title: Next generation sequencing of microRNAs from isogenic neuroblastoma cell lines isolated before and after treatment.
abstract: Neuroblastoma is a pediatric cancer of the developing sympathetic nervous system. High risk neuroblastoma patients typically undergo an initial remission in response to treatment, followed by recurrence of aggressive tumors that have become refractory to further treatment. Recent works have underlined the involvement of microRNAs (miRNAs) in neuroblastoma development and evolution of drug resistance. In this study we have used deep sequencing technology to identify miRNAs differentially expressed in neuroblastoma cell lines isolated from 6 patients at diagnosis and at relapse after intensive treatments. This approach revealed a panel of 42 differentially expressed miRNAs, 8 of which were upregulated and 34 were downregulated. Most strikingly, the 14q32 miRNA clusters encode 22 of the downregulated miRNAs. Reduced expression of 14q32 miRNAs in tumors associated with poor prognosis factors was confirmed in a cohort consisting of 226 primary neuroblastomas. In order to gain insight into the nature of the genes that may be affected by the differentially expressed miRNAs we utilized Ingenuity Pathway Analysis (IPA). This analysis revealed several biological functions and canonical pathways associated with cancer progression and drug resistance. The results of this study contribute to the identification of miRNAs involved in the complex processes of surviving therapeutic treatment and developing drug resistance in neuroblastoma.
authors.affiliation: Pediatric Research Group, Department of Clinical Medicine, Faculty of Health Science, The Arctic University of Norway - UiT, NO-9037 Tromsø, Norway.
authors.forename: Sarah Andrea
authors.initials: SA
authors.lastname: Roth
authors.affiliation: RNA and Molecular Pathology (RAMP), Department of Medical Biology, Faculty of Health Sciences, The Arctic University of Norway - UiT, NO-9037 Tromsø, Norway.
authors.forename: Erik
authors.initials: E
authors.lastname: Knutsen
authors.affiliation: RNA and Molecular Pathology (RAMP), Department of Medical Biology, Faculty of Health Sciences, The Arctic University of Norway - UiT, NO-9037 Tromsø, Norway.
authors.forename: Tonje
authors.initials: T
authors.lastname: Fiskaa
authors.affiliation: Department of Pediatrics, Division of Child and Adolescent Health, UNN - University Hospital of North-Norway, NO-9038 Tromsø, Norway.
authors.forename: Peter
authors.initials: P
authors.lastname: Utnes
authors.affiliation: Pediatric Research Group, Department of Clinical Medicine, Faculty of Health Science, The Arctic University of Norway - UiT, NO-9037 Tromsø, Norway.
authors.forename: Swapnil
authors.initials: S
authors.lastname: Bhavsar
authors.affiliation: Department of Pediatrics, Division of Child and Adolescent Health, UNN - University Hospital of North-Norway, NO-9038 Tromsø, Norway.
authors.forename: Øyvind H
authors.initials: ØH
authors.lastname: Hald
authors.affiliation: Pediatric Research Group, Department of Clinical Medicine, Faculty of Health Science, The Arctic University of Norway - UiT, NO-9037 Tromsø, Norway.
authors.forename: Cecilie
authors.initials: C
authors.lastname: Løkke
authors.affiliation: Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium.
authors.forename: Pieter
authors.initials: P
authors.lastname: Mestdagh
authors.affiliation: RNA and Molecular Pathology (RAMP), Department of Medical Biology, Faculty of Health Sciences, The Arctic University of Norway - UiT, NO-9037 Tromsø, Norway; Marine Genomics Group, Faculty of Biosciences and Aquaculture, University of Nordland, Bodø, Norway.
authors.forename: Steinar D
authors.initials: SD
authors.lastname: Johansen
authors.affiliation: Pediatric Research Group, Department of Clinical Medicine, Faculty of Health Science, The Arctic University of Norway - UiT, NO-9037 Tromsø, Norway; Department of Pediatrics, Division of Child and Adolescent Health, UNN - University Hospital of North-Norway, NO-9038 Tromsø, Norway.
authors.forename: Trond
authors.initials: T
authors.lastname: Flægstad
authors.affiliation: Pediatric Research Group, Department of Clinical Medicine, Faculty of Health Science, The Arctic University of Norway - UiT, NO-9037 Tromsø, Norway; Department of Pediatrics, Division of Child and Adolescent Health, UNN - University Hospital of North-Norway, NO-9038 Tromsø, Norway. Electronic address: christer.einvik@uit.no.
authors.forename: Christer
authors.initials: C
authors.lastname: Einvik
mesh_terms: D000971:Antineoplastic Combined Chemotherapy Protocols / Q000627:therapeutic use*; D014408:Biomarkers, Tumor / Q000235:genetics*; D045744:Cell Line, Tumor; D002469:Cell Separation / Q000379:methods*; D019008:Drug Resistance, Neoplasm / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods*; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D035683:MicroRNAs / Q000235:genetics*; D009364:Neoplasm Recurrence, Local / Q000235:genetics; D009447:Neuroblastoma / Q000188:drug therapy* / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D060888:Real-Time Polymerase Chain Reaction; D016896:Treatment Outcome
chemical_list: D014408:Biomarkers, Tumor; D035683:MicroRNAs
keywords: 14q32 miRNA cluster; Drug resistance; Neuroblastoma; Next generation sequencing; SOLiD; miRNA; microRNA