title: Transcriptome sequencing (RNA-Seq) of human endobronchial biopsies: asthma versus controls.
abstract: The cellular and molecular pathways in asthma are highly complex. Increased understanding can be obtained by unbiased transcriptomic analysis (RNA-Seq). We hypothesised that the transcriptomic profile of whole human endobronchial biopsies differs between asthma patients and controls. First, we investigated the feasibility of obtaining RNA from whole endobronchial biopsies suitable for RNA-Seq. Secondly, we examined the difference in transcriptomic profiles between asthma and controls. This cross-sectional study compared four steroid-free atopic asthma patients and five healthy nonatopic controls. Total RNA from four biopsies per subject was prepared for RNA-Seq. Comparison of the numbers of reads per gene in asthma and controls was based on the Poisson distribution. 46 genes were differentially expressed between asthma and controls, including pendrin, periostin and BCL2. 10 gene networks were found to be involved in cellular morphology, movement and development. RNA isolated from whole human endobronchial biopsies is suitable for RNA-Seq, showing different transcriptomic profiles between asthma and controls. Novel and confirmative genes were found to be linked to asthma. These results indicate that biological processes in the airways of asthma patients are regulated differently when compared to controls, which may be relevant for the pathogenesis and treatment of the disease.
authors: Dept of Respiratory Medicine, Academic Medical Centre, Amsterdam, The Netherlands. c.y.yick@amc.uva.nl
authors: Ching Yong
authors: CY
authors: Yick
authors: Aeilko H
authors: AH
authors: Zwinderman
authors: Peter W
authors: PW
authors: Kunst
authors: Katrien
authors: K
authors: Grünberg
authors: Thais
authors: T
authors: Mauad
authors: Annemiek
authors: A
authors: Dijkhuis
authors: Elisabeth H
authors: EH
authors: Bel
authors: Frank
authors: F
authors: Baas
authors: René
authors: R
authors: Lutter
authors: Peter J
authors: PJ
authors: Sterk
mesh_terms: D000328:Adult; D001249:Asthma / Q000235:genetics* / Q000378:metabolism / Q000503:physiopathology; D001980:Bronchi / Q000378:metabolism*; D001999:Bronchoscopy; D016022:Case-Control Studies; D003430:Cross-Sectional Studies; D005541:Forced Expiratory Volume / Q000502:physiology; D020869:Gene Expression Profiling; D006801:Humans; D017423:Sequence Analysis, RNA; D059467:Transcriptome; D014797:Vital Capacity / Q000502:physiology; D055815:Young Adult