This work was supported in part by grants from the NIH (HL118532, HL120142, CA187692), the David &#38; Lucile Packard Foundation, the Camille &#38; Henry Dreyfus Foundation, and the Burroughs Welcome Fund. A.S.P. was supported in part by a Charlotte Elizabeth Procter Honorific Fellowship.

1. Preparation of Solutions
<ol>
	<li>To prepare a 5 mg/ml solution of insulin, dilute the powdered insulin stock with 5 mM hydrochloric acid (HCl) in dH2O (500 mg insulin in 100 ml solvent). Prepare 100 ml solvent by adding 50 &#956;l of concentrated HCl to 100 ml distilled water (dH2O).</li>
	<li>To make a 1x solution of PBS, dilute the 10x phosphate-buffered saline (PBS) stock solution to 1x with dH2O under sterile conditions.</li>
	<li>Prepare the polydimethylsiloxane (PDMS) elastomer solution as follows: mix the PDMS prepolymer together with the curing agent in a 10:1 (w:w) ratio.</li>
	<li>Prepare the cell culture medium as follows: to 500 ml of stock Dulbecco&#39;s Modified Eagle Medium: Nutrient Mixture F-12 (DMEM/F-12), add 10 ml of sterile fetal bovine serum (FBS), 500 &#956;l of gentamicin reagent, and 500 &#956;l of 5 mg/ml insulin.</li>
	<li>To prepare the 1% bovine serum albumin (BSA) in 1x PBS solution, add 1% (w:v) solution of BSA powder to 1x PBS and mix thoroughly.</li>
	<li>To prepare a 4 mg/ml solution of neutralized bovine type I collagen, add 50 &#181;l 10x Hank&#39;s balanced salt solution (HBSS) buffer, 30 &#181;l 0.1 N sodium hydroxide (NaOH), 30 &#181;l cell culture medium, and 400 &#181;l of stock collagen to a chilled 1.5 ml microcentrifuge tube. Mix slowly by pipetting up and down; avoid introducing bubbles. To remove any bubbles, briefly centrifuge the mixture at 4 &#176;C.</li>
	<li>Prepare a fixative solution by diluting 16% paraformaldehyde 1:4 (v:v) in 1x PBS.</li>
	<li>Prepare a nuclei labeling solution by diluting the stock nuclei labeling solution 1:1,000 (v:v) in 1x PBS.</li>
	<li>Prepare a 0.3% phosphate-buffered saline and detergent (PBST) solution by mixing 1x PBS with 0.3% (v:v) detergent.</li>
	<li>Prepare blocking buffer by diluting goat serum 1:10 (v:v) in 0.3% PBST.</li>
	<li>Prepare a primary antibody solution for a particular protein of interest by diluting primary antibody (for example, rabbit anti-focal adhesion kinase (FAK)) 1:200 (v:v) in blocking buffer.</li>
	<li>Prepare a secondary antibody solution by diluting a fluorescent probe-conjugated antibody (for example, goat anti-rabbit) 1:1,000 (v:v) in blocking buffer.</li>
</ol>
2. Preparation of Elastomeric Stamps for 3D Micropatterning
Note: Elastomeric stamps are made with PDMS.
<ol>
	<li>Make a PDMS solution at the same ratio as described in step 1.3 and mix thoroughly. Place the mixture in a vacuum chamber for 15-30 min to remove any air bubbles that were introduced during the mixing process.</li>
	<li>Pour the degassed solution into a plastic weigh boat or Petri dish containing a silicon master that is lithographically patterned with features of desired geometry. For best results, cure the PDMS solution at 60 &#176;C for ~12 hr. 
	Note: The silicon masters are highly customizable; this protocol uses rectangular structures with dimensions of 50 &#956;m x 200 &#956;m x 50 &#956;m spaced 200 &#956;m apart. The silicon masters can be made using standard photolithography techniques. Briefly, an epoxy-based photoresist is spin-coated on top of a silicon wafer. A mask detailing the desired stamp features is placed on top of the photoresist-coated wafer, which is then exposed to UV light. The desired features not blocked by the mask are exposed to the light and the photoresist at these locations becomes crosslinked, while the remainder of the photoresist coating is soluble and can be washed away.</li>
	<li>After the PDMS has cured around the desired features on the silicon master, remove the PDMS and master from the plastic container. Carefully separate the PDMS from the silicon wafer and remove excess PDMS from around the imprinted features using a clean razor blade.</li>
	<li>Now cut the PDMS patterned with imprinted features into individual rectangular stamps (~8-mm x 5-mm) with a razor blade. Store these feature-side-up in a clean 100-mm-diameter Petri dish.</li>
	<li>Additionally, use the PDMS solution described in step 1.3 to make supports for the rectangular stamps.</li>
	<li>Using a spin coater, spread ~2-3 g of the PDMS solution evenly on a 100-mm-diameter Petri dish and cure the PDMS for ~12 hr at 60 &#176;C as in step 2.1. Then, using a razor blade, cut the thin layer of PDMS into rectangles (~5 mm x 2 mm). 
	Note: Two supports are needed for each PDMS stamp made in step 2.3. The supports can be stored in the 100-mm-diameter Petri dish that contains the PDMS stamps.</li>
	<li>Before the PDMS stamps and supports can be used for cell culture, sterilize by immersion in 70% ethanol and dry using an aspirator in a biosafety cabinet (cell culture hood).</li>
</ol>
3. Preparation of 3D Epithelial Tissues
<ol>
	<li>In a biosafety cabinet, add a drop of approximately 50&#160;&#181;l of 1% BSA in PBS to the top of each stamp. Place the droplet covered stamps at 4 &#176;C for a minimum of 4 hr to ensure that the BSA adsorbs to the surface of the stamp.</li>
	<li>Aspirate BSA solution from the PDMS stamps.</li>
	<li>Wash the surfaces of the stamps twice with cell culture medium (50 &#181;l per wash per stamp should be sufficient), aspirating after each wash.</li>
	<li>Handle the sterilized PDMS stamps and supports using curved stainless steel tweezers. In a biosafety cabinet, lay out one 35-mm-diameter tissue culture dish for each PDMS stamp. In each dish, lay down two PDMS supports separated by a distance slightly less than the length of the PDMS stamps.</li>
	<li>Using the tweezers, sterilize as many circular glass coverslips (15 mm in diameter, #1) as there are PDMS stamps using 70% ethanol. Aspirate the excess liquid from the coverslips while holding them with the tweezers. Store the washed coverslips in a separate 100-mm-diameter Petri dish.</li>
	<li>Dispense ~50 &#181;l of the collagen mixture to evenly coat the surface of each PDMS stamp.</li>
	<li>Pick up each collagen-coated PDMS stamp with the tweezers and gently invert them. Lower the inverted stamps on top of the PDMS supports laid out in 35-mm-diameter tissue culture dished such that the collagen is between the stamp and the bottom of the tissue culture dish. Incubate the dishes at 37 &#176;C for 30 min.</li>
	<li>Dispense ~50 &#181;l of the remaining collagen mixture onto each of the circular coverslips (later, these will be placed on top of the engineered tissues to completely encapsulate them in collagen) and incubate them at 37 &#176;C for 30 min.</li>
	<li>Obtain a 100-mm-diameter tissue culture dish containing epithelial cells (ex. EpH4 mouse mammary epithelial cells) at ~40% confluency. Aspirate the cell culture medium and wash once with 10 ml 1x PBS. Add 2 ml of trypsin to the cells and incubate at 37 &#176;C for 5-10 min.</li>
	<li>Add 8 ml of fresh culture medium to the tissue culture dish containing trypsinized cells, detaching any remaining adherent cells from the dish. Mix gently by pipetting and move the cell mixture to a 15 ml conical tube and centrifuge at 100 &#215; g for 5 min.</li>
	<li>Aspirate the supernatant from the conical tube and resuspend the cell pellet in cell culture medium. Using a hemocytometer, count the cells to determine the concentration of the suspension. Adjust the suspension volume to obtain a final concentration of ~106-107cells/ml.</li>
	<li>Remove the gelled collagen samples from the incubator. Using the tweezers, gently lift the PDMS stamps straight upwards to detach them from the molded collagen and discard them.</li>
	<li>Dispense ~30 &#181;l of the concentrated cell suspension onto the surface of each collagen gel containing molded cavities of desired geometry. Observe the cells under a brightfield microscope with a 10X/0.25 NA objective while gently shaking the dishes side to side to promote cell settling within the cavities. The cavities should be filled within ~5 min.</li>
	<li>To remove excess cells from around the cavities, tilt each tissue culture dish on its side and gently dispense ~400 &#956;l cell culture medium over the surface of the collagen gel. Aspirate the liquid and repeat the wash 1-2 more times, checking the collagen gels under the microscope in between each wash.</li>
	<li>After the excess cells have been cleared from around the cell-filled cavities in the collagen mold, place the tissue culture dishes into a cell culture incubator at 37 &#176;C for 15 min. Then, using the tweezers, gently invert the collagen-coated class coverslips and place them on top of the cell-filled collagen molds such that the collagen from the coverslips forms a cap over the cell-filled cavities. Incubate the samples at 37 &#176;C for 15 min.</li>
	<li>Once the collagen caps have adhered to the cell-filled collagen mold, dispense ~2-2.5 ml cell culture medium slowly over the glass coverslip on top of the gels. Culture the samples at 37 &#176;C for 1-3 days. 
	Note: 24 hr after initial seeding, the epithelial tissues can be treated with growth factors such as epidermal growth factor (EGF) or hepatocyte growth factor (HGF) to induce branching.</li>
</ol>
4. Immunofluorescence and Image Analysis&#160;
<ol>
	<li>Aspirate the cell culture medium from the tissue culture dishes and add enough fixative solution to cover the cell-containing gels. Incubate the dishes at room temperature for 15 min on a shaker at 200 rpm.</li>
	<li>Aspirate the fixative, fill the tissue culture dishes with 1x PBS, and incubate at room temperature for 15 min on a shaker at 200 rpm. Repeat twice for three total washes.</li>
	<li>To label nuclei: Aspirate the PBS from the tissue culture dish and replace with Hoechst solution. Incubate at room temperature for 15-20 min. To stain for FAK or another marker that is detectable with antibodies, skip to Step 4.5.</li>
	<li>Aspirate the nuclear labeling solution and wash the cell-containing gels three times with 1x PBS as in Step 4.2. Stained samples can be stored in 1x PBS at 4 &#176;C until further use.</li>
	<li>To stain for a protein of interest: Aspirate the PBS from the tissue culture dishes, add 300 &#956;l of 0.3% PBST, and incubate the sample at room temperature for 15 min.</li>
	<li>Aspirate the PBS, cover the gels with blocking buffer, and incubate on a shaker (200 rpm) at room temperature for ~4 hr.</li>
	<li>Aspirate the blocking buffer, cover the gels with primary antibody solution, and incubate on a shaker at 200 rpm overnight at 4 &#176;C.</li>
	<li>Aspirate the primary antibody solution, add 0.3% PBST solution, and incubate on a shaker at 200 rpm at room temperature for 30 min. Aspirate the PBST and repeat every 30 min for 3-4 hr.</li>
	<li>Repeat steps 4.7 and 4.8, this time incubating with the secondary antibody solution. Wrap the tissue culture dishes with aluminum foil to prevent photobleaching of the secondary antibody. After the final wash, stained samples can be stored in 1x PBS at 4 &#176;C until further use.</li>
	<li>To visualize samples, use a 10X/0.30 NA objective focused on the midplane of the epithelial tissues.</li>
	<li>To visualize cell nuclei, image fixed samples labeled with a nuclear marker using a 10X/0.30 NA objective under UV illumination.</li>
	<li>To visualize samples stained for a protein of interest, image using a 10X/0.30 NA objective on an inverted fluorescence microscope.</li>
	<li>To create frequency maps of protein staining of multiple tissues (typically 50 or more) of identical initial geometry, first import each of the images using standard image analysis software (see Materials) and convert them to 8-bit grayscale.</li>
	<li>To threshold these images, convert them to binary (i.e., halftone/black and white) by defining a grayscale cutoff point; grayscale values below the threshold become black, and those above the threshold become white. Then, combine each of the individual binary images into a single image stack.</li>
	<li>Next, register the stacked images (i.e., align or match them) in the analysis software. Many image analysis software packages come with a freely available registration plugin.
	<ol>
		<li>Use each image in a stack as a template for the alignment of the next image, such that the images in the entire stack are aligned by propagation. Finally, overlay (project) the images in the aligned image stack based on average intensity to form a single image with a pixel frequency map. This image can then be color-coded using image editing software of choice10,11.</li>
	</ol>
	</li>
</ol>

<ol>
	<li>Affolter, 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=Tube+or+not+tube:+remodeling+epithelial+tissues+by+branching+morphogenesis.">Tube or not tube: remodeling epithelial tissues by branching morphogenesis.</a> Dev Cell. 4 (1), 11-18 (2003).</li><li>Zhu, W., Nelson, C. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=PI3K+signaling+in+the+regulation+of+branching+morphogenesis.">PI3K signaling in the regulation of branching morphogenesis.</a> Biosystems. 109 (3), 403-411 (2012).</li><li>Sternlicht, M. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Key+stages+in+mammary+gland+development:+the+cues+that+regulate+ductal+branching+morphogenesis.">Key stages in mammary gland development: the cues that regulate ductal branching morphogenesis.</a> Breast Cancer Res. 8 (1), 201 (2006).</li><li>Fata, J. E., 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=The+MAPK(ERK-1,2)+pathway+integrates+distinct+and+antagonistic+signals+from+TGFalpha+and+FGF7+in+morphogenesis+of+mouse+mammary+epithelium.">The MAPK(ERK-1,2) pathway integrates distinct and antagonistic signals from TGFalpha and FGF7 in morphogenesis of mouse mammary epithelium.</a> Dev Biol. 306 (1), 193-207 (2007).</li><li>Ip, M. M., Darcy, K. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Three-dimensional+mammary+primary+culture+model+systems.">Three-dimensional mammary primary culture model systems.</a> J Mammary Gland Biol Neoplasia. 1 (1), 91-110 (1996).</li><li>Lo, A. T., Mori, H., Mott, J., 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=Constructing+three-dimensional+models+to+study+mammary+gland+branching+morphogenesis+and+functional+differentiation.">Constructing three-dimensional models to study mammary gland branching morphogenesis and functional differentiation.</a> J Mammary Gland Biol Neoplasia. 17 (2), 103-110 (2012).</li><li>Nelson, C. M., Vanduijn, M. M., Inman, J. L., Fletcher, D. A., 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=Tissue+geometry+determines+sites+of+mammary+branching+morphogenesis+in+organotypic+cultures.">Tissue geometry determines sites of mammary branching morphogenesis in organotypic cultures.</a> Science. 314 (5797), 298-300 (2006).</li><li>Gjorevski, N., Nelson, C. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Endogenous+patterns+of+mechanical+stress+are+required+for+branching+morphogenesis.">Endogenous patterns of mechanical stress are required for branching morphogenesis.</a> Integr Biol (Camb). 2 (9), 424-434 (2010).</li><li>Gjorevski, N., Nelson, C. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mapping+of+mechanical+strains+and+stresses+around+quiescent+engineered+three-dimensional+epithelial+tissues.">Mapping of mechanical strains and stresses around quiescent engineered three-dimensional epithelial tissues.</a> Biophys J. 103 (1), 152-162 (2012).</li><li>Gjorevski, N., Piotrowski, A. S., Varner, V. D., Nelson, C. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Dynamic+tensile+forces+drive+collective+cell+migration+through+three-dimensional+extracellular+matrices.">Dynamic tensile forces drive collective cell migration through three-dimensional extracellular matrices.</a> Sci Rep. 5, 11458 (2015).</li><li>Zhu, W., Nelson, C. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=PI3K+regulates+branch+initiation+and+extension+of+cultured+mammary+epithelia+via+Akt+and+Rac1+respectively.">PI3K regulates branch initiation and extension of cultured mammary epithelia via Akt and Rac1 respectively.</a> Dev Biol. 379 (2), 235-245 (2013).</li><li>Barcellos-Hoff, M. H., Aggeler, J., Ram, T. G., 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=Functional+differentiation+and+alveolar+morphogenesis+of+primary+mammary+cultures+on+reconstituted+basement+membrane.">Functional differentiation and alveolar morphogenesis of primary mammary cultures on reconstituted basement membrane.</a> Development. 105 (2), 223-235 (1989).</li><li>Hirai, Y., 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=Epimorphin+functions+as+a+key+morphoregulator+for+mammary+epithelial+cells.">Epimorphin functions as a key morphoregulator for mammary epithelial cells.</a> J Cell Biol. 140 (1), 159-169 (1998).</li><li>Pavlovich, A. L., Manivannan, S., Nelson, C. 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The authors declare that they have no competing financial interests.

The protocol described above outlines a method to produce identical epithelial tissues of pre-defined shape, enabling spatial control of the mechanical stress experienced by cells in the tissue. An elastomeric mold is used to create cavities in type I collagen that are then filled with epithelial cells and covered with an additional collagen layer such that cells are completely encapsulated in a 3D collagen matrix environment. Further culture of these tissues and treatment with growth factors to induce branching from the...

The development of branched epithelial tissues, known as branching morphogenesis, is regulated by cell-derived, physical, and environmental factors. In the mammary gland, branching morphogenesis is an iterative process through which guided collective cell migration creates a tree-like architecture. The first step is primary bud formation from the milk ducts, followed by branch initiation and elongation1,2. Invasion of branches into the surrounding stroma is induced by the systemic release of steroid hormones at puberty. New primary buds then initiate from the ends of existing branches, and this process continues to create an epithelial tree3. Although many important biochemical signals have been identified, a comprehensive understanding of the cell biological mechanisms that guide this complex developmental process is currently lacking. Moreover, mechanistic studies on the influences of specific cues are difficult to deconstruct from experiments in vivo, as precise spatiotemporal perturbations and measurements are often not possible.
Three-dimensional (3D) culture techniques, such as whole organ culture, primary organoids, and cell culture models, are useful tools for systematically investigating the mechanisms underlying tissue morphogenesis4-6. These can be particularly useful for determining the influences of specific factors individually, such as mechanical forces and biochemical signals, on a variety of cell behaviors, including migration, proliferation, and differentiation.6 Engineered cell culture models, in particular, readily enable the perturbation of individual cells and their microenvironment.
One such culture model uses a microfabrication-based approach to engineer model mammary epithelial tissues with controlled 3D structure that consistently and reproducibly form branches that migrate collectively when induced with the appropriate growth factors. The major advantage of the model is the ability to precisely manipulate and measure the effects of physical and biochemical factors, such as patterns of mechanical stress, with high statistical confidence. This technique, together with computational modeling, has already been used to determine the relative contributions of physical and biochemical signals in the guidance of the normal development of mammary epithelial tissues and other branched epithelia7-11. Presented here is a detailed protocol for building these model tissues, which can be readily extended to other types of cells and extracellular matrix (ECM) gels, and which serves as a potential tool for the testing of therapeutics.

<table><tbody><tr><td>Polydimethylsiloxane (PDMS)</td><td>Ellsworth Adhesives</td><td>Sylgard 184</td><td></td></tr><tr><td>PDMS curing agent</td><td>Ellsworth Adhesives</td><td>Sylgard 184</td><td></td></tr><tr><td>Lithographically patterned silicon master</td><td>self-made</td><td>N/A</td><td></td></tr><tr><td>Plastic weigh boat</td><td>Fisher Scientific</td><td>08-732-115</td><td></td></tr><tr><td>100-mm-diameter Petri dishes</td><td>BioExpress</td><td>D-2550-2</td><td></td></tr><tr><td>Ethyl Alcohol 200 Proof</td><td>Pharmco-Aaper</td><td>111000200</td><td>Make a 70% EtOH (v:v) solution by mixing with dH&lt;sub&gt;2&lt;/sub&gt;O</td></tr><tr><td>Razor blade</td><td>American Safety Razor</td><td>620179</td><td></td></tr><tr><td>1:1 Dulbecco&amp;rsquo;s Modified Eagle&amp;rsquo;s Medium : Ham&amp;rsquo;s F12 Nutrient Mixture (DMEM/F12) (1:1)</td><td>Hyclone</td><td>SH30023FS</td><td></td></tr><tr><td>Fetal Bovine Serum (FBS)</td><td>Atlanta Biologicals</td><td>S11150H</td><td></td></tr><tr><td>10x Hank&amp;rsquo;s balanced salt solution (HBSS)</td><td>Life Technologies</td><td>14185-052</td><td></td></tr><tr><td>Insulin</td><td>Sigma Aldrich</td><td>I6634-500MG</td><td></td></tr><tr><td>Gentamicin</td><td>Life Technologies</td><td>15750-060</td><td></td></tr><tr><td>10x Phosphate-buffered saline (PBS)</td><td>Fisher Scientific</td><td>BP399-500</td><td></td></tr><tr><td>Sodium hydroxide (NaOH)</td><td>Sigma Aldrich</td><td>221465-500G</td><td></td></tr><tr><td>Bovine type I collagen (non-pepsinized)</td><td>Koken</td><td>IAC-50</td><td></td></tr><tr><td>Albumin from bovine serum (BSA)</td><td>Sigma Aldrich</td><td>A-7906</td><td></td></tr><tr><td>Curved stainless steel tweezers</td><td>Dumont</td><td>7</td><td></td></tr><tr><td>35-mm-diameter tissue culture dishes</td><td>BioExpress</td><td>T-2881-6</td><td></td></tr><tr><td>15 ml conical tubes</td><td>BioExpress</td><td>C-3394-2</td><td></td></tr><tr><td>1.5 ml Eppendorf Safe-Lock Tube</td><td>USA Scientific</td><td>1615-5500</td><td></td></tr><tr><td>Circular #1 glass coverslips, 15-mm in diameter</td><td>Bellco Glass Inc.</td><td>Special order</td><td></td></tr><tr><td>0.05% 1x Trypsin-EDTA</td><td>Life Technologies</td><td>25300-054</td><td></td></tr><tr><td>Paraformaldehyde</td><td>VWR</td><td>100503-916</td><td></td></tr><tr><td>Triton X-100</td><td>Perkin Elmer</td><td>N9300260</td><td>Detergent</td></tr><tr><td>HGF</td><td>Sigma Aldrich</td><td>H 9661</td><td>Resuspended in dH&lt;sub&gt;2&lt;/sub&gt;O at 50 mg/ml</td></tr><tr><td>Rabbit anti-mouse FAK antibody</td><td>Life Technologies</td><td>AMO0672</td><td></td></tr><tr><td>Goat anti-rabbit Alexa 488 antibody</td><td>Life Technologies</td><td>A-11034</td><td></td></tr><tr><td>Adobe Photoshop</td><td>Adobe</td><td>N/A</td><td>Used for color-coding pixel frequency maps.</td></tr><tr><td>FIJI (ImageJ)</td><td>NIH</td><td>N/A</td><td>Free image analysis software used for thresholding, registering, and overlaying images to create a pixel frequency map. The StackReg plugin was used for registering binary images.</td></tr></tbody></table>

engineering three-dimensional epithelial tissues embedded within extracellular matrix

The architecture of branched organs such as the lungs, kidneys, and mammary glands arises through the developmental process of branching morphogenesis, which is regulated by a variety of soluble and physical signals in the microenvironment. Described here is a method created to study the process of branching morphogenesis by forming engineered three-dimensional (3D) epithelial tissues of defined shape and size that are completely embedded within an extracellular matrix (ECM). This method enables the formation of arrays of identical tissues and enables the control of a variety of environmental factors, including tissue geometry, spacing, and ECM composition. This method can also be combined with widely used techniques such as traction force microscopy (TFM) to gain more information about the interactions between cells and their surrounding ECM. The protocol can be used to investigate a variety of cell and tissue processes beyond branching morphogenesis, including cancer invasion.

General schematic of mammary epithelial tissue microfabrication
A general schematic of the microfabrication procedure outlining the experimental work flow is shown in Figure 1. The end result is an array of epithelial tissues of identical geometry and spacing that are completely embedded within an ECM gel. A representative experiment uses EpH4 mouse mammary epithelial cells cultured in a gel of bovine type I collagen at a conce...

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Engineering Three-dimensional Epithelial Tissues Embedded within Extracellular Matrix

This manuscript describes a soft lithography-based technique to engineer uniform arrays of three-dimensional (3D) epithelial tissues of defined geometry surrounded by extracellular matrix. This method is amenable to a wide variety of cell types and experimental contexts and allows for high-throughput screening of identical replicates.

The architecture of branched organs such as the lungs, kidneys, and mammary glands arises through the developmental process of branching morphogenesis, ...

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7.5K Views.  Princeton University. This manuscript describes a soft lithography-based technique to engineer uniform arrays of three-dimensional (3D) epithelial tissues of defined geometry surrounded by extracellular matrix. This method is amenable to a wide variety of cell types and experimental contexts and allows for high-throughput screening of identical replicates.

Video: Engineering Three-dimensional Epithelial Tissues Embedded within Extracellular Matrix

Analyzing the Communication Between Monocytes and Primary Breast Cancer Cells in an Extracellular Matrix Extract (ECME)-based Three-dimensional System

Embedded in the extracellular matrix (ECM), normal and neoplastic epithelial cells intimately communicate with hematopoietic and non-hematopoietic cells, thus greatly influencing normal tissue homeostasis and disease outcome. In breast cancer, tumor-associated macrophages (TAMs) play a critical role in disease progression, metastasis, and recurrence; therefore, understanding the mechanisms of monocyte chemoattraction to the tumor microenvironment and their interactions with tumor cells is important to control the disease. Here, we provide a detailed description of a three-dimensional (3D) co-culture system of human breast cancer (BrC) cells and human monocytes. BrC cells produced high basal levels of regulated on-activation, normal T-cell expressed and secreted (RANTES), monocyte chemoattractant protein-1 (MCP-1), and granulocyte-macrophage colony-stimulating factor (G-CSF), while in co-culture with monocytes, pro-inflammatory cytokines Interleukin (IL)-1 beta (IL-1&#946;) and IL-8 were enriched together with matrix metalloproteinases (MMP)-1, MMP-2, and MMP-10. This tumor stroma microenvironment promoted resistance to anoikis in MCF-10A 3D acini-like structures, chemoattraction of monocytes, and invasion of aggressive BrC cells. The protocols presented here provide an affordable alternative to study intra-tumor communication and are an example of the great potential that in vitro 3D cell systems provide to interrogate specific features of tumor biology related to tumor aggression.

Analyzing the Communication Between Monocytes and Primary Breast Cancer Cells in an Extracellular Matrix Extract ECME-based Three-dimensional System

Here, we describe a three-dimensional culture method to analyze the morphology of primary breast cancer cells, as well as to study their direct/indirect interactions with monocytes and the outcomes such as collagen degradation, immune cell recruitment, cell invasion, and promotion of cancer-related inflammation.

Embedded in the extracellular matrix (ECM), normal and neoplastic epithelial cells intimately communicate with hematopoietic and non-hematopoietic cells, ...

Cancer Research

Fibroblast-Derived 3D Matrix System Applicable to Endothelial Tube Formation Assay

The extracellular matrix (ECM) is a three-dimensional scaffold that acts as the main support for cells in tissues. Besides its structural function, the ECM also participates in cell migration, proliferation, and differentiation. Fibroblasts are the main type of cells modifying ECM fiber arrangement and production. In cancer, CAFs (cancer associated fibroblasts) are in permanent activation status, participating in ECM remodeling, facilitating tumor cell migration, and stimulating tumor-associated angiogenesis, among other pro-tumorigenic roles. The objective of this method is to create a three-dimensional matrix with a fiber composition that is similar to in vivo matrices, using immortalized fibroblasts or human primary CAFs. Fibroblasts are cultured in pre-treated cell culture plates and grown under ascorbic acid stimulation. Then, fibroblasts are removed and matrices are blocked for further cell seeding. In this ECM model, fibroblasts can be activated or modified to generate different kinds of matrix, whose effects can be studied in cell culture. 3D matrices are also shaped by cell signals, like degradation or cross-linking enzymes that might modify fiber distribution. In this context, angiogenesis can be studied, along with other cell types such as epithelial tumor cells.

The aim of this method is to obtain fibroblast-derived 3D matrices as a natural scaffold for subsequent cellular assays. Fibroblasts are seeded in a pre-treated culture plate and stimulated with ascorbic acid for matrix generation. Matrices are decellularized and blocked to culture relevant cells (e.g., endothelial cells).

The extracellular matrix (ECM) is a three-dimensional scaffold that acts as the main support for cells in tissues. Besides its structural function, the ...

Tissue Engineering: Construction of a Multicellular 3D Scaffold for the Delivery of Layered Cell Sheets

Many tissues, such as the adult human hearts, are unable to adequately regenerate after damage.2,3 Strategies in tissue engineering propose innovations to assist the body in recovery and repair. For example, TE approaches may be able to attenuate heart remodeling after myocardial infarction (MI) and possibly increase total heart function to a near normal pre-MI level.4 As with any functional tissue, successful regeneration of cardiac tissue involves the proper delivery of multiple cell types with environmental cues favoring integration and survival of the implanted cell/tissue graft. Engineered tissues should address multiple parameters including: soluble signals, cell-to-cell interactions, and matrix materials evaluated as delivery vehicles, their effects on cell survival, material strength, and facilitation of cell-to-tissue organization. Studies employing the direct injection of graft cells only ignore these essential elements.2,5,6 A tissue design combining these ingredients has yet to be developed. Here, we present an example of integrated designs using layering of patterned cell sheets with two distinct types of biological-derived materials containing the target organ cell type and endothelial cells for enhancing new vessels formation in the &#8220;tissue&#8221;. Although these studies focus on the generation of heart-like tissue, this tissue design can be applied to many organs other than heart with minimal design and material changes, and is meant to be an off-the-shelf product for regenerative therapies. The protocol contains five detailed steps. A temperature sensitive Poly(N-isopropylacrylamide) (pNIPAAM) is used to coat tissue culture dishes. Then, tissue specific cells are cultured on the surface of the coated plates/micropattern surfaces to form cell sheets with strong lateral adhesions. Thirdly, a base matrix is created for the tissue by combining porous matrix with neovascular permissive hydrogels and endothelial cells. Finally, the cell sheets are lifted from the pNIPAAM coated dishes and transferred to the base element, making the complete construct.

For creation of highly organized structures of complex tissue, one must assemble multiple material and cell types into an integrated composite. This combinatorial design incorporates organ-specific layered cell sheets with two distinct biologically-derived materials containing a strong fibrous matrix base, and endothelial cells for enhancing new vessels formation.

Many tissues, such as the adult human hearts, are unable to adequately regenerate after damage.2,3 Strategies in tissue engineering propose innovations to ...

Tissue Engineering of Tumor Stromal Microenvironment with Application to Cancer Cell Invasion

3D organotypic cultures of epithelial cells on a matrix embedded with mesenchymal cells are widely used to study epithelial cell differentiation and invasion. Rat tail type I collagen and/or matrix derived from Engelbreth-Holm-Swarm mouse sarcoma cells have been traditionally employed as the substrates to model the matrix or stromal microenvironment into which mesenchymal cells (usually fibroblasts) are populated. Although experiments using such matrices are very informative, it can be argued that due to an overriding presence of a single protein (such as in type I Collagen) or a high content of basement membrane components and growth factors (such as in matrix derived from mouse sarcoma cells), these substrates do not best reflect the contribution to matrix composition made by the stromal cells themselves. To study native matrices produced by primary dermal fibroblasts isolated from patients with a tumor prone, genetic blistering disorder (recessive dystrophic epidermolysis bullosa), we have adapted an existing native matrix protocol to study tumor cell invasion. Fibroblasts are induced to produce their own matrix over a prolonged period in culture. This native matrix is then detached from the culture dish and epithelial cells are seeded onto it before the entire coculture is raised to the air-liquid interface. Cellular differentiation and/or invasion can then be assessed over time. This technique provides the ability to assess epithelial-mesenchymal cell interactions in a 3D setting without the need for a synthetic or foreign matrix with the only disadvantage being the prolonged period of time required to produce the native matrix. Here we describe the application of this technique to assess the ability of a single molecule expressed by fibroblasts, type VII collagen, to inhibit tumor cell invasion.

Tissue engineered fibroblast-derived native matrix is an emerging tool to generate a stromal substrate which supports epithelial cell proliferation and differentiation. Here a protocol applying this methodology to assess the impact of different stromal cell types on tumor cell biology is presented.

3D organotypic cultures of epithelial cells on a matrix embedded with mesenchymal cells are widely used to study epithelial cell differentiation and ...

Development of a Multicellular Three-dimensional Organotypic Model of the Human Intestinal Mucosa Grown Under Microgravity

Because cells growing in a three-dimensional (3-D) environment have the potential to bridge many gaps of cell cultivation in 2-D environments (e.g., flasks or dishes). In fact, it is widely recognized that cells grown in flasks or dishes tend to de-differentiate and lose specialized features of the tissues from which they were derived. Currently, there are mainly two types of 3-D culture systems where the cells are seeded into scaffolds mimicking the native extracellular matrix (ECM): (a) static models and (b) models using bioreactors. The first breakthrough was the static 3-D models. 3-D models using bioreactors such as the rotating-wall-vessel (RWV) bioreactors are a more recent development. The original concept of the RWV bioreactors was developed at NASA&#39;s Johnson Space Center in the early 1990s and is believed to overcome the limitations of static models such as the development of hypoxic, necrotic cores. The RWV bioreactors might circumvent this problem by providing fluid dynamics that allow the efficient diffusion of nutrients and oxygen. These bioreactors consist of a rotator base that serves to support and rotate two different formats of culture vessels that differ by their aeration source type: (1) Slow Turning Lateral Vessels (STLVs) with a co-axial oxygenator in the center, or (2) High Aspect Ratio Vessels (HARVs) with oxygenation via a flat, silicone rubber gas transfer membrane. These vessels allow efficient gas transfer while avoiding bubble formation and consequent turbulence. These conditions result in laminar flow and minimal shear force that models reduced gravity (microgravity) inside the culture vessel. Here we describe the development of a multicellular 3-D organotypic model of the human intestinal mucosa composed of an intestinal epithelial cell line and primary human lymphocytes, endothelial cells and fibroblasts cultured under microgravity provided by the RWV bioreactor.

Cells growing in a three-dimensional (3-D) environment represent a marked improvement over cell cultivation in 2-D environments (e.g., flasks or dishes). Here we describe the development of a multicellular 3-D organotypic model of the human intestinal mucosa cultured under microgravity provided by rotating-wall-vessel (RWV) bioreactors.

Because cells growing in a three-dimensional (3-D) environment have the potential to bridge many gaps of cell cultivation in 2-D environments (e.g., ...

Tunable Hydrogels from Pulmonary Extracellular Matrix for 3D Cell Culture

Here we present a method for establishing multiple component cell culture hydrogels for in vitro lung cell culture. Beginning with healthy en bloc lung tissue from porcine, rat, or mouse, the tissue is perfused and submerged in subsequent chemical detergents to remove the cellular debris. Histological comparison of the tissue before and after processing confirms removal of over 95% of double stranded DNA and alpha galactosidase staining suggests the majority of cellular debris is removed. After decellularization, the tissue is lyophilized and then cryomilled into a powder. The matrix powder is digested for 48 hr in an acidic pepsin digestion solution and then neutralized to form the pregel solution. Gelation of the pregel solution can be induced by incubation at 37 &#176;C and can be used immediately following neutralization or stored at 4 &#176;C for up to two weeks. Coatings can be formed using the pregel solution on a non-treated plate for cell attachment. Cells can be suspended in the pregel prior to self-assembly to achieve a 3D culture, plated on the surface of a formed gel from which the cells can migrate through the scaffold, or plated on the coatings. Alterations to the strategy presented can impact gelation temperature, strength, or protein fragment sizes. Beyond hydrogel formation, the hydrogel stiffness may be increased using genipin.

This is a method to create a 3-dimensional cell culture scaffold from pulmonary extracellular matrix. Intact lung is processed into hydrogels that can support the growth of cells in three-dimensions.

Here we present a method for establishing multiple component cell culture hydrogels for in vitro lung cell culture. Beginning with healthy en bloc lung ...

3D Analysis of Multi-cellular Responses to Chemoattractant Gradients

Various limitations of 2D cell culture systems have sparked interest in 3D cell culture and analysis platforms, which would better mimic the spatial and chemical complexity of living tissues and mimic in vivo tissue functions. Recent advances in microfabrication technologies have facilitated the development of 3D in vitro environments in which cells can be integrated into a well-defined extracellular matrix (ECM) and a defined set of soluble or matrix associated biomolecules. However, technological barriers have limited their widespread use in research laboratories. Here, we describe a method to construct simple devices for 3D culture and experimentation with cells and multicellular organoids in 3D microenvironments with a defined chemoattractant gradient. We illustrate the use of this platform for analysis of the response of epithelial cells and organoids to gradients of growth factors, such as epidermal growth factor (EGF). EGF gradients were stable in the devices for several days leading to directed branch formation in breast organoids. This analysis allowed us to conclude that collective gradient sensing by groups of cells is more sensitive vs. single cells. We also describe the fabrication method, which does not require photolithography facilities nor advanced soft lithography techniques. This method will be helpful to study 3D cellular behaviors in the context of the analysis of development and pathological states, including cancer.

We describe a method to construct devices for 3D culture and experimentation with cells and multicellular organoids. This device allows analysis of cellular responses to soluble signals in 3D microenvironments with defined chemoattractant gradients. Organoids are better than single cells at detection of weak noisy inputs.

Various limitations of 2D cell culture systems have sparked interest in 3D cell culture and analysis platforms, which would better mimic the spatial and ...

Pancreatic Tissue-Derived Extracellular Matrix Bioink for Printing 3D Cell-Laden Pancreatic Tissue Constructs

The transplantation of pancreatic islets is a promising treatment for patients who suffer from type 1 diabetes accompanied by hypoglycemia and secondary complications. However, islet transplantation still has several limitations such as the low viability of transplanted islets due to poor islet engraftment and hostile environments. In addition, the insulin-producing cells differentiated from human pluripotent stem cells have limited ability to secrete sufficient hormones that can regulate the blood glucose level; therefore, improving the maturation by culturing cells with proper microenvironmental cues is strongly required. In this article, we elucidate protocols for preparing a pancreatic tissue-derived decellularized extracellular matrix (pdECM) bioink to provide a beneficial microenvironment that can increase glucose sensitivity of pancreatic islets, followed by describing the processes for generating 3D pancreatic tissue constructs using a microextrusion-based bioprinting technique.

Decellularized extracellular matrix (dECM) can provide suitable microenvironmental cues to recapitulate the inherent functions of target tissues in an engineered construct. This article elucidates the protocols for the decellularization of pancreatic tissue, evaluation of pancreatic tissue-derived dECM bioink, and generation of 3D pancreatic tissue constructs using a bioprinting technique.

The transplantation of pancreatic islets is a promising treatment for patients who suffer from type 1 diabetes accompanied by hypoglycemia and secondary ...

Reconstituting Cytoarchitecture and Function of Human Epithelial Tissues on an Open-Top Organ-Chip

Nearly all human organs are lined with epithelial tissues, comprising one or multiple layers of tightly connected cells organized into three-dimensional (3D) structures. One of the main functions of epithelia is the formation of barriers that protect the underlining tissues against physical and chemical insults and infectious agents. In addition, epithelia mediate the transport of nutrients, hormones, and other signaling molecules, often creating biochemical gradients that guide cell positioning and compartmentalization within the organ. Owing to their central role in determining organ-structure and function, epithelia are important therapeutic targets for many human diseases that are not always captured by animal models. Besides the obvious species-to-species differences, conducting research studies on barrier function and transport properties of epithelia in animals is further compounded by the difficulty of accessing these tissues in a living system. While two-dimensional (2D) human cell cultures are useful for answering basic scientific questions, they often yield poor in vivo predictions. To overcome these limitations, in the last decade, a plethora of micro-engineered biomimetic platforms, known as organs-on-a-chip, have emerged as a promising alternative to traditional in vitro and animal testing. Here, we describe an Open-Top Organ-Chip (or Open-Top Chip), a platform designed for modeling organ-specific epithelial tissues, including skin, lungs, and the intestines. This chip offers new opportunities for reconstituting the multicellular architecture and function of epithelial tissues, including the capability to recreate a 3D stromal component by incorporating tissue-specific fibroblasts and endothelial cells within a mechanically active system. This Open-Top Chip provides an unprecedented tool for studying epithelial/mesenchymal and vascular interactions at multiple scales of resolution, from single cells to multi-layer tissue constructs, thus allowing molecular dissection of the intercellular crosstalk of epithelialized organs in health and disease.

The present protocol describes the capabilities and the essential culture modalities of the Open-Top Organ-Chip for the successful establishment and maturation of full-thickness organ-on-chip cultures of primary tissues (skin, alveolus, airway, and intestine), providing the opportunity to investigate different functional aspects of the human epithelial/mesenchymal and vascular niche interface in vitro.

Nearly all human organs are lined with epithelial tissues, comprising one or multiple layers of tightly connected cells organized into three-dimensional ...

Advanced Two-Layered 3D Co-Culture System for Epithelial and Fibroblast Cells

Establishing a Three-Dimensional Coculture Module of Epithelial Cells Using Nanofibrous Membranes

Technical hurdles in a culture of epithelial cells include dedifferentiation and loss of function. Biomimetic three-dimensional (3D) cell culture methods can enhance cell culture efficiency. This study introduces an advanced two-layered culture system intended to cultivate epithelial cells as tissue-like layers with the culture of fibroblasts within a 3D environment. Polyvinyl alcohol (PVA) and poly(&#949;-caprolactone) (PCL) nanofibrous membranes (NMs) were fabricated via electrospinning and utilized as a physiologically relevant extracellular matrix for the culture of epithelial cells and fibroblasts, respectively. In the upper insert wells, lung epithelial cells were cultivated on the PVA NM, and in the lower chambers, fibroblasts were cultured on the PCL NM. This configuration eliminates direct cell-cell contact and facilitates the examination of paracrine signaling mediated by soluble factors. Confocal microscopy was employed to analyze the distribution, growth pattern, and expression of intracellular proteins, including zona occludens in epithelial cells. Z-stacking techniques enabled detailed 3D reconstructions, providing precise insights into the integrity of tight junctions and spatial organization within the epithelial layer. Scanning electron microscopy (SEM) assessed the morphological characteristics of cell types on the nanofibrous membranes. SEM imaging revealed intricate cell surface structures and interactions with the nanofibers, offering a comprehensive perspective on cellular architecture and cell interaction with nanofibrous structure. The Cell Counting Kit-8 (CCK-8) assay is a simple method for measuring epithelial cell and fibroblast growth rates over time. It provides the proliferative behaviors and potential synergistic effects of coculturing these cells. These findings highlight the effectiveness of a simple insert co-culture system for simultaneous culture of fibroblasts and epithelial cells, which is crucial in various physiological and pharmacological contexts, including epithelial tissue regeneration, tumor microenvironment with endothelial, immune, and other stroma cells, toxicity assay, and drug activity test.

Author Spotlight: Advancing 3D Coculture Systems with PVA-PCL Nanofibrous Membranes 

Here, we demonstrate how epithelial cells cultured with fibroblasts in the nanofibrous membrane-based two-layer system can stably adhere to and grow on the membrane.

Technical hurdles in a culture of epithelial cells include dedifferentiation and loss of function. Biomimetic three-dimensional (3D) cell culture methods ...