Vesiclepedia 2024: an extracellular vesicles and extracellular particles repository

Abstract

Vesiclepedia (http://www.microvesicles.org) is a free web-based compendium of DNA, RNA, proteins, lipids and metabolites that are detected or associated with extracellular vesicles (EVs) and extracellular particles (EPs). EVs are membranous vesicles that are secreted ubiquitously by cells from all domains of life from archaea to eukaryotes. In addition to EVs, it was reported recently that EPs like exomeres and supermeres are secreted by some mammalian cells. Both EVs and EPs contain proteins, nucleic acids, lipids and metabolites and has been proposed to be implicated in several key biological functions. Vesiclepedia catalogues proteins, DNA, RNA, lipids and metabolites from both published and unpublished studies. Currently, Vesiclepedia contains data obtained from 3533 EV studies, 50 550 RNA entries, 566 911 protein entries, 3839 lipid entries, 192 metabolite and 167 DNA entries. Quantitative data for 62 822 entries from 47 EV studies is available in Vesiclepedia. The datasets available in Vesiclepedia can be downloaded as tab-delimited files or accessible through the FunRich-based Vesiclepedia plugin.

Graphical Abstract

Figure 1.

Subtypes of EVs based on their biogenesis pathways. (A) Based on their biogenesis pathways, EVs are classified into various subtypes. Exosomes, range from 30 to 150 nm, originate from the endosomal pathway. Microvesicles/ectosomes, range from 100 to 1000 nm, are produced through outward budding of the plasma membrane. Migrasomes are the vesicles that are left behind by the migratory cells and are in the size of 500 to 3000 nm. Apoptotic bodies with a diameter up to 1–5 μm are the largest class of EV subtypes and are produced through the blebbing and protrusions of the apoptotic cell membrane during cell death. Large oncosomes, range from 1 to 10 μm, are the large class of cancer-derived EVs originating from the shedding of membrane blebs. (B) Based on the operational terms and size, EVs and particles are broadly classified as large EVs, small EVs and EPs.

Figure 2.

Snapshot of Vesiclepedia pages with the example of EV enriched protein TSG101. Search for the molecule of interest provides gene summary page that contains the data on the molecule, experimental details 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. EV-QUANT provides quantitative data for EV studies. For the experiment of interest, the quantification for the cargo identified is available as data table and abundant cargo are visualised as heatmap. Alongside that, for the gene of interest in the study, the relative quantification can be visualised by bar graph. Vesiclepedia plugin in FunRich can be used to automatically download data for downstream analysis.

Figure 3.

Schematic workflow of Vesiclepedia query page. Multiple query options are available for users to access EV/EP contents (A) Search for the proteins/miRNA by entering either gene symbol, gene name or miRNA name to retrieve all the related experiment details. (B) Search for the lipid of interest by entering the lipid name in searchable dropdown menu to retrieve experimental details. (C) For DNA, use searchable dropdown option to retrieve experimental details.