Metabolomics Applied to the Study of Extracellular Vesicles

Abstract

Cell-secreted extracellular vesicles (EVs) have rapidly gained prominence as sources of biomarkers for non-invasive biopsies, owing to their ubiquity across human biofluids and physiological stability. There are many characterisation studies directed towards their protein, nucleic acid, lipid and glycan content, but more recently the metabolomic analysis of EV content has also gained traction. Several EV metabolite biomarker candidates have been identified across a range of diseases, including liver disease and cancers of the prostate and pancreas. Beyond clinical applications, metabolomics has also elucidated possible mechanisms of action underlying EV function, such as the arginase-mediated relaxation of pulmonary arteries or the delivery of nutrients to tumours by vesicles. However, whilst the value of EV metabolomics is clear, there are challenges inherent to working with these entities—particularly in relation to sample production and preparation. The biomolecular composition of EVs is known to change drastically depending on the isolation method used, and recent evidence has demonstrated that changes in cell culture systems impact upon the metabolome of the resulting EVs. This review aims to collect recent advances in the EV metabolomics field whilst also introducing researchers interested in this area to practical pitfalls in applying metabolomics to EV studies.

Urinary extracellular vesicles: A position paper by the Urine Task Force of the International Society for Extracellular Vesicles

“…Such studies include (small) RNA‐Seq and other transcriptomics analyses as well as mass spectrometry‐based proteomics (Carreras‐Planella et al., 2020; Carreras‐Planella et al., 2020; Cheng et al., 2014; Erozenci et al., 2019; Everaert et al., 2019; Park et al., 2020; Rodriguez et al., 2017; Salih et al., 2016; Srinivasan et al., 2019; Stokman et al., 2019; Thomas et al., 2016). Metabolomic and lipidomic studies of uEVs are also under development, but remain rather complicated, with workflows requiring specialized instrumentation and expertise (Clos‐Garcia et al., 2018; Williams et al., 2019).…”

Glycosylation of Cancer Extracellular Vesicles: Capture Strategies, Functional Roles and Potential Clinical Applications

“…Different subpopulations of EVs may share size and biochemical characteristics, which makes it impossible to differentiate or specifically isolate them from a given sample [ 125 , 126 ]. In fact, most of the currently available methods for EV isolation will enrich different sub-populations of EVs carrying diverse molecular compositions [ 127 , 128 , 129 , 130 ]. Our group previously showed that different EV isolation techniques resulted in an enrichment of diverse EV glycosylated profiles, depending on the capacity of each method to separate cancer EVs from the non-EV content [ 86 ].…”

Inclusion Biogenesis, Methods of Isolation and Clinical Application of Human Cellular Exosomes

“…Even though the EVs always have a lipid encapsulation, lipidomics is not the most often used method in EV analysis, and there are few studies regarding proteomic analysis, highlighting as with proteins, different cells release exosomes of diverse lipid composition [53]. The exosome membrane does not exactly reflect plasma membrane of the maternal cell (e.g., enrichment of exosome membrane in sphingomyelin and glycosphingolipids, as well as lower amount of phosphatidylinositol in comparison to releasing cell) [28].…”