Name: in vitro and in vivo approaches to determine intestinal epithelial cell permeability
Uploaded: 2018-10-19T12:30:00
Description: Watch this Scientific Journal Video about In Vitro and In Vivo Approaches to Determine Intestinal Epithelial Cell Permeability at JoVE.com

We thank Dr. Jerrold R. Turner, from Brigham and Women&#39;s Hospital, Harvard Medical School, for his generous help in completing this study. This work is supported by the National Natural Science Foundation of China (grant number&#160;81470804,&#160;31401229, and 81200620), the Natural Science Foundation of Jiangsu Province (grant number&#160;BK20180838, and BK20140319), The Research Innovation Program for College Graduates of Jiangsu Province (grant number KYLX16-0116), Advanced Research Projects of Soochow University (grant number SDY2015_06), and Crohn&#39;s &#38; Colitis Foundation Research Fellowship Award (grant number 310801).

This study was approved by the Animal Care and Use Protocol of Cambridge-Suda Genomic Resource Center (CAM-SU), Soochow University.
1. Plating and Maintenance of Caco-2bbe on Porous Polycarbonate Membranes
<ol>
	<li>Grow cells in a T75 flask with media (DMEM containing 10% FBS). Flasks should be fed regularly, depending on the cell density. 
	NOTE: For optimal plating, cells should divide rapidly and have a flat &#34;fried-egg&#34; shape, which indicates that cells are in the growth pha...

<ol>
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Q., 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=Myosin+light+chain+kinase+is+central+to+smooth+muscle+contraction+and+required+for+gastrointestinal+motility+in+mice.">Myosin light chain kinase is central to smooth muscle contraction and required for gastrointestinal motility in mice.</a> Gastroenterology. 135, 610-620 (2008).</li><li>Li, H. 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=Myosin+regulatory+light+chain+phosphorylation+is+associated+with+leiomyosarcoma+development.">Myosin regulatory light chain phosphorylation is associated with leiomyosarcoma development.</a> Biomed. Pharmacother. 92, 810-818 (2017).</li><li>Clayburgh, D. 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Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cellular+and+molecular+mechanisms+that+mediate+basal+and+tumour+necrosis+factor-alpha-induced+regulation+of+myosin+light+chain+kinase+gene+activity.">Cellular and molecular mechanisms that mediate basal and tumour necrosis factor-alpha-induced regulation of myosin light chain kinase gene activity.</a> J. Cell Mol. Med. 12, 1331-1346 (2008).</li><li>Turner, J. R., Buschmann, M. M., Romero-Calvo, I., Sailer, A., Shen, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+role+of+molecular+remodeling+in+differential+regulation+of+tight+junction+300+permeability.">The role of molecular remodeling in differential regulation of tight junction 300 permeability.</a> Semin. Cell Dev. Biol. 36, 204-212 (2014).</li><li>Srinivasan, B., 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=TEER+measurement+techniques+for+in+vitro+barrier+model+systems.">TEER measurement techniques for in vitro barrier model systems.</a> J. Lab. Autom. 20 (2), 107-126 (2015).</li><li>Wang, F., 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=IFN-gamma-induced+TNFR2+expression+is+required+for+TNF-dependent+intestinal+epithelial+barrier+dysfunction.">IFN-gamma-induced TNFR2 expression is required for TNF-dependent intestinal epithelial barrier dysfunction.</a> Gastroenterology. 131, 1153-1163 (2006).</li><li>Peterson, M. D., Mooseker, M. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Characterization+of+the+enterocyte-like+brush+border+cytoskeleton+of+the+C2BBe+clones+of+the+human+intestinal+cell+line+Caco-2.">Characterization of the enterocyte-like brush border cytoskeleton of the C2BBe clones of the human intestinal cell line Caco-2.</a> J. Cell Sci. 102 (Pt 3), 581-600 (1992).</li><li>Wang, 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=Methods+to+determine+intestinal+permeability+and+bacterial+translocation+during+liver+disease.">Methods to determine intestinal permeability and bacterial translocation during liver disease.</a> J. Immunol. Methods. 421, 44-53 (2015).</li></ol>

There are several critical steps in the protocol. Caco-2BBe (brush border-expressing) cells are always used for TER measurement, selected from the Caco-2 cell line for expression of brush-border proteins. Caco-2BBe cells have a villus absorptive phenotype when fully-differentiated (after about 3 weeks of culture post-confluence)17. It is necessary to avoid contamination during the measurement, and to sterilize the electrode. Because the procedure is non-sterile, measurements can only be performed ...

Intestinal epithelial cells are not only responsible for the absorption of nutrients, but also form an important barrier to defend against pathogenic microorganisms and microbial toxins. This intestinal barrier function is regulated by tight junction permeability and epithelial cell integrity1,2,3, and dysfunction of the epithelial barrier function is associated with inflammatory bowel disease (IBD). The perijunctional actomyosin ring (PAMR) lies within the cell that is closely contiguous to the tight junctions. The contraction of the PAMR, which is regulated by the myosin light chain (MLC), is crucial for the regulation of tight junction permeability4,5,6,7,8,9,10. Tumor necrosis factor (TNF) is central to intestinal barrier loss by upregulating intestinal epithelial MLC kinase (MLCK) expression and inducing occludin internalization11,12,13.
Ions such as Na+ and Cl- can cross the paracellular space by either the pore or leak pathway14. In a &#34;leaky&#34; epithelium, changes in TER primarily reflect altered tight junction permeability. TER measurement is a commonly used electrophysiological approach to quantify tight junction permeability, primarily to Na+ and Cl-, based on the impedance of cell monolayers. Diverse cell types, including intestinal epithelial cells, pulmonary epithelial cells, and vascular endothelial cells, have been reported for TER measurements. Advantages of this method are that TER measurements are non-invasive and can be used to monitor live cells in real-time. In addition, the TER measurement technique is useful for drug toxicity studies15.
Caco-2BBe cells are human epithelial colorectal adenocarcinoma cells with a structure and function similar to the differentiated small intestinal epithelial cells: for example, these cells have microvilli and enzymes associated with small intestinal brush border. Therefore, cultured Caco-2BBe monolayers are utilized as an in vitro model for testing barrier function.
In mice, one way to study intestinal paracellular permeability is by measuring the ability of FITC-dextran to cross from the lumen into the blood. Thus, the intestinal permeability can be assessed by gavaging FITC-dextran directly into mice and measuring the fluorescence within the blood. The following protocol describes two simple methods to assess intestinal epithelium permeability both in vitro and in vivo.

<table>
	<tbody>
		<tr>
			<td>22G gavage needle</td>
			<td>VWR</td>
			<td>20068-608</td>
			<td></td>
		</tr>
		<tr>
			<td>4 kDa FITC-dextran</td>
			<td>Sigma</td>
			<td>46944</td>
			<td></td>
		</tr>
		<tr>
			<td>Avertin</td>
			<td>Sigma</td>
			<td>T48402</td>
			<td></td>
		</tr>
		<tr>
			<td>Black 96-well plates for fluorescence</td>
			<td>Fisher</td>
			<td>14-245-197A</td>
			<td></td>
		</tr>
		<tr>
			<td>C57/B6 mice</td>
			<td>Nanjing Biomedical Research Institute of Nanjing University</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Caco-2BBe cells</td>
			<td>ATCC</td>
			<td>CRL-2102</td>
			<td></td>
		</tr>
		<tr>
			<td>Dextran sulphate sodium</td>
			<td>MP Biomedicals</td>
			<td>2160110</td>
			<td></td>
		</tr>
		<tr>
			<td>DMED with high glucose and sodium pyruvate&#160;</td>
			<td>Hyclone</td>
			<td>SH30243.01B</td>
			<td></td>
		</tr>
		<tr>
			<td>Epithelial (Volt/Ohm) Meter&#160;</td>
			<td>Millicell-ERS</td>
			<td>MERS00002</td>
			<td></td>
		</tr>
		<tr>
			<td>Ethanol</td>
			<td>Sinopharm ChemicalReagent</td>
			<td>10009218</td>
			<td></td>
		</tr>
		<tr>
			<td>Falcon tube (15 mL)</td>
			<td>Corning</td>
			<td>430791</td>
			<td></td>
		</tr>
		<tr>
			<td>FBS</td>
			<td>Gibco</td>
			<td>10437-028</td>
			<td></td>
		</tr>
		<tr>
			<td>Fluorescence microscope</td>
			<td>Olympus&#160;</td>
			<td>FV1000</td>
			<td></td>
		</tr>
		<tr>
			<td>Fluorometer</td>
			<td>Biotek</td>
			<td>Synergy 2</td>
			<td></td>
		</tr>
		<tr>
			<td>HBSS</td>
			<td></td>
			<td></td>
			<td>138 mM NaCl, 0.3 mM Na2HPO4, 0.4 mM MgSO4, 0.5 mM MgCl2, 5.0 mM KCl, 0.3 mM KH2PO4, 15.0 mM HEPES, 1.3 mM CaCl2, 25 mM glucose&#160;</td>
		</tr>
		<tr>
			<td>IFNg</td>
			<td>PeproTech</td>
			<td>315-05-20</td>
			<td></td>
		</tr>
		<tr>
			<td>Modular Tissue Embedding Center&#160;</td>
			<td>Leica</td>
			<td>EG1150H</td>
			<td></td>
		</tr>
		<tr>
			<td>Serum collection tubes</td>
			<td>Sarstedt</td>
			<td>41.1378.005</td>
			<td></td>
		</tr>
		<tr>
			<td>T75 flask&#160;</td>
			<td>corning</td>
			<td>430641</td>
			<td></td>
		</tr>
		<tr>
			<td>TNF</td>
			<td>PeproTech</td>
			<td>315-01A</td>
			<td></td>
		</tr>
		<tr>
			<td>Parraffin</td>
			<td>Sigma</td>
			<td>A6330-1CS</td>
			<td></td>
		</tr>
		<tr>
			<td>Polycarbonate membranes (Transwell)</td>
			<td>Costar</td>
			<td>3413</td>
			<td></td>
		</tr>
		<tr>
			<td>Pressure pump</td>
			<td>AUTOSCIENCE</td>
			<td>AP-9925</td>
			<td></td>
		</tr>
		<tr>
			<td>Rotary Microtomy</td>
			<td>Leica</td>
			<td>RM2235</td>
			<td></td>
		</tr>
		<tr>
			<td>Trypsin-EDTA</td>
			<td>Gibco</td>
			<td>25200-056</td>
			<td></td>
		</tr>
		<tr>
			<td>Xylene</td>
			<td>Sinopharm ChemicalReagent</td>
			<td>10023418</td>
			<td></td>
		</tr>
	</tbody>
</table>

in vitro and in vivo approaches to determine intestinal epithelial cell permeability

The intestinal barrier defends against pathogenic microorganism and microbial toxin. Its function is regulated by tight junction permeability and epithelial cell integrity, and disruption of the intestinal barrier function contributes to progression of gastrointestinal and systemic disease. Two simple methods are described here to measure the permeability of intestinal epithelium. In vitro, Caco-2BBe cells are plated in tissue culture wells as a monolayer and transepithelial electrical resistance (TER) can be measured by an epithelial (volt/ohm) meter. This method is convincing because of its user-friendly operation and repeatability. In vivo, mice are gavaged with 4 kDa fluorescein isothiocyanate (FITC)-dextran, and the FITC-dextran concentrations are measured in collected serum samples from mice to determine the epithelial permeability. Oral gavage provides an accurate dose, and therefore is the preferred method to measure the intestinal permeability in vivo. Taken together, these two methods can measure the permeability of the intestinal epithelium in vitro and in vivo, and hence be used to study the connection between diseases and barrier function.

In culture, Caco-2BBe cells grow as a monolayer and slowly differentiate into mature absorptive enterocytes that have brush borders. In this protocol, Caco-2BBe cells were plated with a high density on polycarbonate membranes, and cells reached 100% confluency one day after seeding. However, cells are undifferentiated at this stage: To fully differentiate the cells, the media is changed every 2-3 days for 3 weeks. Cells were stained with nuclei and F-actin stains to show the differences b...

Watch this Scientific Journal Video about In Vitro and In Vivo Approaches to Determine Intestinal Epithelial Cell Permeability at JoVE.com

In Vitro and In Vivo Approaches to Determine Intestinal Epithelial Cell Permeability

Two methods are presented here to determine intestinal barrier function. An epithelial meter (volt/ohm) is used for measurements of transepithelial electrical resistance of cultured epithelia directly in tissue culture wells. In mice, the FITC-dextran gavage method is used to determine the intestinal permeability in vivo.

In Vitro and In Vivo Approaches to Determine Intestinal Epithelial Cell Permeability

The intestinal barrier defends against pathogenic microorganism and microbial toxin. Its function is regulated by tight junction permeability and ...

The overall goal of this experiment is to study the diseases caused by epithelial barrier dysfunction by measuring the intestinal epithelial cell permeability in vitro and in vivo. This method can help answer key questions in the intestinal barrier function field, such as those related to the inflammatory bowel disease. The main advantage of this technique is that intestinal epithelial cell permeability can be assessed both in vitro and in vivo.The implications of this technique extends towards therapy or diagnosis of gastrointestinal diseases, because intestinal epithelial barrier dysfunction contributes to those diseases. Though this method can provide insight into the intestinal barrier function, it can also be applied to other systems, such as drug toxicity studies and barrier integrity of other cell types. Visual demonstration of this method is critical, as some steps are difficult to learn.An accurate operation of this method can now be understood by textual description. To begin, grow Caco-2bbe cells in a T75 flask with medium. Feed the flasks regularly, depending on the cell density.When the cells are 80%confluent, remove the medium and use 1-2 milliliters of sterile PBS without calcium to rinse them. Add 1.5 milliliters of Trypsin-EDTA, and gently rock the flask. Then, place it in the 37 degree Celsius incubator for 20 minutes, without rocking.While the cells are trypsinizing, place inserts containing porous polycarbonate membranes into 24 well plates. Then add 1 milliliter of culture medium into the basal chamber which is the lower space of the membrane. Add 5 milliliters of medium to the flask, and vigorously pipette the cells against the inside of the flask 5 to 10 times, to separate the culture into loose individual cells, or two to three cell clumps.Plate 0.166 milliliters of the cells into the apical chamber which is the upper space of the membrane. Then incubate the plates at 37 degrees Celsius for up to three weeks. Feed the cells three times weekly, by using a pressure pump to carefully aspirate the medium from the basal compartment of each well.Then gently drip one milliliter of medium into the apical chamber of each insert. For cytokine studies, one day before transepithelial electrical resistance or TER measurements, replace the basal medium with medium, containing 10 nanograms per milliliter of interferon gamma. On the day of the experiment, replace the medium with HBSS containing 2.5 or 7.5 nanograms per milliliter of TNF.To correct the meter, insert the correction electrode into the input port and choose Ohm mode. Then use a screwdriver to adjust the R Adjustment screw until the meter displays a reading of 1, 000 ohms. Sterilize the electrodes in 70%ethanol for 15 to 30 minutes and allow them to air dry for 15 seconds.Then rinse the electrodes in experimental cell culture medium. Next, turn on the power and choose Ohm mode. While keeping the electrodes vertical, carefully place the long ends of electrode bridges into the basal chamber, ensuring that they touch the dish.Then place the short ends into the apical chamber, ensuring that they stay below the surface of the medium, but above the tissue culture inserts. Measure the resistance of the sample and blank inserts at 0, 1, 2, 3 and 4 hours after cytokine treatment. Then record the resistance.To achieve consistency across different plate formats, calculate the product of the resistance and the effective membrane area as shown here. For 24 well inserts, the effective membrane area is 0.33 square centimeters. To induce colitis, add DSS to autoclaved water to a final concentration of 3.5%weight per volume.Then use the DSS solution to replace the drinking water in the cages of 8-week-old male C57 black six mice for a total of seven days. Give regular drinking water without DSS to control mice. After day seven, switch the DSS water to regular drinking water.Each day, weigh the mice and assess the clinical scores as defined according to the disease severity by four parameters:rectal prolapse, stool consistency, bleeding, and activity. Sum the scores from these parameters for a final clinical score. To analyze the histopathological condition of colon tissues seven days post DSS treatment, after euthanizing mice according to the text protocol, isolate the colon and cecum, and measure the length of the colon.Cut 0.5 centimeter segments from the distal colon, and fix the tissue in a 15 milliliter falcon tube containing 10 milliliters of 10%formalin overnight. Wash the fixed tissues with graded ethanol and xylene. Then embed the tissues in paraffin and cut six millimeter sections for the hematoxylin and eosin staining.To measure epithelial barrier permeability in DSS-induced mice, seven days after the start of DSS administration, fast the mice for three hours. Autoclave a gavage needle to ensure sterility, then use 150 microliters of 80 milligrams per milliliter four kilodalton FITC dextran in sterile water to gavage the mice, and keep the unused FITC dextran to measure the standard curve after serum collection. Next, weight the mice for the permeability calculation.Four hours later, after anesthetizing the mice by IP injection, confirm proper anesthetization by the lack of reflexes and whisker movement. Then place the mice on a heat block for five minutes. Using a pair of scissors, clip a one centimeter piece of the tail and collect 100 microliters of blood from the tail into a serum collection tube.Spin the collected blood at 10, 000 times g and room temperature for ten minutes. With water, dilute the serum one to four. Then, to make a standard curve, use water to prepare the dilutions of the unused FITC dextran.Add 100 microliters per well of the serum and the standard curve samples into 96 well plates. Using a plate reader, read the fluorescence at an excitation of 485 and an emission of 528. Calculate the permeability values based on the standard curve, and multiply by four to correct for the dilution.Divide the concentration of FITC dextran by the weight to normalize the values. This helps to normalize the difference in FITC dextran delivery if mice are sick, and have lost weight. The Caco-2bbe cells shown here were labeled with nuclei and F-actin stains to show the difference between undifferentiated and differentiated cells.Stress fibers are clearly seen in undifferentiated cells. Differentiated cells have a smaller volume, larger nuclei, and fewer stress fibers than undifferentiated cells. TNF is central to intestinal barrier loss through MLCK-dependent tight junction regulation.As seen in this figure, TNF significantly decreases the TER of the Caco-2bbe monolayer in a dose-dependent manner, suggesting that TNF increases epithelial permeability. Compared to their initial body weight, mice treated with DSS lose a significant amount of weight. The severity of colitis is scored by rectal prolapse, stool consistency, bleeding, and activity.Cross-sections of colonic tissues stained with hematoxylin and eosin show colonic mucosal damage in DSS-treated mice. In addition, the length of colon crypt, as well as the colon itself, is decreased in DSS-treated mice. Finally, there is an approximately two-fold increase in the levels of FITC dextran staining in DSS-treated mice, compared to control mice.While attempting this procedure, it's important to remember to minimize error, by standardizing operational procedures and utilizing statistical methods. After its development, this technique paved the way to researchers in the field of intestinal barrier function to explore gastrointestinal diseases in both model organisms and cell lines. After watching this video, you should have a good understanding of how to determine intestinal epithelial permeability by measuring the TER, gavaging FITC dextran, and observing morphological and histochemical changes.

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Visualization of MG53-mediated Cell Membrane Repair Using in vivo and in vitro Systems

Repair of acute injury to the cell membrane is an elemental process of normal cellular physiology, and defective membrane repair has been linked to many degenerative human diseases. The recent discovery of MG53 as a key component of the membrane resealing machinery allows for a better molecular understanding of the basic biology of tissue repair, as well as for potential translational applications in regenerative medicine. Here we detail the experimental protocols for exploring the in vivo function of MG53 in repair of muscle injury using treadmill exercise protocols on mouse models, for testing the ex vivo membrane repair capacity by measuring dye entry into isolated muscle fibers, and for monitoring the dynamic process of MG53-mediated vesicle trafficking and cell membrane repair in cultured cells using live cell confocal microscopy.

Visualization of MG53-mediated Cell Membrane Repair Using in vivo and in vitro Systems

Described here are protocols used to visualize the dynamic process of MG53-mediated cell membrane repair in whole animals and at the cellular level. These methods can be applied to investigate the cell biology of plasma membrane resealing and regenerative medicine.

Repair of acute injury to the cell membrane is an elemental process of normal cellular physiology, and defective membrane repair has been linked to many ...

Chromatin Isolation by RNA Purification (ChIRP)

Long noncoding RNAs are key regulators of chromatin states for important biological processes such as dosage compensation, imprinting, and developmental gene expression 1,2,3,4,5,6,7. The recent discovery of thousands of lncRNAs in association with specific chromatin modification complexes, such as Polycomb Repressive Complex 2 (PRC2) that mediates histone H3 lysine 27 trimethylation (H3K27me3), suggests broad roles for numerous lncRNAs in managing chromatin states in a gene-specific fashion 8,9. While some lncRNAs are thought to work in cis on neighboring genes, other lncRNAs work in trans to regulate distantly located genes. For instance, Drosophila lncRNAs roX1 and roX2 bind numerous regions on the X chromosome of male cells, and are critical for dosage compensation 10,11. However, the exact locations of their binding sites are not known at high resolution. Similarly, human lncRNA HOTAIR can affect PRC2 occupancy on hundreds of genes genome-wide 3,12,13, but how specificity is achieved is unclear. LncRNAs can also serve as modular scaffolds to recruit the assembly of multiple protein complexes. The classic trans-acting RNA scaffold is the TERC RNA that serves as the template and scaffold for the telomerase complex 14; HOTAIR can also serve as a scaffold for PRC2 and a H3K4 demethylase complex 13.
Prior studies mapping RNA occupancy at chromatin have revealed substantial insights 15,16, but only at a single gene locus at a time. The occupancy sites of most lncRNAs are not known, and the roles of lncRNAs in chromatin regulation have been mostly inferred from the indirect effects of lncRNA perturbation. Just as chromatin immunoprecipitation followed by microarray or deep sequencing (ChIP-chip or ChIP-seq, respectively) has greatly improved our understanding of protein-DNA interactions on a genomic scale, here we illustrate a recently published strategy to map long RNA occupancy genome-wide at high resolution 17. This method, Chromatin Isolation by RNA Purification (ChIRP) (Figure 1), is based on affinity capture of target lncRNA:chromatin complex by tiling antisense-oligos, which then generates a map of genomic binding sites at a resolution of several hundred bases with high sensitivity and low background. ChIRP is applicable to many lncRNAs because the design of affinity-probes is straightforward given the RNA sequence and requires no knowledge of the RNA's structure or functional domains.

Chromatin Isolation by RNA Purification ChIRP

ChIRP is a novel and rapid technique to map genomic binding sites of long noncoding RNAs (lncRNAs). The method takes advantage of the specificity of anti-sense tiling oligonucleotides to allow the enumeration of lncRNA-bound genomic sites.

Long noncoding RNAs are key regulators of chromatin states for important biological processes such as dosage compensation, imprinting, and developmental ...

Isolation of Ribosome Bound Nascent Polypeptides in vitro to Identify Translational Pause Sites Along mRNA

The rate of translational elongation is non-uniform. mRNA secondary structure, codon usage and mRNA associated proteins may alter ribosome movement on the messagefor review see 1. However, it's now widely accepted that synonymous codon usage is the primary cause of non-uniform translational elongation rates1. Synonymous codons are not used with identical frequency. A bias exists in the use of synonymous codons with some codons used more frequently than others2. Codon bias is organism as well as tissue specific2,3. Moreover, frequency of codon usage is directly proportional to the concentrations of cognate tRNAs4. Thus, a frequently used codon will have higher multitude of corresponding tRNAs, which further implies that a frequent codon will be translated faster than an infrequent one. Thus, regions on mRNA enriched in rare codons (potential pause sites) will as a rule slow down ribosome movement on the message and cause accumulation of nascent peptides of the respective sizes5-8. These pause sites can have functional impact on the protein expression, mRNA stability and protein foldingfor review see 9. Indeed, it was shown that alleviation of such pause sites can alter ribosome movement on mRNA and subsequently may affect the efficiency of co-translational (in vivo) protein folding1,7,10,11. To understand the process of protein folding in vivo, in the cell, that is ultimately coupled to the process of protein synthesis it is essential to gain comprehensive insights into the impact of codon usage/tRNA content on the movement of ribosomes along mRNA during translational elongation.
Here we describe a simple technique that can be used to locate major translation pause sites for a given mRNA translated in various cell-free systems6-8. This procedure is based on isolation of nascent polypeptides accumulating on ribosomes during in vitro translation of a target mRNA. The rationale is that at low-frequency codons, the increase in the residence time of the ribosomes results in increased amounts of nascent peptides of the corresponding sizes. In vitro transcribed mRNA is used for in vitro translational reactions in the presence of radioactively labeled amino acids to allow the detection of the nascent chains. In order to isolate ribosome bound nascent polypeptide complexes the translation reaction is layered on top of 30% glycerol solution followed by centrifugation. Nascent polypeptides in polysomal pellet are further treated with ribonuclease A and resolved by SDS PAGE. This technique can be potentially used for any protein and allows analysis of ribosome movement along mRNA and the detection of the major pause sites. Additionally, this protocol can be adapted to study factors and conditions that can alter ribosome movement and thus potentially can also alter the function/conformation of the protein.

Isolation of Ribosome Bound Nascent Polypeptides in vitro to Identify Translational Pause Sites Along mRNA

A technique to identify translational pause sites on mRNA is described. This procedure is based on isolation of nascent polypeptides accumulating on ribosomes during in vitro translation of a target mRNA, followed by the size analysis of the nascent chains using a denaturing gel electrophoresis.

The rate of translational elongation is non-uniform. mRNA secondary structure, codon usage and mRNA associated proteins may alter ribosome movement on the ...

Rapid Genetic Analysis of Epithelial-Mesenchymal Signaling During Hair Regeneration

Hair follicle morphogenesis, a complex process requiring interaction between epithelia-derived keratinocytes and the underlying mesenchyme, is an attractive model system to study organ development and tissue-specific signaling. Although hair follicle development is genetically tractable, fast and reproducible analysis of factors essential for this process remains a challenge. Here we describe a procedure to generate targeted overexpression or shRNA-mediated knockdown of factors using lentivirus in a tissue-specific manner. Using a modified version of a hair regeneration model 5, 6, 11, we can achieve robust gain- or loss-of-function analysis in primary mouse keratinocytes or dermal cells to facilitate study of epithelial-mesenchymal signaling pathways that lead to hair follicle morphogenesis. We describe how to isolate fresh primary mouse keratinocytes and dermal cells, which contain dermal papilla cells and their precursors, deliver lentivirus containing either shRNA or cDNA to one of the cell populations, and combine the cells to generate fully formed hair follicles on the backs of nude mice. This approach allows analysis of tissue-specific factors required to generate hair follicles within three weeks and provides a fast and convenient companion to existing genetic models.

Tissue-specific analysis of a hair follicle regeneration model using lentivirus to mediate gain- or loss-of-function.

Hair follicle morphogenesis, a complex process requiring interaction between epithelia-derived keratinocytes and the underlying mesenchyme, is an ...

Real Time Analysis of Metabolic Profile in Ex Vivo Mouse Intestinal Crypt Organoid Cultures

The small intestinal mucosa exhibits a repetitive architecture organized into two fundamental structures: villi, projecting into the intestinal lumen and composed of mature enterocytes, goblet cells and enteroendocrine cells; and crypts, residing proximal to the submucosa and the muscularis, harboring adult stem and progenitor cells and mature Paneth cells, as well as stromal and immune cells of the crypt microenvironment. Until the last few years, in vitro studies of small intestine was limited to cell lines derived from either benign or malignant tumors, and did not represent the physiology of normal intestinal epithelia and the influence of the microenvironment in which they reside. Here, we demonstrate a method adapted from Sato et al. (2009) for culturing primary mouse intestinal crypt organoids derived from C57BL/6 mice. In addition, we present the use of crypt organoid cultures to assay the crypt metabolic profile in real time by measurement of basal oxygen consumption, glycolytic rate, ATP production and respiratory capacity. Organoids maintain properties defined by their source and retain aspects of their metabolic adaptation reflected by oxygen consumption and extracellular acidification rates. Real time metabolic studies in this crypt organoid culture system are a powerful tool to study crypt organoid energy metabolism, and how it can be modulated by nutritional and pharmacological factors.

Real Time Analysis of Metabolic Profile in Ex Vivo Mouse Intestinal Crypt Organoid Cultures

Small intestinal crypt organoids cultured ex vivo provide a tissue culture system that recapitulates growth of crypts dependent on stem cells and their niche. We established a method to assay the metabolic profile in real time in primary mouse crypt organoids. We found organoids maintain physiological properties defined by their source.

The small intestinal mucosa exhibits a repetitive architecture organized into two fundamental structures: villi, projecting into the intestinal lumen and ...

Genetic and Biochemical Approaches for In Vivo and In Vitro Assessment of Protein Oligomerization: The Ryanodine Receptor Case Study

Oligomerization is often a structural requirement for proteins to accomplish their specific cellular function. For instance, tetramerization of the ryanodine receptor (RyR) is necessary for the formation of a functional Ca2+ release channel pore. Here, we describe detailed protocols for the assessment of protein self-association, including yeast two-hybrid (Y2H), co-immunoprecipitation (co-IP) and chemical cross-linking assays. In the Y2H system, protein self-interaction is detected by &#946;-galactosidase assay in yeast co-expressing GAL4 bait and target fusions of the test protein. Protein self-interaction is further assessed by co-IP using HA- and cMyc-tagged fusions of the test protein co-expressed in mammalian HEK293 cells. The precise stoichiometry of the protein homo-oligomer is examined by cross-linking and SDS-PAGE analysis following expression in HEK293 cells. Using these different but complementary techniques, we have consistently observed the self-association of the RyR N-terminal domain and demonstrated its intrinsic ability to form tetramers. These methods can be applied to protein-protein interaction and homo-oligomerization studies of other mammalian integral membrane proteins.

Genetic and Biochemical Approaches for In Vivo and In Vitro Assessment of Protein Oligomerization: The Ryanodine Receptor Case Study

Oligomerization of the ryanodine receptor, a homo-tetrameric ion channel mediating Ca2+ release from intracellular stores, is critical for skeletal and cardiac muscle contraction. Here, we present complementary in vivo and in vitro methods to detect protein self-association and determine homo-oligomer stoichiometry.

Oligomerization is often a structural requirement for proteins to accomplish their specific cellular function. For instance, tetramerization of the ...

Glomerular Outgrowth as an Ex Vivo Assay to Analyze Pathways Involved in Parietal Epithelial Cell Activation

Parietal epithelial cell (PEC) activation is one of the key factors involved in the development and progression of glomerulosclerosis. Inhibition of pathways involved in parietal epithelial cell activation could therefore be a tool to attenuate the progression of glomerular diseases. This article describes a method to culture and analyze parietal epithelial cell outgrowth of encapsulated glomeruli isolated from mouse kidney. After dissecting isolated mouse kidneys, the tissue is minced, and glomeruli are isolated by sieving. Encapsulated glomeruli are collected, and single glomeruli are cultured for 6 days to obtain glomerular outgrowth of parietal epithelial cells. During this period, parietal epithelial cell proliferation and migration can be analyzed by determining the cell number or the surface area of outgrowing cells. This assay can therefore be used as a tool to study the effects of an altered gene expression in transgenic- or knockout-mice or the effects of culture conditions on parietal epithelial cell growth characteristics and signaling. Using this method, important pathways involved in the process of parietal epithelial cell activation and consequently in glomerulosclerosis can be studied.

This article describes a method for culturing and analyzing glomerular parietal epithelial cell outgrowths of encapsulated glomeruli isolated from mouse kidney. This method can be used to study pathways involved in parietal epithelial cell proliferation and migration.

Parietal epithelial cell (PEC) activation is one of the key factors involved in the development and progression of glomerulosclerosis. Inhibition of ...

Organoid-Derived Epithelial Monolayer: A Clinically Relevant In Vitro Model for Intestinal Barrier Function

In the past, intestinal epithelial model systems were limited to transformed cell lines and primary tissue. These model systems have inherent limitations as the former do not faithfully represent original tissue physiology, and the availability of the latter is limited. Hence, their application hampers fundamental and drug development research. Adult stem-cell-based organoids (henceforth referred to as organoids) are miniatures of normal or diseased epithelial tissue from which they are derived. They can be established very efficiently from different gastrointestinal (GI) tract regions, have long-term expandability, and simulate tissue- and patient-specific responses to treatments in vitro. Here, the establishment of intestinal organoid-derived epithelial monolayers has been demonstrated along with methods to measure epithelial barrier integrity, permeability and transport,&#160;antimicrobial protein secretion, as well as histology. Moreover, intestinal organoid-derived monolayers can be enriched with proliferating stem and transit-amplifying cells as well as with key differentiated epithelial cells. Therefore, they represent a model system that can be tailored to study the effects of compounds on target cells and their mode of action. Although organoid cultures are technically more demanding than cell lines, once established, they can reduce failures in the later stages of drug development as they truly represent in vivo epithelium complexity and interpatient heterogeneity.

Here, we describe the preparation of human organoid-derived intestinal epithelial monolayers for studying intestinal barrier function, permeability, and transport. As organoids represent original epithelial tissue response to external stimuli, these models combine the advantages of expandability of cell lines and the relevance and complexity of primary tissue.

In the past, intestinal epithelial model systems were limited to transformed cell lines and primary tissue. These model systems have inherent limitations ...

Intestinal Epithelial Regeneration in Response to Ionizing Irradiation

The intestinal epithelium consists of a single layer of cells yet contains multiple types of terminally differentiated cells, which are generated by the active proliferation of intestinal stem cells located at the bottom of intestinal crypts. However, during events of acute intestinal injury, these active intestinal stem cells undergo cell death. Gamma irradiation is a widely used colorectal cancer treatment, which, while therapeutically efficacious, has the side effect of depleting the active stem cell pool. Indeed, patients frequently experience gastrointestinal radiation syndrome while undergoing radiotherapy, in part due to active stem cell depletion. The loss of active intestinal stem cells in intestinal crypts activates a pool of typically quiescent reserve intestinal stem cells and induces dedifferentiation of secretory and enterocyte precursor cells. If not for these cells, the intestinal epithelium would lack the ability to recover from radiotherapy and other such major tissue insults. New advances in lineage-tracing technologies allow tracking of the activation, differentiation, and migration of cells during regeneration and have been successfully employed for studying this in the gut. This study aims to depict a method for the analysis of cells within the mouse intestinal epithelium following radiation injury.

The gastrointestinal tract is one of the most sensitive organs to injury upon radiotherapeutic cancer treatments. It is simultaneously an organ system with one of the highest regenerative capacities following such insults. The presented protocol describes an efficient method to study the regenerative capacity of the intestinal epithelium.

The intestinal epithelium consists of a single layer of cells yet contains multiple types of terminally differentiated cells, which are generated by the ...

In Vivo Vascular Permeability Detection in Mouse Submandibular Gland

Saliva plays an important role in oral and overall health. The intact endothelial barrier function of blood vessels enables saliva secretion, whereas the endothelial barrier dysfunction is related to many salivary gland secretory disorders. The present protocol describes an in vivo paracellular permeability detection method to evaluate the function of endothelial tight junctions (TJs) in mouse submandibular glands (SMG). First, fluorescence-labeled dextrans with different molecular weights (4 kDa, 40 kDa, or 70 kDa) were injected into the angular veins of mice. Afterward, the unilateral SMG was dissected and fixed in the customized holder under a two-photon laser-scanning microscope, and then images were captured for blood vessels, acini, and ducts. Utilizing this method, the real-time dynamic leakage of the different-sized tracers from blood vessels into the basal sides of the acini and even across the acinar epithelia into the ducts was monitored to evaluate the alteration of the endothelial barrier function under physiological or pathophysiological conditions.

In Vivo Vascular Permeability Detection in Mouse Submandibular Gland

In the present protocol, the endothelial barrier function of the submandibular gland (SMG) was evaluated by injecting different molecular weighted fluorescent tracers into the angular veins of test animal models in vivo under a two-photon laser-scanning microscope.

Saliva plays an important role in oral and overall health. The intact endothelial barrier function of blood vessels enables saliva secretion, whereas the ...