Assembling the Genetic Architecture of X-linked Dystonia Parkinsonism

我们将整合基因组和转录组组装使用新的方法和技术作为一个新的 对X连锁肌张力障碍-帕金森综合征（XDP）病因的数十年研究方法， 未解决的罕见疾病和疾病，特别是孤立的人群。XDP是一种神经退行性疾病 一种结合了肌张力障碍和帕金森病（PD）临床特征的疾病，其神经病理学 类似于亨廷顿病（HD）。XDP是菲律宾的土著，特别是在菲律宾的岛屿。 帕奈1991年，基因组片段建立了连锁，但因果突变尚不清楚。我们 初步研究表明，关于这种疾病的遗传结构的先前假设已经被证明是错误的。 受到传统技术的限制。在这里，我们建议强大的新基因组学工具可以解决这个长期- 通过XDP单倍型的无参考重建来识别已知的和隐藏的 序列，然后表征与推定的致病变体相关的功能性基因组改变 以及在诱导多能干细胞（iPSC）衍生的细胞中操纵这些变体的分子后果。 神经组织我们将研究XDP作为未解决的孟德尔疾病或来自孤立的 可能来自创始人单倍型的群体。我们建议确定 通过从头组装，在少数多代XDP家族中共享单倍型，然后定义 在500例XDP病例和1000例对照的大集合中，XDP区域的完整等位基因结构 以及更广泛地患有神经退行性疾病的数万人（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， 来源于一组30例XDP病例和匹配的未受影响的男性家族的神经组织 成员为了将假定的因果突变归因于这些转录特征，我们将在体外进行 用CRISPR/Cas9建模以纠正XDP先证者品系中的缺陷并将其引入未受影响的男性 兄弟系，同时对同基因菲律宾人和 高加索控制线。然后，我们将评估相关基因的后续变化，并共同评估 表达网络遵循这种扰动（目标2）。最后，我们将对基因进行全局分析， 途径和与XDP相关的网络，并将这些分子特征与其他单基因 来自可比RNAseq数据集的神经退行性疾病形式，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有的和新的分子机制。第 结论，本研究将重建XDP单倍型并鉴定所有可能的致病突变， 描述其分子后果，并获得新的见解，更常见的形式， 神经退行性疾病它还可能为孤立的人类疾病研究建立路线图 这避免了依赖于不同人群之间的单一共识人类参考。

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.