Development of a CD9 aptamer for liquid biopsy of extracellular vesicles

Extracellular vesicles (EVs) are nanoscale, membrane-bound particles that play pivotal roles in intercellular communication as well as modulate diverse physiological and pathological processes. As a classical EV surface marker, the tetraspanin CD9 is critically involved in vesicle biogenesis, membrane fusion, and cell-to-cell signaling. While antibodies remain the conventional tool for CD9 detection, their utility in biosensing is constrained by inherent limitations. Aptamers offer a compelling alternative as synthetic single-stranded nucleic acids with high target affinity and specificity. In this study, a novel epitope-specific DNA aptamer, CD9 A3-A, targeting the extracellular domain of CD9 was developed using a peptide-directed Systematic Evolution of Ligands by Exponential Enrichment (SELEX) approach. The aptamer's specificity and binding efficacy toward recombinant CD9 protein, CD9-positive cells, and CD9-enriched EVs, including those from human serum, were validated using ELISA and flow cytometry. Furthermore, this epitope-specific CD9 aptamer enabled the detection and differentiation of EVs from distinct cancer cell origins in a fluorescence polarization-based aptamer detection method for extracellular nanovesicles. Notably, a flow cytometric assay based on a HER2 aptamer successfully detected one HER2-povitive EV amongst 499 HER2-negative sEVs, with sEVs defined by the CD9 A3-A aptamer. These findings suggest that the CD9 aptamer-based biosensing platforms represent a promising next-generation tool for liquid biopsy-based precision medicine.