Identification of Genetic and Molecular Bases of Derived Phenotypes in Primate Brain Development

灵长类动物大脑发育中衍生表型的遗传和分子基础的鉴定

• 批准号: 10841947
• 负责人: NENAD SESTAN
• 金额: $ 36.45万
• 依托单位: YALE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-05-16 至 2024-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10841947
• 关键词: ATAC-seq; Affect; Atlases; Automobile Driving; Autopsy; Biological Assay; Biology; Brain; Brain Diseases; CRISPR/Cas technology; Cataloging; Catalogs; Cell Differentiation process; Cell Nucleus; Cells; Cerebral cortex; Chromatin; Coculture Techniques; Cognition; Collection; Complement; Complex; Data; Development; Disease; Electroporation; Epigenetic Process; Episodic memory; Ethics; Evolution; Exhibits; Fetal Development; Fibroblasts; Freezing; Gene Expression; Gene Expression Profile; Gene Expression Profiling; Genes; Genetic; Genetic Variation; Genome; Genomics; Gorilla gorilla; Grant; Hominidae; Human; Individual; Knowledge; Language; Macaca; Methods; Molecular; Mus; Neonatal; Neuroanatomy; Nucleotides; Organ; Organoids; Pan Genus; Phenotype; Phylogenetic Analysis; Pongidae; Pongo pygmaeus; Population; Prefrontal Cortex; Primates; Regulatory Element; Reporter; Research; Resources; Single Nucleotide Polymorphism; Social Behavior; Specificity; Surveys; Taxonomy; Thinking; Tissues; Variant; base; cell type; cognitive ability; comparative; epigenetic regulation; epigenomics; experimental study; fetal; functional genomics; genetic variant; genome editing; genome resource; genomic variation; in utero; in vivo; induced pluripotent stem cell; infancy; insertion/deletion mutation; lymphoblastoid cell line; molecular phenotype; mouse model; multimodal data; nanopore; neglect; neurodevelopment; neuropsychiatric disorder; nonhuman primate; rare variant; single cell technology; single nucleus RNA-sequencing; species difference; stem cell model; stem cells; syntax; tool; transcriptome; transcriptomics; whole genome; ATAC-seq; Affect; Atlases; Automobile Driving; Autopsy; Biological Assay; Biology; Brain; Brain Diseases; CRISPR/Cas technology; Cataloging; Catalogs; Cell Differentiation process; Cell Nucleus; Cells; Cerebral cortex; Chromatin; Coculture Techniques; Cognition; Collection; Complement; Complex; Data; Development; Disease; Electroporation; Epigenetic Process; Episodic memory; Ethics; Evolution; Exhibits; Fetal Development; Fibroblasts; Freezing; Gene Expression; Gene Expression Profile; Gene Expression Profiling; Genes; Genetic; Genetic Variation; Genome; Genomics; Gorilla gorilla; Grant; Hominidae; Human; Individual; Knowledge; Language; Macaca; Methods; Molecular; Mus; Neonatal; Neuroanatomy; Nucleotides; Organ; Organoids; Pan Genus; Phenotype; Phylogenetic Analysis; Pongidae; Pongo pygmaeus; Population; Prefrontal Cortex; Primates; Regulatory Element; Reporter; Research; Resources; Single Nucleotide Polymorphism; Social Behavior; Specificity; Surveys; Taxonomy; Thinking; Tissues; Variant; base; cell type; cognitive ability; comparative; epigenetic regulation; epigenomics; experimental study; fetal; functional genomics; genetic variant; genome editing; genome resource; genomic variation; in utero; in vivo; induced pluripotent stem cell; infancy; insertion/deletion mutation; lymphoblastoid cell line; molecular phenotype; mouse model; multimodal data; nanopore; neglect; neurodevelopment; neuropsychiatric disorder; nonhuman primate; rare variant; single cell technology; single nucleus RNA-sequencing; species difference; stem cell model; stem cells; syntax; tool; transcriptome; transcriptomics; whole genome

PROJECT SUMMARY (from original grant) Increasingly persuasive evidence suggests genomic variants driving derived features in humans and among primates are enriched in regulatory elements, but the vast majority of these evolutionarily relevant variants have yet to be discovered or characterized. This is unfortunate, as among the approximately 35 million single nucleotide substitutions (SNPs), 5 million insertions or deletions (indels), and 90 megabases of structural variants where the human and chimpanzee genomes differ are countless variants associated with development, function, or disease. Identifying evolutionarily relevant genetic variants, as well as those implicated in disease or function, can be guided by the analysis of species differences in intermediate molecular phenotypes (e.g., transcriptomic and epigenomic signatures), which are most likely the primary effects determined by genomic variation. In this proposal, we propose to perform primate comparative functional genomics to uncover genetic variants explaining lineage-specific phenotypes affecting the human and non-human primate (NHP) brain, an organ exhibiting pronounced molecular and functional differences between species. To do so, in our first aim we will develop a taxonomy of gene expression and open chromatin across primates, applying single nucleus RNA-seq and single nucleus ATAC-seq to study the mid- fetal and neonatal (late fetal and early infancy) development of the post-mortem human and NHP brain, as well as brain organoid co-cultures containing cells differentiated from multiple primate stem cells and fibroblasts and lymphoblastoid cell lines. In our second aim, we will complement this atlas of species differences in gene expression and open chromatin by cataloguing SNPs, indels, and large, complex structural variants in multiple primate species. This will allow us to differentiate between lineage-specific (i.e., human versus chimpanzee and macaque) and Hominidae-specific (i.e., human and chimpanzee versus macaque) genomic variants. Finally, in our third aim we will integrate and functionally validate, using the Massively Parallel Reporter Assay, CRISPR/Cas9 genome editing, human induced pluripotent stem cells, and mouse models of neural development, key regulatory elements and de novo genes identified through these experiments. Through these aims, we will identify and functionally validate genomic variants and patterns of gene expression and open chromatin potentially driving derived phenotypes in the human and non-human brain and consequently plausibly associated with human cognition, social behaviour, and neuropsychiatric disease.

项目摘要（来自原始赠款） 越来越有说服力的证据表明，基因组变体驱动人类和中间的特征 灵长类动物丰富在监管元素中，但是这些进化上相关的绝大多数 尚未发现或表征。这是不幸的，因为在大约3500万单曲中 核苷酸取代（SNP），500万插入或缺失（Indels）和90兆瓦的结构 人类和黑猩猩基因组不同的变体与无数的变体相关 发展，功能或疾病。识别进化相关的遗传变异以及那些 与疾病或功能有关，可以通过分析中间物种差异来指导 分子表型（例如，转录组和表观基因组特征），很可能是主要的 通过基因组变异确定的效果。在此提案中，我们建议进行灵长类动物比较 功能性基因组学发现遗传变异解释了影响人类的谱系特异性表型 和非人类灵长类动物（NHP）大脑，一种具有明显分子和功能差异的器官 物种之间。为此，在我们的第一个目标中，我们将开发基因表达和开放染色质的分类法 跨灵长类 新生儿（胎儿晚期和婴儿早期）的发育后人类和NHP大脑以及大脑 含有多个灵长类动物干细胞和成纤维细胞和成纤维细胞和成纤维细胞的细胞培养物和培养 淋巴母细胞系。在我们的第二个目标中，我们将补充基因物种差异的地图集 通过对多个的SNP，Indels和大型复杂结构变体进行表达和开放染色质 灵长类动物。这将使我们能够区分谱系特异性（即人与黑猩猩和 猕猴）和hominidae特异性（即人和黑猩猩与猕猴）基因组变体。最后，在 我们的第三个目标我们将使用大规模并行的记者测定法进行整合并在功能上验证 CRISPR/CAS9基因组编辑，人类诱导的多能干细胞和神经的小鼠模型 通过这些实验确定的开发，关键调节元素和从头基因。通过这些 目的，我们将识别并在功能上验证基因表达和开放的基因组变异和模式 染色质可能会在人和非人类大脑中驱动衍生的表型，因此 与人类认知，社会行为和神经精神疾病有可能相关。