Digital reconstruction of full embryos during early mouse organogenesis
Early organogenesis is a crucial stage in embryonic development, characterized by extensive cell fate specification to initiate organ formation but also by a high susceptibility to developmental defects. Here, we profiled 285 serial sections from six E7.5-E8.0 embryos to generate full spatiotemporal transcriptome and signal maps during early organogenesis at single-cell resolution. By developing SEU-3D, we reconstructed digital embryos, enabling investigation of regionalized gene expression in the native spatial context. We established a space-informed gene-cell co-embedding approach, systematically characterized the spatial atlas of endoderm and mesoderm derivatives, and elucidated signaling networks across germ layers and cell types. Furthermore, we characterized a primordium determination zone (PDZ) formed along the anterior embryonic-extraembryonic interface at E7.75, and it revealed that the coordinated signaling communications contribute to the formation of cardiac primordium. Collectively, the high-resolution "digital embryo" provides significant insights into early organogenesis and a unique spatial platform for studying development and diseases.
Authors
- Naihe Jing (ORCID: https://orcid.org/0000-0003-1509-6378)
- Chengqi Lin (ORCID: https://orcid.org/0000-0002-2121-584X)
- Chen Wu (ORCID: https://orcid.org/0000-0003-3900-9363)
- Wei Liu (ORCID: https://orcid.org/0000-0001-9037-8792)
- Jin Liu (ORCID: https://orcid.org/0000-0002-5707-2078)
- Guangyao Mao (ORCID: https://orcid.org/0009-0004-3178-9937)
- Xuebiao Yao (ORCID: https://orcid.org/0000-0001-8982-5911)
- Zehong Yang (ORCID: https://orcid.org/0000-0001-7562-3710)
- Xiaodong Fang (ORCID: https://orcid.org/0000-0001-7061-3337)
- Ke Fang (ORCID: https://orcid.org/0000-0002-5387-8138)
- Peng Xie (ORCID: https://orcid.org/0000-0002-9138-9749)
- Hua Cao (ORCID: https://orcid.org/0000-0001-5480-1610)
- Zhuojuan Luo
- Juan Shen (ORCID: https://orcid.org/0000-0001-5048-3838)
- Xueting Chen (ORCID: https://orcid.org/0000-0002-5314-0221)
- Jingjing He
- Xin Xue (ORCID: https://orcid.org/0000-0002-7781-1982)
- Wei Xie (ORCID: https://orcid.org/0000-0002-7840-5652)
- Linjin Chen
- Hailong Cao (ORCID: https://orcid.org/0000-0002-1462-6659)
- Ling Liu (ORCID: https://orcid.org/0000-0002-3468-3933)
- Yi Yang (ORCID: https://orcid.org/0000-0002-9507-7144)
- Xiao Zhang (ORCID: https://orcid.org/0000-0001-9423-1210)
- Chaoyi Wang (ORCID: https://orcid.org/0000-0002-1422-2451)
- Xing Liu (ORCID: https://orcid.org/0000-0001-9798-6432)
- Xinrui Wang (ORCID: https://orcid.org/0009-0002-5888-6783)
- Xu Jiang
- Yanying Zheng
- Weiheng Zheng (ORCID: https://orcid.org/0000-0002-1189-9539)
- Xianfa Yang (ORCID: https://orcid.org/0000-0002-6843-8055)
Institutions
- BGI Group (China) (CN)
- Fujian Medical University (CN)
- Nantong University (CN)
- Sichuan University (CN)
- Fujian Women and Children Hospital (CN)
- Guangzhou Experimental Station (CN)
- Hefei National Center for Physical Sciences at Nanoscale (CN)
- Chinese University of Hong Kong, Shenzhen (CN)
- Botswana Geoscience Institute (BW)
- Southeast University (CN)
Publication Details
- Journal
- Cell
- Published
- 2025-06-18
- DOI
- https://doi.org/10.1016/j.cell.2025.05.035
- Citations
- 11
- Primary Topic
- Congenital heart defects research
- Type
- article
- Field-Weighted Citation Impact
- 9.67
Funders
- National Natural Science Foundation of China
- National Key Research and Development Program of China Stem Cell and Translational Research