Novel surface functionalized superparamagnetic nanoparticles with engineered cellular uptake as a means for intracellular omics

Superparamagnetic nanoparticles (SPMNPs) are appealing for use in organelle isolation strategies. Yet, this potential remains largely unexplored because thus far research has focused on either physicochemical design or on their application in micron-sized beads. For their use in life sciences, the biocompatibility of SPMNPs goes beyond their chemical composition and shape, and features like their size and more importantly their surface properties are becoming more important to exploit extra- and intracellular interactions. Here we introduce thermal decomposition to manufacture iron oxide based SPMNPs (Ø10nm) and demonstrate how different surface functionalizations can lead to different types of cellular interactions. Cationic aminolipid-coated SPMNPs reside surprisingly strong at the outer cell surface. In contrast, anionic dimercaptosuccinic acid-coated SPMNPs are efficiently internalized and accumulate in a time-dependent manner in endosomal and lysosomal populations. These features allowed us to establish a standardized magnetic isolation procedure to selectively isolate plasma membranes and intracellular late endosomes/lysosomes with high yields and purities as consolidated by biochemical and ultrastructural analyses. Subsequent quantitative and qualitative proteome analysis underpins the overall high enrichment for hydrophobic (membrane) proteins as well as plasma membrane and lysosomal constituents in the respective purified fractions. This nano based technology provides therefore a breakthrough in the field of subcellular ‘omics’ as it allows the identification of subtle alterations in the biomolecular composition of different SPMNP-isolated compartments that would be otherwise not detected in total cell or tissue analysis.