Mapping the signaling landscape of vertebrate development at single cell resolution

以单细胞分辨率绘制脊椎动物发育的信号图谱

基本信息

批准号：
9766326
负责人：
Allon Moshe Klein
金额：
$ 62.05万
依托单位：
HARVARD MEDICAL SCHOOL
依托单位国家：
美国
项目类别：
财政年份：
2018
资助国家：
美国
起止时间：
2018-08-20 至 2023-04-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/9766326
关键词：
Acute Address Adult Biological Models CRISPR/Cas technology Cell Differentiation process Cell Lineage Cell Therapy Cells Collaborations Communities Computer software Computing Methodologies Core Facility Coupled Data Data Set Development Developmental Biology Disease Embryo Embryonic Development Engineering Erinaceidae Fertilization Fibroblast Growth Factor Gene Targeting Genomics Goals Hour In Vitro Larva Maps Measures Methods Microfluidics Modeling Molecular Mutagenesis Neural tube Neurons Organ Transplantation Outcome Patients Pattern Phenotype Regulator Genes Resolution Resources Series Signal Pathway Signal Transduction System Systems Biology Technology Time Tissues Work Zebrafish base blastomere structure combinatorial cost data acquisition extracellular indexing insight mutant notch protein pluripotency response single-cell RNA sequencing theories tool transcription factor transcriptome transcriptome sequencing translational impact zebrafish development

项目摘要

Abstract (Project Summary) A major goal of developmental biology is to understand the detailed molecular progression of all embryonic cell lineages, from pluripotency to adulthood, and how signalling pathways control lineage choices at every step of differentiation. Such an understanding addresses several fundamental questions in developmental biology, while having practical implications for re-programming cells in disease, and for in vitro differentiation for cell therapy. Recently, we developed droplet microfluidic single cell RNA-Sequencing (scRNA-Seq) technology, which allows profiling the transcriptome of tens of thousands of single cells at low cost, and we additionally developed a method to combine droplet scRNA-Seq with lineage tracing, and the computational methods required to reconstruct time series of differentiation from scRNA-Seq and lineage data. In preliminary work, we applied these tools to generate a comprehensive map of cell state trajectories in zebrafish development through the first 24 hours post fertilization. In this proposal, we will extend our map of zebrafish development, combining scRNA-Seq with clonal analysis to track every cell state in the developing zebrafish embryo up to 7 days post-fertilization. We will then use staged, acute perturbations of seven major signaling pathways, followed by scRNA-Seq, to define which signaling pathways control the flow of cells down different trajectories throughout development, as well as their context dependent and invariant gene targets. Focusing deeply on neural tube patterning, we will then dissect the transcription factor networks that integrate signaling pathways, by CRISPR/Cas9 perturbation coupled to scRNA-Seq. This proposal builds on a multi-year collaboration between two labs with strong and synergistic expertise -- the Megason lab in the use of zebrafish for developmental systems biology and the Klein lab in single cell genomics and analysis.

摘要（项目概要）发育生物学的一个主要目标是了解所有胚胎细胞的详细分子进展谱系，从多能性到成年，以及信号通路如何控制谱系选择的每一步差异化。这种理解解决了发育生物学中的几个基本问题，同时对疾病中的细胞重编程以及细胞的体外分化具有实际意义治疗。最近，我们开发了液滴微流控单细胞RNA测序（scRNA-Seq）技术，这允许以低成本分析数万个单细胞的转录组，而且我们另外开发了一种将液滴 scRNA-Seq 与谱系追踪相结合的方法，以及计算方法需要从 scRNA-Seq 和谱系数据重建分化的时间序列。在前期工作中，我们应用这些工具生成斑马鱼发育中细胞状态轨迹的综合图受精后的前 24 小时。在这个提案中，我们将扩展我们的斑马鱼发育地图，将 scRNA-Seq 与克隆分析相结合，追踪发育中的斑马鱼胚胎中的每个细胞状态（最多 7 个）受精后天。然后我们将使用七个主要信号通路的阶段性急性扰动，其次是 scRNA-Seq，以确定哪些信号通路控制细胞沿着不同轨迹流动在整个发育过程中，以及它们的背景依赖性和不变的基因目标。深度聚焦神经管模式，然后我们将剖析整合信号通路的转录因子网络，通过与 scRNA-Seq 耦合的 CRISPR/Cas9 扰动。该提案建立在多年合作的基础上两个具有强大协同专业知识的实验室之间的合作——Megason 实验室利用斑马鱼进行研究发育系统生物学和克莱因单细胞基因组学和分析实验室。