We would like to thank Marilaine Fournier for her comments on the manuscript and Jos&#233;e Tessier for technical assistance. C57BL/6-Tg (OT-I)-RAG1&lt;tmMom&gt; #4175 were obtained through the NIAID Exchange Program, NIH. Support for this research is provided by a grant from the SickKids Foundation and CIHR-IHDCYN (NI15-002), an operating grant from the CIHR-III (MOP-142254), and start-up funds from the FRQS (&#201;tablissement de jeunes chercheurs) and H&#244;pital Maisonneuve-Rosemont Foundation to HJM. HJM is a junior 1 scholar of the FRQS, a CIHR New Investigator (MSH-141967), and a Cole Foundation Early Career Transition award recipient.

Protocols for all animal studies were approved by the Animal Care Committee at the Centre de recherche - H&#244;pital Maisonneuve-Rosemont.
1. Harvesting Mouse Thymus for Preparation of Thymic Slices and Single Cell Suspensions
<ol>
	<li>Euthanize the mouse with CO2 followed by cervical dislocation.</li>
	<li>In a laminar flow hood, pin the mouse ventral side up to a dissection board. Spray the mouse with 70% ethanol. Remove any excess alcohol by dabbing with gauze to prevent ethanol from entering the...

Here we describe a protocol for the preparation of thymic slices and representative results of efficient positive and negative selection of overlaid pre-selection MHC class I-restricted TCR transgenic thymocytes by flow cytometry. This system has been used with similar success to support positive selection of MHC class II-restricted CD4+ T cells from pre-selection DP thymocytes32, and, in the presence of agonist antigen, negative selection and thymic Treg development11,12,36,38,39,43...

T cells differentiate through a series of developmental intermediates in the thymus during which time they encounter several checkpoints that ensure the generation of a functional, self-tolerant T cell repertoire1-3. Positive selection promotes the survival of thymocytes with T cell receptors (TCR) capable of recognizing, with low to moderate affinity, peptide presented by major histocompatibility complex molecules (MHC) on cortical thymic epithelial cells (cTEC)2,3. Negative selection and regulatory T (Treg) cell development contribute to the establishment of self-tolerance via the elimination or diversion of thymocytes that respond strongly to self-peptide presented by MHC2,4. Immature CD4+CD8+ double positive (DP) thymocytes expressing TCRs that pass the selection process differentiate into mature T cell subpopulations, the majority of which are MHC class I-restricted CD8+ cytotoxic or MHC class II-restricted CD4+ helper single positive (SP) T cells, before exiting the thymus to perform effector functions in the secondary lymphoid organs1-3.

Adding to the complexity of T cell development is the dynamic migration and cellular encounters of developing thymocytes throughout the stromal cell network5-9. These stromal cells play distinct roles in thymocyte development and are differentially distributed between the thymic cortical and medullary regions where positive and negative selection occur10. Although positive selection takes place primarily in the cortex, there is accumulating evidence that DP thymocytes migrate to the medulla and continue to require TCR signals before they differentiate into mature T cells suggesting that the medulla may provide additional signals necessary for completion of positive selection and lineage differentiation11,12. Further, despite the presence of specialized medullary thymic epithelial cells (mTEC) that express and present tissue-restricted antigens facilitating deletion of autoreactive thymocytes13,14, a large proportion of negative selection occurs in the cortex in response to ubiquitously expressed self-peptide presented by dendritic cells15,16. Thus, accurate models of T cell development must provide a highly organized thymic microenvironment, with intact cortical and medullary regions, that facilitates interaction between thymocytes and stromal cells, and supports thymocyte migration as these cells undergo positive and negative selection.

To complement ex vivo analyses of thymocytes as a means of studying positive and negative selection, a number of in vitro, in situ, and in vivo models of T cell development have been developed17-22. It has been notoriously difficult to recapitulate positive selection in vitro, but coculture of stem cell populations or T cell precursors with stromal cells expressing Notch ligand, notably OP9-DL1/4 cells, has the capability to support T lineage commitment and limited positive selection making it an invaluable in vitro model to study T cell development23-25. Limitations of this system, however, include the fact that these cells lack the unique peptide processing machinery found in thymic stromal cells and the three-dimensional thymic microenvironment.

Though more technically cumbersome, in situ and in vivo models of thymic selection can overcome some of the barriers related to in vitro systems. Reaggregate thymic organ cultures (RTOC) contain defined mixtures of thymocytes and thymic stromal cells18,26,27. These thymic epithelial cell reaggregates maintain MHC class I and II expression and can support development of both conventional T cell subsets, yet still lack defined cortical and medullary structures. Fetal thymic organ culture (FTOC) is a popular model of T cell development that can be seeded with thymocytes via hanging-drop culture of lymphodepleted thymic lobes or via injection of thymocytes into lymphoreplete thymic lobes and support efficient development of CD4+ and CD8+ T cells over time in culture18,28-31. At the initiation of culture of fetal thymic lobes there is a paucity of mTECs, but defined cortical and medullary structures may develop over time depending on conditions. An important consideration is that this model may preferentially support fetal versus adult T cell development. Finally, intrathymic injection of defined thymic precursors in adult mice is technically challenging but clearly provides an environment to support T cell development in vivo. These in situ and in vivo models are excellent tools to study T cell development and their use should be considered on an experiment-by-experiment basis.

Thymic slices, however, have recently emerged as a versatile, complementary model to study thymic selection in situ with the possibility to accommodate unique, complex, and generally higher throughput experiments. Thymic slices maintain the integrity of the cortical and medullary regions and provide a framework of stromal cells that supports thymocyte migration during development as well as efficient positive and negative selection11,32-39. Thymocyte subsets added atop thymic slices migrate into the tissue and to their appropriate microenvironmental niche34,37. The overlaid thymocytes can be distinguished from thymic slice endogenous cells via congenic markers or fluorescent labels and can be maintained in culture for several days. Thymic slice organotypic cultures can be used to study various aspects of T cell development including thymic selection, thymocyte behavior (migration and cellular interactions), and thymocyte localization, among others. Given the ability to generate ~20 thymic slices per mouse, the scalability of experiments is generally greater than other in situ models of thymic selection. Although the preparation of thymic slices requires specialized equipment, such as the vibratome, and the life time of thymic slices in culture is limited owing to loss of cells over time via cell death and the lack of an encapsulating membrane, thymic slices provide an excellent model for analysis of thymic selection of synchronized populations of thymocytes within a mature thymic microenvironment. Here we describe the preparation of thymic slices (including harvesting the thymus, agarose embedding of thymus lobes and vibratome sectioning of the embedded tissue), isolation and overlaying of thymocytes, and dissociation of thymic slices for flow cytometric analysis.

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			<td>Vibratome</td>
			<td>Leica Biosystems</td>
			<td>VT1000S&#160;</td>
			<td></td>
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			<td>NuSieve GTG Agarose</td>
			<td>Lonza</td>
			<td>50080</td>
			<td>Low melting temperature agarose</td>
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		<tr>
			<td>Embedding Mold (Truncated - T12)</td>
			<td>Polyciences</td>
			<td>18986</td>
			<td>22mm x 22mm square, truncated to 12mm x 12mm</td>
		</tr>
		<tr>
			<td>Double Edge Prep Blades</td>
			<td>Personna</td>
			<td>74-0002</td>
			<td></td>
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		<tr>
			<td>Tissue Adhesive</td>
			<td>3M&#160;</td>
			<td>1469SB</td>
			<td></td>
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			<td>0.4 &#181;m Cell Culture Inserts&#160;</td>
			<td>BD Falcon</td>
			<td>353090</td>
			<td>Of several brands tested, these maintained the cells atop the slices the best</td>
		</tr>
		<tr>
			<td>Dulbecco&#39;s Phosphate-Buffered Saline</td>
			<td>ThermoFisher</td>
			<td>21600-010</td>
			<td></td>
		</tr>
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			<td>RPMI-1640 with L-glutamine</td>
			<td>Wisent</td>
			<td>350-000-CL</td>
			<td></td>
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			<td>Fetal Bovine Serum</td>
			<td>Wisent</td>
			<td>080-110</td>
			<td>Heat inactivated</td>
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		<tr>
			<td>L-Glutamine, 200mM</td>
			<td>Wisent</td>
			<td>609-065-EL</td>
			<td></td>
		</tr>
		<tr>
			<td>Penicillin/Streptomycin, 100X</td>
			<td>Wisent</td>
			<td>450-201-EL</td>
			<td></td>
		</tr>
		<tr>
			<td>2-Mercaptoethanol</td>
			<td>Alfa Aesar</td>
			<td>A15890</td>
			<td></td>
		</tr>
		<tr>
			<td>15 ml Tenbroeck Tissue Grinders</td>
			<td>Wheaton</td>
			<td>357426</td>
			<td></td>
		</tr>
		<tr>
			<td>Nylon Mesh Filter</td>
			<td>Component Supply</td>
			<td>U-CMN-255</td>
			<td></td>
		</tr>
		<tr>
			<td>Microcentrifuge Tube Sample Pestle</td>
			<td>Bel-Art</td>
			<td>F19922-0000</td>
			<td></td>
		</tr>
		<tr>
			<td>40 &#181;m Nylon Cell Strainer</td>
			<td>BD Falcon</td>
			<td>352340</td>
			<td></td>
		</tr>
		<tr>
			<td>Forceps Inox Tip</td>
			<td>Dumont&#160;</td>
			<td>RS-5047</td>
			<td>Fine tip curved forceps, size .17&#160;X .10mm&#160;</td>
		</tr>
		<tr>
			<td>Micro Forceps</td>
			<td>Dumont&#160;</td>
			<td>RS-5090&#160;</td>
			<td></td>
		</tr>
	</tbody>
</table>

preparation and applications of organotypic thymic slice cultures

Thymic selection proceeds in a unique and highly organized thymic microenvironment resulting in the generation of a functional, self-tolerant T cell repertoire. In vitro models to study T lineage commitment and development have provided valuable insights into this process. However, these systems lack the complete three-dimensional thymic milieu necessary for T cell development and, therefore, are incomplete approximations of in vivo thymic selection. Some of the challenges related to modeling T cell development can be overcome by using in situ models that provide an intact thymic microenvironment that fully supports thymic selection of developing T cells. Thymic slice organotypic cultures complement existing in situ techniques. Thymic slices preserve the integrity of the thymic cortical and medullary regions and provide a platform to study development of overlaid thymocytes of a defined developmental stage or of endogenous T cells within a mature thymic microenvironment. Given the ability to generate ~20 slices per mouse, thymic slices present a unique advantage in terms of scalability for high throughput experiments. Further, the relative ease in generating thymic slices and potential to overlay different thymic subsets or other cell populations from diverse genetic backgrounds enhances the versatility of this method. Here we describe a protocol for the preparation of thymic slices, isolation and overlay of thymocytes, and dissociation of thymic slices for flow cytometric analysis. This system can also be adapted to study non-conventional T cell development as well as visualize thymocyte migration, thymocyte-stromal cell interactions, and TCR signals associated with thymic selection by two-photon microscopy.

Thymic slices support analysis of different aspects of T cell development such as positive and negative selection. For successful experiments, the quality of the thymic slice is paramount. Thus, thymic slices should be examined to ensure the integrity of the thymic tissue and that the agarose surrounding the thymic slice is intact (Figure 1A). Surface tension can be compromised when the agarose is damaged causing a significant decrease in the number of th...

Watch this Scientific Journal Video about Preparation and Applications of Organotypic Thymic Slice Cultures at JoVE.com

Preparation and Applications of Organotypic Thymic Slice Cultures

We describe the preparation of thymic slices that, in combination with flow cytometry, can be used to model positive and negative selection of developing T cells. Thymic slices can also be adapted for the in situ analysis of thymocyte migration, localization, and signaling via immunofluorescence and two-photon microscopy.

Thymic selection proceeds in a unique and highly organized thymic microenvironment resulting in the generation of a functional, self-tolerant T cell ...