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RNA-seq of TGF-β-Induced A549 cells for comparison with H3K4me3 ChIP-seq data

ABSTRACT: RNA-seq was performed to compare changes in broad H3K4me3 occupancy with gene expression levels during TGF-β-induced epithelial-to-mesenchymal transition (EMT) in A549 lung adenocarcinoma cells, allowing for the identification of transcriptional changes associated with EMT.

ORGANISM(S): Homo sapiens

PROVIDER: GSE285672 | GEO | 2026/07/31

REPOSITORIES: GEO

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Project description:Idiopathic pulmonary fibrosis (IPF) is a refractory and lethal interstitial lung disease; EBV has previously been localised to alveolar epithelial cells of IPF patients. The molecular process of the epithelial mesenchymal transition (EMT) in IPF remains still unknown. Using an oligonucleotide array analysis, we observed dysregulated expression of members of non-canonical Wnt family in EBV infected A549 after TGF?1 exposure. TGF?1 exposure induced EMT increasing ?-Smooth Muscle Actin (ACTC) and Wnt5b gene expression, but decreasing E-cadherin and DKK1. When data were analyzed as a function of Wnt5b in EMT, significance differences in ACTC and E-cadherin gene expression, active TGF?1 protein levels and collagen deposition could be detected. Treatment with 9-cis Retinoic Acid (9-cisRA) significantly inhibited Wnt5b expression in both EBV infected and non-infected A549, followed by decreased collagen deposition and active TGF?1 protein level. Specific non-canonical Wnt-signalling genes are dysregulated in EBV infected cells and A549 treated with TGF?1; while, 9-cisRA treatment appears to attenuate EMT process in vitro. Experiment Overall Design: EBV infected cells and A549 were cultured in RPMI1640+5%FCS, and exposed to 10ng/ml TGF beta1 for 4hours. RNA isolation, cDNA synthesis, in vitro transcription and microarray analysis were performed as previously reported (Kieran et al., 2003). All analysis were microarrayed in duplicate. Image files were obtained through Affymetrix GeneChip software (MAS5), subsequently robust multichip analysis (RMA) was performed. Expression data were compared to control, p<0.05 correlated values and a signal log ratio of 0.6 or greater (equivalent to a fold change in expression of 1.5 or greater) were taken to identify significant differential regulation (Bolstad et al., 2003). All the SLRs data resulting from the comparative analyses in duplicate were reported in a scatter plot graph to determine the reliability of the assay and the linearity by r2. For all the microarray assays r2 value was higher than 0.98. Using normalised RMA values by Gene Cluster Software, Average Linkage Hierarchical Cluster Analysis was performed using TreeView analysis software (Eisen et al., 1998). Lists of dysregulated genes in both TGF?1 exposed cell lines were curated via the publicly available DAVID, Gene-Ontology (GOCharts) and Functional Annotation Clustering databases (Dennis et al., 2003).

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RNA-seq of TGF-β-Induced A549 cells for comparison with H3K4me3 ChIP-seq data

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