Molecular architecture of lineage specification and tissue organization in early mouse embryo

During postimplantation development of the mouse embryo, descendants of the inner cell mass cells in the early epiblast transit from the naive pluripotent state to the primed pluripotent state. Concurrent with the transition of the pluripotency states is the specification of cell lineages and formation of germ layers in the embryos that serves as the blueprint for embryogenesis. Fate mapping and lineage analysis studies have revealed that cells in different regions of the germ layers acquire location-specific cell fates during gastrulation. The regionalization of cell fates heralding the formation of the basic body plan is conserved in vertebrate embryos at a common phylotypic stage of development. Knowledge of the molecular regulation that underpin the lineage specification and tissue patterning is instrumental for understanding embryonic programming and stem cell-based translational study. However, a genome-wide molecular annotation of lineage segregation and tissue architecture of post-implantation embryo has yet to be undertaken. Here, we reported a spatially resolved transcriptome of cell populations at defined positions in the germ layers over the period of pre- to late gastrulation development. This spatio-temporal transcriptome provides high resolution digitized gene expression profiles and defines the molecular attribute of the genealogy of lineages and continuum of pluripotency states in time and space. The transcriptome further identifies the networks of molecular determinants that drive lineage specification and tissue patterning in the early postimplantation mouse embryo. By using spatial transcriptome of Geo-seq, we carried out transcriptome profiling on embryo sections at a high resolution of 20-40 cells per sample. We then constructed a comprehensive spatial transcriptome map from the pre-gastrulation to late-gastrulation embryos that are visualized in a 3D embryonic model based on the sequencing data. Please be aware that the positions for left (L) and right (R) are from mirrored images and should be considered as right and left in real embryo settings. Anterior (A) or Posterior (P) regions do not change.在小鼠胚胎植入后发育过程中，早期上胚层（epiblast）内的内细胞团（inner cell mass）细胞后代会从初始多能性（naive pluripotent）状态转变为始发多能性（primed pluripotent）状态。多能性状态转换的同时，胚胎内的细胞谱系特化与胚层形成过程同步发生，二者共同构成胚胎发生的蓝图。命运图谱与谱系分析研究表明，在原肠胚形成（gastrulation）过程中，胚层不同区域的细胞会获得具有位置特异性的细胞命运。预示基本体型形成的细胞命运区域化特征，在脊椎动物发育的共同系统型阶段的胚胎中得以保守保留。阐明支撑细胞谱系特化与组织模式建成的分子调控机制，有助于理解胚胎编程以及基于干细胞的转化研究。然而，目前尚未有针对植入后胚胎的细胞谱系分离与组织架构的全基因组分子注释研究。本研究报道了原肠胚形成早期至晚期阶段中，胚层内特定位置细胞群体的空间分辨转录组（spatially resolved transcriptome）。该时空转录组提供了高分辨率的数字化基因表达谱，从时间与空间维度阐明了谱系亲缘关系的分子特征以及多能性状态的连续变化过程。该转录组还进一步揭示了驱动植入后早期小鼠胚胎细胞谱系特化与组织模式建成的分子决定因子调控网络。本研究依托Geo-seq空间转录组技术，对胚胎切片进行转录组分析，单样本分辨率可达20~40个细胞。基于测序数据，我们构建了从原肠胚形成前至晚期原肠胚阶段的完整空间转录组图谱，并将其可视化于三维胚胎模型中。请注意：左侧（L）与右侧（R）的标注源自镜像图像，在真实胚胎环境中应对应为右侧与左侧；前侧（A）与后侧（P）的区域划分保持不变。