Next-gen transcriptome analysis (RNA-Seq) of human bronchial biopsies and laser microdissected airway smooth muscle: Asthma vs. controls

Rationale The pathophysiology of asthma is largely unknown. RNA-Seq allows detailed biological characterization of the airways. We hypothesized that the airway transcriptome is different between asthma and controls. Aim We investigated: a) the difference in transcriptomic profiles of whole endobronchial biopsies between steroid-naive asthma and controls; b) the feasibility to obtain RNA from airway smooth muscle (ASM) captured by laser microdissection (LCM) suitable for RNA-Seq Methods 4 biopsies per subject (asthma/control: aim a n=4/n=5; aim b n=24/n=12) were incubated in RNAlater. Whole cryosection or LCM-captured ASM was put into TRIzol. cDNA was obtained with Ovation RNA-Seq System and prepared for RNA-Seq (GS FLX+, 454). Results Sample characteristics are shown below. The 46 differentially expressed genes between asthma and controls were assigned to networks associated with cell cycle, morphology, and development. Conclusion Transcriptomic profiles of whole biopsies were different between asthma and controls. LCM-captured ASM is suitable for RNA-Seq. Regulation of airway biological processes in asthma and controls tends to be fundamentally different. These findings may help develop targeted asthma therapy.