This work was supported by NIH-NEI R01 EY024942, Research to Prevent Blindness, Upstate Medical University Unrestricted Research Funds, and Lions District 20-Y. Microscopy and image analysis of paraffin sections were performed at the Microscopy CORE and histological slide preparation was performed at the Biorepository and Pathology CORE at the Icahn School of Medicine at Mount Sinai.

1. Organ Culture
<ol>
	<li>Preparations
	<ol>
		<li>Prepare agar solution as follows. In a small flask, prepare 1% agar and 1 mg/mL bovine collagen in DMEM-F12 up to 20 mL. Bring to boil on a hot plate. Put the solution into a 50 mL conical tube. Place tube in a water bath on a hot plate to keep the solution from solidifying.</li>
		<li>Prepare supplemented serum-free media (SSFM) as per the composition provided in the Table of Materials. 
		NOTE: The necessary am...

This protocol describes a model for studying wound healing in a natural stratified 3D environment. Use of organ culture as an intermediate between cell culture and in vivo studies significantly reduces costs as well as reducing procedures on live animals. Other 3D models have been of great benefit to the field including self-synthesizing collagen gels made from primary human corneal fibroblasts2 or these same cells embedded in gels made from animal-derived collagens31. The ...

Scarring in the cornea resulting from injury, trauma, or infection can lead to debilitating opacities and permanent vision loss. Thus, there is a critical need to identify pathways that can be targeted for therapeutic intervention. Current treatment options are limited and consist primarily of corneal transplantations, which are not accessible to patients across the world. Both human (Figure 1) and animal corneas can be utilized for 2D and 3D cell culture studies1,2. Human cadaver corneas not suitable for transplant can be obtained from eye banks or centralized tissue banks (National Disease Research Interchange (NDRI)), and animal eyes can be obtained from an abattoir. Primary corneal epithelial cells, stromal fibroblasts, and more recently, endothelial cells, can be isolated and cultured from these tissues for wound healing and toxicology studies3,4,5. In addition to the importance of understanding the molecular basis of blinding eye disease, the accessibility of tissue and the ability to culture primary cells has made the cornea an important model system for study. The cornea is ideal for testing the effects of agents on scarring as the normal cornea is transparent and certain types of wounds create opacities or fibrotic scars (reviewed in6). Several in vivo corneal wound healing models have also been extensively utilized for scarring studies1. Less utilized has been the ex vivo corneal wound healing model7,8 that is describe in detail here. The goal of this method is to quantify scarring outcomes characterized by fibrotic makers in a 3D multicellular corneal ex vivo model system.
Corneal epithelial wounding that does not breach the epithelial basement membrane normally closes within 24-72 h9. Soon after wounding, the cells at the edge of the epithelium start spreading and migrating into the epithelial free surface, to reestablish epithelial barrier function. This activity is sequentially followed by activation of corneal basal cell proliferation first and, in a later stage, of precursor cells located at the outer limbal zone to achieve recovery of epithelial cell mass10,11. These wounds often heal without scarring. However, a wound that penetrates the basement membrane into the stroma often results in scar formation1. After corneal stromal wounding, the stroma is populated with cells of multiple origins including differentiated resident stromal cells as well as bone marrow-derived fibrocytes12,13,14. Fibrotic scarring is characterized by the persistence of myofibroblasts in a healing wound. These pathological myofibroblasts demonstrate increased adhesion through the accumulation of integrins in focal adhesions, contractile &#945;-smooth muscle actin (&#945;-SMA) stress fibers, and local activation of extracellular matrix (ECM)-sequestered latent-transforming growth factor-beta (TGF&#946;). The differentiation of epithelial-derived cells, known as epithelial to mesenchymal transition (EMT), may also contribute to scar formation6.
There is a delicate balance between cell differentiation and apoptosis after wounding. Because of the breach in the basement membrane, growth factors such as platelet-derived growth factor (PDGF) and TGF&#946; from tears and the epithelium bathe the stroma, inducing myofibroblast differentiation, a sustained autocrine loop of TGF&#946;&#160;activation, and the secretion of disorganized fibrotic ECM15,16. The persistence of myofibroblasts in the healed wound promotes haze and scarring in the cornea (Figure 2). However, in regeneratively healed wound although myofibroblasts develop, they apoptose and thus are absent or significantly reduced in number in the healed tissue (reviewed in reference6,10). Thus, research on fibrotic scarring has focused at least in part on targeting molecules that prevent excessive myofibroblast development or myofibroblast persistence17,18. Because myofibroblast persistence characterizes both scarring and fibrotic disease in all tissues19, the cornea may be useful as a model system to study general cellular mechanisms of fibrosis.
In our model system, the cornea is wounded with a cylindrical blade called a trephine while still in the globe. Human and pig corneas can be wounded with either a 6 or 7 mm trephine; for rabbit corneas a 6 mm trephine is preferred. The pig cornea is similar in size to the human cornea. Because they are cost effective and readily available in large numbers, pig corneas are routinely used for organ culture. Furthermore, antibodies and siRNAs made to react with human have consistently cross-reacted with pig7. After wounding, corneas are cut from the globe with the limbus intact and mounted on an agar/collagen base. The corneas are cultured in serum-free media plus stabilized vitamin C to simulate fibroblast proliferation and ECM deposition20. Neither the addition of serum nor growth factors are needed to induce myofibroblast formation7. Corneas are routinely fixed and processed for histology after two weeks of culture. For gene knockdown, or to test the effects of an agent on wound healing, the wound can be treated with siRNA in the wound after wounding7 or a soluble agent can be added to the media, respectively8.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>PBS</td>
			<td>Gibco</td>
			<td>10-010-023</td>
			<td></td>
		</tr>
		<tr>
			<td>Pen Strep&#160;</td>
			<td>MP Biomedicals</td>
			<td>91670049</td>
			<td></td>
		</tr>
		<tr>
			<td>Bovine Collagen Solution</td>
			<td>Advance Biomatrix</td>
			<td>5005</td>
			<td></td>
		</tr>
		<tr>
			<td>Pig eyes with lids attached&#160;</td>
			<td>Pel-freeze, Arkansas</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>6.0 mm trephine&#160;</td>
			<td>Katena</td>
			<td>K28014</td>
			<td></td>
		</tr>
		<tr>
			<td>Surgical Blade&#160;</td>
			<td>Personna</td>
			<td>0.009</td>
			<td></td>
		</tr>
		<tr>
			<td>Small scissor</td>
			<td>Fisher</td>
			<td>895110</td>
			<td></td>
		</tr>
		<tr>
			<td>Forceps</td>
			<td>Fisher</td>
			<td>08953-F</td>
			<td></td>
		</tr>
		<tr>
			<td>Kim Wipes&#160;</td>
			<td>Kimberly-Clark&#8482; 34120</td>
			<td>06-666</td>
			<td></td>
		</tr>
		<tr>
			<td>60 mm cell culture dishes&#160;</td>
			<td>Falcon</td>
			<td>08-772B</td>
			<td></td>
		</tr>
		<tr>
			<td>Supplemented Serum- Free media (SSFM)</td>
			<td></td>
			<td></td>
			<td>Add all of the following components to DMEM/F-12:&#160; ITS, RPMI, Glutathione, L-Glutamine, MEM Non essential amino acids, MEM Sodium Pyruvate, ABAM, Gentamicin, Vitamin C.&#160;</td>
		</tr>
		<tr>
			<td>DMEM/F-12</td>
			<td>Gibco</td>
			<td>11330</td>
			<td></td>
		</tr>
		<tr>
			<td>ITS Liquid Media Supplement&#160;</td>
			<td>Sigma</td>
			<td>I3146</td>
			<td>100X</td>
		</tr>
		<tr>
			<td>RPMI 1640 Vitamins Solution&#160;</td>
			<td>Sigma</td>
			<td>R7256</td>
			<td>100X</td>
		</tr>
		<tr>
			<td>Glutathione</td>
			<td>Sigma</td>
			<td>G6013</td>
			<td>Use at 1 &#181;g/mL. Freeze aliquots; do not reuse after thawing.</td>
		</tr>
		<tr>
			<td>1% L-glutamine solution&#160;</td>
			<td>Gibco</td>
			<td>25030-081</td>
			<td>100X</td>
		</tr>
		<tr>
			<td>MEM Non-essential amino acids solution&#160;</td>
			<td>Gibco</td>
			<td>11140</td>
			<td>100X</td>
		</tr>
		<tr>
			<td>MEM Sodium pyruvate solution&#160;</td>
			<td>Gibco</td>
			<td>11360</td>
			<td>1 M Stocks (1000X) and freeze in single use aliquits.&#160; Use from freezer each time media is made.</td>
		</tr>
		<tr>
			<td>ABAM&#160;</td>
			<td>Sigma</td>
			<td>A7292</td>
			<td>100X</td>
		</tr>
		<tr>
			<td>Gentamicin&#160;</td>
			<td>Sigma</td>
			<td>30-005-CR</td>
			<td>200X</td>
		</tr>
		<tr>
			<td>Vitamin C&#160;</td>
			<td>Wako</td>
			<td>070-0483</td>
			<td>2-0-aD Glucopyranosyl-Ascorbic Acid. 1 mM stocks (1000x)</td>
		</tr>
		<tr>
			<td>10% Iodine&#160;</td>
			<td>Fisher Chemical</td>
			<td>SI86-1</td>
			<td></td>
		</tr>
		<tr>
			<td>Tissue Path Cassettes&#160;</td>
			<td>Fisher</td>
			<td>22-272416</td>
			<td></td>
		</tr>
		<tr>
			<td>Normal Goat Serum (NGS)</td>
			<td>Jackson Immuno Research</td>
			<td>005-000-121</td>
			<td>We use 3% NGS</td>
		</tr>
		<tr>
			<td>Mounting Media&#160;</td>
			<td>Thermo Scientific</td>
			<td>TA-030-FM</td>
			<td></td>
		</tr>
		<tr>
			<td>Safe Clear&#160;</td>
			<td>Fisher</td>
			<td>314-629</td>
			<td></td>
		</tr>
		<tr>
			<td>Ethyl Alcohol</td>
			<td>Ultra Pure</td>
			<td>200CSGP</td>
			<td>200 Proof, diluted at 100%, 70%, 50%)&#160;</td>
		</tr>
		<tr>
			<td>Sodium citrate&#160;</td>
			<td>Fisher</td>
			<td>BP327</td>
			<td>10mM, pH 6.4</td>
		</tr>
		<tr>
			<td>Hematoxylin</td>
			<td>EMD Millipore</td>
			<td>M10742500</td>
			<td></td>
		</tr>
		<tr>
			<td>Bluing agent&#160;</td>
			<td>Ricca Chemical Company</td>
			<td>220-106</td>
			<td></td>
		</tr>
		<tr>
			<td>1% Triton X-100</td>
			<td>Fisher</td>
			<td>9002-93-1</td>
			<td>Diluted in PBS</td>
		</tr>
		<tr>
			<td>0.1% Tween 20&#160;</td>
			<td>Fisher</td>
			<td>BP337</td>
			<td>Diluted in PBS</td>
		</tr>
		<tr>
			<td>3% Hydrogen Peroxide&#160;</td>
			<td>Fisher</td>
			<td>H324</td>
			<td></td>
		</tr>
		<tr>
			<td>DAB Kit&#160;</td>
			<td>Vector Laboratories</td>
			<td>SK-4100</td>
			<td></td>
		</tr>
		<tr>
			<td>Agar&#160;</td>
			<td>Fisher&#160;</td>
			<td>BP1423-500</td>
			<td>Agar solution: prepare 1% agar and 1 mg/mL bovine collagen in DMEM-F12 up to 20 mL</td>
		</tr>
		<tr>
			<td>Parafilm</td>
			<td>Bermis</td>
			<td>13-374-12</td>
			<td></td>
		</tr>
		<tr>
			<td>Moist Chamber</td>
			<td></td>
			<td></td>
			<td>Use any chamber, cover it with wet Wipe Tissue and then put a layer of Parafilm over it.</td>
		</tr>
		<tr>
			<td>Lipofectamine 2000</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Qiagen RNAprotect Cell Reagent</td>
			<td>Qiagen</td>
			<td>&#160;76104</td>
			<td></td>
		</tr>
		<tr>
			<td>Ambion PureLink RNA Mini Kit</td>
			<td>Thermo Scientific</td>
			<td>12183018A</td>
			<td></td>
		</tr>
		<tr>
			<td>Anti-Fibronectin-EDA Antibody</td>
			<td>Sigma</td>
			<td>F6140</td>
			<td>1:200 Diluted in&#160; 3% normal goat serum</td>
		</tr>
		<tr>
			<td>Anti-alpha smooth muscle actin Antibody</td>
			<td>Sigma</td>
			<td>A2547 or C6198 (cy3 conjugated)</td>
			<td>1:200 Diluted in 3% normal goat serum</td>
		</tr>
		<tr>
			<td>Permafluor&#160;</td>
			<td>Thermo Scientific</td>
			<td>TA-030-FM</td>
			<td></td>
		</tr>
		<tr>
			<td>DAPI&#160;</td>
			<td>Invitrogen</td>
			<td>P36931</td>
			<td></td>
		</tr>
		<tr>
			<td>Gt anti -MS IgG (H+L) Secondary Antibody, HRP&#160;</td>
			<td>Invitrogen</td>
			<td>62-6520</td>
			<td>1:100 diluted in 3% normal goat serum (for a-SMA, DAB staining)</td>
		</tr>
		<tr>
			<td>Gt anti -MS IgM (H+L) Secondary Antibody, HRP&#160;</td>
			<td>Thermo Scientific</td>
			<td>PA1-85999</td>
			<td>1:100 diluted in 3% normal goat serum (for FN-EDA, DAB staining)</td>
		</tr>
		<tr>
			<td>Gt anti -MS IgG (H+L) Secondary Antibody, Cy3&#160;</td>
			<td>Jackson Immuno Research</td>
			<td>115-165-146</td>
			<td>1:200 Diluted in&#160; 3% normal goat serum (for a-SMA, Fluorescence staining)</td>
		</tr>
		<tr>
			<td>&#160;Zeiss Axioplan2&#160;</td>
			<td>Zeiss</td>
			<td></td>
			<td>Microscope</td>
		</tr>
		<tr>
			<td>SPOT-2</td>
			<td colspan="2">Diagnostic Instruments, Sterling Heights, Michigan</td>
			<td>CCD camera</td>
		</tr>
	</tbody>
</table>

ex vivo corneal organ culture model for wound healing studies

The cornea has been used extensively as a model system to study wound healing. The ability to generate and utilize primary mammalian cells in two dimensional (2D) and three dimensional (3D) culture has generated a wealth of information not only about corneal biology but also about wound healing, myofibroblast biology, and scarring in general. The goal of the protocol is an assay system for quantifying myofibroblast development, which characterizes scarring. We demonstrate a corneal organ culture ex vivo model using pig eyes. In this anterior keratectomy wound, corneas still in the globe are wounded with a circular blade called a trephine. A plug of approximately 1/3 of the anterior cornea is removed including the epithelium, the basement membrane, and the anterior part of the stroma. After wounding, corneas are cut from the globe, mounted on a collagen/agar base, and cultured for two weeks in supplemented-serum free medium with stabilized vitamin C to augment cell proliferation and extracellular matrix secretion by resident fibroblasts. Activation of myofibroblasts in the anterior stroma is evident in the healed cornea. This model can be used to assay wound closure, the development of myofibroblasts and fibrotic markers, and for toxicology studies. In addition, the effects of small molecule inhibitors as well as lipid-mediated siRNA transfection for gene knockdown can be tested in this system.

Immunohistochemistry is the primary assay utilized to analyze the success of the ex vivo wound healing experiment. Figure 4 depicts the epithelium and anterior stroma in control tissue (Figure 4A, 4B). Six hours after wounding, the epithelium was absent (Figure 4C, 4D). Six days after wounding as expected, the epithelium had regrown (Figure 4E</s...

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Ex Vivo Corneal Organ Culture Model for Wound Healing Studies

A protocol for an ex vivo corneal organ culture model useful for wound healing studies is described. This model system can be used to assess the effects of agents to promote regenerative healing or drug toxicity in an organized 3D multicellular environment.