We thank Magali Guffroy, John Kreeger, and Stephani Bisulco of the Pfizer-Oncology Histopathology and Biomarker group for pathology/histology support and Michael Arensman for critical review of the manuscript. We also thank the Pfizer Postdoctoral Program and the Oncology R&#38;D group, specifically Robert Abraham, Puja Sapra, Karen Widbin and Jennifer Tejeda for their support of the program.

1. Passaging and Culturing TUM622 Cells and CAFs in 2D Cultures
<ol>
	<li>Passaging and culturing TUM622 cells
	<ol>
		<li>Warm 3D culture medium and cell dissociation reagents (see Table of Materials) for TUM622 cells at 37 &#176;C.</li>
		<li>Passage TUM622 cells at 80% confluency in 2D flasks. Usually, this occurs 1 week after passaging.</li>
		<li>Discard old medium from a T75 flask and wash once with 6 mL of HEPES buffer. Avoid pipetting directly onto the cells.</li>
		<li>Aspirate the HEPES buffer. Add 4 mL of trypsin/EDTA (0.25 mg/mL, see Table of Materials) for a quick rinse and discard the trypsin/EDTA.</li>
		<li>Add 2 mL of trypsin/EDTA and incubate at 37 &#176;C for 5 min. Remove flasks from the incubator and tap the flasks to loosen the cells without creating air bubbles and return flasks to the incubator for an additional 5 min. 
		NOTE: Prolonged exposure to trypsin will irreversibly damage the cells and alter their phenotype, thus it is recommended to limit the time cells are exposed to trypsin.</li>
		<li>Confirm cells have detached and dissociated under a light microscope (4x or 10x). Add 4 mL of neutralization buffer (TNS buffer) (see subculture reagent information in the Table of Materials) followed by 10 mL of 3D culture medium (see Table of Materials).</li>
		<li>Pipette up-and-down gently to further dissociate the cells using a 10 mL pipette. Transfer the suspension through a 40 &#181;m cell strainer into a 50 mL conical tube.</li>
		<li>Count cell numbers using a hemocytometer or automated cell counter.</li>
		<li>Seed 0.8 x 106 cells/T75 flask in 20 mL of 3D culture medium (see Table of Materials).</li>
		<li>Feed the cells every other day by replacing half of the spent medium with fresh medium.</li>
	</ol>
	</li>
	<li>Passaging and culturing CAFs
	<ol>
		<li>Passage CAFs when cells reach confluency. Usually, this occurs after 5 days of culturing from a 1:2 split.</li>
		<li>Prepare CAF medium using RPMI basal medium with 20% heat-inactivated fetal bovine serum, 1% L-Glutamine and 1% Penicillin/Streptomycin. Warm the medium to 37 &#176;C.</li>
		<li>In a T75 flask, rinse CAFs with phosphate-buffered saline (PBS) once then add 2 mL of trypsin/EDTA and incubate at 37 &#176;C for 5 min.</li>
		<li>Observe under a light microscope to ensure cells have dissociated in the flask (4x or 10x). If not, extend the incubation for another 2-3 min.</li>
		<li>Once cells have detached and dissociated, add 10 mL of 3D culture medium to neutralize the trypsin/EDTA and pipette up and down several times to further dissociate the CAFs.</li>
		<li>Transfer the cell suspension into a 50 mL conical tube and spin down at 300 x g for 5 min at room temperature.</li>
		<li>Discard the supernatant and resuspend the pellet in an appropriate volume of 3D culture medium (see Table of Materials) and passage into two new T75 flasks.</li>
	</ol>
	</li>
</ol>
2. Plating TUM622 Cells in the Extracellular Matrix for 3D Culturing
<ol>
	<li>The day before the experiment, thaw vials of basement membrane matrix in a 4 &#176;C refrigerator overnight. Cooldown plastic pipettes (2 mL) and tips at -20 &#176;C overnight. 
	NOTE: Not all lots of basement membrane matrix have the same capacity to support the 3D growth of TUM622 cells. Therefore, it is necessary to acquire and test multiple lots of basement membrane matrix to identify those that support robust acini formation. Usually, this requires a higher protein concentration (16-18 mg/mL) in the matrix.</li>
	<li>On the day of the experiment, warm 3D culture medium, HEPES buffer, trypsin/EDTA and trypsin neutralization buffer (TNS) in a 37 &#176;C water bath. Immediately before setting up the culture, take the thawed basement membrane matrix out of the fridge and put the vial on ice.</li>
	<li>Cooldown the tissue culture plates on a metal platform cooler placed on ice. Place centrifuge tubes on a metal cooling rack on ice.</li>
	<li>Using TUM622 cells obtained from step 1.1.7, calculate the desired number of cells needed for plating. Typically, 15,000-30,0000 cells are needed per well of a 24-well plate. Lower density is more suited for imaging and quantification, while higher density is preferred when collecting cells for RNA extraction or western blotting.</li>
	<li>Transfer cell suspension into a cooled centrifuge tube (each tube containing cells for triplicate plating) and spin down at 300 x g in a hanging bucket centrifuge at 4 &#176;C for 5 min.</li>
	<li>Aspirate the supernatant carefully with an aspirating pipette attached to an unfiltered tip (20 &#181;L), leaving approximately 100 &#181;L of the medium in the tube (use markings on the tube as a guide).</li>
	<li>Gently tap on the side of the tube to dislodge and dissociate the pellet before returning it to the cooling rack.</li>
	<li>Using the 2 mL pre-cooled pipettes, gently mix the matrix by pipetting up and down a few times while keeping the vial in contact with the ice. Pipette at an even and moderate speed so that no bubbles are introduced into the matrix during this procedure.</li>
	<li>Transfer the appropriate volume of the matrix into each centrifuge tube. For plating triplicates in a 24-well plate, add 1.1 mL of basement membrane matrix to each tube.</li>
	<li>Using pre-cooled tips, pipette the matrix in each tube up and down about 10 times to make a uniform cell suspension.</li>
	<li>Transfer 310 &#181;L of cell/matrix suspension into each well of a pre-cooled 24-well plate. The pipette is placed at a 90&#176; angle to the plate surface and the suspension added to the center of the well. The suspension should spread and cover the entire well without needing to tilt the plate.</li>
	<li>To facilitate downstream immunofluorescence analysis, plate the cell/matrix suspension in parallel into 2-well chamber slides. Transfer 100 &#181;L of cell/matrix suspension into the center of a well of 2-well chamber slide (see Table of Materials). This allows the matrix to form a dome-like structure with much smaller volume.</li>
	<li>Return the plate and the chamber slide back into a tissue culture incubator and incubate for 30 min to allow the matrix to solidify. Examine the plate/slide under a light microscope to ensure that single cells are evenly distributed within the matrix (4x or 10x).</li>
	<li>Add 1 mL of pre-warmed 3D culture complete medium into each well and 1.5 mL of 3D culture medium to each well of the chamber slide then return them to the incubator.</li>
</ol>
3. 3D Coculturing of TUM622 Cells and CAFs in the Extracellular Matrix
<ol>
	<li>Prepare cell suspensions of TUM622 and CAFs according to section 2.</li>
	<li>Count the CAF cell density by taking 10 &#181;L of cell suspension and mixing it with 10 &#181;L of trypan blue.</li>
	<li>Add 10 &#181;L of the mixture to each of the two chambers on a hemacytometer to count and calculate cell density. 
	NOTE: CAFs have irregular shapes and may not be accurately counted on an automatic cell counter.</li>
	<li>Co-embedding TUM622 cells and CAFs in basement membrane matrix
	<ol>
		<li>Based on the cell density information, calculate the desired number of cells used for plating. CAFs are seeded at a 2:1 ratio of TUM622 cells. For example, for 30,000 TUM622 cells seeded, 60,000 CAFs are co-embedded.</li>
		<li>Transfer the appropriate volume of TUM622 as well as CAFs cell suspension into the same centrifuge tube and follow steps 2.5-2.11 for plating into 24-well plates. For immunofluorescence, transfer 60 &#181;L of TUM622/CAFs mix to chamber slides as described in step 2.12).</li>
	</ol>
	</li>
	<li>Coculturing TUM622 with overlaid CAFs in basement membrane matrix (see Table of Materials)
	<ol>
		<li>Set up TUM622 mono-culture according to steps 2.5-2.13.</li>
		<li>Transfer twice the number of CAFs suspension (compared to the number of TUM622 cells seeded) into a centrifuge tube and spin down at 300 x g for 5 min at room temperature.</li>
		<li>Aspirate the supernatant and resuspend the CAFs in 1 mL of 3D culture medium.</li>
		<li>Transfer the 1 mL of CAFs suspension to the well containing the embedded TUM622 cells.</li>
	</ol>
	</li>
</ol>
4. Harvesting TUM622 Acini for RNA/Protein Extraction and Fluorescence-activated Cell Sorting (FACS)
<ol>
	<li>Prepare wash buffer and cell harvesting buffer according to the 3D cell harvesting kit protocol the previous day and chill overnight at 4 &#176;C.</li>
	<li>Keep plates on a plate cooler and other reagents on ice before starting the extraction process.</li>
	<li>Aspirate media from 3D culture wells without touching the matrix and gently wash the well 3 times with 1 mL of wash buffer.</li>
	<li>Aspirate the final wash and add 1 mL of cell harvesting buffer to each well.</li>
	<li>Use a p1000 pipette tip to scrape the matrix off of each well.</li>
	<li>Pipette up and down to further dissociate the matrix.</li>
	<li>Transfer 1 mL of the mix to a pre-chilled 15 mL conical tube. Add another 1 mL of harvesting buffer to the same well.</li>
	<li>Repeat steps 4.5-4.7, and transfer all mix of the same well into one 15 mL conical tube.</li>
	<li>Cap the tubes and rock at 4 &#176;C for 30 min.</li>
	<li>Fill each tube with ice-cold PBS up to 10 mL and then centrifuge at 300 x g for 5 min at 4 &#176;C.</li>
	<li>Aspirate the supernatant without touching the pellet. The supernatant should contain matrix fragments, but the spheroids should all be collected at the bottom of the tube.</li>
	<li>Add ice-cold PBS for a second wash. Invert the tube a few times to dissociate the pellet. Spin down at 300 x g for 5 min.</li>
	<li>While spinning, prepare lysis buffer for protein and RNA collection.</li>
	<li>Carefully aspirate the supernatant and add lysis buffer for downstream processing to collect protein or RNA. Alternatively, cells could be resuspended for flow analysis/FACS sorting or serial passaging.</li>
</ol>
5. Immunofluorescence of TUM622 Acini
<ol>
	<li>Prepare immunofluorescence buffer (IF buffer: PBS with 0.1% bovine serum albumin (BSA), 0.2% Triton X-100 and 0.05% Tween-20), primary blocking buffer (IF buffer with 10% goat serum), secondary blocking buffer (primary blocking buffer with 20 &#181;g/mL goat anti-mouse F(ab&#39;)2)</li>
	<li>Aspirate medium from 2-well chamber slides, rinse once with PBS and set the slide on metal plate cooler on ice. The chamber slide should remain on the metal plate cooler for the remainder of the protocol.</li>
	<li>Add pre-chilled 4% PFA to fix the acini and incubate on ice for 20 min.</li>
	<li>Remove 4% PFA and wash three times with 2 mL of pre-chilled PBS each for 5 min with gentle rocking on a rocker.</li>
	<li>Aspirate PBS and permeabilize with 1.5 mL of 0.5% Triton X-100 in PBS (pre-chilled) for 20 min. By the end of this procedure, the dome-like structure will become loose.</li>
	<li>Gently aspirate the permeabilization buffer from the chamber slide to avoid sample loss. This is achieved by adding a fine tip (20 &#181;L) to the aspirating pipette and pressing the tip towards the corner of the chamber.</li>
	<li>Wash three times with 2 mL of pre-chilled PBS each for 5 min with gentle rocking on a rocker.</li>
	<li>Block the sample with the primary blocking buffer on ice for 1 h.</li>
	<li>Remove primary blocking buffer and add secondary blocking buffer and block for 30 min.</li>
	<li>Add primary antibodies in primary blocking buffer and incubate overnight at 4 &#176;C. 
	NOTE: The concentration of the antibodies used here should be higher than normally used for staining cells in 2D culture. Most of the primary antibodies used in this study are diluted at 1:100 dilution (see Table of Materials).</li>
	<li>Remove primary antibodies and wash the sample 3 times with 2 mL of cold IF buffer. 
	NOTE: The samples could be loose, take extra caution when aspirating.</li>
	<li>Incubate the samples in secondary antibodies diluted in primary blocking buffer for 1 h at RT. The preferred secondary antibodies should be highly cross-adsorbed to reduce background staining. Most secondary antibodies used in this study are diluted at 1:200 dilution.</li>
	<li>Remove secondary antibodies and wash the sample 3 times with 2 mL of cold IF buffer. 
	NOTE: The samples could be loose, take extra caution when aspirating.</li>
	<li>Add PBS with DAPI (1:1,000 dilution) during the last wash to stain the nucleus. The perform another 2 washes in PBS.</li>
	<li>Image the samples on a confocal microscope within 3 days. 
	NOTE: Due to the size of the organoids and limits in the objective&#39;s working distance, samples are usually imaged at 10x or 20x magnification.</li>
</ol>
6. Preparing 3D Culture Samples for Immunohistochemistry
<ol>
	<li>Aspirate medium from 2-well chamber slides and rinse once with PBS.</li>
	<li>Fix 3D cultures in 4% PFA at 37 &#176;C overnight.</li>
	<li>Remove 4% PFA, surround cultures with 2.5 mL of histology sample gel (see Table of Materials) and place the slide at 4 &#176;C to solidify for at least 1 h.</li>
	<li>Transfer samples surrounded with histological sample gel to tissue cassettes and processed in an automated tissue sample processor overnight.</li>
	<li>Embed samples in paraffin wax and prepare for sectioning12.</li>
</ol>
7. 3D Cytotoxicity Assay for Compound Screening (Example for One 96-well Plate)
<ol>
	<li>Set a 96-well plate on a plate cooler, a 25 mL reservoir on a reservoir cooler and a 15 mL conical tubes on ice before starting the experiment.</li>
	<li>Prepare cell matrix suspensions of TUM622 cells in a pre-chilled 15 mL polypropylene conical tube by adding the appropriate volume of basement membrane matrix to cells. The desired density for TUM622 cells is 10,000 cells per 70-75 &#181;L of basement membrane matrix. Pipette up and down a few times to allow even mixing of cells within the matrix.</li>
	<li>Move the plate with plate cooler and reservoir with a reservoir cooler away from the ice to a dry surface to avoid contact of basement membrane matrix with ice during transfer.</li>
	<li>Transfer the matrix cell mixture to the cooling reservoir without creating bubbles.</li>
	<li>Using a mechanical multichannel pipette (10-300 &#181;L), transfer 70-75 &#181;L of the mix cells into each appropriate well of a 96-well plate.</li>
	<li>Incubate plate at 37 &#176;C and 5% CO2 for 30 min for the basement membrane matrix to solidify.</li>
	<li>Add 100 &#181;L of media in all rows and return the plate to the incubator.</li>
	<li>Start compound dosing the next day or later depending on the goal of the experiment.</li>
	<li>Spheroids can be re-fed and re-dosed every 2-3 days for up to 10 days, by removing spent media with an 8- or 12-well vacuum manifold and replacing with fresh media with or without desired compounds.</li>
	<li>The number of TUM622 spheroids could be quantified using 3D imager according to the manufacturer&#39;s protocol.</li>
</ol>

<ol>
	<li>Cancer Genome Atlas Research Network. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comprehensive+genomic+characterization+of+squamous+cell+lung+cancers.">Comprehensive genomic characterization of squamous cell lung cancers.</a> Nature. 489 (7417), 519-525 (2012).</li><li>Nelson, C. M., Bissell, M. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Of+Extracellular+Matrix,+Scaffolds,+and+Signaling:+Tissue+Architecture+Regulates+Development,+Homeostasis,+and+Cancer.">Of Extracellular Matrix, Scaffolds, and Signaling: Tissue Architecture Regulates Development, Homeostasis, and Cancer.</a> Annual Review of Cell and Developmental Biology. 22 (1), 287-309 (2006).</li><li>Quail, D. F., Joyce, J. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Microenvironmental+regulation+of+tumor+progression+and+metastasis.">Microenvironmental regulation of tumor progression and metastasis.</a> Nature Medicine. 19 (11), 1423-1437 (2013).</li><li>Balkwill, F. R., Capasso, M., Hagemann, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+tumor+microenvironment+at+a+glance.">The tumor microenvironment at a glance.</a> Journal of Cell Science. 125 (23), 5591-5596 (2012).</li><li>Schmeichel, K. L., Bissell, M. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Modeling+tissue-specific+signaling+and+organ+function+in+three+dimensions.">Modeling tissue-specific signaling and organ function in three dimensions.</a> Journal of Cell Science. 116 (Pt 12), 2377-2388 (2003).</li><li>Wu, X., Peters-Hall, J. R., Bose, S., Pena, M. T., Rose, M. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Human+bronchial+epithelial+cells+differentiate+to+3D+glandular+acini+on+basement+membrane+matrix.">Human bronchial epithelial cells differentiate to 3D glandular acini on basement membrane matrix.</a> American Journal of Respiratory Cell and Molecular Biology. 44 (6), 914-921 (2011).</li><li>Godugu, C., Singh, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=AlgiMatrix-Based+3D+Cell+Culture+System+as+an+In+Vitro+Tumor+Model:+An+Important+Tool+in+Cancer+Research.">AlgiMatrix-Based 3D Cell Culture System as an In Vitro Tumor Model: An Important Tool in Cancer Research.</a> Methods in Molecular Biology. 1379, 117-128 (2016).</li><li>Amann, A., 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=Development+of+an+innovative+3D+cell+culture+system+to+study+tumour--stroma+interactions+in+non-small+cell+lung+cancer+cells.">Development of an innovative 3D cell culture system to study tumour--stroma interactions in non-small cell lung cancer cells.</a> PLoS One. 9 (3), e92511 (2014).</li><li>Chen, 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=Cancer-associated+fibroblasts+suppress+SOX2-induced+dysplasia+in+a+lung+squamous+cancer+coculture.">Cancer-associated fibroblasts suppress SOX2-induced dysplasia in a lung squamous cancer coculture.</a> Proceedings of the National Academy of Sciences of the United States of America. 115 (50), E11671-E11680 (2018).</li><li>Damelin, M., 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=Delineation+of+a+cellular+hierarchy+in+lung+cancer+reveals+an+oncofetal+antigen+expressed+on+tumor-initiating+cells.">Delineation of a cellular hierarchy in lung cancer reveals an oncofetal antigen expressed on tumor-initiating cells.</a> Cancer Research. 71 (12), 4236-4246 (2011).</li><li>Sapra, 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=Long-term+tumor+regression+induced+by+an+antibody-drug+conjugate+that+targets+5T4,+an+oncofetal+antigen+expressed+on+tumor-initiating+cells.">Long-term tumor regression induced by an antibody-drug conjugate that targets 5T4, an oncofetal antigen expressed on tumor-initiating cells.</a> Molecular Cancer Therapeutics. 12 (1), 38-47 (2013).</li><li>Fischer, A. 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The authors are employees and shareholders of Pfizer Inc.

Tumors are heterogeneous tissues composed of cancer cells coexisting side-by-side with stromal cells such as cancer-associated fibroblasts, endothelial cells and immune cells within the ECM. Together, these diverse components cross-talk and influence the tumor microenvironment, playing an active role in driving tumorigenesis, a process that involves progressive changes in tumor architecture. Ideally, an in vitro model of tumor development should be able to capture the dynamic tissue architectural changes observed in huma...

Lung cancer is the leading cause of cancer-related mortality worldwide. Lung squamous cell carcinoma (LUSC), which is the second most common type of non-small-cell lung cancer (NSCLC) and accounts for approximately 30% of all lung cancer, is often diagnosed at advanced stages and has a poor prognosis1. Treatment options for LUSC patients are a major unmet need that can be improved by a better understanding of the underlying cellular and molecular mechanisms that drive LUSC tumorigenesis.
As with most human cancers, the pathogenesis of LUSC is characterized by the disruption of the intact, well-ordered epithelial tissue architecture2. During this process, proper apical-basal cell polarity, cell-cell and cell-matrix contacts are lost, permitting uncontrolled growth and invasive behavior of the tumor cells. It is now widely appreciated that the malignant features of cancer cells cannot be manifested without an important interplay between cancer cells and their local tumor microenvironment (TME)3. Key components in the TME including extracellular matrix (ECM), cancer-associated fibroblasts (CAFs) as well as endothelial cells and infiltrating immune cells actively shape the TME and drives tumorigenesis4. Nevertheless, our current understanding of how the tumor cells and these key components in the TME interact to drive tissue architectural changes during LUSC progression is very limited.
Three-dimensional (3D) culture is an important tool to study the biological activities of cell-intrinsic and extrinsic changes in regulating tissue architectural changes in both normal and diseased tissues5. 3D cultures provide the appropriate structural and functional context that is usually lacking in traditional two-dimensional (2D) cultures. The added dimensions of such systems more closely mimic tissue in vivo in many aspects of cell physiology and cellular behaviors, including proliferation, differentiation, migration, protein expression and response to drug treatment. In recent years, efforts from various labs have led to the development of in vitro 3D models for both the normal lung as well as NSCLC6,7,8. However, a model for lung squamous carcinoma that can recapitulate both the dynamic tissue architectural changes during tumorigenesis as well as incorporate key stromal components was unavailable.
Here, we describe the methods for establishing a novel 3-dimensional (3D) coculture system using primary PDX-derived LUSC cells (termed TUM622) and CAFs9,10. Both TUM622 and CAFs are derived from NSCLC patient with poorly differentiated tumors10. When embedded as single cells in ECM, a rare subpopulation of TUM622 cells have the capacity to form organoids with acinar-like structures that display proper apical-basal cell polarity. These acinar-like structures are hyperplastic, display heterogeneous expression of stem-like and differentiation markers similar to the original tumor while remaining non-invasive, and thus mimic the earliest stage of LUSC development. Importantly, we showed that the tissue architecture of the acinar-like structures could be altered by inhibition of cell-intrinsic signaling pathways with small molecule inhibitors or addition of key components in the ECM such as CAFs, the latter of which enhances acini formation and further provokes the acini to become invasive when in close proximity. Together, these data suggest that this 3D co-culture system of LUSC organoids provides a valuable platform for the investigation of the dynamic reciprocity between LUSC cells and the TME and could be adapted for monitoring the response of LUSC cells to drug treatment11.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Bronchial Epithelial Growth Medium</td>
			<td>Lonza</td>
			<td>CC-3170</td>
			<td>BEGM</td>
		</tr>
		<tr>
			<td>Cell Strainer 40um</td>
			<td>ThermoFisher</td>
			<td>352340</td>
			<td>For passing TUM622 cells</td>
		</tr>
		<tr>
			<td>Cleaved Caspase 3 antibody</td>
			<td>Cell Signaling Technology</td>
			<td>9661 (RRID:AB_2341188)</td>
			<td>Rabbit</td>
		</tr>
		<tr>
			<td>CoolRack CFT30</td>
			<td>Biocision</td>
			<td>BCS-138</td>
			<td>For 3D culture</td>
		</tr>
		<tr>
			<td>CoolSink XT96F</td>
			<td>Biocision</td>
			<td>BCS-536</td>
			<td>For 3D culture</td>
		</tr>
		<tr>
			<td>Cultrex 3D Cell Harvesting Kit</td>
			<td>Bio-Techne</td>
			<td>3448-020-K</td>
			<td></td>
		</tr>
		<tr>
			<td>Cultrex (preferred for co-culture)</td>
			<td>Bio-Techne</td>
			<td>3443-005-01</td>
			<td>For 3D culture</td>
		</tr>
		<tr>
			<td>CXCR4 antibody</td>
			<td>Abcam</td>
			<td>Ab124824 (RRID:AB_10975635)</td>
			<td>Rabbit</td>
		</tr>
		<tr>
			<td>E-cadherin antibody</td>
			<td>BD Biosciences</td>
			<td>610182 (RRID:AB_397581)</td>
			<td>Mouse</td>
		</tr>
		<tr>
			<td>GelCount</td>
			<td>Oxford Optronix</td>
			<td></td>
			<td>For Acini counts and measurements</td>
		</tr>
		<tr>
			<td>GM130 antibody</td>
			<td>BD Biosciences</td>
			<td>610822 (RRID:AB_398141)</td>
			<td>Mouse</td>
		</tr>
		<tr>
			<td>Goat Serum</td>
			<td>Vector Labs</td>
			<td>S1000 (RRID:AB_2336615)</td>
			<td>For Immunofluorescence</td>
		</tr>
		<tr>
			<td>Heat-inactivated FBS</td>
			<td>Gibco</td>
			<td>10082-147</td>
			<td>For CAFs</td>
		</tr>
		<tr>
			<td>Histology sample gel</td>
			<td>Richard Allan Scientific</td>
			<td>HG-4000-012</td>
			<td>For Immunofluorescence</td>
		</tr>
		<tr>
			<td>Integrin alpha 6 antibody</td>
			<td>Millipore Sigma</td>
			<td>Mab1378 (RRID:AB_2128317)</td>
			<td>Rat</td>
		</tr>
		<tr>
			<td>Involucrin antibody</td>
			<td>Abcam</td>
			<td>Ab68 (RRID:AB_305656)</td>
			<td>Mouse</td>
		</tr>
		<tr>
			<td>Ki67 antibody</td>
			<td>Abcam</td>
			<td>Ab15580 (RRID:AB_443209)</td>
			<td>Rabbit</td>
		</tr>
		<tr>
			<td>Lab-Tec II chambered #1.5 German Coverglass System</td>
			<td>Nalge Nunc International</td>
			<td>155379 (2)</td>
			<td>For 3D culture</td>
		</tr>
		<tr>
			<td>Lab-Tec II chambered #1.5 German Coverglass System</td>
			<td>Nalge Nunc International</td>
			<td>155409 (8)</td>
			<td>For 3D culture</td>
		</tr>
		<tr>
			<td>L-Glutamine</td>
			<td>Gibco</td>
			<td>25030-081</td>
			<td>For CAFs</td>
		</tr>
		<tr>
			<td>Matrigel (preferred for mono-culture)</td>
			<td>Corning</td>
			<td>356231</td>
			<td>For 3D culture</td>
		</tr>
		<tr>
			<td>p63 antibody</td>
			<td>Cell Signaling Technology</td>
			<td>13109 (SRRID:AB_2637091)</td>
			<td>Rabbit</td>
		</tr>
		<tr>
			<td>Pen/Strep</td>
			<td>Gibco</td>
			<td>15140-122</td>
			<td>For CAFs</td>
		</tr>
		<tr>
			<td>ReagentPack Subculture Reagents</td>
			<td>Lonza</td>
			<td>CC-5034</td>
			<td>For TUM622 cell dissociation</td>
		</tr>
		<tr>
			<td>RPMI</td>
			<td>ThermoFisher</td>
			<td>11875-093</td>
			<td>For CAFs</td>
		</tr>
		<tr>
			<td>Sox2 antibody</td>
			<td>Cell Signaling Technology</td>
			<td>3579 (RRID:AB_2195767)</td>
			<td>Rabbit</td>
		</tr>
		<tr>
			<td>TrypLE Express</td>
			<td>Gibco</td>
			<td>12604-021</td>
			<td>For CAF dissociation</td>
		</tr>
		<tr>
			<td>Vi-Cell</td>
			<td>Bechman Coulter</td>
			<td></td>
			<td>Automatic cell counter</td>
		</tr>
		<tr>
			<td>Vimentin antibody</td>
			<td>Abcam</td>
			<td>Ab92547 (RRID:AB_10562134)</td>
			<td>Rabbit</td>
		</tr>
		<tr>
			<td>&#946;-catenin antibody</td>
			<td>Cell Signaling Technology</td>
			<td>2677s (RRID:AB_1030943)</td>
			<td>Mouse</td>
		</tr>
	</tbody>
</table>

multidimensional coculture system to model lung squamous carcinoma progression

Tumor-stroma interactions play a critical role in the development of lung squamous carcinoma (LUSC). However, understanding how these dynamic interactions contribute to tissue architectural changes observed during tumorigenesis remains challenging due to the lack of appropriate models. In this protocol, we describe the generation of a 3D coculture model using a LUSC primary cell culture known as TUM622. TUM622 cells were established from a LUSC patient-derived xenograft (PDX) and have the unique property to form acinar-like structures when seeded in a basement membrane matrix. We demonstrate that TUM622 acini in 3D coculture recapitulate key features of tissue architecture during LUSC progression as well as the dynamic interactions between LUSC cells and components of the tumor microenvironment (TME), including the extracellular matrix (ECM) and cancer-associated fibroblasts (CAFs). We further adapt our principal 3D culturing protocol to demonstrate how this system could be utilized for various downstream analyses. Overall, this organoid model creates a biologically rich and adaptable platform that enables one to gain insight into the cell-intrinsic and extrinsic mechanisms that promote the disruption of epithelial architectures during carcinoma progression and will aid the search for new therapeutic targets and diagnostic markers.

TUM622 and CAFs in 2D culture 
Figure 1 presents the typical morphology of TUM622 cells and CAFs in 2D culture. TUM622 cells are rounded with large nuclei while CAFs are flat and elongated. TUM622 cells can reach 80%-90% confluency in culture. Further proliferation leads to more, but smaller cells aggregated in colonies that do not come into direct contact. In contrast, CAFs prefer to grow at higher cell density and will keep proliferati...

Watch this Scientific Journal Video about Multidimensional Coculture System to Model Lung Squamous Carcinoma Progression at JoVE.com

Multidimensional Coculture System to Model Lung Squamous Carcinoma Progression

An in vitro model system was developed to capture tissue architectural changes during lung squamous carcinoma (LUSC) progression in a 3-dimensional (3D) co-culture with cancer-associated fibroblasts (CAFs). This organoid system provides a unique platform to investigate the roles of diverse tumor cell-intrinsic and extrinsic changes that modulate the tumor phenotype.

Tumor-stroma interactions play a critical role in the development of lung squamous carcinoma (LUSC). However, understanding how these dynamic interactions ...

multidimensional-coculture-system-to-model-lung-squamous-carcinoma

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JoVE Journal

Cancer Research

7.1K Views.  Pfizer Worldwide Research and Development. An in vitro model system was developed to capture tissue architectural changes during lung squamous carcinoma (LUSC) progression in a 3-dimensional (3D) co-culture with cancer-associated fibroblasts (CAFs). This organoid system provides a unique platform to investigate the roles of diverse tumor cell-intrinsic and extrinsic changes that modulate the tumor phenotype.

Video: Multidimensional Coculture System to Model Lung Squamous Carcinoma Progression

A Model for Perineural Invasion in Head and Neck Squamous Cell Carcinoma

Perineural invasion (PNI) is found in approximately 40% of head and neck squamous cell carcinomas (HNSCC). Despite multimodal treatment with surgery, radiation, and chemotherapy, locoregional recurrences and distant metastases occur at higher rates, and overall survival is decreased by 40% compared to HNSCC without PNI. In vitro studies of the pathways involved in HNSCC PNI have historically been challenging given the lack of a consistent, reproducible assay. Described here is the adaptation of the dorsal root ganglion (DRG) assay for the examination of PNI in HNSCC. In this model, DRG are harvested from the spinal column of a sacrificed nude mouse and placed within a semisolid matrix. Over the subsequent days, neurites are generated and grow in a radial pattern from the cell bodies of the DRG. HNSCC cell lines are then placed peripherally around the matrix and invade preferentially along the neurites toward the DRG. This method allows for rapid evaluation of multiple treatment conditions, with very high assay success rates and reproducibility.

Perineural invasion (PNI) is a common feature of head and neck squamous cell carcinoma (HNSCC), conferring lower survival rates. Its mechanisms are poorly understood. Utilizing neurites generated from murine dorsal root ganglia confined to a semisolid matrix, the pathways involved in the PNI of HNSCC cell lines can be investigated.

Perineural invasion (PNI) is found in approximately 40% of head and neck squamous cell carcinomas (HNSCC). Despite multimodal treatment with surgery, ...

Four-color Fluorescence Immunohistochemistry of T-cell Subpopulations in Archival Formalin-fixed, Paraffin-embedded Human Oropharyngeal Squamous Cell Carcinoma Samples

The four-color fluorescence immunohistochemistry (IHC) technique is a method to quantify cell populations of interest while taking into account their relative distribution and their localization in the tissue. This technique has been extensively applied to study the immune infiltrate in various tumor types. The tumor microenvironment is infiltrated by immune cells that are attracted to the tumor site. Different immune cell populations have been found to play different roles in the tumor microenvironment and to have a different impact on the outcome of disease. This manuscript describes the use of multiparameter fluorescence IHC on oropharyngeal squamous cell carcinoma (OPSCC) as an example. This technique can be extended to other tissue samples and cell types of interest. In the presented study, we analyzed the intraepithelial and stromal compartment of a large OPSCC cohort (n = 162). We focused on total T lymphocytes (CD3+), immunosuppressive regulatory T cells (Tregs; i.e., FoxP3+), and T helper 17 (Th17) cells (i.e., IL-17+CD3+) using a nuclear counterstain to distinguish tumor epithelium from stroma. A high number of T cells was found to be correlated with improved disease-free survival in patients with a low number of intratumoral IL-17+ non-T cells. This suggests that IL-17+ non-T cells may be correlated with a poor immune response in OPSCC, which is in agreement with the correlation described between IL-17 and poor survival in cancer patients. Currently, novel multiparameter fluorescence IHC techniques are being developed using up to 7 different fluorochromes and will enable the more precise characterization and localization of immune cells in the tumor microenvironment.

Multiparameter fluorescence immunohistochemistry can be used to assess the number, relative distribution, and localization of immune cell populations in the tumor microenvironment. This manuscript describes the use of this technique to analyze T-cell subpopulations in oropharyngeal cancer.

The four-color fluorescence immunohistochemistry (IHC) technique is a method to quantify cell populations of interest while taking into account their ...

Therapy Testing in a Spheroid-based 3D Cell Culture Model for Head and Neck Squamous Cell Carcinoma

Current treatment options for advanced and recurrent head and neck squamous cell carcinoma (HNSCC) enclose radiation and chemo-radiation approaches with or without surgery. While platinum-based chemotherapy regimens currently represent the gold standard in terms of efficacy and are given in the vast majority of cases, new chemotherapy regimens, namely immunotherapy are emerging. However, the response rates and therapy resistance mechanisms for either chemo regimen are hard to predict and remain insufficiently understood. Broad variations of chemo and radiation resistance mechanisms are known to date. This study describes the development of a standardized, high-throughput in vitro assay to assess HNSCC cell line&#39;s response to various therapy regimens, and hopefully on primary cells from individual patients as a future tool for personalized tumor therapy. The assay is designed to being integrated into the quality-controlled standard algorithm for HNSCC patients at our tertiary care center; however, this will be subject of future studies. Technical feasibility looks promising for primary cells from tumor biopsies from actual patients. Specimens are then transferred into the laboratory. Biopsies are mechanically separated followed by enzymatic digestion. Cells are then cultured in ultra-low adhesion cell culture vials that promote the reproducible, standardized and spontaneous formation of three-dimensional, spheroid-shaped cell conglomerates. Spheroids are then ready to be exposed to chemo-radiation protocols and immunotherapy protocols as needed. The final cell viability and spheroid size are indicators of therapy susceptibility and therefore could be drawn into consideration in future to assess the patients&#39; likely therapy response. This model could be a valuable, cost-efficient tool towards personalized therapy for head and neck cancer.

We describe the evolution of a spheroid-based, three-dimensional in vitro model that enables us to test the current standard of experimental therapy regimens for head and neck squamous cell carcinoma on cell lines, aiming at evaluating therapy susceptibility and resistance on primary cells from human specimens in the future.

Current treatment options for advanced and recurrent head and neck squamous cell carcinoma (HNSCC) enclose radiation and chemo-radiation approaches with ...

Fabrication of Tongue Extracellular Matrix and Reconstitution of Tongue Squamous Cell Carcinoma In Vitro

In order to construct an effective and realistic model for tongue squamous cell carcinoma (TSCC) in vitro, the methods were created to produce decellularized tongue extracellular matrix (TEM) which provides functional scaffolds for TSCC construction. TEM provides an in vitro niche for cell growth, differentiation, and cell migration. The microstructures of native extracellular matrix (ECM) and biochemical compositions retained in the decellularized matrix provide tissue-specific niches for anchoring cells. The fabrication of TEM can be realized by deoxyribonuclease (DNase) digestion accompanied with a serious of organic or inorganic pretreatment. This protocol is easy to operate and ensures high efficiency for the decellularization. The TEM showed favorable cytocompatibility for TSCC cells under static or stirred culture conditions, which enables the construction of the TSCC model. A self-made bioreactor was also used for the persistent stirred condition for cell culture. Reconstructed TSCC using TEM showed the characteristics and properties resembling clinical TSCC histopathology, suggesting the potential in TSCC research.

Fabrication of Tongue Extracellular Matrix and Reconstitution of Tongue Squamous Cell Carcinoma In Vitro

A method is shown here for the preparation of the tongue extracellular matrix (TEM) with efficient decellularization. The TEM can be used as functional scaffolds for the reconstruction of a tongue squamous cell carcinoma (TSCC) model under static or stirred culture conditions.

In order to construct an effective and realistic model for tongue squamous cell carcinoma (TSCC) in vitro, the methods were created to produce ...

Acellular and Cellular Lung Model to Study Tumor Metastasis

It is difficult to isolate tumor cells at different points of tumor progression. We created an ex vivo lung model that can show the interaction of tumor cells with a natural matrix and continual flow of nutrients, as well as a model that shows the interaction of tumor cells with normal cellular components and a natural matrix. The acellular ex vivo lung model is created by isolating a rat heart-lung block and removing all the cells using the decellularization process. The right main bronchus is tied off and tumor cells are placed in the trachea by a syringe. The cells move and populate the left lung. The lung is then placed in a bioreactor where the pulmonary artery receives a continual flow of media in a closed circuit. The tumor grown on the left lung is the primary tumor. The tumor cells that are isolated in the circulating media are circulating tumor cells and the tumor cells in the right lung are metastatic lesions. The cellular ex vivo lung model is created by skipping the decellularization process. Each model can be used to answer different research questions.

Here, we present a protocol for an ex vivo lung cancer model that mimics the steps of tumor progression and helps to isolate a primary tumor, circulating tumor cells, and metastatic lesions.

It is difficult to isolate tumor cells at different points of tumor progression. We created an ex vivo lung model that can show the interaction of tumor ...

Intramucosal Inoculation of Squamous Cell Carcinoma Cells in Mice for Tumor Immune Profiling and Treatment Response Assessment

Head and neck squamous cell carcinoma (HNSCC) is a debilitating and deadly disease with a high prevalence of recurrence and treatment failure. To develop better therapeutic strategies, understanding tumor microenvironmental factors that contribute to the treatment resistance is important. A major impediment to understanding disease mechanisms and improving therapy has been a lack of murine cell lines that resemble the aggressive and metastatic nature of human HNSCCs. Furthermore, a majority of murine models employ subcutaneous implantations of tumors which lack important physiological features of the head and neck region, including high vascular density, extensive lymphatic vasculature, and resident mucosal flora. The purpose of this study is to develop and characterize an orthotopic model of HNSCC. We employ two genetically distinct murine cell lines and established tumors in the buccal mucosa of mice. We optimize collagenase-based tumor digestion methods for the optimal recovery of single cells from established tumors. The data presented here show that mice develop highly vascularized tumors that metastasize to regional lymph nodes. Single-cell multiparametric mass cytometry analysis shows the presence of diverse immune populations with myeloid cells representing the majority of all immune cells. The model proposed in this study has applications in cancer biology, tumor immunology, and preclinical development of novel therapeutics. The resemblance of the orthotopic model to clinical features of human disease will provide a tool for enhanced translation and improved patient outcomes.

Here we present a reproducible method for developing an orthotopic murine model of head and neck squamous cell carcinoma. Tumors demonstrate clinically relevant histopathological features of the disease, including necrosis, poor differentiation, nodal metastases, and immune infiltration. Tumor-bearing mice develop clinically relevant symptoms including dysphagia, jaw displacement, and weight loss.

Head and neck squamous cell carcinoma (HNSCC) is a debilitating and deadly disease with a high prevalence of recurrence and treatment failure. To develop ...

Detection of Lung Tumor Progression in Mice by Ultrasound Imaging

With ~1.6 million victims per year, lung cancer contributes tremendously to the worldwide burden of cancer. Lung cancer is partly driven by genetic alterations in oncogenes such as the KRAS oncogene, which constitutes ~25% of lung cancer cases. The difficulty in therapeutically targeting KRAS-driven lung cancer partly stems from having poor models that can mimic the progression of the disease in the lab. We describe a method that permits the relative quantification of primary KRAS lung tumors in a Cre-inducible LSL-KRAS G12D mouse model via ultrasound imaging. This method relies on brightness (B)-mode acquisition of the lung parenchyma. Tumors that are initially formed in this model are visualized as B-lines and can be quantified by counting the number of B-lines present in the acquired images. These would represent the relative tumor number formed on the surface of the mouse lung. As the formed tumors develop with time, they are perceived as deep clefts within the lung parenchyma. Since the circumference of the formed tumor is well-defined, calculating the relative tumor volume is achieved by measuring the length and width of the tumor and applying them in the formula used for tumor caliper measurements. Ultrasound imaging is a non-invasive, fast and user-friendly technique that is often used for tumor quantifications in mice. Although artifacts may appear when obtaining ultrasound images, it has been shown that this imaging technique is more advantageous for tumor quantifications in mice compared to other imaging techniques such as computed tomography (CT) imaging and bioluminescence imaging (BLI). Researchers can investigate novel therapeutic targets using this technique by comparing lung tumor initiation and progression between different groups of mice.

This protocol describes the steps taken to induce KRAS lung tumors in mice as well as the quantification of formed tumors by ultrasound imaging. Small tumors are visualized in early timepoints as B-lines. At later timepoints, relative tumor volume measurements are achieved by the measurement tool in the ultrasound software.

With ~1.6 million victims per year, lung cancer contributes tremendously to the worldwide burden of cancer. Lung cancer is partly driven by genetic ...

Analysis of Liver Microenvironment During Early Progression of Non-Alcoholic Fatty Liver Disease-Associated Hepatocellular Carcinoma in Zebrafish

Liver cancer is currently the third&#160;leading cause of cancer related death worldwide, and Hepatocellular Carcinoma (HCC) accounts for 75-90% of all liver cancer cases. With the introduction of effective treatments to prevent and treat hepatitis B/C, non-alcoholic fatty liver disease (NAFLD), and the more aggressive form know as non-alcoholic steatohepatitis (NASH), are quickly becoming the number one risk factors to develop HCC in modern societies. To better understand the role NASH has on the development of HCC we designed a NASH-associated HCC zebrafish. The optical clarity and genetic tractability of the zebrafish larvae make them an appealing and powerful model to study the liver microenvironment and immune cell composition using non-invasive fluorescent live imaging. This protocol describes how to use a NASH-associated HCC zebrafish model to investigate the effect of cholesterol surplus in the liver microenvironment and its impact on immune cell composition at early stages of the disease. First, we feed HCC larvae (s704Tg), which express hepatocyte-specific activated beta-catenin, with a 10% high cholesterol diet for 8 days to develop a NASH-associated HCC model. Here we describe how to make use of different transgenic lines to evaluate several early malignancy features in the liver by non-invasive confocal microscopy, such as liver area, cell, and nuclear morphology (hepatocytes area, nuclear area, nuclear:cytoplasmic ratio (N:C ratio), nuclear circularity, micronuclei/nuclear herniation scoring) and angiogenesis. Then, using transgenic lines with tagged immune cells (neutrophils, macrophages, and T cells) we show how to analyze liver immune cell composition in NASH-associated HCC larvae. The described techniques are useful to evaluate liver microenvironment and immune cell composition at early hepatocarcinogenesis stages, but they can also be modified to study such features in other liver disease models.

Here, we present how to generate a non-alcoholic fatty liver disease (NAFLD)-associated Hepatocellular Carcinoma (HCC) zebrafish model to study the impact of cholesterol surplus on liver microenvironment and immune cell landscape.

Liver cancer is currently the third&#160;leading cause of cancer related death worldwide, and Hepatocellular Carcinoma (HCC) accounts for 75-90% of all ...

A Three-Dimensional Spheroid Model to Investigate the Tumor-Stromal Interaction in Hepatocellular Carcinoma

The aggressiveness and lack of well-tolerated and widely effective treatments for advanced hepatocellular carcinoma (HCC), the predominant form of liver cancer, rationalize its rank as the second most common cause of cancer-related death. Preclinical models need to be adapted to recapitulate the human conditions to select the best therapeutic candidates for clinical development and aid the delivery of personalized medicine. Three-dimensional (3D) cellular spheroid models show promise as an emerging in vitro alternative to two-dimensional (2D) monolayer cultures. Here, we describe a 3D tumor spheroid&#160;model which exploits the ability of individual cells to aggregate when maintained in hanging droplets, and is more representative of an in vivo environment than standard monolayers. Furthermore, 3D spheroids can be produced by combining homotypic or heterotypic cells, more reflective of the cellular heterogeneity in vivo, potentially enabling the study of environmental interactions that can influence progression and treatment responses. The current research optimized the cell density to form 3D homotypic and heterotypic tumor spheroids by immobilizing cell suspensions on the lids of standard 10 cm3 Petri dishes. Longitudinal analysis was performed to generate growth curves for homotypic versus heterotypic tumor/fibroblasts spheroids. Finally, the proliferative impact of fibroblasts (COS7 cells) and liver myofibroblasts (LX2) on homotypic tumor (Hep3B) spheroids was investigated. A seeding density of 3,000 cells (in 20 &#181;L media) successfully yielded Huh7/COS7 heterotypic spheroids, which displayed a steady increase in size up to culture day 8, followed by growth retardation. This finding was corroborated using Hep3B homotypic spheroids cultured in LX2 (human hepatic stellate cell line) conditioned medium (CM). LX2 CM triggered the proliferation of Hep3B spheroids compared to control tumor spheroids. In conclusion, this protocol has shown that 3D tumor spheroids can be used as a simple, economical, and prescreen in vitro tool to study tumor-stromal interactions more comprehensively.

Comprehensive in vitro models that faithfully recapitulate the relevant human disease are lacking. The current study presents three-dimensional (3D) tumor spheroid creation and culture, a reliable in vitro tool to study the tumor-stromal interaction in human hepatocellular carcinoma.

The aggressiveness and lack of well-tolerated and widely effective treatments for advanced hepatocellular carcinoma (HCC), the predominant form of liver ...

Modeling Oral-Esophageal Squamous Cell Carcinoma in 3D Organoids

Esophageal squamous cell carcinoma (ESCC) is prevalent worldwide, accounting for 90% of all esophageal cancer cases each year, and is the deadliest of all human squamous cell carcinomas. Despite recent progress in defining the molecular changes accompanying ESCC initiation and development, patient prognosis remains poor. The functional annotation of these molecular changes is the necessary next step and requires models that both capture the molecular features of ESCC and can be readily and inexpensively manipulated for functional annotation. Mice treated with the tobacco smoke mimetic 4-nitroquinoline 1-oxide (4NQO) predictably form ESCC and esophageal preneoplasia. Of note, 4NQO lesions also arise in the oral cavity, most commonly in the tongue, as well as the forestomach, which all share the stratified squamous epithelium. However, these mice cannot be simply manipulated for functional hypothesis testing, as generating isogenic mouse models is time- and resource-intensive. Herein, we overcome this limitation by generating single cell-derived three-dimensional (3D) organoids from mice treated with 4NQO to characterize murine ESCC or preneoplastic cells ex vivo. These organoids capture the salient features of ESCC and esophageal preneoplasia, can be cheaply and quickly leveraged to form isogenic models, and can be utilized for syngeneic transplantation experiments. We demonstrate how to generate 3D organoids from normal, preneoplastic, and SCC murine esophageal tissue and maintain and cryopreserve these organoids. The applications of these versatile organoids are broad and include the utilization of genetically engineered mice and further characterization by flow cytometry or immunohistochemistry, the generation of isogeneic organoid lines using CRISPR technologies, and drug screening or syngeneic transplantation. We believe that the widespread adoption of the techniques demonstrated in this protocol will accelerate progress in this field to combat the severe burden of ESCC.

This protocol describes the key steps to generate and characterize murine oral-esophageal 3D organoids that represent normal, preneoplastic, and squamous cell carcinoma lesions induced via chemical carcinogenesis.

Esophageal squamous cell carcinoma (ESCC) is prevalent worldwide, accounting for 90% of all esophageal cancer cases each year, and is the deadliest of all ...