Integrating long and short sequencing data for a global overview of the endothelial extracellular vesicle RNA landscape

Background: Although extracellular vesicles (EVs) are well known to be enriched in miRNAs and other short RNA species, long RNA transcripts such as mRNA and lncRNA have been reported by several groups. We use RNA-Seq analysis in conjunction with wet bench techniques to provide a global analysis of the RNA content of endothelial cell EVs. Methods: EVs from primary human umbilical vein endothelial cell (HUVEC) cultures were isolated by sequential ultracentrifugation and immunocapture. RNA was extracted from cells and EVs, then short and long RNA libraries were prepared and sequenced. Reads were mapped to the human genome and transcriptome and mapped reads were analysed to determine transcript type and differential abundance between cells and EVs. RT-PCR was used to investigate integrity of long RNA transcripts. Gene ontology analyses were performed to determine enrichment of functional terms. Results: RNA in primary endothelial EVs is highly diverse in terms of length, type and abundance. As expected, endothelial EV RNA content is dominated by short RNA molecules, in particular snRNA and piRNA. Additionally, long rRNA, mRNA and lncRNA transcripts are present. Many of these transcripts are intact, putatively functional transcripts and are detectable at robust levels. Analysis of differential abundance between EVs and cells reveals significant differences in miRNA, snRNA, piRNA, mRNA and lncRNA profiles. LncRNAs in particular show a striking distribution, with about 13 times more lncRNA transcripts being enriched in EVs than in cells. Few of these lncRNAs have been fully functionally characterized, but gene ontology analysis of EV-enriched mRNA transcripts reveals an overabundance of genes coding for ribosomal proteins, elongation factors and other translation-related proteins. Summary/conclusion: Endothelial EVs are enriched for short and long regulatory RNA with the potential to control gene expression at both transcriptional and post-transcriptional levels