The authors wish to acknowledge support from NIH funding DK055679, DK089763, DK079392, DK061739, DK072564 and the University of Michigan Pathology Slide Scanning Services.

All animal experiments described were approved by the University of Michigan&#39;s Committee on the Use and Care of Animals.
1. Tissue harvest
<ol>
	<li>Euthanize mice humanely using isoflurane anesthesia followed by cervical dislocation, in accordance with approved protocols. For all animal experiments, approval was obtained by a certified review board in accordance with the National and Institutional guidelines for animal handling.</li>
	<li>Place the mouse on a dissecting pad in a supine position. Immobilize mouse extremities using 20 G x 1 1/2-inch G needles.</li>
	<li>Using forceps and scissors, make a small incision on the abdominal skin and pull it to the side to expose the peritoneum.</li>
	<li>Open the abdominal cavity with a midline incision in the peritoneum from the pubic bone to the sides of the abdomen.</li>
	<li>Carefully remove tissues and organs until large intestine is visualized. Cut the pelvic bone on both sides of the colon to fully visualize the organ, extending from the anus towards the cecum.</li>
	<li>Gently remove fat, small veins and arteries attached to the colon, while carefully dissecting the organ, cutting just proximal to the anus and just distal to the cecum. 
	NOTE: The dissected colon should remain at room temperature while completing the Swiss roll procedure.</li>
	<li>Carefully flush the colon with 1x PBS, using a flexible plastic gavage needle inserted through the anus to remove fecal contents.</li>
	<li>Position the colon in a straight line, and open longitudinally along the mesenteric artery. Bisect the colon longitudinally from the distal to the proximal end (Figure 1A). One half of the tissue can be used for histological analysis while the other can be processed for western blot, PCR or rolled into a second Swiss roll for fresh frozen immunofluorescence microscopy12.</li>
</ol>
2. Preparation of swiss rolls
<ol>
	<li>Trim extra tissue from the proximal colon using a razor blade until approximately the same width along the length of the whole colon is obtained.</li>
	<li>Align the colon to expose the lumen facing-up, and flatten the tissue completely using a flexible gavage needle. Add more PBS, if needed, to keep the tissue moist throughout the procedure.</li>
	<li>Remove the excess of PBS using a paper wipe. With a syringe and gavage needle, add 10% neutral buffered formalin solution over the tissue for 2-3 min to fix and flatten the tissue.</li>
	<li>Use straight forceps to grab the end of the distal colon and twist the colon into concentric circles from the distal to proximal end (Figure 1B). 
	NOTE: It is possible to push back the inside of the Swiss roll while rolling using the forefinger to ensure the tissue is inside the roll.</li>
	<li>Insert a 27 G needle to pin the colon in the middle to hold its Swiss roll shape (Figure 1C).</li>
	<li>Place the Swiss roll with the needle into an embedding cassette inside a histologic specimen container. 
	NOTE: Tissue must be oriented in parallel with respect to the cassette before fixation (Figure 1D).</li>
	<li>Fix the tissue in 10% neutral buffered formalin solution overnight at 4 &#176;C13.</li>
	<li>After overnight fixation, wash the tissue 3x with PBS.</li>
	<li>Add 70% ethanol to the tissue prior to the paraffin embedding process. Remove the needle from the Swiss roll before proceeding. Tissue can be stored in ethanol at room temperature until paraffin embedment13.</li>
	<li>Place samples into the tissue processor, embed in paraffin, and prepare 4 &#181;m sections, mounted on positively charged microscopy slides (Figure 1E). This can be an optional stop point. 
	NOTE: Proper tissue orientation is critical to achieve sections suitable for image analysis. Parallel Swiss roll embedding in the paraffin cassette will result in full sections appropriated for image analysis (Figure 1F-1H). Oblique sections must be avoided to prevent incomplete sections (Figure 1I-1K). For more details, see the Discussion section.</li>
	<li>Stain sections with hematoxylin and eosin (H&#38;E)13.</li>
</ol>
3. Digital scanning and analysis
NOTE: For accurate evaluation of mucosal changes, select only sections that include at least 90% of the total colon length.
<ol>
	<li>Scan stained sections using a slide scanner or imager (see Table of Materials). Images produced need a resolution of 0.25 microns per pixel with 40x objective and 40x magnification.</li>
	<li>Install and download an appropriate software for digital analysis of scanned slides (see Table of Materials).</li>
	<li>Open scanned images in the image processing software (Figure 2A). Verify that the entire colon is visible and that there are no missing areas of the sample.</li>
	<li>Activate the label imager and scale bar tools to properly identify scanned slides by clicking Label imager (Figure 2A).</li>
	<li>Open the annotations tool by clicking Annotations, (Figure 2A) and create 3 different layers by clicking New layer (Figure 2B) to quantify the total length the Swiss roll, inflammation/injury, and erosion/ulceration. Choose a different color for each layer by clicking Layer color (Figure 2B).</li>
	<li>Measure the length of each layer/category by clicking the Pen tool (Figure 2A), using the muscularis mucosa as a reference:
	<ol>
		<li>View the image at 400 &#181;m zoom (or more) to facilitate adequate visualization of the muscularis mucosa. 
		NOTE: Magnification is easily controlled using the mouse scroll wheel and will need to be adjusted as necessary while moving across the section to draw all the lines.</li>
		<li>Click on the Pen tool to draw a line following the muscularis mucosa (Figure 2A). Move the pointer as needed to visualize the adjacent area for analysis. 
		NOTE: Each time that the pen is stopped, a small new layer region will be generated. It can be visualized and edited with the Layer regions tab (select desired segment and click Delete Layer in case of mistakes or corrections, Figure 2B).</li>
	</ol>
	</li>
	<li>Once all layers (Figure 2C) are defined, export the data using the Export Grid to Text File button inside the layer regions options (Figure 2B). 
	NOTE: Save files often while creating the layers to ensure data is properly stored.</li>
	<li>Open the text files and copy the data with a spreadsheet software. Total all the segments from each region and calculate percentage of injury and ulceration with respect to total length.</li>
	<li>To calculate the Histological Colitis Score (HCS) and to evaluate the severity of disease, consider three main characteristics as detailed below.
	<ol>
		<li>Check for healthy intestinal mucosa which is characterized by organized epithelial cells in the crypt-luminal axis, lamina propria with few immune cells, and subjacent muscularis mucosa that interfaces the mucosa and submucosa (Figure 3A).</li>
		<li>Check for inflammation/injury which is characterized by epithelial crypts that are attenuated or partially missing epithelial cells and mucosal inflammation with neutrophil infiltration into crypts (Figure 3B).</li>
		<li>Check for the presence of erosion/ulceration which is characterized by areas devoid of surface epithelium or areas completely lacking epithelial crypts with or without associated leukocytes (Figure 3C).</li>
	</ol>
	</li>
	<li>Calculate HCS of injured and ulcerated regions expressed as a percentage of the total length in the following formula: 
	<img alt="Equation 1" src="/files/ftp_upload/62135/62135eq01v2.jpg" /> 
	NOTE: HCS combines the percentage of inflammation/injury and erosion/ulceration adding a factor of two to the latter, based on a reasonable assumption that complete loss of the epithelium results in maximum loss of barrier integrity and hence worse disease. HCS consistently represents the morphological changes caused by DSS induced experimental colitis. Interestingly, we have not seen a clear correlation between the numbers of colonic lymphoid aggregates or follicles and clinical disease severity in DSS colitis and, therefore, we did not include the quantification in this analysis.</li>
	<li>Take a snapshot of the representative images (click Snapshot, Figure 2A), and save. Include scale bars if needed by clicking on Show/Hide Scale Bar (Figure 2A).</li>
</ol>

<ol>
	<li>Kagnoff, M. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+intestinal+epithelium+is+an+integral+component+of+a+communications+network.">The intestinal epithelium is an integral component of a communications network.</a> Journal of Clinical Investigation. 124 (7), 2841-2843 (2014).</li><li>Laukoetter, M. G., Nava, P., Nusrat, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Role+of+the+intestinal+barrier+in+inflammatory+bowel+disease.">Role of the intestinal barrier in inflammatory bowel disease.</a> World Journal of Gastroenterology. 14 (3), 401-407 (2008).</li><li>Baumgart, D. C., Sandborn, W. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Crohn's+disease.">Crohn's disease.</a> Lancet. 380 (9853), 1590-1605 (2012).</li><li>Ordas, I., Eckmann, L., Talamini, M., Baumgart, D. C., Sandborn, W. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ulcerative+colitis.">Ulcerative colitis.</a> Lancet. 380 (9853), 1606-1619 (2012).</li><li>Vowinkel, T., Kalogeris, T. J., Mori, M., Krieglstein, C. F., Granger, D. N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Impact+of+dextran+sulfate+sodium+load+on+the+severity+of+inflammation+in+experimental+colitis.">Impact of dextran sulfate sodium load on the severity of inflammation in experimental colitis.</a> Digestive Diseases and Sciences. 49 (4), 556-564 (2004).</li><li>Kitajima, S., Takuma, S., Morimoto, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Histological+analysis+of+murine+colitis+induced+by+dextran+sulfate+sodium+of+different+molecular+weights.">Histological analysis of murine colitis induced by dextran sulfate sodium of different molecular weights.</a> Experimental Animals. 49 (1), 9-15 (2000).</li><li>Mahler, 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=Differential+susceptibility+of+inbred+mouse+strains+to+dextran+sulfate+sodium-induced+colitis.">Differential susceptibility of inbred mouse strains to dextran sulfate sodium-induced colitis.</a> American Journal of Physiology. 274 (3), 544-551 (1998).</li><li>Wirtz, S., Neufert, C., Weigmann, B., Neurath, M. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Chemically+induced+mouse+models+of+intestinal+inflammation.">Chemically induced mouse models of intestinal inflammation.</a> Nature Protocols. 2 (3), 541-546 (2007).</li><li>Kozlowski, C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=An+entirely+automated+method+to+score+DSS-induced+colitis+in+mice+by+digital+image+analysis+of+pathology+slides.">An entirely automated method to score DSS-induced colitis in mice by digital image analysis of pathology slides.</a> Disease Models &amp; Mechanisms. 6 (3), 855-865 (2013).</li><li>Perse, M., Cerar, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Dextran+sodium+sulphate+colitis+mouse+model:+traps+and+tricks.">Dextran sodium sulphate colitis mouse model: traps and tricks.</a> Journal of Biomedicine and Biotechnology. 2012, 718617 (2012).</li><li>Mizoguchi, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Animal+models+of+inflammatory+bowel+disease.">Animal models of inflammatory bowel disease.</a> Progress in Molecular Biology and Translational Science. 105, 263-320 (2012).</li><li>Flemming, S., 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=Desmocollin-2+promotes+intestinal+mucosal+repair+by+controlling+integrin-dependent+cell+adhesion+and+migration.">Desmocollin-2 promotes intestinal mucosal repair by controlling integrin-dependent cell adhesion and migration.</a> Molecular Biology of the Cell. 31 (6), 407-418 (2020).</li><li>Luna, L. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Armed Forces Institute of Pathology (U.S) &amp; Armed Forces Institute of Pathology (U.S.). Manual of Histologic Staining Methods of the Armed Forces Institute of Pathology. 3d edn. , (1968).</li><li>Kelm, 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=Targeting+epithelium-expressed+sialyl+Lewis+glycans+improves+colonic+mucosal+wound+healing+and+protects+against+colitis.">Targeting epithelium-expressed sialyl Lewis glycans improves colonic mucosal wound healing and protects against colitis.</a> The Journal of Clinical Investigation Insight. 5 (12), (2020).</li><li>Reed, 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=Epithelial+CD47+is+critical+for+mucosal+repair+in+the+murine+intestine+in+vivo.">Epithelial CD47 is critical for mucosal repair in the murine intestine in vivo.</a> Nature Communications. 10 (1), 5004 (2019).</li><li>Laukoetter, M. G., 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=JAM-A+regulates+permeability+and+inflammation+in+the+intestine+in+vivo.">JAM-A regulates permeability and inflammation in the intestine in vivo.</a> Journal of Experimental Medicine. 204 (13), 3067-3076 (2007).</li><li>Khounlotham, 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=Compromised+intestinal+epithelial+barrier+induces+adaptive+immune+compensation+that+protects+from+colitis.">Compromised intestinal epithelial barrier induces adaptive immune compensation that protects from colitis.</a> Immunity. 37 (3), 563-573 (2012).</li></ol>

The authors have nothing to disclose.

Our Histological Colitis Score system constitutes a reliable tool to quantify tissue inflammation and damage in the intestine. This approach provides an improved understanding of the histopathological state of the whole organ without the bias of selecting small areas or incomplete sections. Among the critical steps to successfully execute this protocol are proper preparation of Swiss rolls that allow for analysis of at least 90% of the length of the colon; parallel orientation during paraffin embedding and sectioning to ...

The gastrointestinal epithelial barrier plays a pivotal role in separating luminal antigens and pathogens from underlying tissue compartments1. Epithelial injury and mucosal wounds seen in pathologic conditions such as inflammatory bowel disease (IBD), ischemia, or surgical injury are associated with clinical symptoms that include diarrhea, weight loss, blood in stool, and abdominal pain. In response to injury, epithelial cells migrate and proliferate to re-epithelialize and repair mucosal barrier defects. Resolution of inflammation and restitution of mucosal integrity are crucial to re-establishing intestinal mucosal homeostasis and function2,3,4.
Various animal models have been employed to study the underlying molecular mechanisms that are associated with the damage to the intestinal epithelial barrier. Well-established and easily applicable models of chemically induced colitis are widely used, particularly in studies related to inflammatory injury such as IBD. A common, reproducible, and reliable murine colitis model employs dextran sodium sulfate (DSS) mediated colonic injury and inflammation. The severity of disease varies depending upon mouse strain, dose of DSS, length of DSS administration, and molecular weight of DSS5,6,7.
Intestinal mucosal damage during DSS colitis is usually evaluated using the Disease Activity Index (DAI), a composite score determined by weight loss, fecal blood content, and stool consistency. The fecal blood content can be microscopic (detected using a stool guaiac acid test) or macroscopic; fecal consistency is classified as hard, soft, or liquid (i.e., diarrhea)5,8. Scoring of these clinical parameters can be subjective and may vary depending on the user&#39;s experience and bias, although overall, the data provides reliable information and is thus widely used by IBD researchers. In contrast, there is no generally accepted method for histological evaluation of mucosal damage. Most commonly, selected areas of the colon are inspected by a trained pathologist and scored based on several parameters that usually include crypt injury and leukocyte infiltration9,10,11. However, because the number of investigated parameters and the amount of tissue analyzed varies considerably between individual reports, comparability of many published studies is limited. To reduce observer bias and enhance inter-study concordance, an ideal histological scoring protocol should: 1) include the entire length of the colon, as intestinal mucosal inflammation is most often variable and skip lesions are common, 2) limit analysis to specific key and easily interpretable parameters to reduce subjectivity, 3) facilitate fast, consistent processing of large numbers of samples, and 4) use widely available and affordable tools for data acquisition, analysis and presentation.
Here we describe a technique to process the entire colon or long segments of the small intestine in a &#34;Swiss roll&#34; configuration along with the use of a free computer-assisted scoring system to analyze intestinal mucosal inflammation and damage because of DSS-induced colitis.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Aperio AT2 &#8211; High Volume, Digital Whole Slide Scanning</td>
			<td>Leica Biosystems</td>
			<td>Aperio AT2</td>
			<td></td>
		</tr>
		<tr>
			<td>Absorbent Underpads with waterproof moisture barrier</td>
			<td>VWR International</td>
			<td>56616-032</td>
			<td></td>
		</tr>
		<tr>
			<td>American Line 66-0089 Single Edge Blade, 100 per pkg</td>
			<td>GT Midwest</td>
			<td>TL5837</td>
			<td></td>
		</tr>
		<tr>
			<td>BD Luer-Lok Disposable Syringes without Needles</td>
			<td>Fisher scientific</td>
			<td>14-823-2A</td>
			<td></td>
		</tr>
		<tr>
			<td>Bonn Strabismus Scissors - ToughCut</td>
			<td>Fine Science tools</td>
			<td>11103-09</td>
			<td></td>
		</tr>
		<tr>
			<td>Bonn Strabismus Scissors - ToughCut</td>
			<td>Fine Science tools</td>
			<td>14084-09</td>
			<td></td>
		</tr>
		<tr>
			<td>Dumont #5 Forceps</td>
			<td>Fine Science tools</td>
			<td>11251-20</td>
			<td></td>
		</tr>
		<tr>
			<td>Formalin solution, neutral buffered, 10%</td>
			<td>Sigma</td>
			<td>HT501640-19L</td>
			<td></td>
		</tr>
		<tr>
			<td>HistoPrep 70% Ea</td>
			<td>Fisherbran</td>
			<td>70% denatured ethyl alcohol</td>
			<td></td>
		</tr>
		<tr>
			<td>ImageScope</td>
			<td>Aperio</td>
			<td>Version 12.3.3.5039</td>
			<td>http://www.leicabiosystems.com/pathology-imaging/aperio-epathology/integrate/imagescope/</td>
		</tr>
		<tr>
			<td>LeakBuster Specimen Containers: Sterile</td>
			<td>Starplex Scientific</td>
			<td>B120210</td>
			<td></td>
		</tr>
		<tr>
			<td>Phosphate-Buffere Saline, without calcium &#38; magnesium</td>
			<td>Corning</td>
			<td>21-040-CV</td>
			<td></td>
		</tr>
		<tr>
			<td>Plastic Feeding tubes, 20 GA x 30 mm</td>
			<td>Instech</td>
			<td>FTP2030</td>
			<td></td>
		</tr>
		<tr>
			<td>PrecisionGlide Needle, Size: 20 G x 1 1/2 in</td>
			<td>BD (Becton, Dickinson and Company)</td>
			<td>305176</td>
			<td></td>
		</tr>
		<tr>
			<td>PrecisionGlide Needle, Size: 27 G x 1/2 in</td>
			<td>BD (Becton, Dickinson and Company)</td>
			<td>305109</td>
			<td></td>
		</tr>
		<tr>
			<td>Syringe, 10 ml</td>
			<td>BD (Becton, Dickinson and Company)</td>
			<td>302995</td>
			<td></td>
		</tr>
		<tr>
			<td>Unisette Tissue Cassettes</td>
			<td>Simport</td>
			<td>M505-2</td>
			<td></td>
		</tr>
	</tbody>
</table>

systematic scoring analysis for intestinal inflammation in a murine dextran sodium sulfate-induced colitis model

Murine colitis models are tools that are extensively employed in studies focused on understanding the pathobiology of inflammatory intestinal disorders. However, robust standards for objective and reproducible quantification of disease severity remain to be defined. Most colitis analysis methods rely on limited histological scoring of small segments of intestine, leading to partial or biased analyses. Here, we combine high-resolution image acquisition and longitudinal analysis of the entire colon to quantify intestinal injury and ulceration in the dextran sodium sulfate (DSS) induced model of murine colitis. This protocol allows for the generation of objective and reproducible results without extensive user training. Here, we provide comprehensive details on sample preparation and image analysis using examples of data from DSS induced colitis. This method can be easily adapted to other models of murine colitis that have significant inflammation associated with mucosal injury. We demonstrate that the fraction of inflamed/injured and eroded/ulcerated mucosa relative to the complete length of the colon closely parallels clinical findings such as weight loss amid DSS-induced disease progression. This histological protocol provides a reliable time and cost-effective aid to standardize analyses of disease activity in an unbiased way in DSS colitis experiments.

To illustrate the reliability of this Histological Colitis Score Analysis in the context of mucosal damage after DSS challenge and subsequent recovery from colitis, we administered 2.5% DSS in the drinking water of eight 10 weeks old male C57BL6 wild type mice for 5 days followed by a recovery period with regular water for 5 days. There was no change in body weight during the acute administration of DSS, from day 0 to 5 (Figure 4A). Body weight dramatically d...

Watch this Scientific Journal Video about Systematic Scoring Analysis for Intestinal Inflammation in a Murine Dextran Sodium Sulfate-Induced Colitis Model at JoVE.com

Systematic Scoring Analysis for Intestinal Inflammation in a Murine Dextran Sodium Sulfate-Induced Colitis Model

Systematic scoring of intestinal inflammation using a free computer-assisted system is a powerful tool to quantitatively compare histopathological changes in colitis models characterized by the presence of ulcers and inflammatory changes. Histological colitis score evaluation strengthens clinical observations and facilitates data interpretation.

Murine colitis models are tools that are extensively employed in studies focused on understanding the pathobiology of inflammatory intestinal disorders. ...

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Immunology and Infection

8.9K Views.  University of Michigan. Systematic scoring of intestinal inflammation using a free computer-assisted system is a powerful tool to quantitatively compare histopathological changes in colitis models characterized by the presence of ulcers and inflammatory changes. Histological colitis score evaluation strengthens clinical observations and facilitates data interpretation.

Video: Systematic Scoring Analysis for Intestinal Inflammation in a Murine Dextran Sodium Sulfate-Induced Colitis Model

Trichuris muris Infection: A Model of Type 2 Immunity and Inflammation in the Gut

Trichuris muris is a natural pathogen of mice and is biologically and antigenically similar to species of Trichuris that 
infect humans and livestock1. Infective eggs are given by oral gavage, hatch in the distal small intestine, invade the intestinal epithelial cells (IECs) 
that line the crypts of the cecum and proximal colon and upon maturation the worms release eggs into the environment1. This model is a powerful tool to 
examine factors that control CD4+ T helper (Th) cell activation as well as changes in the intestinal epithelium. The immune response that occurs in 
resistant inbred strains, such as C57BL/6 and BALB/c, is characterized by Th2 polarized cytokines (IL-4, IL-5 and IL-13) and expulsion of worms while Th1-associated 
cytokines (IL-12, IL-18, IFN-&gamma;) promote chronic infections in genetically susceptible AKR/J mice2-6. Th2 cytokines promote physiological changes in 
the intestinal microenvironment including rapid turnover of IECs, goblet cell differentiation, recruitment and changes in epithelial permeability and smooth muscle 
contraction, all of which have been implicated in worm expulsion7-15. Here we detail a protocol for propagating Trichuris muris eggs which can 
be used in subsequent experiments. We also provide a sample experimental harvest with suggestions for post-infection analysis. Overall, this protocol will provide 
researchers with the basic tools to perform a Trichuris muris mouse infection model which can be used to address questions pertaining to Th proclivity in 
the gastrointestinal tract as well as immune effector functions of IECs.

Trichuris muris Infection: A Model of Type 2 Immunity and Inflammation in the Gut

Trichuris muris infection is an intestinal model of Th2 immunity where resistant mice generate a protective Th2 response and susceptible mice generate a pathological Th1 response.

Trichuris muris is a natural pathogen of mice and is biologically and antigenically similar to species of Trichuris that 
infect humans and livestock1. ...

Flow Cytometry Analysis of Immune Cells Within Murine Aortas

Atherosclerosis is a chronic inflammatory process of medium and large size vessels that is characterized by the formation of plaques consisting of foam cells, immune cells, vascular endothelial and smooth muscle cells, platelets, extracellular matrix, and a lipid-rich core with extensive necrosis and fibrosis of surrounding tissues.1 The innate and adaptive arms of the immune response are involved in the initiation, development and persistence of atherosclerosis.2, 3 There is a significant body of evidence that different subsets of the immune cells, such as macrophages, dendritic cells, T and B lymphocytes, are present within the aortas of healthy and atherosclerosis-prone mice4. Additionally, immune cells are found in the surrounding aortic adventitia which suggests an important role of this tissue in atherogenesis.2
For some time, the quantitative detection of different types of immune cells, their activation status, and the cellular composition within the aortic wall was limited by RT-PCR and immunohistochemical methods for the study of atherosclerosis. Few attempts were made to perform flow cytometry using human aortas, and a number of problems, such as a high autofluorescence, have been reported5,6. Human atherosclerotic plaques were digested with collagenase 1, and free cells were collected and stained for CD14+/CD11c+ to highlight macrophage-derived foam cells. In this study, a "mock" channel was used to avoid false-positive staining.6 Necrotic materials accumulating during the digestion process give rise in a large amount of debris that generates a high autofluorescence in aortic samples. To resolve this problem, a panel of negative and positive controls has been proposed, but only double staining could be applied in these samples. We have developed a new flow cytometry-based method7 to analyze the immune cell composition and characterize the activation, proliferation, differentiation of immune cells in healthy and atherosclerosis-prone aorta. This method allows the investigation of the immune cell composition of the aortic wall and opens possibilities to use a broad spectrum of immunological methods for investigations of immune aspects of this disease.

This paper presents a flow cytometry-based method to investigate the immune composition of aortas. The paper also illustrates an additional technique that allows examining surrounding adventitia and vessel wall separately. This method opens possibilities to perform phenotypical analyses of aortic leukocytes and apply several immunological assays for atherosclerosis studies.

Atherosclerosis is a chronic inflammatory process of medium and large size vessels that is characterized by the formation of plaques consisting of foam ...

Analysis of Pulmonary Dendritic Cell Maturation and Migration during Allergic Airway Inflammation

Dendritic cells (DCs) are the key players involved in initiation of adaptive immune response by activating antigen-specific T cells. DCs are present in peripheral tissues in steady state; however in response to antigen stimulation, DCs take up the antigen and rapidly migrate to the draining lymph nodes where they initiate T cell response against the antigen1,2. Additionally, DCs also play a key role in initiating autoimmune as well as allergic immune response3.
DCs play an essential role in both initiation of immune response and induction of tolerance in the setting of lung environment4. Lung environment is largely tolerogenic, owing to the exposure to vast array of environmental antigens5. However, in some individuals there is a break in tolerance, which leads to induction of allergy and asthma. In this study, we describe a strategy, which can be used to monitor airway DC maturation and migration in response to the antigen used for sensitization. The measurement of airway DC maturation and migration allows for assessment of the kinetics of immune response during airway allergic inflammation and also assists in understanding the magnitude of the subsequent immune response along with the underlying mechanisms.
Our strategy is based on the use of ovalbumin as a sensitizing agent. Ovalbumin-induced allergic asthma is a widely used model to reproduce the airway eosinophilia, pulmonary inflammation and elevated IgE levels found during asthma6,7. After sensitization, mice are challenged by intranasal delivery of FITC labeled ovalbumin, which allows for specific labeling of airway DCs which uptake ovalbumin. Next, using several DC specific markers, we can assess the maturation of these DCs and can also assess their migration to the draining lymph nodes by employing flow cytometry.

We describe a strategy to monitor maturation and migration of pulmonary dendritic cells in response to ovalbumin in the setting of ovalbumin induced allergic airway inflammation. This strategy can be modified to assess migration of pulmonary dendritic cells in settings of infection.

Dendritic cells (DCs) are the key players involved in initiation of adaptive immune response by activating antigen-specific T cells. DCs are present in ...

The Citrobacter rodentium Mouse Model: Studying Pathogen and Host Contributions to Infectious Colitis

This protocol outlines the steps required to produce a robust model of infectious disease and colitis, as well as the methods used to characterize Citrobacter rodentium infection in mice. C. rodentium is a gram negative, murine specific bacterial pathogen that is closely related to the clinically important human pathogens enteropathogenic E. coli and enterohemorrhagic E. coli. Upon infection with C. rodentium, immunocompetent mice suffer from modest and transient weight loss and diarrhea. Histologically, intestinal crypt elongation, immune cell infiltration, and goblet cell depletion are observed. Clearance of infection is achieved after 3 to 4 weeks. Measurement of intestinal epithelial barrier integrity, bacterial load, and histological damage at different time points after infection, allow the characterization of mouse strains susceptible to infection.
The virulence mechanisms by which bacterial pathogens colonize the intestinal tract of their hosts, as well as specific host responses that defend against such infections are poorly understood. Therefore the C. rodentium model of enteric bacterial infection serves as a valuable tool to aid in our understanding of these processes. Enteric bacteria have also been linked to Inflammatory Bowel Diseases (IBDs). It has been hypothesized that the maladaptive chronic inflammatory responses seen in IBD patients develop in genetically susceptible individuals following abnormal exposure of the intestinal mucosal immune system to enteric bacteria. Therefore, the study of models of infectious colitis offers significant potential for defining potentially pathogenic host responses to enteric bacteria. C. rodentium induced colitis is one such rare model that allows for the analysis of host responses to enteric bacteria, furthering our understanding of potential mechanisms of IBD pathogenesis; essential in the development of novel preventative and therapeutic treatments.

The Citrobacter rodentium Mouse Model: Studying Pathogen and Host Contributions to Infectious Colitis

Citrobacter rodentium infection provides a valuable model to study enteric bacterial infections as well as host immune responses and colitis in mice. This protocol outlines the measurement of barrier integrity, pathogen load and histological damage allowing for the thorough characterization of pathogen and host contributions to murine infectious colitis.

This protocol  outlines the steps required to produce a robust model of infectious disease and  colitis, as well as the methods used to characterize ...

A Mouse Model for Pathogen-induced Chronic Inflammation at Local and Systemic Sites

Chronic inflammation is a major driver of pathological tissue damage and a unifying characteristic of many chronic diseases in humans including neoplastic, autoimmune, and chronic inflammatory diseases. Emerging evidence implicates pathogen-induced chronic inflammation in the development and progression of chronic diseases with a wide variety of clinical manifestations. Due to the complex and multifactorial etiology of chronic disease, designing experiments for proof of causality and the establishment of mechanistic links is nearly impossible in humans. An advantage of using animal models is that both genetic and environmental factors that may influence the course of a particular disease can be controlled. Thus, designing relevant animal models of infection represents a key step in identifying host and pathogen specific mechanisms that contribute to chronic inflammation.
Here we describe a mouse model of pathogen-induced chronic inflammation at local and systemic sites following infection with the oral pathogen Porphyromonas gingivalis, a bacterium closely associated with human periodontal disease. Oral infection of specific-pathogen free mice induces a local inflammatory response resulting in destruction of tooth supporting alveolar bone, a hallmark of periodontal disease. In an established mouse model of atherosclerosis, infection with P. gingivalis accelerates inflammatory plaque deposition within the aortic sinus and innominate artery, accompanied by activation of the vascular endothelium, an increased immune cell infiltrate, and elevated expression of inflammatory mediators within lesions. We detail methodologies for the assessment of inflammation at local and systemic sites. The use of transgenic mice and defined bacterial mutants makes this model particularly suitable for identifying both host and microbial factors involved in the initiation, progression, and outcome of disease. Additionally, the model can be used to screen for novel therapeutic strategies, including vaccination and pharmacological intervention.

Animal models have proven to be invaluable tools in defining host and pathogen specific mechanisms that contribute to the development of chronic inflammation. Here we describe a mouse model of oral infection with the human pathogen Porphyromonas gingivalis and detail methodologies to assess the progression of inflammation at local and systemic sites.

Chronic inflammation is a major driver of pathological tissue damage and a unifying characteristic of many chronic diseases in humans including ...

Induction of Murine Intestinal Inflammation by Adoptive Transfer of Effector CD4+CD45RBhigh T Cells into Immunodeficient Mice

There are many different animal models available for studying the pathogenesis of human inflammatory bowel diseases (IBD), each with its own advantages and disadvantages. We describe here an experimental colitis model that is initiated by adoptive transfer of syngeneic splenic CD4+CD45RBhigh T cells into T and B cell deficient recipient mice. The CD4+CD45RBhigh T cell population that largely consists of na&#239;ve effector cells is capable of inducing chronic intestinal inflammation, closely resembling key aspects of human IBD. This method can be manipulated to study aspects of disease onset and progression. Additionally it can be used to study the function of innate, adaptive, and regulatory immune cell populations, and the role of environmental exposures, i.e., the microbiota, in intestinal inflammation. In this article we illustrate the methodology for inducing colitis with a step-by-step protocol. This includes a video demonstration of key technical aspects required to successfully develop this murine model of experimental colitis for research purposes.

Induction of Murine Intestinal Inflammation by Adoptive Transfer of Effector CD4+CD45RBhigh T Cells into Immunodeficient Mice

Here, we present a protocol to induce colonic inflammation in mice by adoptive transfer of syngeneic CD4+CD45RBhigh T cells into T and B cell deficient recipients. Clinical and histopathological features mimic human inflammatory bowel diseases. This method allows the study of the initiation of colonic inflammation and progression of disease.

There are many different animal models available for studying the pathogenesis of human inflammatory bowel diseases (IBD), each with its own advantages ...

An Optimized Method for Isolating and Expanding Invariant Natural Killer T Cells from Mouse Spleen

The ability to rapidly secrete cytokines upon stimulation is a functional characteristic of the invariant natural killer T (iNKT) cell lineage. iNKT cells are therefore characterized as an innate T cell population capable of activating and steering adaptive immune responses. The development of improved techniques for the culture and expansion of murine iNKT cells facilitates the study of iNKT cell biology in in vitro and in vivo model systems. Here we describe an optimized procedure for the isolation and expansion of murine splenic iNKT cells.
Spleens from C57Bl/6 mice are removed, dissected and strained and the resulting cellular suspension is layered over density gradient media. Following centrifugation, splenic mononuclear cells (MNCs) are collected and CD5-positive (CD5+) lymphocytes are enriched for using magnetic beads. iNKT cells within the CD5+ fraction are subsequently stained with &#945;GalCer-loaded CD1d tetramer and purified by fluorescence activated cell sorting (FACS). FACS sorted iNKT cells are then initially cultured in vitro using a combination of recombinant murine cytokines and plate-bound T cell receptor (TCR) stimuli before being expanded in the presence of murine recombinant IL-7. Using this technique, approximately 108 iNKT cells can be generated within 18-20 days of culture, after which they can be used for functional assays in vitro, or for in vivo transfer experiments in mice.

Here we present an adapted protocol that can be used to generate a large number of murine invariant natural killer T cells from mouse spleen. The protocol outlines an approach by which splenic iNKT cells can be enriched for, isolated and expanded in vitro using a limited number of animals and reagents.

The ability to rapidly secrete cytokines upon stimulation is a functional characteristic of the invariant natural killer T (iNKT) cell lineage. iNKT cells ...

Dextran Enhances the Lentiviral Transduction Efficiency of Murine and Human Primary NK Cells

The efficient transduction of specific genes into natural killer (NK) cells has been a major challenge. Successful transductions are critical to defining the role of the gene of interest in the development, differentiation, and function of NK cells. Recent advances related to chimeric antigen receptors (CARs) in cancer immunotherapy accentuate the need for an efficient method to deliver exogenous genes to effector lymphocytes. The efficiencies of lentiviral-mediated gene transductions into primary human or mouse NK cells remain significantly low, which is a major limiting factor. Recent advances using cationic polymers, such as polybrene, show an improved gene transduction efficiency in T cells. However, these products failed to improve the transduction efficiencies of NK cells. This work shows that dextran, a branched glucan polysaccharide, significantly improves the transduction efficiency of human and mouse primary NK cells. This highly reproducible transduction methodology provides a competent tool for transducing human primary NK cells, which can vastly improve clinical gene delivery applications and thus NK cell-based cancer immunotherapy.

The goal of this study was to formulate technologies that allow for successful gene transduction in primary natural killer (NK) cells. The dextran-mediated lentiviral transduction of human or mouse primary NK cells results in higher gene expression efficiencies. This method of gene transduction will vastly improve NK cell genetic manipulation.

The efficient transduction of specific genes into natural killer (NK) cells has been a major challenge. Successful transductions are critical to defining ...

Induction and Scoring of Graft-Versus-Host Disease in a Xenogeneic Murine Model and Quantification of Human T Cells in Mouse Tissues using Digital PCR

Acute graft-versus-host disease (GVHD) is a significant limitation for patients receiving hematopoietic stem cell transplant as therapy for hematological deficiencies and malignancies. Acute GVHD occurs when donor T cells recognize host tissues as a foreign antigen and mount an immune response to the host. Current treatments involve toxic immunosuppressive drugs that render patients susceptible to infection and recurrence. Thus, there is ongoing research to provide an acute GVHD therapy that can effectively target donor T cells and reduce side effects. Much of this pre-clinical work uses the xenogenic GVHD (xenoGVHD) murine model that allows for testing of immunosuppressive therapies on human cells rather than murine cells in an in vivo system. This protocol outlines how to induce xenoGVHD and how to blind and standardize clinical scoring to ensure consistent results. Additionally, this protocol describes how to use digital PCR to detect human T cells in mouse tissues, which can subsequently be used to quantify efficacy of tested therapies. The xenoGVHD model not only provides a model to test GVHD therapies but any therapy that can suppress human T cells, which could then be applied to many inflammatory diseases.

Here, we present a protocol to induce and score disease in a xenogeneic graft-versus-host disease (xenoGVHD) model. xenoGVHD provides an in vivo model to study immunosuppression of human T cells. Additionally, we describe how to detect human T cells in tissues with digital PCR as a tool to quantify immunosuppression.

Acute graft-versus-host disease (GVHD) is a significant limitation for patients receiving hematopoietic stem cell transplant as therapy for hematological ...

Intravital Imaging of Intraepithelial Lymphocytes in Murine Small Intestine

Intraepithelial lymphocytes expressing &#947;&#948; T cell receptor (&#947;&#948; IEL) play a key role in immune surveillance of the intestinal epithelium. Due in part to the lack of a definitive ligand for the &#947;&#948; T cell receptor, our understanding of the regulation of &#947;&#948; IEL activation and their function in vivo remains limited. This necessitates the development of alternative strategies to interrogate signaling pathways involved in regulating &#947;&#948; IEL function and the responsiveness of these cells to the local microenvironment. Although &#947;&#948; IELs are widely understood to limit pathogen translocation, the use of intravital imaging has been critical to understanding the spatiotemporal dynamics of IEL/epithelial interactions at steady-state and in response to invasive pathogens. Herein, we present a protocol for visualizing IEL migratory behavior in the small intestinal mucosa of a GFP &#947;&#948; T cell reporter mouse using inverted spinning disk confocal laser microscopy. Although the maximum imaging depth of this approach is limited relative to the use of two-photon laser-scanning microscopy, spinning disk confocal laser microscopy provides the advantage of high speed image acquisition with reduced photobleaching and photodamage. Using 4D image analysis software, T cell surveillance behavior and their interactions with neighboring cells can be analyzed following experimental manipulation to provide additional insight into IEL activation and function within the intestinal mucosa.

We describe a method to visualize GFP-labeled &#947;&#948; IELs using intravital imaging of murine small intestine by inverted spinning disk confocal microscopy. This technique enables the tracking of live cells within the mucosa for up to 4 h and can be used to investigate a variety of intestinal immune-epithelial interactions. &#160;