Name: a video protocol of retroviral infection in primary intestinal organoid culture
Uploaded: 2014-08-11T18:30:00.000+00:00
Duration: 9 min 18 s
Description: Watch this Scientific Journal Video about A Video Protocol of Retroviral Infection in Primary Intestinal Organoid Culture at JoVE.com

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><tbody><tr><td>Advanced DMEM/F12&amp;nbsp;</td><td>Invitrogen</td><td>12634-034</td><td></td></tr><tr><td>Glutamax 100x&amp;nbsp;</td><td>Invitrogen</td><td>35050-068</td><td></td></tr><tr><td>HEPES 1 M</td><td>Invitrogen</td><td>15630-056</td><td></td></tr><tr><td>Penicillin-streptomycin 100x</td><td>Invitrogen</td><td>15140-122</td><td></td></tr><tr><td>B27 supplement 50x</td><td>Invitrogen</td><td>17504-044</td><td></td></tr><tr><td>N2 supplement 100x&amp;nbsp;</td><td>Invitrogen</td><td>17502-048</td><td></td></tr><tr><td>n-Acetylcysteine 500 mM</td><td>Sigma-Aldrich</td><td>A9165-5G</td><td></td></tr><tr><td>Mouse EGF 500 &amp;micro;g/ml</td><td>Invitrogen Biosource</td><td>PMG8043</td><td></td></tr><tr><td>Mouse Noggin 100 &amp;micro;g/ml</td><td>Peprotech</td><td>250-38</td><td></td></tr><tr><td>R-Spondin conditioned medium</td><td></td><td></td><td>The conditioned media is generated from HEK293 cells, for details see Sato and Clevers 2013.</td></tr><tr><td>Wnt conditioned medium</td><td></td><td></td><td>The conditioned media is generated from L cells, for details see Sato and Clevers 2013.</td></tr><tr><td>Nicotinamide 1 M</td><td>Sigma</td><td>N0636</td><td></td></tr><tr><td>Y-27632 10 &amp;micro;M</td><td>Sigma</td><td>Y0503-1MG</td><td></td></tr><tr><td>Polybrene (8 &amp;micro;g/ml)</td><td>Sigma</td><td>H9268-5G</td><td></td></tr><tr><td>Standard BD Matrigel matrix</td><td>BD Biosciences</td><td>356231</td><td>Basement Matrix Extract (Cultrex PathClear BME Reduced Growth Factor Type 2, 3533-005-02)&lt;br/&gt; supplied by AMSBIO can be used as an alterntive.</td></tr><tr><td>24-well Plate</td><td>Greiner Bio One</td><td>662960</td><td></td></tr><tr><td>48-well Plate</td><td>Greiner Bio One</td><td>677980</td><td></td></tr><tr><td>CHIR99021</td><td>Sigma</td><td>A3734-1MG</td><td></td></tr><tr><td>Platinum-E cells</td><td>Cell Biolabs</td><td>RV-102</td><td></td></tr><tr><td>Puromycin</td><td>Invitrogen</td><td>A1113802</td><td></td></tr><tr><td>Blasticidin</td><td>Invitrogen</td><td>A1113902</td><td></td></tr><tr><td>Polyethyleneimine (PEI)</td><td>Polysciences</td><td>23966</td><td></td></tr><tr><td>opti-MEM</td><td>Life Technologies</td><td>51985-034</td><td></td></tr><tr><td>TrypLE</td><td>Invitrogen</td><td>12605-010</td><td></td></tr><tr><td>Parafilm</td><td>Sigma</td><td>P7793-1EA</td><td></td></tr><tr><td>4-OHT</td><td>Sigma</td><td>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 ...

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Nanyang Technological University

Research

JoVE Journal

Biology

29.7K 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

High-sensitivity Detection of Micrometastases Generated by GFP Lentivirus-transduced Organoids Cultured from a Patient-derived Colon Tumor

Despite current advances in human colorectal cancer (CRC) treatment, few radical therapies are effective for the late stages of CRC. To overcome this clinical challenge, tumor xenograft mouse models using long-established human carcinoma cell lines and many transgenic mouse models with tumors have been developed as preclinical models. They partially mimic the features of human carcinomas, but often fail to recapitulate the key aspects of human malignancies including invasion and metastasis. Thus, alternative models that better represent the malignant progression in human CRC have long been awaited.
We herein show generation of patient-derived tumor xenografts (PDXs) by subcutaneous implantation of small CRC fragments surgically dissected from a patient. The colon PDXs develop and histopathologically resemble the CRC in the patient. However, few spontaneous micrometastases are detectable in conventional cross-sections of affected distant organs in the PDX model. To facilitate the detection of metastatic dissemination into distant organs, we extracted the tumor organoid cells from the colon PDXs in culture and infected them with GFP lentivirus prior to injection into highly immunodeficient NOD/Shi-scid IL2R&#947;null (NOG) mice. Orthotopically injected PDX-derived CRC organoid cells consistently form primary tumors positive for GFP in recipient mice. Moreover, spontaneously developing micrometastatic colonies expressing GFP are notably detected in the lungs of these mice by fluorescence microscopy. Moreover, intrasplenic injection of CRC organoids frequently produces hepatic colonization. Taken together, these findings indicate GFP-labelled PDX-derived CRC organoid cells to be visually detectable during a multistep process termed the invasion-metastasis cascade. The described protocols include the establishment of PDXs of human CRC and 3D culture of the corresponding CRC organoid cells transduced by GFP lentiviral particles.

To allow highly sensitive detection of the disseminating human colorectal cancer (CRC) cells colonizing tissues, we herein show a protocol for efficient transduction of green fluorescent protein (GFP) lentiviral particles into PDX-derived CRC organoid cells prior to their injection into recipient mice, with stereo-fluorescence microscopic observation.

Despite current advances in human colorectal cancer (CRC) treatment, few radical therapies are effective for the late stages of CRC. To overcome this ...

Cancer Research

Genetic Engineering of Primary Mouse Intestinal Organoids Using Magnetic Nanoparticle Transduction Viral Vectors for Frozen Sectioning

Intestinal organoid cultures provide a unique opportunity to investigate intestinal stem cell and crypt biology in vitro, although efficient approaches to manipulate gene expression in organoids have made limited progress in this arena. While CRISPR/Cas9 technology allows for precise genome editing of cells for organoid generation, this strategy requires extensive selection and screening by sequence analysis, which is both time-consuming and costly. Here, we provide a detailed protocol for efficient viral transduction of intestinal organoids. This approach is rapid and highly efficient, thus decreasing the time and expense inherent in CRISPR/Cas9 technology. We also present a protocol to generate frozen sections from intact organoid cultures for further analysis with immunohistochemical or immunofluorescent staining, which can be used to confirm gene expression or silencing. After successful transduction of viral vectors for gene expression or silencing is achieved, intestinal stem cell and crypt function can be rapidly assessed. Although most organoid studies employ in vitro assays, organoids can also be delivered to mice for in vivo functional analyses. Moreover, our approaches are advantageous for predicting therapeutic responses to drugs because currently available therapies generally function by modulating gene expression or protein function rather than altering the genome.

We describe step-by-step instructions to: 1) efficiently engineer intestinal organoids using magnetic nanoparticles for lenti- or retroviral transduction, and, 2) generate frozen sections from engineered organoids. This approach provides a powerful tool to efficiently alter gene expression in organoids for investigation of downstream effects.

Intestinal organoid cultures provide a unique opportunity to investigate intestinal stem cell and crypt biology in vitro, although efficient approaches to ...

Developmental Biology

The Ex Vivo Culture and Pattern Recognition Receptor Stimulation of Mouse Intestinal Organoids

Primary intestinal organoids are a valuable model system that has the potential to significantly impact the field of mucosal immunology. However, the complexities of the organoid growth characteristics carry significant caveats for the investigator. Specifically, the growth patterns of each individual organoid are highly variable and create a heterogeneous population of epithelial cells in culture. With such caveats, common tissue culture practices cannot be simply applied to the organoid system due to the complexity of the cellular structure. Counting and plating based solely on cell number, which is common for individually separated cells, such as cell lines, is not a reliable method for organoids unless some normalization technique is applied. Normalizing to total protein content is made complex due to the resident protein matrix. These characteristics in terms of cell number, shape and cell type should be taken into consideration when evaluating secreted contents from the organoid mass. This protocol has been generated to outline a simple procedure to culture and treat small intestinal organoids with microbial pathogens and pathogen associated molecular patterns (PAMPs). It also emphasizes the normalization techniques that should be applied when protein analysis are conducted after such a challenge.

The Ex Vivo Culture and Pattern Recognition Receptor Stimulation of Mouse Intestinal Organoids

Here, a protocol to harvest, maintain, and treat mouse small intestinal organoids with pathogen associated molecular patterns (PAMPs) and Listeria monocytogenes is described, as well as emphasis on gene expression and proper normalization techniques for protein.

Primary intestinal organoids are a valuable model system that has the potential to significantly impact the field of mucosal immunology. However, the ...

Immunology and Infection

Live Imaging of Primary Cerebral Cortex Cells Using a 2D Culture System

During cerebral cortex development, progenitor cells undergo several rounds of symmetric and asymmetric cell divisions to generate new progenitors or postmitotic neurons. Later, some progenitors switch to a gliogenic fate, adding to the astrocyte and oligodendrocyte populations. Using time-lapse video-microscopy of primary cerebral cortex cell cultures, it is possible to study the cellular and molecular mechanisms controlling the mode of cell division and cell cycle parameters of progenitor cells. Similarly, the fate of postmitotic cells can be examined using cell-specific fluorescent reporter proteins or post-imaging immunocytochemistry. More importantly, all these features can be analyzed at the single-cell level, allowing the identification of progenitors committed to the generation of specific cell types. Manipulation of gene expression can also be performed using viral-mediated transfection, allowing the study of cell-autonomous and non-cell-autonomous phenomena. Finally, the use of fusion fluorescent proteins allows the study of symmetric and asymmetric distribution of selected proteins during division and the correlation with daughter cells fate. Here, we describe the time-lapse video-microscopy method to image primary cerebral cortex murine cells for up to several days and analyze the mode of cell division, cell cycle length and fate of newly generated cells. We also describe a simple method to transfect progenitor cells, which can be applied to manipulate genes of interest or simply label cells with reporter proteins.

Live imaging is a powerful tool to study cellular behaviors in real time. Here, we describe a protocol for time-lapse video-microscopy of primary cerebral cortex cells that allows a detailed examination of the phases enacted during the lineage progression from primary neural stem cells to differentiated neurons and glia.

During cerebral cortex development, progenitor cells undergo several rounds of symmetric and asymmetric cell divisions to generate new progenitors or ...

Neuroscience

Adapting Gastrointestinal Organoids for Pathogen Infection and Single Cell Sequencing under Biosafety Level 3 (BSL-3) Conditions

Human intestinal organoids constitute the best cellular model to study pathogen infections of the gastrointestinal tract. These organoids can be derived from all sections of the GI tract (gastric, jejunum, duodenum, ileum, colon, rectum) and, upon differentiation, contain most of the cell types that are naturally found in each individual section. For example, intestinal organoids contain nutrient-absorbing enterocytes, secretory cells (Goblet, Paneth, and enteroendocrine), stem cells, as well as all lineage-specific differentiation intermediates (e.g.,&#160;early or immature cell types). The greatest advantage in using gastrointestinal tract-derived organoids to study infectious diseases is the possibility of precisely identifying which cell type is targeted by the enteric pathogen and to address whether the different sections of the gastrointestinal tract and their specific cell types similarly respond to pathogen challenges. Over the past years, gastrointestinal models, as well as organoids from other tissues, have been employed to study viral tropism and the mechanisms of pathogenesis. However, utilizing all the advantages of using organoids when employing highly pathogenic viruses represents a technical challenge and requires strict biosafety considerations. Additionally, as organoids are often grown in three dimensions, the basolateral side of the cells is facing the outside of the organoid while their apical side is facing the inside (lumen) of the organoids. This organization poses a challenge for enteric pathogens as many enteric infections initiate from the apical/luminal side of the cells following ingestion. The following manuscript will provide a comprehensive protocol to prepare human intestinal organoids for infection with enteric pathogens by considering the infection side (apical vs. basolateral) to perform single-cell RNA sequencing to characterize cell-type-specific host/pathogen interactions. This method details the preparation of the organoids as well as the considerations needed to perform this work under biosafety level 3 (BSL-3) containment conditions.

Adapting Gastrointestinal Organoids for Pathogen Infection and Single Cell Sequencing under Biosafety Level 3 BSL-3 Conditions

This protocol describes how to infect human intestinal organoids from either their apical or basolateral side to characterize host/pathogen interactions at the single-cell level using single-cell RNA sequencing (scRNAseq) technology.

Human intestinal organoids constitute the best cellular model to study pathogen infections of the gastrointestinal tract. These organoids can be derived ...

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 ...

Calcium Imaging of Virus-Infected Human Intestinal Organoid Monolayers

Live Calcium Imaging of Virus-Infected Human Intestinal Organoid Monolayers Using Genetically Encoded Calcium Indicators

Calcium signaling is an integral regulator of nearly every tissue. Within the intestinal epithelium, calcium is involved in the regulation of secretory activity, actin dynamics, inflammatory responses, stem cell proliferation, and many other uncharacterized cellular functions. As such, mapping calcium signaling dynamics within the intestinal epithelium can provide insight into homeostatic cellular processes and unveil unique responses to various stimuli. Human intestinal organoids (HIOs) are a high-throughput, human-derived model to study the intestinal epithelium and thus represent a useful system to investigate calcium dynamics. This paper describes a protocol to stably transduce HIOs with genetically encoded calcium indicators (GECIs), perform live fluorescence microscopy, and analyze imaging data to meaningfully characterize calcium signals. As a representative example, 3-dimensional HIOs were transduced with lentivirus to stably express GCaMP6s, a green fluorescent protein-based cytosolic GECI. The engineered HIOs were then dispersed into a single-cell suspension and seeded as monolayers. After differentiation, the HIO monolayers were infected with rotavirus and/or treated with drugs known to stimulate a calcium response. An epifluorescence microscope fitted with a temperature-controlled, humidified live-imaging chamber allowed for long-term imaging of infected or drug-treated monolayers. Following imaging, acquired images were analyzed using the freely available analysis software, ImageJ. Overall, this work establishes an adaptable pipeline for characterizing cellular signaling in HIOs.

Author Spotlight: Investigating Viral Disruption of Intestinal Epithelial Signaling &#8211; Research Insights and Future Directions 

This protocol describes an approach for performing calcium imaging in virus-infected human intestinal organoids and offers an approach to analysis.

Calcium signaling is an integral regulator of nearly every tissue. Within the intestinal epithelium, calcium is involved in the regulation of secretory ...

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 ...

Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites

Retroviruses exhibit signature integration preferences on both the local and global scales. Here, we present a detailed protocol for (1) generation of diverse libraries of retroviral integration sites using ligation-mediated PCR (LM-PCR) amplification and next-generation sequencing (NGS), (2) mapping the genomic location of each virus-host junction using BEDTools, and (3) analyzing the data for statistical relevance. Genomic DNA extracted from infected cells is fragmented by digestion with restriction enzymes or by sonication. After suitable DNA end-repair, double-stranded linkers are ligated onto the DNA ends, and semi-nested PCR is conducted using primers complementary to both the long terminal repeat (LTR) end of the virus and the ligated linker DNA. The PCR primers carry sequences required for DNA clustering during NGS, negating the requirement for separate adapter ligation. Quality control (QC) is conducted to assess DNA fragment size distribution and adapter DNA incorporation prior to NGS. Sequence output files are filtered for LTR-containing reads, and the sequences defining the LTR and the linker are cropped away. Trimmed host cell sequences are mapped to a reference genome using BLAT and are filtered for minimally 97% identity to a unique point in the reference genome. Unique integration sites are scrutinized for adjacent nucleotide (nt) sequence and distribution relative to various genomic features. Using this protocol, integration site libraries of high complexity can be constructed from genomic DNA in three days. The entire protocol that encompasses exogenous viral infection of susceptible tissue culture cells to integration site analysis can therefore be conducted in approximately one to two weeks. Recent applications of this technology pertain to longitudinal analysis of integration sites from HIV-infected patients.

We describe a protocol for amplifying retroviral integration sites from the genomic DNA of infected cells, sequencing the amplified virus-host junctions, and then mapping these sequences to a reference genome. We also describe techniques to quantify the distribution of integration sites relative to various genomic annotations using BEDTools.

Retroviruses exhibit signature integration preferences on both the local and global scales. Here, we present a detailed protocol for (1) generation of ...

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 ...

A Video Protocol of Retroviral Infection in Primary Intestinal Organoid Culture

Summary

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Chapters in this video

High-sensitivity Detection of Micrometastases Generated by GFP Lentivirus-transduced Organoids Cultured from a Patient-derived Colon Tumor

Genetic Engineering of Primary Mouse Intestinal Organoids Using Magnetic Nanoparticle Transduction Viral Vectors for Frozen Sectioning

The Ex Vivo Culture and Pattern Recognition Receptor Stimulation of Mouse Intestinal Organoids

Live Imaging of Primary Cerebral Cortex Cells Using a 2D Culture System

Adapting Gastrointestinal Organoids for Pathogen Infection and Single Cell Sequencing under Biosafety Level 3 (BSL-3) Conditions

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

Live Calcium Imaging of Virus-Infected Human Intestinal Organoid Monolayers Using Genetically Encoded Calcium Indicators

A Protocol for Lentiviral Transduction and Downstream Analysis of Intestinal Organoids

Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites

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