Quantitative and qualitative analysis of small RNAs in human endothelial cells and exosomes provides insights into localized RNA processing, degradation and sorting

Abstract

Exosomes are small vesicles that mediate cell–cell communication. They contain proteins, lipids and RNA, and evidence is accumulating that these molecules are specifically sorted for release via exosomes. We recently showed that endothelial-cell-produced exosomes promote angiogenesis in vivo in a small RNA-dependent manner. Recent deep sequencing studies in exosomes from lymphocytic origin revealed a broad spectrum of small RNAs. However, selective depletion or incorporation of small RNA species into endothelial exosomes has not been studied extensively. With next generation sequencing, we identified all known non-coding RNA classes, including microRNAs (miRNAs), small nucleolar RNAs, yRNAs, vault RNAs, 5p and 3p fragments of miRNAs and miRNA-like fragments. In addition, we mapped many fragments of messenger RNAs (mRNAs) and mitochondrial RNAs (mtRNAs). The distribution of small RNAs in exosomes revealed a considerable overlap with the distribution in the producing cells. However, we identified a remarkable enrichment of yRNA fragments and mRNA degradation products in exosomes consistent with yRNAs having a role in degradation of structured and misfolded RNAs in close proximity to endosomes. We propose that endothelial endosomes selectively sequester cytoplasmic RNA-degrading machineries taking part in gene regulation. The release of these regulatory RNAs via exosomes may have implications for endothelial cell–cell communication.

• extracellular vesicles
• microvesicles
• next generation sequencing
• quality control

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Acknowledgements

BWMvB was supported by the Netherlands Organization for Scientific Research (NGI/ZonMw Horizon project 935190280), a UMC Utrecht Focus and Massa grant (grant DIGD-DGK-DHL), and the Netherlands Institute for Regenerative Medicine (grant FES0908). MCV is supported by the Netherlands Organisation for Scientific Research (ZonMw-TAS grant 116001026; Vidi grant 016.096.359). We thank Olivier G. de Jong (Department of Nephrology and Hypertension, University Medical Center Utrecht, the Netherlands) for excellent technical assistance.

Conflict of interest and funding

The authors have not received any funding or benefits from industry or elsewhere to conduct this study.

Notes

To access the supplementary material to this article, please see Supplementary files under ‘Article Tools’.