10779/rcsi.10767908.v1 Isabella Bray Isabella Bray Kenneth Bryan Kenneth Bryan Suzanne Prenter Suzanne Prenter Patrick G. Buckley Patrick G. Buckley Niamh H. Foley Niamh H. Foley Derek M. Murphy Derek M. Murphy Leah Alcock Leah Alcock Pieter Mestdagh Pieter Mestdagh Jo Vandesompele Jo Vandesompele Frank Speleman Frank Speleman Wendy B. London Wendy B. London Patrick W. McGrady Patrick W. McGrady Desmond G. Higgins Desmond G. Higgins Anne O'Meara Anne O'Meara Maureen O'Sullivan Maureen O'Sullivan Raymond L. Stallings Raymond L. Stallings Widespread dysregulation of MiRNAs by MYCN amplification and chromosomal imbalances in neuroblastoma: association of miRNA expression with survival. Royal College of Surgeons in Ireland 2019 Cell Line Tumor Chromosome Aberrations Cluster Analysis Cohort Studies Gene Expression Regulation Neoplastic Humans MicroRNAs/metabolism Nervous System Neoplasms/genetics/metabolism Neuroblastoma/*genetics Nuclear Proteins/*biosynthesis/*genetics Nucleic Acid Hybridization Oncogene Proteins/*biosynthesis/*genetics Reverse Transcriptase Polymerase Chain Reaction Sensitivity and Specificity Sequence Analysis DNA Sympathetic Nervous System/pathology Treatment Outcome Cancer Genetics 2019-11-22 15:17:52 Journal contribution https://repository.rcsi.com/articles/journal_contribution/Widespread_dysregulation_of_MiRNAs_by_MYCN_amplification_and_chromosomal_imbalances_in_neuroblastoma_association_of_miRNA_expression_with_survival_/10767908 <p>MiRNAs regulate gene expression at a post-transcriptional level and their dysregulation can play major roles in the pathogenesis of many different forms of cancer, including neuroblastoma, an often fatal paediatric cancer originating from precursor cells of the sympathetic nervous system. We have analyzed a set of neuroblastoma (n = 145) that is broadly representative of the genetic subtypes of this disease for miRNA expression (430 loci by stem-loop RT qPCR) and for DNA copy number alterations (array CGH) to assess miRNA involvement in disease pathogenesis. The tumors were stratified and then randomly split into a training set (n = 96) and a validation set (n = 49) for data analysis. Thirty-seven miRNAs were significantly over- or under-expressed in MYCN amplified tumors relative to MYCN single copy tumors, indicating a potential role for the MYCN transcription factor in either the direct or indirect dysregulation of these loci. In addition, we also determined that there was a highly significant correlation between miRNA expression levels and DNA copy number, indicating a role for large-scale genomic imbalances in the dysregulation of miRNA expression. In order to directly assess whether miRNA expression was predictive of clinical outcome, we used the Random Forest classifier to identify miRNAs that were most significantly associated with poor overall patient survival and developed a 15 miRNA signature that was predictive of overall survival with 72.7% sensitivity and 86.5% specificity in the validation set of tumors. We conclude that there is widespread dysregulation of miRNA expression in neuroblastoma tumors caused by both over-expression of the MYCN transcription factor and by large-scale chromosomal imbalances. MiRNA expression patterns are also predicative of clinical outcome, highlighting the potential for miRNA mediated diagnostics and therapeutics.</p>