Pompe disease is an autosomal recessive glycogen storage disease caused by mutations in alpha‐glucosidase (GAA) ‐ an enzyme responsible of hydrolyzing lysosomal glycogen. GAA deficiency results in systemic lysosomal glycogen accumulation and cellular disruption. Skeletal muscle, motor neuron pathology and airway smooth muscle cells are known to contribute to respiratory insufficiency in Pompe disease, but the role of distal airway cells including alveolar type 1 and type 2 cells (AT1 and AT2, respectively) has not been evaluated. AT1 cells depend on lysosomes for cellular homeostasis to maintain a thin barrier for gas exchange whereas AT2 cells depend on lysosomal structures for surfactant production. Using an established mouse model of Pompe disease, the Gaa−/− mouse, we compared lung histology using Periodic acid‐Schiff staining, quantification of immunohistochemistry staining and electron microscopy, and pulmonary mechanics using forced oscillometry FlexiVent system, between Gaa−/− and age‐matched wild‐type (WT) mice. We also perfomed single cell‐RNA seq (scRNA‐seq) on the distal airways of Gaa‐/‐ mice. Lysosomal glycogen accumulation and engorged lamellar bodies were observed in the AT2 cells in Gaa−/− but not WT mice. Furthermore, AT2 positive surfactant protein‐C (SPC) staining and lysosomal positive lysosomal associated membrane protein 1 (LAMP1) staining is more evident with increased colocalization of LAMP1 with the type 2 cell marker after quantification of each marker in Gaa−/− airway cells. The Gaa−/− mice exhibited a significant decrease in total and central airway resistance (Rrs and Rn, respectively), as well as a significant increase in lung compliance (Crs) versus WT mice. Moreover, in the dimensionless and volume‐independent shape constant k that describes the curvature of the upper portion of the deflation limb of the Pressure‐Volume curves, a statistically significant change was observed in Gaa−/− mice. This indicates a change in the intrinsic elastic properties of the respiratory system in Pompe disease. Finally, a robust transcriptomic dysregulation in AT1 and AT2 cells was detected scRNA‐seq in Gaa‐/‐mice relative to WT mice. We conclude that GAA enzyme deficiency leads to glycogen accumulation in the distal airway stem cells that may contribute to respiratory impairments in Pompe disease. Our findings will inform the clinical care of patients with Pompe disease and will provide essential information for the development of novel therapies in Pompe disease that will address this airway pathology.
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