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

基本信息

批准号：
10523550
负责人：
Paola Arlotta
金额：
$ 936.46万
依托单位：
HARVARD 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：
2022-09-01 至 2027-06-30
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10523550
关键词：
3-Dimensional ATAC-seq Adult Age Anatomy Atlases Bar Codes Brain CRISPR screen Cell Differentiation process Cell Lineage Cell Maturation Cell Nucleus Cell physiology Cells Censuses Classification Clone Cells Communities Comparative Study Complex Computational algorithm Computing Methodologies Data Data Set Development Disease Embryo Embryonic Development Event Evolution Experimental Models Foundations 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 TimeLine Translating Validation Viral Vector base brain cell brain circuitry cell motility cell type comparative data resource 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-cell RNA sequencing spatial relationship transcriptome sequencing transcriptomics

项目摘要

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.

项目概要发育中的小鼠大脑是研究细胞类型起源的基础实验模型哺乳动物的大脑。小鼠大脑发育的全面知识对于比较研究至关重要神经发育过程的关键，这是理解显着的进化创新的关键将人类与其他物种区分开来。此外，发育信息能够完善细胞分类学通过将细胞类型和谱系起源的知识纳入成体细胞分类来研究成体大脑。尽管最近创建的成年小鼠大脑分子图谱带来了变革性的见解，我们目前缺乏对发育中的小鼠大脑的细胞类型的全面普查，以及将其联系起来的谱系关系他们与成年同行。在这里，我们寻求生成一个全面的、空间和时间分辨率的、细胞分辨率的图集。整个发育中的小鼠大脑，在胚胎和出生后的整个时期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的方法来生成全面的多组学单细胞概况：10x Genomics 单细胞 RNA-seq (scRNA-seq)、10x Genomics 多组（同时单核 RNA-seq 和 ATAC-seq，用于组合转录组和表观基因组分析）和 Smart-seq3（用于全长深度 RNA 测序）。同时，我们将使用空间分辨转录组方法 MERFISH 跨越相同的密集采样时间线，以确定空间分布所有细胞类型以及整个小鼠大脑中细胞状态的动态变化。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育谱系关系的方法，并通过基于条形码的体内谱系追踪和通过实验验证谱系关系使用多重子宫内 CRISPR 筛选 (Perturb-seq) 对候选分子效应器进行功能测试。最后，我们将试点整合跨物种的发育数据集，绘制单细胞组学数据集从正在发育的人类和非人类灵长类动物大脑到全面的小鼠大脑发育细胞此处建立的类型图集，用于创建发育时间的计算对齐，这将使了解跨物种特定发育事件的差异调节。总体来说，这个项目汇集了一组研究人员，他们在大脑发育、电路、单细胞基因组学和脑图谱组装以产生全面的发育脑细胞图谱，旨在作为神经科学界研究的首个基础资源哺乳动物大脑发育和神经发育障碍的机制。我们提出的项目将为 BICAN 生成有关不同细胞的基础知识的总体目标做出了重大贡献生命周期和进化过程中大脑中的类型及其三维组织原则。