar lavage fluid (BALF) offers insights into both host and microbe dynamics and potential interactions. However, detection of microbial proteins, and analysis of their interaction with host proteins is analytically challenging. As a solution, we have developed a novel, integrated workflow coupling deep MS-based BALF analysis, with customized bioinformatic processing of both host and microbial proteins, generating a panel of verified host and microbe peptide candidates suitable for targeted analysis within individual patient samples. We have utilized this workflow in our ongoing work to identify a promising host and microbe peptide panel for application to CF disease progression studies.
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Project description:Progression of the bronchoalveolar lavage microbiome and disease markers in pre-school children with Cystic Fibrosis
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Project description:Application of a mass spectrometry -based approach to assess the lung microbiota composition and the associated metaproteomic functionality of subjects with cystic fibrosis
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Project description:16S bacterial profiling in bronchoalveolar lavage fluid from patients with Cystic Fibrosis
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Project description:We used the scRNA-seq to characterize disease-related heterogeneity within cell populations of macrophages/monocytes in the bronchoalveolar lavage fluid from West Highland white terriers either healthy or affected with canine idioapthic pulmonary fibrosis. The disease is still not well understood, occurs in old West Highland white terriers and results from deposition of fibrotic tissue in the lung parenchyma causing respiratory failure.
2020-12-02 | E-MTAB-9623 | biostudies-arrayexpress
Project description:The pathogenesis of idiopathic pulmonary fibrosis is multifactorial and characterized by progressive fibrosis and excessive accumulation of extracellular matrix in the interstitium of the lung, and driven by an imbalance between anti-fibrotic and pro-fibrotic factors leading to collagen deposition. In the present study we wanted to identify proteins involved in these processes, and performed high-resolution proteomic profiling of bronchoalveolar lavage (BAL) from IPF patients and controls. The proteomic analysis of BAL demonstrated that the complement system was highly differentially regulated in IPF patients as compared with controls.
2023-07-31 | PXD036638 | Pride
Project description:AJ mouse is susceptible to lung carcinogenesis from urethane treatment and is a good model for human adenocarcinoma. We completed a study using microarray analysis of bronchoalveolar lavage cells from control or urethane treated mice. A unique macrophage expression signature in the lung tumor microenvironment was able to correctly classify the lavage samples. Experiment Overall Design: RNA from bronchoalveolar lavage cells of age matched untreated AJ mice controls (C) or from urethane treated (T) AJ mice was prepared. Datasets were accurately classified using a unique macrophage gene expression signature derived from the tumor microenvironment.
2008-04-07 | E-GEOD-7258 | biostudies-arrayexpress
Project description:To determine if differences in the severity of pulmonary infection in cystic fibrosis been seen in late isolates od Pseudomonas aeruginosa and Burkholderia cepacia are associated with differences in the initial repsonse of alveolar macrophages (AM) to these pathogens, we assessed gene expression changes in human AM in response to infection with a laboratoty strain, early and late clinical isolates of P. aeruginosa, and B. cepacia. Experiment Overall Design: Alveolar macrophages were obtained from bronchoalveolar lavage. Experiment Overall Design: Two clinical strains isolated from the sputum of an individual with CF, AD2A and AD15B (provided by J. Burns, University of Washington, Seattle). AD2A is an early clinical isolate, and AD15B is a late clinical isolate; both were derived from the same individual.
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Project description:Mucus accumulation is a key feature of respiratory diseases such as cystic fibrosis (CF) and chronic obstructive pulmonary disease (COPD). This is associated with goblet cell metaplasia and mucin overexpression, which can be induced by the increased activity of neutrophil elastase. The aim of the study was to characterization of mucus and epithelial cell proteomics in a porcine pancreatic elastase (PPE) mouse model of COPD/CF. The major proteins detected in mucus plugs obtained from PPE-treated mice included mucins Muc5ac and Muc5b, mucus-related proteins Clca1, Fcgbp, and Bpifb1. These proteins were upregulated in bronchoalveolar lavage (BAL) fluid and epithelial cells in mice exposed to elastase. Similar changes were found in BAL fluid of COPD patients.
2018-10-22 | PXD006770 | Pride