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.

项目总结/摘要 脊髓小脑性共济失调10型（SCA 10）是一种罕见的常染色体显性共济失调，由大量扩增的 ATXN 10基因内含子9中的（ATTCT）n重复序列。SCA 10仅在拉丁美洲（LA）存在 美洲原住民和东亚（EA）人口。我们所有的SCA 10患者都有一个 包括rs 41524745处的G等位基因的单个单倍型。G等位基因的次要等位基因频率为2- 100%。 在EA和LA人群中为4%，但在其他地方为0%。这些数据表明，单一的祖先突变 早在15，000 - 20，000年前，在人类进入美洲之前，就已经出现在EA的G（+）单倍型上。虽然 rs 41524547和SCA 10重复序列之间的距离足够长，可以进行多次历史重组 在正常人群中，我们的SCA 10人群没有显示G等位基因与SCA 10分离。 扩张.此外，G等位基因位于miR 4762 - 5 p的种子序列附近。我们获得 G（+）DNA来自1000个基因组储存库和我们自己的一般人群样本，并进行了测试， SCA 10扩展。我们发现这些样本中高达25%显示SCA 10重复扩增。我们的研究 进一步表明，SCA 10扩增中断（ATTCC）n或（ATCCT）n（ATCCC）n重复完全 渗透而纯（ATTCT）n扩展显示出降低的渗透率。根据这些观察，我们 本文拟验证以下假设：（1）rs 41524547的G等位基因倾向于SCA 10重复， 纯（ATTCT）n重复膨胀（A型膨胀），其保持大部分非渗透性，以及（2） （ATTCT）n-（ATTCC）n（B型）或（ATTCT）n-（ATCCT）n-（ATCCC）n（C型）重复插入A型 扩展驱动SCA 10致病性。为了验证这些假设，我们将致力于： 目的1）确定SCA 10扩增与rs 41524547处的G等位基因之间的关系： (1a)病例对照研究，以记录SCA 10扩增与G（+）单倍型的紧密关联。 (1b)确定SCA 10患者和其他G（+）个体的重复结构。 目的2）确认B型和C型（而不是A型）扩张是完全致病的。 (2a)表征表达A、B和C型扩增的转基因小鼠的表型。 (2b)确定来源于SCA 10患者iPS细胞的浦肯野样细胞（PC）的表型， A、B和C展开。 (2c)在≥50岁的SCA 10同胞中确定A、B和C型扩增的检出率。 (2d)从具有A、B和C型扩增的SCA 10家族成员中获得横断面临床数据。 目的3）确定rs 41524547处的G等位基因是否降低下游重组率， 对抗SCA 10 RNA扩增的毒性，或促进SCA 10重复的扩增状态： (3a)确定SCA 10患者精子中rs 41524547-SCA 10区间的重组率。 (3b)确定iPSC衍生的SCA 10 PC中rs 41524547处的G至C基因组编辑的影响。