Integrating Proteomes for Lung Tissue and Lavage Reveals Pathways that Link Responses in Allergen-Challenged Mice

To capture interplay between biological pathways we analyzed the proteome from matched lung tissue and bronchoalveolar lavage fluid (BALF) of individual allergen-naïve and house dust mite (HDM)-challenged BALB/c mice, a model of allergic asthma. Unbiased label-free LC-MS/MS analysis quantified 2,675 proteins from tissue and BALF of allergen-naïve and HDM-exposed mice. In comparing the four datasets we found significantly greater diversity in proteins between lung tissue and BALF than in the changes induced by HDM challenge. The biological pathways enriched after allergen exposure were compartment-dependent. Lung tissue featured innate immune responses and oxidative stress, while BALF most strongly revealed changes in metabolism. We combined lung tissue and BALF proteomes, which principally highlighted oxidation reduction (redox) pathways, a finding influenced chiefly by the lung tissue dataset. Integrating lung and BALF proteomes also uncovered new proteins and biological pathways that may mediate lung tissue and BALF interactions after allergen challenge, for example, B Cell Receptor signaling. We demonstrate that enhanced insight is fostered when different biological compartments from the lung are investigated in parallel. Integration of proteomes from lung tissue and BALF compartments reveals new information about protein networks in the response to environmental challenge and interaction between intracellular and extracellular process.