SGLT2 Inhibitors Rescue Lysosomal mTORC1 Hyperactivity and Proximal Tubulopathy in Preclinical Models of Cystinosis

The loss of lysosomal cystine transporter cystinosin (CTNS) disrupts kidney proximal tubule (PT) function, causing cystinosis - a prototypical lysosomal storage disorder characterized by cystine accumulation and metabolic dyshomeostasis. Cystine storage disrupts lysosomal nutrient sensing and downstream mTORC1 signalling, driving loss of PT differentiation and proximal tubulopathy. Here, using cross-species disease models, differentiated cellular systems, lysosome-based assays, and transcriptomics profiling, we demonstrate that sodium-glucose co-transporter 2 (SGLT2) inhibitors (empagliflozin or dapagliflozin) ameliorate proximal tubulopathy in cystinosis. In CTNS-deficient PT cells, SGLT2 inhibition restores lysosome proteolysis, autophagic flux, metabolic homeostasis, and epithelial differentiation and function, independently of cystine clearance. Mechanistically, SGLT2 inhibition reduces the assembly of the v-ATPase-Ragulator-Rag scaffolding complex at lysosomes, thereby decoupling cystine storage from pathological mTORC1 activation. These effects reprogram PT metabolic trajectories and differentiation states, mitigating proximal tubulopathy across zebrafish and rodent models of cystinosis. Together, these findings define a lysosome-metabolism crosstalk that links glucose handling to mTORC1 regulation and provide a rationale for repurposing SGLT2 inhibitors as a disease-modifying therapy for cystinosis and related lysosome-driven PT disorders.