title: Network analysis of quantitative proteomics on asthmatic bronchi: effects of inhaled glucocorticoid treatment.
abstract: BACKGROUND
  Proteomic studies of respiratory disorders have the potential to identify protein biomarkers for diagnosis and disease monitoring. Utilisation of sensitive quantitative proteomic methods creates opportunities to determine individual patient proteomes. The aim of the current study was to determine if quantitative proteomics of bronchial biopsies from asthmatics can distinguish relevant biological functions and whether inhaled glucocorticoid treatment affects these functions.
  
  
  METHODS
  Endobronchial biopsies were taken from untreated asthmatic patients (n = 12) and healthy controls (n = 3). Asthmatic patients were randomised to double blind treatment with either placebo or budesonide (800 μg daily for 3 months) and new biopsies were obtained. Proteins extracted from the biopsies were digested and analysed using isobaric tags for relative and absolute quantitation combined with a nanoLC-LTQ Orbitrap mass spectrometer. Spectra obtained were used to identify and quantify proteins. Pathways analysis was performed using Ingenuity Pathway Analysis to identify significant biological pathways in asthma and determine how the expression of these pathways was changed by treatment.
  
  
  RESULTS
  More than 1800 proteins were identified and quantified in the bronchial biopsies of subjects. The pathway analysis revealed acute phase response signalling, cell-to-cell signalling and tissue development associations with proteins expressed in asthmatics compared to controls. The functions and pathways associated with placebo and budesonide treatment showed distinct differences, including the decreased association with acute phase proteins as a result of budesonide treatment compared to placebo.
  
  
  CONCLUSIONS
  Proteomic analysis of bronchial biopsy material can be used to identify and quantify proteins using highly sensitive technologies, without the need for pooling of samples from several patients. Distinct pathophysiological features of asthma can be identified using this approach and the expression of these features is changed by inhaled glucocorticoid treatment. Quantitative proteomics may be applied to identify mechanisms of disease that may assist in the accurate and timely diagnosis of asthma.
  
  
  BACKGROUND
  ClinicalTrials.gov registration NCT01378039.
authors.affiliation: Krefting Research Centre, Department of Internal Medicine, University of Gothenburg, Sweden. serena.oneil@lungall.gu.se
authors.forename: Serena E
authors.initials: SE
authors.lastname: O'Neil
authors.forename: Brigita
authors.initials: B
authors.lastname: Sitkauskiene
authors.forename: Agne
authors.initials: A
authors.lastname: Babusyte
authors.forename: Algirda
authors.initials: A
authors.lastname: Krisiukeniene
authors.forename: Kristina
authors.initials: K
authors.lastname: Stravinskaite-Bieksiene
authors.forename: Raimundas
authors.initials: R
authors.lastname: Sakalauskas
authors.forename: Carina
authors.initials: C
authors.lastname: Sihlbom
authors.forename: Linda
authors.initials: L
authors.lastname: Ekerljung
authors.forename: Elisabet
authors.initials: E
authors.lastname: Carlsohn
authors.forename: Jan
authors.initials: J
authors.lastname: Lötvall
mesh_terms: D000280:Administration, Inhalation; D000328:Adult; D000368:Aged; D001249:Asthma / Q000188:drug therapy* / Q000235:genetics / Q000378:metabolism*; D001980:Bronchi / Q000187:drug effects / Q000276:immunology; D001993:Bronchodilator Agents / Q000008:administration & dosage*; D004311:Double-Blind Method; D053263:Gene Regulatory Networks / Q000187:drug effects* / Q000276:immunology; D005938:Glucocorticoids / Q000008:administration & dosage*; D006801:Humans; D008875:Middle Aged; D040901:Proteomics / Q000379:methods*
chemical_list: D001993:Bronchodilator Agents; D005938:Glucocorticoids