The SNSF grant 310030_219210 to J.H.N. supported the publication of this manuscript without restrictions. Figure 1 has been created with the help of BioRender.com.

The procedures were approved by the ethics committee of Northwest and Central Switzerland (EKNZ; Project-ID 2019-00273). All patients provided written informed consent for the experimental use of biopsies before the endoscopic examination. The reagents and equipment used in the study are listed in the Table of Materials.
1. Cell isolation for patient-derived esophageal organoids
NOTE: A list of the medium constituents for culturing human esophageal organoids is provided in Table 1.
<ol>
	<li>Obtain the biopsies. 
	NOTE: In the present study, two biopsies from one esophagus segment are obtained during esophagogastroduodenoscopy with biopsy forceps using a gastroscope with a 2.8 mm working channel.</li>
	<li>Transfer the biopsies into commercially available keratinocyte serum-free medium (KSFM; Ca2+ 0.09 mM, 1 ng/mL EGF, 50 &#181;g/mL BPE). 
	NOTE: Biopsies can be stored on ice for several hours until use.</li>
	<li>Replace the KSFM medium with 1 mL of Dispase I (10 U/mL) and incubate the biopsies for 10 min at room temperature.</li>
	<li>Centrifuge the biopsies at room temperature at 300 x g for 2 min.</li>
	<li>Aspirate the Dispase using a 1000 &#181;L pipette without touching the biopsies and the cell debris pellet.</li>
	<li>Rinse the biopsies with 1 mL Dulbecco&#39;s Phosphate-Buffered Saline (DPBS).</li>
	<li>Centrifuge the biopsies at room temperature at 300 x g for 2 min.</li>
	<li>Aspirate the supernatant using a 1000 &#181;L pipette.</li>
	<li>Incubate the biopsies with 500 &#181;L of Trypsin-EDTA (0.05%) at 37 &#176;C for 10 min while shaking at 800 rpm.</li>
	<li>Perform mechanical disruption by repeated up-and-down pipetting until a single-cell suspension is obtained.</li>
	<li>Filter the cells through a 70 &#181;m cell strainer using the rubber plunger head of a tuberculin syringe.</li>
	<li>Wash the strainer with 2-4 mL of soybean trypsin inhibitor (250 &#181;g/mL).</li>
	<li>Filter the cells through a 35 &#181;m cell strainer with a snap-on cap on a 5 mL round-bottomed polystyrene tube.</li>
	<li>Transfer the single-cell solution to a 15 mL conical tube.</li>
	<li>Centrifuge at 300 x g for 5 min at 4 &#176;C.</li>
	<li>Aspirate the supernatant using a 1000 &#181;L pipette.</li>
	<li>Resuspend the cells in 100 &#181;L of KSFM medium.</li>
	<li>Mix 10 &#181;L of trypan blue with 10 &#181;L of cell suspension.</li>
	<li>Count the cells using an automated cell counter.</li>
</ol>
2. Patient-derived organoid culture
<ol>
	<li>Add 1-2 mL of KSFM to the cell suspension after counting.</li>
	<li>Centrifuge at 300 x g for 5 min at 4 &#176;C.</li>
	<li>Aspirate the supernatant with a 1000 &#181;L pipette without disturbing the cell pellet.</li>
	<li>Resuspend the cell pellet in Basement membrane extract (BME) hydrogel matrix (40 &#181;L of BME per 20,000 cells). 
	NOTE: After adding the BME, keep the cells on ice to prevent premature solidification of the BME.</li>
	<li>Cut off a 200 &#181;L pipette tip to aspirate the viscous BME-cell suspension mixture.</li>
	<li>Form 40 &#181;L droplets in a pre-warmed (37 &#176;C) suspension cell culture plate.</li>
	<li>Incubate the plate without medium for 20-30 min at 37 &#176;C to ensure solidification of the BME droplets.</li>
	<li>Add pre-warmed KSFM-C medium supplemented with 10 &#181;M of Y27632 (ROCK-inhibitor) for the first two days of culture.</li>
	<li>Replace the medium with new KSFM-C medium (without Y27632 and +/- cytokine of interest) every other day.</li>
	<li>Aspirate the medium and scratch off droplets with the pipet tip while continuously adding 1 mL of Dispase II (1.5 U/mL) to the well.</li>
	<li>Transfer the BME-dispase mixture into a 15 mL centrifuge tube and incubate it for 20 min at 37 &#176;C in a shaking water bath to digest the BME.</li>
	<li>Centrifuge at 250 x g for 3 min at 4 &#176;C and aspirate the Dispase II.</li>
	<li>Proceed according to the protocol of the interest readout (e.g., RNA isolation, protein isolation, or fixation with 4% PFA for histology).</li>
</ol>
3. Cell isolation for patient-derived air-liquid interface (ALI) cultures
<ol>
	<li>Obtain the biopsies. During esophagogastroduodenoscopy using a gastroscope with a 2.8 mm working channel, two biopsies are taken from one esophagus segment with biopsy forceps.</li>
	<li>Place the biopsies into commercially available keratinocyte serum-free medium (KSFM; Ca2+ 0.09 mM, 1 ng/mL EGF, 50 &#181;g/mL BPE) and store on ice for several hours until use.</li>
	<li>Exchange KSFM with 1 mL of Dispase (10 U/mL). Afterward, incubate the biopsies for 10 min at room temperature.</li>
	<li>Centrifuge the biopsies at room temperature at 300 x g for 2 min.</li>
	<li>Remove the Dispase using a 1000 &#181;L pipette without touching the biopsies and cell debris pellet.</li>
	<li>Wash the biopsies with 1 mL of DPBS.</li>
	<li>At room temperature, spin down the biopsies at 300 x g for 2 min.</li>
	<li>Aspirate the supernatant with a 1000 &#181;L pipette.</li>
	<li>Incubate the biopsies in 500 &#181;L of Trypsin-EDTA (0.05%) at 37 &#176;C for 10 min and continuously mix at 800 rpm during incubation.</li>
	<li>Disrupt the biopsies mechanically with repeated up-and-down pipetting till a single-cell suspension is obtained.</li>
	<li>Pass the dissociated cells through a 70 &#181;m cell strainer with a rubber plunger head from a tuberculin syringe and collect the cells in a 50 mL conical tube.</li>
	<li>Wash the strainer with 2-4 mL of soybean trypsin inhibitor (250 &#181;g/mL) to remove the remaining cells from the strainer.</li>
	<li>Filter the cells with a 35 &#181;m cell strainer snap cap into a 5 mL round bottom polystyrene tube.</li>
	<li>Transfer cells into a 15 mL conical tube.</li>
	<li>Centrifuge at 300 x g at 4 &#176;C for 5 min.</li>
	<li>Remove the supernatant with a 1,000 &#181;L pipette.</li>
	<li>Resuspend the cell pellet in 4 mL of KSFM medium (Ca2+ 0.09 mM), including 10 &#181;M Y27632.</li>
	<li>Transfer the cells into a T25 cell culture flask.</li>
	<li>To expand the primary keratinocytes, culture the cells till 60%-80% confluency for approximately 1 week. 
	NOTE: Passage (P)0 forms islet-like cell conglomerates and is not a monolayer. Primary keratinocytes form monolayers from P1 on.</li>
	<li>Passage at 60%-80% confluency and reseed P1 in 2-3 T25 or 1-2 T75 cell culture flasks.</li>
	<li>Passage P1 again when keratinocytes form a monolayer with 60%-80% confluency.</li>
</ol>
4. Patient-derived air-liquid interface (ALI) culture
<ol>
	<li>Seed P2 primary keratinocytes onto transwell inserts for the ALI culture. 
	NOTE: Seed 400,000 cells in 12 well-inserts (200,000 keratinocytes per 0.6 cm2) in 500 &#181;L of KSFM (Ca2+ 0.09 mM, 1 ng/mL EGF, 50 &#181;g/mL BPE).
	<ol>
		<li>Seed 150,000 cells in 24 well-inserts (155,000 keratinocytes per 0.5 cm2) in 100 &#181;L of KSFM (Ca2+ 0.09 mM, 1 ng/mL EGF, 50 &#181;g/mL BPE).</li>
		<li>Alternatively, freeze in the KSFM medium (Ca2+ 0.09 mM + 10% DMSO) at -80 &#176;C for 24 h and then transfer the frozen cells to liquid nitrogen for later use. 
		NOTE: When using frozen vials, passage once more after thawing before using the cells for the ALI culture.</li>
	</ol>
	</li>
	<li>Add medium to the lower well beneath the insert of the transwell culture plate. 
	NOTE: For 12 well plates: 1.5 mL of KSFM (Ca2+ 0.09 mM, 1 ng/mL EGF, 50 &#181;g/mL BPE). For 24 well-plates: 600 &#181;L of KSFM (Ca2+ 0.09 mM, 1 ng/mL EGF, 50 &#181;g/mL BPE).</li>
	<li>Replace the medium to high calcium KSFM (Ca2+ 1.8 mM, 1 ng/mL EGF, 50 &#181;g/mL BPE) after 2 days.</li>
	<li>Change the high calcium KSFM medium every second day until day 7.</li>
	<li>Perform airlift on day 7 by aspirating the medium from the upper chamber and replacing the medium in the lower chamber with high calcium KSFM (Ca2+ 1.8 mM, 1 ng/mL EGF, 50 &#181;g/mL BPE) containing 10 ng/mL KGF (=FGF7), 75 &#181;g/mL ascorbic acid (AA).
	<ol>
		<li>Optional: Add cytokine of interest at the desired concentration to the medium.</li>
	</ol>
	</li>
	<li>Change the medium every second day until day 14.</li>
</ol>
5. Transepithelial electrical resistance (TEER) measurement
<ol>
	<li>Sterilize the electrode of the TEER meter by immersing it in a well of a 24-well plate with 5% sodium hypochlorite for 10-15 min.</li>
	<li>Wash off the 5% sodium hypochlorite by immersing the electrode into 4 subsequential wells with sterile ddH2O and letting the electrode air dry.</li>
	<li>Set the blank by placing one electrode in the well and the second electrode into the transwell insert, filling it with PBS, and measuring the TEER. 
	NOTE: Recommended volumes for TEER measurements: For 12 well-plate (1900 &#181;L in the well and 900 &#181;L in the insert). For 24 well-plate (750-1000 &#181;L in the well and 250 &#181;L in the insert).</li>
	<li>Replace the medium of the ALI cultures with room-temperature sterile PBS. 
	NOTE: Remove the medium from the lower well and, in a second step, from the transwell insert. Similarly, add PBS first to the insert and then to the lower well to prevent detachment of the ALI culture from the transwell membrane.</li>
	<li>Place the TEER meter electrodes in the experimental wells with ALI cultures and perform the TEER measurement1. 
	NOTE: Perform TEER measurements every second day before the medium is changed.</li>
</ol>
6. Macromolecular flux
<ol>
	<li>Dilute the FITC-Dextran (3-5 kDa) stock solution to a working 1 mg/mL concentration. 
	NOTE: Always protect FITC-Dextran from light exposure.</li>
	<li>Prepare a dilution row with decreasing FITC concentration (1000 &#181;g/mL to 0.25 &#181;g/mL) as a standard for the readout.</li>
	<li>Add 500 &#181;L of FITC-dextran solution (1 mg/mL) to the upper chamber of the transwell and 1.5 mL medium (+/- cytokine of interest) into the lower compartment and place the plate in the incubator.</li>
	<li>Collect 120 &#181;L of medium from the lower compartment at the respective time points (e.g., 0 min, 15 min, 30 min, 60 min, 90 min, 120 min, 150 min, and 180 min).</li>
	<li>Pipette duplicates (50 &#181;L/well) of each timepoint into a black 96-well transparent flat bottom plate.</li>
	<li>Excite the FITC-dextran at 490 nm and read the emission at a wavelength of 520 nm using a plate reader.</li>
	<li>Calculate the amount of macromolecular flux according to the standard.</li>
</ol>

Human Esophageal Organoids and Air-Liquid Interface Culture Protocols

The authors have nothing to disclose.

The provided procedures allow the cultivation of patient-derived organoids and ALI cultures with high prospects of success. The organoid protocol has been adapted from the first published protocol reporting the generation of human esophageal organoids26 and from a recently published protocol32. Sherill and colleagues have described the ALI model22. Organoids and ALI culture models assist each other in studying the impact of cytokines and other mediat...

Esophageal inflammation compromises the epithelial barrier integrity1,2,3,4,5, as observed in eosinophilic esophagitis (EoE), a Th2-dominated chronic inflammatory disease of the esophagus6. EoE was first described in the 1990s7,8 and is predominantly induced by food antigens9,10,11,12,13. The most frequently occurring symptoms of EoE in the adult population are dysphagia and food impaction14. In children, EoE typically manifests with failure to thrive, food refusal, vomiting, and abdominal pain15. Genome-wide association studies (GWAS) have identified EoE risk genes involved in epithelial barrier integrity, moving the epithelium into the focus of EoE research16,17,18. EoE transcriptomics further revealed that an impaired differentiation process and a reactive basal zone hyperplasia cause the compromised barrier function of the esophageal epithelium3,5,19,20,21,22. The early understanding of EoE being a Th2-mediated disease6 led to the discovery of IL-13 as a driving mediator by disturbing epithelial integrity3,4,21,23. Experimental systems allowing the dissection of cytokine-mediated effects on epithelial integrity from intrinsic barrier impairment through genetic predisposition provide the possibility to study the complex interplay between immune cells and the epithelium in EoE. Human esophageal organoids and air-liquid interface (ALI) cultures have been proposed as valuable tools to analyze the consequence of cytokine stimulation on epithelial integrity5.
The first protocol for generating adult tissue-specific stem cell (ASC)-derived esophageal organoids was established five years after the first published reports of intestinal organoids in 2009 using intestinal Lgr5+ ASCs recapitulating the epithelial compartment of the small intestine24. DeWard et al. pioneered generating organoids from murine esophageal epithelial cells25. In 2018, Kasagi et al. generated human esophageal organoids from the immortalized human esophageal squamous epithelium cell line EPC2-hTERT and primary patient-derived cells26. In the same year, Zhang et al. successfully generated induced pluripotent stem cell (iPSC)-derived esophageal organoids. They delineated the significance of TGF&#946; and bone morphogenetic protein (BMP) inhibition for esophageal progenitor cell (EPC) development and the crucial role of Notch signaling in the differentiation of the stratified squamous epithelium26,27. Trisno and colleagues complemented these findings by identifying Sox2 as a Wnt inhibitor that directs the developmental fate towards esophageal differentiation28. The subsequent refinements of protocols, medium composition, and culture conditions increased the organoid formation rate and made subculturing and recovering organoids after cryopreservation possible26,29,30,31,32. Although these organoids are powerful tools for studying tissue architecture and expression of potential target genes after stimulation with cytokines, esophageal organoids will not offer the possibility to measure transepithelial resistance (TEER) or macromolecule flux as direct measures for barrier integrity. As previously described by Sherrill and colleagues22, ALI cultures modeling epithelial differentiation4&#160;allow direct assessments of epithelial integrity. Combining patient-derived organoids and ALI cultures is a powerful tool for investigating tissue architecture and epithelial barrier integrity in EoE.
Here are procedures with instructions for isolating viable cells from esophageal biopsies and establishing esophageal organoid and ALI cultures that can further be used to study the effects of cytokines on barrier integrity.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>1250 &#181;L Griptip - Filter</td>
			<td>Integra</td>
			<td>4445</td>
			<td></td>
		</tr>
		<tr>
			<td>300 &#181;L Griptip - Filter</td>
			<td>Integra</td>
			<td>4435</td>
			<td></td>
		</tr>
		<tr>
			<td>70 &#181;M cell strainer</td>
			<td>Sarstedt</td>
			<td>83.3945.070</td>
			<td></td>
		</tr>
		<tr>
			<td>Ascorbic Acid</td>
			<td>Sigma-Aldrich (Merck)</td>
			<td>A4544</td>
			<td></td>
		</tr>
		<tr>
			<td>Bovine pituitary extract</td>
			<td>Gibco (Thermo Fischer Scientific)</td>
			<td>3700015</td>
			<td></td>
		</tr>
		<tr>
			<td>Calcium chloride</td>
			<td>Sigma-Aldrich (Merck)</td>
			<td>21115</td>
			<td></td>
		</tr>
		<tr>
			<td>Cell Culture Multiwell Plates CELLSTAR for suspension cultures</td>
			<td>Greiner Bio-One</td>
			<td>7.657 185</td>
			<td></td>
		</tr>
		<tr>
			<td>Cultrex Basement Membrane Extract (BME), Type 2, Pathclear</td>
			<td>R&#38;D Systems (Bio-Techne)</td>
			<td>3532-010-02</td>
			<td></td>
		</tr>
		<tr>
			<td>Dimethyl sulfoxide (DMSO), >99,5% BioScience Grade</td>
			<td>Carl Roth</td>
			<td>A994</td>
			<td></td>
		</tr>
		<tr>
			<td>Dispase I</td>
			<td>Corning</td>
			<td>354235</td>
			<td></td>
		</tr>
		<tr>
			<td>Dispase II</td>
			<td>Sigma-Aldrich (Merck)</td>
			<td>D4693</td>
			<td></td>
		</tr>
		<tr>
			<td>Dulbeccos Phosphate Buffered Saline&#160; (DPBS)</td>
			<td>Sigma-Aldrich (Merck)</td>
			<td>D8537</td>
			<td></td>
		</tr>
		<tr>
			<td>EVE Automated Cell Counter</td>
			<td>NanoEntek</td>
			<td>EVE-MC</td>
			<td></td>
		</tr>
		<tr>
			<td>EVE Cell counting slide</td>
			<td>NanoEntek</td>
			<td>EVS-050</td>
			<td></td>
		</tr>
		<tr>
			<td>Falcon 5 mL Round Bottom Polystyrene Test Tube, with Cell Strainer Snap Cap</td>
			<td>Falcon</td>
			<td>352235</td>
			<td></td>
		</tr>
		<tr>
			<td>Fluorescin isothiocyanate (FITC)-dextran</td>
			<td>Sigma-Aldrich (Merck)</td>
			<td>FD4</td>
			<td>average mol wt 3000-5000</td>
		</tr>
		<tr>
			<td>Heraeus - Megafuge&#160; 40R&#160;</td>
			<td>Thermo Fisher Scientific</td>
			<td>75004518</td>
			<td></td>
		</tr>
		<tr>
			<td>Human recombinant epidermal growth factor</td>
			<td>Gibco (Thermo Fischer Scientific)</td>
			<td>3700015</td>
			<td></td>
		</tr>
		<tr>
			<td>Keratinocyte-SFM</td>
			<td>Gibco (Thermo Fischer Scientific)</td>
			<td>17005042</td>
			<td></td>
		</tr>
		<tr>
			<td>Penicillin-Streptomycin</td>
			<td>Gibco (Thermo Fischer Scientific)</td>
			<td>15140122</td>
			<td></td>
		</tr>
		<tr>
			<td>Recombinant Human KGF/FGF-7 Protein</td>
			<td>R&amp;D Systems (Bio-Techne)</td>
			<td>251-KG-010/CF</td>
			<td></td>
		</tr>
		<tr>
			<td>Screw cap tube, 15 mL</td>
			<td>Sarstedt</td>
			<td>62.554.502</td>
			<td></td>
		</tr>
		<tr>
			<td>Single Channel EVOLVE 100-1000 &#181;L&#160;</td>
			<td>Integra</td>
			<td>3018</td>
			<td></td>
		</tr>
		<tr>
			<td>Single Channel EVOLVE 20-200 &#181;L&#160;</td>
			<td>Integra</td>
			<td>3016</td>
			<td></td>
		</tr>
		<tr>
			<td>Syringe 1 mL</td>
			<td></td>
			<td>1134950</td>
			<td></td>
		</tr>
		<tr>
			<td>ThermoMixer C</td>
			<td>Eppendorf</td>
			<td>5382000015</td>
			<td></td>
		</tr>
		<tr>
			<td>Trypsin inhibitor from Glycine max (soybean)</td>
			<td>Sigma-Aldrich (Merck)</td>
			<td>T9128</td>
			<td></td>
		</tr>
		<tr>
			<td>Trypsin-EDTA</td>
			<td>SAFC Biosciences (Merck)</td>
			<td>59418C</td>
			<td></td>
		</tr>
		<tr>
			<td>Y27632 dihydrochloride</td>
			<td>Tocris (Bio-Techne)</td>
			<td>1254</td>
			<td></td>
		</tr>
	</tbody>
</table>

three-dimensional cell culture models to investigate the epithelial barrier in eosinophilic esophagitis 

The squamous epithelium of the esophagus is directly exposed to the environment, continuously facing foreign antigens, including food antigens and microbes. Maintaining the integrity of the epithelial barrier is critical for preventing infections and avoiding inflammation caused by harmless food-derived antigens. This article provides simplified protocols for generating human esophageal organoids and air-liquid interface cultures from patient biopsies to study the epithelial compartment of the esophagus in the context of tissue homeostasis and disease. These protocols have been significant scientific milestones in the last decade, describing three-dimensional organ-like structures from patient-derived primary cells, organoids, and air-liquid interface cultures. They offer the possibility to investigate the function of specific cytokines, growth factors, and signaling pathways in the esophageal epithelium within a three-dimensional framework while maintaining the phenotypic and genetic properties of the donor. Organoids provide information on tissue microarchitecture by assessing the transcriptome and proteome after cytokine stimulation. In contrast, air-liquid interface cultures allow the assessment of the epithelial barrier integrity through transepithelial resistance (TEER) or macromolecule flux measurements. Combining these organoids and air-liquid interface cultures is a powerful tool to advance research in impaired esophageal epithelial barrier conditions.

Author Spotlight: Investigating the Pathophysiology of Eosinophilic Esophagitis

Three-Dimensional Cell Culture Models to Investigate the Epithelial Barrier in Eosinophilic Esophagitis 

Esophageal organoids will grow from primary cells extracted from patient biopsies according to the instructions of the provided protocol, as documented with an inverted brightfield microscope (Figure 1). Epithelial ASCs start forming cell clusters in a self-organizing manner within the first two days of culture after seeding the isolated cells in the basement membrane extract, serving as a scaffold. The size and number of cell clusters, noticeable with an inverted brightfield microscope, inc...

Read this Scientific Article Protocol about Author Spotlight: Investigating the Pathophysiology of Eosinophilic Esophagitis at JoVE.com

Here, a protocol for the culture of human esophageal organoids and air-liquid interface culture is provided. Esophageal organoids' air-liquid interface culture can be used to study the impact of cytokines on the esophageal epithelial barrier.

The squamous epithelium of the esophagus is directly exposed to the environment, continuously facing foreign antigens, including food antigens and ...

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Patient-Derived Esophageal Organoids Culture Using Cells Isolated from Esophagus Biopsies

Establishment of Patient-Derived Air-Liquid Interface (ALI) Cultures from Esophagus Biopsies

422 Views.  University of Basel.  Here, a protocol for the culture of human esophageal organoids and air-liquid interface culture is provided. Esophageal organoids' air-liquid interface culture can be used to study the impact of cytokines on the esophageal epithelial barrier.

Human Esophageal Organoids and Air-Liquid Interface Culture Protocols

Summary