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Bierlaagh MC, Ramalho AS, Silva IAL, Vonk AM, van den Bor RM, van Mourik P, Pott J, Suen SWF, Boj SF, Vries RGJ, Lammertyn E, Vermeulen F, Amaral MD, de Boeck K, van der Ent CK, Beekman JM. Repeatability and reproducibility of the Forskolin-induced swelling (FIS) assay on intestinal organoids from people with Cystic Fibrosis. J Cyst Fibros 2024; 23:693-702. [PMID: 38749892 DOI: 10.1016/j.jcf.2024.04.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 04/05/2024] [Accepted: 04/26/2024] [Indexed: 08/31/2024]
Abstract
BACKGROUND The forskolin-induced swelling (FIS) assay measures CFTR function on patient-derived intestinal organoids (PDIOs) and may guide treatment selection for individuals with Cystic Fibrosis (CF). The aim of this study is to demonstrate the repeatability and reproducibility of the FIS assay following a detailed Standard Operating Procedure (SOP), thus advancing the validation of the assay for precision medicine (theranostic) applications. METHODS Over a 2-year period, FIS responses to CFTR modulators were measured in four European labs. PDIOs from six subjects with CF carrying different CFTR genotypes were used to assess the repeatability and reproducibility across the dynamic range of the assay. RESULTS Technical, intra-assay repeatability was high (Lin's concordance correlation coefficient (CCC) 0.95-0.98). Experimental, within-subject repeatability was also high within each lab (CCCs all >0.9). Longer-term repeatability (>1 year) showed more variability (CCCs from 0.67 to 0.95). The reproducibility between labs was also high (CCC ranging from 0.92 to 0.97). Exploratory analysis also found that between-lab percentage of agreement of dichotomized CFTR modulator outcomes for predefined FIS thresholds ranged between 78 and 100 %. CONCLUSIONS The observed repeatability and reproducibility of the FIS assay within and across different labs is high and support the use of FIS as biomarker of CFTR function in the presence or absence of CFTR modulators.
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Affiliation(s)
- Marlou C Bierlaagh
- Dept. of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands; Regenerative Medicine Center Utrecht, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | | | - Iris A L Silva
- BioISI- Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Lisboa, Portugal
| | - Annelotte M Vonk
- Dept. of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands; Regenerative Medicine Center Utrecht, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Rutger M van den Bor
- Dept. of Data Science and Biostatistics, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Peter van Mourik
- Dept. of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands; Regenerative Medicine Center Utrecht, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Johanna Pott
- HUB Organoids B.V. (HUB), Utrecht, The Netherlands
| | - Sylvia W F Suen
- Dept. of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands; Regenerative Medicine Center Utrecht, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Sylvia F Boj
- HUB Organoids B.V. (HUB), Utrecht, The Netherlands
| | | | - Elise Lammertyn
- Cystic Fibrosis Europe & the Belgian Cystic Fibrosis Association, Brussels, Belgium
| | | | - Margarida D Amaral
- BioISI- Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Lisboa, Portugal
| | - Kris de Boeck
- KULeuven, Dept. of Development and Regeneration, Leuven, Belgium
| | - Cornelis K van der Ent
- Regenerative Medicine Center Utrecht, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Jeffrey M Beekman
- Dept. of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands; Regenerative Medicine Center Utrecht, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands; Centre for Living Technologies, Alliance Eindhoven University of Technology, Wageningen University & Research, Utrecht University and University Medical Center Utrecht (EWUU), Utrecht, The Netherlands.
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2
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Angyal D, Kleinfelder K, Ciciriello F, Groeneweg TA, De Marchi G, de Pretis N, Bernardoni L, Rodella L, Tomba F, De Angelis P, Surace C, Pintani E, Alghisi F, de Jonge HR, Melotti P, Sorio C, Lucidi V, Bijvelds MJC, Frulloni L. CFTR function is impaired in a subset of patients with pancreatitis carrying rare CFTR variants. Pancreatology 2024; 24:394-403. [PMID: 38493004 DOI: 10.1016/j.pan.2024.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 03/07/2024] [Accepted: 03/08/2024] [Indexed: 03/18/2024]
Abstract
BACKGROUND Many affected by pancreatitis harbor rare variants of the cystic fibrosis (CF) gene, CFTR, which encodes an epithelial chloride/bicarbonate channel. We investigated CFTR function and the effect of CFTR modulator drugs in pancreatitis patients carrying CFTR variants. METHODS Next-generation sequencing was performed to identify CFTR variants. Sweat tests and nasal potential difference (NPD) assays were performed to assess CFTR function in vivo. Intestinal current measurement (ICM) was performed on rectal biopsies. Patient-derived intestinal epithelial monolayers were used to evaluate chloride and bicarbonate transport and the effects of a CFTR modulator combination: elexacaftor, tezacaftor and ivacaftor (ETI). RESULTS Of 32 pancreatitis patients carrying CFTR variants, three had CF-causing mutations on both alleles and yielded CF-typical sweat test, NPD and ICM results. Fourteen subjects showed a more modest elevation in sweat chloride levels, including three that were provisionally diagnosed with CF. ICM indicated impaired CFTR function in nine out of 17 non-CF subjects tested. This group of nine included five carrying a wild type CFTR allele. In epithelial monolayers, a reduction in CFTR-dependent chloride transport was found in six out of 14 subjects tested, whereas bicarbonate secretion was reduced in only one individual. In epithelial monolayers of four of these six subjects, ETI improved CFTR function. CONCLUSIONS CFTR function is impaired in a subset of pancreatitis patients carrying CFTR variants. Mutations outside the CFTR locus may contribute to the anion transport defect. Bioassays on patient-derived intestinal tissue and organoids can be used to detect such defects and to assess the effect of CFTR modulators.
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Affiliation(s)
- Dora Angyal
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center, P.O. Box 2040, 3000, CA, Rotterdam, the Netherlands
| | - Karina Kleinfelder
- Department of Medicine, University of Verona, Division of General Pathology, Verona, Italy
| | - Fabiana Ciciriello
- Cystic Fibrosis Unit, Bambino Gesù Children's Hospital, IRCCS, Piazza di Sant'Onofrio 4, 00165, Rome, Italy
| | - Tessa A Groeneweg
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center, P.O. Box 2040, 3000, CA, Rotterdam, the Netherlands
| | - Giulia De Marchi
- Gastroenterology Unit, Department of Medicine, Borgo Roma Hospital, Piazzale L.A. Scuro 10, 37134, Verona, Italy
| | - Nicolò de Pretis
- Gastroenterology Unit, Department of Medicine, Borgo Roma Hospital, Piazzale L.A. Scuro 10, 37134, Verona, Italy
| | - Laura Bernardoni
- Gastroenterology Unit, Department of Medicine, Borgo Roma Hospital, Piazzale L.A. Scuro 10, 37134, Verona, Italy
| | - Luca Rodella
- Endoscopy Surgery Unit, Azienda Ospedaliera Universitaria Integrata Verona, 37126, Verona, Italy
| | - Francesco Tomba
- Endoscopy Surgery Unit, Azienda Ospedaliera Universitaria Integrata Verona, 37126, Verona, Italy
| | - Paola De Angelis
- Digestive Endoscopy and Surgery Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Cecilia Surace
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Viale di San Paolo 15, 00146, Rome, Italy
| | - Emily Pintani
- Cystic Fibrosis Centre, Azienda Ospedaliera Universitaria Integrata Verona, Verona, Italy
| | - Federico Alghisi
- Cystic Fibrosis Unit, Bambino Gesù Children's Hospital, IRCCS, Piazza di Sant'Onofrio 4, 00165, Rome, Italy
| | - Hugo R de Jonge
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center, P.O. Box 2040, 3000, CA, Rotterdam, the Netherlands
| | - Paola Melotti
- Cystic Fibrosis Centre, Azienda Ospedaliera Universitaria Integrata Verona, Verona, Italy
| | - Claudio Sorio
- Department of Medicine, University of Verona, Division of General Pathology, Verona, Italy
| | - Vincenzina Lucidi
- Cystic Fibrosis Unit, Bambino Gesù Children's Hospital, IRCCS, Piazza di Sant'Onofrio 4, 00165, Rome, Italy
| | - Marcel J C Bijvelds
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center, P.O. Box 2040, 3000, CA, Rotterdam, the Netherlands.
| | - Luca Frulloni
- Gastroenterology Unit, Department of Medicine, Borgo Roma Hospital, Piazzale L.A. Scuro 10, 37134, Verona, Italy
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3
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Furstova E, Drevinek P, Novotna S, Libik M, Benesova K, Borek-Dohalska L, Sakmarova K, Modrak M, Macek M, Dousova T. Precision medicine in cystic fibrosis: predictive role of forskolin-induced swelling assay. Eur Respir J 2024; 63:2400156. [PMID: 38485147 DOI: 10.1183/13993003.00156-2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 03/06/2024] [Indexed: 04/20/2024]
Affiliation(s)
- Eva Furstova
- Department of Paediatrics, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Pavel Drevinek
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Stepanka Novotna
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Malgorzata Libik
- Department of Biology and Medical Genetics, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Klara Benesova
- Department of Clinical Psychology, Motol University Hospital, Prague, Czech Republic
- Department of Neurology and Centre for Clinical Neuroscience, 1st Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Lucie Borek-Dohalska
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Kristina Sakmarova
- Department of Bioinformatics, 2nd Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Martin Modrak
- Department of Bioinformatics, 2nd Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Milan Macek
- Department of Biology and Medical Genetics, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Tereza Dousova
- Department of Paediatrics, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
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4
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Lefferts JW, Kroes S, Smith MB, Niemöller PJ, Nieuwenhuijze NDA, Sonneveld van Kooten HN, van der Ent CK, Beekman JM, van Beuningen SFB. OrgaSegment: deep-learning based organoid segmentation to quantify CFTR dependent fluid secretion. Commun Biol 2024; 7:319. [PMID: 38480810 PMCID: PMC10937908 DOI: 10.1038/s42003-024-05966-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 02/23/2024] [Indexed: 03/17/2024] Open
Abstract
Epithelial ion and fluid transport studies in patient-derived organoids (PDOs) are increasingly being used for preclinical studies, drug development and precision medicine applications. Epithelial fluid transport properties in PDOs can be measured through visual changes in organoid (lumen) size. Such organoid phenotypes have been highly instrumental for the studying of diseases, including cystic fibrosis (CF), which is characterized by genetic mutations of the CF transmembrane conductance regulator (CFTR) ion channel. Here we present OrgaSegment, a MASK-RCNN based deep-learning segmentation model allowing for the segmentation of individual intestinal PDO structures from bright-field images. OrgaSegment recognizes spherical structures in addition to the oddly-shaped organoids that are a hallmark of CF organoids and can be used in organoid swelling assays, including the new drug-induced swelling assay that we show here. OrgaSegment enabled easy quantification of organoid swelling and could discriminate between organoids with different CFTR mutations, as well as measure responses to CFTR modulating drugs. The easy-to-apply label-free segmentation tool can help to study CFTR-based fluid secretion and possibly other epithelial ion transport mechanisms in organoids.
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Affiliation(s)
- Juliet W Lefferts
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA, Utrecht, The Netherlands
- Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT, Utrecht, The Netherlands
| | - Suzanne Kroes
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA, Utrecht, The Netherlands
- Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT, Utrecht, The Netherlands
| | - Matthew B Smith
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA, Utrecht, The Netherlands
- Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT, Utrecht, The Netherlands
- Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, 3584 CB, Utrecht, The Netherlands
| | - Paul J Niemöller
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA, Utrecht, The Netherlands
- Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT, Utrecht, The Netherlands
| | - Natascha D A Nieuwenhuijze
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA, Utrecht, The Netherlands
- Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT, Utrecht, The Netherlands
- Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, 3584 CB, Utrecht, The Netherlands
| | - Heleen N Sonneveld van Kooten
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA, Utrecht, The Netherlands
- Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT, Utrecht, The Netherlands
- Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, 3584 CB, Utrecht, The Netherlands
| | - Cornelis K van der Ent
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA, Utrecht, The Netherlands
| | - Jeffrey M Beekman
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA, Utrecht, The Netherlands.
- Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT, Utrecht, The Netherlands.
- Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, 3584 CB, Utrecht, The Netherlands.
| | - Sam F B van Beuningen
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA, Utrecht, The Netherlands.
- Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT, Utrecht, The Netherlands.
- Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, 3584 CB, Utrecht, The Netherlands.
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5
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Bacalhau M, Camargo M, Lopes-Pacheco M. Laboratory Tools to Predict CFTR Modulator Therapy Effectiveness and to Monitor Disease Severity in Cystic Fibrosis. J Pers Med 2024; 14:93. [PMID: 38248793 PMCID: PMC10820563 DOI: 10.3390/jpm14010093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 12/28/2023] [Accepted: 01/11/2024] [Indexed: 01/23/2024] Open
Abstract
The implementation of cystic fibrosis (CF) transmembrane conductance regulator (CFTR) modulator drugs into clinical practice has been attaining remarkable therapeutic outcomes for CF, a life-threatening autosomal recessive genetic disease. However, there is elevated CFTR allelic heterogeneity, and various individuals carrying (ultra)rare CF genotypes remain without any approved modulator therapy. Novel translational model systems based on individuals' own cells/tissue are now available and can be used to interrogate in vitro CFTR modulator responses and establish correlations of these assessments with clinical features, aiming to provide prediction of therapeutic effectiveness. Furthermore, because CF is a progressive disease, assessment of biomarkers in routine care is fundamental in monitoring treatment effectiveness and disease severity. In the first part of this review, we aimed to focus on the utility of individual-derived in vitro models (such as bronchial/nasal epithelial cells and airway/intestinal organoids) to identify potential responders and expand personalized CF care. Thereafter, we discussed the usage of CF inflammatory biomarkers derived from blood, bronchoalveolar lavage fluid, and sputum to routinely monitor treatment effectiveness and disease progression. Finally, we summarized the progress in investigating extracellular vesicles as a robust and reliable source of biomarkers and the identification of microRNAs related to CFTR regulation and CF inflammation as novel biomarkers, which may provide valuable information for disease prognosis.
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Affiliation(s)
- Mafalda Bacalhau
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal;
| | - Mariana Camargo
- Department of Surgery, Division of Urology, Sao Paulo Federal University, Sao Paulo 04039-060, SP, Brazil
| | - Miquéias Lopes-Pacheco
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal;
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Spelier S, de Winter-de Groot K, Keijzer-Nieuwenhuijze N, Liem Y, van der Ent K, Beekman J, Kamphuis LS. Organoid-guided synergistic treatment of minimal function CFTR mutations with CFTR modulators, roflumilast and simvastatin: a personalised approach. Eur Respir J 2024; 63:2300770. [PMID: 37857424 PMCID: PMC10809127 DOI: 10.1183/13993003.00770-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 09/23/2023] [Indexed: 10/21/2023]
Abstract
Highly effective cystic fibrosis transmembrane conductance regulator (CFTR) protein-targeting modulator therapies (HEMTs) facilitate strong clinical improvements in a large proportion of people with cystic fibrosis (CF) [1, 2]. More specifically, the European Medicines Agency and US Food and Drug Administration (FDA) approved combination of the CFTR modulators elexacaftor/tezacaftor/ivacaftor (ETI) for people with CF with at least one F508del allele, while the FDA extended eligibility for several rare genotypes [3, 4]. However, 10–15% of those with CF carry CFTR mutations that are unresponsive to HEMTs as monotherapy [1]; furthermore, some suffer from HEMT intolerance, and HEMTs are sometimes not accessible due to practical challenges, such as lack of access due to high costs or legislation and approval challenges. Consequently, the focus in the CF research field has shifted towards filling the unmet clinical need for the people with CF that will not benefit from HEMTs. This study describes how preclinical research has guided a successful personalised clinical treatment regimen in a person with minimal function CFTR, upon a synergistic treatment regimen consisting of CFTR modulators, simvastatin and roflumilast https://bit.ly/3rDTHZL
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Affiliation(s)
- Sacha Spelier
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, The Netherlands
- Regenerative Medicine Utrecht, University Medical Center, Utrecht University, Utrecht, The Netherlands
| | - Karin de Winter-de Groot
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, The Netherlands
| | - Natascha Keijzer-Nieuwenhuijze
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, The Netherlands
- Regenerative Medicine Utrecht, University Medical Center, Utrecht University, Utrecht, The Netherlands
| | - Yves Liem
- Department of Clinical Pharmacy, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, The Netherlands
| | - Kors van der Ent
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, The Netherlands
| | - Jeffrey Beekman
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, The Netherlands
- Regenerative Medicine Utrecht, University Medical Center, Utrecht University, Utrecht, The Netherlands
- J. Beekman and L.S. Kamphuis contributed equally to this article as lead authors and supervised the work
| | - Lieke S Kamphuis
- Department of Respiratory Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
- J. Beekman and L.S. Kamphuis contributed equally to this article as lead authors and supervised the work
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7
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Velez Lopez A, Waddell A, Antonacci S, Castillo D, Santucci N, Ollberding NJ, Eshleman EM, Denson LA, Alenghat T. Microbiota-derived butyrate dampens linaclotide stimulation of the guanylate cyclase C pathway in patient-derived colonoids. Neurogastroenterol Motil 2023; 35:e14681. [PMID: 37736865 PMCID: PMC10841278 DOI: 10.1111/nmo.14681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 06/25/2023] [Accepted: 08/29/2023] [Indexed: 09/23/2023]
Abstract
BACKGROUND & AIMS Disorders of gut-brain interaction (DGBI) are complex conditions that result in decreased quality of life and a significant cost burden. Linaclotide, a guanylin cyclase C (GCC) receptor agonist, is approved as a DGBI treatment. However, its efficacy has been limited and variable across DGBI patients. Microbiota and metabolomic alterations are noted in DGBI patients, provoking the hypothesis that the microbiota may impact the GCC response to current therapeutics. METHODS Human-derived intestinal organoids were grown from pediatric DGBI, non-IBD colon biopsies (colonoids). Colonoids were treated with 250 nM linaclotide and assayed for cGMP to develop a model of GCC activity. Butyrate was administered to human colonoids overnight at a concentration of 1 mM. Colonoid lysates were analyzed for cGMP levels by ELISA. For the swelling assay, colonoids were photographed pre- and post-treatment and volume was measured using ImageJ. Principal coordinate analyses (PCoA) were performed on the Bray-Curtis dissimilarity and Jaccard distance to assess differences in the community composition of short-chain fatty acid (SCFA) producing microbial species in the intestinal microbiota from pediatric patients with IBS and healthy control samples. KEY RESULTS Linaclotide treatment induced a significant increase in [cGMP] and swelling of patient-derived colonoids, demonstrating a human in vitro model of linaclotide-induced GCC activation. Shotgun sequencing analysis of pediatric IBS patients and healthy controls showed differences in the composition of commensal SCFA-producing bacteria. Butyrate exposure significantly dampened linaclotide-induced cGMP levels and swelling in patient-derived colonoids. CONCLUSIONS & INFERENCES Patient-derived colonoids demonstrate that microbiota-derived butyrate can dampen human colonic responses to linaclotide. This study supports incorporation of microbiota and metabolomic assessment to improve precision medicine for DGBI patients.
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Affiliation(s)
- Alejandro Velez Lopez
- Division of Gastroenterology, Hepatology, and Nutrition, Cincinnati Children’s Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH USA
| | - Amanda Waddell
- Division of Immunobiology and Center for Inflammation and Tolerance, Cincinnati Children’s Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH USA
| | - Simona Antonacci
- Division of Immunobiology and Center for Inflammation and Tolerance, Cincinnati Children’s Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH USA
| | - Daniel Castillo
- Division of Gastroenterology, Hepatology, and Nutrition, Cincinnati Children’s Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH USA
| | - Neha Santucci
- Division of Gastroenterology, Hepatology, and Nutrition, Cincinnati Children’s Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH USA
| | - Nicholas J. Ollberding
- Division of Biostatistics and Epidemiology, Cincinnati Children’s Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH USA
| | - Emily M. Eshleman
- Division of Immunobiology and Center for Inflammation and Tolerance, Cincinnati Children’s Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH USA
| | - Lee A. Denson
- Division of Gastroenterology, Hepatology, and Nutrition, Cincinnati Children’s Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH USA
| | - Theresa Alenghat
- Division of Immunobiology and Center for Inflammation and Tolerance, Cincinnati Children’s Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH USA
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8
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Naderi-Meshkin H, Cornelius VA, Eleftheriadou M, Potel KN, Setyaningsih WAW, Margariti A. Vascular organoids: unveiling advantages, applications, challenges, and disease modelling strategies. Stem Cell Res Ther 2023; 14:292. [PMID: 37817281 PMCID: PMC10566155 DOI: 10.1186/s13287-023-03521-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 09/26/2023] [Indexed: 10/12/2023] Open
Abstract
Understanding mechanisms and manifestations of cardiovascular risk factors, including diabetes, on vascular cells such as endothelial cells, pericytes, and vascular smooth muscle cells, remains elusive partly due to the lack of appropriate disease models. Therefore, here we explore different aspects for the development of advanced 3D in vitro disease models that recapitulate human blood vessel complications using patient-derived induced pluripotent stem cells, which retain the epigenetic, transcriptomic, and metabolic memory of their patient-of-origin. In this review, we highlight the superiority of 3D blood vessel organoids over conventional 2D cell culture systems for vascular research. We outline the key benefits of vascular organoids in both health and disease contexts and discuss the current challenges associated with organoid technology, providing potential solutions. Furthermore, we discuss the diverse applications of vascular organoids and emphasize the importance of incorporating all relevant cellular components in a 3D model to accurately recapitulate vascular pathophysiology. As a specific example, we present a comprehensive overview of diabetic vasculopathy, demonstrating how the interplay of different vascular cell types is critical for the successful modelling of complex disease processes in vitro. Finally, we propose a strategy for creating an organ-specific diabetic vasculopathy model, serving as a valuable template for modelling other types of vascular complications in cardiovascular diseases by incorporating disease-specific stressors and organotypic modifications.
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Affiliation(s)
- Hojjat Naderi-Meshkin
- The Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, UK
| | - Victoria A Cornelius
- The Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, UK
| | - Magdalini Eleftheriadou
- The Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, UK
| | - Koray Niels Potel
- The Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, UK
| | - Wiwit Ananda Wahyu Setyaningsih
- The Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, UK
- Department of Anatomy, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Sleman, D.I. Yogyakarta, 55281, Indonesia
| | - Andriana Margariti
- The Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, UK.
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Beri P, Woo YJ, Schierenbeck K, Chen K, Barnes SW, Ross O, Krutil D, Quackenbush D, Fang B, Walker J, Barnes W, Toyama EQ. A high-throughput cigarette smoke-treated bronchosphere model for disease-relevant phenotypic compound screening. PLoS One 2023; 18:e0287809. [PMID: 37384771 PMCID: PMC10310037 DOI: 10.1371/journal.pone.0287809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 06/13/2023] [Indexed: 07/01/2023] Open
Abstract
Cigarette smoking (CS) is the leading cause of COPD, and identifying the pathways that are driving pathogenesis in the airway due to CS exposure can aid in the discovery of novel therapies for COPD. An additional barrier to the identification of key pathways that are involved in the CS-induced pathogenesis is the difficulty in building relevant and high throughput models that can recapitulate the phenotypic and transcriptomic changes associated with CS exposure. To identify these drivers, we have developed a cigarette smoke extract (CSE)-treated bronchosphere assay in 384-well plate format that exhibits CSE-induced decreases in size and increase in luminal secretion of MUC5AC. Transcriptomic changes in CSE-treated bronchospheres resemble changes that occur in human smokers both with and without COPD compared to healthy groups, indicating that this model can capture human smoking signature. To identify new targets, we ran a small molecule compound deck screening with diversity in target mechanisms of action and identified hit compounds that attenuated CSE induced changes, either decreasing spheroid size or increasing secreted mucus. This work provides insight into the utility of this bronchopshere model to examine human respiratory disease impacted by CSE exposure and the ability to screen for therapeutics to reverse the pathogenic changes caused by CSE.
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Affiliation(s)
- Pranjali Beri
- Novartis Institutes for Biomedical Research, San Diego, California, United States of America
| | - Young Jae Woo
- Novartis Institutes for Biomedical Research, San Diego, California, United States of America
| | - Katie Schierenbeck
- Novartis Institutes for Biomedical Research, San Diego, California, United States of America
| | - Kaisheng Chen
- Novartis Institutes for Biomedical Research, San Diego, California, United States of America
| | - S. Whitney Barnes
- Novartis Institutes for Biomedical Research, San Diego, California, United States of America
| | - Olivia Ross
- Novartis Institutes for Biomedical Research, San Diego, California, United States of America
| | - Douglas Krutil
- Novartis Institutes for Biomedical Research, San Diego, California, United States of America
| | - Doug Quackenbush
- Novartis Institutes for Biomedical Research, San Diego, California, United States of America
| | - Bin Fang
- Novartis Institutes for Biomedical Research, San Diego, California, United States of America
| | - John Walker
- Novartis Institutes for Biomedical Research, San Diego, California, United States of America
| | - William Barnes
- Novartis Institutes for Biomedical Research, San Diego, California, United States of America
| | - Erin Quan Toyama
- Novartis Institutes for Biomedical Research, San Diego, California, United States of America
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Barillaro M, Gonska T. Assessing accuracy of testing and diagnosis in cystic fibrosis. Expert Rev Respir Med 2023:1-13. [PMID: 37190981 DOI: 10.1080/17476348.2023.2213438] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Affiliation(s)
- Malina Barillaro
- Department of Physiology, University of Toronto, Toronto ON, Canada
- Translational Medicine, Research Institute, Hospital for Sick Children, Toronto, ON, Canada
| | - Tanja Gonska
- Translational Medicine, Research Institute, Hospital for Sick Children, Toronto, ON, Canada
- Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, University of Toronto, Toronto ON, Canada
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11
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de Poel E, Spelier S, Hagemeijer MC, van Mourik P, Suen SWF, Vonk AM, Brunsveld JE, Ithakisiou GN, Kruisselbrink E, Oppelaar H, Berkers G, de Winter de Groot KM, Heida-Michel S, Jans SR, van Panhuis H, Bakker M, van der Meer R, Roukema J, Dompeling E, Weersink EJM, Koppelman GH, Blaazer AR, Muijlwijk-Koezen JE, van der Ent CK, Beekman JM. FDA-approved drug screening in patient-derived organoids demonstrates potential of drug repurposing for rare cystic fibrosis genotypes. J Cyst Fibros 2023; 22:548-559. [PMID: 37147251 DOI: 10.1016/j.jcf.2023.03.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 01/06/2023] [Accepted: 03/03/2023] [Indexed: 05/07/2023]
Abstract
BACKGROUND Preclinical cell-based assays that recapitulate human disease play an important role in drug repurposing. We previously developed a functional forskolin induced swelling (FIS) assay using patient-derived intestinal organoids (PDIOs), allowing functional characterization of CFTR, the gene mutated in people with cystic fibrosis (pwCF). CFTR function-increasing pharmacotherapies have revolutionized treatment for approximately 85% of people with CF who carry the most prevalent F508del-CFTR mutation, but a large unmet need remains to identify new treatments for all pwCF. METHODS We used 76 PDIOs not homozygous for F508del-CFTR to test the efficacy of 1400 FDA-approved drugs on improving CFTR function, as measured in FIS assays. The most promising hits were verified in a secondary FIS screen. Based on the results of this secondary screen, we further investigated CFTR elevating function of PDE4 inhibitors and currently existing CFTR modulators. RESULTS In the primary screen, 30 hits were characterized that elevated CFTR function. In the secondary validation screen, 19 hits were confirmed and categorized in three main drug families: CFTR modulators, PDE4 inhibitors and tyrosine kinase inhibitors. We show that PDE4 inhibitors are potent CFTR function inducers in PDIOs where residual CFTR function is either present, or created by additional compound exposure. Additionally, upon CFTR modulator treatment we show rescue of CF genotypes that are currently not eligible for this therapy. CONCLUSION This study exemplifies the feasibility of high-throughput compound screening using PDIOs. We show the potential of repurposing drugs for pwCF carrying non-F508del genotypes that are currently not eligible for therapies. ONE-SENTENCE SUMMARY We screened 1400 FDA-approved drugs in CF patient-derived intestinal organoids using the previously established functional FIS assay, and show the potential of repurposing PDE4 inhibitors and CFTR modulators for rare CF genotypes.
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Affiliation(s)
- E de Poel
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, EA 3584, the Netherlands; Regenerative Medicine Utrecht, University Medical Center, Utrecht University, Utrecht, CT 3584, the Netherlands
| | - S Spelier
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, EA 3584, the Netherlands; Regenerative Medicine Utrecht, University Medical Center, Utrecht University, Utrecht, CT 3584, the Netherlands
| | - M C Hagemeijer
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, EA 3584, the Netherlands; Regenerative Medicine Utrecht, University Medical Center, Utrecht University, Utrecht, CT 3584, the Netherlands; Center for Lysosomal and Metabolic Diseases, Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, GD 3015, the Netherlands
| | - P van Mourik
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, EA 3584, the Netherlands
| | - S W F Suen
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, EA 3584, the Netherlands; Regenerative Medicine Utrecht, University Medical Center, Utrecht University, Utrecht, CT 3584, the Netherlands
| | - A M Vonk
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, EA 3584, the Netherlands; Regenerative Medicine Utrecht, University Medical Center, Utrecht University, Utrecht, CT 3584, the Netherlands
| | - J E Brunsveld
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, EA 3584, the Netherlands; Regenerative Medicine Utrecht, University Medical Center, Utrecht University, Utrecht, CT 3584, the Netherlands
| | - G N Ithakisiou
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, EA 3584, the Netherlands; Regenerative Medicine Utrecht, University Medical Center, Utrecht University, Utrecht, CT 3584, the Netherlands
| | - E Kruisselbrink
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, EA 3584, the Netherlands; Regenerative Medicine Utrecht, University Medical Center, Utrecht University, Utrecht, CT 3584, the Netherlands
| | - H Oppelaar
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, EA 3584, the Netherlands; Regenerative Medicine Utrecht, University Medical Center, Utrecht University, Utrecht, CT 3584, the Netherlands
| | - G Berkers
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, EA 3584, the Netherlands
| | - K M de Winter de Groot
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, EA 3584, the Netherlands
| | - S Heida-Michel
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, EA 3584, the Netherlands
| | - S R Jans
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, EA 3584, the Netherlands
| | - H van Panhuis
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, EA 3584, the Netherlands
| | - M Bakker
- Department of Pulmonology, Erasmus MC, University Medical Center, Rotterdam, GD 3015, the Netherlands
| | - R van der Meer
- Haga Teaching Hospital, The Hague, CH 2545, the Netherlands
| | - J Roukema
- Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, XZ 6525, the Netherlands
| | - E Dompeling
- Maastricht University Medical Center, Maastricht, HX 6229, the Netherlands
| | - E J M Weersink
- Amsterdam University Medical Center, location AMC, Amsterdam, AZ 1105, the Netherlands
| | - G H Koppelman
- University of Groningen, University Medical Center Groningen, Beatrix Children's Hospital, Department of Pediatric Pulmonology and Pediatric Allergology, Groningen, the Netherlands; University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, the Netherlands
| | - A R Blaazer
- Division of Medicinal Chemistry, Vrije Universiteit Amsterdam, Amsterdam, HZ 1081, the Netherlands
| | - J E Muijlwijk-Koezen
- Division of Medicinal Chemistry, Vrije Universiteit Amsterdam, Amsterdam, HZ 1081, the Netherlands
| | - C K van der Ent
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, EA 3584, the Netherlands
| | - J M Beekman
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, EA 3584, the Netherlands; Regenerative Medicine Utrecht, University Medical Center, Utrecht University, Utrecht, CT 3584, the Netherlands; Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, Princetonlaan 6, Utrecht, CB 3584, the Netherlands.
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12
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Spelier S, de Poel E, Ithakisiou GN, Suen SW, Hagemeijer MC, Muilwijk D, Vonk AM, Brunsveld JE, Kruisselbrink E, van der Ent CK, Beekman JM. High-throughput functional assay in cystic fibrosis patient-derived organoids allows drug repurposing. ERJ Open Res 2023; 9:00495-2022. [PMID: 36726369 PMCID: PMC9885274 DOI: 10.1183/23120541.00495-2022] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 10/27/2022] [Indexed: 12/24/2022] Open
Abstract
Background Cystic fibrosis (CF) is a rare hereditary disease caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Recent therapies enable effective restoration of CFTR function of the most common F508del CFTR mutation. This shifts the unmet clinical need towards people with rare CFTR mutations such as nonsense mutations, of which G542X and W1282X are most prevalent. CFTR function measurements in patient-derived cell-based assays played a critical role in preclinical drug development for CF and may play an important role to identify new drugs for people with rare CFTR mutations. Methods Here, we miniaturised the previously described forskolin-induced swelling (FIS) assay in intestinal organoids from a 96-well to a 384-well plate screening format. Using this novel assay, we tested CFTR increasing potential of a 1400-compound Food and Drug Administration (FDA)-approved drug library in organoids from donors with W1282X/W1282X CFTR nonsense mutations. Results The 384-well FIS assay demonstrated uniformity and robustness based on coefficient of variation and Z'-factor calculations. In the primary screen, CFTR induction was limited overall, yet interestingly, the top five compound combinations that increased CFTR function all contained at least one statin. In the secondary screen, we indeed verified that four out of the five statins (mevastatin, lovastatin, simvastatin and fluvastatin) increased CFTR function when combined with CFTR modulators. Statin-induced CFTR rescue was concentration-dependent and W1282X-specific. Conclusions Future studies should focus on elucidating genotype specificity and mode-of-action of statins in more detail. This study exemplifies proof of principle of large-scale compound screening in a functional assay using patient-derived organoids.
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Affiliation(s)
- Sacha Spelier
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, The Netherlands,Regenerative Medicine Utrecht, University Medical Center, Utrecht University, Utrecht, The Netherlands,These authors contributed equally to this work,Corresponding author: Sacha Spelier ()
| | - Eyleen de Poel
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, The Netherlands,Regenerative Medicine Utrecht, University Medical Center, Utrecht University, Utrecht, The Netherlands,These authors contributed equally to this work
| | - Georgia N. Ithakisiou
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, The Netherlands,Regenerative Medicine Utrecht, University Medical Center, Utrecht University, Utrecht, The Netherlands
| | - Sylvia W.F. Suen
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, The Netherlands,Regenerative Medicine Utrecht, University Medical Center, Utrecht University, Utrecht, The Netherlands
| | - Marne C. Hagemeijer
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, The Netherlands,Regenerative Medicine Utrecht, University Medical Center, Utrecht University, Utrecht, The Netherlands,Center for Lysosomal and Metabolic Diseases, Department of Clinical Genetics Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Danya Muilwijk
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, The Netherlands
| | - Annelotte M. Vonk
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, The Netherlands,Regenerative Medicine Utrecht, University Medical Center, Utrecht University, Utrecht, The Netherlands
| | - Jesse E. Brunsveld
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, The Netherlands,Regenerative Medicine Utrecht, University Medical Center, Utrecht University, Utrecht, The Netherlands
| | - Evelien Kruisselbrink
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, The Netherlands,Regenerative Medicine Utrecht, University Medical Center, Utrecht University, Utrecht, The Netherlands
| | - Cornelis K. van der Ent
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, The Netherlands
| | - Jeffrey M. Beekman
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, The Netherlands,Regenerative Medicine Utrecht, University Medical Center, Utrecht University, Utrecht, The Netherlands
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Novelli G, Spitalieri P, Murdocca M, Centanini E, Sangiuolo F. Organoid factory: The recent role of the human induced pluripotent stem cells (hiPSCs) in precision medicine. Front Cell Dev Biol 2023; 10:1059579. [PMID: 36699015 PMCID: PMC9869172 DOI: 10.3389/fcell.2022.1059579] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 12/22/2022] [Indexed: 01/11/2023] Open
Abstract
During the last decades, hiPSC-derived organoids have been extensively studied and used as in vitro models for several applications among which research studies. They can be considered as organ and tissue prototypes, especially for those difficult to obtain. Moreover, several diseases can be accurately modeled and studied. Hence, patient-derived organoids (PDOs) can be used to predict individual drug responses, thus paving the way toward personalized medicine. Lastly, by applying tissue engineering and 3D printing techniques, organoids could be used in the future to replace or regenerate damaged tissue. In this review, we will focus on hiPSC-derived 3D cultures and their ability to model human diseases with an in-depth analysis of gene editing applications, as well as tumor models. Furthermore, we will highlight the state-of-the-art of organoid facilities that around the world offer know-how and services. This is an increasing trend that shed the light on the need of bridging the publicand the private sector. Hence, in the context of drug discovery, Organoid Factories can offer biobanks of validated 3D organoid models that can be used in collaboration with pharmaceutical companies to speed up the drug screening process. Finally, we will discuss the limitations and the future development that will lead hiPSC-derived technology from bench to bedside, toward personalized medicine, such as maturity, organoid interconnections, costs, reproducibility and standardization, and ethics. hiPSC-derived organoid technology is now passing from a proof-of-principle to real applications in the clinic, also thanks to the applicability of techniques, such as CRISPR/Cas9 genome editing system, material engineering for the scaffolds, or microfluidic systems. The benefits will have a crucial role in the advance of both basic biological and translational research, particularly in the pharmacological field and drug development. In fact, in the near future, 3D organoids will guide the clinical decision-making process, having validated patient-specific drug screening platforms. This is particularly important in the context of rare genetic diseases or when testing cancer treatments that could in principle have severe side effects. Therefore, this technology has enabled the advancement of personalized medicine in a way never seen before.
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Affiliation(s)
- Giuseppe Novelli
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
- IRCCS Neuromed, Pozzilli, IS, Italy
- Department of Pharmacology, School of Medicine, University of Nevada, Reno, NV, United States
| | - Paola Spitalieri
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Michela Murdocca
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Eleonora Centanini
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, CS, Italy
| | - Federica Sangiuolo
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
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Organoid Technology and Its Role for Theratyping Applications in Cystic Fibrosis. CHILDREN (BASEL, SWITZERLAND) 2022; 10:children10010004. [PMID: 36670555 PMCID: PMC9856584 DOI: 10.3390/children10010004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/14/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
Abstract
Cystic fibrosis (CF) is a autosomal recessive, multisystemic disease caused by different mutations in the CFTR gene encoding CF transmembrane conductance regulator. Although symptom management is important to avoid complications, the approval of CFTR modulator drugs in the clinic has demonstrated significant improvements by targeting the primary molecular defect of CF and thereby preventing problems related to CFTR deficiency or dysfunction. CFTR modulator therapies have positively changed the patients' quality of life, especially for those who start their use at the onset of the disease. Due to early diagnosis with the implementation of newborn screening programs and considerable progress in the treatment options, nowadays pediatric mortality was dramatically reduced. In any case, the main obstacle to treat CF is to predict the drug response of patients due to genetic complexity and heterogeneity. Advances in 3D culture systems have led to the extrapolation of disease modeling and individual drug response in vitro by producing mini organs called "organoids" easily obtained from nasal and rectal mucosa biopsies. In this review, we focus primarily on patient-derived intestinal organoids used as in vitro model for CF disease. Organoids combine high-validity of outcomes with a high throughput, thus enabling CF disease classification, drug development and treatment optimization in a personalized manner.
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Guimbellot JS, Nichols DP, Brewington JJ. Novel Applications of Biomarkers and Personalized Medicine in Cystic Fibrosis. Clin Chest Med 2022; 43:617-630. [PMID: 36344070 DOI: 10.1016/j.ccm.2022.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
As routine care in cystic fibrosis (CF) becomes increasingly personalized, new opportunities to further focus care on the individual have emerged. These opportunities are increasingly filled through research in tools aiding drug selection, drug monitoring and titration, disease-relevant biomarkers, and evaluation of therapeutic benefits. Herein, we will discuss such research tools presently being translated into the clinic to improve the personalization of care in CF.
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Affiliation(s)
- Jennifer S Guimbellot
- Department of Pediatrics, Division of Pulmonary and Sleep Medicine, Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham; 1600 7th Avenue South, ACC 620, Birmingham, AL 35233, USA
| | - David P Nichols
- Department of Pediatrics, Division of Pulmonary Medicine, Seattle Children's Hospital, University of Washington School of Medicine, Building Cure, 1920 Terry Avenue, Office 4-209, Seattle, WA 98109, USA
| | - John J Brewington
- Department of Pediatrics, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH 45267, USA; Division of Pulmonary Medicine, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, MLC 2021, Cincinnati, OH 45229, USA.
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Berg P, Sorensen MV, Rousing AQ, Vebert Olesen H, Jensen-Fangel S, Jeppesen M, Leipziger J. Challenged Urine Bicarbonate Excretion as a Measure of Cystic Fibrosis Transmembrane Conductance Regulator Function in Cystic Fibrosis. Ann Intern Med 2022; 175:1543-1551. [PMID: 36315944 DOI: 10.7326/m22-1741] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND In cystic fibrosis (CF), renal base excretion is impaired. Accordingly, challenged urine bicarbonate excretion may be an in vivo biomarker of cystic fibrosis transmembrane conductance regulator (CFTR) function. OBJECTIVE To evaluate the association between challenged bicarbonate excretion and clinical characteristics at baseline, quantify the CFTR modulator drug elexacaftor/tezacaftor/ivacaftor-induced changes of challenged bicarbonate excretion after 6 months of treatment, and characterize the intraindividual variation in healthy adults. DESIGN Prospective observational study. SETTING Cystic fibrosis clinic, Aarhus University Hospital, Denmark. PATIENTS Fifty adult patients with CF starting CFTR modulator therapy with elexacaftor/tezacaftor/ivacaftor between May 2020 and June 2021. MEASUREMENTS Quantification of urine bicarbonate excretion after an acute oral sodium bicarbonate challenge before and 6 months after elexacaftor/tezacaftor/ivacaftor treatment. RESULTS At baseline, challenged urine bicarbonate excretion was associated with several CF disease characteristics. Bicarbonate excretion was higher in patients with residual function mutations. A higher bicarbonate excretion was associated with better lung function, pancreatic sufficiency, and lower relative risk for chronic pseudomonas infections. Elexacaftor/tezacaftor/ivacaftor treatment increased bicarbonate excretion by 3.9 mmol/3 h (95% CI, 1.6 to 6.1 mmol/3 h), reaching about 70% of that seen in healthy control participants. In healthy control participants, individual bicarbonate excretion at each visit correlated with the individual mean bicarbonate excretion. The median coefficient of variation was 31%. LIMITATION Single-center study without a placebo-controlled group. CONCLUSION Although further studies are needed to address the performance and sensitivity of this approach, this early-stage evaluation shows that challenged urine bicarbonate excretion may offer a new, simple, and safe quantification of CFTR function and the extent of its pharmacologic improvement. Elexacaftor/tezacaftor/ivacaftor partially restores renal CFTR function in patients with CF, likely resulting in decreased risk for electrolyte disorders and metabolic alkalosis. PRIMARY FUNDING SOURCE Innovation Fund Denmark.
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Affiliation(s)
- Peder Berg
- Department of Biomedicine, Aarhus University, Aarhus, Denmark (P.B., M.V.S., A.Q.R., J.L.)
| | - Mads V Sorensen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark (P.B., M.V.S., A.Q.R., J.L.)
| | - Amalie Quist Rousing
- Department of Biomedicine, Aarhus University, Aarhus, Denmark (P.B., M.V.S., A.Q.R., J.L.)
| | - Hanne Vebert Olesen
- Department of Pediatrics and Adolescent Medicine, Aarhus University Hospital, Aarhus, Denmark (H.V.O.)
| | - Søren Jensen-Fangel
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark (S.J., M.J.)
| | - Majbritt Jeppesen
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark (S.J., M.J.)
| | - Jens Leipziger
- Department of Biomedicine, Aarhus University, Aarhus, Denmark (P.B., M.V.S., A.Q.R., J.L.)
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Sermet-Gaudelus I, Girodon E, Vermeulen F, Solomon G, Melotti P, Graeber S, Bronsveld I, Rowe S, Wilschanski M, Tümmler B, Cutting G, Gonska T. ECFS standards of care on CFTR-related disorders: Diagnostic criteria of CFTR dysfunction. J Cyst Fibros 2022; 21:922-936. [DOI: 10.1016/j.jcf.2022.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 09/06/2022] [Accepted: 09/14/2022] [Indexed: 11/06/2022]
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Advances in Preclinical In Vitro Models for the Translation of Precision Medicine for Cystic Fibrosis. J Pers Med 2022; 12:jpm12081321. [PMID: 36013270 PMCID: PMC9409685 DOI: 10.3390/jpm12081321] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/12/2022] [Accepted: 08/16/2022] [Indexed: 11/19/2022] Open
Abstract
The development of preclinical in vitro models has provided significant progress to the studies of cystic fibrosis (CF), a frequently fatal monogenic disease caused by mutations in the gene encoding the CF transmembrane conductance regulator (CFTR) protein. Numerous cell lines were generated over the last 30 years and they have been instrumental not only in enhancing the understanding of CF pathological mechanisms but also in developing therapies targeting the underlying defects in CFTR mutations with further validation in patient-derived samples. Furthermore, recent advances toward precision medicine in CF have been made possible by optimizing protocols and establishing novel assays using human bronchial, nasal and rectal tissues, and by progressing from two-dimensional monocultures to more complex three-dimensional culture platforms. These models also enable to potentially predict clinical efficacy and responsiveness to CFTR modulator therapies at an individual level. In parallel, advanced systems, such as induced pluripotent stem cells and organ-on-a-chip, continue to be developed in order to more closely recapitulate human physiology for disease modeling and drug testing. In this review, we have highlighted novel and optimized cell models that are being used in CF research to develop novel CFTR-directed therapies (or alternative therapeutic interventions) and to expand the usage of existing modulator drugs to common and rare CF-causing mutations.
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19
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Muilwijk D, de Poel E, van Mourik P, Suen SWF, Vonk AM, Brunsveld JE, Kruisselbrink E, Oppelaar H, Hagemeijer MC, Berkers G, de Winter-de Groot KM, Heida-Michel S, Jans SR, van Panhuis H, van der Eerden MM, van der Meer R, Roukema J, Dompeling E, Weersink EJM, Koppelman GH, Vries R, Zomer-van Ommen DD, Eijkemans MJC, van der Ent CK, Beekman JM. Forskolin-induced Organoid Swelling is Associated with Long-term CF Disease Progression. Eur Respir J 2022; 60:13993003.00508-2021. [PMID: 35086832 PMCID: PMC9386333 DOI: 10.1183/13993003.00508-2021] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 12/23/2021] [Indexed: 11/30/2022]
Abstract
Rationale Cystic fibrosis (CF) is a monogenic life-shortening disease associated with highly variable individual disease progression which is difficult to predict. Here we assessed the association of forskolin-induced swelling (FIS) of patient-derived organoids with long-term CF disease progression in multiple organs and compared FIS with the golden standard biomarker sweat chloride concentration (SCC). Methods We retrieved 9-year longitudinal clinical data from the Dutch CF Registry of 173 people with mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Individual CFTR function was defined by FIS, measured as the relative size increase of intestinal organoids after stimulation with 0.8 µM forskolin, quantified as area under the curve (AUC). We used linear mixed-effect models and multivariable logistic regression to estimate the association of FIS with long-term forced expiratory volume in 1 s % predicted (FEV1pp) decline and development of pancreatic insufficiency, CF-related liver disease and diabetes. Within these models, FIS was compared with SCC. Results FIS was strongly associated with longitudinal changes of lung function, with an estimated difference in annual FEV1pp decline of 0.32% (95% CI 0.11–0.54%; p=0.004) per 1000-point change in AUC. Moreover, increasing FIS levels were associated with lower odds of developing pancreatic insufficiency (adjusted OR 0.18, 95% CI 0.07–0.46; p<0.001), CF-related liver disease (adjusted OR 0.18, 95% CI 0.06–0.54; p=0.002) and diabetes (adjusted OR 0.34, 95% CI 0.12–0.97; p=0.044). These associations were absent for SCC. Conclusion This study exemplifies the prognostic value of a patient-derived organoid-based biomarker within a clinical setting, which is especially important for people carrying rare CFTR mutations with unclear clinical consequences. Forskolin-induced swelling of patient-derived intestinal organoids is associated with long-term cystic fibrosis disease progression, expressed as FEV1pp decline and development of pancreatic insufficiency, CF-related liver disease and CF-related diabeteshttps://bit.ly/3tjjJzU
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Affiliation(s)
- Danya Muilwijk
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, The Netherlands.,These authors contributed equally to this work
| | - Eyleen de Poel
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, The Netherlands.,Regenerative Medicine Utrecht, University Medical Center, Utrecht University, Utrecht, The Netherlands.,These authors contributed equally to this work
| | - Peter van Mourik
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, The Netherlands
| | - Sylvia W F Suen
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, The Netherlands.,Regenerative Medicine Utrecht, University Medical Center, Utrecht University, Utrecht, The Netherlands
| | - Annelotte M Vonk
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, The Netherlands.,Regenerative Medicine Utrecht, University Medical Center, Utrecht University, Utrecht, The Netherlands
| | - Jesse E Brunsveld
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, The Netherlands.,Regenerative Medicine Utrecht, University Medical Center, Utrecht University, Utrecht, The Netherlands
| | - Evelien Kruisselbrink
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, The Netherlands.,Regenerative Medicine Utrecht, University Medical Center, Utrecht University, Utrecht, The Netherlands
| | - Hugo Oppelaar
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, The Netherlands.,Regenerative Medicine Utrecht, University Medical Center, Utrecht University, Utrecht, The Netherlands
| | - Marne C Hagemeijer
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, The Netherlands.,Regenerative Medicine Utrecht, University Medical Center, Utrecht University, Utrecht, The Netherlands.,Current affiliation: Center for Lysosomal and Metabolic Diseases, Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Gitte Berkers
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, The Netherlands
| | - Karin M de Winter-de Groot
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, The Netherlands
| | - Sabine Heida-Michel
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, The Netherlands
| | - Stephan R Jans
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, The Netherlands
| | - Hannah van Panhuis
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, The Netherlands
| | - Menno M van der Eerden
- Department of Pulmonology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | | | - Jolt Roukema
- Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, The Netherlands
| | - Edward Dompeling
- Maastricht University Medical Center, Maastricht, The Netherlands
| | - Els J M Weersink
- Amsterdam University Medical Center, location AMC, Amsterdam, The Netherlands
| | - Gerard H Koppelman
- Department of Pediatric Pulmonology and Pediatric Allergology, University of Groningen, University Medical Center Groningen, Beatrix Children's Hospital, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
| | - Robert Vries
- Hubrecht Organoid Technology (HUB), Utrecht, The Netherlands
| | | | - Marinus J C Eijkemans
- Department of Data Science and Biostatistics, Julius Center for Health Sciences and Primary Care, University Medical Center, Utrecht University, Utrecht, The Netherlands
| | - Cornelis K van der Ent
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, The Netherlands.,These authors contributed equally to this work and are both corresponding authors
| | - Jeffrey M Beekman
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, Utrecht, The Netherlands .,Regenerative Medicine Utrecht, University Medical Center, Utrecht University, Utrecht, The Netherlands.,These authors contributed equally to this work and are both corresponding authors
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20
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Ramalho AS, Boon M, Proesmans M, Vermeulen F, Carlon MS, De Boeck K. Assays of CFTR Function In Vitro, Ex Vivo and In Vivo. Int J Mol Sci 2022; 23:1437. [PMID: 35163362 PMCID: PMC8836180 DOI: 10.3390/ijms23031437] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/12/2022] [Accepted: 01/21/2022] [Indexed: 12/22/2022] Open
Abstract
Cystic fibrosis, a multi-organ genetic disease, is characterized by abnormal function of the cystic fibrosis transmembrane conductance regulator (CFTR) protein, a chloride channel at the apical membrane of several epithelia. In recent years, therapeutic strategies have been developed to correct the CFTR defect. To evaluate CFTR function at baseline for diagnosis, or the efficacy of CFTR-restoring therapy, reliable tests are needed to measure CFTR function, in vitro, ex vivo and in vivo. In vitro techniques either directly or indirectly measure ion fluxes; direct measurement of ion fluxes and quenching of fluorescence in cell-based assays, change in transmembrane voltage or current in patch clamp or Ussing chamber, swelling of CFTR-containing organoids by secondary water influx upon CFTR activation. Several cell or tissue types can be used. Ex vivo and in vivo assays similarly evaluate current (intestinal current measurement) and membrane potential differences (nasal potential difference), on tissues from individual patients. In the sweat test, the most frequently used in vivo evaluation of CFTR function, chloride concentration or stimulated sweat rate can be directly measured. Here, we will describe the currently available bio-assays for quantitative evaluation of CFTR function, their indications, advantages and disadvantages, and correlation with clinical outcome measures.
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Affiliation(s)
- Anabela S. Ramalho
- CF Research Lab, Woman and Child Unit, Department of Development and Regeneration, KU Leuven (Catholic University of Leuven), B-3000 Leuven, Belgium; (M.B.); (M.P.); (F.V.); (K.D.B.)
| | - Mieke Boon
- CF Research Lab, Woman and Child Unit, Department of Development and Regeneration, KU Leuven (Catholic University of Leuven), B-3000 Leuven, Belgium; (M.B.); (M.P.); (F.V.); (K.D.B.)
- Department of Pediatrics, Pediatric Pulmonology, University Hospital of Leuven, B-3000 Leuven, Belgium
| | - Marijke Proesmans
- CF Research Lab, Woman and Child Unit, Department of Development and Regeneration, KU Leuven (Catholic University of Leuven), B-3000 Leuven, Belgium; (M.B.); (M.P.); (F.V.); (K.D.B.)
- Department of Pediatrics, Pediatric Pulmonology, University Hospital of Leuven, B-3000 Leuven, Belgium
| | - François Vermeulen
- CF Research Lab, Woman and Child Unit, Department of Development and Regeneration, KU Leuven (Catholic University of Leuven), B-3000 Leuven, Belgium; (M.B.); (M.P.); (F.V.); (K.D.B.)
- Department of Pediatrics, Pediatric Pulmonology, University Hospital of Leuven, B-3000 Leuven, Belgium
| | - Marianne S. Carlon
- Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven (Catholic University of Leuven), B-3000 Leuven, Belgium;
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department CHROMETA, KU Leuven (Catholic University of Leuven), B-3000 Leuven, Belgium
| | - Kris De Boeck
- CF Research Lab, Woman and Child Unit, Department of Development and Regeneration, KU Leuven (Catholic University of Leuven), B-3000 Leuven, Belgium; (M.B.); (M.P.); (F.V.); (K.D.B.)
- Department of Pediatrics, Pediatric Pulmonology, University Hospital of Leuven, B-3000 Leuven, Belgium
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21
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Little MH, Humphreys BD. Regrow or Repair: An Update on Potential Regenerative Therapies for the Kidney. J Am Soc Nephrol 2022; 33:15-32. [PMID: 34789545 PMCID: PMC8763179 DOI: 10.1681/asn.2021081073] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Fifteen years ago, this journal published a review outlining future options for regenerating the kidney. At that time, stem cell populations were being identified in multiple tissues, the concept of stem cell recruitment to a site of injury was of great interest, and the possibility of postnatal renal stem cells was growing in momentum. Since that time, we have seen the advent of human induced pluripotent stem cells, substantial advances in our capacity to both sequence and edit the genome, global and spatial transcriptional analysis down to the single-cell level, and a pandemic that has challenged our delivery of health care to all. This article will look back over this period of time to see how our view of kidney development, disease, repair, and regeneration has changed and envision a future for kidney regeneration and repair over the next 15 years.
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Affiliation(s)
- Melissa H. Little
- Murdoch Children’s Research Institute, Parkville, Melbourne, Victoria, Australia,Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Melbourne, Victoria, Australia,Department of Anatomy and Neuroscience, The University of Melbourne, Parkville, Melbourne, Victoria, Australia
| | - Benjamin D. Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, Missouri,Department of Developmental Biology, Washington University in St. Louis School of Medicine, Missouri
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22
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Angyal D, Bijvelds MJC, Bruno MJ, Peppelenbosch MP, de Jonge HR. Bicarbonate Transport in Cystic Fibrosis and Pancreatitis. Cells 2021; 11:cells11010054. [PMID: 35011616 PMCID: PMC8750324 DOI: 10.3390/cells11010054] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 12/12/2022] Open
Abstract
CFTR, the cystic fibrosis (CF) gene-encoded epithelial anion channel, has a prominent role in driving chloride, bicarbonate and fluid secretion in the ductal cells of the exocrine pancreas. Whereas severe mutations in CFTR cause fibrosis of the pancreas in utero, CFTR mutants with residual function, or CFTR variants with a normal chloride but defective bicarbonate permeability (CFTRBD), are associated with an enhanced risk of pancreatitis. Recent studies indicate that CFTR function is not only compromised in genetic but also in selected patients with an acquired form of pancreatitis induced by alcohol, bile salts or smoking. In this review, we summarize recent insights into the mechanism and regulation of CFTR-mediated and modulated bicarbonate secretion in the pancreatic duct, including the role of the osmotic stress/chloride sensor WNK1 and the scaffolding protein IRBIT, and current knowledge about the role of CFTR in genetic and acquired forms of pancreatitis. Furthermore, we discuss the perspectives for CFTR modulator therapy in the treatment of exocrine pancreatic insufficiency and pancreatitis and introduce pancreatic organoids as a promising model system to study CFTR function in the human pancreas, its role in the pathology of pancreatitis and its sensitivity to CFTR modulators on a personalized basis.
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23
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van der Vaart J, Böttinger L, Geurts MH, van de Wetering WJ, Knoops K, Sachs N, Begthel H, Korving J, Lopez‐Iglesias C, Peters PJ, Eitan K, Gileles‐Hillel A, Clevers H. Modelling of primary ciliary dyskinesia using patient-derived airway organoids. EMBO Rep 2021; 22:e52058. [PMID: 34693619 PMCID: PMC8647008 DOI: 10.15252/embr.202052058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 09/19/2021] [Accepted: 09/21/2021] [Indexed: 01/08/2023] Open
Abstract
Patient-derived human organoids can be used to model a variety of diseases. Recently, we described conditions for long-term expansion of human airway organoids (AOs) directly from healthy individuals and patients. Here, we first optimize differentiation of AOs towards ciliated cells. After differentiation of the AOs towards ciliated cells, these can be studied for weeks. When returned to expansion conditions, the organoids readily resume their growth. We apply this condition to AOs established from nasal inferior turbinate brush samples of patients suffering from primary ciliary dyskinesia (PCD), a pulmonary disease caused by dysfunction of the motile cilia in the airways. Patient-specific differences in ciliary beating are observed and are in agreement with the patients' genetic mutations. More detailed organoid ciliary phenotypes can thus be documented in addition to the standard diagnostic procedure. Additionally, using genetic editing tools, we show that a patient-specific mutation can be repaired. This study demonstrates the utility of organoid technology for investigating hereditary airway diseases such as PCD.
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Affiliation(s)
- Jelte van der Vaart
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW)University Medical Centre UtrechtUtrechtThe Netherlands
- Oncode InstituteHubrecht InstituteUtrechtThe Netherlands
| | - Lena Böttinger
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW)University Medical Centre UtrechtUtrechtThe Netherlands
| | - Maarten H Geurts
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW)University Medical Centre UtrechtUtrechtThe Netherlands
- Oncode InstituteHubrecht InstituteUtrechtThe Netherlands
| | | | - Kèvin Knoops
- The Maastricht Multimodal Molecular Imaging InstituteMaastricht UniversityMaastrichtThe Netherlands
| | - Norman Sachs
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW)University Medical Centre UtrechtUtrechtThe Netherlands
- Present address:
Vertex IncSan DiegoCAUSA
| | - Harry Begthel
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW)University Medical Centre UtrechtUtrechtThe Netherlands
- Oncode InstituteHubrecht InstituteUtrechtThe Netherlands
| | - Jeroen Korving
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW)University Medical Centre UtrechtUtrechtThe Netherlands
- Oncode InstituteHubrecht InstituteUtrechtThe Netherlands
| | - Carmen Lopez‐Iglesias
- The Maastricht Multimodal Molecular Imaging InstituteMaastricht UniversityMaastrichtThe Netherlands
| | - Peter J Peters
- The Maastricht Multimodal Molecular Imaging InstituteMaastricht UniversityMaastrichtThe Netherlands
| | - Kerem Eitan
- Division of Cell Biology, Immunology and Cancer ResearchHebrew University‐Hadassah Medical SchoolJerusalemIsrael
| | - Alex Gileles‐Hillel
- Division of Cell Biology, Immunology and Cancer ResearchHebrew University‐Hadassah Medical SchoolJerusalemIsrael
- Department of Paediatrics, Paediatric Pulmonology and SleepHadassah Hebrew University Medical CentreJerusalemIsrael
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW)University Medical Centre UtrechtUtrechtThe Netherlands
- Oncode InstituteHubrecht InstituteUtrechtThe Netherlands
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24
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Benden C, Schwarz C. CFTR Modulator Therapy and Its Impact on Lung Transplantation in Cystic Fibrosis. Pulm Ther 2021; 7:377-393. [PMID: 34406641 PMCID: PMC8589902 DOI: 10.1007/s41030-021-00170-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 08/03/2021] [Indexed: 01/05/2023] Open
Abstract
Cystic fibrosis (CF) is the most common autosomal recessive disorder in Caucasian people and is caused by mutations in the gene encoding for the CF transmembrane conductance regulator (CFTR) protein. It is a multisystem disorder; however, CF lung disease causes most of its morbidity and mortality. Although survival for CF has improved over time due to a multifaceted symptomatic management approach, CF remains a life-limiting disease. For individuals with progressive advanced CF lung disease (ACFLD), lung transplantation is considered the ultimate treatment option if compatible with goals of care. Since 2012, newer drugs, called CFTR modulators, have gradually become available, revolutionizing CF care, as these small-molecule drugs target the underlying defect in CF that causes decreased CFTR protein synthesis, function, or stability. Because of their extremely high efficacy and overall respectable tolerability, CFTR modulator drugs have already proven to have a substantial positive impact on the lives of individuals with CF. Individuals with ACFLD have generally been excluded from initial clinical trials. Now, however, these drugs are being used in clinical practice in selected individuals with ACFLD, showing promising results, although randomized controlled trial data for CFTR modulators in this subgroup of patients are lacking. Such data need to be gathered, ideally in randomized controlled trials including patients with ACFLD. Furthermore, the efficacy and tolerability of the newer modulator therapies in individuals with ACFLD need to be monitored, and their impact on lung disease progression and the need for lung transplantation as the ultimate therapy call for an objective evaluation in larger patient cohorts. As of today, guidelines for referral and listing of lung transplant candidates with CF have not incorporated the status of the new CFTR modulator therapies in the referral and listing process. The purpose of this review article, therefore, is threefold: first, to describe the effects of new therapies, with a focus on the subgroup of individuals with ACFLD; second, to provide an update on the recent outcomes after lung transplantation for individuals with CF; and third, to discuss the referral, evaluation, and timing for lung transplantation as the ultimate therapeutic option in view of the new treatments available in CF.
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Affiliation(s)
- Christian Benden
- Faculty of Medicine, University of Zurich, Raemistrasse 71, 8006, Zurich, Switzerland.
| | - Carsten Schwarz
- Division of Cystic Fibrosis, CF Center Westbrandenburg, Campus Potsdam, Potsdam, Germany
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25
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Noel S, Servel N, Hatton A, Golec A, Rodrat M, Ng DRS, Li H, Pranke I, Hinzpeter A, Edelman A, Sheppard DN, Sermet-Gaudelus I. Correlating genotype with phenotype using CFTR-mediated whole-cell Cl - currents in human nasal epithelial cells. J Physiol 2021; 600:1515-1531. [PMID: 34761808 DOI: 10.1113/jp282143] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 11/01/2021] [Indexed: 12/20/2022] Open
Abstract
Dysfunction of the epithelial anion channel cystic fibrosis transmembrane conductance regulator (CFTR) causes a wide spectrum of disease, including cystic fibrosis (CF) and CFTR-related diseases (CFTR-RDs). Here, we investigate genotype-phenotype-CFTR function relationships using human nasal epithelial (hNE) cells from a small cohort of non-CF subjects and individuals with CF and CFTR-RDs and genotypes associated with either residual or minimal CFTR function using electrophysiological techniques. Collected hNE cells were either studied directly with the whole-cell patch-clamp technique or grown as primary cultures at an air-liquid interface after conditional reprogramming. The properties of cAMP-activated whole-cell Cl- currents in freshly isolated hNE cells identified them as CFTR-mediated. Their magnitude varied between hNE cells from individuals within the same genotype and decreased in the rank order: non-CF > CFTR residual function > CFTR minimal function. CFTR-mediated whole-cell Cl- currents in hNE cells isolated from fully differentiated primary cultures were identical to those in freshly isolated hNE cells in both magnitude and behaviour, demonstrating that conditional reprogramming culture is without effect on CFTR expression and function. For the cohort of subjects studied, CFTR-mediated whole-cell Cl- currents in hNE cells correlated well with CFTR-mediated transepithelial Cl- currents measured in vitro with the Ussing chamber technique, but not with those determined in vivo with the nasal potential difference assay. Nevertheless, they did correlate with the sweat Cl- concentration of study subjects. Thus, this study highlights the complexity of genotype-phenotype-CFTR function relationships, but emphasises the value of conditionally reprogrammed hNE cells in CFTR research and therapeutic testing. KEY POINTS: The genetic disease cystic fibrosis is caused by pathogenic variants in the cystic fibrosis transmembrane conductance regulator (CFTR), an ion channel, which controls anion flow across epithelia lining ducts and tubes in the body. This study investigated CFTR function in nasal epithelial cells from people with cystic fibrosis and CFTR variants with a range of disease severity. CFTR function varied widely in nasal epithelial cells depending on the identity of CFTR variants, but was unaffected by conditional reprogramming culture, a cell culture technique used to grow large numbers of patient-derived cells. Assessment of CFTR function in vitro in nasal epithelial cells and epithelia, and in vivo in the nasal epithelium and sweat gland highlights the complexity of genotype-phenotype-CFTR function relationships.
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Affiliation(s)
- Sabrina Noel
- INSERM U1151, Institut Necker-Enfants Malades, Paris, France.,Université de Paris, Paris, France
| | - Nathalie Servel
- INSERM U1151, Institut Necker-Enfants Malades, Paris, France.,Université de Paris, Paris, France
| | - Aurélie Hatton
- INSERM U1151, Institut Necker-Enfants Malades, Paris, France.,Université de Paris, Paris, France
| | - Anita Golec
- INSERM U1151, Institut Necker-Enfants Malades, Paris, France.,Université de Paris, Paris, France
| | - Mayuree Rodrat
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, UK.,Center of Research and Development for Biomedical Instrumentation, Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Demi R S Ng
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, UK
| | - Hongyu Li
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, UK
| | - Iwona Pranke
- INSERM U1151, Institut Necker-Enfants Malades, Paris, France.,Université de Paris, Paris, France
| | - Alexandre Hinzpeter
- INSERM U1151, Institut Necker-Enfants Malades, Paris, France.,Université de Paris, Paris, France
| | - Aleksander Edelman
- INSERM U1151, Institut Necker-Enfants Malades, Paris, France.,Université de Paris, Paris, France
| | - David N Sheppard
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, UK
| | - Isabelle Sermet-Gaudelus
- INSERM U1151, Institut Necker-Enfants Malades, Paris, France.,Université de Paris, Paris, France.,Centre de Référence Maladies Rares, Mucoviscidose et Maladies Apparentées, Hôpital Necker-Enfants Malades, Paris, France.,European Reference Network on rare respiratory diseases, Frankfurt, Germany
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26
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Functional Restoration of CFTR Nonsense Mutations in Intestinal Organoids. J Cyst Fibros 2021; 21:246-253. [PMID: 34666947 DOI: 10.1016/j.jcf.2021.09.020] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 09/16/2021] [Accepted: 09/17/2021] [Indexed: 11/20/2022]
Abstract
BACKGROUND Pharmacotherapies for people with cystic fibrosis (pwCF) who have premature termination codons (PTCs) in the cystic fibrosis transmembrane conductance regulator (CFTR) gene are under development. Thus far, clinical studies focused on compounds that induce translational readthrough (RT) at the mRNA PTC location. Recent studies using primary airway cells showed that PTC functional restoration can be achieved through combining compounds with multiple mode-of-actions. Here, we assessed induction of CFTR function in PTC-containing intestinal organoids using compounds targeting RT, nonsense mRNA mediated decay (NMD) and CFTR protein modulation. METHODS Rescue of PTC CFTR protein was assessed by forskolin-induced swelling of 12 intestinal organoid cultures carrying distinct PTC mutations. Effects of compounds on mRNA CFTR level was assessed by RT-qPCRs. RESULTS Whilst response varied between donors, significant rescue of CFTR function was achieved for most donors with the quintuple combination of a commercially available pharmacological equivalent of the RT compound (ELX-02-disulfate or ELX-02ds), NMD inhibitor SMG1i, correctors VX-445 and VX-661 and potentiator VX-770. The quintuple combination of pharmacotherapies reached swelling quantities higher than the mean swelling of three VX-809/VX-770-rescued F508del/F508del organoid cultures, indicating level of rescue is of clinical relevance as VX-770/VX-809-mediated F508del/F508del rescue in organoids correlate with substantial improvement of clinical outcome. CONCLUSIONS Whilst variation in efficacy was observed between genotypes as well as within genotypes, the data suggests that strong pharmacological rescue of PTC requires a combination of drugs that target RT, NMD and protein function.
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27
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Staab JF, Lemme-Dumit JM, Latanich R, Pasetti MF, Zachos NC. Co-Culture System of Human Enteroids/Colonoids with Innate Immune Cells. ACTA ACUST UNITED AC 2021; 131:e113. [PMID: 33166041 DOI: 10.1002/cpim.113] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Human intestinal enteroids derived from adult stem cells offer a relevant ex vivo system to study biological processes of the human gut. They recreate cellular and functional features of the intestinal epithelium of the small intestine (enteroids) or colon (colonoids) albeit limited by the lack of associated cell types that help maintain tissue homeostasis and respond to external challenges. In the gut, innate immune cells interact with the epithelium, support barrier function, and deploy effector functions. We have established a co-culture system of enteroid/colonoid monolayers and underlying macrophages and polymorphonuclear neutrophils to recapitulate the cellular framework of the human intestinal epithelial niche. Enteroids are generated from biopsies or resected tissue from any segment of the human gut and maintained in long-term cultures as three-dimensional structures through supplementation of stem cell growth factors. Immune cells are isolated from fresh human whole blood or frozen peripheral blood mononuclear cells (PBMC). Monocytes from PBMC are differentiated into macrophages by cytokine stimulation prior to co-culture. The methods are divided into the two main components of the model: (1) generating enteroid/colonoid monolayers and isolating immune cells and (2) assembly of enteroid/colonoid-immune cell co-cultures with separate apical and basolateral compartments. Co-cultures containing macrophages can be maintained for 48 hr while those involving neutrophils, due to their shorter life span, remain viable for 4 hr. Enteroid-immune co-cultures enable multiple outcome measures, including transepithelial resistance, production of cytokines/chemokines, phenotypic analysis of immune cells, tissue immunofluorescence imaging, protein or mRNA expression, antigen or microbe uptake, and other cellular functions. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Seeding enteroid fragments onto Transwells for monolayer formation Alternate Protocol: Seeding enteroid fragments for monolayer formation using trituration Basic Protocol 2: Isolation of monocytes and derivation of immune cells from human peripheral blood Basic Protocol 3: Isolation of neutrophils from human peripheral blood Basic Protocol 4: Assembly of enteroid/macrophage or enteroid/neutrophil co-culture.
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Affiliation(s)
- Janet F Staab
- Department of Medicine, Division of Gastroenterology and Hepatology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jose M Lemme-Dumit
- Department of Pediatrics, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland
| | - Rachel Latanich
- Department of Medicine, Division of Gastroenterology and Hepatology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Marcella F Pasetti
- Department of Pediatrics, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland
| | - Nicholas C Zachos
- Department of Medicine, Division of Gastroenterology and Hepatology, Johns Hopkins University School of Medicine, Baltimore, Maryland
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Calucho M, Gartner S, Barranco P, Fernández-Álvarez P, Pérez RG, Tizzano EF. Validation of nasospheroids to assay CFTR functionality and modulator responses in cystic fibrosis. Sci Rep 2021; 11:15511. [PMID: 34330959 PMCID: PMC8324871 DOI: 10.1038/s41598-021-94798-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 07/05/2021] [Indexed: 02/07/2023] Open
Abstract
The availability of a simple, robust and non-invasive in vitro airway model would be useful to study the functionality of the cystic fibrosis transmembrane regulator (CFTR) protein and to personalize modulator therapy for cystic fibrosis (CF) patients. Our aim was to validate a CFTR functional study using nasospheroids, a patient-derived nasal cell 3D-culture. We performed live-cell experiments in nasospheroids obtained from wild-type individuals and CF patients with different genotypes and phenotypes. We extended the existing method and expanded the analysis to upgrade measurements of CFTR activity using forskolin-induced shrinking. We also tested modulator drugs in CF samples. Immobilizing suspended-nasospheroids provided a high number of samples for live-cell imaging. The diversity observed in basal sizes of nasospheroids did not affect the functional analysis of CFTR. Statistical analysis with our method was simple, making this protocol easy to reproduce. Moreover, we implemented the measurement of inner fluid reservoir areas to further differentiate CFTR functionality. In summary, this rapid methodology is helpful to analyse response to modulators in CF samples to allow individualized treatment for CF patients.
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Affiliation(s)
- Maite Calucho
- Medicine Genetics Group, Vall D'Hebron Research Institute, 08035, Barcelona, Spain.,Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron , 08035, Barcelona, Spain
| | - Silvia Gartner
- Cystic Fibrosis Unit, Hospital Universitari Vall d'Hebron, 08035, Barcelona, Spain
| | - Paula Barranco
- Medicine Genetics Group, Vall D'Hebron Research Institute, 08035, Barcelona, Spain.,Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron , 08035, Barcelona, Spain
| | - Paula Fernández-Álvarez
- Medicine Genetics Group, Vall D'Hebron Research Institute, 08035, Barcelona, Spain.,Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron , 08035, Barcelona, Spain
| | | | - Eduardo F Tizzano
- Medicine Genetics Group, Vall D'Hebron Research Institute, 08035, Barcelona, Spain. .,Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron , 08035, Barcelona, Spain.
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29
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Orr JC, Hynds RE. Stem Cell-derived Respiratory Epithelial Cell Cultures as Human Disease Models. Am J Respir Cell Mol Biol 2021; 64:657-668. [PMID: 33428856 PMCID: PMC8456877 DOI: 10.1165/rcmb.2020-0440tr] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 01/11/2021] [Indexed: 12/11/2022] Open
Abstract
Advances in stem cell biology and the understanding of factors that determine lung stem cell self-renewal have enabled long-term in vitro culture of human lung cells derived from airway basal and alveolar type II cells. Improved capability to expand and study primary cells long term, including in clonal cultures that are recently derived from a single cell, will allow experiments that address fundamental questions about lung homeostasis and repair, as well as translational questions in asthma, chronic obstructive pulmonary disease, pulmonary fibrosis, and lung cancer research. Here, we provide a brief history of postnatal lung epithelial cell culture and describe recent methodological advances. We further discuss the applications of primary cultures in defining "normal" epithelium, in modeling lung disease, and in future cell therapies.
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Affiliation(s)
- Jessica C Orr
- Lungs for Living Research Centre, UCL Respiratory, Division of Medicine, and
| | - Robert E Hynds
- UCL Cancer Institute, University College London, London, United Kingdom
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30
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Anderson JD, Liu Z, Odom LV, Kersh L, Guimbellot JS. CFTR function and clinical response to modulators parallel nasal epithelial organoid swelling. Am J Physiol Lung Cell Mol Physiol 2021; 321:L119-L129. [PMID: 34009038 DOI: 10.1152/ajplung.00639.2020] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
In vitro biomarkers to assess cystic fibrosis transmembrane conductance regulator activity are desirable for precision modulator selection and as a tool for clinical trials. Here, we describe an organoid swelling assay derived from human nasal epithelia using commercially available reagents and equipment and an automated imaging process. Cells were collected in nasal brush biopsies, expanded in vitro, and cultured as spherical organoids or as monolayers. Organoids were used in a functional swelling assay with automated measurements and analysis, whereas monolayers were used for short-circuit current measurements to assess ion channel activity. Clinical data were collected from patients on modulators. Relationships between swelling data and short-circuit current, as well as between swelling data and clinical outcome measures, were assessed. The organoid assay measurements correlated with short-circuit current measurements for ion channel activity. The functional organoid assay distinguished individual responses as well as differences between groups. The organoid assay distinguished incremental drug responses to modulator monotherapy with ivacaftor and combination therapy with ivacaftor, tezacaftor, and elexacaftor. The swelling activity paralleled the clinical response. In conclusion, an in vitro biomarker derived from patients' cells can be used to predict responses to drugs and is likely to be useful as a preclinical tool to aid in the development of novel treatments and as a clinical trial outcome measure for a variety of applications, including gene therapy or editing.
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Affiliation(s)
- Justin D Anderson
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama.,Division of Pulmonary and Sleep Medicine, Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Zhongyu Liu
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama.,Division of Pulmonary and Sleep Medicine, Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama
| | - L Victoria Odom
- Division of Pulmonary and Sleep Medicine, Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Latona Kersh
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama
| | - Jennifer S Guimbellot
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama.,Division of Pulmonary and Sleep Medicine, Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama
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31
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Silva IAL, Railean V, Duarte A, Amaral MD. Personalized Medicine Based on Nasal Epithelial Cells: Comparative Studies with Rectal Biopsies and Intestinal Organoids. J Pers Med 2021; 11:421. [PMID: 34065744 PMCID: PMC8156700 DOI: 10.3390/jpm11050421] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 05/09/2021] [Accepted: 05/12/2021] [Indexed: 12/20/2022] Open
Abstract
As highly effective CFTR modulator therapies (HEMT) emerge, there is an unmet need to find effective drugs for people with CF (PwCF) with ultra-rare mutations who are too few for classical clinical trials and for whom there are no drug discovery programs. Therefore, biomarkers reliably predicting the benefit from CFTR modulator therapies are essential to find effective drugs for PwCF through personalized approaches termed theranostics. Here, we assess CFTR basal function and the individual responses to CFTR modulators in primary human nasal epithelial (pHNE) cells from PwCF carrying rare mutations and compare these measurements with those in native rectal biopsies and intestinal organoids, respectively, in the same individual. The basal function in pHNEs shows good correlation with CFTR basal function in rectal biopsies. In parallel, CFTR rescue in pHNEs by CFTR modulators correlates to that in intestinal organoids. Altogether, results show that pHNEs are a bona fide theranostic model to assess CFTR rescue by CFTR modulator drugs, in particular for PwCF and rare mutations.
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Affiliation(s)
| | | | | | - Margarida D. Amaral
- BioISI—Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisboa, Portugal; (I.A.L.S.); (V.R.); (A.D.)
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32
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Graeber SY, Vitzthum C, Mall MA. Potential of Intestinal Current Measurement for Personalized Treatment of Patients with Cystic Fibrosis. J Pers Med 2021; 11:jpm11050384. [PMID: 34066648 PMCID: PMC8151208 DOI: 10.3390/jpm11050384] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/02/2021] [Accepted: 05/04/2021] [Indexed: 12/14/2022] Open
Abstract
Refinement of personalized treatment of cystic fibrosis (CF) with emerging medicines targeting the CF basic defect will likely benefit from biomarkers sensitive to detect improvement of cystic fibrosis transmembrane conductance regulator (CFTR) function in individual patients. Intestinal current measurement (ICM) is a technique that enables quantitative assessment of CFTR chloride channel function in rectal tissues or other intestinal epithelia. ICM was originally developed to study the CF ion transport defect in the intestine and has been established as a sensitive biomarker of CFTR function and diagnostic test for CF. With the emergence of CFTR-directed therapeutics, ICM has become an important tool to estimate the level of rescue of CFTR function achieved by approved CFTR modulators, both at the level of CFTR genotype groups, as well as individual patients with CF. In combination with preclinical patient-derived cell culture models, ICM may aid the development of targeted therapies for patients with rare CFTR mutations. Here, we review the principles of ICM and examine how this CFTR biomarker may be used to support diagnostic testing and enhance personalized medicine for individual patients with common as well as rare CFTR mutations in the new era of medicines targeting the underlying cause of CF.
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Affiliation(s)
- Simon Y. Graeber
- Charité—Universitätsmedizin Berlin, Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, 13353 Berlin, Germany; (S.Y.G.); (C.V.)
- Berlin Institute of Health, Charité—Universitätsmedizin Berlin, 10117 Berlin, Germany
- German Centre for Lung Research (DZL), 13353 Berlin, Germany
| | - Constanze Vitzthum
- Charité—Universitätsmedizin Berlin, Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, 13353 Berlin, Germany; (S.Y.G.); (C.V.)
- German Centre for Lung Research (DZL), 13353 Berlin, Germany
| | - Marcus A. Mall
- Charité—Universitätsmedizin Berlin, Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, 13353 Berlin, Germany; (S.Y.G.); (C.V.)
- Berlin Institute of Health, Charité—Universitätsmedizin Berlin, 10117 Berlin, Germany
- German Centre for Lung Research (DZL), 13353 Berlin, Germany
- Correspondence: ; Tel.: +49-(30)-450-566-182; Fax: +49-(30)-450-566-931
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33
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Schutgens F, Rookmaaker M, Verhaar M. A Perspective on a Urine-Derived Kidney Tubuloid Biobank from Patients with Hereditary Tubulopathies. Tissue Eng Part C Methods 2021; 27:177-182. [PMID: 33544041 DOI: 10.1089/ten.tec.2020.0366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Inherited kidney tubulopathies comprise a group of rare diseases with a significant societal impact, as lifelong treatment is often required and no therapies are available to prevent progression of renal damage. Diagnosis of inherited tubulopathies has improved with the advances of next generation sequencing. However, difficulties remain, such as a lack of genotype-phenotype correlation and unknown pathogenicity of newly identified variants. In addition, treatment remains mainly symptomatic. Both diagnosis and treatment can be improved by addition of in vitro functional studies to clinical care. Urine-derived kidney organoids ("tubuloids") are a promising platform for these studies. International collections of patient-derived tubuloids in a living biobank offer additional advantages for drug development and pathophysiological studies. In this review, we discuss how diagnosis and treatment of tubulopathies can be improved by in vitro studies using a tubuloid biobank. We also address practical challenges in the development of such biobank. Impact statement This review provides readers insight into aspects related to diagnosis and treatment of hereditary kidney tubulopathies that can be improved. In addition, it explains why in vitro functional analyses using a kidney organoid model (tubuloids) may be useful as a method to improve these aspects. Finally, the additional advantages and practical hurdles of collecting tubuloid lines in a biobank are discussed.
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Affiliation(s)
- Frans Schutgens
- Department of Nephrology and Hypertension, University Medical Centre Utrecht, Utrecht, The Netherlands.,Hubrecht Institute-Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Maarten Rookmaaker
- Department of Nephrology and Hypertension, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Marianne Verhaar
- Department of Nephrology and Hypertension, University Medical Centre Utrecht, Utrecht, The Netherlands
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34
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Hof L, Moreth T, Koch M, Liebisch T, Kurtz M, Tarnick J, Lissek SM, Verstegen MMA, van der Laan LJW, Huch M, Matthäus F, Stelzer EHK, Pampaloni F. Long-term live imaging and multiscale analysis identify heterogeneity and core principles of epithelial organoid morphogenesis. BMC Biol 2021; 19:37. [PMID: 33627108 PMCID: PMC7903752 DOI: 10.1186/s12915-021-00958-w] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 01/12/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Organoids are morphologically heterogeneous three-dimensional cell culture systems and serve as an ideal model for understanding the principles of collective cell behaviour in mammalian organs during development, homeostasis, regeneration, and pathogenesis. To investigate the underlying cell organisation principles of organoids, we imaged hundreds of pancreas and cholangiocarcinoma organoids in parallel using light sheet and bright-field microscopy for up to 7 days. RESULTS We quantified organoid behaviour at single-cell (microscale), individual-organoid (mesoscale), and entire-culture (macroscale) levels. At single-cell resolution, we monitored formation, monolayer polarisation, and degeneration and identified diverse behaviours, including lumen expansion and decline (size oscillation), migration, rotation, and multi-organoid fusion. Detailed individual organoid quantifications lead to a mechanical 3D agent-based model. A derived scaling law and simulations support the hypotheses that size oscillations depend on organoid properties and cell division dynamics, which is confirmed by bright-field microscopy analysis of entire cultures. CONCLUSION Our multiscale analysis provides a systematic picture of the diversity of cell organisation in organoids by identifying and quantifying the core regulatory principles of organoid morphogenesis.
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Affiliation(s)
- Lotta Hof
- Physical Biology Group, Buchmann Institute for Molecular Life Sciences (BMLS), Goethe-Universität Frankfurt am Main, Frankfurt am Main, Germany
| | - Till Moreth
- Physical Biology Group, Buchmann Institute for Molecular Life Sciences (BMLS), Goethe-Universität Frankfurt am Main, Frankfurt am Main, Germany
| | - Michael Koch
- Physical Biology Group, Buchmann Institute for Molecular Life Sciences (BMLS), Goethe-Universität Frankfurt am Main, Frankfurt am Main, Germany
| | - Tim Liebisch
- Frankfurt Institute for Advanced Studies and Faculty of Biological Sciences, Goethe-Universität Frankfurt am Main, Frankfurt am Main, Germany
| | - Marina Kurtz
- Department of Physics, Goethe Universität Frankfurt am Main, Frankfurt am Main, Germany
| | - Julia Tarnick
- Deanery of Biomedical Science, University of Edinburgh, Edinburgh, UK
| | - Susanna M Lissek
- Experimental Medicine and Therapy Research, University of Regensburg, Regensburg, Germany
| | - Monique M A Verstegen
- Department of Surgery, Erasmus MC - University Medical Center, Rotterdam, The Netherlands
| | - Luc J W van der Laan
- Department of Surgery, Erasmus MC - University Medical Center, Rotterdam, The Netherlands
| | - Meritxell Huch
- The Wellcome Trust/CRUK Gurdon Institute, University of Cambridge, Cambridge, UK
- Present address: Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Franziska Matthäus
- Frankfurt Institute for Advanced Studies and Faculty of Biological Sciences, Goethe-Universität Frankfurt am Main, Frankfurt am Main, Germany
| | - Ernst H K Stelzer
- Physical Biology Group, Buchmann Institute for Molecular Life Sciences (BMLS), Goethe-Universität Frankfurt am Main, Frankfurt am Main, Germany
| | - Francesco Pampaloni
- Physical Biology Group, Buchmann Institute for Molecular Life Sciences (BMLS), Goethe-Universität Frankfurt am Main, Frankfurt am Main, Germany.
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Padoan R, Quattrucci S, Amato A, Carnovale V, Salvatore D, Salvatore M, Campagna G. The Diagnosis of Cystic Fibrosis in Adult Age. Data from the Italian Registry. Diagnostics (Basel) 2021; 11:diagnostics11020321. [PMID: 33669477 PMCID: PMC7920411 DOI: 10.3390/diagnostics11020321] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/13/2021] [Accepted: 02/15/2021] [Indexed: 11/16/2022] Open
Abstract
Cystic Fibrosis (CF) registries are an essential resource of epidemiological and clinical data. Although the median age at diagnosis is usually reported in the first months of life, a minority of individuals is diagnosed during adulthood. The aim of this study was to describe demographic, genetic, and clinical characteristics of this subgroup of the Italian CF population by using data from the Italian CF Registry (ICFR). Patients ≥18 years at diagnosis were selected and clinical data at diagnosis were analyzed from the 2012-2018 ICFR data (Cohort A). Subjects with diagnosis ≥18 years were selected from 2018 ICFR dataset (Cohort B) to describe their clinical status. In 2012-18 the incidence of late diagnosis was 18.2%, whereas, in 2018, the prevalence of patients diagnosed ≥18 years was 12.54%. The median age of late diagnosis was 36.2 years, ranging from 19.0 to 68.3. The male patients were diagnosed because of infertility in the 45.9% of cases. Median sweat chloride value (SCL) was 69 mmol/L (range 9-150). F508del mutation accounted for 28.3% of alleles. A wide variability in respiratory function was present with a median percent predicted Forced Expiratory Volume in the first second (ppFEV1) of 90.8% (range 20-147%). Low prevalence of pancreatic insufficiency (25%) and of Pseudomonas aeruginosa (Pa) infection (17%) suggest a mild CF phenotype in the majority of patients. The assessment of the clinical status in the 2018 dataset and the comparison between genders showed a greater nutritional and respiratory impairment in females. Further studies are needed to clarify the importance of a true diagnostic delay or of late onset of CF symptoms.
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Affiliation(s)
- Rita Padoan
- Regional Support Center for Cystic Fibrosis, Department of Pediatrics, Children’s Hospital–ASST Spedali Civili, University of Brescia, 25123 Brescia, Italy
- Italian Cystic Fibrosis Registry, 00162 Rome, Italy; (S.Q.); (V.C.); (D.S.); (M.S.); (G.C.)
- Correspondence: ; Tel.: +39-349-742-4291
| | - Serena Quattrucci
- Italian Cystic Fibrosis Registry, 00162 Rome, Italy; (S.Q.); (V.C.); (D.S.); (M.S.); (G.C.)
- Italian League of Cystic Fibrosis–ONLUS, 00198 Rome, Italy;
| | - Annalisa Amato
- Italian League of Cystic Fibrosis–ONLUS, 00198 Rome, Italy;
| | - Vincenzo Carnovale
- Italian Cystic Fibrosis Registry, 00162 Rome, Italy; (S.Q.); (V.C.); (D.S.); (M.S.); (G.C.)
- Cystic Fibrosis Center, Adult Unit, Department of Translational Medical Science, University of Naples “Federico II”, 80138 Naples, Italy
| | - Donatello Salvatore
- Italian Cystic Fibrosis Registry, 00162 Rome, Italy; (S.Q.); (V.C.); (D.S.); (M.S.); (G.C.)
- Cystic Fibrosis Center, Hospital San Carlo, 85100 Potenza, Italy
| | - Marco Salvatore
- Italian Cystic Fibrosis Registry, 00162 Rome, Italy; (S.Q.); (V.C.); (D.S.); (M.S.); (G.C.)
- National Center for Rare Diseases, Undiagnosed Rare Diseases Unit, Istituto Superiore di Sanità, 00162 Rome, Italy
| | - Giuseppe Campagna
- Italian Cystic Fibrosis Registry, 00162 Rome, Italy; (S.Q.); (V.C.); (D.S.); (M.S.); (G.C.)
- Italian League of Cystic Fibrosis–ONLUS, 00198 Rome, Italy;
- Department of Medical-Surgical Sciences and Translational Medicine, Faculty of Medicine and Psychology, “Sapienza” University, 00198 Rome, Italy
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36
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Targeting G542X CFTR nonsense alleles with ELX-02 restores CFTR function in human-derived intestinal organoids. J Cyst Fibros 2021; 20:436-442. [PMID: 33558100 DOI: 10.1016/j.jcf.2021.01.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/19/2020] [Accepted: 01/21/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND Promoting full-length protein production is a requisite step to address some of the remaining unmet medical need for those with Cystic Fibrosis (CF) nonsense alleles. ELX-02 promotes read-through of mRNA transcripts bearing nonsense mutations, including the most common CF nonsense allele G542X, in several different preclinical models including human bronchial epithelial cells. Here we evaluate ELX-02 mediated read-through using the CFTR-dependent Forskolin-induced swelling (FIS) assay across a selection of G542X genotype patient derived organoids (PDOs). METHODS CFTR functional restoration was evaluated in ELX-02 treated G542X homozygous and heterozygous PDOs in the CFTR-dependent FIS assay. CFTR mRNA abundance and integrity were evaluated by qPCR and Nanostring analysis while PDO protein was detected by capillary based size-exclusion chromatography. RESULTS PDOs homozygous for G542X or heterozygous with a second minimally functional allele had significantly increased CFTR activity with ELX-02 in a dose-dependent fashion across a variety of forskolin induction concentrations. The functional increases are similar to those obtained with tezacaftor/ivacaftor in F508del homozygous PDOs. Increased CFTR C- and B-band protein was observed in accordance with increased function. In addition, ELX-02 treatment of a G542X/G542X PDO results in a 5-fold increase in CFTR mRNA compared with vehicle treated, resulting in normalization of CFTR mRNA as measured via Nanostring. CONCLUSIONS These data with ELX-02 in PDOs are consistent with previous G542X model evaluations. These results also support the on-going clinical evaluation of ELX-02 as a read-through agent for CF caused by the G542X allele.
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37
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Ramalho AS, Fürstová E, Vonk AM, Ferrante M, Verfaillie C, Dupont L, Boon M, Proesmans M, Beekman JM, Sarouk I, Vazquez Cordero C, Vermeulen F, De Boeck K. Correction of CFTR function in intestinal organoids to guide treatment of cystic fibrosis. Eur Respir J 2021; 57:13993003.02426-2019. [PMID: 32747394 DOI: 10.1183/13993003.02426-2019] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 06/29/2020] [Indexed: 11/05/2022]
Abstract
RATIONALE Given the vast number of cystic fibrosis transmembrane conductance regulator (CFTR) mutations, biomarkers predicting benefit from CFTR modulator therapies are needed for subjects with cystic fibrosis (CF). OBJECTIVES To study CFTR function in organoids of subjects with common and rare CFTR mutations and evaluate correlations between CFTR function and clinical data. METHODS Intestinal organoids were grown from rectal biopsies in a cohort of 97 subjects with CF. Residual CFTR function was measured by quantifying organoid swelling induced by forskolin and response to modulators by quantifying organoid swelling induced by CFTR correctors, potentiator and their combination. Organoid data were correlated with clinical data from the literature. RESULTS Across 28 genotypes, residual CFTR function correlated (r2=0.87) with sweat chloride values. When studying the same genotypes, CFTR function rescue by CFTR modulators in organoids correlated tightly with mean improvement in lung function (r2=0.90) and sweat chloride (r2=0.95) reported in clinical trials. We identified candidate genotypes for modulator therapy, such as E92K, Q237E, R334W and L159S. Based on organoid results, two subjects started modulator treatment: one homozygous for complex allele Q359K_T360K, and the second with mutation E60K. Both subjects had major clinical benefit. CONCLUSIONS Measurements of residual CFTR function and rescue of function by CFTR modulators in intestinal organoids correlate closely with clinical data. Our results for reference genotypes concur with previous results. CFTR function measured in organoids can be used to guide precision medicine in patients with CF, positioning organoids as a potential in vitro model to bring treatment to patients carrying rare CFTR mutations.
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Affiliation(s)
- Anabela S Ramalho
- Dept of Development and Regeneration, Woman and Child Unit, CF Research Lab, KU Leuven, Leuven, Belgium
| | - Eva Fürstová
- Dept of Pediatrics, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Annelotte M Vonk
- Dept of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Centre, Utrecht, The Netherlands.,Regenerative Medicine Center, University Medical Centre, Utrecht, The Netherlands
| | - Marc Ferrante
- Dept of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders (TARGID), KU Leuven, Leuven, Belgium.,Dept of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
| | - Catherine Verfaillie
- Dept of Development and Regeneration, Stem Cell Biology and Embryology, KU Leuven, Leuven, Belgium
| | - Lieven Dupont
- Dept of Chronic Diseases, Metabolism and Ageing; Pneumology, KU Leuven, Leuven, Belgium.,Dept of Respiratory Diseases, University Hospital of Leuven, Leuven, Belgium
| | - Mieke Boon
- Dept of Development and Regeneration, Woman and Child Unit, CF Research Lab, KU Leuven, Leuven, Belgium.,Dept of Pediatrics, Pediatric Pulmonology, University Hospital of Leuven, Leuven, Belgium
| | - Marijke Proesmans
- Dept of Development and Regeneration, Woman and Child Unit, CF Research Lab, KU Leuven, Leuven, Belgium.,Dept of Pediatrics, Pediatric Pulmonology, University Hospital of Leuven, Leuven, Belgium
| | - Jeffrey M Beekman
- Dept of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Centre, Utrecht, The Netherlands.,Regenerative Medicine Center, University Medical Centre, Utrecht, The Netherlands
| | - Ifat Sarouk
- Pulmonology Pediatrics and National CF Center Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | | | - Francois Vermeulen
- Dept of Development and Regeneration, Woman and Child Unit, CF Research Lab, KU Leuven, Leuven, Belgium.,Dept of Pediatrics, Pediatric Pulmonology, University Hospital of Leuven, Leuven, Belgium
| | - Kris De Boeck
- Dept of Development and Regeneration, Woman and Child Unit, CF Research Lab, KU Leuven, Leuven, Belgium.,Dept of Pediatrics, Pediatric Pulmonology, University Hospital of Leuven, Leuven, Belgium
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Hagemeijer MC, Vonk AM, Awatade NT, Silva IAL, Tischer C, Hilsenstein V, Beekman JM, Amaral MD, Botelho HM. An open-source high-content analysis workflow for CFTR function measurements using the forskolin-induced swelling assay. Bioinformatics 2020; 36:5686-5694. [PMID: 33367496 DOI: 10.1093/bioinformatics/btaa1073] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 11/13/2020] [Accepted: 12/14/2020] [Indexed: 01/20/2023] Open
Abstract
MOTIVATION The forskolin-induced swelling (FIS) assay has become the preferential assay to predict the efficacy of approved and investigational CFTR-modulating drugs for individuals with cystic fibrosis (CF). Currently, no standardized quantification method of FIS data exists thereby hampering inter-laboratory reproducibility. RESULTS We developed a complete open-source workflow for standardized high-content analysis of CFTR function measurements in intestinal organoids using raw microscopy images as input. The workflow includes tools for (i) file and metadata handling; (ii) image quantification and (iii) statistical analysis. Our workflow reproduced results generated by published proprietary analysis protocols and enables standardized CFTR function measurements in CF organoids. AVAILABILITY All workflow components are open-source and freely available: the htmrenamer R package for file handling https://github.com/hmbotelho/htmrenamer; CellProfiler and ImageJ analysis scripts/pipelines https://github.com/hmbotelho/FIS_image_analysis; the Organoid Analyst application for statistical analysis https://github.com/hmbotelho/organoid_analyst; detailed usage instructions and a demonstration dataset https://github.com/hmbotelho/FIS_analysis. Distributed under GPL v3.0. SUPPLEMENTARY INFORMATION Supplementary information and a stepwise guide for software installation and data analysis for training purposes are available at Bioinformatics online.
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Affiliation(s)
- Marne C Hagemeijer
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands; Regenerative Medicine Center Utrecht, University Medical Centre Utrecht, 3584 EA, Utrecht, The Netherlands.,Department of Clinical Genetics, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Annelotte M Vonk
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands; Regenerative Medicine Center Utrecht, University Medical Centre Utrecht, 3584 EA, Utrecht, The Netherlands
| | - Nikhil T Awatade
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016, Lisboa, Portugal.,>School of Women's & Children's Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Iris A L Silva
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016, Lisboa, Portugal
| | - Christian Tischer
- European Molecular Biology Laboratory (EMBL), Centre for Bioimage Analysis (CBA), 69117, Heidelberg, Germany
| | - Volker Hilsenstein
- European Molecular Biology Laboratory (EMBL), Advanced Light Microscopy Facility (ALMF), 69117, Heidelberg, Germany.,Monash Micro Imaging, Monash University, Melbourne, Australia
| | - Jeffrey M Beekman
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands; Regenerative Medicine Center Utrecht, University Medical Centre Utrecht, 3584 EA, Utrecht, The Netherlands
| | - Margarida D Amaral
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016, Lisboa, Portugal
| | - Hugo M Botelho
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016, Lisboa, Portugal
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Graeber SY, van Mourik P, Vonk AM, Kruisselbrink E, Hirtz S, van der Ent CK, Mall MA, Beekman JM. Comparison of Organoid Swelling and In Vivo Biomarkers of CFTR Function to Determine Effects of Lumacaftor-Ivacaftor in Patients with Cystic Fibrosis Homozygous for the F508del Mutation. Am J Respir Crit Care Med 2020; 202:1589-1592. [PMID: 32687398 DOI: 10.1164/rccm.202004-1200le] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Simon Y Graeber
- Charité - Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health (BIH), Berlin, Germany.,German Centre for Lung Research (DZL), Berlin, Germany.,University of Heidelberg, Heidelberg, Germany and
| | | | | | | | | | | | - Marcus A Mall
- Charité - Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health (BIH), Berlin, Germany.,German Centre for Lung Research (DZL), Berlin, Germany.,University of Heidelberg, Heidelberg, Germany and
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40
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Berkers G, van der Meer R, van Mourik P, Vonk AM, Kruisselbrink E, Suen SW, Heijerman HG, Majoor CJ, Koppelman GH, Roukema J, Janssens HM, de Rijke YB, Kemper EM, Beekman JM, van der Ent CK, de Jonge HR. Clinical effects of the three CFTR potentiator treatments curcumin, genistein and ivacaftor in patients with the CFTR-S1251N gating mutation. J Cyst Fibros 2020; 19:955-961. [PMID: 32499204 DOI: 10.1016/j.jcf.2020.04.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 04/21/2020] [Accepted: 04/23/2020] [Indexed: 12/19/2022]
Abstract
BACKGROUND The natural food supplements curcumin and genistein, and the drug ivacaftor were found effective as CFTR potentiators in the organoids of individuals carrying a S1251N gating mutation, possibly in a synergistic fashion. Based on these in vitro findings, we evaluated the clinical efficacy of a treatment with curcumin, genistein and ivacaftor, in different combinations. METHODS In three multi-center trials people with CF carrying the S1251N mutation were treated for 8 weeks with curcumin+genistein, ivacaftor and ivacaftor+genistein. We evaluated change in lung function, sweat chloride concentration, CFQ-r, BMI and fecal elastase to determine the clinical effect. We evaluated the pharmacokinetic properties of the compounds by evaluating the concentration in plasma collected after treatment and the effect of the same plasma on the intestinal organoids. RESULTS A clear clinical effect of treatment with ivacaftor was observed, evidenced by a significant improvement in clinical parameters. In contrast we observed no clear clinical effect of curcumin and/or genistein, except for a small but significant reduction in sweat chloride and airway resistance. Plasma concentrations of the food supplements were low, as was the response of the organoids to this plasma. CONCLUSIONS We observed a clear clinical effect of treatment with ivacaftor, which is in line with the high responsiveness of the intestinal organoids to this drug. No clear clinical effect was observed of the treatment with curcumin and/or genistein, the low plasma concentration of these compounds emphasizes that pharmacokinetic properties of a compound have to be considered when in vitro experiments are performed.
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Affiliation(s)
- Gitte Berkers
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Renske van der Meer
- Department of Pulmonology, Haga Teaching Hospital, The Hague, the Netherlands
| | - Peter van Mourik
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Annelotte M Vonk
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands; Regenerative Medicine Center Utrecht, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Evelien Kruisselbrink
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands; Regenerative Medicine Center Utrecht, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Sylvia Wf Suen
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands; Regenerative Medicine Center Utrecht, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Harry Gm Heijerman
- Department of Pulmonology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Christof J Majoor
- Department of Respiratory Medicine, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Gerard H Koppelman
- Department of Pediatric Pulmonology and Pediatric Allergology and GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Beatrix Children's Hospital, Groningen, the Netherlands
| | - Jolt Roukema
- Department of Pediatric Pulmonology, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Hettie M Janssens
- Department of Pediatrics, division of Respiratory Medicine and Allergology, Erasmus Medical Center/Sophia Children's Hospital, University Hospital Rotterdam, the Netherlands
| | - Yolanda B de Rijke
- Department of Clinical Chemistry, Erasmus Medical Center, University Hospital Rotterdam, the Netherlands
| | - E Marleen Kemper
- Department of Pharmacy, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Jeffrey M Beekman
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands; Regenerative Medicine Center Utrecht, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Cornelis K van der Ent
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands.
| | - Hugo R de Jonge
- Department of Gastroenterology and Hepatology, Erasmus Medical Center, University Hospital Rotterdam, the Netherlands
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41
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Liu Z, Anderson JD, Deng L, Mackay S, Bailey J, Kersh L, Rowe SM, Guimbellot JS. Human Nasal Epithelial Organoids for Therapeutic Development in Cystic Fibrosis. Genes (Basel) 2020; 11:genes11060603. [PMID: 32485957 PMCID: PMC7349680 DOI: 10.3390/genes11060603] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/22/2020] [Accepted: 05/27/2020] [Indexed: 12/12/2022] Open
Abstract
We describe a human nasal epithelial (HNE) organoid model derived directly from patient samples that is well-differentiated and recapitulates the airway epithelium, including the expression of cilia, mucins, tight junctions, the cystic fibrosis transmembrane conductance regulator (CFTR), and ionocytes. This model requires few cells compared to airway epithelial monolayer cultures, with multiple outcome measurements depending on the application. A novel feature of the model is the predictive capacity of lumen formation, a marker of baseline CFTR function that correlates with short-circuit current activation of CFTR in monolayers and discriminates the cystic fibrosis (CF) phenotype from non-CF. Our HNE organoid model is amenable to automated measurements of forskolin-induced swelling (FIS), which distinguishes levels of CFTR activity. While the apical side is not easily accessible, RNA- and DNA-based therapies intended for systemic administration could be evaluated in vitro, or it could be used as an ex vivo biomarker of successful repair of a mutant gene. In conclusion, this highly differentiated airway epithelial model could serve as a surrogate biomarker to assess correction of the mutant gene in CF or other diseases, recapitulating the phenotypic and genotypic diversity of the population.
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Affiliation(s)
- Zhongyu Liu
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham (UAB), Birmingham, AL 35294, USA; (Z.L.); (J.D.A.); (S.M.); (L.K.); (S.M.R.)
- Department of Pediatrics, Division of Pulmonary and Sleep Medicine, UAB, Birmingham, AL 35233, USA; (L.D.); (J.B.)
| | - Justin D. Anderson
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham (UAB), Birmingham, AL 35294, USA; (Z.L.); (J.D.A.); (S.M.); (L.K.); (S.M.R.)
- Department of Pediatrics, Division of Pulmonary and Sleep Medicine, UAB, Birmingham, AL 35233, USA; (L.D.); (J.B.)
| | - Lily Deng
- Department of Pediatrics, Division of Pulmonary and Sleep Medicine, UAB, Birmingham, AL 35233, USA; (L.D.); (J.B.)
| | - Stephen Mackay
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham (UAB), Birmingham, AL 35294, USA; (Z.L.); (J.D.A.); (S.M.); (L.K.); (S.M.R.)
- Department of Pediatrics, Division of Pulmonary and Sleep Medicine, UAB, Birmingham, AL 35233, USA; (L.D.); (J.B.)
| | - Johnathan Bailey
- Department of Pediatrics, Division of Pulmonary and Sleep Medicine, UAB, Birmingham, AL 35233, USA; (L.D.); (J.B.)
| | - Latona Kersh
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham (UAB), Birmingham, AL 35294, USA; (Z.L.); (J.D.A.); (S.M.); (L.K.); (S.M.R.)
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, UAB, Birmingham, AL 35294, USA
| | - Steven M. Rowe
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham (UAB), Birmingham, AL 35294, USA; (Z.L.); (J.D.A.); (S.M.); (L.K.); (S.M.R.)
- Department of Pediatrics, Division of Pulmonary and Sleep Medicine, UAB, Birmingham, AL 35233, USA; (L.D.); (J.B.)
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, UAB, Birmingham, AL 35294, USA
- Department of Cell, Developmental and Integrative Biology, UAB, Birmingham, AL 35294, USA
| | - Jennifer S. Guimbellot
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham (UAB), Birmingham, AL 35294, USA; (Z.L.); (J.D.A.); (S.M.); (L.K.); (S.M.R.)
- Department of Pediatrics, Division of Pulmonary and Sleep Medicine, UAB, Birmingham, AL 35233, USA; (L.D.); (J.B.)
- Correspondence: ; Tel.: +1-205-234-0250; Fax: +1-205-975-5983
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42
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Rectal Organoids Enable Personalized Treatment of Cystic Fibrosis. Cell Rep 2020; 26:1701-1708.e3. [PMID: 30759382 DOI: 10.1016/j.celrep.2019.01.068] [Citation(s) in RCA: 189] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 10/08/2018] [Accepted: 01/17/2019] [Indexed: 12/16/2022] Open
Abstract
In vitro drug tests using patient-derived stem cell cultures offer opportunities to individually select efficacious treatments. Here, we provide a study that demonstrates that in vitro drug responses in rectal organoids from individual patients with cystic fibrosis (CF) correlate with changes in two in vivo therapeutic endpoints. We measured individual in vitro efficaciousness using a functional assay in rectum-derived organoids based on forskolin-induced swelling and studied the correlation with in vivo effects. The in vitro organoid responses correlated with both change in pulmonary response and change in sweat chloride concentration. Receiver operating characteristic curves indicated good-to-excellent accuracy of the organoid-based test for defining clinical responses. This study indicates that an in vitro assay using stem cell cultures can prospectively select efficacious treatments for patients and suggests that biobanked stem cell resources can be used to tailor individual treatments in a cost-effective and patient-friendly manner.
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43
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Geurts MH, de Poel E, Amatngalim GD, Oka R, Meijers FM, Kruisselbrink E, van Mourik P, Berkers G, de Winter-de Groot KM, Michel S, Muilwijk D, Aalbers BL, Mullenders J, Boj SF, Suen SWF, Brunsveld JE, Janssens HM, Mall MA, Graeber SY, van Boxtel R, van der Ent CK, Beekman JM, Clevers H. CRISPR-Based Adenine Editors Correct Nonsense Mutations in a Cystic Fibrosis Organoid Biobank. Cell Stem Cell 2020; 26:503-510.e7. [PMID: 32084388 DOI: 10.1016/j.stem.2020.01.019] [Citation(s) in RCA: 112] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 12/11/2019] [Accepted: 01/27/2020] [Indexed: 02/06/2023]
Abstract
Adenine base editing (ABE) enables enzymatic conversion from A-T into G-C base pairs. ABE holds promise for clinical application, as it does not depend on the introduction of double-strand breaks, contrary to conventional CRISPR/Cas9-mediated genome engineering. Here, we describe a cystic fibrosis (CF) intestinal organoid biobank, representing 664 patients, of which ~20% can theoretically be repaired by ABE. We apply SpCas9-ABE (PAM recognition sequence: NGG) and xCas9-ABE (PAM recognition sequence: NGN) on four selected CF organoid samples. Genetic and functional repair was obtained in all four cases, while whole-genome sequencing (WGS) of corrected lines of two patients did not detect off-target mutations. These observations exemplify the value of large, patient-derived organoid biobanks representing hereditary disease and indicate that ABE may be safely applied in human cells.
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Affiliation(s)
- Maarten H Geurts
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Eyleen de Poel
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, the Netherlands; Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT Utrecht, the Netherlands
| | - Gimano D Amatngalim
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, the Netherlands; Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT Utrecht, the Netherlands
| | - Rurika Oka
- Princess Maxima Center, 3584 CS Utrecht, the Netherlands; Oncode Institute, Princess Maxima Center, 3584 CS Utrecht, the Netherlands
| | - Fleur M Meijers
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, the Netherlands; Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT Utrecht, the Netherlands
| | - Evelien Kruisselbrink
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, the Netherlands; Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT Utrecht, the Netherlands
| | - Peter van Mourik
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, the Netherlands
| | - Gitte Berkers
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, the Netherlands
| | - Karin M de Winter-de Groot
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, the Netherlands
| | - Sabine Michel
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, the Netherlands
| | - Danya Muilwijk
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, the Netherlands
| | - Bente L Aalbers
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, the Netherlands
| | | | - Sylvia F Boj
- Hubrecht Organoid Technology, 3584 CM, Utrecht, the Netherlands
| | - Sylvia W F Suen
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, the Netherlands; Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT Utrecht, the Netherlands
| | - Jesse E Brunsveld
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, the Netherlands; Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT Utrecht, the Netherlands
| | - Hettie M Janssens
- Department of Pediatrics, division of Respiratory Medicine and Allergology, ErasmusMC-Sophia Children's Hospital, University Hospital Rotterdam, 3015 GD Rotterdam, the Netherlands
| | - Marcus A Mall
- Department of Pediatric Pulmonology, Immunology and Critical Care Medicine, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany; Berlin Institute of Health (BIH), 10178 Berlin, Germany
| | - Simon Y Graeber
- Department of Pediatric Pulmonology, Immunology and Critical Care Medicine, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany; Berlin Institute of Health (BIH), 10178 Berlin, Germany
| | - Ruben van Boxtel
- Princess Maxima Center, 3584 CS Utrecht, the Netherlands; Oncode Institute, Princess Maxima Center, 3584 CS Utrecht, the Netherlands
| | - Cornelis K van der Ent
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, the Netherlands
| | - Jeffrey M Beekman
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, the Netherlands; Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT Utrecht, the Netherlands.
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands.
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44
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Lopes-Pacheco M. CFTR Modulators: The Changing Face of Cystic Fibrosis in the Era of Precision Medicine. Front Pharmacol 2020; 10:1662. [PMID: 32153386 PMCID: PMC7046560 DOI: 10.3389/fphar.2019.01662] [Citation(s) in RCA: 275] [Impact Index Per Article: 68.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 12/19/2019] [Indexed: 12/22/2022] Open
Abstract
Cystic fibrosis (CF) is a lethal inherited disease caused by mutations in the CF transmembrane conductance regulator (CFTR) gene, which result in impairment of CFTR mRNA and protein expression, function, stability or a combination of these. Although CF leads to multifaceted clinical manifestations, the respiratory disorder represents the major cause of morbidity and mortality of these patients. The life expectancy of CF patients has substantially lengthened due to early diagnosis and improvements in symptomatic therapeutic regimens. Quality of life remains nevertheless limited, as these individuals are subjected to considerable clinical, psychosocial and economic burdens. Since the discovery of the CFTR gene in 1989, tremendous efforts have been made to develop therapies acting more upstream on the pathogenesis cascade, thereby overcoming the underlying dysfunctions caused by CFTR mutations. In this line, the advances in cell-based high-throughput screenings have been facilitating the fast-tracking of CFTR modulators. These modulator drugs have the ability to enhance or even restore the functional expression of specific CF-causing mutations, and they have been classified into five main groups depending on their effects on CFTR mutations: potentiators, correctors, stabilizers, read-through agents, and amplifiers. To date, four CFTR modulators have reached the market, and these pharmaceutical therapies are transforming patients' lives with short- and long-term improvements in clinical outcomes. Such breakthroughs have paved the way for the development of novel CFTR modulators, which are currently under experimental and clinical investigations. Furthermore, recent insights into the CFTR structure will be useful for the rational design of next-generation modulator drugs. This review aims to provide a summary of recent developments in CFTR-directed therapeutics. Barriers and future directions are also discussed in order to optimize treatment adherence, identify feasible and sustainable solutions for equitable access to these therapies, and continue to expand the pipeline of novel modulators that may result in effective precision medicine for all individuals with CF.
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Affiliation(s)
- Miquéias Lopes-Pacheco
- Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
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45
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de Poel E, Lefferts JW, Beekman JM. Intestinal organoids for Cystic Fibrosis research. J Cyst Fibros 2019; 19 Suppl 1:S60-S64. [PMID: 31787574 DOI: 10.1016/j.jcf.2019.11.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 10/14/2019] [Accepted: 11/07/2019] [Indexed: 11/30/2022]
Abstract
Significant progress has been made in the development of CFTR modulator therapy; however, current CFTR modulator therapies are only available for a minority of the CF-patient population. Additionally, heterogeneity in in vivo modulator response has been reported among individuals carrying homozygous F508del-CFTR, adding to the desire for an optimal prediction of response-to-therapy on an individual level. In the last decade, a lot of progress has been made in the development of primary cell cultures into 3D patient-derived disease models. The advantage of these models is that the endogenous CFTR function is affected by the patient's mutation as well as other genetic or environmental factors. In this review we focus on intestinal organoids as in vitro model for CF, enabling for CF disease classification, drug development and treatment optimization in a personalized manner, taking into account rare CFTR mutations and clinical heterogeneity among individuals with CF.
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Affiliation(s)
- E de Poel
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, the Netherlands; Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT Utrecht, the Netherlands
| | - J W Lefferts
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, the Netherlands; Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT Utrecht, the Netherlands
| | - J M Beekman
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584 EA Utrecht, the Netherlands; Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584 CT Utrecht, the Netherlands.
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46
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Forskolin-induced swelling of intestinal organoids correlates with disease severity in adults with cystic fibrosis and homozygous F508del mutations. J Cyst Fibros 2019; 19:614-619. [PMID: 31735562 DOI: 10.1016/j.jcf.2019.10.022] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 10/01/2019] [Accepted: 10/22/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND CFTR function measurements in intestinal organoids may help to better characterise individual disease expression in F508del homozygous people. Our objective was to study correlations between CFTR function as measured with forskolin-induced swelling in rectal organoids with clinical parameters in adult patients with homozygous F508del mutations. METHODS Multicentre observational study. Thirty-four adults underwent rectal biopsy, pulmonary function tests (FEV1 and FVC), chest X-ray and chest CT. Body-mass index (BMI) was assessed at study visit and exacerbation rate was determined during five years prior to study visit. Organoids were cultured and measured after stimulation with 5 µm forskolin for three hours to quantitate CFTR residual function. FINDINGS FIS was positively correlated with FEV1 (r = 0.36, 95% CI 0.02-0.62, p = 0.04) and BMI (r = 0.42, 95% CI 0.09-0.66, p = 0.015). FIS was negatively correlated with PRAGMA-CF CT score for% of disease (r = -0.37, 95% CI -0.62- -0.03, p = 0.049). We found no significant correlation between FIS and chest radiography score for CF (r = -0.16, 95% CI -0.48-0.20, p = 0.44). We observed a trend between higher FIS and a lower mean number of exacerbations over the last 5 years of observation, but this was not statistically significant (Poisson regression, p = 0.089). INTERPRETATION FIS of intestinal organoids varied between subjects with homozygous F508del and correlated with pulmonary and nutritional parameters. These findings suggest that differences at low CFTR residual function may contribute to clinical heterogeneity in F508del homozygous patients and small changes in CFTR residual function might impact long-term disease expression.
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Is it cystic fibrosis? The challenges of diagnosing cystic fibrosis. Paediatr Respir Rev 2019; 31:6-8. [PMID: 30967347 DOI: 10.1016/j.prrv.2019.02.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 02/20/2019] [Indexed: 01/10/2023]
Abstract
The spectrum of conditions caused by abnormal CFTR function is broad - from 'classic' cystic fibrosis (CF) to single organ conditions termed CFTR-related disorders. Defining and securing the diagnosis in an important minority of patients can be a challenge as the sweat test is equivocal or normal; the impact this has on the patient (at different stages of their life) can be very significant as it has the potential to lead to misdiagnosis and over (or under) treatment with associated psychological burden. The nasal potential difference test and intestinal current measurements are physiological measurements of CFTR function and thus can provide important diagnostic information. This article provides an overview of the latest developments in CF diagnostics, outlining the approach to be taken when the diagnosis is unclear and some of the areas of uncertainty.
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van Mourik P, Beekman JM, van der Ent CK. Intestinal organoids to model cystic fibrosis. Eur Respir J 2019; 54:13993003.02379-2018. [PMID: 31023844 DOI: 10.1183/13993003.02379-2018] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 04/07/2019] [Indexed: 12/18/2022]
Affiliation(s)
- Peter van Mourik
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Jeffrey M Beekman
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.,Regenerative Medicine Center Utrecht, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Cornelis K van der Ent
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
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Yin YB, de Jonge HR, Wu X, Yin YL. Mini-gut: a promising model for drug development. Drug Discov Today 2019; 24:1784-1794. [PMID: 31212027 DOI: 10.1016/j.drudis.2019.06.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 05/01/2019] [Accepted: 06/11/2019] [Indexed: 02/08/2023]
Abstract
Until recently, major advances in drug development have been hampered by a lack of proper cell and tissue models; but the introduction of organoid technology has revolutionized this field. At the level of the gastrointestinal tract, the so-called mini-gut comprises all major cell types of native intestine and recapitulates the composition and function of native intestinal epithelium. The mini-gut can be classified as an intestinal organoid (IO), derived from pluripotent stem cells, or as an enteroid, consisting only of epithelial cells and generated from adult stem cells. Both classifications have been used as models to develop drugs against cystic fibrosis, cancer and infectious disease, as well as for drug screening, personalized medicine and the development of new medical tools. In this review, we highlight and discuss the importance of mini-guts for drug development and point out their limitations and future prospects.
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Affiliation(s)
- Yue-Bang Yin
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences; National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production; Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production, Changsha, Hunan, 410125, China; Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Hugo R de Jonge
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Xin Wu
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences; National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production; Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production, Changsha, Hunan, 410125, China; Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang 330096, China.
| | - Yu-Long Yin
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences; National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production; Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production, Changsha, Hunan, 410125, China.
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Chen KG, Zhong P, Zheng W, Beekman JM. Pharmacological analysis of CFTR variants of cystic fibrosis using stem cell-derived organoids. Drug Discov Today 2019; 24:2126-2138. [PMID: 31173911 DOI: 10.1016/j.drudis.2019.05.029] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 05/09/2019] [Accepted: 05/30/2019] [Indexed: 12/29/2022]
Abstract
Cystic fibrosis (CF) is a life-shortening genetic disease caused by mutations of CFTR, the gene encoding cystic fibrosis transmembrane conductance regulator. Despite considerable progress in CF therapies, targeting specific CFTR genotypes based on small molecules has been hindered because of the substantial genetic heterogeneity of CFTR mutations in patients with CF, which is difficult to assess by animal models in vivo. There are broadly four classes (e.g., II, III, and IV) of CF genotypes that differentially respond to current CF drugs (e.g., VX-770 and VX-809). In this review, we shed light on the pharmacogenomics of diverse CFTR mutations and the emerging role of stem cell-based organoids in predicting the CF drug response. We discuss mechanisms that underlie differential CF drug responses both in organoid-based assays and in CF clinical trials, thereby facilitating the precision design of safer and more effective therapies for individual patients with CF.
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Affiliation(s)
- Kevin G Chen
- NIH Stem Cell Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA; Department of Microbiology and Immunology, Georgetown University Medical Center, Washington DC, 20057, USA.
| | - Pingyu Zhong
- Singapore Immunology Network, Agency for Science, Technology and Research (A⁎STAR), 8A Biomedical Grove, Singapore 138648, Singapore
| | - Wei Zheng
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jeffrey M Beekman
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, Regenerative Medicine Center Utrecht, University Medical Center, Utrecht University, Utrecht, The Netherlands
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