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Plate IV.92 · Publications

An integrated transcriptomic cell atlas of human endoderm-derived organoids

Article in Nature Genetics, May 2025.

Open accessCell Atlas, Integration

  1. Quan Xu
  2. Lennard Halle
  3. Soroor Hediyeh-zadeh
  4. Merel Kuijs
  5. Rya Riedweg
  6. Umut Kilik
  7. Timothy Recaldin
  8. Qianhui Yu
  9. Isabell Rall
  10. Tristan Frum
  11. Lukas Adam
  12. Shrey Parikh
  13. Raphael Kfuri-Rubens
  14. Manuel Gander
  15. Dominik Klein
  16. Fabiola Curion
  17. Zhisong He
  18. Jonas Simon Fleck
  19. Koen Oost
  20. Maurice Kahnwald
  21. Silvia Barbiero
  22. Olga Mitrofanova
  23. Grzegorz Jerzy Maciag
  24. Kim B. Jensen
  25. Matthias Lutolf
  26. Prisca Liberali
  27. Jason R. Spence
  28. Nikolche Gjorevski
  29. Joep Beumer
  30. Barbara Treutlein
  31. Fabian J. Theis
  32. J. Gray Camp

Abstract

Human pluripotent stem cells and tissue-resident fetal and adult stem cells can generate epithelial tissues of endodermal origin in vitro that recapitulate aspects of developing and adult human physiology. Here, we integrate single-cell transcriptomes from 218 samples covering organoids and other models of diverse endoderm-derived tissues to establish an initial version of a human endoderm-derived organoid cell atlas. The integration includes nearly one million cells across diverse conditions, data sources and protocols. We compare cell types and states between organoid models and harmonize cell annotations through mapping to primary tissue counterparts. Focusing on the intestine and lung, we provide examples of mapping data from new protocols and show how the atlas can be used as a diverse cohort to assess perturbations and disease models. The human endoderm-derived organoid cell atlas makes diverse datasets centrally available and will be valuable to assess fidelity, characterize perturbed and diseased states, and streamline protocol development.

Versions2

  1. PublishedNature Genetics10.1038/s41588-025-02182-6
  2. PreprintbioRxiv10.1101/2023.11.20.567825

Cite

@article{xu2025integrated,
  title = {{An integrated transcriptomic cell atlas of human endoderm-derived organoids}},
  author = {Xu, Quan and Halle, Lennard and Hediyeh-zadeh, Soroor and Kuijs, Merel and Riedweg, Rya and Kilik, Umut and Recaldin, Timothy and Yu, Qianhui and Rall, Isabell and Frum, Tristan and Adam, Lukas and Parikh, Shrey and Kfuri-Rubens, Raphael and Gander, Manuel and Klein, Dominik and Curion, Fabiola and He, Zhisong and Fleck, Jonas Simon and Oost, Koen and Kahnwald, Maurice and Barbiero, Silvia and Mitrofanova, Olga and Maciag, Grzegorz Jerzy and Jensen, Kim B. and Lutolf, Matthias and Liberali, Prisca and Spence, Jason R. and Gjorevski, Nikolche and Beumer, Joep and Treutlein, Barbara and Theis, Fabian J. and Camp, J. Gray},
  journal = {Nature Genetics},
  publisher = {Springer Science and Business Media LLC},
  year = {2025},
  month = may,
  doi = {10.1038/s41588-025-02182-6},
  url = {https://doi.org/10.1038/s41588-025-02182-6},
  pmid = {40355592},
  pmcid = {PMC12081310}
}
.bib file