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Patterned gastrointestinal monolayers with bilateral access as observable models of parasite gut infection

Nature Biomedical Engineering volume 9, pages 1075–1085 (2025)Cite this article

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An Author Correction to this article was published on 20 January 2025

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Abstract

Organoids for modelling the physiology and pathology of gastrointestinal tissues are constrained by a poorly accessible lumen. Here we report the development and applicability of bilaterally accessible organoid-derived patterned epithelial monolayers that allow the independent manipulation of their apical and basal sides. We constructed gastric, small-intestinal, caecal and colonic epithelial models that faithfully reproduced their respective tissue geometries and that exhibited stem cell regionalization and transcriptional resemblance to in vivo epithelia. The models’ enhanced observability allowed single-cell tracking and studies of the motility of cells in immersion culture and at the air–liquid interface. Models mimicking infection of the caecal epithelium by the parasite Trichuris muris allowed us to live image syncytial tunnel formation. The enhanced observability of bilaterally accessible organoid-derived gastrointestinal tissue will facilitate the study of the dynamics of epithelial cells and their interactions with pathogens.

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Fig. 1: A microfluidic system for a stem cell-derived epithelial monolayer with bilateral accessibility.
Fig. 2: Generation of observable epithelial organoid monolayer of GI tissues.
Fig. 3: Gastric transgel organoids in ALI cultures show enhanced transcriptional relevance and increased motility.
Fig. 4: Infection of caecal transgel organoids with L1 larvae of T. muris.

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Data availability

The main data supporting the results in this study are available within the article and its Supplementary Information. RNA sequencing source data are available from the Gene Expression Omnibus repository via the accession code GSE241012.

Code availability

Custom analysis code is available from the corresponding authors on request.

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References

  1. Clevers, H. Modeling development and disease with organoids. Cell 165, 1586–1597 (2016).

    Article  CAS  PubMed  Google Scholar 

  2. Fatehullah, A., Tan, S. H. & Barker, N. Organoids as an in vitro model of human development and disease. Nat. Cell Biol. 18, 246–254 (2016).

    Article  PubMed  Google Scholar 

  3. Lancaster, M. A. & Knoblich, J. A. Organogenesisin a dish: modeling development and disease using organoid technologies. Science 345, 1247125 (2014).

    Article  PubMed  Google Scholar 

  4. Sato, T. et al. Single Lgr5 stem cells build crypt–villus structures in vitro without a mesenchymal niche. Nature 459, 262–265 (2009).

    Article  CAS  PubMed  Google Scholar 

  5. Hofer, M. & Lutolf, M. P. Engineering organoids. Nat. Rev. Mater. 6, 402–420 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Boccellato, F. et al. Polarised epithelial monolayers of the gastric mucosa reveal insights into mucosal homeostasis and defence against infection. Gut 68, 400–413 (2019).

    Article  CAS  PubMed  Google Scholar 

  7. Liu, Y., Qi, Z., Li, X., Du, Y. & Chen, Y. G. Monolayer culture of intestinal epithelium sustains Lgr5+ intestinal stem cells. Cell Discov. 4, 4–6 (2018).

    Article  Google Scholar 

  8. VanDussen, K. L. et al. Development of an enhanced human gastrointestinal epithelial culture system to facilitate patient-based assays. Gut 64, 911–920 (2015).

    Article  CAS  PubMed  Google Scholar 

  9. Wang, Y. et al. Long-term culture captures injury–repair cycles of colonic stem cells. Cell 179, 1144–1159.e15 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Roodsant, T. et al. A human 2D primary organoid-derived epithelial monolayer model to study host–pathogen interaction in the small intestine. Front. Cell Infect. Microbiol. 10, 1–14 (2020).

    Article  Google Scholar 

  11. Thorne, C. A. et al. Enteroid monolayers reveal an autonomous WNT and BMP circuit controlling intestinal epithelial growth and organization. Dev. Cell 44, 624–633.e4 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Jabaji, Z. et al. Use of collagen gel as an alternative extracellular matrix for the in vitro and in vivo growth of murine small intestinal epithelium. Tissue Eng. Part C 19, 961–969 (2013).

    Article  CAS  Google Scholar 

  13. Duque-Correa, M. A. et al. Defining the early stages of intestinal colonisation by whipworms. Nat. Commun. 13, 1725 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Wang, Y. et al. Formation of human colonic crypt array by application of chemical gradients across a shaped epithelial monolayer. Cell Mol. Gastroenterol. Hepatol. 5, 113–130 (2018).

    Article  PubMed  Google Scholar 

  15. Costello, C. M. et al. 3-D intestinal scaffolds for evaluating the therapeutic potential of probiotics. Mol. Pharm. 11, 2030–2039 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Wang, Y. et al. A microengineered collagen scaffold for generating a polarized crypt-villus architecture of human small intestinal epithelium. Biomaterials 128, 44–55 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Creff, J. et al. Fabrication of 3D scaffolds reproducing intestinal epithelium topography by high-resolution 3D stereolithography. Biomaterials https://doi.org/10.1016/j.biomaterials.2019.119404 (2019).

  18. Verhulsel, M. et al. Developing an advanced gut on chip model enabling the study of epithelial cell/fibroblast interactions. Lab Chip 21, 365–377 (2021).

    Article  CAS  PubMed  Google Scholar 

  19. Gjorevski, N. et al. Tissue geometry drives deterministic organoid patterning. Science https://doi.org/10.1126/science.aaw9021 (2022).

  20. Nikolaev, M. et al. Homeostatic mini-intestines through scaffold-guided organoid morphogenesis. Nature 585, 574–578 (2020).

    Article  PubMed  Google Scholar 

  21. Barker, N. et al. Lgr5+ve stem cells drive self-renewal in the stomach and build long-lived gastric units in vitro. Cell Stem Cell 6, 25–36 (2010).

    Article  CAS  PubMed  Google Scholar 

  22. Zhu, G., Hu, J. & Xi, R. The cellular niche for intestinal stem cells: a team effort. Cell Regen. 10, 1–16 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Casteleyn, C., Rekecki, A., Van Der Aa, A., Simoens, P. & Van Den Broeck, W. Surface area assessment of the murine intestinal tract as a prerequisite for oral dose translation from mouse to man. Lab Anim. 44, 176–183 (2010).

    Article  CAS  PubMed  Google Scholar 

  24. Choi, E. et al. Cell lineage distribution atlas of the human stomach reveals heterogeneous gland populations in the gastric antrum. Gut 63, 1711–1720 (2014).

    Article  PubMed  Google Scholar 

  25. Ootani, A., Toda, S., Fujimoto, K. & Sugihara, H. An air–liquid interface promotes the differentiation of gastric surface mucous cells (GSM06) in culture. Biochem. Biophys. Res. Commun. 271, 741–746 (2000).

    Article  CAS  PubMed  Google Scholar 

  26. Zhang, Y., Zeng, F., Han, X., Weng, J. & Gao, Y. Lineage tracing: technology tool for exploring the development, regeneration, and disease of the digestive system. Stem Cell Res. Ther. 11, 1–16 (2020).

    Article  Google Scholar 

  27. Bartfeld, S. et al. In vitro expansion of human gastric epithelial stem cells and their responses to bacterial infection. Gastroenterology 148, 126–136.e6 (2015).

    Article  PubMed  Google Scholar 

  28. Co, J. Y. et al. Controlling epithelial polarity: a human enteroid model for host–pathogen interactions. Cell Rep. 26, 2509–2520.e4 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Dutta, D. & Clevers, H. Organoid culture systems to study host–pathogen interactions. Curr. Opin. Immunol. 48, 15–22 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. White, R., Blow, F., Buck, A. H. & Duque-Correa, M. A. Organoids as tools to investigate gastrointestinal nematode development and host interactions. Front. Cell Infect. Microbiol. 12, 1–9 (2022).

    Article  Google Scholar 

  31. Duque-Correa, M. A., Maizels, R. M., Grencis, R. K. & Berriman, M. Organoids—new models for host–helminth interactions. Trends Parasitol. 36, 170–181 (2020).

    Article  PubMed  Google Scholar 

  32. Yousefi, Y., Haq, S., Banskota, S., Kwon, Y. H. & Khan, W. I. Trichuris muris model: role in understanding intestinal immune response, inflammation and host defense. Pathogens 10, 1–21 (2021).

    Article  Google Scholar 

  33. Bancroft, A. J. et al. The major secreted protein of the whipworm parasite tethers to matrix and inhibits interleukin-13 function. Nat Commun. 10, 2344 (2019).

  34. Panesar, T. S. & Croll, N. A. The location of parasites within their hosts: site selection by Trichuris muris in the laboratory mouse. Int J. Parasitol. 10, 261–273 (1980).

    Article  CAS  PubMed  Google Scholar 

  35. Gjorevski, N. et al. Designer matrices for intestinal stem cell and organoid culture. Nature 539, 560–564 (2016).

    Article  CAS  PubMed  Google Scholar 

  36. Ramanujan, S. et al. Diffusion and convection in collagen gels: implications for transport in the tumor interstitium. Biophys. J. 83, 1650–1660 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Miyoshi, H. & Stappenbeck, T. S. In vitro expansion and genetic modification of gastrointestinal stem cells in spheroid culture. Nat. Protoc. 8, 2471–2482 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Bartfeld, S. & Clevers, H. Organoids as model for infectious diseases: culture of human and murine stomach organoids and microinjection of Helicobacter pylori. J. Vis. Exp. https://doi.org/10.3791/53359 (2015)

  39. Duque-Correa, M. A. et al. Development of caecaloids to study host-pathogen interactions: new insights into immunoregulatory functions of Trichuris muris extracellular vesicles in the caecum. Int. J. Parasitol. 50, 707–718 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Nik, A. M. & Carlsson, P. Separation of intact intestinal epithelium from mesenchyme. Biotechniques 55, 42–44 (2013).

    Article  CAS  PubMed  Google Scholar 

  41. Stirling, D. R. et al. CellProfiler 4: improvements in speed, utility and usability. BMC Bioinf. 22, 1–11 (2021).

    Article  Google Scholar 

  42. Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).

    Article  CAS  PubMed  Google Scholar 

  43. Chen, Y., Lun, A. T. L. & Smyth, G. K. From reads to genes to pathways: differential expression analysis of RNA-seq experiments using Rsubread and the edgeR quasi-likelihood pipeline. F1000Research. 5, 1–51 (2016).

    Google Scholar 

  44. Pachitariu, M. & Stringer, C. Cellpose 2.0: how to train your own model. Nat. Methods 19, 1634–1641 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Tinevez, J. Y. et al. TrackMate: an open and extensible platform for single-particle tracking. Methods 115, 80–90 (2017).

    Article  CAS  PubMed  Google Scholar 

  46. Berg, S. et al. ilastik: interactive machine learning for (bio)image analysis. Nat. Methods 16, 1226–1232 (2019).

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

We thank K. Sharma from the Laboratory of John McKinney (EPFL) and A. Widmer from the EPFL Organ/Tissue Sharing Program for providing cadavers of mice and R. Grencis (University of Manchester) for the p43 antibody. We thank M. Nikolaev for help producing the microfabricated moulds for stamps, S. Li for help generating colonic organoids, T. Hübscher, A. Chrisnandy and B. Sen Elci for valuable discussions and primers and J. Prébandier, L. Tillard and C. Tolley for administrative and technical support. We acknowledge support from CMi, BIOP, GECF, FCCF and HCF EPFL core facilities. This work was funded by the National Center of Competence in Research Bio-Inspired Materials, the EU Horizon 2020 research programme INTENS (www.intens.info; no. 668294-2) and the Swiss National Science Foundation research grant no. 310030_179447. This work was supported by the Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society (222546/Z/21/Z, M.A.D.-C.) and the Wellcome Trust (203151/A/16/Z, M.A.D.-C.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Author information

Authors and Affiliations

  1. Laboratory of Stem Cell Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland

    Moritz Hofer & Matthias P. Lutolf

  2. Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK

    Maria A. Duque-Correa

  3. Institute of Human Biology (IHB), Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland

    Matthias P. Lutolf

Authors
  1. Moritz Hofer
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Contributions

M.H. and M.P.L. conceived the study, designed experiments, interpreted data and wrote the paper. M.H. conducted all experiments and analysis. M.A.D.-C. proposed and supervised T. muris infection experiments, provided T. muris eggs, contributed to data interpretation and edited the paper.

Corresponding authors

Correspondence to Maria A. Duque-Correa or Matthias P. Lutolf.

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M.P.L. is an employee of Hoffmann-La Roche. The other authors declare no competing interests.

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Nature Biomedical Engineering thanks Martin Beaumont and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Supplementary information

Supplementary Information

Supplementary figures, tables and video captions.

Reporting Summary

Supplementary Video 1

Animated confocal live-acquired stack images of stomach, small intestine, caecum and colon transgel organoids.

Supplementary Video 2

Cellular motility of gastric transgel organoids in IMM and ALI cultures.

Supplementary Video 3

Infection of T. muris larvae on caecal transgel organoids.

Supplementary Video 4

T. muris larvae moving through epithelium by tunnel formation.

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Hofer, M., Duque-Correa, M.A. & Lutolf, M.P. Patterned gastrointestinal monolayers with bilateral access as observable models of parasite gut infection. Nat. Biomed. Eng 9, 1075–1085 (2025). https://doi.org/10.1038/s41551-024-01313-4

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