Progress in understanding early human development has been impeded by the scarcity of reference datasets from natural embryos, particularly those with spatial information during crucial stages like gastrulation. We conducted high-resolution spatial transcriptomics profiling on 38,562 spots from 62 transverse sections of an intact Carnegie stage (CS) 8 human embryo. From this spatial transcriptomic dataset, we constructed a 3D model of the CS8 embryo, in which a range of cell subtypes are identified, based on gene expression patterns and positional register, along the anterior-posterior, medial-lateral, and dorsal-ventral axis in the embryo. We further characterized the lineage trajectories of embryonic and extra-embryonic tissues and associated regulons and the regionalization of signaling centers and signaling activities that underpin lineage progression and tissue patterning during gastrulation. Collectively, the findings of this study provide insights into gastrulation and post-gastrulation development of the human embryo.

由于自然胚胎参考数据集的缺乏，特别是那些在原肠胚形成等关键阶段具有空间信息的数据集，阻碍了理解早期人类发育的进展。我们对完整的卡内基阶段 (CS) 8 人类胚胎的 62 个横切面的 38,562 个点进行了高分辨率空间转录组学分析。根据这个空间转录组数据集，我们构建了 CS8 胚胎的 3D 模型，其中根据基因表达模式和位置​​记录，沿着前后轴、内侧轴和背腹轴识别了一系列细胞亚型在胚胎中。我们进一步表征了胚胎和胚胎外组织以及相关调节子的谱系轨迹，以及支持原肠胚形成期间谱系进展和组织模式的信号中心和信号活动的区域化。总的来说，这项研究的结果提供了对人类胚胎原肠胚形成和原肠胚形成后发育的见解。