Palmitoyltransferase DHHC13 controls lysosomal cholesterol egress through palmitoylating Niemann-Pick C1

Protein S-palmitoylation provides a key regulatory mechanism for diverse cellular activities. Although palmitoylated proteins are frequently observed in cholesterol-enriched membrane microdomains, how protein palmitoylation reciprocally regulates cholesterol metabolism remains elusive. Here, we identify DHHC13 as a critical regulator linking protein palmitoylation to lysosomal cholesterol egress. Through an shRNA screen, we found that lack of DHHC13 led to pronounced lysosomal cholesterol accumulation. Mechanistically, DHHC13 directly palmitoylated Niemann-Pick C1 (NPC1). Loss of palmitoylation disrupted NPC1 association with lysosomes and caused its degradation, thereby impairing lysosomal cholesterol egress. Dhhc13 ^-/- mice phenocopied Npc1 ^-/- mice, displaying cholesterol deposition in the brain, liver, spleen, and kidney, along with significant Purkinje cell loss. Furthermore, two clinically relevant DHHC13 mutants (Q173H and R451Q) associated with neurodegenerative disorders showed diminished catalytic activity and failed to restore NPC1 palmitoylation or lysosomal cholesterol egress. Collectively, our findings uncover DHHC13 as a critical regulator of lysosomal cholesterol metabolism via NPC1 palmitoylation, providing mechanistic insights into cholesterol-related neurological disorders.