title: An integrated analysis of miRNA and gene copy numbers in xenografts of Ewing's sarcoma.
abstract: BACKGROUND
  Xenografts have been shown to provide a suitable source of tumor tissue for molecular analysis in the absence of primary tumor material. We utilized ES xenograft series for integrated microarray analyses to identify novel biomarkers.
  
  
  METHODS
  Microarray technology (array comparative genomic hybridization (aCGH) and micro RNA arrays) was used to screen and identify copy number changes and differentially expressed miRNAs of 34 and 14 passages, respectively. Incubated cells used for xenografting (Passage 0) were considered to represent the primary tumor. Four important differentially expressed miRNAs (miR-31, miR-31*, miR-145, miR-106) were selected for further validation by real time polymerase chain reaction (RT-PCR). Integrated analysis of aCGH and miRNA data was performed on 14 xenograft passages by bioinformatic methods.
  
  
  RESULTS
  The most frequent losses and gains of DNA copy number were detected at 9p21.3, 16q and at 8, 15, 17q21.32-qter, 1q21.1-qter, respectively. The presence of these alterations was consistent in all tumor passages. aCGH profiles of xenograft passages of each series resembled their corresponding primary tumors (passage 0). MiR-21, miR-31, miR-31*, miR-106b, miR-145, miR-150*, miR-371-5p, miR-557 and miR-598 showed recurrently altered expression. These miRNAS were predicted to regulate many ES-associated genes, such as genes of the IGF1 pathway, EWSR1, FLI1 and their fusion gene (EWS-FLI1). Twenty differentially expressed miRNAs were pinpointed in regions carrying altered copy numbers.
  
  
  CONCLUSIONS
  In the present study, ES xenografts were successfully applied for integrated microarray analyses. Our findings showed expression changes of miRNAs that were predicted to regulate many ES associated genes, such as IGF1 pathway genes, FLI1, EWSR1, and the EWS-FLI1 fusion genes.
authors.affiliation: Department of Pathology, Haartman Institute and HUSLAB, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland.
authors.forename: Neda
authors.initials: N
authors.lastname: Mosakhani
authors.forename: Mohamed
authors.initials: M
authors.lastname: Guled
authors.forename: Gayle
authors.initials: G
authors.lastname: Leen
authors.forename: Silvia
authors.initials: S
authors.lastname: Calabuig-Fariñas
authors.forename: Tarja
authors.initials: T
authors.lastname: Niini
authors.forename: Isidro
authors.initials: I
authors.lastname: Machado
authors.forename: Suvi
authors.initials: S
authors.lastname: Savola
authors.forename: Katia
authors.initials: K
authors.lastname: Scotlandi
authors.forename: José Antonio
authors.initials: JA
authors.lastname: López-Guerrero
authors.forename: Antonio
authors.initials: A
authors.lastname: Llombart-Bosch
authors.forename: Sakari
authors.initials: S
authors.lastname: Knuutila
mesh_terms: D000818:Animals; D016000:Cluster Analysis; D056915:DNA Copy Number Variations; D018628:Gene Dosage; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D008297:Male; D051379:Mice; D008819:Mice, Nude; D035683:MicroRNAs / Q000235:genetics*; D015203:Reproducibility of Results; D012512:Sarcoma, Ewing / Q000235:genetics* / Q000378:metabolism; D014183:Transplantation, Heterologous
chemical_list: D035683:MicroRNAs