利用单细胞转录组和空间转录组技术建立小鼠胚胎原肠运动时期的单细胞时空转录组图谱

The paradigm and blueprint of lineage segregation of early mouse embryo is established during gastrulation in which progenitors of various cell fates are regionalized and patterned in specific embryo locations. Despite the central importance of this period of mammalian development, we currently lack a comprehensive understanding of the underlying developmental trajectories and molecular processes, principally because research efforts either employed in vitro systems, focused on small numbers of genes, or limited the number of developmental stages or cell types that were studied.. Single-cell RNA sequencing has emerged as a powerful method to simultaneously measure cell-to-cell expression variability of thousands of genes. This technique has enormous applications in stem cell and developmental biology. However, the spatial information has been lost during the isolation of single cells. Previous spatial mapping of single cells requires the prior knowledge of location landmarks, which is often missing in many particular contexts.. In this project, our lab propose to study the regulatory landscape of gastrulation by combining single-cell RNA-seq (A total of ~50,000 single cells isolated at E6.5, E6.75, E7.0, E7.25, E7.5) and geographical position sequencing (Geo-seq) technique, and we will establish a de novo identification of spatial “zipcodes” and a method to enable retrospective locating of single cells to their origins in the embryo. This work will provide insights into the exit from pluripotency and priming for differentiation, and the emergence of regulatory networks associated with cell fate decisions. We will also reconstruct the spatio-temporal roadmap of gastrula mouse embryo in single-cell resolution and uncover the cell migration trajectories and molecular processes associated with lineage segregation.. This project will offer new insights into the genealogy of cell population in real time and real space during gastrulation, and provide references for early human embryo development.

哺乳动物的早期胚胎发育，尤其是原肠运动建立了整个动物体发育的蓝图，研究不同胚层的发育来源，尤其是决定这一过程的分子机制，具有极其重要的生物学意义。由于早期胚胎组织异乎微小，着床后胚胎取材非常困难，以往的研究大多集中在单个基因某一个方面的功能，无法反映体内真实而复杂的发育状况。单细胞转录组测序技术可以从整体转录组水平研究单个细胞之间的相互作用，但无法获取细胞的位置信息。我们实验室建立了小鼠早期胚胎的空间转录组技术，保留了细胞原有的位置信息，将应用于转录图谱的三维构建。.本项目旨在结合单细胞转录组和空间转录组技术，三维重建单细胞精度的早期胚胎发育图谱，在时间和空间四维层面上考察小鼠原肠运动时期三个胚层建立过程的分子机制，阐明内源因子和外源信号的调控网络，揭示不同胚层细胞的发育起源和迁移轨迹。本研究将加深人们对胚胎早期发育各胚层细胞谱系的认识，并对探索人的早期发育以及发育相关疾病的机理提供借鉴。

哺乳动物的早期胚胎发育，尤其是原肠运动建立了整个动物体发育的蓝图，研究不同胚层的发育来源，尤其是决定这一过程的分子机制，具有极其重要的生物学意义。由于早期胚胎组织异乎微小，着床后胚胎取材非常困难，以往的研究大多集中在单个基因某一个方面的功能，无法反映体内真实而复杂的发育状况。单细胞转录组测序技术可以从整体转录组水平研究单个细胞之间的相互作用，但无法获取细胞的位置信息。我们实验室建立了小鼠早期胚胎的空间转录组技术，保留了细胞原有的位置信息，将应用于转录图谱的三维构建。. 本项目旨在结合单细胞转录组和空间转录组技术，三维重建单细胞精度的早期胚胎发育图谱，在时间和空间四维层面上考察小鼠原肠运动时期三个胚层建立过程的分子机制，阐明内源因子和外源信号的调控网络，揭示不同胚层细胞的发育起源和迁移轨迹。本研究将加深人们对胚胎早期发育各胚层细胞谱系的认识，并对探索人的早期发育以及发育相关疾病的机理提供借鉴。. 目前我们的研究已经取得阶段性成果，发表于国际学术期刊Genomics, Proteomics & Bioinformatics..Ran Wang, Guangdun Peng, Patrick P L Tam, Naihe Jing. Integration of Computational Analysis and Spatial Transcriptomics in Single-cell Study. Genomics, Proteomics & Bioinformatics (2022), online ahead of print, doi: https://doi.org/10.1016/j.gpb.2022.06.006