Discovery of genetic modifiers of PTEN-ASD severity in a library of genetically diverse iPSC lines

在遗传多样性 iPSC 系库中发现 PTEN-ASD 严重程度的遗传修饰剂

• 批准号: 10571430
• 负责人: Justin Wolter
• 金额: $ 18.4万
• 依托单位: UNIV OF NORTH CAROLINA CHAPEL HILL
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-09-16 至 2023-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10571430
• 关键词: ASD patient; Address; Affect; Behavioral; Bioinformatics; Brain imaging; California; Cell Culture Techniques; Cell Differentiation process; Cell Line; Censuses; Child; Clinical; Clinical Data; Cognitive deficits; Data; Disease; Disease Outcome; Disease model; Environmental Risk Factor; Etiology; Experimental Designs; Fibrinogen; Foundations; Gene Expression; Genes; Genetic; Genetic Determinism; Genetic Predisposition to Disease; Genetic Risk; Genetic Variation; Genetic study; Genome; Genomics; Genotype; Goals; Heterogeneity; Human; Human Genome; Image Analysis; Individual; Induced Mutation; Infant; Institutes; Knowledge; Libraries; Macrocephaly; Magnetic Resonance Imaging; Measures; Mentors; Methods; Modeling; Molecular; Mutation; Neurocognitive; Neurodevelopmental Disorder; Noise; Outcome; Pathogenesis; Pathway interactions; Patient-Focused Outcomes; Patients; Phenotype; Population; Regenerative Medicine; Research; Resources; Risk; Risk Factors; Sample Size; Severities; Severity of illness; Sex Bias; Shapes; Source; Syndrome; System; Testing; Training; Validation; Variant; autism spectrum disorder; base; brain overgrowth; brain size; career; causal variant; cost effective; disorder subtype; experimental study; genetic risk factor; genetic variant; genome wide association study; genomic locus; imaging study; improved outcome; induced pluripotent stem cell; nerve stem cell; neurodevelopment; neuropsychiatry; novel; polygenic risk score; post-doctoral training; prevent; rational design; repository; response; sex; stem cell proliferation; targeted treatment; trait

ABSTRACT It is increasingly apparent that both common and rare genetic variation influences the risk and severity of syndromic autism spectrum disorders (ASD). Among patients with highly penetrant ASD associated mutations there is often substantial heterogeneity in the severity of physical, behavioral, and cognitive deficits. However, precisely which regions of the human genome affect disease outcomes in the context of any high confidence ASD mutation are currently unknown. This critical gap in knowledge prevents the rational design of therapies that target underlying molecular and cellular deficiencies. Here, I will leverage genetically diverse iPSC lines to test the hypothesis that common genetic variation shapes the severity of hyperproliferation phenotypes caused by mutations in PTEN, a highly penetrant ASD associated gene. I will employ a novel pooled cell culture method, which allows rapid and efficient phenotyping of dozens of distinct lines in the same culture dish, to quantify the variation in hyperproliferation induced by PTEN haploinsufficiency. This will allow me to identify regions of the genome which modulate this ASD relevant phenotype, and test for the presence of sex specific genetic effects. I will then mechanistically validate associated loci with three distinct approaches. First, we will expand and validate our culture-based findings in patients with 1) idiopathic autism with brain overgrowth with longitudinal MRI and neurocognitive profiling, from whom these lines were generated, 2) ~600 deeply phenotyped patients with a variety of PTEN mutations and clinical presentations. Second, we will correlate our findings with those from other genome wide association studies to identify causal genes, and loci with shared genetic risk with other diseases. Third, we will validate associated loci in isogenic PTEN(+/-) lines, and test hypotheses aimed at the mechanisms by which genetic variants protect/exacerbate the effects of PTEN mutations. In all, the proposed studies will identify common genetic modifiers of phenotypic severity and patient outcomes in a genetically defined ASD subtype. To develop the expertise necessary for this cross-disciplinary project, I will undergo comprehensive training in bioinformatics, statistical genetics, and molecular neurodevelopment under the guidance of my primary mentor Jason Stein. I will also undergo supplemental training from my advisors in iPSC differentiation methods (Beltran), MRI image analysis (Piven/Styner), ASD pathogenesis (Piven/Zylka/Eng), and approaches to correlate genetic and clinical data (Stein/Piven/Eng). They will train me in the methods and principles required to successfully complete this project. This training will facilitate a successfully transition into my independent scientific career, where I will study genetic modifiers of neurodevelopmental disorders.

摘要 越来越明显的是，常见和罕见的遗传变异都影响着疾病的风险和严重程度。 综合征型自闭症谱系障碍（ASD）。在具有高渗透性ASD相关突变的患者中， 在身体、行为和认知缺陷的严重程度上常常存在实质上的异质性。然而，在这方面， 人类基因组的哪些区域在任何高置信度的背景下影响疾病结果 ASD突变目前尚不清楚。这一知识上的关键差距阻碍了治疗的合理设计 针对潜在的分子和细胞缺陷。 在这里，我将利用遗传多样性的iPSC系来检验共同的遗传变异 形成了由PTEN突变引起的过度增殖表型的严重程度， 相关基因我将采用一种新的混合细胞培养方法，该方法可以快速有效地进行表型分析 在同一个培养皿中的几十个不同的线，以量化的变化，在过度增殖诱导 PTEN单倍不足。这将使我能够确定基因组中调节ASD的区域 相关表型，并测试性别特异性遗传效应的存在。然后我将机械地验证 与三种不同方法相关的基因座。首先，我们将扩展和验证我们基于文化的发现， 患有1）具有纵向MRI和神经认知特征的脑过度生长的特发性自闭症患者， 2）约600名具有各种PTEN突变的深度表型化患者， 临床表现。第二，我们将把我们的发现与其他基因组广泛关联的发现相关联， 研究确定致病基因和与其他疾病具有共同遗传风险的基因位点。第三，我们将验证 相关基因座在等基因PTEN（+/-）线，并测试假设，旨在机制，遗传 突变保护/加剧了PTEN突变的影响。总之，拟议的研究将确定共同的 在遗传学定义的ASD亚型中，表型严重程度和患者结局的遗传修饰剂。 为了发展这个跨学科项目所需的专业知识，我将接受全面的培训 在生物信息学，统计遗传学和分子神经发育的指导下，我的主要 我的导师杰森·斯坦我还将接受我的顾问在iPSC分化方法方面的补充培训 （Beltran），MRI图像分析（Piven/Styner），ASD发病机制（Piven/Zylka/Eng），以及 将遗传和临床数据相关联（Stein/Piven/Eng）。他们将训练我所需的方法和原则 成功完成这个项目。这次培训将有助于我成功地过渡到独立工作。 科学生涯，在那里我将研究神经发育障碍的遗传修饰剂。