Lysosomal multi-omics reveals altered sphingolipid catabolism associated with lysosomal dysfunction in the aging brain

Lipids dynamically reside in multiple intracellular locations, and their organellar distribution is important for function. During brain aging, lysosomal lipid changes have been noted, but lipid identity, interactions, and functional relevance have not been characterized. We used mass spectrometry to assess longitudinal changes in the lipidome and proteome of lysosomal fractions from the murine cortex, from 3 to 24 months, followed by multi-omics factor analysis (MOFA) to identify factors underlying lysosomal aging. Our data uncover an age-dependent increase in lysosomal abundance of lipid and protein myelin components and suggest altered sphingolipid catabolism favoring degradation of sphingomyelins over glycosphingolipids. We experimentally corroborate MOFA predictions to demonstrate that age-dependent accumulation of myelin-derived glycosphingolipids is associated with lysosomal enlargement and dysfunction and is most pronounced in microglia. Our findings suggest that age-related lysosomal lipidome changes resemble those observed in lysosomal storage diseases and underscore the importance of organelle-specific analyses for elucidating lipid function.