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E-GEOD-7524 - Transcription profiling of human whole blood isolated form RA disease pre and post anti-TNF treatment

Status
Submitted on 16 April 2007, released on 15 June 2008, last updated on 10 June 2011
Organism
Homo sapiens
Samples (6)
Array (1)
Protocols (2)
Description
The purpose of this study was (1) to identify novel genes involved in the pathogenesis of Rheumatoid Arthritis (RA) disease, which may provide additional targets for therapeutic intervention and (2) to examine the molecular mechanisms associated with the response to anti-TNF treatment. Microarray analysis of LPS-stimulated whole blood from RA patients pre and post anti-TNF treatment was conducted. This study identified 818 transcripts, differentially expressed in RA patients pre-treatment compared to non-RA control samples. While a number of these genes were associated with RA in previous studies, validating our data, a number of novel genes with possible functions in RA disease were also identified. The number of transcripts (1051) significantly altered post anti-TNF treatment indicates the impact of anti-TNF therapy on systemic gene expression. A number of these transcripts were confirmed to be altered in a larger patient group and may represent potential genetic markers of a patient’s clinical response to anti-TNF treatment. Experiment Overall Design: Transcriptome profiling was performed on two RA patients, pre- and three months post-Enbrel therapy and two matched non-RA controls. The whole blood model described by Wang et al (2000) was used with minor modifications. Briefly, to EDTA anti-coagulated blood, LPS (30ng/ml) was added immediately after drawing, and incubated at 37oC for 4 hours, mixing at 80s. After 4 hours red blood cells were lysed and pelleted, white cells were washed once in PBS (Gibco) and frozen at –70oC for subsequent RNA extraction. Total RNA was extracted using the RNeasy kit (QIAGEN) as per manufacturer’s instructions. Samples were treated with DNA-Free (Ambion) to remove genomic DNA and checked using intron-overlapping primers prior to generating cRNA probes or cDNA (data not shown). Affymetrix array data was normalised (globally) and statistically (t-test) analysed using GeneSight software (Biodiscovery). Gene expression changes with a p value of < 0.05 and a fold change of 3 or greater were considered differentially expressed.
Experiment types
transcription profiling by array, unknown experiment type
Contact
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-7524.idf.txt
Sample and data relationshipE-GEOD-7524.sdrf.txt
Raw data (1)E-GEOD-7524.raw.1.zip
Processed data (1)E-GEOD-7524.processed.1.zip
Array designA-AFFY-33.adf.txt
R ExpressionSetE-GEOD-7524.eSet.r
Links