Co-enrichment of proteins in extracellular vesicles

Extracellular vesicles are cell-derived secretions that mediate tissue homeostasis and intercellular communication through their diverse cargos, including proteins. Distinct extracellular vesicle biogenesis pathways suggest specific association and co-enrichment of proteins sharing a biogenesis pathway, and non-association and co-depletion of proteins segregated into distinct pathways. Yet these associations elude conventional protein expression or co-expression measurements. Here, we propose and define pairwise protein co-enrichment relative to its overall expression to quantify whether a given protein is co-enriched or co-depleted with another protein. We measure co-enrichment, and differential co-enrichment between a stimulus and a reference condition, of up to 240 protein pairs in extracellular vesicles using antibody microarrays. We validate co-enrichment by modulating well-known extracellular vesicle biogenesis pathways, and find that differential co-enrichment measures expected changes between perturbed and reference conditions. Co-enrichment and differential co-enrichment in three model cell lines and parental and organotropic breast cancer progeny cell lines reveal both preserved and variable co-enrichment that may warrant further studies. Collectively, our result suggest that co-enrichment reflects cell physiology and extracellular biogenesis, is readily measurable, and could serve as quality control in extracellular vesicle biomanufacturing. Distinct extracellular vesicle biogenesis pathways suggest specific co-enrichment of proteins sharing a biogenesis pathway. Here, the authors design an approach to examine this co-enrichment and show that it reflects vesicle biogenesis.