Identification of the gene expression in IPF lung fibroblasts after demethylation
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE69764 | GEO | 2016/02/16
SECONDARY ACCESSION(S): PRJNA286695
REPOSITORIES: GEO
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Project description:Idiopathic pulmonary fibrosis (IPF) is a progressive lung disease. Although the pathogenesis is poorly understood, evidence suggests that genetic and epigenetic alterations, such as DNA methylation, may play a key role. We used microarrays to see the gene expression in IPF fibroblasts after demethylation agent 5'-azacytidine treatment. Human IPF lung fibroblasts were cultured and then treated with 5'-azacytidine 5uM 24 hours. RNA were extracted and hybridized on Affymetrix microarrays.
2016-02-16 | E-GEOD-69764 | biostudies-arrayexpress
Project description:The activated fibroblast is the central effector cell for the progressive fibrotic process that characterizes idiopathic pulmonary fibrosis (IPF). An understanding of the genomic phenotype of this cell in isolation is essential to the understanding of disease pathogenesis and is integral to strategizing therapeutic trials. Employing a unique technique that minimizes cellular phenotypic alterations, we characterized the genomic phenotype of non-cultured pulmonary fibroblasts from the lungs of patients with advanced IPF. This approach revealed several novel genes and pathways previously unreported in IPF fibroblasts. Specifically, we demonstrate altered expression in proteasomal constituents, ubiquitination mediators, the Wnt pathway and several cell cycle regulators suggestive of loss of normal cell cycle controls. The pro-inflammatory cytokine CXCL12 was also up-regulated which may provide a mechanism for fibrocytes’ recruitment, while up-regulated oncogenic KIT may promote fibroblast over proliferation. Paradoxically, pro-apoptotic inducers such as death inducing ligand TRAIL (TNFSF10) and pro-apoptotic Bax were also up-regulated. This comprehensive description of altered gene expression within IPF fibroblasts sheds further light on the complex interactions that characterize IPF. Further studies including therapeutic interventions directed at these pathways hold promise for the treatment of this devastating disease. 58 samples of total RNA isolated from 12 lungs of patients with end-stage idiopathic pulmonary fibrosis and 6 donors of normal lungs (controls) who were designated brain dead, non-diseased donors whose lungs failed criteria for transplantation and who were organ donors for research. RNA extraction followed the Qiagen RNeasy Kit using QIshredder columns for shredding of DNA contiminants. Experimental/control samples were amplified amino-allylated RNA labeled with Cy5 and Stratagene Reference RNA was amplified and amino-allylated and labeled with Cy3. Amplification was one round using Ambion MessageAmp II kit with amino-allylated UTP according to the protocol of the Duke University Institute for Genome Sciences and Policy. Amplification and amino-allylation of the Stratagene Reference RNA and Hybridization of Reference with patient samples and controls was done by the Duke Institute for Genomic Sciences and Policy.
2010-05-19 | E-GEOD-17978 | biostudies-arrayexpress
Project description:Idiopathic pulmonary fibrosis (IPF) is a chronic progressive interstitial lung disease characterized by patchy scarring of the distal lung with limited therapeutic options and poor prognosis. Here, we show that conditional deletion of the ubiquitin ligase Nedd4-2 in lung epithelial cells in adult mice produces chronic lung disease that shares key features with IPF including progressive fibrosis and bronchiolization with increased expression of Muc5b in peripheral airways, honeycombing and characteristic alterations in the lung proteome
2020-03-20 | PXD011116 | Pride
Project description:The activated fibroblast is the central effector cell for the progressive fibrotic process that characterizes idiopathic pulmonary fibrosis (IPF). An understanding of the genomic phenotype of this cell in isolation is essential to the understanding of disease pathogenesis and is integral to strategizing therapeutic trials. Employing a unique technique that minimizes cellular phenotypic alterations, we characterized the genomic phenotype of non-cultured pulmonary fibroblasts from the lungs of patients with advanced IPF. This approach revealed several novel genes and pathways previously unreported in IPF fibroblasts. Specifically, we demonstrate altered expression in proteasomal constituents, ubiquitination mediators, the Wnt pathway and several cell cycle regulators suggestive of loss of normal cell cycle controls. The pro-inflammatory cytokine CXCL12 was also up-regulated which may provide a mechanism for fibrocytes’ recruitment, while up-regulated oncogenic KIT may promote fibroblast over proliferation. Paradoxically, pro-apoptotic inducers such as death inducing ligand TRAIL (TNFSF10) and pro-apoptotic Bax were also up-regulated. This comprehensive description of altered gene expression within IPF fibroblasts sheds further light on the complex interactions that characterize IPF. Further studies including therapeutic interventions directed at these pathways hold promise for the treatment of this devastating disease.
2010-05-19 | GSE17978 | GEO
Project description:Viruses in acute exacerbations of idiopathic pulmonary fibrosis Keywords: viral detection BAL from patients with acute exacerbations of IPF and stable IPF were hybridized to a pan-viral cDNA microarray to evaluate the presence of virus during these episodes
2011-03-03 | E-GEOD-27578 | biostudies-arrayexpress
Project description:Idiopathic pulmonary fibrosis (IPF) is a chronic progressive interstitial lung disease characterized by patchy scarring of the distal lung with limited therapeutic options and poor prognosis. Here, we show that conditional deletion of the ubiquitin ligase Nedd4-2 in lung epithelial cells in adult mice produces chronic lung disease that shares key features with IPF including progressive fibrosis and bronchiolization with increased expression of Muc5b in peripheral airways, honeycombing and characteristic alterations in the lung proteome.
2020-03-20 | PXD011129 | Pride
Project description:Idiopathic Pulmonary Fibrosis (IPF) is a chronic, progressive, and often fatal disorder. Using an in-silico data-driven approach, we identified a robust connection between the transcriptomic perturbations in IPF disease and those induced by saracatinib, a selective Src kinase inhibitor, originally developed for oncological indications.We investigated the anti-fibrotic efficacy of saracatinib in two in vivo modeles (bleomycin and recombinant adenovirus transforming growth factor-beta (Ad-TGF-β) murine models of pulmonary fibrosis).
2022-08-30 | GSE178457 | GEO
Project description:Idiopathic pulmonary fibrosis (IPF) is a progressive lethal interstitial lung disease of unkown etiology with limited effective therapies. The pathogenic mechanisms of IPF remain unkown. Emerging evidences indicate that abnormal behaviors of fibroblasts in IPF are associated with a variety of genetic alterations and aberrant reactivation of developmental signaling pathways. We compared gene expression profiles in fibrotic lung tissues from IPF patients and normal lung tissues from patients with primary spontaneous pneumothorax using cDNA microarray to examine the mechnisms involved in the pathogenesis of IPF.
2015-08-15 | GSE72073 | GEO
Project description:Idiopathic pulmonary fibrosis (IPF) is an untreatable fibrotic lung disease characterized by fibroblast proliferation and epithelial mesenchymal transition.miRNA let-7d and mir30b were found to be signifcantly down regulated in IPF. Compared to control we over expressed these miRNAs in Human Fetal Lung Fibroblast cell line
2013-06-06 | GSE38530 | GEO
Project description:The activated fibroblast is the putative effector cell for the progressive fibrotic phenotype idiopathic pulmonary fibrosis (IPF). Recent studies investigating global gene expression differences between normal and IPF fibroblasts indicate that changes in gene expression occur in these fibroblasts in culture. Employing a technique that minimizes cellular phenotypic alterations, we characterized the global gene expression changes in pulmonary fibroblasts by comparing both cultured and non-cultured IPF and normal cells. The results revealed dramatic difference between IPF and normal fibroblast as they progressed in culture. While there are significant differences in gene expression between IPF and normal fibroblast at P0, after 3 passages in culture, no statistically significant difference was observed. This study is a comprehensive investigation of gene expression within IPF and normal fibroblasts in culture and sheds light on the efficacy of in vitro models of pulmonary fibroblasts.
2017-09-07 | GSE87175 | GEO