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
基本信息
- 批准号:10358636
- 负责人:
- 金额:$ 35.31万
- 依托单位:
- 依托单位国家:美国
- 项目类别:
- 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:
- 关键词:AddressAlternative SplicingAwarenessBindingBinding SitesBiochemicalBioinformaticsBiological AssayBiologyBreast Cancer PatientBreast cancer metastasisClinicalCodeCollaborationsCommunitiesComplexComprehensive Cancer CenterComputational BiologyDissectionElementsEnhancersEventExonsFamilyGenetic TranscriptionGenomicsGoalsHumanIn VitroKnowledgeMalignant NeoplasmsMeasurementMediatingMessenger RNAMetastatic breast cancerMethodologyModelingMolecularMusMutationNeoplasm MetastasisNonmetastaticPathologicPathway interactionsPatientsPlayPositioning AttributePost-Transcriptional RegulationProtein IsoformsPublic HealthRNARNA ProcessingRNA SequencesRNA SplicingRNA-Binding ProteinsRegulationRegulatory ElementRegulatory PathwayRegulonReporterResearchRoleSamplingSmall Nuclear RibonucleoproteinsStructureSurvival AnalysisTrans-SplicingTranscriptUp-RegulationWorkXenograft procedurebasebreast cancer progressioncancer cellclinically relevantcomputer frameworkexperimental studyin silicoin vivoinnovationinterdisciplinary approachknock-downlung colonizationmouse modelnoveloverexpressionpatient derived xenograft modelprogramspromotershape analysistargeted treatmenttumor progressiontumorigenesis
项目摘要
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.
项目摘要
现在,广泛的异常剪接被认为是癌症的标志,许多由此产生的成绩单
同工型在功能上与肿瘤发生有关。但是,基本的监管途径
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未知。
由于我们对剪接法规的了解有限,我们不能仅依靠注释的途径来学习
转录本同工型的变化。而且,经常用于发现的生物信息学策略
转录调节途径通常无法捕获转录后调节的复杂性。为了
例如,顺式元素发现的常见方法专注于单独的序列,并在很大程度上忽略了
RNA结构代码在剪接中的积分作用。为了应对这一挑战,我们已经开发了
对替代剪接事件进行上下文感知分析的计算框架以识别已知的
和RNA处理的新型调节剂。使用这种方法,我们发现并部分表征了
以前未知的RNA结构剪接增强子(SSE)在高度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,该蛋白是反式因子
与这部小说SSE互动。我们已经表明,该途径驱动异种移植中的转移性进展
小鼠模型,其活性与患者的存活不良密切相关。在此提案中,我们将
基于以前的工作(i)对这种非规范的监管途径进行详细的解剖
替代剪接,其潜在的分子机械及其管理RNA结构代码; (ii)评估
这种途径对乳腺癌进展的贡献; (iii)建立了这一点的临床相关性
途径及其对癌症的调节。
项目成果
期刊论文数量(0)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
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Hani Goodarzi其他文献
Hani Goodarzi的其他文献
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$ 35.31万 - 项目类别:
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
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10654522 - 财政年份:2021
- 资助金额:
$ 35.31万 - 项目类别:
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
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10117466 - 财政年份:2021
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$ 35.31万 - 项目类别:
Editing CG and non-CG DNA methylation to identify genomic elements that regulate gene expression
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An antisense RNA-mediated regulatory program that drives cancer metastasis
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An antisense RNA-mediated regulatory program that drives cancer metastasis
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反义RNA介导的驱动癌症转移的调控程序
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10177973 - 财政年份:2019
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