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 thoracic cavity and damaging the tissue.</li>
	<li>Lift the skin at the base of the sternum with a pair of forceps and make a cut through the skin. Extend the cut of the skin upwards to each forelimb.</li>
	<li>Make an additional cut at the base of the sternum to separate the diaphragm from the rib cage. Then cut each side of the rib cage towards the clavicle. Flip the rib cage over towards the head exposing the thoracic cavity. The two lobes of the thymus lie on top of the heart.</li>
	<li>Remove the connective tissue around the thymic lobes using forceps, micro-dissection scissors, and/or sharp curved scissors. Use a pair of fine tip curved forceps to lift the individual lobes from underneath or via remaining connective tissue. 
	Note: Do not grasp the thymus directly.</li>
	<li>Place the thymic lobes in a 15 ml conical tube containing PBS and set aside on ice until needed.</li>
</ol>
2. Agarose Embedding and Vibratome Slicing of Thymic Lobes
<ol>
	<li>Prepare 4% agarose solution for embedding by dissolving 2 g low-melting point agarose in 50 ml sterile PBS and microwaving on a low setting until the agarose has completely dissolved. Cover flask with aluminum foil and place in a water bath at 55 &#176;C until ready for use.</li>
	<li>In a tissue culture hood, prepare complete RPMI-1640 media that contains 10% fetal bovine serum (FBS), 4 mM L glutamine, 1x penicillin/streptomycin, and 10 &#181;M 2-mercaptoethanol.</li>
	<li>Add 1.5 ml complete RPMI-1640 media per well to a 6-well cell culture plate and place a cell culture insert in each well. Set the plate aside in an incubator at 37 &#176;C until needed.</li>
	<li>Prepare a slushy ice water bath with water and ice in an ice bucket.</li>
	<li>Carefully remove all remaining connective tissue surrounding each thymic lobe using fine tip forceps. Do this while the thymic lobe is submerged in PBS in a tissue culture dish, after transfer onto a tissue wipe soaked with PBS, or under a dissecting microscope.</li>
	<li>Allow the agarose to cool below 40 &#176;C, when the flask is just warm to the touch, to avoid overheating the tissue. Pour the cooled 4% agarose into a tissue mold to a height of ~1 cm.</li>
	<li>Use a pair of forceps to carefully transfer the thymic lobe to a tissue wipe and roll it gently to dry it without damaging the tissue. Ensure that the tissue dries completely or it will slide out of the agarose during slicing.</li>
	<li>Carefully insert the lobe into the agarose and position it either horizontally (to increase surface area of each slice) or vertically (to increase number of slices) at the bottom of the mold. Place the mold in ice water for 5-10 min to allow the agarose to solidify.</li>
	<li>During this time, prepare the vibratome for slicing by mounting the buffer tray, assembling the specimen disc, and inserting the vibratome blade. Place a piece of laboratory tape on the specimen disc. Sterilize the clean, assembled workspace with 70% ethanol.</li>
	<li>Once the agarose solidifies, invert the mold and press gently at its center to release the agarose embedded lobe.</li>
	<li>Use a sharp blade to trim the excess agarose surrounding the lobe leaving ~2 mm of agarose on each side and ~0.5 cm at the bottom.</li>
	<li>Secure each agarose block with a drop of tissue glue to the piece of tape on the specimen disc. Multiple blocks can be glued on the tape.</li>
	<li>Align the vibratome blade with the top of the agarose block. Fill the buffer tray with sterile PBS until the blade and agarose block(s) are fully immersed.</li>
	<li>Section the agarose embedded tissue to obtain slices with a thickness of 400-500 &#181;m. Set the vibratome to 0.225 mm/sec speed, 100 Hz frequency, and 5&#176; angle.</li>
	<li>Use a bent spatula to collect the thymic slices into a tissue culture plate containing sterile PBS as they are cut. Discard the first and last slice.</li>
	<li>Examine the slices under a light microscope at 4X magnification. Choose the slices with intact thymic tissue and surrounding agarose (Figure 1A).</li>
	<li>Transfer the slices to the plate prepared in step 2.3 by using a pipette tip to gently slide the thymic slice from the bent spatula onto the cell culture insert. Each insert can accommodate ~3 slices. Make sure the slices do not touch each other or the cell culture insert walls.</li>
	<li>Maintain the plate at 37 &#176;C until needed.</li>
</ol>
3. Preparation of Thymocytes for Overlaying
<ol>
	<li>Isolate thymic lobes as described in section 1. Dissociate the lobes manually to make a single cell suspension using a sterilized 15 ml tissue grinder filled with 5 ml of sterile PBS containing 2% FBS. Transfer the cells to a 15 ml conical tube.</li>
	<li>Centrifuge the cells at 545 x g for 5 min at 4 &#176;C. Discard the supernatant and resuspend the cells in 1 ml of 1x ACK lysis buffer (0.15 M NH4Cl, 10 mM KHCO3, 0.1 mM Na2EDTA) at room temperature for 3 min to lyse red blood cells.</li>
	<li>Fill the tube to 15 ml with PBS containing 2% FBS. Centrifuge the cells at 545 x g for 5 min at 4 &#176;C.</li>
	<li>Resuspend the cells in 10 ml of PBS containing 2% FBS and pass cells through a 255 &#181;m mesh filter.</li>
	<li>Count cells using a hemocytometer. Centrifuge the cells at 545 x g for 5 min at 4 &#176;C, and resuspend the cell pellet in PBS containing 2% FBS at a concentration of 1 x 107 cells per ml.</li>
	<li>Label the cells with cellular dyes such as carboxyfluorescein succinimidyl ester (CFSE) according to manufacturer protocols if not using thymocytes from mice expressing congenic markers or genetically encoded fluorescent reporters to distinguish from slice endogenous cells.</li>
	<li>After the final wash of the labeled cells, resuspend the cell pellet in complete RPMI-1640 media at 1-3 x 106 cells per 15 &#181;l.</li>
</ol>
4. Overlaying Thymocytes onto the Thymic Slices
<ol>
	<li>Use a pipette to aspirate any liquid&#160;surrounding the thymic slices on the insert. 
	Note: Take care to avoid damaging the agarose. If the agarose is damaged, the overlaid thymocytes will not attach to the slice surface due to loss of surface tension.</li>
	<li>Without touching the slice with the pipette tip, overlay 15 &#181;l of thymocytes prepared in section 3 onto each thymic slice.</li>
	<li>Incubate the plate at 37 &#176;C for 2 hr to allow the cells to migrate into the thymic slices.</li>
	<li>After 2 hr, rinse the thymic slices 3 times with 1 ml PBS to remove excess overlaid thymocytes that have not yet migrated into the tissue.</li>
	<li>Incubate the plate at 37 &#176;C until the thymic slices are ready to be harvested, typically 1-72 hr depending on the experiment.</li>
</ol>
5. Dissociation of Thymic Slices for Flow Cytometry
<ol>
	<li>Prepare a microcentrifuge tube for each slice by adding 150 &#181;l of PBS containing 2% FBS.</li>
	<li>Add 1 ml of PBS containing 2% FBS to the tissue culture insert with the thymic slices and gently stir with a bent spatula to detach the slices from the surface of the cell culture insert.</li>
	<li>Transfer the slice from the insert to the microcentrifuge tube using a bent spatula.</li>
	<li>Manually disrupt the slice using a microcentrifuge tube sample pestle. Add 150 &#181;l of PBS containing 2% FBS to a final volume 300 &#181;l.</li>
	<li>Filter the dissociated tissue through a 40 &#181;m filter into a new microcentrifuge tube. The filtered cells are ready to be stained for flow cytometric analysis40.</li>
	<li>Filter cells a second time before passing them on a flow cytometer to ensure that all the agarose is removed and does not clog the flow cytometer.</li>
	<li>Acquire the cells on a flow cytometer and analyze data as has been previously described40.</li>
</ol>

The authors declare that they have no competing financial interests.

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.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Vibratome</td>
			<td>Leica Biosystems</td>
			<td>VT1000S&#160;</td>
			<td></td>
		</tr>
		<tr>
			<td>NuSieve GTG Agarose</td>
			<td>Lonza</td>
			<td>50080</td>
			<td>Low melting temperature agarose</td>
		</tr>
		<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>
		</tr>
		<tr>
			<td>Tissue Adhesive</td>
			<td>3M&#160;</td>
			<td>1469SB</td>
			<td></td>
		</tr>
		<tr>
			<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>
		<tr>
			<td>RPMI-1640 with L-glutamine</td>
			<td>Wisent</td>
			<td>350-000-CL</td>
			<td></td>
		</tr>
		<tr>
			<td>Fetal Bovine Serum</td>
			<td>Wisent</td>
			<td>080-110</td>
			<td>Heat inactivated</td>
		</tr>
		<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 ...

preparation-and-applications-of-organotypic-thymic-slice-cultures

Research

JoVE Journal

Immunology and Infection

8.0K Views.  Hôpital Maisonneuve-Rosemont. 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.

Video: Preparation and Applications of Organotypic Thymic Slice Cultures

Derivation of Thymic Lymphoma T-cell Lines from Atm-/- and p53-/- Mice

Established cell lines are a critical research tool that can reduce the use of laboratory animals in research. Certain strains of genetically modified mice, such as Atm-/- and p53-/- consistently develop thymic lymphoma early in life 1,2, and thus, can serve as a reliable source for derivation of murine T-cell lines. Here we present a detailed protocol for the development of established murine thymic lymphoma T-cell lines without the need to add interleukins as described in previous protocols 1,3. Tumors were harvested from mice aged three to six months, at the earliest indication of visible tumors based on the observation of hunched posture, labored breathing, poor grooming and wasting in a susceptible strain 1,4. We have successfully established several T-cell lines using this protocol and inbred strains ofAtm-/- [FVB/N-Atmtm1Led/J] 2 and p53-/- [129/S6-Trp53tm1Tyj/J] 5 mice. We further demonstrate that more than 90% of the established T-cell population expresses CD3, CD4 and CD8. Consistent with stably established cell lines, the T-cells generated by using the present protocol have been passaged for over a year.

Derivation of Thymic Lymphoma T-cell Lines from Atm-/- and p53-/- Mice

In this video we demonstrate a protocol to establish mouse thymic lymphoma cell lines. By following this protocol, we have successfully established several T-cell lines from Atm-/- and p53-/- mice with thymic lymphoma.

Established cell lines are a critical research tool that can reduce the use of laboratory animals in research. Certain strains of genetically modified ...

Rapid Diagnosis of Avian Influenza Virus in Wild Birds: Use of a Portable rRT-PCR and Freeze-dried Reagents in the Field

Wild birds have been implicated in the spread of highly pathogenic avian influenza (HPAI) of the H5N1 subtype, prompting surveillance along migratory flyways. Sampling of wild birds for avian influenza virus (AIV) is often conducted in remote regions, but results are often delayed because of the need to transport samples to a laboratory equipped for molecular testing. Real-time reverse transcriptase polymerase chain reaction (rRT-PCR) is a molecular technique that offers one of the most accurate and sensitive methods for diagnosis of AIV. The previously strict lab protocols needed for rRT-PCR are now being adapted for the field. Development of freeze-dried (lyophilized) reagents that do not require cold chain, with sensitivity at the level of wet reagents has brought on-site remote testing to a practical goal.
Here we present a method for the rapid diagnosis of AIV in wild birds using an rRT-PCR unit (Ruggedized Advanced Pathogen Identification Device or RAPID, Idaho Technologies, Salt Lake City, UT) that employs lyophilized reagents (Influenza A Target 1 Taqman; ASAY-ASY-0109, Idaho Technologies). The reagents contain all of the necessary components for testing at appropriate concentrations in a single tube: primers, probes, enzymes, buffers and internal positive controls, eliminating errors associated with improper storage or handling of wet reagents. The portable unit performs a screen for Influenza A by targeting the matrix gene and yields results in 2-3 hours. Genetic subtyping is also possible with H5 and H7 primer sets that target the hemagglutinin gene.
The system is suitable for use on cloacal and oropharyngeal samples collected from wild birds, as demonstrated here on the migratory shorebird species, the western sandpiper (Calidrus mauri) captured in Northern California. Animal handling followed protocols approved by the Animal Care and Use Committee of the U.S. Geological Survey Western Ecological Research Center and permits of the U.S. Geological Survey Bird Banding Laboratory. The primary advantage of this technique is to expedite diagnosis of wild birds, increasing the chances of containing an outbreak in a remote location. On-site diagnosis would also prove useful for identifying and studying infected individuals in wild populations. The opportunity to collect information on host biology (immunological and physiological response to infection) and spatial ecology (migratory performance of infected birds) will provide insights into the extent to which wild birds can act as vectors for AIV over long distances.

This study describes diagnosis of avian influenza in wild birds using a portable rRT-PCR system. The method takes advantage of freeze-dried reagents to screen wild birds in a non-laboratory setting, typical of an outbreak scenario. Use of molecular tools provides accurate and sensitive alternatives for rapid diagnosis.

Wild birds have been implicated in the spread of highly pathogenic avian influenza (HPAI) of the H5N1 subtype, prompting surveillance along migratory ...

Preparation of Viral DNA from Nucleocapsids

Viruses are obligate cellular parasites, and thus the study of their DNA requires isolating viral material away from host cell contaminants and DNA. Several downstream applications require large quantities of pure viral DNA, which is provided by this protocol. These applications include viral genome sequencing, where the removal of host DNA is crucial to optimize data output for viral sequences, and the production of new viral recombinant strains, where co-transfection of purified plasmid and linear viral DNA facilitates recombination.1,2,3 
This procedure utilizes a combination of extractions and density-based centrifugation to isolate purified linear herpesvirus nucleocapsid DNA from infected cells.4,5 The initial purification steps aim to isolate purified viral capsids, which contain and protect the viral DNA during the extractions and centrifugation steps that remove cellular proteins and DNA. Lysis of nucleocapsids then releases viral DNA, and two final phenol-chloroform steps remove remaining proteins. The final DNA captured from solution is highly concentrated and pure, with an average OD260/280 of 1.90. Depending on the quantity of infected cells used, yields of viral DNA range from 150-800 &mu;g or more. The purity of this DNA makes it stable during long-term storage at 4C. This DNA is thus ideally suited for high-throughput sequencing, high fidelity PCR reactions, and transfections. 
Prior to beginning the protocol, it is important to know the average number of cells per dish (e.g. an average of 8 x 106 PK-15 cells in a confluent 15 cm dish), and the titer of the viral stock to be used (e.g. 1 x 108 plaque-forming units per ml). These are necessary to calculate the appropriate multiplicity of infection (MOI) for the protocol.6 For instance, to infect one 15 cm dish of PK-15 cells with the above viral stock, at an MOI of 5, you would use 400 &mu;l of viral stock and dilute it with 3.6 ml of medium (total inoculation volume of 4 ml for one 15 cm plate).
Multiple viral DNA preparations can be prepared at the same time. The number of simultaneous preparations is limited only by the number of tubes held by the ultracentrifuge rotor (one per virus; see step 3.9 below). Here we describe the procedure as though being done for one virus.

We describe the process of isolating high purity herpesvirus nucleocapsid DNA from infected cells. The final DNA captured from solution is of high concentration and purity, making it ideally suited for high-throughput sequencing, high fidelity PCR reactions, and transfections to produce new viral recombinants.

Viruses are obligate cellular parasites, and thus the study of their DNA requires isolating viral material away from host cell contaminants and DNA. ...

Generation of Organotypic Raft Cultures from Primary Human Keratinocytes

The development of organotypic epithelial raft cultures has provided researchers with an efficient in vitro system that faithfully recapitulates epithelial differentiation. There are many uses for this system. For instance, the ability to grow three-dimensional organotypic raft cultures of keratinocytes has been an important milestone in the study of human papillomavirus (HPV)1. The life cycle of HPV is tightly linked to the differentiation of squamous epithelium2. Organotypic epithelial raft cultures as demonstrated here reproduce the entire papillomavirus life cycle, including virus production3,4,5. In addition, these raft cultures exhibit dysplastic lesions similar to those observed upon in vivo infection with HPV. Hence this system can also be used to study epithelial cell cancers, as well as the effect of drugs on epithelial cell differentiation in general. Originally developed by Asselineau and Prunieras6 and modified by Kopan et al.7, the organotypic epithelial raft culture system has matured into a general, relatively easy culture model, which involves the growth of cells on collagen plugs maintained at an air-liquid interface (Figure 1A). Over the course of 10-14 days, the cells stratify and differentiate, forming a full thickness epithelium that produces differentiation-specific cytokeratins. Harvested rafts can be examined histologically, as well as by standard molecular and biochemical techniques. In this article, we describe a method for the generation of raft cultures from primary human keratinocytes. The same technique can be used with established epithelial cell lines, and can easily be adapted for use with epithelial tissue from normal or diseased biopsies8. Many viruses target either the cutaneous or mucosal epithelium as part of their replicative life cycle. Over the past several years, the feasibility of using organotypic raft cultures as a method of studying virus-host cell interactions has been shown for several herpesviruses, as well as adenoviruses, parvoviruses, and poxviruses9. Organotypic raft cultures can thus be adapted to examine viral pathogenesis, and are the only means to test novel antiviral agents for those viruses that are not cultivable in permanent cell lines.

An in vitro method to mimic in vivo epithelial differentiation is described. Many viruses target epithelial cells as part of their viral life cycle, and this method provides a means of examining virus:host interactions that more closely resembles that which occurs in vivo. This technique can be used with primary keratinocytes, established cell lines, as well as normal or diseased biopsy tissue.

The development of organotypic epithelial raft cultures has provided researchers with an efficient in vitro system that faithfully recapitulates ...

Examination of Thymic Positive and Negative Selection by Flow Cytometry

A healthy immune system requires that T cells respond to foreign antigens while remaining tolerant to self-antigens. Random rearrangement of the T cell receptor (TCR) &alpha; and &beta; loci generates a T cell repertoire with vast diversity in antigen specificity, both to self and foreign. Selection of the repertoire during development in the thymus is critical for generating safe and useful T cells. Defects in thymic selection contribute to the development of autoimmune and immunodeficiency disorders1-4. 
T cell progenitors enter the thymus as double negative (DN) thymocytes that do not express CD4 or CD8 co-receptors. Expression of the &alpha;&beta;TCR and both co-receptors occurs at the double positive (DP) stage. Interaction of the &alpha;&beta;TCR with self-peptide-MHC (pMHC) presented by thymic cells determines the fate of the DP thymocyte. High affinity interactions lead to negative selection and elimination of self-reactive thymocytes. Low affinity interactions result in positive selection and development of CD4 or CD8 single positive (SP) T cells capable of recognizing foreign antigens presented by self-MHC5.
Positive selection can be studied in mice with a polyclonal (wildtype) TCR repertoire by observing the generation of mature T cells. However, they are not ideal for the study of negative selection, which involves deletion of small antigen-specific populations. Many model systems have been used to study negative selection but vary in their ability to recapitulate physiological events6. For example, in vitro stimulation of thymocytes lacks the thymic environment that is intimately involved in selection, while administration of exogenous antigen can lead to non-specific deletion of thymocytes7-9. Currently, the best tools for studying in vivo negative selection are mice that express a transgenic TCR specific for endogenous self-antigen. However, many classical TCR transgenic models are characterized by premature expression of the transgenic TCR&alpha; chain at the DN stage, resulting in premature negative selection. Our lab has developed the HYcd4 model, in which the transgenic HY TCR&alpha; is conditionally expressed at the DP stage, allowing negative selection to occur during the DP to SP transition as occurs in wildtype mice10.
Here, we describe a flow cytometry-based protocol to examine thymic positive and negative selection in the HYcd4 mouse model. While negative selection in HYcd4 mice is highly physiological, these methods can also be applied to other TCR transgenic models. We will also present general strategies for analyzing positive selection in a polyclonal repertoire applicable to any genetically manipulated mice.

We present a flow cytometry-based method to examine T cell development in vivo using genetically manipulated mice on a wildtype or T cell receptor transgenic background.

A healthy immune system requires that T cells respond to foreign  antigens while remaining tolerant to self-antigens. Random rearrangement of the  T cell ...

Preparation of Tumor Antigen-loaded Mature Dendritic Cells for Immunotherapy

While clinical studies have established that antigen-loaded DC vaccines are safe and promising therapy for tumors 1, their clinical efficacy remains to be established. The method described below, prepared in accordance with Good Manufacturing Process (GMP) guidelines, is an optimization of the most common ex vivo preparation method for generating large numbers of DCs for clinical studies 2.
Our method utilizes the synthetic TLR 3 agonist Polyinosinic-Polycytidylic Acid-poly-L-lysine Carboxymethylcellulose (Poly-ICLC) to stimulate the DCs. Our previous study established that Poly-ICLC is the most potent individual maturation stimulus for human DCs as assessed by an upregulation of CD83 and CD86, induction of interleukin-12 (IL-12), tumor necrosis factor (TNF), interferon gamma-induced protein 10 (IP-10), interleukmin 1 (IL-1), and type I interferons (IFN), and minimal interleukin 10 (IL-10) production.
DCs are differentiated from frozen peripheral blood mononuclear cells (PBMCs) obtained by leukapheresis. PBMCs are isolated by Ficoll gradient centrifugation and frozen in aliquots. On Day 1, PBMCs are thawed and plated onto tissue culture flasks to select for monocytes which adhere to the plastic surface after 1-2 hr incubation at 37 &deg;C in the tissue culture incubator. After incubation, the lymphocytes are washed off and the adherent monocytes are cultured for 5 days in the presence of interleukin-4 (IL-4) and granulocyte macrophage-colony stimulating factor (GM-CSF) to differentiate to immature DCs. On Day 6, immature DCs are pulsed with the keyhole limpet hemocyanin (KLH) protein which serves as a control for the quality of the vaccine and may boost the immunogenicity of the vaccine 3. The DCs are stimulated to mature, loaded with peptide antigens, and incubated overnight. On Day 7, the cells are washed, and frozen in 1 ml aliquots containing 4 - 20 x 106 cells using a controlled-rate freezer. Lot release testing for the batches of DCs is performed and must meet minimum specifications before they are injected into patients.

The most commonly used method for generating large numbers of autologous dendritic cells (DCs) for use in tumor immunotherapy is described. The method uses IL-4 and GM-CSF to differentiate DCs from monocytes. The immature DCs are stimulated to mature and then loaded with antigens before they are injected back into the patient.

While clinical studies have established that antigen-loaded DC vaccines are safe and promising therapy for tumors 1, their clinical efficacy remains to be ...

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.

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 ...

Isolation and Transplantation of Different Aged Murine Thymic Grafts.

The mechanisms that regulate the efficacy of thymic selection remain ill-defined. The method presented here allows in vivo analyses of the development and selection of T cells specific for self and foreign antigens. The approach entails implantation of thymic grafts derived from various aged mice into immunodeficient scid recipients. Over a relatively short period of time the recipients are fully reconstituted with T cells derived from the implanted thymus graft. Only thymocytes seeding the thymus at the time of isolation undergo selection and develop into mature T cells. As such, changes in the nature and specificity of the engrafted T cells as a function of age-dependent thymic events can be assessed. Although technical expertise is required for successful thymic transplantation, this method provides a unique strategy to study in vivo a wide range of pathologies that are due to or a result of aberrant thymic function and/or homeostasis.

This report provides a detailed description of transplanting murine thymi from different aged donor mice under the kidney capsule of immunodeficient mouse recipients. The goal of this approach is to model T cell development and thymic selection events in vivo.

The mechanisms that regulate the efficacy of thymic selection remain ill-defined. The method presented here allows in vivo analyses of the development and ...

Automated Cell Enrichment of Cytomegalovirus-specific T cells for Clinical Applications using the Cytokine-capture System

The adoptive transfer of pathogen-specific T cells can be used to prevent and treat opportunistic infections such as cytomegalovirus (CMV) infection occurring after allogeneic hematopoietic stem-cell transplantation. Viral-specific T cells from allogeneic donors, including third party donors, can be propagated ex vivo in compliance with current good manufacturing practice (cGMP), employing repeated rounds of antigen-driven stimulation to selectively propagate desired T cells. The identification and isolation of antigen-specific T cells can also be undertaken based upon the cytokine capture system of T cells that have been activated to secrete gamma-interferon (IFN-&#947;). However, widespread human application of the cytokine capture system (CCS) to help restore immunity has been limited as the production process is time-consuming and requires a skilled operator. The development of a second-generation cell enrichment device such as CliniMACS Prodigy now enables investigators to generate viral-specific T cells using an automated, less labor-intensive system. This device separates magnetically labeled cells from unlabeled cells using magnetic activated cell sorting technology to generate clinical-grade products, is engineered as a closed system and can be accessed and operated on the benchtop. We demonstrate the operation of this new automated cell enrichment device to manufacture CMV pp65-specific T cells obtained from a steady-state apheresis product obtained from a CMV seropositive donor. These isolated T cells can then be directly infused into a patient under institutional and federal regulatory supervision. All the bio-processing steps including removal of red blood cells, stimulation of T cells, separation of antigen-specific T cells, purification, and washing are fully automated. Devices such as this raise the possibility that T cells for human application can be manufactured outside of dedicated good manufacturing practice (GMP) facilities and instead be produced in blood banking facilities where staff can supervise automated protocols to produce multiple products.

The goal of this protocol is to manufacture pathogen-specific clinical-grade T cells using a bench-top, automated, second generation cell enrichment device that incorporates a closed cytokine capture system and does not require dedicated staff or use of a GMP facility. The cytomegalovirus pp65-specific-T cells generated can be directly administered to patients.

The adoptive transfer of pathogen-specific T cells can be used to prevent and treat opportunistic infections such as cytomegalovirus (CMV) infection ...

Promoting 3-D Aggregation of FACS Purified Thymic Epithelial Cells with EAK 16-II/EAKIIH6 Self-assembling Hydrogel

Thymus involution, associated with aging or pathological insults, results in diminished output of mature T-cells. Restoring the function of a failing thymus is crucial to maintain effective T cell-mediated acquired immune response against invading pathogens. However, thymus regeneration and revitalization proved to be challenging, largely due to the difficulties of reproducing the unique 3D microenvironment of the thymic stroma that is critical for the survival and function of thymic epithelial cells (TECs). We developed a novel hydrogel system to promote the formation of TEC aggregates, based on the self-assembling property of the amphiphilic EAK16-II oligopeptides and its histidinylated analogue EAKIIH6. TECs were enriched from isolated thymic cells with density-gradient, sorted with fluorescence-activated cell sorting (FACS), and labeled with anti-epithelial cell adhesion molecule (EpCAM) antibodies that were anchored, together with anti-His IgGs, on the protein A/G adaptor complexes. Formation of cell aggregates was promoted by incubating TECs with EAKIIH6 and EAK16-II oligopeptides, and then by increasing the ionic concentration of the medium to initiate gelation. TEC aggregates embedded in EAK hydrogel can effectively promote the development of functional T cells in vivo when transplanted into the athymic nude mice.

This video demonstrates a protocol to enrich thymic epithelial cells (TECs) with density gradient for FACS isolation. It also shows the use of EAK16-II/EAKIIH6 peptides to promote the TEC aggregate formation. The microenvironments of EAK16-II/EAKIIH6 hydrogel provide the 3-D configuration necessary to maintain the survival and function of the TECs.

Thymus involution, associated with aging or pathological insults, results in diminished output of mature T-cells. Restoring the function of a failing ...