Defining the gene regulatory roles of non-coding variants in the pathogenesis of autism

定义非编码变异在自闭症发病机制中的基因调控作用

基本信息

批准号：
10537043
负责人：
Eric Alexander Sosa
金额：
$ 5.18万
依托单位：
ALBERT EINSTEIN COLLEGE OF MEDICINE
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：
2022-08-01 至 2026-07-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10537043
关键词：
ATAC-seq Address Affect Astrocytes Binding Sites Brain region Cells Child Chromatin Clustered Regularly Interspaced Short Palindromic Repeats Code Computational Biology DNA Data Databases Diagnosis Diagnostic Doctor of Philosophy Electrophysiology (science)Family Fellowship Foundations Future Gene Expression Genes Genetic Genetic Diseases Genetic Services Genetic Transcription Genome Genomic approach Genomics Goals Human Genetics Human Genome Impairment In Vitro Individual Link Location Mediating Medical Medical Genetics Membrane Potentials Mentors Minority Groups Molecular Neurodevelopmental Disorder Neuroglia Neurology Neurons Neurosciences Nucleic Acid Regulatory Sequences Outcome Parents Pathogenesis Pathogenicity Patients Phenotype Physicians Physiological Process Property Regulation Regulator Genes Regulatory Element Research Role Scientist Susceptibility Gene System Techniques Testing Time Tissues Training Transcriptional Regulation Translating Untranslated RNA Variant autism spectrum disorder autistic children base brain cell career cell type cellular engineering clinical diagnostics cohort de novo mutation disease phenotype exome genetic variant genome editing genome sequencing human disease improved in vivo individuals with autism spectrum disorder induced pluripotent stem cell insight large datasets member neuroregulation offspring pre-doctoral proband programs stem cells success synaptogenesis tool transcription factor transcriptome sequencing whole genome

项目摘要

ABSTRACT In this Predoctoral Fellowship proposal, I will be trained for a future as a physician-scientist with my own independent research program at the interface of genomics, computational biology, and neuroscience. During my MD/PhD training, I will be co-mentored by two physician-scientists, Drs. John Greally (Medical Genomics) and Pablo Castillo (Neurology), addressing a question that is timely with the imminent widespread use of whole genome sequencing (WGS) in clinical diagnostics – how do we interpret variants in the non- coding majority of the human genome when a patient presents with a medical problem? I will focus on autism, as a condition that represents a substantial proportion of patients seen by medical genetics services, for which there is extensive WGS information from thousands of families. Despite this wealth of research sequencing, only a small minority of individuals with autism receive a positive outcome of diagnostic exome or WGS. I propose that the currently limited diagnostic success rates are mostly due to our inability to interpret pathogenic variants in the non-coding majority of the genome of these patients. By improving our insights into non-coding variants, we will be able to offer diagnostic information to many more families seeking answers than currently. My strategy is to focus on de novo variants (DNVs) in offspring with autism born to unaffected parents. My hypothesis is that DNVs can be pathogenic when they occur in the cis-regulatory regions of cell types mediating autism. The project is therefore based on a computational genomics foundation, using WGS and DNV calls from large datasets from thousands of families who have a member with autism. In my preliminary data, I show that DNVs in individuals with autism are enriched at cis-regulatory loci in glial and neuronal cells in particular, and at genes known to be causative for autism. In my project, I will test these associations more rigorously, and will define a high-confidence set of DNVs for functional testing. Two types of functional testing will be performed. One will test whether the DNVs alter molecular genomic properties, including chromatin accessibility and gene expression. The second will test the physiological properties of the cells. To generate the appropriate cells for testing, I plan to use induced pluripotent stem cells (iPSCs) that are in vitro differentiated to GABAergic neurons and astrocytes. By performing CRISPR-mediated genomic editing in the iPSCs, I can generate cells with the candidate pathogenic DNVs, and test whether they have effects on cellular properties like dendritogenesis, synaptogenesis, and electrophysiology, increasing the confidence that these DNVs have pathogenic effects. I will have the privilege of getting training in sophisticated computational, stem cell and neuroscience techniques, under the guidance of two leaders in their fields, as part of a comprehensive training plan that will equip me to become the independent physician-scientist I aspire to be in my career.

抽象的在这个奖学金的奖学金提案中，我将接受我自己的身体科学家的未来培训基因组学，计算生物学和神经科学界面的独立研究计划。在我的MD/PhD培训期间，我将由两位物理科学家Drs共同征收。约翰·格雷利（John Greally）（医疗基因组学）和帕勃罗·卡斯蒂略（Pablo Castillo）（神经学在临床诊断中使用整个基因组测序（WGS） - 我们如何解释非 - 当患者出现医疗问题时，编码大多数人基因组？我将专注于自闭症，作为代表医疗看到的大部分患者的疾病遗传学服务，有成千上万个家庭的WGS信息。尽管有这些财富在研究测序中，只有少数自闭症的人获得了积极的结果诊断外显子或WGS。我建议目前有限的诊断成功率主要是由于我们的无法解释这些患者基因组的非编码大多数的致病变异。经过改善我们对非编码变体的见解，我们将能够向更多信息提供诊断信息寻求答案的家庭比目前。我的策略是专注于后代的从头变体（DNV），自闭症父母生于未受影响的父母。我的假设是DNV发生在细胞类型的顺式调节区域中时可能是致病性的调解自闭症。因此，该项目基于计算基因组基础，使用WGS和 DNV来自数千个有自闭症成员的家庭的大型数据集的呼叫。在我的初步中数据，我表明自闭症患者的DNV在神经胶质细胞和神经元细胞中的顺式调节中富含特别，并且在已知的基因上是自闭症的原因。在我的项目中，我将进一步测试这些关联严格地，将定义用于功能测试的高信心DNV。将执行两种类型的功能测试。一个人将测试DNV是否改变分子基因组特性，包括染色质访问性和基因表达。第二个将测试生理细胞的特性。为了生成适当的细胞进行测试，我计划使用诱导的多能干细胞（IPSC）在体外与GABA能神经元和星形胶质细胞区分开。通过执行CRISPR介导 IPSC中的基因组编辑，我可以使用候选病原DNV产生细胞，并测试它们是否对细胞特性，例如树突生成，突触发生和电生理学，增加对这些DNV具有致病作用的信心。我将有幸接受复杂的计算，干细胞和神经科学的培训在其领域的两名领导人的指导下，技术是一项全面的培训计划的一部分让我成为我渴望成为职业生涯的独立身体科学家。