We wish to thank Dr. Rossant and Dr. Bilodeau for the Nkx2-1mcherry ESC used in experiments depicted in Figures 1-3. FACS was performed in The SickKids-UHN Flow Cytometry Facility. This work was supported by operating grants from the Canadian Institutes for Health Research and an infrastructure grant (CSCCD) from the Canadian Foundation of Innovation.

Animal experiments were carried out in accordance with the Animal Care Committee guidelines of the Hospital for Sick Children Research Institute.
1. Scaffold Preparation
<ol>
	<li>Decellularization of lungs
	<ol>
		<li>Euthanize adult Wistar rats using CO2 chamber. Place animal in the chamber and start 100% CO2 exposure at a fill rate of 10-30% of chamber volume per minute.
		<ol>
			<li>Observe animal for unconsciousness; this will occur after approximately 2-3 min. If unconsciousness does...

<ol>
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There are no competing financial interests to declare.

The protocol described here generates mature ESC-derived airway epithelia using only natural lung scaffolds to direct differentiation with no other supplementation. This culture setup is defined, serum-free, inexpensive, and reproducible. No growth factor supplementation of base differentiation media is required. Previously published methods for generating stem cell-derived lung epithelial cells have used 2-dimensional strategies with growth factor supplementation to promote lineage restriction3,4,8,18,19. The...

Directed differentiation of pluripotent cells to the lung lineage is dependent on precise signaling events in the microenvironment 1,2. Due to the dynamic nature of this process it has been challenging to mimic the precise events of lung organogenesis in vitro. Recent reports have used step-wise lineage restriction strategies with soluble growth factor supplementation of two-dimensional cultures to achieve lung differentiation3-8. In step-wise differentiation protocols, pluripotent cells, whether embryonic stem cells (ESC) or induced pluripotent stem cells, were first differentiated to the definitive endoderm germ layer. Endodermal cells were subsequently pushed to an anterior endoderm fate and thereafter to lung progenitor cells, as identified by the expression of homeodomain-containing transcription factor NKX2-1. These lung progenitors were further differentiated to proximal (airway) or distal (alveolar) lung epithelial cells with continued growth factor supplementation. Such 2-dimensional strategies have had some success in generating lung epithelial cells, however there are several limitations including unclear efficiencies, possible contamination from other endodermal lineages, lack of a 3-dimensional (3D) structure, and in some instances use of undefined cultures with serum supplementation. Culture of pluripotent or differentiated cells on decellularized lung scaffolds is increasingly used as an assay to assess the regenerative potential of seeded cells in forming lung epithelial structures3,5,6,8,9. Such reports culture seeded cells on scaffolds with continued growth factor or serum supplementation.
Lung development involves the division, migration, gene expression and differentiation of individual cells in response to environmental cues. The extra cellular matrix (ECM) is a latticework of glycoproteins that in addition to providing structural support, directs tissue morphogenesis by integrating and regulating these processes10,11. By using the lung ECM scaffold as a natural platform for endoderm culture to better mimic the in vivo lung developmental milieu, we have generated stem cell-derived airway epithelial cells in a defined 3D-culture setting with high efficiency and reproducibility.
Rat lung ECM scaffolds were generated by decellularization as well as mouse ESC-derived endodermal cells were generated and subsequently seeded onto these scaffolds. Dual expression of CXCR4 &#38; c-KIT proteins indicates a definitive endoderm cell identity and cells positive for both SOX2 &#38; NKX2-1 expression are identified as airway (proximal lung) progenitor cells. Definitive endoderm cells were cultured at air liquid interface (ALI) for up to three weeks to generate functional airway epithelial cells in vitro.
This protocol promotes lung lineage differentiation of definitive endoderm as early as 7 days, observed with the emergence of NKX2-1+/SOX2+ early proximal lung progenitors. By day 14 and 21 of culture mature airway epithelial cell populations emerge including ciliated (TUBB4A+), club (SCGB1A1+), and basal (TRP63+, KRT5+) cells with morphological and functional resemblance to native mouse airways. This protocol demonstrates the importance of the 3D-matrix microenvironment for achieving robust differentiation to airway epithelial cells.

<table border="0" cellpadding="0" cellspacing="0" width="901">
	<tbody>
		<tr height="22">
			<td height="22" style="height:22px;width:291px;">Reagents</td>
			<td style="width:163px;"></td>
			<td style="width:168px;"></td>
			<td style="width:281px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:291px;">Perfusion solution</td>
			<td style="width:163px;">Sigma</td>
			<td style="width:168px;">H0777</td>
			<td style="width:281px;">10U/mL heparin</td>
		</tr>
		<tr height="39">
			<td height="39" style="height:39px;width:291px;">Perfusion solution</td>
			<td style="width:163px;">Gibco</td>
			<td align="right" style="width:168px;">14170112</td>
			<td style="width:281px;">dissolved in Hank&#39;s balanced salt solution (HBSS-)</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:291px;">Decellularization solution</td>
			<td style="width:163px;">BioShop</td>
			<td style="width:168px;">CHA003</td>
			<td style="width:281px;">8mM CHAPS&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:291px;">Decellularization solution</td>
			<td style="width:163px;">Sigma</td>
			<td style="width:168px;">E9884</td>
			<td style="width:281px;">25mM EDTA&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:291px;">Decellularization solution</td>
			<td style="width:163px;">BioShop</td>
			<td style="width:168px;">SOD002</td>
			<td style="width:281px;">1M NaCl</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:291px;">Decellularization solution</td>
			<td style="width:163px;">Gibco</td>
			<td style="width:168px;">14190-144</td>
			<td style="width:281px;">dissolved in PBS</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:291px;">Benzonase nuclease</td>
			<td style="width:163px;">Novagen</td>
			<td style="width:168px;">70664-3</td>
			<td style="width:281px;">90U/mL Benzonase nuclease&#160;</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:291px;">Benzonase nuclease</td>
			<td style="width:163px;">Gibco</td>
			<td style="width:168px;">14190-144</td>
			<td style="width:281px;">diluted in PBS</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:291px;">Antimicrobial solution&#160;</td>
			<td style="width:163px;">Gibco</td>
			<td align="right" style="width:168px;">15140</td>
			<td style="width:281px;">200U/mL penicillin streptomycin&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:291px;">Antimicrobial solution&#160;</td>
			<td style="width:163px;">Gibco</td>
			<td align="right" style="width:168px;">15290</td>
			<td style="width:281px;">25&#956;g/mL amphotericin B&#160;</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:291px;">Antimicrobial solution&#160;</td>
			<td style="width:163px;">Gibco</td>
			<td style="width:168px;">14190-144</td>
			<td style="width:281px;">diluted in PBS</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:291px;">Trypsinization&#160;</td>
			<td style="width:163px;">Gibco</td>
			<td style="width:168px;">12605-028</td>
			<td style="width:281px;">TrypLE</td>
		</tr>
		<tr height="39">
			<td height="39" style="height:39px;width:291px;">Serum free differentiation media (SFDM)</td>
			<td style="width:163px;">Gibco</td>
			<td style="width:168px;">IMDM 2440-053, F12 11765-054</td>
			<td style="width:281px;">3:1 ratio of IMDM and Ham&#8217;s modified F12 medium</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:291px;">Serum free differentiation media (SFDM)</td>
			<td style="width:163px;">Gibco</td>
			<td style="width:168px;">12587-010</td>
			<td style="width:281px;">B27 supplement (50x dilution)&#160;</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:291px;">Serum free differentiation media (SFDM)</td>
			<td style="width:163px;">Gibco</td>
			<td style="width:168px;">17502-048</td>
			<td style="width:281px;">N2 supplement (100x dilution)&#160;</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:291px;">Serum free differentiation media (SFDM)</td>
			<td style="width:163px;">Gibco</td>
			<td style="width:168px;">15260-037</td>
			<td style="width:281px;">0.05% (Fraction V) bovine serum albumin</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:291px;">Serum free differentiation media (SFDM)</td>
			<td style="width:163px;">Gibco</td>
			<td style="width:168px;">35050-061</td>
			<td style="width:281px;">200mM Glutamax&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:291px;">Serum free differentiation media (SFDM)</td>
			<td style="width:163px;">Sigma</td>
			<td style="width:168px;">M6145</td>
			<td style="width:281px;">4&#956;M monothioglycerol</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:291px;">Serum free differentiation media (SFDM)</td>
			<td style="width:163px;">Sigma</td>
			<td style="width:168px;">A4403&#160;</td>
			<td style="width:281px;">0.05mg/mL ascobic acid</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:291px;">Endoderm induction</td>
			<td style="width:163px;">R&#38;D</td>
			<td style="width:168px;">338-AC/CF</td>
			<td style="width:281px;">Activin A</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:291px;">Antibodies</td>
			<td style="width:163px;"></td>
			<td style="width:168px;"></td>
			<td style="width:281px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:291px;">CDH1</td>
			<td style="width:163px;">BD Biosciences</td>
			<td align="right" style="width:168px;">610181</td>
			<td style="width:281px;">Mouse, non-conjugated, 1:100</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:291px;">C-KIT</td>
			<td style="width:163px;">BD Biosciences</td>
			<td align="right" style="width:168px;">558163</td>
			<td style="width:281px;">Rat, PE-Cy7, 1:100</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:291px;">CXCR4</td>
			<td style="width:163px;">BD Biosciences</td>
			<td align="right" style="width:168px;">558644</td>
			<td style="width:281px;">Rat, APC, 1:100</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:291px;">KRT5</td>
			<td style="width:163px;">Abcam</td>
			<td style="width:168px;">ab24647</td>
			<td style="width:281px;">Rabbit, non-conjugated, 1:1000</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:291px;">NKX2-1</td>
			<td style="width:163px;">Abcam</td>
			<td style="width:168px;">ab76013</td>
			<td style="width:281px;">Rabbit, non-conjugated, 1:200</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:291px;">Laminin</td>
			<td style="width:163px;">Novus Biologicals</td>
			<td style="width:168px;">NB300-144</td>
			<td style="width:281px;">Rabbit, non-conjugated, 1:200</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:291px;">SCGB1A1</td>
			<td style="width:163px;">Santa Cruz</td>
			<td style="width:168px;">sc-9772&#160;</td>
			<td style="width:281px;">Goat, non-conjugated, 1:1000</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:291px;">SOX2</td>
			<td style="width:163px;">R&#38;D Systems</td>
			<td style="width:168px;">AF2018&#160;</td>
			<td style="width:281px;">Goat, non-conjugated, 1:400</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:291px;">TRP63</td>
			<td style="width:163px;">Santa Cruz</td>
			<td style="width:168px;">sc-8431</td>
			<td style="width:281px;">Mouse, non-conjugated, 1:200</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:291px;">TUBB4A</td>
			<td style="width:163px;">BioGenex</td>
			<td style="width:168px;">MU178-UC</td>
			<td style="width:281px;">Mouse, non-conjugated, 1:500</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:291px;">Goat IgG&#160;</td>
			<td style="width:163px;">Invitrogen</td>
			<td style="width:168px;">A-11055</td>
			<td style="width:281px;">Donkey, Alexa Fluor 488, 1:200</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:291px;">Mouse IgG&#160;</td>
			<td style="width:163px;">Invitrogen</td>
			<td style="width:168px;">A-21202</td>
			<td style="width:281px;">Donkey, Alexa Fluor 488, 1:200</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:291px;">Mouse IgG&#160;</td>
			<td style="width:163px;">Invitrogen</td>
			<td style="width:168px;">A-31571</td>
			<td style="width:281px;">Donkey, Alexa Fluor 647, 1:200</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:291px;">Rabbit IgG&#160;</td>
			<td style="width:163px;">Invitrogen</td>
			<td style="width:168px;">A-21206</td>
			<td style="width:281px;">Donkey, Alexa Fluor 488, 1:200</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:291px;">Rabbit IgG&#160;</td>
			<td style="width:163px;">Invitrogen</td>
			<td style="width:168px;">A-31573</td>
			<td style="width:281px;">Donkey, Alexa Fluor 647, 1:200</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:291px;">Other Materials</td>
			<td style="width:163px;"></td>
			<td style="width:168px;"></td>
			<td style="width:281px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Low adherent plates</td>
			<td style="width:163px;">Nunc</td>
			<td style="width:168px;">Z721050&#160;</td>
			<td style="width:281px;">Low cell binding plates,&#160; 6 wells&#160;&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Air-liquid interface membranes&#160;</td>
			<td>Whatman</td>
			<td align="right">110614</td>
			<td>Hydrophobic Nucleopore membrane, 8&#956;m pore size</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Vibratome</td>
			<td>Leica</td>
			<td>VT1200S&#160;</td>
			<td>Leica Vibratome</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">Tissue Adhesive</td>
			<td>Ted Pella</td>
			<td align="right">10033</td>
			<td>Pelco tissue adhesive</td>
		</tr>
	</tbody>
</table>

generation of esc-derived mouse airway epithelial cells using decellularized lung scaffolds

Lung lineage differentiation requires integration of complex environmental cues that include growth factor signaling, cell-cell interactions and cell-matrix interactions. Due to this complexity, recapitulation of lung development in vitro to promote differentiation of stem cells to lung epithelial cells has been challenging. In this protocol, decellularized lung scaffolds are used to mimic the 3-dimensional environment of the lung and generate stem cell-derived airway epithelial cells. Mouse embryonic stem cell are first differentiated to the endoderm lineage using an embryoid body (EB) culture method with activin A. Endoderm cells are then seeded onto decellularized scaffolds and cultured at air-liquid interface for up to 21 days. This technique promotes differentiation of seeded cells to functional airway epithelial cells (ciliated cells, club cells, and basal cells) without additional growth factor supplementation. This culture setup is defined, serum-free, inexpensive, and reproducible. Although there is limited contamination from non-lung endoderm lineages in culture, this protocol only generates airway epithelial populations and does not give rise to alveolar epithelial cells. Airway epithelia generated with this protocol can be used to study cell-matrix interactions during lung organogenesis and for disease modeling or drug-discovery platforms of airway-related pathologies such as cystic fibrosis.

As outlined in this protocol, robust differentiation of definitive endoderm to mature airway epithelial cells can be achieved using extended culture of seeded cells on decellularized lung scaffold sections. It is recommended that decellularized scaffolds be characterized to ensure (1) host cells are completely removed, and (2) extracellular matrix proteins are preserved prior to using scaffolds for differentiation. Decellularization can be assessed using tissue staining with hematoxylin a...

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Generation of ESC-derived Mouse Airway Epithelial Cells Using Decellularized Lung Scaffolds

This protocol efficiently directs mouse embryonic stem cell-derived definitive endoderm to mature airway epithelial cells. This differentiation technique uses 3-dimensional decellularized lung scaffolds to direct lung lineage specification, in a defined, serum-free culture setting.

Lung lineage differentiation requires integration of complex environmental cues that include growth factor signaling, cell-cell interactions and ...

The overall goal of this procedure, is to direct the differentiation of mouse embryonic stem cells into mature airway epithelial cells, using a 3D culture set up with decellularized lung scaffolds.This method can help answer key questions in the area of lung development, such as the role of cell matrix contractions and growth factor signalling during lung lineage differentiation.The main advantage of this technique is that it uses a 3D culture system in a defined serum free setting, and achieves robust airway epithelial differentiation with limited contamination from other endoderm lineages.After euthanizing an adult wistar rat, according to the text protocol, secure the animal to a dissecting surface by fixing forepaws and hindlegs, and use 70%ethanol to spray down the chest and abdomen.Create an incision just below the rib cage.Cut through the skin and expose the diaphragm.Then, make small incisions through the diaphragm, to cause the lungs to retract, reducing the chance of puncturing the lungs.Next, create a vertical incision along the sternum, and open the thoracic cavity to access the heart and lungs.Then with a suture, ligate the inferior vena cava, and use small dissecting scissors to place a small incision in the left atrium.Using a prepared 10ml syringe with a 25 gauge needle filled with heparinized Hank's Balance salt solution, start lung perfusion by inserting the needle into the right ventricle, and push the buffer through the pulmonary circulation.Continue the perfusion until the lungs turn white, and the fluid flowing from the left atrium runs clear.Following perfusion, expose the trachea, and make a small incision near the thyroid cartilage for canulation.Then, with a plastic catheter, canulate the trachea and use a suture to secure it in place.Now, set up a gravity perfusion system by fixing a 10ml syringe to a retort stand and clamp.Then, remove and discard the syringe plunger.Secure the maximum filling point on the syringe barrel at 20 cm above the lungs, then attach a two way stopcock to the end of the syringe, and a long plastic tubing to the other end of the stopcock.Gently pull out the catheter from the trachea, and attach to the end of the plastic tubing.Then, pour decellularization solution into the syringe and allow the solution to completely fill the attached plastic tubing and catheter.Place the solution filled catheter back into the trachea and lavage the lungs by filling to total lung capacity for one minute.Then remove the catheter from the trachea to allow the fluid to flow out of the lungs.Repeat the lavage of the lungs eight times with decellularization solution, followed by ten rinses with PBS.The lungs will appear white with the completion of the lavage steps.Then dissect the trachea and lungs from the neck and chest cavity.Remove excess tissue from the dissected lungs, including the esophagus and heart, then transfer the lungs into cold PBS until preparation for vibratome sectioning.To prepare thick sections, make approximately 15ml of 2%and 4%low melting point agarose in PBS, and enough 6%agarose for embedding all lobes into small rectangular blocks.After transferring the agarose to 15ml tubes, place the tubes on a heat block and maintain the temperature above 40 degrees celsius to avoid gelling.Using small scissors, dissect the decellularized lung at the end of each lobar bronchus, and detach each lobe.Then use absorbent sheets to remove excess PBS, and transfer the lobes to 2%agarose on the heating block for five minutes to coat the tissue.After transferring each lobe to a petri dish, place the dish on a cold plate and allow the surface to gel for one minute.Gently place the lobes into 4%agarose, and after incubating for five minutes and cooling, repeat the coating with 6%agarose.After coating, use metal base molds to embed each lobe separately in 6%agarose, with at least 3ml of agarose surrounding the tissue from the edges.Next, with forceps, orient each lobe by positioning the tissue's largest flat edge at the surface of the metal mold facing the experimentor, and complete the embedding using plastic cassettes.Allow the blocks to gel on a cold plate for at least 30 minutes before vibratome sectioning.Alternatively, store the blocks in a humidified chamber for up to 12 hours at four degrees celsius prior to vibratome sectioning.To prepare sections, set up the vibratome by filling the sectioning chamber with cold PBS.Set up a surrounding ice bath to maintain a cold temperature throughout sectioning.Now, remove the blocks from the metal molds, and use a razor blade to trim down the excess agarose surrounding the lobes, while keeping approximately three millimetres from the edge of the tissue.Using adhesive, fix the tissue to the center of the specimen plate, and submerge the plate into the PBS filled sectioning chamber.Load the sectioning blade on the vibratome.Set the sectioning boundaries on the vibratome, by selecting the following speed, amplitude, and thickness values respectively.Section each lobe completely, and if sections do not fully separate from each other, use small scissors to manually cut the sections free.Then, gently collect scaffold sections, and transfer into cold PBS.Using forceps, gently free each section from the surrounding agarose.To decontaminate scaffold sections, after transferring them from PBS to microcentrifuge tubes, add 90 units per milliliter of nuclease in PBS, and incubate on a rotator at room temperature for 12 to 24 hours.After transferring sections to new microcentrifuge tubes, according to the text protocol, under sterile conditions add antimicrobial solution, and incubate on a rotator at room temperature for six hours.Then under sterile conditions, use PBS to rinse the scaffolds twice and transfer them into serum free medium, or SFDM, prior to seeding with cells.To set up an air liquid interface culture, use sterile forceps to place hydrophobic membranes on a petri dish.Then, transfer each decellularized scaffold section from SFDM onto a membrane, ensuring the sections are spread evenly on the membrane.Prepare six or twelve well plates by filling wells with 1ml or 0.5ml of SFDM respectively.Then, gently place the membranes into the wells, allowing the membrane to float on top of the medium creating an air liquid culture set up.To seed 3D scaffolds, following the preparation of endodermal cells and fluorescence activated cell sorting, to enrich for a definitive endoderm, use a haemocytometer to count the sorted cells.Then spin down the cells at 400 Gs for five minutes.Using SFDM, re-suspend the pelleted cells to approximately 100, 000 cells in 10

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8.6K visualizações.  Hospital for Sick Children. The overall goal of this procedure, is to direct the differentiation of mouse embryonic stem cells into mature airway epithelial cells, using a 3D culture set up with decellularized lung scaffolds.This method can help answer key questions in the area of lung development, such as the role of cell matrix contractions and growth factor signalling during lung lineage differentiation.The main advantage of this technique is that it uses a 3D culture system in a defined serum free setting, and achie...