51
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Mondejar-Lopez P, Zolin A, Garcia-Marcos PW, Pastor-Vivero MD, Rosa-Silvestre M, de Asis Sanchez-Martinez F, Salvatore D, Cimino G, Majo F, Sole-Jover A, Asensio de la Cruz O, Calderazzo MA, Pizzamiglio G, Castillo-Corullon S, Alvarez-Fernandez A, Gartner S, Padoan R, Carnovale V, Salvatore M, Moya-Quiles MR, Orenti A, Glover G, Sanchez-Solis M. Geographic distribution and phenotype of European people with cystic fibrosis carrying A1006E mutation. Respir Med 2022; 192:106736. [PMID: 35032736 DOI: 10.1016/j.rmed.2022.106736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 01/03/2022] [Accepted: 01/04/2022] [Indexed: 10/19/2022]
Abstract
BACKGROUND A1006E is a Cystic Fibrosis (CF) mutation that is still not widely known. We report phenotypic features and geographic distribution of the largest cohort of people with CF (pwCF) carrying A1006E to date. METHODS Study of European pwCF carrying A1006E mutation, included in the European CF Society Patient Registry (ECFSPR). Genotype, ancestries and all variables recorded were compared to a cohort of F508del/F508del patients. Rate of decline in percentage-of-predicted FEV1 (ppFEV1) was also analyzed using the 2010-2017 ECFSPR. RESULTS 44 pwCF carrying A1006E were reported (59% males), median age 33 years old (3-58), 54.5% Spanish and 40.9% Italian, most with ancestry in Murcia (Spain) and Lazio (Italy) regions. Compared to F508del homozygous, A1006E-pwCF were significantly older (75% vs. 52.5% ≥ 18 years old) and diagnosed at later median age (6.98 vs. 0.29 years); showed lower rates of meconium ileus (2.33% vs. 17.7%), pancreatic insufficiency (27.91% vs. 99.26%), diabetes (2.33% vs. 21.98%), liver disease (6.98% vs. 36.72%) and Pseudomonas aeruginosa chronic colonization (30.95% vs. 42.51%); and presented better nutrition (BMI z-score 0.44 vs. -0.43) and ppFEV1 (90.8% vs. 78.6%), with 18.9% (most >40 years old) having a ppFEV1<70%. Additional ppFEV1 decline (0.96% per year) was attributed to F508del/F508del genotype (p = 0.0007). None died or needed organ transplantation during the study period. CONCLUSIONS A1006E-pwCF are mainly of Western Mediterranean Spanish and Italian descent. When compared with F508del/F508del-pwCF, they usually have a milder form of the disease, associated with pancreatic sufficiency and slower FEV1 decline. However, some will develop progressive respiratory impairment during adulthood.
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Affiliation(s)
- Pedro Mondejar-Lopez
- Pediatric Pulmonology and Cystic Fibrosis Unit, Hospital Clinico Universitario Virgen de la Arrixaca, Murcia, Spain; Department of Surgery, Paediatrics, Obstetrics and Genecology, Universidad de Murcia, Spain. Biomedical Research Institute of Murcia (IMIB), Murcia, Spain.
| | - Anna Zolin
- Department of Clinical Sciences and Community Health, Laboratory of Medical Statistics, Epidemiology and Biometry G. A. Maccacaro, University of Milan, Milan, Italy
| | - Patricia W Garcia-Marcos
- Pediatric Pulmonology and Cystic Fibrosis Unit, Hospital Clinico Universitario Virgen de la Arrixaca, Murcia, Spain
| | - Mª Dolores Pastor-Vivero
- Osakidetza. Organizacion Sanitaria Integrada Ezkerraldea-Enkarterri-Cruces, Hospital Universitario Cruces, Paediatrics, Cystic Fibrosis Unit, Bizkaia, Spain
| | - Maria Rosa-Silvestre
- Pediatric Pulmonology and Cystic Fibrosis Unit, Hospital Clinico Universitario Virgen de la Arrixaca, Murcia, Spain
| | | | | | - Giuseppe Cimino
- Lazio Reference Center for Cystic Fibrosis, Policlinico Umberto I University Hospital, Rome, Italy
| | - Fabio Majo
- Cystic Fibrosis Centre, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Amparo Sole-Jover
- Lung Transplantation and Cystic Fibrosis Unit, Hospital Universitario La Fe, Universidad de Valencia, Valencia, Spain
| | - Oscar Asensio de la Cruz
- Cystic Fibrosis Unit, Pediatric Pulmonology and Allergy Unit, Hospital Universitari Parc Tauli, Sabadell, Barcelona, Spain
| | | | - Giovanna Pizzamiglio
- Cystic Fibrosis Center - Adult Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Antonio Alvarez-Fernandez
- Adult Cystic Fibrosis Unit, Pulmonology Service, Hospital Universitari Vall D'Hebron, Barcelona, Spain
| | - Silvia Gartner
- Pediatric Pulmonology and Cystic Fibrosis Unit, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Rita Padoan
- Department of Paediatrics, Cystic Fibrosis Regional Support Centre, University of Brescia, ASST Spedali Civili Brescia, Brescia, Italy
| | - Vincenzo Carnovale
- Department of Translational Medical Science, Cystic Fibrosis Centre, Adult Unit, University of Naples "Federico II", Italy
| | - Marco Salvatore
- Italian Cystic Fibrosis Registry, Rome, Italy, National Centre for Rare Diseases, Undiagnosed Rare Diseases Unit, Istituto Superiore di Sanità, Rome, Italy
| | - Mª Rosa Moya-Quiles
- Immunology Service, University Clinical Hospital Virgen de la Arrixaca-Biomedical Research Institute of Murcia (IMIB), Murcia, Spain
| | - Annalisa Orenti
- Department of Clinical Sciences and Community Health, Laboratory of Medical Statistics, Epidemiology and Biometry G. A. Maccacaro, University of Milan, Milan, Italy
| | - Guillermo Glover
- Biochemistry and Clinical Genetic Centre. Hospital Clinico Universitario Virgen de la Arrixaca, Murcia, Spain
| | - Manuel Sanchez-Solis
- Pediatric Pulmonology and Cystic Fibrosis Unit, Hospital Clinico Universitario Virgen de la Arrixaca, Murcia, Spain; Department of Surgery, Paediatrics, Obstetrics and Genecology, Universidad de Murcia, Spain. Biomedical Research Institute of Murcia (IMIB), Murcia, Spain
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52
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Allan KM, Astore MA, Fawcett LK, Wong SL, Chen PC, Griffith R, Jaffe A, Kuyucak S, Waters SA. S945L-CFTR molecular dynamics, functional characterization and tezacaftor/ivacaftor efficacy in vivo and in vitro in matched pediatric patient-derived cell models. Front Pediatr 2022; 10:1062766. [PMID: 36467478 PMCID: PMC9709344 DOI: 10.3389/fped.2022.1062766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 10/28/2022] [Indexed: 11/18/2022] Open
Abstract
Cystic Fibrosis (CF) results from over 400 different disease-causing mutations in the CF Transmembrane Conductance Regulator (CFTR) gene. These CFTR mutations lead to numerous defects in CFTR protein function. A novel class of targeted therapies (CFTR modulators) have been developed that can restore defects in CFTR folding and gating. This study aimed to characterize the functional and structural defects of S945L-CFTR and interrogate the efficacy of modulators with two modes of action: gating potentiator [ivacaftor (IVA)] and folding corrector [tezacaftor (TEZ)]. The response to these modulators in vitro in airway differentiated cell models created from a participant with S945L/G542X-CFTR was correlated with in vivo clinical outcomes of that participant at least 12 months pre and post modulator therapy. In this participants' airway cell models, CFTR-mediated chloride transport was assessed via ion transport electrophysiology. Monotherapy with IVA or TEZ increased CFTR activity, albeit not reaching statistical significance. Combination therapy with TEZ/IVA significantly (p = 0.02) increased CFTR activity 1.62-fold above baseline. Assessment of CFTR expression and maturation via western blot validated the presence of mature, fully glycosylated CFTR, which increased 4.1-fold in TEZ/IVA-treated cells. The in vitro S945L-CFTR response to modulator correlated with an improvement in in vivo lung function (ppFEV1) from 77.19 in the 12 months pre TEZ/IVA to 80.79 in the 12 months post TEZ/IVA. The slope of decline in ppFEV1 significantly (p = 0.02) changed in the 24 months post TEZ/IVA, becoming positive. Furthermore, there was a significant improvement in clinical parameters and a fall in sweat chloride from 68 to 28 mmol/L. The mechanism of dysfunction of S945L-CFTR was elucidated by in silico molecular dynamics (MD) simulations. S945L-CFTR caused misfolding of transmembrane helix 8 and disruption of the R domain, a CFTR domain critical to channel gating. This study showed in vitro and in silico that S945L causes both folding and gating defects in CFTR and demonstrated in vitro and in vivo that TEZ/IVA is an efficacious modulator combination to address these defects. As such, we support the utility of patient-derived cell models and MD simulations in predicting and understanding the effect of modulators on CFTR function on an individualized basis.
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Affiliation(s)
- Katelin M Allan
- School of Clinical Medicine, Discipline of Paediatrics and Child Health, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia.,Molecular and Integrative Cystic Fibrosis Research Centre, UNSW Sydney, Sydney, NSW, Australia
| | - Miro A Astore
- School of Physics, The University of Sydney, Sydney, NSW, Australia
| | - Laura K Fawcett
- School of Clinical Medicine, Discipline of Paediatrics and Child Health, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia.,Molecular and Integrative Cystic Fibrosis Research Centre, UNSW Sydney, Sydney, NSW, Australia.,Department of Respiratory Medicine, Sydney Children's Hospital, Sydney, NSW, Australia
| | - Sharon L Wong
- School of Clinical Medicine, Discipline of Paediatrics and Child Health, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia.,Molecular and Integrative Cystic Fibrosis Research Centre, UNSW Sydney, Sydney, NSW, Australia
| | - Po-Chia Chen
- School of Physics, The University of Sydney, Sydney, NSW, Australia
| | - Renate Griffith
- School of Natural Sciences (Chemistry), University of Tasmania, Hobart, TAS, Australia
| | - Adam Jaffe
- School of Clinical Medicine, Discipline of Paediatrics and Child Health, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia.,Molecular and Integrative Cystic Fibrosis Research Centre, UNSW Sydney, Sydney, NSW, Australia.,Department of Respiratory Medicine, Sydney Children's Hospital, Sydney, NSW, Australia
| | - Serdar Kuyucak
- School of Physics, The University of Sydney, Sydney, NSW, Australia
| | - Shafagh A Waters
- School of Clinical Medicine, Discipline of Paediatrics and Child Health, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia.,Molecular and Integrative Cystic Fibrosis Research Centre, UNSW Sydney, Sydney, NSW, Australia.,Department of Respiratory Medicine, Sydney Children's Hospital, Sydney, NSW, Australia.,School of Biomedical Sciences, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
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53
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Infield DT, Strickland KM, Gaggar A, McCarty NA. The molecular evolution of function in the CFTR chloride channel. J Gen Physiol 2021; 153:212705. [PMID: 34647973 PMCID: PMC8640958 DOI: 10.1085/jgp.202012625] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 08/11/2021] [Accepted: 09/09/2021] [Indexed: 12/13/2022] Open
Abstract
The ATP-binding cassette (ABC) transporter superfamily includes many proteins of clinical relevance, with genes expressed in all domains of life. Although most members use the energy of ATP binding and hydrolysis to accomplish the active import or export of various substrates across membranes, the cystic fibrosis transmembrane conductance regulator (CFTR) is the only known animal ABC transporter that functions primarily as an ion channel. Defects in CFTR, which is closely related to ABCC subfamily members that bear function as bona fide transporters, underlie the lethal genetic disease cystic fibrosis. This article seeks to integrate structural, functional, and genomic data to begin to answer the critical question of how the function of CFTR evolved to exhibit regulated channel activity. We highlight several examples wherein preexisting features in ABCC transporters were functionally leveraged as is, or altered by molecular evolution, to ultimately support channel function. This includes features that may underlie (1) construction of an anionic channel pore from an anionic substrate transport pathway, (2) establishment and tuning of phosphoregulation, and (3) optimization of channel function by specialized ligand–channel interactions. We also discuss how divergence and conservation may help elucidate the pharmacology of important CFTR modulators.
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Affiliation(s)
- Daniel T Infield
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA
| | | | - Amit Gaggar
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL.,Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL.,Program in Protease and Matrix Biology, University of Alabama at Birmingham, Birmingham, AL.,Birmingham Veterans Administration Medical Center, Birmingham, AL
| | - Nael A McCarty
- Department of Pediatrics, Emory University, Atlanta, GA.,Children's Healthcare of Atlanta Center for Cystic Fibrosis and Airways Disease Research, Emory University, Atlanta, GA
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54
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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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55
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Measurements of spontaneous CFTR-mediated ion transport without acute channel activation in airway epithelial cultures after modulator exposure. Sci Rep 2021; 11:22616. [PMID: 34799640 PMCID: PMC8605007 DOI: 10.1038/s41598-021-02044-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 10/25/2021] [Indexed: 12/13/2022] Open
Abstract
Quantitation of CFTR function in vitro is commonly performed by acutely stimulating then inhibiting ion transport through CFTR and measuring the resulting changes in transepithelial voltage (Vte) and current (ISC). While this technique is suitable for measuring the maximum functional capacity of CFTR, it may not provide an accurate estimate of in vivo CFTR activity. To test if CFTR-mediated ion transport could be measured in the absence of acute CFTR stimulation, primary airway epithelia were analyzed in an Ussing chamber with treatment of amiloride followed by CFTR(inh)-172 without acute activation of CFTR. Non-CF epithelia demonstrated a decrease in Vte and ISC following exposure to CFTR(inh)-172 and in the absence of forskolin/IBMX (F/I); this decrease is interpreted as a measure of spontaneous CFTR activity present in these epithelia. In F508del/F508del CFTR epithelia, F/I-induced changes in Vte and ISC were ~ fourfold increased after treatment with VX-809/VX-770, while the magnitude of spontaneous CFTR activities were only ~ 1.6-fold increased after VX-809/VX-770 treatment. Method-dependent discrepancies in the responses of other CF epithelia to modulator treatments were observed. These results serve as a proof of concept for the analysis of CFTR modulator responses in vitro in the absence of acute CFTR activation. Future studies will determine the usefulness of this approach in the development of novel CFTR modulator therapies.
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56
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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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57
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Lukasiak A, Zajac M. The Distribution and Role of the CFTR Protein in the Intracellular Compartments. MEMBRANES 2021; 11:membranes11110804. [PMID: 34832033 PMCID: PMC8618639 DOI: 10.3390/membranes11110804] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/18/2021] [Accepted: 10/21/2021] [Indexed: 12/11/2022]
Abstract
Cystic fibrosis is a hereditary disease that mainly affects secretory organs in humans. It is caused by mutations in the gene encoding CFTR with the most common phenylalanine deletion at position 508. CFTR is an anion channel mainly conducting Cl− across the apical membranes of many different epithelial cells, the impairment of which causes dysregulation of epithelial fluid secretion and thickening of the mucus. This, in turn, leads to the dysfunction of organs such as the lungs, pancreas, kidney and liver. The CFTR protein is mainly localized in the plasma membrane; however, there is a growing body of evidence that it is also present in the intracellular organelles such as the endosomes, lysosomes, phagosomes and mitochondria. Dysfunction of the CFTR protein affects not only the ion transport across the epithelial tissues, but also has an impact on the proper functioning of the intracellular compartments. The review aims to provide a summary of the present state of knowledge regarding CFTR localization and function in intracellular compartments, the physiological role of this localization and the consequences of protein dysfunction at cellular, epithelial and organ levels. An in-depth understanding of intracellular processes involved in CFTR impairment may reveal novel opportunities in pharmacological agents of cystic fibrosis.
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58
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Shaughnessy CA, Zeitlin PL, Bratcher PE. Elexacaftor is a CFTR potentiator and acts synergistically with ivacaftor during acute and chronic treatment. Sci Rep 2021; 11:19810. [PMID: 34615919 PMCID: PMC8494914 DOI: 10.1038/s41598-021-99184-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 09/03/2021] [Indexed: 02/07/2023] Open
Abstract
Cystic fibrosis (CF) is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR), which lead to early death due to progressive lung disease. The development of small-molecule modulators that directly interact with CFTR to aid in protein folding (“correctors”) and/or increase channel function (“potentiators”) have proven to be highly effective in the therapeutic treatment of CF. Notably, incorporation of the next-generation CFTR corrector, elexacaftor, into a triple combination therapeutic (marketed as Trikafta) has shown tremendous clinical promise in treating CF caused by F508del-CFTR. Here, we report on a newly-described role of elexacaftor as a CFTR potentiator. We explore the acute and chronic actions, pharmacology, and efficacy of elexacaftor as a CFTR potentiator in restoring function to multiple classes of CFTR mutations. We demonstrate that the potentiating action of elexacaftor exhibits multiplicative synergy with the established CFTR potentiator ivacaftor in rescuing multiple CFTR class defects, indicating that a new combination therapeutic of ivacaftor and elexacaftor could have broad impact on CF therapies.
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Affiliation(s)
| | - Pamela L Zeitlin
- Department of Pediatrics, National Jewish Health, Denver, CO, USA.,Department of Pediatrics, University of Colorado Anschutz Medical Center, Aurora, CO, USA
| | - Preston E Bratcher
- Department of Pediatrics, National Jewish Health, Denver, CO, USA.,Department of Pediatrics, University of Colorado Anschutz Medical Center, Aurora, CO, USA
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59
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Weaver JL, Wu W, Hyland PL, Lim R, Smpokou P, Pacanowski M. Expanding Approved Patient Populations for Rare Disease Treatment Using In Vitro Data. Clin Pharmacol Ther 2021; 112:58-61. [PMID: 34496049 PMCID: PMC9293129 DOI: 10.1002/cpt.2414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 08/17/2021] [Indexed: 11/06/2022]
Abstract
In vitro cell-based data can be used to support the extension of pharmaceutical approval to patient subsets with unique genetic variants. A set of conditions should be satisfied to support the extension of approval. The disease mechanism should be well described, and the impact of variants on protein function should be reasonably understood. The incidence data should show that clinical trials for the variants in question are not practical. The overall safety and efficacy of the drug should be clear in adequate and well-controlled clinical trials. The clinical trial should include patients found to be responders and nonresponders so that both positive and negative predictive power of the in vitro assay may be measured. The mechanism of action of the drug should be clearly defined and should be consistent with the disease mechanism. The assay system should be qualified, including the following points: (i) each variant construct should be confirmed by bidirectional sequencing; (ii) the in vitro assay should directly measure the variant protein function in comparison with the reference protein; (iii) the assay should be formally validated to the extent possible, clearly demonstrating precision, reproducibility, and sensitivity used to support the efficacy claim; and (iv) the primary data should be available for inspection and analytical validation. The overall goal is a robust and validated cell-based system that can be shown to predict the outcome of targeted therapy.
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Affiliation(s)
- James L Weaver
- Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Wendy Wu
- Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Paula L Hyland
- Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Robert Lim
- Division of Pulmonology, Allergy and Critical Care, Office of Immunology & Inflammation, Office of New Drugs, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Patroula Smpokou
- Division of Rare Disease and Medical Genetics, Office of Rare Diseases, Pediatrics, Urologic, and Reproductive Medicine, Office of New Drugs, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Michael Pacanowski
- Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
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60
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Abstract
Rationale: Ivacaftor’s clinical effects in the residual function mutations 3849 + 10kb C→T and D1152H warrant further characterization. Objectives: To evaluate ivacaftor’s effect in people with cystic fibrosis aged ≥6 years with 3849 + 10kb C→T or D1152H residual function mutations and to explore the correlation between ivacaftor-induced organoid-based cystic fibrosis transmembrane conductance regulator function measurements and clinical response to ivacaftor. Methods: Participants were randomized (1:1) in this placebo-controlled crossover study; each treatment sequence included two 8-week treatments with an 8-week washout period. The primary endpoint was absolute change in lung clearance index2.5 from baseline through Week 8. Additional endpoints included lung function, patient-reported outcomes, and in vitro intestinal organoid–based measurements of ivacaftor-induced cystic fibrosis transmembrane conductance regulator function. Results: Of 38 participants, 37 completed the study. The primary endpoint was met; the Bayesian posterior probability of improvement in lung clearance index2.5 with ivacaftor versus placebo was >99%. Additional endpoints improved with ivacaftor. Safety findings were consistent with ivacaftor’s known safety profile. Dose-dependent swelling was observed in 23 of 25 viable organoid cultures with ivacaftor treatment. Correlations between ivacaftor-induced organoid swelling and clinical endpoints were negligible to low. Conclusions: In people with cystic fibrosis aged ≥6 years with a 3849 + 10kb C→T or D1152H mutation, ivacaftor treatment improved clinical endpoints compared with placebo; however, there was no correlation between organoid swelling and change in clinical endpoints. The organoid assay may assist in identification of ivacaftor-responsive mutations but in this study did not predict magnitude of clinical benefit for individual people with cystic fibrosis with these two mutations. Clinical trial registered with ClinicalTrials.gov (NCT03068312).
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A Precision Medicine Approach to Optimize Modulator Therapy for Rare CFTR Folding Mutants. J Pers Med 2021; 11:jpm11070643. [PMID: 34357110 PMCID: PMC8307171 DOI: 10.3390/jpm11070643] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 06/30/2021] [Accepted: 07/05/2021] [Indexed: 12/23/2022] Open
Abstract
Trikafta, a triple-combination drug, consisting of folding correctors VX-661 (tezacaftor), VX-445 (elexacaftor) and the gating potentiator VX-770 (ivacaftor) provided unprecedented clinical benefits for patients with the most common cystic fibrosis (CF) mutation, F508del. Trikafta indications were recently expanded to additional 177 mutations in the CF transmembrane conductance regulator (CFTR). To minimize life-long pharmacological and financial burden of drug administration, if possible, we determined the necessary and sufficient modulator combination that can achieve maximal benefit in preclinical setting for selected mutants. To this end, the biochemical and functional rescue of single corrector-responsive rare mutants were investigated in a bronchial epithelial cell line and patient-derived human primary nasal epithelia (HNE), respectively. The plasma membrane density of P67L-, L206W- or S549R-CFTR corrected by VX-661 or other type I correctors was moderately increased by VX-445. Short-circuit current measurements of HNE, however, uncovered that correction comparable to Trikafta was achieved for S549R-CFTR by VX-661 + VX-770 and for P67L- and L206W-CFTR by the VX-661 + VX-445 combination. Thus, introduction of a third modulator may not provide additional benefit for patients with a subset of rare CFTR missense mutations. These results also underscore that HNE, as a precision medicine model, enable the optimization of mutation-specific modulator combinations to maximize their efficacy and minimize life-long drug exposure of CF patients.
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Cystic Fibrosis Human Organs-on-a-Chip. MICROMACHINES 2021; 12:mi12070747. [PMID: 34202364 PMCID: PMC8305167 DOI: 10.3390/mi12070747] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/19/2021] [Accepted: 06/23/2021] [Indexed: 11/17/2022]
Abstract
Cystic fibrosis (CF) is an autosomal recessive disease caused by mutations in the cystic fibrosis transmembrane regulator (CFTR) gene: the gene product responsible for transporting chloride and bicarbonate ions through the apical membrane of most epithelial cells. Major clinical features of CF include respiratory failure, pancreatic exocrine insufficiency, and intestinal disease. Many CF animal models have been generated, but some models fail to fully capture the phenotypic manifestations of human CF disease. Other models that better capture the key characteristics of the human CF phenotype are cost prohibitive or require special care to maintain. Important differences have been reported between the pathophysiology seen in human CF patients and in animal models. These limitations present significant limitations to translational research. This review outlines the study of CF using patient-derived organs-on-a-chip to overcome some of these limitations. Recently developed microfluidic-based organs-on-a-chip provide a human experimental model that allows researchers to manipulate environmental factors and mimic in vivo conditions. These chips may be scaled to support pharmaceutical studies and may also be used to study organ systems and human disease. The use of these chips in CF discovery science enables researchers to avoid the barriers inherent in animal models and promote the advancement of personalized medicine.
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Hubert D, Marguet C, Benichou J, DeSouza C, Payen-Champenois C, Kinnman N, Chandarana K, Munck A, Fajac I. Real-World Long-Term Ivacaftor for Cystic Fibrosis in France: Clinical Effectiveness and Healthcare Resource Utilization. Pulm Ther 2021; 7:455-468. [PMID: 34101145 PMCID: PMC8589905 DOI: 10.1007/s41030-021-00158-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 04/22/2021] [Indexed: 11/29/2022] Open
Abstract
Introduction Ivacaftor is a cystic fibrosis transmembrane conductance regulator (CFTR) potentiator that has demonstrated clinical benefits in phase 3 trials. We report results from a real-world study (BRIO) to assess the effectiveness of ivacaftor in people with cystic fibrosis (pwCF) in France. Methods BRIO was an observational study conducted at 35 centers in France. Both pwCF initiating ivacaftor treatment and those already taking ivacaftor were included and prospectively followed for 24 months. The primary objective was to evaluate the effect of ivacaftor on percent predicted forced expiratory volume in 1 s (ppFEV1); secondary objectives were evaluating the effect of ivacaftor on clinical effectiveness, healthcare resource utilization (HCRU), and safety. Results A total of 129 pwCF were enrolled; 58.9% were aged < 18 years; 64.3% had a G551D-CFTR allele. Mean age at ivacaftor initiation was 19.1 years (range, 2–64 years); ppFEV1 increased by a least squares mean of 8.49 percentage points in the first 6 months and was sustained through 36 months of ivacaftor use. Growth metrics increased during the first 12 months post-ivacaftor and remained stable. The rate of pulmonary exacerbations (PEx) decreased during the 12 months post-ivacaftor compared with the 12 months pre-ivacaftor; estimated rate ratios (95% CI) were 0.57 (0.43–0.75) for PEx events and 0.25 (0.13–0.48) for PEx requiring hospitalization. No new safety concerns were identified; no deaths occurred. Conclusions The results from this real-world study of ivacaftor usage in France were consistent with prior clinical trial outcomes, confirming the clinical effectiveness of ivacaftor, as well as an associated reduction in HCRU. Supplementary Information The online version contains supplementary material available at 10.1007/s41030-021-00158-5.
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Affiliation(s)
- Dominique Hubert
- Respiratory Medicine and National Cystic Fibrosis Reference Center, Cochin Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France.
| | - Christophe Marguet
- Pediatric Respiratory Diseases and Cystic Fibrosis Center, Rouen University Hospital, INSERM CIC1404, EA 2656 UNI ROUEN, Normandy University, Rouen, France
| | - Jacques Benichou
- Department of Biostatistics and Clinical Research, Rouen University Hospital and INSERM U 1018, University of Rouen, Rouen, France
| | | | | | - Nils Kinnman
- Vertex Pharmaceuticals (Europe) Limited, London, UK
| | | | - Anne Munck
- Cystic Fibrosis Center, Hôpital Robert Debré, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Isabelle Fajac
- Respiratory Medicine and National Cystic Fibrosis Reference Center, Cochin Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France.,Physiology Department, AP-HP Centre-Université de Paris, Hôpital Cochin, Paris, France.,Université de Paris, Paris, France
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McGarry ME, McColley SA. Cystic fibrosis patients of minority race and ethnicity less likely eligible for CFTR modulators based on CFTR genotype. Pediatr Pulmonol 2021; 56:1496-1503. [PMID: 33470563 PMCID: PMC8137541 DOI: 10.1002/ppul.25285] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/21/2020] [Accepted: 12/31/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND Cystic fibrosis transmembrane conductance regulator (CFTR) modulators are disease-modifying medications for cystic fibrosis (CF) and are shown to be efficacious for only specific CFTR mutations. CFTR mutation frequency varies by ancestry, which is different from but related to demographic racial and ethnic group. Eligibility for CFTR modulator therapy has not been previously reported by race and ethnicity. METHODS We conducted a cross-sectional study of patients in the 2018 CF Foundation Patient Registry. We analyzed the percentage of patients in each US Census defined racial and ethnic group eligible for CFTR modulators based on CFTR mutations approved by the US FDA and then based on both mutations and FDA approval by age. We compared lung function based on CFTR modulator eligibility and prescription. FINDINGS Based on CFTR mutations alone, 92.4% of non-Hispanic White patients, 69.7% of Black/African American patients, 75.6% of Hispanic patients, and 80.5% of other race patients eligible for CFTR modulators. For each CFTR modulator, Black/African American patients were least likely to have eligible mutations, and non-Hispanic White patients were most likely. There was no difference in the disparity between racial and/or ethnic groups with the addition of current FDA approval by age. The lowest pulmonary function in the cohort was seen in non-Hispanic White, Black/African American, and Hispanic patients not eligible for CFTR modulators. INTERPRETATION Patients with CF from minority groups are less likely to be eligible for CFTR modulators. Because people with CF who are racial and ethnic minorities have increased disease severity and earlier mortality, this will further contribute to health disparities.
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Affiliation(s)
- Meghan E McGarry
- Department of Pediatrics, University of California, San Francisco, California, USA
| | - Susanna A McColley
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Department of Pediatrics, Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
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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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Long-Term Impact of Ivacaftor on Healthcare Resource Utilization Among People with Cystic Fibrosis in the United States. Pulm Ther 2021; 7:281-293. [PMID: 33913076 PMCID: PMC8137794 DOI: 10.1007/s41030-021-00154-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 03/19/2021] [Indexed: 12/18/2022] Open
Abstract
INTRODUCTION Ivacaftor was first approved in 2012 for the treatment of a select population of individuals with cystic fibrosis (CF), a rare, life-shortening genetic disease. Reductions in healthcare resource utilization (HCRU) associated with ivacaftor have been observed during limited follow-up and for selected outcomes in real-world studies. This study aimed to further describe the long-term impact of ivacaftor treatment on multiple measures of HCRU among people with CF (pwCF). METHODS This retrospective study used US commercial and Medicaid claims data from 2011-2018. We included pwCF ≥ 6 years of age with ≥ 1 claim for ivacaftor and 12 months of continuous health plan enrollment before ivacaftor initiation ("pre-ivacaftor" period) who also had 36 months of continuous enrollment and persistent ivacaftor use (i.e., no gap ≥ 90 days between refills) following initiation ("post-ivacaftor" period). We compared comorbidities occurring pre-ivacaftor versus the last 12 months post-ivacaftor. HCRU outcomes included medication use, inpatient admissions, and outpatient office visits. We compared medication use pre-ivacaftor versus the last 12 months post-ivacaftor and inpatient admissions and outpatient office visits pre-ivacaftor versus the post-ivacaftor period annualized across 36 months. RESULTS Seventy-nine pwCF met all criteria, including persistent ivacaftor use during the post-ivacaftor period. Ivacaftor treatment was associated with a significant reduction in pneumonia prevalence (10.1% vs. 26.6%; p < 0.001) and significantly fewer mean [SD] antibiotics claims (8.0 [7.3] vs. 12.3 [11.1]; p < 0.001) in the last 12 months post-ivacaftor versus pre-ivacaftor. In comparing the 36-month post-ivacaftor period to the pre-ivacaftor period, we also observed fewer mean [SD] annual inpatient admissions (0.2 [0.4] vs. 0.4 [0.7]), CF-related inpatient admissions (0.1 [0.2] vs. 0.2 [0.5]), and outpatient office visits (8.8 [4.9] vs. 9.9 [5.4]) (all, p < 0.05). CONCLUSION Long-term ivacaftor treatment reduced HCRU, consistent with trends observed in prior real-world studies. Our results support the sustained, long-term value of ivacaftor treatment in reducing CF burden.
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Kristensen MI, de Winter-de Groot KM, Berkers G, Chu MLJN, Arp K, Ghijsen S, Heijerman HGM, Arets HGM, Majoor CJ, Janssens HM, van der Meer R, Bogaert D, van der Ent CK. Individual and Group Response of Treatment with Ivacaftor on Airway and Gut Microbiota in People with CF and a S1251N Mutation. J Pers Med 2021; 11:jpm11050350. [PMID: 33925519 PMCID: PMC8146888 DOI: 10.3390/jpm11050350] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/15/2021] [Accepted: 04/25/2021] [Indexed: 12/19/2022] Open
Abstract
Ivacaftor has been shown to restore the functionality of the S1251N (also known as c.3752G>A) mutated CFTR, which may cause alterations in both airway and gut physiology and micro-environment, resulting in a change of microbiota in these organs. The aim of the present study was to analyze the effects of ivacaftor on the microbial community composition of both airway and gut in subjects with CF carrying one S1251N mutation, using a 16S rRNA gene-based sequencing approach. In 16 subjects with CF, repetitive samples from airways and gut were collected just before, and 2 months after, and, for 8 patients, also 9 and 12 months after, start of ivacaftor. 16S rRNA based sequencing identified 344 operational taxonomical units (OTUs) in a total of 139 samples (35 nasopharyngeal, 39 oropharyngeal, 29 sputum, and 36 fecal samples). Ivacaftor significantly enhanced bacterial diversity and overall microbiota composition in the gut (p < 0.01). There were no significant changes in the overall microbial composition and alpha diversity in upper and lower airways of these patients after ivacaftor treatment. Treatment with ivacaftor induces changes in gut microbiota whereas airway microbiota do not change significantly over time.
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Affiliation(s)
- Maartje I. Kristensen
- Department of Pediatric Pulmonology and Allergology, Wilhelmina Children’s Hospital—University Medical Center, Utrecht University, P.O. Box 85090, 3508 AB Utrecht, The Netherlands; (M.I.K.); (K.M.d.W.-d.G.); (G.B.); (S.G.); (H.G.M.A.); (C.K.v.d.E.)
| | - Karin M. de Winter-de Groot
- Department of Pediatric Pulmonology and Allergology, Wilhelmina Children’s Hospital—University Medical Center, Utrecht University, P.O. Box 85090, 3508 AB Utrecht, The Netherlands; (M.I.K.); (K.M.d.W.-d.G.); (G.B.); (S.G.); (H.G.M.A.); (C.K.v.d.E.)
| | - Gitte Berkers
- Department of Pediatric Pulmonology and Allergology, Wilhelmina Children’s Hospital—University Medical Center, Utrecht University, P.O. Box 85090, 3508 AB Utrecht, The Netherlands; (M.I.K.); (K.M.d.W.-d.G.); (G.B.); (S.G.); (H.G.M.A.); (C.K.v.d.E.)
| | - Mei Ling J. N. Chu
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children’s Hospital—University Medical Center, Utrecht University, P.O. Box 85090, 3508 AB Utrecht, The Netherlands; (M.L.J.N.C.); (K.A.)
| | - Kayleigh Arp
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children’s Hospital—University Medical Center, Utrecht University, P.O. Box 85090, 3508 AB Utrecht, The Netherlands; (M.L.J.N.C.); (K.A.)
| | - Sophie Ghijsen
- Department of Pediatric Pulmonology and Allergology, Wilhelmina Children’s Hospital—University Medical Center, Utrecht University, P.O. Box 85090, 3508 AB Utrecht, The Netherlands; (M.I.K.); (K.M.d.W.-d.G.); (G.B.); (S.G.); (H.G.M.A.); (C.K.v.d.E.)
| | - Harry G. M. Heijerman
- Department of Pulmonology, University Medical Center, Utrecht University, P.O. Box 85500, 3508 GA Utrecht, The Netherlands;
| | - Hubertus G. M. Arets
- Department of Pediatric Pulmonology and Allergology, Wilhelmina Children’s Hospital—University Medical Center, Utrecht University, P.O. Box 85090, 3508 AB Utrecht, The Netherlands; (M.I.K.); (K.M.d.W.-d.G.); (G.B.); (S.G.); (H.G.M.A.); (C.K.v.d.E.)
| | - Christof J. Majoor
- Department of Respiratory Medicine, Amsterdam University Medical Center, P.O. Box 22660, 1100 DD Amsterdam, The Netherlands;
| | - Hettie M. Janssens
- Department of Pediatric Pulmonology, Erasmus Medical Center/Sophia Children’s Hospital, 3015 GD Rotterdam, The Netherlands;
| | - Renske van der Meer
- Department of Pulmonology, Haga Teaching Hospital, 2545 AA The Hague, The Netherlands;
| | - Debby Bogaert
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children’s Hospital—University Medical Center, Utrecht University, P.O. Box 85090, 3508 AB Utrecht, The Netherlands; (M.L.J.N.C.); (K.A.)
- The Queen’s Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
- Correspondence:
| | - Cornelis K. van der Ent
- Department of Pediatric Pulmonology and Allergology, Wilhelmina Children’s Hospital—University Medical Center, Utrecht University, P.O. Box 85090, 3508 AB Utrecht, The Netherlands; (M.I.K.); (K.M.d.W.-d.G.); (G.B.); (S.G.); (H.G.M.A.); (C.K.v.d.E.)
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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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Nasal Epithelial Cell-Based Models for Individualized Study in Cystic Fibrosis. Int J Mol Sci 2021; 22:ijms22094448. [PMID: 33923202 PMCID: PMC8123210 DOI: 10.3390/ijms22094448] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 12/11/2022] Open
Abstract
The emergence of highly effective CFTR modulator therapy has led to significant improvements in health care for most patients with cystic fibrosis (CF). For some, however, these therapies remain inaccessible due to the rarity of their individual CFTR variants, or due to a lack of biologic activity of the available therapies for certain variants. One proposed method of addressing this gap is the use of primary human cell-based models, which allow preclinical therapeutic testing and physiologic assessment of relevant tissue at the individual level. Nasal cells represent one such tissue source and have emerged as a powerful model for individual disease study. The ex vivo culture of nasal cells has evolved over time, and modern nasal cell models are beginning to be utilized to predict patient outcomes. This review will discuss both historical and current state-of-the art use of nasal cells for study in CF, with a particular focus on the use of such models to inform personalized patient care.
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Lopes-Pacheco M, Pedemonte N, Veit G. Discovery of CFTR modulators for the treatment of cystic fibrosis. Expert Opin Drug Discov 2021; 16:897-913. [PMID: 33823716 DOI: 10.1080/17460441.2021.1912732] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
INTRODUCTION Cystic fibrosis (CF) is a life-threatening inherited disease caused by mutations in the gene encoding the CF transmembrane conductance regulator (CFTR) protein, an anion channel expressed at the apical membrane of secretory epithelia. CF leads to multiorgan dysfunction with progressive deterioration of lung function being the major cause of untimely death. Conventional CF therapies target only symptoms and consequences downstream of the primary genetic defect and the current life expectancy and quality of life of these individuals are still very limited. AREA COVERED CFTR modulator drugs are novel-specialized therapies that enhance or even restore functional expression of CFTR mutants and have been approved for clinical use for individuals with specific CF genotypes. This review summarizes classical approaches used for the pre-clinical development of CFTR correctors and potentiators as well as emerging strategies aiming to accelerate modulator development and expand theratyping efforts. EXPERT OPINION Highly effective CFTR modulator drugs are expected to deeply modify the disease course for the majority of individuals with CF. A multitude of experimental approaches have been established to accelerate the development of novel modulators. CF patient-derived specimens are valuable cell models to predict therapeutic effectiveness of existing (and novel) modulators in a precision medicine approach.
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Affiliation(s)
| | | | - Guido Veit
- Department of Physiology, McGill University, Montréal, Canada
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Davies JC, Wainwright CE, Sawicki GS, Higgins MN, Campbell D, Harris C, Panorchan P, Haseltine E, Tian S, Rosenfeld M. Ivacaftor in Infants Aged 4 to <12 Months with Cystic Fibrosis and a Gating Mutation. Results of a Two-Part Phase 3 Clinical Trial. Am J Respir Crit Care Med 2021; 203:585-593. [PMID: 33023304 PMCID: PMC7924576 DOI: 10.1164/rccm.202008-3177oc] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Rationale: We previously reported that ivacaftor was safe and well tolerated in cohorts aged 12 to <24 months with cystic fibrosis and gating mutations in the ARRIVAL study; here, we report results for cohorts aged 4 to <12 months. Objectives: To evaluate the safety, pharmacokinetics, and pharmacodynamics of ivacaftor in infants aged 4 to <12 months with one or more gating mutations. Methods: ARRIVAL is a single-arm phase 3 study. Infants received 25 mg or 50 mg ivacaftor every 12 hours on the basis of age and weight for 4 days in part A and 24 weeks in part B. Measurements and Main Results: Primary endpoints were safety (parts A and B) and pharmacokinetics (part A). Secondary/tertiary endpoints (part B) included pharmacokinetics and changes in sweat chloride levels, growth, and markers of pancreatic function. Twenty-five infants received ivacaftor, 12 in part A and 17 in part B (four infants participated in both parts). Pharmacokinetics was consistent with that in older groups. Most adverse events were mild or moderate. In part B, cough was the most common adverse event (n = 10 [58.8%]). Five infants (part A, n = 1 [8.3%]; part B, n = 4 [23.5%]) had serious adverse events, all of which were considered to be not or unlikely related to ivacaftor. No deaths or treatment discontinuations occurred. One infant (5.9%) experienced an alanine transaminase elevation >3 to ≤5× the upper limit of normal at Week 24. No other adverse trends in laboratory tests, vital signs, or ECG parameters were reported. Sweat chloride concentrations and measures of pancreatic obstruction improved. Conclusions: This study of ivacaftor in the first year of life supports treating the underlying cause of cystic fibrosis in children aged ≥4 months with one or more gating mutations. Clinical trial registered with clinicaltrials.gov (NCT02725567).
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Affiliation(s)
- Jane C Davies
- National Heart & Lung Institute, Imperial College London and Royal Brompton Hospital, London, United Kingdom
| | - Claire E Wainwright
- Queensland Children's Hospital, University of Queensland, Brisbane, Queensland, Australia
| | - Gregory S Sawicki
- Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Mark N Higgins
- Vertex Pharmaceuticals Incorporated, Boston, Massachusetts; and
| | - Daniel Campbell
- Vertex Pharmaceuticals Incorporated, Boston, Massachusetts; and
| | | | - Paul Panorchan
- Vertex Pharmaceuticals Incorporated, Boston, Massachusetts; and
| | - Eric Haseltine
- Vertex Pharmaceuticals Incorporated, Boston, Massachusetts; and
| | - Simon Tian
- Vertex Pharmaceuticals Incorporated, Boston, Massachusetts; and
| | - Margaret Rosenfeld
- Seattle Children's Hospital, University of Washington School of Medicine, Seattle, Washington
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72
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He L, Kennedy AS, Houck S, Aleksandrov A, Quinney NL, Cyr-Scully A, Cholon DM, Gentzsch M, Randell SH, Ren HY, Cyr DM. DNAJB12 and Hsp70 triage arrested intermediates of N1303K-CFTR for endoplasmic reticulum-associated autophagy. Mol Biol Cell 2021; 32:538-553. [PMID: 33534640 PMCID: PMC8101465 DOI: 10.1091/mbc.e20-11-0688] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 01/19/2021] [Accepted: 01/26/2021] [Indexed: 11/11/2022] Open
Abstract
The transmembrane Hsp40 DNAJB12 and cytosolic Hsp70 cooperate on the endoplasmic reticulum's (ER) cytoplasmic face to facilitate the triage of nascent polytopic membrane proteins for folding versus degradation. N1303K is a common mutation that causes misfolding of the ion channel CFTR, but unlike F508del-CFTR, biogenic and functional defects in N1303K-CFTR are resistant to correction by folding modulators. N1303K is reported to arrest CFTR folding at a late stage after partial assembly of its N-terminal domains. N1303K-CFTR intermediates are clients of JB12-Hsp70 complexes, maintained in a detergent-soluble state, and have a relatively long 3-h half-life. ER-associated degradation (ERAD)-resistant pools of N1303K-CFTR are concentrated in ER tubules that associate with autophagy initiation sites containing WIPI1, FlP200, and LC3. Destabilization of N1303K-CFTR or depletion of JB12 prevents entry of N1303K-CFTR into the membranes of ER-connected phagophores and traffic to autolysosomes. In contrast, the stabilization of intermediates with the modulator VX-809 promotes the association of N1303K-CFTR with autophagy initiation machinery. N1303K-CFTR is excluded from the ER-exit sites, and its passage from the ER to autolysosomes does not require ER-phagy receptors. DNAJB12 operates in biosynthetically active ER microdomains to triage membrane protein intermediates in a conformation-specific manner for secretion versus degradation via ERAD or selective-ER-associated autophagy.
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Affiliation(s)
- Lihua He
- Department of Cell Biology and Physiology and the Cystic Fibrosis/Pulmonary Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Andrew S. Kennedy
- Department of Cell Biology and Physiology and the Cystic Fibrosis/Pulmonary Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Scott Houck
- Department of Cell Biology and Physiology and the Cystic Fibrosis/Pulmonary Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Andrei Aleksandrov
- Department of Cell Biology and Physiology and the Cystic Fibrosis/Pulmonary Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Nancy L. Quinney
- Department of Cell Biology and Physiology and the Cystic Fibrosis/Pulmonary Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Alexandra Cyr-Scully
- Department of Cell Biology and Physiology and the Cystic Fibrosis/Pulmonary Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Deborah M. Cholon
- Department of Cell Biology and Physiology and the Cystic Fibrosis/Pulmonary Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Martina Gentzsch
- Department of Cell Biology and Physiology and the Cystic Fibrosis/Pulmonary Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Scott H. Randell
- Department of Cell Biology and Physiology and the Cystic Fibrosis/Pulmonary Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Hong Yu Ren
- Department of Cell Biology and Physiology and the Cystic Fibrosis/Pulmonary Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Douglas M. Cyr
- Department of Cell Biology and Physiology and the Cystic Fibrosis/Pulmonary Research and Treatment Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
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73
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Sanders M, Lawlor JMJ, Li X, Schuen JN, Millard SL, Zhang X, Buck L, Grysko B, Uhl KL, Hinds D, Stenger CL, Morris M, Lamb N, Levy H, Bupp C, Prokop JW. Genomic, transcriptomic, and protein landscape profile of CFTR and cystic fibrosis. Hum Genet 2021; 140:423-439. [PMID: 32734384 PMCID: PMC7855842 DOI: 10.1007/s00439-020-02211-w] [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: 05/16/2020] [Accepted: 07/25/2020] [Indexed: 01/18/2023]
Abstract
Cystic Fibrosis (CF) is caused most often by removal of amino acid 508 (Phe508del, deltaF508) within CFTR, yet dozens of additional CFTR variants are known to give rise to CF and many variants in the genome are known to contribute to CF pathology. To address CFTR coding variants, we developed a sequence-to-structure-to-dynamic matrix for all amino acids of CFTR using 233 vertebrate species, CFTR structure within a lipid membrane, and 20 ns of molecular dynamic simulation to assess known variants from the CFTR1, CFTR2, ClinVar, TOPmed, gnomAD, and COSMIC databases. Surprisingly, we identify 18 variants of uncertain significance within CFTR from diverse populations that are heritable and a likely cause of CF that have been understudied due to nonexistence in Caucasian populations. In addition, 15 sites within the genome are known to modulate CF pathology, where we have identified one genome region (chr11:34754985-34836401) that contributes to CF through modulation of expression of a noncoding RNA in epithelial cells. These 15 sites are just the beginning of understanding comodifiers of CF, where utilization of eQTLs suggests many additional genomics of CFTR expressing cells that can be influenced by genomic background of CFTR variants. This work highlights that many additional insights of CF genetics are needed, particularly as pharmaceutical interventions increase in the coming years.
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Affiliation(s)
- Morgan Sanders
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, 400 Monroe Ave NW, Grand Rapids, MI, 49503, USA
| | - James M J Lawlor
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Xiaopeng Li
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, 400 Monroe Ave NW, Grand Rapids, MI, 49503, USA
| | - John N Schuen
- Pediatric Pulmonology, Helen DeVos Children's Hospital, Grand Rapids, MI, 49503, USA
| | - Susan L Millard
- Pediatric Pulmonology, Helen DeVos Children's Hospital, Grand Rapids, MI, 49503, USA
| | - Xi Zhang
- Department of Pediatrics, Division of Pulmonary Medicine, National Jewish Health, Denver, CO, 80206, USA
| | - Leah Buck
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, 400 Monroe Ave NW, Grand Rapids, MI, 49503, USA
- Department of Mathematics, University of North Alabama, Florence, AL, 35632, USA
| | - Bethany Grysko
- Spectrum Health Medical Genetics, Grand Rapids, MI, 49503, USA
| | - Katie L Uhl
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, 400 Monroe Ave NW, Grand Rapids, MI, 49503, USA
| | - David Hinds
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, 400 Monroe Ave NW, Grand Rapids, MI, 49503, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Cynthia L Stenger
- Department of Mathematics, University of North Alabama, Florence, AL, 35632, USA
| | - Michele Morris
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Neil Lamb
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Hara Levy
- Department of Pediatrics, Division of Pulmonary Medicine, National Jewish Health, Denver, CO, 80206, USA
| | - Caleb Bupp
- Spectrum Health Medical Genetics, Grand Rapids, MI, 49503, USA
| | - Jeremy W Prokop
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, 400 Monroe Ave NW, Grand Rapids, MI, 49503, USA.
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, 48824, USA.
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74
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Spanò V, Barreca M, Cilibrasi V, Genovese M, Renda M, Montalbano A, Galietta LJV, Barraja P. Evaluation of Fused Pyrrolothiazole Systems as Correctors of Mutant CFTR Protein. Molecules 2021; 26:molecules26051275. [PMID: 33652850 PMCID: PMC7956813 DOI: 10.3390/molecules26051275] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 02/07/2023] Open
Abstract
Cystic fibrosis (CF) is a genetic disease caused by mutations that impair the function of the CFTR chloride channel. The most frequent mutation, F508del, causes misfolding and premature degradation of CFTR protein. This defect can be overcome with pharmacological agents named “correctors”. So far, at least three different classes of correctors have been identified based on the additive/synergistic effects that are obtained when compounds of different classes are combined together. The development of class 2 correctors has lagged behind that of compounds belonging to the other classes. It was shown that the efficacy of the prototypical class 2 corrector, the bithiazole corr-4a, could be improved by generating conformationally-locked bithiazoles. In the present study, we investigated the effect of tricyclic pyrrolothiazoles as analogues of constrained bithiazoles. Thirty-five compounds were tested using the functional assay based on the halide-sensitive yellow fluorescent protein (HS-YFP) that measured CFTR activity. One compound, having a six atom carbocyle central ring in the tricyclic pyrrolothiazole system and bearing a pivalamide group at the thiazole moiety and a 5-chloro-2-methoxyphenyl carboxamide at the pyrrole ring, significantly increased F508del-CFTR activity. This compound could lead to the synthesis of a novel class of CFTR correctors.
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Affiliation(s)
- Virginia Spanò
- Department of Biological, Chemical, and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Via Archirafi 32, 90123 Palermo, Italy; (V.S.); (M.B.); (V.C.); (P.B.)
| | - Marilia Barreca
- Department of Biological, Chemical, and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Via Archirafi 32, 90123 Palermo, Italy; (V.S.); (M.B.); (V.C.); (P.B.)
| | - Vincenzo Cilibrasi
- Department of Biological, Chemical, and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Via Archirafi 32, 90123 Palermo, Italy; (V.S.); (M.B.); (V.C.); (P.B.)
| | - Michele Genovese
- Telethon Institute of Genetics and Medicine (TIGEM), Campi Flegrei 34, 80078 Naples, Italy; (M.G.); (M.R.); (L.J.V.G.)
| | - Mario Renda
- Telethon Institute of Genetics and Medicine (TIGEM), Campi Flegrei 34, 80078 Naples, Italy; (M.G.); (M.R.); (L.J.V.G.)
| | - Alessandra Montalbano
- Department of Biological, Chemical, and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Via Archirafi 32, 90123 Palermo, Italy; (V.S.); (M.B.); (V.C.); (P.B.)
- Correspondence: ; Tel.: +39-091-238-968-22
| | - Luis Juan Vicente Galietta
- Telethon Institute of Genetics and Medicine (TIGEM), Campi Flegrei 34, 80078 Naples, Italy; (M.G.); (M.R.); (L.J.V.G.)
- Department of Translational Medical Sciences (DISMET), University of Naples, “Federico II”, Via Sergio Pansini 5, 80131 Naples, Italy
| | - Paola Barraja
- Department of Biological, Chemical, and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Via Archirafi 32, 90123 Palermo, Italy; (V.S.); (M.B.); (V.C.); (P.B.)
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75
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Salvatore D, Carnovale V, Majo F, Padoan R, Salvatore M, Taruscio D, Amato A, Ferrari G, Campagna G. Cystic fibrosis with non-G551D gating mutations in Italy: Epidemiology and clinical characteristics. Pediatr Pulmonol 2021; 56:442-449. [PMID: 33219628 DOI: 10.1002/ppul.25179] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 11/10/2020] [Accepted: 11/12/2020] [Indexed: 12/25/2022]
Abstract
BACKGROUND Cystic fibrosis transmembrane conductance regulator (CFTR) gating mutations (GMs) result in CFTR that is present at the cell surface but nonfunctional. Patients with the G551D mutation, the most prevalent worldwide, have been well studied. Italian GM patients have mainly non-G551D mutations. We studied their epidemiology and clinical characteristics in the period spanning the pre/post ivacaftor introduction to the Italian market. METHODS Data from the Italian CF Registry were used to describe patients with GMs and compare them with F508del homozygous (F/F) patients. RESULTS In total, 186 patients with GMs (median [range] age, 21.96 [0.13-63.38] years) were identified among the 5552 patients included in the study (3.3%). They had lower sweat chloride values at diagnosis than the F/F and a lower ratio of males. In the GM group, examining the data of the years 2012 and 2017 and comparing with F/F, lung infection by Staphylococcus aureus and diabetes became less prevalent, and better FEV1 and nutritional status were observed in 2017. The cross-sectional evaluation year-by-year from 2012 to 2017 of the GM group showed improving trends in lung function and body mass index, and the decreasing prevalence of diabetes compared with F/F. Longitudinal evaluation of GM patients showed improvement in percent predicted (pp)FEV1 and nutrition in the 2012-2017 period. These variations correspond to the introduction of treatment with the CFTR potentiator ivacaftor (2014/2015). CONCLUSIONS Italian patients with GMs are few and are characterized by milder phenotypes than F/F patients. Improved outcomes are likely influenced by treatment with ivacaftor.
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Affiliation(s)
- Donatello Salvatore
- Cystic Fibrosis Centre, Hospital San Carlo, Potenza, Italy.,Italian Cystic Fibrosis Registry, Rome, Italy
| | - Vincenzo Carnovale
- Italian Cystic Fibrosis Registry, Rome, Italy.,Cystic Fibrosis Centre, Adult Unit, Department of Translational Medical Science, University "Federico II", Naples, Italy
| | - Fabio Majo
- Italian Cystic Fibrosis Registry, Rome, Italy.,Cystic Fibrosis Centre, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Rita Padoan
- Italian Cystic Fibrosis Registry, Rome, Italy.,Cystic Fibrosis Regional Support Centre, Department of Pediatrics, University of Brescia, ASST Spedali Civili Brescia, Brescia, Italy
| | - Marco Salvatore
- Italian Cystic Fibrosis Registry, Rome, Italy.,Undiagnosed Rare Diseases Unit, National Centre for Rare Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Domenica Taruscio
- Italian Cystic Fibrosis Registry, Rome, Italy.,Undiagnosed Rare Diseases Unit, National Centre for Rare Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Annalisa Amato
- Italian Cystic Fibrosis Registry, Rome, Italy.,Lega Italiana Fibrosi Cistica, Rome, Italy
| | - Gianluca Ferrari
- Italian Cystic Fibrosis Registry, Rome, Italy.,Undiagnosed Rare Diseases Unit, National Centre for Rare Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Giuseppe Campagna
- Italian Cystic Fibrosis Registry, Rome, Italy.,Lega Italiana Fibrosi Cistica, Rome, Italy.,Department of Clinical and Molecular Medicine, University of Rome "La Sapienza", Rome, Italy
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76
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Lee JH, Kweon S, Park YR. Sharing genetic variants with the NGS pipeline is essential for effective genomic data sharing and reproducibility in health information exchange. Sci Rep 2021; 11:2268. [PMID: 33500538 PMCID: PMC7838410 DOI: 10.1038/s41598-021-82006-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 01/07/2021] [Indexed: 11/09/2022] Open
Abstract
Genetic variants causing underlying pharmacogenetic and disease phenotypes have been used as the basis for clinical decision-making. However, due to the lack of standards for next-generation sequencing (NGS) pipelines, reproducing genetic variants among institutions is still difficult. The aim of this study is to show how many important variants for clinical decisions can be individually detected using different pipelines. Genetic variants were derived from 105 breast cancer patient target DNA sequences via three different variant-calling pipelines. HaplotypeCaller, Mutect2 tumor-only mode in the Genome Analysis ToolKit (GATK), and VarScan were used in variant calling from the sequence read data processed by the same NGS preprocessing tools using Variant Effect Predictor. GATK HaplotypeCaller, VarScan, and MuTect2 found 25,130, 16,972, and 4232 variants, comprising 1491, 1400, and 321 annotated variants with ClinVar significance, respectively. The average number of ClinVar significant variants in the patients was 769.43, 16.50% of the variants were detected by only one variant caller. Despite variants with significant impact on clinical decision-making, the detected variants are different for each algorithm. To utilize genetic variants in the clinical field, a strict standard for NGS pipelines is essential.
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Affiliation(s)
- Jeong Hoon Lee
- Lunit Inc., 175 Yeoksamro, Gangnam-gu, Seoul, Republic of Korea
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Solbi Kweon
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Yu Rang Park
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, Republic of Korea.
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77
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Farley H, Poole S, Chapman S, Flight W. Diagnosis of cystic fibrosis in adulthood and eligibility for novel CFTR modulator therapy. Postgrad Med J 2021; 98:341-345. [PMID: 33452147 DOI: 10.1136/postgradmedj-2020-139278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 12/08/2020] [Accepted: 12/12/2020] [Indexed: 11/04/2022]
Abstract
BACKGROUND Cystic fibrosis (CF) is an autosomal recessive condition that primarily manifests as a chronic respiratory disease. CF is usually diagnosed in early childhood or through newborn screening although in a small but important group, diagnosis is not made until adulthood. Highly effective cystic fibrosis transmembrane conductance regulator (CFTR) modulator therapies are now available for most genetic causes of CF highlighting the importance of identifying people with late presentations of CF. AIM We aimed to identify the clinical characteristics of people diagnosed with CF in adulthood and their resulting eligibility for novel CFTR modulator therapies. DESIGN Retrospective single-centre cohort study. METHODS Patients diagnosed with CF at age 18 years or older were identified from a patient database. Paper and electronic medical records were reviewed and clinical, microbiological and radiological data at diagnosis were recorded. RESULTS Nineteen patients were identified. Median age at diagnosis was 38 years (range: 19-71) and 9 (47%) were female. All patients had a history of chronic respiratory symptoms and 18/19 (94%) had radiological evidence of bronchiectasis. All patients had two pathogenic CFTR mutations identified with 16/19 (84%) compound heterozygotes for the F508del mutation. The majority of patients had a CFTR genotype considered eligible for CFTR modulator therapy (84% and 89% according to European and US licences, respectively). CONCLUSIONS Adult patients with unexplained chronic bronchiectasis should be thoroughly investigated for CF. A low index of suspicion will help to identify adults with undiagnosed CF who are likely to benefit from CFTR modulator therapy.
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Affiliation(s)
| | - Sarah Poole
- Respiratory Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, Oxfordshire, UK
| | - Stephen Chapman
- Respiratory Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, Oxfordshire, UK
| | - William Flight
- Respiratory Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, Oxfordshire, UK
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78
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Fidler MC, Buckley A, Sullivan JC, Statia M, Boj SF, Vries RGJ, Munck A, Higgins M, Moretto Zita M, Negulescu P, van Goor F, De Boeck K. G970R-CFTR Mutation (c.2908G>C) Results Predominantly in a Splicing Defect. Clin Transl Sci 2020; 14:656-663. [PMID: 33278322 PMCID: PMC7993255 DOI: 10.1111/cts.12927] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 10/25/2020] [Indexed: 01/23/2023] Open
Abstract
In previous work, participants with a G970R mutation in cystic fibrosis transmembrane conductance regulator (CFTR) (c.2908G>C) had numerically lower sweat chloride responses during ivacaftor treatment than participants with other CFTR gating mutations. The objective of this substudy was to characterize the molecular defect of the G970R mutation in vitro and assess the benefit of ivacaftor in participants with this mutation. This substudy assessed sweat chloride, spirometry findings, and nasal potential difference on and off ivacaftor treatment in three participants with a G970R/F508del genotype. Intestinal organoids derived from rectal biopsy specimens were used to assess ivacaftor response ex vivo and conduct messenger RNA splice and protein analyses. No consistent or meaningful trends were observed between on-treatment and off-treatment clinical assessments. Organoids did not respond to ivacaftor in forskolin-induced swelling assays; no mature CFTR protein was detected in Western blots. Organoid RNA analysis demonstrated that 3 novel splice variants were created by G970R-CFTR: exon 17 truncation, exons 13-15 and 17 skipping, and intron 17 retention. Functional and molecular analyses indicated that the c.2908G>C mutation caused a cryptic splicing defect. Organoids lacked an ex vivo response with ivacaftor and supported identification of the mechanism underlying the CFTR defect caused by c.2908G>C. Analysis of CFTR mutations indicated that cryptic splicing was a rare cause of mutation misclassification in engineered cell lines. This substudy used organoids as an alternative in vitro model for mutations, such as cryptic splice mutations that cannot be fully assessed using cDNA expressed in recombinant cell systems.
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Affiliation(s)
| | | | | | - Marvin Statia
- Foundation Hubrecht Organoid Technology, Utrecht, The Netherlands
| | - Sylvia F Boj
- Foundation Hubrecht Organoid Technology, Utrecht, The Netherlands
| | - Robert G J Vries
- Foundation Hubrecht Organoid Technology, Utrecht, The Netherlands
| | - Anne Munck
- Hôpital Universitaire Robert-Debré, AP-HP, Université Paris Diderot, Paris, France
| | - Mark Higgins
- Vertex Pharmaceuticals Incorporated, Boston, Massachusetts, USA
| | | | - Paul Negulescu
- Vertex Pharmaceuticals Incorporated, Boston, Massachusetts, USA
| | | | - Kris De Boeck
- University Hospital Gasthuisberg, University of Leuven, Leuven, Belgium
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79
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Prins S, Langron E, Hastings C, Hill EJ, Stefan AC, Griffin LD, Vergani P. Fluorescence assay for simultaneous quantification of CFTR ion-channel function and plasma membrane proximity. J Biol Chem 2020; 295:16529-16544. [PMID: 32934006 PMCID: PMC7864054 DOI: 10.1074/jbc.ra120.014061] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 08/21/2020] [Indexed: 11/21/2022] Open
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) is a plasma membrane anion channel that plays a key role in controlling transepithelial fluid movement. Excessive activation results in intestinal fluid loss during secretory diarrheas, whereas CFTR mutations underlie cystic fibrosis (CF). Anion permeability depends both on how well CFTR channels work (permeation/gating) and on how many are present at the membrane. Recently, treatments with two drug classes targeting CFTR-one boosting ion-channel function (potentiators) and the other increasing plasma membrane density (correctors)-have provided significant health benefits to CF patients. Here, we present an image-based fluorescence assay that can rapidly and simultaneously estimate both CFTR ion-channel function and the protein's proximity to the membrane. We monitor F508del-CFTR, the most common CF-causing variant, and confirm rescue by low temperature, CFTR-targeting drugs and second-site revertant mutation R1070W. In addition, we characterize a panel of 62 CF-causing mutations. Our measurements correlate well with published data (electrophysiology and biochemistry), further confirming validity of the assay. Finally, we profile effects of acute treatment with approved potentiator drug VX-770 on the rare-mutation panel. Mapping the potentiation profile on CFTR structures raises mechanistic hypotheses on drug action, suggesting that VX-770 might allow an open-channel conformation with an alternative arrangement of domain interfaces. The assay is a valuable tool for investigation of CFTR molecular mechanisms, allowing accurate inferences on gating/permeation. In addition, by providing a two-dimensional characterization of the CFTR protein, it could better inform development of single-drug and precision therapies addressing the root cause of CF disease.
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Affiliation(s)
- Stella Prins
- Department of Neuroscience, Physiology, and Pharmacology, University College London, London, United Kingdom
| | - Emily Langron
- Department of Neuroscience, Physiology, and Pharmacology, University College London, London, United Kingdom
| | - Cato Hastings
- CoMPLEX, University College London, London, United Kingdom
| | - Emily J Hill
- Department of Neuroscience, Physiology, and Pharmacology, University College London, London, United Kingdom
| | - Andra C Stefan
- Natural Sciences, University College London, London, United Kingdom
| | | | - Paola Vergani
- Department of Neuroscience, Physiology, and Pharmacology, University College London, London, United Kingdom.
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80
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Vincent F, Loria PM, Weston AD, Steppan CM, Doyonnas R, Wang YM, Rockwell KL, Peakman MC. Hit Triage and Validation in Phenotypic Screening: Considerations and Strategies. Cell Chem Biol 2020; 27:1332-1346. [DOI: 10.1016/j.chembiol.2020.08.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 05/31/2020] [Accepted: 08/14/2020] [Indexed: 02/06/2023]
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81
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Joynt AT, Evans TA, Pellicore MJ, Davis-Marcisak EF, Aksit MA, Eastman AC, Patel SU, Paul KC, Osorio DL, Bowling AD, Cotton CU, Raraigh KS, West NE, Merlo CA, Cutting GR, Sharma N. Evaluation of both exonic and intronic variants for effects on RNA splicing allows for accurate assessment of the effectiveness of precision therapies. PLoS Genet 2020; 16:e1009100. [PMID: 33085659 PMCID: PMC7605713 DOI: 10.1371/journal.pgen.1009100] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 11/02/2020] [Accepted: 09/08/2020] [Indexed: 12/21/2022] Open
Abstract
Elucidating the functional consequence of molecular defects underlying genetic diseases enables appropriate design of therapeutic options. Treatment of cystic fibrosis (CF) is an exemplar of this paradigm as the development of CFTR modulator therapies has allowed for targeted and effective treatment of individuals harboring specific genetic variants. However, the mechanism of these drugs limits effectiveness to particular classes of variants that allow production of CFTR protein. Thus, assessment of the molecular mechanism of individual variants is imperative for proper assignment of these precision therapies. This is particularly important when considering variants that affect pre-mRNA splicing, thus limiting success of the existing protein-targeted therapies. Variants affecting splicing can occur throughout exons and introns and the complexity of the process of splicing lends itself to a variety of outcomes, both at the RNA and protein levels, further complicating assessment of disease liability and modulator response. To investigate the scope of this challenge, we evaluated splicing and downstream effects of 52 naturally occurring CFTR variants (exonic = 15, intronic = 37). Expression of constructs containing select CFTR intronic sequences and complete CFTR exonic sequences in cell line models allowed for assessment of RNA and protein-level effects on an allele by allele basis. Characterization of primary nasal epithelial cells obtained from individuals harboring splice variants corroborated in vitro data. Notably, we identified exonic variants that result in complete missplicing and thus a lack of modulator response (e.g. c.2908G>A, c.523A>G), as well as intronic variants that respond to modulators due to the presence of residual normally spliced transcript (e.g. c.4242+2T>C, c.3717+40A>G). Overall, our data reveals diverse molecular outcomes amongst both exonic and intronic variants emphasizing the need to delineate RNA, protein, and functional effects of each variant in order to accurately assign precision therapies. Genetic variants that impact pre-mRNA splicing are a common cause of genetic disease and have varying downstream molecular consequences. As a result, precision therapies that function at the protein level are not always effective for these variants and thus careful assessment is necessary. Here we evaluate RNA-level effects of 52 variants in the cystic fibrosis transmembrane conductance regulator (CFTR) gene and show that study of splicing and its consequences allows for more accurate assignment of precision therapies.
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Affiliation(s)
- Anya T. Joynt
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Taylor A. Evans
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Matthew J. Pellicore
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Emily F. Davis-Marcisak
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Melis A. Aksit
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Alice C. Eastman
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Shivani U. Patel
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, United States of America
| | - Kathleen C. Paul
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Derek L. Osorio
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Alyssa D. Bowling
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Calvin U. Cotton
- Departments of Pediatrics, Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Karen S. Raraigh
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Natalie E. West
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, United States of America
| | - Christian A. Merlo
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, United States of America
| | - Garry R. Cutting
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- * E-mail: (GRC); (NS)
| | - Neeraj Sharma
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- * E-mail: (GRC); (NS)
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82
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Moheet A, Beisang D, Zhang L, Sagel SD, VanDalfsen JM, Heltshe SL, Frederick C, Mann M, Antos N, Billings J, Rowe SM, Moran A. Lumacaftor/ivacaftor therapy fails to increase insulin secretion in F508del/F508del CF patients. J Cyst Fibros 2020; 20:333-338. [PMID: 32917547 DOI: 10.1016/j.jcf.2020.09.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 07/13/2020] [Accepted: 09/02/2020] [Indexed: 01/05/2023]
Abstract
BACKGROUND Glucose tolerance abnormalities including cystic fibrosis related diabetes (CFRD) are common in patients with cystic fibrosis (CF). The underlying pathophysiology is not fully understood. Emerging evidence suggests that CFTR dysfunction may directly or indirectly impact β-cell function, offering the potential for improvement with CFTR modulator therapy. In small pilot studies, treatment with ivacaftor improved insulin secretion in patients with the G551D CFTR mutation. In the current study, we examined the impact of lumacaftor/ivacaftor therapy on glucose tolerance and insulin secretion in patients with CF who were homozygous for the F508del mutation. METHODS 39 subjects from the PROSPECT Part B study who had been prescribed lumacaftor/ivacaftor by their CF care team at a CF Foundation's Therapeutic Development Network center were recruited. Subjects underwent 2-hour oral glucose tolerance tests (OGTTs) at baseline prior to first dose of lumacaftor/ivacaftor, and at 3, 6 and 12 months on therapy. OGTT glucose, insulin and c-peptide parameters were compared. RESULTS Compared to baseline, OGTT fasting and 2 hour glucose levels, glucose area under the curve, insulin area under the curve and time to peak insulin level were not significantly different at 3, 6 and 12 months on lumacaftor/ivacaftor therapy. Similarly, C-peptide levels were no different. CONCLUSIONS Lumacaftor/ivacaftor therapy did not improve insulin secretion or glucose tolerance in patients with CF who were homozygous for the F508del mutation.
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Affiliation(s)
- Amir Moheet
- Department of Medicine, University of Minnesota, Minneapolis, MN, United States
| | - Daniel Beisang
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States
| | - Lin Zhang
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, United States
| | - Scott D Sagel
- Department of Pediatrics, Children's Hospital Colorado and University of Colorado Anshutz Medical Campus, Aurora, CO, United States
| | - Jill M VanDalfsen
- Cystic Fibrosis Foundation Therapeutics Development Network Coordinating Center, Seattle, Children's Research, Seattle, WA, United States
| | - Sonya L Heltshe
- Cystic Fibrosis Foundation Therapeutics Development Network Coordinating Center, Seattle, Children's Research, Seattle, WA, United States; Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, United States
| | - Carla Frederick
- Jacobs School of Medicine and Biomedical Sciences of the University at Buffalo and UBMD Internal Medicine, Buffalo, NY, United States
| | - Michelle Mann
- Baylor College of Medicine, Houston, TX, United States
| | - Nicholas Antos
- Medical College of Wisconsin, Milwaukee, WI, United States
| | - Joanne Billings
- Department of Medicine, University of Minnesota, Minneapolis, MN, United States
| | - Steven M Rowe
- Department of Medicine and the Gregory Flemming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Antoinette Moran
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States.
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83
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Wang W, Fu L, Liu Z, Wen H, Rab A, Hong JS, Kirk KL, Rowe SM. G551D mutation impairs PKA-dependent activation of CFTR channel that can be restored by novel GOF mutations. Am J Physiol Lung Cell Mol Physiol 2020; 319:L770-L785. [PMID: 32877225 DOI: 10.1152/ajplung.00262.2019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
G551D is a major disease-associated gating mutation in the cystic fibrosis transmembrane conductance regulator (CFTR) protein, an ATP- and phosphorylation-dependent chloride channel. G551D causes severe cystic fibrosis (CF) disease by disrupting ATP-dependent channel opening; however, whether G551D affects phosphorylation-dependent channel activation is unclear. Here, we use macropatch recording and Ussing chamber approaches to demonstrate that G551D impacts on phosphorylation-dependent activation of CFTR, and PKA-mediated phosphorylation regulates the interaction between the x-loop in nucleotide-binding domain 2 (NBD2) and cytosolic loop (CL) 1. We show that G551D not only disrupts ATP-dependent channel opening but also impairs phosphorylation-dependent channel activation by largely reducing PKA sensitivity consistent with the reciprocal relationship between channel opening/gating, ligand binding, and phosphorylation. Furthermore, we identified two novel GOF mutations: D1341R in the x-loop near the ATP-binding cassette signature motif in NBD2 and D173R in CL1, each of which strongly increased PKA sensitivity both in the wild-type (WT) background and when introduced into G551D-CFTR. When D1341R was combined with a second GOF mutation (e.g., K978C in CL3), we find that the double GOF mutation maximally increased G551D channel activity such that VX-770 had no further effect. We further show that a double charge-reversal mutation of D1341R/D173R-CFTR exhibited similar PKA sensitivity when compared with WT-CFTR. Together, our results suggest that charge repulsion between D173 and D1341 of WT-CFTR normally inhibits channel activation at low PKA activity by reducing PKA sensitivity, and negative allostery by the G551D is coupled to reduced PKA sensitivity of CFTR that can be restored by second GOF mutations.
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Affiliation(s)
- Wei Wang
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama.,Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama
| | - Lianwu Fu
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama.,Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama
| | - Zhiyong Liu
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama
| | - Hui Wen
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama
| | - Andras Rab
- Department of Pediatrics, Emory University, Atlanta, Georgia
| | - Jeong S Hong
- Department of Pediatrics, Emory University, Atlanta, Georgia
| | - Kevin L Kirk
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama.,Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama
| | - Steven M Rowe
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama.,Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama.,School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama.,Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama
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84
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Bradbury NA. Cystic Fibrosis and Genotype-Dependent Therapy: Is There a Need for a Sex-Specific Therapy? GENDER AND THE GENOME 2020. [DOI: 10.1177/2470289720937025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Cystic fibrosis (CF) is an autosomal recessive genetic disease caused by mutations in the cystic fibrosis transmembrane conductance regulation (CFTR) anion channel. Loss of CFTR protein and/or function disrupts chloride, bicarbonate, and fluid transport and also impacts epithelial sodium transport. Such altered ion and fluid transport produces mucus obstruction, inflammation, pulmonary infection, and damage to multiple organs. Although an autosomal disease, it is apparent that gender differences in life expectancy and quality of life do exist. Conventionally established therapies have treated the downstream sequelae of CFTR dysfunction and have led to a steady increase in life expectancy. Physicians now have access to medications that treat the basic defect in CF, in the form of CFTR modulators. These drugs target the trafficking and/or function of CFTR to improve clinical outcomes for patients. This review summarizes the science behind CFTR modulators and shows how these drugs have dramatically changed how patients with CF are treated. Surprisingly, although the drug target(s) are identical in males and females, CF females seem to display a greater improvement than their male counterparts.
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Affiliation(s)
- Neil A. Bradbury
- Department of Physiology and Biophysics and Center for Genetic Diseases, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL, USA
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85
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Gostelie R, Stegeman I, Berkers G, Bittermann J, Ligtenberg-van der Drift I, van Kipshagen PJ, de Winter - de Groot K, Speleman L. The impact of ivacaftor on sinonasal pathology in S1251N-mediated cystic fibrosis patients. PLoS One 2020; 15:e0235638. [PMID: 32687499 PMCID: PMC7371187 DOI: 10.1371/journal.pone.0235638] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/19/2020] [Indexed: 12/19/2022] Open
Abstract
IMPORTANCE Sinonasal symptoms in patients suffering from cystic fibrosis can negatively influence the quality of life and sinuses can be a niche for pathogens causing infection and inflammation leading to a decrease of lung function. Ivacaftor, a potentiator of the Cystic Fibrosis Transmembrane Conductance Regulator protein, has shown improvement in pulmonary function in cystic fibrosis patients with different forms of class III gating mutations. However, the effects of ivacaftor on sinonasal pathology have hardly been studied. OBJECTIVE To determine the impact of ivacaftor therapy on sinonasal pathology in patients with cystic fibrosis with an S1251N mutation. DESIGN Prospective observational mono-center cohort study, between June 2015 and December 2016. SETTING A tertiary referral center in Utrecht, The Netherlands. PARTICIPANTS Eight patients with cystic fibrosis with an S1251N mutation, treated with the potentiator ivacaftor were investigated. EXPOSURES Ivacaftor (Kalydeco, VX-770) therapy. Computed tomography imaging of paranasal sinuses. Nasal nitric oxide concentration measurements and nasal endoscopy. MAIN OUTCOMES AND MEASURES Primary outcome is opacification of paranasal sinuses examined with computed tomography scan analysis and scaled by the modified Lund-Mackay score before and one year after treatment. Secondary outcomes are nasal nitric oxide concentration levels, sinonasal symptoms and nasal endoscopic findings before and approximately two months and in some cases one year after treatment. RESULTS Computed tomography scan analysis showed a significant decrease in opacification of the majority of paranasal sinuses comparing the opacification score per paranasal sinus before and after one year of treatment with ivacaftor. Median nasal nitric oxide levels significantly improved from 220.00 (IQR:136.00-341.18) to 462.84 (IQR:233.17-636.25) (p = 0.017) parts per billion. Likewise, the majority of sinonasal symptoms and nasal endoscopic pathology decreased or resolved at two months after the use of ivacaftor. CONCLUSION AND RELEVANCE Ivacaftor appears to improve sinonasal outcome parameters and thereby sinonasal health in patients with cystic fibrosis with an S1251N mutation.
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Affiliation(s)
- Romee Gostelie
- University Medical Center, Utrecht University, Utrecht, The Netherlands
| | - Inge Stegeman
- Department of Otorhinolaryngology, Head and Neck Surgery, University Medical Center, Utrecht University, Utrecht, The Netherlands
| | - Gitte Berkers
- Department of Pediatric Respiratory Medicine and Allergology, Cystic Fibrosis Center, University Medical Center, Utrecht University, Utrecht, The Netherlands
| | - Joost Bittermann
- Department of Pediatric Otorhinolaryngology, University Medical Center, Utrecht University, Utrecht, The Netherlands
| | - Ivonne Ligtenberg-van der Drift
- Department of Otorhinolaryngology, Head and Neck Surgery, University Medical Center, Utrecht University, Utrecht, The Netherlands
| | | | - Karin de Winter - de Groot
- Department of Pediatric Respiratory Medicine and Allergology, Cystic Fibrosis Center, University Medical Center, Utrecht University, Utrecht, The Netherlands
| | - Lucienne Speleman
- Department of Pediatric Otorhinolaryngology, University Medical Center, Utrecht University, Utrecht, The Netherlands
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86
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Sidhom E, O'Brien J, Underwood BR. The application of stratified medicine to dementia care. BJPSYCH ADVANCES 2020. [DOI: 10.1192/bja.2020.28] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
SUMMARYStratified medicine has been successfully used in many areas of medicine, perhaps most notably oncology. There is now both a growing evidence base and mounting enthusiasm, supported at a governmental level and across industry, academia and clinical medicine, to apply this approach to neurodegenerative illnesses, including dementia, as these provide the greatest clinical and social challenge of our times. In this article we consider definitions of stratified medicine, look at its application in other medical specialties, review the national context in the UK and consider the current state, future potential and specific considerations of applying stratified medicine to dementia.
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87
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GM1 as Adjuvant of Innovative Therapies for Cystic Fibrosis Disease. Int J Mol Sci 2020; 21:ijms21124486. [PMID: 32599772 PMCID: PMC7350007 DOI: 10.3390/ijms21124486] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/20/2020] [Accepted: 06/21/2020] [Indexed: 01/26/2023] Open
Abstract
Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) protein is expressed at the apical plasma membrane (PM) of different epithelial cells. The most common mutation responsible for the onset of cystic fibrosis (CF), F508del, inhibits the biosynthesis and transport of the protein at PM, and also presents gating and stability defects of the membrane anion channel upon its rescue by the use of correctors and potentiators. This prompted a multiple drug strategy for F508delCFTR aimed simultaneously at its rescue, functional potentiation and PM stabilization. Since ganglioside GM1 is involved in the functional stabilization of transmembrane proteins, we investigated its role as an adjuvant to increase the effectiveness of CFTR modulators. According to our results, we found that GM1 resides in the same PM microenvironment as CFTR. In CF cells, the expression of the mutated channel is accompanied by a decrease in the PM GM1 content. Interestingly, by the exogenous administration of GM1, it becomes a component of the PM, reducing the destabilizing effect of the potentiator VX-770 on rescued CFTR protein expression/function and improving its stabilization. This evidence could represent a starting point for developing innovative therapeutic strategies based on the co-administration of GM1, correctors and potentiators, with the aim of improving F508del CFTR function.
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88
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Patel SD, Bono TR, Rowe SM, Solomon GM. CFTR targeted therapies: recent advances in cystic fibrosis and possibilities in other diseases of the airways. Eur Respir Rev 2020; 29:29/156/190068. [PMID: 32554756 PMCID: PMC9131734 DOI: 10.1183/16000617.0068-2019] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 03/09/2020] [Indexed: 12/11/2022] Open
Abstract
Cystic fibrosis transmembrane conductance regulator (CFTR) is an ion transporter that regulates mucus hydration, viscosity and acidity of the airway epithelial surface. Genetic defects in CFTR impair regulation of mucus homeostasis, causing severe defects of mucociliary clearance as seen in cystic fibrosis. Recent work has established that CFTR dysfunction can be acquired in chronic obstructive pulmonary disease (COPD) and may also contribute to other diseases that share clinical features of cystic fibrosis, such as asthma, allergic bronchopulmonary aspergillosis and bronchiectasis. Protean causes of CFTR dysfunction have been identified including cigarette smoke exposure, toxic metals and downstream effects of neutrophil activation pathways. Recently, CFTR modulators, small molecule agents that potentiate CFTR or restore diminished protein levels at the cell surface, have been successfully developed for various CFTR gene defects, prompting interest in their use to treat diseases of acquired dysfunction. The spectrum of CFTR dysfunction, strategies for CFTR modulation, and candidate diseases for CFTR modulation beyond cystic fibrosis will be reviewed in this manuscript. CFTR dysfunction may be part of the pathophysiology of many diseases of the airways. Exploration of mechanisms of dysfunction and options for CFTR-directed therapies are examined in this article. http://bit.ly/33o6nDu
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Affiliation(s)
- Sheylan D Patel
- Dept of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA.,Both authors contributed equally
| | - Taylor R Bono
- Dept of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA.,The Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL, USA.,Both authors contributed equally
| | - Steven M Rowe
- Dept of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA .,The Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - George M Solomon
- Dept of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA.,The Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL, USA
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89
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Alexander M, Reyfman PA. RNA Sequencing: A Potentiator of Discovery-based Research. Am J Respir Cell Mol Biol 2020; 61:558-559. [PMID: 31091961 PMCID: PMC6827071 DOI: 10.1165/rcmb.2019-0156ed] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
| | - Paul A Reyfman
- Feinberg School of MedicineNorthwestern UniversityChicago, Illinois
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90
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Sutcliffe M, Radley G, Barton A. Personalized medicine in rheumatic diseases: how close are we to being able to use genetic biomarkers to predict response to TNF inhibitors? Expert Rev Clin Immunol 2020; 16:389-396. [DOI: 10.1080/1744666x.2020.1740594] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Megan Sutcliffe
- Versus Arthritis Centre for Genetics and Genomics, Centre for Musculoskeletal Research, The University of Manchester, Manchester, UK
| | - Gemma Radley
- Versus Arthritis Centre for Genetics and Genomics, Centre for Musculoskeletal Research, The University of Manchester, Manchester, UK
| | - Anne Barton
- Versus Arthritis Centre for Genetics and Genomics, Centre for Musculoskeletal Research, The University of Manchester, Manchester, UK
- NIHR Manchester Biomedical Research Centre, Manchester University NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK
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91
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Froux L, Elbahnsi A, Boucherle B, Billet A, Baatallah N, Hoffmann B, Alliot J, Zelli R, Zeinyeh W, Haudecoeur R, Chevalier B, Fortuné A, Mirval S, Simard C, Lehn P, Mornon JP, Hinzpeter A, Becq F, Callebaut I, Décout JL. Targeting different binding sites in the CFTR structures allows to synergistically potentiate channel activity. Eur J Med Chem 2020; 190:112116. [DOI: 10.1016/j.ejmech.2020.112116] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 01/24/2020] [Accepted: 02/03/2020] [Indexed: 02/06/2023]
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92
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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: 269] [Impact Index Per Article: 67.3] [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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93
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Meng X, Clews J, Ciuta AD, Martin ER, Ford RC. CFTR structure, stability, function and regulation. Biol Chem 2020; 400:1359-1370. [PMID: 30738013 DOI: 10.1515/hsz-2018-0470] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 01/30/2019] [Indexed: 12/15/2022]
Abstract
Cystic fibrosis transmembrane conductance regulator (CFTR) is a unique member of the ATP-binding cassette family of proteins because it has evolved into a channel. Mutations in CFTR cause cystic fibrosis, the most common genetic disease in people of European origin. The F508del mutation is found in about 90% of patients and here we present data that suggest its main effect is on CFTR stability rather than on the three-dimensional (3D) folded state. A survey of recent cryo-electron microscopy studies was carried out and this highlighted differences in terms of CFTR conformation despite similarities in experimental conditions. We further studied CFTR structure under various phosphorylation states and with the CFTR-interacting protein NHERF1. The coexistence of outward-facing and inward-facing conformations under a range of experimental conditions was suggested from these data. These results are discussed in terms of structural models for channel gating, and favour the model where the mostly disordered regulatory-region of the protein acts as a channel plug.
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Affiliation(s)
- Xin Meng
- School of Biological Sciences, Faculty of Biology Medicine and Health, Michael Smith Building, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Jack Clews
- School of Biological Sciences, Faculty of Biology Medicine and Health, Michael Smith Building, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Anca D Ciuta
- School of Biological Sciences, Faculty of Biology Medicine and Health, Michael Smith Building, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Eleanor R Martin
- School of Biological Sciences, Faculty of Biology Medicine and Health, Michael Smith Building, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Robert C Ford
- School of Biological Sciences, Faculty of Biology Medicine and Health, Michael Smith Building, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
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Wang C, Balch WE. Bridging Genomics to Phenomics at Atomic Resolution through Variation Spatial Profiling. Cell Rep 2020; 24:2013-2028.e6. [PMID: 30134164 PMCID: PMC6261431 DOI: 10.1016/j.celrep.2018.07.059] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 06/25/2018] [Accepted: 07/16/2018] [Indexed: 01/04/2023] Open
Abstract
To understand the impact of genome sequence variation (the genotype) responsible for biological diversity and human health (the phenotype) including cystic fibrosis and Alzheimer's disease, we developed a Gaussian-process-based machine learning (ML) approach, variation spatial profiling (VSP). VSP uses a sparse collection of known variants found in the population that perturb the protein fold to define unknown variant function based on the emergent general principle of spatial covariance (SCV). SCV quantitatively captures the role of proximity in genotype-to-phenotype spatial-temporal relationships. Phenotype landscapes generated through SCV provide a platform that can be used to describe the functional properties that drive sequence-to-function-to-structure design of the polypeptide fold at atomic resolution. We provide proof of principle that SCV can enable the use of population-based genomic platforms to define the origins and mechanism of action of genotype-to-phenotype transformations contributing to the health and disease of an individual.
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Affiliation(s)
- Chao Wang
- Department of Molecular Medicine, The Scripps Research Institute (TSRI), La Jolla, CA 92037, USA
| | - William E Balch
- Department of Molecular Medicine, The Scripps Research Institute (TSRI), La Jolla, CA 92037, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute (TSRI), La Jolla, CA 92037, USA.
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95
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Ivey G, Youker RT. Disease-relevant mutations alter amino acid co-evolution networks in the second nucleotide binding domain of CFTR. PLoS One 2020; 15:e0227668. [PMID: 31978131 PMCID: PMC6980524 DOI: 10.1371/journal.pone.0227668] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Accepted: 12/25/2019] [Indexed: 01/23/2023] Open
Abstract
Cystic Fibrosis (CF) is an inherited disease caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) ion channel. Mutations in CFTR cause impaired chloride ion transport in the epithelial tissues of patients leading to cardiopulmonary decline and pancreatic insufficiency in the most severely affected patients. CFTR is composed of twelve membrane-spanning domains, two nucleotide-binding domains (NBDs), and a regulatory domain. The most common mutation in CFTR is a deletion of phenylalanine at position 508 (ΔF508) in NBD1. Previous research has primarily concentrated on the structure and dynamics of the NBD1 domain; However numerous pathological mutations have also been found in the lesser-studied NBD2 domain. We have investigated the amino acid co-evolved network of interactions in NBD2, and the changes that occur in that network upon the introduction of CF and CF-related mutations (S1251N(T), S1235R, D1270N, N1303K(T)). Extensive coupling between the α- and β-subdomains were identified with residues in, or near Walker A, Walker B, H-loop and C-loop motifs. Alterations in the predicted residue network varied from moderate for the S1251T perturbation to more severe for N1303T. The S1235R and D1270N networks varied greatly compared to the wildtype, but these CF mutations only affect ion transport preference and do not severely disrupt CFTR function, suggesting dynamic flexibility in the network of interactions in NBD2. Our results also suggest that inappropriate interactions between the β-subdomain and Q-loop could be detrimental. We also identified mutations predicted to stabilize the NBD2 residue network upon introduction of the CF and CF-related mutations, and these predicted mutations are scored as benign by the MUTPRED2 algorithm. Our results suggest the level of disruption of the co-evolution predictions of the amino acid networks in NBD2 does not have a straightforward correlation with the severity of the CF phenotypes observed.
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Affiliation(s)
- Gabrianne Ivey
- Kyder Christian Academy, Franklin, North Carolina, United States of America
- Southwestern Community College, Sylva, North Carolina, United States of America
| | - Robert T. Youker
- Department of Biology, Western Carolina University, Cullowhee, North Carolina, United States of America
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96
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McCague AF, Raraigh KS, Pellicore MJ, Davis-Marcisak EF, Evans TA, Han ST, Lu Z, Joynt AT, Sharma N, Castellani C, Collaco JM, Corey M, Lewis MH, Penland CM, Rommens JM, Stephenson AL, Sosnay PR, Cutting GR. Correlating Cystic Fibrosis Transmembrane Conductance Regulator Function with Clinical Features to Inform Precision Treatment of Cystic Fibrosis. Am J Respir Crit Care Med 2020; 199:1116-1126. [PMID: 30888834 DOI: 10.1164/rccm.201901-0145oc] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Rationale: The advent of precision treatment for cystic fibrosis using small-molecule therapeutics has created a need to estimate potential clinical improvements attributable to increases in cystic fibrosis transmembrane conductance regulator (CFTR) function. Objectives: To derive CFTR function of a variety of CFTR genotypes and correlate with key clinical features (sweat chloride concentration, pancreatic exocrine status, and lung function) to develop benchmarks for assessing response to CFTR modulators. Methods: CFTR function assigned to 226 unique CFTR genotypes was correlated with the clinical data of 54,671 individuals enrolled in the Clinical and Functional Translation of CFTR (CFTR2) project. Cross-sectional FEV1% predicted measurements were plotted by age at which measurement was obtained. Shifts in sweat chloride concentration and lung function reported in CFTR modulator trials were compared with function-phenotype correlations to assess potential efficacy of therapies. Measurements and Main Results: CFTR genotype function exhibited a logarithmic relationship with each clinical feature. Modest increases in CFTR function related to differing genotypes were associated with clinically relevant improvements in cross-sectional FEV1% predicted over a range of ages (6-82 yr). Therapeutic responses to modulators corresponded closely to predictions from the CFTR2-derived relationship between CFTR genotype function and phenotype. Conclusions: Increasing CFTR function in individuals with severe disease will have a proportionally greater effect on outcomes than similar increases in CFTR function in individuals with mild disease and should reverse a substantial fraction of the disease process. This study provides reference standards for clinical outcomes that may be achieved by increasing CFTR function.
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Affiliation(s)
- Allison F McCague
- 1 McKusick-Nathans Institute of Genetic Medicine, School of Medicine
| | - Karen S Raraigh
- 1 McKusick-Nathans Institute of Genetic Medicine, School of Medicine
| | | | | | - Taylor A Evans
- 1 McKusick-Nathans Institute of Genetic Medicine, School of Medicine
| | - Sangwoo T Han
- 1 McKusick-Nathans Institute of Genetic Medicine, School of Medicine
| | - Zhongzhou Lu
- 1 McKusick-Nathans Institute of Genetic Medicine, School of Medicine
| | - Anya T Joynt
- 1 McKusick-Nathans Institute of Genetic Medicine, School of Medicine
| | - Neeraj Sharma
- 1 McKusick-Nathans Institute of Genetic Medicine, School of Medicine
| | - Carlo Castellani
- 2 Cystic Fibrosis Center, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Joseph M Collaco
- 3 Eudowood Division of Pediatric Respiratory Sciences, School of Medicine
| | | | | | | | - Johanna M Rommens
- 7 Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Anne L Stephenson
- 8 Department of Respirology, Adult Cystic Fibrosis Program, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Patrick R Sosnay
- 9 Pulmonary and Critical Care Medicine, School of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Garry R Cutting
- 1 McKusick-Nathans Institute of Genetic Medicine, School of Medicine
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97
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Regulation of CFTR Biogenesis by the Proteostatic Network and Pharmacological Modulators. Int J Mol Sci 2020; 21:ijms21020452. [PMID: 31936842 PMCID: PMC7013518 DOI: 10.3390/ijms21020452] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 01/06/2020] [Accepted: 01/08/2020] [Indexed: 12/14/2022] Open
Abstract
Cystic fibrosis (CF) is the most common lethal inherited disease among Caucasians in North America and a significant portion of Europe. The disease arises from one of many mutations in the gene encoding the cystic fibrosis transmembrane conductance regulator, or CFTR. The most common disease-associated allele, F508del, along with several other mutations affect the folding, transport, and stability of CFTR as it transits from the endoplasmic reticulum (ER) to the plasma membrane, where it functions primarily as a chloride channel. Early data demonstrated that F508del CFTR is selected for ER associated degradation (ERAD), a pathway in which misfolded proteins are recognized by ER-associated molecular chaperones, ubiquitinated, and delivered to the proteasome for degradation. Later studies showed that F508del CFTR that is rescued from ERAD and folds can alternatively be selected for enhanced endocytosis and lysosomal degradation. A number of other disease-causing mutations in CFTR also undergo these events. Fortunately, pharmacological modulators of CFTR biogenesis can repair CFTR, permitting its folding, escape from ERAD, and function at the cell surface. In this article, we review the many cellular checkpoints that monitor CFTR biogenesis, discuss the emergence of effective treatments for CF, and highlight future areas of research on the proteostatic control of CFTR.
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98
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Targeting the Underlying Defect in CFTR with Small Molecule Compounds. Respir Med 2020. [DOI: 10.1007/978-3-030-42382-7_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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99
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Volkova N, Moy K, Evans J, Campbell D, Tian S, Simard C, Higgins M, Konstan MW, Sawicki GS, Elbert A, Charman SC, Marshall BC, Bilton D. Disease progression in patients with cystic fibrosis treated with ivacaftor: Data from national US and UK registries. J Cyst Fibros 2020; 19:68-79. [DOI: 10.1016/j.jcf.2019.05.015] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 04/22/2019] [Accepted: 05/20/2019] [Indexed: 11/25/2022]
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100
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Bell SC, Mall MA, Gutierrez H, Macek M, Madge S, Davies JC, Burgel PR, Tullis E, Castaños C, Castellani C, Byrnes CA, Cathcart F, Chotirmall SH, Cosgriff R, Eichler I, Fajac I, Goss CH, Drevinek P, Farrell PM, Gravelle AM, Havermans T, Mayer-Hamblett N, Kashirskaya N, Kerem E, Mathew JL, McKone EF, Naehrlich L, Nasr SZ, Oates GR, O'Neill C, Pypops U, Raraigh KS, Rowe SM, Southern KW, Sivam S, Stephenson AL, Zampoli M, Ratjen F. The future of cystic fibrosis care: a global perspective. THE LANCET RESPIRATORY MEDICINE 2020; 8:65-124. [DOI: 10.1016/s2213-2600(19)30337-6] [Citation(s) in RCA: 351] [Impact Index Per Article: 87.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 07/19/2019] [Accepted: 08/14/2019] [Indexed: 02/06/2023]
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