1
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Lyu Z, Villanueva P, O’Malley L, Murphy P, Augenstreich J, Briken V, Singh A, Ling J. Genome-wide screening reveals metabolic regulation of stop-codon readthrough by cyclic AMP. Nucleic Acids Res 2023; 51:9905-9919. [PMID: 37670559 PMCID: PMC10570021 DOI: 10.1093/nar/gkad725] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/12/2023] [Accepted: 08/21/2023] [Indexed: 09/07/2023] Open
Abstract
Translational fidelity is critical for microbial fitness, survival and stress responses. Much remains unknown about the genetic and environmental control of translational fidelity and its single-cell heterogeneity. In this study, we used a high-throughput fluorescence-based assay to screen a knock-out library of Escherichia coli and identified over 20 genes critical for stop-codon readthrough. Most of these identified genes were not previously known to affect translational fidelity. Intriguingly, we show that several genes controlling metabolism, including cyaA and crp, enhance stop-codon readthrough. CyaA catalyzes the synthesis of cyclic adenosine monophosphate (cAMP). Combining RNA sequencing, metabolomics and biochemical analyses, we show that deleting cyaA impairs amino acid catabolism and production of ATP, thus repressing the transcription of rRNAs and tRNAs to decrease readthrough. Single-cell analyses further show that cAMP is a major driver of heterogeneity in stop-codon readthrough and rRNA expression. Our results highlight that carbon metabolism is tightly coupled with stop-codon readthrough.
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Affiliation(s)
- Zhihui Lyu
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD, USA
| | - Patricia Villanueva
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD, USA
| | - Liam O’Malley
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD, USA
| | - Parker Murphy
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD, USA
| | - Jacques Augenstreich
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD, USA
| | - Volker Briken
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD, USA
| | - Abhyudai Singh
- Department of Electrical and Computer Engineering and Biomedical Engineering, University of Delaware, Newark, DE, USA
| | - Jiqiang Ling
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, MD, USA
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2
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Rab A, Yang X, Tracy WF, Hong JS, Joshi D, Manfredi C, Ponnaluri SS, Kolykhalov AA, Qui M, Fu H, Du Y, Davies HML, Sorscher EJ. A Novel 7 H-[1,2,4]Triazolo[3,4- b]thiadiazine-based Cystic Fibrosis Transmembrane Conductance Regulator Potentiator Directed toward Treatment of Cystic Fibrosis. ACS Med Chem Lett 2023; 14:1338-1343. [PMID: 37849531 PMCID: PMC10577695 DOI: 10.1021/acsmedchemlett.3c00155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 08/25/2023] [Indexed: 10/19/2023] Open
Abstract
Cystic fibrosis (CF) is an autosomal genetic disorder caused by disrupted anion transport in epithelial cells lining tissues in the human airways and digestive system. While cystic fibrosis transmembrane conductance regulator (CFTR) modulator compounds have provided transformative improvement in CF respiratory function, certain patients exhibit marginal clinical benefit or detrimental effects or have a form of the disease not approved or unlikely to respond using CFTR modulation. We tested hit compounds from a 300,000-drug screen for their ability to augment CFTR transepithelial transport alone or in combination with the FDA-approved CFTR potentiator ivacaftor (VX-770). A subsequent SAR campaign led us to a class of 7H-[1,2,4]triazolo[3,4-b][1,3,4]thiadiazines that in combination with VX-770 rescued function of G551D mutant CFTR channels to approximately 400% above the activity of VX-770 alone and to nearly wild-type CFTR levels in the same Fischer rat thyroid model system.
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Affiliation(s)
- Andras Rab
- Department
of Pediatrics, Emory University School of
Medicine, Atlanta, Georgia 30322, United States
| | - Xun Yang
- Department
of Chemistry, Emory University, 1515 Dickey Dr., Atlanta, Georgia 30329, United States
| | - William F. Tracy
- Department
of Chemistry, Emory University, 1515 Dickey Dr., Atlanta, Georgia 30329, United States
| | - Jeong S. Hong
- Department
of Pediatrics, Emory University School of
Medicine, Atlanta, Georgia 30322, United States
| | - Disha Joshi
- Department
of Pediatrics, Emory University School of
Medicine, Atlanta, Georgia 30322, United States
| | - Candela Manfredi
- Department
of Pediatrics, Emory University School of
Medicine, Atlanta, Georgia 30322, United States
| | - Sadhana S. Ponnaluri
- Department
of Pediatrics, Emory University School of
Medicine, Atlanta, Georgia 30322, United States
| | | | - Min Qui
- Department
of Pharmacology and Chemical Biology, Emory
University School of Medicine, Atlanta, Georgia 30322, United States
- Emory
Chemical Biology Discovery Center, Emory
University School of Medicine, Atlanta, Georgia 30322, United States
| | - Haian Fu
- Department
of Pharmacology and Chemical Biology, Emory
University School of Medicine, Atlanta, Georgia 30322, United States
- Emory
Chemical Biology Discovery Center, Emory
University School of Medicine, Atlanta, Georgia 30322, United States
| | - Yuhong Du
- Department
of Pharmacology and Chemical Biology, Emory
University School of Medicine, Atlanta, Georgia 30322, United States
- Emory
Chemical Biology Discovery Center, Emory
University School of Medicine, Atlanta, Georgia 30322, United States
| | - Huw M. L. Davies
- Department
of Chemistry, Emory University, 1515 Dickey Dr., Atlanta, Georgia 30329, United States
| | - Eric J. Sorscher
- Department
of Pediatrics, Emory University School of
Medicine, Atlanta, Georgia 30322, United States
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3
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Chen J, Thrasher K, Fu L, Wang W, Aghamohammadzadeh S, Wen H, Tang L, Keeling KM, Falk Libby E, Bedwell DM, Rowe SM. The synthetic aminoglycoside ELX-02 induces readthrough of G550X-CFTR producing superfunctional protein that can be further enhanced by CFTR modulators. Am J Physiol Lung Cell Mol Physiol 2023; 324:L756-L770. [PMID: 37014818 PMCID: PMC10202470 DOI: 10.1152/ajplung.00038.2023] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/29/2023] [Accepted: 04/02/2023] [Indexed: 04/05/2023] Open
Abstract
Ten percent of cystic fibrosis (CF) patients carry a premature termination codon (PTC); no mutation-specific therapies exist for these individuals. ELX-02, a synthetic aminoglycoside, suppresses translation termination at PTCs (i.e., readthrough) by promoting the insertion of an amino acid at the PTC and restoring expression of full-length CFTR protein. The identity of amino acids inserted at PTCs affects the processing and function of the resulting full-length CFTR protein. We examined readthrough of the rare G550X-CFTR nonsense mutation due to its unique properties. We found that forskolin-induced swelling in G550X patient-derived intestinal organoids (PDOs) was significantly higher than in G542X PDOs (both UGA PTCs) with ELX-02 treatment, indicating greater CFTR function from the G550X allele. Using mass spectrometry, we identified tryptophan as the sole amino acid inserted in the G550X position during ELX-02- or G418-mediated readthrough, which differs from the three amino acids (cysteine, arginine, and tryptophan) inserted in the G542X position after treatment with G418. Compared with wild-type CFTR, Fischer rat thyroid (FRT) cells expressing the G550W-CFTR variant protein exhibited significantly increased forskolin-activated Cl- conductance, and G550W-CFTR channels showed increased PKA sensitivity and open probability. After treatment with ELX-02 and CFTR correctors, CFTR function rescued from the G550X allele in FRTs reached 20-40% of the wild-type level. These results suggest that readthrough of G550X produces greater CFTR function because of gain-of-function properties of the CFTR readthrough product that stem from its location in the signature LSGGQ motif found in ATP-binding cassette (ABC) transporters. G550X may be a particularly sensitive target for translational readthrough therapy.NEW & NOTEWORTHY We found that forskolin-induced swelling in G550X-CFTR patient-derived intestinal organoids (PDOs) was significantly higher than in G542X-CFTR PDOs after treatment with ELX-02. Tryptophan (W) was the sole amino acid inserted in the G550X position after readthrough. Resulting G550W-CFTR protein exhibited supernormal CFTR activity, PKA sensitivity, and open probability. These results show that aminoglycoside-induced readthrough of G550X produces greater CFTR function because of the gain-of-function properties of the CFTR readthrough product.
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Affiliation(s)
- Jianguo Chen
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Kari Thrasher
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, United States
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Lianwu Fu
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, United States
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Wei Wang
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | | | - Hui Wen
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Liping Tang
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Kim M Keeling
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, United States
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Emily Falk Libby
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - David M Bedwell
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, United States
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Steven M Rowe
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States
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4
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Spelier S, van Doorn EPM, van der Ent CK, Beekman JM, Koppens MAJ. Readthrough compounds for nonsense mutations: bridging the translational gap. Trends Mol Med 2023; 29:297-314. [PMID: 36828712 DOI: 10.1016/j.molmed.2023.01.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/28/2022] [Accepted: 01/19/2023] [Indexed: 02/24/2023]
Abstract
Approximately 10% of all pathological mutations are nonsense mutations that are responsible for several severe genetic diseases for which no treatment regimens are currently available. The most widespread strategy for treating nonsense mutations is by enhancing ribosomal readthrough of premature termination codons (PTCs) to restore the production of the full-length protein. In the past decade several compounds with readthrough potential have been identified. However, although preclinical results on these compounds are promising, clinical studies have not yielded positive outcomes. We review preclinical and clinical research related to readthrough compounds and characterize factors that contribute to the observed translational gap.
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Affiliation(s)
- Sacha Spelier
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584, EA, Utrecht, The Netherlands; Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584, CT, Utrecht, The Netherlands
| | - Eveline P M van Doorn
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584, EA, Utrecht, The Netherlands
| | - Cornelis K van der Ent
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584, EA, Utrecht, The Netherlands; Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584, CT, Utrecht, The Netherlands
| | - Jeffrey M Beekman
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584, EA, Utrecht, The Netherlands; Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584, CT, Utrecht, The Netherlands; Center for Living Technologies, Eindhoven-Wageningen-Utrecht Alliance, Utrecht, The Netherlands
| | - Martijn A J Koppens
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584, EA, Utrecht, The Netherlands; Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584, CT, Utrecht, The Netherlands; Department of Metabolic Diseases, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584, EA, Utrecht, The Netherlands.
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5
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Allen L, Allen L, Carr SB, Davies G, Downey D, Egan M, Forton JT, Gray R, Haworth C, Horsley A, Smyth AR, Southern KW, Davies JC. Future therapies for cystic fibrosis. Nat Commun 2023; 14:693. [PMID: 36755044 PMCID: PMC9907205 DOI: 10.1038/s41467-023-36244-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 01/20/2023] [Indexed: 02/10/2023] Open
Abstract
We are currently witnessing transformative change for people with cystic fibrosis with the introduction of small molecule, mutation-specific drugs capable of restoring function of the defective protein, cystic fibrosis transmembrane conductance regulator (CFTR). However, despite being a single gene disorder, there are multiple cystic fibrosis-causing genetic variants; mutation-specific drugs are not suitable for all genetic variants and also do not correct all the multisystem clinical manifestations of the disease. For many, there will remain a need for improved treatments. Those patients with gene variants responsive to CFTR modulators may have found these therapies to be transformational; research is now focusing on safely reducing the burden of symptom-directed treatment. However, modulators are not available in all parts of the globe, an issue which is further widening existing health inequalities. For patients who are not suitable for- or do not have access to- modulator drugs, alternative approaches are progressing through the trials pipeline. There will be challenges encountered in design and implementation of these trials, for which the established global CF infrastructure is a major advantage. Here, the Cystic Fibrosis National Research Strategy Group of the UK NIHR Respiratory Translational Research Collaboration looks to the future of cystic fibrosis therapies and consider priorities for future research and development.
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Affiliation(s)
| | | | - Siobhan B Carr
- Royal Brompton & Harefield Hospital, Guy's & St Thomas' Trust, London, UK
- National Heart & Lung Institute, Imperial College London, London, UK
| | - Gwyneth Davies
- UCL Great Ormond Street Institute of Child Health, University College London, London, UK
- Great Ormond Street Hospital for Children, London, UK
| | - Damian Downey
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
| | | | - Julian T Forton
- Noah's Ark Children's Hospital for Wales, Cardiff, UK
- School of Medicine, Cardiff University, Cardiff, UK
| | - Robert Gray
- Centre for Inflammation Research, University of Edinburgh, Edinburgh, UK
- Western General Hospital, Edinburgh, UK
| | - Charles Haworth
- Royal Papworth Hospital and Department of Medicine, Cambridge, UK
- University of Cambridge, Cambridge, UK
| | - Alexander Horsley
- Division of Infection, Immunity and Respiratory Medicine, University of Manchester, Manchester, UK
- Manchester Adult CF Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - Alan R Smyth
- School of Medicine, University of Nottingham, Nottingham, UK
- NIHR Nottingham Biomedical Research Centre, Nottingham, UK
| | - Kevin W Southern
- Department of Women's and Children's Health, University of Liverpool, Liverpool, UK
- Institute in the Park, Alder Hey Children's Hospital, Liverpool, UK
| | - Jane C Davies
- Royal Brompton & Harefield Hospital, Guy's & St Thomas' Trust, London, UK.
- National Heart & Lung Institute, Imperial College London, London, UK.
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6
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Britto CJ, Taylor-Cousar JL. Cystic Fibrosis in the Era of Highly Effective CFTR Modulators. Clin Chest Med 2022; 43:xiii-xvi. [PMID: 36344084 DOI: 10.1016/j.ccm.2022.07.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Clemente J Britto
- Department of Internal Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, Yale University School of Medicine, 300 Cedar Street, TAC-S419, New Haven, CT 06520, USA.
| | - Jennifer L Taylor-Cousar
- Departments of Medicine and Pediatrics, Divisions of Pulmonary Sciences and Critical Care Medicine and Pediatric Pulmonology, University of Colorado, Anschutz Medical Campus, 1400 Jackson Street, J318, Denver, CO 80206, USA.
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7
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Abstract
Muscular dystrophies are a group of genetic disorders characterized by varying degrees of progressive muscle weakness and degeneration. They are clinically and genetically heterogeneous but share the common histological features of dystrophic muscle. There is currently no cure for muscular dystrophies, which is of particular concern for the more disabling and/or lethal forms of the disease. Through the years, several therapies have encouragingly been developed for muscular dystrophies and include genetic, cellular, and pharmacological approaches. In this chapter, we undertake a comprehensive exploration of muscular dystrophy therapeutics under current development. Our review includes antisense therapy, CRISPR, gene replacement, cell therapy, nonsense suppression, and disease-modifying small molecule compounds.
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8
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Complementary Dual Approach for In Silico Target Identification of Potential Pharmaceutical Compounds in Cystic Fibrosis. Int J Mol Sci 2022; 23:ijms232012351. [PMID: 36293229 PMCID: PMC9604016 DOI: 10.3390/ijms232012351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/10/2022] [Accepted: 10/12/2022] [Indexed: 11/06/2022] Open
Abstract
Cystic fibrosis is a genetic disease caused by mutation of the CFTR gene, which encodes a chloride and bicarbonate transporter in epithelial cells. Due to the vast range of geno- and phenotypes, it is difficult to find causative treatments; however, small-molecule therapeutics have been clinically approved in the last decade. Still, the search for novel therapeutics is ongoing, and thousands of compounds are being tested in different assays, often leaving their mechanism of action unknown. Here, we bring together a CFTR-specific compound database (CandActCFTR) and systems biology model (CFTR Lifecycle Map) to identify the targets of the most promising compounds. We use a dual inverse screening approach, where we employ target- and ligand-based methods to suggest targets of 309 active compounds in the database amongst 90 protein targets from the systems biology model. Overall, we identified 1038 potential target–compound pairings and were able to suggest targets for all 309 active compounds in the database.
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9
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Berical A, Lee RE, Lu J, Beermann ML, Le Suer JA, Mithal A, Thomas D, Ranallo N, Peasley M, Stuffer A, Bukis K, Seymour R, Harrington J, Coote K, Valley H, Hurley K, McNally P, Mostoslavsky G, Mahoney J, Randell SH, Hawkins FJ. A multimodal iPSC platform for cystic fibrosis drug testing. Nat Commun 2022; 13:4270. [PMID: 35906215 PMCID: PMC9338271 DOI: 10.1038/s41467-022-31854-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 07/06/2022] [Indexed: 01/27/2023] Open
Abstract
Cystic fibrosis is a monogenic lung disease caused by dysfunction of the cystic fibrosis transmembrane conductance regulator anion channel, resulting in significant morbidity and mortality. The progress in elucidating the role of CFTR using established animal and cell-based models led to the recent discovery of effective modulators for most individuals with CF. However, a subset of individuals with CF do not respond to these modulators and there is an urgent need to develop novel therapeutic strategies. In this study, we generate a panel of airway epithelial cells using induced pluripotent stem cells from individuals with common or rare CFTR variants representative of three distinct classes of CFTR dysfunction. To measure CFTR function we adapt two established in vitro assays for use in induced pluripotent stem cell-derived airway cells. In both a 3-D spheroid assay using forskolin-induced swelling as well as planar cultures composed of polarized mucociliary airway epithelial cells, we detect genotype-specific differences in CFTR baseline function and response to CFTR modulators. These results demonstrate the potential of the human induced pluripotent stem cell platform as a research tool to study CF and in particular accelerate therapeutic development for CF caused by rare variants.
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Affiliation(s)
- Andrew Berical
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, 02118, USA
- The Pulmonary Center and Department of Medicine, Boston University and Boston Medical Center, Boston, MA, 02118, USA
| | - Rhianna E Lee
- Marsico Lung Institute and Cystic Fibrosis Research Center, Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Junjie Lu
- Cystic Fibrosis Foundation, Lexington, MA, 02421, USA
| | - Mary Lou Beermann
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, 02118, USA
| | - Jake A Le Suer
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, 02118, USA
| | - Aditya Mithal
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, 02118, USA
| | - Dylan Thomas
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, 02118, USA
| | - Nicole Ranallo
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, 02118, USA
| | - Megan Peasley
- Cystic Fibrosis Foundation, Lexington, MA, 02421, USA
| | - Alex Stuffer
- Cystic Fibrosis Foundation, Lexington, MA, 02421, USA
| | | | | | | | - Kevin Coote
- Cystic Fibrosis Foundation, Lexington, MA, 02421, USA
| | | | - Killian Hurley
- Department of Medicine, Royal College of Surgeons in Ireland, Education and Research Centre, Beaumont Hospital, Dublin, Ireland
- Tissue Engineering Research Group, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Paul McNally
- RCSI University of Medicine and Health Sciences, Dublin, Ireland
- Children's Health Ireland, Dublin, Ireland
| | - Gustavo Mostoslavsky
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, 02118, USA
| | - John Mahoney
- Cystic Fibrosis Foundation, Lexington, MA, 02421, USA
| | - Scott H Randell
- Marsico Lung Institute and Cystic Fibrosis Research Center, Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Finn J Hawkins
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, 02118, USA.
- The Pulmonary Center and Department of Medicine, Boston University and Boston Medical Center, Boston, MA, 02118, USA.
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10
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Lee RE, Lewis CA, He L, Bulik-Sullivan EC, Gallant SC, Mascenik TM, Dang H, Cholon DM, Gentzsch M, Morton LC, Minges JT, Theile JW, Castle NA, Knowles MR, Kimple AJ, Randell SH. Small molecule eRF3a degraders rescue CFTR nonsense mutations by promoting premature termination codon readthrough. J Clin Invest 2022; 132:154571. [PMID: 35900863 PMCID: PMC9479597 DOI: 10.1172/jci154571] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 07/26/2022] [Indexed: 11/22/2022] Open
Abstract
The vast majority of people with cystic fibrosis (CF) are now eligible for CF transmembrane regulator (CFTR) modulator therapy. The remaining individuals with CF harbor premature termination codons (PTCs) or rare CFTR variants with limited treatment options. Although the clinical modulator response can be reliably predicted using primary airway epithelial cells, primary cells carrying rare CFTR variants are scarce. To overcome this obstacle, cell lines can be created by overexpression of mouse Bmi-1 and human TERT (hTERT). Using this approach, we developed 2 non-CF and 6 CF airway epithelial cell lines, 3 of which were homozygous for the W1282X PTC variant. The Bmi-1/hTERT cell lines recapitulated primary cell morphology and ion transport function. The 2 F508del-CFTR cell lines responded robustly to CFTR modulators, which was mirrored in the parent primary cells and in the cell donors’ clinical response. Cereblon E3 ligase modulators targeting eukaryotic release factor 3a (eRF3a) rescued W1282X-CFTR function to approximately 20% of WT levels and, when paired with G418, rescued G542X-CFTR function to approximately 50% of WT levels. Intriguingly, eRF3a degraders also diminished epithelial sodium channel (ENaC) function. These studies demonstrate that Bmi-1/hTERT cell lines faithfully mirrored primary cell responses to CFTR modulators and illustrate a therapeutic approach to rescue CFTR nonsense mutations.
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Affiliation(s)
- Rhianna E Lee
- Marsico Lung Institute/Cystic Fibrosis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - Catherine A Lewis
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - Lihua He
- Marsico Lung Institute/Cystic Fibrosis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - Emily C Bulik-Sullivan
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - Samuel C Gallant
- Marsico Lung Institute/Cystic Fibrosis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - Teresa M Mascenik
- Marsico Lung Institute/Cystic Fibrosis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - Hong Dang
- Marsico Lung Institute/Cystic Fibrosis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - Deborah M Cholon
- Marsico Lung Institute/Cystic Fibrosis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - Martina Gentzsch
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - Lisa C Morton
- Marsico Lung Institute/Cystic Fibrosis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - John T Minges
- Marsico Lung Institute/Cystic Fibrosis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | | | - Neil A Castle
- Research and Development, Icagen, Durham, United States of America
| | - Michael R Knowles
- Marsico Lung Institute/Cystic Fibrosis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - Adam J Kimple
- Department of Otolaryngology, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - Scott H Randell
- Marsico Lung Institute/Cystic Fibrosis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
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11
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Mutyam V, Sharma J, Li Y, Peng N, Chen J, Tang LP, Falk Libby E, Singh AK, Conrath K, Rowe SM. Novel Correctors and Potentiators Enhance Translational Readthrough in CFTR Nonsense Mutations. Am J Respir Cell Mol Biol 2021; 64:604-616. [PMID: 33616476 DOI: 10.1165/rcmb.2019-0291oc] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Premature-termination codons (PTCs) in CFTR (cystic fibrosis [CF] transmembrane conductance regulator) result in nonfunctional CFTR protein and are the proximate cause of ∼11% of CF-causing alleles, for which no treatments exist. The CFTR corrector lumacaftor and the potentiator ivacaftor improve CFTR function with terminal PTC mutations and enhance the effect of readthrough agents. Novel correctors GLPG2222 (corrector 1 [C1]), GLPG3221 (corrector 2 [C2]), and potentiator GLPG1837 compare favorably with lumacaftor and ivacaftor in vitro. Here, we evaluated the effect of correctors C1a and C2a (derivatives of C1 and C2) and GLPG1837 alone or in combination with the readthrough compound G418 on CFTR function using heterologous Fischer rat thyroid (FRT) cells, the genetically engineered human bronchial epithelial (HBE) 16HBE14o- cell lines, and primary human cells with PTC mutations. In FRT lines pretreated with G418, GLPG1837 elicited dose-dependent increases in CFTR activity that exceeded those from ivacaftor in FRT-W1282X and FRT-R1162X cells. A three-mechanism strategy consisting of G418, GLPG1837, and two correctors (C1a + C2a) yielded the greatest functional improvements in FRT and 16HBE14o- PTC variants, noting that correction and potentiation without readthrough was sufficient to stimulate CFTR activity for W1282X cells. GLPG1837 + C1a + C2a restored substantial function in G542X/F508del HBE cells and restored even more function for W1282X/F508del cells, largely because of the corrector/potentiator effect, with no additional benefit from G418. In G542X/R553X or R1162X/R1162X organoids, enhanced forskolin-induced swelling was observed with G418 + GLPG1837 + C1a + C2a, although GLPG1837 + C1a + C2a alone was sufficient to improve forskolin-induced swelling in W1282X/W1282X organoids. Combination of CFTR correctors, potentiators, and readthrough compounds augments the functional repair of CFTR nonsense mutations, indicating the potential for novel correctors and potentiators to restore function to truncated W1282X CFTR.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Steven M Rowe
- Department of Medicine.,Department of Pediatrics.,Department of Cell Developmental and Integrative Biology, and.,Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama
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12
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Pinto MC, Silva IAL, Figueira MF, Amaral MD, Lopes-Pacheco M. Pharmacological Modulation of Ion Channels for the Treatment of Cystic Fibrosis. J Exp Pharmacol 2021; 13:693-723. [PMID: 34326672 PMCID: PMC8316759 DOI: 10.2147/jep.s255377] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 06/30/2021] [Indexed: 12/12/2022] Open
Abstract
Cystic fibrosis (CF) is a life-shortening monogenic disease caused by mutations in the gene encoding the CF transmembrane conductance regulator (CFTR) protein, an anion channel that transports chloride and bicarbonate across epithelia. Despite clinical progress in delaying disease progression with symptomatic therapies, these individuals still develop various chronic complications in lungs and other organs, which significantly restricts their life expectancy and quality of life. The development of high-throughput assays to screen drug-like compound libraries have enabled the discovery of highly effective CFTR modulator therapies. These novel therapies target the primary defect underlying CF and are now approved for clinical use for individuals with specific CF genotypes. However, the clinically approved modulators only partially reverse CFTR dysfunction and there is still a considerable number of individuals with CF carrying rare CFTR mutations who remain without any effective CFTR modulator therapy. Accordingly, additional efforts have been pursued to identify novel and more potent CFTR modulators that may benefit a larger CF population. The use of ex vivo individual-derived specimens has also become a powerful tool to evaluate novel drugs and predict their effectiveness in a personalized medicine approach. In addition to CFTR modulators, pro-drugs aiming at modulating alternative ion channels/transporters are under development to compensate for the lack of CFTR function. These therapies may restore normal mucociliary clearance through a mutation-agnostic approach (ie, independent of CFTR mutation) and include inhibitors of the epithelial sodium channel (ENaC), modulators of the calcium-activated channel transmembrane 16A (TMEM16, or anoctamin 1) or of the solute carrier family 26A member 9 (SLC26A9), and anionophores. The present review focuses on recent progress and challenges for the development of ion channel/transporter-modulating drugs for the treatment of CF.
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Affiliation(s)
- Madalena C Pinto
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, Lisboa, Portugal
| | - Iris A L Silva
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, Lisboa, Portugal
| | - Miriam F Figueira
- Marsico Lung Institute/Cystic Fibrosis Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Margarida D Amaral
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, Lisboa, Portugal
| | - Miquéias Lopes-Pacheco
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, Lisboa, Portugal
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13
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CFTR Lifecycle Map-A Systems Medicine Model of CFTR Maturation to Predict Possible Active Compound Combinations. Int J Mol Sci 2021; 22:ijms22147590. [PMID: 34299207 PMCID: PMC8306775 DOI: 10.3390/ijms22147590] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/07/2021] [Accepted: 07/13/2021] [Indexed: 02/07/2023] Open
Abstract
Different causative therapeutics for CF patients have been developed. There are still no mutation-specific therapeutics for some patients, especially those with rare CFTR mutations. For this purpose, high-throughput screens have been performed which result in various candidate compounds, with mostly unclear modes of action. In order to elucidate the mechanism of action for promising candidate substances and to be able to predict possible synergistic effects of substance combinations, we used a systems biology approach to create a model of the CFTR maturation pathway in cells in a standardized, human- and machine-readable format. It is composed of a core map, manually curated from small-scale experiments in human cells, and a coarse map including interactors identified in large-scale efforts. The manually curated core map includes 170 different molecular entities and 156 reactions from 221 publications. The coarse map encompasses 1384 unique proteins from four publications. The overlap between the two data sources amounts to 46 proteins. The CFTR Lifecycle Map can be used to support the identification of potential targets inside the cell and elucidate the mode of action for candidate substances. It thereby provides a backbone to structure available data as well as a tool to develop hypotheses regarding novel therapeutics.
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14
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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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15
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Airway Redox Homeostasis and Inflammation Gone Awry: From Molecular Pathogenesis to Emerging Therapeutics in Respiratory Pathology. Int J Mol Sci 2020; 21:ijms21239317. [PMID: 33297418 PMCID: PMC7731288 DOI: 10.3390/ijms21239317] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 12/05/2020] [Indexed: 02/06/2023] Open
Abstract
As aerobic organisms, we are continuously and throughout our lifetime subjected to an oxidizing atmosphere and, most often, to environmental threats. The lung is the internal organ most highly exposed to this milieu. Therefore, it has evolved to confront both oxidative stress induced by reactive oxygen species (ROS) and a variety of pollutants, pathogens, and allergens that promote inflammation and can harm the airways to different degrees. Indeed, an excess of ROS, generated intrinsically or from external sources, can imprint direct damage to key structural cell components (nucleic acids, sugars, lipids, and proteins) and indirectly perturb ROS-mediated signaling in lung epithelia, impairing its homeostasis. These early events complemented with efficient recognition of pathogen- or damage-associated recognition patterns by the airway resident cells alert the immune system, which mounts an inflammatory response to remove the hazards, including collateral dead cells and cellular debris, in an attempt to return to homeostatic conditions. Thus, any major or chronic dysregulation of the redox balance, the air-liquid interface, or defects in epithelial proteins impairing mucociliary clearance or other defense systems may lead to airway damage. Here, we review our understanding of the key role of oxidative stress and inflammation in respiratory pathology, and extensively report current and future trends in antioxidant and anti-inflammatory treatments focusing on the following major acute and chronic lung diseases: acute lung injury/respiratory distress syndrome, asthma, chronic obstructive pulmonary disease, pulmonary fibrosis, and cystic fibrosis.
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16
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Bajko J, Duguid M, Altmann S, Hurlbut GD, Kaczmarek JS. Pendrin stimulates a chloride absorption pathway to increase CFTR-mediated chloride secretion from Cystic Fibrosis airway epithelia. FASEB Bioadv 2020; 2:526-537. [PMID: 32923987 PMCID: PMC7475303 DOI: 10.1096/fba.2020-00012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 03/24/2020] [Accepted: 06/26/2020] [Indexed: 01/04/2023] Open
Abstract
Cystic Fibrosis (CF), an inherited multi-system disease, is caused by mutations in the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) that disrupt its ability to secrete anions from epithelia. Recovery of functional anion secretion may be curative for CF, so different components of the ion transport machinery have become attractive therapeutic targets. Several members of the SLC26 ion transporter family have been linked to epithelial ion flux, some through putative functional interactions with CFTR. Using a small-scale qPCR screen, we confirmed that the anion transporter SLC26A4 (pendrin) is downregulated in CF. Upregulation of pendrin using interleukins IL-4 or IL-13 increased Cl- secretion through CFTR in human bronchial epithelial cell (HBEC) derived epithelia differentiated in vitro and measured in the Ussing Chamber. Inhibition or knockdown of pendrin prevented this increased secretion. Increased CFTR activity was not driven by increases in CFTR protein or upstream regulatory pathway components. When basolateral Cl- absorption through NKCC1 was inhibited, a pendrin-dependent Cl- absorption pathway allowing CFTR to continue secreting Cl- from the epithelium was revealed. Although CFTR is often considered the bottleneck in the transepithelial Cl- transport pathway, these studies indicate that basolateral Cl- permeability becomes limiting as CFTR activity increases. Therefore, an increase of epithelial Cl- absorption via pendrin might have additional therapeutic benefit in combination with CFTR modulators.
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17
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Keenan MM, Huang L, Jordan NJ, Wong E, Cheng Y, Valley HC, Mahiou J, Liang F, Bihler H, Mense M, Guo S, Monia BP. Nonsense-mediated RNA Decay Pathway Inhibition Restores Expression and Function of W1282X CFTR. Am J Respir Cell Mol Biol 2020; 61:290-300. [PMID: 30836009 DOI: 10.1165/rcmb.2018-0316oc] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The recessive genetic disease cystic fibrosis (CF) is caused by loss-of-function mutations in the CFTR (CF transmembrane conductance regulator) gene. Approximately 10% of patients with CF have at least one allele with a nonsense mutation in CFTR. Nonsense mutations generate premature termination codons that can subject mRNA transcripts to rapid degradation through the nonsense-mediated mRNA decay (NMD) pathway. Currently, there are no approved therapies that specifically target nonsense mutations in CFTR. Here, we identified antisense oligonucleotides (ASOs) that target the NMD factor SMG1 to inhibit the NMD pathway, and determined their effects on the W1282X CFTR mutation. First, we developed and validated two in vitro models of the W1282X CFTR mutation. Next, we treated these cells with antisense oligonucleotides to inhibit NMD and measured the effects of these treatments on W1282X expression and function. SMG1-ASO-mediated NMD inhibition upregulated the RNA, protein, and surface-localized protein expression of the truncated W1282X gene product. Additionally, these ASOs increased the CFTR chloride channel function in cells homozygous for the W1282X mutation. Our approach suggests a new therapeutic strategy for patients harboring nonsense mutations and may be beneficial as a single agent in patients with CF and the W1282X mutation.
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Affiliation(s)
| | - Lulu Huang
- Ionis Pharmaceuticals, Carlsbad, California; and
| | - Nikole J Jordan
- Cystic Fibrosis Foundation Therapeutics Lab, Cystic Fibrosis Foundation, Lexington, Massachusetts
| | - Eric Wong
- Cystic Fibrosis Foundation Therapeutics Lab, Cystic Fibrosis Foundation, Lexington, Massachusetts
| | - Yi Cheng
- Cystic Fibrosis Foundation Therapeutics Lab, Cystic Fibrosis Foundation, Lexington, Massachusetts
| | - Hillary C Valley
- Cystic Fibrosis Foundation Therapeutics Lab, Cystic Fibrosis Foundation, Lexington, Massachusetts
| | - Jerome Mahiou
- Cystic Fibrosis Foundation Therapeutics Lab, Cystic Fibrosis Foundation, Lexington, Massachusetts
| | - Feng Liang
- Cystic Fibrosis Foundation Therapeutics Lab, Cystic Fibrosis Foundation, Lexington, Massachusetts
| | - Hermann Bihler
- Cystic Fibrosis Foundation Therapeutics Lab, Cystic Fibrosis Foundation, Lexington, Massachusetts
| | - Martin Mense
- Cystic Fibrosis Foundation Therapeutics Lab, Cystic Fibrosis Foundation, Lexington, Massachusetts
| | - Shuling Guo
- Ionis Pharmaceuticals, Carlsbad, California; and
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18
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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: 257] [Impact Index Per Article: 64.3] [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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19
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Valley HC, Bukis KM, Bell A, Cheng Y, Wong E, Jordan NJ, Allaire NE, Sivachenko A, Liang F, Bihler H, Thomas PJ, Mahiou J, Mense M. Isogenic cell models of cystic fibrosis-causing variants in natively expressing pulmonary epithelial cells. J Cyst Fibros 2018; 18:476-483. [PMID: 30563749 DOI: 10.1016/j.jcf.2018.12.001] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 11/30/2018] [Accepted: 12/02/2018] [Indexed: 11/29/2022]
Abstract
BACKGROUND Assessment of approved drugs and developmental drug candidates for rare cystic fibrosis (CF)-causing variants of the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) requires abundant material from relevant models. METHODS Isogenic cell lines harboring CFTR variants in the native genomic context were created through the development and utilization of a footprint-less, CRISPR/Cas9 gene editing pipeline in 16HBE14o- immortalized bronchial epithelial cells. RESULTS Isogenic, homozygous cell lines for three CFTR variants (F508del and the two most common CF-causing nonsense variants, G542X and W1282X) were established and characterized. The F508del model recapitulates the known molecular pathology and pharmacology. The two models of nonsense variants (G542X and W1282X) are sensitive to Nonsense Mediated mRNA Decay (NMD) and responsive to reference compounds that inhibit NMD and promote ribosomal readthrough. CONCLUSIONS We present a versatile, efficient gene editing pipeline that can be used to create CFTR variants in the native genomic context and the utilization of this pipeline to create homozygous cell models for the CF-causing variants F508del, G542X, and W1282X. The resulting cell lines provide a virtually unlimited source of material with specific pathogenic mutations that can be used in a variety of assays, including functional assays.
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Affiliation(s)
- Hillary C Valley
- Cystic Fibrosis Foundation, CFFT Lab, 44 Hartwell Ave., Lexington, MA 02421, USA
| | - Katherine M Bukis
- Cystic Fibrosis Foundation, CFFT Lab, 44 Hartwell Ave., Lexington, MA 02421, USA
| | - Alisa Bell
- Cystic Fibrosis Foundation, CFFT Lab, 44 Hartwell Ave., Lexington, MA 02421, USA
| | - Yi Cheng
- Cystic Fibrosis Foundation, CFFT Lab, 44 Hartwell Ave., Lexington, MA 02421, USA
| | - Eric Wong
- Cystic Fibrosis Foundation, CFFT Lab, 44 Hartwell Ave., Lexington, MA 02421, USA
| | - Nikole J Jordan
- Cystic Fibrosis Foundation, CFFT Lab, 44 Hartwell Ave., Lexington, MA 02421, USA
| | - Normand E Allaire
- Cystic Fibrosis Foundation, CFFT Lab, 44 Hartwell Ave., Lexington, MA 02421, USA
| | - Andrey Sivachenko
- Cystic Fibrosis Foundation, CFFT Lab, 44 Hartwell Ave., Lexington, MA 02421, USA
| | - Feng Liang
- Cystic Fibrosis Foundation, CFFT Lab, 44 Hartwell Ave., Lexington, MA 02421, USA
| | - Hermann Bihler
- Cystic Fibrosis Foundation, CFFT Lab, 44 Hartwell Ave., Lexington, MA 02421, USA
| | - Philip J Thomas
- Cystic Fibrosis Foundation, CFFT Lab, 44 Hartwell Ave., Lexington, MA 02421, USA; University of Texas - Southwestern, UT Southwestern Medical Ctr., 6001 Forrest Park Rd ND12.126B, Dallas, TX 75390-9040, USA
| | - Jerome Mahiou
- Cystic Fibrosis Foundation, CFFT Lab, 44 Hartwell Ave., Lexington, MA 02421, USA
| | - Martin Mense
- Cystic Fibrosis Foundation, CFFT Lab, 44 Hartwell Ave., Lexington, MA 02421, USA.
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20
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Young R, Purton S. CITRIC: cold-inducible translational readthrough in the chloroplast of Chlamydomonas reinhardtii using a novel temperature-sensitive transfer RNA. Microb Cell Fact 2018; 17:186. [PMID: 30474564 PMCID: PMC6260665 DOI: 10.1186/s12934-018-1033-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 11/16/2018] [Indexed: 01/17/2023] Open
Abstract
Background The chloroplast of eukaryotic microalgae such as Chlamydomonas reinhardtii is a potential platform for metabolic engineering and the production of recombinant proteins. In industrial biotechnology, inducible expression is often used so that the translation or function of the heterologous protein does not interfere with biomass accumulation during the growth stage. However, the existing systems used in bacterial or fungal platforms do not transfer well to the microalgal chloroplast. We sought to develop a simple inducible expression system for the microalgal chloroplast, exploiting an unused stop codon (TGA) in the plastid genome. We have previously shown that this codon can be translated as tryptophan when we introduce into the chloroplast genome a trnWUCA gene encoding a plastidial transfer RNA with a modified anticodon sequence, UCA. Results A mutated version of our trnWUCA gene was developed that encodes a temperature-sensitive variant of the tRNA. This allows transgenes that have been modified to contain one or more internal TGA codons to be translated differentially according to the culture temperature, with a gradient of recombinant protein accumulation from 35 °C (low/off) to 15 °C (high). We have named this the CITRIC system, an acronym for cold-inducible translational readthrough in chloroplasts. The exact induction behaviour can be tailored by altering the number of TGA codons within the transgene. Conclusions CITRIC adds to the suite of genetic engineering tools available for the microalgal chloroplast, allowing a greater degree of control over the timing of heterologous protein expression. It could also be used as a heat-repressible system for studying the function of essential native genes in the chloroplast. The genetic components of CITRIC are entirely plastid-based, so no engineering of the nuclear genome is required. Electronic supplementary material The online version of this article (10.1186/s12934-018-1033-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rosanna Young
- Algal Research Group, Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK.,Department of Medicine, Sir Alexander Fleming Building, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Saul Purton
- Algal Research Group, Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK.
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21
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Sharma N, Evans TA, Pellicore MJ, Davis E, Aksit MA, McCague AF, Joynt AT, Lu Z, Han ST, Anzmann AF, Lam ATN, Thaxton A, West N, Merlo C, Gottschalk LB, Raraigh KS, Sosnay PR, Cotton CU, Cutting GR. Capitalizing on the heterogeneous effects of CFTR nonsense and frameshift variants to inform therapeutic strategy for cystic fibrosis. PLoS Genet 2018; 14:e1007723. [PMID: 30444886 PMCID: PMC6267994 DOI: 10.1371/journal.pgen.1007723] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 11/30/2018] [Accepted: 09/28/2018] [Indexed: 12/18/2022] Open
Abstract
CFTR modulators have revolutionized the treatment of individuals with cystic fibrosis (CF) by improving the function of existing protein. Unfortunately, almost half of the disease-causing variants in CFTR are predicted to introduce premature termination codons (PTC) thereby causing absence of full-length CFTR protein. We hypothesized that a subset of nonsense and frameshift variants in CFTR allow expression of truncated protein that might respond to FDA-approved CFTR modulators. To address this concept, we selected 26 PTC-generating variants from four regions of CFTR and determined their consequences on CFTR mRNA, protein and function using intron-containing minigenes expressed in 3 cell lines (HEK293, MDCK and CFBE41o-) and patient-derived conditionally reprogrammed primary nasal epithelial cells. The PTC-generating variants fell into five groups based on RNA and protein effects. Group A (reduced mRNA, immature (core glycosylated) protein, function <1% (n = 5)) and Group B (normal mRNA, immature protein, function <1% (n = 10)) variants were unresponsive to modulator treatment. However, Group C (normal mRNA, mature (fully glycosylated) protein, function >1% (n = 5)), Group D (reduced mRNA, mature protein, function >1% (n = 5)) and Group E (aberrant RNA splicing, mature protein, function > 1% (n = 1)) variants responded to modulators. Increasing mRNA level by inhibition of NMD led to a significant amplification of modulator effect upon a Group D variant while response of a Group A variant was unaltered. Our work shows that PTC-generating variants should not be generalized as genetic 'nulls' as some may allow generation of protein that can be targeted to achieve clinical benefit.
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Affiliation(s)
- Neeraj Sharma
- 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 Davis
- 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
| | - Allison F. McCague
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Anya T. Joynt
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Zhongzhu Lu
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Sangwoo T. Han
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Arianna F. Anzmann
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Anh-Thu N. Lam
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Abigail Thaxton
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, United States of America
| | - Natalie West
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, United States of America
| | - Christian Merlo
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, United States of America
| | - Laura B. Gottschalk
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, 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
| | - Patrick R. Sosnay
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins Hospital, 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
| | - Garry R. Cutting
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
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Filatova EN, Utkin OV. The Role of Noncoding mRNA Isoforms in the Regulation of Gene Expression. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418080057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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McHugh DR, Steele MS, Valerio DM, Miron A, Mann RJ, LePage DF, Conlon RA, Cotton CU, Drumm ML, Hodges CA. A G542X cystic fibrosis mouse model for examining nonsense mutation directed therapies. PLoS One 2018; 13:e0199573. [PMID: 29924856 PMCID: PMC6010256 DOI: 10.1371/journal.pone.0199573] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 06/08/2018] [Indexed: 12/22/2022] Open
Abstract
Nonsense mutations are present in 10% of patients with CF, produce a premature termination codon in CFTR mRNA causing early termination of translation, and lead to lack of CFTR function. There are no currently available animal models which contain a nonsense mutation in the endogenous Cftr locus that can be utilized to test nonsense mutation therapies. In this study, we create a CF mouse model carrying the G542X nonsense mutation in Cftr using CRISPR/Cas9 gene editing. The G542X mouse model has reduced Cftr mRNA levels, demonstrates absence of CFTR function, and displays characteristic manifestations of CF mice such as reduced growth and intestinal obstruction. Importantly, CFTR restoration is observed in G542X intestinal organoids treated with G418, an aminoglycoside with translational readthrough capabilities. The G542X mouse model provides an invaluable resource for the identification of potential therapies of CF nonsense mutations as well as the assessment of in vivo effectiveness of these potential therapies targeting nonsense mutations.
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Affiliation(s)
- Daniel R. McHugh
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
- Department of Pediatrics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Miarasa S. Steele
- Department of Pediatrics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Dana M. Valerio
- Department of Pediatrics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Alexander Miron
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Rachel J. Mann
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - David F. LePage
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Ronald A. Conlon
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Calvin U. Cotton
- Department of Pediatrics, Case Western Reserve University, Cleveland, Ohio, United States of America
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Mitchell L. Drumm
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
- Department of Pediatrics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Craig A. Hodges
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
- Department of Pediatrics, Case Western Reserve University, Cleveland, Ohio, United States of America
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Guimbellot J, Sharma J, Rowe SM. Toward inclusive therapy with CFTR modulators: Progress and challenges. Pediatr Pulmonol 2017; 52:S4-S14. [PMID: 28881097 PMCID: PMC6208153 DOI: 10.1002/ppul.23773] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 06/29/2017] [Indexed: 12/29/2022]
Abstract
Cystic fibrosis is caused by gene mutations that result in an abnormal Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) protein on the surface of cells. CFTR modulators are a novel class of drugs that directly target the molecular defect. CFTR modulators include potentiators that result in improved activity of the channel; correctors that help the protein traffic to the cell surface properly; and readthrough agents that restore full-length CFTR by suppression of premature termination codons, among other novel classes more recently established. While some of these drugs, CFTR potentiators in particular, have provided remarkable improvements for CF patients, others have yet to achieve profoundly improved outcomes, and many CF patients are not yet impacted by CFTR modulators due to lack of knowledge regarding susceptibility of their mutations to treatment. One limitation to expanding these types of therapies to the maximum number of patients with CF is the lack of rigorously validated clinical biomarkers that can determine efficacy on an individual basis, as well as few pre-clinical tools that can predict whether an individual with a rare combination of mutant alleles will respond to a particular CFTR modulator regimen. In this review, we discuss the various groups of CFTR modulators and their status in clinical development, as well as address the current literature on biomarkers, pre-clinical cell-based tools, and the role of pharmacometrics in creating therapeutic strategies to improve the lives of all patients with cystic fibrosis, regardless of their specific mutation.
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Affiliation(s)
- Jennifer Guimbellot
- Departments of Pediatrics, The University of Alabama at Birmingham, Birmingham, Alabama
- Gregory Fleming James Cystic Fibrosis Research Center, The University of Alabama at Birmingham, Birmingham, Alabama
| | - Jyoti Sharma
- Gregory Fleming James Cystic Fibrosis Research Center, The University of Alabama at Birmingham, Birmingham, Alabama
- Cell Developmental and Integrative Biology, The University of Alabama at Birmingham, Birmingham, Alabama
| | - Steven M. Rowe
- Departments of Pediatrics, The University of Alabama at Birmingham, Birmingham, Alabama
- Gregory Fleming James Cystic Fibrosis Research Center, The University of Alabama at Birmingham, Birmingham, Alabama
- Cell Developmental and Integrative Biology, The University of Alabama at Birmingham, Birmingham, Alabama
- Departments of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama
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Marson FAL, Bertuzzo CS, Ribeiro JD. Personalized or Precision Medicine? The Example of Cystic Fibrosis. Front Pharmacol 2017; 8:390. [PMID: 28676762 PMCID: PMC5476708 DOI: 10.3389/fphar.2017.00390] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 06/02/2017] [Indexed: 01/01/2023] Open
Abstract
The advent of the knowledge on human genetics, by the identification of disease-associated variants, culminated in the understanding of human variability. With the genetic knowledge, the specificity of the clinical phenotype and the drug response of each individual were understood. Using the cystic fibrosis (CF) as an example, the new terms that emerged such as personalized medicine and precision medicine can be characterized. The genetic knowledge in CF is broad and the presence of a monogenic disease caused by mutations in the CFTR gene enables the phenotype–genotype association studies (including the response to drugs), considering the wide clinical and laboratory spectrum dependent on the mutual action of genotype, environment, and lifestyle. Regarding the CF disease, personalized medicine is the treatment directed at the symptoms, and this treatment is adjusted depending on the patient’s phenotype. However, more recently, the term precision medicine began to be widely used, although its correct application and understanding are still vague and poorly characterized. In precision medicine, we understand the individual as a response to the interrelation between environment, lifestyle, and genetic factors, which enabled the advent of new therapeutic models, such as conventional drugs adjustment by individual patient dosage and drug type and response, development of new drugs (read through, broker, enhancer, stabilizer, and amplifier compounds), genome editing by homologous recombination, zinc finger nucleases, TALEN (transcription activator-like effector nuclease), CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats-CRISPR-associated endonuclease 9), and gene therapy. Thus, we introduced the terms personalized medicine and precision medicine based on the CF.
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Affiliation(s)
- Fernando A L Marson
- Department of Medical Genetics, Faculty of Medical Sciences, State University of CampinasCampinas, Brazil.,Department of Pediatrics, Faculty of Medical Sciences, State University of CampinasCampinas, Brazil
| | - Carmen S Bertuzzo
- Department of Medical Genetics, Faculty of Medical Sciences, State University of CampinasCampinas, Brazil
| | - José D Ribeiro
- Department of Pediatrics, Faculty of Medical Sciences, State University of CampinasCampinas, Brazil
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Affiliation(s)
- Dean Ho
- Professor of Oral Biology and Medicine, and Bioengineering, The Jane and Jerry Weintraub Center for Reconstructive Biotechnology, School of Dentistry and Henry Samueli School of Engineering and Applied Science, University of California, Los Angeles, CA, USA
| | - Ali Zarrinpar
- Division of Liver and Pancreas Transplantation, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
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