1
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Bulcaen M, Kortleven P, Liu RB, Maule G, Dreano E, Kelly M, Ensinck MM, Thierie S, Smits M, Ciciani M, Hatton A, Chevalier B, Ramalho AS, Casadevall I Solvas X, Debyser Z, Vermeulen F, Gijsbers R, Sermet-Gaudelus I, Cereseto A, Carlon MS. Prime editing functionally corrects cystic fibrosis-causing CFTR mutations in human organoids and airway epithelial cells. Cell Rep Med 2024; 5:101544. [PMID: 38697102 PMCID: PMC11148721 DOI: 10.1016/j.xcrm.2024.101544] [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: 07/26/2023] [Revised: 01/16/2024] [Accepted: 04/10/2024] [Indexed: 05/04/2024]
Abstract
Prime editing is a recent, CRISPR-derived genome editing technology capable of introducing precise nucleotide substitutions, insertions, and deletions. Here, we present prime editing approaches to correct L227R- and N1303K-CFTR, two mutations that cause cystic fibrosis and are not eligible for current market-approved modulator therapies. We show that, upon DNA correction of the CFTR gene, the complex glycosylation, localization, and, most importantly, function of the CFTR protein are restored in HEK293T and 16HBE cell lines. These findings were subsequently validated in patient-derived rectal organoids and human nasal epithelial cells. Through analysis of predicted and experimentally identified candidate off-target sites in primary stem cells, we confirm previous reports on the high prime editor (PE) specificity and its potential for a curative CF gene editing therapy. To facilitate future screening of genetic strategies in a translational CF model, a machine learning algorithm was developed for dynamic quantification of CFTR function in organoids (DETECTOR: "detection of targeted editing of CFTR in organoids").
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Affiliation(s)
- Mattijs Bulcaen
- Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Belgium; Department of Chronic Diseases and Metabolism, KU Leuven, 3000 Leuven, Belgium.
| | - Phéline Kortleven
- Department of Chronic Diseases and Metabolism, KU Leuven, 3000 Leuven, Belgium
| | - Ronald B Liu
- Department of Biosystems, KU Leuven, 3000 Leuven, Belgium; School of Engineering, University of Edinburgh, EH9 3JL Edinburgh, UK
| | - Giulia Maule
- Department of CIBIO, University of Trento, 38123 Povo-Trento, Italy
| | - Elise Dreano
- INSERM, CNRS, Institut Necker Enfants Malades, 75015 Paris, France; Université Paris-Cité, 75015 Paris, France
| | - Mairead Kelly
- INSERM, CNRS, Institut Necker Enfants Malades, 75015 Paris, France; Université Paris-Cité, 75015 Paris, France
| | - Marjolein M Ensinck
- Department of Chronic Diseases and Metabolism, KU Leuven, 3000 Leuven, Belgium
| | - Sam Thierie
- Department of Chronic Diseases and Metabolism, KU Leuven, 3000 Leuven, Belgium
| | - Maxime Smits
- Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Belgium; Leuven Viral Vector Core, KU Leuven, 3000 Leuven, Belgium
| | - Matteo Ciciani
- Department of CIBIO, University of Trento, 38123 Povo-Trento, Italy
| | - Aurelie Hatton
- INSERM, CNRS, Institut Necker Enfants Malades, 75015 Paris, France; Université Paris-Cité, 75015 Paris, France
| | - Benoit Chevalier
- INSERM, CNRS, Institut Necker Enfants Malades, 75015 Paris, France; Université Paris-Cité, 75015 Paris, France
| | - Anabela S Ramalho
- Department of Development and Regeneration, KU Leuven, 3000 Leuven, Belgium
| | | | - Zeger Debyser
- Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Belgium; Leuven Viral Vector Core, KU Leuven, 3000 Leuven, Belgium
| | - François Vermeulen
- Department of Development and Regeneration, KU Leuven, 3000 Leuven, Belgium; Department of Pediatrics, UZ Leuven, 3000 Leuven, Belgium
| | - Rik Gijsbers
- Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Belgium; Leuven Viral Vector Core, KU Leuven, 3000 Leuven, Belgium
| | - Isabelle Sermet-Gaudelus
- INSERM, CNRS, Institut Necker Enfants Malades, 75015 Paris, France; Université Paris-Cité, 75015 Paris, France; Cystic Fibrosis National Pediatric Reference Center, Pneumo-Allergologie Pédiatrique, Hôpital Necker Enfants Malades, Assistance Publique Hôpitaux de Paris (AP-HP), 75015 Paris, France; European Reference Network, ERN-Lung CF, 60596 Frankfurt am Mein, Germany
| | - Anna Cereseto
- Department of CIBIO, University of Trento, 38123 Povo-Trento, Italy
| | - Marianne S Carlon
- Department of Chronic Diseases and Metabolism, KU Leuven, 3000 Leuven, Belgium; Leuven Viral Vector Core, KU Leuven, 3000 Leuven, Belgium.
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2
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Ferreira FC, Buarque CD, Lopes-Pacheco M. Organic Synthesis and Current Understanding of the Mechanisms of CFTR Modulator Drugs Ivacaftor, Tezacaftor, and Elexacaftor. Molecules 2024; 29:821. [PMID: 38398574 PMCID: PMC10891718 DOI: 10.3390/molecules29040821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/02/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
The monogenic rare disease Cystic Fibrosis (CF) is caused by mutations in the gene encoding the CF transmembrane conductance (CFTR) protein, an anion channel expressed at the apical plasma membrane of epithelial cells. The discovery and subsequent development of CFTR modulators-small molecules acting on the basic molecular defect in CF-have revolutionized the standard of care for people with CF (PwCF), thus drastically improving their clinical features, prognosis, and quality of life. Currently, four of these drugs are approved for clinical use: potentiator ivacaftor (VX-770) alone or in combination with correctors lumacaftor, (VX-809), tezacaftor (VX-661), and elexacaftor (VX-445). Noteworthily, the triple combinatorial therapy composed of ivacaftor, tezacaftor, and elexacaftor constitutes the most effective modulator therapy nowadays for the majority of PwCF. In this review, we exploit the organic synthesis of ivacaftor, tezacaftor, and elexacaftor by providing a retrosynthetic drug analysis for these CFTR modulators. Furthermore, we describe the current understanding of the mechanisms of action (MoA's) of these compounds by discussing several studies that report the key findings on the molecular mechanisms underlying their action on the CFTR protein.
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Affiliation(s)
- Filipa C. Ferreira
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal
| | - Camilla D. Buarque
- Department of Chemistry, Pontifical Catholic University of Rio de Janeiro (PUC-Rio), Rio de Janeiro 22435-900, RJ, Brazil
| | - Miquéias Lopes-Pacheco
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal
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3
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Cao L, Wu Y, Gong Y, Zhou Q. Small molecule modulators of cystic fibrosis transmembrane conductance regulator (CFTR): Structure, classification, and mechanisms. Eur J Med Chem 2024; 265:116120. [PMID: 38194776 DOI: 10.1016/j.ejmech.2023.116120] [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: 11/18/2023] [Revised: 12/28/2023] [Accepted: 12/31/2023] [Indexed: 01/11/2024]
Abstract
The advent of small molecule modulators targeting the cystic fibrosis transmembrane conductance regulator (CFTR) has revolutionized the treatment of persons with cystic fibrosis (CF) (pwCF). Presently, these small molecule CFTR modulators have gained approval for usage in approximately 90 % of adult pwCF. Ongoing drug development endeavors are focused on optimizing the therapeutic benefits while mitigating potential adverse effects associated with this treatment approach. Based on their mode of interaction with CFTR, these drugs can be classified into two distinct categories: specific CFTR modulators and non-specific CFTR modulators. Specific CFTR modulators encompass potentiators and correctors, whereas non-specific CFTR modulators encompass activators, proteostasis modulators, stabilizers, reader-through agents, and amplifiers. Currently, four small molecule modulators, all classified as potentiators and correctors, have obtained marketing approval. Furthermore, numerous novel small molecule modulators, exhibiting diverse mechanisms of action, are currently undergoing development. This review aims to explore the classification, mechanisms of action, molecular structures, developmental processes, and interrelationships among small molecule CFTR modulators.
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Affiliation(s)
- Luyang Cao
- China Pharmaceutical University, Nanjing, 210009, PR China
| | - Yong Wu
- Jiangsu Vcare PharmaTech Co., Ltd., Huakang Road 136, Biotech and Pharmaceutical Valley, Jiangbei New Area, Nanjing, 211800, PR China
| | - Yanchun Gong
- Jiangsu Vcare PharmaTech Co., Ltd., Huakang Road 136, Biotech and Pharmaceutical Valley, Jiangbei New Area, Nanjing, 211800, PR China.
| | - Qingfa Zhou
- China Pharmaceutical University, Nanjing, 210009, PR China.
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4
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Tiroille V, Krug A, Bokobza E, Kahi M, Bulcaen M, Ensinck MM, Geurts MH, Hendriks D, Vermeulen F, Larbret F, Gutierrez-Guerrero A, Chen Y, Van Zundert I, Rocha S, Rios AC, Medaer L, Gijsbers R, Mangeot PE, Clevers H, Carlon MS, Bost F, Verhoeyen E. Nanoblades allow high-level genome editing in murine and human organoids. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:57-74. [PMID: 37435135 PMCID: PMC10331042 DOI: 10.1016/j.omtn.2023.06.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 06/04/2023] [Indexed: 07/13/2023]
Abstract
Genome engineering has become more accessible thanks to the CRISPR-Cas9 gene-editing system. However, using this technology in synthetic organs called "organoids" is still very inefficient. This is due to the delivery methods for the CRISPR-Cas9 machinery, which include electroporation of CRISPR-Cas9 DNA, mRNA, or ribonucleoproteins containing the Cas9-gRNA complex. However, these procedures are quite toxic for the organoids. Here, we describe the use of the "nanoblade (NB)" technology, which outperformed by far gene-editing levels achieved to date for murine- and human tissue-derived organoids. We reached up to 75% of reporter gene knockout in organoids after treatment with NBs. Indeed, high-level NB-mediated knockout for the androgen receptor encoding gene and the cystic fibrosis transmembrane conductance regulator gene was achieved with single gRNA or dual gRNA containing NBs in murine prostate and colon organoids. Likewise, NBs achieved 20%-50% gene editing in human organoids. Most importantly, in contrast to other gene-editing methods, this was obtained without toxicity for the organoids. Only 4 weeks are required to obtain stable gene knockout in organoids and NBs simplify and allow rapid genome editing in organoids with little to no side effects including unwanted insertion/deletions in off-target sites thanks to transient Cas9/RNP expression.
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Affiliation(s)
- Victor Tiroille
- Université Côte d’Azur, INSERM, C3M, 06204 Nice, France
- Equipe labélisée Ligue National Contre le Cancer, Basel, Switzerland
| | - Adrien Krug
- Université Côte d’Azur, INSERM, C3M, 06204 Nice, France
| | - Emma Bokobza
- Université Côte d’Azur, INSERM, C3M, 06204 Nice, France
- Equipe labélisée Ligue National Contre le Cancer, Basel, Switzerland
| | - Michel Kahi
- Université Côte d’Azur, INSERM, C3M, 06204 Nice, France
- Equipe labélisée Ligue National Contre le Cancer, Basel, Switzerland
| | - Mattijs Bulcaen
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, Faculty of Medicine, KU Leuven, Leuven, Belgium
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Marjolein M. Ensinck
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, Faculty of Medicine, KU Leuven, Leuven, Belgium
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Maarten H. Geurts
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
- Oncode Institute, Hubrecht Institute, Utrecht, the Netherlands
| | - Delilah Hendriks
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
- Oncode Institute, Hubrecht Institute, Utrecht, the Netherlands
| | | | | | - Alejandra Gutierrez-Guerrero
- CIRI – International Center for Infectiology Research, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Université Lyon, F-69007 Lyon, France
| | - Yu Chen
- Human Oncology and Pathogenesis Program, Department of Medicine, Memorial Sloan; Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Indra Van Zundert
- Synthetic Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, the Netherlands
| | - Susana Rocha
- Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Anne C. Rios
- Oncode Institute, Hubrecht Institute, Utrecht, the Netherlands
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Louise Medaer
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, Faculty of Medicine, KU Leuven, Leuven, Belgium
| | - Rik Gijsbers
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, Faculty of Medicine, KU Leuven, Leuven, Belgium
| | - Philippe E. Mangeot
- CIRI – International Center for Infectiology Research, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Université Lyon, F-69007 Lyon, France
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
- Oncode Institute, Hubrecht Institute, Utrecht, the Netherlands
| | - Marianne S. Carlon
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, Faculty of Medicine, KU Leuven, Leuven, Belgium
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Frédéric Bost
- Université Côte d’Azur, INSERM, C3M, 06204 Nice, France
- Equipe labélisée Ligue National Contre le Cancer, Basel, Switzerland
| | - Els Verhoeyen
- Université Côte d’Azur, INSERM, C3M, 06204 Nice, France
- CIRI – International Center for Infectiology Research, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Université Lyon, F-69007 Lyon, France
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5
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Graeber SY, Balázs A, Ziegahn N, Rubil T, Vitzthum C, Piehler L, Drescher M, Seidel K, Rohrbach A, Röhmel J, Thee S, Duerr J, Mall MA, Stahl M. Personalized CFTR Modulator Therapy for G85E and N1303K Homozygous Patients with Cystic Fibrosis. Int J Mol Sci 2023; 24:12365. [PMID: 37569738 PMCID: PMC10418744 DOI: 10.3390/ijms241512365] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/28/2023] [Accepted: 07/31/2023] [Indexed: 08/13/2023] Open
Abstract
CFTR modulator therapy with elexacaftor/tezacaftor/ivacaftor (ETI) has been approved for people with CF and at least one F508del allele in Europe. In the US, the ETI label has been expanded to 177 rare CFTR mutations responsive in Fischer rat thyroid cells, including G85E, but not N1303K. However, knowledge on the effect of ETI on G85E or N1303K CFTR function remains limited. In vitro effects of ETI were measured in primary human nasal epithelial cultures (pHNECs) of a G85E homozygous patient and an N1303K homozygous patient. Effects of ETI therapy in vivo in these patients were assessed using clinical outcomes, including multiple breath washout and lung MRI, and the CFTR biomarkers sweat chloride concentration (SCC), nasal potential difference (NPD) and intestinal current measurement (ICM), before and after initiation of ETI. ETI increased CFTR-mediated chloride transport in G85E/G85E and N1303K/N1303K pHNECs. In the G85E/G85E and the N1303K/N1303K patient, we observed an improvement in lung function, SCC, and CFTR function in the respiratory and rectal epithelium after initiation of ETI. The approach of combining preclinical in vitro testing with subsequent in vivo verification can facilitate access to CFTR modulator therapy and enhance precision medicine for patients carrying rare CFTR mutations.
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Affiliation(s)
- Simon Y. Graeber
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine and Cystic Fibrosis Center, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 13353 Berlin, Germany
- German Centre for Lung Research (DZL), Associated Partner Site, 13353 Berlin, Germany
- Berlin Institute of Health (BIH) at Charité–Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Anita Balázs
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine and Cystic Fibrosis Center, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 13353 Berlin, Germany
- German Centre for Lung Research (DZL), Associated Partner Site, 13353 Berlin, Germany
| | - Niklas Ziegahn
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine and Cystic Fibrosis Center, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 13353 Berlin, Germany
| | - Tihomir Rubil
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine and Cystic Fibrosis Center, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 13353 Berlin, Germany
- German Centre for Lung Research (DZL), Associated Partner Site, 13353 Berlin, Germany
| | - Constanze Vitzthum
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine and Cystic Fibrosis Center, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 13353 Berlin, Germany
- German Centre for Lung Research (DZL), Associated Partner Site, 13353 Berlin, Germany
| | - Linus Piehler
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine and Cystic Fibrosis Center, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 13353 Berlin, Germany
- German Centre for Lung Research (DZL), Associated Partner Site, 13353 Berlin, Germany
| | - Marika Drescher
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine and Cystic Fibrosis Center, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 13353 Berlin, Germany
- German Centre for Lung Research (DZL), Associated Partner Site, 13353 Berlin, Germany
| | - Kathrin Seidel
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine and Cystic Fibrosis Center, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 13353 Berlin, Germany
- German Centre for Lung Research (DZL), Associated Partner Site, 13353 Berlin, Germany
| | - Alexander Rohrbach
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine and Cystic Fibrosis Center, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 13353 Berlin, Germany
- German Centre for Lung Research (DZL), Associated Partner Site, 13353 Berlin, Germany
| | - Jobst Röhmel
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine and Cystic Fibrosis Center, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 13353 Berlin, Germany
- German Centre for Lung Research (DZL), Associated Partner Site, 13353 Berlin, Germany
- Berlin Institute of Health (BIH) at Charité–Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Stephanie Thee
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine and Cystic Fibrosis Center, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 13353 Berlin, Germany
- German Centre for Lung Research (DZL), Associated Partner Site, 13353 Berlin, Germany
- Berlin Institute of Health (BIH) at Charité–Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Julia Duerr
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine and Cystic Fibrosis Center, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 13353 Berlin, Germany
- German Centre for Lung Research (DZL), Associated Partner Site, 13353 Berlin, Germany
| | - Marcus A. Mall
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine and Cystic Fibrosis Center, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 13353 Berlin, Germany
- German Centre for Lung Research (DZL), Associated Partner Site, 13353 Berlin, Germany
- Berlin Institute of Health (BIH) at Charité–Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Mirjam Stahl
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine and Cystic Fibrosis Center, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 13353 Berlin, Germany
- German Centre for Lung Research (DZL), Associated Partner Site, 13353 Berlin, Germany
- Berlin Institute of Health (BIH) at Charité–Universitätsmedizin Berlin, 10117 Berlin, Germany
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6
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Pedrazzoli E, Bianchi A, Umbach A, Amistadi S, Brusson M, Frati G, Ciciani M, Badowska KA, Arosio D, Miccio A, Cereseto A, Casini A. An optimized SpCas9 high-fidelity variant for direct protein delivery. Mol Ther 2023; 31:2257-2265. [PMID: 36905119 PMCID: PMC10362380 DOI: 10.1016/j.ymthe.2023.03.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/08/2023] [Accepted: 03/07/2023] [Indexed: 03/12/2023] Open
Abstract
Electroporation of the Cas9 ribonucleoprotein (RNP) complex offers the advantage of preventing off-target cleavages and potential immune responses produced by long-term expression of the nuclease. Nevertheless, the majority of engineered high-fidelity Streptococcus pyogenes Cas9 (SpCas9) variants are less active than the wild-type enzyme and are not compatible with RNP delivery. Building on our previous studies on evoCas9, we developed a high-fidelity SpCas9 variant suitable for RNP delivery. The editing efficacy and precision of the recombinant high-fidelity Cas9 (rCas9HF), characterized by the K526D substitution, was compared with the R691A mutant (HiFi Cas9), which is currently the only available high-fidelity Cas9 that can be used as an RNP. The comparative analysis was extended to gene substitution experiments where the two high fidelities were used in combination with a DNA donor template, generating different ratios of non-homologous end joining (NHEJ) versus homology-directed repair (HDR) for precise editing. The analyses revealed a heterogeneous efficacy and precision indicating different targeting capabilities between the two variants throughout the genome. The development of rCas9HF, characterized by an editing profile diverse from the currently used HiFi Cas9 in RNP electroporation, increases the genome editing solutions for the highest precision and efficient applications.
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Affiliation(s)
- Eleonora Pedrazzoli
- Department CIBIO, Laboratory of Molecular Virology, University of Trento, Via Sommarive 9, 38123 Trento, Italy
| | - Andrea Bianchi
- Department CIBIO, Laboratory of Molecular Virology, University of Trento, Via Sommarive 9, 38123 Trento, Italy
| | - Alessandro Umbach
- Department CIBIO, Laboratory of Molecular Virology, University of Trento, Via Sommarive 9, 38123 Trento, Italy
| | - Simone Amistadi
- Department CIBIO, Laboratory of Molecular Virology, University of Trento, Via Sommarive 9, 38123 Trento, Italy
| | - Mégane Brusson
- Imagine Institute, Laboratory of Chromatin and Gene Regulation During Development, Université de Paris, INSERM UMR 1163, Paris, France
| | - Giacomo Frati
- Imagine Institute, Laboratory of Chromatin and Gene Regulation During Development, Université de Paris, INSERM UMR 1163, Paris, France
| | - Matteo Ciciani
- Department CIBIO, Laboratory of Molecular Virology, University of Trento, Via Sommarive 9, 38123 Trento, Italy
| | | | - Daniele Arosio
- Biophysics Institute, National Research Council of Italy, 38123 Trento, Italy
| | - Annarita Miccio
- Imagine Institute, Laboratory of Chromatin and Gene Regulation During Development, Université de Paris, INSERM UMR 1163, Paris, France
| | - Anna Cereseto
- Department CIBIO, Laboratory of Molecular Virology, University of Trento, Via Sommarive 9, 38123 Trento, Italy.
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7
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Amistadi S, Maule G, Ciciani M, Ensinck MM, De Keersmaecker L, Ramalho AS, Guidone D, Buccirossi M, Galietta LJV, Carlon MS, Cereseto A. Functional restoration of a CFTR splicing mutation through RNA delivery of CRISPR adenine base editor. Mol Ther 2023; 31:1647-1660. [PMID: 36895161 PMCID: PMC10277887 DOI: 10.1016/j.ymthe.2023.03.004] [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: 11/04/2022] [Revised: 01/07/2023] [Accepted: 03/03/2023] [Indexed: 03/11/2023] Open
Abstract
Cystic fibrosis (CF) is a genetic disease caused by mutations in the CF transmembrane conductance regulator (CFTR) gene. The 2789+5G>A CFTR mutation is a quite frequent defect causing an aberrant splicing and a non-functional CFTR protein. Here we used a CRISPR adenine base editing (ABE) approach to correct the mutation in the absence of DNA double-strand breaks (DSB). To select the strategy, we developed a minigene cellular model reproducing the 2789+5G>A splicing defect. We obtained up to 70% editing in the minigene model by adapting the ABE to the PAM sequence optimal for targeting 2789+5G>A with a SpCas9-NG (NG-ABE). Nonetheless, the on-target base correction was accompanied by secondary (bystander) A-to-G conversions in nearby nucleotides, which affected the wild-type CFTR splicing. To decrease the bystander edits, we used a specific ABE (NG-ABEmax), which was delivered as mRNA. The NG-ABEmax RNA approach was validated in patient-derived rectal organoids and bronchial epithelial cells showing sufficient gene correction to recover the CFTR function. Finally, in-depth sequencing revealed high editing precision genome-wide and allele-specific correction. Here we report the development of a base editing strategy to precisely repair the 2789+5G>A mutation resulting in restoration of the CFTR function, while reducing bystander and off-target activities.
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Affiliation(s)
- Simone Amistadi
- University of Trento, Department of Computational, Cellular and Integrative Biology, Laboratory of Molecular Virology, 38123 Trento, Italy
| | - Giulia Maule
- University of Trento, Department of Computational, Cellular and Integrative Biology, Laboratory of Molecular Virology, 38123 Trento, Italy.
| | - Matteo Ciciani
- University of Trento, Department of Computational, Cellular and Integrative Biology, Laboratory of Molecular Virology, 38123 Trento, Italy
| | - Marjolein M Ensinck
- KU Leuven, Department of Pharmaceutical and Pharmacological Sciences, Laboratory for Molecular Virology and Gene Therapy, 3000 Leuven, Belgium
| | - Liesbeth De Keersmaecker
- KU Leuven, Department of Pharmaceutical and Pharmacological Sciences, Laboratory for Molecular Virology and Gene Therapy, 3000 Leuven, Belgium
| | - Anabela S Ramalho
- CF Research Lab, Woman and Child Unit, Department of Development and Regeneration, KU Leuven, 3000 Leuven, Belgium
| | - Daniela Guidone
- Telethon Institute of Genetics and Medicine, 80078 Pozzuoli, Italy
| | | | - Luis J V Galietta
- Telethon Institute of Genetics and Medicine, 80078 Pozzuoli, Italy; Department of Translational Medical Sciences, University of Napoli "Federico II," 80138 Napoli, Italy
| | - Marianne S Carlon
- KU Leuven, Department of Pharmaceutical and Pharmacological Sciences, Laboratory for Molecular Virology and Gene Therapy, 3000 Leuven, Belgium; KU Leuven, Department of Chronic Diseases and Metabolism, BREATHE Laboratory, 3000 Leuven, Belgium
| | - Anna Cereseto
- University of Trento, Department of Computational, Cellular and Integrative Biology, Laboratory of Molecular Virology, 38123 Trento, Italy.
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Bergougnoux A, Billet A, Ka C, Heller M, Degrugillier F, Vuillaume ML, Thoreau V, Sasorith S, Bareil C, Thèze C, Ferec C, Gac GL, Bienvenu T, Bieth E, Gaston V, Lalau G, Pagin A, Malinge MC, Dufernez F, Lemonnier L, Koenig M, Fergelot P, Claustres M, Taulan-Cadars M, Kitzis A, Reboul MP, Becq F, Fanen P, Mekki C, Audrezet MP, Girodon E, Raynal C. The multi-faceted nature of 15 CFTR exonic variations: Impact on their functional classification and perspectives for therapy. J Cyst Fibros 2022:S1569-1993(22)01423-0. [PMID: 36567205 DOI: 10.1016/j.jcf.2022.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 09/30/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND The majority of variants of unknown clinical significance (VUCS) in the CFTR gene are missense variants. While change on the CFTR protein structure or function is often suspected, impact on splicing may be neglected. Such undetected splicing default of variants may complicate the interpretation of genetic analyses and the use of an appropriate pharmacotherapy. METHODS We selected 15 variants suspected to impact CFTR splicing after in silico predictions on 319 missense variants (214 VUCS), reported in the CFTR-France database. Six specialized laboratories assessed the impact of nucleotide substitutions on splicing (minigenes), mRNA expression levels (quantitative PCR), synthesis and maturation (western blot), cellular localization (immunofluorescence) and channel function (patch clamp) of the CFTR protein. We also studied maturation and function of the truncated protein, consecutive to in-frame aberrant splicing, on additional plasmid constructs. RESULTS Six of the 15 variants had a major impact on CFTR splicing by in-frame (n = 3) or out-of-frame (n = 3) exon skipping. We reclassified variants into: splicing variants; variants causing a splicing defect and the impairment of CFTR folding and/or function related to the amino acid substitution; deleterious missense variants that impair CFTR folding and/or function; and variants with no consequence on the different processes tested. CONCLUSION The 15 variants have been reclassified by our comprehensive approach of in vitro experiments that should be used to properly interpret very rare exonic variants of the CFTR gene. Targeted therapies may thus be adapted to the molecular defects regarding the results of laboratory experiments.
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Affiliation(s)
- A Bergougnoux
- Génétique Moléculaire, CHU Montpellier, Montpellier, France; PhyMedExp, INSERM, CNRS UMR, Montpellier, France; Université de Montpellier, Montpellier, France
| | - A Billet
- Laboratoire STIM, Université de Poitiers, Poitiers, France
| | - C Ka
- Service de génétique moléculaire, CHRU Brest, Brest, France; Université de Brest, Inserm, UMR 1078, GGB, Brest, France
| | - M Heller
- Service de Médecine Génomique des Maladies de Système et d'Organe, APHP Centre - Université de Paris, Hôpital Cochin, Paris, France
| | - F Degrugillier
- Université Paris-Est Créteil, INSERM, IMRB, Créteil F-94010, France
| | - M-L Vuillaume
- Génétique Moléculaire, CHU Bordeaux, Bordeaux, France
| | - V Thoreau
- Laboratoire NEUVACOD-3808, Université de Poitiers, Poitiers, France
| | - S Sasorith
- Génétique Moléculaire, CHU Montpellier, Montpellier, France; PhyMedExp, INSERM, CNRS UMR, Montpellier, France
| | - C Bareil
- Génétique Moléculaire, CHU Montpellier, Montpellier, France
| | - C Thèze
- Génétique Moléculaire, CHU Montpellier, Montpellier, France
| | - C Ferec
- Université de Brest, Inserm, UMR 1078, GGB, Brest, France
| | - G Le Gac
- Service de génétique moléculaire, CHRU Brest, Brest, France; Université de Brest, Inserm, UMR 1078, GGB, Brest, France
| | - T Bienvenu
- Service de Médecine Génomique des Maladies de Système et d'Organe, APHP Centre - Université de Paris, Hôpital Cochin, Paris, France
| | - E Bieth
- Génétique Médicale, CHU Toulouse, Toulouse, France
| | - V Gaston
- Génétique Médicale, CHU Toulouse, Toulouse, France
| | - G Lalau
- Biochimie et Biologie Moléculaire, CHU Lille, Lille, France
| | - A Pagin
- Biochimie et Biologie Moléculaire, CHU Lille, Lille, France
| | - M-C Malinge
- Biochimie et Génétique, CHU Angers, Angers, France
| | - F Dufernez
- Génétique, CHU Poitiers, Poitiers, France
| | - L Lemonnier
- Association Vaincre la Mucoviscidose, Paris, France
| | - M Koenig
- Génétique Moléculaire, CHU Montpellier, Montpellier, France; PhyMedExp, INSERM, CNRS UMR, Montpellier, France; Université de Montpellier, Montpellier, France
| | - P Fergelot
- MRGM, INSERM UMR 1211 Université de Bordeaux, Bordeaux, France
| | - M Claustres
- Université de Montpellier, Montpellier, France
| | - M Taulan-Cadars
- PhyMedExp, INSERM, CNRS UMR, Montpellier, France; Université de Montpellier, Montpellier, France
| | - A Kitzis
- Génétique, CHU Poitiers, Poitiers, France
| | - M-P Reboul
- Génétique Moléculaire, CHU Bordeaux, Bordeaux, France
| | - F Becq
- Laboratoire STIM, Université de Poitiers, Poitiers, France
| | - P Fanen
- AP-HP, Département de Biochimie-Biologie Moléculaire, Pharmacologie, Génétique Médicale, Hôpital Henri Mondor, Créteil F-94010, France
| | - C Mekki
- AP-HP, Département de Biochimie-Biologie Moléculaire, Pharmacologie, Génétique Médicale, Hôpital Henri Mondor, Créteil F-94010, France
| | - M-P Audrezet
- Service de génétique moléculaire, CHRU Brest, Brest, France; Université de Brest, Inserm, UMR 1078, GGB, Brest, France
| | - E Girodon
- Service de Médecine Génomique des Maladies de Système et d'Organe, APHP Centre - Université de Paris, Hôpital Cochin, Paris, France; INSERM U1151, Institut Necker Enfants Malades, Université de Paris, Paris, France
| | - C Raynal
- Génétique Moléculaire, CHU Montpellier, Montpellier, France; PhyMedExp, INSERM, CNRS UMR, Montpellier, France.
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Hillenaar T, Beekman J, van der Sluijs P, Braakman I. Redefining Hypo- and Hyper-Responding Phenotypes of CFTR Mutants for Understanding and Therapy. Int J Mol Sci 2022; 23:ijms232315170. [PMID: 36499495 PMCID: PMC9735543 DOI: 10.3390/ijms232315170] [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: 09/12/2022] [Revised: 11/11/2022] [Accepted: 11/23/2022] [Indexed: 12/03/2022] Open
Abstract
Mutations in CFTR cause misfolding and decreased or absent ion-channel function, resulting in the disease Cystic Fibrosis. Fortunately, a triple-modulator combination therapy (Trikafta) has been FDA-approved for 178 mutations, including all patients who have F508del on one allele. That so many CFTR mutants respond well to modulators developed for a single mutation is due to the nature of the folding process of this multidomain protein. We have addressed the question 'What characterizes the exceptions: the mutants that functionally respond either not or extremely well'. A functional response is the product of the number of CFTR molecules on the cell surface, open probability, and conductivity of the CFTR chloride channel. By combining biosynthetic radiolabeling with protease-susceptibility assays, we have followed CF-causing mutants during the early and late stages of folding in the presence and absence of modulators. Most CFTR mutants showed typical biochemical responses for each modulator, such as a TMD1 conformational change or an increase in (cell-surface) stability, regardless of a functional response. These modulators thus should still be considered for hypo-responder genotypes. Understanding both biochemical and functional phenotypes of outlier mutations will boost our insights into CFTR folding and misfolding, and lead to improved therapeutic strategies.
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Affiliation(s)
- Tamara Hillenaar
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Science for Life, Faculty of Science, Utrecht University, 3584 CS Utrecht, The Netherlands; (T.H.); (P.v.d.S.)
| | - Jeffrey Beekman
- Department of Pediatric Pulmonology, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht University, Member of ERN-LUNG, 3584 EA Utrecht, The Netherlands;
- Regenerative Medicine Center Utrecht, University Medical Center Utrecht, Utrecht University, 3584 CT Utrecht, The Netherlands
- Centre for Living Technologies, Alliance TU/e, WUR, UU, UMC Utrecht, 3584 CB Utrecht, The Netherlands
| | - Peter van der Sluijs
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Science for Life, Faculty of Science, Utrecht University, 3584 CS Utrecht, The Netherlands; (T.H.); (P.v.d.S.)
| | - Ineke Braakman
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Science for Life, Faculty of Science, Utrecht University, 3584 CS Utrecht, The Netherlands; (T.H.); (P.v.d.S.)
- Correspondence: ; Tel.: +31-30-253-2759
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10
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Moni SS, Al Basheer A. Molecular targets for cystic fibrosis and therapeutic potential of monoclonal antibodies. Saudi Pharm J 2022; 30:1736-1747. [PMID: 36601503 PMCID: PMC9805982 DOI: 10.1016/j.jsps.2022.10.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 10/01/2022] [Indexed: 12/24/2022] Open
Abstract
Cystic fibrosis (CF) is a genetic disease that affects the exocrine glands and is caused by cystic fibrosis transmembrane conductance regulator gene (CFTR) mutations. Lung disease is the leading cause of morbidity in patients. Target-specific treatment of CF has been achieved using monoclonal antibodies (mAbs). The purpose of this article is to discuss the possibility of treating CF with mAbs through their significant target specificity. We searched electronic databases in Web of Science, PubMed, EMBASE, Scopus, and Google Scholar from 1984 to 2021. We discussed the critical role of targeted therapy in cystic fibrosis, as it will be more effective at suppressing the molecular networks. After conducting a critical review of the available literature, we concluded that it is critical to understand the fundamental molecular mechanisms underlying CF prior to incorporating biologics into the therapy regimen. Omalizumab, Mepolizumab, Benralizumab, Dupilumab and KB001-A have been successfully screened for asthma-complicated CF, and their efficacies have been well reported. Despite the availability of effective targeted biologics, treating CF has remained a difficult task, particularly when it comes to reduction of secondary inflammatory mediators. This review emphasizes the overall views on CF, the immunological mechanism of CF, and the prospective therapeutic use of mAbs as potential targeted biologics for enhancing the overall status of human health.
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11
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Mun KS, Nathan JD, Jegga AG, Wikenheiser-Brokamp KA, Abu-El-Haija M, Naren AP. Personalized medicine approaches in cystic fibrosis related pancreatitis. Am J Transl Res 2022; 14:7612-7620. [PMID: 36398272 PMCID: PMC9641468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/27/2022] [Indexed: 06/16/2023]
Abstract
We report a rare case of a patient with cystic fibrosis suffering from debilitating abdominal pain due to chronic pancreatitis. This 13-year-old patient was evaluated for surgical intervention to relieve pain from chronic pancreatitis and to improve quality of life. The patient carried two mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene; the most common ΔF508 variant and a second variant, p.Glu1044Gly, which has not been previously described. The patient's condition did not improve despite medical management and multiple endoscopic interventions, and therefore total pancreatectomy with islet autotransplantation and a near-total duodenectomy was offered for definitive management. Patient-derived duodenal crypts were isolated and cultured from the resected duodenum, and duodenal organoids were generated to test CFTR function. Our studies demonstrate that this novel mutation (ΔF508/p.Glu1044Gly) caused severely impaired CFTR function in vitro. The Food and Drug Administration (FDA)-approved drug ivacaftor, a CFTR potentiator, was identified to robustly improve CFTR function in the context of this novel mutation. Herein, we describe a personalized medicine approach consisting of performing drug testing on individual patient derived organoids that has potential to guide management of patients with novel CFTR genetic mutations. Identified effective medical therapeutics using this approach may avoid irreversible surgical treatments such as total pancreatectomy with islet autotransplantation in the future.
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Affiliation(s)
- Kyu Shik Mun
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Cedars-Sinai Medical Center127 South San Vicente Boulevard, Los Angeles 90048, CA, USA
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center127 South San Vicente Boulevard, Los Angeles 90048, CA, USA
| | - Jaimie D Nathan
- Department of Abdominal Transplant and Hepatopancreatobiliary Surgery, Nationwide Children’s Hospital700 Children’s Drive, Columbus 43205, OH, USA
- Department of Surgery, The Ohio State University Wexner Medical Center395 West 12th Avenue, Columbus 43210, OH, USA
| | - Anil G Jegga
- Department of Pediatrics, College of Medicine, University of Cincinnati3230 Eden Avenue, Cincinnati 45267, OH, USA
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center3333 Burnet Avenue, Cincinnati 45229, OH, USA
| | - Kathryn A Wikenheiser-Brokamp
- Division of Pathology and Laboratory Medicine, The Perinatal Institute, and Division of Pulmonary Biology, Cincinnati Children’s Hospital Medical Center3333 Burnet Avenue, Cincinnati 45229, OH, USA
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine3333 Burnet Avenue, Cincinnati 45267, OH, USA
| | - Maisam Abu-El-Haija
- Department of Pediatrics, College of Medicine, University of Cincinnati3230 Eden Avenue, Cincinnati 45267, OH, USA
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Cincinnati Children’s Hospital Medical Center3333 Burnet Avenue, Cincinnati 45229, OH, USA
| | - Anjaparavanda P Naren
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Cedars-Sinai Medical Center127 South San Vicente Boulevard, Los Angeles 90048, CA, USA
- Division of Pulmonary Medicine, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center3333 Burnet Avenue, Cincinnati 45229, OH, USA
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12
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Current state of CFTR modulators for treatment of Cystic Fibrosis. Curr Opin Pharmacol 2022; 65:102239. [DOI: 10.1016/j.coph.2022.102239] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 03/31/2022] [Accepted: 04/13/2022] [Indexed: 12/23/2022]
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13
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Ensinck MM, Carlon MS. One Size Does Not Fit All: The Past, Present and Future of Cystic Fibrosis Causal Therapies. Cells 2022; 11:cells11121868. [PMID: 35740997 PMCID: PMC9220995 DOI: 10.3390/cells11121868] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 05/25/2022] [Accepted: 05/28/2022] [Indexed: 02/04/2023] Open
Abstract
Cystic fibrosis (CF) is the most common monogenic disorder, caused by mutations in the CF transmembrane conductance regulator (CFTR) gene. Over the last 30 years, tremendous progress has been made in understanding the molecular basis of CF and the development of treatments that target the underlying defects in CF. Currently, a highly effective CFTR modulator treatment (Kalydeco™/Trikafta™) is available for 90% of people with CF. In this review, we will give an extensive overview of past and ongoing efforts in the development of therapies targeting the molecular defects in CF. We will discuss strategies targeting the CFTR protein (i.e., CFTR modulators such as correctors and potentiators), its cellular environment (i.e., proteostasis modulation, stabilization at the plasma membrane), the CFTR mRNA (i.e., amplifiers, nonsense mediated mRNA decay suppressors, translational readthrough inducing drugs) or the CFTR gene (gene therapies). Finally, we will focus on how these efforts can be applied to the 15% of people with CF for whom no causal therapy is available yet.
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Affiliation(s)
- Marjolein M. Ensinck
- Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Flanders, Belgium;
| | - Marianne S. Carlon
- Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Flanders, Belgium;
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, 3000 Leuven, Flanders, Belgium
- Correspondence:
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14
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Ensinck MM, De Keersmaecker L, Ramalho AS, Cuyx S, Van Biervliet S, Dupont L, Christ F, Debyser Z, Vermeulen F, Carlon MS. Novel CFTR modulator combinations maximize rescue of G85E and N1303K in rectal organoids. ERJ Open Res 2022; 8:00716-2021. [PMID: 35449760 PMCID: PMC9016267 DOI: 10.1183/23120541.00716-2021] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 01/21/2022] [Indexed: 11/05/2022] Open
Abstract
Introduction Cystic fibrosis (CF) is a severe monogenic disorder caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Several types of CFTR modulators (correctors/potentiators) have been developed to overcome protein dysfunction associated with these mutations. CFTR modulator therapy is now available for the major CF-causing mutations; however, 10% of people with CF remain without causal treatments. By combining investigational and market-approved CFTR modulators, we aimed to maximise functional rescue of iva-, luma- and tezacaftor refractory mutants G85E and N1303K. Methods We used the well-established forskolin-induced swelling (FIS) in primary rectal organoids to assess responses to different CFTR corrector and potentiator types. The FIS analysis was performed with brightfield microscopy, allowing both 1-h and 24-h follow-up. Corrector and potentiator activity of elexacaftor was investigated. Results For G85E, maximal rescue was observed by a combination of elexacaftor and corr4a. For N1303K, the quadruple combination teza-elexa-ivacaftor with apigenin was required to obtain a rescue similar to that of luma-ivacaftor rescued F508del. Elexacaftor rescued G85E and N1303K by different mechanisms, with chronic corrector effects on G85E and acute potentiation of N1303K only in the presence of ivacaftor. Synergy in N1303K rescue for iva-elexacaftor and apigenin suggests at least three potentiator mechanisms for this mutant. 24-h FIS identified ivacaftor as the main CFTR modulator for N1303K and elexacaftor and apigenin as co-potentiators. Conclusions Novel combinations of CFTR modulators can further improve functional rescue of G85E and N1303K in rectal organoids, although for N1303K, more effective CFTR modulators are still needed. Organoids can guide personalised medicine in cystic fibrosis. Novel modulator combinations rescue G85E and N1303K beyond Trikafta. Label-free, long-term organoid monitoring unravels major contributors to the functional rescue of these rare CFTR mutants.https://bit.ly/3AKYJnz
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Assays of CFTR Function In Vitro, Ex Vivo and In Vivo. Int J Mol Sci 2022; 23:ijms23031437. [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] [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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16
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Terlizzi V, Claut L, Colombo C, Tosco A, Castaldo A, Fabrizzi B, Lucarelli M, Cimino G, Carducci C, Dolce D, Biffi A, Bonomi P, Timpano S, Padoan R. Outcomes of early repeat sweat testing in infants with cystic fibrosis transmembrane conductance regulator-related metabolic syndrome/CF screen-positive, inconclusive diagnosis. Pediatr Pulmonol 2021; 56:3785-3791. [PMID: 34549893 DOI: 10.1002/ppul.25683] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 09/13/2021] [Accepted: 09/15/2021] [Indexed: 01/05/2023]
Abstract
BACKGROUND Reaching early and definitive diagnosis in infants with cystic fibrosis (CF) transmembrane conductance regulator-related metabolic syndrome (CRMS)/CF screen-positive, inconclusive diagnosis (CFSPID) is a priority of all CF newborn screening programs. Currently, sweat testing (ST) is the gold standard for CF diagnosis or exclusion. We assessed outcomes in a cohort of Italian CRMS/CFSPID infants who underwent repeat ST in the 1st year of life. METHODS This multicentre, prospective study analysed clinical data and outcomes in CRMS/CFSPID infants born between September 1, 2018, and December 31, 2019, and followed until June 30, 2020. All subjects underwent CF transmembrane conductance regulator (CFTR) gene sequencing and the search for CFTR macrodeletions/macroduplications, and repeat ST in the 1st year of life. RESULTS Fifty subjects (median age at end of follow-up, 16 months [range, 7-21 months]) were enrolled. Forty-one (82%) had the first sweat chloride (SC) in the intermediate range. During follow up, 150 STs were performed (range, 1-7/infant). After a median follow-up of 8.5 months (range, 1-16.2 months), 11 (22%) subjects were definitively diagnosed as follows: CF (n = 2 [4%]) at 2 and 5 months, respectively; healthy carrier (n = 8 [16%]), at a median age of 4 months (range, 2-8 months); and healthy (n = 1 [2%]) at 2 months of age. Inconclusive diagnosis remained in 39 (78%) infants. CONCLUSIONS Early repeat ST in the 1st year of life can shorten the time to definitive diagnosis in screening positive subjects with initial SC levels in the intermediate range.
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Affiliation(s)
- Vito Terlizzi
- Department of Paediatric Medicine, Cystic Fibrosis Regional Reference Center, Anna Meyer Children's University, Florence, Italy
| | - Laura Claut
- Department of Pathophysiology and Transplantation, Cystic Fibrosis Regional Reference Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Milan, Milan, Italy
| | - Carla Colombo
- Department of Pathophysiology and Transplantation, Cystic Fibrosis Regional Reference Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Milan, Milan, Italy
| | - Antonella Tosco
- Paediatric Unit, Department of Translational Medical Sciences, Cystic Fibrosis Regional Reference Center, University of Naples Federico II, Naples, Italy
| | - Alice Castaldo
- Paediatric Unit, Department of Translational Medical Sciences, Cystic Fibrosis Regional Reference Center, University of Naples Federico II, Naples, Italy
| | - Benedetta Fabrizzi
- Mother - Child Department, Cystic Fibrosis Regional Reference Center, United Hospitals, Ancona, Italy
| | - Marco Lucarelli
- Dept. of Experimental Medicine, Sapienza University of Rome, Rome, Italy.,Pasteur Institute Cenci Bolognetti Foundation, Rome, Italy
| | - Giuseppe Cimino
- Cystic Fibrosis Regional Reference Center, A.O.U. Policlinico Umberto I, Rome, Italy
| | - Carla Carducci
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Daniela Dolce
- Department of Paediatric Medicine, Cystic Fibrosis Regional Reference Center, Anna Meyer Children's University, Florence, Italy
| | - Arianna Biffi
- Department of Pathophysiology and Transplantation, Cystic Fibrosis Regional Reference Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Milan, Milan, Italy
| | | | - Silviana Timpano
- Department of Pediatrics, Cystic Fibrosis Regional Support Center, ASST Spedali Civili Brescia, University of Brescia, Brescia, Italy
| | - Rita Padoan
- Department of Pediatrics, Cystic Fibrosis Regional Support Center, ASST Spedali Civili Brescia, University of Brescia, Brescia, Italy
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Peters KW, Gong X, Frizzell RA. Cystic Fibrosis Transmembrane Conductance Regulator Folding Mutations Reveal Differences in Corrector Efficacy Linked to Increases in Immature Cystic Fibrosis Transmembrane Conductance Regulator Expression. Front Physiol 2021; 12:695767. [PMID: 34764878 PMCID: PMC8576290 DOI: 10.3389/fphys.2021.695767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 07/05/2021] [Indexed: 11/17/2022] Open
Abstract
Background: Most cystic fibrosis is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene that lead to protein misfolding and degradation by the ubiquitin–proteasome system. Previous studies demonstrated that PIAS4 facilitates the modification of wild-type (WT) and F508del CFTR by small ubiquitin-like modifier (SUMO)-1, enhancing CFTR biogenesis by slowing immature CFTR degradation and producing increased immature CFTR band B. Methods: We evaluated two correction strategies using misfolding mutants, including the common variant, F508del. We examined the effects on mutant expression of co-expression with PIAS4 (E3 SUMO ligase), and/or the corrector, C18. To study the impact of these correction conditions, we transfected CFBE410- cells, a bronchial epithelial cell line, with a CFTR mutant plus: (1) empty vector, (2) empty vector plus overnight 5 μM C18, (3) PIAS4, and (4) PIAS4 plus C18. We assessed expression at steady state by immunoblot of CFTR band B, and if present, band C, and the corresponding C:B band ratio. The large PIAS4-induced increase in band B expression allowed us to ask whether C18 could act on the now abundant immature protein to enhance correction above the control level, as reported by the C:B ratio. Results: The data fell into three mutant CFTR categories as follows: (1) intransigent: no observable band C under any condition (i.e., C:B = 0); (2) throughput responsive: a C:B ratio less than control, but suggesting that the increased band C resulted from PIAS4-induced increases in band B production; and (3) folding responsive: a C:B ratio greater than control, reflecting C18-induced folding greater than that expected from increased throughput due to the PIAS4-induced band B level. Conclusion: These results suggest that the immature forms of CFTR folding intermediates occupy different loci within the energetic/kinetic folding landscape of CFTR. The evaluation of their properties could assist in the development of correctors that can target the more difficult-to-fold mutant conformations that occupy different sites within the CFTR folding pathway.
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Affiliation(s)
- Kathryn W Peters
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Xiaoyan Gong
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Raymond A Frizzell
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
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18
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Ensinck M, Mottais A, Detry C, Leal T, Carlon MS. On the Corner of Models and Cure: Gene Editing in Cystic Fibrosis. Front Pharmacol 2021; 12:662110. [PMID: 33986686 PMCID: PMC8111007 DOI: 10.3389/fphar.2021.662110] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 03/15/2021] [Indexed: 12/11/2022] Open
Abstract
Cystic fibrosis (CF) is a severe genetic disease for which curative treatment is still lacking. Next generation biotechnologies and more efficient cell-based and in vivo disease models are accelerating the development of novel therapies for CF. Gene editing tools, like CRISPR-based systems, can be used to make targeted modifications in the genome, allowing to correct mutations directly in the Cystic Fibrosis Transmembrane conductance Regulator (CFTR) gene. Alternatively, with these tools more relevant disease models can be generated, which in turn will be invaluable to evaluate novel gene editing-based therapies for CF. This critical review offers a comprehensive description of currently available tools for genome editing, and the cell and animal models which are available to evaluate them. Next, we will give an extensive overview of proof-of-concept applications of gene editing in the field of CF. Finally, we will touch upon the challenges that need to be addressed before these proof-of-concept studies can be translated towards a therapy for people with CF.
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Affiliation(s)
- Marjolein Ensinck
- Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Angélique Mottais
- Institut de Recherche Expérimentale et Clinique, Louvain Centre for Toxicology and Applied Pharmacology, Université Catholique de Louvain, Brussels, Belgium
| | - Claire Detry
- Institut de Recherche Expérimentale et Clinique, Louvain Centre for Toxicology and Applied Pharmacology, Université Catholique de Louvain, Brussels, Belgium
| | - Teresinha Leal
- Institut de Recherche Expérimentale et Clinique, Louvain Centre for Toxicology and Applied Pharmacology, Université Catholique de Louvain, Brussels, Belgium
| | - Marianne S. Carlon
- Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
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19
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Barben J, Castellani C, Munck A, Davies JC, de Winter-de Groot KM, Gartner S, Kashirskaya N, Linnane B, Mayell SJ, McColley S, Ooi CY, Proesmans M, Ren CL, Salinas D, Sands D, Sermet-Gaudelus I, Sommerburg O, Southern KW. Updated guidance on the management of children with cystic fibrosis transmembrane conductance regulator-related metabolic syndrome/cystic fibrosis screen positive, inconclusive diagnosis (CRMS/CFSPID). J Cyst Fibros 2020; 20:810-819. [PMID: 33257262 DOI: 10.1016/j.jcf.2020.11.006] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/30/2020] [Accepted: 11/07/2020] [Indexed: 02/06/2023]
Abstract
Over the past two decades there has been considerable progress with the evaluation and management of infants with an inconclusive diagnosis following Newborn Screening (NBS) for cystic Fibrosis (CF). In addition, we have an increasing amount of evidence on which to base guidance on the management of these infants and, importantly, we have a consistent designation being used across the globe of CRMS/CFSPID. There is still work to be undertaken and research questions to answer, but these infants now receive more consistent and appropriate care pathways than previously. It is clear that the majority of these infants remain healthy, do not convert to a diagnosis of CF in childhood, and advice on management should reflect this. However, it is also clear that some will convert to a CF diagnosis and monitoring of these infants should facilitate their early recognition. Those infants that do not convert to a CF diagnosis have some potential of developing a CFTR-RD later in life. At present, it is not possible to quantify this risk, but families need to be provided with clear information of what to look out for. This paper contains a number of changes from previous guidance in light of developing evidence, but the major change is the recommendation of a detailed assessment of the child with CRMS/CFSPID in the sixth year of age, including respiratory function assessment and imaging. With these data, the CF team can discuss future care arrangements with the family and come to a shared decision on the best way forward, which may include discharge to primary care with appropriate information. Information is key for these families, and we recommend consideration of a further appointment when the individual is a young adult to directly communicate the implications of the CRMS/CFSPID designation.
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Affiliation(s)
- Jürg Barben
- Paediatric Pulmonology & CF Centre, Children's Hospital of Eastern Switzerland, St. Gallen, Switzerland.
| | - Carlo Castellani
- Istituto Giannina Gaslini, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Anne Munck
- CF referent physician for the French Society of Newborn Screening, Hopital Necker Enfants-Malades, AP-HP, CF centre, Université Paris Descartes, France
| | - Jane C Davies
- National Heart & Lung Institute, Imperial College London, UK; Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Karin M de Winter-de Groot
- Department of Paediatric Pulmonology & Allergology, Wilhelmina Children's Hospital/University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Silvia Gartner
- Pediatric Pulmonology and Cystic Fibrosis Unit, Hospital Universitari Vall d´Hebron, Barcelona, Spain
| | - Nataliya Kashirskaya
- Laboratory of genetic epidemiology, Research Centre for Medical Genetics, Moscow, Russian Federation
| | - Barry Linnane
- Graduate Entry Medical School and Centre for Interventions in Infection, Inflammation & Immunity (4i), University of Limerick, Limerick, Ireland
| | - Sarah J Mayell
- Regional Paediatric CF Centre, Alder Hey Children's Hospital, Liverpool, UK
| | - Susanna McColley
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Stanley Manne Children's Research Institute, Ann and Robert H Lurie Children's Hospital of Chicago, USA
| | - Chee Y Ooi
- Discipline of Paediatrics, School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Australia; Department of Gastroenterology and Molecular and Integrative Cystic Fibrosis Research Centre, Sydney Children's Hospital, Randwick, NSW, Australia
| | - Marijke Proesmans
- Division of Woman and Child, Department of Pediatrics, University Hospitals Leuven, Leuven, Belgium
| | - Clement L Ren
- Department of Pediatrics, Indiana University School of Medicine, Division of Pediatric Pulmonology, Allergy and Sleep Medicine, Riley Hospital for Children, Indianapolis, USA
| | - Danieli Salinas
- Department of Pediatric Pulmonology, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, USA
| | - Dorota Sands
- Cystic Fibrosis Department, Institute of Mother and Child, Warsaw, Poland
| | - Isabelle Sermet-Gaudelus
- Institut Necker Enfants Malades/INSERM U1151, Service de Pneumologie et Allergologie Pédiatriques Centre de Référence Maladies Rares, Mucoviscidose et maladies de CFTR, Hôpital Necker Enfants Malades Paris. Université de Paris. ERN Lung, France
| | - Olaf Sommerburg
- Paediatric Pulmonology, Allergology & CF Centre, Department of Paediatrics III, and Translational Lung Research Center, German Lung Research Center, University Hospital Heidelberg, Germany
| | - Kevin W Southern
- Department of Women's and Children's Health, University of Liverpool, UK
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20
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Ubiquitination of disease-causing CFTR variants in a microsome-based assay. Anal Biochem 2020; 604:113829. [PMID: 32621804 DOI: 10.1016/j.ab.2020.113829] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/10/2020] [Accepted: 06/11/2020] [Indexed: 12/14/2022]
Abstract
Soluble secreted proteins and membrane proteins are subjected to protein quality control pathways during their synthesis in the endoplasmic reticulum (ER) and delivery to other destinations. Foremost among these quality control pathways is the selection of misfolded proteins for ER-associated degradation (ERAD). A growing number of diseases, including Cystic Fibrosis, are linked to the ERAD pathway. In most cases, a membrane protein known as the Cystic Fibrosis Transmembrane Conductance Regulator, or CFTR, is prematurely degraded by ERAD. Cell-based assays and in vitro studies have elucidated factors required for the recognition and degradation of CFTR, yet mechanistic details on how these factors target specific disease-causing variants is limited. Given the possibility that variants might exhibit unique susceptibilities to ubiquitin modification, which is required for proteasome-mediated degradation, we devised an assay that recapitulates this event. Here, we demonstrate that ER-enriched membranes from transfected human cells support CFTR ubiquitination when combined with radiolabeled ubiquitin and isolated enzymes in the ubiquitination cascade. We also show that select disease-causing variants are ubiquitinated more extensively than wild-type channels and to varying degrees. Our system provides a platform to examine how other purified factors impact CFTR ubiquitination and the ubiquitination of additional disease-associated membrane proteins.
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21
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The CFTR Mutation c.3453G > C (D1152H) Confers an Anion Selectivity Defect in Primary Airway Tissue that Can Be Rescued by Ivacaftor. J Pers Med 2020; 10:jpm10020040. [PMID: 32414100 PMCID: PMC7354675 DOI: 10.3390/jpm10020040] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 04/29/2020] [Accepted: 05/08/2020] [Indexed: 02/07/2023] Open
Abstract
The Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene variant, c.3453G > C (D1152H), is associated with mild Cystic Fibrosis (CF) disease, though there is considerable clinical variability ranging from no detectable symptoms to lung disease with early acquisition of Pseudomonas aeruginosa. The approval extension of ivacaftor, the first CFTR modulator drug approved, to include D1152H was based on a positive drug response of defective CFTR-D1152H chloride channel function when expressed in FRT cells. Functional analyses of primary human nasal epithelial cells (HNE) from an individual homozygous for D1152H now revealed that while CFTR-D1152H demonstrated normal, wild-type level chloride conductance, its bicarbonate-selective conductance was impaired. Treatment with ivacaftor increased this bicarbonate-selective conductance. Extensive genetic, protein and functional analysis of the nasal cells of this D1152H/D1152H patient revealed a 90% reduction of CFTR transcripts due to the homozygous presence of the 5T polymorphism in the poly-T tract forming a complex allele with D1152H. Thus, we confirm previous observation in patient-derived tissue that 10% normal CFTR transcripts confer normal, wild-type level chloride channel activity. Together, this study highlights the benefit of patient-derived tissues to study the functional expression and pharmacological modulation of CF-causing mutations, in order to understand pathogenesis and therapeutic responses.
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