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

描述（由申请方提供）：HD基因产物亨廷顿蛋白外显子1中的CAG重复扩增导致亨廷顿病（HD），这是一种致命的神经退行性疾病，目前尚无治愈或神经保护性治疗方法。转录失调是HD发病机制的一个主要特征，如使用RNA阵列技术的大量工作所示，并对特定转录因子及其靶点进行了研究。最近的研究也表明亨廷顿蛋白在RNA加工中的作用。 关于HD脑组织中基因表达改变的先前工作使用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，异常的替代性前mRNA剪接的发生越来越重要。然而，传统的基因表达技术不太适合于可变剪接模式的定量分析，并且不能很好地对稀有转录物进行采样。 从我们的初步工作的几个证据表明全球剪接异常的HD。例如，我们之前报道过microRNA miR-124在HD大脑中显著减少。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片段结合蛋白（PTBP 1）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PTBP 1 mRNA水平显著增加。此外，初步数据表明，PTBP 1调控的基因中的几个外显子在HD脑中表现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可以对转录物稳定性和蛋白质活性具有显著影响。因此，HD中的转录组改变可能超出上调和下调基因，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，以测试它们对HD表型的相关性。 这些研究联合收割机了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。将使用Davidson和Ross实验室的功能获得和丧失研究阐明这些变化的功能相关性，其中两组均具有丰富的HD模型经验。

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.