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.

项目概要/摘要 脊髓小脑性共济失调 10 型 (SCA10) 是一种罕见的常染色体显性共济失调，由脊髓小脑大量扩张引起 (ATTCT)n 重复位于 ATXN10 基因的内含子 9 中，仅存在于拉丁美洲 (LA)。 美洲原住民血统和东亚 (EA) 人群我们所有的 SCA10 患者都有一个共同点。 包含 rs41524745 处 G 等位基因的单一单倍型 G 等位基因的次要等位基因频率为 2-。 EA 和 LA 人群中为 4%，但其他地区为 0%。这些数据表明单一祖先突变存在。 15,000-20,000 年前，在美洲出现之前，G(+) 单倍型就在 EA 中出现。 rs41524547和SCA10重复之间的距离足够长以进行多次历史重组 在正常人群中发生的事件中，我们的 SCA10 人群没有显示 G 等位基因与 SCA10 的分离 此外，G 等位基因位于 miR4762-5p 的种子序列附近。 来自 1000 个基因组存储库和我们自己的一般人群样本的 G(+) DNA 并进行了测试 我们的研究发现，高达 25% 的样本显示 SCA10 重复扩增。 进一步表明，被 (ATTCC)n 或 (ATCCT)n(ATCCC)n 重复中断的 SCA10 扩展是完全 渗透性而纯 (ATTCT)n 扩展显示渗透性降低。根据这些观察，我们。 建议测试以下假设：（1）rs41524547 处的 G 等位基因倾向于 SCA10 重复 纯 (ATTCT)n 重复扩展（A 型扩展），大部分仍为非渗透性，以及 (2) (ATTCT)n-(ATTCC)n（B 型）或 (ATTCT)n-(ATCCT)n-(ATCCC)n（C 型）重复插入 A 型 为了检验这些假设，我们的目标是： 目标 1) 确定 SCA10 扩展与 rs41524547 处的 G 等位基因之间的关系： (1a) 病例对照研究，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。 目标 2) 确认 B 型和 C 型（而非 A 型）扩展具有完全致病性。 (2a) 表征表达 A、B 和 C 型扩增的转基因小鼠的表型。 (2b) 确定源自 SCA10 型患者 iPS 细胞的浦肯野样细胞 (PC) 的表型 A、B 和 C 扩展。 (2c) 确定年龄≥50 岁的 SCA10 同胞中 A、B 和 C 型扩展的外显率。 (2d) 从具有 A、B 和 C 型扩展的 SCA10 家族成员获得横断面临床数据。 目标 3) 确定 rs41524547 处的 G 等位基因是否会降低下游重组率、保护 对抗 SCA10 RNA 扩增的毒性，或促进 SCA10 重复的扩增状态： (3a)确定SCA10患者精子中rs41524547-SCA10间隔的重组率。 (3b) 确定 iPSC 衍生的 SCA10 PC 中 rs41524547 处的 G 到 C 基因组编辑的效果。