Multiple RNA classes display cell stimulation-dependent association with extracellular vesicles

The release and uptake of nano-sized extracellular vesicles (EV) is a highly conserved means of intercellular communication. The molecular composition of EV, and thereby their signaling function to target cells, is regulated by cellular activation and differentiation stimuli. EV are regarded as snapshots of cells and are, therefore, in the limelight as biomarkers for disease. Although research on EV-associated RNA has predominantly focused on microRNAs, the transcriptome of EV consists of multiple classes of small non-coding RNAs with potential gene-regulatory functions. It is not known whether environmental cues imposed on cells induce specific changes in a broad range of EV-associated RNA classes.

Researchers from Utrecht University investigated whether immune-activating or -suppressing stimuli imposed on primary dendritic cells affected the release of various small non-coding RNAs via EV. The small RNA transcriptomes of highly pure EV populations free from ribonucleoprotein particles were analyzed by RNA sequencing and RT-qPCR. Immune stimulus-specific changes were found in the miRNA, snoRNA, and Y-RNA content of EV from dendritic cells, whereas tRNA and snRNA levels were much less affected. Only part of the changes in EV-RNA content reflected changes in cellular RNA, which urges caution in interpreting EV as snapshots of cells. By comprehensive analysis of RNA obtained from highly purified EV, the researchers demonstrate that multiple RNA classes contribute to genetic messages conveyed via EV. The identification of multiple RNA classes that display cell stimulation-dependent association with EV is the prelude to unraveling the function and biomarker potential of these EV-RNAs.

Cells and EV differ in the relative abundance of different small RNA classes


af The relative abundance of the indicated ncRNA classes in cells versus EV was assessed by small RNAseq analysis of cellular and EV-associated RNA. Total read count for each RNA class was normalized to total library size. To compare the distribution of ncRNA classes between cells and EV, normalized RNA class read counts in EV were scaled to the normalized RNA class read counts in cellular RNA (set to 1). Indicated are mean values ± SD of n = 3 independent experiments (two-tailed t test on normalized CPM values, *p < 0.05)

Driedonks TAP, van der Grein SG, Ariyurek Y, Buermans HPJ, Jekel H, Chow FWN, Wauben MHM, Buck AH, ‘t Hoen PAC, Nolte-‘t Hoen ENM. (2018) Immune stimuli shape the small non-coding transcriptome of extracellular vesicles released by dendritic cells. Cell Mol Life Sci 75(20):3857-3875. [abstract]

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