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Protocol collection for “Global cellular proteo-lipidomic profiling of diverse lysosomal storage disease mutants using nMOST”
Output Details
Description
Lysosomal storage diseases (LSDs) comprise ~50 monogenic diseases display accumulation of cellular material in lysosomes and associated defects in lysosomal function, but systematic lipid-proteome phenotyping remains challenging. Here, we report a sensitive nanoflow-based multi-omic single-shot technology (nMOST) workflow allowing simultaneous quantification of proteomes and lipidomes. Benchmarking nMOST using LSD mutants linked with cholesterol trafficking revealed aberrant accumulation of autophagy receptors and ferritinophagy cargo, which correlated with accumulation of lyso-phosphatidylcholine species and multi-lamellar membrane structures visualized by cryo-electron-tomography, especially in NPC2-/- cells. Ferritinophagy defects correlated with loss of mitochondrial cristae and iron-sulfur cluster-containing electron transport chain complexes that could be rescued by extracellular iron. To further demonstrate the value of nMOST, we profiled more than two dozen diverse LSD mutant cell lines. We provide an accompanying web-portal resource of lipid-protein correlations across the entire dataset and demonstrate how the resource can be used to reveal common and distinct molecular phenotypes.
Identifier (DOI)
10.17504/protocols.io.5qpvokmmzl4o/v1