Deconstruction and in vivo functionalization of the ceRNA cancer network (PQ-11)

描述（由申请人提供）：我们最近发现了一种新的基因调控手段，由此蛋白质编码和非编码RNA都能够通过新的RNA语言进行交互。在这种新的调控维度中，蛋白质编码和非编码RNA（例如假基因）可以通过竞争共同的microRNA而彼此通信，因此充当“竞争性内源RNA”或ceRNA。我们已经描述了几种调节肿瘤抑制因子PTEN的ceRNA，从而将肿瘤抑制功能归因于许多与癌症无关的mRNA和非编码RNA。此外，我们还开发了一种方法，根据其microRNA响应元件（MRE）的身份来计算预测癌症相关基因的ceRNA，这是这种新语言的基础。这允许预测和鉴定新的推定的肿瘤抑制因子和癌基因，并且，关键地，允许整个癌症相关基因的功能化。 转录组因此，我们建议在体外进一步表征致癌和肿瘤抑制ceRNA网络。此外，为了探索ceRNA在体内基础生物学中的功能，我们已经建立了一系列以诱导方式表达假基因或3 'UTR或缺乏已建立的PTEN ceRNA的小鼠模型。我们将这些小鼠与现有的小鼠癌症模型杂交，以表征ceRNA对体内恶性表型的贡献。我们提出了解决这些悬而未决的问题与这个新的变革性的生物学维度与以下具体目标：（1）鉴定和功能表征新的肿瘤抑制性PTEN ceRNA以及分析缺乏真正的PTEN ceRNA的小鼠模型，如ZEB 2和VHL;（2）探讨PTEN 3 'UTR过表达对PTEN杂合性或靶向miR 106 b ~（-1）的PTEN过表达诱导的恶性表型的影响。25簇;（3）分析假基因BRAFps在体外和体内对其祖先基因原癌基因BRAF的ceRNA活性及其对癌症发展的贡献。我们坚信，我们的应用是高度创新和及时的，有可能大大加深我们对癌症遗传学和生物学中基因调控这一新过程的理解。

DESCRIPTION (provided by applicant): We have recently discovered a novel means of gene regulation whereby both protein-coding and non-coding RNAs are able to cross-talk through a new RNA language. In this new regulatory dimension, both protein-coding and non-coding RNAs (e.g. pseudogenes) can communicate with each other by competing for common microRNAs, hence acting as "competing endogenous RNAs" or ceRNAs. We have described several ceRNAs that regulate the tumor suppressor PTEN, thereby ascribing tumor suppressive functions to numerous cancer-unrelated mRNAs and non-coding RNAs. Moreover, we have developed a methodology to computationally predict ceRNAs for cancer-associated genes based upon the identity of their microRNA response elements (MREs), which are the foundation of this new language. This allows for the prediction and identification of novel putative tumor suppressors and oncogenes, and, critically, for the functionalization of the entire cancer-relevant transcriptome. We therefore propose to further characterize oncogenic and tumor suppressive ceRNA networks in vitro. Additionally, to explore the function of ceRNAs in basic biology in vivo, we have created a series of mouse models that express pseudogenes or 3'UTRs or lack established PTEN ceRNAs in an inducible manner. We will cross these mice to existing mouse models of cancer to characterize the contribution of ceRNAs to the malignant phenotype in vivo. We propose to address these outstanding questions pertaining to this new transformative biological dimension with the following specific aims: (1) to identify and functionally characteriz novel tumor suppressive PTEN ceRNAs as well as to analyze mouse models lacking bona fide PTEN ceRNAs such as ZEB2 and VHL; (2) to explore the effect of PTEN 3'UTR overexpression on the malignant phenotype elicited by either PTEN heterozygosity or overexpression of the PTEN targeting miR106b~25 cluster; (3) to analyze the ceRNA activity of the pseudogene BRAFps towards its ancestral gene, the proto-oncogene BRAF, in vitro and in vivo and its contribution to cancer development. We strongly believe that our application is both highly innovative and timely, with the potential to significantly further our understanding of this novel process of gene regulation in cancer genetics and biology.