This work was supported by National Institutes of Health Grant R01 AI088209 (to K.A.H.). We also thank the University of Minnesota Flow Cytometry Resource.

In this study, adult (6 - 8 weeks) female C57Bl/6 mice were used. Mice were purchased from the National Cancer Institute and maintained under specific pathogen free conditions. The University of Minnesota Institutional Animal Care and Use Committee (IACUC) approved all animal experimentation.
1. Preparation of Instruments and Buffers
<ol>
	<li>Prepare enzyme solution (RPMI1640 medium with 0.05% [w/v] of Liberase TH and 100 U/ml of DNase I), albumin-rich buffer (1X PBS [Ca2+/Mg<sup...

<ol>
	<li>Rothenberg, E. V., Moore, J. E., Yui, M. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Launching+the+T-cell-lineage+developmental+programme.">Launching the T-cell-lineage developmental programme.</a> Nat. Rev. Immunol. 8, 9-21 (2008).</li><li>Anderson, G., Takahama, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Thymic+epithelial+cells:+working+class+heroes+for+T+cell+development+and+repertoire+selection.">Thymic epithelial cells: working class heroes for T cell development and repertoire selection.</a> Trends Immunol. 33, 256-263 (2012).</li><li>Klein, L., Hinterberger, M., Wirnsberger, G., Kyewski, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Antigen+presentation+in+the+thymus+for+positive+selection+and+central+tolerance+induction.">Antigen presentation in the thymus for positive selection and central tolerance induction.</a> Nat. Rev. Immunol. 9, 833-844 (2009).</li><li>Starr, T. K., Jameson, S. C., Hogquist, K. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Positive+and+negative+selection+of+T+cells.">Positive and negative selection of T cells.</a> Annu. Rev. Immunol. 21, 139-176 (2003).</li><li>Takahama, Y., Takada, K., Murata, S., Tanaka, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=beta5t-containing+thymoproteasome:+specific+expression+in+thymic+cortical+epithelial+cells+and+role+in+positive+selection+of+CD8.">beta5t-containing thymoproteasome: specific expression in thymic cortical epithelial cells and role in positive selection of CD8.</a> T cells. Curr. Opin. 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C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Zoned+out:+functional+mapping+of+stromal+signaling+microenvironments+in+the+thymus.">Zoned out: functional mapping of stromal signaling microenvironments in the thymus.</a> Annu. Rev. Immunol. 25, 649-679 (2007).</li><li>Rezzani, R., Bonomini, F., Rodella, L. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Histochemical+and+molecular+overview+of+the+thymus+as+site+for+T-cells+development.">Histochemical and molecular overview of the thymus as site for T-cells development.</a> Prog. Histochem. Cytochem. 43, 73-120 (2008).</li><li>Rodewald, H. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Thymus+organogenesis.">Thymus organogenesis.</a> Annu. Rev. 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Immunol. 163, 5781-5785 (1999).</li><li>Murata, 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=Regulation+of+CD8++T+cell+development+by+thymus-specific+proteasomes.">Regulation of CD8+ T cell development by thymus-specific proteasomes.</a> Science. 316, 1349-1353 (2007).</li><li>Chidgey, A. P., Pircher, H., MacDonald, H. R., Boyd, R. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=An+adult+thymic+stromal-cell+suspension+model+for+in+vitro+positive+selection.">An adult thymic stromal-cell suspension model for in vitro positive selection.</a> Dev. Immunol. 6, 157-170 (1998).</li><li>Izon, D. J., Nieland, J. D., Godfrey, D. I., Boyd, R. L., Kruisbeek, A. 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In the protocol, critical steps are the preparation of thymus stromal cells (Section 3) and the enrichment of TECs (Section 4). It is strongly recommended that fresh enzyme solution is prepared each time and the tissue is treated as soon as possible. For pooled thymi, optimizing the volume of enzyme solution is required depending upon the number of thymi. If any tissue residue is left after the processing, adding more enzyme solution and extension of incubation time could increase cell yield. During enrichment of TECs, c...

Early in T cell development, bone marrow hematopoietic stem cell-derived multipotent progenitors are recruited to the cortex of the thymus, undergo commitment to T lineage and become T cell precursors1. In the cortex, T cell precursor CD4 and CD8 double negative (DN) thymocytes expand and differentiate into immature CD4 and CD8 double positive (DP) thymocytes, forming a large pool of progenitors with highly variable T cell receptors1. Only a select MHC-restricted subset of DP cells will become CD4 or CD8 single positive (SP) thymocytes, migrate to the medulla of the thymus, and differentiate into functionally competent mature T cells, an event that is referred to as positive selection2-6. In contrast, clones of auto-reactive thymocytes undergo negative selection and are removed via apoptosis, converted to regulatory T cells for self-tolerance, or diverted to intraepithelial lymphocytes for purposes that are not yet clear3,7-10.
In the thymus, thymic stromal cells form a unique microenvironment providing signals for these various T cell development fates5,11,12. Thymic stromal cells are composed of thymic epithelial cells (TECs) - including cortical TECs (cTECs) and medullary TECs (mTECs), dendritic cells, macrophages, fibroblasts, endothelial cells, neural crest-derived pericytes and other mesenchymal cells13-15. Among these, TECs are crucial at the various stages of T cell development1,2,16,17. However, lack of a robust way to isolate TECs has hampered a comprehensive understanding of their functions16. In particular, cTECs, which form a three-dimensional network surrounding progenitors in the cortex, are essential for positive selection13,18,19 for reasons that are not yet clear. Earlier studies provided clues as to the heterogeneity and role of TECs, mostly relying on morphological and histological tools13. Recently the unique roles of TEC subsets were addressed by genetic approaches in mouse models12,20. A robust and reproducible way to isolate TECs is fundamental to achieve unbiased characterization of TEC subsets, quantitative and qualitative assessment of TEC functions, and clarification of mechanisms how cTECs support positive selection.
Due to the rarity of TECs in the thymus and the tight interactions they form in the intact organ, the isolation of TECs has been challenging. The protocol described here is based on previous discoveries, currently available reagents, techniques, and knowledge of thymus structure and stromal composition. Nearly two decades ago, several procedures were reported to disaggregate thymus tissues21-27, in which different enzymes were used during digestion, including Trypsin, Collagenase and Dispase. Gray et al. compared those enzymes in their precedure28, and reported an improved method with a multiple-step digestion of enzyme cocktails29 that became widely used20,30. However, this method involves a long preparation time and complex digestion steps and results in variable final cell numbers and proportions of TECs even in the same murine cohort29,30. Several years ago, Liberase research grade enzyme, containing highly purified Collagenase and neutral protease started to be used in thymus tissue dissociation30. Here, we describe a Liberase digestion-based protocol, with optimized mechanical separation procedures, that yields a high number of viable TECs from mouse thymus tissues.
To enrich dissociated stromal cells, previous studies have used either density gradients or magnetic bead separation21,29. However, both methods cause severe lost of certain populations of thymic stromal cells, particularly the population of cTECs29. Cytotoxic elimination and panning techniques31,32 have widely been used for depletion or separation of lymphocytes in the immunological field12,31. After comparison of these techniques, we established the current panning protocol for enrichment of TECs. The gentle condition during the enrichment procedure leads to less cell death and unbiased and increased TEC recovery.
The isolated thymus cell suspension described in Section 3 can be directly applied to flow cytometric analysis for identification and characterization of TEC subsets and dendritic cells. Section 4 describes a simple and useful way to identify TEC subsets using multiparameter flow cytometer. For experiments that seek to obtain purified cTECs or mTECs, TEC enrichment and cell sorting procedures can be found in Section 5 and 6.

<table border="0" cellpadding="0" cellspacing="0">
	<tbody>
		<tr height="20">
			<td height="20" style="height:20px;width:487px;">Anti-mouse EpCAM</td>
			<td style="width:153px;">eBioscience</td>
			<td style="width:133px;">XX-5791-YY*</td>
			<td style="width:163px;">Clone G8.8</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Anti-mouse MHC II</td>
			<td>eBioscience</td>
			<td>XX-5321-YY*</td>
			<td>Clone M5/114.15.2</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Anti-mouse Ly51</td>
			<td>eBioscience</td>
			<td>XX-5891-YY*</td>
			<td>Clone 6C3</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">UEA-1</td>
			<td>Vector Laboratory</td>
			<td>FL-1061</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Flow cytometer</td>
			<td>BD Biosciences&#160;</td>
			<td>LSRFortessa</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Flow cell sorter</td>
			<td>BD Biosciences&#160;</td>
			<td>FACSAria</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">FACS tubes</td>
			<td>BD Biosciences</td>
			<td>352052</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Flow cytometry analysis software</td>
			<td>TreeStar - Flowjo</td>
			<td>FlowJo v7/9</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">*XX varies by fluorochrome and YY varies by vial size.</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
	</tbody>
</table>

isolation, identification, and purification of murine thymic epithelial cells

The thymus is a vital organ for T lymphocyte development. Of thymic stromal cells, thymic epithelial cells (TECs) are particularly crucial at multiple stages of T cell development: T cell commitment, positive selection and negative selection. However, the function of TECs in the thymus remains incompletely understood. In the article, we provide a method to isolate TEC subsets from fresh mouse thymus using a combination of mechanical disruption and enzymatic digestion. The method allows thymic stromal cells and thymocytes to be efficiently released from cell-cell and cell-extracellular matrix connections and to form a single-cell suspension. Using the isolated cells, multiparameter flow cytometry can be applied to identification and characterization of TECs and dendritic cells. Because TECs are a rare cell population in the thymus, we also describe an effective way to enrich and purify TECs by depleting thymocytes, the most abundant cell type in the thymus. Following the enrichment, cell sorting time can be decreased so that loss of cell viability can be minimized during purification of TECs. Purified cells are suitable for various downstream analyses like Real Time-PCR, Western blot and gene expression profiling. The protocol will promote research of TEC function and as well as the development of in vitro T cell reconstitution.

Using this protocol, a thymus organ was removed from an adult mouse (Section 2) and a thymic cell suspension was prepared as outlined in Section 3. The obtained cell suspension consisted of thymocytes, hematopoietic-derived stromal cells and non-hematopoietic stromal cells. CD45 is a hematopoietic pan-marker expressed on both thymocytes and hematopoietic stromal cells such as macrophages and dendritic cells. In contrast, TECs are not of hematopoietic origin and do not express CD4515. Cell staining and flow cyt...

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Isolation, Identification, and Purification of Murine Thymic Epithelial Cells

Here we describe an efficient method for isolation, identification, and purification of mouse thymic epithelial cells (TECs). The protocol can be utilized for studies of thymus function for normal T cell development, thymus dysfunction, and T cell reconstitution.

The thymus is a vital organ for T lymphocyte development. Of thymic stromal cells, thymic epithelial cells (TECs) are particularly crucial at multiple ...

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31.5K Views.  University of Minnesota. Here we describe an efficient method for isolation, identification, and purification of mouse thymic epithelial cells (TECs). The protocol can be utilized for studies of thymus function for normal T cell development, thymus dysfunction, and T cell reconstitution.