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

描述(申请人提供)：我们最近发现了一种新的基因调控方法，通过这种方法，蛋白质编码和非编码RNA都能够通过一种新的RNA语言进行串扰。在这个新的调控维度中，蛋白质编码和非编码RNA(如假基因)都可以通过竞争共同的microRNA来相互通信，从而起到“竞争内源RNAs”或ceRNAs的作用。我们已经描述了几个调控肿瘤抑制基因PTEN的CERNAs，从而将肿瘤抑制功能归因于许多与癌症无关的mRNAs和非编码RNA。此外，我们还开发了一种方法，根据癌症相关基因的microRNA响应元件(MRE)的身份来计算预测CERNA，这是这种新语言的基础。这使得可以预测和鉴定新的假定的肿瘤抑制基因和癌基因，关键的是，可以实现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的Cerna网络。此外，为了探索ceRNAs在体内基础生物学中的功能，我们建立了一系列以诱导方式表达假基因或3‘UTRs或缺乏已建立的PTEN ceRNAs的小鼠模型。我们将把这些小鼠与现有的小鼠癌症模型进行交叉，以表征ceRNAs在体内对恶性表型的贡献。我们建议解决与这一新的具有转化作用的生物学维度相关的这些悬而未决的问题，具体目标如下：(1)鉴定和功能鉴定新的抑癌基因PTEN ceRNAs，并分析缺乏真正PTEN ceRNAs的小鼠模型，如ZEB2和VHL；(2)探讨PTEN 3‘UTR过表达对PTEN杂合性或针对miR106b~25簇的PTEN过表达所诱导的恶性表型的影响；(3)分析假基因BRAFps针对其祖先基因原癌基因BRAF的Cerna活性及其在肿瘤发展中的作用。我们坚信，我们的应用具有很高的创新性和时效性，有可能极大地促进我们对癌症遗传学和生物学中这一新的基因调控过程的理解。

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.