Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland.
Oncogene. 2013 Jun 13;32(24):2927-36. doi: 10.1038/onc.2012.311. Epub 2012 Jul 16.
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.
微小 RNA（miRNA）有助于多种形式的癌症的发病机制，包括儿科癌症神经母细胞瘤，但导致 miRNA 表达改变的潜在机制通常未知。在这里，一种新的分析 DNA 甲基化与 miRNA 和 mRNA 表达数据集的综合方法鉴定了神经母细胞瘤中 67 个受表观遗传调控的 miRNA。当这些 miRNA 在肿瘤中低表达时，其中很大一部分（42%）与患者生存不良相关。此外，我们证明，这组表观遗传沉默的 miRNA 靶向一组大量基因，这些基因在生存不良的患者肿瘤中以高度冗余的方式过表达。受表观遗传调控的 miRNA 靶向的基因富集了许多生物学过程，包括细胞分化的调节。涉及几个表观遗传沉默 miRNA 的异位过表达的功能研究对神经母细胞瘤细胞活力有负面影响，进一步支持了这些 miRNA 的失活对神经母细胞瘤发病机制很重要的概念。一个位点 miR-340 以细胞上下文依赖的方式诱导分化或凋亡，表明该 miRNA 具有肿瘤抑制功能。有趣的是，确定 miR-340 是通过全反式视黄酸（ATRA）诱导的神经母细胞瘤细胞分化过程中上游基因组区域的去甲基化而上调的。对 miR-340 的进一步生物学研究表明，它通过靶向其 3'非翻译区直接抑制 SOX2 转录因子，解释了 ATRA 下调 SOX2 的机制。虽然 SOX2 有助于未分化状态下干细胞的维持，但我们证明 miR-340 介导的 SOX2 下调对于 ATRA 诱导的分化发生不是必需的。总之，我们的结果说明了 miRNA 表观基因组的动态性质，并确定了一个显著的 miRNA/mRNA 相互作用网络，对神经母细胞瘤发病机制有重要贡献。
