Koo BK and Mustata RC are supported by the Sir Henry Dale Fellowship from the Wellcome Trust and Andersson-Rolf A is supported by the Medical Research Council (MRC). Fink J is supported by the Wellcome Trust 4-year PhD-Programme.

All mice used in the following protocol were kept in specific pathogen-free conditions, and all procedures were performed according to the United Kingdom Home Office regulations.
1. Preparation
<ol>
	<li>Prepare media 1 hr in advance of use (see Table 1 and List of Materials for more details) and pre-warm in a 37 &#176;C water bath at least 10 min before use.</li>
</ol>
2. Culturing Small Intestinal (SI) Organoids
NOTE: Unless otherwise stated, all incubations are performed at 37 &#176;C, 5% CO2 in a humidified incubator. Equipment and reagents coming into contact with living cells must be sterile.
Pre-warming the tissue culture plate is important as it prevents the basement matrix (Matrigel or BME) drops from spreading out when seeding. Also, the basement matrix should be kept on ice at all times. Store at -20 &#176;C and thaw on ice before use.
<ol>
	<li>Isolating Crypts
	<ol>
		<li>For isolation of the small intestine sacrifice the mouse according to the national rules and regulations, then place the animal on its back and wash the abdomen with 70% ethanol. Perform a longitudinal midline incision from the groin to the sternum. First, cut the skin and then the subcutaneous tissue. Remove the small intestine from the cecum to the stomach. Crypts isolated from duodenum, jejunum and ileum can be used for organoid culture.</li>
		<li>Wash the isolated small intestine with pre-cooled Phosphate-Buffered Saline without calcium or magnesium (PBS0).</li>
		<li>Cut the tissue into 3-5 cm long pieces and use scissors to cut it open longitudinally. Spread the tissue by using forceps.</li>
		<li>Scrape off villi using a coverslip. Caution, too much force will cause the tissue to tear and will reduce the yield of crypts in following steps.</li>
		<li>Transfer the tissue to a 50 ml tube containing pre-cooled PBS0 using forceps. Wash the tissue fragments through vigorous shaking and change the PBS0. Repeat 2-3x&#160;or until the PBS0 turns less cloudy.</li>
		<li>Incubate the tissue in a 50 ml tube containing 30 ml of PBS0 with 1 mM ethylenediaminetetraacetic acid (EDTA) for 30 min at 4 &#176;C on a tube roller.</li>
		<li>Vigorously shake the tube and transfer the tissue to another 50 ml tube containing 30 ml of PBS0 with 5 mM EDTA. The 1 mM EDTA solution (previously containing the tissue) will contain a mixture of crypts and villi. This fraction is not suitable for seeding of organoids as it often contains a high percentage of villi.</li>
		<li>Incubate the tissue further for 1 hr at 4 &#176;C on a tube roller.</li>
		<li>Vigorously shake the tube and collect the solution in a clean 50 ml tube. Confirm the presence of crypts and estimate the number, e.g., by counting crypts in 50 &#181;l by light microscopy. Calculate the volume needed to obtain 50-100 crypts and transfer it to a 1.5 ml tube.</li>
		<li>Spin at 300 x g for 5 min. Discard the supernatant, resuspend the pellet in 50 &#181;l of basement matrix, and seed in a pre-warmed 24-well plate. Incubate the plate in a tissue culture incubator for 5-15 min so the basement matrix polymerizes.</li>
		<li>Overlay with 500 &#181;l ENR medium (see Table 1). Approximately 24 hr after seeding the organoids will show a small round cystic shape and after another 2-3 days budding structures become visible. Change to fresh ENR media every 3 days.</li>
		<li>Passage organoid cultures every 7 days.</li>
	</ol>
	</li>
	<li>Passaging and Maintaining Organoids
	<ol>
		<li>Maintain the organoids by refreshing the media every 3 days and passage 1:3 or 1:5 as the lumen becomes filled with dead cells, approximately every 7 days.</li>
		<li>Break the basement matrix dome with medium using 1 ml pipetman tip and transfer it from the well to a 1.5 ml tube.</li>
		<li>Mechanically dissociate the organoids through pipetting approximately 50x&#160;using a fine (e.g., 200 &#181;l) tip.</li>
		<li>Spin at 300 x g for 5 min.</li>
		<li>Discard the supernatant and resuspend the pellet in 150-250 &#181;l of basement matrix. Seed in a pre-warmed 24-well plate (50 &#181;l of basement matrix /well). Before seeding pipette the basement matrix up and down once to coat the wall of the tip. Pipette slowly to avoid bubbles and seed in the middle of the well to prevent the basement matrix from spreading out. It is desired to get a dome of basement matrix in the center of the well.</li>
		<li>Incubate in a tissue culture incubator for 5-15 min so the basement matrix polymerizes. Overlay with 500 &#181;l ENR media per well.</li>
	</ol>
	</li>
</ol>
3. Pre-infection Treatment of SI Organoids
NOTE: Figure 1 illustrates the transduction procedure.
<ol>
	<li>Exchange ENR to ENRWntNic (see Table 1) medium and grow the organoids in this medium for a minimum of 3 days or until they have adopted a cystic morphology. Wnt3a increases the number of stem and Paneth cells while Nicotinamide (Nic) improves culture efficiency.</li>
</ol>
4. Virus Production
<ol>
	<li>One 150 mm dish of Platinum-E cells is needed per infection. Seed approximately 5 x 106 cells with 15-18 ml media (DMEM + 10% FBS) in the presence of puromycin (1 &#181;g/ml) and blasticidin (10 &#181;g/ml). Transfect cells after 2-3 days, when they have reached 70-80% confluency. Change the medium to DMEM + 10% FBS without puromycin and blasticidin prior to transfection.</li>
	<li>Add 30 &#181;g of retroviral DNA construct and 240 &#181;l of polyethylenimine (PEI) to separate tubes containing 1 ml of opti-MEM. Mix and incubate at room temperature for 5 min.</li>
	<li>Pool the two solutions and incubate at room temperature for 20-30 min. Add the complete mixture to the medium of Platinum-E cells and carefully shake the plate to ensure equal distribution of the DNA-PEI complexes.</li>
	<li>Incubate the Platinum-E cells with the transfection mixture overnight and refresh the medium the following day. Keep the cells in the new medium for 2 days.</li>
	<li>Collect only the medium in a 50 ml Falcon tube, pass it through a 0.45 &#181;m filter and centrifuge at 8,000 x g at 4 &#176;C for 12-16 hr. Discard the supernatant and resuspend the pellet in 250 &#181;l of Transduction medium (see Table 1).</li>
</ol>
5. Organoid Fragment Preparation
<ol>
	<li>For one infection one well from a 24-well plate is needed. Break the basement matrix dome with medium using 1 ml pipetman tip and transfer it to a 1.5 ml tube.</li>
	<li>Use a finer volume tip (e.g., 200 &#181;l tips) to mechanically disrupt the organoids through pipetting (30-50x). The solution will become cloudy and no whole organoids should be visible.</li>
	<li>Centrifuge at room temperature, 900 x g for 5 min.</li>
	<li>Discard the supernatant and resuspend the pellet in 500 &#181;l of cell culture grade recombinant protease (e.g., TrypLE). Incubate at 37 &#176;C for 5 min. Following incubation check the size of the organoid fragments using light microscopy, counting the number of cells per fragment. Fragments containing 5-10 cells are ideal. If the majority of the fragments contain a higher number of cells the incubation time can be increased by 2 min at a time.</li>
	<li>Terminate the dissociation process by adding 500 &#181;l of ENR medium.</li>
	<li>Centrifuge at room temperature, 900 x g for 5 min. Remove the supernatant and keep the pellet on ice or 4 &#176;C.</li>
</ol>
6. Retroviral Transduction
<ol>
	<li>Combine organoid fragments with 250 &#181;l of the retroviral solution (from section 4.5) in one well of a 48-well plate. Mix gently by slow pipetting using 1 ml pipetman tip.</li>
	<li>Seal the plate with Parafilm.</li>
</ol>
7. Spinoculation and Plating
<ol>
	<li>Centrifuge the plate at 32 &#176;C, 600 x g, for 1 hr. Carefully remove the Parafilm and incubate the plate in a tissue culture incubator for 6 hr.</li>
</ol>
8. Seeding of Infected Organoid Fragments
<ol>
	<li>Transfer the infected organoid fragments and transduction media from the well to a 1.5 ml tube, and spin at 900 x g for 5 min.</li>
	<li>Discard the supernatant and put the tube containing the pellet on ice for 5 min to cool. Add 100 &#181;l of basement matrix and resuspend the pellet by pipetting slowly up and down.</li>
	<li>Seed drops of 50 &#181;l &#8216;basement matrix -cell mix&#8217; in a new 24-well plate. Incubate the plate at 37 &#176;C for 5-15 min until the basement matrix solidifies.</li>
	<li>Add transduction media without polybrene to the wells and incubate the plate in a tissue culture incubator. Change media every 2-3 days.</li>
</ol>
9. Selection
<ol>
	<li>Start selection after 2-3 days by adding puromycin (1 &#181;g/ml) to the media.</li>
	<li>When the fragments are starting to form organoids replace the Transduction media with ENR media supplemented with puromycin (1 &#181;g/ml).</li>
</ol>
10. Post-infection Treatment of SI Organoids
<ol>
	<li>Culture transduced organoids according to the &#8220;Passaging and maintaining organoids&#8221; protocol (section 2.2.1). After 1-2 weeks the SI organoids will regain their budding structures.</li>
	<li>Following the appearance of budding structures induce the expression of miRNA or cDNA by adding 4-hydroxytamoxifen (4-OHT) in a working concentration of 1 &#181;M. Note that this step is valid only if using retroviral vectors from Addgene (pMSCV-loxp-dsRed-loxp-eGFP-Puro-WPRE (32702), pMSCV-loxp-dsRed-loxp-3xHA-Puro-WPRE (32703), and pMSCV-FLIP-puro-dsRed-GFP-miRNA (32704)) and organoids expressing Cre-ERT2.</li>
</ol>
11. Confirmation of Infection and Expression/Suppression of the Gene of Interest
<ol>
	<li>If using retroviral vectors from Addgene (32702, 32703 and 32704) transduction efficiency can be confirmed by observation of dsRed expression. Furthermore, the expression or suppression of the gene of interest can be confirmed by Western Blot, using the GFP or 3xHA epitope (for gene overexpression) and qPCR (for gene knockdown), as exemplified in Koo&#160;et al4.</li>
</ol>

<ol>
	<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, 262-265 (2009).</li><li>Sato, T., Clevers, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Growing+self-organizing+mini-guts+from+a+single+intestinal+stem+cell:+mechanism+and+applications.">Growing self-organizing mini-guts from a single intestinal stem cell: mechanism and applications.</a> Science. 340, 1190-1194 (2013).</li><li>Stelzner, 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=A+nomenclature+for+intestinal+in+vitro+cultures.+American+journal+of+physiology.">A nomenclature for intestinal in vitro cultures. American journal of physiology.</a> Gastrointestinal and liver physiology. 302, G1359-G1363 (2012).</li><li>Koo, B. 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=Controlled+gene+expression+in+primary+Lgr5+organoid+cultures.">Controlled gene expression in primary Lgr5 organoid cultures.</a> Nature. 9, 81-83 (2012).</li><li>Schwank, G., Andersson-Rolf, A., Koo, B. K., Sasaki, N., Clevers, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Generation+of+BAC+Transgenic+Epithelial+Organoids.">Generation of BAC Transgenic Epithelial Organoids.</a> PloS one. 8, e76871 (2013).</li><li>Mustata, R. 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=Lgr4+is+required+for+Paneth+cell+differentiation+and+maintenance+of+intestinal+stem+cells+ex+vivo.">Lgr4 is required for Paneth cell differentiation and maintenance of intestinal stem cells ex vivo.</a> EMBO reports. 12, 558-564 (2011).</li><li>Lau, W., 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=Lgr5+homologues+associate+with+Wnt+receptors+and+mediate+R-spondin+signalling.">Lgr5 homologues associate with Wnt receptors and mediate R-spondin signalling.</a> Nature. 476, 293-297 (2011).</li><li>Koo, B. 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=Tumour+suppressor+RNF43+is+a+stem-cell+E3+ligase+that+induces+endocytosis+of+Wnt+receptors.">Tumour suppressor RNF43 is a stem-cell E3 ligase that induces endocytosis of Wnt receptors.</a> Nature. 488, 665-669 (2012).</li><li>Huch, 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=Unlimited+in+vitro+expansion+of+adult+bi-potent+pancreas+progenitors+through+the+Lgr5/R-spondin+axis.">Unlimited in vitro expansion of adult bi-potent pancreas progenitors through the Lgr5/R-spondin axis.</a> The EMBO journal. 32, 2708-2721 (2013).</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=Long-term+expansion+of+epithelial+organoids+from+human+colon,+adenoma,+adenocarcinoma,+and+Barrett's+epithelium.">Long-term expansion of epithelial organoids from human colon, adenoma, adenocarcinoma, and Barrett's epithelium.</a> Gastroenterology. 141, 1762-1772 (2011).</li><li>Huch, 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=In+vitro+expansion+of+single+Lgr5++liver+stem+cells+induced+by+Wnt-driven+regeneration.">In vitro expansion of single Lgr5+ liver stem cells induced by Wnt-driven regeneration.</a> Nature. 494, 247-250 (2013).</li></ol>

The authors have nothing to disclose. The authors have no conflict of interest declared.

To achieve high transduction efficiency certain aspects are critical. One is the pre-treatment of organoids with ENRWntNic media until they adopt a round cystic shape. This increases the number of stem cells and thereby the chance of obtaining a stable integration of the transgene, as well as increasing the survival rate of the SI organoids throughout the transduction procedure. Another parameter is the incubation time following spinoculation. Too short or too long incubation results in poor transduction efficiency and poor survival of the organoids, respectively. The spinoculation step is not essential although it significantly increases the percentage of transduced organoids. Finally, high-titer virus is key for successful transduction. This is dependent on the type of packaging cell line and virus. The combination of Platinum-E cell line and murine stem cell virus (MSCV), was found to produce a titer high enough for transduction of organoids.
Below are tips for troubleshooting which may help to achieve successful transduction. First, if the transfection of the packaging cell line is poor, make sure that the confluency of the cells is between 70-80% and that the incubation time of the pooled PEI-DNA mixture is between 20-30 min. The survival of the organoids during transduction highly depends on the fragment size. Too long trypsinization causes the majority of fragments to consist of less than 3 cells and thereby decreases organoid survivability. Another factor is the activity of the Wnt conditioned medium, if the activity is too low boosting it through addition of CHIR99021 in a working concentration of 5 &#956;M can increase the survival. CHIR99021 inhibits GSK3, resulting in increased Wnt signaling. Furthermore, Y-27362, which prevents anoikis is added to the transduction media to improve organoid survivability, since the organoids are disrupted to fragments (containing 1-10 cells) prior to transduction. As&#160;mentioned above, the incubation time after spinoculation should not exceed 6 hr. Lastly, if poor transduction is observed the aforementioned factors influencing the viral titer and the size limit of the insert for the retroviral vector should be considered. The efficiency of the knockdown is highly dependent on the miRNA. Since the efficiency varies with the combination of the target gene and miRNA it is worth performing an efficiency screen to identify those that work best.
The technique is restricted to the epithelial phenomena of the organoid system. In the future it might be possible to study infectious or immune-mediated diseases through co-culture of pathogens or reconstitution with components derived from the immune system, respectively. Moreover, retroviruses can only carry inserts of a relatively small size. Consequently, naturally occurring regulatory regions have to be excluded and therefore the expression of the transgene cannot mimic that of the endogenous gene. As mentioned above, the knockdown efficiency is dependent on the target gene and miRNA. If no miRNA with suitable knockdown efficiency can be found it may limit the use of the technique for that particular target gene.
Theoretically, organoids are compatible with all standardized manipulative techniques used for cell lines. Retroviral transduction was the first method to be reported4, and recently BAC (bacterial artificial chromosome)-transgenesis has become available5. With a total generation time of 2-3 weeks, after transfection of the viral plasmid into the packaging cell line, it is significantly faster than the generation of a transgenic (tg) mouse. By maintaining the in vivo crypt-villus architecture while containing stem cells as well as all differentiated cell lineages of the intestinal epithelium, the organoid culture system bridges the gap between tg animal and previously used cell culture.
The protocol described here provides a method to perform phenotypic analysis of endodermal epithelium in vitro through gain- and loss- of function studies. This makes it feasible to address physiologically relevant questions in adult stem cell biology, with a minimal need of tg mice. For example, the generation of conditional knockout mice could be avoided by using organoids derived from newborn mutants with perinatal lethality6. In addition, the technique can be applied to organoids derived from previously established knockout mice to study the role of paralogues by performing additional knockdown7,8.
Following the establishment of small intestinal organoids, adaptation of the original culture protocol has allowed culturing of pancreatic, liver, colon and stomach epithelia9-11. Furthermore, human intestinal organoids and tumor organoids have been derived from normal human biopsies, primary adenoma and colorectal cancer biopsies10. The viral infection protocol can easily be extended to these types of organoids and provides an unprecedented way of performing functional studies in human derived tissues.
Taken together, retroviral transduction of small intestinal organoids is a valuable resource for investigating stem cell maintenance, differentiation, and cell fate decision, as well as cell signaling and cell- cell interactions.

High-throughput functional genetics is needed to increase our biological understanding of the body, to improve current basic science and medicine. Mouse genetics has been the gold standard for investigating gene function in vivo, although it is both time-consuming and costly. Cell lines, being the other common choice, have a higher throughput capacity while being less expensive. However, they are impeded by their inability to reproduce the proper microenvironment and thereby the physiological responses seen in vivo. Hence, there is an unambiguous need for an easy-to-handle model system, which allows cost/time-efficient high throughput analysis while mimicking the physiological responses observed in in vivo transgenic (tg) mouse experiments.
For the endodermal epithelium one such model system appeared in 20091. Among the knowledge gained from the discovery of Lgr5-positive intestinal stem cells was information about the niche corresponding to the extra-cellular matrix and growth factors necessary for stem cell maintenance. Utilizing this information it became possible to establish &#8216;mini-guts&#8217; also known as organoids2. Recently a consensus nomenclature for in vitro cultures, where organoids are referred to as &#8216;enteroids&#8217;, was suggested3. Like cell lines, the organoids are ever-expanding and easy to treat with ligands and inhibitors. However, instead of being two-dimensional they are three-dimensional self-organizing structures that retain the crypt-villus organization as well as stem cells and differentiated cell lineages of the small intestine (SI). Organoids consist of a single layer of epithelial cells that surround a luminal area. Protruding budding structures correspond to small intestinal crypts containing the stem cell compartment. Starting from the tip of the budding structure progenitor cells differentiate as they migrate towards the epithelial lining, where terminally differentiated cells are shed into the lumen. Compared to cell lines, this ex vivo system more closely recapitulates the normal physiology and is therefore a promising model system for the small intestinal epithelium.
In this video protocol of retroviral transduction, we present a method that enables ex vivo gene function studies in this novel organoid culture system. We start by describing organoid culture in a step-by-step manner, and continue by demonstrating&#160;the generation of retroviruses followed by the transduction procedure. Finally, there is a section for additional advice for troubleshooting. An advantage of this technique is that it can be combined with live imaging or drug screening to study homeostasis, cell fate decisions and cell-cell interactions in the intestinal epithelium. Due to their simple architecture and fast turnover rate, organoids represent an ideal model system for studying adult stem cell biology. In addition retroviral transduction can be applied to organoids derived from pre-established transgenic mice as well as human patient samples. As knock-in and knock-out approaches cannot be extended to humans, the human SI organoids constitute an attractive alternative.
In summary, gene manipulation through retroviral transduction allows phenotypic analysis in small intestinal organoids derived from mice or human tissue samples, thereby complementing mouse genetics and cell lines while opening new avenues for studies in human derived tissues. Retroviral transduction enables gain- and loss-of-function studies to be performed in the organoid culture system4. This makes it a valuable resource for investigating gene function, adult stem cell biology and disease while being in accordance with the three Rs (reduction, refinement, and replacement).

<table border="0" cellpadding="0" cellspacing="0" width="1090">
	<tbody>
		<tr height="19">
			<td height="19" style="height:19px;width:220px;">Advanced DMEM/F12&#160;</td>
			<td style="width:157px;">Invitrogen</td>
			<td style="width:119px;">12634-034</td>
			<td style="width:595px;"></td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">Glutamax 100x&#160;</td>
			<td style="width:157px;">Invitrogen</td>
			<td style="width:119px;">35050-068</td>
			<td></td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">Hepes 1M&#160;</td>
			<td style="width:157px;">Invitrogen</td>
			<td>15630-056</td>
			<td></td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">Penicillin- Streptomycin 100x</td>
			<td style="width:157px;">Invitrogen</td>
			<td>15140-122</td>
			<td></td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">B27 supplement 50x</td>
			<td style="width:157px;">Invitrogen</td>
			<td>17504-044</td>
			<td></td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">N2 supplement 100x&#160;</td>
			<td>Invitrogen&#160;</td>
			<td>17502-048</td>
			<td></td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">n-Acetylcysteine 500 mM&#160;&#160;</td>
			<td>Sigma-Aldrich</td>
			<td>A9165-5G</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">mouse EGF 500 &#181;g/ml</td>
			<td>Invitrogen Biosource</td>
			<td>PMG8043</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">mouse Noggin 100 &#181;g/ml&#160;&#160;</td>
			<td>Peprotech</td>
			<td>250-38</td>
			<td></td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">R-Spondin conditioned medium</td>
			<td></td>
			<td></td>
			<td>The conditioned media is generated&#160; from HEK293 cells, for details see Sato and Clevers 2013</td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">Wnt conditioned medium</td>
			<td></td>
			<td></td>
			<td>The conditioned media is generated&#160; from L cells, for details see Sato and Clevers 2013</td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">Nicotinamide 1 M</td>
			<td>Sigma</td>
			<td>N0636</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Y-27632 10 &#181;M</td>
			<td>Sigma</td>
			<td>Y0503-1MG</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Polybrene 8 &#181;g/ml)</td>
			<td>Sigma</td>
			<td>H9268-5G</td>
			<td></td>
		</tr>
		<tr height="39">
			<td height="39" style="height:39px;">Standard BD Matrigel matrix</td>
			<td>BD Biosciences</td>
			<td>356231</td>
			<td style="width:595px;">Basement Matrix Extract (Cultrex PathClear BME Reduced Growth Factor Type 2, 3533-005-02 ) 
			supplied by AMSBIO can be used as an alterntive.</td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;width:220px;">24 well plate</td>
			<td>Greiner Bio One</td>
			<td>662960</td>
			<td></td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">48 well plate</td>
			<td>Greiner Bio One</td>
			<td>677980</td>
			<td></td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">CHIR99021</td>
			<td>Sigma</td>
			<td>A3734-1MG</td>
			<td></td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">Platinum- E cells</td>
			<td>Cell biolabs</td>
			<td>RV-102</td>
			<td></td>
		</tr>
		<tr height="19">
			<td height="19" style="height:19px;">Puromycin</td>
			<td>Invitrogen</td>
			<td>A1113802</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:220px;">Blasticidin</td>
			<td style="width:157px;">Invitrogen</td>
			<td style="width:119px;">A1113902</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:220px;">Polyethyleneimine (PEI)</td>
			<td style="width:157px;">Polysciences</td>
			<td style="width:119px;">23966</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:220px;">opti-MEM</td>
			<td style="width:157px;">Life Technologies</td>
			<td style="width:119px;">51985-034</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:220px;">TrypLE</td>
			<td style="width:157px;">Invitrogen</td>
			<td style="width:119px;">12605-010</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:220px;">Parafilm</td>
			<td style="width:157px;">Sigma</td>
			<td style="width:119px;">P7793-1EA</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:220px;">4-OHT</td>
			<td style="width:157px;">Sigma</td>
			<td style="width:119px;">H7904</td>
			<td></td>
		</tr>
	</tbody>
</table>

a video protocol of retroviral infection in primary intestinal organoid culture

Lgr5-positive stem cells can be supplemented with the essential growth factors Egf, Noggin, and R-Spondin, which allows us to culture ever-expanding primary 3D epithelial structures in vitro. Both the architecture and physiological properties of these &#39;mini-guts&#39;, also called organoids, closely resemble their in vivo counterparts. This makes them an attractive model system for the small intestinal epithelium. Using retroviral transduction, functional genetics can now be performed by conditional gene overexpression or knockdown. This video demonstrates the procedure of organoid culture, the generation of retroviruses, and the retroviral transduction of organoids to assist phenotypic analysis of the small intestinal epithelium in vitro. This novel organotypic model system in combination with retroviral mediated gene expression provides a valuable tool for rapid analysis of gene function in vitro without the need of costly and time-consuming generation for transgenic animals.

Organoids are ready to be split when the central lumen is darkened due to the presence of dead cells (Figure 2). After 2-3 days of pre-treatment organoids should adopt a round cystic morphology (Figure 3). This increases the number of stem cells, enhancing the chances of obtaining stable integration. The size of the viral pellet may vary following centrifugation of the viral supernatant, most likely due to varying contribution of cell debris to the pellet size. No clear correlation to transduction efficiency has been observed. During the selection procedure non-transduced organoids will die, while the ones having a stable integration will remain. The fluorescent protein from MSCV-eGFP retrovirus can be observed in cells originating from surviving organoids, which have a cystic morphology, within 2-3 days following transduction (Figure 4).
<img alt="Figure 1" fo:content-width="6in" src="/files/ftp_upload/51765/51765fig1highres.jpg" width="600" /> 
Figure 1. A schematic drawing of the retroviral transduction procedure. Prior to infection organoids are pre-treated using ENRWntNic until they adopt a cystic structure (step 1). Platinum-E cells are used as the packaging cell line, and are cultured until they reach 70-80% confluency. Thereafter they are transfected with the retroviral construct using PEI. Viruses are harvested 2 days later (step 2). Organoids are trypsinized to obtain fragments containing 1-10 cells (step 3), and are then infected (step 4). Following spinoculation to increase the infection efficiency (step 5), the infected organoid fragments are seeded (step 6) and 2-3 days later selection for positive clones with stable integration can be performed (step 7).
<img alt="Figure 2" fo:content-width="5in" src="/files/ftp_upload/51765/51765fig2highres.jpg" width="500" /> 
Figure 2. Representative image of organoids after 4-6 days of culture. The lumen is filled with dead cells, making it appear dark. Organoids at this stage are ready to be passaged.
<img alt="Figure 3" fo:content-width="5in" src="/files/ftp_upload/51765/51765fig3highres.jpg" width="500" /> 
Figure 3. Representative image of small intestinal organoids cultured in ENRWntNic media for 3-4 days. The organoids adopt a cystic morphology.
<img alt="Figure 4" fo:content-width="5in" src="/files/ftp_upload/51765/51765fig4highres.jpg" width="500" /> 
Figure 4. Representative image of small intestinal organoids&#160;(a) that show viral transgene expression (b, eGFP).
<table border="0" cellpadding="0" cellspacing="0">
	<tbody>
		<tr>
			<td colspan="2">Advanced DMEM/F12 +++</td>
		</tr>
		<tr>
			<td colspan="2">Store at 4 &#176;C for 4 weeks</td>
		</tr>
		<tr>
			<td>Advanced DMEM/F12</td>
			<td>500 ml</td>
		</tr>
		<tr>
			<td>Glutamax 100x</td>
			<td>5 ml</td>
		</tr>
		<tr>
			<td>Hepes 1 M&#160;&#160;</td>
			<td>5 ml</td>
		</tr>
		<tr>
			<td>Antibiotics 100x&#160;</td>
			<td>5 ml</td>
		</tr>
		<tr>
			<td colspan="2">ENRWntNic medium (for 20 ml)</td>
		</tr>
		<tr>
			<td colspan="2">Store at 4 &#176;C for 2 weeks</td>
		</tr>
		<tr>
			<td>Advanced DMEM/F12 +++</td>
			<td>7.2 ml</td>
		</tr>
		<tr>
			<td>B27 supplement (50x)</td>
			<td>400 &#181;l</td>
		</tr>
		<tr>
			<td>N2 supplement (100x)</td>
			<td>200 &#181;l</td>
		</tr>
		<tr>
			<td>n-Acetylcysteine (500 mM)</td>
			<td>50 &#181;l</td>
		</tr>
		<tr>
			<td>mouse EGF (500 &#181;g/ml)</td>
			<td>2 &#181;l</td>
		</tr>
		<tr>
			<td>mouse Noggin (100 &#181;g/ml)&#160;</td>
			<td>20 &#181;l</td>
		</tr>
		<tr>
			<td>R-Spondin conditioned medium</td>
			<td>2 ml</td>
		</tr>
		<tr>
			<td>Wnt3a conditioned medium&#160;</td>
			<td>10 ml</td>
		</tr>
		<tr>
			<td>Nicotinamide (1 M)&#160;</td>
			<td>200 &#181;l</td>
		</tr>
		<tr>
			<td colspan="2">Transduction medium (for 20 ml)</td>
		</tr>
		<tr>
			<td colspan="2">Prepare fresh</td>
		</tr>
		<tr>
			<td>ENRWntNic medium&#160;&#160;</td>
			<td>20 ml</td>
		</tr>
		<tr>
			<td>Y-27632 (10 &#181;M)&#160;</td>
			<td>20 &#181;l</td>
		</tr>
		<tr>
			<td>Polybrene (8 &#181;g/ml)&#160;</td>
			<td>20 &#181;l</td>
		</tr>
		<tr>
			<td colspan="2">ENR medium (for 20 ml)</td>
		</tr>
		<tr>
			<td colspan="2">Store at 4 &#176;C for 4 weeks</td>
		</tr>
		<tr>
			<td>Advanced DMEM/F12 +++&#160;</td>
			<td>17.4 ml</td>
		</tr>
		<tr>
			<td>B27 supplement (50x)</td>
			<td>400 &#181;l</td>
		</tr>
		<tr>
			<td>N2 supplement (100x)</td>
			<td>200 &#181;l</td>
		</tr>
		<tr>
			<td>n-Acetylcysteine (500 mM)</td>
			<td>50 &#181;l</td>
		</tr>
		<tr>
			<td>mouse EGF (500 &#181;g/ml)</td>
			<td>2 &#181;l</td>
		</tr>
		<tr>
			<td>mouse Noggin (100 &#181;g/ml)</td>
			<td>20 &#181;l</td>
		</tr>
		<tr>
			<td>R-Spondin conditioned medium&#160;</td>
			<td>2 ml</td>
		</tr>
		<tr>
			<td colspan="2">Media for Platinum-E cells&#160; (for 500 ml)</td>
		</tr>
		<tr>
			<td colspan="2">Store at 4 &#176;C for 12 weeks</td>
		</tr>
		<tr>
			<td>DMEM&#160;</td>
			<td>449.45 ml</td>
		</tr>
		<tr>
			<td>Fetal Bovine Serum (FBS)</td>
			<td>50 ml</td>
		</tr>
		<tr>
			<td>Puromycin (1 &#956;g/ml)&#160;</td>
			<td>50 &#181;l</td>
		</tr>
		<tr>
			<td>Blasticidin (10 &#956;g/ml)</td>
			<td>500 &#181;l</td>
		</tr>
	</tbody>
</table>
Table 1. Media composition for Advanced DMEM/F12 +++, ENRWntNic medium, Transduction medium, ENR medium, and medium for Platinum-E cells.

Watch this Scientific Journal Video about A Video Protocol of Retroviral Infection in Primary Intestinal Organoid Culture at JoVE.com

A Video Protocol of Retroviral Infection in Primary Intestinal Organoid Culture

This protocol explains primary Lgr5-positve organoid culture and the subsequent performance of retroviral transduction. This enables Cre-inducible overexpression or knockdown of the delivered transgene and allows functional studies to be carried out in the novel in vitro organotypic model system.

Lgr5-positive stem cells can be supplemented with the essential growth factors Egf, Noggin, and R-Spondin, which allows us to culture ever-expanding ...

a-video-protocol-retroviral-infection-primary-intestinal-organoid

Research

JoVE Journal

Biology

29.5K Views.  University of Cambridge. This protocol explains primary Lgr5-positve organoid culture and the subsequent performance of retroviral transduction. This enables Cre-inducible overexpression or knockdown of the delivered transgene and allows functional studies to be carried out in the novel in vitro organotypic model system. 

Video: A Video Protocol of Retroviral Infection in Primary Intestinal Organoid Culture

Protocol for Dengue Infections in Mosquitoes (A. aegypti) and Infection Phenotype Determination

The purpose of this procedure is to infect the Aedes mosquito with dengue virus in a laboratory condition and examine the infection level and dynamic of the virus in the mosquito tissues. This protocol is routinely used for studying mosquito-virus interactions, especially for identification of novel host factors that are able to determine vector competence. The entire experiment must be conducted in a BSL2 laboratory. Similar to Plasmodium falciparum infections, proper attire including gloves and lab coat must be worn at all times. After the experiment, all the materials that came in contact with the virus need to be treated with 75% ethanol and bleached before proceeding with normal washing. All other materials need to be autoclaved before discarding them.

Protocol for Dengue Infections in Mosquitoes A. aegypti and Infection Phenotype Determination

Once a gene is identified as potentially refractory for the dengue virus, it must be evaluated for it's role in preventing viral infections within the mosquito. This protocol illustrates how the extent of dengue infections of mosquitoes can be assayed. The techniques for growing up the virus in culture, membrane feeding mosquitoes human blood, and assaying viral titers in the mosquito midgut are demonstrated.

The purpose of this procedure is to infect the Aedes mosquito with dengue virus in a laboratory condition and examine the infection level and dynamic of ...

Primary Culture and Plasmid Electroporation of the Murine Organ of Corti. 

In all mammals, the sensory epithelium for audition is located along the spiraling organ of Corti that resides within the conch shaped cochlea of the inner ear (fig 1). Hair cells in the developing cochlea, which are the mechanosensory cells of the auditory system, are aligned in one row of inner hair cells and three (in the base and mid-turns) to four (in the apical turn) rows of outer hair cells that span the length of the organ of Corti. Hair cells transduce sound-induced mechanical vibrations of the basilar membrane into neural impulses that the brain can interpret. Most cases of sensorineural hearing loss are caused by death or dysfunction of cochlear hair cells.
An increasingly essential tool in auditory research is the isolation and in vitro culture of the organ explant 1,2,9. Once isolated, the explants may be utilized in several ways to provide information regarding normative, anomalous, or therapeutic physiology. Gene expression, stereocilia motility, cell and molecular biology, as well as biological approaches for hair cell regeneration are examples of experimental applications of organ of Corti explants.
This protocol describes a method for the isolation and culture of the organ of Corti from neonatal mice. The accompanying video includes stepwise directions for the isolation of the temporal bone from mouse pups, and subsequent isolation of the cochlea, spiral ligament, and organ of Corti. Once isolated, the sensory epithelium can be plated and cultured in vitro in its entirety, or as a further dissected micro-isolate that lacks the spiral limbus and spiral ganglion neurons. Using this method, primary explants can be maintained for 7-10 days. As an example of the utility of this procedure, organ of Corti explants will be electroporated with an exogenous DsRed reporter gene. This method provides an improvement over other published methods because it provides reproducible, unambiguous, and stepwise directions for the isolation, microdissection, and primary culture of the organ of Corti.

Primary Culture and Plasmid Electroporation of the Murine Organ of Corti.

This procedure describes a method for the isolation and culture of the murine organ of Corti with or without the spiral limbus and spiral ganglion neurons. We also demonstrate a method for the expression of an exogenous reporter gene in the organ of Corti explant by electroporation.

In all mammals, the sensory epithelium for audition is located along the spiraling organ of Corti that resides within the conch shaped cochlea of the ...

Isolation and Primary Culture of Rat Hepatic Cells

Primary hepatocyte culture is a valuable tool that has been extensively used in basic research of liver function, disease, pathophysiology, pharmacology and other related subjects. The method based on two-step collagenase perfusion for isolation of intact hepatocytes was first introduced by Berry and Friend in 1969 1 and, since then, has undergone many modifications. The most commonly used technique was described by Seglenin 1976 2. Essentially, hepatocytes are dissociated from anesthetized adult rats by a non-recirculating collagenase perfusion through the portal vein. The isolated cells are then filtered through a 100 &mu;m pore size mesh nylon filter, and cultured onto plates. After 4-hour culture, the medium is replaced with serum-containing or serum-free medium, e.g. HepatoZYME-SFM, for additional time to culture. These procedures require surgical and sterile culture steps that can be better demonstrated by video than by text. Here, we document the detailed steps for these procedures by both video and written protocol, which allow consistently in the generation of viable hepatocytes in large numbers.

Primary hepatocytes provide a valuable tool to evaluate biochemical, molecular, and metabolic functions in a physiologically relevant experimental system. We describe a reliable protocol for rat in situ liver perfusion, which consistently generates viable hepatocytes up to 1.0 &times; 108 cells per preparation with cell viability between 88 ~ 96%.

Primary hepatocyte culture is a valuable tool that has been extensively used in basic research of liver function, disease, pathophysiology, pharmacology ...

Retroviral Infection of Murine Embryonic Stem Cell Derived Embryoid Body Cells for Analysis of Hematopoietic Differentiation

Embryonic stem cells (ESCs) are an outstanding model for elucidating the molecular mechanisms of cellular differentiation. They are especially useful for investigating the development of early hematopoietic progenitor cells (HPCs). Gene expression in ESCs can be manipulated by several techniques that allow the role for individual molecules in development to be determined. One difficulty is that expression of specific genes often has different phenotypic effects dependent on their temporal expression. This problem can be circumvented by the generation of ESCs that inducibly express a gene of interest using technology such as the doxycycline-inducible transgene system. However, generation of these inducible cell lines is costly and time consuming. Described here is a method for disaggregating ESC-derived embryoid bodies (EBs) into single cell suspensions, retrovirally infecting the cell suspensions, and then reforming the EBs by hanging drop. Downstream differentiation is then evaluated by flow cytometry. Using this protocol, it was demonstrated that exogenous expression of a microRNA gene at the beginning of ESC differentiation blocks HPC generation. However, when expressed in EB derived cells after nascent mesoderm is produced, the microRNA gene enhances hematopoietic differentiation. This method is useful for investigating the role of genes after specific germ layer tissue is derived.

Manipulating temporal gene expression in differentiating embryonic stem cells (ESCs) can be achieved using inducible gene systems. However, generation of these cell lines is costly and time consuming. This protocol achieves rapid expression of a transgene in differentiating ES-derived cells and subsequent analysis of downstream hematopoietic differentiation.

Embryonic stem cells (ESCs) are an outstanding model for elucidating the molecular mechanisms of cellular differentiation. They are especially useful for ...

Real Time Analysis of Metabolic Profile in Ex Vivo Mouse Intestinal Crypt Organoid Cultures

The small intestinal mucosa exhibits a repetitive architecture organized into two fundamental structures: villi, projecting into the intestinal lumen and composed of mature enterocytes, goblet cells and enteroendocrine cells; and crypts, residing proximal to the submucosa and the muscularis, harboring adult stem and progenitor cells and mature Paneth cells, as well as stromal and immune cells of the crypt microenvironment. Until the last few years, in vitro studies of small intestine was limited to cell lines derived from either benign or malignant tumors, and did not represent the physiology of normal intestinal epithelia and the influence of the microenvironment in which they reside. Here, we demonstrate a method adapted from Sato et al. (2009) for culturing primary mouse intestinal crypt organoids derived from C57BL/6 mice. In addition, we present the use of crypt organoid cultures to assay the crypt metabolic profile in real time by measurement of basal oxygen consumption, glycolytic rate, ATP production and respiratory capacity. Organoids maintain properties defined by their source and retain aspects of their metabolic adaptation reflected by oxygen consumption and extracellular acidification rates. Real time metabolic studies in this crypt organoid culture system are a powerful tool to study crypt organoid energy metabolism, and how it can be modulated by nutritional and pharmacological factors.

Real Time Analysis of Metabolic Profile in Ex Vivo Mouse Intestinal Crypt Organoid Cultures

Small intestinal crypt organoids cultured ex vivo provide a tissue culture system that recapitulates growth of crypts dependent on stem cells and their niche. We established a method to assay the metabolic profile in real time in primary mouse crypt organoids. We found organoids maintain physiological properties defined by their source.

The small intestinal mucosa exhibits a repetitive architecture organized into two fundamental structures: villi, projecting into the intestinal lumen and ...

A Protocol for Lentiviral Transduction and Downstream Analysis of Intestinal Organoids

Intestinal crypt-villus structures termed organoids, can be kept in sustained culture three dimensionally when supplemented with the appropriate growth factors. Since organoids are highly similar to the original tissue in terms of homeostatic stem cell differentiation, cell polarity and presence of all terminally differentiated cell types known to the adult intestinal epithelium, they serve as an essential resource in experimental research on the epithelium. The possibility to express transgenes or interfering RNA using lentiviral or retroviral vectors in organoids has increased opportunities for functional analysis of the intestinal epithelium and intestinal stem cells, surpassing traditional mouse transgenics in speed and cost. In the current video protocol we show how to utilize transduction of small intestinal organoids with lentiviral vectors illustrated by use of doxycylin inducible transgenes, or IPTG inducible short hairpin RNA for overexpression or gene knockdown. Furthermore, considering organoid culture yields minute cell counts that may even be reduced by experimental treatment, we explain how to process organoids for downstream analysis aimed at quantitative RT-PCR, RNA-microarray and immunohistochemistry. Techniques that enable transgene expression and gene knock down in intestinal organoids contribute to the research potential that these intestinal epithelial structures hold, establishing organoid culture as a new standard in cell culture.

In this video protocol we give a step by step explanation of lentiviral transduction in organoids of primary intestinal epithelium and of processing and downstream analysis of these cultures by quantitative RT-PCR, RNA-microarray and immunohistochemistry.

Intestinal crypt-villus structures termed organoids, can be kept in sustained culture three dimensionally when supplemented with the appropriate growth ...

Isolation and Culture of Primary Mouse Keratinocytes from Neonatal and Adult Mouse Skin

The keratinocyte (KC) is the predominant cell type in the epidermis, the outermost layer of the skin. Epidermal KCs play a critical role in providing skin defense by forming an intact skin barrier against environmental insults, such as UVB irradiation or pathogens, and also by initiating an inflammatory response upon those insults. Here we describe methods to isolate KCs from neonatal mouse skin and from adult mouse tail skin. We also describe culturing conditions using defined growth supplements (dGS) in comparison to chelexed fetal bovine serum (cFBS). Functionally, we show that both neonatal and adult KCs are highly responsive to high calcium-induced terminal differentiation, tight junction formation and stratification. Additionally, cultured adult KCs are susceptible to UVB-triggered cell death and can release large amounts of TNF upon UVB irradiation. Together, the methods described here will be useful to researchers for the setup of in vitro models to study epidermal biology in the neonatal mouse and/or the adult mouse.

Epidermal keratinocytes form a functional skin barrier and are positioned at the front line of host defense against external environmental insults. Here we describe methods for isolation and primary culture of epidermal keratinocytes from neonatal and adult mouse skin, and induction of terminal differentiation and UVB-triggered inflammatory response from keratinocytes.

The keratinocyte (KC) is the predominant cell type in the epidermis, the outermost layer of the skin. Epidermal KCs play a critical role in providing skin ...

Apoptosis Induction and Detection in a Primary Culture of Sea Cucumber Intestinal Cells

Primary cultured cells are used in a variety of scientific disciplines as exceptionally important tools for the functional evaluation of biological substances or characterization of specific biological activities. However, due to the lack of universally applicable cell culture media and protocols, well described cell culture methods for marine organisms are still limited. Meanwhile, the commonly occurring microbial contamination and polytropic properties of marine invertebrate cells further impede the establishment of an effective cell culture strategy for marine invertebrates. Here, we describe an easy-to-handle method for culturing intestinal cells from sea cucumber Apostichopus japonicus; additionally, we provide an example of in vitro apoptosis induction and detection in primary cultured intestinal cells. Moreover, this experiment provides details about the appropriate culture medium and cell collection method. The described protocol is compatible with a variety of widely available tissue samples from marine organisms including Echinodermata, Mollusca, and Crustacea, and it can provide sufficient cells for multiple in vitro experimental applications. This technique would enable researchers to efficiently manipulate primary cell cultures from marine invertebrates and to facilitate the functional evaluation of targeted biological materials on cells.

This protocol provides an easy-to-handle method to culture the intestinal cells from sea cucumber Apostichopus japonicus and is compatible with a variety of widely available tissue samples from marine organisms including Echinodermata, Mollusca, and Crustacea.

Primary cultured cells are used in a variety of scientific disciplines as exceptionally important tools for the functional evaluation of biological ...

Organoid-Derived Epithelial Monolayer: A Clinically Relevant In Vitro Model for Intestinal Barrier Function

In the past, intestinal epithelial model systems were limited to transformed cell lines and primary tissue. These model systems have inherent limitations as the former do not faithfully represent original tissue physiology, and the availability of the latter is limited. Hence, their application hampers fundamental and drug development research. Adult stem-cell-based organoids (henceforth referred to as organoids) are miniatures of normal or diseased epithelial tissue from which they are derived. They can be established very efficiently from different gastrointestinal (GI) tract regions, have long-term expandability, and simulate tissue- and patient-specific responses to treatments in vitro. Here, the establishment of intestinal organoid-derived epithelial monolayers has been demonstrated along with methods to measure epithelial barrier integrity, permeability and transport,&#160;antimicrobial protein secretion, as well as histology. Moreover, intestinal organoid-derived monolayers can be enriched with proliferating stem and transit-amplifying cells as well as with key differentiated epithelial cells. Therefore, they represent a model system that can be tailored to study the effects of compounds on target cells and their mode of action. Although organoid cultures are technically more demanding than cell lines, once established, they can reduce failures in the later stages of drug development as they truly represent in vivo epithelium complexity and interpatient heterogeneity.

Here, we describe the preparation of human organoid-derived intestinal epithelial monolayers for studying intestinal barrier function, permeability, and transport. As organoids represent original epithelial tissue response to external stimuli, these models combine the advantages of expandability of cell lines and the relevance and complexity of primary tissue.

In the past, intestinal epithelial model systems were limited to transformed cell lines and primary tissue. These model systems have inherent limitations ...

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 ...