Proteogenomic analysis reveals exosomes are more oncogenic than ectosomes

Abstract

Extracellular vesicles (EVs) include the exosomes (30-100 nm) that are produced through the endocytic pathway via the multivesicular bodies and the ectosomes (100-1000 nm) that are released through the budding of the plasma membrane. Despite the differences in the mode of biogenesis and size, reliable markers that can distinguish between exosomes and ectosomes are non-existent. Moreover, the precise functional differences between exosomes and ectosomes remains poorly characterised. Here, using label-free quantitative proteomics, we highlight proteins that could be exploited as markers to discriminate between exosomes and ectosomes. For the first time, a global proteogenomics analysis unveiled the secretion of mutant proteins that are implicated in cancer progression through tumor-derived EVs. Follow up integrated bioinformatics analysis highlighted the enrichment of oncogenic cargo in exosomes and ectosomes. Interestingly, exosomes induced significant cell proliferation and migration in recipient cells compared to ectosomes confirming the oncogenic nature of exosomes. These findings ascertain that cancer cells facilitate oncogenesis by the secretion of mutant and oncoproteins into the tumor microenvironment via exosomes and ectosomes. The integrative proteogenomics approach utilized in this study has the potential to identify disease biomarker candidates which can be later assayed in liquid biopsies obtained from cancer patients.

Proteomic comparison defines novel markers to characterize heterogeneous populations of extracellular vesicle subtypes

“…Comparing the molecular signatures of tumor- (26)(27)(28)(29) and DC-derived (our work) medium EVs will surely provide additional specific markers. So far, we have not identified a protein that would be exclusively in medium EVs, and not also in the largest ones, which the other groups working on tumorderived EVs did not evaluate: although it would be very useful, finding a specific marker for these particular EVs may be challenging.…”

“…To obtain these results, it was necessary to combine several separation procedures and to follow a nonbiased approach, rather than a molecule-or EV subtype-targeted one. Some groups have recently performed comparative proteomic analyses of medium-sized and small EVs (with or without floatation into a gradient) from platelets (19) or tumor cells (26)(27)(28)(29). Another group has compared the expression of a few surface proteins on B lymphoma-EVs immunoprecipitated with either CD9, CD63, or CD81 (30).…”

Tracing Cellular Origin of Human Exosomes Using Multiplex Proximity Extension Assays

“…The presence of integrins on exosomes has previously been reported (6,49). Exosome-associated integrins are important in cancer metastasis and preferential exosome uptake by specific cells (12).…”

“…EVs, encompassing subcategories such as exosomes, microvesicles and apoptotic bodies, constitute structures secreted from cells and are surrounded by a phospholipid bilayer membrane whose constituents may reflect their cells of origin (2,3). It has been demonstrated that the content of exosomes may be selectively incorporated (4,5), with examples of oncogenic proteins enriched in exosomes compared with their cells of origin (6). The largest of the EVs are apoptotic bodies and microvesicles, both originating from the plasma membrane (7), whereas smaller EVs, so called exosomes, are formed intracellularly by multiple invaginations of the late endocytic membrane, leading to formation of vesicle-containing endosomes called multivesicular bodies (8,9).…”

Adaptor Protein CD2AP and L-type Lectin LMAN2 Regulate Exosome Cargo Protein Trafficking through the Golgi Complex

“…Proteomics studies, however, have discovered a growing set of GPCR family proteins, including GPR179 (14), GPR155 (15), GPR100 (16), and GPRC5 family proteins (17), that are cargos of extracellular vesicles. This suggests that GPCR family proteins may also mediate intercellular communications when transported to target cells via extracellular vesicles.…”