Superparamagnetic Nanoparticles for Lysosome Isolation to Identify Spatial Alterations in Lysosomal Protein and Lipid Composition

Lysosomes are dynamic organelles that serve as regulatory hubs in cellular homeostasis. Changes in lysosome morphology, composition, and turnover are typically linked to disease. These characteristics make enrichment protocols based on biophysical parameters challenging. However, organelle enrichment methods are essential to facilitate their biomolecular analysis. We describe the synthesis and use of superparamagnetic iron oxide nanoparticles (SPIONs) for high-yield purification of lysosomes compatible with “omics” analysis. NANOLYSE (Nanoparticles for Lysosome Isolation) provides a reliable strategy in fingerprinting the biomolecular composition of lysosomes. For complete details on the use and execution of this protocol, please refer to Tharkeshwar et al. (2017). [Display omitted] •Lysosome isolation from adherent cells using superparamagnetic iron oxide nanoparticles•Enriched lysosomes with high intactness, compatible for functional, biochemical studies•NANOLYSE is highly reproducible and compatible for proteome and lipidome profiling•NANOLYSE is an unbiased method to identify lysosomal dyshomeostasis in a disease context Lysosomes are dynamic organelles that serve as regulatory hubs in cellular homeostasis. Changes in lysosome morphology, composition, and turnover are typically linked to disease. These characteristics make enrichment protocols based on biophysical parameters challenging. However, organelle enrichment methods are essential to facilitate their biomolecular analysis. We describe the synthesis and use of superparamagnetic iron oxide nanoparticles (SPIONs) for high-yield purification of lysosomes compatible with “omics” analysis. NANOLYSE (Nanoparticles for Lysosome Isolation) provides a reliable strategy in fingerprinting the biomolecular composition of lysosomes.