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Exomeres, Supermeres and the Revised Map of Exosome Composition

Revisado por el equipo editorial de ExaVeyra Sciences · Actualizado el 20 de octubre de 2026

Exomeres and supermeres are amembranous nanoparticles that cells release alongside exosomes, and their discovery changed the accepted picture of exosome composition.¹ High-resolution separation showed that many proteins and RNAs once credited to exosomes travel in these and other non-vesicular extracellular particles.²

This page follows that revision: the separation methods that resolved the particle classes, the markers that moved to non-vesicular fractions, the structure of Argonaute2 as the best-understood non-vesicular RNA carrier, and the MISEV2023 terms that now describe the whole population.

Early exosome preparations captured a mixture of particle classes

Valadi and colleagues reported in 2007 that exosomes from mast cells contain messenger RNA and microRNA, and that the messenger RNA can be translated after transfer to another cell.³ That finding framed exosomes as the main vehicle for extracellular RNA for the following decade.

Kowal and colleagues then compared vesicle populations separated by sedimentation speed, density floatation and immuno-isolation. Several classic exosome markers, including MHC proteins, flotillin and HSP70, were present at similar levels in all vesicle types.⁴

The MISEV2018 guidelines drew the practical conclusion. Ascribing a function to exosomes in particular requires evidence beyond a crude, heterogeneous preparation, because exosomes are difficult to separate from biophysically similar particles.⁵

Asymmetric-flow field-flow fractionation resolved exomeres and two exosome subsets

Zhang and colleagues applied asymmetric-flow field-flow fractionation (AF4) to small vesicle preparations in 2018. AF4 sorts particles by hydrodynamic size between a channel flow and a perpendicular cross-flow, and it resolved two exosome subsets and a third, smaller population.⁶

• Large exosome vesicles (Exo-L), 90 to 120 nm, with proteins of the mitotic spindle and IL-2/STAT5 signalling.⁶
• Small exosome vesicles (Exo-S), 60 to 80 nm, with proteins of endosomal function and secretion pathways.⁶
• Exomeres, about 35 nm, which appeared as amembranous particles in electron micrographs and were enriched in metabolic enzymes.⁶

The companion protocol reports that AF4 separates particles from a few nanometres upward at a resolution of about 1 nm, with the fractionation step itself taking about an hour.⁷ The size classes it defined anchor the map of extracellular particles used on this page (Fig. 1).

Density gradients and direct capture reassessed exosome composition

Jeppesen and colleagues took a complementary route in 2019. They floated crude small vesicle pellets upward through high-resolution iodixanol gradients, then pulled classical exosomes out of the vesicle fractions with beads carrying antibodies to CD63, CD81 or CD9 (Fig. 2).⁸

Membrane vesicles collected in low-density fractions, and most classical exosomes floated at 1.08 to 1.13 g/mL in iodixanol. Non-vesicular material stayed in high-density fractions, and a second round of fractionation showed that it was released as such, independent of vesicle damage.⁸

The two pools differed sharply. Syntenin-1 and ALIX were among the most abundant proteins of the purified vesicles, while the non-vesicular fractions were dominated by metabolic enzymes such as GAPDH, PKM and ENO1, together with HSP90, tubulins and histones H2A and H3.⁸

Direct capture placed Argonaute 1 to 4, glycolytic enzymes and cytoskeletal proteins outside classical exosomes.⁸ The same study identified annexin A1 as a specific marker of microvesicles shed directly from the plasma membrane, which float at slightly lower density than exosomes.⁸

Argonaute complexes carry most extracellular microRNA outside vesicles

Arroyo and colleagues fractionated human plasma and serum by differential centrifugation and size-exclusion chromatography in 2011. Most circulating microRNAs co-fractionated with protein complexes, eluted with Argonaute2, and were recovered by Argonaute2 immunoprecipitation, while a minority associated mainly with vesicles.⁹

Turchinovich and colleagues reached the same conclusion independently. Most microRNA in plasma and culture medium passed 0.22 micrometre filters, stayed in the supernatant after centrifugation at 110,000 g, and co-immunoprecipitated with the 96 kDa Argonaute2 protein.¹⁰

Jeppesen and colleagues later found that microRNAs in non-vesicular fractions showed marked trimming of their 3 prime ends, and that vault RNAs were associated with the same fractions.⁸ They concluded that cells secrete Argonaute proteins independently of exosomes.⁸

Lipoproteins, vaults and ribosomes extend the set of RNA carriers

Vickers and colleagues showed that high-density lipoprotein (HDL) carries endogenous microRNAs in plasma and delivers them to cells, where they act on reporter messenger RNAs. Delivery depended on scavenger receptor class B type I, and export to HDL was regulated by neutral sphingomyelinase.¹¹

Vaults are a further ribonucleoprotein class in the non-vesicular pool. MVP makes up more than 70 percent of the protein of these 41 by 72.5 nm particles, and Jeppesen and colleagues found MVP in non-vesicular fractions alongside vault RNAs.⁸

Tosar and colleagues added full ribosomes and full-length tRNAs to the extracellular RNA map. Their fragmentation outside the cell generates small RNAs that resist degradation, so the extracellular abundance of a fragment reflects processing as well as secretion.¹²

The structure of Argonaute2 explains how it holds a microRNA

Argonaute2 is the human Argonaute protein encoded by AGO2, a highly basic protein with a PAZ domain and a PIWI domain.¹³ Liu and colleagues identified it in 2004 as the one mammalian Argonaute that cleaves target messenger RNA, the catalytic engine of RNA interference.¹⁴

Schirle and MacRae solved the first crystal structure of human Argonaute2 in 2012. It is a bilobed molecule with a central cleft for guide and target RNA, and guide nucleotides 2 to 6 sit in an A-form conformation ready to base pair with a target.¹⁵

Elkayam and colleagues solved Argonaute2 bound to a single defined microRNA, miR-20a, at 2.2 Å (Fig. 3). The microRNA is anchored at both ends by the MID and PAZ domains and makes several kinks and turns along the binding groove.¹⁶

The same study found that microRNA binding locks the otherwise flexible enzyme into a stable conformation.¹⁶ Arroyo and colleagues saw plasma microRNAs lost after protease digestion of plasma, indicating that protein complexes protect them from plasma RNases.⁹

Schirle and colleagues then captured Argonaute2 with guide and target RNA paired across the seed (Fig. 4). Target recognition proceeds stepwise: guide nucleotides 2 to 5 are exposed first, and pairing there opens guide positions 2 to 8 and 13 to 16 for further recognition.¹⁷

Exomeres and supermeres carry distinct protein and RNA cargo

Exomeres are small, lipid-poor particles rich in metabolic enzymes

Exomeres in the AF4 study were smaller than 50 nm, weakly negatively charged, stiffer than exosomes, and 5.8 to 7.0 nm in average height by atomic force microscopy.⁶ They contained fewer lipids than exosomes, with relatively more triglycerides and ceramides, and were enriched in glycolysis and mTOR pathway proteins.⁶

Zhang and colleagues then pelleted exomeres directly by ultracentrifugation and found them enriched in Argonaute 1 to 3 and amyloid precursor protein.¹⁸ Exomeres transferred functional β-galactoside α2,6-sialyltransferase 1 to recipient cells, raising α2,6-sialylation of surface proteins that included β1 integrin.¹⁸

Exomeres also carried the EGFR ligand amphiregulin. Amphiregulin-containing exomeres prolonged EGFR signalling in recipient cells and modulated EGFR trafficking in normal intestinal organoids, establishing exomeres as carriers of active cargo.¹⁸

Supermeres are the smallest particles in the series

Supermeres take their name from the supernatant of exomeres, the fraction in which they were found. They are smaller than exomeres by atomic force microscopy and are pelleted from that supernatant at higher force.² Yu and colleagues give their diameter as about 22 to 32 nm, roughly half the volume of an exomere.¹⁹

Glycolytic enzymes trace the shift in thinking. Earlier small vesicle preparations contained them, direct capture placed them outside classical exosomes, and they are enriched in exomeres and more highly enriched in supermeres.²

Supermeres from many cell types are rich in transforming growth factor beta-induced protein (TGFBI), while fatty acid synthase is more associated with exomeres. Their membrane-protein content consists of ectodomain cleavage products, including those of APP, glypican-1, MET and amphiregulin.²

Supermeres contain high quantities of extracellular RNA and are enriched in miR-1246.²⁰ Tosar, Cayota and Witwer reanalysed the published data and found that the top-ranking supermere RNAs are footprints of protein complexes protecting fragments of U2 small nuclear RNA and 28S ribosomal RNA.²⁰

The same authors noted that several exomere-enriched proteins self-assemble into defined particles: LGALS3BP forms ring-like decamers of 30 to 40 nm, and VCP forms hexamers 15.6 nm across.²⁰

Jeppesen and colleagues answered with further analyses of their supermere data, isolated from the exomere supernatant after a 16 h ultracentrifugation, that support supermeres as a distinct nanoparticle.²¹ The same group lists the relationship between exomeres and supermeres among the open questions now driving the field.²

MISEV2023 names non-vesicular extracellular particles

MISEV2023 introduced a nomenclature for this material. Extracellular particles (EPs) is the umbrella term, extracellular vesicles are particles delimited by a lipid bilayer, and non-vesicular extracellular particles (NVEPs) are cell-derived multimolecular assemblies without a delimiting bilayer.²²

The guideline leaves the naming of specific classes such as lipoprotein particles, ribonucleoprotein particles, exomeres and supermeres to their own fields. It notes that NVEPs may greatly outnumber EVs and that most separation methods co-isolate the two.²²

Its protein reference table builds on the reassessment. MISEV2023 lists Argonautes and 14-3-3 proteins as generally more abundant in NVEPs, and HSP90AA and HSP90AB, TGFBI, HSPA13 and LDHA and LDHB as exomere- or supermere-enriched components for purity control.²²

Liu and colleagues summarise the consequence in a 2026 review. Most NVEPs are smaller than 50 nm and carry protein and RNA cargo once thought to belong to exosomes, so some functions attributed to exosomes are being reassigned.²³

Separation method defines which particles a preparation contains

Size and density overlap between particle classes, so each method enriches a different mixture (Fig. 1). Jeppesen and colleagues note that EVs and NVEPs of similar size differ in density because their lipid, protein and nucleic acid content differs, which is why density gradients separate them.²

• Size-exclusion chromatography of plasma places vesicle markers in the same fractions as lipoprotein particles; adding a density cushion reduced lipoprotein carry-over about 100-fold.²⁴
• Low-density lipoprotein, about 25 nm across, remained in plasma vesicle preparations after each isolation method tested and associated with vesicles when mixed in vitro.²⁵
• HDL floats at 1.063 to 1.21 g/mL, a range that overlaps the density of exosomes.²⁵
• A sequential protocol now isolates large and small EVs, non-vesicular fractions, exomeres and supermeres from one starting sample by ultracentrifugation, filtration and bottom-loaded density gradients.²⁶

In that protocol, exomeres are pelleted at 167,000 g and supermeres from the remaining supernatant at 367,000 g, each for 16 h.²⁶ Reviews comparing ultracentrifugation, density gradients, size-exclusion chromatography and flow field-flow fractionation describe strategies for combining them.²³

Particle counting is equally method-dependent. NVEPs smaller than EVs may fall below the detection range of some characterisation methods, so their share of a preparation can go unmeasured.²² Reporting the separation method, density and marker panel with every composition claim makes results comparable across laboratories.

Where to go from here

The cargo sorting reference covers how proteins and RNAs enter vesicles, and the uptake reference covers what happens when vesicles reach a recipient cell. The quality references on MISEV2023 and on particle counting explain how purity and particle number are measured.

Verified practices can request lot-specific characterization data with the certificate of analysis. Our team can explain how a preparation was separated and what its marker panel represents.