Assembling the Genetic Architecture of X-linked Dystonia Parkinsonism

组装 X 连锁肌张力障碍帕金森症的遗传结构

• 批准号: 10241557
• 负责人: David Cristopher Bragg
• 金额: $ 70.54万
• 依托单位: MASSACHUSETTS GENERAL HOSPITAL
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-09-01 至 2023-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10241557
• 关键词: Ablation; Alleles; Alternative Splicing; Architecture; Autopsy; Brain; CRISPR/Cas technology; Caucasians; Clinical; Collection; Complex; Consensus; Corpus striatum structure; DNA Sequence Alteration; Data; Data Set; Defect; Detection; Disease; Dystonia; Family; Family member; Filipino; Future; Gene Expression Profile; Genes; Genetic; Genetic Recombination; Genetic Transcription; Genome; Genomic Segment; Genomics; Genotype; Haplotypes; Human; Huntington Disease; Indigenous; Individual; Inherited; International; Island; LRRK2 gene; Lead; Link; Mediating; Mendelian disorder; Methods; Minisatellite Repeats; Molecular; Molecular Profiling; Movement Disorders; Mutation; NF-kappa B; Nerve Degeneration; Neurochip; Neurodegenerative Disorders; Neurons; Parkinson Disease; Pathogenicity; Pathology; Pathway interactions; Patients; Peripheral; Phenotype; Philippines; Population; Population Heterogeneity; Primary Lesion; Rare Diseases; Recording of previous events; Research; Retrotransposon; Short Interspersed Nucleotide Elements; Siblings; Structure; Syndrome; Target Populations; Technology; Therapeutic; Tissues; Variant; X Chromosome; X-linked dystonia parkinsonism; base; brain tissue; causal variant; disease phenotype; disorder control; functional genomics; genetic architecture; genome editing; genomic tools; human disease; in vitro Model; induced pluripotent stem cell; insight; male; member; nerve stem cell; nervous system disorder; neuropathology; novel; novel strategies; proband; reconstruction; relating to nervous system; stem cells; targeted sequencing; transcriptome; transcriptome sequencing

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.

我们将使用新方法和技术作为一种新颖的方法整合基因组和转录组组件 几十年来寻找X连锁肌张力障碍 - 帕金森主义（XDP）的方法，对 未解决的罕见疾病和特定于分离人群的疾病。 XDP是一种神经退行性 结合了肌张力障碍和帕金森氏病（PD）的临床特征的疾病，与神经病理学结合了 类似于亨廷顿氏病（HD）。 XDP是菲律宾的土著，特别是 Panay。 1991年建立了与基因组段建立的联系，但因果突变尚不清楚。我们的 初步研究表明，关于这种疾病遗传结构的先前假设已 受传统技术的限制。在这里，我们建议强大的新基因组学工具可以解决这一长期 通过XDP单倍型的无参考重建来识别已知和加密的站立问题 序列，然后表征与推定因果变体相关的功能基因组改变 以及在诱导多能干细胞（IPSC）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的典范或分离株的XDP 可能是由创始人单倍型引起的人群。我们建议确定 从头大会上的少数多代XDP家族中共享的单倍型，然后定义 XDP区域的完整等位基因架构在大量的500 XDP案例和1000个控件中 从Panay以及成千上万的神经退行性疾病的人更广泛（AIM） 1）。然后，我们将比较外围和IPSC-中与XDP单倍型相关的分子特征 来自30个XDP病例的良好表征的派生神经组织，并匹配，未受影响的男性 成员。为了将推定的因果突变归因于这些转录特征，我们将在体外执行 使用CRISPR/CAS9建模以纠正XDP概率线中的缺陷，并将其引入未受影响的男性 同级线，同时对等源性菲律宾和所有特定突变进行相同的分析和 高加索控制线。然后，我们将评估相关基因和共同基因的变化 表达网络遵循这种扰动（AIM 2）。最后，我们将对基因进行全球分析， 途径和与XDP相关的网络，并将这些分子特征与其他单基因进行比较 来自可比较的RNASEQ数据集的神经退行性疾病的形式，包括遗传的肌张力蛋白酶， LRRK2相关的PD和HD探索这些疾病中共享和新颖的分子机制。在它的 结论，这项研究将重建XDP单倍型并确定所有合理的因果突变， 表征它们的分子后果，并获得对更常见形式的新见解 神经退行性疾病。它也可能为分离株的人类疾病研究建立路线图 消除了潜水员人群中单一共识的人类参考的人群。