title: The RNA binding protein HuR differentially regulates unique subsets of mRNAs in estrogen receptor negative and estrogen receptor positive breast cancer.
abstract: BACKGROUND
  The discordance between steady-state levels of mRNAs and protein has been attributed to posttranscriptional control mechanisms affecting mRNA stability and translation. Traditional methods of genome wide microarray analysis, profiling steady-state levels of mRNA, may miss important mRNA targets owing to significant posttranscriptional gene regulation by RNA binding proteins (RBPs).
  
  
  METHODS
  The ribonomic approach, utilizing RNA immunoprecipitation hybridized to microarray (RIP-Chip), provides global identification of putative endogenous mRNA targets of different RBPs. HuR is an RBP that binds to the AU-rich elements (ARE) of labile mRNAs, such as proto-oncogenes, facilitating their translation into protein. HuR has been shown to play a role in cancer progression and elevated levels of cytoplasmic HuR directly correlate with increased invasiveness and poor prognosis for many cancers, including those of the breast. HuR has been described to control genes in several of the acquired capabilities of cancer and has been hypothesized to be a tumor-maintenance gene, allowing for cancers to proliferate once they are established.
  
  
  RESULTS
  We used HuR RIP-Chip as a comprehensive and systematic method to survey breast cancer target genes in both MCF-7 (estrogen receptor positive, ER+) and MDA-MB-231 (estrogen receptor negative, ER-) breast cancer cell lines. We identified unique subsets of HuR-associated mRNAs found individually or in both cell types. Two novel HuR targets, CD9 and CALM2 mRNAs, were identified and validated by quantitative RT-PCR and biotin pull-down analysis.
  
  
  CONCLUSIONS
  This is the first report of a side-by-side genome-wide comparison of HuR-associated targets in wild type ER+ and ER- breast cancer. We found distinct, differentially expressed subsets of cancer related genes in ER+ and ER- breast cancer cell lines, and noted that the differential regulation of two cancer-related genes by HuR was contingent upon the cellular environment.
authors.affiliation: Department of Surgery, University of Missouri, Columbia, Missouri 65212, USA.
authors.forename: Robert
authors.initials: R
authors.lastname: Calaluce
authors.forename: Matthew M
authors.initials: MM
authors.lastname: Gubin
authors.forename: J Wade
authors.initials: JW
authors.lastname: Davis
authors.forename: Joseph D
authors.initials: JD
authors.lastname: Magee
authors.forename: Jing
authors.initials: J
authors.lastname: Chen
authors.forename: Yuki
authors.initials: Y
authors.lastname: Kuwano
authors.forename: Myriam
authors.initials: M
authors.lastname: Gorospe
authors.forename: Ulus
authors.initials: U
authors.lastname: Atasoy
mesh_terms: D015703:Antigens, CD / Q000235:genetics / Q000378:metabolism; D000954:Antigens, Surface / Q000235:genetics* / Q000378:metabolism; D001710:Biotin / Q000737:chemistry; D001943:Breast Neoplasms / Q000235:genetics* / Q000378:metabolism; D002147:Calmodulin / Q000235:genetics / Q000378:metabolism; D045744:Cell Line, Tumor; D051959:ELAV Proteins; D000067780:ELAV-Like Protein 1; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D047468:Immunoprecipitation; D008562:Membrane Glycoproteins / Q000235:genetics / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D012333:RNA, Messenger / Q000096:biosynthesis / Q000235:genetics*; D016601:RNA-Binding Proteins / Q000235:genetics* / Q000378:metabolism; D011960:Receptors, Estrogen / Q000096:biosynthesis* / Q000235:genetics; D060245:Tetraspanin 29
chemical_list: D015703:Antigens, CD; D000954:Antigens, Surface; C488659:CALM2 protein, human; C554869:CD9 protein, human; D002147:Calmodulin; D051959:ELAV Proteins; D000067780:ELAV-Like Protein 1; C098770:ELAVL1 protein, human; D008562:Membrane Glycoproteins; D012333:RNA, Messenger; D016601:RNA-Binding Proteins; D011960:Receptors, Estrogen; D060245:Tetraspanin 29; D001710:Biotin