Gene-Environment interactions in Autism

自闭症的基因与环境相互作用

• 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
• 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

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.

摘要 自闭症谱系障碍(ASD)是一组以社交障碍为特征的神经发育疾病 相互作用、重复或限制性行为，以及沟通困难。ASD非常普遍， 在美国，每54名儿童中就有一名受到影响。全基因组和外显子组测序研究确定192个高 自信ASD相关基因，其中许多在大脑中的不同细胞系中早期表达 皮质发育，包括神经前体细胞、未成熟和成熟神经元以及神经胶质细胞。此外, Gwas的研究表明，存在导致ASD表型的非编码基因组变异。 小鼠暴露于环境中的化学物质，包括双酚A(BPA)，会导致类似ASD的疾病 表型，大脑皮层细胞成分的变化，以及结合的变化 ASD相关基因中的转录因子(TF)。基于这些观察结果，我们假设 序列变异存在于不同个体的非编码基因组中，当改变调控时 序列，可能会影响转录因子与其目标位置的相互作用，以响应环境化学品。 在携带特定序列变异的个体中，表型效应可能很弱或检测不到，但 暴露在环境化学品中可能会放大这些变种对其与转铁蛋白和 接下来的表型。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自闭症患者。这些IPSC将被用来增长 大脑皮质类器官，在分化过程中会在不同的时间暴露于BPA 改变不同细胞类型的神经谱系的基因表达。单核(SN)RNA序列和SnATAC- SEQ将被用来分析在特定细胞群体中的转铁蛋白的占有率和基因表达 双酚A存在或不存在时脑器官的分化。这将使我们能够监测 双酚A对不同神经细胞系分化途径和相对比例的影响。然后我们将确定 不同IPSCs产生的脑器官中BPA反应ATAC-SEQ峰的差异 与ASD相关的细胞分化和基因表达表型。我们预计这些差额 ATAC-SEQ峰对应于不同IPSC品系的调控序列中存在的序列变体 影响与ASD相关的特定基因的表达。这将使用大规模并行报告程序进行测试 与受影响的细胞类型和脑器官相对应的细胞系中的分析(MPRA)。的作用 基因表达中的特定SNPs将使用单碱基无疤痕基因组编辑进行进一步测试。最后， 这些对BPA有反应的SNP对自闭症表型的可能贡献将通过执行 ASD患者死后脑标本中的SnATAC-seq。这些结果将填补我们在 了解基因组变异对化学物质的基本原理。 环境影响神经细胞的谱系承诺，并引发ASD症状。