This work has been supported by the German Cancer Research Center (DKFZ), the EU-consortium &#8220;Tolerage&#8221;, the Deutsche Forschungsgemeinschaft (SFB 938) and the Landesstiftung Baden-W&#252;rttemberg.

This study has been approved by the ethics committee of the Regierungspr&#228;sidium Karlsruhe. All animals were housed under specific pathogen-free conditions at the German Cancer Research Center (DKFZ). For all culture experiments mouse pups ranging from 1 to 7 days of age were used.
1. Isolation of mTECs from Thymus
NOTE: The following digestion steps were performed as described previously1 under sterile conditions with some modifications as follows.
<ol>
	<li>Decapitate the mouse pups and remove the thymus. Place the thymi on ice in a Petri plate containing RPMI 1640 medium (containing 5% FCS).</li>
	<li>Cut the thymi into fine, small pieces and place in a round bottom tube with ~5-30 ml RPMI media and gently stir using a magnet for 10 min at RT.</li>
	<li>Thereafter, decant the supernatant containing mainly thymocytes and digest the remaining tissue sequentially with one round of collagenase type IV (0.2 mg/ml and 57 U/ml final concentartion) for 15 min each at 37 &#176;C, followed by collagenase/dispase (0.2 mg/ml and 1.2 U/ml final concentration) for 25 min each at 37 &#176;C in a water bath with magnetic stirring until the thymi are completely digested. Use 1 ml enzyme per two to three thymi.</li>
	<li>Agitate the tissue once every 7-10 min with a Pasteur pipette. Pool the collagenase/dispase fractions and filter through a 70 &#181;m gauze.</li>
	<li>Enrich the mTECs by magnetic cell sorting (MACS). Perform the purification of mTECs by magnetic cell sorting as described previously11, and shown in Figure 1. 
	NOTE: For magnetic sorting of mTECs we used the following antibodies: anti-CD80-PE (16-10A1, use at 1:100 dilution) and anti-EpCAM-bio (G8.8, use at 1:100 dilution)12. Immature and mature mTECs using MACS were defined as: CD45- EpCAM+ CD80- and CD45- CD80+ respectively.</li>
	<li>After MACS purification (purity of immature mTECs = 83.1 &#177; 6.3 % and mature mTECs = 79.23 &#177; 3.42%), seed the mTECs onto the organotypic cultures as described below (Section 2.3).</li>
	<li>Alternatively, sort mTECs by FACS (using 100 &#181;m nozzle) after CD45 MACS depletion using the following antibodies: anti-CD45-PerCP (30-F11, use at 1:100 dilution), anti-Ly51-FITC (6C3, use at 1:100 dilution), anti-EpCAM-Alexa647 (G8.8, use at 1:500 dilution) and anti-CD80-PE (16-10A1, use at 1:100 dilution). Exclude dead cells using propidium iodide (1:5,000) (Day 4). Immature and mature mTECs using FACS were defined as: PI- CD45- Ly51-EpCAM+ CD80- and PI- CD45- Ly51- EpCAM+ CD80+, respectively.</li>
</ol>
2. 3D Organotypic Co-cultures (OTCs)
NOTE: The 3D-dermal constructs for organotypic cultivation of keratinocytes were prepared as described previously9,13. At all steps cells were incubated at 37 &#176;C and 5% CO2. The OTCs using mTECs were prepared with slight modifications as follows.
<ol>
	<li>Preparation of Human Fibroblasts 
	NOTE: The human dermal fibroblasts were obtained from explant cultures of de-epidermised dermis as described previously9.
	<ol>
		<li>In brief, cut strips of human skin ( ~5 cm length) and treat with thermolysin (0.5 mg/ml in saline with 10 mM Hepes pH 7.4) O/N at 4 &#176;C.</li>
		<li>Thereafter, separate the epidermis from the dermis using forceps.</li>
		<li>Finely cut the dermis into small pieces, place in a 10 cm Petri plate and allow to dry for 1-2 hr under a sterile airflow. Supplement the explants regularly with DMEM containing 20 % FBS.</li>
		<li>Split the out-growing fibroblasts when confluent (usually around 3 weeks) using 0.1 % trypsin making sure that the explants continue to adhere to the plate for further consecutive rounds of outgrowth.</li>
		<li>Expand the fibroblasts from the same explants for up to 3 times in DMEM with 10 % FBS and cryo-preserve them14. Use the same batch of fibroblasts for each experimental series. 
		NOTE: The fibroblasts were not irradiated for the set-up of the dermal equivalents.</li>
	</ol>
	</li>
	<li>Preparation of the Scaffold
	<ol>
		<li>Cut the 0.4-0.6 mm thick viscose, nonwoven fibrous material (product details in supporting excel sheet) into well demarcated circles using a sharp 11 mm diameter metal puncher to exactly fit into 12 well-filter inserts. Then place it into the 12- well filter insert (polyester capillary pore membrane, 3 &#181;m pore size) as a scaffold. Place the complete filter setup into a sterile 12-well plate.</li>
		<li>Prepare the fibrin gel using a fibrin glue-kit for surgery consisting of a combination of fibrinogen and thrombin. Pre-dilute the fibrinogen- as well as the thrombin-component of the kit to 8 mg/ml and 10 units/ml, respectively. For a single well of a 12-well plate proceed as follows.
		<ol>
			<li>Dilute 100 &#181;l fibrinogen (8 mg/ml) with 100 &#181;l phosphate buffered saline (PBS) without Ca2+ and Mg2+, pH 7.0. Dilute 100 &#181;l thrombin (10 units/ml) with 100 &#181;l FCS containing 270,000 fibroblasts.</li>
			<li>Dispense 200 &#181;l of the thrombin containing fibroblasts cell-mix onto the scaffold, to which add 200 &#181;l fibrinogen (1:1 mixture), resulting in a final concentration of fibrinogen of 2 mg/ml and of thrombin of 2.5 units/ml. Mix well and distribute evenly over the whole area of the scaffold by gentle pipetting (Day 1). 
			NOTE: After 30 min at 37 &#176;C a clot enclosing the fibroblasts will have formed, filling completely the internal spaces of the scaffold and forming a smooth upper surface.</li>
		</ol>
		</li>
	</ol>
	</li>
	<li>Co-culture with mTECs
	<ol>
		<li>For pre-culture, submerse the organ cultures in DMEM with 10 % FBS, 50 &#181;g/ml L-ascorbic acid and 1 ng/ml TGF-&#946;1 with a medium change every other day for 4-5 days.</li>
		<li>On the day of mTEC seeding, replace the medium by rFAD medium (1:1 DMEM + DMEM/F12) with 10% FBS, 10-10 M cholera toxin, 0.4 mg/ml hydrocortisone, 50 &#181;g/ml L-ascorbic acid, RANK ligand (0.1 &#956;g/ml) and 500 units/ml of Aprotinin, thus preventing precocious fibrinolysis by serine proteases secreted by fibroblasts.</li>
		<li>7-8 hr later, set-up the co-cultures by seeding 250,000 mTECs (either complete mTECs, or CD80lo and CD80hi subsets), in a volume of 100 &#181;l per well on top of the fibroblast scaffold. Count the cells using a Neubauer chamber (Day 4). 
		NOTE: At all times the thymus 3D organotypic cultures are submersed in media unlike skin OTCs which are air-lifted.</li>
		<li>After 24 hr incubation, supply the cultures with medium (total medium exchange) as mentioned above (step 2.3.2) now containing reduced amounts of Aprotinin, 250 units/ml (Day 5).</li>
		<li>In order to assess the proliferative activity of mTECs, add EdU (6.7 &#181;M/ml, i.e.,&#160;10 &#181;M/well) to OTCs for 4 hr before termination of the cultures. Perform the staining of OTC cryo-sections as described in the EdU Imaging Kit combined with co-staining of keratin 14. Determine the proliferative indices of mTECs, by either counting the K14+ EdU+ cells in two sections of each culture specimen or by flow cytometry (EdU flow cytometry, Section 1.7 but instead of Ly51-FITC use CDR1-PB15 at a 1:100 dilution and 2.3.6.4).</li>
		<li>Following 4-7 days of co-culture, terminate the OTCs and process for RNA isolation, cryo-sectioning or FACS analysis (Day 8-11).
		<ol>
			<li>Terminate the cultures using a forceps, separating the scaffold/dermal equivalent from the filter of the well insert.</li>
			<li>For cryo-sectioning, embed the entire OTC in OCT compound and freeze in liquid nitrogen vapor before cryo-sectioning. Prepare 5-7 &#181;m thick OTC sections using a cryostat and store at -20 &#176;C until use. For immuno-histochemistry of cryo-sectioned OTCs use anti-keratin 14 (AF64, use at 1:1,000 dilution), and anti-vimentin (GP53, use at 1:100 dilution) antibodies. Perform the indirect immuno-histochemistry staining using respective secondary antibodies.</li>
			<li>For RNA isolation, add 1 ml Denaturing solution (containing phenol and guanidinium thiocyanate) in a screw cap of a 2 ml RNase free tube. Cut the entire OTC into pieces with a scalpel and add into the tube containing denaturing solution. Mechanically shred the OTCs with FastPrep instrument twice for 30 sec at a speed of 6.0, place in between on ice for 2 min (the sample can be stored at -80 &#176;C after this point). If frozen at -80 &#176;C, thaw on ice. Centrifuge the tubes at 11,500-13,000 rpm for 10 min at 4 &#176;C. Transfer the supernatant to a fresh tube, incubate for 5 min at RT and follow RNA isolation protocols using Acid guanidinium thiocyanate-phenol-chloroform extraction as described by the manufacturer.</li>
			<li>For FACS analysis, remove the scaffold and separate the membrane from the fibrin/fibroblast/mTEC gel. Finely cut the gel with a scalpel and digest it in a FACS tube for ~20 min or until completely digested with 2 ml of collagenase/dispase at 37 &#176;C in a water bath with magnetic stirring. Agitate the enzyme solution with a Pasteur pipette once every 5 min. After complete digestion, filter the cell suspension through a 70 &#181;m filter; stain the single cell suspension using the antibodies as described in 1.7 and analyze by flow cytometry.</li>
		</ol>
		</li>
	</ol>
	</li>
</ol>

<ol>
	<li>Derbinski, J., Schulte, A., Kyewski, B., Klein, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Promiscuous+gene+expression+in+medullary+thymic+epithelial+cells+mirrors+the+peripheral+self.">Promiscuous gene expression in medullary thymic epithelial cells mirrors the peripheral self.</a> Nat Immunol. 2, 1032-1039 (2001).</li><li>Kyewski, B., Klein, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+central+role+for+central+tolerance.">A central role for central tolerance.</a> Annual review of immunology. 24, 571-606 (2006).</li><li>Bonfanti, P., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Microenvironmental+reprogramming+of+thymic+epithelial+cells+to+skin+multipotent+stem+cells.">Microenvironmental reprogramming of thymic epithelial cells to skin multipotent stem cells.</a> Nature. 466, 978-982 (2010).</li><li>Kont, V., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Modulation+of+Aire+regulates+the+expression+of+tissue-restricted+antigens.">Modulation of Aire regulates the expression of tissue-restricted antigens.</a> Molecular Immunology. 45, 25-33 (2008).</li><li>Mohtashami, M., Zuniga-Pflucker, J. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Three-dimensional+architecture+of+the+thymus+is+required+to+maintain+delta-like+expression+necessary+for+inducing+T+cell+development.">Three-dimensional architecture of the thymus is required to maintain delta-like expression necessary for inducing T cell development.</a> J Immunol. 176, 730-734 (2006).</li><li>Palumbo, M. O., Levi, D., Chentoufi, A. A., Polychronakos, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Isolation+and+characterization+of+proinsulin-producing+medullary+thymic+epithelial+cell+clones.">Isolation and characterization of proinsulin-producing medullary thymic epithelial cell clones.</a> Diabetes. 55, 2595-2601 (2006).</li><li>White, A., Jenkinson, E., Anderson, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Reaggregate+thymus+cultures.">Reaggregate thymus cultures.</a> Journal of visualized experiments : JoVE. , (2008).</li><li>Stark, H. J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Epidermal+homeostasis+in+long-term+scaffold-enforced+skin+equivalents.">Epidermal homeostasis in long-term scaffold-enforced skin equivalents.</a> J Investig Dermatol Symp Proc. 11, 93-105 (2006).</li><li>Boehnke, K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Effects+of+fibroblasts+and+microenvironment+on+epidermal+regeneration+and+tissue+function+in+long-term+skin+equivalents.">Effects of fibroblasts and microenvironment on epidermal regeneration and tissue function in long-term skin equivalents.</a> Eur J Cell Biol. 86, 731-746 (2007).</li><li>Pinto, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=An+organotypic+coculture+model+supporting+proliferation+and+differentiation+of+medullary+thymic+epithelial+cells+and+promiscuous+gene+expression.">An organotypic coculture model supporting proliferation and differentiation of medullary thymic epithelial cells and promiscuous gene expression.</a> J Immunol. 190, 1085-1093 (2013).</li><li>Gabler, J., Arnold, J., Kyewski, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Promiscuous+gene+expression+and+the+developmental+dynamics+of+medullary+thymic+epithelial+cells.">Promiscuous gene expression and the developmental dynamics of medullary thymic epithelial cells.</a> Eur J Immunol. 37, 3363-3372 (2007).</li><li>Farr, A., Nelson, A., Truex, J., Hosier, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Epithelial+heterogeneity+in+the+murine+thymus:+a+cell+surface+glycoprotein+expressed+by+subcapsular+and+medullary+epithelium.">Epithelial heterogeneity in the murine thymus: a cell surface glycoprotein expressed by subcapsular and medullary epithelium.</a> The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society. 39, 645-653 (1991).</li><li>Stark, H. J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Authentic+fibroblast+matrix+in+dermal+equivalents+normalises+epidermal+histogenesis+and+dermoepidermal+junction+in+organotypic+co-culture.">Authentic fibroblast matrix in dermal equivalents normalises epidermal histogenesis and dermoepidermal junction in organotypic co-culture.</a> Eur J Cell Biol. 83, 631-645 (2004).</li><li>Schoop, V. M., Mirancea, N., Fusenig, N. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Epidermal+organization+and+differentiation+of+HaCaT+keratinocytes+in+organotypic+coculture+with+human+dermal+fibroblasts.">Epidermal organization and differentiation of HaCaT keratinocytes in organotypic coculture with human dermal fibroblasts.</a> J Invest Dermatol. 112, 343-353 (1999).</li><li>Rouse, R. V., Bolin, L. M., Bender, J. R., Kyewski, B. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Monoclonal+antibodies+reactive+with+subsets+of+mouse+and+human+thymic+epithelial+cells.">Monoclonal antibodies reactive with subsets of mouse and human thymic epithelial cells.</a> The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society. 36, 1511-1517 (1988).</li></ol>

The authors declare no financial or commercial conflict of interest.

Alongside RTOCs, the 3D OTCs have been by far superior in terms of TEC differentiation and pGE maintenance/induction (Table 1) compared to other (i) &#8216;simplified 3D cultures&#8217; using - fibroblasts alone without the scaffold; (ii) 2D systems using - fibroblasts/feeder cells co-cultured with TECs10, (iii) 3T3-J2 cells wherein TEC clones develop, but pGE is lost, (iv) matrigel or (v) ECM components (unpublished data). PGE was maintained for up to 7 days in the 3D OTCs, 4 days being the o...

Developing thymocytes make up about 98 % of the thymus, while the remaining 2 % consists of a variety of cells that collectively compose the thymic stroma (i.e., epithelial cells, dendritic cells, macrophages, B cells, fibroblasts, endothelial cells). The outer cortical epithelial cells (cTECs) procure immigration of pro-T cells from the bone marrow, T cell lineage induction in multipotent pre-T cells and positive selection of self-MHC restricted immature thymocytes. The inner medullary thymic epithelial cells (mTECs) are involved in tolerance induction of those thymocytes with a high-affinity TCR for self-peptide/MHC complexes by either inducing negative selection or their deviation into the T regulatory cell lineage. In the context of central tolerance induction, mTECs are unique in that they express a wide spectrum of tissue-restricted self-antigens (TRAs) thus mirroring the peripheral self. This phenomenon is called promiscuous gene expression (pGE)1,2.
Most current studies on this fascinating cell type rely on ex vivo isolated cells, as various short-term 2D culture systems invariably resulted in the loss of pGE and key regulator molecules like MHC class II, FoxN1 and Aire within the first 2 days3-6. It remained however unclear, which particular components and features of the intact 3D meshwork of the thymus were missing in 2D models. The re-aggregation thymic organ culture (RTOC) has been so far the only 3D system that allows the study of T cell development, on the one hand, and stromal cell biology, on the other hand, in an intact thymic microenvironment7. Yet, RTOCs have certain limitations, i.e., they already contain a complex mixture of cells, require the input of fetal stromal cells and endure a maximal culture period of 5 to 10 days.
The lack of reductionist in vitro culture systems has hampered the study of several aspects of T cell development and thymic organogenesis not least the molecular regulation of pGE and its relationship to the developmental biology of mTECs.
Owing to the close-relatedness of the structured organization of the epithelial cells of skin and thymus, we opted for a 3D organotypic culture (OTC) system that had been developed originally to emulate the differentiation of keratinocytes in vitro and thus create a dermal equivalent. The OTC system consists of an inert scaffold matrix overlaid with dermal fibroblasts that are trapped in a fibrin gel, onto which keratinocytes are seeded8,9. Here, we replaced keratinocytes with purified mTECs. While keeping the basic features of this model, we optimized certain parameters.
In the adopted OTC model mTECs proliferated, underwent terminal differentiation and maintained mTEC identity and pGE, thus closely mimicking in vivo mTECs development10. This technical note provides a detailed protocol allowing the stepwise set-up of thymus OTCs.

<table border="0" cellpadding="0" cellspacing="0">
	<tbody>
		<tr>
			<td>Pregnant C57BL/6 mice&#160;</td>
			<td>Charles River WIGA</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>LS columns</td>
			<td>Miltenyi Biotec</td>
			<td>130-042-401</td>
			<td></td>
		</tr>
		<tr>
			<td>MS columns</td>
			<td>Miltenyi Biotec</td>
			<td>130-042-201</td>
			<td></td>
		</tr>
		<tr>
			<td>CD45 Microbeads, mouse</td>
			<td>Miltenyi Biotec</td>
			<td>130-052-301</td>
			<td></td>
		</tr>
		<tr>
			<td>Anti-PE Microbeads</td>
			<td>Miltenyi Biotec</td>
			<td>130-048-801</td>
			<td></td>
		</tr>
		<tr>
			<td>Streptavidin Microbeads</td>
			<td>Miltenyi Biotec</td>
			<td>130-048-101</td>
			<td></td>
		</tr>
		<tr>
			<td>EpCAM (G8.8 -Alexa 647 and -biotin)</td>
			<td>Ref. 12</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>CD80-PE antibody</td>
			<td>BD Pharmingen</td>
			<td>553769</td>
			<td></td>
		</tr>
		<tr>
			<td>CD45-PerCP antibody</td>
			<td>BD Pharmingen</td>
			<td>557235</td>
			<td></td>
		</tr>
		<tr>
			<td>Ly51-FITC antibody</td>
			<td>BD Pharmingen</td>
			<td>553160</td>
			<td></td>
		</tr>
		<tr>
			<td>CDR1-Pacific Blue</td>
			<td>Ref. 15</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Keratin 14 antibody</td>
			<td>Covance</td>
			<td>PRB-155P</td>
			<td></td>
		</tr>
		<tr>
			<td>Vimentin antibody</td>
			<td>Progen</td>
			<td>GP58</td>
			<td></td>
		</tr>
		<tr>
			<td>Cy3-conjugated AffiniPure Goat anti-Rabbit IgG (H+L)</td>
			<td>Jackson ImmunoResearch&#160;</td>
			<td>111-165-003</td>
			<td></td>
		</tr>
		<tr>
			<td>Alexa 488-conjugated AffiniPure F(ab&#39;)2 Fragment Goat anti-Guinea Pig IgG (H+L)</td>
			<td>Jackson ImmunoResearch&#160;</td>
			<td>106-546-003</td>
			<td></td>
		</tr>
		<tr>
			<td>Goat anti-Rabbit IgG (H+L) Secondary Antibody, Alexa Fluor 488 conjugate</td>
			<td>Molecular Probes (Invitrogen GmbH)</td>
			<td>A-11008</td>
			<td></td>
		</tr>
		<tr>
			<td><a href="https://www.lifetechnologies.com/order/catalog/product/C10339">Click-iT EdU Alexa Fluor 594 Imaging Kit</a></td>
			<td>Invitrogen</td>
			<td><a href="https://www.lifetechnologies.com/order/catalog/product/C10339">C10339</a></td>
			<td></td>
		</tr>
		<tr>
			<td><a href="https://www.lifetechnologies.com/order/catalog/product/C10425">Click-iT EdU Alexa Fluor 488 Flow Cytometry Assay Kit</a></td>
			<td>Invitrogen</td>
			<td><a href="https://www.lifetechnologies.com/order/catalog/product/C10425">C10425</a></td>
			<td></td>
		</tr>
		<tr>
			<td>12-well filter inserts (thincerts)</td>
			<td>Greiner bio-one</td>
			<td>657631</td>
			<td></td>
		</tr>
		<tr>
			<td>12-well plate</td>
			<td>Greiner</td>
			<td>665180-01</td>
			<td></td>
		</tr>
		<tr>
			<td>Jettex 2005/45</td>
			<td>ORSA, Giorla Minore, Italy</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Fibrinogen TISSUECOL-Kit Immuno</td>
			<td>Baxter</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Thrombin TISSUECOL-Kit Immuno</td>
			<td>Baxter</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>PBS</td>
			<td>Serva</td>
			<td>47302.03</td>
			<td></td>
		</tr>
		<tr>
			<td>DMEM</td>
			<td>Lonza</td>
			<td>BE12-604F</td>
			<td></td>
		</tr>
		<tr>
			<td>DMEM/F12</td>
			<td>Lonza</td>
			<td>BE12-719F</td>
			<td></td>
		</tr>
		<tr>
			<td>HEPES</td>
			<td>Gibco</td>
			<td>15630-049&#160;</td>
			<td></td>
		</tr>
		<tr>
			<td>FBS Gold</td>
			<td>GE Healthcare</td>
			<td>A11-151</td>
			<td></td>
		</tr>
		<tr>
			<td>Aprotinin (Trasylol)</td>
			<td>Bayer</td>
			<td>4032037</td>
			<td></td>
		</tr>
		<tr>
			<td>Cholera toxin</td>
			<td>Biomol</td>
			<td>G117</td>
			<td></td>
		</tr>
		<tr>
			<td>Hydrocortisone</td>
			<td>Seromed (Biochrom)</td>
			<td>K3520</td>
			<td></td>
		</tr>
		<tr>
			<td>L-ascorbic acid</td>
			<td>Sigma</td>
			<td>A4034</td>
			<td></td>
		</tr>
		<tr>
			<td>TGF-&#223;1</td>
			<td>Invitrogen</td>
			<td>PHG9214</td>
			<td></td>
		</tr>
		<tr>
			<td>RANKL</td>
			<td>R&#38;D systems</td>
			<td>462-TR-010</td>
			<td></td>
		</tr>
		<tr>
			<td>Thermolysin</td>
			<td>Sigma Aldrich</td>
			<td>&#160;T-7902</td>
			<td></td>
		</tr>
		<tr>
			<td>OCT Compound</td>
			<td>TissueTek</td>
			<td>4583</td>
			<td></td>
		</tr>
		<tr>
			<td>Trizol (aka. Denaturing solution - Acid guanidinium thiocyanate-phenol-chloroform extraction)</td>
			<td>Invitrogen</td>
			<td>10296028</td>
			<td></td>
		</tr>
		<tr>
			<td>FastPrep FP120</td>
			<td>Thermo Scientific</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Collagenase Type IV&#160;</td>
			<td>CellSystems</td>
			<td>LS004189</td>
			<td>0.2 mg/ml and 57U/ml final conc.</td>
		</tr>
		<tr>
			<td>Neutrale Protease (Dispase)</td>
			<td>CellSystems</td>
			<td>LS002104</td>
			<td>0.2 mg/ml and 1.2U/ml final conc.</td>
		</tr>
		<tr>
			<td>DNase I&#160;</td>
			<td>Roche</td>
			<td>11 284 932 001</td>
			<td>25 &#181;g/ml final conc.</td>
		</tr>
	</tbody>
</table>

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.

We adopted a 3D organotypic co-culture model (3D OTC) which had been originally developed for in vitro long term culture of keratinocytes9. MACS-enriched mTECs (see MACS enrichment scheme Figure 1) were seeded onto a scaffold comprising of a fibrin gel and entrapped fibroblasts. The fibroblasts provide the essential extracellular matrix (ECM) supporting mTECs in vitro. MTECs were cultivated in OTCs for 4-14 days in the presence of RANKL in submerged cultures unlike keratinocy...

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

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 ...

3d-organotypic-co-culture-model-supporting-medullary-thymic

Research

JoVE Journal

Developmental Biology

10.6K Views.  German Cancer Research Center (DKFZ). 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. 

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

Culture and Co-Culture of Mouse Ovaries and Ovarian Follicles

The mammalian ovary is composed of ovarian follicles, each follicle consisting of a single oocyte surrounded by somatic granulosa cells, enclosed together within a basement membrane. A finite pool of follicles is laid down during embryonic development, when oocytes in meiotic arrest form a close association with flattened granulosa cells, forming primordial follicles. By or shortly after birth, mammalian ovaries contain their lifetime&#8217;s supply of primordial follicles, from which point onwards there is a steady release of follicles into the growing follicular pool.
The ovary is particularly amenable to development in vitro, with follicles growing in a highly physiological manner in culture. This work describes the culture of whole neonatal ovaries containing primordial follicles, and the culture of individual ovarian follicles, a method which can support the development of follicles from an immature through to the preovulatory stage, after which their oocytes are able to undergo fertilization in vitro. The work outlined here uses culture systems to determine how the ovary is affected by exposure to external compounds. We also describe a co-culture system, which allows investigation of the interactions that occur between growing follicles and the non-growing pool of primordial follicles.

This protocol describes the primary culture/co-culture of mouse ovarian tissue, using ovaries from neonatal mice and individual ovarian follicles from prepubertal mice. The culture techniques support development in a highly physiological manner, allowing investigation of the effect of extrinsic agents on the ovary, and of interactions between ovarian follicles.

The mammalian ovary is composed of ovarian follicles, each follicle consisting of a single oocyte surrounded by somatic granulosa cells, enclosed together ...

Generation of Genetically Modified Organotypic Skin Cultures Using Devitalized Human Dermis

Organotypic cultures allow the reconstitution of a 3D environment critical for cell-cell contact and cell-matrix interactions which mimics the function and physiology of their in vivo tissue counterparts. This is exemplified by organotypic skin cultures which faithfully recapitulates the epidermal differentiation and stratification program. Primary human epidermal keratinocytes are genetically manipulable through retroviruses where genes can be easily overexpressed or knocked down. These genetically modified keratinocytes can then be used to regenerate human epidermis in organotypic skin cultures providing a powerful model to study genetic pathways impacting epidermal growth, differentiation, and disease progression. The protocols presented here describe methods to prepare devitalized human dermis as well as to genetically manipulate primary human keratinocytes in order to generate organotypic skin cultures. Regenerated human skin can be used in downstream applications such as gene expression profiling, immunostaining, and chromatin immunoprecipitations followed by high throughput sequencing. Thus, generation of these genetically modified organotypic skin cultures will allow the determination of genes that are critical for maintaining skin homeostasis.

The goal of this paper is to provide a comprehensive and detailed protocol on how to generate genetically modified human organotypic skin from epidermal keratinocytes and devitalized human dermis.

Organotypic cultures allow the reconstitution of a 3D environment critical for cell-cell contact and cell-matrix interactions which mimics the function ...

Prediction and Validation of Gene Regulatory Elements Activated During Retinoic Acid Induced Embryonic Stem Cell Differentiation

Embryonic development is a multistep process involving activation and repression of many genes. Enhancer elements in the genome are known to contribute to tissue and cell-type specific regulation of gene expression during the cellular differentiation. Thus, their identification and further investigation is important in order to understand how cell fate is determined. Integration of gene expression data (e.g., microarray or RNA-seq) and results of chromatin immunoprecipitation (ChIP)-based genome-wide studies (ChIP-seq) allows large-scale identification of these regulatory regions. However, functional validation of cell-type specific enhancers requires further in vitro and in vivo experimental procedures. Here we describe how active enhancers can be identified and validated experimentally. This protocol provides a step-by-step workflow that includes: 1) identification of regulatory regions by ChIP-seq data analysis, 2) cloning and experimental validation of putative regulatory potential of the identified genomic sequences in a reporter assay, and 3) determination of enhancer activity in vivo by measuring enhancer RNA transcript level. The presented protocol is detailed enough to help anyone to set up this workflow in the lab. Importantly, the protocol can be easily adapted to and used in any cellular model system.

In this work we provide an experimental workflow of how active enhancers can be identified and experimentally validated.

Embryonic development is a multistep process involving activation and repression of many genes. Enhancer elements in the genome are known to contribute to ...

Adenoviral Gene Therapy for Diabetic Keratopathy: Effects on Wound Healing and Stem Cell Marker Expression in Human Organ-cultured Corneas and Limbal Epithelial Cells

The goal of this protocol is to describe molecular alterations in human diabetic corneas and demonstrate how they can be alleviated by adenoviral gene therapy in organ-cultured corneas. The diabetic corneal disease is a complication of diabetes with frequent abnormalities of corneal nerves and epithelial wound healing. We have also documented significantly altered expression of several putative epithelial stem cell markers in human diabetic corneas. To alleviate these changes, adenoviral gene therapy was successfully implemented using the upregulation of c-met proto-oncogene expression and/or the downregulation of proteinases matrix metalloproteinase-10 (MMP-10) and cathepsin F. This therapy accelerated wound healing in diabetic corneas even when only the limbal stem cell compartment was transduced. The best results were obtained with combined treatment. For possible patient transplantation of normalized stem cells, an example is also presented of the optimization of gene transduction in stem cell-enriched cultures using polycationic enhancers. This approach may be useful not only for the selected genes but also for the other mediators of corneal epithelial wound healing and stem cell function.

An example of adenoviral gene therapy in the human diabetic organ-cultured corneas is presented towards the normalization of delayed wound healing and markedly reduced epithelial stem cell marker expression in these corneas. It also describes the optimization of this process in stem cell-enriched limbal epithelial cultures.

The goal of this protocol is to describe molecular alterations in human diabetic corneas and demonstrate how they can be alleviated by adenoviral gene ...

Temporal Ordering of Dynamic Expression Data from Detailed Spatial Expression Maps

During somitogenesis, pairs of epithelial somites form in a progressive manner, budding off from the anterior end of the pre-somitic mesoderm (PSM) with a strict species-specific periodicity. The periodicity of the process is regulated by a molecular oscillator, known as the "segmentation clock," acting in the PSM cells. This clock drives the oscillatory patterns of gene expression across the PSM in a posterior-anterior direction. These so-called clock genes are key components of three signaling pathways: Wnt, Notch, and fibroblast growth factor (FGF). In addition, Notch signaling is essential for synchronizing intracellular oscillations in neighboring cells. We recently gained insight into how this may be mechanistically regulated. Upon ligand activation, the Notch receptor is cleaved, releasing the intracellular domain (NICD), which moves to the nucleus and regulates gene expression. NICD is highly labile, and its phosphorylation-dependent turnover acts to restrict Notch signaling. The profile of NICD production (and degradation) in the PSM is known to be oscillatory and to resemble that of a clock gene. We recently reported that both the Notch receptor and the Delta ligand, which mediate intercellular coupling, themselves exhibit dynamic expression at both the mRNA and protein levels. In this article, we describe the sensitive detection methods and detailed image analysis tools that we used, in combination with the computational modeling that we designed, to extract and overlay expression data from distinct points in the expression cycle. This allowed us to construct a spatio-temporal picture of the dynamic expression profile for the receptor, the ligand, and the Notch target clock genes throughout an oscillation cycle. Here, we describe the protocols used to generate and culture the PSM explants, as well as the procedure to stain for the mRNA or protein. We also explain how the confocal images were subsequently analyzed and temporally ordered computationally to generate ordered sequences of clock expression snapshots, hereafter defined as "kymographs," for the visualization of the spatiotemporal expression of Delta-like1 (Dll1) and Notch1 throughout the PSM.

The segmentation clock drives oscillatory gene expression across the pre-somitic mesoderm (PSM). Dynamic Notch activity is key to this process. We use imaging and computational analyses to extract temporal dynamics from spatial expression data to demonstrate that Delta ligand and Notch receptor expression oscillate in the vertebrate PSM.

During somitogenesis, pairs of epithelial somites form in a progressive manner, budding off from the anterior end of the pre-somitic mesoderm (PSM) with a ...

Rapid, Directed Differentiation of Retinal Pigment Epithelial Cells from Human Embryonic or Induced Pluripotent Stem Cells

We describe a robust method to direct the differentiation of pluripotent stem cells into retinal pigment epithelial cells (RPE). The purpose of providing a detailed and thorough protocol is to clearly demonstrate each step and to make this readily available to researchers in the field. This protocol results in a homogenous layer of RPE with minimal or no manual dissection needed. The method presented here has been shown to be effective for induced pluripotent stem cells (iPSC) and human embryonic stem cells. Additionally, we describe methods for cryopreservation of intermediate cell banks that allow long-term storage. RPE generated using this protocol might be useful for iPSC disease-in-a-dish modeling or clinical application.

This protocol describes how to produce retinal pigment epithelial cells (RPE) from pluripotent stem cells. The method uses a combination of growth factors and small molecules to direct the differentiation of stem cells into immature RPE in fourteen days and mature, functional RPE after three months.

We describe a robust method to direct the differentiation of pluripotent stem cells into retinal pigment epithelial cells (RPE). The purpose of providing ...

Streamlined 3D Cerebellar Differentiation Protocol with Optional 2D Modification

Reducing the complexity and cost of differentiation protocols is important for researchers. This interest fits with concerns about possible unintended effects that extrinsic patterning factors might introduce into human pluripotent stem cell (hPSC) models of brain development or pathophysiology, such as masking disease phenotype. Here, we present two cerebellar differentiation protocols for hPSCs, designed with simpler startup method, fewer patterning factors, and less material requirements than previous protocols. Recently, we developed culture procedures, which generate free-floating 3-dimensional (3D) products consistent with other brain &#34;organoid&#34; protocols, including morphologies relevant to modeling brain development such as sub/ventricular zone- and rhombic lip-like structures. The second uses an adherent, 2D monolayer procedure to complete differentiation, which is shown capable of generating functional cerebellar neurons, as products are positive for cerebellar-associated markers, and exhibit neuron-like calcium influxes. Together, these protocols offer scientists a choice of options suited to different research purposes, as well as a basic model for testing other types of streamlined neural differentiations.

We describe a simplified 3D differentiation protocol for hPSCs, using defined medium and reduced growth factors, capable of generating cell aggregates with early neuroepithelial structures and positive for cerebellar-associated markers, as well as an optional 2D modification for differentiating cells as a monolayer to generate functional neurons.

Reducing the complexity and cost of differentiation protocols is important for researchers. This interest fits with concerns about possible unintended ...

Clonal Analysis of Embryonic Hematopoietic Stem Cell Precursors Using Single Cell Index Sorting Combined with Endothelial Cell Niche Co-culture

The ability to study hematopoietic stem cell (HSC) genesis during embryonic development has been limited by the rarity of HSC precursors in the early embryo and the lack of assays that functionally identify the long-term multilineage engraftment potential of individual putative HSC precursors. Here, we describe methodology that enables the isolation and characterization of functionally validated HSC precursors at the single cell level. First, we utilize index sorting to catalog the precise phenotypic parameter of each individually sorted cell, using a combination of phenotypic markers to enrich for HSC precursors with additional markers for experimental analysis. Second, each index-sorted cell is co-cultured with vascular niche stroma from the aorta-gonad-mesonephros (AGM) region, which supports the maturation of non-engrafting HSC precursors to functional HSC with multilineage, long-term engraftment potential in transplantation assays. This methodology enables correlation of phenotypic properties of clonal hemogenic precursors with their functional engraftment potential or other properties such as transcriptional profile, providing a means for the detailed analysis of HSC precursor development at the single cell level.

Here we present methodology for the clonal analysis of hematopoietic stem cell precursors during murine embryonic development. We combine index sorting of single cells from the embryonic aorta-gonad-mesonephros region with endothelial cell co-culture and transplantation to characterize the phenotypic properties and engraftment potential of single hematopoietic precursors.

The ability to study hematopoietic stem cell (HSC) genesis during embryonic development has been limited by the rarity of HSC precursors in the early ...

Proliferation and Differentiation of Murine Myeloid Precursor 32D/G-CSF-R Cells

Understanding of the hematopoietic stem and progenitor cell biology has important implications for regenerative medicine and the treatment of hematological pathologies. Despite the most relevant data that can be acquired using in vivo models or primary cultures, the low abundance of hematopoietic stem and progenitor cells considerably restricts the pool of suitable techniques for their investigation. Therefore, the use of cell lines allows sufficient production of biological material for the performance of screenings or assays that require large cell numbers. Here we present a detailed description, readout, and interpretation of proliferation and differentiation assays which are used for the investigation of processes involved in myelopoiesis and neutrophilic differentiation. These experiments employ the 32D/G-CSF-R cytokine dependent murine myeloid cell line, which possesses the ability to proliferate in the presence of IL-3 and differentiate in G-CSF. We provide optimized protocols for handling 32D/G-CSF-R cells and discuss major pitfalls and drawbacks that might compromise the described assays and expected results. Additionally, this article contains protocols for lentiviral and retroviral production, titration, and transduction of 32D/G-CSF-R cells. We demonstrate that genetic manipulation of these cells can be employed to successfully perform functional and molecular studies, which can complement results obtained with primary hematopoietic stem and progenitor cells or in vivo models.

Here detailed protocols for culturing the murine myeloid precursor 32D/G-CSF-R cell line, performing viral infections, and carrying out proliferation and differentiation assays are presented. This cell line is suitable for studying myeloid cell development, and the role of genes of interest in myeloid cell growth and neutrophilic differentiation.

Understanding of the hematopoietic stem and progenitor cell biology has important implications for regenerative medicine and the treatment of ...

Hemogenic Reprogramming of Human Fibroblasts by Enforced Expression of Transcription Factors

The cellular and molecular mechanisms underlying specification of human hematopoietic stem cells (HSCs) remain elusive. Strategies to recapitulate human HSC emergence in vitro are required to overcome limitations in studying this complex developmental process. Here, we describe a protocol to generate hematopoietic stem and progenitor-like cells from human dermal fibroblasts employing a direct cell reprogramming approach. These cells transit through a hemogenic intermediate cell-type, resembling the endothelial-to-hematopoietic transition (EHT) characteristic of HSC specification. Fibroblasts were reprogrammed to hemogenic cells via transduction with GATA2, GFI1B and FOS transcription factors. This combination of three factors induced morphological changes, expression of hemogenic and hematopoietic markers and dynamic EHT transcriptional programs. Reprogrammed cells generate hematopoietic progeny and repopulate immunodeficient mice for three months. This protocol can be adapted towards the mechanistic dissection of the human EHT process as exemplified here by defining GATA2 targets during the early phases of reprogramming. Thus, human hemogenic reprogramming provides a simple and tractable approach to identify novel markers and regulators of human HSC emergence. In the future, faithful induction of hemogenic fate in fibroblasts may lead to the generation of patient-specific HSCs for transplantation.

This protocol demonstrates the induction of a hemogenic program in human dermal fibroblasts by enforced expression of the transcription factors GATA2, GFI1B and FOS to generate hematopoietic stem and progenitor cells.

The cellular and molecular mechanisms underlying specification of human hematopoietic stem cells (HSCs) remain elusive. Strategies to recapitulate human ...