Extracellular Vesicle Proteomes Shed Light on the Evolutionary, Interactive, and Functional Divergence of Their Biogenesis Mechanisms

Hyobin Julianne Lim; Haejin Yoon; Hyeyeon Kim; Yun-Won Kang; Ji-Eun Kim; Oh Youn Kim; Eun-Young Lee; Jean-Claude Twizere; Janusz Rak; Dae-Kyum Kim

doi:10.3389/fcell.2021.734950

Extracellular Vesicle Proteomes Shed Light on the Evolutionary, Interactive, and Functional Divergence of Their Biogenesis Mechanisms

Front Cell Dev Biol. 2021 Oct 1:9:734950. doi: 10.3389/fcell.2021.734950. eCollection 2021.

Authors

Hyobin Julianne Lim¹, Haejin Yoon², Hyeyeon Kim³, Yun-Won Kang¹, Ji-Eun Kim^{4

5}, Oh Youn Kim⁶, Eun-Young Lee⁷, Jean-Claude Twizere^{8

9}, Janusz Rak¹⁰, Dae-Kyum Kim¹

Affiliations

¹ Center for Personalized Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States.
² Department of Cell Biology, Blavatnik Institute and Harvard Medical School, Boston, MA, United States.
³ Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
⁴ Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada.
⁵ Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
⁶ College of Medicine, Yonsei University, Seoul, South Korea.
⁷ Infection and Immunity Research Laboratory, Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea.
⁸ Laboratory of Viral Interactomes, GIGA Institute, University of Liège, Liege, Belgium.
⁹ TERRA Teaching and Research Centre, University of Liège, Liege, Belgium.
¹⁰ Research Institute of the McGill University Health Centre, Glen Site, McGill University, Montreal, QC, Canada.

Abstract

Extracellular vesicles (EVs) are membranous structures containing bioactive molecules, secreted by most cells into the extracellular environment. EVs are classified by their biogenesis mechanisms into two major subtypes: ectosomes (enriched in large EVs; lEVs), budding directly from the plasma membrane, which is common in both prokaryotes and eukaryotes, and exosomes (enriched in small EVs; sEVs) generated through the multivesicular bodies via the endomembrane system, which is unique to eukaryotes. Even though recent proteomic analyses have identified key proteins associated with EV subtypes, there has been no systematic analysis, thus far, to support the general validity and utility of current EV subtype separation methods, still largely dependent on physical properties, such as vesicular size and sedimentation. Here, we classified human EV proteomic datasets into two main categories based on distinct centrifugation protocols commonly used for isolating sEV or lEV fractions. We found characteristic, evolutionarily conserved profiles of sEV and lEV proteins linked to their respective biogenetic origins. This may suggest that the evolutionary trajectory of vesicular proteins may result in a membership bias toward specific EV subtypes. Protein-protein interaction (PPI) network analysis showed that vesicular proteins formed distinct clusters with proteins in the same EV fraction, providing evidence for the existence of EV subtype-specific protein recruiters. Moreover, we identified functional modules enriched in each fraction, including multivesicular body sorting for sEV, and mitochondria cellular respiration for lEV proteins. Our analysis successfully captured novel features of EVs embedded in heterogeneous proteomics studies and suggests specific protein markers and signatures to be used as quality controllers in the isolation procedure for subtype-enriched EV fractions.

Keywords: biogenesis; evolution; extracellular vesicle; network; purification.