Prostate-specific EV capture with sufficient RNA yield to enable transcriptomic profiling

Yang, Y.; Doo, J.; Perez, D.; Franzen, K.; Nguyen, S.; Mirabal, J.; Mitsock, E.; Punnen, S.; Gaston, S.; Gerard, T.; Pollack, A.; Cortizas, E.; Chakrabortty, S. K.; Skog, J.; Johnson, J. M.

doi:10.1101/2025.09.08.674937

bioRxiv · 10.1101/2025.09.08.674937

Prostate-specific EV capture with sufficient RNA yield to enable transcriptomic profiling

Yang, Y.·Doo, J.·Perez, D.·Franzen, K.·Nguyen, S.·Mirabal, J.·Mitsock, E.·Punnen, S.·Gaston, S.·Gerard, T.·Pollack, A.·Cortizas, E.·Chakrabortty, S. K.·Skog, J.·Johnson, J. M.

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Abstract

Prostate-specific antigen (PSA) screening has reduced prostate cancer (PCa) mortality but suffers from limited specificity, contributing to unnecessary biopsies and overdiagnosis of indolent disease. There is a critical need for biofluid-based biomarkers that improve the precision of PCa detection. Extracellular vesicles (EVs) offer a promising platform for noninvasive diagnostics, as they carry molecular cargo reflective of their tissue of origin. The ExoDx Prostate IntelliScore (EPI) test, a urine-based EV assay, is currently the only commercial EV diagnostic for clinically significant (cs)PCa, but its performance may be constrained by contamination from renal and bladder-derived EVs. To address this, we developed Exosome Diagnostics Depletion and Enrichment (EDDE), a novel immunocapture-based method for isolating prostate-derived EVs with high specificity. By targeting Prostate Specific Membrane Antigen (PSMA), we optimized EDDE to selectively enrich prostate EVs from post-DRE urine and recover sufficient RNA for transcriptomic analysis. Throughout development, we implemented a quantitative framework to track EV stoichiometry and assess depletion efficiency and yield, enabling rigorous optimization of the workflow. Our findings demonstrate that PSMA EDDE enriches prostate-specific EVs and yields RNA quantities compatible with sequencing. This platform enhances the specificity of EV-based biomarker discovery and holds promise for determining if tissue-specific EV biomarkers contribute advantages over bulk EVs.

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Yang, Y., Doo, J., Perez, D., Franzen, K., Nguyen, S., Mirabal, J., Mitsock, E., Punnen, S., Gaston, S., Gerard, T., Pollack, A., Cortizas, E., Chakrabortty, S. K., Skog, J., Johnson, J. M.. 2025-09-13. Prostate-specific EV capture with sufficient RNA yield to enable transcriptomic profiling. https://doi.org/10.1101/2025.09.08.674937

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