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

转移中RNA剪接病理调控的RNA结构密码

• 批准号: 10654522
• 负责人: Hani Goodarzi
• 金额: $ 35.31万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-07-01 至 2026-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10654522
• 关键词: Address; Alternative Splicing; Awareness; Binding; Binding Sites; Biochemical; Bioinformatics; Biological Assay; Biology; Breast Cancer Patient; Breast cancer metastasis; Clinical; Code; Collaborations; Communities; Complex; Comprehensive Cancer Center; Computational Biology; Dissection; Elements; Enhancers; Event; Exons; Family; Genetic Transcription; Genomics; Goals; Human; In Vitro; Knowledge; Malignant Neoplasms; Measurement; Mediating; Messenger RNA; Metastatic breast cancer; Methodology; Modeling; Molecular; Mus; Mutation; Neoplasm Metastasis; Nonmetastatic; Pathologic; Pathway interactions; Patients; Positioning Attribute; Post-Transcriptional Regulation; Protein Isoforms; Public Health; RNA; RNA Processing; RNA Sequences; RNA Splicing; RNA-Binding Proteins; Regulation; Regulatory Element; Regulatory Pathway; Regulon; Reporter; Research; Role; Sampling; Small Nuclear Ribonucleoproteins; Structure; Survival Analysis; Trans-Splicing; Transcript; Up-Regulation; Work; Xenograft procedure; breast cancer progression; cancer cell; clinically relevant; computer framework; experimental study; in silico; in vivo; innovation; interdisciplinary approach; knock-down; lung colonization; mouse model; novel; overexpression; patient derived xenograft model; programs; promoter; shape analysis; targeted treatment; tumor progression; tumorigenesis

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.

项目概要 广泛的异常剪接现在被认为是癌症的标志，并且许多由此产生的转录本 同种型在功能上与肿瘤发生有关。然而，潜在的监管途径 控制 RNA 剪接以及它们在癌症进展中发挥作用的程度仍然很大程度上未知。 由于我们对剪接调控的了解有限，我们不能仅仅依靠注释的途径来研究 转录亚型的变化。此外，生物信息学策略经常用于发现 转录调控途径通常无法捕捉转录后调控的复杂性。为了 例如，顺式元件发现的常见方法仅关注序列，而很大程度上忽略了序列 RNA结构密码在剪接中的不可或缺的作用。为了应对这一挑战，我们开发了 对选择性剪接事件进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，我们发现并部分表征了 先前未知的 RNA 结构剪接增强子 (SSE)，可在高度转移性细胞中驱动异常剪接 乳腺癌。我们已经鉴定出相关的 RNA 结合蛋白，它作为反式因子 与这个新颖的 SSE 互动。我们已经证明该途径驱动异种移植物的转移进展 小鼠模型，其活性与患者的不良生存率密切相关。在本提案中，我们将 以之前的工作为基础，（i）对这种非规范监管途径进行详细剖析 选择性剪接、其基础分子机制及其控制 RNA 结构代码； (ii) 评估 该途径对乳腺癌进展的贡献； (iii) 确定该研究的临床相关性 途径及其对癌症的调节。

项目成果

Integrative identification of non-coding regulatory regions driving metastatic prostate cancer.

驱动转移性前列腺癌的非编码调控区的综合识别。

• 发表时间: 2023-06-02
• 作者: Woo, Brian J;Moussavi;Karner, Heather;Karimzadeh, Mehran;Garcia, Kristle;Joshi, Tanvi;Yin, Keyi;Navickas, Albertas;Gilbert, Luke A;Wang, Bo;Asgharian, Hosseinali;Feng, Felix Y;Goodarzi, Hani
• 通讯作者: Goodarzi, Hani

RPL22 is a tumor suppressor in MSI-high cancers and a key splicing regulator of MDM4.

RPL22 是 MSI 高癌症中的肿瘤抑制因子，也是 MDM4 的关键剪接调节因子。

• 发表时间: 2023-12-10
• 作者: Weinstein, Hannah N W;Hu, Kevin;Fish, Lisa;Chen, Yih;Allegakoen, Paul;Hui, Keliana S F;Pham, Julia H;Baco, Maria B;Song, Hanbing;Giacomelli, Andrew O;Vazquez, Francisca;Ghandi, Mahmoud;Goodarzi, Hani;Huang, Franklin W
• 通讯作者: Huang, Franklin W