HITS-CLIP reveals key regulators of nuclear receptor signaling in breast cancer

Breast Cancer Res Treat. 2014 Jul;146(1):85-97. doi: 10.1007/s10549-014-3004-9. Epub 2014 Jun 7.


miRNAs regulate the expression of genes in both normal physiology and disease. While miRNAs have been demonstrated to play a pivotal role in aspects of cancer biology, these reports have generally focused on the regulation of single genes. Such single-gene approaches have significant limitations, relying on miRNA expression levels and heuristic predictions of mRNA-binding sites. This results in only circumstantial evidence of miRNA-target interaction and typically leads to large numbers of false positive predictions. Here, we used a genome-wide approach (high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation, HITS-CLIP) to define direct miRNA-mRNA interactions in three breast cancer subtypes (estrogen receptor positive, Her2 amplified, and triple negative). Focusing on steroid receptor signaling, we identified two novel regulators of the ER pathway (miR-9-5p and miR-193a/b-3p), which together target multiple genes involved in ER signaling. Moreover, this approach enabled the definition of miR-9-5p as a global regulator of steroid receptor signaling in breast cancer. We show that miRNA targets and networks defined by HITS-CLIP under physiologic conditions are predictive of patient outcomes and provide global insight into miRNA regulation in breast cancer.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Breast Neoplasms / diagnosis
  • Breast Neoplasms / genetics*
  • Breast Neoplasms / metabolism*
  • Breast Neoplasms / mortality
  • Cell Line, Tumor
  • Cluster Analysis
  • Estrogens / metabolism
  • Female
  • Gene Expression Profiling
  • Gene Regulatory Networks
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Immunoprecipitation
  • MicroRNAs / genetics
  • Neoplasm Grading
  • Prognosis
  • RNA Interference
  • RNA, Messenger / genetics
  • Receptors, Cytoplasmic and Nuclear / genetics*
  • Receptors, Cytoplasmic and Nuclear / metabolism*
  • Receptors, Estrogen / genetics
  • Receptors, Estrogen / metabolism
  • Receptors, Steroid / genetics
  • Receptors, Steroid / metabolism
  • Severity of Illness Index
  • Signal Transduction*


  • Estrogens
  • MIRN92 microRNA, human
  • MicroRNAs
  • RNA, Messenger
  • Receptors, Cytoplasmic and Nuclear
  • Receptors, Estrogen
  • Receptors, Steroid