Characterization of human plasma-derived exosomal RNAs by deep sequencingReportar como inadecuado

Characterization of human plasma-derived exosomal RNAs by deep sequencing - Descarga este documento en PDF. Documentación en PDF para descargar gratis. Disponible también para leer online.

BMC Genomics

, 14:319



BackgroundExosomes, endosome-derived membrane microvesicles, contain specific RNA transcripts that are thought to be involved in cell-cell communication. These RNA transcripts have great potential as disease biomarkers. To characterize exosomal RNA profiles systemically, we performed RNA sequencing analysis using three human plasma samples and evaluated the efficacies of small RNA library preparation protocols from three manufacturers. In all we evaluated 14 libraries 7 replicates.

ResultsFrom the 14 size-selected sequencing libraries, we obtained a total of 101.8 million raw single-end reads, an average of about 7.27 million reads per library. Sequence analysis showed that there was a diverse collection of the exosomal RNA species among which microRNAs miRNAs were the most abundant, making up over 42.32% of all raw reads and 76.20% of all mappable reads. At the current read depth, 593 miRNAs were detectable. The five most common miRNAs miR-99a-5p, miR-128, miR-124-3p, miR-22-3p, and miR-99b-5p collectively accounted for 48.99% of all mappable miRNA sequences. MiRNA target gene enrichment analysis suggested that the highly abundant miRNAs may play an important role in biological functions such as protein phosphorylation, RNA splicing, chromosomal abnormality, and angiogenesis. From the unknown RNA sequences, we predicted 185 potential miRNA candidates. Furthermore, we detected significant fractions of other RNA species including ribosomal RNA 9.16% of all mappable counts, long non-coding RNA 3.36%, piwi-interacting RNA 1.31%, transfer RNA 1.24%, small nuclear RNA 0.18%, and small nucleolar RNA 0.01%; fragments of coding sequence 1.36%, 5 untranslated region 0.21%, and 3 untranslated region 0.54% were also present. In addition to the RNA composition of the libraries, we found that the three tested commercial kits generated a sufficient number of DNA fragments for sequencing but each had significant bias toward capturing specific RNAs.

ConclusionsThis study demonstrated that a wide variety of RNA species are embedded in the circulating vesicles. To our knowledge, this is the first report that applied deep sequencing to discover and characterize profiles of plasma-derived exosomal RNAs. Further characterization of these extracellular RNAs in diverse human populations will provide reference profiles and open new doors for the development of blood-based biomarkers for human diseases.

KeywordsExosome microRNA Next generation sequencing Plasma Biomarker Electronic supplementary materialThe online version of this article doi:10.1186-1471-2164-14-319 contains supplementary material, which is available to authorized users.

Download fulltext PDF

Autor: Xiaoyi Huang - Tiezheng Yuan - Michael Tschannen - Zhifu Sun - Howard Jacob - Meijun Du - Meihua Liang - Rachel L Dittmar


Documentos relacionados