Loss of the batten disease protein CLN3 leadsto mis-trafficking of M6PR and defective autophagic-lysosomal reformation

Batten disease, one of the most devastating types of neurodegenerativelysosomal storage disorders, is caused by mutations in CLN3. Here, we showthat CLN3 is a vesicular trafficking hub connecting the Golgi and lysosomecompartments. Proteomic analysis reveals that CLN3 interacts with severalendo-lysosomal trafficking proteins, including the cation-independent man-nose 6 phosphate receptor (CI-M6PR), which coordinates the targeting oflysosomal enzymes to lysosomes. CLN3 depletion results in mis-trafficking ofCI-M6PR, mis-sorting of lysosomal enzymes, and defective autophagic lyso-somal reformation. Conversely, CLN3 overexpression promotes the formationof multiple lysosomal tubules, which are autophagy and CI-M6PR-dependent,generating newly formed proto-lysosomes. Together, our findings reveal thatCLN3 functions as a link between the M6P-dependent trafficking of lysosomalenzymes and lysosomal reformation pathway, explaining the global impair-ment of lysosomal function in Batten disease.