E-GEOD-5457 - Transcription profiling of EBV infected human A549 cells exposed to 10ng/ml TGF beta1 for 4 hours

Status
Released on 13 June 2008, last updated on 12 October 2011
Organism
Homo sapiens
Samples (8)
Array (1)
Protocols (2)
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).
Experiment types
transcription profiling by array, unknown experiment type
Contact
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-GEOD-5457.idf.txt
Sample and data relationshipE-GEOD-5457.sdrf.txt
Raw data (1)E-GEOD-5457.raw.1.zip
Processed data (1)E-GEOD-5457.processed.1.zip
Array designA-AFFY-33.adf.txt
R ExpressionSetE-GEOD-5457.eSet.r
Links