Assembling the Genetic Architecture of X-linked Dystonia Parkinsonism

我们将使用新的方法和技术将基因组和转录组组装整合为一种新的 对数十年来寻找X连锁肌张力障碍-帕金森综合征(XDP)病因的方法，及其对 未解决的罕见疾病和疾病，这些疾病是孤立人群特有的。XDP是一种神经退行性疾病 这种疾病结合了肌张力障碍和帕金森病(PD)的临床特征，并具有 类似亨廷顿病(HD)。XDP是菲律宾的土生土长的，特别是 帕奈。1991年建立了与基因组片段的联系，但原因突变尚不清楚。我们的 初步研究表明，先前关于这种疾病的遗传结构的假设是 受传统技术的限制。在这里，我们提出强大的新基因组学工具可以解决这一长期- 通过XDP单倍型的无参考重构来识别已知和神秘的存在的问题 序列，然后描述与推测的因果变异相关的功能性基因组改变 在诱导多能干细胞(IPSC)中操纵这些变异的分子后果 神经组织。我们将研究XDP作为未解决的孟德尔疾病的样本或来自 可能来自创始人单倍型的群体。我们建议确定准确的序列 通过重新组装少数多代XDP家族中的共享单倍型，然后定义 500例XDP病例和1000例对照中XDP区域的完整等位基因架构 来自Panay，以及更广泛的数万名患有神经退行性疾病的个人(Aim 1)。然后，我们将比较外周和IPSC中与XDP单倍型相关的分子特征。 来自一组特征良好的XDP患者和匹配的未受影响的男性家庭的神经组织 会员。为了将推测的因果突变归因于这些转录信号，我们将在体外进行 用CRISPR/CAS9建模纠正XDP先证系缺陷并将其引入未患病男性 兄弟姐妹系，同时对同一基因的菲律宾人和 高加索控制线。然后我们将评估相关基因的后续变化，并共同- 这种扰动之后的表达网络(目标2)。最后，我们将对基因进行全球分析， 与XDP相关的通路和网络，并将这些分子特征与其他单基因进行比较 来自可比的RNAseq数据集的神经退行性疾病的形式，包括遗传性肌张力障碍， LRRK2相关的PD和HD，以探索这些疾病中共同的和新的分子机制。在ITS 结论，本研究将重建XDP单倍型，并确定所有可能的原因突变， 描述它们的分子后果，并对更常见的形式得出新的见解 神经退行性疾病。它还可能为人类疾病研究建立一个路线图 消除对不同人群中单一共识人类参照的依赖。

We will integrate genome and transcriptome assemblies using new methods and technologies as a novel approach to the decades-old search for cause of X-linked dystonia-parkinsonism (XDP), with implications for unsolved rare disorders and diseases that are specific to isolate populations. XDP is a neurodegenerative disease that combines clinical features of dystonia and Parkinson’s disease (PD), with a neuropathology that resembles Huntington’s disease (HD). XDP is indigenous to the Philippines, and specifically to the island of Panay. Linkage was established to a genomic segment in 1991, yet the causal mutation is unknown. Our Preliminary Studies suggest that prior assumptions about the genetic architecture of this disorder have been limited by conventional technologies. Here, we propose that powerful new genomics tools can solve this long- standing problem through reference-free reconstruction of the XDP haplotype to identify known and cryptic sequences, then to characterize the functional genomic alterations associated with the putative causal variants and the molecular consequences of manipulating those variants in induced pluripotent stem cell (iPSC) derived neural tissues. We will investigate XDP as an exemplar of unsolved Mendelian disorders or those from isolate populations that have likely arisen from a founder haplotype. We propose to determine the exact sequence of the shared haplotype in a small number of multigenerational XDP families by de novo assembly, then to define the complete allelic architecture of the XDP region in a large collection of 500 XDP cases and 1000 controls from Panay, as well as tens of thousands of individuals with neurodegenerative conditions more broadly (Aim 1). We will then compare molecular signatures associated with the XDP haplotype in peripheral and iPSC- derived neural tissue from a well characterized group of 30 XDP cases and matched, unaffected male family members. To attribute the putative causal mutation to these transcriptional signatures, we will perform in vitro modeling with CRISPR/Cas9 to correct the defect in XDP proband lines and introduce it into unaffected male sibling lines, while performing the same analyses for all specific mutations in an isogenic Filipino and Caucasian control lines. We will then evaluate consequent changes to the associated genes and co- expression networks following this perturbation (Aim 2). Finally, we will perform global analyses of genes, pathways, and networks associated with XDP and compare these molecular signatures to other monogenic forms of neurodegenerative disorders from comparable RNAseq datasets, including inherited dystonias, LRRK2-associated PD, and HD, to explore shared and novel molecular mechanisms in these disorders. At its conclusion, this study will reconstruct the XDP haplotype and identify all plausible causal mutations, characterize their molecular consequences, and derive new insights into more common forms of neurodegenerative disorders. It may also establish a roadmap for human disease research in isolate populations that obviates reliance on a single consensus human reference among diverse populations.