Center for Medical Genetics, Ghent University, Ghent, 9000, Belgium.
Cancer Research Institute Ghent (CRIG), Ghent, 9000, Belgium.
Sci Rep. 2019 Apr 5;9(1):5685. doi: 10.1038/s41598-019-42107-y.
Long intergenic non-coding RNAs (lincRNAs) are emerging as integral components of signaling pathways in various cancer types. In neuroblastoma, only a handful of lincRNAs are known as upstream regulators or downstream effectors of oncogenes. Here, we exploit RNA sequencing data of primary neuroblastoma tumors, neuroblast precursor cells, neuroblastoma cell lines and various cellular perturbation model systems to define the neuroblastoma lincRNome and map lincRNAs up- and downstream of neuroblastoma driver genes MYCN, ALK and PHOX2B. Each of these driver genes controls the expression of a particular subset of lincRNAs, several of which are associated with poor survival and are differentially expressed in neuroblastoma tumors compared to neuroblasts. By integrating RNA sequencing data from both primary tumor tissue and cancer cell lines, we demonstrate that several of these lincRNAs are expressed in stromal cells. Deconvolution of primary tumor gene expression data revealed a strong association between stromal cell composition and driver gene status, resulting in differential expression of these lincRNAs. We also explored lincRNAs that putatively act upstream of neuroblastoma driver genes, either as presumed modulators of driver gene activity, or as modulators of effectors regulating driver gene expression. This analysis revealed strong associations between the neuroblastoma lincRNAs MIAT and MEG3 and MYCN and PHOX2B activity or expression. Together, our results provide a comprehensive catalogue of the neuroblastoma lincRNome, highlighting lincRNAs up- and downstream of key neuroblastoma driver genes. This catalogue forms a solid basis for further functional validation of candidate neuroblastoma lincRNAs.
长链非编码 RNA（lincRNAs）作为各种癌症类型信号通路的组成部分正在出现。在神经母细胞瘤中，仅有少数 lincRNAs 被认为是癌基因的上游调节剂或下游效应物。在这里，我们利用原发性神经母细胞瘤肿瘤、神经母细胞前体细胞、神经母细胞瘤细胞系和各种细胞扰动模型系统的 RNA 测序数据，定义神经母细胞瘤 lincRNome，并绘制神经母细胞瘤驱动基因 MYCN、ALK 和 PHOX2B 上下游的 lincRNAs。这些驱动基因中的每一个都控制着特定亚群 lincRNAs 的表达，其中有几个与不良预后相关，并且在神经母细胞瘤肿瘤与神经母细胞相比时存在差异表达。通过整合来自原发性肿瘤组织和癌细胞系的 RNA 测序数据，我们证明了其中一些 lincRNAs 在基质细胞中表达。对原发性肿瘤基因表达数据的去卷积分析表明，基质细胞组成与驱动基因状态之间存在很强的关联，导致这些 lincRNAs 的差异表达。我们还探索了可能位于神经母细胞瘤驱动基因上游的 lincRNAs，这些 lincRNAs要么作为驱动基因活性的假定调节剂，要么作为调节驱动基因表达的效应物调节剂。这种分析揭示了神经母细胞瘤 lincRNAs MIAT 和 MEG3 与 MYCN 和 PHOX2B 活性或表达之间的强烈关联。总之，我们的研究结果提供了神经母细胞瘤 lincRNome 的综合目录，突出了关键神经母细胞瘤驱动基因上下游的 lincRNAs。该目录为进一步验证候选神经母细胞瘤 lincRNAs 的功能提供了坚实的基础。
