Gastrulation controls the emergence of cellular diversity and axis patterning in the early embryo. In mammals, this transformation is orchestrated by dynamic signalling centres at the interface of embryonic and extraembryonic tissues^1–3. Elucidating the molecular framework of axis formation in vivo is fundamental for our understanding of human development^4–6 and to advance stem-cell-based regenerative approaches⁷. Here, we illuminate early gastrulation of marmoset embryos in utero by spatial transcriptomics and stem cell-based embryo models. Gaussian process regression-based 3D-transcriptomes delineate the emergence of the anterior visceral endoderm, which is hallmarked by conserved (HHEX, LEFTY2, LHX1) and primate-specific (POSTN, SDC4, FZD5) factors. WNT signalling spatially coordinates primitive streak formation in the embryonic disc and is counteracted by SFRP1/2 to sustain pluripotency in the anterior domain. Amnion specification occurs at the boundaries of the embryonic disc through ID1/2/3 in response to BMP-signalling, providing a developmental rationale for amnion differentiation of primate pluripotent stem cells (PSCs). Spatial identity mapping demonstrates that primed marmoset PSCs exhibit highest similarity to the anterior embryonic disc, while naïve PSCs resemble the preimplantation epiblast. Our 3D-transcriptome models reveal the molecular code of lineage specification in the primate embryo and provide an in vivo reference to decipher human development.

原肠胚形成控制早期胚胎中细胞多样性和轴模式的出现。在哺乳动物中，这种转变是由胚胎和胚胎外组织界面上的动态信号中心精心策划的^1-3。阐明体内轴形成的分子框架对于我们理解人类发育^4-6和推进基于干细胞的再生方法⁷至关重要。在这里，我们通过空间转录组学和基于干细胞的胚胎模型阐明了狨猴胚胎在子宫内的早期原肠胚形成。基于高斯过程回归的 3D 转录组描绘了前内脏内胚层的出现，其特征是保守的（HHEX、LEFTY2、LHX1）和灵长类特异性（POSTN、SDC4、FZD5）因子。WNT 信号在空间上协调胚胎盘中原条的形成，并被SFRP1/2抵消以维持前域的多能性。羊膜特化发生在胚胎盘的边界处，通过ID1/2/3响应 BMP 信号，为灵长类多能干细胞 (PSC) 的羊膜分化提供了发育原理。空间同一性图谱表明，引发的狨猴 PSC 与前胚盘表现出最高的相似性，而幼稚的 PSC 类似于植入前外胚层。我们的 3D 转录组模型揭示了灵长类动物胚胎中谱系规范的分子密码，并为破译人类发育提供了体内参考。