Coding and noncoding landscape of extracellular RNA released by human glioma stem cells

Nature Communications
Zhiyun WeiAnna M Krichevsky

Abstract

Tumor-released RNA may mediate intercellular communication and serve as biomarkers. Here we develop a protocol enabling quantitative, minimally biased analysis of extracellular RNAs (exRNAs) associated with microvesicles, exosomes (collectively called EVs), and ribonucleoproteins (RNPs). The exRNA complexes isolated from patient-derived glioma stem-like cultures exhibit distinct compositions, with microvesicles most closely reflecting cellular transcriptome. exRNA is enriched in small ncRNAs, such as miRNAs in exosomes, and precisely processed tRNA and Y RNA fragments in EVs and exRNPs. EV-enclosed mRNAs are mostly fragmented, and UTRs enriched; nevertheless, some full-length mRNAs are present. Overall, there is less than one copy of non-rRNA per EV. Our results suggest that massive EV/exRNA uptake would be required to ensure functional impact of transferred RNA on brain recipient cells and predict the most impactful miRNAs in such conditions. This study also provides a catalog of diverse exRNAs useful for biomarker discovery and validates its feasibility on cerebrospinal fluid.

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Datasets Mentioned

BETA
GSE93143

Methods Mentioned

BETA
biopsy
gel filtration
RNAseq
PCR
CLIP-Seq
RNA Assay
RNA-Seq
reverse transcription PCR
Protein Assay

Software Mentioned

R package
MultiExperiment Viewer
MS Excel Macro
TopHat2
Cuffdiff
Cuffmerge
SPSS
Cufflinks
R package rgl
SOAP2

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