Oncotarget

Research Papers:

Role of microRNAs in epigenetic silencing of the CHD5 tumor suppressor gene in neuroblastomas

Koumudi Naraparaju, Venkatadri Kolla, Tiangang Zhuang, Mayumi Higashi, Radhika Iyer, Sriharsha Kolla, Erin R. Okawa, Gerd A. Blobel and Garrett M. Brodeur _

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Oncotarget. 2016; 7:15977-15985. https://doi.org/10.18632/oncotarget.7434

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Abstract

Koumudi Naraparaju1, Venkatadri Kolla1, Tiangang Zhuang1, Mayumi Higashi1, Radhika Iyer1, Sriharsha Kolla1, Erin R. Okawa1, Gerd A. Blobel2, Garrett M. Brodeur1

1Division of Oncology and Hematology, The Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA

2Department of Pediatrics, The Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA

Correspondence to:

Garrett M. Brodeur, e-mail: Brodeur@email.chop.edu

Keywords: neuroblastoma, CHD5, miRNA, tumor suppressor, MYCN

Abbreviations: TSG: Tumor Suppressor Gene; CHD5: Chromodomain Helicase DNA binding protein 5; NB: Neuroblastoma; SRD: Smallest Region of consistent Deletion

Received: October 06, 2015     Accepted: February 05, 2016     Published: February 16, 2016

ABSTRACT

Neuroblastoma (NB), a tumor of the sympathetic nervous system, is the most common extracranial solid tumor of childhood. We and others have identified distinct patterns of genomic change that underlie diverse clinical behaviors, from spontaneous regression to relentless progression. We first identified CHD5 as a tumor suppressor gene that is frequently deleted in NBs. Mutation of the remaining CHD5 allele is rare in these tumors, yet expression is very low or absent, so expression is likely regulated by epigenetic mechanisms. In order to understand the potential role of miRNA regulation of CHD5 protein expression in NBs, we examined all miRNAs that are predicted to target the 3’-UTR using miRanda, TargetScan and other algorithms. We identified 18 miRNAs that were predicted by 2 or more programs: miR-204, -211, -216b, -17, -19ab, -20ab, -93, -106ab, -130ab, -301ab, -454, -519d, -3666. We then performed transient transfections in two NB cell lines, NLF (MYCN amplified) and SY5Y (MYCN non-amplified), with the reporter plasmid and miRNA mimic, as well as appropriate controls. We found seven miRNAs that significantly downregulated CHD5 expression in NB: miR-211, 17, -93, -20b, -106b, -204, and -3666. Interestingly, MYCN upregulates several of the candidates we identified: miR-17, -93, -106b & -20b. This suggests that miRNAs driven by MYCN and other genes represent a potential epigenetic mechanism to regulate CHD5 expression.


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