We thank the department of Pathology of the IRCCS Policlinico Hospital, Milan for technical support and the IEO Animal Facility for assistance in animal husbandry.

Animal procedures were approved by the Italian Ministry of Health (Auth. 127/15, 27/13) and followed the animal care guidelines of the European Institute of Oncology IACUC (Institutional Animal Care and Use Committee)
1. Chronic Colitis Induction by Repetitive DSS Administration
<ol>
	<li>Separate age and sex matched mice in 2 groups (treatment DSS vs. control H2O, at least 5 mice littermates per experimental group).</li>
	<li>Administer 2.5% DSS (40 kDa) in the drinking water for...

<ol>
	<li>Gibson-Corley, K. 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=Successful+Integration+of+the+Histology+Core+Laboratory+in+Translational+Research.">Successful Integration of the Histology Core Laboratory in Translational Research.</a> Journal of histotechnology. 35, 17-21 (2012).</li><li>Olivier, A. K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Genetically+modified+species+in+research:+Opportunities+and+challenges+for+the+histology+core+laboratory.">Genetically modified species in research: Opportunities and challenges for the histology core laboratory.</a> Journal of histotechnology. 35, 63-67 (2012).</li><li>Gibson-Corley, K. N., Olivier, A. K., Meyerholz, D. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Principles+for+valid+histopathologic+scoring+in+research.">Principles for valid histopathologic scoring in research.</a> Veterinary pathology. 50, 1007-1015 (2013).</li><li>Stolfi, 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=Involvement+of+interleukin-21+in+the+regulation+of+colitis-associated+colon+cancer.">Involvement of interleukin-21 in the regulation of colitis-associated colon cancer.</a> The Journal of experimental medicine. 208, 2279-2290 (2011).</li><li>Begley, C. G., Ellis, L. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Drug+development:+Raise+standards+for+preclinical+cancer+research.">Drug development: Raise standards for preclinical cancer research.</a> Nature. 483, 531-533 (2012).</li><li>Peters, S. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> A Practical Guide to Frozen Section Technique. , (2010).</li><li>Rosai, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Rosai and Ackerman's Surgical Pathology. , (2011).</li><li>Blumberg, R. S., Saubermann, L. J., Strober, W. <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+mucosal+inflammation+and+their+relation+to+human+inflammatory+bowel+disease.">Animal models of mucosal inflammation and their relation to human inflammatory bowel disease.</a> Current opinion in immunology. 11, 648-656 (1999).</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. 2, 541-546 (2007).</li><li>Kaser, A., Zeissig, S., Blumberg, R. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Inflammatory+bowel+disease.">Inflammatory bowel disease.</a> Annual review of immunology. 28, 573-621 (2010).</li><li>Cribi&#249;, F. M., Burrello, 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=Implementation+of+an+automated+inclusion+system+for+the+histological+analysis+of+murine+tissue+samples:+A+feasibility+study+in+DSS-induced+chronic+colitis.">Implementation of an automated inclusion system for the histological analysis of murine tissue samples: A feasibility study in DSS-induced chronic colitis.</a> European Journal of Inflammation. 16, 1-12 (2018).</li></ol>

We utilize different automated steps during the preparation of murine tissues for histopathologic analysis. This protocol aims at providing technical hints to increase the reproducibility and the standardization of the whole process, thus enhancing the overall quality of the final histopathological evaluation. We implemented automated instruments and methods for the preparation and embedding of tissues, routinely used in pathology core facilities for the study of human specimens.
To demonstrat...

An erratum was issued for: <a href="https://www.jove.com/video/58654/using-robotic-systems-to-process-embed-colonic-murine-samples-for">Using Robotic Systems to Process and Embed Colonic Murine Samples for Histological Analyses</a>.&#160; An author affiliation&#160;was updated.
The affiliation for Claudia&#160;Burrello and Federica Facciotti was updated from:
Department of Experimental Oncology, European Institute of Oncology
to:
Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS

An erratum was issued for: <a href="https://www.jove.com/video/58654/using-robotic-systems-to-process-embed-colonic-murine-samples-for">Using Robotic Systems to Process and Embed Colonic Murine Samples for Histological Analyses</a>.&#160; An author affiliation&#160;was updated.

Erratum: Using Robotic Systems to Process and Embed Colonic Murine Samples for Histological Analyses

In the last decades, several experimental models have been developed to dissect the pathogenic mechanisms leading to human diseases1,2. In order to assess the severity of a disease, researchers must evaluate the effect of a treatment and study the cytological and histological architectural variations or the amount of inflammation3. To perform on those experimental models, detailed histopathological analyses are needed, often comparing murine and human samples4,5.
Additionally, human samples are commonly processed and scored by histopathology core facilities and experienced human pathologists through standardized histopathological criteria and methods. Conversely, murine tissues are usually fixed, embedded and analyzed by researchers with limited experience of histopathological protocols. The quality and reliability of histopathological examination begins with the preparation of high-quality tissue sections. Several factors critically contribute to increase or decrease the quality of the final analysis, including fixation, macroscopic sectioning, processing, paraffin embedding, and embedding of the samples6,7.
All these passages involving manipulation of the sample are subjected to manual errors, including manual embedding of the samples and, to a lesser extent, manual microtome sectioning and staining. At present, the whole process of murine tissue preparation for histological evaluation relies on protocols that vary from laboratory to laboratory and manual protocols. The goal of this study is to implement standardized automated protocols to reduce errors and variability in murine histopathological examination.
To our knowledge, we describe here the first protocols for fully automated tissue processing and embedding for the histological evaluation of murine tissues; these are routinely used in pathology units for the analyses of human specimens. As a practical example of the feasibility of the method, a murine model of intestinal inflammation has been analyzed, i.e., the chronic colitis model caused by repeated administration of dextran sodium sulphate (DSS) in the drinking water8,9. This experimental setting closely resembles human inflammatory bowel diseases (IBD)10 since DSS-treated animals exhibit signs of intestinal inflammation, e.g., weight loss, loose stool or diarrhea, and shortening of the colon as well as fibrosis8,9,11. As observed for human IBD patients, DSS treatment generates a complex disease course. In this context, elaborate histological evaluations are required to understand the profound alteration of the tissue architecture. Thus, the implementation of the described protocols for increasing sample preparation quality might benefit researchers relying on the interpretation of histological and immunohistochemical analyses for murine experimental settings. Murine experimental models of human diseases involving alterations of the tissue architecture, the presence of cellular tissue infiltrate or inflammation in different tissues and organs (intestine, brain, liver, skin) could use the increased quality of the sample preparation for histopathological examination.

<table>
	<tbody>
		<tr>
			<td>Absolute Ethanol anhydrous</td>
			<td>Carlo Erba</td>
			<td>414605</td>
			<td>reagent</td>
		</tr>
		<tr>
			<td>Absolute ETOH</td>
			<td>Honeywell</td>
			<td>02860-1L</td>
			<td>reagent</td>
		</tr>
		<tr>
			<td>Aluminium Potassium Sulfate</td>
			<td>SIGMA</td>
			<td>A6435</td>
			<td>reagent</td>
		</tr>
		<tr>
			<td>Aniline Blue</td>
			<td>SIGMA</td>
			<td>415049</td>
			<td>reagent</td>
		</tr>
		<tr>
			<td>carbol Fuchsin</td>
			<td>SIGMA</td>
			<td>C4165</td>
			<td>reagent</td>
		</tr>
		<tr>
			<td>CD11b (clone M1/70)</td>
			<td>TONBO biosciences</td>
			<td>35-0112-U100</td>
			<td>antibody</td>
		</tr>
		<tr>
			<td>CD20 IHC (clone SA275A11)</td>
			<td>Biolegend</td>
			<td>150403</td>
			<td>antibody</td>
		</tr>
		<tr>
			<td>CD3 (17A2)</td>
			<td>TONBO biosciences</td>
			<td>35-0032-U100</td>
			<td>antibody</td>
		</tr>
		<tr>
			<td>CD4 (GK1.5)</td>
			<td>BD Biosciences</td>
			<td>552051</td>
			<td>antibody</td>
		</tr>
		<tr>
			<td>CD45.2 (clone 104)</td>
			<td>BioLegend</td>
			<td>109837</td>
			<td>antibody</td>
		</tr>
		<tr>
			<td>CD8 (53-6.7)</td>
			<td>BD Biosciences</td>
			<td>553031</td>
			<td>antibody</td>
		</tr>
		<tr>
			<td>Citrate Buffer pH 6 10X</td>
			<td>SIGMA</td>
			<td>C9999</td>
			<td>reagent</td>
		</tr>
		<tr>
			<td>Dab</td>
			<td>Vector Laboratories</td>
			<td>SK-4100</td>
			<td>reagent</td>
		</tr>
		<tr>
			<td>DPBS 1X</td>
			<td>Microgem</td>
			<td>L0615-500</td>
			<td>reagent</td>
		</tr>
		<tr>
			<td>DSS</td>
			<td>TdB Consultancy</td>
			<td>DB001</td>
			<td>reagent</td>
		</tr>
		<tr>
			<td>EDTA</td>
			<td>SIGMA</td>
			<td>E9884</td>
			<td>reagent</td>
		</tr>
		<tr>
			<td>EnVision Flex Peroxidase-Blocking Reagent</td>
			<td>DAKO</td>
			<td></td>
			<td>compreso in GV80011-2</td>
		</tr>
		<tr>
			<td>EnVision Flex Substrate</td>
			<td>DAKO</td>
			<td></td>
			<td>compreso in GV80011-2</td>
		</tr>
		<tr>
			<td>EnVision Flex/HRP</td>
			<td>DAKO</td>
			<td></td>
			<td>compreso in GV80011-2</td>
		</tr>
		<tr>
			<td>EnVision Flex+ Rat Linker</td>
			<td>DAKO</td>
			<td></td>
			<td>compreso in GV80011-2</td>
		</tr>
		<tr>
			<td>Eosin</td>
			<td>VWR</td>
			<td>1.09844</td>
			<td>reagent</td>
		</tr>
		<tr>
			<td>F4/80 (clone BM8)</td>
			<td>BioLegend</td>
			<td>123108</td>
			<td>antibody</td>
		</tr>
		<tr>
			<td>Formalin</td>
			<td>PanReac</td>
			<td>2,529,311,215</td>
			<td>reagent</td>
		</tr>
		<tr>
			<td>glacial acetic acid</td>
			<td>SIGMA</td>
			<td>71251</td>
			<td>reagent</td>
		</tr>
		<tr>
			<td>Goat-anti-Rat-HRP</td>
			<td>Agilent DAKO</td>
			<td>P0448</td>
			<td>antibody</td>
		</tr>
		<tr>
			<td>Haematoxylin</td>
			<td>DIAPATH</td>
			<td>C0303</td>
			<td>reagent</td>
		</tr>
		<tr>
			<td>LEICA Rotary microtome (RM2255)</td>
			<td>Leica</td>
			<td>RM2255</td>
			<td>equipment</td>
		</tr>
		<tr>
			<td>Ly6g (clone 1A8)</td>
			<td>BD Biosciences</td>
			<td>551459</td>
			<td>antibody</td>
		</tr>
		<tr>
			<td>Mercury II Oxide</td>
			<td>SIGMA</td>
			<td>203793</td>
			<td>reagent</td>
		</tr>
		<tr>
			<td>Omnis Clearify Clearing Agent</td>
			<td>DAKO</td>
			<td>CACLEGAL</td>
			<td>reagent</td>
		</tr>
		<tr>
			<td>Omnis EnVision Flex TRS</td>
			<td>DAKO</td>
			<td>GV80011-2</td>
			<td>reagent</td>
		</tr>
		<tr>
			<td>Orange G</td>
			<td>SIGMA</td>
			<td>O3756</td>
			<td>reagent</td>
		</tr>
		<tr>
			<td>Paraffin</td>
			<td>Sakura</td>
			<td>7052</td>
			<td>reagent</td>
		</tr>
		<tr>
			<td>Peloris</td>
			<td>LEICA</td>
			<td></td>
			<td>equipment</td>
		</tr>
		<tr>
			<td>Percoll</td>
			<td>SIGMA</td>
			<td>P4937</td>
			<td>reagent</td>
		</tr>
		<tr>
			<td>RPMI 1640 without L-Glutamine</td>
			<td>Microgem</td>
			<td>L0501-500</td>
			<td>reagent</td>
		</tr>
		<tr>
			<td>STS020</td>
			<td>Leica</td>
			<td></td>
			<td>equipment</td>
		</tr>
		<tr>
			<td>Tissue-Teck Paraform Sectionable Cassette</td>
			<td>SAKURA</td>
			<td>7022</td>
			<td>equipment</td>
		</tr>
		<tr>
			<td>Tissue-Tek Automated paraffin embedder</td>
			<td>Sakura</td>
			<td></td>
			<td>equipment</td>
		</tr>
		<tr>
			<td>Xylene</td>
			<td>J.T.Baker</td>
			<td>8080.1000</td>
			<td>reagent</td>
		</tr>
	</tbody>
</table>

using robotic systems to process and embed colonic murine samples for histological analyses

The understanding of human diseases has been greatly expanded thanks to the study of animal models. Nonetheless, histopathological evaluation of experimental models needs to be as rigorous as that applied for human samples. Indeed, drawing reliable and accurate conclusions is critically influenced by the quality of tissue section preparation. Here, we describe a protocol for histopathological analysis of murine tissues that implements several automated steps during the procedure, from the initial preparation to the paraffin embedding of the murine samples. The reduction of methodological variables through rigorous protocol standardization from automated procedures contributes to increased overall reliability of murine pathological analysis. Specifically, this protocol describes the utilization of automated processing and embedding robotic systems, routinely used for the tissue processing and paraffin embedding of human samples, to process murine specimens of intestinal inflammation. We conclude that the reliability of histopathological examination of murine tissues is significantly increased upon introduction of standardized and automated techniques.

Experimental chronic colitis induced by repeated administration of DSS in the drinking water is a murine model of intestinal inflammation closely resembling human IBD8,9. Figure 1 describes the effects of DSS treatment, including colon shortening (Figure 1A), a widely-used parameter to score the presence of DSS-induced inflammation, and colonic expression of pro-inflammat...

Watch this Scientific Journal Video about Using Robotic Systems to Process and Embed Colonic Murine Samples for Histological Analyses at JoVE.com

Using Robotic Systems to Process and Embed Colonic Murine Samples for Histological Analyses

Lack of standardization for murine tissue processing reduces the quality of murine histopathological analysis as compared to human specimens. Here, we present a protocol to perform histopathological examination of murine inflamed and uninflamed colonic tissues to show the feasibility of robotic systems routinely used for processing and embedding&#160;human samples.

The understanding of human diseases has been greatly expanded thanks to the study of animal models. Nonetheless, histopathological evaluation of ...

This automated protocol allows the histopathological preparation of murine tissues with robotic systems routinely used for processing and embedding of human samples, greatly increasing the quality of the samples. The main advantages of this technique, are that it reduces the number of methodological variables and it improves the standardization of procedural steps. Demonstrating the procedure, will be Francesca Boggio.Francesca Boggio is a pathologist working in my laboratory. Begin by using small tweezers to transfer the fixed murine colon tissue samples from the neutral buffered formalin, onto a sectioning work plate in a Petri dish. Use a sterile scalpel to cut the colon into 0.2 to 0.3 centimeter fragments, and use the tweezers to place one segment into each of three non-adjacent plastic-protruding tips of an oriented paraffin-embedding cassette.Carefully push the four edges to close the cassette and insert the grid into a plastic supporting frame. Then, label the supporting frame to identify the sample and transfer the cassette into the grid. One hour before processing, turn the automated processor.When the instrument indicates that the paraffin has melted, manually insert the metal basket in the automated processor. When all of the cassettes have been inserted, close the basket and open the lid of the retort. Insert the basket into the dedicated housing of the processor and close the retort lid.Use the touchscreen on the instrument computer to define the working protocol selecting the sequence of solutions, timing, and temperature, to be implemented according to the scheme provided in the table. Click on the dedicated computer icon to assign the protocol to the retort containing the cassette basket, and click the start button. When the instrument confirms the end of the protocol with a dedicated icon and an alarm tone, open the retort lid and remove the basket from the processor.An hour before the tissue embedding, turn on the automated embedder and wait until the paraffin is completely melted as indicated by the paraffin bath thermometer on the instrument. Manually transfer up to 32 processed cassettes from the processor basket to the embedder rack and open the main embedder lid. Use the touchscreen to signal to the robotic system that a rack is being inserted and open the inlet housing lid.Insert up to four racks into the inlet housing and close the inlet housing lid. Then, use the touchscreen to start the embedding procedure as indicated in the table. When the instrument confirms the end of the protocol with the dedicated icon, remove the outlet rack and close the main embedder lid.Then, transfer the embedded blocks from the rack into a storage box. Colon shortening, and colonic expression of pro inflammatory genes, are widely used parameters for scoring the presence of dextran sodium sulfate or DSS induced inflammation. The infiltration of inflammatory cells into the intestinal lamina propria is also greatly enhanced by DSS treatment.H&E staining of untreated samples processed by automation as demonstrated, reveals fewer infiltrating inflammatory cells, epithelial alterations, and changes in mucosal architecture compared to samples from DSS treated animals. The quality of the murine tissue preparation and embedding performed by the automated instruments can be additionally confirmed by immunohistochemical staining for CD20 and Mallory Trichrome Staining. Notably, automated sample processing consistently allows the evaluation of a higher proportion of histological parameters, than do samples processed by the manual method.Take care to correctly insert the tissue into the grid to wait for the automated processor to be ready, and to wait for the paraffin to be completely melted. This method can be used to perform histological analysis of any murine tissue, with the qualitive of human histological samples which will be used in murine models of human pathologists. This technique has already been successful study for studying inflammatory tissue inflammation, and will be useful for studying models of colorectal murine cancer.As some reagents used in this protocol are hazardous, remember to always wear protective gloves, goggles and a lab coat when performing this procedure.

Using Robotic Systems to Process and Embed Colonic Murine Samples for Histological Analyses

Abstract