Transcriptome sequencing (RNA-Seq) of human endobronchial biopsies: asthma versus controls

Ching Yong Yick, Aeilko H. Zwinderman, Peter W. Kunst, Katrien Grünberg, Thais Mauad, Annemiek Dijkhuis, Elisabeth H. Bel, Frank Baas, René Lutter, Peter J. Sterk

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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
Original languageEnglish
Pages (from-to)662-670
JournalEuropean respiratory journal
Volume42
Issue number3
DOIs
Publication statusPublished - 2013

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