title: Identification of distinct miRNA target regulation between breast cancer molecular subtypes using AGO2-PAR-CLIP and patient datasets.
abstract: BACKGROUND
  Various microRNAs (miRNAs) are up- or downregulated in tumors. However, the repression of cognate miRNA targets responsible for the phenotypic effects of this dysregulation in patients remains largely unexplored. To define miRNA targets and associated pathways, together with their relationship to outcome in breast cancer, we integrated patient-paired miRNA-mRNA expression data with a set of validated miRNA targets and pathway inference.
  
  
  RESULTS
  To generate a biochemically-validated set of miRNA-binding sites, we performed argonaute-2 photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation (AGO2-PAR-CLIP) in MCF7 cells. We then defined putative miRNA-target interactions using a computational model, which ranked and selected additional TargetScan-predicted interactions based on features of our AGO2-PAR-CLIP binding-site data. We subselected modeled interactions according to the abundance of their constituent miRNA and mRNA transcripts in tumors, and we took advantage of the variability of miRNA expression within molecular subtypes to detect miRNA repression. Interestingly, our data suggest that miRNA families control subtype-specific pathways; for example, miR-17, miR-19a, miR-25, and miR-200b show high miRNA regulatory activity in the triple-negative, basal-like subtype, whereas miR-22 and miR-24 do so in the HER2 subtype. An independent dataset validated our findings for miR-17 and miR-25, and showed a correlation between the expression levels of miR-182 targets and overall patient survival. Pathway analysis associated miR-17, miR-19a, and miR-200b with leukocyte transendothelial migration.
  
  
  CONCLUSIONS
  We combined PAR-CLIP data with patient expression data to predict regulatory miRNAs, revealing potential therapeutic targets and prognostic markers in breast cancer.
authors.forename: Thalia A
authors.initials: TA
authors.lastname: Farazi
authors.forename: Jelle J
authors.initials: JJ
authors.lastname: Ten Hoeve
authors.forename: Miguel
authors.initials: M
authors.lastname: Brown
authors.forename: Aleksandra
authors.initials: A
authors.lastname: Mihailovic
authors.forename: Hugo M
authors.initials: HM
authors.lastname: Horlings
authors.forename: Marc J
authors.initials: MJ
authors.lastname: van de Vijver
authors.forename: Thomas
authors.initials: T
authors.lastname: Tuschl
authors.forename: Lodewyk F A
authors.initials: LF
authors.lastname: Wessels
mesh_terms: D001943:Breast Neoplasms / Q000235:genetics*; D005260:Female; D015972:Gene Expression Regulation, Neoplastic; D018390:Gene Targeting; D015316:Genetic Therapy; D006801:Humans; D047468:Immunoprecipitation; D061986:MCF-7 Cells; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism
chemical_list: C524941:MIRN17 microRNA, human; C534451:MIRN20a microRNA, human; C543351:MIRN25 microRNA, human; D035683:MicroRNAs; C538984:Mirn182 microRNA, human; D012333:RNA, Messenger