In collaboration with the Coon Lab (University of Wisconsin, Madison), the Gygi Lab (HMS Cell Bio) and the Max Planck Institute of Biochemistry in Munich, the Harper Lab has pioneered the application of nanoflow-based multiomic single-shot technology (nMOST) to study lysosomal storage diseases (LSDs). These over 50 rare genetic disorders involve the accumulation of cellular material in lysosomes, leading to cellular dysfunction and links to neurodegenerative conditions like Parkinson’s Disease.

Using the nMOST approach, the Harper/Coon teams profiled the proteome and lipidome of HeLa cell lines representing various LSD mutants. This work uncovered key insights into molecular phenotypes and autophagy defects. For example, the team focuses on NPC mutants, characterised by disruptions in lysosomal cholesterol trafficking and the formation of membrane-laden organelles (beautifully visualized at nanometer resolution using in situ cryo-electron tomography by the Wilfling and Schulman labs at the Max Planck) cause autophagy deficiencies due to fusion defects with the lysosome. Specifically, mutations in NPCs causes defects in iron homeostasis (ferritinophagy), which ultimately leads to mitochondrial dysfunction.  

Interestingly, the mitochondrial defects were alleviated by exogenous iron supplementation, accompanied by extensive remodeling of the mitochondrial proteome. This remodeling was observed in both HeLa cells and stem-cell-derived iNeurons using TMT and nDIA workflows in collaboration with the Gygi Lab. 

The multi-omic data is available online and will hopefully provide a valuable resource for the scientific community and pave the way for developing targeted therapies. For more details, see the Harper Lab’s recent publication in Science Advances.