Laboratory for extracellular vesicle research

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Research

 

Understanding EV Biology

We use HIV infection as a model system to investigate the cellular mechanisms that regulate EV biogenesis, cargo composition, and biological function, and how these processes are reshaped by changes in cellular state. Our research focuses on the HIV accessory protein Nef, which profoundly remodels cellular signaling, membrane trafficking, lipid metabolism, and autophagy—processes that are closely linked to EV biogenesis and intercellular communication.

To address these questions, we integrate complementary imaging, biochemical, single-particle, and functional approaches in diverse cellular models. We investigate how Nef alters intracellular trafficking and EV biogenesis, characterize the molecular composition and heterogeneity of released EV populations, and determine how these EVs communicate with and influence recipient cells.

Despite effective antiretroviral therapy, HIV-associated neurocognitive disorders (HAND) remain a major clinical challenge. Our research investigates how Nef-containing EVs contribute to the development and persistence of HAND, providing new insights into disease mechanisms and potential therapeutic targets.

Representative publications:
Lavrin T, Loboda J, Ferdin J, Levak V, Sitar S, Holcar M, Resnik N, Stenovec M, Trampuš Bakija A, Veranič P, Žagar E, Tušek Žnidarič M, Pužar Dominkuš P, Lenassi M. HIV protein Nef expression in human microglia drives the release of distinct Nef-containing extracellular vesicles. Extracell Vesicles Circ Nucl Acids. 2025 Dec 2;6(4):895-920. doi: 10.20517/evcna.2025.106. 

Stenovec M, Lasič E, Dominkuš PP, Bobnar ST, Zorec R, Lenassi M, Kreft M. Slow Release of HIV-1 Protein Nef from Vesicle-like Structures Is Inhibited by Cytosolic Calcium Elevation in Single Human Microglia. Mol Neurobiol. 2019 Jan;56(1):102-118. doi: 10.1007/s12035-018-1072-2.
Erratum in: Mol Neurobiol. 2019 Sep;56(9):6668. doi: 10.1007/s12035-019-01709-3. 

Lenassi M, Cagney G, Liao M, Vaupotic T, Bartholomeeusen K, Cheng Y, Krogan NJ, Plemenitas A, Peterlin BM. HIV Nef is secreted in exosomes and triggers apoptosis in bystander CD4+ T cells. Traffic. 2010 Jan;11(1):110-22. doi: 10.1111/j.1600-0854.2009.01006.x. 

Complete publication list: PubMed

 

Translational EV Biomarkers

The potential of EVs as biomarkers is considerable, yet their promise has not yet translated into clinical use. Translation is challenged by several factors, including pre-analytical sample quality, the complexity of EV biology, and limited reproducibility. We address these bottlenecks through methodological innovation by developing workflows for sample processing, EV isolation, and EV characterization from blood and urine; contributing to resources that advance reproducibility in EV research; and evaluating these approaches in collaborative biomarker studies with clinical partners.

Kidney transplantation provides an excellent clinical model for developing and evaluating EV biomarkers. In this setting, we investigate the potential of EVs for non-invasive diagnosis and monitoring of kidney allograft injury. We have established well-characterized cross-sectional and longitudinal patient cohorts with matched, quality-controlled urine, blood plasma, and biopsy tissue samples. We pioneered the use of urinary EV-bound DNA as a biomarker for kidney allograft rejection and are currently investigating urinary EV phenotypes associated with allograft injury. Complementary studies of blood EVs in healthy individuals are establishing reference profiles needed for the future clinical implementation of EV-based diagnostics.

Representative publications:
Holcar M, Marić I, Tertel T, Goričar K, Čegovnik Primožič U, Černe D, Giebel B, Lenassi M. Comprehensive Phenotyping of Extracellular Vesicles in Plasma of Healthy Humans - Insights Into Cellular Origin and Biological Variation. J Extracell Vesicles. 2025 Jan;14(1):e70039. doi: 10.1002/jev2.70039. 

Sedej I, Štalekar M, Tušek Žnidarič M, Goričar K, Kojc N, Kogovšek P, Dolžan V, Arnol M, Lenassi M. Extracellular vesicle-bound DNA in urine is indicative of kidney allograft injury. J Extracell Vesicles. 2022 Sep;11(9):e12268. doi: 10.1002/jev2.12268. 

Holcar M, Ferdin J, Sitar S, Tušek-Žnidarič M, Dolžan V, Plemenitaš A, Žagar E, Lenassi M. Enrichment of plasma extracellular vesicles for reliable quantification of their size and concentration for biomarker discovery. Sci Rep. 2020 Dec 7;10(1):21346. doi: 10.1038/s41598-020-78422-y. 

Droste M, Puhka M, van Royen ME, Ng MSY, Blijdorp C, Alvarez-Llamas G, Borràs FE, Büscher AK, Bussolati B, Dear JW, Falcón-Pérez JM, Giebel B, Grange C, Hoorn EJ, Leivo J, Lenassi M, Llorente A, Lucien F, Mertens I, Mischak H, Pink D, Tertel T, Tiwari S, Di Vizio D, Yuen PST, Zarovni N, Jenster G, Burger D, Martens-Uzunova ES, Erdbrügger U. Roadblocks of Urinary EV Biomarkers: Moving Toward the Clinic. J Extracell Vesicles. 2025 Jul;14(7):e70120. doi: 10.1002/jev2.70120. 

Lucien F, Gustafson D, Lenassi M, Li B, Teske JJ, Boilard E, von Hohenberg KC, Falcón-Perez JM, Gualerzi A, Reale A, Jones JC, Lässer C, Lawson C, Nazarenko I, O'Driscoll L, Pink R, Siljander PR, Soekmadji C, Hendrix A, Welsh JA, Witwer KW, Nieuwland R. MIBlood-EV: Minimal information to enhance the quality and reproducibility of blood extracellular vesicle research. J Extracell Vesicles. 2023 Dec;12(12):e12385. doi: 10.1002/jev2.12385. 

Complete publication list: PubMed