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Modulation of neuroblastoma disease pathogenesis by an extensive network of epigenetically regulated microRNAs

Oncogene volume 32, pages 2927–2936 (2013)Cite this article

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Abstract

MicroRNAs (miRNAs) contribute to the pathogenesis of many forms of cancer, including the pediatric cancer neuroblastoma, but the underlying mechanisms leading to altered miRNA expression are often unknown. Here, a novel integrated approach for analyzing DNA methylation coupled with miRNA and mRNA expression data sets identified 67 epigenetically regulated miRNA in neuroblastoma. A large proportion (42%) of these miRNAs was associated with poor patient survival when underexpressed in tumors. Moreover, we demonstrate that this panel of epigenetically silenced miRNAs targets a large set of genes that are overexpressed in tumors from patients with poor survival in a highly redundant manner. The genes targeted by the epigenetically regulated miRNAs are enriched for a number of biological processes, including regulation of cell differentiation. Functional studies involving ectopic overexpression of several of the epigenetically silenced miRNAs had a negative impact on neuroblastoma cell viability, providing further support to the concept that inactivation of these miRNAs is important for neuroblastoma disease pathogenesis. One locus, miR-340, induced either differentiation or apoptosis in a cell context dependent manner, indicating a tumor suppressive function for this miRNA. Intriguingly, it was determined that miR-340 is upregulated by demethylation of an upstream genomic region that occurs during the process of neuroblastoma cell differentiation induced by all-trans retinoic acid (ATRA). Further biological studies of miR-340 revealed that it directly represses the SOX2 transcription factor by targeting of its 3′-untranslated region, explaining the mechanism by which SOX2 is downregulated by ATRA. Although SOX2 contributes to the maintenance of stem cells in an undifferentiated state, we demonstrate that miR-340-mediated downregulation of SOX2 is not required for ATRA induced differentiation to occur. In summary, our results exemplify the dynamic nature of the miRNA epigenome and identify a remarkable network of miRNA/mRNA interactions that significantly contribute to neuroblastoma disease pathogenesis.

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Acknowledgements

This work was supported by grants from Science Foundation Ireland (07/IN.1/B1776), Children′s Medical and Research Foundation and NIH (5R01CA127496).

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Author notes

  1. S Das and K Bryan: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland

    S Das, K Bryan, P G Buckley, O Piskareva, I M Bray, N Foley, J Ryan, J Lynch, L Creevey, J Fay, S Prenter & R L Stallings

  2. National Children′s Research Centre, Our Lady′s Children′s Hospital, Dublin, Ireland

    S Das, K Bryan, P G Buckley, O Piskareva, I M Bray, N Foley, J Ryan, J Lynch, L Creevey, J Fay, S Prenter & R L Stallings

  3. Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands

    J Koster, P van Sluis & R Versteeg

  4. University Children′s Hospital, Essen, Germany

    A Eggert, J H Schulte & A Schramm

  5. Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium

    P Mestdagh, J Vandesompele & F Speleman

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Das, S., Bryan, K., Buckley, P. et al. Modulation of neuroblastoma disease pathogenesis by an extensive network of epigenetically regulated microRNAs. Oncogene 32, 2927–2936 (2013). https://doi.org/10.1038/onc.2012.311

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