TAILS proteomics reveals dynamic changes in airway proteolysis controlling protease activity and innate immunity during COPD exacerbations.

Dysregulated protease activity is thought to cause parenchymal and airway damage in COPD. Multiple proteases have been implicated in COPD and identifying their substrates may reveal new disease mechanisms and treatments. However as proteases interact with many substrates which may be protease inhibitors or proteases themselves, these webs of protease interactions make the wider consequences of therapeutically targeting proteases difficult to predict. We therefore used a systems approach to determine protease substrates and protease activity in COPD airways. Protease substrates were determined by proteomics using Terminal Amine Isotopic Labelling of Substrates (TAILS) methodology in paired sputum samples during stable COPD and exacerbations. Protease activity and specific protein degradation in airway samples were assessed using western blotting, substrate assays and ex vivo cleavage assays. 299 proteins were identified in human COPD sputum, 125 of which were proteolytically processed including proteases, protease inhibitors, mucins, defensins, complement and other innate immune proteins. During exacerbations, airway neutrophils and neutrophil proteases increased. More proteins were cleaved, particularly at multiple sites, consistent with degradation and inactivation. During exacerbations, different substrates were processed including protease inhibitors, mucins and complement proteins. Exacerbations were associated with increasing airway elastase activity and increased processing of specific elastase substrates including secretory leukocyte protease inhibitor. Proteolysis regulates multiple processes including elastase activity and innate immune proteins in COPD airways and differs during stable disease and exacerbations. The complexity of protease, inhibitor and substrate networks makes the effect of protease inhibitors hard to predict which should be used cautiously.