This publication was supported by Award Number K22 CA218462-03 from the NIH National Cancer Institute. The HEK293-T cells expressing R-Spondin1 was a generous gift from Dr. Michael P. Verzi.

All the mouse experiments conducted, including the use of Tamoxifen and euthanasia by cervical dislocation, had the approval of the Institutional Animal Care and Use Committee at Stevens Institute of echnology.
1. Mice
NOTE: The generation of Smad4f/f; Catnblox(ex3)/+; Villin-CreERT2 mice have been previously described3. Adult female mice between eight to twelve weeks of agewere used...

<ol>
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P., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=De+novo+crypt+formation+and+juvenile+polyposis+on+BMP+inhibition+in+mouse+intestine.">De novo crypt formation and juvenile polyposis on BMP inhibition in mouse intestine.</a> Science. 303 (5664), 1684-1686 (2004).</li><li>Madison, B. B., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Epithelial+hedgehog+signals+pattern+the+intestinal+crypt-villus+axis.">Epithelial hedgehog signals pattern the intestinal crypt-villus axis.</a> Development. 132 (2), 279-289 (2005).</li><li>van Es, J. H., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Dll1++secretory+progenitor+cells+revert+to+stem+cells+upon+crypt+damage.">Dll1+ secretory progenitor cells revert to stem cells upon crypt damage.</a> Nature Cell Biology. 14 (10), 1099-1104 (2012).</li><li>Tetteh, P. 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=Replacement+of+Lost+Lgr5-Positive+Stem+Cells+through+Plasticity+of+Their+Enterocyte-Lineage+Daughters.">Replacement of Lost Lgr5-Positive Stem Cells through Plasticity of Their Enterocyte-Lineage Daughters.</a> Cell Stem Cell. 18 (2), 203-213 (2016).</li><li>Baulies, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+Transcription+Co-Repressors+MTG8+and+MTG16+Regulate+Exit+of+Intestinal+Stem+Cells+From+Their+Niche+and+Differentiation+Into+Enterocyte+vs+Secretory+Lineages.">The Transcription Co-Repressors MTG8 and MTG16 Regulate Exit of Intestinal Stem Cells From Their Niche and Differentiation Into Enterocyte vs Secretory Lineages.</a> Gastroenterology. 159 (4), 1328-1341 (2020).</li><li>Zeilstra, J., 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=Stem+cell+CD44v+isoforms+promote+intestinal+cancer+formation+in+Apc(min)+mice+downstream+of+Wnt+signaling.">Stem cell CD44v isoforms promote intestinal cancer formation in Apc(min) mice downstream of Wnt signaling.</a> Oncogene. 33 (5), 665-670 (2014).</li><li>Gracz, A. D., 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=Brief+report:+CD24+and+CD44+mark+human+intestinal+epithelial+cell+populations+with+characteristics+of+active+and+facultative+stem+cells.">Brief report: CD24 and CD44 mark human intestinal epithelial cell populations with characteristics of active and facultative stem cells.</a> Stem Cells. 31 (9), 2024-2030 (2013).</li><li>Gao, N., White, P., Kaestner, K. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Establishment+of+intestinal+identity+and+epithelial-mesenchymal+signaling+by+Cdx2.">Establishment of intestinal identity and epithelial-mesenchymal signaling by Cdx2.</a> Developmental Cell. 16 (4), 588-599 (2009).</li><li>Verzi, M. P., Shin, H., Ho, L. L., Liu, X. S., Shivdasani, R. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Essential+and+redundant+functions+of+caudal+family+proteins+in+activating+adult+intestinal+genes.">Essential and redundant functions of caudal family proteins in activating adult intestinal genes.</a> Molecular and Cellular Biology. 31 (10), 2026-2039 (2011).</li><li>Verzi, M. P., Shin, H., San Roman, A. K., Liu, X. S., Shivdasani, R. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Intestinal+master+transcription+factor+CDX2+controls+chromatin+access+for+partner+transcription+factor+binding.">Intestinal master transcription factor CDX2 controls chromatin access for partner transcription factor binding.</a> Molecular and Cellular Biology. 33 (2), 281-292 (2013).</li><li>Grainger, S., Hryniuk, A., Lohnes, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cdx1+and+Cdx2+exhibit+transcriptional+specificity+in+the+intestine.">Cdx1 and Cdx2 exhibit transcriptional specificity in the intestine.</a> PLoS One. 8 (1), 54757 (2013).</li><li>Stringer, E. J., 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=Cdx2+determines+the+fate+of+postnatal+intestinal+endoderm.">Cdx2 determines the fate of postnatal intestinal endoderm.</a> Development. 139 (3), 465-474 (2012).</li></ol>

The authors declare no conflicts of interest.

This method can confirm the self-renewal capacity of dedifferentiating villi epithelium that acquire stem cell markers in vivo. The normal intestinal epithelium can give rise to organoids from the crypt but not the villi compartment, when cultured in 3D because of the presence of stem cells in the crypts1. Thus, organoid formation from the dedifferentiated villi epithelium&#160;cultured in 3D cultures confirms stem cell formation from cell fate reversal. Reports on cell fate reversal in t...

The intestinal crypts but not villi, form organoids when cultured in Matrigel or BME-R1 matrix. These organoids are self-organizing structures, often referred to as the &#34;mini-gut&#34; owing to the presence of the various differentiated lineages, progenitor, and stem cells present in the intestinal epithelium in vivo. The potential to form organoids from crypts is attributed to the presence of stem cells1. The intestinal villi on the other hand consist only of differentiated cells, and hence cannot form organoids. However, mutations2 or conditions that permit dedifferentiation of the villus epithelium may lead to stem cells in the villi2,3. This fate change resulting in stemness in the villi epithelium can be confirmed by plating the dedifferentiating villus epithelium in 3D matrix to determine their organoid-forming potential as an indicator of de-novo stemness in the villus epithelium. Hence, the critical aspect of this procedure is to ensure absence of crypt contamination.
The Smad4KO:&#946;-cateninGOF conditional mutation causes dedifferentiation in the intestinal epithelium marked by the expression of proliferation and stem cell markers in the villi, and eventually the formation of crypt-like structures in the villi referred to as ectopic crypts The presence of stem cells these dedifferentiated villi was determined by the expression of stem cell markers in the ectopic crypts (in vivo) and the ability of the mutant villi to form organoids when plated Matrigel3. The below mentioned procedure elaborates the methodology used to confirm the stemness of the dedifferentiating intestinal epithelium in the Smad4KO:&#946;-cateninGOF mutant mice. A key feature of this methodology for isolating villi was the use of scraping of the intestinal lumen, as opposed to the EDTA chelation method4. Unlike in the EDTA chelation method, villi isolation by scraping retains majority of the underlying mesenchyme and allows adjust the pressure of scraping to yield villi without tethered crypts. The pressure of scraping is subjective to the operator, hence, the optimal pressure to yield villi without crypts tethered must be determined empirically by the operator. The critical aspect of this procedure is to ensure the absence of crypt contamination by microscopic examination of the villi both before and after plating in the BME-R1 matrix.
Intestinal villi are scraped off the intestinal lumen with glass slides and placed in a 70 &#181;m filter and washed with PBS to get rid of loose cells or crypts, if any, prior to plating in BME-R1 matrix. The method stresses on the following criteria to avoid crypt contamination: a) confining the villi harvest the proximal half of the duodenum where the villi are the longest, b) minimizing the number of villi-yielding scrapes, c) washing the filter containing the villi through a series of PBS in a six-well dish, and d) confirming the absence of crypt contamination by microscopic examination prior to and after plating in BME-R1 matrix. Villi isolation by scraping, rather than by EDTA chelation, prevents the complete loss of the underlying mesenchyme that may provide the niche signals5, 6, 7, 8, if required, for organoid initiation from the villus epithelium.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Advanced DMEM F-12 media</td>
			<td>Gibco</td>
			<td>12634010</td>
			<td></td>
		</tr>
		<tr>
			<td>3,3-diaminobenzidine</td>
			<td>Vector Labs</td>
			<td>SK-4105</td>
			<td></td>
		</tr>
		<tr>
			<td>96 well U-bottom plate</td>
			<td>Fisher Scientific</td>
			<td>FB012932</td>
			<td></td>
		</tr>
		<tr>
			<td>ABC kit</td>
			<td>Vector Labs</td>
			<td>&#160;PK4001</td>
			<td></td>
		</tr>
		<tr>
			<td>Angled scissor</td>
			<td>Fisher Scientific</td>
			<td>11-999</td>
			<td></td>
		</tr>
		<tr>
			<td>Animal-Free Recombinant Human EGF</td>
			<td>Peprotech</td>
			<td>AF-100-15</td>
			<td></td>
		</tr>
		<tr>
			<td>B-27 Supplement (50X), minus vitamin A</td>
			<td>Gibco</td>
			<td>12587010</td>
			<td></td>
		</tr>
		<tr>
			<td>Bovine Serum Albumin (BSA) Protease-free Powder</td>
			<td>Fisher Scientific</td>
			<td>BP9703100</td>
			<td></td>
		</tr>
		<tr>
			<td>CD44 antibody</td>
			<td>BioLegend</td>
			<td>1030001</td>
			<td></td>
		</tr>
		<tr>
			<td>Cdx2 antibody</td>
			<td>Cell Signaling</td>
			<td>12306</td>
			<td></td>
		</tr>
		<tr>
			<td>Corn oil</td>
			<td>Sigma-Aldrich</td>
			<td>C8267-500ML</td>
			<td></td>
		</tr>
		<tr>
			<td>Corning 70-micron cell strainer</td>
			<td>Life Sciences</td>
			<td>431751</td>
			<td></td>
		</tr>
		<tr>
			<td>Cultrex Reduced Growth Factor Basement Membrane Extract, Type R1</td>
			<td>R&#38;D</td>
			<td>3433-005-R1</td>
			<td></td>
		</tr>
		<tr>
			<td>Dissection scissors</td>
			<td>Fisher Scientific</td>
			<td>22-079-747</td>
			<td></td>
		</tr>
		<tr>
			<td>Forceps</td>
			<td>Fisher Scientific</td>
			<td>17-456-209</td>
			<td></td>
		</tr>
		<tr>
			<td>Glutamax (100X)</td>
			<td>Gibco</td>
			<td>35050-061</td>
			<td></td>
		</tr>
		<tr>
			<td>HEK 293-T cells expressing RSPO-1</td>
			<td>Gift from Dr. Michael Verzi</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>HEPES (1M)</td>
			<td>Gibco</td>
			<td>15630-080</td>
			<td></td>
		</tr>
		<tr>
			<td>Histogel</td>
			<td>Thermoscientific</td>
			<td>HG-4000-012</td>
			<td></td>
		</tr>
		<tr>
			<td>Mesh filter</td>
			<td>Fisher Scientific</td>
			<td>07-201-431</td>
			<td></td>
		</tr>
		<tr>
			<td>Micrscope glass slide</td>
			<td>VWR</td>
			<td>89218-844</td>
			<td></td>
		</tr>
		<tr>
			<td>N-2 Supplement (100X)</td>
			<td>Gibco</td>
			<td>17502048</td>
			<td></td>
		</tr>
		<tr>
			<td>N-acetyl cysteine</td>
			<td>Sigma-Aldrich</td>
			<td>A9165</td>
			<td></td>
		</tr>
		<tr>
			<td>p200 Blunt tips</td>
			<td>VWR</td>
			<td>46620-642</td>
			<td></td>
		</tr>
		<tr>
			<td>Penicillin-Streptomycin (10,000 U/mL)</td>
			<td>Gibco</td>
			<td>15140-122</td>
			<td></td>
		</tr>
		<tr>
			<td>Primocin (50mg/mL)</td>
			<td>Invivogen</td>
			<td>ant-pm-1</td>
			<td></td>
		</tr>
		<tr>
			<td>Quality Biological Inc PBS (10X)</td>
			<td>Fisher Scientific</td>
			<td>50-146-770</td>
			<td></td>
		</tr>
		<tr>
			<td>Recombinant Murine Noggin</td>
			<td>Peprotech</td>
			<td>250-38</td>
			<td></td>
		</tr>
		<tr>
			<td>Signal diluent</td>
			<td>Cell Signaling</td>
			<td>8112L</td>
			<td></td>
		</tr>
		<tr>
			<td>Tamoxifen</td>
			<td>Sigma-Aldrich</td>
			<td>T5648-1G</td>
			<td></td>
		</tr>
		<tr>
			<td>6-well tissue culture plate</td>
			<td>Fisher Scientific</td>
			<td>50-146-770</td>
			<td></td>
		</tr>
	</tbody>
</table>

3d culturing of organoids from the intestinal villi epithelium undergoing dedifferentiation

Clonogenicity of organoids from the intestinal epithelium is attributed to the presence of stem cells therein. The mouse small intestinal epithelium is compartmentalized into crypts and villi: the stem and proliferating cells are confined to the crypts, whereas the villi epithelium contains only differentiated cells. Hence, the normal intestinal crypts, but not the villi, can give rise to organoids in 3D cultures. The procedure described here is applicable only to villus epithelium undergoing dedifferentiation leading to stemness. The method described uses the Smad4-loss-of-function:&#946;-catenin gain-of-function (Smad4KO:&#946;-cateninGOF) conditional mutant mouse. The mutation causes the intestinal villi to dedifferentiate and generate stem cells in the villi. Intestinal villi undergoing dedifferentiation are scraped off the intestine using glass slides, placed in a 70 &#181;m strainer and washed several times to filter out any loose cells or crypts prior to plating in BME-R1 matrix to determine their organoid-forming potential. Two main criteria were used to ensure that the resulting organoids were developed from the dedifferentiating villus compartment and not from the crypts: 1) microscopically evaluating&#160;the isolated villi to ensure absence of any tethered crypts, both before and after plating in the 3D matrix, and 2) monitoring the time course of organoid development from the villi. Organoid initiation from the villi occurs only two to five days after plating and appears irregularly shaped, whereas the crypt-derived organoids from the same intestinal epithelium are apparent within sixteen hours of plating and appear spherical. The limitation of the method, however, is that the number of organoids formed, and the time required for organoid initiation from the villi vary depending on the degree of dedifferentiation. Hence, depending upon the specificity of the mutation or the insult causing the dedifferentiation, the optimal stage at which villi can be harvested to assay their organoid forming potential, must be determined empirically.

The determining factor for the success of the procedure is preventing crypt contamination. Organoid development from the villi (and not from any contaminating crypts) is ensured by confirming four major criteria: 1) ensuring the purity of the harvested villi by microscopic examination before and after plating the villi in BME-R1, 2) plating limited number of villi per well to allow visualization of all the plated villi individually, 3) onitoring the development of organoid daily; images of the time course show developmen...

Watch this Scientific Journal Video about 3D Culturing of Organoids from the Intestinal Villi Epithelium Undergoing Dedifferentiation at JoVE.com

3D Culturing of Organoids from the Intestinal Villi Epithelium Undergoing Dedifferentiation

The procedure describes isolation of the villi from the mouse intestinal epithelium undergoing dedifferentiation to determine their organoid forming potential.

Clonogenicity of organoids from the intestinal epithelium is attributed to the presence of stem cells therein. The mouse small intestinal epithelium is ...

This method can confirm the organoid-forming capacity of de-differentiating villi epithelium that acquire stem cell markers in vivo. The collection of villi is performed via scraping rather than the EDTA chelation method preventing the complete loss of the underlying mesenchyme that may provide the niche signals if required for organoid initiation. This method is applicable in epithelial tissues where proliferative and differentiated compartments are physically delineated and the de-differentiating cells express stem cell markers in vivo.Some factors in this protocol need to be determined empirically, including the optimal stage for harvesting the villi and the optimal pressure for scraping the villi, which will take time and practice. Induce the Smad4 knockout and beta-catenin gain of function mutation in mutant mice with intraperitoneal injection of tamoxifen and corn oil for four consecutive days. After euthanizing the mouse, spray the abdomen with 70%ethanol to prevent mouse fur from getting into the peritoneal cavity.Open the abdominal cavity with dissection scissors to expose the intestine and isolate the intestine using scissors and forceps. Dissect out the proximal half of the duodenum, then flush the duodenum with five milliliters of ice cold PBS in a 10 milliliter syringe to clear the luminal content. Open the duodenum longitudinally with an angled scissor and lay the duodenum flat on a 15 centimeter Petri dish on ice with the lumen of the duodenum facing the operator.Prior to beginning the scraping, place a 70 micrometer mesh strainer in one of the wells of a six-well tissue culture plate. Fill all the wells with four milliliters of 1X PBS and place the plate on ice. Scrape the villi using two microscopic glass slides, one to hold the duodenum down and the other to scrape.Scrape the luminal side of the duodenum superficially twice to remove the mucus without removing the villi, then scrape the duodenum two more times to collect the villi on the slides without tethering the crypts. Use a one milliliter transfer pipette containing PBS to transfer the villi to a 70 micrometer mesh strainer in the six-well dish. Collect the villi after every scrape.To remove loose crypts, wash the villi collected with the 70 micrometer strainer by transferring the strainer through a series of wells in the six-well dish containing four milliliters of ice cold PBS per well. Using a P1000 pipette, transfer the villi suspension in about three milliliters of PBS from the 70 micrometer strainer to a new 15 milliliter tube on ice. Use a 0.1%BSA-coated blunt-ended P200 pipette tip to transfer a 50 microliter volume of the villi suspension onto a glass slide.Count the number of villi in the 50 microliter droplet under 4X magnification to determine the concentration of villi in the PBS suspension and to confirm the absence of tethered crypts. To plate the villi, use a 0.1%BSA-coated P200 blunt-ended pipette tip to transfer the villi to a microcentrifuge tube for a plating density of six villi per well in 12.5 microliters of BME-R1 matrix. Spin down the villi for two minutes at 200 times G at four degrees Celsius.Remove the supernatant and repeat the centrifugation to remove any residual PBS. In a laminar flow hood, resuspend the villi pellet gently in the required amount of cold BME-R1 thawed on ice. Using a P20 pipette, plate 12.5 microliters of the villi in BME-R1 matrix per well of a 96-well U-bottomed plate pre-warmed to 37 degrees Celsius.Incubate the plate in a tissue culture incubator at 37 degrees Celsius for 15 minutes to allow solidification of the BME-R1 matrix. To each well, add 125 microliters of pre-warmed ENR media supplemented as described in the text manuscript. Incubate the plated villi in a tissue culture incubator at 37 degrees Celsius with 5%carbon dioxide and change the media every other day.Discard any well in which organoids appear before two days. There's a difference in appearance of the organoids emerging from the crypts versus the de-differentiated villi epithelium from the same mouse intestine. The crypt-derived organoids appear overnight as spherical structures with well-defined borders.The kinetics and morphological appearance of the organoids initiated from villi was examined, which appear irregularly shaped at first and take two to five days before they can be seen under a microscope. Organoid initiation from two different villi is shown. The villi with organoid-forming potential appears dense, possibly due to the retention of the underlying mesenchyme.Organoid initiation from the villas is apparent at day two from one of the villi. While in the other villas, the organoid appears at day four. It's crucial to take the proper steps to avoid crypt contamination when harvesting the villi and growing the resulting organoids.Phenotypic differences between the organoids emerging from the crypts and villi of the same mutant were observed following this procedure, so further experimentation could be carried out to look for molecular differences between the two. This protocol could be used to study the differences between organoids arising from endogenous crypts versus ectopic crypts arising from de-differentiation, thus implications of de-differentiation could be addressed.

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4.7K Görüntüleme.  Stevens Institute of Technology. Bu yöntem, kök hücre belirteçlerini in vivo edinen villi epitelin ayrıştırıcı organoid oluşturma kapasitesini doğrulayabilir. Villi koleksiyonu, organoid başlatma için gerektiğinde niş sinyalleri sağlayabilecek alttaki mezenkimlerin tamamen kaybını önleyen EDTA şelasyon yöntemi yerine kazıma yoluyla gerçekleştirilir. Bu yöntem, proliferatif ve farklılaştırılmış bölmelerin fiziksel olarak tanımlandığı ve farklılaşan hücrelerin kök hücre işaretleyiciler...