Both exosome isolation methods proved to be suitable for miRNA
profiling as around 100 exosomal miRNAs were detected from a relatively
small amount of blood serum. The overall exosomal miRNA profiles
were similar regardless of the isolation method used, however,
the miRNA levels showed a slight variation between the two methods.
Hierarchical clustering of 17 miRNAs generated a distinguishable pattern
where the samples were grouped according to the used exosome
isolation method indicating that the observed exosomal miRNA profile
is somewhat dependent upon the extracellular vesicle isolation method.
We must consider that both methods used in the present study do not
ensure stringent criteria for exosome specific isolation, being based on
their physical features, rather than on their unique molecular composition.
The purity of material isolated with ultracentrifugation is inferior
compared to othermethods such as sucrose gradient or immunocapture
based isolation [10], however combinedwith differential centrifugation
and microfiltration steps ultracentrifugation yields pellets that are consistently
enriched with fairly intact exosome like vesicles, being only
slightly contaminated by other membrane vesicles or fragments, while
containing large amount of protein complexes [11]. Additional disadvantage
of this method regards poor recovery of exosomes from highly
viscous biofluids such as plasma and serum [12,13]. ExoQuick on the
other hand precipitates very efficiently most of the vesicles and protein–
protein, lipoprotein or protein–RNA complexes present in the
serumregardless of their origin. This can also explain differences in particular
miRNA species detected in this study in differently processed
samples where miR-486-5p and miR-92a showed lower relative expression
in ultracentrifugation isolated samples compared to ExoQuick
precipitated samples. Arroyo et al. showed that miR-92a and miR-486-
5p are mostly bound to ribonucleoprotein complexes rather than confined
inside vesicles [14]. However, in our study the experiments with
protease treatment unveiled a similar slight decrease in miR-92a levels
from pellets isolated with both methods suggesting that the detected
fluctuations were probably not because of different levels of proteinbound
miRNAs but rather due to the differences in the composition of
extracellular vesicles isolated with EQ and UC methods.