The authors have no acknowledgements.

The experimental procedures and ethical treatment of animals was approved by the University of Pittsburgh IACUC (protocol #1104674).
1. Preparation of G6PD Staining Mixture
NOTE: Ensure that the final concentration of each reagents is as follows; 5 mM glucose-6-phosphate (G6P); 2 mM NADP, 5 mM MgCl2, 0.35 mM 1-methoxy-5-methylphenazinium methyl sulfate (MMPMS) and 0.8 mM NBT.1,8,9 For each reagent the initial concentration was derived for a 40 ml final volume. Solutions were freshly prepared and used each day.
<ol>
	<li>Add 2 ml of 200 mM pH 7.4 phosphate buffer (PB) to 35 ml of OCT medium in a 50 ml tube and shake vigorously. Confirm with pH paper that the solution is ~pH 7.4. If not discard the solution.</li>
	<li>Add 61 mg G6P dissolved in 0.94 ml of 200 mM PB, 61 mg NADP dissolved in 0.94 ml of 200 mM PB, and 41 mg MgCl2 dissolved in 0.96 ml of 100 mM PB. Reconfirm that the pH is ~7.4 with pH paper. If not ~7.4, discard the solution.</li>
	<li>Add 5 mg of MMPMS dissolved in 0.25 ml of 200 mM PB (pH 7.4). Vigorously shake the resulting reaction mixture to generate a clear dark red homogenate. If the solution is turbid, the mixture should be discarded. The tube containing the reaction mixture is wrapped in foil to minimize exposure to light. Store the reaction mixture at RT while the final component, NBT, is prepared.</li>
	<li>Prepare separately a 5 mM NBT solution by adding 0.4 ml anhydrous dimethyl formamide (DMF) and 0.4 ml anhydrous ethanol to 164 mg of NBT in a 2 ml tube with an O-ring lid. Close the lid loosely (not tightly sealed) and bring the solution to a vigorous boil in an oil bath until the NBT is in solution.8</li>
	<li>Allow the solubilized NBT to cool to RT and then add all of the solution to the OCT reaction mixture and shake vigorously to obtain a clear solution. Observe the solution color change from initial orange-red to a dark-red or purple color over time. This is normal.</li>
	<li>Place the final G6PD staining mixture in a 37&#160;&#176;C warm room for 1 hr before use.</li>
</ol>
2. Animal Treatment and Tissue Collection
<ol>
	<li>Treat 6-week-old C57Bl/6 male mice with DNA damaging agent, e.g., 10 mg/kg azoxymethane (AOM) in a volume of 200 &#181;l PBS by i.p. injection. Treat control mice with 200 &#181;l of PBS by i.p. injection.</li>
	<li>At 90 days, euthanize mice by CO2 asphyxiation followed by cervical dislocation as approved by IACUC protocol.</li>
	<li>Surgically open the abdominal cavity from just above the anus to the base of the sternum. Move the small intestine out of the body cavity but do not excise it. Excise the lower intestine just below the cecum to the rectum.10</li>
	<li>Carefully slice along one side of the colon using a micro-dissection scissor and remove feces from the opened colon by washing with clean sterile PBS. Swiss roll the excised colon with the luminal side facing outward, and place in a tissue mold.10</li>
	<li>Completely immerse the colon in OCT medium and place mold in a Dewar containing liquid N2. Hold the mold so that the plastic base is just in contact with the liquid N2 until the OCT medium is frozen solid.</li>
	<li>Store the frozen tissue block at -80 &#160;until cutting frozen sections. Do not use any fixative, which would result in the inactivation of the G6PD enzyme.</li>
</ol>
3. Preparation of Frozen Sections
<ol>
	<li>Cut frozen tissue sections at a thickness of 7 &#181;m using a cryostat at -25 &#176;C. Cut 4 consecutive 7 &#181;m sections and place two of them on the same slide (Figure 1). Prepare 2 slides, or four consecutive 7 &#181;m sections to represent one level of the colon (Figure 1).</li>
	<li>Repeat for the next level with a minimum distance of &#62;50 &#181;m from the last section of the previous level. This distance ensured that the crypts assessed for each level did not duplicate one another.</li>
	<li>Frequently wipe the cryostat blade with 100% ethanol to remove the OCT residue that accumulates during cutting. Before sectioning is resumed, the dry blade is wiped with an antistatic dryer sheet to dissipate accumulated static charge. Store slides with the frozen sections at -80 oC.</li>
</ol>
4. Staining of Frozen Section Tissue
<ol>
	<li>Perform the enzyme histochemistry reaction in a 37 &#176;C&#160;warm room with high humidity. 
	NOTE: Attempting the enzymatic reaction in an incubation oven or on a slide warmer led to poor and inconsistent G6PD staining.</li>
	<li>Build wells for tissue staining using two 1.5 cm x 0.15 cm steel washers (interior diameter x height) that are bonded together using silicone grease (Figure 1). Cut the parafilm to fit the base of the well with the center cut out and the well placed over the tissue section on the slide. 
	NOTE: The parafilm on the bottom of the washer creates a seal between the slide and the washer that maintains the viscous G6PD staining mixture on the tissue section. This construct gives a well with a 0.4 - 0.5 ml volume so that each tissue section in the study receives the same volume of the G6PD reaction staining mixture.</li>
	<li>Incubate frozen tissue slides at 37 oC in a warm room for 10 min. At 37 &#176;C, add the G6PD staining reaction mixture to each tissue section well (2 sections per slide) for 45-50 min. Remove slides from warm room, and carefully lift the stainless steel wells off the slides.</li>
	<li>Set slides on their long edge to allow the reaction medium to drain. Place slides in 100 mM PB (pH 7.4) for 30-60 min to remove the G6PD staining reaction mixture from the tissue without disturbing the tissue staining. Submerge slides in distilled water for 5-10 min to remove PB salts</li>
	<li>Seal the tissue by adding fluoro-gel from a dropper onto the tissue and waiting ~ 30 min for it to dry. Avoid bubbles that can confound the identification of mutated crypts. 
	NOTE: If bubbles form, the procedure can be repeated after removal of the fluoro-gel by soaking in distilled water. Do not use cover slips as they tend to trap air bubbles.</li>
</ol>
5. Determination of G6PD Mutant Crypts and Mutation Frequency
<ol>
	<li>Analyze slides for G6PD mutant crypts under a light microscope. 
	NOTE: The criteria used to identify a fully mutant crypt were: (i) the entire crypt was devoid of blue color; (ii) the outer structure of the crypt was intact, (iii) the mutant crypt was observed on adjacent 7 &#181;m sections and, (iv) two observers had to identify the same crypt as a mutant. Mutants observed on adjacent 7 &#181;m sections are counted as one mutant.</li>
	<li>Image each G6PD mutant crypt at 40x magnification and catalogue the images using a 5.0 megapixel camera with imaging software.</li>
	<li>Quantify the total number of crypts examined in a mouse by selecting a representative section for each mouse from the level with the smallest surface area and image it at 10x magnification (Figure 1C). 
	NOTE: A level represents four consecutive 7 &#181;m sections (Figure 1D), which due to their proximity often show mutated crypts on more than one section. The levels are separated by &#62;50 &#181;m to visualize crypts from different areas of the colon.</li>
	<li>Open each image file and visually count the number of crypts on a level by analyzing the files (shown as boxes in Figure 1C). Images files will vary in the number of crypts observed from as low as 20 to &#62;300 crypts in one file.</li>
	<li>Multiply the total number of crypts from the selected level (Figure 1C) for each mouse by the number of levels screened for G6PD mutant crypts for each colon. For example, a total count of 1,250 crypts per selected level multiplied by 8 levels screened for mutant crypts equals a total count of 10,000 crypts. Evaluate a minimum of 10,000 crypts for each colon for statistical analysis.</li>
	<li>Combine the number of mutants observed in all of the animals by the total number of crypts screened to calculate the MF for each treatment. The background stem cell MF level in untreated mice is &#60; 0.1x10-4 (Table 1), which is close to that previously reported in C57Bl/6 mice.11</li>
</ol>

<ol>
	<li>Griffiths, D. F., Davies, S. J., Williams, S., Williams, G. T., Williams, E. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Demonstration+of+somatic+mutation+and+colonic+crypt+clonality+by+X-linked+enzyme+histochemistry.">Demonstration of somatic mutation and colonic crypt clonality by X-linked enzyme histochemistry.</a> Nature. 333 (6172), 461-463 (1988).</li><li>Griffiths, D. F., Sacco, P., Williams, G. T., Williams, E. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+clonal+origin+of+experimental+large+bowel+tumours.">The clonal origin of experimental large bowel tumours.</a> Br. J. Cancer. 59 (3), 385-387 (1989).</li><li>Kuraguchi, M., Thomas, G. A., Williams, E. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Somatic+mutation+of+the+glucose-6-phosphate+dehydrogenase+(g6pd)+gene+in+colonic+stem+cells+and+crypt+restricted+loss+of+G6PD+activity.">Somatic mutation of the glucose-6-phosphate dehydrogenase (g6pd) gene in colonic stem cells and crypt restricted loss of G6PD activity.</a> Mutat. Res. 379 (1), (1997).</li><li>Van Noorden, C. J., Vogels, I. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Polyvinyl+alcohol+and+other+tissue+protectants+in+enzyme+histochemistry:+a+consumer&#8217;s+guide.">Polyvinyl alcohol and other tissue protectants in enzyme histochemistry: a consumer&#8217;s guide.</a> Histochem. J. 21 (7), 373-379 (1989).</li><li>Giardina Rosenberg, D. W., C, T., Tanaka, <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mouse+models+for+the+study+of+colon+carcinogenesis.">Mouse models for the study of colon carcinogenesis.</a> Carcinogenesis. 30 (2), 183-196 (2009).</li><li>Tanaka, T., Kohno, H., Suzuki, R., Yamada, Y., Sugie, S., Mori, 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+novel+inflammation-related+mouse+colon+carcinogenesis+model+induced+by+azoxymethane+and+dextran+sodium+sulfate.">A novel inflammation-related mouse colon carcinogenesis model induced by azoxymethane and dextran sodium sulfate.</a> Cancer Sci. 94 (11), 965-973 (2003).</li><li>Suzuki, R., Kohno, H., Sugie, S., Tanaka, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Dose-dependent+promoting+effect+of+dextran+sodium+sulfate+on+mouse+colon+carcinogenesis+initiated+with+azoxymethane.">Dose-dependent promoting effect of dextran sodium sulfate on mouse colon carcinogenesis initiated with azoxymethane.</a> Histol. Histopathol. 20 (2), 483-492 (2005).</li><li>Frederiks, W. M., Vreeling-Sindalarova, H., Van Noorden, C. J. <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+peroxisomes+causes+oxygen+insensitivity+of+the+histochemical+assay+of+glucose-6-phosphate+dehydrogenase+activity+to+detect+cancer+cells.">Loss of peroxisomes causes oxygen insensitivity of the histochemical assay of glucose-6-phosphate dehydrogenase activity to detect cancer cells.</a> J. Histochem. Cytochem. 55 (2), 175-181 (2007).</li><li>Hisada, R., Yagi, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=1-Methoxy-5-methylphenazinium+methyl+sulfate.">1-Methoxy-5-methylphenazinium methyl sulfate.</a> Biochem. 82 (5), 1469-1473 (1977).</li><li>Whittem, C. G., Williams, A. D., Williams, C. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Murine+Colitis+modeling+using+Dextran+Sulfate+Sodium+(DSS).">Murine Colitis modeling using Dextran Sulfate Sodium (DSS).</a> J Vis Exp. (35), (2010).</li><li>Kuraguchi, M., Cook, H., Williams, E. D., Thomas GA, . <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Differences+in+susceptibility+to+colonic+stem+cell+somatic+mutation+in+three+strains+of+mice.">Differences in susceptibility to colonic stem cell somatic mutation in three strains of mice.</a> J. Pathol. 193 (4), 517-521 (2001).</li><li>Whetstone, R. D., Gold, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=T-Cells+Enhance+Stem+Cell+Mutagenesis+in+the+Mouse+Colon.">T-Cells Enhance Stem Cell Mutagenesis in the Mouse Colon.</a> Mutat. Res. 744, 1-5 (2015).</li><li>Van Noorden, C. J., Vogel, I. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Histochemistry+and+cytochemistry+of+glucose-6-phosphate+dehydrogenase.">Histochemistry and cytochemistry of glucose-6-phosphate dehydrogenase.</a> Prog. Histochem. Cytochem. 15 (4), 1-85 (1985).</li><li>Van Noorden, C. J., Vogels, I. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+sensitive+cytochemical+staining+method+for+glucose-6-phosphate+dehydrogenase+activity+in+individual+erythrocytes.+II.+Further+improvements+of+the+staining+procedure+and+some+observations+with+glucose-6-phosphate+dehydrogenase+deficiency.">A sensitive cytochemical staining method for glucose-6-phosphate dehydrogenase activity in individual erythrocytes. II. Further improvements of the staining procedure and some observations with glucose-6-phosphate dehydrogenase deficiency.</a> Br. J. Haematol. 60 (1), 57-63 (1985).</li><li>Cook, H. A., Williams, D., Thomas, G. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Crypt-restricted+metallothionein+immunopositivity+in+murine+colon:+validation+of+a+model+for+studies+of+somatic+stem+cell+mutation.">Crypt-restricted metallothionein immunopositivity in murine colon: validation of a model for studies of somatic stem cell mutation.</a> J. Pathol. 191 (3), 306-312 (2000).</li></ol>

The authors have nothing to disclose.

Often the genotoxic effect of a compound is determined by its ability to modify DNA. This is normally done by isolating the tissue and measuring the global level of DNA adducts. For AOM, this would involve quantifying O6-methylguanine adducts in the colon. Using this approach information on damage within specific cell types, such as in the stem cell niche, is lost. In addition, a DNA adduct is not the same as a mutation since only a small subset of adducts are eventually converted into fixed mutations.12<...

Colon cancer is thought to involve exposure to environmental agents and dietary components that can damage DNA and produce activating somatic mutations in oncogenes (e.g., &#223;-catenin) or inactivating mutations in tumor suppressor genes (e.g., APC). It is assumed that these critical mutations occur in colonic stem cells. Because of the unique crypt architecture of the colonic epithelium, it is possible to measure stem cell mutations in the colon after exposing animals to chemicals associated with colon carcinogenesis. Several X-linked enzymes can serve as indicators for mutations that occur in stem cells, as the mutations will be present in all cells within a crypt.
Previously, a procedure was published demonstrating that chemicals that induce colon tumors in mice also generated somatic stem cell mutations in the colon via analysis of mutations in the X-linked glucose-6-phosphate dehydrogenase (G6PD) gene.1-3 The method quantifies the incidence of random somatic mutations in colonic stem cells without any selection pressure. The procedure involves the production of unfixed frozen colon sections from treated and control mice and the identification of crypts devoid of cells that produce functional G6PD activity. These mutated crypts, which appear white, indicate that the mutation occurred in a stem cell that gave rise to progeny also harboring a mutated G6PD gene. In the enzymatic assay, G6PD deficient mutant crypts cannot oxidize glucose-6-phosphate, which is required for the reduction of nitro blue tetrazolium (NBT). When the G6PD enzyme is functional, the NBT in the staining mixture is reduced to insoluble formazan and precipitates, accumulating at the location of the enzyme and &#8220;staining&#8221; cells blue. Cells that are G6PD mutants remain whitish in contrast to blue stained wild type crypts. This method measures mutations that have a &#8220;null&#8221; phenotype. Because enzymes, such as G6PD, can diffuse out of the cells on an unfixed tissue section if the sections are placed in an aqueous solution, it is necessary to stabilize the enzyme in the tissue sections to be analyzed.4 The stabilization of the enzyme in the tissue must not interfere with diffusion of small reagent molecules necessary for the G6PD enzymatic reaction.
We have made a number of significant changes to the original procedure. The medium for the critical enzymatic staining has been changed from polyvinyl alcohol to Optimal Cutting Temperature Compound (OCT), which facilitates pH control and solubilization of the components used in the assay. The staining is performed using 0.4 &#8211; 0.5 ml wells made of steel washers so that each tissue section received the same volume of the G6PD reaction mixture. A procedure was developed to estimate the number of crypts in an imaged section that provides a large sampling of the colonic tissue without having to manually count &#62;105 crypts for each colon. The analysis of adjacent 7 &#181;m tissue sections affords visualization of a mutant crypt on more than one slide, which reduces potential staining artifacts. These changes make the procedure more efficient and reproducible.
Using this revised protocol, we have quantified the mutation frequency in colonic stem cells after exposure of C57Bl/6 mice to azoxymethane, a well-known colon carcinogen in rodents.5-7

<table border="0" cellpadding="0" cellspacing="0">
	<tbody>
		<tr>
			<td>reagents</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>nitroblue tetrazolium</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>NADP</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>glucose-6-phosphate</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>1-methoxy-5-methylphenazinium methyl sulfate</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>dimethyl formamide</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>phosphate buffer (pH 7.4</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Optimal Cutting Temperature Compound (OCT)&#160;</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Equipment</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>light microscope equipped with 5 megapixel camera</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>cryostat</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>warm room&#160;</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
	</tbody>
</table>

quantification of  colonic stem cell mutations

The ability to measure stem cell mutations is a powerful tool to quantify in a critical cell population if, and to what extent, a chemical can induce mutations that potentially lead to cancer. The use of an enzymatic assay to quantify stem cell mutations in the X-linked glucose-6-phosphate dehydrogenase gene has been previously reported.1 This method requires the preparation of frozen sections and incubation of the sectioned tissue with a reaction mixture that yields a blue color if the cells produce functional glucose-6-phosphate dehydrogenase (G6PD) enzyme. If not, the cells appear whitish. We have modified the reaction mixture using Optimal Cutting Temperature Compound (OCT) medium in place of polyvinyl alcohol. This facilitates pH measurement, increases solubilization of the G6PD staining components and restricts diffusion of the G6PD enzyme. To demonstrate that a mutation occurred in a stem cell, the entire crypt must lack G6PD enzymatic activity. Only if a stem cell harbors a phenotypic G6PD mutation will all of the progeny in the crypt lack G6PD enzymatic activity. To identify crypts with a stem cell mutation, four consecutive adjacent frozen sections (a level) were cut at 7 &#181;m thicknesses. This approach of making adjacent cuts provides conformation that a crypt was fully mutated since the same mutated crypt will be observed in adjacent sections. Slides with tissue samples that were more than 50 &#181;m apart were prepared to assess a total of &#62;104 crypts per mouse. The mutation frequency is the number of observed mutated (white) crypts &#247; by the number of wild type (blue) crypts in a treatment group.

The ability to measure colonic stem cell mutations in animals provides a unique way to correlate mutations to cancer induction. Normally, it is assumed that the critical step in carcinogenesis involves activating mutations in oncogenes and/or inactivating mutations in tumor suppressor genes. We injected C57Bl/6 mice with 200 &#181;l of PBS or 10 mg/kg AOM in 200 &#181;l of PBS. AOM is a known colon carcinogen.5-7 At 90 days the colons were analyzed for stem cell mutations. This time is required to allow stem c...

Watch this Scientific Journal Video about Quantification of  Colonic Stem Cell Mutations at JoVE.com

Quantification of  Colonic Stem Cell Mutations

We report significant improvements for the reproducible measurement of somatic colonic stem cell mutations after exposure of mice to potential DNA damaging agents.

The ability to measure stem cell mutations is a powerful tool to quantify in a critical cell population if, and to what extent, a chemical can induce ...

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6.5K Views.  University of Pittsburgh. We report significant improvements for the reproducible measurement of somatic colonic stem cell mutations after exposure of mice to potential DNA damaging agents.

Video: Quantification of  Colonic Stem Cell Mutations

Generation of Murine Cardiac Pacemaker Cell Aggregates Based on ES-Cell-Programming in Combination with Myh6-Promoter-Selection

Treatment of the &#8220;sick sinus syndrome&#8221; is based on artificial pacemakers. These bear hazards such as battery failure and infections. Moreover, they lack hormone responsiveness and the overall procedure is cost-intensive. &#8220;Biological pacemakers&#8221; generated from PSCs may become an alternative, yet the typical content of pacemaker cells in Embryoid Bodies (EBs) is extremely low. The described protocol combines &#8220;forward programming&#8221; of murine PSCs via the sinus node inducer TBX3 with Myh6-promoter based antibiotic selection. This yields cardiomyocyte aggregates consistent of &#62;80% physiologically functional pacemaker cells. These &#8220;induced-sinoatrial-bodies&#8221; (&#8220;iSABs&#8221;) are spontaneously contracting at yet unreached frequencies (400-500 bpm) corresponding to nodal cells isolated from mouse hearts and are able to pace murine myocardium ex vivo. Using the described protocol highly pure sinus nodal single cells can be generated which e.g. can be used for in vitro drug testing. Furthermore, the iSABs generated according to this protocol may become a crucial step towards heart tissue engineering.

This protocol describes how to produce functional sinus nodal tissue from murine pluripotent stem cells (PSC). T-Box3 (TBX3) overexpression plus cardiac Myosin-heavy-chain (Myh6) promoter antibiotic selection leads to highly pure pacemaker cell aggregates. These &#8220;Induced-sinoatrial-bodies&#8221; (&#8220;iSABs&#8221;) contain over 80% pacemaker cells, show highly increased beating rates and are able to pace myocardium ex vivo.

Treatment of the &#8220;sick sinus syndrome&#8221; is based on artificial pacemakers. These bear hazards such as battery failure and infections. Moreover, ...

Automated Quantification of Hematopoietic Cell &#8211; Stromal Cell Interactions in Histological Images of Undecalcified Bone

Confocal microscopy is the method of choice for the analysis of localization of multiple cell types within complex tissues such as the bone marrow. However, the analysis and quantification of cellular localization is difficult, as in many cases it relies on manual counting, thus bearing the risk of introducing a rater-dependent bias and reducing interrater reliability. Moreover, it is often difficult to judge whether the co-localization between two cells results from random positioning, especially when cell types differ strongly in the frequency of their occurrence. Here, a method for unbiased quantification of cellular co-localization in the bone marrow is introduced. The protocol describes the sample preparation used to obtain histological sections of whole murine long bones including the bone marrow, as well as the staining protocol and the acquisition of high-resolution images. An analysis workflow spanning from the recognition of hematopoietic and non-hematopoietic cell types in 2-dimensional (2D) bone marrow images to the quantification of the direct contacts between those cells is presented. This also includes a neighborhood analysis, to obtain information about the cellular microenvironment surrounding a certain cell type. In order to evaluate whether co-localization of two cell types is the mere result of random cell positioning or reflects preferential associations between the cells, a simulation tool which is suitable for testing this hypothesis in the case of hematopoietic as well as stromal cells, is used. This approach is not limited to the bone marrow, and can be extended to other tissues to permit reproducible, quantitative analysis of histological data.

Automated Quantification of Hematopoietic Cell &amp;#8211; Stromal Cell Interactions in Histological Images of Undecalcified Bone

A strategy to quantitatively analyze histological data in the bone marrow is presented. Confocal microscopy of fluorescently labeled cells in tissue sections results in 2-dimensional images, which are automatically analyzed. Co-localization analyses of different cell types are compared to data from simulated images, giving quantitative information about cellular interactions.

Confocal microscopy is the method of choice for the analysis of localization of multiple cell types within complex tissues such as the bone marrow. ...

Generation of Genetically Modified Organotypic Skin Cultures Using Devitalized Human Dermis

Organotypic cultures allow the reconstitution of a 3D environment critical for cell-cell contact and cell-matrix interactions which mimics the function and physiology of their in vivo tissue counterparts. This is exemplified by organotypic skin cultures which faithfully recapitulates the epidermal differentiation and stratification program. Primary human epidermal keratinocytes are genetically manipulable through retroviruses where genes can be easily overexpressed or knocked down. These genetically modified keratinocytes can then be used to regenerate human epidermis in organotypic skin cultures providing a powerful model to study genetic pathways impacting epidermal growth, differentiation, and disease progression. The protocols presented here describe methods to prepare devitalized human dermis as well as to genetically manipulate primary human keratinocytes in order to generate organotypic skin cultures. Regenerated human skin can be used in downstream applications such as gene expression profiling, immunostaining, and chromatin immunoprecipitations followed by high throughput sequencing. Thus, generation of these genetically modified organotypic skin cultures will allow the determination of genes that are critical for maintaining skin homeostasis.

The goal of this paper is to provide a comprehensive and detailed protocol on how to generate genetically modified human organotypic skin from epidermal keratinocytes and devitalized human dermis.

Organotypic cultures allow the reconstitution of a 3D environment critical for cell-cell contact and cell-matrix interactions which mimics the function ...

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.

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.

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

Temporal Ordering of Dynamic Expression Data from Detailed Spatial Expression Maps

During somitogenesis, pairs of epithelial somites form in a progressive manner, budding off from the anterior end of the pre-somitic mesoderm (PSM) with a strict species-specific periodicity. The periodicity of the process is regulated by a molecular oscillator, known as the "segmentation clock," acting in the PSM cells. This clock drives the oscillatory patterns of gene expression across the PSM in a posterior-anterior direction. These so-called clock genes are key components of three signaling pathways: Wnt, Notch, and fibroblast growth factor (FGF). In addition, Notch signaling is essential for synchronizing intracellular oscillations in neighboring cells. We recently gained insight into how this may be mechanistically regulated. Upon ligand activation, the Notch receptor is cleaved, releasing the intracellular domain (NICD), which moves to the nucleus and regulates gene expression. NICD is highly labile, and its phosphorylation-dependent turnover acts to restrict Notch signaling. The profile of NICD production (and degradation) in the PSM is known to be oscillatory and to resemble that of a clock gene. We recently reported that both the Notch receptor and the Delta ligand, which mediate intercellular coupling, themselves exhibit dynamic expression at both the mRNA and protein levels. In this article, we describe the sensitive detection methods and detailed image analysis tools that we used, in combination with the computational modeling that we designed, to extract and overlay expression data from distinct points in the expression cycle. This allowed us to construct a spatio-temporal picture of the dynamic expression profile for the receptor, the ligand, and the Notch target clock genes throughout an oscillation cycle. Here, we describe the protocols used to generate and culture the PSM explants, as well as the procedure to stain for the mRNA or protein. We also explain how the confocal images were subsequently analyzed and temporally ordered computationally to generate ordered sequences of clock expression snapshots, hereafter defined as "kymographs," for the visualization of the spatiotemporal expression of Delta-like1 (Dll1) and Notch1 throughout the PSM.

The segmentation clock drives oscillatory gene expression across the pre-somitic mesoderm (PSM). Dynamic Notch activity is key to this process. We use imaging and computational analyses to extract temporal dynamics from spatial expression data to demonstrate that Delta ligand and Notch receptor expression oscillate in the vertebrate PSM.

During somitogenesis, pairs of epithelial somites form in a progressive manner, budding off from the anterior end of the pre-somitic mesoderm (PSM) with a ...

Bioengineering of Humanized Bone Marrow Microenvironments in Mouse and Their Visualization by Live Imaging

Human hematopoietic stem cells (HSCs) reside in the bone marrow (BM) niche, an intricate, multifactorial network of components producing cytokines, growth factors, and extracellular matrix. The ability of HSCs to remain quiescent, self-renew or differentiate, and acquire mutations and become malignant depends upon the complex interactions they establish with different stromal components. To observe the crosstalk between human HSCs and the human BM niche in physiological and pathological conditions, we designed a protocol to ectopically model and image a humanized BM niche in immunodeficient mice. We show that the use of different cellular components allows for the formation of humanized structures and the opportunity to sustain long-term human hematopoietic engraftment. Using two-photon microscopy, we can live-image these structures in situ at the single-cell resolution, providing a powerful new tool for the functional characterization of the human BM microenvironment and its role in regulating normal and malignant hematopoiesis.

A method to create and live-image different humanized bone-marrow niches in mice is presented. Based on the supportive niche created by human mesenchymal cells, the addition of human endothelial cells induces the formation of human vessels, while the addition of rhBMP-2 induces the formation of human-mouse chimeric mature bone tissue.

Human hematopoietic stem cells (HSCs) reside in the bone marrow (BM) niche, an intricate, multifactorial network of components producing cytokines, growth ...

Evaluation of Injury-induced Senescence and In Vivo Reprogramming in the Skeletal Muscle

Cellular senescence is a stress response that is characterized by a stable cellular growth arrest, which is important for many physiological and pathological processes, such as cancer and ageing. Recently, senescence has also been implicated in tissue repair and regeneration. Therefore, it has become increasingly critical to identify senescent cells in vivo. Senescence-associated &#946;-galactosidase (SA-&#946;-Gal) assay is the most widely used assay to detect senescent cells both in culture and in vivo. This assay is based on the increased lysosomal contents in the senescent cells, which allows the histochemical detection of lysosomal &#946;-galactosidase activity at suboptimum pH (6 or 5.5). In comparison with other assays, such as flow cytometry, this allows the identification of senescent cells in their resident environment, which offers valuable information such as the location relating to the tissue architecture, the morphology, and the possibility of coupling with other markers via immunohistochemistry&#160;(IHC). The major limitation of the SA-&#946;-Gal assay is the requirement of fresh or frozen samples.
Here, we present a detailed protocol to understand how cellular senescence promotes cellular plasticity and tissue regeneration in vivo. We use SA-&#946;-Gal to detect senescent cells in the skeletal muscle upon injury, which is a well-established system to study tissue regeneration. Moreover, we use&#160;IHC to detect Nanog, a marker of pluripotent stem cells, in a transgenic mouse model. This protocol enables us to examine and quantify cellular senescence in the context of induced cellular plasticity and in vivo reprogramming.

Evaluation of Injury-induced Senescence and In Vivo Reprogramming in the Skeletal Muscle

Here we present a detailed protocol to detect both senescent and pluripotent stem cells in the skeletal muscle upon injury while inducing in vivo reprogramming. This method is suitable for evaluating the role of cellular senescence during tissue regeneration and reprogramming in vivo.

Cellular senescence is a stress response that is characterized by a stable cellular growth arrest, which is important for many physiological and ...

Rapid, Directed Differentiation of Retinal Pigment Epithelial Cells from Human Embryonic or Induced Pluripotent Stem Cells

We describe a robust method to direct the differentiation of pluripotent stem cells into retinal pigment epithelial cells (RPE). The purpose of providing a detailed and thorough protocol is to clearly demonstrate each step and to make this readily available to researchers in the field. This protocol results in a homogenous layer of RPE with minimal or no manual dissection needed. The method presented here has been shown to be effective for induced pluripotent stem cells (iPSC) and human embryonic stem cells. Additionally, we describe methods for cryopreservation of intermediate cell banks that allow long-term storage. RPE generated using this protocol might be useful for iPSC disease-in-a-dish modeling or clinical application.

This protocol describes how to produce retinal pigment epithelial cells (RPE) from pluripotent stem cells. The method uses a combination of growth factors and small molecules to direct the differentiation of stem cells into immature RPE in fourteen days and mature, functional RPE after three months.

We describe a robust method to direct the differentiation of pluripotent stem cells into retinal pigment epithelial cells (RPE). The purpose of providing ...

Efficient Differentiation of Human Pluripotent Stem Cells into Liver Cells

The liver detoxifies harmful substances, secretes vital proteins, and executes key metabolic activities, thus sustaining life. Consequently, liver failure&#8212;which can be caused by chronic alcohol intake, hepatitis, acute poisoning, or other insults&#8212;is a severe condition that can culminate in bleeding, jaundice, coma, and eventually death. However, approaches to treat liver failure, as well as studies of liver function and disease, have been stymied in part by the lack of a plentiful supply of human liver cells. To this end, this protocol details the efficient differentiation of human pluripotent stem cells (hPSCs) into hepatocyte-like cells, guided by a developmental roadmap that describes how liver fate is specified across six consecutive differentiation steps. By manipulating developmental signaling pathways to promote liver differentiation and to explicitly suppress the formation of unwanted cell fates, this method efficiently generates populations of human liver bud progenitors and hepatocyte-like cells by days 6 and 18 of PSC differentiation, respectively. This is achieved through the temporally-precise control of developmental signaling pathways, exerted by small molecules and growth factors in a serum-free culture medium. Differentiation in this system occurs in monolayers and yields hepatocyte-like cells that express characteristic hepatocyte enzymes and have the ability to engraft a mouse model of chronic liver failure. The ability to efficiently generate large numbers of human liver cells in vitro has ramifications for treatment of liver failure, for drug screening, and for mechanistic studies of liver disease.

This protocol details a monolayer, serum-free method to efficiently generate hepatocyte-like cells from human pluripotent stem cells (hPSCs) in 18 days. This entails six steps as hPSCs sequentially differentiate into intermediate cell-types such as the primitive streak, definitive endoderm, posterior foregut and liver bud progenitors before forming hepatocyte-like cells.

The liver detoxifies harmful substances, secretes vital proteins, and executes key metabolic activities, thus sustaining life. Consequently, liver ...

Analysis of Cardiac Chamber Development During Mouse Embryogenesis Using Whole Mount Epifluorescence

The goal of this protocol is to describe a method for the dissection of mouse embryos and visualization of embryonic mouse ventricular chambers during heart development using ventricular specific fluorescent reporter knock-in mice (MLC-2v-tdTomato mice). Heart development involves a linear heart tube formation, the heart tube looping, and four chamber septation. These complex processes are highly conserved in all vertebrates. The mouse embryonic heart has been widely used for heart developmental studies. However, due to their extremely small size, dissecting mouse embryonic hearts is technically challenging. In addition, visualization of cardiac chamber formation often needs in situ hybridization, beta-galactosidase staining using LacZ reporter mice, or immunostaining of sectioned embryonic hearts. Here, we describe how to dissect mouse embryonic hearts and directly visualize ventricular chamber formation of MLC-2v-tdTomato mice using whole mount epifluorescent microscopy. With this method, it is possible to directly examine heart tube formation and looping, and four chamber formation without further experimental manipulation of mouse embryos. Although the MLC-2v-tdTomato reporter knock-in mouse line is used in this protocol as an example, this protocol can be applied to other heart-specific fluorescent reporter transgenic mouse lines.

We present the protocols to examine mouse heart development using whole mount epifluorescent microscopy on mouse embryos dissected from ventricular specific MLC-2v-tdTomato reporter knock-in mice. This method allows us to directly visualize each stage of the ventricular formation during mouse heart development without labor-intensive histochemical methods.

The goal of this protocol is to describe a method for the dissection of mouse embryos and visualization of embryonic mouse ventricular chambers during ...