title: Quantitative proteomics of bronchoalveolar lavage fluid in idiopathic pulmonary fibrosis.
abstract: The proteomic analysis of bronchoalveolar lavage fluid (BALF) can give insight into pulmonary disease pathology and response to therapy. Here, we describe the first gel-free quantitative analysis of BALF in idiopathic pulmonary fibrosis (IPF), a chronic and fatal scarring lung disease. We utilized two-dimensional reversed-phase liquid chromatography and ion-mobility-assisted data-independent acquisition (HDMSE) for quantitation of >1000 proteins in immunodepleted BALF from the right middle and lower lobes of normal controls and patients with IPF. Among the analytes that were increased in IPF were well-described mediators of pulmonary fibrosis (osteopontin, MMP7, CXCL7, CCL18), eosinophil- and neutrophil-derived proteins, and proteins associated with fibroblast foci. For additional discovery and targeted validation, BALF was also screened by multiple reaction monitoring (MRM), using the JPT Cytokine SpikeMix library of >400 stable isotope-labeled peptides. A refined MRM assay confirmed the robust expression of osteopontin, and demonstrated, for the first time, upregulation of the pro-fibrotic cytokine, CCL24, in BALF in IPF. These results show the utility of BALF proteomics for the molecular profiling of fibrotic lung diseases and the targeted quantitation of soluble markers of IPF. More generally, this study addresses critical quality control measures that should be widely applicable to BALF profiling in pulmonary disease.
authors.affiliation: Pulmonary, Allergy and Critical Care Medicine, ‡Duke Proteomics and Metabolomics Shared Resource, §Department of Surgery, Duke University Medical Center , Durham, North Carolina 27710, United States , and.
authors.forename: Matthew W
authors.initials: MW
authors.lastname: Foster
authors.forename: Lake D
authors.initials: LD
authors.lastname: Morrison
authors.forename: Jamie L
authors.initials: JL
authors.lastname: Todd
authors.forename: Laurie D
authors.initials: LD
authors.lastname: Snyder
authors.forename: J Will
authors.initials: JW
authors.lastname: Thompson
authors.forename: Erik J
authors.initials: EJ
authors.lastname: Soderblom
authors.forename: Kelly
authors.initials: K
authors.lastname: Plonk
authors.forename: Kent J
authors.initials: KJ
authors.lastname: Weinhold
authors.forename: Robert
authors.initials: R
authors.lastname: Townsend
authors.forename: Anne
authors.initials: A
authors.lastname: Minnich
authors.forename: M Arthur
authors.initials: MA
authors.lastname: Moseley
mesh_terms: D001992:Bronchoalveolar Lavage Fluid; D004591:Electrophoresis, Polyacrylamide Gel; D006801:Humans; D054990:Idiopathic Pulmonary Fibrosis / Q000378:metabolism*; D040901:Proteomics; D015203:Reproducibility of Results; D053719:Tandem Mass Spectrometry
keywords: CRAC1; PEDF; airway lining fluid; immunodepletion; label-free; targeted proteomics