Comparing the Composition of Small RNA in Blood Plasma Fractions Containing Exomeres and Supermeres

It is known that small RNAs contained within extracellular vesicles can serve as agents of intercellular signaling. However, recent studies have shown that these molecules are carried not only by vesicles but also by smaller, non-membranous particles known as exomeres and supermeres. At the same time, the specific repertoire of small RNAs in these particles, as well as the extent to which the RNA profiles of exomeres and supermeres in human blood plasma differ—remains insufficiently studied. The aim of this study was to compare the small RNA patterns in blood plasma fractions containing these particles. Extracellular vesicles were first pelleted from platelet-poor plasma via ultracentrifugation (170,000× g, 4 h); subsequently, a fraction containing exomeres (FCE; pellet from 170,000× g, 20 h centrifugation) and a fraction containing supermeres (FCS; pellet from 370,000× g, 20 h centrifugation) were sequentially isolated. Subsequently, the small RNA composition was analyzed (FCE from eight donors and FCS from fourteen donors). It was found that the FCE and FCS fractions differed significantly in their non-coding RNA composition. Compared to FCE, FCS showed a significantly higher GC content in the small RNA fraction, as well as higher proportions of rRNA, tRNA, snoRNA, and snRNA, and lower proportions of miRNA, piRNA, lncRNA, and scaRNA. Analysis of the sequenced fragments length distribution revealed that, compared to FCE, the FCS sample contained a higher proportion of sequences shorter than 20 nucleotides (17–20 nt) and longer than 24 nucleotides (24–50 nt). A comparison of the major sequences showed that miRNA-451a accounts for approximately 50% of the total miRNA in FCE and 25% in FCS, while piRNA-45195 constitutes about 50% of the total in both FCS and FCE. A comparison of the levels of various miRNAs in the two fractions showed that the levels of 184 miRNAs were significantly higher (p-adj < 0.05, fold change > 2) in the FCE fraction, while 3 miRNAs were significantly higher in the FCS fraction. Additionally, the levels of 13 piRNAs were significantly higher in FCE, and 34 in FCS. Thus, despite the fact that the patterns of the most abundant small RNAs in these fractions are quite similar, FCS and FCE most likely exhibit different signaling functions.