Molecular characterisation of the establishment of and exit from pluripotency in the mouse embryo by combining live-imaging and single-cell RNA-seq

了解哺乳动物囊胚中多能内细胞团（ICM）细胞形成和分化的分子机制对于干细胞生物学和转化医学至关重要。我们最近在小鼠胚胎中的研究揭示了由于动态细胞重排和基因表达的随机细胞间异质性导致的这一过程的意想不到的复杂性。因此，机械的理解需要定量表征细胞行为和全球基因表达动态在单细胞分辨率。本项目旨在利用小鼠胚胎在体内绘制多能细胞特化和分化过程中的分子图谱。我们将联合收割机结合两个实验室的领先专业知识; Hiiragi实验室的荧光谱系报告胚胎的实时成像分析和Tang实验室的早期哺乳动物胚胎的单细胞RNA-seq。这项联合工作将使该团队能够对发育历史和结果可用的单细胞的全转录组进行分析，从而为在前所未有的水平上研究早期小鼠发育和干细胞生物学提供独特的机会。我们将特别关注ICM标记基因在单碱基分辨率下的细胞间表达异质性，并讨论其在建立和退出多能性中的动力学、相关性和潜在作用。这项研究将为理解干细胞形成、维持和谱系特异性分化的分子和细胞机制奠定基础。

Understanding of the molecular mechanism underlying formation and differentiation of the pluripotent inner cell mass (ICM) cells in the mammalian blastocyst is essential for stem cell biology and translational medicine. Our recent studies in the mouse embryo revealed unexpected complexities in this process due to dynamic cell rearrangement and stochastic cell-to-cell heterogeneity in gene expression. Thus the mechanistic understanding requires quantitative characterisation of cell behaviour and global gene expression dynamics at a single-cell resolution. This project aims at mapping the molecular profile during specification and differentiation of the pluripotent cells in vivo using mouse embryos. We will combine the leading expertise of the two labs; live-imaging analysis of fluorescence lineage-reporter embryos in the Hiiragi lab and single-cell RNA-seq of early mammalian embryos in the Tang lab. This joint work will allow the team to characterise the full transcriptome of the single cells for which developmental history and outcome is available, thus providing the unique opportunity to study early mouse development and stem cell biology at an unprecedented level. We will particularly focus on the cell-to-cell expression heterogeneity of the ICM marker genes at a single-base resolution and address its dynamics, correlations and potential role in the establishment of and exit from pluripotency. Together this study will form the basis for understanding the molecular and cellular mechanisms of stem cell formation, maintenance and lineage-specific differentiation.