Analysis of sputum gene expression data in Asthma and COPD
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ABSTRACT:
PROVIDER: PRJNA622797 | ENA |
REPOSITORIES: ENA
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Project description:In addition to analyzing whole-genome methylation, we concomitantly evaluated sputum cell gene expression in the context of chronic inflammatory lung disease. Nucleic acids were purified from sputum samples of subjects with Asthma, COPD as well as healthy controls. Gene expression was analyzed on the Agilent Human GE 4x44k v2 platform.
2020-10-25 | GSE148004 | GEO
Project description:We evaluated the applicability and usability of whole-genome methylomics of sputum samples in molecular profiling of chronic inflammatory lung diseases. Genomic DNA was purified from sputum samples of subjects with Asthma, COPD as well as healthy controls and analyzed on the Illumina Infinium HumanMethylation 450k platform.
2020-10-25 | GSE148000 | GEO
Project description:Background: Macrophages are important cells in pathogenesis of obstructive lung diseases including asthma and chronic obstructive pulmonary disease (COPD). The aim of the study was a multivariate, genetic, comparative analysis of macrophages from patients with asthma and COPD. Methods: Macrophages were isolated from induced sputum (IS) by magnetic bead separation. Transcriptomic measurements were carried out using Affymetrix Human Gene 2.1 ST ArrayStrip in 17 samples: 8 asthma (4 ICS naive , 4 ICS treated), 4 COPD and 5 control samples. The expression of the most significantly differentiating genes was evaluated by real time PCR in 34 samples (15 patients with asthma, 11 patients with COPD and 17 controls). Results: USP53 was the only gene differentially expressed (p adjusted clue =0.09) in the comparison between ICS naïve and ICS treated asthma. The PCR verification showed increased expression of BTF3, CDS2, DNAJC13, DDX5, GNAI2, SCGB1A1, SIRPB1, TRAF3IP, USP53, WDR49 in the asthma compared to COPD group. The changed gene expression profile of macrophages were characterized mostly by gene ontology terms linked with cell motility, cilium function, cell junction and adhesion organization. Conclusions: Gene expression profiling of sputum macrophages revealed distinct molecular capacity in asthma and COPD. The role of sputum macrophages in the pathophysiology of obstructive lung diseases is probably connected with biological processes associated with their motility, cilium dysfunction and cell junction organization.
2018-08-09 | GSE112260 | GEO
Project description:Analysis of sputum methylation data in Asthma and COPD
| PRJNA622793 | ENA
Project description:Gene expression profiles were generated from induced sputum samples in asthma and healthy controls. The study identified differential gene expression and pathways in severe asthma.
2019-09-12 | GSE137268 | GEO
Project description:This study identifies differentially expression genes in the sputum of people with eosinophilic, neutrophilic and paucigranulocytic asthma. A selection of markers identified using this microarray were further validated using qPCR on a wider sample set. Gene expression profiles were generated from induced sputum samples from 47 asthma patients and were grouped by the inflammatory phenotype assigned using sputum cell counts into neutrophilic asthma (n=12), eosinophilic asthma (n=17) and paucigranulocytic asthma (n=18). RNA was extracted, amplified and hybridised to Illumina Sentrix HumanRef-8 Version 2 Expression BeadChips, and genes that were differentially expressed between asthma inflammatory phenotypes were compared.
2014-03-25 | E-GEOD-45111 | biostudies-arrayexpress
Project description:Genetic characterization of macrophages from induced sputum of asthma and COPD patients
| PRJNA445404 | ENA
Project description:Background: MicroRNAs are potent regulators of biologic systems that are critical to tissue homeostasis. Individual microRNAs have been identified in airway samples. However, a systems analysis of the microRNA-mRNA networks present in the sputum that contribute to airway inflammation in asthma has not been published. Methods: We conducted a genome-wide analysis of microRNA and messenger RNA (mRNA) in the sputum from patients with asthma and correlated expression with clinical phenotypes. Weighted gene correlation network analysis (WGCNA) was implemented to identify microRNA networks (modules) that significantly correlate with clinical features of asthma and mRNA expression networks. MicroRNA expression in peripheral blood neutrophils and lymphocytes, and in situ hybridization of the sputum were used to identify the cellular sources of microRNAs. MicroRNA expression obtained before and after ozone exposure was also used to identify changes associated with neutrophil counts in the airway. Results: Six microRNA modules were associated with clinical features of asthma. A single module (nely) was associated with a history of hospitalizations, lung function impairment, and numbers of neutrophils and lymphocytes in the sputum. Of the 12 microRNAs in the nely module, hsa-miR-223-3p was the highest expressed microRNA in neutrophils and was associated with increased neutrophil counts in the sputum in response to ozone exposure. Multiple microRNAs in the nely module correlated with two mRNA modules enriched for toll-like receptor (TLR) and Th17 signaling, and endoplasmic reticulum stress. Hsa-miR-223-3p was a key regulator of the TLR and Th17 pathways in the sputum of subjects with asthma. Conclusions: This study of sputum microRNA and mRNA expression from patients with asthma demonstrates the existence of microRNA networks and genes that are associated with features of asthma severity. Among these, hsa-miR-223-3p, a neutrophil-derived microRNA, regulates TLR/Th17 signaling and endoplasmic reticulum stress.
2020-03-04 | GSE146306 | GEO
Project description:The role of eosinophilic inflammation in chronic obstructive pulmonary disease (COPD) pathogenesis is unknown and is probably different than in asthma. The molecular processes underlying the differences between eosinophils from asthma and COPD have not been studied. The study group included 5 patients with asthma and 4 patients with COPD. The RNA-Seq data analysis identified 26 differentially expressed genes between COPD and asthma (according to adjusted p-value). In total, 6 genes were up-regulated (CCL3L1, CCL4L2, SERPINB2, PRSS21, GPR82) and 20 were down-regulated (e.g. JUN, IFITM3, DUSP1, GNG7, ZNF107, BCL6) in peripheral eosinophils of COPD patients compared to asthma. Biological processes associated with down-regulated genes were cell differentiation, positive regulation of RNA metabolic process. The genes associated with signaling of IL-4 and IL-13 pathway were down-regulated in COPD eosinophils compared to asthma. Peripheral eosinophils from COPD and asthma patients present different transcriptomic profiles suggesting their different function in pathobiology of both obstructive airway diseases.
2024-01-01 | GSE237284 | GEO
Project description:This study identifies differentially expression genes in the sputum of people with eosinophilic, neutrophilic and paucigranulocytic asthma. A selection of markers identified using this microarray were further validated using qPCR on a wider sample set.
2014-03-25 | GSE45111 | GEO