MicroRNA profiling in kidney disease: Plasma versus plasma-derived exosomes

Abstract

Liquid biopsies have advanced rapidly in recent years for use in diagnostic and prognostic applications. One important aspect of this advancement is the growth in our understanding of microRNA (miRNA) biology. The measurement of miRNAs packaged within exosomes, which are constantly released into the blood stream, may reflect pathological changes within the body. The current study performed miRNA profiling using plasma and plasma-derived exosome samples from two animal models of kidney disease, the 5/6th partial nephrectomy (PNx) and two-kidney-one-clip (2K1C) models. The RT-qPCR-based profiling results revealed that the overall miRNA expression level was much higher in plasma than in plasma-derived exosomes. With 200 µl of either plasma or exosomes derived from the same volume of plasma, 629 out of 665 total miRNAs analyzed were detectable in plasma samples from sham-operated rats, while only 403 were detectable in exosomes with a cutoff value set at 35 cycles. Moreover, the average miRNA expression level in plasma was about 16-fold higher than that in exosomes. We also found a select subset of miRNAs that were enriched within exosomes. The number of detectable miRNAs from plasma-derived exosomes was increased in rats subjected to PNx or 2K1C surgery compared to sham-operated animals. Importantly, we found that the changes of individual miRNAs measured in plasma had very poor concordance with that measured in plasma-derived exosomes in both animal models, suggesting that miRNAs in plasma and plasma-derived exosomes are differentially regulated in these disease conditions. Interestingly, PNx and 2K1C surgeries induced similar changes in miRNA expression, implying that common pathways were activated in these two disease models. Pathway analyses using DIANA-miRPath v3.0 showed that significantly changed exosomal miRNAs were associated with extracellular matrix (ECM) receptor interaction and mucin type-O-glycan synthesis pathways, which are related with tissue fibrosis and kidney injury, respectively. In conclusion, our results demonstrated that due to the differential changes in miRNAs, the measurement of exosomal miRNAs cannot be replaced by the measurement of miRNAs in plasma, or vice versa. We also showed that a set of miRNAs related with kidney injury and organ fibrosis were dysregulated in plasma-derived exosomes from animal models of kidney disease.

Circulating Small Noncoding RNAs Have Specific Expression Patterns in Plasma and Extracellular Vesicles in Myelodysplastic Syndromes and Are Predictive of Patient Outcome

“…In summary, our results suggest that the two materials represent distinctive snapshots of the disease taken from two different points of view and may not be replaced by one another. This is in agreement with the results of another study comparing miRNA content in total plasma and plasma-derived exosomes in kidney disease [37]. The authors showed that miRNAs in plasma and in exosomes are differentially regulated and thus the measurement of exosomal miRNAs cannot be replaced by the measurement of miRNAs in plasma, or vice versa [37].…”

“…Other studies also found no significant difference between plasma and exosomal miRNAs from healthy people [36]. On the other hand, differential regulation of miRNA levels between plasma and exosomes in different disease animal models has been described as well [37]. Therefore, it seems that export of sncRNAs into blood circulation may be specifically affected in various disease states.…”

“…These disproportions might indicate that miRNAs probably use at least partly different mechanisms of export than mechanisms exploited for other non-miRNA species of sncRNAs and that these mechanisms may be affected in MDS in different ways. Other studies have also demonstrated that different sncRNA species are preferentially loaded into different types of carriers [33,38] and that packaging of specific RNA molecules into carriers is selective within individual RNA species [37,39].…”

MicroRNA-451a in extracellular, blood-resident vesicles attenuates macrophage and dendritic cell responses to influenza whole-virus vaccine

“…Therefore, it is possible that serum miRNAs that are not included in EVs affected macrophage response. However, this possibility is weakened by the observation that EV miRNA levels do not correlate with the blood miRNA levels (47). In addition, we showed that the cytokine expression in macrophages correlated with EV miR-451a levels (Fig.…”

miR-126 in Peripheral Blood Mononuclear Cells Negatively Correlates with Risk and Severity and is Associated with Inflammatory Cytokines as well as Intercellular Adhesion Molecule-1 in Patients with Coronary Artery Disease

“…Through decades of investigations, thousands of miRNAs have been found in humans and animals, among which a notable proportion of miRNAs are found to be critical in the pathogenesis of various diseases, including cardiovascular diseases [9,10,11,12,13,14]. Moreover, some circulating miRNAs predominantly express in CAD patients [15,16].…”