Compartmental analysis of the pulmonary proteome reveals novel functions of the aryl hydrocarbon receptor

As a barrier organ, the lungs are continuously exposed to environmental stimuli and rely on molecular sensors to detect and respond to these external cues. One such sensor is the aryl hydrocarbon receptor (AhR), a ligand-activated transcription factor traditionally recognized for its role in xenobiotic metabolism. However, this function is a relatively recent evolutionary adaptation of the AhR. Beyond its detoxification role, AhR has been implicated in developmental and homeostatic processes, as evidenced by defects in AhR-deficient mice. Despite this, the contribution of endogenous AhR activity to pulmonary homeostasis remains poorly defined. To address this gap, we leveraged high-resolution proteomics from lung tissue, bronchoalveolar lavage fluid (BALF), and extracellular vesicles (EVs) of AhR-expressing and AhR-knockout mice to define the role of AhR in shaping the pulmonary proteomic landscape. Our analysis reveals that each compartment exhibits a distinct proteomic signature and that AhR plays a central role dictating that composition within each compartment. Notably, AhR regulates proteins involved in epithelial barrier function, alveolar macrophage lipid handling, and the selective packaging of bioactive cargo into EVs. These findings identify AhR as a key regulator of structural and immune balance in the lung and uncover new functions of this receptor in maintaining pulmonary homeostasis. Furthermore, our work highlights the potential of EVs as sensitive indicators of AhR activity and offers new insight into therapeutic strategies targeting AhR signaling in respiratory disease.