Genetic mechanism of conserved ancestral haplotype in SCA10

SCA10保守祖先单倍型的遗传机制

• 批准号: 10093170
• 负责人: TETSUO ASHIZAWA
• 金额: $ 15.91万
• 依托单位: METHODIST HOSPITAL RESEARCH INSTITUTE
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-02-01 至 2023-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10093170
• 关键词: Age; Age-Years; Alleles; American; Americas; Asian Americans; Asians; Ataxia; Biopsy; Birth; Brain; Brazil; Case-Control Studies; Cell Death; Cells; Characteristics; Clinical; Clinical Data; DNA; Data; Disease; Dissociation; Electroencephalography; Electron Microscopy; Event; Exhibits; Family; Family member; Far East; Frequencies; Gel; Gene Frequency; General Population; Genes; Genetic; Genetic Recombination; Genome; Genotype; Goals; Haplotypes; Individual; Inherited Spinocerebellar Degenerations; Interruption; Introns; Latin American; Length; Magnetic Resonance Imaging; Minor; Molecular; Morphology; Mutation; Native American Ancestry; Pathogenicity; Pathway interactions; Patients; Penetrance; Phenotype; Physiologic pulse; Play; Population; RNA; Research Design; Risk; Role; Sampling; Seeds; Single Nucleotide Polymorphism; Skin; Spinocerebellar Ataxias; Structure; Testing; Toxic effect; Transgenic Mice; Variant; base; digital; genome editing; high throughput screening; human migration; induced pluripotent stem cell; molecular phenotype; mouse model; neurobehavioral; phenotypic data; repository; sex; single molecule real time sequencing; sperm cell; transcriptome sequencing

PROJECT SUMMARY/ABSTRACT Spinocerebellar ataxia type 10 (SCA10) is a rare autosomal dominant ataxia caused by a large expansion of (ATTCT)n repeat in intron 9 of the ATXN10 gene. SCA10 exists exclusively in Latin American (LA) populations of Native American Ancestry and East Asian (EA) populations. All our SCA10 patients share a single haplotype that includes the G allele at rs41524745. The G allele has the minor allele frequency of 2- 4% in EA and LA populations but 0% elsewhere. These data suggest that the single ancestral mutation has risen on the G(+) haplotype in EA 15,000-20,000 years ago before peopling Americas. Although the distance between rs41524547 and the SCA10 repeat is long enough for multiple historical recombination events in normal populations, our SCA10 population shows no dissociation of the G allele from the SCA10 expansion. Furthermore, the G allele is located adjacent to the seed sequence of miR4762-5p. We obtained G(+) DNA from the 1000 Genomes repository and our own general population samples and tested for SCA10 expansions. We found up to 25% of these samples show SCA10 repeat expansions. Our studies further suggest that SCA10 expansions interrupted by (ATTCC)n or (ATCCT)n(ATCCC)n repeat are fully penetrant while pure (ATTCT)n expansions show reduced penetrance. Based on these observations we propose to test following hypotheses: (1) the G allele at rs41524547 predisposes the SCA10 repeat for pure (ATTCT)n repeat expansion (Type A expansion), that remains mostly non-penetrant, and (2) the (ATTCT)n-(ATTCC)n (Type B) or (ATTCT)n-(ATCCT)n-(ATCCC)n (Type C) repeat insertion into Type A expansion drives the SCA10 pathogenicity. To test these hypotheses we will aim to: Aim 1) Determine the relationship between SCA10 expansions and the G allele at rs41524547: (1a) Case-control study to document the tight association of SCA10 expansion with the G(+) haplotype. (1b) Determine repeat structures in SCA10 patients and other G(+) individuals. Aim 2) Confirm that Type B and Type C, but not Type A, expansions are fully pathogenic. (2a) Characterize phenotypes of transgenic mice expressing each of Types A, B and C expansion. (2b) Determine phenotype of Purkinje-like cells (PC) derived from iPS cells of SCA10 patients with Types A, B and C expansions. (2c) Establish penetrance rates of Type A, B and C expansions in SCA10 sibships ≥50 years of age. (2d) Obtain cross-sectional clinical data from SCA10 family members with Types A, B and C expansions. Aim 3) Determine if the G allele at rs41524547 reduces downstream recombination rates, protects against the toxicity of SCA10 RNA expansions, or promote expanded states of the SCA10 repeat: (3a) Determine the recombination rate in the rs41524547-SCA10 interval in sperm from SCA10 patients. (3b) Determine the effect of G-to-C genome editing at rs41524547 in iPSC-derived SCA10 PC.

项目摘要/摘要 脊髓脑性共济失调类型10（SCA10）是由大量扩张引起的罕见的常染色体主要共济失调 （ATTCT）N ATXN10基因的重复内含子9。 SCA10仅存在于拉丁美洲（LA）中 美国原住民血统和东亚（EA）人口的种群。我们所有的SCA10患者共享 单个单倍型，包括rs41524745的G等位基因。 G等位基因的次要等位基因频率为2- EA和LA人口中有4％，但其他地方为0％。这些数据表明单一祖传突变具有 EA 15,000-20，000年前的G（+）单倍型上升，然后在persinging美洲之前。虽然 RS41524547与SCA10重复之间的距离足够长，足以进行多个历史重组 在正常人群中，我们的SCA10人口显示G等位基因与SCA10没有分离 扩张。此外，G等位基因位于MiR4762-5p的种子序列附近。我们获得了 G（+）DNA来自1000个基因组存储库和我们自己的一般人群样本，并测试了 SCA10扩展。我们发现其中多达25％的样品显示了SCA10重复扩展。我们的研究 进一步表明SCA10扩展被（ATTCC）N或（ATCCT）N（ATCCC）N重复完全 纯净（ATTCT）n膨胀的渗透物显示出降低的外观。根据这些观察，我们 提出以下假设测试的建议：（1）rs41524547的G等位基因易感SCA10重复 纯（ATTCT）n重复扩展（A型膨胀），主要是非渗透剂，（2） （attct）n-（attcc）n（b）或（attct）n-（atcct）n-（atccc）n（cype c）重复插入A型 扩展驱动SCA10致病性。为了检验这些假设，我们将旨在： 目标1）在RS41524547上确定SCA10扩展与G等位基因之间的关系： （1a）病例对照研究，以记录SCA10扩展与G（+）单倍型的紧密关联。 （1B）确定SCA10患者和其他G（+）个体的重复结构。 AIM 2）确认B型和C型，但不是A型，扩展是完全致病的。 （2a）表征表达每种类型A，B和C膨胀的转基因小鼠的表型。 （2b）确定源自SCA10患者IPS细胞的Purkinje样细胞（PC）的表型 A，B和C扩展。 （2C）在Sca10 sibships中建立A，B和C型扩张的外观≥50岁。 （2D）从A，B型和C型扩展的SCA10家族成员那里获取横断面临床数据。 目标3）确定RS41524547的G等位基因是否降低下游重组率，保护 反对SCA10 RNA扩展的毒性，或促进SCA10重复的扩展状态： （3a）确定SCA10患者精子的RS41524547-SCA10间隔中的重组率。 （3b）确定在IPSC衍生的SCA10 PC中，G-C-C基因组编辑在RS41524547上的影响。