Three-dimensional molecular architecture of mouse organogenesis

Fangfang Qu, Wenjia Li, Jian Xu, Ruifang Zhang, Jincan Ke, Xiaodie Ren, Xiaogao Meng, Lexin Qin, Jingna Zhang, Fangru Lu, Xin Zhou, Xi Luo, Zhen Zhang, Minhan Wang, Guangming Wu, Duanqing Pei, Jiekai Chen, Guizhong Cui (), Shengbao Suo () and Guangdun Peng ()
Additional contact information
Fangfang Qu: Bioland Laboratory
Wenjia Li: Bioland Laboratory
Jian Xu: Bioland Laboratory
Ruifang Zhang: Bioland Laboratory
Jincan Ke: Chinese Academy of Sciences
Xiaodie Ren: Bioland Laboratory
Xiaogao Meng: Chinese Academy of Sciences
Lexin Qin: Chinese Academy of Sciences
Jingna Zhang: Bioland Laboratory
Fangru Lu: Bioland Laboratory
Xin Zhou: Bioland Laboratory
Xi Luo: Chinese Academy of Sciences
Zhen Zhang: Chinese Academy of Sciences
Minhan Wang: Chinese Academy of Sciences
Guangming Wu: Bioland Laboratory
Duanqing Pei: Westlake University
Jiekai Chen: Bioland Laboratory
Guizhong Cui: Bioland Laboratory
Shengbao Suo: Guangzhou Laboratory
Guangdun Peng: Bioland Laboratory

Nature Communications, 2023, vol. 14, issue 1, 1-18

Abstract: Abstract Mammalian embryos exhibit sophisticated cellular patterning that is intricately orchestrated at both molecular and cellular level. It has recently become apparent that cells within the animal body display significant heterogeneity, both in terms of their cellular properties and spatial distributions. However, current spatial transcriptomic profiling either lacks three-dimensional representation or is limited in its ability to capture the complexity of embryonic tissues and organs. Here, we present a spatial transcriptomic atlas of all major organs at embryonic day 13.5 in the mouse embryo, and provide a three-dimensional rendering of molecular regulation for embryonic patterning with stacked sections. By integrating the spatial atlas with corresponding single-cell transcriptomic data, we offer a detailed molecular annotation of the dynamic nature of organ development, spatial cellular interactions, embryonic axes, and divergence of cell fates that underlie mammalian development, which would pave the way for precise organ engineering and stem cell-based regenerative medicine.

Date: 2023
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DOI: 10.1038/s41467-023-40155-7

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