Abstract
Defining the precise regionalization of specified definitive endoderm progenitors is critical for understanding the mechanisms underlying the generation and regeneration of respiratory and digestive organs, yet the patterning of endoderm progenitors remains unresolved, particularly in humans. We performed single-cell RNA sequencing on endoderm cells during the early somitogenesis stages in mice and humans. We developed molecular criteria to define four major endoderm regions (foregut, lip of anterior intestinal portal, midgut, and hindgut) and their developmental pathways. We identified the cell subpopulations in each region and their spatial distributions and characterized key molecular features along the body axes. Dorsal and ventral pancreatic progenitors appear to originate from the midgut population and follow distinct pathways to develop into an identical cell type. Finally, we described the generally conserved endoderm patterning in humans and clear differences in dorsal cell distribution between species. Our study comprehensively defines single-cell endoderm patterning and provides novel insights into the spatiotemporal process that drives establishment of early endoderm domains.
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Data availability
The RNA-seq data from this publication have been deposited in the Genome Sequence Archive (GSA) and assigned the identifiers CRA003104 and HRA000280.
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Acknowledgements
We thank Drs. Ken Zaret, Chris Wright, and Erfei Bi for their critical advice; Drs. Genji Qin and Peng Du for assistance with imaging; Drs. Jing Zhang and Yi Wang for assistance with human embryo collection; members of the Xu laboratory for advice and comments; Ms. Yanzhu Yue and Dr. Aibin He for assistance with the rat serum preparation and tissue culture; and the Peking-Tsinghua Center for Life Science Computing Platform. We thank the flow cytometry Core at National Center for Protein Sciences at Peking University, particularly Ms. Fei Wang and Ms. Yinghua Guo for technical help, and Mr. Ming Du from the Core Facility of the School of Life Sciences for drawing schematics. This work was supported by the National Key R&D Program of China (2019YFA0801500), the National Basic Research Program of China (2015CB942800), the National Natural Science Foundation of China (31521004, 31471358, and 31522036), and funding from Peking-Tsinghua Center for Life Sciences.
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C.-R.X. conceived the project; C.-R.X., L.-C.L., and X.W. designed the study; L.-C.L., Z.-R.X., Y.-C.W, Y.F., Liu Y., and Li Y. performed the experiments; L.-C.L., X.W., W.-L.Q., Z.-R.X., X.-X.Y., J.G. and C.-R.X. analyzed the data; L.-C.L., X.W., X.-X.Y., and C.-R.X. wrote the manuscript.
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Li, LC., Wang, X., Xu, ZR. et al. Single-cell patterning and axis characterization in the murine and human definitive endoderm. Cell Res 31, 326–344 (2021). https://doi.org/10.1038/s41422-020-00426-0
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DOI: https://doi.org/10.1038/s41422-020-00426-0
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