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A three-dimensional spatial transcriptome atlas reconstructs early organogenesis in primate Carnegie stages 9 and 10 embryos

Nature Cell Biology (2026)Cite this article

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Abstract

The early organogenesis stage is a critical phase of embryogenesis that lays the foundation for organ development, and is characterized by dynamic and spatially organized transcriptional programs. However, limited spatial transcriptomic information has constrained our understanding of early primate organogenesis. Here we present a comprehensive three-dimensional (3D) spatial transcriptomic atlas of cynomolgus monkey embryos at Carnegie stages (CS) 9 and 10, capturing key morphogenetic events including cardiogenesis, gut tube regionalization, neurulation, axial mesendoderm patterning and early somitogenesis. Using high-resolution spatial transcriptomics and 3D reconstruction, we identify spatially defined lineage domains across germ layers and resolve regionally restricted gene expression, transcription factor activity, and signalling landscapes along major embryonic axes, exemplified by the emergence of dorsoventrally patterned spinal cord subpopulations during neurulation. Cross-species comparisons with human and mouse datasets reveal conserved and species-biased transcriptional programs. Together, this atlas provides a foundational reference for studying early primate development.

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Fig. 1: Spatial transcriptomic characterization and 3D reconstruction of CS9 and CS10 cynomolgus monkey embryos.
The alternative text for this image may have been generated using AI.
Fig. 2: Molecular regulatory programs and signalling patterns along the embryo A–P axis.
The alternative text for this image may have been generated using AI.
Fig. 3: Spatial transcriptomic profiling of heart tube development in CS9 and CS10 embryos.
The alternative text for this image may have been generated using AI.
Fig. 4: Spatial molecular landscape of gut tube patterning.
The alternative text for this image may have been generated using AI.
Fig. 5: Spatial cellular dynamics of neurulation in CS9 and CS10 embryos.
The alternative text for this image may have been generated using AI.
Fig. 6: Spatial characterization of somitogenesis and axial development.
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Fig. 7: Spatial transcriptomic profiling of notochord development.
The alternative text for this image may have been generated using AI.
Fig. 8: Cross-species comparison of embryonic tissues during early organogenesis.
The alternative text for this image may have been generated using AI.

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Data availability

The raw sequencing data supporting the findings of this study have been deposited in the China National GeneBank database (CNGBdb) under accession code CNP0007017. Previously published cynomolgus monkey embryo data that were re-analysed in this study are available under accession code GSE193007. Previously published mouse embryo data that were re-analysed in this study are available under accession code E-MTAB-6967. Previously published human CS9 embryo data that were re-analysed in this study are available under accession code HRA007284. Previously published in vitro models of somitogenesis data that were re-analysed in this study are available under accession codes GSE199576 and GSE195467. An online portal allowing visualization of spatial gene expression, lineage annotations, and three-dimensional reconstructions of the CS9 and CS10 embryos can be accessed at https://3dprimate.lab.westlake.edu.cn/. Data supporting the findings of this study are available from the corresponding author on reasonable request. Source data are provided with this paper.

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Acknowledgements

We thank all members of the Liu Labs for insightful advice and comments on the manuscript. We thank the Imaging Platform at Westlake University for the use of microscopes and technical support. We thank the staff and veterinarians from Huazhen Biosciences (HZ-Bio) for help with animal care and operational assistance on obtaining embryo samples. We also thank BGI-Research for technical support. This work was supported by the the National Key R&D Program of China (2022YFA1105700 to Xiaodong Liu, 2022YFC3400400 to L. Liu, 2022YFA1104300 to L.Y.), the National Natural Science Foundation of China (32370784 to Xiaodong Liu, 22DAA01467 to Xiaodong Liu, 82525028 to L.Y.), the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB0820000 to L.Y.) and the Westlake Education Foundation to Xiaodong Liu.

Author information

Author notes

  1. These authors contributed equally: Jia Ping Tan, Yifang Liu, Yuting Fu, Langchao Liang, Yan Wu, Tiantian Guo.

Authors and Affiliations

  1. School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China

    Jia Ping Tan, Yifang Liu, Yuting Fu, Shikai Jia, Tingli Yuan, Xixi Yan, Zizhuo Liao, Xiaojing Liu, Bowen Hu, Shujie Fu & Xiaodong Liu

  2. Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China

    Jia Ping Tan, Yifang Liu, Yuting Fu, Shikai Jia, Tingli Yuan, Xixi Yan, Zizhuo Liao, Xiaojing Liu, Bowen Hu, Shujie Fu & Xiaodong Liu

  3. Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China

    Jia Ping Tan, Yifang Liu, Yuting Fu, Shikai Jia, Tingli Yuan, Xixi Yan, Zizhuo Liao, Xiaojing Liu, Bowen Hu, Shujie Fu & Xiaodong Liu

  4. Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China

    Jia Ping Tan, Yifang Liu, Yuting Fu, Shikai Jia, Tingli Yuan, Xixi Yan, Zizhuo Liao, Xiaojing Liu, Bowen Hu, Shujie Fu & Xiaodong Liu

  5. State Key Laboratory of Genome and Multi-omics Technologies, BGI Research, Hangzhou, Zhejiang, China

    Langchao Liang, Yan Wu, Yujia Jiang, Yixin Li, Zhi Huang, Shenglong Li, Shijie Hao & Longqi Liu

  6. School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China

    Langchao Liang, Zhi Huang, Shenglong Li & Shijie Hao

  7. Key Laboratory of Brain Cell Mapping of Zhejiang Province, BGI Research, Hangzhou, Zhejiang, China

    Langchao Liang, Shijie Hao & Longqi Liu

  8. State Key Laboratory of Organ Regeneration and Reconstruction, Human Organ Physiopathology Emulation System, Institute of Zoology, Chinese Academy of Sciences, Beijing, China

    Tiantian Guo, Yixin Li & Leqian Yu

  9. School of Software Engineering, Beijing Jiaotong University, Beijing, China

    Tiantian Guo

  10. Department of Biology, University of Copenhagen, Copenhagen, Denmark

    Yujia Jiang

  11. Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, China

    Jie Li, Jie Li & Zhen Liu

  12. Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, China

    Jie Li, Jie Li & Zhen Liu

  13. Guangzhou National Laboratory, Guangzhou, China

    Luyi Tian

  14. GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, China

    Luyi Tian

  15. Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China

    Leqian Yu

  16. University of Chinese Academy of Sciences, Beijing, China

    Leqian Yu

Authors
  1. Jia Ping Tan
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  2. Yifang Liu
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  3. Yuting Fu
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  4. Langchao Liang
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  5. Yan Wu
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  6. Tiantian Guo
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  7. Shikai Jia
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  8. Yujia Jiang
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  9. Tingli Yuan
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  10. Jie Li
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  11. Yixin Li
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  12. Zhi Huang
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  13. Shenglong Li
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  14. Jie Li
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  15. Xixi Yan
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  16. Zizhuo Liao
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  17. Xiaojing Liu
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  18. Bowen Hu
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  19. Shujie Fu
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  20. Shijie Hao
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  21. Luyi Tian
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  22. Zhen Liu
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  23. Leqian Yu
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  24. Longqi Liu
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  25. Xiaodong Liu
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Contributions

Xiaodong Liu and L. Liu conceived and supervised the project. Y.F. and J.P.T. prepared samples for Stereo-seq and performed all other wet experiments with help from T.Y., J.L. (http://orcid.org/0000-0002-5446-894X), S.J., J.L. (http://orcid.org/0000-0003-1754-2378), Y.J., Y. Li, Xiaojing Liu, B.H. and S.F. Y. Liu, L. Liang, Y.W., T.G. analysed the data with support from Z.H., S.L., X.Y., Z.L., and input from S.H., L. Liu, L.T., L.Y., J.P.T. and Xiaodong Liu. J.P.T., Y. Liu, Y.F., L. Liang, Y.W., T.G. and Xiaodong Liu wrote and revised the manuscript with input from all authors.

Corresponding authors

Correspondence to Leqian Yu, Longqi Liu or Xiaodong Liu.

Ethics declarations

Competing interests

X.L. is a co-founder of iCamuno Biotherapeutics Ltd. The remaining authors declare no competing interests.

Peer review

Peer review information

Nature Cell Biology thanks Junyue Cao, Alfonso Martinez-Arias and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

Extended Data Fig. 1 Quality control-related analyses on embryo slices used for Stereo-seq, related to Fig. 1.

a, Spatial visualization of the segmented cells (nucleic acid staining) on 10 slices of CS9 cynomolgus monkey embryo. b, Spatial visualization of the segmented cells (nucleic acid staining) on 10 slices of CS9 cynomolgus monkey embryo. c, Violin plots of gene numbers, read counts, and percentage of mitochondrial reads detected in each slice of CS9 embryo. d, Violin plots of gene numbers, read counts, and percentage of mitochondrial reads detected in each slice of CS10 embryo.

Extended Data Fig. 2 Cellular composition analysis of CS9 and CS10 embryos, related to Fig. 1.

a, Spatial distribution of 22 lineage clusters on all slices of CS9 and CS10 embryo. b, Stacked bar plot depicting the proportion of each lineage cluster across 10 slices from CS9 and CS10 embryos. c, Separate UMAP plots respectively showing the 22 lineage clusters of CS9 and CS10 embryos. d, Cell cycle analysis examining cell cycle phase distribution of each lineage cluster from CS9 and CS10 embryos.

Source data

Extended Data Fig. 3 Integrative benchmarking analysis with single-cell transcriptomic dataset of CS8-11 cynomolgus monkey embryo, related to Fig. 1.

a, UMAP plot of integration analysis of spatial transcriptomic dataset from this study with scRNA-seq dataset of CS8-CS11 cynomolgus monkey embryo from Zhai et al. Cells are coloured by Carnegie stage and dataset of origin. b, UMAP feature plots showing the distribution of lineage clusters annotated in this study, with each panel highlighting one cell type overlaid on the integrated UMAP embedding while all other cells are shown in grey. c, UMAP feature plots showing the distribution of cell types annotated by Zhai et al. projected onto the same integrated UMAP embedding, with each panel highlighting one annotated cell type and all other cells shown in grey.

Extended Data Fig. 4 Spatial molecular landscape of CS9 and CS10 embryo, related to Fig. 2.

a, Heatmap showing module scores for each gene module across 22 annotated cell lineages in the CS10 embryo. b, Spatial visualization of representative gene modules identified by Hotspot analysis in the three-dimensional reconstructed CS10 embryo. Cells are coloured by module score. c, Heatmap of genes exhibiting significant spatial autocorrelation in the three-dimensional reconstructed CS10 embryo, grouped into 11 gene modules based on pairwise local correlation. Representative genes and enriched Gene Ontology (GO) terms for the modules are indicated on the right.

Source data

Extended Data Fig. 5 Profiling of HOX gene expression in CS9 and CS10 embryos, related to Fig. 2.

a, Heatmap showing the scaled average expression of HOX genes across annotated cell lineages in the CS9 embryo. b, Heatmap showing the scaled average expression of HOX genes across annotated cell lineages in the CS10 embryo. c, Ridgeline plots showing the distribution of HOX gene expression along the anterior–posterior (A–P) axis of the three-dimensionally reconstructed CS10 embryo. Cells are ordered according to their spatial position along the A–P axis.

Source data

Extended Data Fig. 6 Expression pattern of key signaling ligands in CS9 and CS10 embryos, related to Fig. 2.

a, Dot plot showing the expression of ligands from the FGF, NODAL, BMP, WNT, and Hh signaling pathways across annotated cell lineages in the CS9 embryo. Dot size represents the fraction of cells expressing each gene, and colour indicates scaled average expression. b, Dot plot showing the expression of ligands from the FGF, NODAL, BMP, WNT, and Hh signaling pathways across annotated cell lineages in the CS10 embryo. c, Spatial feature plots showing the expression of selected signaling ligands (FGF3, FGF7, FGF8, FGF10, FGF17, WNT2, WNT3A, and WNT5A) projected onto the three-dimensional reconstructed CS9 embryo. d, Spatial feature plots showing the expression of FGF3, FGF7, FGF8, FGF10, FGF17, WNT2, WNT3A, and WNT5A projected onto the three-dimensional reconstructed CS10 embryo.

Source data

Extended Data Fig. 7 Additional spatial analysis on gut tube development and PGC migration, related to Fig. 4.

a, Spatial expression of representative PGC markers on endodermal clusters of 3D reconstructed CS9 cynomolgus monkey embryo. b, Spatial expression of representative PGC markers on endodermal clusters of 3D reconstructed CS10 cynomolgus monkey embryo. c, Dotplot depicting the expression of chemokine and chemokine receptors in gut tube-related subclusters. d, Spatial expression of CXCR4 and CXCL12 on gut tube clusters of CS9 and CS10 cynomolgus monkey embryos. e, Immunofluorescence analysis of CS9 cynomolgus monkey embryo slice for NANOG, SOX17 and CXCR4. White box on the leftmost panel indicates the region magnified for locating PGCs. Red arrows indicate CXCR4-expressing PGCs (n = 1 embryo). Scale bar, 100 μm. f, Immunofluorescence analysis of CS9 cynomolgus monkey embryo slice for OCT4, SOX17 and CXCR4. White box on the leftmost panel indicates the region magnified for locating PGCs. Red arrows indicate CXCR4-expressing PGCs (n = 1 embryo). Scale bar, 100 μm.

Source data

Extended Data Fig. 8 Molecular dynamics of neurulation between CS9 and CS10 embryos, related to Fig. 5.

a, Dot plot showing representative genes upregulated in the ectodermal clusters of the CS9 embryo relative to CS10. Dot size indicates the fraction of cells expressing each gene, and colour represents scaled average expression. b, Dot plot showing representative genes upregulated in the ectodermal clusters of the CS10 embryo relative to CS9. c, Spatial feature plots showing the expression of selected CS9-enriched genes in the brain and spinal cord clusters projected onto the three-dimensionally reconstructed CS9 and CS10 cynomolgus monkey embryos. d, Spatial feature plots showing the expression of selected CS10-enriched genes in the brain and spinal cord clusters projected onto the three-dimensionally reconstructed CS9 and CS10 embryos. e, Spatial projection of regional neural signatures, including forebrain, midbrain, hindbrain, caudal hindbrain, neuroblast, spinal cord roof plate, spinal cord neural plate, spinal cord floor plate, and caudal neuroectoderm, derived from cynomolgus monkey scRNA-seq data and mapped onto the three-dimensionally reconstructed CS9 and CS10 embryos.

Source data

Extended Data Fig. 9 Additional spatial analysis on neurulation, related to Fig. 5.

a, Bar plot showing the relative proportions of brain and spinal cord–associated subclusters in CS9 and CS10 cynomolgus monkey embryos, highlighting stage-dependent changes in neurulation-related cell composition. b, UMAP plot of neurulation-associated subclusters (as in Fig. 5b) overlaid with RNA velocity vectors, illustrating inferred developmental trajectories among Spinal Cord 1, Spinal Cord 2, and Spinal Cord 3 subclusters. c-d, UMAP embedding and spatial projection of an independent biological replicate CS10 embryo profiled by Stereo-seq, showing annotated lineage clusters. e, Stacked bar plot showing the relative proportions of Spinal Cord 1, Spinal Cord 2, and Spinal Cord 3 subclusters across the three embryos analysed in this study (one CS9 embryo and two CS10 embryos). f, Feature plots showing expression of representative marker genes for spinal cord subclusters, corresponding to the dot plot in Fig. 5h, projected onto the integrated UMAP plot.

Source data

Extended Data Fig. 10 Additional spatial analysis on somitogenesis and notochord development, related to Fig. 6 and Fig. 7.

a, Dot plot showing the expression of representative DEGs and canonical markers across somitogenesis and spinal cord-related subclusters. Dot size indicates the fraction of spots expressing each gene, and colour denotes scaled average expression. b, Pseudotime trajectory inferred from Monocle3 analysis of somitogenesis- and spinal cord–associated subclusters. c, Spatial distribution of NMP cluster in selected CS9 and CS10 embryo slices. The other spots were depicted in grey. d, Spatial distribution of anterior and posterior domains within the notochord-associated cluster in the CS9 embryo. e, Dot plot of representative DEGs distinguishing anterior and posterior notochord domains in the CS9 embryo. Dot size represents the percentage of expressing spots and colour indicates scaled expression levels. f, Chord diagram summarizing predicted cell–cell communication networks between anterior and posterior notochord domains and ectodermal subclusters in the CS9 embryo, inferred by CellChat analysis. Line thickness reflects the relative number of ligand–receptor interactions. g, Bubble plot showing selected ligand–receptor pairs mediating interactions between anterior or posterior notochord domains and forebrain or Spinal Cord 1 clusters in the CS9 embryo. Bubble size denotes interaction significance (–log10 P value), and colour indicates communication probability. Statistical significance of each ligand–receptor interaction was assessed using a one-sided permutation test (n = 100 permutations) as implemented in CellChat. P values were not adjusted for multiple comparisons.

Source data

Supplementary information

Supplementary Information (download PDF )

Supplementary Figs. 1–4

Reporting Summary (download PDF )

Supplementary Table 1 (download XLSX )

Gene Ontology (GO) terms of Hotspot modules of CS9 cynomolgus monkey embryo

Supplementary Table 2 (download XLSX )

Gene Ontology (GO) terms of Hotspot modules of CS10 cynomolgus monkey embryo

Supplementary Data 1 (download XLSX )

Source data for Supplementary Fig. 3

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Tan, J.P., Liu, Y., Fu, Y. et al. A three-dimensional spatial transcriptome atlas reconstructs early organogenesis in primate Carnegie stages 9 and 10 embryos. Nat Cell Biol (2026). https://doi.org/10.1038/s41556-026-01956-2

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