High-resolution proteomic and lipidomic analysis of exosomes and microvesicles

Extracellular vesicles (EVs), including exosomes and microvesicles (MVs), are explored for use in diagnostics, therapeutics and drug delivery. However, little is known about the relationship of protein and lipid composition of EVs and their source cells. Here, researchers from the University of Massachusetts Medical School report high-resolution lipidomic and proteomic analyses of exosomes and MVs derived by differential ultracentrifugation from 3 different cell types: U87 glioblastoma cells, Huh7 hepatocellular carcinoma cells and human bone marrow-derived mesenchymal stem cells (MSCs). The researchers identified 3,532 proteins and 1,961 lipid species in the screen.

Exosomes differed from MVs in several different areas:

(a) The protein patterns of exosomes were more likely different from their cells of origin than were the protein patterns of MVs;

(b) The proteomes of U87 and Huh7 exosomes were similar to each other but different from the proteomes of MSC exosomes, whereas the lipidomes of Huh7 and MSC exosomes were similar to each other but different from the lipidomes of U87 exosomes;

(c) exosomes exhibited proteins of extracellular matrix, heparin-binding, receptors, immune response and cell adhesion functions, whereas MVs were enriched in endoplasmic reticulum, proteasome and mitochondrial proteins.

Lipid enrichment in EVs correlates with head group charge
and fatty acid tail length and saturation


Lipid species levels in EVs were normalized to the corresponding lipid levels in source cells, expressed on a log(2) scale and colour-coded. Depletion is depicted in blue and enrichment in red. Sidebar on the left encodes 3 characteristics of a lipid species: headgroup charge (in colour), average length of fatty acid tails (greyscale) and average level of saturation of fatty acid tails (greyscale). Lipid species clustered not only according to head group charge but also according to length and saturation of tails.

Exosomes and MVs also differed in their types of lipid contents. Enrichment in glycolipids and free fatty acids characterized exosomes, whereas enrichment in ceramides and sphingomyelins characterized MVs. Furthermore, Huh7 and MSC exosomes were specifically enriched in cardiolipins; U87 exosomes were enriched in sphingomyelins. This study comprehensively analyses the protein and lipid composition of exosomes, MVs and source cells in 3 different cell types.

Haraszti RA, Didiot MC, Sapp E, Leszyk J, Shaffer SA, Rockwell HE, Gao F, Narain NR, DiFiglia M, Kiebish MA, Aronin N, Khvorova A. (2016) High-resolution proteomic and lipidomic analysis of exosomes and microvesicles from different cell sources. J Extracell Vesicles 5:32570. [article]

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