The authors thank the UVM autopsy services for human lung procurement and Robert Pouliot PhD for contributions to the overall dissection techniques. These studies were supported by R01 HL127144-01 (DJW).

All animal studies have been performed in accordance with the IACUC of University of Vermont (UVM). All human lungs were acquired from UVM Autopsy Services and related studies were performed as per the guidelines of IRB of UVM.
NOTE: Decellularization of pig and human lungs has been previously described by our group7,8,9,10, 21. In brief, whole lung lobes are decellularized through sequential perfusion of the airways and vasculature with a series of 2 L detergent and enzyme solutions using a peristaltic pump: 0.1% Triton-X 100, 2% sodium deoxycholate, 1 M sodium chloride, 30 &#181;g/mL DNase/1.3 mM MgSO4/2 mM CaCl2, 0.1% peracetic acid/4% ethanol, and a deionized water wash. Standard methods for confirming efficient decellularization include the determination of &#60;50 ng/mg residual double-stranded DNA within decellularized lungs and the absence of DNA fragments by gel electrophoresis, and nuclear staining by hematoxylin and eosin (H&#38;E) staining9,21.
1. Setup
<ol>
	<li>Gather all necessary equipment required for the dissection procedure, including a glass casserole dish, two pairs of surgical tweezers, one pair of forceps, and one pair of surgical scissors, and autoclave before use.</li>
	<li>Obtain a section of the lung, place it in the glass casserole dish, and orient it so that the superior end of the airway can be seen clearly.</li>
	<li>Identify the proximal end of the vasculature and keep it intact until later steps. The end of the vasculature should be clearly visible and entirely opaque white in color.</li>
	<li>Using a pair of tweezers and surgical scissors, remove any pleura that may be lining the exterior of the lung and discard.</li>
</ol>
2. Exposing the airway
<ol>
	<li>Using a spreading technique with the surgical scissors, gently work to expose the additional airway.
	<ol>
		<li>Locate the largest airway, which will typically have a diameter of approximately 2-4 cm. Another way to identify an airway is through the observation of cartilage rings, which can be detected visually or via palpation of the tissue.</li>
		<li>Using a pair of forceps, palpate down the length of the airway in order to determine the location of the unseen airway to a depth of approximately 1 in. 
		NOTE: Being lined with cartilage rings, the airway is characteristically harder than the other lung tissues. As such, finding and palpating the unseen airway should be relatively simple.</li>
		<li>Holding the surgical scissors parallel to the airway, insert the closed tips into the tissue directly surrounding the unseen airway.</li>
		<li>Slowly open the surgical scissors to gently pull apart the surrounding membrane. Subsequently, remove the surgical scissors and avoid cutting any tissue whatsoever.</li>
		<li>Repeat this process intermittently throughout the dissection procedure to continue exposing the airway.</li>
	</ol>
	</li>
	<li>Using the surgical scissors, cut the airway at the branching points and dissect along either branch independently. 
	NOTE: A branching point is a location at which one airway splits into two separate airways.</li>
	<li>Sever regions of the airway once confident that the intact ends will remain identifiable and easily located for further dissection.</li>
	<li>Place severed regions of the airway into the corresponding tube. The size of the severed regions will vary depending on the sample but, in general, will range between 1-5 cm in length. The width varies based on the relative location along the airway tree, with the distal regions maintaining smaller widths than the more proximal regions.</li>
</ol>
3. Exposing and excising regions of the vasculature
<ol>
	<li>Apply gentle pressure to the vasculature and slowly pull away from the airway. Allow the vasculature to stretch slightly and use surgical scissors to further separate the vasculature from the airway. 
	NOTE: Too much pressure will rip the vasculature. If the vasculature rips, simply place that section of vasculature in the corresponding labeled tube and identify its intact end.</li>
	<li>When a branching point in the vascular tree has been exposed, use surgical scissors and tweezers to expose more inferior regions of the vasculature.
	<ol>
		<li>Begin by inserting the closed tips of the surgical scissors just below a branching point and between the two corresponding vasculature regions.</li>
		<li>Slowly open the scissors to spread apart the underlying tissues.</li>
		<li>Intermittently, use a pair of tweezers to remove the tissue that was spread apart using the surgical scissors, as well as any other tissue directly surrounding the vasculature.</li>
	</ol>
	</li>
	<li>When the vasculature is covering regions of the airway or becoming cumbersome to any step in the dissection procedure, cut the vasculature at a branching point and further dissect along either branch independently.</li>
	<li>Sever regions of the vasculature once confident that the intact ends will remain identifiable and easily located for further dissection.</li>
</ol>
4. Identifying and excising alveolar tissue
<ol>
	<li>Using a pair of forceps or tweezers, pinch and then gently tear away small regions of alveolar tissue.
	<ol>
		<li>Locate a region of tissue that is not in the direct vicinity of the airway or the vasculature.</li>
		<li>Using the tweezers, pinch a small region of the tissue that appears to be devoid of any vasculature or airway.</li>
		<li>Tear the pinched region of the tissue from the lung.</li>
	</ol>
	</li>
	<li>Observe the region of tissue removed and confirm whether or not it is alveolar tissue. 
	NOTE: Alveolar tissue is present throughout the lung, so it can and should be removed throughout the dissection procedure. Any tissue that cannot easily be identified as primarily alveoli, vasculature, or airway should be categorized as bulk tissue and placed in the corresponding labeled tube.</li>
</ol>

Regional Decellularized Lung Tissue Isolation to Study Cell-Cell and Cell-ECM Interactions

<ol>
	<li>L&#243;pez-Campos, J. L., Tan, W., Soriano, J. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Global+burden+of+COPD.">Global burden of COPD.</a> Respirology. 21 (1), 14-23 (2016).</li><li>Raherison, C., Girodet, P. -. O. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Epidemiology+of+COPD.">Epidemiology of COPD.</a> European Respiratory Review. 18 (114), 213-221 (2009).</li><li>Glass, D. 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=Idiopathic+pulmonary+fibrosis:+Current+and+future+treatment.">Idiopathic pulmonary fibrosis: Current and future treatment.</a> The Clinical Respiratory Journal. 16 (2), 84-96 (2022).</li><li>Dickinson, K. M., Collaco, J. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cystic+Fibrosis.">Cystic Fibrosis.</a> Pediatrics in Review. 42 (2), 55-67 (2021).</li><li>DeFreitas, M. R., McAdams, H. P., Azfar Ali, H., Iranmanesh, A. M., Chalian, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Complications+of+lung+transplantation:+update+on+imaging+manifestations+and+management.">Complications of lung transplantation: update on imaging manifestations and management.</a> Radiology: Cardiothoracic Imaging. 3 (4), e190252 (2021).</li><li>Young, K. A., Dilling, D. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+future+of+lung+transplantation.">The future of lung transplantation.</a> Chest. 155 (3), 465-473 (2019).</li><li>Wagner, D. 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=Comparative+decellularization+and+recellularization+of+normal+versus+emphysematous+human+lungs.">Comparative decellularization and recellularization of normal versus emphysematous human lungs.</a> Biomaterials. 35 (10), 3281-3297 (2014).</li><li>Booth, A. J., 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=Acellular+normal+and+fibrotic+human+lung+matrices+as+a+culture+system+for+in+vitro+investigation.">Acellular normal and fibrotic human lung matrices as a culture system for in vitro investigation.</a> American Journal of Respiratory and Critical Care Medicine. 186 (9), 866-876 (2012).</li><li>Uhl, F. E., Wagner, D. E., Weiss, D. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Preparation+of+decellularized+lung+matrices+for+cell+culture+and+protein+analysis.">Preparation of decellularized lung matrices for cell culture and protein analysis.</a> Methods in Molecular Biology. 1627, 253-283 (2017).</li><li>Wagner, D. 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=Three-dimensional+scaffolds+of+acellular+human+and+porcine+lungs+for+high+throughput+studies+of+lung+disease+and+regeneration.">Three-dimensional scaffolds of acellular human and porcine lungs for high throughput studies of lung disease and regeneration.</a> Biomaterials. 35 (9), 2664-2679 (2014).</li><li>Uhl, F. 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=Functional+role+of+glycosaminoglycans+in+decellularized+lung+extracellular+matrix.">Functional role of glycosaminoglycans in decellularized lung extracellular matrix.</a> Acta Biomaterialia. 102, 231-246 (2020).</li><li>Saldin, L. T., Cramer, M. C., Velankar, S. S., White, L. J., Badylak, S. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Extracellular+matrix+hydrogels+from+decellularized+tissues:+structure+and+function.">Extracellular matrix hydrogels from decellularized tissues: structure and function.</a> Acta Biomaterialia. 49, 1-15 (2017).</li><li>Giobbe, G. G., 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=Extracellular+matrix+hydrogel+derived+from+decellularized+tissues+enables+endodermal+organoid+culture.">Extracellular matrix hydrogel derived from decellularized tissues enables endodermal organoid culture.</a> Nature Communications. 10 (1), 5658 (2019).</li><li>Petrou, C. L., 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=Clickable+decellularized+extracellular+matrix+as+a+new+tool+for+building+hybrid-hydrogels+to+model+chronic+fibrotic+diseases+in+vitro.">Clickable decellularized extracellular matrix as a new tool for building hybrid-hydrogels to model chronic fibrotic diseases in vitro.</a> Journal of Materials Chemistry. B. 8 (31), 6814-6826 (2020).</li><li>Nizamoglu, 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=An+in+vitro+model+of+fibrosis+using+crosslinked+native+extracellular+matrix-derived+hydrogels+to+modulate+biomechanics+without+changing+composition.">An in vitro model of fibrosis using crosslinked native extracellular matrix-derived hydrogels to modulate biomechanics without changing composition.</a> Acta Biomaterialia. 147, 50-62 (2022).</li><li>Marhuenda, 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=Lung+extracellular+matrix+hydrogels+enhance+preservation+of+type+ii+phenotype+in+primary+alveolar+epithelial+cells.">Lung extracellular matrix hydrogels enhance preservation of type ii phenotype in primary alveolar epithelial cells.</a> International Journal of Molecular Sciences. 23 (9), 4888 (2022).</li><li>Zhou, J., 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=Lung+tissue+extracellular+matrix-derived+hydrogels+protect+against+radiation-induced+lung+injury+by+suppressing+epithelial-mesenchymal+transition.">Lung tissue extracellular matrix-derived hydrogels protect against radiation-induced lung injury by suppressing epithelial-mesenchymal transition.</a> Journal of Cellular Physiology. 235 (3), 2377-2388 (2020).</li><li>Pouliot, R. 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+and+characterization+of+a+naturally+derived+lung+extracellular+matrix+hydrogel.">Development and characterization of a naturally derived lung extracellular matrix hydrogel.</a> Journal of Biomedical Materials Research. Part A. 104 (8), 1922-1935 (2016).</li><li>Pouliot, R. 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=Porcine+lung-derived+extracellular+matrix+hydrogel+properties+are+dependent+on+pepsin+digestion+time.">Porcine lung-derived extracellular matrix hydrogel properties are dependent on pepsin digestion time.</a> Tissue Engineering. Part C, Methods. 26 (6), 332-346 (2020).</li><li>de Hilster, R. H. J., 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=Human+lung+extracellular+matrix+hydrogels+resemble+the+stiffness+and+viscoelasticity+of+native+lung+tissue.">Human lung extracellular matrix hydrogels resemble the stiffness and viscoelasticity of native lung tissue.</a> American Journal of Physiology. Lung Cellular and Molecular Physiology. 318 (4), L698-L704 (2020).</li><li>Hoffman, E. T., 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=Regional+and+disease+specific+human+lung+extracellular+matrix+composition.">Regional and disease specific human lung extracellular matrix composition.</a> Biomaterials. 293, 121960 (2023).</li><li>Sicard, D., 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=Aging+and+anatomical+variations+in+lung+tissue+stiffness.">Aging and anatomical variations in lung tissue stiffness.</a> American Journal of Physiology. Lung Cellular and Molecular Physiology. 314 (6), L946-L955 (2018).</li></ol>

None of the authors have any conflicts of interest.

Decellularized tissues from humans and other species are frequently utilized as biomaterials for studying ECM composition as well as cell-ECM interactions in ex vivo culture models, including 3D hydrogels12,13. Similar to other organs, decellularized lungs have previously been utilized to determine ECM compositional differences in healthy versus diseased (i.e., emphysematous and IPF) lungs and are increasingly being utilized as hydrogels for studying ECM...

Lung diseases, including chronic obstructive pulmonary disease (COPD), idiopathic pulmonary fibrosis (IPF), and cystic fibrosis (CF), currently remain without a cure1,2,3,4. Lung transplantation is often the only option for patients in later stages, however this remains a limited option both due to the supply of suitable donor lungs and both acute and chronic rejection after transplantation3,5,6. As such, there is a critical need for new treatment strategies. One promising approach in respiratory bioengineering is the application of tissue-derived scaffolds prepared from decellularized native lung tissue. As acellular whole lung scaffolds retain much of the complexity of the native extracellular matrix (ECM) composition and bioactivity, they have been intensively studied for whole-organ engineering and as improved models for studying lung disease mechanisms7,8,9,10. In parallel, there is increasing interest in utilizing decellularized tissues from different organs, including lungs, as hydrogels and other substrates for studying cell-cell and cell-ECM interactions in organoid and other tissue culture models11,12,13,14,15,16,17. These provide more relevant models than commercially available substrates, such as Matrigel, derived from tumor sources. However, information on human lung-derived hydrogels is relatively limited at present. We have previously described hydrogels derived from decellularized pig lungs and have characterized both their mechanical and material properties, as well as demonstrated their utility as cell culture models18,19.&#160;A recent report detailed the initial mechanical and viscoelastic characterization of hydrogels derived from decellularized normal and diseased (COPD, IPF) human lungs20. We have also presented initial data characterizing the glycosaminoglycan content of decellularized normal and COPD human lungs, as well as their applicability for studying cell-cell and cell-ECM interactions11.
These examples illustrate the power of utilizing decellularized human lung ECMs for investigative purposes. However, the lung is a complex organ, and both the structure and function vary in different regions of the lung, including ECM composition and other properties such as stiffness21,22. As such, it is of interest to study the ECM in individual regions of the lung, including the trachea and large airways, medium-sized and small airways, and alveoli, as well as large, medium-sized, and small blood vessels. To this end, we have developed a reliable and reproducible method for dissecting decellularized human and pig lungs and subsequently isolating each of those anatomic regions. This has allowed detailed differential analysis of regional protein content in both normal and diseased lungs21.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Bonn Scissors</td>
			<td>Fine Science Tools</td>
			<td>14184-09</td>
			<td></td>
		</tr>
		<tr>
			<td>Dumont #5 - Fine Forceps</td>
			<td>Fine Science Tools</td>
			<td>11254-02</td>
			<td></td>
		</tr>
		<tr>
			<td>Forceps, Curved, S/S, Blunt, Serrated - 130mm</td>
			<td>CellPath</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>Hardened Fine Scissors</td>
			<td>Fine Science Tools</td>
			<td>14090-11</td>
			<td></td>
		</tr>
		<tr>
			<td>Moria Iris Forceps</td>
			<td>Fine Science Tools</td>
			<td>11373-22</td>
			<td></td>
		</tr>
		<tr>
			<td>Pyrex Glass Casserole Dish</td>
			<td>Cole-Parmer</td>
			<td>3175-10</td>
			<td></td>
		</tr>
	</tbody>
</table>

dissection and isolation of region-specific decellularized lung tissue

Lung transplantation is often the only option for patients in the later stages of severe lung disease, but this is limited both due to the supply of suitable donor lungs and both acute and chronic rejection after transplantation. Ascertaining novel bioengineering approaches for the replacement of diseased lungs is imperative for improving patient survival and avoiding complications associated with current transplantation methodologies. An alternative approach involves the use of decellularized whole lungs lacking cellular constituents that are typically the cause of acute and chronic rejection. Since the lung is such a complex organ, it is of interest to examine the extracellular matrix components of specific regions, including the vasculature, airways, and alveolar tissue. The purpose of this approach is to establish simple and reproducible methods by which researchers may dissect and isolate region-specific tissue from fully decellularized lungs. The current protocol has been devised for pig and human lungs, but may be applied to other species as well. For this protocol, four regions of the tissue were specified: airway, vasculature, alveoli, and bulk lung tissue. This procedure allows for the procurement of samples of tissue that more accurately represent the contents of the decellularized lung tissue as opposed to traditional bulk analysis methods.

An overall schematic of the protocol is depicted in Figure 1. Once mastered, the regional dissection of decellularized lung tissue is easily reproducible. Determining the categorization of each severed tissue sample is imperative to the success of the dissection procedure. Vascular tissue is substantially more elastic than airway, so using forceps to stretch the tissue is often a strong indicator of whether a particular sample is vasculature or airway. Typically, vascular tissue runs paralle...

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Author Spotlight: Dissection and Isolation of Region-Specific Decellularized Lung Tissue  

Presented here is a protocol for the isolation of regional decellularized lung tissue. This protocol provides a powerful tool for studying complexities in the extracellular matrix and cell-matrix interactions.

Dissection and Isolation of Region-Specific Decellularized Lung Tissue

Lung transplantation is often the only option for patients in the later stages of severe lung disease, but this is limited both due to the supply of ...

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Research

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Bioengineering

5.1K Views.  University of Vermont. Presented here is a protocol for the isolation of regional decellularized lung tissue. This protocol provides a powerful tool for studying complexities in the extracellular matrix and cell-matrix interactions.

Video: Author Spotlight: Dissection and Isolation of Region-Specific Decellularized Lung Tissue  

Expression, Isolation, and Purification of Soluble and Insoluble Biotinylated Proteins for Nerve Tissue Regeneration

Recombinant protein engineering has utilized Escherichia coli (E. coli) expression systems for nearly 4 decades, and today E. coli is still the most widely used host organism. The flexibility of the system allows for the addition of moieties such as a biotin tag (for streptavidin interactions) and larger functional proteins like green fluorescent protein or cherry red protein. Also, the integration of unnatural amino acids like metal ion chelators, uniquely reactive functional groups, spectroscopic probes, and molecules imparting post-translational modifications has enabled better manipulation of protein properties and functionalities. As a result this technique creates customizable fusion proteins that offer significant utility for various fields of research. More specifically, the biotinylatable protein sequence has been incorporated into many target proteins because of the high affinity interaction between biotin with avidin and streptavidin. This addition has aided in enhancing detection and purification of tagged proteins as well as opening the way for secondary applications such as cell sorting. Thus, biotin-labeled molecules show an increasing and widespread influence in bioindustrial and biomedical fields. For the purpose of our research we have engineered recombinant biotinylated fusion proteins containing nerve growth factor (NGF) and semaphorin3A (Sema3A) functional regions. We have reported previously how these biotinylated fusion proteins, along with other active protein sequences, can be tethered to biomaterials for tissue engineering and regenerative purposes. This protocol outlines the basics of engineering biotinylatable proteins at the milligram scale, utilizing&#160; a T7 lac inducible vector and E. coli expression hosts, starting from transformation to scale-up and purification.

Developing biotinylatable fusion proteins has many potential applications in various fields of research. Recombinant protein engineering is a straight forward procedure that is cost-effective, providing high yields of custom-designed proteins.

Recombinant protein engineering has utilized Escherichia coli (E. coli) expression systems for nearly 4 decades, and today E. coli is still the most ...

A Combined 3D Tissue Engineered In Vitro/In Silico Lung Tumor Model for Predicting Drug Effectiveness in Specific Mutational Backgrounds

In the present study, we combined an in vitro 3D lung tumor model with an in silico model to optimize predictions of drug response based on a specific mutational background. The model is generated on a decellularized porcine scaffold that reproduces tissue-specific characteristics regarding extracellular matrix composition and architecture including the basement membrane. We standardized a protocol that allows artificial tumor tissue generation within 14 days including three days of drug treatment. Our article provides several detailed descriptions of 3D read-out screening techniques like the determination of the proliferation index Ki67 staining&#39;s, apoptosis from supernatants by M30-ELISA and assessment of epithelial to mesenchymal transition (EMT), which are helpful tools for evaluating the effectiveness of therapeutic compounds. We could show compared to 2D culture a reduction of proliferation in our 3D tumor model that is related to the clinical situation. Despite of this lower proliferation, the model predicted EGFR-targeted drug responses correctly according to the biomarker status as shown by comparison of the lung carcinoma cell lines HCC827 (EGFR -mutated, KRAS wild-type) and A549 (EGFR wild-type, KRAS-mutated) treated with the tyrosine-kinase inhibitor (TKI) gefitinib. To investigate drug responses of more advanced tumor cells, we induced EMT by long-term treatment with TGF-beta-1 as assessed by vimentin/pan-cytokeratin immunofluorescence staining. A flow-bioreactor was employed to adjust culture to physiological conditions, which improved tissue generation. Furthermore, we show the integration of drug responses upon gefitinib treatment or TGF-beta-1 stimulation - apoptosis, proliferation index and EMT - into a Boolean in silico model. Additionally, we explain how drug responses of tumor cells with a specific mutational background and counterstrategies against resistance can be predicted. We are confident that our 3D in vitro approach especially with its in silico expansion provides an additional value for preclinical drug testing in more realistic conditions than in 2D cell culture.

A Combined 3D Tissue Engineered In Vitro/In Silico Lung Tumor Model for Predicting Drug Effectiveness in Specific Mutational Backgrounds

We present a three-dimensional (3D) lung cancer model based on a biological collagen scaffold to study sensitivity towards non-small-cell-lung-cancer-(NSCLC)-targeted therapies. We demonstrate different read-out techniques to determine the proliferation index, apoptosis and epithelial-mesenchymal transition (EMT) status. Collected data are integrated into an in silico model for prediction of drug sensitivity.

In the present study, we combined an in vitro 3D lung tumor model with an in silico model to optimize predictions of drug response based on a specific ...

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

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

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

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

A Microfluidic Platform for High-throughput Single-cell Isolation and Culture

Studying the heterogeneity of single cells is crucial for many biological questions, but is technically difficult. Thus, there is a need for a simple, yet high-throughput, method to perform single-cell culture experiments. Here, we report a microfluidic chip-based strategy for high-efficiency single-cell isolation (~77%) and demonstrate its capability of performing long-term single-cell culture (up to 7 d) and cellular heterogeneity analysis using clonogenic assay. These applications were demonstrated with KT98 mouse neural stem cells, and A549 and MDA-MB-435 human cancer cells. High single-cell isolation efficiency and long-term culture capability are achieved by using different sizes of microwells on the top and bottom of the microfluidic channel. The small microwell array is designed for precisely isolating single-cells, and the large microwell array is used for single-cell clonal culture in the microfluidic chip. This microfluidic platform constitutes an attractive approach for single-cell culture applications, due to its flexibility of adjustable cell culture spaces for different culture strategies, without decreasing isolation efficiency.

Here, we present a protocol for isolating and culturing single cells with a microfluidic platform, which utilizes a new microwell design concept to allow for high-efficiency single cell isolation and long-term clonal culture.

Studying the heterogeneity of single cells is crucial for many biological questions, but is technically difficult. Thus, there is a need for a simple, yet ...

Isolation of Murine Adipose Tissue-derived Microvascular Fragments as Vascularization Units for Tissue Engineering

A functional microvascular network is of pivotal importance for the survival and integration of engineered tissue constructs. For this purpose, several angiogenic and prevascularization strategies have been established. However, most cell-based approaches include time-consuming in vitro steps for the formation of a microvascular network. Hence, they are not suitable for intraoperative one-step procedures. Adipose tissue-derived microvascular fragments (ad-MVF) represent promising vascularization units. They can be easily isolated from fat tissue and exhibit a functional microvessel morphology. Moreover, they rapidly reassemble into new microvascular networks after in vivo implantation. In addition, ad-MVF have been shown to induce lymphangiogenesis. Finally, they are a rich source of mesenchymal stem cells, which may further contribute to their high vascularization potential. In previous studies we have demonstrated the remarkable vascularization capacity of ad-MVF in engineered bone and skin substitutes. In the present study, we report on a standardized protocol for the enzymatic isolation of ad-MVF from murine fat tissue.

We present a protocol to isolate adipose tissue-derived microvascular fragments that represent promising vascularization units. They can be rapidly isolated, do not require in vitro processing and, thus, may be used for one-step prevascularization in different fields of tissue engineering.

A functional microvascular network is of pivotal importance for the survival and integration of engineered tissue constructs. For this purpose, several ...

Fabrication of Decellularized Cartilage-derived Matrix Scaffolds

Osteochondral defects lack sufficient intrinsic repair capacity to regenerate functionally sound bone and cartilage tissue. To this extent, cartilage research has focused on the development of regenerative scaffolds. This article describes the development of scaffolds that are completely derived from natural cartilage extracellular matrix, coming from an equine donor. Potential applications of the scaffolds include producing allografts for cartilage repair, serving as a scaffold for osteochondral tissue engineering, and providing in vitro models to study tissue formation. By decellularizing the tissue, the donor cells are removed, but many of the natural bioactive cues are thought to be retained. The main advantage of using such a natural scaffold in comparison to a synthetically produced scaffold is that no further functionalization of polymers is required to drive osteochondral tissue regeneration. The cartilage-derived matrix scaffolds can be used for bone and cartilage tissue regeneration in both in vivo and in vitro settings.

Decellularized cartilage-derived scaffolds can be used as a scaffold to guide cartilage repair and as a means to regenerate osteochondral tissue. This paper describes the decellularization process in detail and provides suggestions to use these scaffolds in in vitro settings.

Osteochondral defects lack sufficient intrinsic repair capacity to regenerate functionally sound bone and cartilage tissue. To this extent, cartilage ...

Novel Process for 3D Printing Decellularized Matrices

3D bioprinting aims to create custom scaffolds that are biologically active and accommodate the desired size and geometry. A thermoplastic backbone can provide mechanical stability similar to native tissue while biologic agents offer compositional cues to progenitor cells, leading to their migration, proliferation, and differentiation to reconstitute the original tissues/organs1,2. Unfortunately, many 3D printing compatible, bioresorbable polymers (such as polylactic acid, PLA) are printed at temperatures of 210 &#176;C or higher - temperatures that are detrimental to biologics. On the other hand, polycaprolactone (PCL), a different type of polyester, is a bioresorbable, 3D printable material that has a gentler printing temperature of 65 &#176;C. Therefore, it was hypothesized that decellularized extracellular matrix (DM) contained within a thermally protective PLA barrier could be printed within PCL filament and remain in its functional conformation. In this work, osteochondral repair was the application for which the hypothesis was tested. As such, porcine cartilage was decellularized and encapsulated in polylactic acid (PLA) microspheres which were then extruded with polycaprolactone (PCL) into filament to produce 3D constructs via fused deposition modeling. The constructs with or without the microspheres (PLA-DM/PCL and PCL(-), respectively) were evaluated for differences in surface features.

This protocol describes the production of polycaprolactone (PCL) filament with embedded polylactic acid (PLA) microspheres which contain decellularized matrices (DM) for 3D printing of structural tissue engineering constructs.

3D bioprinting aims to create custom scaffolds that are biologically active and accommodate the desired size and geometry. A thermoplastic backbone can ...

Isolation and Culture of Primary Human Gingival Epithelial Cells using Y-27632

The gingival tissue is the first structure that protects periodontal tissues and plays meaningful roles in many oral functions. The gingival epithelium is an important structure of gingival tissue, especially in the repair and regeneration of periodontal tissue. Studying the functions of gingival epithelial cells has crucial scientific value, such as repairing oral defects and detecting the compatibility of biomaterials. As human gingival epithelial cells are highly differentiated keratinized cells, their lifespan is short, and they are difficult to passage. So far, there are only two ways to isolate and culture gingival epithelial cells, a direct explant method and an enzymatic method. However, the time required to obtain epithelial cells using the direct explant method is longer, and the cell survival rate of the enzymatic method is lower. Clinically, the acquisition of gingival tissue is limited, so a stable, efficient, and simple in vitro isolation and culture system is needed. We improved the traditional enzymatic method by adding Y-27632, a Rho-associated kinase (ROCK) inhibitor, which can selectively promote the growth of epithelial cells. Our modified enzymatic method simplifies the steps of the traditional enzymatic method and increases the efficiency of culturing epithelial cells, which has significant advantages over the direct explant method and the enzymatic method.

Here we present a modified method for the isolation and culture of human gingival epithelial cells by adding the Rock inhibitor, Y-27632, to the traditional method. This method is easier, less time-consuming, enhances stem cell properties, and produces larger numbers of high-potential epithelial cells both for the laboratory and for clinical applications.

The gingival tissue is the first structure that protects periodontal tissues and plays meaningful roles in many oral functions. The gingival epithelium is ...

Engineered Lung Tissues Prepared from Decellularized Lung Slices

There is a need for improved 3-dimensional (3D) lung models that recapitulate the architectural and cellular complexity of the native lung alveolus ex vivo. Recently developed organoid models have facilitated the expansion and study of lung epithelial progenitors in vitro, but these platforms typically rely on mouse tumor-derived matrix and/or serum, and incorporate just one or two cellular lineages. Here, we describe a protocol for generating engineered lung tissues (ELTs) based on the multi-lineage recellularization of decellularized precision-cut lung slices (PCLS). ELTs contain alveolar-like structures comprising alveolar epithelium, mesenchyme, and endothelium, within an extracellular matrix (ECM) substrate closely resembling that of native lung. To generate the tissues, rat lungs are inflated with agarose, sliced into 450 &#181;m-thick slices, cut into strips, and decellularized. The resulting acellular ECM scaffolds are then reseeded with primary endothelial cells, fibroblasts, and alveolar epithelial type 2 cells (AEC2s). AEC2s can be maintained in ELT culture for at least 7 days with a serum-free, chemically-defined growth medium. Throughout the tissue preparation and culture process, the slices are clipped into a cassette system that facilitates handling and standardized cell seeding of multiple ELTs in parallel. These ELTs represent an organotypic culture platform that should facilitate investigations of cell-cell and cell-matrix interactions within the alveolus as well as biochemical signals regulating AEC2s and their niche.

This protocol describes a method to generate reproducible, small-scale engineered lung tissues, by repopulating decellularized precision-cut lung slices with alveolar epithelial type 2 cells, fibroblasts, and endothelial cells.

There is a need for improved 3-dimensional (3D) lung models that recapitulate the architectural and cellular complexity of the native lung alveolus ex ...

Combining Human Organoids and Organ-on-a-Chip Technology to Model Intestinal Region-Specific Functionality

The intestinal mucosa is a complex physical and biochemical barrier that fulfills a myriad of important functions. It enables the transport, absorption, and metabolism of nutrients and xenobiotics while facilitating a symbiotic relationship with microbiota and restricting the invasion of microorganisms. Functional interaction between various cell types and their physical and biochemical environment is vital to establish and maintain intestinal tissue homeostasis. Modeling these complex interactions and integrated intestinal physiology in vitro is a formidable goal with the potential to transform the way new therapeutic targets and drug candidates are discovered and developed.
Organoids and Organ-on-a-Chip technologies have recently been combined to generate human-relevant intestine chips suitable for studying the functional aspects of intestinal physiology and pathophysiology in vitro. Organoids derived from the biopsies of the small (duodenum) and large intestine are seeded into the top compartment of an organ chip and then successfully expand&#160;as monolayers while preserving the distinct cellular, molecular, and functional features of each intestinal region. Human intestine tissue-specific microvascular endothelial cells are incorporated in the bottom compartment of the organ chip to recreate the epithelial-endothelial interface. This novel platform facilitates luminal exposure to nutrients, drugs, and microorganisms, enabling studies of intestinal transport, permeability, and host-microbe interactions.
Here, a detailed protocol is provided for the establishment of intestine chips representing the human duodenum (duodenum chip) and colon (colon chip), and their subsequent culture under continuous flow and peristalsis-like deformations. We demonstrate methods for assessing drug metabolism and CYP3A4 induction in duodenum chip using prototypical inducers and substrates. Lastly, we provide a step-by-step procedure&#160;for the in vitro modeling of interferon gamma (IFN&#947;)-mediated barrier disruption (leaky gut syndrome) in a colon chip, including methods for evaluating the alteration of paracellular permeability, changes in cytokine secretion, and transcriptomic profiling of the cells within the chip.

Biopsy-derived intestinal organoids and organ-on-a-chips technologies are combined into a microphysiological platform to recapitulate region-specific intestinal functionality.

The intestinal mucosa is a complex physical and biochemical barrier that fulfills a myriad of important functions. It enables the transport, absorption, ...

Dissection and Isolation of Region-Specific Decellularized Lung Tissue

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Chapters in this video

Expression, Isolation, and Purification of Soluble and Insoluble Biotinylated Proteins for Nerve Tissue Regeneration

A Combined 3D Tissue Engineered In Vitro/In Silico Lung Tumor Model for Predicting Drug Effectiveness in Specific Mutational Backgrounds

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

A Microfluidic Platform for High-throughput Single-cell Isolation and Culture

Isolation of Murine Adipose Tissue-derived Microvascular Fragments as Vascularization Units for Tissue Engineering

Fabrication of Decellularized Cartilage-derived Matrix Scaffolds

Novel Process for 3D Printing Decellularized Matrices

Isolation and Culture of Primary Human Gingival Epithelial Cells using Y-27632

Engineered Lung Tissues Prepared from Decellularized Lung Slices

Combining Human Organoids and Organ-on-a-Chip Technology to Model Intestinal Region-Specific Functionality