Lysosomes are critical for maintaining protein homeostasis and cellular metabolism. Lysosomal dysfunction and disrupted protein trafficking contribute to cell death in neurodegenerative disorders, including Parkinson's disease and dementia. We describe three complementary protocols—the use of protein glycosylation, western blotting, immunofluorescence, and hydrolase activity measurement—to analyze the trafficking and activity of lysosomal proteins in patient-derived neurons differentiated from iPSCs. These methods should help to identify lysosomal phenotypes in patient-derived cultures and aid the discovery of therapeutics that augment lysosomal function.

For complete details on the use and execution of this protocol, please refer to Cuddy et al. (2019).