Researchers comprehensively characterize human brain-derived extracellular vesicles using multiple isolation methods

Extracellular vesicles (EVs) have emerged as critical mediators of intercellular communication and promising biomarkers and therapeutics in the central nervous system (CNS). Human brain-derived EVs (BDEVs) provide a comprehensive snapshot of physiological changes in the brain’s environment, however, the isolation of BDEVs and the comparison of different methods for this purpose have not been fully investigated. In this study, Mayo Clinic Florida researchers compared the yield, morphology, subtypes and protein cargo composition of EVs isolated from the temporal cortex of aged human brains using three established separation methods: size-exclusion chromatography (SEC), phosphatidylserine affinity capture (MagE) and sucrose gradient ultracentrifugation (SG-UC). Their results showed that SG-UC method provided the highest yield and collected larger EVs compared to SEC and MagE methods as assessed by transmission electron microscopy and nanoparticle tracking analysis (NTA). Quantitative tandem mass-tag (TMT) mass spectrometry analysis of EV samples from three different isolation methods identified a total of 1158 proteins, with SG-UC showing the best enrichment of common EV proteins with less contamination of non-EV proteins. In addition, SG-UC samples were enriched in proteins associated with ATP activity and CNS maintenance, and were abundant in neuronal and oligodendrocytic molecules. In contrast, MagE samples were more enriched in molecules related to lipoproteins, cell-substrate junction and microglia, whereas SEC samples were highly enriched in molecules related to extracellular matrix, Alzheimer’s disease and astrocytes. Finally, the researchers validated the proteomic results by performing single-particle analysis using the super-resolution microscopy and flow cytometry. Overall, these findings demonstrate the differences in yield, size, enrichment of EV cargo molecules and single EV assay by different isolation methods, suggesting that the choice of isolation method will have significant impact on the downstream analysis and protein discovery.

The workflow for comparative analysis of BDEVs
separated from human brain tissue using three different methods

Following digestion, serial centrifugation, and filtration steps, the resulting supernatant was contracted and divided into three portions and subjected to three different isolation methods: sucrose gradient ultracentrifugation [SG-UC], size-exclusion chromatography (SEC) and phosphatidylserine affinity capture [MagE]. The total digestion (Total), prior supernatant (Super) and enrichment EVs were then collected and analysed using mass spectrometry. We also performed multi-approaches to evaluate EV size and concentration using NTA, Flow Nanoanalyzer and Nanoimager. The morphology of EVs was observed by TEM, while molecular profiling was conducted using mass spectrometry. Moreover, Flow Nanoanalyzer was used to detect EV subpopulations and visualize the protein patten at a single EV level using Nanoimager.

Zhang Z, Yu K, You Y, Jiang P, Wu Z, DeTure MA, Dickson DW, Ikezu S, Peng J, Ikezu T. (2023) Comprehensive characterization of human brain-derived extracellular vesicles using multiple isolation methods: Implications for diagnostic and therapeutic applications. J Extracell Vesicles 12(8):e12358. [article]

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