Enrichment Performance Assessment of Extracellular Vesicles Using Different Functionalized Magnetic Materials and Application in Urinary Proteomics of Prostate Cancer

Extracellular vesicles (EVs) are lipid bilayer nanovesicles that mediate intercellular communication and hold significant potential for clinical applications. Although material-based isolation strategies offer promising alternatives to conventional methods, their relative performances have not been systematically evaluated. In this study, we conducted a comparative assessment of magnetic nanomaterials with distinct surface functionalities, including metal oxides (TiO2), metal-organic frameworks (UiO-66), biopolymeric materials (chitosan), and lipid probes (DSPE-PEG, DOPE-PEG, and CLS-PEG). A comprehensive evaluation across multiple dimensions including capture capacity, capture rate, sample volume, and product purity reveals that the bifunctional magnetic nanomaterial Fe3O4@UiO-66@DSPE material exhibits superior EV capture performance. This material enables the efficient and stable enrichment of high-purity EVs by synergizing Zr4+-phosphate coordination with lipid bilayer anchoring, and preserves EV biological integrity and activity. Meanwhile, this method could be highly compatible with proteomics, and over 1000 proteins are identified by proteomic analysis of urinary EVs, while 34 proteins are upregulated and 25 proteins are downregulated in prostate cancer patients relative to healthy donors. Notably, the differentially expressed proteins, such as AGT, ITIH4, and PGLYRP2, are associated with disease progression. Overall, this work highlights the superior performance of the Fe3O4@UiO-66@DSPE material for efficient and selective EV isolation. It provides a powerful tool for clinical liquid biopsy and proteomic biomarker discovery, enabling early diagnosis, prognostic evaluation, and precision therapy.