The authors would like to thank Mark Bishop, Mathew Zverev, Victoria Marsh-Durban, Adam Blackwood and Sylvie Robine. This work was funded by a programme grant from Cancer Research UK.

<ol>
	<li>Cheng, H., Origin Leblond, C. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=differentiation+and+renewal+of+the+four+main+epithelial+cell+types+in+the+mouse+small+intestine.+V.+Unitarian+Theory+of+the+origin+of+the+four+epithelial+cell+types.">differentiation and renewal of the four main epithelial cell types in the mouse small intestine. V. Unitarian Theory of the origin of the four epithelial cell types.</a> Am J Anat. 141 (4), 537-561 (1974).</li><li>Barker, N., 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=Identification+of+stem+cells+in+small+intestine+and+colon+by+marker+gene+Lgr5.">Identification of stem cells in small intestine and colon by marker gene Lgr5.</a> Nature. 449 (7165), 1003-1007 (2007).</li><li>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=.">.</a> The gut, a clonal conveyor belt. , (2015).</li><li>Snippert, 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=Intestinal+crypt+homeostasis+results+from+neutral+competition+between+symmetrically+dividing+Lgr5+stem+cells.">Intestinal crypt homeostasis results from neutral competition between symmetrically dividing Lgr5 stem cells.</a> Cell. 143 (1), 134-144 (2010).</li><li>Lopez-Garcia, C., Klein, A. M., Simons, B. D., Winton, D. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Intestinal+stem+cell+replacement+follows+a+pattern+of+neutral+drift.">Intestinal stem cell replacement follows a pattern of neutral drift.</a> Science. 330 (6005), 822-825 (2010).</li><li>Buczacki, S. 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=Intestinal+label-retaining+cells+are+secretory+precursors+expressing+Lgr5.">Intestinal label-retaining cells are secretory precursors expressing Lgr5.</a> Nature. 495 (7439), 65-69 (2013).</li><li>Basak, O., 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=Mapping+early+fate+determination+in+Lgr5++crypt+stem+cells+using+a+novel+Ki67-RFP+allele.">Mapping early fate determination in Lgr5+ crypt stem cells using a novel Ki67-RFP allele.</a> EMBO J. 33 (18), 2057-2068 (2014).</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=Paneth+cells+constitute+the+niche+for+Lgr5+stem+cells+in+intestinal+crypts.">Paneth cells constitute the niche for Lgr5 stem cells in intestinal crypts.</a> Nature. 469 (7330), 415-418 (2011).</li><li>Young, M., Ordonez, L., Clarke, A. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=What+are+the+best+routes+to+effectively+model+human+colorectal+cancer.">What are the best routes to effectively model human colorectal cancer.</a> Molecular oncology. 7 (2), 178-189 (2013).</li><li>Sauer, B., Henderson, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Site-specific+DNA+recombination+in+mammalian+cells+by+the+Cre+recombinase+of+bacteriophage+P1.">Site-specific DNA recombination in mammalian cells by the Cre recombinase of bacteriophage P1.</a> Proc Natl Acad Sci U.S.A. 85 (14), 5166-5170 (1988).</li><li>Brault, V., 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=Inactivation+of+the+beta-catenin+gene+by+Wnt1-Cre-mediated+deletion+results+in+dramatic+brain+malformation+and+failure+of+craniofacial+development.">Inactivation of the beta-catenin gene by Wnt1-Cre-mediated deletion results in dramatic brain malformation and failure of craniofacial development.</a> Development. 128 (8), 1253-1264 (2001).</li><li>Fevr, T., Robine, S., Louvard, D., Huelsken, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Wnt/&#946;-catenin+is+essential+for+intestinal+homeostasis+and+maintenance+of+intestinal+stem+cells.">Wnt/&#946;-catenin is essential for intestinal homeostasis and maintenance of intestinal stem cells.</a> Molecular and Cellular Biology. 27 (21), 7551-7559 (2007).</li><li>Ireland, 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=Inducible+Cre-mediated+control+of+gene+expression+in+the+murine+gastrointestinal+tract:+effect+of+loss+of+beta-catenin.">Inducible Cre-mediated control of gene expression in the murine gastrointestinal tract: effect of loss of beta-catenin.</a> Gastroenterology. 126 (5), 1236-1246 (2004).</li><li>Kemp, R., 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=Elimination+of+background+recombination:+somatic+induction+of+Cre+by+combined+transcriptional+regulation+and+hormone+binding+affinity.">Elimination of background recombination: somatic induction of Cre by combined transcriptional regulation and hormone binding affinity.</a> Nucleic Acids Res. 32 (11), e92 (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=Cis+elements+of+the+villin+gene+control+expression+in+restricted+domains+of+the+vertical+(crypt)+and+horizontal+(duodenum,+cecum)+axes+of+the+intestine.">Cis elements of the villin gene control expression in restricted domains of the vertical (crypt) and horizontal (duodenum, cecum) axes of the intestine.</a> J Biol Chem. 277 (36), 33275-33283 (2002).</li><li>Parry, L., Young, M., El Marjou, F., Clarke, A. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Evidence+for+a+crucial+role+of+paneth+cells+in+mediating+the+intestinal+response+to+injury.">Evidence for a crucial role of paneth cells in mediating the intestinal response to injury.</a> Stem Cells. 31 (4), 776-785 (2013).</li><li>Soriano, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Generalized+lacZ+expression+with+the+ROSA26+Cre+reporter+strain.">Generalized lacZ expression with the ROSA26 Cre reporter strain.</a> Nat Genet. 21 (1), 70-71 (1999).</li><li>el Marjou, F., 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=Tissue-specific+and+inducible+Cre-mediated+recombination+in+the+gut+epithelium.">Tissue-specific and inducible Cre-mediated recombination in the gut epithelium.</a> Genesis. 39 (3), 186-193 (2004).</li><li>Guillemot, F., Nagy, A., Auerbach, A., Rossant, J., Joyner, A. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Essential+role+of+Mash-2+in+extraembryonic+development.">Essential role of Mash-2 in extraembryonic development.</a> Nature. 371 (6495), 333-336 (1994).</li><li>Gregorieff, 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=Expression+pattern+of+Wnt+signaling+components+in+the+adult+intestine.">Expression pattern of Wnt signaling components in the adult intestine.</a> Gastroenterology. 129 (2), 626-638 (2005).</li><li>van der Flier, L. G., Haegebarth, A., Stange, D. E., van de Wetering, M., 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=OLFM4+is+a+robust+marker+for+stem+cells+in+human+intestine+and+marks+a+subset+of+colorectal+cancer+cells.">OLFM4 is a robust marker for stem cells in human intestine and marks a subset of colorectal cancer cells.</a> Gastroenterology. 137 (1), 15-17 (2009).</li><li>Merritt, A., Allen, T., Potten, C., Hickman, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Apoptosis+in+small+intestinal+epithelial+from+p53-null+mice:+evidence+for+a+delayed,+p53-independent+G2/M-associated+cell+death+after+gamma-irradiation.">Apoptosis in small intestinal epithelial from p53-null mice: evidence for a delayed, p53-independent G2/M-associated cell death after gamma-irradiation.</a> Oncogene. 14 (23), 2759-2766 (1997).</li><li>Marshman, E., Ottewell, P., Potten, C., Watson, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Caspase+activation+during+spontaneous+and+radiation-induced+apoptosis+in+the+murine+intestine.">Caspase activation during spontaneous and radiation-induced apoptosis in the murine intestine.</a> J Pathol. 195 (3), 285-292 (2001).</li><li>Fevr, T., Robine, S., Louvard, D., Huelsken, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Wnt/beta-catenin+is+essential+for+intestinal+homeostasis+and+maintenance+of+intestinal+stem+cells.">Wnt/beta-catenin is essential for intestinal homeostasis and maintenance of intestinal stem cells.</a> Mol Cell Biol. 27 (21), 7551-7559 (2007).</li><li>Barker, N., 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=Crypt+stem+cells+as+the+cells-of-origin+of+intestinal+cancer.">Crypt stem cells as the cells-of-origin of intestinal cancer.</a> Nature. 457 (7229), 608-611 (2009).</li><li>Tian, H., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+reserve+stem+cell+population+in+small+intestine+renders+Lgr5-positive+cells+dispensable.">A reserve stem cell population in small intestine renders Lgr5-positive cells dispensable.</a> Nature. 478 (7368), 255-259 (2011).</li><li>Yilmaz, O. 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=mTORC1+in+the+Paneth+cell+niche+couples+intestinal+stem-cell+function+to+calorie+intake.">mTORC1 in the Paneth cell niche couples intestinal stem-cell function to calorie intake.</a> Nature. 486 (7404), 490-495 (2012).</li><li>Adolph, T. E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Paneth+cells+as+a+site+of+origin+for+intestinal+inflammation.">Paneth cells as a site of origin for intestinal inflammation.</a> Nature. 503 (7475), 272-276 (2013).</li><li>Marsh, V., 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+Pten+is+dispensable+for+intestinal+homeostasis+but+suppresses+adenoma+development+and+progression+after+Apc+mutation.">Epithelial Pten is dispensable for intestinal homeostasis but suppresses adenoma development and progression after Apc mutation.</a> Nat Genet. 40 (12), 1436-1444 (2008).</li><li>Jard&#233;, 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=In+vivo+and+in+vitro+models+for+the+therapeutic+targeting+of+Wnt+signaling+using+a+Tet-O&#916;N89&#946;-catenin+system.">In vivo and in vitro models for the therapeutic targeting of Wnt signaling using a Tet-O&#916;N89&#946;-catenin system.</a> Oncogene. 32 (7), 883-893 (2013).</li><li>Hung, K. E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Development+of+a+mouse+model+for+sporadic+and+metastatic+colon+tumors+and+its+use+in+assessing+drug+treatment.">Development of a mouse model for sporadic and metastatic colon tumors and its use in assessing drug treatment.</a> Proc Natl Acad Sci U S A. 107 (4), 1565-1570 (2010).</li><li>Dacquin, R., Starbuck, M., Schinke, T., Karsenty, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mouse+alpha1(I)-collagen+promoter+is+the+best+known+promoter+to+drive+efficient+Cre+recombinase+expression+in+osteoblast.">Mouse alpha1(I)-collagen promoter is the best known promoter to drive efficient Cre recombinase expression in osteoblast.</a> Dev Dyn. 224 (2), 245-251 (2002).</li><li>Hinoi, 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=Mouse+model+of+colonic+adenoma-carcinoma+progression+based+on+somatic+Apc+inactivation.">Mouse model of colonic adenoma-carcinoma progression based on somatic Apc inactivation.</a> Cancer Res. 67 (20), 9721-9730 (2007).</li><li>Sansom, O. 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=Loss+of+Apc+allows+phenotypic+manifestation+of+the+transforming+properties+of+an+endogenous+K-ras+oncogene+in+vivo.">Loss of Apc allows phenotypic manifestation of the transforming properties of an endogenous K-ras oncogene in vivo.</a> Proc Natl Acad Sci U.S.A. 103 (38), 14122-14127 (2006).</li><li>Wong, V. 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=Lrig1+controls+intestinal+stem-cell+homeostasis+by+negative+regulation+of+ErbB+signalling.">Lrig1 controls intestinal stem-cell homeostasis by negative regulation of ErbB signalling.</a> Nat Cell Biol. 14 (4), 401-408 (2012).</li><li>Sato, T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Single+Lgr5+stem+cells+build+crypt-villus+structures+in+vitro+without+a+mesenchymal+niche.">Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche.</a> Nature. 459 (7244), 262-265 (2009).</li><li>van de Wetering, 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=Prospective+Derivation+of+a+Living+Organoid+Biobank+of+Colorectal+Cancer+Patients.">Prospective Derivation of a Living Organoid Biobank of Colorectal Cancer Patients.</a> Cell. 161 (4), 933-945 (2015).</li></ol>

The authors have nothing to disclose.

Using conditional cre-lox transgenic mice to dissect the function of genes and cells is a commonly used approach. These models have been used with great success in the intestine to identify and characterize the stem cells2,4-6 and understand their role in disease25. To fully exploit these models requires a comprehensive characterization of the system to enable data to be interpreted correctly. A complete understanding of these systems is difficult to achieve due to genes rarely being specific to a solitary cell type or location, a lack of biological knowledge and inefficiency of the systems used to induce Cre expression. The methods described here demonstrate how we overcome these issues through experimental design and application of existing knowledge. Although we used these methods to answer a specific research question the techniques presented here are generic and can be exploited for any research investigating the murine intestine.
Preparation of Intestinal Tissue
The crucial step for ensuring robust results is the harvesting and processing of the tissue, which needs to be processed in a timely manner and fixation protocols strictly adhered to. As almost all significant issues downstream can be attributed to artefacts associated with the tissue drying out and/or incomplete fixation. Timing is crucial to prevent degradation of tissue architecture and/or nucleic acids and proteins. Incomplete or overzealous fixation can result in loss of histochemical resolution. Incomplete fixation due to insufficient time or sections too thick to allow fixative penetration can result in loss of resolution within the intestinal crypts that can be observed as a &#8220;tide mark&#8221; upon IHC analysis. Further it is crucial that fixation does not extend for too long, as nuclear &#946;-catenin can diffuse out of the nucleus unless immediately processed and wax embedded following formalin fixation.
Role of Paneth Cells in the ISC Niche
The data presented here effectively show the importance of Paneth cells in crypt regeneration in the adult intestine following ISC loss. However there remained the possibility that Ah-cre spares a population of ISCs that vil-Cre-ERT2 targets. Tian et al.26 elegantly demonstrated that the Lgr5hi ISCs are replaced by a population of Lgr5lo reserve ISCs. It now seems likely that these ISCs are spared in the Ah-cre system due to the reserve population having been identified as secretory cell precursors6,7. The importance of the mature Paneth cell in supporting these secretory cell precursors when required to revert to an ISC state remains to be answered. As Paneth cells constitute the ISC niche8 and play roles in regulating the ISC responses to calorie intake27 and inflammation28 it remains likely that their nursing functions will extend to their own precursors.
New Approaches and Technologies to Effectively Model Human Colorectal Cancer
The discovery of the ISC led to the identification of genes which are now being used to generate new mouse models for investigating the roles of genes and cells in intestinal biology and disease, reviewed by Clarke et al9. The only limitations to this technique is the identification of genes to express the Cre protein. Currently ISCs are routinely investigated using conditional transgenic mice based on the Lgr5 gene expression pattern. Mice which express Cre from the Lgr5 promoter have been used to delete Apc, the gene most commonly mutated in colorectal cancer (CRC), demonstrating the ISC as the cell of origin25. Selectively deleting other CRC genes in these cells is providing insight into disease progression and spread e.g. PTEN29. Further insight into ISC function is being retrieved by specifically ablating Lgr5-expressing cells in mice using a human diphtheria toxin receptor (DTR) gene knocked into the Lgr5 locus26. Other strategies use the Tet-O system which enables ongoing reversible expression of mutant proteins30. Using these tools to modify gene(s) in different cells31 and locations32,33 is used to understand how cancer initiate, progress and metastasize34. Alternatively mutagenesis using the sleeping beauty transposon system is identifying new drivers of CRC. The continuing development of mice, techniques and genetic alteration strategies is continuing to develop more patient relevant models.
New methods have been developed for characterization of the intestinal epithelia and ISCs. Characterization of the ratio of epithelial cell types can be achieved using flow cytometry based on the differential expression of lectin and CD2435. Potentially the biggest progress in understanding ISC biology and their role in disease will be made using the ex vivo organoid culture system36. This system allows normal and malignant ISCs to culture in 3D, where they replicate and differentiate in a more physiologically relevant way. It is hoped that these will enable direct testing of drugs on patient samples in vitro, paving the way for personalized medicine37.

The luminal surface of the mammalian intestine features repeating units of crypts and finger like projections, termed villi, which protrude into the lumen. This surface is a continuous sheet of epithelia which undergoes complete self-renewal approximately every 3 - 4 days1. This dynamic tissue is supported by a population of rapidly cycling stem cells (ISCs; also known as crypt base columnar cells), which were initially identified by their expression of the Lgr5 gene2,3. These cells exist in a specialized niche at the bottom of the crypts of Lieberkuhn. Initially, the discovery that ISCs were rapidly cycling was discordant with the prevailing idea that a stem cell was quiescent in nature. Previous to the identification of the Lgr5+ ISC it was postulated that a population of quiescent label retaining cells at the +4 position, relative to the base of the crypt, were the ISCs1. Recent research has now reconciled these observations by demonstrating that primarily there is a pool of equipotent cycling ISCs in each crypt whose fate are regulated by its neighbors4,5. In the event they are lost these can be replaced by quiescent cells that ordinarily are committed to the secretory lineage but can revert to ISCs if the ISC population is damaged6.
ISC neighbors can either be ISCs or their daughter cells. The ISCs produce na&#239;ve daughter cells which multiply and differentiate into the specialized cell types that comprise the epithelial sheet which lines the intestinal lumen1. The goblet, enteroendocrine, enterocytes, tuft and M cells migrate upwards to the luminal surface where they provide various absorptive and regulatory functions, however, the Paneth cells remain at the bottom of the crypt where they exist intermingled with the ISCs. In recent years it has been demonstrated that a proportion of the na&#239;ve daughter cells destined for a secretory lineage are quiescent label retaining Lgr5lo cells capable of reverting to an ISC upon injury6,7.
Due to its importance in crypt regeneration a priority was placed on understanding the interactions between the ISCs and its neighbors, particularly the Paneth cells. The Paneth cells play a crucial role in the niche which supports the ISCs8. In addition to bactericidal products the Paneth cells produce signaling molecules that activate the pathways which govern ISC renewal or differentiation. Previous studies showed that the Lgr5+ ISCs could only exist when they could compete for essential niche signals provided by their daughter Paneth cells8. These studies examined the role of Paneth cells on normal Lgr5+ ISCs and not in a situation where they are damaged and require replenishment from an Lgr5lo population.
To understand intestinal biology and model disease we examine the functional role of cells and/or genes using transgenic mouse models9,10. Frequently these models utilize cre-lox technology to conditionally modify gene(s)9,10. Cre (Causes recombination) recombinase is a site specific recombinase of the integrase family, isolated from bacteriophage P1. Cre catalyses site specific recombination between defined 34 bp &#8216;Lox P&#8217; (locus &#967; of crossover P1) sites. Mice are genetically engineered to contain LoxP sites that flank regions of interest which upon expression of Cre recombinase are excised. Linking the expression of the Cre gene to a cell or developmental specific promoter allows for alteration to be made in a spatial fashion9,10, this is especially useful in overcoming embryonic lethal mutations. Further linking the Cre expression to a receptor pathway, that can be activated artificially, permits temporal alterations.
Using this technology we inactivated the CatnB gene11 in the intestinal epithelia. &#946;-catenin, the CatnB gene product, is a key regulator of the canonical Wnt signaling pathway which governs ISC homeostasis. Two previous studies using this strategy produced conflicting results12,13. The study by Fevr et al.12, demonstrated loss of stem cells and intestinal homeostasis. Whereas the Ireland et al.14study reported that following a reduction in cell viability the crypt-villus axis was repopulated from wild type cells expressing CatnB. The major difference in these studies was the promoter used to express Cre in the intestinal epithelia. The Fevr et al., study used the villin gene promoter linked to the estrogen receptor which can be activated by administering tamoxifen (vil-Cre-ERT2)15,16. In contrast Ireland et al., utilized the promoter element of the rat cytochrome P450A1 (CYP1A1) gene to drive Cre expression in response to the xenobiotic &#946;-naphthoflavone (Ah-cre). The characteristics of these different systems generated two hypotheses to account for these different observations. The first that CatnB is more efficiently deleted in the ISC using the vil-Cre-ERT2 system compared to the Ah-cre, thereby reducing the number of ISCs to sub-repopulation levels. Alternatively it was due to differential CatnB deletion in the differentiated cell population. The vil-Cre-ERT2 system targets all epithelial cells of the crypt and villus whereas the Ah-cre system only targets the non-Paneth cells of the ISC niche and crypt. These systems provided ideal tools for examining the behavior of the ISCs and their interaction with the Paneth cells. Here we present several detailed protocols based on how we used these systems to determine that Paneth cells play a crucial role in mediating the intestinal response to injury17.

<table border="0" cellpadding="0" cellspacing="0">
	<colgroup>
		<col />
		<col />
		<col />
		<col />
	</colgroup>
	<tbody>
		<tr>
			<td>Acetate buffer</td>
			<td>*</td>
			<td>*</td>
			<td>To make 100ml: 4.8ml 0.2M Acetic acid, 45.2ml 0.2M Sodium acetate &#38; 50ml distilled water</td>
		</tr>
		<tr>
			<td>Acetic acid</td>
			<td>Fisher Scientific</td>
			<td>C/0400/PB17</td>
			<td></td>
		</tr>
		<tr>
			<td>Acetic anhydride</td>
			<td>Sigma</td>
			<td>A6404</td>
			<td></td>
		</tr>
		<tr>
			<td>Acetic anhydride solution</td>
			<td>*</td>
			<td>*</td>
			<td>2 M Acetic anhydride in 0.1 M triethanolamine hydrochloride</td>
		</tr>
		<tr>
			<td>Alcian Blue</td>
			<td>Sigma</td>
			<td>A5268</td>
			<td></td>
		</tr>
		<tr>
			<td>Alcian Blue ph2.5</td>
			<td>*</td>
			<td>*</td>
			<td>To make 500ml: 15ml acetic acid, 5g Alcian Blue &#38; 485ml distilled water</td>
		</tr>
		<tr>
			<td>anti-digoxigenin alkaline phosphatase conjugated antibody</td>
			<td>Abcam</td>
			<td>ab119345</td>
			<td></td>
		</tr>
		<tr>
			<td>B(beta)-Naphthoflavone</td>
			<td>Sigma</td>
			<td>N3633</td>
			<td>BNF, inject without allowing the solution to cool too much as compound will drop out of solution. Solution can be re-used &#8211; store at -20&#176;C between uses, do not reheat more than twice.</td>
		</tr>
		<tr>
			<td>Bloxall</td>
			<td>Vector Labs</td>
			<td>SP-6000</td>
			<td></td>
		</tr>
		<tr>
			<td>BM purple</td>
			<td>Roche</td>
			<td>11442074001</td>
			<td></td>
		</tr>
		<tr>
			<td>BSA</td>
			<td>Sigma</td>
			<td>A4503</td>
			<td>Bovine serum albumin</td>
		</tr>
		<tr>
			<td>Chloroform</td>
			<td>Fisher Scientific</td>
			<td>C/4920/17</td>
			<td></td>
		</tr>
		<tr>
			<td>Citrate Buffer/Antigen Unmasking Solution</td>
			<td>Vector Labs</td>
			<td>H-3300</td>
			<td></td>
		</tr>
		<tr>
			<td>Corn oil</td>
			<td>Sigma</td>
			<td>C8627</td>
			<td></td>
		</tr>
		<tr>
			<td>Demucifiying solution</td>
			<td>*</td>
			<td>*</td>
			<td>For 500ml: 50ml glycerol, 50ml Tris 0.1M pH8.8, 100ml EtOH, 300ml saline (0.9% NaCl in water), DTT 1.7g.&#160; Demucifying solution can be made in advance and stored, but DTT sholud be added just before incubation (340mg/100ml).</td>
		</tr>
		<tr>
			<td>DEPC treated water</td>
			<td>Life Technologies</td>
			<td>750023</td>
			<td></td>
		</tr>
		<tr>
			<td>DTT</td>
			<td>Sigma</td>
			<td>101509944</td>
			<td></td>
		</tr>
		<tr>
			<td>EDTA</td>
			<td>Sigma</td>
			<td>O3690</td>
			<td>0.5M</td>
		</tr>
		<tr>
			<td>Ethanol</td>
			<td>Fisher Scientific</td>
			<td>E/0650DF/17</td>
			<td></td>
		</tr>
		<tr>
			<td>Filter paper</td>
			<td>Whatman</td>
			<td>3000917</td>
			<td></td>
		</tr>
		<tr>
			<td>Formaldehyde</td>
			<td>Sigma</td>
			<td>F8775</td>
			<td></td>
		</tr>
		<tr>
			<td>Formalin&#160;</td>
			<td>Sigma</td>
			<td>SLBL11382V</td>
			<td>Neutral buffered formalin</td>
		</tr>
		<tr>
			<td>Formamide</td>
			<td>Sigma</td>
			<td>F5786</td>
			<td></td>
		</tr>
		<tr>
			<td>Glutaraldehye</td>
			<td>Sigma</td>
			<td>G6257</td>
			<td></td>
		</tr>
		<tr>
			<td>H2O2</td>
			<td>Sigma</td>
			<td>216763</td>
			<td></td>
		</tr>
		<tr>
			<td>Haematoxylin</td>
			<td>Raymond A Lamb</td>
			<td>12698616</td>
			<td></td>
		</tr>
		<tr>
			<td>HBSS</td>
			<td>Gibco</td>
			<td>14175-053</td>
			<td>HBSS (-MgCl2+; -CaCl2)</td>
		</tr>
		<tr>
			<td>Hybridisation buffer</td>
			<td>*</td>
			<td>*</td>
			<td>&#160;5&#215; SSC, 50% formamide, 5% SDS, 1 mg/ml heparin, 1 mg/ml calf liver tRNA</td>
		</tr>
		<tr>
			<td>Hydroquinone</td>
			<td>Sigma</td>
			<td>H9003</td>
			<td></td>
		</tr>
		<tr>
			<td>ImmPACT DAB Peroxidase</td>
			<td>Vector Labs</td>
			<td>SK-4105</td>
			<td></td>
		</tr>
		<tr>
			<td>Immpress HRP Anti-Mouse IgG Kit</td>
			<td>Vector Labs</td>
			<td>MP-7402</td>
			<td></td>
		</tr>
		<tr>
			<td>Immpress HRP Anti-Rabbit IgG Kit</td>
			<td>Vector Labs</td>
			<td>MP-7401</td>
			<td></td>
		</tr>
		<tr>
			<td>Intestinal tissue powder</td>
			<td>*</td>
			<td>*</td>
			<td>The small intestines of 5 adult mice were combined and homogenised in the minimum volume of ice cold PBS. 4 volumes of ice cold acetone were added to the homogenised intestine, which was mixed thoroughly and incubated on ice for 30 minutes. This was centrifuged and the pellet was washed using ice cold acetone. This was further centrifuged and the resulting pellet spread onto filter paper and allowed to dry. Once thoroughly dry the material was ground to a fine powder using a pestle and mortar.&#160;</td>
		</tr>
		<tr>
			<td>K-ferricyanide</td>
			<td>Sigma</td>
			<td>P-3667</td>
			<td></td>
		</tr>
		<tr>
			<td>K-ferrocyanide</td>
			<td>Sigma</td>
			<td>P3289</td>
			<td></td>
		</tr>
		<tr>
			<td>Levamisole</td>
			<td>Sigma</td>
			<td>L0380000</td>
			<td></td>
		</tr>
		<tr>
			<td>Methacarn</td>
			<td>*</td>
			<td>*</td>
			<td>60% Methanol:30% Chloroform:10% Acetic acid</td>
		</tr>
		<tr>
			<td>Methanol</td>
			<td>Fisher Scientific</td>
			<td>M/4000/17</td>
			<td></td>
		</tr>
		<tr>
			<td>MgCl2</td>
			<td>Sigma</td>
			<td>M8266</td>
			<td></td>
		</tr>
		<tr>
			<td>Normal goat serum</td>
			<td>Vector Labs</td>
			<td>S-1012</td>
			<td>NGS</td>
		</tr>
		<tr>
			<td>Normal rabbit serum</td>
			<td>Dako</td>
			<td>X0902</td>
			<td>NRS</td>
		</tr>
		<tr>
			<td>NTMT</td>
			<td>*</td>
			<td>*</td>
			<td>100 mM NaCl, 100 mM Tris HCl, 50 mM MgCl2, 0.1% Tween20, 2 mM Levamisole</td>
		</tr>
		<tr>
			<td>PAP pen</td>
			<td>Vector</td>
			<td>H-400</td>
			<td></td>
		</tr>
		<tr>
			<td>Paraformaldehyde</td>
			<td>Sigma</td>
			<td>P6148</td>
			<td></td>
		</tr>
		<tr>
			<td>PBT</td>
			<td>*</td>
			<td>*</td>
			<td>0.5M NaCl, 10mM TrisHCL pH7.5, 0.1% Tween 20</td>
		</tr>
		<tr>
			<td>Penicillin/Streptomycin</td>
			<td>Gibco</td>
			<td>15140-122</td>
			<td>100x solutiuon.</td>
		</tr>
		<tr>
			<td>Phosphate buffered saline (10x)</td>
			<td>Fisher Scientific</td>
			<td>BP3994</td>
			<td>Dilluted 1:10 with distilled water to make 1x</td>
		</tr>
		<tr>
			<td>PLL slides</td>
			<td>Sigma</td>
			<td>P0425-72EA</td>
			<td>Poly-L-lysine microscope slides</td>
		</tr>
		<tr>
			<td>Proteinase K</td>
			<td>Sigma</td>
			<td>P2308</td>
			<td></td>
		</tr>
		<tr>
			<td>Proteinase k solution</td>
			<td>*</td>
			<td>*</td>
			<td>Dilute Proteinase K at 200 &#181;g/ml in 50 mM Tris, 5 mM EDTA.</td>
		</tr>
		<tr>
			<td>Ralwax</td>
			<td>BDH</td>
			<td>36154 7N</td>
			<td></td>
		</tr>
		<tr>
			<td>Reducer Solution</td>
			<td>*</td>
			<td>*</td>
			<td>To make 100ml: 1g Hydroquinone, 5g sodium sulphite &#38; 100ml distilled water</td>
		</tr>
		<tr>
			<td>RnaseA</td>
			<td>Sigma</td>
			<td>R6148</td>
			<td></td>
		</tr>
		<tr>
			<td>Saline</td>
			<td>*</td>
			<td>*</td>
			<td>0.9% NaCl in distilled water</td>
		</tr>
		<tr>
			<td>SDS</td>
			<td>Sigma</td>
			<td>I3771</td>
			<td></td>
		</tr>
		<tr>
			<td>Sheep serum</td>
			<td>Sigma</td>
			<td>S3772</td>
			<td></td>
		</tr>
		<tr>
			<td>Silver nitrate</td>
			<td>Sigma</td>
			<td>S/1240/46</td>
			<td></td>
		</tr>
		<tr>
			<td>Silver solution</td>
			<td>*</td>
			<td>*</td>
			<td>To make 100ml: 10ml Acetate buffer, 87ml distilled water, 3ml 1% silver nitrate</td>
		</tr>
		<tr>
			<td>Sodium acetate</td>
			<td>Fisher Scientific</td>
			<td>S/2120/53</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium Chloride</td>
			<td>Sigma</td>
			<td>S6753</td>
			<td>NaCl</td>
		</tr>
		<tr>
			<td>Sodium sulfite</td>
			<td>Sigma</td>
			<td>239321</td>
			<td></td>
		</tr>
		<tr>
			<td>SSC</td>
			<td>Sigma</td>
			<td>93017</td>
			<td>20x saline sodium citrate</td>
		</tr>
		<tr>
			<td>Surgical tape</td>
			<td>Fisher Scientific</td>
			<td>12960495</td>
			<td></td>
		</tr>
		<tr>
			<td>Tamoxifen</td>
			<td>Sigma</td>
			<td>T5648</td>
			<td>TAM, inject without allowing the solution to cool too much as compound will drop out of solution. Solution can be re-used &#8211; store at -20&#176;C between uses, do not reheat more than twice.</td>
		</tr>
		<tr>
			<td>TBS/T</td>
			<td>Cell Signalling</td>
			<td>#9997</td>
			<td></td>
		</tr>
		<tr>
			<td>Triethanolamine hydrochloride</td>
			<td>Sigma</td>
			<td>T1502</td>
			<td></td>
		</tr>
		<tr>
			<td>Tris-HCL</td>
			<td>Invitrogen</td>
			<td>15567-027</td>
			<td></td>
		</tr>
		<tr>
			<td>Tween20</td>
			<td>Sigma</td>
			<td>TP9416</td>
			<td></td>
		</tr>
		<tr>
			<td>VectaMount</td>
			<td>Vector Labs</td>
			<td>H-5000</td>
			<td></td>
		</tr>
		<tr>
			<td>VectaShield Hardset mounting Medium with DAPI</td>
			<td>Vector Labs</td>
			<td>H-1500</td>
			<td></td>
		</tr>
		<tr>
			<td>Vectastain ABC Kit</td>
			<td>Vector Labs</td>
			<td>PK-4001</td>
			<td></td>
		</tr>
		<tr>
			<td>X-gal</td>
			<td>Promega</td>
			<td>V3941</td>
			<td></td>
		</tr>
		<tr>
			<td>X-gal fixative</td>
			<td>*</td>
			<td>*</td>
			<td>2% formaldehyde, 0.1% glutaraldehyde in 1xPBS</td>
		</tr>
		<tr>
			<td>X-gal stain</td>
			<td>*</td>
			<td>*</td>
			<td>X-gal stain; 200ul X-gal (A) in 50ml solution B (0.214g MgCl2, 0.48g K-ferricyanide, 0.734g K-ferrocyanide in 500ml PBS).&#160; Solution B can be made up oin advance and stored at 4&#176;C</td>
		</tr>
		<tr>
			<td>Xylene</td>
			<td>Fisher Scientific</td>
			<td>X/0200/21</td>
			<td></td>
		</tr>
	</tbody>
</table>

protocols for analyzing the role of paneth cells in regenerating the murine intestine using conditional cre-lox mouse models

The epithelial surface of the mammalian intestine is a dynamic tissue that renews every 3 - 7 days. Understanding this renewal process identified a population of rapidly cycling intestinal stem cells (ISCs) characterized by their expression of the Lgr5 gene. These are supported by a quiescent stem cell population, marked by Bmi-1 expression, capable of replacing them in the event of injury. Investigating the interactions between these populations is crucial to understanding their roles in disease and cancer. The ISCs exist within crypts on the intestinal surface, these niches support the ISC in replenishing the epithelia. The interaction between active and quiescent ISCs likely involves other differentiated cells within the niche, as it has previously been demonstrated that the &#8216;&#8216;stemness&#8217;&#8217; of the Lgr5 ISC is closely tied to the presence of their neighboring Paneth cells. Using conditional cre-lox mouse models we tested the effect of deleting the majority of active ISCs in the presence or absence of the Paneth cells. Here we describe the techniques and analysis undertaken to characterize the intestine and demonstrate that the Paneth cells play a crucial role within the ISC niche in aiding recovery following substantial insult.

Watch this Scientific Journal Video about Protocols for Analyzing the Role of Paneth Cells in Regenerating the Murine Intestine using Conditional Cre-lox Mouse Models at JoVE.com

Protocols for Analyzing the Role of Paneth Cells in Regenerating the Murine Intestine using Conditional Cre-lox Mouse Models

Intestinal epithelial stem cells (ISCs) are intermingled with Paneth cells. These cells are differentiated progeny of the ISC, which support the ISCs and provide antibacterial protection. Here we demonstrate how we used transgenic conditional mouse models to establish that Paneth cells play a crucial role in maintaining the intestinal epithelia.

Protocols for Analyzing the Role of Paneth Cells in Regenerating the Murine Intestine using Conditional Cre-lox Mouse Models

The epithelial surface of the mammalian intestine is a dynamic tissue that renews every 3 - 7 days. Understanding this renewal process identified a ...

protocols-for-analyzing-role-paneth-cells-regenerating-murine

Research

JoVE Journal

Developmental Biology

17.5K Views.  Cardiff University. Intestinal epithelial stem cells (ISCs) are intermingled with Paneth cells. These cells are differentiated progeny of the ISC, which support the ISCs and provide antibacterial protection. Here we demonstrate how we used transgenic conditional mouse models to establish that Paneth cells play a crucial role in maintaining the intestinal epithelia.