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Series GSE38003 Query DataSets for GSE38003
Status Public on Aug 15, 2014
Title Transcriptomic Analysis of Airway Smooth Muscle by Next-Generation Sequencing (RNA-Seq): Asthma versus Healthy Controls
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Rationale: Asthma and atopy shares common features including Th2-inflammation. However, impairment of airway function seems to be absent in atopy. Increased understanding of the complex cellular and molecular pathways defining the similarities and differences between asthma and atopy may be achieved by transcriptomic analysis (RNA-Seq).
Hypothesis and Aims: As the airway smooth muscle (ASM) layer plays an important role in airway function, we hypothesized that the transcriptomic profile of the ASM layer in endobronchial biopsies is different between atopic asthma patients and atopic healthy controls. First, we examined the differences in transcriptomic profiles of the ASM layer in endobronchial biopsies between atopic mild, steroid-free asthma patients, and atopic and non-atopic healthy controls. Second, we investigated the association between the transcriptomic profiles of the ASM layer and airway function.
Methods: This cross-sectional study included 12 steroid-free atopic asthma patients, 6 atopic, and 6 non-atopic healthy controls. RNA of ASM from 4 endobronchial biopsies per subject was isolated and sequenced (GS FLX+, 454/Roche). Ingenuity Pathway Analysis was used to identify gene networks. Comparison of the numbers of reads per gene in asthma and controls was based on the negative binomial distribution. At the current sample size the estimated false discovery rate was approximately 1%.
Results: Yield of isolated RNA was 30-821ng. We identified 174 differentially expressed genes between asthma and atopic controls, 108 between asthma and non-atopic controls, and 135 between atopic and non-atopic controls. A set of 8 genes was identified, which seems to define asthma patients from non-asthmatic controls regardless of atopy. Four of these genes were significantly associated with airway hyperresponsiveness.
Conclusion: A difference in transcriptomic profile of the airway smooth muscle layer in asthma patients compared to atopic and non-atopic healthy controls may lead to a different regulation of inflammatory pathways and of airway smooth muscle function and development resulting in impaired airway function.
 
Overall design This cross-sectional transcriptomics study consisted of 2 visits. At visit 1, asthma patients (n=12), and healthy atopic (n=6) and non-atopic (n=6) controls were screened for eligibility to participate according to the in- and exclusion criteria. Spirometry and a methacholine bronchoprovocation test were performed. At visit 2, FEV1 reversibility was measured and 4 endobronchial biopsies per subject were collected during a bronchoscopy. Airway smooth muscle was collected from the biopsies by laser capture microdissection and total RNA isolated. cDNA was prepared using the Ovation RNA-Seq System (NuGEN). RNA-Seq was performed using the GS FLX+ instrument (454/Roche). Sequence reads were mapped against the human genome (hg19; UCSC). Comparison of the numbers of reads per gene between asthma and healthy controls was based on the negative binomial distribution and carried out with the R package DESeq including correction for multiple testing.
 
Contributor(s) Yick C
Citation(s) 24888725
Submission date May 16, 2012
Last update date May 15, 2019
Contact name Ching Yong Yick
E-mail(s) c.y.yick@amc.uva.nl
Phone +31-20-5661660
Organization name Academic Medical Center
Department Respiratory Medicine
Street address Meibergdreef 9
City Amsterdam
ZIP/Postal code 1105AZ
Country Netherlands
 
Platforms (1)
GPL14603 454 GS FLX Titanium (Homo sapiens)
Samples (24)
GSM931711 Atopic asthma airway smooth muscle A1
GSM931712 Atopic asthma airway smooth muscle A2
GSM931713 Atopic asthma airway smooth muscle A3
Relations
SRA SRP013217
BioProject PRJNA167090

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE38003_RAW.tar 750.0 Kb (http)(custom) TAR (of CSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
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