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Series GSE5457 Query DataSets for GSE5457
Status Public on Aug 05, 2006
Title Retinoic Acids Exposure Alters TGFbeta1 -Induced Epithelial Mesenchymal Transition via Wnt5b expression.
Organism Homo sapiens
Experiment type Expression profiling by array
Summary 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.
Keywords: EBV infection, EMT and non-canonical Wnt pathway in A549 detected by oligonucleotide array
 
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).
 
Contributor(s) Malizia AP, Keating DT, Smith SM, Walls D, Wood AE, Doran PP, Egan JJ
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Submission date Aug 04, 2006
Last update date Aug 10, 2018
Contact name Andrea Patricelli Malizia
E-mail amalizia@mater.ie
Phone 0035317166381
Fax 0035317166309
Organization name University College Dublin
Lab Genome Resource Unit
Street address 21, Nelson Street
City Dublin
ZIP/Postal code 7
Country Ireland
 
Platforms (1)
GPL96 [HG-U133A] Affymetrix Human Genome U133A Array
Samples (8)
GSM124905 A549_rep1
GSM124906 A549_rep2
GSM124907 AAKata_rep1
Relations
BioProject PRJNA95963

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE5457_RAW.tar 26.4 Mb (http)(custom) TAR (of CEL)
Raw data provided as supplementary file

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