The Lung Macroautophagy Substrate Proteome: A SYSTEMS BIOLOGY Analysis

Abstract

RationaleMacroautophagy is a lysosome‐based catabolic process that is implicated in the pathogenesis of multiple diseases. Although macroautophagy is ubiquitous, its physiologic role may be specialized in various tissue types and we know little of how this process contributes specifically to homeostasis in the lung. Since standard markers of macroautophagy cannot convey information about tissue‐specific patterns of catabolism we used a proteomic approach to compare autophagosome substrate turnover in mouse lung to that of mouse liver.Methods:We measured macroautophagic activity in the lungs and liver of GFP‐LC3 expressing transgenic mice using a leupeptin based protocol we developed previously. GFP‐LC3+ vesicles were were analyzed via 1D‐SDS PAGE followed by label‐free LC‐MS‐MS.Results:The macroautophagy substrate proteome of the lung was highly divergent than that of livers. Specific to lung macroautophagy, tight junction components were part of the substrate proteome in this organ. Lung macroautophagy had a higher predilection than liver for secreted proteins, possibly reflecting increased input from retrograde endocytic traffic to amphisomes. There was also a greater contingent of leukocyte‐associated proteins among lung macroautophagy substrates.ConclusionsA proteomics‐based approach successfully identified organ specific variations in macroautophagy. We believe this approach will prove useful for understanding how disease states reprogram macroautophagy, and conversely how macroautophagy regulation brought about by interventions are likely to affect cellular physiology in different cell types.