Scanning electron microscopy of retained extracellular vesicles on the filter membrane.

Platform Enhances Purity and Reproducibility of Extracellular Vesicle Proteomics

Low-cost, high-throughput method improves purity and reproducibility of EV-based proteomics

Ghent, 07 July 2025 – A group of researchers at the VIB-UGent Center for Medical Biotechnology has developed a new platform to isolate and analyse extracellular vesicles (EVs), nanosized particles secreted by cells and playing a role in cellular communication and disease development. Called FAEVEr, the method increases the throughput of EV enrichment and is significantly more cost-efficient than existing methods. The study was published in the Journal of Extracellular Vesicles.

Extracellular Vesicles (EVs) are small particles that carry proteins, RNA, and other biomolecules from their cell of origin. They hold much promise for diagnostics and therapeutics, but isolating them from complex biofluids at high purity and throughput remains a major challenge. EVs are incredibly small - between 30 and 150 nanometers in size. To capture these tiny containers of messengers, scientists need to rely on sophisticated equipment such as ultracentrifuges. Unfortunately, these traditional methods of EV enrichment are time-consuming and resource-intensive with relatively low throughput.

Now, researchers in the lab of Prof. Kris Gevaert at the VIB-UGent Center for Medical Biotechnology have developed a novel EV-enrichment method. Building on their earlier work published in Molecular & Cellular Proteomics (January 2025), they demonstrated the effectiveness of Filter-Aided Extracellular Vesicle Enrichment, or FAEVEr in enriching EVs from individual samples in a miniaturized and 96-well high-throughput format.

Transmission electron microscopy reveals intact EVs with their distinct morphology and low background after their enrichment and purification using FAEVEr including 5% Tween-20 (size bar of 100 nm).

Cost-efficient and fast

The new platform promises a much faster and more affordable alternative to existing EV-enrichment methods. Using 96-well filter plates, FAEVEr enables a much higher throughput volume by parallel processing of samples in under 2 hours.

Essential to the FAEVEr method is the use of Tween-20, a mild and inexpensive detergent added during EV washing steps. Its inclusion proved critical for improving the purity of the EV proteome by preventing fouling of the filter membranes used to trap EVs and by breaking weak interactions between EVs and contaminating abundant proteins. Importantly, this improvement in purity does not require complex chemistry or costly reagents, making the method accessible for both labs and clinical research settings using standard lab equipment.

Dr. Jarne Pauwels, first author of the study: “We noticed that the addition of higher concentrations of Tween-20 led to a marked reduction in contaminating non-EV proteins and a significant increase in the identification of transmembrane proteins, a key metric in our studies.”
Schematic overview of the streamlined, high-throughput FAEVEr approach for characterization and proteome analysis.

Doing clinicians a FAEVEr

This innovation paves the way for more reproducible EV-based proteomics and strengthens the foundation for future clinical applications of EVs in diagnostics.

“We hope this new approach can find its way into clinical practice”, adds Prof. Kris Gevaert, Director of the VIB-UGent Center for Medical Biotechnology. “FAEVEr lowers the barrier for EV enrichment and offers a significantly faster and much more cost-efficient approach to analyzing plasma or urine biopsies for biomarkers. We hope this new technology can contribute to faster diagnoses for patients.”

The method is already being applied in collaborations focused on prostate cancer, where enriched EV analysis may help identify disease-specific protein signatures from a simple urine sample.


Publication

Pauwels et al. “A 96well ultrafiltration approach for the high-throughput proteome analysis of extracellular vesicles isolated from conditioned medium” Journal of Extracellular Vesicles, 2025.

Funding

The research team at the VIB-UGent Center for Medical Biotechnology was financially supported by FWO, the Ghent University Concerted Research Actions and the interuniversity BOF program.


Joran Lauwers

Joran Lauwers

Press Contact, VIB

About the VIB-UGent Center for Medical Biotechnology

Research at the VIB-UGent Center for Medical Biotechnology can lead to more effective medicine. If we know the causes and mechanisms of a disease, we can then deal with it in a better way. This is much more efficient than treating the symptoms, which is how things are often done at the moment. The research helps to prevent, diagnose or treat diseases.

Share

Latest stories

Website preview
Animab Secures EUR 10 Million in Series B Financing to Launch Nanoprotec® in Europe and Expand Pipeline
Zwijnaarde, 1 July 2025 – Animab (“the Company”), a leader in pioneering first-in-class oral antibody solutions for unmet needs in production animals, announces the successful closing of a EUR 10 million Series B funding round. The investment will support the commercial launch of Animab Nanoprotec® as well as the advancement of its broader pipeline. This financing round follows shortly after Animab’s exclusive distribution agreement with Huvepharma1, reinforcing the strong momentum behind the upcoming commercialization of Nanoprotec® in the European market.
press.vib.be
Website preview
Researchers uncover surprising role of 'natural killer' cells in resistance to cancer immunotherapy
Targeting NK cells could open the door to more effective immunotherapy in resistant tumors
press.vib.be
Website preview
Killing cancer cells by boosting organelle bridges
Endoplasmic reticulum-mitochondria contact sites drive ferroptosis
press.vib.be

About VIB

VIB is an independent research institute that translates insights in biology into impactful innovations for society. Collaborating with the five Flemish universities, it conducts research in plant biology, cancer, neuroscience, microbiology, inflammatory diseases, artificial intelligence and more. VIB connects science with entrepreneurship and stimulates the growth of the Flemish biotech ecosystem. The institute contributes to solutions for societal challenges such as new methods for diagnostics and treatments, as well as innovations for agriculture. 

Learn more at www.vib.be.

Contact

Suzanne Tassierstraat 1 9052 Zwijnaarde

+32 9 244 66 11

press@vib.be

vib.be