The heterogeneity of exosomal populations has hindered our understanding
of their biogenesis, molecular composition, biodistribution, and functions. By
employing asymmetric-flow field-flow fractionation (AF4), we identified two
exosome subpopulations (large exosome vesicles, Exo-L, 90-120 nm; small exosome
vesicles, Exo-S, 60-80 nm) and discovered an abundant population of
non-membranous nanoparticles termed “exomeres” (~35 nm).
Exomere proteomic profiling revealed an enrichment in metabolic enzymes and
hypoxia, microtubule and coagulation proteins and specific pathways, such as
glycolysis and mTOR signaling. Exo-S and Exo-L contained proteins involved in
endosomal function and secretion pathways, and mitotic spindle and IL-2/STAT5
signaling pathways, respectively. Exo-S, Exo-L, and exomeres each had unique
N-glycosylation, protein, lipid, and DNA and RNA profiles
and biophysical properties. These three nanoparticle subsets demonstrated
diverse organ biodistribution patterns, suggesting distinct biological
functions. This study demonstrates that AF4 can serve as an improved analytical
tool for isolating and addressing the complexities of heterogeneous nanoparticle
subpopulations.