Gene-Environment interactions in Autism

自闭症的基因与环境相互作用

基本信息

批准号：
10552617
负责人：
Victor G. Corces
金额：
$ 61.1万
依托单位：
EMORY UNIVERSITY
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：
2022-01-20 至 2026-11-30
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10552617
关键词：
ASD patient ATAC-seq Affect Age Air Alleles Autopsy Bar Codes Behavior Behavioral Binding Biological Assay Blood Brain Brain region Cell Differentiation process Cell Line Cell Lineage Cells Cerebral cortex Cerebrovascular system Cerebrum Chemicals Child Chromatin Chronic Disease Code Collection Communication Cosmetics Dendritic Spines Dependence Development Diagnosis Disease Endocrine Disruptors Environment Exposure to Family Female Fetal Development Food Gene Expression Genes Genome Goals Growth Heart Diseases Household Products Human Impairment Incidence Individual Knowledge Laboratory Animals Malignant neoplasm of testis Monitor Mus Mutation Neurodevelopmental Disorder Neuroglia Neurons Nuclear Hormone Receptors Nucleic Acid Regulatory Sequences Obesity Organoids Paper Pathway interactions Patients Penetrance Phenotype Plastics Population Process Race Reporter Research Risk Role Sampling Site Social Interaction Societies Symptoms Testing Time Untranslated RNA Urine Variant Water autism spectrum disorder autistic children base bisphenol A brain tissue building materials cell type combinatorial density environmental chemical exome sequencing experimental study exposed human population gene environment interaction genome editing genome sequencing genome wide association study genome-wide gray matter induced pluripotent stem cell malignant breast neoplasm nerve stem cell neural novel pregnant programs protein function response sex single nucleus RNA-sequencing social communication social integration transcription factor white matter whole genome

项目摘要

ABSTRACT Autism spectrum disorder (ASD) is group of neurodevelopmental conditions characterized by impaired social interactions, repetitive or restrictive behaviors, and difficulties with communication. ASD is highly prevalent, affecting 1 in 54 children in the US. Whole genome and exome sequencing studies identified 192 high confidence ASD-associated genes, many of which are expressed early in various cell lineages during brain cortex development, including neural progenitors, immature and maturing neurons, and glial cells. In addition, GWAS studies suggest the existence of non-coding genome variants that contribute to ASD phenotypes. Exposure of mice to chemicals present in the environment, including bisphenol A (BPA), result in ASD-like phenotypes, alterations in the cellular composition of the brain cortex, and changes in the binding of transcription factors (TFs) in genes implicated in ASD. Based on these observations we hypothesize that sequence variants present in the non-coding genome of different individuals, when altering regulatory sequences, may influence the interaction of TFs with their target sites in response to environmental chemicals. Phenotypic effects may be weak or undetectable in individuals carrying specific sequence variants but exposure to environmental chemicals may amplify the effect of these variants on their interaction with TFs and the ensuing phenotypes. To test these hypotheses, we propose to use a collection of iPSCs obtained from normal and ASD individuals from different sex, age, and racial backgrounds. These iPSCs will be used to grow cerebral cortical organoids, which will be exposed to BPA at different times during the differentiation process to alter gene expression in different cell types of neural lineages. Single nucleus (sn) RNA-seq and snATAC- seq will be employed to analyze TF occupancy and gene expression in specific cell populations during the differentiation of brain organoids in the presence or absence of BPA. This will allow us to monitor the effect of BPA on differentiation pathways and relative ratios of different neural cell lineages. We will then identify differential BPA-responsive ATAC-seq peaks among brain organoids arising from different iPSCs that correlate with cellular differentiation and gene expression phenotypes related to ASD. We expect that these differential ATAC-seq peaks will correspond to sequence variants present in regulatory sequences of different iPSC lines that affect the expression of specific genes involved in ASD. This will be tested using massively parallel reporter assays (MPRAs) in cell lines corresponding to the affected cell type, and cerebral organoids. The role of specific SNPs in gene expression will be further tested using single-base scarless genome editing. Finally, the possible contribution of these BPA-responsive SNPs to autism phenotypes will be analyzed by performing snATAC-seq in post-mortem brain samples from ASD patients. These results will fill an important gap in our knowledge of the fundamental principles by which genome variants can respond to chemicals present in the environment to affect lineage commitment of neural cells and elicit ASD symptoms.

抽象的自闭症谱系障碍 (ASD) 是一组以社交能力受损为特征的神经发育疾病互动、重复或限制性行为以及沟通困难。 ASD 非常普遍，影响美国五分之一的儿童。全基因组和外显子组测序研究确定了 192 个高信心 ASD 相关基因，其中许多在大脑发育过程的早期各种细胞谱系中表达皮质发育，包括神经祖细胞、未成熟和成熟神经元以及神经胶质细胞。此外， GWAS 研究表明，存在导致 ASD 表型的非编码基因组变异。小鼠暴露于环境中存在的化学物质（包括双酚 A (BPA)）会导致类似自闭症谱系障碍 (ASD) 表型、大脑皮层细胞组成的改变以及结合的变化与 ASD 相关的基因中的转录因子 (TF)。根据这些观察，我们假设当改变监管时，不同个体的非编码基因组中存在序列变异序列，可能会影响转录因子与其靶位点响应环境化学物质的相互作用。在携带特定序列变异的个体中，表型效应可能很弱或无法检测到，但暴露于环境化学物质可能会放大这些变体与转录因子相互作用的影响随后的表型。为了检验这些假设，我们建议使用从以下来源获得的 iPSC 集合：来自不同性别、年龄和种族背景的正常人和 ASD 个体。这些 iPSC 将用于生长大脑皮质类器官，在分化过程中的不同时间会接触BPA 改变神经谱系不同细胞类型的基因表达。单核 (sn) RNA-seq 和 snATAC- seq将用于分析特定细胞群中的TF占据和基因表达在存在或不存在 BPA 的情况下大脑类器官的分化。这将使我们能够监控效果 BPA 对不同神经细胞谱系的分化途径和相对比率的影响。然后我们将识别不同 iPSC 产生的脑类器官之间 BPA 响应 ATAC-seq 峰的差异与 ASD 相关的细胞分化和基因表达表型。我们预计这些差异 ATAC-seq 峰将对应于不同 iPSC 系调控序列中存在的序列变异影响 ASD 相关特定基因的表达。这将使用大规模并行报告器进行测试在与受影响的细胞类型相对应的细胞系和脑类器官中进行分析（MPRA）。的作用基因表达中的特定 SNP 将使用单碱基无痕基因组编辑进一步测试。最后，将通过执行以下操作来分析这些 BPA 响应 SNP 对自闭症表型的可能贡献自闭症谱系障碍 (ASD) 患者死后大脑样本中的 snATAC-seq。这些结果将填补我们的一个重要空白了解基因组变异对存在于体内的化学物质作出反应的基本原理影响神经细胞谱系定型并引发 ASD 症状的环境。