This work was supported by Institut Carnot France Futur Elevage (&#34;OrganoPig&#34; project) and by INRAE HOLOFLUX (&#34;Holopig&#34; project). The authors are grateful to the Genotoul core facilities (TRI). We acknowledge Christelle Knudsen (GenPhySE, INRAE, Toulouse) for&#160; careful proofreading.

<ol>
	<li>Peterson, L. W., Artis, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Intestinal+epithelial+cells:+regulators+of+barrier+function+and+immune+homeostasis.">Intestinal epithelial cells: regulators of barrier function and immune homeostasis.</a> Nature Reviews Immunology. 14 (3), 141-153 (2014).</li><li>In, J. G., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Human+mini-guts:+new+insights+into+intestinal+physiology+and+host-pathogen+interactions.">Human mini-guts: new insights into intestinal physiology and host-pathogen interactions.</a> Nature Reviews Gastroenterology &amp; Hepatology. 13 (11), 633-642 (2016).</li><li>Sato, T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Single+Lgr5+stem+cells+build+crypt-villus+structures+in+vitro+without+a+mesenchymal+niche.">Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche.</a> Nature. 459 (7244), 262-265 (2009).</li><li>Beaumont, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Intestinal+organoids+in+farm+animals.">Intestinal organoids in farm animals.</a> Veterinary Research. 52 (1), 33 (2021).</li><li>Gonzalez, L. M., Williamson, I., Piedrahita, J. A., Blikslager, A. T., Magness, S. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cell+lineage+identification+and+stem+cell+culture+in+a+porcine+model+for+the+study+of+intestinal+epithelial+regeneration.">Cell lineage identification and stem cell culture in a porcine model for the study of intestinal epithelial regeneration.</a> PLoS One. 8 (6), 66465 (2013).</li><li>Holthaus, D., Delgado-Betancourt, E., Aebischer, T., Seeber, F., Klotz, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Harmonization+of+protocols+for+multi-species+organoid+platforms+to+study+the+intestinal+biology+of+toxoplasma+gondii+and+other+protozoan+infections.">Harmonization of protocols for multi-species organoid platforms to study the intestinal biology of toxoplasma gondii and other protozoan infections.</a> Frontiers in Cellular and Infection Microbiology. 10, 610368 (2021).</li><li>Powell, R. H., Behnke, M. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=WRN+conditioned+media+is+sufficient+for+in+vitro+propagation+of+intestinal+organoids+from+large+farm+and+small+companion+animals.">WRN conditioned media is sufficient for in vitro propagation of intestinal organoids from large farm and small companion animals.</a> Biology Open. 6 (5), 698-705 (2017).</li><li>Li, L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Porcine+intestinal+enteroids:+a+new+model+for+studying+enteric+coronavirus+porcine+epidemic+diarrhea+virus+infection+and+the+host+innate+response.">Porcine intestinal enteroids: a new model for studying enteric coronavirus porcine epidemic diarrhea virus infection and the host innate response.</a> Journal of Virology. 93 (5), 01682 (2019).</li><li>vander Hee, B., Madsen, O., Vervoort, J., Smidt, H., Wells, J. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Congruence+of+transcription+programs+in+adult+stem+cell-derived+jejunum+organoids+and+original+tissue+during+long-term+culture.">Congruence of transcription programs in adult stem cell-derived jejunum organoids and original tissue during long-term culture.</a> Frontiers in Cell and Developmental Biology. 8, 375 (2020).</li><li>Barnett, A. M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Porcine+colonoids+and+enteroids+keep+the+memory+of+their+origin+during+regeneration.">Porcine colonoids and enteroids keep the memory of their origin during regeneration.</a> American Journal of Physiology. Cell Physiology. 320 (5), 794-805 (2021).</li><li>Mussard, E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+phenotype+of+the+gut+region+is+more+stably+retained+than+developmental+stage+in+piglet+intestinal+organoids.">The phenotype of the gut region is more stably retained than developmental stage in piglet intestinal organoids.</a> Frontiers in Cell and Developmental Biology. 10, 983031 (2022).</li><li>Zhu, M., Qin, Y. -. C., Gao, C. -. Q., Yan, H. -. C., Wang, X. -. Q. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=l-Glutamate+drives+porcine+intestinal+epithelial+renewal+by+increasing+stem+cell+activity+via+upregulation+of+the+EGFR-ERK-mTORC1+pathway.">l-Glutamate drives porcine intestinal epithelial renewal by increasing stem cell activity via upregulation of the EGFR-ERK-mTORC1 pathway.</a> Food &amp; Function. 11 (3), 2714-2724 (2020).</li><li>Wang, Z., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Dietary+vitamin+A+affects+growth+performance,+intestinal+development,+and+functions+in+weaned+piglets+by+affecting+intestinal+stem+cells.">Dietary vitamin A affects growth performance, intestinal development, and functions in weaned piglets by affecting intestinal stem cells.</a> Journal of Animal Science. 98 (2), (2020).</li><li>Derricott, H., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Developing+a+3D+intestinal+epithelium+model+for+livestock+species.">Developing a 3D intestinal epithelium model for livestock species.</a> Cell and Tissue Research. 375 (2), 409-424 (2019).</li><li>Khalil, H. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+novel+culture+system+for+adult+porcine+intestinal+crypts.">A novel culture system for adult porcine intestinal crypts.</a> Cell and Tissue Research. 365 (1), 123-134 (2016).</li><li>Stewart, A. S., Freund, J. M., Gonzalez, L. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Advanced+three-dimensional+culture+of+equine+intestinal+epithelial+stem+cells.">Advanced three-dimensional culture of equine intestinal epithelial stem cells.</a> Equine Veterinary Journal. 50 (2), 241-248 (2018).</li><li>Tsai, Y. -. H., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+method+for+cryogenic+preservation+of+human+biopsy+specimens+and+subsequent+organoid+culture.">A method for cryogenic preservation of human biopsy specimens and subsequent organoid culture.</a> Cellular and Molecular Gastroenterology and Hepatology. 6 (2), 218-222 (2018).</li><li>Wilson, S. S., Tocchi, A., Holly, M. K., Parks, W. C., Smith, J. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+small+intestinal+organoid+model+of+non-invasive+enteric+pathogen-epithelial+cell+interactions.">A small intestinal organoid model of non-invasive enteric pathogen-epithelial cell interactions.</a> Mucosal Immunology. 8 (2), 352-361 (2015).</li><li>Li, Y., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Next-generation+porcine+intestinal+organoids:+an+apical-out+organoid+model+for+swine+enteric+virus+infection+and+immune+response+investigations.">Next-generation porcine intestinal organoids: an apical-out organoid model for swine enteric virus infection and immune response investigations.</a> Journal of Virology. 94 (21), 01006-01020 (2020).</li><li>Moon, C., VanDussen, K. L., Miyoshi, H., Stappenbeck, T. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Development+of+a+primary+mouse+intestinal+epithelial+cell+monolayer+culture+system+to+evaluate+factors+that+modulate+IgA+transcytosis.">Development of a primary mouse intestinal epithelial cell monolayer culture system to evaluate factors that modulate IgA transcytosis.</a> Mucosal Immunology. 7 (4), 818-828 (2014).</li><li>vander Hee, B., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Optimized+procedures+for+generating+an+enhanced,+near+physiological+2D+culture+system+from+porcine+intestinal+organoids.">Optimized procedures for generating an enhanced, near physiological 2D culture system from porcine intestinal organoids.</a> Stem Cell Research. 28, 165-171 (2018).</li><li>Hoffmann, P., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Intestinal+organoid-based+2D+monolayers+mimic+physiological+and+pathophysiological+properties+of+the+pig+intestine.">Intestinal organoid-based 2D monolayers mimic physiological and pathophysiological properties of the pig intestine.</a> PLoS One. 16 (8), 0256143 (2021).</li><li>Vermeire, B., Gonzalez, L. M., Jansens, R. J. J., Cox, E., Devriendt, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Porcine+small+intestinal+organoids+as+a+model+to+explore+ETEC-host+interactions+in+the+gut.">Porcine small intestinal organoids as a model to explore ETEC-host interactions in the gut.</a> Veterinary Research. 52 (1), 94 (2021).</li><li>Luo, H., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Utility+evaluation+of+porcine+enteroids+as+PDCoV+infection+model+in+vitro.">Utility evaluation of porcine enteroids as PDCoV infection model in vitro.</a> Frontiers in Microbiology. 11, 821 (2020).</li><li>Resende, T. P., Medida, R. L., Vannucci, F. A., Saqui-Salces, M., Gebhart, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Evaluation+of+swine+enteroids+as+in+vitro+models+for+Lawsonia+intracellularis+infection1,2.">Evaluation of swine enteroids as in vitro models for Lawsonia intracellularis infection1,2.</a> Journal of Animal Science. 98 (2), 011 (2020).</li><li>Engevik, A. C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Editing+myosin+VB+gene+to+create+porcine+model+of+microvillus+inclusion+disease,+with+microvillus-lined+inclusions+and+alterations+in+sodium+transporters.">Editing myosin VB gene to create porcine model of microvillus inclusion disease, with microvillus-lined inclusions and alterations in sodium transporters.</a> Gastroenterology. 158 (8), 2236-2249 (2020).</li><li>Watanabe, K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+ROCK+inhibitor+permits+survival+of+dissociated+human+embryonic+stem+cells.">A ROCK inhibitor permits survival of dissociated human embryonic stem cells.</a> Nature Biotechnology. 25 (6), 681-686 (2007).</li><li>Gracz, A. D., Puthoff, B. J., Magness, S. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Identification,+isolation,+and+culture+of+intestinal+epithelial+stem+cells+from+murine+intestine.">Identification, isolation, and culture of intestinal epithelial stem cells from murine intestine.</a> Somatic Stem Cells: Methods and Protocols. 879, 89-107 (2012).</li><li>Ferrandis Vila, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Dietary+fiber+sources+and+non-starch+polysaccharide-degrading+enzymes+modify+mucin+expression+and+the+immune+profile+of+the+swine+ileum.">Dietary fiber sources and non-starch polysaccharide-degrading enzymes modify mucin expression and the immune profile of the swine ileum.</a> PloS One. 13 (11), 0207196 (2018).</li><li>Li, L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=IFN-lambda+3+mediates+antiviral+protection+against+porcine+epidemic+diarrhea+virus+by+inducing+a+distinct+antiviral+transcript+profile+in+porcine+intestinal+epithelia.">IFN-lambda 3 mediates antiviral protection against porcine epidemic diarrhea virus by inducing a distinct antiviral transcript profile in porcine intestinal epithelia.</a> Frontiers in Immunology. 10, 2394 (2019).</li><li>VanDussen, K. L., Sonnek, N. M., Stappenbeck, T. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=L-WRN+conditioned+medium+for+gastrointestinal+epithelial+stem+cell+culture+shows+replicable+batch-to-batch+activity+levels+across+multiple+research+teams.">L-WRN conditioned medium for gastrointestinal epithelial stem cell culture shows replicable batch-to-batch activity levels across multiple research teams.</a> Stem Cell Research. 37, 101430 (2019).</li><li>Sutton, K. M., Orr, B., Hope, J., Jensen, S. R., Vervelde, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Establishment+of+bovine+3D+enteroid-derived+2D+monolayers.">Establishment of bovine 3D enteroid-derived 2D monolayers.</a> Veterinary Research. 53 (1), 15 (2022).</li></ol>

The authors have nothing to disclose.

This protocol describes a method used to cryopreserve epithelial crypts from the piglet intestine for the long-term storage and subsequent culture of 3D organoids. This protocol uses a freezing solution containing DMSO, FBS, the Y27632 ROCK inhibitor, DMEM, and antibiotics. Another study in pigs obtained organoids from crypts cryopreserved in a similar freezing solution but without the ROCK inhibitor15. The Y27632 ROCK inhibitor was included to prevent apoptosis and maintain the stem cell pool since, after thawing, epithelial crypt cells are dissociated, which may lead to cell death (&#39;anoikis&#39;)27,28. Interestingly, equine enteroids have been obtained from epithelial crypts frozen in a culture medium containing only DMEM and DMSO16; this simple method has not been tested for pig epithelial crypts yet. Other methods have been published to grow human and pig organoids from frozen tissues or biopsies instead of epithelial crypts4,17. The advantage of this method is the ability to directly cryopreserve the intestinal tissues without performing the crypt isolation procedure, which requires time and laboratory equipment. This might be convenient when the tissues have to be collected far from the lab. However, when isolating the crypts immediately after slaughter, large segments of the intestine can be processed to obtain a very high number of crypts, which is not the case when starting from small frozen tissue fragments. After the thawing of epithelial crypts, organoids were observed from 3-4 days post-seeding and split&#160;after 10 days. This is a slower growth rate than when starting the culture from fresh epithelial crypts, for which the organoids were obtained from day 1 post-seeding, and can usually be split at around day 511. Khalil et al. also reported a delayed growth of pig enteroids when starting from frozen crypts15, suggesting that stem cells might require time to recover their proliferative capacity. We also obtained a lower number of organoids when starting from frozen crypts compared to fresh crypts, which might be due to the death of stem cells during the freezing process. In some attempts of crypts thawing (&#60;20%), we did not obtain organoids from frozen crypts, probably due to a suboptimal cryopreservation procedure (e.g., delayed freezing after crypt isolation of probably more than 1 h). Thus, we recommend keeping the crypts on ice until counting, and freezing them as quickly as possible.
For 3D organoids, we chose to use a commercial organoid culture medium formulated for humans. Indeed, previous reports have showed that pig intestinal organoids grow efficiently with this medium8,11,14,19,25,26,29,30. It is of interest for this culture medium to be ready-to-use and have a standardized concentration of growth factors within a batch. However, this culture medium is costly, its composition is undisclosed, and it is thus not possible to modulate its composition. In contrast, other studies have cultured pig intestinal organoids in customized media containing pharmacological inhibitors, recombinant growth factor, and/or conditioned media5,6,7,21. Although highly flexible and cheaper, this method is time-consuming for the production of conditioned media and might lack reproducibility due to potential variability in the concentration of growth factors in conditioned media. Thus, the quality of each batch of conditioned media should be validated by measuring organoid growth or marker gene expression31.
A study has showed that pig jejunal organoids cultured in the same commercial organoid culture medium used here grew faster and seemed less differentiated, compared to enteroids cultured with media containing recombinant growth factor and/or conditioned media23. A high proliferative state facilitates the culture of 3D organoids, but might require inducing differentiation to be more representative of intestinal physiological characteristics. In this protocol, for the passage of 3D organoids, the cells are fully dissociated for counting, allowing to control the number of cells seeded in ECM. This increases the reproducibility of the phenotype of organoids, which is highly influenced by their density. Moreover, counting the cells avoids obtaining too low or an overcrowded culture, that requires adapting the culture schedule. Most other studies prepared organoid fragments not fully dissociated to single cells, and used a dilution ratio for passaging. This method is more straightforward, but might induce variability according to the organoid density of the culture.
For the culture in monolayers, organoid cells are seeded in culture inserts precoated with a thin layer of ECM, that allows the attachment of cells but avoids the growth of organoids in 3D. This protocol used collagen type IV as an ECM protein, as described previously in pigs23. Other studies with pig organoid monolayers used the same tumor-derived ECM used here to culture 3D organoids6,8,9,21,25,30. The advantage of using collagen is the ability to standardize the protein concentration with a fully defined composition, which is not the case in the tumor-derived ECM. A critical step for the success of the culture of cell monolayers is to pay attention to the visual appearance of the precursor 3D organoids, which should have well-defined edges and an empty lumen without black debris. Indeed, organoids with a high maturation level and a low proliferative rate are not an appropriate source of cells for 2D culture. Thus, the timing of the dissociation of 3D organoids into single cells is crucial for the success of this step.
The culture of 2D monolayers from single cells allows standardizing the number of cells seeded, which is more difficult when starting from organoid fragments, as performed in some other methods. We seeded 7.6 x 105 cells per cm2, which is high compared to most other studies21,22,23 in pigs that used a lower cell density, ranging from 0.25 x 105 cells per cm2 to 1.78 x 105 cells per cm2. The requirement of a high number of organoid cells constitutes a limitation of this protocol, but it allowed us to quickly obtain a confluent monolayer, fully covering the culture insert after 1 day. In contrast, Vermeire et al.23 obtained confluency after 4-7 days with a lower density of cells seeded (from 0.25 x 105 cells/cm2 to 0.4 x 105 cells/cm2). Some studies have also used pig organoid cell monolayers that did not fully cover the culture surface for infections with viruses8,30. In these conditions, the apical side of epithelial cells is accessible for treatments, but fully confluent monolayers are required if the objective is to study nutrient absorption or epithelial permeability.
For organoid cell monolayers, a commercial organoid culture medium supplemented with 20% FBS was used, based on a recent study on bovine enteroid-derived monolayers32. In our tests, the supplementation with 20% FBS was necessary to obtain fully confluent monolayers, probably due to a high growth factor requirement. On the contrary, other studies using the same commercial medium have established monolayers without additional FBS8,25,30, but without reaching full confluency. Other studies have also used supplementation with 20% FBS in a customized medium for the culture of pig organoid cell monolayers21,22. In our experiments, TEER is high 1 day after seeding (around 700 &#8486;&#183;cm2), and remains high until day 3 (around 1,500 &#8486;&#183;cm2; this is consistent with the formation of tight junctions, as indicated by the expression of occludin. Van der Hee et al. obtained similar TEER values over 72 h for jejunum organoid cell monolayers21. They also demonstrated that monolayers can be maintained until day 12-15 with daily media changes. In contrast, other studies have reported much lower TEER values (around 200 &#8486;&#183;cm2) for pig organoid cell monolayers6,22. These differences between studies might be related to the gut segment studied or to the media used that influence epithelial differentiation.
In conclusion, the above protocol to grow pig intestinal 3D organoids from frozen epithelial crypts facilitates the organization of the culture work. It reduces the need for fresh tissues to be obtained from living animals. We also explain how to establish fully confluent cell monolayers derived from pig organoids in less than 3 days. Thus, our protocols could be useful resources for scientists studying the pig intestinal epithelium for veterinary or biomedical research.

The intestinal epithelium is formed by a monolayer of cells covering the digestive mucosa at the interface with the luminal environment. This position is associated with diverse functions, such as nutrient absorption and barrier function, that are supported by the presence of stem cells and multiple differentiated epithelial cell types (absorptive, enteroendocrine, Paneth, and goblet cells)1. Immortalized cell lines traditionally used to study epithelial cells have major limitations, since they do not reflect the cellular complexity of the intestinal epithelium and present genomic abnormalities2. The development of three-dimensional (3D) organoids by Sato et al.3 provided a new model to study the intestinal epithelium with an improved physiological relevance. Indeed, intestinal organoids are derived from non-transformed stem cells, are composed of multiple cell types, and recapitulate the functionality of the intestinal epithelium. Intestinal organoids are increasingly being used to understand the development and functions of the intestinal epithelium and its interactions with pathogens, nutrients, toxins, drugs, the microbiota, and its metabolites2.
Initially developed for humans and mice, the methods used to culture intestinal organoids have recently been adapted to other species, including pigs4. Gonzales et al.5 were the first to culture pig organoids from the jejunum ; since then, porcine organoids have been described for other gut segments (duodenum, ileum, and colon)6,7,8, and have been shown to retain a location-specific phenotype9,10,11. Pig intestinal 3D organoids are now commonly used to study the effect of nutrients12,13 or enteric infections6,8,14.
Most of the studies have described the culture of intestinal organoids starting from freshly isolated epithelial crypts. However, this is not always feasible for logistical reasons, notably when working with large animals such as pigs. Indeed, animal facilities for pigs can be located far from the lab where organoids are cultured, which complicates the work organization. Moreover, organoid culture is time-consuming; thus, it is not practical to simultaneously grow multiple organoid lines, for instance, from different gut segments or several animals. To circumvent these issues, a few studies in humans, horses, and pigs have described methods to culture organoids from frozen intestinal tissues (or biopsies) or from isolated epithelial crypts4,15,16,17. These methods allow the cryopreservation of intestinal epithelial stem cells from multiple gut segments of a single animal, which can then be used to grow organoids when needed. Moreover, this allows a strong reduction in the number of live animals used as donors of stem cells, since large stocks of cryopreserved crypts can be created (principles of 3R). Another advantage of this method is the growth of intestinal organoids only from animals of interest after obtaining phenotypic or genotypic results, which is highly cost-effective.
In vivo, intestinal epithelial cells are polarized, with the apical side directed toward the lumen. In vitro, in 3D organoids, the apical side of epithelial cells is also facing the lumen (i.e., inside the organoids)4. This organization prevents access to the apical side, which is an issue when studying the effects of luminal components (e.g., nutrients, microbes, metabolites) on epithelial cells. To circumvent this disadvantage, several methods have been developed, such as the culture of organoid cells as 2D monolayers, microinjection, and polarity reversal (&#34;apical-out organoids&#34;)18,19. The culture of organoid cell monolayers is emerging as the most efficient and tractable system. The principle is to dissociate 3D organoids into single cells and seed them on a cell culture vessel previously coated with a thin layer of extracellular matrix (ECM)20. In these culture conditions, the apical side of the epithelial cells is facing upward, and is thus accessible to experimental treatments20. The culture of organoid cell monolayers was recently adapted for the pig intestine21,22; cell monolayers derived from pig 3D organoids have been used for multiple applications, including the study of enteric infections6,23,24,25, the transport of nutrients9, and digestive disease modeling26.
Here, this study first presents a detailed protocol for the culture and maintenance of pig intestinal 3D organoids derived from cryopreserved epithelial crypts (Figure 1). Then, a protocol is described to establish cell monolayers from pig intestinal 3D organoids. The methods described here provide experimental tools that can be used to study the pig intestinal epithelium for nutrient transport, barrier function, and host-microorganism interactions.

<table><tbody><tr><td>0.5 M EDTA, pH 8.0</td><td>Thermo Fisher Scientific</td><td>AM9260G</td><td>Store at room temperature.</td></tr><tr><td>15 mL conical tube</td><td>Sarstedt</td><td>62.554.502</td><td></td></tr><tr><td>24-well cell culture plate </td><td>Corning</td><td>003526</td><td></td></tr><tr><td>48-well cell culture plate </td><td>Corning</td><td>003548</td><td></td></tr><tr><td>50 mL polypropylene conical tube</td><td>Falcon</td><td>352070</td><td></td></tr><tr><td>Bovine Serum Albumine (BSA)</td><td>Euromedex</td><td>A6003</td><td>Store at 4 &amp;deg;C.</td></tr><tr><td>Centrifuge Universal 320 R</td><td>Hettich</td><td>1406</td><td></td></tr><tr><td>Collagene type IV from human placenta</td><td>Sigma</td><td>C5533</td><td>Prepare the stock solution at 1 mg/mL in acetic acid according to the manufacturer&#039;s recommendation. Aliquot (500 &amp;micro;L) and store at -20 &amp;deg;C. </td></tr><tr><td>CoolCell LX Cell Freezing Container</td><td>Corning</td><td>432003</td><td>Used to cryopreserve crypts and organoids. </td></tr><tr><td>Countess 3 Automated Cell Counter</td><td>Thermo Fisher Scientific</td><td>16842556</td><td></td></tr><tr><td>Coverslips, 22 mm x 50 mm</td><td>VWR</td><td>630-1845</td><td></td></tr><tr><td>Cryotube ClearLine 1 mL</td><td>Clear line </td><td>390706</td><td>Used to cryopreserve crypts and organoids. </td></tr><tr><td>DAPI</td><td>Invitrogen</td><td>D1306</td><td>Prepare the stock solution at 5 mg/mL in water according to the manufacturer&amp;rsquo;s recommendation. Aliquot (20 &amp;micro;L) and store at -20 &amp;deg;C </td></tr><tr><td>Dithiothreitol (DTT) </td><td>Merck</td><td>10197777001</td><td>Store at 4 &amp;deg;C.</td></tr><tr><td>DMEM, high glucose, GlutaMAX Supplement, pyruvate</td><td>Thermo Fisher Scientific</td><td>31966047</td><td>Store at 4 &amp;deg;C.</td></tr><tr><td>DMSO (Dimethyl Sulfoxide)</td><td>Corning</td><td>25-950-CQC</td><td>Store at room temperature.</td></tr><tr><td>Epredia Superfrost Plus Adhesion microscopic slide</td><td>VWR</td><td>631-9483 </td><td></td></tr><tr><td>Fetal Bovine Serum (FBS)</td><td>Thermo Fisher Scientific</td><td>10270-106</td><td>Store 5 mL aliquots at -20 &amp;deg;C.</td></tr><tr><td>Fisherbrand Sterile Cell Strainers</td><td>Thermo Fisher Scientific</td><td>22363549</td><td>Used for crypt isolation. </td></tr><tr><td>Fixed Tilt 3D Platform Rotator </td><td>VWR</td><td> 97025-564 </td><td>Used for incubations in the immunostaining protocol. </td></tr><tr><td>Gibco PBS, pH 7.4</td><td>Thermo Fisher Scientific</td><td>10010015</td><td>Store at 4 &amp;deg;C.</td></tr><tr><td>Gibco TrypLE Express Enzyme (1x), phenol red</td><td>Thermo Fisher Scientific</td><td>12605-010</td><td>Enzyme dissociation reagent. Store at room temperature.</td></tr><tr><td>Goat anti-rabbit IgG, Alexa fluor 488</td><td>Thermo Fisher Scientific</td><td>A-11008</td><td>Secondary antibody. Store at 4 &amp;deg;C. Working dilution 1:1000. </td></tr><tr><td>IntestiCult Organoid Growth Medium (Human)</td><td>Stem Cell Technology</td><td>6010</td><td>Organoid culture medium. Store at -20 &amp;deg;C. Thaw the basal medium and organoid supplement at room temperature and mix (1:1). Store the mix at 4 &amp;deg;C for up to 1 week. </td></tr><tr><td>Insert with PET membrane transparent Falcon for plate 24 wells</td><td>Corning</td><td>353095</td><td></td></tr><tr><td>Inverted microscope</td><td>Nikon</td><td> Eclipse TS2</td><td></td></tr><tr><td>Matrigel Basement Membrane Matrix</td><td>Corning</td><td>354234</td><td>Tumor-derived extracellular matrix used for the 3D culture of organoids. Matrigel polymerizes at room temperature. Use cooled tips to pipet the Matrigel. Prepare 500 &amp;micro;L aliquots and store at -20 &amp;deg;C.</td></tr><tr><td>Mounting medium for fluorescence with DAPI</td><td>Vectashield</td><td>H1250</td><td> Store at 4 &amp;deg;C. </td></tr><tr><td>Occludin polyclonal antibody</td><td>Thermo Fisher Scientific</td><td>71-1500</td><td>Primary antibody. Store at -20 &amp;deg;C. Working dilution 1:200. </td></tr><tr><td>Paraformaldehyde 32%</td><td>Electron microscopy science</td><td>15714</td><td>Prepare 4% paraformaldehyde (PFA) solution under chemical hood by adding 5 mL of 32% PFA to 35 mL of PBS. Aliquot by 10 mL and store at -20 &amp;deg;C.</td></tr><tr><td>Penicillin-Streptomycin</td><td>Sigma</td><td>P4333</td><td>Antibacterial. Store 5 mL aliquots at -20 &amp;deg;C.</td></tr><tr><td>Phalloidin TRITC</td><td>Sigma</td><td>P1951</td><td>Probe for actin staining. 1 mg/mL stock solution. Store at 4 &amp;deg;C.</td></tr><tr><td>Primocin</td><td>InvivoGen</td><td>ant-pm-05</td><td>Antimicrobial agent for primary cells acting on bacteria, mycoplasma and fungi. Store at -20 &amp;deg;C.</td></tr><tr><td>ROCK Inhibitor (Y27632)</td><td>ATCC</td><td>ACS-3030</td><td>Used to maintain the stem cells. Prepare the stock solution at 10 mM in sterile water according to the manufacturer&#039;s recommendation and store aliquots (50 &amp;micro;L) at -20 &amp;deg;C.</td></tr><tr><td>Rotating shaker mix XL</td><td>Clear line </td><td>062646CL</td><td>Used for crypt isolation. </td></tr><tr><td>Stripette Serological Pipets 10 mL</td><td>Corning</td><td>4488</td><td></td></tr><tr><td>Tissue Culture Dish </td><td>TPP</td><td>93100</td><td></td></tr><tr><td>Triton X100</td><td>Sigma</td><td>8787</td><td>Store at room temperature.</td></tr><tr><td>Trypan Blue stain 0.4% </td><td>Thermo Fisher Scientific</td><td>T10282</td><td>Store at room temperature.</td></tr><tr><td>Vacuum system Vacusip</td><td>Integra</td><td>159000</td><td>Used to remove the medium of organoid wells. </td></tr></tbody></table>

culture of piglet intestinal 3d organoids from cryopreserved epithelial crypts and establishment of cell monolayers

Intestinal organoids are increasingly being used to study the gut epithelium for digestive disease modeling, or to investigate interactions with drugs, nutrients, metabolites, pathogens, and the microbiota. Methods to culture intestinal organoids are now available for multiple species, including pigs, which is a species of major interest both as a farm animal and as a translational model for humans, for example, to study zoonotic diseases. Here, we give an in-depth description of a procedure used to culture pig intestinal 3D organoids from frozen epithelial crypts. The protocol describes how to cryopreserve epithelial crypts from the pig intestine and the subsequent procedures to culture 3D intestinal organoids. The main advantages of this method are (i) the temporal dissociation of the isolation of crypts from the culture of 3D organoids, (ii) the preparation of large stocks of cryopreserved crypts derived from multiple intestinal segments and from several animals at once, and thus (iii) the reduction in the need to sample fresh tissues from living animals. We also detail a protocol to establish cell monolayers derived from 3D organoids to allow access to the apical side of epithelial cells, which is the site of interactions with nutrients, microbes, or drugs. Overall, the protocols described here is a useful resource for studying the pig intestinal epithelium in veterinary and biomedical research.

Following the protocol described above, epithelial crypts are obtained from the pig intestine and cryopreserved for long-term storage in liquid nitrogen (Figure 1 and Figure 2A). After thawing, the crypt stem cells are seeded in the ECM (Figure 2B). The crypt structure is usually lost after this step, due to the disintegration of the crypt structure in the ECM. The organoids can be observed within 3-4 days, and then rapidly grow and develop budding structures (Figure 2B). We successfully obtained organoids after thawing frozen crypts in &#62;80% of attempts. Approximately 10 days after thawing (according to the growth rate of organoids), a passage of organoids is performed to expand the culture (Figure 3). The organoids grow faster after splitting, and they present diverse morphologies, with some cystic and a majority of budding organoids. For optimal maintenance of the culture, the organoids used for passaging must present a clear and empty lumen and well-defined edges (examples indicated by green arrows) with no black debris in the lumen (indicated by red arrows), as observed in mature organoids (Figure 3). We found that black cell debris starts accumulating around day 6 post-passaging. Thus, splitting or freezing the organoids at day 4-5 post-passaging is recommended.
The maturity stage of the organoids is also an important point in obtaining cell monolayers. Organoids with advanced maturity (indicated by the presence of black cell debris in the lumen) are not optimal to seed monolayers. We usually dissociate 3D organoids 4 days after passage to collect cells for 2D culture. Approximately one to three wells of 3D organoids cultured at 3,000 cells per 50 &#181;L dome of the ECM are needed for seeding one culture insert with 2.5 x 105 cells. Cells attach and form a fully confluent monolayer within 1 day (Figure 4A), which is confirmed by the high TEER of around 700 &#8486;&#183;cm2 (Figure 4B). However, the cell edges are difficult to visualize by brightfield microscopy at this early time point, probably due to a low differentiation level. The TEER remains high for 3 days (Figure 4B).
Actin staining indicates that the apical side of the epithelial cells is oriented toward the lumen in 3D organoids (Figure 5A). Organoid cells seeded in culture insert form a confluent single layer of epithelial cells, with the apical side oriented toward the upper compartment (Figure 4B,C). Occludin staining reveals the presence of tight junctions at the apical side of the epithelial cells in 3D organoids and in cell monolayers (Figure 5A-C).
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/64917/64917fig01.jpg" /> 
Figure 1: Schematic representation of the methods used to culture 3D organoids and cell monolayers derived from organoids. Epithelial crypts are isolated from the piglet intestine. These crypts can i) be used immediately to culture 3D organoids or ii) be frozen and stored in a biobank in liquid nitrogen. Cryopreserved crypts can be thawed and used to culture 3D organoids. The 3D organoid culture can be maintained with successive splitting, or frozen and stored in the biobank. Cell monolayers can be obtained from the 3D organoid culture to allow access to the apical side of the cells and study the epithelial barrier function. <a href="https://www.jove.com/files/ftp_upload/64917/64917fig01large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 2" class="xfigimg" src="/files/ftp_upload/64917/64917fig02v2.jpg" /> 
Figure 2: Culture of pig intestinal 3D organoids from cryopreserved epithelial crypts. (A) Representative microscopic image of freshly isolated jejunal crypts. (B)&#160;Representative microscopic images of 3D organoids obtained after thawing of the jejunal crypts. The organoids were cultured in a 25 &#181;L dome of ECM in a 48-well plate. The figure shows images of the 3D organoids at 4, 7, 8, 9, and 10 days post-seeding. The scale bar represents 500 &#181;m. <a href="https://www.jove.com/files/ftp_upload/64917/64917fig02large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 3" class="xfigimg" src="/files/ftp_upload/64917/64917fig03v2.jpg" /> 
Figure 3: Morphology of pig intestinal 3D organoids derived from cryopreserved epithelial crypts after the first passage. Representative microscopic images showing the development of organoids derived from cryopreserved jejunum crypts after the first passage from day 4 to day 7. Green arrows indicate clear organoids appropriate for the passage or seeding of monolayers. Red arrows indicate mature organoids not suitable for splitting or seeding monolayers; thus, wells should be used before the apparition of this morphology. The scale bar represents 500 &#181;m. <a href="https://www.jove.com/files/ftp_upload/64917/64917fig03large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 4" class="xfigimg" src="/files/ftp_upload/64917/64917fig04v2.jpg" /> 
Figure 4: Characteristics of cell monolayers derived from pig intestinal 3D organoids. (A) Representative microscopic images of the monolayer morphology over 3 days. Jejunum organoid cells were seeded at 2.5 x 105 cells into 0.33 cm2 cell culture inserts coated with collagen IV at 50 ng/mL. The scale bar represents 500 &#181;m. (B) Transepithelial electrical resistance (TEER) of organoid cell monolayers over 3 days. Dots connected by a line correspond to the same well at different times. <a href="https://www.jove.com/files/ftp_upload/64917/64917fig04large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 5" class="xfigimg" src="/files/ftp_upload/64917/64917fig05v2.jpg" /> 
Figure 5: Imaging of pig jejunum organoids cultured in 3D or 2D. Confocal microscopy imaging of (A) 3D organoids 5 days after splitting and (B,C) organoid cell monolayers 3 days after seeding (B: XZ section; C:&#160;XY section). DNA (blue) was stained with DAPI. Actin (red) was stained with phalloidin. Occludin (green) was stained with a polyclonal antibody. White arrows indicate occludin localized at the tight junction. The scale bar represents 20 &#181;m. <a href="https://www.jove.com/files/ftp_upload/64917/64917fig05large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>

Watch this Scientific Journal Video about Culture of Piglet Intestinal 3D Organoids from Cryopreserved Epithelial Crypts and Establishment of Cell Monolayers at JoVE.com

Culture of Piglet Intestinal 3D Organoids from Cryopreserved Epithelial Crypts and Establishment of Cell Monolayers

Here, we describe a protocol to culture pig intestinal 3D organoids from cryopreserved epithelial crypts. We also describe a method to establish cell monolayers derived from 3D organoids, allowing access to the apical side of epithelial cells.

Intestinal organoids are increasingly being used to study the gut epithelium for digestive disease modeling, or to investigate interactions with drugs, ...

culture-piglet-intestinal-3d-organoids-from-cryopreserved-epithelial

Research

JoVE Journal

Biology

2.3K Views.  Université de Toulouse, INRAE, ENVT. Ons protocol biedt hulpmiddelen om het darmepitheel van varkens te bestuderen voor veterinair en biomedisch onderzoek. Intestinale organoïden van varkens kunnen worden gebruikt om het transport van voedingsstoffen, de barrièrefunctie en interacties tussen gastheer en microben te bestuderen. Door het behoud van varkensdarmepitheelcrypten maken het mogelijk om een grote voorraad stamcellen te creëren die later kunnen worden gebruikt om organoïden in 3D- of 2D-monolagen te kweken.Dit ...

Video: Culture of Piglet Intestinal 3D Organoids from Cryopreserved Epithelial Crypts and Establishment of Cell Monolayers

Three-Dimensional Culture of Murine Colonic Crypts to Study Intestinal Stem Cell Function Ex Vivo

The intestinal epithelium regenerates every 5-7 days, and is controlled by the intestinal epithelial stem cell (IESC) population located at the bottom of the crypt region. IESCs include active stem cells, which self-renew and differentiate into various epithelial cell types, and quiescent stem cells, which serve as the reserve stem cells in the case of injury. Regeneration of the intestinal epithelium is controlled by the self-renewing and differentiating capabilities of these active IESCs. In addition, the balance of the crypt stem cell population and maintenance of the stem cell niche are essential for intestinal regeneration. Organoid culture is an important and attractive approach to studying proteins, signaling molecules, and environmental cues that regulate stem cell survival and functions. This model is less expensive, less time-consuming, and more manipulatable than animal models. Organoids also mimic the tissue microenvironment, providing in vivo relevance. The present protocol describes the isolation of colonic crypts, embedding these isolated crypt cells into a three-dimensional gel matrix system and culturing crypt cells to form colonic organoids capable of self-organization, proliferation, self-renewal, and differentiation. This model allows one to manipulate the environment-knocking out specific proteins such as claudin-7, activating/deactivating signaling pathways, etc.-to study how these effects influence the functioning of colonic stem cells. Specifically, the role of tight junction protein claudin-7 in colonic stem cell function was examined. Claudin-7 is vital for maintaining intestinal homeostasis and barrier function and integrity. Knockout of claudin-7 in mice induces an inflammatory bowel disease-like phenotype exhibiting intestinal inflammation, epithelial hyperplasia, weight loss, mucosal ulcerations, epithelial cell sloughing, and adenomas. Previously, it was reported that claudin-7 is required for intestinal epithelial stem cell functions in the small intestine. In this protocol, a colonic organoid culture system is established to study the role of claudin-7 in the large intestine.

Three-Dimensional Culture of Murine Colonic Crypts to Study Intestinal Stem Cell Function Ex Vivo

The present protocol describes establishing a murine colonic organoid system to study the activity and functioning of colonic stem cells in a claudin-7 knockout model.

The intestinal epithelium regenerates every 5-7 days, and is controlled by the intestinal epithelial stem cell (IESC) population located at the bottom of ...

Cancer Research

Establishment of Human Epithelial Enteroids and Colonoids from Whole Tissue and Biopsy

The epithelium of the gastrointestinal tract is constantly renewed as it turns over. This process is triggered by the proliferation of intestinal stem cells (ISCs) and progeny that progressively migrate and differentiate toward the tip of the villi. These processes, essential for gastrointestinal homeostasis, have been extensively studied using multiple approaches. Ex vivo technologies, especially primary cell cultures have proven to be promising for understanding intestinal epithelial functions. A long-term primary culture system for mouse intestinal crypts has been established to generate 3-dimensional epithelial organoids. These epithelial structures contain crypt- and villus-like domains reminiscent of normal gut epithelium. Commonly, termed &#8220;enteroids&#8221; when derived from small intestine and &#8220;colonoids&#8221; when derived from colon, they are different from organoids that also contain mesenchyme tissue. Additionally, these enteroids/colonoids continuously produce all cell types found normally within the intestinal epithelium. This in vitro organ-like culture system is rapidly becoming the new gold standard for investigation of intestinal stem cell biology and epithelial cell physiology. This technology has been recently transferred to the study of human gut. The establishment of human derived epithelial enteroids and colonoids from small intestine and colon has been possible through the utilization of specific culture media that allow their growth and maintenance over time. Here, we describe a method to establish a small intestinal and colon crypt-derived system from human whole tissue or biopsies. We emphasize the culture modalities that are essential for the successful growth and maintenance of human enteroids and colonoids.

We describe a method to establish human enteroids from small intestinal crypts and colonoids from colon crypts collected from both surgical tissue and biopsies. In this methodological article, we present the culture modalities that are essential for the successful growth and maintenance of human enteroids and colonoids.

The epithelium of the gastrointestinal tract is constantly renewed as it turns over. This process is triggered by the proliferation of intestinal stem ...

Medicine

Human Colonoid Monolayers to Study Interactions Between Pathogens, Commensals, and Host Intestinal Epithelium

Human 3-dimensional (3D) enteroid or colonoid cultures derived from crypt base stem cells are currently the most advanced ex vivo model of the intestinal epithelium. Due to their closed structures and significant supporting extracellular matrix, 3D cultures are not ideal for host-pathogen studies. Enteroids or colonoids can be grown as epithelial monolayers on permeable tissue culture membranes to allow manipulation of both luminal and basolateral cell surfaces and accompanying fluids. This enhanced luminal surface accessibility facilitates modeling bacterial-host epithelial interactions such as the mucus-degrading ability of enterohemorrhagic E. coli (EHEC) on colonic epithelium. A method for 3D culture fragmentation, monolayer seeding, and transepithelial electrical resistance (TER) measurements to monitor the progress towards confluency and differentiation are described. Colonoid monolayer differentiation yields secreted mucus that can be studied by the immunofluorescence or immunoblotting techniques. More generally, enteroid or colonoid monolayers enable a physiologically-relevant platform to evaluate specific cell populations that may be targeted by pathogenic or commensal microbiota.

Here, we present a protocol to culture human enteroid or colonoid monolayers that have intact barrier function to study host epithelial-microbiota interactions at the cellular and biochemical level.

Human 3-dimensional (3D) enteroid or colonoid cultures derived from crypt base stem cells are currently the most advanced ex vivo model of the intestinal ...

Immunology and Infection

Co-Culture of Murine Small Intestine Epithelial Organoids with Innate Lymphoid Cells

Complex co-cultures of organoids with immune cells provide a versatile tool for interrogating the bi-directional interactions that underpin the delicate balance of mucosal homeostasis. These 3D, multi-cellular systems offer a reductionist model for addressing multi-factorial diseases and resolving technical difficulties that arise when studying rare cell types such as tissue-resident innate lymphoid cells (ILCs). This article describes a murine system that combines small intestine organoids and small intestine lamina propria derived helper-like type-1 ILCs (ILC1s), which can be readily extended to other ILC or immune populations. ILCs are a tissue-resident population that is particularly enriched in the mucosa, where they promote homeostasis and rapidly respond to damage or infection. Organoid co-cultures with ILCs have already begun shedding light on new epithelial-immune signaling modules in the gut, revealing how different ILC subsets impact intestinal epithelial barrier integrity and regeneration. This protocol will enable further investigations into reciprocal interactions between epithelial and immune cells, which hold the potential to provide new insights into the mechanisms of mucosal homeostasis and inflammation.

This protocol offers detailed instructions for establishing murine small intestine organoids, isolating type-1 innate lymphoid cells from the murine small intestine lamina propria, and establishing 3-dimensional (3D) co-cultures between both cell types to study bi-directional interactions between intestinal epithelial cells and type-1 innate lymphoid cells.

Complex co-cultures of organoids with immune cells provide a versatile tool for interrogating the bi-directional interactions that underpin the delicate ...

Establishment of a 2D Monolayer from 3D Bovine Ileal Enteroid Culture

Generation of a Bovine Primary Enteroid-Derived Two-Dimensional Monolayer Culture System for Applications in Translational Biomedical Research

Organoid cell culture systems can recapitulate the complexity observed in tissues, making them useful in studying host-pathogen interactions, evaluating drug efficacy and toxicity, and tissue bioengineering. However, applying these models for the described reasons may be limited because of the three-dimensional (3D) nature of these models. For example, using 3D enteroid culture systems to study digestive diseases is challenging due to the inaccessibility of the intestinal lumen and its secreted substances. Indeed, stimulation of 3D organoids with pathogens requires either luminal microinjection, mechanical disruption of the 3D structure, or generation of apical-out enteroids. Moreover, these organoids cannot be co-cultured with immune and stromal cells, limiting in-depth mechanistic analysis into pathophysiological dynamics. To circumvent this, we optimized a bovine primary cell two-dimensional (2D) enteroid-derived monolayer culture system, allowing co-culture with other relevant cell types. Ileal crypts isolated from healthy adult cattle were cultured to generate 3D organoids that were cryopreserved for future use. A 2D monolayer was created using revived 3D enteroids that were passaged and disrupted to yield single cells, which were seeded on basement membrane extract-coated transwell cell culture inserts, thereby exposing their apical surface. The intestinal monolayer polarity, cellular differentiation, and barrier function were characterized using immunofluorescence microscopy and measuring transepithelial electrical resistance. Stimulation of the apical surface of the monolayer revealed the expected functionality of the monolayer, as demonstrated by cytokine secretion from both apical and basal compartments. The described 2D enteroid-derived monolayer model holds great promise in investigating host-pathogen interactions and intestinal physiology, drug development, and regenerative medicine.

Author Spotlight: Advanced Enteroid Model for Studying Host-Pathogen Interactions 

Enteroids are emerging as a novel model for studying tissue physiology and pathophysiology, drug development, and regenerative medicine. Here, we describe a bovine primary cell 2D enteroid-derived culture system that permits co-culture with relevant tissue cell types. This model offers a translational advantage for gastrointestinal research modeling.

Organoid cell culture systems can recapitulate the complexity observed in tissues, making them useful in studying host-pathogen interactions, evaluating ...

Generation of Murine Primary Colon Epithelial Monolayers from Intestinal Crypts

The intestinal epithelium is comprised of a single layer of cells that act as a barrier between the gut lumen and the interior of the body. Disruption in the continuity of this barrier can result in inflammatory disorders such as inflammatory bowel disease. One of the limitations in the study of intestinal epithelial biology has been the lack of primary cell culture models, which has obliged researchers to use model cell lines derived from carcinomas. The advent of three dimensional (3D) enteroids has given epithelial biologists a powerful tool to generate primary cell cultures, nevertheless, these structures are embedded in extracellular matrix and lack the maturity characteristic of differentiated intestinal epithelial cells. Several techniques to generate intestinal epithelial monolayers have been published, but most are derived from established 3D enteroids making the process laborious and expensive. Here we describe a protocol to generate primary epithelial colon monolayers directly from murine intestinal crypts. We also detail experimental approaches that can be used with this model such as the generation of confluent cultures on permeable filters, confluent monolayer for scratch wound healing studies and sparse and confluent monolayers for immunofluorescence analysis.

In this protocol, we describe how to generate murine primary epithelial colon monolayers directly from intestinal crypts. We provide experimental approaches to generate confluent monolayers on permeable filters, confluent monolayers for scratch wound healing and biochemical studies, and sparse and confluent monolayers for immunofluorescence analysis.

The intestinal epithelium is comprised of a single layer of cells that act as a barrier between the gut lumen and the interior of the body. Disruption in ...

Culture Methods to Study Apical-Specific Interactions using Intestinal Organoid Models

The lining of the gut epithelium is made up of a simple layer of specialized epithelial cells that expose their apical side to the lumen and respond to external cues. Recent optimization of in vitro culture conditions allows for the re-creation of the intestinal stem cell niche and the development of advanced 3-dimensional (3D) culture systems that recapitulate the cell composition and the organization of the epithelium. Intestinal organoids embedded in an extracellular matrix (ECM) can be maintained for long-term and self-organize to generate a well-defined, polarized epithelium that encompasses an internal lumen and an external exposed basal side. This restrictive nature of the intestinal organoids presents challenges in accessing the apical surface of the epithelium in vitro and limits the investigation of biological mechanisms such as nutrient uptake and host-microbiota/host-pathogen interactions. Here, we describe two methods that facilitate access to the apical side of the organoid epithelium and support the differentiation of specific intestinal cell types. First, we show how ECM removal induces an inversion of the epithelial cell polarity and allows for the generation of apical-out 3D organoids. Second, we describe how to generate 2-dimensional (2D) monolayers from single cell suspensions derived from intestinal organoids, comprised of&#160;mature and differentiated cell types. These techniques provide novel tools to study apical-specific interactions of the epithelium with external cues in vitro and promote the use of organoids as a platform to facilitate precision medicine.

Here we present two protocols that allow the modeling of intestinal apical-specific interactions. Organoid-derived intestinal monolayers and Air-Liquid Interface (ALI) cultures facilitate the generation of well-differentiated epithelia accessible from both luminal and basolateral sides, whereas polarity-inverted intestinal organoids expose their apical side and are amenable to high throughput assays.

The lining of the gut epithelium is made up of a simple layer of specialized epithelial cells that expose their apical side to the lumen and respond to ...

Generation and Characterization of Murine Oral Mucosal Organoid Cultures

The mucous lining covering the inside of our mouth, the oral mucosa, is a highly compartmentalized tissue and can be subdivided into the buccal mucosa, gingiva, lips, palate, and tongue. Its uppermost layer, the oral epithelium, is maintained by adult stem cells throughout life. Proliferation and differentiation of adult epithelial stem cells have been intensively studied using in vivo mouse models as well as two-dimensional (2D) feeder-cell based in vitro models. Complementary to these methods is organoid technology, where adult stem cells are embedded into an extracellular matrix (ECM)-rich hydrogel and provided with a culture medium containing a defined cocktail of growth factors. Under these conditions, adult stem cells proliferate and spontaneously form three-dimensional (3D) cell clusters, the so-called organoids. Organoid cultures were initially established from murine small intestinal epithelial stem cells. However, the method has since been adapted for other epithelial stem cell types. Here, we describe a protocol for the generation and characterization of murine oral mucosal organoid cultures. Primary epithelial cells are isolated from murine tongue tissue, embedded into an ECM hydrogel, and cultured in a medium containing: epidermal growth factor (EGF), R-spondin, and fibroblast growth factor (FGF) 10. Within 7 to 14 days of initial seeding, the resulting organoids can be passaged for further expansion and cryopreservation. We additionally present strategies for the characterization of established organoid cultures via 3D whole-mount imaging and gene-expression analysis. This protocol may serve as a tool to investigate oral epithelial stem cell behavior ex vivo in a reductionist manner.

We present a method for the generation and characterization of oral mucosal organoid cultures derived from the tongue epithelium of adult mice.

The mucous lining covering the inside of our mouth, the oral mucosa, is a highly compartmentalized tissue and can be subdivided into the buccal mucosa, ...

3D Culture of Organoids from Murine Intestinal Crypts and Single Stem Cell

The 3D Culturing of Organoids from Murine Intestinal Crypts and a Single Stem Cell for Organoid Research

At present, organoid culture represents an important tool for in vitro studies of different biological aspects and diseases in different organs. Murine small intestinal crypts can form organoids that mimic the intestinal epithelium when cultured in a 3D extracellular matrix. The organoids are composed of all cell types that fulfill various intestinal homeostatic functions. These include Paneth cells, enteroendocrine cells, enterocytes, goblet cells, and tuft cells. Well-characterized molecules are added into the culture medium to enrich the intestinal stem cells (ISCs) labeled with leucine-rich repeats containing G protein-coupled receptor 5 and are used to drive differentiation down specific lineages; these molecules include epidermal growth factor, Noggin (a bone morphogenetic protein), and R-spondin 1. Additionally, a protocol to generate organoids from a single erythropoietin-producing hepatocellular receptor B2 (EphB2)-positive ISC is also detailed. In this methods article, techniques to isolate small intestinal crypts and a single ISC from tissues and ensure the efficient establishment of organoids are described.

Author Spotlight: The 3D Culturing of Organoids from Murine Intestinal Crypts and a Single Stem Cell for Organoid Research  

We describe a protocol to isolate murine small intestinal crypts and culture intestinal 3D organoids from the crypts. Additionally, we describe a method to generate organoids from a single intestinal stem cell in the absence of a sub-epithelial cellular niche.

At present, organoid culture represents an important tool for in vitro studies of different biological aspects and diseases in different organs. Murine ...

Rat Intestinal Crypts Isolation and Intestinal Organoids Generation

Generation and Manipulation of Rat Intestinal Organoids

When using organoids to assess physiology and cell fate decisions, it is important to use a model that closely recapitulates in vivo contexts. Accordingly, patient-derived organoids are used for disease modeling, drug discovery, and personalized treatment screening. Mouse intestinal organoids are commonly utilized to understand aspects of both intestinal function/physiology and stem cell dynamics/fate decisions. However, in many disease contexts, rats are often preferred over mice as a model due to their greater physiological similarity to humans in terms of disease pathophysiology. The rat model has been limited by a lack of genetic tools available in vivo, and rat intestinal organoids have proven fragile and difficult to culture long-term. Here, we build upon previously published protocols to robustly generate rat intestinal organoids from the duodenum and jejunum. We provide an overview of several downstream applications utilizing rat intestinal organoids, including functional swelling assays, whole mount staining, the generation of 2D enteroid monolayers, and lentiviral transduction. The rat organoid model provides a practical solution to the need of the field for an in vitro model which retains physiological relevance to humans, can be quickly genetically manipulated, and is easily obtained without the barriers involved in procuring human intestinal organoids.

Author Spotlight: Generation and Manipulation of Rat Intestinal Organoids  

Here, we present a protocol to generate rat intestinal organoids and use them in several downstream applications. Rats are often a preferred preclinical model, and the robust intestinal organoid system fills the need for an in vitro system to accompany in vivo studies.

Culture of Piglet Intestinal 3D Organoids from Cryopreserved Epithelial Crypts and Establishment of Cell Monolayers

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