Quantitative proteomics identifies the core proteome of exosomes with syntenin-1 as the highest abundant protein and a putative universal biomarker

• Published in: Nature cell biology Vol. 23; no. 6; pp. 631 - 641
• Main Authors: Kugeratski, Fernanda G., Hodge, Kelly, Lilla, Sergio, McAndrews, Kathleen M., Zhou, Xunian, Hwang, Rosa F., Zanivan, Sara, Kalluri, Raghu
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 01.06.2021; Nature Publishing Group
• Subjects: 631/1647/1407/2163; 631/45/475; 631/80; 82/58; Amino acids; Analysis; Animals; Biological markers; Biomarkers; Biomarkers, Tumor - genetics; Biomarkers, Tumor - metabolism; Biomedical and Life Sciences; Cancer Research; Case-Control Studies; Cell Biology; Cell culture; Cell interaction; Cell signaling; Chemical properties; Depletion; Developmental Biology; Exosomes; Exosomes - genetics; Exosomes - metabolism; Exosomes - ultrastructure; Extracellular vesicles; Female; HEK293 Cells; Humans; Isotope Labeling; Jurkat Cells; Life Sciences; Male; Mass spectrometry; Mass spectroscopy; MCF-7 Cells; Membrane proteins; Methods; Mice; Mice, Inbred C57BL; Neoplasms - genetics; Neoplasms - metabolism; Neoplasms - ultrastructure; NIH 3T3 Cells; Proteins; Proteome; Proteomes; Proteomics; RAW 264.7 Cells; Resource; Spectrometry, Mass, Electrospray Ionization; Stable isotopes; Stem Cells; Syntenins - genetics; Syntenins - metabolism; Tandem Mass Spectrometry; THP-1 Cells; United States
• ISSN: 1465-7392; 1476-4679
• DOI: 10.1038/s41556-021-00693-y

Exosomes are extracellular vesicles derived from the endosomal compartment that are potentially involved in intercellular communication. Here, we found that frequently used biomarkers of exosomes are heterogeneous, and do not exhibit universal utility across different cell types. To uncover ubiquitous and abundant proteins, we used an unbiased and quantitative proteomic approach based on super-stable isotope labeling with amino acids in cell culture (super-SILAC), coupled to high-resolution mass spectrometry. In total, 1,212 proteins were quantified in the proteome of exosomes, irrespective of the cellular source or isolation method. A cohort of 22 proteins was universally enriched. Fifteen proteins were consistently depleted in the proteome of exosomes compared to cells. Among the enriched proteins, we identified biogenesis-related proteins, GTPases and membrane proteins, such as CD47 and ITGB1. The cohort of depleted proteins in exosomes was predominantly composed of nuclear proteins. We identified syntenin-1 as a consistently abundant protein in exosomes from different cellular origins. Syntenin-1 is also present in exosomes across different species and biofluids, highlighting its potential use as a putative universal biomarker of exosomes. Our study provides a comprehensive quantitative atlas of core proteins ubiquitous to exosomes that can serve as a resource for the scientific community. Using an unbiased and quantitative proteomic approach, Kugeratski et al. identified the core constituents of exosomes and found that syntenin-1 was the most abundant component, making it a putative universal biomarker.