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Comprehensive proteomic profiling of plasma and serum phosphatidylserine-positive extracellular vesicles reveals tissue-specific proteins.

ABSTRACT: Extracellular vesicles (EVs) are ubiquitously secreted by almost all tissues and carry many cargoes, including proteins, RNAs, and lipids, which are related to various biological processes. EVs are shed from tissues into the blood and expected to be used as biomarkers for diseases. Here, we isolated EVs from EDTA plasma and serum of six healthy subjects by an affinity capture isolation method, and a total of 4,079 proteins were successfully identified by comprehensive EV proteomics. Our reliable and detailed catalog of the differential expression profiles of EV proteins in plasma and serum between healthy individuals could be useful as a reference for biomarker discovery. Furthermore, tissue-specific protein groups co-regulated between blood EVs from healthy individuals were identified. These EV proteins are expected to be used for more specific and sensitive enrichment of tissue-specific EVs and for screening and monitoring of disease without diagnostic imaging in patient blood in the future.

SUBMITTER: Muraoka S

PROVIDER: S-EPMC8941215 | biostudies-literature | 2022 Apr

REPOSITORIES: biostudies-literature

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Comprehensive proteomic profiling of plasma and serum phosphatidylserine-positive extracellular vesicles reveals tissue-specific proteins.

Muraoka Satoshi S Hirano Masayo M Isoyama Junko J Nagayama Satoshi S Tomonaga Takeshi T Adachi Jun J

iScience 20220301 4

Extracellular vesicles (EVs) are ubiquitously secreted by almost all tissues and carry many cargoes, including proteins, RNAs, and lipids, which are related to various biological processes. EVs are shed from tissues into the blood and expected to be used as biomarkers for diseases. Here, we isolated EVs from EDTA plasma and serum of six healthy subjects by an affinity capture isolation method, and a total of 4,079 proteins were successfully identified by comprehensive EV proteomics. Our reliable ...[more]

PMID: 35340435

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Project description:BackgroundCirculating small extracellular vesicles (sEVs) and its associated proteins are of great interest in the early detection of many diseases. However, there is no gold standard for plasma sEVs isolation, especially for proteomic profiling which could be largely affected by contamination such as lipoproteins and plasma proteins. Previous studies suggested combinations of different sEVs isolation methods could improve the yield and purity of the isolated fractions. Nevertheless, there is no systematic evaluation of size-exclusion chromatography (SEC), ultracentrifugation (UC), and their combination in a proteomic perspective.ResultsPlasma samples were collected from healthy individuals, and sEVs were separated by one-step SEC, one-step UC, and combining SEC with UC, respectively. Here we exhibited that the purity of sEVs was improved by SEC in contrast to traditional UC. Furthermore, by conducting a SEC procedure followed by UC, we separated sEVs with the highest purity. In the proteomic analysis, 992 protein species were identified in the plasma sEVs isolated by our novel separation method, of which several proteins are sEVs-associated proteins but hitherto never been identified in the previous studies and database, much more than plasma sEVs isolated by UC (453) or SEC (682) alone. As compared to Vesiclepedia and Exocarta databases, plasma sEVs isolated by the new procedure kept 584 previously identified sEVs-associated proteins and 360 other proteins that have not been detected before. Detailed analysis suggested that more kinds of sEVs biomarkers, such as CD9, ALIX, and FLOT1, could be identified in plasma sEVs isolated by the novel isolation method as compared to one-step UC/SEC. Furthermore, the lower abundance ranks of common contaminants, such as lipoproteins and IgG chains, in the sEVs fractions obtained by our new method as compared to one-step UC/SEC also demonstrated the purity of sEVs had been improved.ConclusionsCombining SEC with UC could significantly improve the performance of mass spectrometry-based proteomic profiling in analyzing plasma-derived sEVs.

Dataset Information

Comprehensive proteomic profiling of plasma and serum phosphatidylserine-positive extracellular vesicles reveals tissue-specific proteins.

Publications

Comprehensive proteomic profiling of plasma and serum phosphatidylserine-positive extracellular vesicles reveals tissue-specific proteins.

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