title: Gene expression profiling of laser microdissected airway smooth muscle tissue in asthma and atopy.
abstract: BACKGROUND
  Asthma and atopy share common characteristics including type 2 helper-T-cell-mediated inflammation. However, only asthma is associated with variable airways obstruction. The complex cellular and molecular pathways distinguishing asthma and atopy can now be captured by transcriptomic analysis (RNA-Seq). We hypothesized that the transcriptomic profile of airway smooth muscle (ASM) distinguishes atopic asthma from atopic healthy controls. First, we compared the ASM transcriptomic profiles of endobronchial biopsies between glucocorticoid-free, atopic asthma patients, and atopic and nonatopic healthy controls. Second, we investigated the association between ASM transcriptomic profiles and airway function.
  
  
  METHODS
  Twelve asthma patients and 12 control subjects (six atopic, six nonatopic) underwent bronchoscopy. RNA of laser-dissected ASM from 96 bronchial biopsy specimens was sequenced with Roche GS FLX. Gene networks were identified using Ingenuity Pathway Analysis. RNA-Seq reads were assumed to follow a negative binomial distribution. With the current sample size, the estimated false discovery rate was approximately 1%.
  
  
  RESULTS
  One hundred and seventy four ASM genes were differentially expressed between asthma patients and atopic controls, 108 between asthma patients and nonatopic controls, and 135 between atopic and nonatopic controls. A set of eight genes discriminated asthma patients from nonasthmatic controls, irrespective of atopy. Four of these genes (RPTOR, VANGL1, FAM129A, LEPREL1) were associated with airway hyper-responsiveness (P < 0.05).
  
  
  CONCLUSIONS
  Airway smooth muscle from asthma patients can be distinguished from that of atopic and nonatopic control subjects by a specific gene expression profile, which is associated with airway hyper-responsiveness.
authors.affiliation: Department of Respiratory Medicine, Academic Medical Center, Amsterdam, The Netherlands.
authors.forename: C Y
authors.initials: CY
authors.lastname: Yick
authors.forename: A H
authors.initials: AH
authors.lastname: Zwinderman
authors.forename: P W
authors.initials: PW
authors.lastname: Kunst
authors.forename: K
authors.initials: K
authors.lastname: Grünberg
authors.forename: T
authors.initials: T
authors.lastname: Mauad
authors.forename: S
authors.initials: S
authors.lastname: Chowdhury
authors.forename: E H
authors.initials: EH
authors.lastname: Bel
authors.forename: F
authors.initials: F
authors.lastname: Baas
authors.forename: R
authors.initials: R
authors.lastname: Lutter
authors.forename: P J
authors.initials: PJ
authors.lastname: Sterk
mesh_terms: D000328:Adult; D001249:Asthma / Q000235:genetics*; D005260:Female; D020869:Gene Expression Profiling; D006801:Humans; D006967:Hypersensitivity / Q000235:genetics*; D061346:Laser Capture Microdissection; D008297:Male; D009130:Muscle, Smooth; D059467:Transcriptome / Q000235:genetics*; D055815:Young Adult
keywords: RNA-Seq; airway smooth muscle; asthma; gene expression analysis; transcriptomics