Deep sequencing of RNA from immune cell-derived vesicles uncovers the selective incorporation of small non-coding RNA biotypes with potential regulatory functions

Abstract

Cells release RNA-carrying vesicles and membrane-free RNA/protein complexes into the extracellular milieu. Horizontal vesicle-mediated transfer of such shuttle RNA between cells allows dissemination of genetically encoded messages, which may modify the function of target cells. Other studies used array analysis to establish the presence of microRNAs and mRNA in cell-derived vesicles from many sources. Here, we used an unbiased approach by deep sequencing of small RNA released by immune cells. We found a large variety of small non-coding RNA species representing pervasive transcripts or RNA cleavage products overlapping with protein coding regions, repeat sequences or structural RNAs. Many of these RNAs were enriched relative to cellular RNA, indicating that cells destine specific RNAs for extracellular release. Among the most abundant small RNAs in shuttle RNA were sequences derived from vault RNA, Y-RNA and specific tRNAs. Many of the highly abundant small non-coding transcripts in shuttle RNA are evolutionary well-conserved and have previously been associated to gene regulatory functions. These findings allude to a wider range of biological effects that could be mediated by shuttle RNA than previously expected. Moreover, the data present leads for unraveling how cells modify the function of other cells via transfer of specific non-coding RNA species.

Towards mechanisms and standardization in extracellular vesicle and extracellular RNA studies: results of a worldwide survey

“…Communication via extracellular RNA (exRNA) was soon accepted as a novel set of mechanisms to explain the increasingly appreciated paracrine effects of EVs. Meanwhile, RNA profiling technologies advanced quickly, allowing comprehensive characterization from the small amounts of material often obtained from extracellular samples [6,7]. Coincidence or not, EV research outputs including patents and publications grew rapidly following the initial reports of EVs and exRNA [8].…”

141 Small RNA deep sequencing discriminates subsets of extracellular vesicles released by melanoma cells - evidence of unique microRNA cargos

“…The presence of snRNA in exosomes is interesting, as to date most of the RNA species in exosomes are considered to be of cytoplasmic origin. 23 We also observed an enrichment of RNU12 snRNA in exosomes -which was absent in apoptotic bodies and microvesicles. The enrichment of mitochondrial associated RNA (mt-RNA) in apoptotic bodies and microvesicles suggest that mt-RNA is more prone to be loaded into apoptotic bodies and microvesicles than into the exosomes (Fig.…”

“…[17][18][19][20][21] Importantly, many small RNAs are released in the extracellular environment as EV cargo, which has been specifically documented for the exosomes. [22][23][24][25][26][27] Importantly, many cellular RNAs, including miRNAs are detected in the extracellular space, especially in extracellular vesicles. 28,29 Currently, extracellular RNA communication is also considered to be putatively important in animals, with important implications for biology, disease and medicine.…”

Evaluation of The Diagnostic Role of Non-Coding RNA and Exosomal Related Gene Association in Lung Cancer

“…In addition to mRNA and miRNA, exosomal cargo also include a large different species of other small noncoding RNAs, including RNA transcripts overlapping with protein coding regions, repeat sequences, structural RNAs, tRNA fragments, vault RNA, Y RNA, and small interfering RNAs. Exosomes are enriched with RNA profiles relative to that found in the originating cells, indicating the selective incorporation of RNA molecules into exosomes (16) .…”