Name: rectal organoid morphology analysis (roma): a diagnostic assay in cystic fibrosis
Uploaded: 2022-06-10T14:30:00
Description: Watch this Scientific Journal Video about Rectal Organoid Morphology Analysis ROMA: A Diagnostic Assay in Cystic Fibrosis at JoVE.com

We thank the patients and parents who participated in this study. We thank Abida Bibi for all culturing work with the organoids. We thank Els Aertgeerts, Karolien Bruneel, Claire Collard, Liliane Collignon, Monique Delfosse, Anja Delporte, Nathalie Feyaerts, C&#233;cile Lambremont, Lut Nieuwborg, Nathalie Peeters, Ann Raman, Pim Sansen, Hilde Stevens, Marianne Schulte, Els Van Ransbeeck, Christel Van de Brande, Greet Van den Eynde, Marleen Vanderkerken, Inge Van Dijck, Audrey Wagener, Monika Waskiewicz, and Bernard Wenderickx for logistic support. We also thank the Mucovereniging/Association Muco, and specifically Stefan Joris and Dr. Jan Vanleeuwe, for their support and financing. We thank all collaborators from the Belgian Organoid Project: Hedwige Boboli (CHR Citadelle, Li&#232;ge, Belgium), Linda Boulanger (University Hospitals Leuven, Belgium), Georges Casimir (HUDERF, Brussels, Belgium), Benedicte De Meyere (University Hospital Ghent, Belgium), Elke De Wachter (University Hospital Brussels, Belgium), Danny De Looze (University Hospital Ghent, Belgium), Isabelle Etienne (CHU Erasme, Brussels, Belgium), Laurence Hanssens (HUDERF, Brussels), Christiane Knoop (CHU Erasme, Brussels, Belgium), Monique Lequesne (University Hospital Antwerp, Belgium), Vicky Now&#233; (GZA St. Vincentius Hospital Antwerp), Dirk Staessen (GZA St. Vincentius Hospital Antwerp), Stephanie Van Biervliet (University Hospital Ghent, Belgium), Eva Van Braeckel (University Hospital Ghent, Belgium), Kim Van Hoorenbeeck (University Hospital Antwerp, Belgium), Eef Vanderhelst (University Hospital Brussels, Belgium), Stijn Verhulst (University Hospital Antwerp, Belgium), Stefanie Vincken (University Hospital Brussels, Belgium).

For all procedures involving human tissue, approval by the Ethics Committee Research UZ/KU Leuven (EC research) was acquired. All research was performed with informed consent and/or assent from parents, representatives, and/or patients.
NOTE: All procedures involving rectal biopsies and organoids should be performed in a laminar flow to protect the researcher from any biological hazard and to minimize the risk of contamination of the cultures. As for any lab procedure, researchers should at al...

<ol>
	<li>Riordan, J. R., 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=Identification+of+the+cystic+fibrosis+gene:+Cloning+and+characterization+of+complementary+DNA.">Identification of the cystic fibrosis gene: Cloning and characterization of complementary DNA.</a> Science. 245 (4922), 1066-1073 (1989).</li><li>Castellani, C., 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=ECFS+best+practice+guidelines:+the+2018+revision.">ECFS best practice guidelines: the 2018 revision.</a> Journal of Cystic Fibrosis. 17 (2), 153-178 (2018).</li><li>. CFTR2 Available from: <a target="_blank" href="https://www.cftr2.org/">https://www.cftr2.org/</a> (2022)</li><li>Farrell, P. 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=Diagnosis+of+cystic+fibrosis:+Consensus+guidelines+from+the+cystic+fibrosis+foundation.">Diagnosis of cystic fibrosis: Consensus guidelines from the cystic fibrosis foundation.</a> The Journal of Pediatrics. 181, 4-15 (2017).</li><li>Vermeulen, F., Lebecque, P., De Boeck, K., Leal, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Biological+variability+of+the+sweat+chloride+in+diagnostic+sweat+tests:+A+retrospective+analysis.">Biological variability of the sweat chloride in diagnostic sweat tests: A retrospective analysis.</a> Journal of Cystic Fibrosis: Official Journal of the European Cystic Fibrosis Society. 16 (1), 30-35 (2017).</li><li>Sato, 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=Long-term+expansion+of+epithelial+organoids+from+human+colon,+adenoma,+adenocarcinoma,+and+Barrett's+epithelium.">Long-term expansion of epithelial organoids from human colon, adenoma, adenocarcinoma, and Barrett's epithelium.</a> Gastroenterology. 141 (5), 1762-1772 (2011).</li><li>Boj, S. 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=Forskolin-induced+swelling+in+intestinal+organoids:+An+in+vitro+assay+for+assessing+drug+response+in+cystic+fibrosis+patients.">Forskolin-induced swelling in intestinal organoids: An in vitro assay for assessing drug response in cystic fibrosis patients.</a> Journal of Visualized Experiments: JoVE. (120), e55159 (2017).</li><li>Friedmacher, F., Puri, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rectal+suction+biopsy+for+the+diagnosis+of+Hirschsprung's+disease:+a+systematic+review+of+diagnostic+accuracy+and+complications.">Rectal suction biopsy for the diagnosis of Hirschsprung's disease: a systematic review of diagnostic accuracy and complications.</a> Pediatric Surgery International. 31 (9), 821-830 (2015).</li><li>Dekkers, J. 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=A+functional+CFTR+assay+using+primary+cystic+fibrosis+intestinal+organoids.">A functional CFTR assay using primary cystic fibrosis intestinal organoids.</a> Nature Medicine. 19 (7), 939-945 (2013).</li><li>Dekkers, J. 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=Characterizing+responses+to+CFTR-modulating+drugs+using+rectal+organoids+derived+from+subjects+with+cystic+fibrosis.">Characterizing responses to CFTR-modulating drugs using rectal organoids derived from subjects with cystic fibrosis.</a> Science Translational Medicine. 8 (344), (2016).</li><li>Vonk, A. 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=Protocol+for+application,+standardization+and+validation+of+the+forskolin-induced+swelling+assay+in+cystic+fibrosis+human+colon+organoids.">Protocol for application, standardization and validation of the forskolin-induced swelling assay in cystic fibrosis human colon organoids.</a> STAR Protocols. 1 (1), 100019 (2020).</li><li>Cuyx, 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=Rectal+organoid+morphology+analysis+(ROMA)+as+a+promising+diagnostic+tool+in+cystic+fibrosis.">Rectal organoid morphology analysis (ROMA) as a promising diagnostic tool in cystic fibrosis.</a> Thorax. 76 (11), 1146-1149 (2021).</li><li>Wilschanski, 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=Mutations+in+the+cystic+fibrosis+transmembrane+regulator+gene+and+in+vivo+transepithelial+potentials.">Mutations in the cystic fibrosis transmembrane regulator gene and in vivo transepithelial potentials.</a> American Journal of Respiratory and Critical Care Medicine. 174 (7), 787-794 (2006).</li><li>Derichs, N., 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=Intestinal+current+measurement+for+diagnostic+classification+of+patients+with+questionable+cystic+fibrosis:+validation+and+reference+data.">Intestinal current measurement for diagnostic classification of patients with questionable cystic fibrosis: validation and reference data.</a> Thorax. 65 (7), 594-599 (2010).</li><li>Ramalho, A. 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=Correction+of+CFTR+function+in+intestinal+organoids+to+guide+treatment+of+Cystic+Fibrosis.">Correction of CFTR function in intestinal organoids to guide treatment of Cystic Fibrosis.</a> European Respiratory Journal. 57, 1902426 (2020).</li></ol>

We provide a detailed protocol for rectal organoid morphology analysis (ROMA). The two indexes calculated with ROMA, IR, and CI, distinguished organoids from subjects with CF from those without CF with perfect accuracy. ROMA could thus function as a novel physiological CFTR assay complementary to SCC and other currently available tests13,14,15.
The protocol is dependent on the use of intestinal organo...

Cystic fibrosis (CF) is an autosomal recessive disease caused by mutations in the CF transmembrane conductance regulator (CFTR) gene. The CFTR protein is a chloride and bicarbonate channel, ensuring hydration of several epithelia1. CF is a high-burden, life-shortening, multi-system disease, manifesting primarily as a respiratory disease, but also affecting the gastrointestinal tract, pancreas, liver, and reproductive tract2.
Disease-causing CFTR mutations lead to a decrease in the amount or function of CFTR, in turn causing mucus dehydration. More than 2,000 variants in the CFTR gene have been described3, of which only 466 have been thoroughly characterized4.
A diagnosis of CF can be made when either sweat chloride concentration (SCC) is above the threshold of 60 mmol/L or when two disease-causing CFTR mutations (according to the CFTR2 database) are identified4,5. In subjects with only intermediately elevated (30-60 mmol/L) SCC, which occurs in about 4%-5% of sweat tests6, and CFTR mutations of varying or unknown clinical consequence, the diagnosis cannot be confirmed nor ruled out, even when they have CF compatible symptoms or a positive neonatal screening test. For these cases, second-line physiological CFTR assays (nasal potential difference (NPD) and intestinal current measurements (ICM)) have been included in the diagnostic algorithm. These tests are not readily available at most centers nor feasible at all ages, especially in infants5.
Rectal organoids are 3D structures grown from Lgr5(+) adult intestinal stem cells from intestinal crypts obtained through rectal biopsy7. Organoids are being used increasingly in biomedical research, such as testing modulator treatment in CF8. A viable biopsy can be obtained by either suction or forceps biopsy, a procedure that causes only minimal discomfort and is safe even in infants, with low complication rates9. The crypts isolated from the rectal biopsies are enriched in stem cells, and under specific culturing conditions, these self-organize into rectal organoids. The morphology of these organoids is determined by the expression and function of CFTR, located at the apical membrane of epithelial cells. Functional CFTR allows chloride and water to enter the organoid lumen, thereby inducing swelling of non-CF organoids. CF organoids do not swell and have no visible lumen10,11.
Rectal organoid morphology analysis (ROMA) allows the discrimination between CF and non-CF organoids based on these differences in organoid morphology. Non-CF organoids are more round and have a visible lumen, while the opposite is true for CF organoids. For this assay, patient-specific organoids are plated in 32 wells of a 96-well plate. After 1 day of growing, the organoids are stained with calcein green and imaged in a confocal microscope. The non-CF organoids show a more circular shape and a less fluorescent central part, as the lumen contains fluid and calcein stains only cells. These differences in morphology are quantified using two ROMA indexes: the circularity index (CI) quantifies the roundness of organoids, while the intensity ratio (IR) is a measure of the presence or absence of a central lumen. In this report, we describe in detail the protocol to obtain these discriminative indexes, to allow replication of the technique.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>1.5 mL microcentrifuge tubes</td>
			<td>Sorenson</td>
			<td>17040</td>
			<td></td>
		</tr>
		<tr>
			<td>15 mL conical tubes</td>
			<td>VWR</td>
			<td>525-0605</td>
			<td></td>
		</tr>
		<tr>
			<td>24 well plates</td>
			<td>Corning</td>
			<td>3526</td>
			<td></td>
		</tr>
		<tr>
			<td>96 well plates</td>
			<td>Greiner</td>
			<td>655101</td>
			<td></td>
		</tr>
		<tr>
			<td>Brightfield microscope</td>
			<td>Zeiss</td>
			<td>Axiovert 40C</td>
			<td></td>
		</tr>
		<tr>
			<td>Centrifuge</td>
			<td>Eppendorf</td>
			<td>5702</td>
			<td></td>
		</tr>
		<tr>
			<td>CO2 incubator</td>
			<td>Binder</td>
			<td>CB160</td>
			<td></td>
		</tr>
		<tr>
			<td>Computer</td>
			<td>Hewlett-Packard</td>
			<td>Z240</td>
			<td></td>
		</tr>
		<tr>
			<td>Confocal microscope&#160;</td>
			<td>Zeiss</td>
			<td>LSM 800</td>
			<td></td>
		</tr>
		<tr>
			<td>Laminar flow hood</td>
			<td>Thermo Fisher</td>
			<td>51025413</td>
			<td></td>
		</tr>
		<tr>
			<td>Material for organoid culture as detailed in previous protocol10</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Micropipettes (20, 200, and 1000 &#181;L)</td>
			<td>Eppendorf</td>
			<td>3123000039, 3123000055, 3123000063</td>
			<td></td>
		</tr>
		<tr>
			<td>Microsoft Excel</td>
			<td>Microsoft</td>
			<td>Microsoft Excel 2019 MSO 64-bit</td>
			<td>Spreadsheet software</td>
		</tr>
		<tr>
			<td>NIS-Elements Advanced Research Analysis Imaging Software&#160;</td>
			<td>Nikon</td>
			<td>v.5.02.00</td>
			<td>Imaging software</td>
		</tr>
		<tr>
			<td>Pipette tips (20, 200, and 1000 &#181;L)</td>
			<td>Greiner</td>
			<td>774288, 775353, 750288</td>
			<td></td>
		</tr>
		<tr>
			<td>Zeiss Zen Blue software&#160;</td>
			<td>Zeiss</td>
			<td>v2.6</td>
			<td>Imaging software</td>
		</tr>
	</tbody>
</table>

rectal organoid morphology analysis (roma): a diagnostic assay in cystic fibrosis

Diagnosis of cystic fibrosis (CF) is not always straightforward, especially when sweat chloride concentration is intermediate and/or less than two disease-causing CFTR mutations can be identified. Physiological CFTR assays (nasal potential difference, intestinal current measurement) have been included in the diagnostic algorithm but are not always readily available or feasible (e.g., in infants). Rectal organoids are 3D structures that grow from stem cells isolated from crypts of a rectal biopsy when cultured under specific conditions. Organoids from non-CF subjects have a round shape and a fluid-filled lumen, as CFTR-mediated chloride transport drives water into the lumen. Organoids with defective CFTR function do not swell, retaining an irregular shape and having no visible lumen. Differences in morphology between CF and non-CF organoids are quantified in the &#39;Rectal Organoid Morphology Analysis&#39; (ROMA) as a novel CFTR physiological assay. For the ROMA assay, organoids are plated in 96-well plates, stained with calcein, and imaged in a confocal microscope. Morphological differences are quantified using two indexes: The circularity index (CI) quantifies the roundness of organoids, and the intensity ratio (IR) is a measure of the presence of a central lumen. Non-CF organoids have a high CI and low IR compared to CF organoids. ROMA indexes perfectly discriminated 167 subjects with CF from 22 subjects without CF, making ROMA an appealing physiological CFTR assay to aid in CF diagnosis. Rectal biopsies can be routinely performed at all ages in most hospitals and tissue can be sent to a central lab for organoid culture and ROMA. In the future, ROMA might also be applied to test the efficacy of CFTR modulators in vitro. The aim of the present report is to fully explain the methods used for ROMA, to allow replication in other labs.

Organoids from 212 subjects were collected during routine clinical visits. No adverse events occurred during or after the rectal biopsy procedure. Organoids were imaged by one researcher blinded to subject characteristics such as genotype and clinical information. Due to low-quality images, 23 subjects were excluded. Examples of successful and failed organoid cultures and image acquisition can be seen in Figure 2.
Organoids of 167 subjects with CF and two disease-...

Watch this Scientific Journal Video about Rectal Organoid Morphology Analysis ROMA: A Diagnostic Assay in Cystic Fibrosis at JoVE.com

Rectal Organoid Morphology Analysis ROMA: A Diagnostic Assay in Cystic Fibrosis

This protocol describes rectal organoid morphology analysis (ROMA), a novel diagnostic assay for cystic fibrosis (CF). Morphological characteristics, namely the roundness (circularity index, CI) and the presence of a lumen (intensity ratio, IR), are a measure of CFTR function. Analysis of 189 subjects showed perfect discrimination between CF and non-CF.

Rectal Organoid Morphology Analysis (ROMA): A Diagnostic Assay in Cystic Fibrosis

Diagnosis of cystic fibrosis (CF) is not always straightforward, especially when sweat chloride concentration is intermediate and/or less than two ...

ROMA can discriminate between organoids from subjects with and without cystic fibrosis when less than two disease-causing CFTR mutations are found and when sweat fluoride is intermediate. ROMA can be performed at all ages and with low complication rates. The analysis is semi-automated and standardized and biopsies can be sent to a central laboratory for analysis.Organoids used for ROMA can also be used to access CFTR modulatory efficacy, and ROMA could help with measuring the degree of restoration of CFTR function. One day after plating, stain the organoids with calcium green. Rotate and slightly tilt the plate with the lid on a few times to ensure homogenous distribution of the calcium green in the whole well.Incubate the plate again, for 15 to 30 minutes at 37 degrees Celsius and 5%carbon dioxide to ensure staining of all organoids in the wells. To focus on the organoids, determine the optimal X and Y position, and focus on the organoids in each well manually, using the confocal microscope. And save these positions in the imaging software.Next, using live cell imaging settings, set the emission at 488 nanometers and excitation at 515 nanometers, and a LD magnification objective at 5X. To acquire organoid pictures, take images in a unit directional way with a resolution of 1024 pixels by 1024 pixels, and a depth of 16 bits with the confocal microscope. Choose the laser intensity and master gain for optimal visualization of morphological differences between cystic fibrosis and non-cystic fibrosis organoids.Start the experiment to capture the images. Afterward, save one picture per well for all 32 wells in the microscope format and export them as TIFF files. First, load the TIFF files in the image analysis software and then perform the first quality check based on exclusion criteria determined by the operator.Exclude the set of pictures if many differentiated or dead structures or debris are present when plating density is inadequate, when too many or too few organoids are present, and in case of inadequate fluorescence distribution. To prepare images for analysis, create and open one network data file of all 32 pictures for each organoid culture, enabling simultaneous analysis of all 32 pictures per subject. And recalibrate images so one pixel corresponds to 2.5 by 2.5 micrometers.Then, delineate structures using a lower intensity threshold of 4, 500, and an upper threshold of 65, 535, turning off the smooth and clean functions, turning on the fill holes function, and putting the separate function at 3X. To count the organoids, select all structures more than or equal to 40 micrometers. Next, click the update ND measurement button, and the counted organoids will be numbered.To measure intensity and circularity for calculation, select all structures more than or equal to 60 micrometers and count. Then, remove all structures touching the borders of the picture. Next, erode one pixel from the border of each, more than, or equal to 60 micrometers structure, and measure the mean intensity of each structure.Afterward, select all structures more than or equal to 60 micrometers again, and erode 10 pixels from the border of each, more than, or equal to 60 micrometers structure. Then, measure the mean intensity of each eroded structure and the circularity of each structure. Then, calculate the intensity ratio by dividing the intensity measurement after eroding 25 micrometers from the border of each, more than, or equal to 60 micrometers structure by the mean of the intensity measurement after eroding 2.5 micrometers from the border of each, more than, or equal to 60 micrometers structure.Perform the second quality check based on exclusion criteria determined by the software as described in the manuscript. Organoids from 212 subjects were collected and imaged. After exclusion of 23 sets of pictures, organoid pictures from 167 subjects with cystic fibrosis and two disease causing CFTR mutations and from 22 non-cystic fibrosis subjects were analyzed, the mean number of organoids per culture was found to be 1, 519.The intensity ratio and circularity index were determined for organoids from subjects with and without cystic fibrosis. Using these two indexes, perfect discrimination was obtained between organoids from subjects with and without cystic fibrosis not only when using data from all 32 wells, but also when eight wells were chosen randomly for each culture. Histograms for four illustrative cultures were obtained, showing the distribution of values for circularity, the intensity of the central part of the organoid, and the intensity of the whole organoid.Quality control is essential, as high quality pictures are required for accurate calculation of the intensity ratio and circularity index. Organoid cultures established for ROMA can also be used for physics aids to test the effect of CFTR treatment. RNA, DNA, and protein can be extracted for further characterization of CFTR variants.

rectal-organoid-morphology-analysis-roma-diagnostic-assay-cystic

Research

JoVE Journal

Medicine

Diagnostic Ultrasound Imaging of Mouse Diaphragm Function

Function analysis of rodent respiratory skeletal muscles, particularly the diaphragm, is commonly performed by isolating muscle strips using invasive surgical procedures. Although this is an effective method of assessing in vitro diaphragm activity, it involves non-survival surgery. The application of non-invasive ultrasound imaging as an in vivo procedure is beneficial since it not only reduces the number of animals sacrificed, but is also suitable for monitoring disease progression in live mice. Thus, our ultrasound imaging method may likely assist in the development of novel therapies that alleviate muscle injury induced by various respiratory diseases. Particularly, in clinical diagnoses of obstructive lung diseases, ultrasound imaging has the potential to be used in conjunction with other standard tests to detect the early onset of diaphragm muscle fatigue. In the current protocol, we describe how to accurately evaluate diaphragm contractility in a mouse model using a diagnostic ultrasound imaging technique.

Diagnostic ultrasound imaging has proven to be effective in diagnosing various respiratory diseases in human and animal subjects. We demonstrate a comprehensive ultrasound protocol utilized by Dr. Zuo's lab to analyze diaphragm kinetics specifically in mouse models. This is also a non-invasive research technique which can provide quantitative information on mouse respiratory muscle function.

Function analysis of rodent respiratory skeletal muscles, particularly the diaphragm, is commonly performed by isolating muscle strips using invasive ...

Carotid Artery Infusions for Pharmacokinetic and Pharmacodynamic Analysis of Taxanes in Mice

When proposing the use of a drug, drug combination, or drug delivery into a novel system, one must assess the pharmacokinetics of the drug in the study model. As the use of mouse models are often a vital step in preclinical drug discovery and drug development1-8, it is necessary to design a system to introduce drugs into mice in a uniform, reproducible manner. Ideally, the system should permit the collection of blood samples at regular intervals over a set time course. The ability to measure drug concentrations by mass-spectrometry, has allowed investigators to follow the changes in plasma drug levels over time in individual mice1, 9, 10. In this study, paclitaxel was introduced into transgenic mice as a continuous arterial infusion over three hours, while blood samples were simultaneously taken by retro-orbital bleeds at set time points. Carotid artery infusions are a potential alternative to jugular vein infusions, when factors such as mammary tumors or other obstructions make jugular infusions impractical. Using this technique, paclitaxel concentrations in plasma and tissue achieved similar levels as compared to jugular infusion. In this tutorial, we will demonstrate how to successfully catheterize the carotid artery by preparing an optimized catheter for the individual mouse model, then show how to insert and secure the catheter into the mouse carotid artery, thread the end of the catheter out through the back of the mouse&#8217;s neck, and hook the mouse to a pump to deliver a controlled rate of drug influx. Multiple low volume retro-orbital bleeds allow for analysis of plasma drug concentrations over time.

This method was developed with the goal of delivering a steady drug solution via the carotid artery, to assess the pharmacokinetics of novel drugs in mouse models.

When proposing the use of a drug, drug combination, or drug delivery into a novel system, one must assess the pharmacokinetics of the drug in the study ...

Forskolin-induced Swelling in Intestinal Organoids: An In Vitro Assay for Assessing Drug Response in Cystic Fibrosis Patients

Recently-developed cystic fibrosis transmembrane conductance regulator (CFTR)-modulating drugs correct surface expression and/or function of the mutant CFTR channel in subjects with cystic fibrosis (CF). Identification of subjects that may benefit from these drugs is challenging because of the extensive heterogeneity of CFTR mutations, as well as other unknown factors that contribute to individual drug efficacy. Here, we describe a simple and relatively rapid assay for measuring individual CFTR function and response to CFTR modulators in vitro. Three dimensional (3D) epithelial organoids are grown from rectal biopsies in standard organoid medium. Once established, the organoids can be bio-banked for future analysis. For the assay, 30-80 organoids are seeded in 96-well plates in basement membrane matrix and are then exposed to drugs. One day later, the organoids are stained with calcein green, and forskolin-induced swelling is monitored by confocal live cell microscopy at 37 &#176;C. Forskolin-induced swelling is fully CFTR-dependent and is sufficiently sensitive and precise to allow for discrimination between the drug responses of individuals with different and even identical CFTR mutations. In vitro swell responses correlate with the clinical response to therapy. This assay provides a cost-effective approach for the identification of drug-responsive individuals, independent of their CFTR mutations. It may also be instrumental in the development of future CFTR modulators.

Forskolin-induced Swelling in Intestinal Organoids: An In Vitro Assay for Assessing Drug Response in Cystic Fibrosis Patients

This protocol describes an assay for measuring CFTR function and CFTR modulator responses in cultured tissue from subjects with cystic fibrosis (CF). Biopsy-derived intestinal organoids swell in a cAMP-driven fashion, a response that is defective (or strongly reduced) in CF organoids and can be restored by exposure to CFTR modulators.

Recently-developed cystic fibrosis transmembrane conductance regulator (CFTR)-modulating drugs correct surface expression and/or function of the mutant ...

Semi-automated Analysis of Mouse Skeletal Muscle Morphology and Fiber-type Composition

For years, distinctions between skeletal muscle fiber types were best visualized by myosin-ATPase staining. More recently, immunohistochemical staining of myosin heavy chain (MyHC) isoforms has emerged as a finer discriminator of fiber-type. Type I, type IIA, type IIX and type IIB fibers can now be identified with precision based on their MyHC profile; however, manual analysis of these data can be slow and down-right tedious. In this regard, rapid, accurate assessment of fiber-type composition and morphology is a very desirable tool. Here, we present a protocol for state-of-the-art immunohistochemical staining of MyHCs in frozen sections obtained from mouse hindlimb muscle in concert with a novel semi-automated algorithm that accelerates analysis of fiber-type and fiber morphology. As expected, the soleus muscle displayed staining for type I and type IIA fibers, but not for type IIX or type IIB fibers. On the other hand, the tibialis anterior muscle was composed predominantly of type IIX and type IIB fibers, a small fraction of type IIA fibers and little or no type I fibers. Several image transformations were used to generate probability maps for the purpose of measuring different aspects of fiber morphology (i.e., cross-sectional area (CSA), maximal and minimal Feret diameter). The values obtained for these parameters were then compared with manually-obtained values. No significant differences were observed between either mode of analysis with regards to CSA, maximal or minimal Feret diameter (all p &#62; 0.05), indicating the accuracy of our method. Thus, our immunostaining analysis protocol may be applied to the investigation of effects on muscle composition in many models of aging and myopathy.

Immunohistochemical staining of myosin heavy chain isoforms has emerged as the state-of-the-art discriminator of skeletal muscle fiber-type (i.e., type I, type IIA, type IIX, type IIB). Here, we present a staining protocol along with a novel semi-automated algorithm that facilitates rapid assessment of fiber-type and fiber morphology.

For years, distinctions between skeletal muscle fiber types were best visualized by myosin-ATPase staining. More recently, immunohistochemical staining of ...

Optimized LC-MS/MS Method for the High-throughput Analysis of Clinical Samples of Ivacaftor, Its Major Metabolites, and Lumacaftor in Biological Fluids of Cystic Fibrosis Patients

Defects in the cystic fibrosis trans-membrane conductance regulator (CFTR) are the cause of cystic fibrosis (CF), a disease with life-threatening pulmonary manifestations. Ivacaftor (IVA) and ivacaftor-lumacaftor (LUMA) combination are two new breakthrough CF drugs that directly modulate the activity and trafficking of the defective CFTR-protein. However, there is still a dearth of understanding on pharmacokinetic/pharmacodynamic parameters and the pharmacology of ivacaftor and lumacaftor. The HPLC-MS technique for the simultaneous analysis of the concentrations of ivacaftor, hydroxymethyl-ivacaftor, ivacaftor-carboxylate, and lumacaftor in biological fluids in patients receiving standard ivacaftor or ivacaftor-lumacaftor combination therapy has previously been developed by our group and partially validated to FDA standards. However, to allow the high-throughput analysis of a larger number of patient samples, our group has optimized the reported method through the use of a smaller pore size reverse-phase chromatography column (2.6 &#181;m, C8 100 &#197;; 50 x 2.1 mm) and a gradient solvent system (0-1 min: 40% B; 1-2 min: 40-70% B; 2-2.7 min: held at 70% B; 2.7-2.8 min: 70-90% B; 2.8-4.0 min: 90% B washing; 4.0-4.1 min: 90-40% B; 4.1-6.0 min: held at 40% B) instead of an isocratic elution. The goal of this study was to reduce the HPLC-MS analysis time per sample dramatically from ~15 min to only 6 min per sample, which is essential for the analysis of a large amount of patient samples. This expedient method will be of considerable utility for studies into the exposure-response relationships of these breakthrough CF drugs.

Ivacaftor and ivacaftor-lumacaftor combination are two new CF drugs. However, there is still a dearth of understanding on their PK/PD and pharmacology. We present an optimized HPLC-MS technique for the simultaneous analysis of ivacaftor and its major metabolites, and lumacaftor.

Defects in the cystic fibrosis trans-membrane conductance regulator (CFTR) are the cause of cystic fibrosis (CF), a disease with life-threatening ...

Standardized Measurement of Nasal Membrane Transepithelial Potential Difference (NPD)

We describe a standardized measurement of nasal potential difference (NPD). In this technique, cystic fibrosis transmembrane conductance regulator (CFTR) and the epithelial sodium channel (ENaC) function are monitored by the change in voltage across the nasal epithelium after the superfusion of solutions that modify ion channel activity. This is enabled by the measurement of the potential difference between the subcutaneous compartment and the airway epithelium in the nostril, utilizing a catheter in contact with the inferior nasal turbinate.
The test allows the measurement of the stable baseline voltage and the successive net voltage changes after perfusion of 100 &#181;M amiloride, an inhibitor of Na+ reabsorption in Ringer&#39;s solution; a chloride-free solution containing amiloride to drive chloride secretion and 10 &#181;M isoproterenol in a chloride-free solution with amiloride to stimulate the cyclic adenosine monophosphate (cAMP)-dependent chloride conductance related to CFTR.
This technique has the advantage of demonstrating the electrophysiological properties of two key components establishing the hydration of the airway surface liquid of the respiratory epithelium, ENaC, and CFTR. Therefore, it is a useful research tool for phase 2 and proof of concept trials of agents that target CFTR and ENaC activity for the treatment of cystic fibrosis (CF) lung disease. It is also a key follow-up procedure to establish CFTR dysfunction when genetic testing and sweat testing are equivocal. Unlike sweat chloride, the test is relatively more time consuming and costly. It also requires operator training and expertise to conduct the test effectively. Inter- and intra-subject variability has been reported in this technique especially in young or uncooperative subjects. To assist with this concern, interpretation has been improved through a recently validated algorithm.

Standardized Measurement of Nasal Membrane Transepithelial Potential Difference NPD

Here, we present a standardized protocol to measure the nasal potential difference (NPD). Cystic fibrosis transmembrane conductance regulator (CFTR) and epithelial sodium channel (ENaC) function are evaluated by the change in the voltage across the nasal epithelium after superfusion of solutions that modify ion channel activity, providing an outcome measure.

We describe a standardized measurement of nasal potential difference (NPD). In this technique, cystic fibrosis transmembrane conductance regulator (CFTR) ...

Generation of Human Nasal Epithelial Cell Spheroids for Individualized Cystic Fibrosis Transmembrane Conductance Regulator Study

While the introduction of Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) modulator drugs has revolutionized care in Cystic Fibrosis (CF), the genotype-directed therapy model currently in use has several limitations. First, rare or understudied mutation groups are excluded from definitive clinical trials. Moreover, as additional modulator drugs enter the market, it will become difficult to optimize the modulator choices for an individual subject. Both of these issues are addressed with the use of patient-derived, individualized preclinical model systems of CFTR function and modulation. Human nasal epithelial cells (HNEs) are an easily accessible source of respiratory tissue for such a model. Herein, we describe the generation of a three-dimensional spheroid model of CFTR function and modulation using primary HNEs. HNEs are isolated from subjects in a minimally invasive fashion, expanded in conditional reprogramming conditions, and seeded into the spheroid culture. Within 2 weeks of seeding, spheroid cultures generate HNE spheroids that can be stimulated with 3',5'-cyclic adenosine monophosphate (cAMP)-generating agonists to activate CFTR function. Spheroid swelling is then quantified as a proxy of CFTR activity. HNE spheroids capitalize on the minimally invasive, yet respiratory origin of nasal cells to generate an accessible, personalized model relevant to an epithelium reflecting disease morbidity and mortality. Compared to the air-liquid interface HNE cultures, spheroids are relatively quick to mature, which reduces the overall contamination rate. In its current form, the model is limited by low throughput, though this is offset by the relative ease of tissue acquisition. HNE spheroids can be used to reliably quantify and characterize CFTR activity at the individual level. An ongoing study to tie this quantification to in vivo drug response will determine if HNE spheroids are a true preclinical predictor of patient response to CFTR modulation.

Here we describe a method to generate three-dimensional spheroid cultures of human nasal epithelial cells. Spheroids are then stimulated to drive Cystic Fibrosis Transmembrane Conductance Regulator (CFTR)-dependent ion and fluid secretion, quantifying the change in the spheroid luminal size as a proxy for CFTR function.

While the introduction of Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) modulator drugs has revolutionized care in Cystic Fibrosis (CF), the ...

Quantitative Micro-CT Analysis of Aortopathy in a Mouse Model of &#946;-aminopropionitrile-induced Aortic Aneurysm and Dissection

Aortic aneurysm and dissection is associated with significant morbidity and mortality in the population and can be highly lethal. While animal models of aortic disease exist, in vivo imaging of the vasculature has been limited. In recent years, micro-computerized tomography (micro-CT) has emerged as a preferred modality for imaging both large and small vessels both in vivo and ex vivo. In conjunction with a method of vascular casting, we have successfully used micro-CT to characterize the frequency and distribution of aortic pathology in &#946;-aminopropionitrile-treated C57/Bl6 mice. Technical limitations of this method include variations in the quality of the perfusion introduced by poor animal preparation, the application of proper methodologies for vessel size quantification, and the non-survivability of this procedure. This article details a methodology for the intravascular perfusion of a lead-based radiopaque silicone rubber for the quantitative characterization of aortopathy in a mouse model of aneurysm and dissection. In addition to visualizing aortic pathology, this method may be used for examining other vascular beds in vivo or vascular beds removed post-mortem.

Quantitative Micro-CT Analysis of Aortopathy in a Mouse Model of &amp;#946;-aminopropionitrile-induced Aortic Aneurysm and Dissection

This article describes a detailed methodology of using a radiopaque lead-based silicone rubber to perfuse the murine vasculature for aortic diameter quantification in a mouse model of aortic aneurysm and dissection.

Aortic aneurysm and dissection is associated with significant morbidity and mortality in the population and can be highly lethal. While animal models of ...

Design and Development of a Model to Study the Effect of Supplemental Oxygen on the Cystic Fibrosis Airway Microbiome

Airway microbial communities are thought to play an important role in the progression of cystic fibrosis (CF) and other chronic pulmonary diseases. Microbes have traditionally been classified based on their ability to use or tolerate oxygen. Supplemental oxygen is a common medical therapy administered to people with cystic fibrosis (pwCF); however, existing studies on oxygen and the airway microbiome have focused on how hypoxia (low oxygen) rather than hyperoxia (high oxygen) affects the predominantly aerobic and facultative anaerobic lung microbial communities. To address this critical knowledge gap, this protocol was developed using an artificial sputum medium that mimics the composition of sputum from pwCF. The use of filter sterilization, which yields a transparent medium, allows optical methods to follow the growth of single-celled microbes in suspension cultures. To create hyperoxic conditions, this model system takes advantage of established anaerobic culturing techniques to study hyperoxic conditions; instead of removing oxygen, oxygen is added to cultures by daily sparging of serum bottles with a mixture of compressed oxygen and air. Sputum from 50 pwCF underwent daily sparging for a 72-h period to verify the ability of this model to maintain differential oxygen conditions. Shotgun metagenomic sequencing was performed on cultured and uncultured sputum samples from 11 pwCF to verify the ability of this medium to support the growth of commensal and pathogenic microbes commonly found in cystic fibrosis sputum. Growth curves were obtained from 112 isolates obtained from pwCF to verify the ability of this artificial sputum medium to support the growth of common cystic fibrosis pathogens. We find that this model can culture a wide variety of pathogens and commensals in CF sputum, recovers a community highly similar to uncultured sputum under normoxic conditions, and creates different culture phenotypes under varying oxygen conditions. This new approach might lead to a better understanding of unanticipated effects induced by the use of oxygen in pwCF on airway microbial communities and common respiratory pathogens.

The goal of this protocol is to develop a model system for the effect of hyperoxia on cystic fibrosis airway microbial communities. Artificial sputum medium emulates the composition of sputum, and hyperoxic culture conditions model the effects of supplemental oxygen on lung microbial communities.

Airway microbial communities are thought to play an important role in the progression of cystic fibrosis (CF) and other chronic pulmonary diseases. ...

Culture and Imaging of Human Nasal Epithelial Organoids

Individualized therapy for cystic fibrosis (CF) patients can be achieved with an in vitro disease model to understand baseline Cystic Fibrosis Transmembrane conductance Regulator (CFTR) activity and restoration from small molecule compounds. Our group recently focused on establishing a well-differentiated organoid model directly derived from primary human nasal epithelial cells (HNE). Histology of sectioned organoids, whole-mount immunofluorescent staining, and imaging (using confocal microscopy, immunofluorescent microscopy, and bright field) are essential to characterize organoids and confirm epithelial differentiation in preparation for functional assays. Furthermore, HNE organoids produce lumens of varying sizes that correlate with CFTR activity, distinguishing between CF and non-CF organoids. In this manuscript, the methodology for culturing HNE organoids are described in detail, focusing on the assessment of differentiation using the imaging modalities, including the measurement of baseline lumen area (a method of CFTR activity measurement in organoids that any laboratory with a microscope can employ) as well as the developed automated approach to a functional assay (which requires more specialized equipment).

A detailed protocol is presented here to describe an in vitro organoid model from human nasal epithelial cells. The protocol has options for measurements requiring standard laboratory equipment, with additional possibilities for specialized equipment and software.