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Widespread Dysregulation of MiRNAs by MYCN Amplification and Chromosomal Imbalances in Neuroblastoma: Association of miRNA Expression with Survival

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 an...

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Autores principales: Bray, Isabella, Bryan, Kenneth, Prenter, Suzanne, Buckley, Patrick G., Foley, Niamh H., Murphy, Derek M., Alcock, Leah, Mestdagh, Pieter, Vandesompele, Jo, Speleman, Frank, London, Wendy B., McGrady, Patrick W., Higgins, Desmond G., O'Meara, Anne, O'Sullivan, Maureen, Stallings, Raymond L.
Formato: Texto
Lenguaje:English
Publicado: Public Library of Science 2009
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2773120/
https://www.ncbi.nlm.nih.gov/pubmed/19924232
http://dx.doi.org/10.1371/journal.pone.0007850
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author Bray, Isabella
Bryan, Kenneth
Prenter, Suzanne
Buckley, Patrick G.
Foley, Niamh H.
Murphy, Derek M.
Alcock, Leah
Mestdagh, Pieter
Vandesompele, Jo
Speleman, Frank
London, Wendy B.
McGrady, Patrick W.
Higgins, Desmond G.
O'Meara, Anne
O'Sullivan, Maureen
Stallings, Raymond L.
author_facet Bray, Isabella
Bryan, Kenneth
Prenter, Suzanne
Buckley, Patrick G.
Foley, Niamh H.
Murphy, Derek M.
Alcock, Leah
Mestdagh, Pieter
Vandesompele, Jo
Speleman, Frank
London, Wendy B.
McGrady, Patrick W.
Higgins, Desmond G.
O'Meara, Anne
O'Sullivan, Maureen
Stallings, Raymond L.
author_sort Bray, Isabella
collection PubMed
description 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.
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spelling pubmed-27731202009-11-19 Widespread Dysregulation of MiRNAs by MYCN Amplification and Chromosomal Imbalances in Neuroblastoma: Association of miRNA Expression with Survival Bray, Isabella Bryan, Kenneth Prenter, Suzanne Buckley, Patrick G. Foley, Niamh H. Murphy, Derek M. Alcock, Leah Mestdagh, Pieter Vandesompele, Jo Speleman, Frank London, Wendy B. McGrady, Patrick W. Higgins, Desmond G. O'Meara, Anne O'Sullivan, Maureen Stallings, Raymond L. PLoS One Research Article 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. Public Library of Science 2009-11-16 /pmc/articles/PMC2773120/ /pubmed/19924232 http://dx.doi.org/10.1371/journal.pone.0007850 Text en Bray et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Bray, Isabella
Bryan, Kenneth
Prenter, Suzanne
Buckley, Patrick G.
Foley, Niamh H.
Murphy, Derek M.
Alcock, Leah
Mestdagh, Pieter
Vandesompele, Jo
Speleman, Frank
London, Wendy B.
McGrady, Patrick W.
Higgins, Desmond G.
O'Meara, Anne
O'Sullivan, Maureen
Stallings, Raymond L.
Widespread Dysregulation of MiRNAs by MYCN Amplification and Chromosomal Imbalances in Neuroblastoma: Association of miRNA Expression with Survival
title Widespread Dysregulation of MiRNAs by MYCN Amplification and Chromosomal Imbalances in Neuroblastoma: Association of miRNA Expression with Survival
title_full Widespread Dysregulation of MiRNAs by MYCN Amplification and Chromosomal Imbalances in Neuroblastoma: Association of miRNA Expression with Survival
title_fullStr Widespread Dysregulation of MiRNAs by MYCN Amplification and Chromosomal Imbalances in Neuroblastoma: Association of miRNA Expression with Survival
title_full_unstemmed Widespread Dysregulation of MiRNAs by MYCN Amplification and Chromosomal Imbalances in Neuroblastoma: Association of miRNA Expression with Survival
title_short Widespread Dysregulation of MiRNAs by MYCN Amplification and Chromosomal Imbalances in Neuroblastoma: Association of miRNA Expression with Survival
title_sort widespread dysregulation of mirnas by mycn amplification and chromosomal imbalances in neuroblastoma: association of mirna expression with survival
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2773120/
https://www.ncbi.nlm.nih.gov/pubmed/19924232
http://dx.doi.org/10.1371/journal.pone.0007850
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