Vesiclepedia 2019: a compendium of RNA, proteins, lipids and metabolites in extracellular vesicles

Abstract

Extracellular vesicles (EVs) are membranous vesicles that are released by both prokaryotic and eukaryotic cells into the extracellular microenvironment. EVs can be categorised as exosomes, ectosomes or shedding microvesicles and apoptotic bodies based on the mode of biogenesis. EVs contain biologically active cargo of nucleic acids, proteins, lipids and metabolites that can be altered based on the precise state of the cell. Vesiclepedia (http://www.microvesicles.org) is a web-based compendium of RNA, proteins, lipids and metabolites that are identified in EVs from both published and unpublished studies. Currently, Vesiclepedia contains data obtained from 1254 EV studies, 38 146 RNA entries, 349 988 protein entries and 639 lipid/metabolite entries. Vesiclepedia is publicly available and allows users to query and download EV cargo based on different search criteria. The mode of EV isolation and characterization, the biophysical and molecular properties and EV-METRIC are listed in the database aiding biomedical scientists in assessing the quality of the EV preparation and the corresponding data obtained. In addition, FunRich-based Vesiclepedia plugin is incorporated aiding users in data analysis.

Figure 1.

Snapshot of Vesiclepedia pages Vesiclepedia gene summary page of EV enriched protein Alix (PDCD6IP) is displayed. The gene summary page provides data on the molecule of interest, experimental description pertaining to the studies that identified the molecule, Western blotting data to support the identification (if applicable) and mass spectrometry-based peptide details along with the tandem MS spectra is provided wherever possible. Furthermore, the experiment details are supported with EV-METRIC and linked to the EV-TRACK website to provide additional information on the scoring. The entire data from Vesiclepedia can be automatically downloaded through FunRich via the Vesiclepedia plugin and analysed.

Figure 2.

Distribution of EV studies based on the isolation method A histogram depicting the distribution of isolation methods employed by the EV studies catalogued in Vesiclepedia is depicted. Differential centrifugation has been used by >73% of the studies to isolate EVs while 57.7% of the studies have used ultracentrifugation. Although the data is depicted as individual methods, most studies have employed a combination of these methods. For instance, filtration accounted for 34% of the EV studies and is always used in conjunction with other procedures to isolate EVs.