Integrating Lung Tissue and Lavage Proteomes Reveals Unique Pathways in Allergen-Challenged Mice

Independent proteomic analysis do not capture the biological interactions between the tissue and extracellular biological compartments when examined in isolation. To address this, we analyzed and compared the proteome from lung tissue and from bronchoalveolar lavage fluid (BALF) of individual allergen-naive and allergen-challenged BALB/c mice, a common pre-clinical model of allergic asthma. Collectively, we quantified 2,695 proteins from both tissue and BALF of allergen-naive and -exposed mice. We created an integrated dataset to examine tissue-BALF proteome interactions. Multivariate analysis identified this Integrated-Tissue-BALF (ITB) dataset as being distinct from either the lung tissue or the BALF dataset. Pathway and network analysis of the ITB dataset uncovered protein hubs that span both the tissue and BALF, but are not significantly enriched in either sample dataset alone. This work reveals that by combining individual datasets provides insight about protein networks that integrate biology in lung tissue and the airway space in response to allergen challenge.