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TitleProteome Landscapes Decode Organelle Vulnerabilities in cortical and dopaminergic-like induced neurons Across Lysosomal Storage Disorders.
Journal, issue, pagesbioRxiv, Year 2025
Publish dateOct 8, 2025
AuthorsFelix Kraus / Yuchen He / Yizhi Jiang / Delong Li / Yohannes A Ambaw / Federico M Gasparoli / Joao A Paulo / Tobias C Walther / Robert V Farese / Steven P Gygi / Florian Wilfling / J Wade Harper /
PubMed AbstractLysosomes maintain cellular homeostasis by degrading proteins delivered via endocytosis and autophagy and recycling building blocks for organelle biogenesis. Lysosomal Storage Disorders (LSDs) ...Lysosomes maintain cellular homeostasis by degrading proteins delivered via endocytosis and autophagy and recycling building blocks for organelle biogenesis. Lysosomal Storage Disorders (LSDs) comprise a broad group of diseases affecting lysosomal degradation, ion flux, and lipid catabolism. Within this group, sphingolipidoses genes involved in glycosphingolipid breakdown are known () or candidate (, ) risk factors for Parkinson's Disease, though disease mechanisms remain unclear. Using our previously reported LSD mutant proteomic landscape in HeLa cells, we observed pronounced variability in endolysosomal proteome signatures among sphingolipid pathway mutants, with cells showing altered lysosomal lipid composition, impaired endocytic trafficking, and disrupted ultrastructure by cryo-electron tomography. To extend these findings in a more physiologic context, we generated a human embryonic stem (ES) cell library comprising 23 LSD gene knockouts and profiled proteomic changes during differentiation into cortical and midbrain dopaminergic neurons over a 7 to 10 week period. LSD mutants exhibited lineage-specific alterations in organellar proteomes, revealing diverse vulnerabilities. Notably, and dopaminergic neurons showed disruptions in synaptic and mitochondrial compartments, correlating with impaired dopaminergic neuronal firing and disrupted presynaptic protein localization. This LSD mutant toolkit and associated proteomic landscape provides a resource for defining molecular signatures of LSD gene loss and highlights convergence of lysosomal dysfunction, synaptic integrity, and mitochondrial health as potential links between sphingolipidoses and PD risk.
External linksbioRxiv / PubMed:41279717 / PubMed Central
MethodsEM (tomography)
Structure data

EMDB-55210: In situ cryo-ET tomogram of HeLa TMEM192-3xHA Control cell showcasing an endolysosomal structure.
Method: EM (tomography)

EMDB-55211: In situ cryo-ET tomogram of HeLa TMEM192-3xHA ASAH1-/- cell showcasing an endolysosomal structure
Method: EM (tomography)

Source
  • Homo sapiens (human)

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