This work was supported in part by the National Institutes of Health grants R21 AI113000 (W.S.M) and R01 AI123392 (Y.F.).

All the animals used in the experiments were housed in the animal facility at Allegheny-Singer Research Institute under the protocol reviewed and approved by the Institutional Animal Care and Use Committee of the Allegheny Health Network/Allegheny Singer Research Institute.
1. Digesting the Thymus with Collagenase
<ol>
	<li>Harvest thymus glands.
	<ol>
		<li>Euthanize 3-5 week-old C57BL6/J mice in a carbon dioxide (CO2) chamber to harvest thymus glands. In detail, place the mice in the chamber under CO2 induction for 3-5 min and confirm death by verifying cardiac or respiratory arrest.</li>
		<li>Lay the carcass on its back and wet the body with 70% ethanol. Make a small horizontal incision with a sharp, straight dissecting scissors on its abdomen through the skin. Pull the skin on both ends (head and legs) so that it is turned inside out.</li>
		<li>Make a horizontal cut with the dissecting scissors just under the lowest rib and cut through the diaphragm sideways. Hold the xiphoid process with a forceps and cut the middle of the ribs proceeding up on both sides. Pull up the ribs/sternum so that the thymus is clearly visible. 
		Note: Thymus lies directly on top of the heart, consists of 2 lobes and is of a white translucent color.</li>
		<li>Using a curved forceps, gently scoop and pull the thymus lobes off of the connective tissue and transfer in washing solution (see List of Materials).</li>
	</ol>
	</li>
	<li>Prepare digestion solution by mixing 9 ml RPMI-1640 (Roswell Park Memorial Institute medium-1640), 0.025 mg/ml purified collagenase, 10 mM HEPES [4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid], and 0.2 mg/ml DNase I in a 50 ml centrifuge tube. Keep the digestion solution in 37 &#176;C water bath until use. 
	Note: The amount of the digestion solution prepared is sufficient for up to five adult mouse thymi, which can be incubated together in one 5 ml polystyrene round-bottom tube.</li>
	<li>Transfer the thymus to a 60 mm tissue culture dish containing 5-6 ml RPMI-1640.</li>
	<li>Dissect the thymus with 28 G insulin syringe needle into small pieces (about 1 mm3 square) to let the lymphocytes flow out.</li>
	<li>Rinse the thymic pieces with RPMI-1640 that is in the petri dish with glass Pasteur pipette. Tilt the dish and let the thymic fragments settle to the bottom. Slowly aspirate and discard the RPMI-1640 supernatant using a glass pipette. Repeat this rinsing step with 5-6 ml RPMI-1640 for 4-5 times with glass pipette until the solution is less opaque. 
	Note: Glass pipettes are recommended at this step, since thymic fragments tend to stick to plastic, resulting in excessive loss of thymic tissues. For the rest of the procedure, use plastic pipettes.</li>
	<li>After the final rinse, discard the supernatant as described in step 1.5. Add 3 ml digestion solution and transfer the thymus pieces and the solution into a 5 ml round-bottom polystyrene tube.</li>
	<li>Place the tube on a tube rotator and incubate at 37 &#176;C for 6 min at a rotation speed of 12 rpm.</li>
	<li>After incubation, let the thymic fragments settle to the bottom of the tube by gravity. Collect the supernatant with Pasteur pipette and transfer into a 50 ml centrifuge tube with 10 ml of washing solution. Centrifuge at 300 x g for 5 min, discard the supernatant and resuspend the cells in 10 ml washing solution. Keep on ice.</li>
	<li>Repeat steps 1.6-1.8 twice on the thymic fragments in the 5 ml round-bottom polystyrene tube. Pool the supernatant in the same 50 ml tube. 
	Note: Centrifugation is not necessary for the second and the third wash.</li>
	<li>After the final digestion, pipet up and down with 2 ml plastic serological pipette to break down any remaining fragments in the tube and transfer to the 50 ml centrifuge tube.</li>
	<li>Centrifuge the 50 ml tube at 300 x g for 5 min, aspirate the supernatant, resuspend in 10 ml of washing buffer and filter through 100 &#181;m cell strainer. Keep on ice.</li>
</ol>
2. Enrichment of TECs with Discontinuous Density Gradient
<ol>
	<li>Prepare 21% density gradient solution by mixing 2.4 ml density gradient medium (60% w/v of iodixanol in water) and 9.6 ml washing solution.</li>
	<li>Centrifuge the dissociated thymic cells in the 50 ml collection tube from step 1.11 at 300 x g for 5 min and resuspend in 2.5 ml washing buffer.</li>
	<li>Add 20 ml RPMI-1640 medium to the cell suspension.</li>
	<li>Fill 12 ml of 21% density gradient solution in a 10 ml serological pipet with an electronic pipettor. Place the tip of the serological pipet at the bottom of the 50 ml centrifuge tube containing cells, and allow the density gradient solution to drain to the bottom of the tube via gravity.
	<ol>
		<li>Gently expel the density gradient solution from the pipet to finish generating the two layers of different densities.</li>
	</ol>
	</li>
	<li>Centrifuge at 600 x g for 20 min at RT in a swinging-bucket rotor. Set the deceleration rate at the slowest level.</li>
	<li>Transfer the top layer and the interface to a new 50 ml tube. 
	Note: Most of the TECs are retained in the interface. Lymphocytes will precipitate to the bottom of the tube after centrifugation. If these cells are to be used for other purposes, rinse the pellet with 20 ml washing solution for three times. Resuspend the cells in 10 ml of washing buffer.</li>
	<li>Add washing solution up to 40 ml to the tube in step 2.6 and centrifuge at 400 x g for 6 min at 4 &#176;C. To remove the supernatant, aspirate with a pipet.</li>
	<li>Repeat the washing and the aspiration 2 more times as described in step 2.7.</li>
	<li>Resuspend in 2 ml of washing solution and count the cells with a hemocytometer.</li>
</ol>
3. Isolating TECs with FACS
<ol>
	<li>Adjust cells from step 2.9 at the concentration of 1x106 cells/100 &#181;l with washing solution and transfer the cells to a 5 ml round-bottom tube (polypropylene or polystyrene, as recommended by the instructions of the flow sorter).</li>
	<li>Add 2 &#181;l anti-Fc receptor IgG per 1x106 cells and incubate at 4 &#176;C for 10 min.</li>
	<li>Add anti-CD45 (1:150 dilution, 10 &#181;l per sample) and anti-EpCAM (1:100 dilution, 10 &#181;l per sample) antibodies and incubate at 4 &#176;C for more than 20 min.</li>
	<li>Wash the cells with 2 ml washing solution and centrifuge at 400 x g for 6 min at 4 &#176;C. Aspirate the supernatant with a pipette.</li>
	<li>Resuspend the cells in 1 ml 1x phosphate-buffered saline (PBS).</li>
	<li>Filter through 100 &#181;m strainer.</li>
	<li>Apply the cells to the sorting instrument. Select the lymphocyte and TEC population excluding the smallest cells on side-scattered light (SSC) / forward-scattered light (FSC) panel (dead cells), then gate on the selected population for CD45- EpCAM+ for sorting13.</li>
</ol>
4. Generation of TEC/EAK Aggregates
Note: Perform reagent preparation and steps involving cell mixing under the laminar hood.
<ol>
	<li>Prepare pA/G adaptor complexes by mixing 4 &#181;l of anti-His-tag IgG, 8 &#181;l of anti-EpCAM IgG and 2.6 &#181;l of pA/G in a sterile 1.5 ml microcentrifuge tube, and incubate at RT for 5 min.</li>
	<li>Adjust the sorted TECs from step 3.7 to 5x104 cells/ml with washing solution, and pipet 100 &#181;l to one well of a low evaporative, 96-well round-bottom tissue culture plate. Add 14.6 &#181;l pA/G adaptor complexes to the cells. Place the plate on a rocking platform for 20 min at 4 &#176;C.</li>
	<li>Wash once with 200 &#181;l washing solution. Centrifuge the plate at 400 x g for 6 min. Discard the supernatant with a micropipette.</li>
	<li>Wash once with 200 &#181;l 10% sucrose solution. Centrifuge at 400 x g for 6 min. Discard the supernatant with a micropipette.</li>
	<li>Resuspend cells in 30 &#181;l 10% sterile sucrose solution per well.</li>
	<li>Add 10 &#181;l of EAKIIH6 (7.5 mg/ml) and incubate for 5 min at RT.</li>
	<li>Add 20 &#181;l of EAK16-II (10 mg/ml) to the TEC mixture.</li>
	<li>Add 100 &#181;l of complete medium to the system to initiate gelation. Place the plate on a platform shaker for 15-20 min at RT.</li>
	<li>Place the plate in the incubator at 37 &#176;C and 5% CO2. After 2-4 hr, add another 100 &#181;l of complete medium.</li>
	<li>Change medium every other day until use.
	<ol>
		<li>Aspirate 100 &#181;l of the medium from the surface without disturbing the gel using a micropipette and gently add 100 &#181;l of pre-warmed medium by placing the pipette tip to the wall of the well.</li>
	</ol>
	</li>
</ol>
5. Characterization of the TEC/EAK Aggregates
<ol>
	<li>To examine the function of the TEC/EAK aggregates in vivo, collect the TEC/EAK hydrogel after O/N culture and transplant under the kidney capsule of an athymic nude mouse, using previously described procedure 11,14.</li>
	<li>Monitor the development of T cells in the periphery by harvesting 50-100 &#181;l blood samples into the EDTA-containing blood collection tube from the nude mice 4-6 weeks post transplantation and stain with a cocktail of anti-CD4, -CD8, -CD45, and -CD3 antibodies12.</li>
	<li>Analyze the percentages of T-lymphocytes in the peripheral blood leukocytes with flow cytometry (FCM), using single cell analysis software12.</li>
</ol>

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Authors declare no conflict of interest.

While TECs are the predominant population of the thymic stroma and play essential roles for the structure and function of the thymus glands, they represent only about 0.1-0.5% of the total thymic cellularity. They are also fragile cells as high percentages of cell death are occasionally observed following collagenase digestion, i.e., the treatment to dissociate TECs from the extracellular matrix (ECM). Their rarity (~200,000 per mouse thymus) and fragility made it a challenging task to isolate TECs. The recent u...

The thymus is the primary lymphoid organ responsible for the generation of a diverse population of pathogen-reactive, self-tolerant T cells that is essential to the function of the acquired immune system. It is a dynamic organ where developing thymocytes, immigrated from the bone marrow as lymphocyte progenitor cells, migrate through the sponge-like three-dimensional (3-D) matrix of the thymic stroma, undergo lineage-specification and differentiation, and eventually emigrate as mature T-cells. The success of this well programmed process depends largely on the cross-talk between the migrating thymocytes and the residential thymic epithelial cells (TECs), the predominant population of the thymic stroma that are essential for establishing and maintaining the integrity of the thymus microenvironment.
Based on their anatomical location and unique function, TECs can be divided into two subsets: the TECs in the cortex (cTECs) that are responsible for selecting self-MHC (major histocompatibility complex) restricted T-cells (positive selection), and the TECs in the medulla (mTECs) that are essential for eliminating autoreactive T-cells (negative selection) 1,2. Many factors (e.g., aging, infection, irradiation, drug treatments) can cause irreversible damages to the thymic epithelium, resulting in compromised adaptive immunity. Despite numerous attempts, restoring the thymic function has been challenging due to the difficulty to reproduce the thymic microenvironment. Notably, thymic three-dimensional (3-D) configuration is critical to the survival and function of TECs, whereas TECs cultured in a 2-D environment rapidly decrease the expression of genes critical for thymopoiesis 3,4.
EAK16-II (AEAEKAKAEAEAKAK) and its C-terminal histidinylated analogue EAKIIH6 (AEAEKAKAEAEAKAKHHHHHH) are low-molecular weight, amphiphilic oligopeptides that are soluble in deionized water, but undergo gelation to form &#946;-fibrils when exposed to ionic strength higher than 20 mM NaCl (normal salt concentration in human body fluid is 154 mM). This environmental responsive property makes them versatile building blocks to form 3D structures. The His-tag on EAKII-H6 provides a docking mechanism, by which the anti-His IgGs/Fc-binding recombinant protein A/G (&#945;H6:pA/G) complexes can serve as an adaptor to anchor protein drugs and other biomolecules (e.g., antibodies) on the hydrogel composite 5-8.
We have previously demonstrated that fluorescent-labeled IgG molecules anchored on the hydrogel can be retained at the injection site for up to 13 days 9. Furthermore, when the &#945;H6:pA/G adaptors anchored with anti-CD4 IgGs were added to the EAK16-II/EAKIIH6 (EAK) hydrogel, CD4+ T cells were specifically captured 10. Using similar technique, we have recently demonstrated that 3-D aggregation of TECs could be promoted in EAK hydrogel with adaptor complexes carrying TEC-specific anti-EpCAM antibodies (&#945;H6:pA/G:&#945;EpCAM). When transplanted underneath the kidney capsules of nude mice, the TEC clusters embedded in EAK hydrogel can effectively support the development of functional T cells in vivo11,12.
Here we illustrate our method to quickly and effectively purify TECs with fluorescence-activated cell sorting (FACS) and generate 3-D TEC aggregates with the EAK hydrogel system.

<table><tbody><tr><td>&lt;strong&gt;TEC Isolation&lt;/strong&gt;</td><td></td><td></td><td></td></tr><tr><td>70% Ethanol</td><td>Decon Laboratories</td><td>2701(1 Gallon)</td><td>Ethanol 200 Proof, deionized water</td></tr><tr><td>Dissecting scissors, straight</td><td>Fine Science Tools, Inc.</td><td>91460-11</td><td></td></tr><tr><td>Graefe forceps, straight</td><td>Fine Science Tools, Inc.</td><td>11053-10</td><td></td></tr><tr><td>Graefe forceps, curved</td><td>Fine Science Tools, Inc.</td><td>11052-10</td><td></td></tr><tr><td>Washing solution</td><td></td><td></td><td>1x PBS, 0.1% BSA, 2&amp;nbsp;mM EDTA</td></tr><tr><td>1x PBS (Phosphate buffered saline)</td><td>Gibco</td><td>10010-023</td><td></td></tr><tr><td>BSA (Bovine serum albumin)</td><td>Sigma</td><td>A1470-100G</td><td></td></tr><tr><td>EDTA (ethylenediaminetetraacetic acid)</td><td>Invitrogen</td><td>15575-038</td><td></td></tr><tr><td>Digestion solution</td><td></td><td></td><td>9 ml RPMI-1640, 0.025&amp;nbsp;mg/ml Liberase TM Research grade, 10&amp;nbsp;mM HEPES, 0.2&amp;nbsp;mg/ml DNaseI</td></tr><tr><td>RPMI-1640</td><td>Gibco</td><td>11879-020</td><td></td></tr><tr><td>Liberase TM Research Grade</td><td>Roche</td><td>05 401 127 001</td><td>referred as &quot;purified collagenase&quot;</td></tr><tr><td>1&amp;nbsp;M HEPES</td><td>Lonza</td><td>17-737E</td><td></td></tr><tr><td>Dnase I</td><td>Roche</td><td>10 104 159 001</td><td></td></tr><tr><td>50&amp;nbsp;ml Centrifuge tube</td><td>Corning</td><td>430290</td><td></td></tr><tr><td>60&amp;nbsp;mm tissue culture dish</td><td>Falcon</td><td>353002</td><td></td></tr><tr><td>1/2&amp;nbsp;cc U-100 Insulin syringe 28&amp;nbsp;1/2&amp;nbsp;G</td><td>Becton Dickinson</td><td>329461</td><td></td></tr><tr><td>5&amp;nbsp;ml Polystyrene round-bottom tube</td><td>Falcon</td><td>352058</td><td></td></tr><tr><td>5&amp;nbsp;ml glass pipet</td><td>Fisher Healthcare</td><td>13-678-27E</td><td>Use for rinsing the thymic fragments. Thymic fragments tend to stick to the wall with plastic pipets.</td></tr><tr><td>MACSmix tube rotator</td><td>Miltenyi</td><td>130-090-753</td><td></td></tr><tr><td>100&amp;nbsp;&amp;micro;m Cell strainer</td><td>Falcon</td><td>352360</td><td></td></tr><tr><td>Density gradient medium: OptiPrep</td><td>Axis-Shield</td><td></td><td></td></tr><tr><td>&lt;strong&gt;Cell Sorting&lt;/strong&gt;</td><td></td><td></td><td></td></tr><tr><td>5&amp;nbsp;ml Polypropylene round-bottom tube</td><td>Falcon</td><td>352063</td><td></td></tr><tr><td>Anti-mouse CD16/CD32 (Fc Block)</td><td>BD Biosciences</td><td>553142</td><td>Use as undiluted, 2&amp;nbsp;&amp;micro;l per sample</td></tr><tr><td>Anti-mouse CD45-PercpCy5.5</td><td>eBioscience</td><td>45-0451-80</td><td>Use at 1:150, 10&amp;nbsp;&amp;micro;l per sample</td></tr><tr><td>Anti-mouse CD326 (EpCAM)-PE</td><td>eBioscience</td><td>12-5791-82</td><td>Use at 1:100, 10&amp;nbsp;&amp;micro;l per sample</td></tr><tr><td>BD Influx</td><td>BD Biosciences</td><td></td><td></td></tr><tr><td>Single cell analysis software</td><td>FlowJo</td><td></td><td></td></tr><tr><td>&lt;strong&gt;EAK Gel Assembly&lt;/strong&gt;</td><td></td><td></td><td></td></tr><tr><td>Anti-His-Tag</td><td>AnaSpec</td><td>29673</td><td>&quot;anti-His-Tag IgG&quot;</td></tr><tr><td>Purified anti-mouse CD326 (EpCAM)</td><td>BioLegend</td><td>118202</td><td>&quot;anti-EpCAM IgG&quot;</td></tr><tr><td>Recombinant protein A/G</td><td>Pierce Biotechnology</td><td></td><td></td></tr><tr><td>1.5&amp;nbsp;ml Safe-Lock Tubes, Biopur, Sterile</td><td>Fisher Healthcare</td><td>05-402-24B</td><td>referred as &quot;1.5&amp;nbsp;ml microcentrifuge tube&quot;</td></tr><tr><td>96-well, Tissue culture plate, Round-bottom with low evaporation lid</td><td>BD Falcon</td><td>353917</td><td></td></tr><tr><td>Rocking platform: Nutator Mixer no.1105</td><td>BD Clay Adams</td><td></td><td></td></tr><tr><td>10% sucrose</td><td>Sigma</td><td>S0389</td><td>Prepare with sterile distilled water</td></tr><tr><td>EAK16-II (AcNH-AEAEAKAKAEAEAKAK-CONH&lt;sub&gt;2&lt;/sub&gt;)</td><td>American Peptide Company&amp;nbsp;</td><td></td><td>custom synthesized, 10&amp;nbsp;mg/ml</td></tr><tr><td>EAKIIH6 (AcNH-AEAEAKAKAEAEAKAKHHHHHH-CONH&lt;sub&gt;2&lt;/sub&gt;)</td><td>American Peptide Company&amp;nbsp;</td><td></td><td>custom synthesized, 7.5&amp;nbsp;mg/ml</td></tr><tr><td>Complete medium</td><td></td><td></td><td>RPMI-1640, 10% FBS, 1% Pen/Strep, 1% L-glutamine, 1% NEAA, 5&amp;nbsp;mM HEPES, 50&amp;nbsp;&amp;micro;M 2-Mercaptoethanol</td></tr><tr><td>RPMI-1640</td><td>Gibco</td><td>11879-020</td><td></td></tr><tr><td>FBS (Fetal Bovine Serum)</td><td>Atlanta Biologicals</td><td>S11150</td><td>Heat inactivated before use</td></tr><tr><td>Pen/Strep</td><td>Gibco</td><td>15140-122</td><td></td></tr><tr><td>L-glutamine 200&amp;nbsp;mM (100x)</td><td>Gibco</td><td>25030-081</td><td></td></tr><tr><td>NEAA (non-essential amino acid) 100x</td><td>Gibco</td><td>11140-050</td><td></td></tr><tr><td>1&amp;nbsp;M HEPES</td><td>BioWhittaker</td><td>17-737E</td><td></td></tr><tr><td>2-Mercaptoethanol (100x)</td><td>Millipore</td><td>ES-007-E</td><td></td></tr><tr><td>Platform shaker: The Belly Dancer</td><td>Stovall Life Sciences Inc.</td><td>model: USBDbo</td><td></td></tr></tbody></table>

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.

To examine the effectiveness of using the density gradient separation protocol to enrich the CD45- stromal cells, cells harvested from both the interface and the precipitated lymphocyte pellets were stained with anti-CD45 and anti-EpCAM antibodies. Both anti-Ulex Europaeus Agglutinin 1 (UEA1) and anti-MHC Class II antibodies were also included in the staining cocktail to further identify the cTEC and mTEC subsets. As shown in Figure 1, we were able to routinely achieve cl...

Watch this Scientific Journal Video about Promoting 3-D Aggregation of FACS Purified Thymic Epithelial Cells with EAK 16-II/EAKIIH6 Self-assembling Hydrogel at JoVE.com

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

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 ...

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Research

JoVE Journal

Immunology and Infection

6.5K Views.  Allegheny Health Network. 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.

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

3D Organotypic Co-culture Model Supporting Medullary Thymic Epithelial Cell Proliferation, Differentiation and Promiscuous Gene Expression

Intra-thymic T cell development requires an intricate three-dimensional meshwork composed of various stromal cells, i.e., non-T cells. Thymocytes traverse this scaffold in a highly coordinated temporal and spatial order while sequentially passing obligatory check points, i.e., T cell lineage commitment, followed by T cell receptor repertoire generation and selection prior to their export into the periphery. The two major resident cell types forming this scaffold are cortical (cTECs) and medullary thymic epithelial cells (mTECs). A key feature of mTECs is the so-called promiscuous expression of numerous tissue-restricted antigens. These tissue-restricted antigens are presented to immature thymocytes directly or indirectly by mTECs or thymic dendritic cells, respectively resulting in self-tolerance.
Suitable in vitro models emulating the developmental pathways and functions of cTECs and mTECs are currently lacking. This lack of adequate experimental models has for instance hampered the analysis of promiscuous gene expression, which is still poorly understood at the cellular and molecular level. We adapted a 3D organotypic co-culture model to culture ex vivo isolated mTECs. This model was originally devised to cultivate keratinocytes in such a way as to generate a skin equivalent in vitro. The 3D model preserved key functional features of mTEC biology: (i) proliferation and terminal differentiation of CD80lo, Aire-negative into CD80hi, Aire-positive mTECs, (ii) responsiveness to RANKL, and (iii) sustained expression of FoxN1, Aire and tissue-restricted genes in CD80hi mTECs.

Studying medullary thymic epithelial cells in vitro has been largely unsuccessful, as current 2D culture systems do not mimic the in vivo scenario. The 3D culture system described herein - a modified skin organotypic culture model - has proven superior in recapitulating mTEC proliferation, differentiation and maintenance of promiscuous gene expression.

Intra-thymic T cell development requires an intricate three-dimensional meshwork composed of various stromal cells, i.e., non-T cells. Thymocytes traverse ...

Developmental Biology

Cultivation of Human Neural Progenitor Cells in a 3-dimensional Self-assembling Peptide Hydrogel

The influence of 3-dimensional (3D) scaffolds on growth, proliferation and finally neuronal differentiation is of great interest in order to find new methods for cell-based and standardised therapies in neurological disorders or neurodegenerative diseases. 3D structures are expected to provide an environment much closer to the in vivo situation than 2D cultures. In the context of regenerative medicine, the combination of biomaterial scaffolds with neural stem and progenitor cells holds great promise as a therapeutic tool.1-5 Culture systems emulating a three dimensional environment have been shown to influence proliferation and differentiation in different types of stem and progenitor cells. Herein, the formation and functionalisation of the 3D-microenviroment is important to determine the survival and fate of the embedded cells.6-8 Here we used PuraMatrix9,10 (RADA16, PM), a peptide based hydrogel scaffold, which is well described and used to study the influence of a 3D-environment on different cell types.7,11-14 PuraMatrix can be customised easily and the synthetic fabrication of the nano-fibers provides a 3D-culture system of high reliability, which is in addition xeno-free.
Recently we have studied the influence of the PM-concentration on the formation of the scaffold.13 In this study the used concentrations of PM had a direct impact on the formation of the 3D-structure, which was demonstrated by atomic force microscopy. A subsequent analysis of the survival and differentiation of the hNPCs revealed an influence of the used concentrations of PM on the fate of the embedded cells. However, the analysis of survival or neuronal differentiation by means of immunofluorescence techniques posses some hurdles. To gain reliable data, one has to determine the total number of cells within a matrix to obtain the relative number of e.g. neuronal cells marked by &beta;III-tubulin. This prerequisites a technique to analyse the scaffolds in all 3-dimensions by a confocal microscope or a comparable technique like fluorescence microscopes able to take z-stacks of the specimen. Furthermore this kind of analysis is extremely time consuming. 
Here we demonstrate a method to release cells from the 3D-scaffolds for the later analysis e.g. by flow cytometry. In this protocol human neural progenitor cells (hNPCs) of the ReNcell VM cell line (Millipore USA) were cultured and differentiated in 3D-scaffolds consisting of PuraMatrix (PM) or PuraMatrix supplemented with laminin (PML). In our hands a PM-concentration of 0.25% was optimal for the cultivation of the cells13, however the concentration might be adapted to other cell types.12 The released cells can be used for e.g. immunocytochemical studies and subsequently analysed by flow cytometry. This speeds up the analysis and more over, the obtained data rest upon a wider base, improving the reliability of the data.

Here we describe the use of a self-assembling 3-dimensional scaffold to culture human neural progenitor cells. We present a protocol to release the cells from the scaffolds to be analysed subsequently e.g. by flow cytometry. This protocol might be adapted to other cell types to perform detailed mechanistically studies.

The  influence of 3-dimensional (3D) scaffolds on growth, proliferation and finally  neuronal differentiation is of great interest in order to find new ...

Bioengineering

Generation and Recovery of &beta;-cell Spheroids From Step-growth PEG-peptide Hydrogels

Hydrogels are hydrophilic crosslinked polymers that provide a three-dimensional microenvironment with tissue-like elasticity and high permeability for culturing therapeutically relevant cells or tissues. Hydrogels prepared from poly(ethylene glycol) (PEG) derivatives are increasingly used for a variety of tissue engineering applications, in part due to their tunable and cytocompatible properties. In this protocol, we utilized thiol-ene step-growth photopolymerizations to fabricate PEG-peptide hydrogels for encapsulating pancreatic MIN6 b-cells. The gels were formed by 4-arm PEG-norbornene (PEG4NB) macromer and a chymotrypsin-sensitive peptide crosslinker (CGGYC). The hydrophilic and non-fouling nature of PEG offers a cytocompatible microenvironment for cell survival and proliferation in 3D, while the use of chymotrypsin-sensitive peptide sequence (CGGY&darr;C, arrow indicates enzyme cleavage site, while terminal cysteine residues were added for thiol-ene crosslinking) permits rapid recovery of cell constructs forming within the hydrogel. The following protocol elaborates techniques for: (1) Encapsulation of MIN6 &beta;-cells in thiol-ene hydrogels; (2) Qualitative and quantitative cell viability assays to determine cell survival and proliferation; (3) Recovery of cell spheroids using chymotrypsin-mediated gel erosion; and (4) Structural and functional analysis of the recovered spheroids.

Generation and Recovery of &#946;-cell Spheroids From Step-growth PEG-peptide Hydrogels

The following protocol provides techniques for encapsulating pancreatic &#x03B2;-cells in step-growth PEG-peptide hydrogels formed by thiol-ene photo-click reactions. This material platform not only offers a cytocompatible microenvironment for cell encapsulation, but also permits user-controlled rapid recovery of cell structures formed within the hydrogels.

Hydrogels are hydrophilic crosslinked polymers that provide a three-dimensional  microenvironment with tissue-like elasticity and high permeability for  ...

Reaggregate Thymus Cultures

Stromal cells within lymphoid tissues are organized into three-dimensional structures that provide a scaffold that is thought to control the migration and development of haemopoeitic cells. Importantly, the maintenance of this three-dimensional organization appears to be critical for normal stromal cell function, with two-dimensional monolayer cultures often being shown to be capable of supporting only individual fragments of lymphoid tissue function. In the thymus, complex networks of cortical and medullary epithelial cells act as a framework that controls the recruitment, proliferation, differentiation and survival of lymphoid progenitors as they undergo the multi-stage process of intrathymic T-cell development. Understanding the functional role of individual stromal compartments in the thymus is essential in determining how the thymus imposes self/non-self discrimination. Here we describe a technique in which we exploit the plasticity of fetal tissues to re-associate into intact three-dimensional structures in vitro, following their enzymatic disaggregation. The dissociation of fetal thymus lobes into heterogeneous cellular mixtures, followed by their separation into individual cellular components, is then combined with the in vitro re-association of these desired cell types into three-dimensional reaggregate structures at defined ratios, thereby providing an opportunity to investigate particular aspects of T-cell development under defined cellular conditions. (This article is based on work first reported Methods in Molecular Biology 2007, Vol. 380 pages 185-196).

In this video the preparation of 2-dGuo-treated reaggregate thymus cultures is demonstrated.

Stromal cells within lymphoid tissues are organized into three-dimensional structures that provide a scaffold that is thought to control the migration and ...

Biology

Cellular Encapsulation in 3D Hydrogels for Tissue Engineering 

The 3D encapsulation of cells within hydrogels represents an increasingly important and popular technique for culturing cells and towards the development of constructs for tissue engineering. This environment better mimics what cells observe in vivo, compared to standard tissue culture, due to the tissue-like properties and 3D environment. Synthetic polymeric hydrogels are water-swollen networks that can be designed to be stable or to degrade through hydrolysis or proteolysis as new tissue is deposited by encapsulated cells. A wide variety of polymers have been explored for these applications, such as poly(ethylene glycol) and hyaluronic acid. Most commonly, the polymer is functionalized with reactive groups such as methacrylates or acrylates capable of undergoing crosslinking through various mechanisms. In the past decade, much progress has been made in engineering these microenvironments - e.g., via the physical or pendant covalent incorporation of biochemical cues - to improve viability and direct cellular phenotype, including the differentiation of encapsulated stem cells (Burdick et al.).
The following methods for the 3D encapsulation of cells have been optimized in our and other laboratories to maximize cytocompatibility and minimize the number of hydrogel processing steps. In the following protocols (see Figure 1 for an illustration of the procedure), it is assumed that functionalized polymers capable of undergoing crosslinking are already in hand; excellent reviews of polymer chemistry as applied to the field of tissue engineering may be found elsewhere (Burdick et al.) and these methods are compatible with a range of polymer types. Further, the Michael-type addition (see Lutolf et al.) and light-initiated free radical (see Elisseeff et al.) mechanisms focused on here constitute only a small portion of the reported crosslinking techniques. Mixed mode crosslinking, in which a portion of reactive groups is first consumed by addition crosslinking and followed by a radical mechanism, is another commonly used and powerful paradigm for directing the phenotype of encapsulated cells (Khetan et al., Salinas et al.).

Cellular Encapsulation in 3D Hydrogels for Tissue Engineering

We present protocols for the 3-dimensional (3D) encapsulation of cells within synthetic hydrogels. The encapsulation procedure is outlined for two commonly used methods of crosslinking (michael-type addition and light-initiated free radical mechanisms), as well as a number of techniques for assessing encapsulated cell behavior.

The 3D encapsulation of cells within hydrogels represents an increasingly important and popular technique for culturing cells and towards the development ...

Production of Elastin-like Protein Hydrogels for Encapsulation and Immunostaining of Cells in 3D

Two-dimensional (2D) tissue culture techniques have been essential for our understanding of fundamental cell biology. However, traditional 2D tissue culture systems lack a three-dimensional (3D) matrix, resulting in a significant disconnect between results collected in vitro and in vivo. To address this limitation, researchers have engineered 3D hydrogel tissue culture platforms that can mimic the biochemical and biophysical properties of the in vivo cell microenvironment. This research has motivated the need to develop material platforms that support 3D cell encapsulation and downstream biochemical assays. Recombinant protein engineering offers a unique toolset for 3D hydrogel material design and development by allowing for the specific control of protein sequence and therefore, by extension, the potential mechanical and biochemical properties of the resultant matrix. Here, we present a protocol for the expression of recombinantly-derived elastin-like protein (ELP), which can be used to form hydrogels with independently tunable mechanical properties and cell-adhesive ligand concentration. We further present a methodology for cell encapsulation within ELP hydrogels and subsequent immunofluorescent staining of embedded cells for downstream analysis and quantification.

Recombinant protein-engineered hydrogels are advantageous for 3D cell culture as they allow for complete tunability of the polymer backbone and therefore, the cell microenvironment. Here, we describe the process of recombinant elastin-like protein purification and its application in 3D hydrogel cell encapsulation.

Two-dimensional (2D) tissue culture techniques have been essential for our understanding of fundamental cell biology. However, traditional 2D tissue ...

Initial 3D Cell Cluster Control in a Hybrid Gel Cube Device for Repeatable Pattern Formations

The importance of in vitro 3D cultures is considerably emphasized in cell/tissue culture. However, the lack of experimental repeatability is one of its restrictions. Producing few repeatable results of pattern formation deteriorates the analysis of the mechanisms underlying the self-organization. Reducing variation in initial culture conditions, such as the cell density and distribution in the extracellular matrix (ECM), is crucial to enhance the repeatability of a 3D culture. In this article, we demonstrate a simple but robust procedure for controlling the initial cell cluster shape in a 3D extracellular matrix to obtain highly repeatable pattern formations. A micromold with a desired shape was fabricated by using photolithography or a machining process, and it formed a 3D pocket in the ECM contained in a hybrid gel cube (HGC). Highly concentrated cells were then injected in the pocket so that the cell cluster shape matched with the fabricated mold shape. The employed HGC allowed multi-directional scanning by its rotation, which enabled high-resolution imaging and the capture of the entire tissue structure even though a low-magnification lens was used. Normal human bronchial epithelial cells were used to demonstrate the methodology.&#160;

We present a procedure for controlling the initial cell cluster shape in a 3D extracellular matrix to obtain a repeatable pattern formation. A cubic device containing two different hydrogels is employed to achieve multi-directional imaging for tissue pattern formation.

The importance of in vitro 3D cultures is considerably emphasized in cell/tissue culture. However, the lack of experimental repeatability is one of its ...

Recreating the Thymic Microenvironment with iPSC-Derived Organoids

Formation of Human Thymus Organoids in Three-Dimensional Fibrin Hydrogels

Generation of a functional and self-tolerant T cell repertoire is a complex process dependent on the thymic microenvironment and, primarily, on the properties of its extracellular matrix (ECM). Thymic epithelial cells (TECs) are crucial in thymopoiesis, nurturing and selecting developing T cells by filtering self-reactive clones. TECs have been empirically demonstrated to be particularly sensitive to physical and chemical clues supplied by the ECM and classical monolayer cell culture leads to a quick loss of functionality until their death. Because of this delicate maintenance combined with relative rarity, and despite the high stakes in modeling thymus biology in vitro, models able to faithfully mimic the TEC niche at scale and over time are still lacking. Here, we describe the formation of a multicellular human thymic organoid model, in which the TEC compartment is derived from human induced pluripotent stem cells (iPSC) and reaggregated with primary early thymocyte progenitors in a three-dimensional (3D) fibrin-based hydrogel. This model answers current needs for a scalable culture system that reproduces the thymic microenvironment ex vivo and demonstrates functionality, i.e., the ability to produce T cells and to support thymus organoid growth over several weeks. Thus, we propose a practical in vitro model of thymus functionality through iPSC-derived organoids that would benefit research on TEC biology and T cell generation ex vivo.

Author Spotlight: Advancing Thymic Epithelial Cells and T-Cell Research with Human Thymic Organoids

Here, we describe a protocol for the formation of human iPSC-derived thymus organoids grown in 3D fibrin hydrogels aiming to support thymic epithelial cell (TEC) maturation and prolonged maintenance, as well as thymopoiesis in vitro.

Generation of a functional and self-tolerant T cell repertoire is a complex process dependent on the thymic microenvironment and, primarily, on the ...

Patterning the Geometry of Human Embryonic Stem Cell Colonies on Compliant Substrates to Control Tissue-Level Mechanics

Human embryonic stem cells demonstrate a unique ability to respond to morphogens in vitro by self-organizing patterns of cell fate specification that correspond to primary germ layer formation during embryogenesis. Thus, these cells represent a powerful tool with which to examine the mechanisms that drive early human development. We have developed a method to culture human embryonic stem cells in confined colonies on compliant substrates that provides control over both the geometry of the colonies and their mechanical environment in order to recapitulate the physical parameters that underlie embryogenesis. The key feature of this method is the ability to generate polyacrylamide hydrogels with defined patterns of extracellular matrix ligand at the surface to promote cell attachment. This is achieved by fabricating stencils with the desired geometric patterns, using these stencils to create patterns of extracellular matrix ligand on glass coverslips, and transferring these patterns to polyacrylamide hydrogels during polymerization. This method is also compatible with traction force microscopy, allowing the user to measure and map the distribution of cell-generated forces within the confined colonies. In combination with standard biochemical assays, these measurements can be used to examine the role mechanical cues play in fate specification and morphogenesis during early human development.

Extracellular matrix ligands can be patterned onto polyacrylamide hydrogels to enable the culture of human embryonic stem cells in confined colonies on compliant substrates. This method can be combined with traction force microscopy and biochemical assays to examine the interplay between tissue geometry, cell-generated forces, and fate specification.

Human embryonic stem cells demonstrate a unique ability to respond to morphogens in vitro by self-organizing patterns of cell fate specification that ...

Hydrogel Arrays Enable Increased Throughput for Screening Effects of Matrix Components and Therapeutics in 3D Tumor Models

Cell-matrix interactions mediate complex physiological processes through biochemical, mechanical, and geometrical cues, influencing pathological changes and therapeutic responses. Accounting for matrix effects earlier in the drug development pipeline is expected to increase the likelihood of clinical success of novel therapeutics. Biomaterial-based strategies recapitulating specific tissue microenvironments in 3D cell culture exist but integrating these with the 2D culture methods primarily used for drug screening has been challenging. Thus, the protocol presented here details the development of methods for 3D culture within miniaturized biomaterial matrices in a multi-well plate format to facilitate integration with existing drug screening pipelines and conventional assays for cell viability. Since the matrix features critical for preserving clinically relevant phenotypes in cultured cells are expected to be highly tissue- and disease-specific, combinatorial screening of matrix parameters will be necessary to identify appropriate conditions for specific applications. The methods described here use a miniaturized culture format to assess cancer cell responses to orthogonal variation of matrix mechanics and ligand presentation. Specifically, this study demonstrates the use of this platform to investigate the effects of matrix parameters on the responses of patient-derived glioblastoma (GBM) cells to chemotherapy.

The present protocol describes an experimental platform to assess the effects of mechanical and biochemical cues on chemotherapeutic responses of patient-derived glioblastoma cells in 3D matrix-mimetic cultures using a custom-made UV illumination device facilitating high-throughput photocrosslinking of hydrogels with tunable mechanical features.

Cell-matrix interactions mediate complex physiological processes through biochemical, mechanical, and geometrical cues, influencing pathological changes ...

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

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