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

基本信息

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
项目类别：
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

项目摘要

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.

抽象的越来越明显的是，常见和罕见的遗传变异都会影响疾病的风险和严重程度综合征型自闭症谱系障碍 (ASD)。具有高渗透性 ASD 相关突变的患者身体、行为和认知缺陷的严重程度往往存在很大的异质性。然而，在任何高置信度的背景下，人类基因组的哪些区域会影响疾病的结果 ASD 突变目前未知。这种知识上的重大差距阻碍了疗法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 系来检验以下假设：常见的遗传变异决定了由 PTEN（一种高度渗透性 ASD）突变引起的过度增殖表型的严重程度相关基因。我将采用一种新颖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同一培养皿中数十个不同的细胞系，以量化由 PTEN单倍体不足。这将使我能够识别调节这种 ASD 的基因组区域相关表型，并测试是否存在性别特异性遗传效应。然后我会机械地验证与三种不同方法相关的基因座。首先，我们将扩展并验证我们基于文化的发现患有 1) 特发性自闭症并伴有大脑过度生长的患者，经纵向 MRI 和神经认知分析，来自这些细胞系是由谁产生的，2) 约 600 名具有多种 PTEN 突变的深度表型患者临床表现。其次，我们将把我们的发现与其他全基因组关联的发现联系起来研究以确定致病基因以及与其他疾病具有共同遗传风险的基因座。第三，我们将验证等基因 PTEN(+/-) 系中的相关位点，并测试针对遗传机制的假设变体保护/加剧 PTEN 突变的影响。总之，拟议的研究将确定常见的在基因定义的 ASD 亚型中，表型严重程度和患者结果的基因修饰剂。为了培养这个跨学科项目所需的专业知识，我将接受全面的培训在我的主要指导下，我从事生物信息学、统计遗传学和分子神经发育方面的研究导师贾森·斯坦。我还将接受顾问关于 iPSC 分化方法的补充培训 (Beltran)、MRI 图像分析 (Piven/Styner)、ASD 发病机制 (Piven/Zylka/Eng) 以及治疗方法关联遗传和临床数据（Stein/Piven/Eng）。他们将培训我所需的方法和原则来顺利完成这个项目。这次培训将有助于我成功过渡到独立科学生涯，我将研究神经发育障碍的基因修饰剂。