Developing cell type-specific enhancers and connectivity mapping pipelines for marmosets

开发狨猴的细胞类型特异性增强剂和连接映射管道

基本信息

批准号：
10271630
负责人：
Guoping Feng
金额：
$ 151.94万
依托单位：
MASSACHUSETTS INSTITUTE OF TECHNOLOGY
依托单位国家：
美国
项目类别：
财政年份：
2021
资助国家：
美国
起止时间：
2021-09-01 至 2024-06-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10271630
关键词：
ATAC-seq Affect Antibodies Area Atlases Automobile Driving Bar Codes Brain Brain Diseases CRISPR/Cas technology Callithrix Callithrix jacchus jacchus Cell Nucleus Cells Cercopithecidae Chromatin Communities Corpus striatum structure DNA Sequence Data Data Analytics Data Set Development Disease model Enhancers Gene Expression Profile Genes Genetic Genetic Engineering Genetic Enhancer Element Genetic Models Genetic Research Human Human Genetics Injections Late-Onset Disorder Longevity Macaca Maps Mediating Methods Modeling Mus Neurons Neurosciences Neurosciences Research Output Phase Phylogenetic Analysis Physiology Primates Reproduction Rodent Rodent Model Small Nuclear RNA Specificity Structure Study models Testing Thalamic structure Virus Work analytical tool brain cell cell type cognitive function comparative computational pipelines cost improved in vivo multimodality nonhuman primate novel promoter single-cell RNA sequencing tool transcriptome sequencing transcriptomics

项目摘要

PROJECT SUMMARY Although genetic tools have dramatically advanced our understanding of brain function, they have largely been confined to mice. While mice are essential models for many areas of neuroscience, there are also many aspects of higher brain function that cannot be adequately modeled in rodents. Similarly, many brain disorders affect higher cognitive functions that have no clear parallels in rodents. Furthermore, recent large- scale single cell transcriptomic analyses have revealed many neuron types, connections and gene expression patterns that are unique to primates. Thus, there is an urgent need for new genetic models that have brain structure and function closer to humans. Non-human primates (NHP) are much more closely related to humans than are rodents, and this is reflected in their brain development, structure and physiology. Hence, it is increasingly recognized that they provide an attractive model to study higher brain function and brain disorders. A promising emerging NHP model is the common marmoset, a small new world primate that has many advantages for neuroscience and genetic research. However, lack of tools with cell type specificity has been a major obstacle in advancing structural and functional studies in NHP. With the combined single cell RNA-seq and single cell ATAC-seq, it is now possible to nominate short cell type-specific enhancer sequences. If validated, these enhancers will provide an effective tool to map connectivity and interrogate function using virus mediated expression. The difficulty lies in the identification of functional enhancers from the hundreds or thousands of nominated potential enhancer sequences in NHP. Here we propose (1) to use a novel high throughput in vivo approach to identify functional enhancers, and (2) to establish a whole-brain circuit mapping pipeline for use striatal circuitry to validate our approach for cell type-specific connectivity mapping in marmosets. When completed, these studies will provide much needed essential tools, methods and computational pipelines for cell type-specific mapping and functional interrogation of the marmoset brain in healthy and disease models.

项目概要尽管遗传工具极大地促进了我们对大脑功能的理解，但它们很大程度上仅限于小鼠。虽然小鼠是神经科学许多领域的重要模型，但也有高级大脑功能的许多方面无法在啮齿类动物中充分建模。同样，很多大脑疾病会影响较高的认知功能，而这在啮齿类动物中没有明显的相似之处。此外，最近的大规模单细胞转录组分析揭示了许多神经元类型、连接和基因表达灵长类动物独有的图案。因此，迫切需要具有大脑功能的新遗传模型结构和功能更接近人类。非人类灵长类动物（NHP）与人类的关系更为密切与啮齿类动物相比，这反映在它们的大脑发育、结构和生理机能上。因此，它是人们越来越认识到它们为研究高级大脑功能和大脑疾病提供了一个有吸引力的模型。一种有前途的新兴 NHP 模型是普通狨猴，它是一种小型新世界灵长类动物，具有许多特征神经科学和遗传学研究的优势。然而，缺乏具有细胞类型特异性的工具一直是一个问题推进 NHP 结构和功能研究的主要障碍。结合单细胞 RNA-seq 和单细胞 ATAC-seq，现在可以指定短细胞类型特异性增强子序列。如果经过验证，这些增强器将提供一个有效的工具来映射连接和询问功能病毒介导的表达。困难在于从数百个或多个功能增强子中识别出功能增强子。 NHP 中数千个指定的潜在增强子序列。在这里我们建议（1）使用一种新颖的高体内吞吐量方法来识别功能增强子，以及（2）建立全脑回路图谱使用纹状体电路来验证我们的细胞类型特定连接映射方法的管道狨猴。完成后，这些研究将提供急需的基本工具、方法和用于细胞类型特异性映射和狨猴大脑功能询问的计算管道健康和疾病模型。