Selective Lipoprotein Removal Enables High-Purity EV Isolation from Plasma via Aptamer-Based Mesh Filtration

Lipoproteins pose a major challenge to plasma extracellular vesicle (EV) isolation due to their abundance and physical similarity to EVs. Here, we present ApoFilter, a rapid and selective aptamer-based mesh-filtration platform that efficiently depletes ApoA1- and ApoB100-positive lipoproteins. High-affinity aptamers immobilized onto nylon mesh layers capture targeted lipoproteins in a spin-column format, enabling rapid (1 min) separation under gravity-driven flow. ApoFilter removed >99% of targeted lipoproteins (HDL and (V)LDL) from purified and plasma samples, with negligible capture of non-target components and no compromise to EV integrity. When integrated with conventional EV isolation methods-including ultracentrifugation (UC), size-exclusion chromatography (SEC), and ExoTFF-ApoFilter consistently eliminated lipoprotein contaminants across all workflows. This simple and rapid system addresses a key bottleneck in EV research, enabling the collection of ultrapure EVs suitable for downstream molecular analyses and translational applications.