title: HITS-CLIP reveals key regulators of nuclear receptor signaling in breast cancer.
abstract: 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.
authors.affiliation: Section of Hematology, Yale Cancer Center, New Haven, CT, USA.
authors.forename: Manoj M
authors.initials: MM
authors.lastname: Pillai
authors.forename: Austin E
authors.initials: AE
authors.lastname: Gillen
authors.forename: Tomomi M
authors.initials: TM
authors.lastname: Yamamoto
authors.forename: Enos
authors.initials: E
authors.lastname: Kline
authors.forename: Joseph
authors.initials: J
authors.lastname: Brown
authors.forename: Kale
authors.initials: K
authors.lastname: Flory
authors.forename: Jay R
authors.initials: JR
authors.lastname: Hesselberth
authors.forename: Peter
authors.initials: P
authors.lastname: Kabos
mesh_terms: D001943:Breast Neoplasms / Q000175:diagnosis / Q000235:genetics* / Q000378:metabolism* / Q000401:mortality; D045744:Cell Line, Tumor; D016000:Cluster Analysis; D004967:Estrogens / Q000378:metabolism; D005260:Female; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D047468:Immunoprecipitation; D035683:MicroRNAs / Q000235:genetics; D060787:Neoplasm Grading; D011379:Prognosis; D034622:RNA Interference; D012333:RNA, Messenger / Q000235:genetics; D018160:Receptors, Cytoplasmic and Nuclear / Q000235:genetics* / Q000378:metabolism*; D011960:Receptors, Estrogen / Q000235:genetics / Q000378:metabolism; D011987:Receptors, Steroid / Q000235:genetics / Q000378:metabolism; D012720:Severity of Illness Index; D015398:Signal Transduction
chemical_list: D004967:Estrogens; C541874:MIRN92 microRNA, human; D035683:MicroRNAs; D012333:RNA, Messenger; D018160:Receptors, Cytoplasmic and Nuclear; D011960:Receptors, Estrogen; D011987:Receptors, Steroid