The RNA structural code underlying pathological regulation of RNA splicing in metastasis

项目总结 广泛的异常剪接现在被认为是癌症的标志，以及由此产生的许多转录本 异构体在功能上与肿瘤的发生有关。然而，潜在的监管途径 管理RNA剪接以及它们在癌症进展中发挥作用的程度在很大程度上仍不清楚。 由于我们对剪接调控的了解有限，我们不能仅仅依靠注释路径来研究 转录异构体的变化。此外，生物信息学策略经常被用于发现 转录调控途径往往不能捕捉到转录后调控的复杂性。为 例如，常见的顺式元件发现方法只关注序列，而在很大程度上忽略了 RNA结构密码在剪接中的整体作用。为了应对这一挑战，我们开发了一种 对备选剪接事件执行上下文感知分析以识别已知的计算框架 以及RNA加工的新型调节剂。使用这种方法，我们已经发现并部分描述了一个 先前未知的RNA结构剪接增强子(SSE)在高转移中驱动异常剪接 乳腺癌。我们已经确定了相关的RNA结合蛋白，它作为反式因子 与这部小说《上海证交所》互动。我们已经证明，这一途径推动了异种移植的转移进展。 该基因的活性与患者的低存活率密切相关。在这项提案中，我们将 在之前工作的基础上，(I)对这一非规范的调控途径进行详细剖析 选择性剪接，其潜在的分子机制，及其支配的RNA结构编码；(Ii)评估 这一途径对乳腺癌进展的贡献；以及(Iii)确定这一途径的临床相关性 致癌途径及其调控因子。

PROJECT SUMMARY Widespread aberrant splicing is now considered a hallmark of cancer, and many of the resulting transcript isoforms have been functionally implicated in tumorigenesis. However, the underlying regulatory pathways that govern RNA splicing and the extent to which they play a role in cancer progression remain largely unknown. Due to our limited knowledge of splicing regulation, we cannot solely rely on annotated pathways to study changes in transcript isoforms. Moreover, bioinformatic strategies that are often used in discovering transcriptional regulatory pathways often fail to capture the complexities of post-transcriptional regulation. For example, common methodologies for cis-element discovery focus on sequence alone and largely ignore the integral role of the RNA structural code in splicing. To address this challenge, we have developed a computational framework that performs context-aware analysis of alternative splicing events to identify known and novel regulators of RNA processing. Using this approach, we have discovered and partly characterized a previously unknown RNA structural splicing enhancer (SSE) that drives aberrant splicing in highly metastatic breast cancer. We have identified the associated RNA-binding protein that serves as the trans factor that interacts with this novel SSE. We have shown that this pathway drives metastatic progression in xenograft mouse models and that its activity is strongly associated with poor survival in patients. In this proposal, we will build on this previous work to (i) perform a detailed dissection of this non-canonical regulatory pathway of alternative splicing, its underlying molecular machinery, and its governing RNA structural code; (ii) evaluate the contribution of this pathway to breast cancer progression; and (iii) establish the clinical relevance of this pathway and its regulon to cancer.