Genomic and functional analysis of transcriptome changes in Huntington's Disease

亨廷顿病转录组变化的基因组和功能分析

• 批准号: 8742006
• 负责人: Beverly L. Davidson
• 金额: $ 68.1万
• 依托单位: CHILDREN'S HOSP OF PHILADELPHIA
• 依托单位国家: 美国
• 财政年份: 2013
• 资助国家: 美国
• 起止时间: 2013-09-30 至 2018-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8742006
• 关键词: Affect; Alternative Splicing; Bioinformatics; Biological Models; Brain; Brain region; CAG repeat; Cell model; Cells; Collection; Computing Methodologies; Data; Data Set; Disease; Disease model; Drug Targeting; Event; Exclusion; Exons; Functional disorder; Gene Expression; Gene Expression Alteration; Gene Expression Profile; Gene Proteins; Genes; Genetic Transcription; Genomics; Human; Huntington Disease; In Vitro; Lead; Messenger RNA; Methodology; MicroRNAs; Molecular Target; Mus; Neurodegenerative Disorders; Neurons; Onset of illness; Pathogenesis; Pathway interactions; Patients; Pattern; Polypyrimidine Tract-Binding Protein; Protein Isoforms; Proteins; RNA; RNA Processing; RNA Sequence Analysis; RNA Sequences; RNA Splicing; Reporting; Research Personnel; Role; Sampling; Specificity; Spliced Genes; Techniques; Testing; Tissue Model; Tissue-Specific Splicing; Transcript; Untranslated RNA; Validation; Work; brain tissue; cell type; disease phenotype; disorder control; experience; functional genomics; human Huntingtin protein; human disease; in vivo; loss of function; mRNA Precursor; mouse model; new therapeutic target; novel; protein function; public health relevance; therapeutic development; transcription factor; validation studies

DESCRIPTION (provided by applicant): A CAG repeat expansion in exon 1 of the HD gene product, huntingtin, causes Huntington's disease (HD), a fatal neurodegenerative disease for which there is no cure or neuroprotective treatment. Dysregulation of transcription is a major feature of HD pathogenesis, as indicated by a large body of work using RNA array techniques, and work on specific transcription factors and their targets. More recent studies have also suggested a role for huntingtin in RNA processing. Prior work on gene expression alterations in HD brain tissues used 3' biased gene expression arrays. Of increasing importance in many human diseases, particularly neurodegenerative diseases, is the occurrence of aberrant alternative pre-mRNA splicing. However, conventional gene expression techniques are not well suited to quantitative analysis of alternative splicing patterns, and do not sample rare transcript well. Several lines of evidence from our preliminary work suggest global splicing abnormalities in HD. For example, we reported earlier that microRNA miR-124 was significantly reduced in HD brains. Work by Maniatis and colleagues showed that miR-124 promotes neuronal-specific alternative splicing events by down- regulating an important tissue-specific splicing regulator, polypyrimidine tract-binding protein (PTBP1). Consistent with the decrease in miR-124, we have preliminary evidence for significantly increased PTBP1 mRNA levels in HD patient samples. Moreover, preliminary data suggest that several exons in genes regulated by PTBP1 show corresponding changes in exon inclusion/exclusion in HD brain. Inclusion or exclusion of non-constitutive exons can have dramatic effects on transcript stability and protein activity. Thus transcriptome alterations in HD may extend beyond up- and down-regulated genes to include changes in gene and protein isoforms. Assessing these events on a global scale for HD will aid efforts to unravel disease pathophysiology, and may identify new drug targets for therapy. In our work, which encompasses 3 aims, we will move from identification of the altered HD transcriptome, to validation, to in vitro and in vivo studies to test their relevance on HD phenotypes. These studies combine the genomics and bioinformatics expertise of the Xing lab and the HD expertise of the Ross and Davidson labs. The functional relevance of those changes will be elucidated using gain and loss of function studies in the Davidson and Ross labs, where both groups have substantial experience with HD models.

描述（由申请人提供）：HD 基因产物亨廷顿蛋白的外显子 1 中的 CAG 重复扩增会导致亨廷顿病 (HD)，这是一种致命的神经退行性疾病，无法治愈或进行神经保护治疗。使用 RNA 阵列技术以及针对特定转录因子及其靶标的大量研究表明，转录失调是 HD 发病机制的一个主要特征。最近的研究还表明亨廷顿蛋白在 RNA 加工中发挥着作用。 先前对 HD 脑组织中基因表达改变的研究使用了 3' 偏向基因表达阵列。在许多人类疾病，特别是神经退行性疾病中，异常的选择性前 mRNA 剪接的发生变得越来越重要。然而，传统的基因表达技术不太适合选择性剪接模式的定量分析，并且不能很好地对稀有转录本进行采样。 我们的初步工作中的几条证据表明 HD 中存在整体剪接异常。例如，我们之前报道称，HD 大脑中的 microRNA miR-124 显着减少。 Maniatis 及其同事的工作表明，miR-124 通过下调重要的组织特异性剪接调节因子聚嘧啶束结合蛋白 (PTBP1) 来促进神经元特异性选择性剪接事件。与 miR-124 的减少一致，我们有初步证据表明 HD 患者样本中 PTBP1 mRNA 水平显着增加。此外，初步数据表明，受PTBP1调控的基因中的几个外显子在HD脑中显示出相应的外显子包含/排除变化。包含或排除非组成型外显子会对转录稳定性和蛋白质活性产生巨大影响。因此，HD 中转录组的改变可能不仅限于上调和下调基因，还包括基因和蛋白质亚型的变化。在全球范围内评估 HD 的这些事件将有助于阐明疾病的病理生理学，并可能确定新的治疗药物靶点。在我们的工作中，包括 3 个目标，我们将从鉴定改变的 HD 转录组，到验证，再到体外和体内研究，以测试它们与 HD 表型的相关性。 这些研究结合了 Xing 实验室的基因组学和生物信息学专业知识以及 Ross 和 Davidson 实验室的 HD 专业知识。这些变化的功能相关性将通过戴维森和罗斯实验室的功能获得和丧失研究来阐明，两个小组在 HD 模型方面都有丰富的经验。