3D reconstruction of a human Carnegie stage 9 embryo provides a snapshot of early body plan formation

Yang Yuan; Xiaoyan Wang; Xiaodi Yan; Nannan He; Xiaojian Lu; Jingyu Yang; Xinwei Xie; Huiyao Yuan; Naixin Chen; Yinbo Liu; Hongan Ren; Runzhao Zhang; Lina Cui; Pengcheng Ren; Sirui Lin; Shuhan Cheng; Xiaolong Yang; Yifei Guo; Rong Li; Tianyi Yan; Jingtao Guo; Zhenyu Xiao; Yulei Wei; Leqian Yu

doi:10.1016/j.stem.2025.04.007

3D reconstruction of a human Carnegie stage 9 embryo provides a snapshot of early body plan formation

Yang Yuan, Xiaoyan Wang, Xiaodi Yan, Nannan He, Xiaojian Lu, Jingyu Yang, Xinwei Xie, Huiyao Yuan, Naixin Chen, Yinbo Liu, Hongan Ren, Runzhao Zhang, Lina Cui, Pengcheng Ren, Sirui Lin, Shuhan Cheng, Xiaolong Yang, Yifei Guo, Rong Li, Tianyi YanJingtao Guo^*, Zhenyu Xiao^*, Yulei Wei^*, Leqian Yu^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

Abstract

The Carnegie stage 9 (CS9) embryo is a pivotal phase signifying the conclusion of gastrulation and the onset of early organogenesis, crucial for initiating major organ system development. Utilizing spatial transcriptomics, we analyzed an intact CS9 human embryo in a spatially detailed manner. Through the examination of 75 transverse cryosections, we digitally reconstructed a 3D model, allowing us to identify diverse cell types, including those from brain and spine regions, the primitive gut tube, distinct somite formation stages, somatic mesoderm, splanchnic mesoderm, etc. Notably, we observed two distinct trajectories of hindbrain development, pinpointed the isthmic organizer at the midbrain-hindbrain boundary, delineated the bi-layered structure of neuromesodermal progenitor (NMP) cells, and described the early aorta formation and primordial germ cells (PGCs) presence in the aorta-gonad-mesonephros (AGM) region. This study provides key insights into the transcriptomic and spatial intricacies shaping the human body plan.

Original language	English
Pages (from-to)	1006-1024.e5
Journal	Cell Stem Cell
Volume	32
Issue number	6
DOIs	https://doi.org/10.1016/j.stem.2025.04.007
Publication status	Published - 5 Jun 2025
Externally published	Yes

Keywords

3D reconstruction
AGM
Carnegie stage 9
cardiogenesis
hindbrain
human embryo
primitive gut tube
somitogenesis
spatial transcriptomics sequencing
stereo-seq

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.1016/j.stem.2025.04.007

Cite this

Yuan, Y., Wang, X., Yan, X., He, N., Lu, X., Yang, J., Xie, X., Yuan, H., Chen, N., Liu, Y., Ren, H., Zhang, R., Cui, L., Ren, P., Lin, S., Cheng, S., Yang, X., Guo, Y., Li, R., ... Yu, L. (2025). 3D reconstruction of a human Carnegie stage 9 embryo provides a snapshot of early body plan formation. Cell Stem Cell, 32(6), 1006-1024.e5. https://doi.org/10.1016/j.stem.2025.04.007

@article{fc352138893845d39dca8bb019d00fe8,

title = "3D reconstruction of a human Carnegie stage 9 embryo provides a snapshot of early body plan formation",

abstract = "The Carnegie stage 9 (CS9) embryo is a pivotal phase signifying the conclusion of gastrulation and the onset of early organogenesis, crucial for initiating major organ system development. Utilizing spatial transcriptomics, we analyzed an intact CS9 human embryo in a spatially detailed manner. Through the examination of 75 transverse cryosections, we digitally reconstructed a 3D model, allowing us to identify diverse cell types, including those from brain and spine regions, the primitive gut tube, distinct somite formation stages, somatic mesoderm, splanchnic mesoderm, etc. Notably, we observed two distinct trajectories of hindbrain development, pinpointed the isthmic organizer at the midbrain-hindbrain boundary, delineated the bi-layered structure of neuromesodermal progenitor (NMP) cells, and described the early aorta formation and primordial germ cells (PGCs) presence in the aorta-gonad-mesonephros (AGM) region. This study provides key insights into the transcriptomic and spatial intricacies shaping the human body plan.",

keywords = "3D reconstruction, AGM, Carnegie stage 9, cardiogenesis, hindbrain, human embryo, primitive gut tube, somitogenesis, spatial transcriptomics sequencing, stereo-seq",

author = "Yang Yuan and Xiaoyan Wang and Xiaodi Yan and Nannan He and Xiaojian Lu and Jingyu Yang and Xinwei Xie and Huiyao Yuan and Naixin Chen and Yinbo Liu and Hongan Ren and Runzhao Zhang and Lina Cui and Pengcheng Ren and Sirui Lin and Shuhan Cheng and Xiaolong Yang and Yifei Guo and Rong Li and Tianyi Yan and Jingtao Guo and Zhenyu Xiao and Yulei Wei and Leqian Yu",

note = "Publisher Copyright: {\textcopyright} 2025 Elsevier Inc.",

year = "2025",

month = jun,

day = "5",

doi = "10.1016/j.stem.2025.04.007",

language = "English",

volume = "32",

pages = "1006--1024.e5",

journal = "Cell Stem Cell",

issn = "1934-5909",

publisher = "Cell Press",

number = "6",

}

Yuan, Y, Wang, X, Yan, X, He, N, Lu, X, Yang, J, Xie, X, Yuan, H, Chen, N, Liu, Y, Ren, H, Zhang, R, Cui, L, Ren, P, Lin, S, Cheng, S, Yang, X, Guo, Y, Li, R, Yan, T, Guo, J, Xiao, Z, Wei, Y & Yu, L 2025, '3D reconstruction of a human Carnegie stage 9 embryo provides a snapshot of early body plan formation', Cell Stem Cell, vol. 32, no. 6, pp. 1006-1024.e5. https://doi.org/10.1016/j.stem.2025.04.007

TY - JOUR

T1 - 3D reconstruction of a human Carnegie stage 9 embryo provides a snapshot of early body plan formation

AU - Yuan, Yang

AU - Wang, Xiaoyan

AU - Yan, Xiaodi

AU - He, Nannan

AU - Lu, Xiaojian

AU - Yang, Jingyu

AU - Xie, Xinwei

AU - Yuan, Huiyao

AU - Chen, Naixin

AU - Liu, Yinbo

AU - Ren, Hongan

AU - Zhang, Runzhao

AU - Cui, Lina

AU - Ren, Pengcheng

AU - Lin, Sirui

AU - Cheng, Shuhan

AU - Yang, Xiaolong

AU - Guo, Yifei

AU - Li, Rong

AU - Yan, Tianyi

AU - Guo, Jingtao

AU - Xiao, Zhenyu

AU - Wei, Yulei

AU - Yu, Leqian

PY - 2025/6/5

Y1 - 2025/6/5

N2 - The Carnegie stage 9 (CS9) embryo is a pivotal phase signifying the conclusion of gastrulation and the onset of early organogenesis, crucial for initiating major organ system development. Utilizing spatial transcriptomics, we analyzed an intact CS9 human embryo in a spatially detailed manner. Through the examination of 75 transverse cryosections, we digitally reconstructed a 3D model, allowing us to identify diverse cell types, including those from brain and spine regions, the primitive gut tube, distinct somite formation stages, somatic mesoderm, splanchnic mesoderm, etc. Notably, we observed two distinct trajectories of hindbrain development, pinpointed the isthmic organizer at the midbrain-hindbrain boundary, delineated the bi-layered structure of neuromesodermal progenitor (NMP) cells, and described the early aorta formation and primordial germ cells (PGCs) presence in the aorta-gonad-mesonephros (AGM) region. This study provides key insights into the transcriptomic and spatial intricacies shaping the human body plan.

AB - The Carnegie stage 9 (CS9) embryo is a pivotal phase signifying the conclusion of gastrulation and the onset of early organogenesis, crucial for initiating major organ system development. Utilizing spatial transcriptomics, we analyzed an intact CS9 human embryo in a spatially detailed manner. Through the examination of 75 transverse cryosections, we digitally reconstructed a 3D model, allowing us to identify diverse cell types, including those from brain and spine regions, the primitive gut tube, distinct somite formation stages, somatic mesoderm, splanchnic mesoderm, etc. Notably, we observed two distinct trajectories of hindbrain development, pinpointed the isthmic organizer at the midbrain-hindbrain boundary, delineated the bi-layered structure of neuromesodermal progenitor (NMP) cells, and described the early aorta formation and primordial germ cells (PGCs) presence in the aorta-gonad-mesonephros (AGM) region. This study provides key insights into the transcriptomic and spatial intricacies shaping the human body plan.

KW - 3D reconstruction

KW - AGM

KW - Carnegie stage 9

KW - cardiogenesis

KW - hindbrain

KW - human embryo

KW - primitive gut tube

KW - somitogenesis

KW - spatial transcriptomics sequencing

KW - stereo-seq

UR - http://www.scopus.com/inward/record.url?scp=105004818194&partnerID=8YFLogxK

U2 - 10.1016/j.stem.2025.04.007

DO - 10.1016/j.stem.2025.04.007

M3 - Article

AN - SCOPUS:105004818194

SN - 1934-5909

VL - 32

SP - 1006-1024.e5

JO - Cell Stem Cell

JF - Cell Stem Cell

IS - 6

ER -

3D reconstruction of a human Carnegie stage 9 embryo provides a snapshot of early body plan formation

Abstract

Keywords

UN SDGs

Access to Document

Other files and links

Fingerprint

Cite this