This study was supported by the National Natural Science Foundation of China (82090013).

The overall protocol requires 44 days, including 1 day for preparation of airway epithelial cells isolated from murine tracheas, 15 days for cell proliferation, and 28 days for CSE stimulation at the air-liquid interface. All experimental animals are housed in the SPF Barrier Animal Room of the Animal Experiment Center of Capital Medical University and have been reviewed and approved by the Animal Experiment and Laboratory Animal Ethics Committee of Capital Medical University (AEEI-2020-100) to meet the requirements of ARRIVE guidelines7.
1. Isolation of primary murine airway epithelial cells from murine tracheas
<ol>
	<li>Preparation
	<ol>
		<li>Prepare complete expansion medium by combining 1 mL of 50x supplement and 0.05 mL of hydrocortisone stock with 48.95 mL expansion basal medium. Store at 4 &#176;C and use within 4 weeks.</li>
		<li>Dissolve 7.5 mg of proteinase and 5 mg of deoxyribonuclease I in 5 mL of Ham&#39;s F-12 to prepare a proteinase solution. Filter it to sterilize and store at 4 &#176;C and use within 4 weeks.</li>
		<li>Prepare antibiotic solutions by adding 0.05 mL of 100x penicillin/streptomycin and 0.01 mL of 500x gentamicin/amphotericin to 5 mL of complete expansion medium, PBS, and proteinase solution (100 U/mL Penicillin, 100 U/mL Streptomycin, 10 &#181;g/mL gentamicin and 0.25 &#181;g/mL amphotericin B). Store at 4 &#176;C and use within 4 weeks.</li>
		<li>Sterilize surgical instruments and prepare the biological safety cabinet for cell isolation. Simultaneously, ensure that standard cell culture equipment is ready for use.</li>
		<li>Prepare rat tail collagen-coated dishes by adding rat tail collagen (100 &#181;g/mL in 0.02 N acetic acid) into 100 mm culture dishes and 24 mm transwells (0.05 mL/cm2). Leave open overnight under UV light for sterilization.</li>
	</ol>
	</li>
	<li>Isolation of primary murine airway epithelial cells
	<ol>
		<li>Use C57BL/6 mice (6-8 weeks old, male, SPF-raised) for tracheal epithelial cell isolation. Euthanize with 1% pentobarbital sodium solution overdose (about 200 mg/kg). Use five mice for sufficient cell yield.</li>
		<li>Sterilize the mouse by immersion in 75% ethanol solution, not immersing the nose and mouth in alcohol to prevent alcohol from flowing into the trachea.</li>
		<li>Dissect the mouse.
		<ol>
			<li>Use surgical blades and forceps, one set of devices for cutting and opening the epidermis from the lower jaw to the abdominal cavity of the mouse.</li>
			<li>Use another set of surgical instruments to tear apart the thyroid glands on both sides and remove the connections between the trachea, the surrounding muscle tissue, and the esophagus.</li>
			<li>After that, carefully cut into the chest, use forceps to delve deeper into the chest cavity, take out the entire lung, and find the end of the trachea.</li>
		</ol>
		</li>
		<li>Process the trachea.
		<ol>
			<li>Cut out the trachea from the thyroid cartilage to the tracheo-bronchial branch and put it in a pre-cold expansion medium containing four antibiotics.</li>
			<li>Shake the tube to rinse as much blood as possible off the surface of the trachea, keep it on ice, and then start the surgery for the next mouse.</li>
		</ol>
		</li>
		<li>Transfer all collected tracheas to pre-cold PBS buffer containing four antibiotics (200 U/mL Penicillin, 200 U/mL Streptomycin, 20 &#181;g/mL gentamicin, and 0.5 &#181;g/mL amphotericin B) for pretreatment before digestion.</li>
		<li>Use a set of surgical instruments to remove clots and other tissue from the surfaces of the trachea, and then cut them into 1 cm2 size.</li>
		<li>Incubate tracheal tissue in proteinase solution at 37 &#176;C for 40 min.</li>
		<li>After 40 min, rock the tube several times and use a 40 &#181;m cell strainer to remove the remaining tissues. Rinse the chopped tracheas on a strainer with 5 mL of expansion medium, centrifuge the cell suspension at 400 x g for 5 min at 4 &#176;C, and discard the supernatant.</li>
		<li>Resuspend the obtained cells in 8 mL of expansion medium.</li>
		<li>Count the viable cells using trypan blue and a hemocytometer.</li>
		<li>Plate P0 cell suspension on 100 mm dishes (1 x 104 live cells/cm2) precoated with rat tail collagen, and culture the cells in an incubator at 37 &#176;C, 5% CO2.</li>
	</ol>
	</li>
</ol>
2. Expansion culture and passage of primary murine airway epithelial cells
<ol>
	<li>Replace the medium for the P0 cell culture every 3 days until cells reach 70%-80% confluency, usually within 6 days. At this point, murine tracheal epithelial cells can form an intact monolayer with a cobblestone appearance (Figure 1A-D).</li>
	<li>Pre-warm sufficient volumes of PBS, complete expansion medium, and animal component-free (ACF) cell dissociation kit to 37 &#176;C.</li>
	<li>Gently rinse the cells with 3 mL of PBS.</li>
	<li>Perform enzymatic dissociation.
	<ol>
		<li>Add 3 mL of ACF enzymatic dissociation solution to the dish and incubate at 37 &#176;C for 5 min. After pipetting, dislodge the cells gently and transfer the cell suspension to 3 mL of ACF enzyme inhibition solution.</li>
		<li>Repeat the addition of 3 mL of ACF enzymatic dissociation solution and incubate again for 5 min to ensure maximum cell detachment.</li>
	</ol>
	</li>
	<li>Spin the cell suspension at 400 x g for 5 min at 4 &#176;C. Discard the supernatant.</li>
	<li>Resuspend the cells in 1 mL of expansion medium.</li>
	<li>Count the viable cells using trypan blue and a hemocytometer.</li>
	<li>Plate P1 cell suspension on several 100 mm dishes (5 x 104 live cells/cm2) pre-coated with rat tail collagen, and culture the cells in an incubator at 37 &#176;C, 5% CO2.</li>
</ol>
3. Differentiation and CSE stimulation of primary murine airway epithelial cells at air-liquid interface
<ol>
	<li>Confirm the cell type.
	<ol>
		<li>Verify the epithelial origin of isolated cells using an immunofluorescence assay (IFA) with antibodies against cytokeratins. Seed cells on glass slides coated by rat tail collagen and use paraformaldehyde to fix them for at least 12 h after cells reach 80% confluency.</li>
		<li>Wash slides 3 times with PBS solution for 5 min and incubate them with 3% BSA and 0.1% triton X-100 in PBS solution at room temperature (RT) for 1 h.</li>
		<li>Incubate slides overnight at 4 &#176;C with commercial anti-pan cytokeratin antibody at a dilution of 1:500.</li>
		<li>The next day, wash slides 3 times with PBS solution for 5 min and incubate them with secondary antibody buffer at a dilution of 1:1000 at RT for 2 h in the dark.</li>
		<li>After incubation, wash slides 3 times with PBS (5 min per wash), and add DAPI at a dilution of 1:1000 to them. After incubation at RT for 15 min, wash slides once with PBS for 5 min.</li>
		<li>Observe slides under a fluorescence microscope and compare expression patterns to a positive control (A549 cell line) and a negative control (Raw264.7 cell line) (Figure 2).</li>
	</ol>
	</li>
	<li>Seed the cells for differentiation.
	<ol>
		<li>Detach and centrifuge P2 cells as previously described, and resuspend the cell pellet in an appropriate volume of expansion medium to facilitate plating of 1 x 104 live cells/cm2.</li>
		<li>Pipette 1 mL of cell suspension onto the apical chamber of the transwell polycarbonate membrane insert. To the basal compartment of the transwell, add 1.5 mL of proliferation media.</li>
	</ol>
	</li>
	<li>Incubate the cells at 37 &#176;C and fully change all medium in the basal and apical chambers every 3 days using expansion medium until confluence is reached. This typically takes 3-6 days.</li>
	<li>Prepare 50 mL of complete differentiation medium by adding 5 mL of ALI 10x Supplement, 500 &#181;L of ALI Maintenance Supplement, 100 &#181;L of heparin solution, and 250 &#181;L of hydrocortisone stock solution to 44.15 mL of ALI Basal Medium.</li>
	<li>Prepare CSE.
	<ol>
		<li>Bubble one cigarette through 12.5 mL of differentiation medium and then filter it through a 0.22 &#181;m pore filter to prepare CSE. To ensure standardization between experiments and batches of CSE, measure the absorbance at 320 nm on a spectrophotometer and define optical density (OD) of 1 as 100%8.</li>
	</ol>
	</li>
	<li>Use the differentiation medium containing an appropriate concentration of CSE to stimulate primary murine airway epithelial cells to detect effects on the differentiation of the cells.</li>
	<li>Allow cells to differentiate for 28 days, during which the basal chamber media is changed, and the apical side is washed twice a week by removing the apical chamber media and replacing the basal chamber media with the differentiation medium containing the appropriate concentration of CSE.</li>
	<li>Analyze the cells post-exposure.
	<ol>
		<li>After exposure to differentiation medium containing CSE, harvest the cells and the culture supernatants at any time point (i.e., 0-28 days) for detecting morphological changes (i.e., immunofluorescence assay (IFA) or hematoxylin-eosin staining (HE) or for bioinformatics analytical procedures (i.e., transcriptomics, proteomics, metabolomics, etc.).</li>
	</ol>
	</li>
</ol>

In Vitro Model of Murine Airway Epithelial Cells and Chronic Smoke Exposure

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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=Barrier+disrupting+effects+of+alternaria+alternata+extract+on+bronchial+epithelium+from+asthmatic+donors.">Barrier disrupting effects of alternaria alternata extract on bronchial epithelium from asthmatic donors.</a> PLoS One. 8 (8), e71278 (2013).</li><li>Benediktsd&#243;ttir, B. E., Arason, A. J., Halld&#243;rsson, S., Gudj&#243;nsson, T., M&#225;sson, M., Baldursson, &. #. 2. 1. 1. ;. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Drug+delivery+characteristics+of+the+progenitor+bronchial+epithelial+cell+line+VA10.">Drug delivery characteristics of the progenitor bronchial epithelial cell line VA10.</a> Pharm Res. 30 (3), 781-791 (2013).</li><li>Walters, M. 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The authors have nothing to disclose.

COPD is a common chronic airway inflammatory disease. Exposure to tobacco smoke leads to chronic airway inflammation, airway remodeling, and lung structural destruction, which is the result of the interaction of various structural cells and immune cells10. As the front line of the innate immune system in the lung, airway epithelial cells play a very important role during the development of the disease11. In this point of view, clarifying how epithelial cells change and regu...

Chronic obstructive pulmonary disease (COPD) is a heterogeneous lung condition with complex characteristics, while patients with COPD gradually tend to be younger1. Smoking, a primary risk factor for COPD2, has a profound impact on airway epithelial cells, which serve as the initial barrier against tobacco smoke. Despite this known association, the detailed mechanisms through which tobacco smoke induces changes in airway epithelial cells remain inadequately explored. A thorough understanding of these molecular alterations is essential for identifying early diagnostic markers and therapeutic targets for COPD.
To address this gap, we developed a novel in vitro model using murine airway epithelial cells. These cells were subjected to long-term stimulation with cigarette smoke extract (CSE), enabling us to monitor dynamic cellular changes and explore the changes in airway epithelial cells under long-term tobacco stimulation and the underlying mechanism. In this model, transwell was used to provide the air-liquid interface of airway epithelial cells, and cigarette smoke extract was stimulated in the early stage of epithelial cell differentiation until the end of differentiation at 28 days. Previous studies investigated only the differentiation and short-term stimulation of airway epithelial cells (cell line dominance). They were limited to a single regulatory pathway3,4,5,6. However, the protocol presented here uses primary mouse airway epithelial cells and optimizes the cell extraction process for better cell activity than previous airway epithelial cell culture methods. This model focuses on alterations in cellular differentiation alongside comprehensive transcriptomic, proteomic, metabolomic, and epigenomic analyses. Employing immunofluorescence and advanced multi-omics techniques, we aimed to elucidate the cellular responses of airway epithelial cells to chronic tobacco smoke exposure, thereby contributing to a deeper understanding of COPD pathogenesis. This model can be used to explore the changes in airway epithelial cell differentiation pattern and its mechanism caused by long-term stimulation of various pollutants.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>100x Penicillin/Streptomycin solution</td>
			<td>Gibco</td>
			<td>15140122</td>
			<td></td>
		</tr>
		<tr>
			<td>24 mm Transwell with 0.4 &#181;m Pore Polyester Membrane Insert, Sterile</td>
			<td>BIOFIL</td>
			<td>TCS016012</td>
			<td></td>
		</tr>
		<tr>
			<td>40 &#181;m Cell Strainer</td>
			<td>Falcon</td>
			<td>352340</td>
			<td></td>
		</tr>
		<tr>
			<td>500x Gentamicin/Amphotericin Solution</td>
			<td>Gibco</td>
			<td>R01510</td>
			<td></td>
		</tr>
		<tr>
			<td>acetylated &#945;-Tubulin</td>
			<td>CST</td>
			<td>#5335</td>
			<td></td>
		</tr>
		<tr>
			<td>Acetyl-&#945;-Tubulin (Lys40) (D20G3)XP Rabbit mAb&#160;</td>
			<td>cellsignal</td>
			<td>#5335</td>
			<td></td>
		</tr>
		<tr>
			<td>Animal Component Free Cell Dissociation Kit</td>
			<td>Stemcell</td>
			<td>05426</td>
			<td></td>
		</tr>
		<tr>
			<td>Anti-pan Cytokeratin antibody</td>
			<td>abcam</td>
			<td>ab7753</td>
			<td></td>
		</tr>
		<tr>
			<td>Cigarette</td>
			<td>Marlboro</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Claudin3</td>
			<td>immunoway</td>
			<td>YT0949</td>
			<td></td>
		</tr>
		<tr>
			<td>Deoxyribonuclase I from bovine pancreas</td>
			<td>Sigma-Aldrich</td>
			<td>DN25</td>
			<td></td>
		</tr>
		<tr>
			<td>Deoxyribonuclase I from bovine pancreas</td>
			<td>Sigma</td>
			<td>DN25</td>
			<td></td>
		</tr>
		<tr>
			<td>Ham&#8217;s F-12</td>
			<td>Sigma-Aldrich</td>
			<td>N6658</td>
			<td></td>
		</tr>
		<tr>
			<td>Heparin Solution&#160;</td>
			<td>Stemcell</td>
			<td>07980</td>
			<td></td>
		</tr>
		<tr>
			<td>Hydrocortisone Stock Solution</td>
			<td>Stemcell</td>
			<td>07925</td>
			<td></td>
		</tr>
		<tr>
			<td>Mucin 5AC</td>
			<td>abcam</td>
			<td>ab212636</td>
			<td></td>
		</tr>
		<tr>
			<td>Occludin</td>
			<td>proteintech</td>
			<td>27260-1-AP</td>
			<td></td>
		</tr>
		<tr>
			<td>PBS</td>
			<td>Cytosci</td>
			<td>CBS004S-BR500</td>
			<td></td>
		</tr>
		<tr>
			<td>Penicillin-Streptomycin Solution</td>
			<td>Gibco</td>
			<td>15140122</td>
			<td></td>
		</tr>
		<tr>
			<td>PneumaCult-ALI 
			Basal Medium</td>
			<td>Stemcell</td>
			<td>05002&#160;</td>
			<td></td>
		</tr>
		<tr>
			<td>PneumaCult-ALI 10x Supplement</td>
			<td>Stemcell</td>
			<td>05003&#160;</td>
			<td></td>
		</tr>
		<tr>
			<td>PneumaCult-ALI Maintenance Supplement</td>
			<td>Stemcell</td>
			<td>05006</td>
			<td></td>
		</tr>
		<tr>
			<td>PneumaCult-Ex Plus 50x Supplement</td>
			<td>Stemcell</td>
			<td>05042</td>
			<td></td>
		</tr>
		<tr>
			<td>PneumaCult-Ex Plus Basal Medium</td>
			<td>Stemcell</td>
			<td>05041</td>
			<td></td>
		</tr>
		<tr>
			<td>Pronase E</td>
			<td>Sigma-Aldrich</td>
			<td>P5147</td>
			<td></td>
		</tr>
		<tr>
			<td>Rat tail collagen</td>
			<td>Corning</td>
			<td>354236</td>
			<td></td>
		</tr>
		<tr>
			<td>Trypan Blue</td>
			<td>Stemcell</td>
			<td>07050&#160;</td>
			<td></td>
		</tr>
	</tbody>
</table>

in vitro model for studying differentiation and changes of multi-omics on murine airway epithelial cells stimulated with cigarette smoke extract

Chronic obstructive pulmonary disease (COPD) is largely attributed to tobacco smoke exposure. Investigating how airway epithelial cells functionally adapt to tobacco smoke is crucial for understanding the pathogenesis of COPD. The present study was to set up an in vitro model using primary murine airway epithelial cells to mimic the real-life impact of tobacco smoke. Unlike established cell lines, primary cells retain more in vivo-like properties, including growth patterns, aging, and differentiation. These cells exhibit a sensitive inflammatory response and efficient differentiation, thus closely representing physiological conditions. In this model, primary murine airway epithelial cells were cultured for 28 days under an air-liquid interface with an optimal concentration of cigarette smoke extract (CSE), which led to the transformation of a monolayer of undifferentiated cells into a pseudostratified columnar epithelium, indicative of CSE acclimation. Comprehensive multi-omics analyses were then applied to elucidate the mechanisms by which CSE influences the differentiation of basal airway cells. These insights provide a deeper understanding of the cellular processes underpinning COPD progression in response to tobacco smoke exposure.

Differentiation 
Murine airway epithelial cells successfully differentiated after culturing at an air-liquid interface with a differentiation medium for 28 days. The presence of ciliated and goblet cells was demonstrated by immunofluorescence assay of cilia marker acetylated &#945;-Tubulin (green; Figure 3A) and the goblet cell marker Mucin5AC, respectively6 (red; Figure 3B).
Determination of CSE concentr...

Author Spotlight: Development and Characterization of an In Vitro Model to Study Chronic Cigarette Smoke Exposure and Its Impact on Airway Epithelial Cells in COPD Research

Here, we describe an in vitro model for isolating and differentiating murine airway epithelial cells, focusing on their acclimation to chronic cigarette smoke extract (CSE). The model could be utilized to comprehensively characterize the multi-omics impact of CSE, which possibly provides insights into the cellular responses under chronic smoke exposure.

In Vitro Model for Studying Differentiation and Changes of Multi-Omics on Murine Airway Epithelial Cells Stimulated with Cigarette Smoke Extract

Chronic obstructive pulmonary disease (COPD) is largely attributed to tobacco smoke exposure. Investigating how airway epithelial cells functionally adapt ...

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Research

JoVE Journal

Biology

518 Views.  Capital Medical University. Here, we describe an in vitro model for isolating and differentiating murine airway epithelial cells, focusing on their acclimation to chronic cigarette smoke extract (CSE). The model could be utilized to comprehensively characterize the multi-omics impact of CSE, which possibly provides insights into the cellular responses under chronic smoke exposure.

Video: Author Spotlight: Development and Characterization of an In Vitro Model to Study Chronic Cigarette Smoke Exposure and Its Impact on Airway Epithelial Cells in COPD Research

Preparation and Culture of Rat Lens Epithelial Explants for Studying Terminal Differentiation

The anterior surface of the ocular lens is covered by a monolayer of epithelial cells, which proliferate in an annular zone underlying the ciliary body.  Following division, these cells migrate posteriorly, where FGF diffusing from the retina induces them to differentiate into a posterior array of elongated lens fiber cells, which compose the bulk of the lens.  Differentiation of lens epithelial cells into lens fibers can be induced in vitro by culturing explants of the central region of the anterior epithelium in the presence of FGF-2.  Explants are prepared from lenses of neonatal rats by removing the lens from the eye and grasping the lens capsule on the posterior side with dissecting tweezers.  The posterior capsule is then gently torn open and pressed down into the plastic bottom of a tissue culture dish. The peripheral regions of the explant are removed with a scalpel and the central area is then cultured in the presence of 100ng/ml FGF-2 for as long as 2-3 weeks, depending on the parameters to be studied.  Since epithelial cells in cultured explants differentiate in approximate synchrony over a period of days to weeks, the time course of signaling and gene expression can be determined using molecular, biochemical, and pharmacological techniques.  Immunofluorescence microscopy is a powerful adjunct to these methods as it demonstrates the subcellular localization of proteins of interest and can reveal the physiological consequences of experimental manipulations of signaling pathways.

Explants of the central region of rat lens epithelia differentiate synchronously when cultured in the presence of FGF-2. Immunofluorescence microscopy of such cultures can provides novel information about gene expression and signaling events associated with terminal differentiation.

The anterior surface of the ocular lens is covered by a monolayer of epithelial cells, which proliferate in an annular zone underlying the ciliary body.  ...

Analyzing the Function of Small GTPases by Microinjection of Plasmids into Polarized Epithelial Cells

Epithelial cells polarize their plasma membrane into biochemically and functionally distinct apical and basolateral domains where the apical domain faces the 'free' surfaces and the basolateral membrane is in contact with the substrate and neighboring cells. Both membrane domains are separated by tight junctions, which form a diffusion barrier. Apical-basolateral polarization can be recapitulated successfully in culture when epithelial cells such as Madin-Darby Canine Kidney (MDCK) cells are seeded at high density on polycarbonate filters and cultured for several days 1 2. Establishment and maintenance of cell polarity is regulated by an array of small GTPases of the Ras superfamily such as RalA, Cdc42, Rab8, Rab10 and Rab13 3 4 5 6 7. Like all GTPases these proteins cycle between an inactive GDP-bound state and an active GTP-bound state. Specific mutations in the nucleotide binding regions interfere with this cycling 8. For example, Rab13T22N is permanently locked in the GDP-form and thus dubbed 'dominant negative', whereas Rab13Q67L can no longer hydrolyze GTP and is thus locked in a 'dominant active' state 7. To analyze their function in cells both dominant negative and dominant active alleles of GTPases are typically expressed at high levels to interfere with the function of the endogenous proteins 9. An elegant way to achieve high levels of overexpression in a short amount of time is to introduce the plasmids encoding the relevant proteins directly into the nuclei of polarized cells grown on filter supports using microinjection technique. This is often combined with the co-injection of reporter plasmids that encode plasma membrane receptors that are specifically sorted to the apical or basolateral domain. A cargo frequently used to analyze cargo sorting to the basolateral domain is a temperature sensitive allele of the vesicular stomatitis virus glycoprotein (VSVGts045) 10. This protein cannot fold properly at 39&deg;C and will thus be retained in the endoplasmic reticulum (ER) while the regulatory protein of interest is assembled in the cytosol. A shift to 31&deg;C will then allow VSVGts045 to fold properly, leave the ER and travel to the plasma membrane 11. This chase is typically performed in the presence of cycloheximide to prevent further protein synthesis leading to cleaner results. Here we describe in detail the procedure of microinjecting plasmids into polarized cells and subsequent incubations including temperature shifts that allow a comprehensive analysis of regulatory proteins involved in basolateral sorting.

This article details the procedures involved in overexpression and analysis of small GTPases in polarized epithelial cells using microinjection technique.

Epithelial cells polarize their plasma membrane into biochemically and functionally distinct apical and basolateral domains where the apical domain faces ...

Induction and Analysis of Epithelial to Mesenchymal Transition

Epithelial to mesenchymal transition (EMT) is essential for proper morphogenesis during development. Misregulation of this process has been implicated as a key event in fibrosis and the progression of carcinomas to a metastatic state. Understanding the processes that underlie EMT is imperative for the early diagnosis and clinical control of these disease states. Reliable induction of EMT in vitro is a useful tool for drug discovery as well as to identify common gene expression signatures for diagnostic purposes. Here we demonstrate a straightforward method for the induction of EMT in a variety of cell types. Methods for the analysis of cells pre- and post-EMT induction by immunocytochemistry are also included. Additionally, we demonstrate the effectiveness of this method through antibody-based array analysis and migration/invasion assays.

A straightforward method is described for the induction of epithelial to mesenchymal transition (EMT) in a variety of cell types. Methods for the analysis of cells in EMT states by immunocytochemistry are included.

Epithelial  to mesenchymal transition (EMT) is essential for proper morphogenesis during  development. Misregulation of this  process has been implicated ...

Cryosectioning Method for Microdissection of Murine Colonic Mucosa

The colonic mucosal tissue provides a vital barrier to luminal antigens. This barrier is composed of a monolayer of simple columnar epithelial cells. The colonic epithelium is dynamically turned over and epithelial cells are generated in the stem cell containing crypts of Lieberk&#252;hn. Progenitor cells produced in the crypt-bases migrate toward the luminal surface, undergoing a process of cellular differentiation before being shed into the gut lumen. In order to study these processes at the molecular level, we have developed a simple method for the microdissection of two spatially distinct regions of the colonic mucosa; the proliferative crypt zone, and the differentiated surface epithelial cells. Our objective is to isolate specific crypt and surface epithelial cell populations from mouse colonic mucosa for the isolation of RNA and protein.

Here we describe a simple method for the isolation of spatially distinct murine colonic epithelial surface cells from the underlying crypt-base cells.

The colonic mucosal tissue provides a vital barrier to luminal antigens. This barrier is composed of a monolayer of simple columnar epithelial cells. The ...

An In Vitro Model for Studying Cellular Transformation by Kaposi Sarcoma Herpesvirus

Kaposi sarcoma (KS) is an unusual tumor composed of proliferating spindle cells that is initiated by infection of endothelial cells (EC) with KSHV, and develops most often in the setting of immunosuppression. Despite decades of research, optimal treatment of KS remains poorly defined and clinical outcomes are especially unfavorable in resource-limited settings. KS lesions are driven by pathological angiogenesis, chronic inflammation, and oncogenesis, and various in vitro cell culture models have been developed to study these processes. KS arises from KSHV-infected cells of endothelial origin, so EC-lineage cells provide the most appropriate in vitro surrogates of the spindle cell precursor. However, because EC have a limited in vitro lifespan, and as the oncogenic mechanisms employed by KSHV are less efficient than those of other tumorigenic viruses, it has been difficult to assess the processes of transformation in primary or telomerase-immortalized EC. Therefore, a novel EC-based culture model was developed that readily supports transformation following infection with KSHV. Ectopic expression of the E6 and E7 genes of human papillomavirus type 16 allows for extended culture of age- and passage-matched mock- and KSHV-infected EC and supports the development of a truly transformed (i.e., tumorigenic) phenotype in infected cell cultures. This tractable and highly reproducible model of KS has facilitated the discovery of several essential signaling pathways with high potential for translation into clinical settings.

An In Vitro Model for Studying Cellular Transformation by Kaposi Sarcoma Herpesvirus

Kaposi sarcoma (KS) is a tumor induced by infection with the oncogenic virus human herpesvirus-8/KS herpesvirus (HHV-8/KSHV). The endothelial cell culture model described here is uniquely suited for studying the mechanisms by which KSHV transforms host cells.

Kaposi sarcoma (KS) is an unusual tumor composed of proliferating spindle cells that is initiated by infection of endothelial cells (EC) with KSHV, and ...

In Vitro Analysis of E3 Ubiquitin Ligase Function

The covalent attachment of ubiquitin (Ub) to internal lysine residue(s) of a substrate protein, a process termed ubiquitylation, represents one of the most important post-translational modifications in eukaryotic organisms. Ubiquitylation is mediated by a sequential cascade of three enzyme classes including ubiquitin-activating enzymes (E1 enzymes), ubiquitin-conjugating enzymes (E2 enzymes), and ubiquitin ligases (E3 enzymes), and sometimes, ubiquitin-chain elongation factors (E4 enzymes). Here, in vitro protocols for ubiquitylation assays are provided, which allow the assessment of E3 ubiquitin ligase activity, the cooperation between E2-E3 pairs, and substrate selection. Cooperating E2-E3 pairs can be screened by monitoring the generation of free poly-ubiquitin chains and/or auto-ubiquitylation of the E3 ligase. Substrate ubiquitylation is defined by selective binding of the E3 ligase and can be detected by western blotting of the in vitro reaction. Furthermore, an E2~Ub discharge assay is described, which is a useful tool for the direct assessment of functional E2-E3 cooperation. Here, the E3-dependent transfer of ubiquitin is followed from the corresponding E2 enzyme onto free lysine amino acids (mimicking substrate ubiquitylation) or internal lysines of the E3 ligase itself (auto-ubiquitylation). In conclusion, three different in vitro protocols are provided that are fast and easy to perform to address E3 ligase catalytic functionality.

In Vitro Analysis of E3 Ubiquitin Ligase Function

The present study provides detailed in vitro ubiquitylation assay protocols for the analysis of E3 ubiquitin ligase catalytic activity. Recombinant proteins were expressed using prokaryotic systems such as Escherichia coli culture.

The covalent attachment of ubiquitin (Ub) to internal lysine residue(s) of a substrate protein, a process termed ubiquitylation, represents one of the ...

Isolation of Endothelial Cells from the Lumen of Mouse Carotid Arteries for Single-Cell Multi-Omics Experiments

Atherosclerosis is an inflammatory disease of the arterial regions exposed to disturbed blood flow (d-flow). D-flow regulates the expression of genes in the endothelium at the transcriptomic and epigenomic levels, resulting in proatherogenic responses. Recently, single-cell RNA sequencing (scRNAseq) and single-cell Assay for Transposase Accessible Chromatin sequencing (scATACseq) studies were performed to determine the transcriptomic and chromatin accessibility changes at a single-cell resolution using the mouse partial carotid ligation (PCL) model. As endothelial cells (ECs) represent a minor fraction of the total cell populations in the artery wall, a luminal digestion method was used to obtain EC-enriched single-cell preparations. For this study, mice were subjected to PCL surgery to induce d-flow in the left carotid artery (LCA) while using the right carotid artery (RCA) as a control. The carotid arteries were dissected out two days or two weeks post PCL surgery. The lumen of each carotid was subjected to collagenase digestion, and endothelial-enriched single cells or single nuclei were obtained. These single-cell and single-nuclei preparations were subsequently barcoded using a 10x Genomics microfluidic setup. The barcoded single-cells and single-nuclei were then utilized for RNA preparation, library generation, and sequencing on a high-throughput DNA sequencer. Post bioinformatics processing, the scRNAseq and scATACseq datasets identified various cell types from the luminal digestion, primarily consisting of ECs. Smooth muscle cells, fibroblasts, and immune cells were also present. This EC-enrichment method aided in understanding the effect of blood flow on the endothelium, which could have been difficult with the total artery digestion method. The EC-enriched single-cell preparation method can be used to perform single-cell omics studies in EC-knockouts and transgenic mice where the effect of blood flow on these genes has not been studied. Importantly, this technique can be adapted to isolate EC-enriched single cells from human artery explants to perform similar mechanistic studies.

We present a method for isolating endothelial cells and nuclei from the lumen of mouse carotid arteries exposed to stable or disturbed flow conditions to perform single-cell omics experiments.

Atherosclerosis is an inflammatory disease of the arterial regions exposed to disturbed blood flow (d-flow). D-flow regulates the expression of genes in ...

Epithelial Effects of Intestinal Inflammation on Established Murine Colonoids

Studying the Epithelial Effects of Intestinal Inflammation In Vitro on Established Murine Colonoids

The intestinal epithelium plays an essential role in human health, providing a barrier between the host and the external environment. This highly dynamic cell layer provides the first line of defense between microbial and immune populations and helps to modulate the intestinal immune response. Disruption of the epithelial barrier is a hallmark of inflammatory bowel disease (IBD) and is of interest for therapeutic targeting. The 3-dimensional colonoid culture system is an extremely useful in vitro model for studying intestinal stem cell dynamics and epithelial cell physiology in IBD pathogenesis. Ideally, establishing colonoids from the inflamed epithelial tissue of animals would be most beneficial in assessing the genetic and molecular influences on disease. However, we have shown that in vivo epithelial changes are not necessarily retained in colonoids established from mice with acute inflammation. To address this limitation, we have developed a protocol to treat colonoids with a cocktail of inflammatory mediators that are typically elevated during IBD. While this system can be applied ubiquitously to various culture conditions, this protocol emphasizes treatment on both differentiated colonoids and 2-dimensional monolayers derived from established colonoids. In a traditional culture setting, colonoids are enriched with intestinal stem cells, providing an ideal environment to study the stem cell niche. However, this system does not allow for an analysis of the features of intestinal physiology, such as barrier function. Further, traditional colonoids do not offer the opportunity to study the cellular response of terminally differentiated epithelial cells to proinflammatory stimuli. The methods presented here provide an alternative experimental framework to address these limitations. The 2-dimensional monolayer culture system also offers an opportunity for therapeutic drug screening ex vivo. This polarized layer of cells can be treated with inflammatory mediators on the basal side of the cell and concomitantly with putative therapeutics apically to determine their utility in IBD treatment.

Author Spotlight: Studying the Epithelial Effects of Intestinal Inflammation In Vitro on Established Murine Colonoids  

We describe a protocol detailing the isolation of murine colonic crypts for the development of 3-dimensional colonoids. The established colonoids can then be terminally differentiated to reflect the cellular composition of the host epithelium prior to receiving an inflammatory challenge or being directed to establish an epithelial monolayer.

The intestinal epithelium plays an essential role in human health, providing a barrier between the host and the external environment. This highly dynamic ...

Optimizing Pinewood Nematode Infection in Pinus pinaster

Infection of In Vivo and In Vitro Pines with the Pinewood Nematode Bursaphelenchus xylophilus and Isolation of Induced Volatiles

The pinewood nematode (PWN) is a phytoparasite that causes pine wilt disease (PWD) in conifer species. This plant parasitic nematode has heavily contributed to pine deforestation in Asian countries, e.g., Japan, China, and Korea. Over the last two decades, in Europe, Portugal and Spain have been greatly affected. Research on the mechanisms of PWN infection and/or PWD progression in susceptible host species relies on the controlled infection of pine seedlings under greenhouse conditions. This technique is laborious and mobilizes substantial economic and human resources. Additionally, it can be prone to variability that results from the genetic diversity associated with some pine species but also from the interference of external factors. As an alternative, in vitro co-cultures of pine with PWNs offer a more advantageous system for studying biochemical changes since they a) allow controlling single environmental or nutritional variables, b) occupy less space, c) require less time to obtain, and d) are&#160;free from contamination or from host genetic variation. The following protocol details the standard in vivo PWN infection of Pinus pinaster, the maritime pine, and the establishment of the novel in vitro co-cultures of pine shoots with the PWN as an improved methodology to study this phytoparasite influence on pine volatiles. PWN-induced volatiles are extracted from in vivo and in vitro infected pines by hydrodistillation and distillation-extraction, and the emitted volatiles are captured by solid phase microextraction (SPME), using fiber or packed column techniques.

Author Spotlight: In Vitro Co-Culture System of Pine Shoots and Pinewood Nematode for Studying Host Volatile Response

The protocol describes the in vivo and in vitro pinewood nematode infection of Pinus pinaster and their volatilome analysis through Gas Chromatography (GC) and GC coupled to Mass Spectrometry (GC-MS).