Rapid and high-yield recovery of plasma-derived extracellular vesicles using modified chromatography with soluble protein depletion for biomarker discovery

Extracellular vesicles (EVs) are critical mediators of intercellular communication by transferring proteins, lipid and nucleic acids between cells. EVs in biofluids, particularly blood, have gathered significant interest as potential biomarkers for disease diagnosis. However, isolating EVs from blood poses a challenge due to the high concentration of plasma proteins, which obscure the detection of low abundant EV-associated proteins. Here, we optimized a simplified and efficient method for isolating plasma-derived EVs by combining size exclusion chromatography (SEC) with flow-through chromatography using Capto Core 700 beads. A brief incubation of SEC-derived EV fractions with Capto Core beads (qEV + CC) enabled us to isolate intact, high-purity EVs with reduced soluble plasma protein contamination. As a comparison, MagReSyn-based method was not compatible with elution of intact EVs after the purification and showed significant contamination of soluble plasma proteins. Data-independent acquisition-based liquid chromatography-mass spectrometry of isolated plasma-EVs using the qEV + CC approach identified over 1,000 EV-associated proteins, including an increased presence of brain derived proteins and markers linked to neurodegenerative diseases, such as amyloid precursor protein and apolipoprotein E. These findings were further validated by super-resolution microscopy at a single EV resolution. Bioinformatic pathway and network analyses revealed enrichment of pathways involved in RNA processing, cell adhesion and synaptic function, highlighting the potential of EV molecules for broad disease biomarker discovery. Our findings present an optimized method for efficient purification of plasma-derived EVs, providing a valuable tool for advancing EV-based biomarker development.