Defining the precise regionalization of specified definitive endoderm progenitors is critical for understanding the mechanisms underlying the generation and regeneration of respiratory and digestive organs, yet the patterning of endoderm progenitors remains unresolved, particularly in humans. We performed single-cell RNA sequencing on endoderm cells during the early somitogenesis stages in mice and humans. We developed molecular criteria to define four major endoderm regions (foregut, lip of anterior intestinal portal, midgut, and hindgut) and their developmental pathways. We identified the cell subpopulations in each region and their spatial distributions and characterized key molecular features along the body axes. Dorsal and ventral pancreatic progenitors appear to originate from the midgut population and follow distinct pathways to develop into an identical cell type. Finally, we described the generally conserved endoderm patterning in humans and clear differences in dorsal cell distribution between species. Our study comprehensively defines single-cell endoderm patterning and provides novel insights into the spatiotemporal process that drives establishment of early endoderm domains.

定义特定定形内胚层祖细胞的精确区域化对于理解呼吸和消化器官产生和再生的机制至关重要，但内胚层祖细胞的模式仍未解决，特别是在人类中。我们在小鼠和人类的早期体节发生阶段对内胚层细胞进行了单细胞 RNA 测序。我们制定了分子标准来定义四个主要内胚层区域（前肠、前肠入口唇、中肠和后肠）及其发育途径。我们确定了每个区域的细胞亚群及其空间分布，并沿体轴表征了关键分子特征。背侧和腹侧胰腺祖细胞似乎起源于中肠群，并遵循不同的途径发展成相同的细胞类型。最后，我们描述了人类普遍保守的内胚层模式和物种间背侧细胞分布的明显差异。我们的研究全面定义了单细胞内胚层模式，并为推动早期内胚层结构域建立的时空过程提供了新的见解。