Intestinal organoid cocultures with microbes

Hans Clevers, Jens Puschhof, Joep Beumer, Cayetano Pleguezuelos-Manzano, Adriana Martinez-Silgado, Ninouk Akkerman, Aurelia Saftien, Charelle Boot, Amy de Waal, Devanjali Dutta, Inha Heo

Published: 2021-08-10 DOI: 10.1038/s41596-021-00589-z

fluorescence microscopy

organoid coculture

host-microbe interaction

microinjection

RNA sequencing

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Adult-stem-cell-derived organoids model human epithelial tissues exvivo, which enables the study of host–nobreakmicrobe interactions with great experimental control. This protocol comprises methods to coculture organoids with microbes, particular
Introduction
Materials
Procedure
Troubleshooting
Timing
Anticipated results
- Reporting Summary
- References
References
ACKNOWLEDGMENTS

Sato, T. et al. Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche. Nature 459, 262–265 (2009).
Dutta, D., Heo, I. & Clevers, H. Disease modeling in stem cell-derived 3D organoid systems. Trends Mol. Med. 23, 393–410 (2017).
Min, S., Kim, S. & Cho, S.-W. Gastrointestinal tract modeling using organoids engineered with cellular and microbiota niches. Exp. Mol. Med. 52, 227–237 (2020).
Leslie, J. L. & Young, V. B. A whole new ball game: stem cell-derived epithelia in the study of host-microbe interactions. Anaerobe 37, 25–28 (2016).
Heo, I. et al. Modelling Cryptosporidium infection in human small intestinal and lung organoids. Nat. Microbiol. 3, 814–823 (2018).
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).
Ettayebi, K. et al. Replication of human noroviruses in stem cell-derived human enteroids. Science 353, 1387–1393 (2016).
Lamers, M. M. et al. SARS-CoV-2 productively infects human gut enterocytes. Science https://doi.org/10.1126/science.abc1669 (2020).
Zhou, J. et al. Infection of bat and human intestinal organoids by SARS-CoV-2. Nat. Med. 26, 1077–1083 (2020).
Pleguezuelos-Manzano, C. et al. Mutational signature in colorectal cancer caused by genotoxic pks+ E. coli. Nature 580, 269–273 (2020).
Andersson-Rolf, A., Fink, J., Mustata, R. C. & Koo, B.-K. A video protocol of retroviral infection in primary intestinal organoid culture. J. Vis. Exp. https://doi.org/10.3791/51765 (2014).
Holthaus, D., Delgado-Betancourt, E., Aebischer, T., Seeber, F. & Klotz, C. Harmonization of protocols for multi-species organoid platforms to study the intestinal biology of Toxoplasma gondii and other protozoan infections. Front. Cell. Infect. Microbiol. 10, 610368 (2021).
Dutta, D., Heo, I. & O’Connor, R. Studying Cryptosporidium infection in 3D tissue-derived human organoid culture systems by microinjection. J. Vis. Exp. https://doi.org/10.3791/59610 (2019).
Sato, T. et al. Long-term expansion of epithelial organoids from human colon, adenoma, adenocarcinoma, and Barrett’s epithelium. Gastroenterology 141, 1762–1772 (2011).
Fakhiri, J. et al. Novel chimeric gene therapy vectors based on adeno-associated virus and four different mammalian bocaviruses. Mol. Ther. Methods Clin. Dev. 12, 202–222 (2019).
Pleguezuelos‐Manzano, C. et al. Establishment and culture of human intestinal organoids derived from adult stem cells. Curr. Protoc. Immunol. 130, (2020).
Beumer, J. et al. High-resolution mRNA and secretome atlas of human enteroendocrine cells. Cell 181, 1291–1306.e19 (2020).
Boonekamp, K. E., Dayton, T. L. & Clevers, H. Intestinal organoids as tools for enriching and studying specific and rare cell types: advances and future directions. J. Mol. Cell Biol. https://doi.org/10.1093/jmcb/mjaa034 (2020).
Bar-Ephraim, Y. E., Kretzschmar, K. & Clevers, H. Organoids in immunological research. Nat. Rev. Immunol. 20, 279–293 (2020).
Dijkstra, K. K. et al. Generation of tumor-reactive T cells by co-culture of peripheral blood lymphocytes and tumor organoids. Cell 174, 1586–1598.e12 (2018).
Greicius, G. et al. PDGFRα+ pericryptal stromal cells are the critical source of Wnts and RSPO3 for murine intestinal stem cells in vivo. Proc. Natl Acad. Sci. USA 115, E3173–E3181 (2018).
Noel, G. et al. A primary human macrophage-enteroid co-culture model to investigate mucosal gut physiology and host-pathogen interactions. Sci. Rep. 7, 45270 (2017).
Round, J. L. & Mazmanian, S. K. The gut microbiome shapes intestinal immune responses during health and disease. Nat. Rev. Immunol. 9, 313–323 (2009).
Spence, J. R. et al. Directed differentiation of human pluripotent stem cells into intestinal tissue in vitro. Nature 470, 105–109 (2011).
McCauley, H. A. & Wells, J. M. Pluripotent stem cell-derived organoids: using principles of developmental biology to grow human tissues in a dish. Development 144, 958–962 (2017).
Forbester, J. L. et al. Interaction of Salmonella enterica serovar Typhimurium with intestinal organoids derived from human induced pluripotent stem cells. Infect. Immun. 83, 2926–2934 (2015).
Holokai, L. et al. Increased programmed death ligand-1 is an early epithelial cell response to Helicobacter pylori infection. PLoS Pathog. 15, e1007468 (2019).
Finkbeiner, S. R. et al. Stem cell–derived human intestinal organoids as an infection model for rotaviruses. mBio 3, e00159-12 (2012).
Nikolaev, M. et al. Homeostatic mini-intestines through scaffold-guided organoid morphogenesis. Nature 585, 574–578 (2020).
Jalili-Firoozinezhad, S. et al. A complex human gut microbiome cultured in an anaerobic intestine-on-a-chip. Nat. Biomed. Eng. 3, 520–531 (2019).
Steinway, S. N., Saleh, J., Koo, B.-K., Delacour, D. & Kim, D.-H. Human microphysiological models of intestinal tissue and gut microbiome. Front. Bioeng. Biotechnol. 8, 725 (2020).
Hinman, S. S., Wang, Y. & Allbritton, N. L. Photopatterned membranes and chemical gradients enable scalable phenotypic organization of primary human colon epithelial models. Anal. Chem. 91, 15240–15247 (2019).
Avraham, R. et al. A highly multiplexed and sensitive RNA-seq protocol for simultaneous analysis of host and pathogen transcriptomes. Nat. Protoc. 11, 1477–1491 (2016).
Marsh, J. W., Humphrys, M. S. & Myers, G. S. A. A laboratory methodology for dual RNA-sequencing of bacteria and their host cells in vitro. Front. Microbiol. 8, 1830 (2017).
Westermann, A. J. et al. Dual RNA-seq unveils noncoding RNA functions in host–pathogen interactions. Nature 529, 496–501 (2016).
Sezonov, G., Joseleau-Petit, D. & D’Ari, R. Escherichia coli physiology in Luria–Bertani broth. J. Bacteriol. 189, 8746–8749 (2007).
Sim, K. et al. Improved detection of bifidobacteria with optimised 16S rRNA-gene based pyrosequencing. PLoS ONE 7, e32543 (2012).
Blokzijl, F. et al. Tissue-specific mutation accumulation in human adult stem cells during life. Nature 538, 260–264 (2016).

Intestinal organoid cocultures with microbes

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