Diverse Long RNAs Are Differentially Sorted into Extracellular Vesicles Secreted by Colorectal Cancer Cells

Cell Rep. 2018 Oct 16;25(3):715-725.e4. doi: 10.1016/j.celrep.2018.09.054.

Abstract

The regulation and functional roles of secreted coding and long noncoding RNAs (lncRNAs; >200 nt) are largely unknown. We previously showed that mutant KRAS colorectal cancer (CRC) cells release extracellular vesicles (EVs) containing distinct proteomes, microRNAs (miRNAs), and circular RNAs. Here, we comprehensively identify diverse classes of CRC extracellular long RNAs secreted in EVs and demonstrate differential export of specific RNAs. Distinct noncoding RNAs, including antisense transcripts and transcripts derived from pseudogenes, are enriched in EVs compared to cellular profiles. We detected strong enrichment of Rab13 in mutant KRAS EVs and demonstrate functional delivery of Rab13 mRNA to recipient cells. To assay functional transfer of lncRNAs, we implemented a CRISPR/Cas9-based RNA-tracking system to monitor delivery to recipient cells. We show that gRNAs containing export signals from secreted RNAs can be transferred from donor to recipient cells. Our data support the existence of cellular mechanisms to selectively export diverse classes of RNA.

Keywords: CRISPR display; KRAS; RNAseq; Rab13; colorectal cancer; exosomes; extracellular RNA; extracellular vesicles; lncRNA.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Biological Transport
  • Cell Communication*
  • Cell Movement
  • Colorectal Neoplasms / genetics
  • Colorectal Neoplasms / metabolism*
  • Exosomes / genetics
  • Exosomes / metabolism*
  • Extracellular Vesicles / metabolism*
  • Humans
  • Mutation*
  • Proto-Oncogene Proteins p21(ras) / genetics
  • RNA, Long Noncoding / genetics
  • RNA, Long Noncoding / metabolism*
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism*
  • Tumor Cells, Cultured
  • rab GTP-Binding Proteins / genetics
  • rab GTP-Binding Proteins / metabolism

Substances

  • KRAS protein, human
  • RNA, Long Noncoding
  • RNA, Messenger
  • RAB13 protein, human
  • Proto-Oncogene Proteins p21(ras)
  • rab GTP-Binding Proteins