Mapping the chemotherapy-induced RNA interactome in Glioblastoma [smallRNA-Seq]. Homo sapiens

Long non-coding RNAs (lncRNAs) are increasingly recognized as important players in transcription and epigenetic-driven cell diversification. So far, lncRNA function in more dynamic transcriptional reprogramming, i.e drug response, has been largely unexplored. Here, we investigated the regulatory circuits induced by chemotherapy in glioblastoma, the most aggressive and clinically refractory brain cancer. We performed a detailed characterization of the cellular and transcriptional response of glioblastoma stem-like cells to the alkylating agent temozolomide (TMZ). We found that in addition to mRNAs, TMZ affects the expression of a large number of non-coding RNAs (miRNAs, snoRNAs, lncRNAs). Our global transcriptome analysis provides a comprehensive characterization of regulatory circuits involving transcription factors, mRNAs, miRNAs and lncRNAs. To analyse the putative functions of these largely unknown RNA molecules, we developed a pipeline to integrate small and large RNA-seq data from multiple public databases and our own experiments. This led to the identification of the RNA interactome of glioblastoma and allowed us to define regulatory loops mediated by lncRNAs. We identified 22 key lncRNAs involved in transcriptional regulatory motifs, and three lncRNAs associated with patient prognosis, independent of other known response predictors. The investigation of TMZ-induced molecular networks in glioblastoma highlights novel coding and non-coding RNA-based predictors of glioblastoma chemoresistance, as well as potential targets to counteract such resistance. Overall design: RNA and small RNA profiling of 3 GBM stem-like cells and neural stem cells under TMZ treatment or vehicle in triplicate. This Series represents the small RNA profiling dataset.

长链非编码RNA（long non-coding RNAs，lncRNAs）如今愈发被认为是转录过程与表观遗传驱动的细胞分化进程中的关键调控因子。迄今为止，针对长链非编码RNA在更具动态性的转录重编程（即药物应答）中的功能，尚未得到系统性探索。本研究针对胶质母细胞瘤——一种恶性程度极高、临床治疗极具挑战性的脑部恶性肿瘤——中化疗诱导的调控网络展开了系统探究。我们对胶质母细胞瘤干细胞样细胞在烷化剂替莫唑胺（temozolomide，TMZ）处理下的细胞应答与转录应答进行了详尽的表征分析。我们发现，除信使RNA（messenger RNAs，mRNAs）外，替莫唑胺还可调控大量非编码RNA的表达，涵盖微小RNA（microRNAs，miRNAs）、核仁小RNA（small nucleolar RNAs，snoRNAs）以及长链非编码RNA（lncRNAs）。本研究的全局转录组分析对涉及转录因子、信使RNA、微小RNA及长链非编码RNA的调控网络进行了全面表征。为解析这些尚未被充分研究的RNA分子的潜在功能，我们开发了一套整合分析流程，用于整合来自多个公共数据库及本研究实验的小RNA与大RNA测序数据。该流程成功解析了胶质母细胞瘤的RNA互作组，并使我们得以明确由长链非编码RNA介导的调控环路。我们共鉴定出22个参与转录调控基序的关键长链非编码RNA，以及3个与患者预后显著相关的长链非编码RNA，且该相关性独立于其他已知的应答预测因子。本研究对替莫唑胺诱导的胶质母细胞瘤分子网络的探究，揭示了全新的基于编码RNA与非编码RNA的胶质母细胞瘤化疗耐药预测标志物，同时也为对抗该耐药性提供了潜在治疗靶点。
实验整体设计：对3株GBM干细胞样细胞及神经干细胞分别进行替莫唑胺处理与溶剂对照处理，并设置三次生物学重复，随后开展RNA与小RNA表达谱分析。本数据集即为其中的小RNA表达谱分析数据集。