Metabolite profiles from extracellular vesicles hold promise as disease biomarkers

Researchers from the University of Helsinki have characterized, for the first time, small metabolite profiles from urine and platelet-derived extracellular vesicles. Their work provides insights both into the methodological aspects of EV metabolite profiling and to the changes in the metabolite profiles associated with prostate cancer. The study can serve as a basis for development of new, non-invasive tools to monitor health and disease.

Extracellular vesicles (EVs) are known as a promising source of biomarkers. So far, the focus has been on protein, (mi)RNA, DNA and lipid cargo and small molecule metabolites have attracted far less attention even though they might reveal dynamic changes in the metabolism downstream of genetic and proteomic regulation.

To study the metabolite content of EVs, EV researchers from the Institute for Molecular Medicine Finland (FIMM), Department of Biosciences and the Faculty of Pharmacy of the University of Helsinki profiled over hundred polar metabolites in the urinary EVs, platelet EVs from plasma and in the original source samples. The metabolate analyses were carried out at the FIMM Technology Centre's Metabolomics Unit. The results of the study have recently been published in the Theranostics – journal.

The results showed that a selection of cytosolic metabolites were enriched in EVs. The profiles of the urinary and platelet EVs overlapped with each other and with those of the source materials, but they also contained unique metabolites.

“Our results suggest that EVs enrich a selection of metabolites from the cytoplasm and that metabolomics of EVs could offer new kind of disease profiles unlike the conventional analysis of the original sample materials”, explain Taija af Hällström and Pia Siljander, the last authors of the study.

The study also focused on developing methods for EV sample preparation and data normalization that are suitable for EV metabolomics and potential biomarker discovery. Importantly, exploration of the metabolite content of EVs in the body fluids could offer a sensitive and non-invasive method to detect dynamic cancer-related biomarkers, especially since cancer cells tend to secrete more vesicles than normal cells.

To find out whether the metabolites from urinary EVs have biomarker potential related to prostate cancer, the researchers compared several different data normalization methods applying them to EV samples from prostate cancer patients before and after prostatectomy and from healthy controls.

The team demonstrated that levels of three metabolites (glucuronate, D-ribose 5-phosphate and isobutyryl-L-carnitine) were significantly lower in the pre-prostatectomy samples compared to the healthy control and post-prostatectomy samples. These changes were only detected from EVs by normalization to EV-derived factors or with metabolite ratios, and not from the original urine samples.

“Our results suggest that metabolite analysis of EVs from different samples is feasible using a high-throughput platform and relatively small amount of sample material. With the knowledge about the specific enrichment of metabolites and normalization methods, EV metabolomics could offer novel biomarker data not revealed by the analysis of the original EV source materials”, concludes Maija Puhka from FIMM, the first author of the study.


Original publication:

Puhka M, Takatalo M, Nordberg M-E, Valkonen S, Nandania J, Aatonen M, Yliperttula M, Laitinen S, Velagapudi V, Mirtti T, Kallioniemi O, Rannikko A, Siljander P R-M* and Af Hällström T M*. 2017. Metabolomic Profiling of Extracellular Vesicles and Alternative Normalization Methods Reveal Enriched Metabolites and Strategies to Study Prostate Cancer-Related Changes. Theranostics, 7:16, pp. 3824-3841. DOI: 10.7150/thno.19890 * Equal contribution.

Contact information:

Maija Puhka, Postdoctoral Researcher, Head of EV core FIMM, Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, maija.puhka at