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Abstract Extracellular vesicles (EVs) – nanoscale membranous particles that carry multiple proteins and nucleic acid cargoes from their mother cells of origin into circulation – have enormous potential as biomarkers. However, devices appropriately scaled to the nanoscale to match the size of EVs (30–200 nm) have orders of magnitude too low throughput to process clinical samples (10¹²EVs mL⁻¹in serum). To address this challenge, we develop a novel approach that incorporates billions of nanomagnetic sorters that act in parallel to precisely isolate sparse EVs based on immunomagnetic labeling directly from clinical samples at flow rates billions of times greater than that of a single nanofluidic device. To fabricate these chips, the ferromagnetic metals are electro‐deposited into a self‐assembled microlattice, achieving >10⁹nanoscale magnetophoretic sorting devices in a 3D postage stamp‐sized lattice with >70x magnetic traps and >20x enrichment of magnetic nanoparticles versus our previous work. The immunomagnetically labeled EVs are isolated and achieve a ≈100% increase in yield as well as increased purity compared to conventional methods. Building on the proof‐of‐concept demonstrations in this manuscript, this new approach has the potential to enhance the future clinical translation of EV biomarkers by enabling rapid, sensitive, and specific isolation of EV subpopulations from clinical samples.