Internally twin-Strep tagged CD63 for rapid and efficient isolation of engineered extracellular vesicles encapsulating functional proteins

Extracellular vesicles (EVs) are key mediators of intercellular communication and hold great promise as vehicles for delivering proteins of interest (POIs) for therapeutic applications. Conventional methods for isolating engineered EVs containing POIs typically rely on bulk EV isolation techniques such as tangential flow filtration, ultracentrifugation, size-exclusion chromatography, or precipitation. However, these approaches cannot effectively separate engineered EVs from the much more abundant unmodified vesicles and contaminants derived from cells and cell culture serum. To address this, we engineered the EV-sorting scaffold protein CD63 to include an internal twin-Strep tag, enabling efficient and rapid affinity-based isolation of engineered EVs using Strep technology. Furthermore, coding sequences of POIs were fused to the C-terminus of CD63, allowing functional POIs to be loaded into the lumen of twin-Strep-tagged EVs. Proteomic analysis of isolated EVs demonstrated high purity, with ∼97% of contaminants removed. Importantly, we also observed efficient removal of contaminating virus particles that resemble EVs in size and density. Notably, affinity-isolated EVs successfully delivered POIs into target cells, where the delivered proteins remained functional. This method may serve as a broadly applicable tool for the efficient isolation of engineered EVs encapsulating functional POIs.