Assessment of small RNA sorting into different extracellular fractions revealed by high-throughput sequencing of breast cell lines

Nucleic Acids Res. 2015 Jun 23;43(11):5601-16. doi: 10.1093/nar/gkv432. Epub 2015 May 4.


Intercellular communication can be mediated by extracellular small regulatory RNAs (sRNAs). Circulating sRNAs are being intensively studied for their promising use as minimally invasive disease biomarkers. To date, most attention is centered on exosomes and microRNAs as the vectors and the secreted species, respectively. However, this field would benefit from an increased understanding of the plethora of sRNAs secreted by different cell types in different extracellular fractions. It is still not clear if specific sRNAs are selected for secretion, or if sRNA secretion is mostly passive. We sequenced the intracellular sRNA content (19-60 nt) of breast epithelial cell lines (MCF-7 and MCF-10A) and compared it with extracellular fractions enriched in microvesicles, exosomes and ribonucleoprotein complexes. Our results are consistent with a non-selective secretion model for most microRNAs, although a few showed secretion patterns consistent with preferential secretion. On the contrary, 5' tRNA halves and 5' RNA Y4-derived fragments of 31-33 were greatly and significantly enriched in the extracellular space (even in non-mammary cell lines), where tRNA halves were detected as part of ∼45 kDa ribonucleoprotein complexes. Overall, we show that different sRNA families have characteristic secretion patterns and open the question of the role of these sRNAs in the extracellular space.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Breast Neoplasms / genetics*
  • Breast Neoplasms / metabolism
  • Cell Line, Tumor
  • Extracellular Space / genetics*
  • Female
  • High-Throughput Nucleotide Sequencing
  • Humans
  • MCF-7 Cells
  • MicroRNAs / metabolism
  • RNA, Small Untranslated / analysis
  • RNA, Small Untranslated / metabolism*
  • RNA, Transfer, Glu / isolation & purification
  • RNA, Transfer, Gly / isolation & purification
  • Ribonucleoproteins / isolation & purification
  • Sequence Analysis, RNA
  • Transport Vesicles / metabolism
  • Transport Vesicles / ultrastructure


  • MicroRNAs
  • RNA, Small Untranslated
  • RNA, Transfer, Glu
  • RNA, Transfer, Gly
  • Ribonucleoproteins

Associated data

  • BioProject/PRJNA270876