Comprehensive single-cell atlas of the developing mouse brain

发育中的小鼠大脑的综合单细胞图谱

• 批准号: 10686208
• 负责人: Paola Arlotta
• 金额: $ 529.86万
• 依托单位: HARVARD UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-09-01 至 2027-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10686208
• 关键词: 3-Dimensional; ATAC-seq; Adult; Age; Anatomy; Atlases; Bar Codes; Brain; CRISPR screen; Cell Differentiation process; Cell Lineage; Cell Maturation; Cell physiology; Cells; Censuses; Classification; Communities; Comparative Study; Complex; Computational algorithm; Computing Methodologies; Data; Data Set; Development; Embryo; Event; Evolution; Experimental Models; Funding; Gene Expression; Genetic Transcription; Genomics; Goals; Human; Human Development; In Situ; Investigation; Knowledge; Laboratories; Length; Link; Longevity; Maps; Methods; Modality; Molecular; Mus; Nature; Neurodevelopmental Disorder; Neurosciences; Pattern; Process; Protein Isoforms; Regulation; Research Personnel; Resolution; Resources; Sampling; Science; Second Pregnancy Trimester; Somatosensory Cortex; Spatial Distribution; Taxonomy; Technology; Testing; Time; Translating; Validation; Viral Vector; base; brain cell; brain circuitry; candidate identification; cell motility; cell type; comparative; data integration; data resource; epigenomic profiling; epigenomics; experience; genomic data; human disease; in utero; in vivo; innovation; insight; large scale data; mouse model; multiple omics; nerve stem cell; nonhuman primate; postnatal; postnatal development; prenatal; prospective; response; scale up; sensory input; single nucleus RNA-sequencing; single-cell RNA sequencing; spatial relationship; temporal measurement; timeline; transcriptome sequencing; transcriptomic profiling; transcriptomics

PROJECT SUMMARY The developing mouse brain is a foundational experimental model for investigation of the origins of cell types in the mammalian brain. Comprehensive knowledge of mouse brain development is critical for comparative studies of neurodevelopmental processes, which are key to understanding the remarkable evolutionary innovations that distinguish humans from other species. In addition, developmental information enables refining cell taxonomy in the adult brain by incorporating knowledge of cell type and lineage origins into adult cell classification. Despite the transformative insights enabled by the recently created molecular atlas of the adult mouse brain, we currently lack a comprehensive census of cell types of the developing mouse brain, and the lineage relationships that link them to their adult counterparts. Here we seek to generate a comprehensive, spatially- and temporally-resolved, cellular-resolution atlas of the whole developing mouse brain, sampled at high resolution through the entire period of embryonic and postnatal brain development (from E8.0 to P28). We will employ three complementary approaches to generate comprehensive multi-omic single-cell profiles: 10x Genomics single-cell RNA-seq (scRNA-seq), 10x Genomics Multiome (simultaneous single-nucleus RNA-seq and ATAC-seq, for combined transcriptomic and epigenomic profiling), and Smart-seq3 (for full-length deep RNA-sequencing). In parallel, we will use the spatially resolved transcriptomic method MERFISH across the same densely-sampled timeline, to identify the spatial distribution of all cell types and dynamic changes in cell states across the entire mouse brain. We will apply computational methods to predict developmental lineage relationships from these spatially and temporally resolved datasets, and experimentally validate lineage relationships through both barcode-based in vivo lineage tracing and by functionally testing candidate molecular effectors using multiplexed in utero CRISPR screening (Perturb-seq). Finally, we will pilot integration of developmental datasets across species, mapping single-cell omics datasets from the developing human and non-human primate brains onto the comprehensive mouse brain developing cell type atlas established here, to create a computational alignment of developmental time that will enable understanding of differential regulation of specific developmental events across species. Overall, this project brings together a team of investigators with extensive, demonstrated expertise in brain development, circuitry, single-cell genomics, and assembly of brain atlases to produce a comprehensive developmental brain cell atlas, intended to serve as a first-of-its-kind foundational resource to the neuroscience community for the study of mechanisms of mammalian brain development and neurodevelopmental disorders. Our proposed project will contribute substantially to the overarching goal of BICAN to generate fundamental knowledge on diverse cell types and their three-dimensional organizational principles in the brain across lifespan and evolution.

项目摘要 发育中的小鼠大脑是研究细胞类型的起源的基础实验模型 哺乳动物的大脑。对小鼠脑发育的全面了解对于比较研究至关重要 神经发育过程，这是理解非凡的进化创新的关键 将人与其他物种区分开。此外，发育信息还可以精炼细胞分类学 成人大脑通过将细胞类型的知识和谱系起源纳入成人细胞分类。尽管 最近创建的成年小鼠大脑的分子图集实现了变革性见解，我们目前 缺乏对发育中的小鼠大脑细胞类型的全面人口普查，以及链接的谱系关系 他们到成年人。 在这里，我们试图产生一个全面的，空间和时间分辨的，细胞分辨率的地图集 整个发育中的小鼠大脑，在整个胚胎和产后的整个时期都以高分辨率采样 大脑发育（从E8.0到P28）。我们将采用三种互补方法来生成 全面的多摩尼克单细胞曲线：10倍基因组学单细胞RNA-seq（SCRNA-SEQ），10x基因组学 多组件（同时使用单核RNA-Seq和ATAC-Seq，用于联合转录组和表观基因组学 分析）和smart-seq3（用于全长深的RNA序列）。同时，我们将使用空间解决 转录组方法在同一密集采样的时间轴上Merfish，以识别空间分布 在整个小鼠大脑中的所有细胞类型和细胞状态的动态变化中。我们将应用计算 从这些空间和时间解析的数据集中预测发展性谱系关系的方法， 并通过基于条形码的体内谱系跟踪和通过实验验证谱系关系 在功能上使用子宫CRISPR筛选（werturb-seq）中的多路复用来测试候选分子效应子。 最后，我们将跨物种的开发数据集进行绘制单细胞OMICS数据集集成 从发展中的人类和非人类灵长类动物大脑到全面的小鼠脑发育细胞 在此建立的类型地图集，以创建一个开发时间的计算对齐，以启用 了解对各种物种特定发展事件的差异调节。总体而言，这个项目 汇集了一个研究人员团队，具有广泛的，具有广泛的大脑开发专业知识，电路， 单细胞基因组学和脑图集的组装，以产生全面的发育性脑细胞地图集， 旨在作为神经科学社区的首个基础资源，以研究 哺乳动物脑发育和神经发育障碍的机制。我们提议的项目将 为BICAN的总体目标做出了基本贡献，以产生有关各种细胞的基本知识 类型及其三维组织原理在大脑中跨越寿命和进化。