1
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Lakli M, Onnée M, Carrez T, Becq F, Falguières T, Fanen P. ABC transporters involved in respiratory and cholestatic diseases: From rare to very rare monogenic diseases. Biochem Pharmacol 2024; 229:116468. [PMID: 39111603 DOI: 10.1016/j.bcp.2024.116468] [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: 02/26/2024] [Revised: 07/16/2024] [Accepted: 08/03/2024] [Indexed: 08/24/2024]
Abstract
ATP-binding cassette (ABC) transporters constitute a 49-member superfamily in humans. These proteins, most of them being transmembrane, allow the active transport of an important variety of substrates across biological membranes, using ATP hydrolysis as an energy source. For an important proportion of these ABC transporters, genetic variations of the loci encoding them have been correlated with rare genetic diseases, including cystic fibrosis and interstitial lung disease (variations in CFTR/ABCC7 and ABCA3) as well as cholestatic liver diseases (variations in ABCB4 and ABCB11). In this review, we first describe these ABC transporters and how their molecular dysfunction may lead to human diseases. Then, we propose a classification of the genetic variants according to their molecular defect (expression, traffic, function and/or stability), which may be considered as a general guideline for all ABC transporters' variants. Finally, we discuss recent progress in the field of targeted pharmacotherapy, which aim to correct specific molecular defects using small molecules. In conclusion, we are opening the path to treatment repurposing for diseases involving similar deficiencies in other ABC transporters.
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Affiliation(s)
- Mounia Lakli
- Inserm, Université Paris-Saclay, Physiopathogenèse et traitement des maladies du foie, UMR_S 1193, Hepatinov, 91400 Orsay, France
| | - Marion Onnée
- Univ Paris Est Creteil, INSERM, IMRB, F-94010, Créteil, France
| | - Thomas Carrez
- Université de Poitiers, Laboratoire Physiopathologie et Régulation des Transports Ioniques, Pôle Biologie Santé, 86000 Poitiers, France; ManRos Therapeutics, Hôtel de Recherche, Centre de Perharidy, 29680, Roscoff, France
| | - Frédéric Becq
- Université de Poitiers, Laboratoire Physiopathologie et Régulation des Transports Ioniques, Pôle Biologie Santé, 86000 Poitiers, France
| | - Thomas Falguières
- Inserm, Université Paris-Saclay, Physiopathogenèse et traitement des maladies du foie, UMR_S 1193, Hepatinov, 91400 Orsay, France
| | - Pascale Fanen
- Univ Paris Est Creteil, INSERM, IMRB, F-94010, Créteil, France; AP-HP, Département de Génétique Médicale, Hôpital Henri Mondor, F-94010, Créteil, France.
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2
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Karri S, Cornu D, Serot C, Biri L, Hatton A, Dréanot E, Rullaud C, Pranke I, Sermet-Gaudelus I, Hinzpeter A, Bidou L, Namy O. TLN468 changes the pattern of tRNA used to read through premature termination codons in CFTR. J Cyst Fibros 2024:S1569-1993(24)00802-6. [PMID: 39098506 DOI: 10.1016/j.jcf.2024.07.017] [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: 11/20/2023] [Revised: 07/22/2024] [Accepted: 07/24/2024] [Indexed: 08/06/2024]
Abstract
Nonsense mutations account for 12 % of cystic fibrosis (CF) cases. The presence of a premature termination codon (PTC) leads to gene inactivation, which can be countered by the use of drugs stimulating PTC readthrough, restoring production of the full-length protein. We recently identified a new readthrough inducer, TLN468, more efficient than gentamicin. We measured the readthrough induced by these two drugs with different cystic fibrosis transmembrane conductance regulator (CFTR) PTCs. We then determined the amino acids inserted at the S1196X, G542X, W846X and E1417X PTCs of CFTR during readthrough induced by gentamicin or TLN468. TLN468 significantly promoted the incorporation of one specific amino acid, whereas gentamicin did not greatly modify the proportions of the various amino acids incorporated relative to basal conditions. The function of the engineered missense CFTR channels corresponding to these four PTCs was assessed with and without potentiator. For the recoded CFTR, except for E1417Q and G542W, the PTC readthrough induced by TLN468 allowed the expression of CFTR variants that were correctly processed and had significant activity that was enhanced by CFTR modulators. These results suggest that it would be relevant to assess the therapeutic benefit of TLN468 PTC suppression in combination with CFTR modulators in preclinical assays.
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Affiliation(s)
- Sabrina Karri
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette, 91198, France
| | - David Cornu
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette, 91198, France
| | - Claudia Serot
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette, 91198, France
| | - Lynda Biri
- CNRS, INSERM, Institut Necker Enfants Malades-INEM, Université Paris Cité, Paris, F-75015, France
| | - Aurélie Hatton
- CNRS, INSERM, Institut Necker Enfants Malades-INEM, Université Paris Cité, Paris, F-75015, France
| | - Elise Dréanot
- CNRS, INSERM, Institut Necker Enfants Malades-INEM, Université Paris Cité, Paris, F-75015, France
| | - Camille Rullaud
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette, 91198, France
| | - Iwona Pranke
- CNRS, INSERM, Institut Necker Enfants Malades-INEM, Université Paris Cité, Paris, F-75015, France
| | - Isabelle Sermet-Gaudelus
- CNRS, INSERM, Institut Necker Enfants Malades-INEM, Université Paris Cité, Paris, F-75015, France
| | - Alexandre Hinzpeter
- CNRS, INSERM, Institut Necker Enfants Malades-INEM, Université Paris Cité, Paris, F-75015, France
| | - Laure Bidou
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette, 91198, France; Sorbonne Université, 4 Place Jussieu, Paris, 75005, France
| | - Olivier Namy
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette, 91198, France.
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3
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Premchandar A, Ming R, Baiad A, Da Fonte DF, Xu H, Faubert D, Veit G, Lukacs GL. Readthrough-induced misincorporated amino acid ratios guide mutant-specific therapeutic approaches for two CFTR nonsense mutations. Front Pharmacol 2024; 15:1389586. [PMID: 38725656 PMCID: PMC11079177 DOI: 10.3389/fphar.2024.1389586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 03/28/2024] [Indexed: 05/12/2024] Open
Abstract
Cystic fibrosis (CF) is a monogenic disease caused by mutations in the CF transmembrane conductance regulator (CFTR) gene. Premature termination codons (PTCs) represent ∼9% of CF mutations that typically cause severe expression defects of the CFTR anion channel. Despite the prevalence of PTCs as the underlying cause of genetic diseases, understanding the therapeutic susceptibilities of their molecular defects, both at the transcript and protein levels remains partially elucidated. Given that the molecular pathologies depend on the PTC positions in CF, multiple pharmacological interventions are required to suppress the accelerated nonsense-mediated mRNA decay (NMD), to correct the CFTR conformational defect caused by misincorporated amino acids, and to enhance the inefficient stop codon readthrough. The G418-induced readthrough outcome was previously investigated only in reporter models that mimic the impact of the local sequence context on PTC mutations in CFTR. To identify the misincorporated amino acids and their ratios for PTCs in the context of full-length CFTR readthrough, we developed an affinity purification (AP)-tandem mass spectrometry (AP-MS/MS) pipeline. We confirmed the incorporation of Cys, Arg, and Trp residues at the UGA stop codons of G542X, R1162X, and S1196X in CFTR. Notably, we observed that the Cys and Arg incorporation was favored over that of Trp into these CFTR PTCs, suggesting that the transcript sequence beyond the proximity of PTCs and/or other factors can impact the amino acid incorporation and full-length CFTR functional expression. Additionally, establishing the misincorporated amino acid ratios in the readthrough CFTR PTCs aided in maximizing the functional rescue efficiency of PTCs by optimizing CFTR modulator combinations. Collectively, our findings contribute to the understanding of molecular defects underlying various CFTR nonsense mutations and provide a foundation to refine mutation-dependent therapeutic strategies for various CF-causing nonsense mutations.
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Affiliation(s)
| | - Ruiji Ming
- Department of Physiology, McGill University, Montréal, QC, Canada
| | - Abed Baiad
- Department of Physiology, McGill University, Montréal, QC, Canada
| | | | - Haijin Xu
- Department of Physiology, McGill University, Montréal, QC, Canada
| | - Denis Faubert
- IRCM Mass Spectrometry and Proteomics Platform, Institut de Recherches Cliniques de Montréal, Montréal, QC, Canada
| | - Guido Veit
- Department of Physiology, McGill University, Montréal, QC, Canada
| | - Gergely L. Lukacs
- Department of Physiology, McGill University, Montréal, QC, Canada
- Department of Biochemistry, McGill University, Montréal, QC, Canada
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Gemmati D, D’Aversa E, Antonica B, Grisafi M, Salvatori F, Pizzicotti S, Pellegatti P, Ciccone M, Moratelli S, Serino ML, Tisato V. Gene Dosage of F5 c.3481C>T Stop-Codon (p.R1161Ter) Switches the Clinical Phenotype from Severe Thrombosis to Recurrent Haemorrhage: Novel Hypotheses for Readthrough Strategy. Genes (Basel) 2024; 15:432. [PMID: 38674367 PMCID: PMC11050146 DOI: 10.3390/genes15040432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
Inherited defects in the genes of blood coagulation essentially express the severity of the clinical phenotype that is directly correlated to the number of mutated alleles of the candidate leader gene (e.g., heterozygote vs. homozygote) and of possible additional coinherited traits. The F5 gene, which codes for coagulation factor V (FV), plays a two-faced role in the coagulation cascade, exhibiting both procoagulant and anticoagulant functions. Thus, defects in this gene can be predisposed to either bleeding or thrombosis. A Sanger sequence analysis detected a premature stop-codon in exon 13 of the F5 gene (c.3481C>T; p.R1161Ter) in several members of a family characterised by low circulating FV levels and contrasting clinical phenotypes. The propositus, a 29 y.o. male affected by recurrent haemorrhages, was homozygous for the F5 stop-codon and for the F5 c.1691G>A (p.R506Q; FV-Leiden) inherited from the heterozygous parents, which is suggestive of combined cis-segregation. The homozygous condition of the stop-codon completely abolished the F5 gene expression in the propositus (FV:Ag < 1%; FV:C < 1%; assessed by ELISA and PT-based one-stage clotting assay respectively), removing, in turn, any chance for FV-Leiden to act as a prothrombotic molecule. His father (57 y.o.), characterised by severe recurrent venous thromboses, underwent a complete molecular thrombophilic screening, revealing a heterozygous F2 G20210A defect, while his mother (56 y.o.), who was negative for further common coagulation defects, reported fully asymptomatic anamnesis. To dissect these conflicting phenotypes, we performed the ProC®Global (Siemens Helthineers) coagulation test aimed at assessing the global pro- and anticoagulant balance of each family member, investigating the responses to the activated protein C (APC) by means of an APC-sensitivity ratio (APC-sr). The propositus had an unexpectedly poor response to APC (APC-sr: 1.09; n.v. > 2.25), and his father and mother had an APC-sr of 1.5 and 2.0, respectively. Although ProC®Global prevalently detects the anticoagulant side of FV, the exceptionally low APC-sr of the propositus and his discordant severe-moderate haemorrhagic phenotype could suggest a residual expression of mutated FV p.506QQ through a natural readthrough or possible alternative splicing mechanisms. The coagulation pathway may be physiologically rebalanced through natural and induced strategies, and the described insights might be able to track the design of novel treatment approaches and rebalancing molecules.
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Affiliation(s)
- Donato Gemmati
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
- University Strategic Centre for Studies on Gender Medicine, University of Ferrara, 44121 Ferrara, Italy
- Centre Haemostasis & Thrombosis, University of Ferrara, 44121 Ferrara, Italy
| | - Elisabetta D’Aversa
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
| | - Bianca Antonica
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
| | - Miriana Grisafi
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
| | - Francesca Salvatori
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
| | | | | | - Maria Ciccone
- Haematology Unit, Hospital-University of Ferrara, 44121 Ferrara, Italy
| | - Stefano Moratelli
- Centre Haemostasis & Thrombosis, University of Ferrara, 44121 Ferrara, Italy
| | - Maria Luisa Serino
- Centre Haemostasis & Thrombosis, University of Ferrara, 44121 Ferrara, Italy
| | - Veronica Tisato
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
- University Strategic Centre for Studies on Gender Medicine, University of Ferrara, 44121 Ferrara, Italy
- Laboratory of Technology for Advanced Therapies (LTTA) Centre, University of Ferrara, 44121 Ferrara, Italy
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5
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Mangkalaphiban K, Fu L, Du M, Thrasher K, Keeling KM, Bedwell DM, Jacobson A. Extended stop codon context predicts nonsense codon readthrough efficiency in human cells. Nat Commun 2024; 15:2486. [PMID: 38509072 PMCID: PMC10954755 DOI: 10.1038/s41467-024-46703-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 03/06/2024] [Indexed: 03/22/2024] Open
Abstract
Protein synthesis terminates when a stop codon enters the ribosome's A-site. Although termination is efficient, stop codon readthrough can occur when a near-cognate tRNA outcompetes release factors during decoding. Seeking to understand readthrough regulation we used a machine learning approach to analyze readthrough efficiency data from published HEK293T ribosome profiling experiments and compared it to comparable yeast experiments. We obtained evidence for the conservation of identities of the stop codon, its context, and 3'-UTR length (when termination is compromised), but not the P-site codon, suggesting a P-site tRNA role in readthrough regulation. Models trained on data from cells treated with the readthrough-promoting drug, G418, accurately predicted readthrough of premature termination codons arising from CFTR nonsense alleles that cause cystic fibrosis. This predictive ability has the potential to aid development of nonsense suppression therapies by predicting a patient's likelihood of improvement in response to drugs given their nonsense mutation sequence context.
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Affiliation(s)
- Kotchaphorn Mangkalaphiban
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, 368 Plantation Street, Worcester, MA, 01655, USA
- Department of Genomics and Computational Biology, UMass Chan Medical School, 368 Plantation Street, Worcester, MA, 01655, USA
| | - Lianwu Fu
- Department of Biochemistry and Molecular Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, 845 19th Street South, Birmingham, AL, 35294, USA
| | - Ming Du
- Department of Biochemistry and Molecular Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, 845 19th Street South, Birmingham, AL, 35294, USA
| | - Kari Thrasher
- Department of Biochemistry and Molecular Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, 845 19th Street South, Birmingham, AL, 35294, USA
| | - Kim M Keeling
- Department of Biochemistry and Molecular Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, 845 19th Street South, Birmingham, AL, 35294, USA
| | - David M Bedwell
- Department of Biochemistry and Molecular Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, 845 19th Street South, Birmingham, AL, 35294, USA
| | - Allan Jacobson
- Department of Microbiology and Physiological Systems, UMass Chan Medical School, 368 Plantation Street, Worcester, MA, 01655, USA.
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Staedtke V, Anstett K, Bedwell D, Giovannini M, Keeling K, Kesterson R, Kim Y, Korf B, Leier A, McManus ML, Sarnoff H, Vitte J, Walker JA, Plotkin SR, Wallis D. Gene-targeted therapy for neurofibromatosis and schwannomatosis: The path to clinical trials. Clin Trials 2024; 21:51-66. [PMID: 37937606 DOI: 10.1177/17407745231207970] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
Numerous successful gene-targeted therapies are arising for the treatment of a variety of rare diseases. At the same time, current treatment options for neurofibromatosis 1 and schwannomatosis are limited and do not directly address loss of gene/protein function. In addition, treatments have mostly focused on symptomatic tumors, but have failed to address multisystem involvement in these conditions. Gene-targeted therapies hold promise to address these limitations. However, despite intense interest over decades, multiple preclinical and clinical issues need to be resolved before they become a reality. The optimal approaches to gene-, mRNA-, or protein restoration and to delivery to the appropriate cell types remain elusive. Preclinical models that recapitulate manifestations of neurofibromatosis 1 and schwannomatosis need to be refined. The development of validated assays for measuring neurofibromin and merlin activity in animal and human tissues will be critical for early-stage trials, as will the selection of appropriate patients, based on their individual genotypes and risk/benefit balance. Once the safety of gene-targeted therapy for symptomatic tumors has been established, the possibility of addressing a wide range of symptoms, including non-tumor manifestations, should be explored. As preclinical efforts are underway, it will be essential to educate both clinicians and those affected by neurofibromatosis 1/schwannomatosis about the risks and benefits of gene-targeted therapy for these conditions.
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Affiliation(s)
- Verena Staedtke
- Department of Neurology, Johns Hopkins University, Baltimore, MD, USA
| | - Kara Anstett
- Department of Neurology, NYU Grossman School of Medicine, New York, NY, USA
| | - David Bedwell
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Marco Giovannini
- Department of Head and Neck Surgery, David Geffen School of Medicine at UCLA and Jonsson Comprehensive Cancer Center (JCCC), University of California Los Angeles, Los Angeles, CA, USA
| | - Kim Keeling
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Robert Kesterson
- Department of Cancer Precision Medicine, Pennington Biomedical Research Center, Baton Rouge, LA, USA
| | - YooRi Kim
- Gilbert Family Foundation, Detroit, MI, USA
| | - Bruce Korf
- Department of Genetics, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - André Leier
- Department of Genetics, The University of Alabama at Birmingham, Birmingham, AL, USA
| | | | | | - Jeremie Vitte
- Department of Head and Neck Surgery, David Geffen School of Medicine at UCLA and Jonsson Comprehensive Cancer Center (JCCC), University of California Los Angeles, Los Angeles, CA, USA
| | - James A Walker
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Scott R Plotkin
- Department of Neurology and Cancer Center, Massachusetts General Hospital, Boston, MA, USA
| | - Deeann Wallis
- Department of Genetics, The University of Alabama at Birmingham, Birmingham, AL, USA
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7
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Coller J, Ignatova Z. tRNA therapeutics for genetic diseases. Nat Rev Drug Discov 2024; 23:108-125. [PMID: 38049504 DOI: 10.1038/s41573-023-00829-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/11/2023] [Indexed: 12/06/2023]
Abstract
Transfer RNAs (tRNAs) have a crucial role in protein synthesis, and in recent years, their therapeutic potential for the treatment of genetic diseases - primarily those associated with a mutation altering mRNA translation - has gained significant attention. Engineering tRNAs to readthrough nonsense mutation-associated premature termination of mRNA translation can restore protein synthesis and function. In addition, supplementation of natural tRNAs can counteract effects of missense mutations in proteins crucial for tRNA biogenesis and function in translation. This Review will present advances in the development of tRNA therapeutics with high activity and safety in vivo and discuss different formulation approaches for single or chronic treatment modalities. The field of tRNA therapeutics is still in its early stages, and a series of challenges related to tRNA efficacy and stability in vivo, delivery systems with tissue-specific tropism, and safe and efficient manufacturing need to be addressed.
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Affiliation(s)
- Jeff Coller
- Department of Molecular Biology and Genetics, School of Medicine, Johns Hopkins University, Baltimore, MD, USA.
| | - Zoya Ignatova
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany.
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Mention K, Cavusoglu-Doran K, Joynt AT, Santos L, Sanz D, Eastman AC, Merlo C, Langfelder-Schwind E, Scallan MF, Farinha CM, Cutting GR, Sharma N, Harrison PT. Use of adenine base editing and homology-independent targeted integration strategies to correct the cystic fibrosis causing variant, W1282X. Hum Mol Genet 2023; 32:3237-3248. [PMID: 37649273 PMCID: PMC10656707 DOI: 10.1093/hmg/ddad143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 07/21/2023] [Accepted: 08/12/2023] [Indexed: 09/01/2023] Open
Abstract
Small molecule drugs known as modulators can treat ~90% of people with cystic fibrosis (CF), but do not work for premature termination codon variants such as W1282X (c.3846G>A). Here we evaluated two gene editing strategies, Adenine Base Editing (ABE) to correct W1282X, and Homology-Independent Targeted Integration (HITI) of a CFTR superexon comprising exons 23-27 (SE23-27) to enable expression of a CFTR mRNA without W1282X. In Flp-In-293 cells stably expressing a CFTR expression minigene bearing W1282X, ABE corrected 24% of W1282X alleles, rescued CFTR mRNA from nonsense mediated decay and restored protein expression. However, bystander editing at the adjacent adenine (c.3847A>G), caused an amino acid change (R1283G) that affects CFTR maturation and ablates ion channel activity. In primary human nasal epithelial cells homozygous for W1282X, ABE corrected 27% of alleles, but with a notably lower level of bystander editing, and CFTR channel function was restored to 16% of wild-type levels. Using the HITI approach, correct integration of a SE23-27 in intron 22 of the CFTR locus in 16HBEge W1282X cells was detected in 5.8% of alleles, resulting in 7.8% of CFTR transcripts containing the SE23-27 sequence. Analysis of a clonal line homozygous for the HITI-SE23-27 produced full-length mature protein and restored CFTR anion channel activity to 10% of wild-type levels, which could be increased three-fold upon treatment with the triple combination of CF modulators. Overall, these data demonstrate two different editing strategies can successfully correct W1282X, the second most common class I variant, with a concomitant restoration of CFTR function.
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Affiliation(s)
- Karen Mention
- Department of Physiology, University College Cork, College Road, Cork, T12 K8AF, Ireland
- School of Microbiology, University College Cork, College Road, Cork, T12 K8AF, Ireland
| | - Kader Cavusoglu-Doran
- Department of Physiology, University College Cork, College Road, Cork, T12 K8AF, Ireland
| | - Anya T Joynt
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, United States
| | - Lúcia Santos
- Department of Physiology, University College Cork, College Road, Cork, T12 K8AF, Ireland
- Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, University of Lisboa, Campo Grande, C8 bdg, Lisboa 1749-016, Portugal
| | - David Sanz
- Department of Physiology, University College Cork, College Road, Cork, T12 K8AF, Ireland
| | - Alice C Eastman
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, United States
| | - Christian Merlo
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins Hospital, 1800 Orleans St, Baltimore, MD 21287, United States
| | - Elinor Langfelder-Schwind
- The Cystic Fibrosis Center, Lenox Hill Hospital, 100 E. 77th Street, 4E, New York, NY 10075, United States
| | - Martina F Scallan
- School of Microbiology, University College Cork, College Road, Cork, T12 K8AF, Ireland
| | - Carlos M Farinha
- Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, University of Lisboa, Campo Grande, C8 bdg, Lisboa 1749-016, Portugal
| | - Garry R Cutting
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, United States
| | - Neeraj Sharma
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, United States
| | - Patrick T Harrison
- Department of Physiology, University College Cork, College Road, Cork, T12 K8AF, Ireland
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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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10
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Wagner RN, Wießner M, Friedrich A, Zandanell J, Breitenbach-Koller H, Bauer JW. Emerging Personalized Opportunities for Enhancing Translational Readthrough in Rare Genetic Diseases and Beyond. Int J Mol Sci 2023; 24:6101. [PMID: 37047074 PMCID: PMC10093890 DOI: 10.3390/ijms24076101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/17/2023] [Accepted: 03/21/2023] [Indexed: 04/14/2023] Open
Abstract
Nonsense mutations trigger premature translation termination and often give rise to prevalent and rare genetic diseases. Consequently, the pharmacological suppression of an unscheduled stop codon represents an attractive treatment option and is of high clinical relevance. At the molecular level, the ability of the ribosome to continue translation past a stop codon is designated stop codon readthrough (SCR). SCR of disease-causing premature termination codons (PTCs) is minimal but small molecule interventions, such as treatment with aminoglycoside antibiotics, can enhance its frequency. In this review, we summarize the current understanding of translation termination (both at PTCs and at cognate stop codons) and highlight recently discovered pathways that influence its fidelity. We describe the mechanisms involved in the recognition and readthrough of PTCs and report on SCR-inducing compounds currently explored in preclinical research and clinical trials. We conclude by reviewing the ongoing attempts of personalized nonsense suppression therapy in different disease contexts, including the genetic skin condition epidermolysis bullosa.
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Affiliation(s)
- Roland N. Wagner
- Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria
| | - Michael Wießner
- Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria
| | - Andreas Friedrich
- Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria
- Department of Biosciences, University of Salzburg, 5020 Salzburg, Austria
| | - Johanna Zandanell
- Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria
| | | | - Johann W. Bauer
- Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria
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11
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Manjunath LE, Singh A, Som S, Eswarappa SM. Mammalian proteome expansion by stop codon readthrough. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1739. [PMID: 35570338 DOI: 10.1002/wrna.1739] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 04/11/2022] [Accepted: 04/16/2022] [Indexed: 12/20/2022]
Abstract
Recognition of a stop codon by translation machinery as a sense codon results in translational readthrough instead of termination. This recoding process, termed stop codon readthrough (SCR) or translational readthrough, is found in all domains of life including mammals. The context of the stop codon, local mRNA topology, and molecules that interact with the mRNA region downstream of the stop codon determine SCR. The products of SCR can have localization, stability, and function different from those of the canonical isoforms. In this review, we discuss how recent technological and computational advances have increased our understanding of the SCR process in the mammalian system. Based on the known molecular events that occur during SCR of multiple mRNAs, we propose transient molecular roadblocks on an mRNA downstream of the stop codon as a possible mechanism for the induction of SCR. We argue, with examples, that the insights gained from the natural SCR events can guide us to develop novel strategies for the treatment of diseases caused by premature stop codons. This article is categorized under: Translation > Regulation.
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Affiliation(s)
- Lekha E Manjunath
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Anumeha Singh
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Saubhik Som
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Sandeep M Eswarappa
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
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12
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Honrubia JM, Gutierrez-Álvarez J, Sanz-Bravo A, González-Miranda E, Muñoz-Santos D, Castaño-Rodriguez C, Wang L, Villarejo-Torres M, Ripoll-Gómez J, Esteban A, Fernandez-Delgado R, Sánchez-Cordón PJ, Oliveros JC, Perlman S, McCray PB, Sola I, Enjuanes L. SARS-CoV-2-Mediated Lung Edema and Replication Are Diminished by Cystic Fibrosis Transmembrane Conductance Regulator Modulators. mBio 2023; 14:e0313622. [PMID: 36625656 PMCID: PMC9973274 DOI: 10.1128/mbio.03136-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 12/01/2022] [Indexed: 01/11/2023] Open
Abstract
Coronaviruses (CoVs) of genera α, β, γ, and δ encode proteins that have a PDZ-binding motif (PBM) consisting of the last four residues of the envelope (E) protein (PBM core). PBMs may bind over 400 cellular proteins containing PDZ domains (an acronym formed by the combination of the first letter of the names of the three first proteins where this domain was identified), making them relevant for the control of cell function. Three highly pathogenic human CoVs have been identified to date: severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV), and SARS-CoV-2. The PBMs of the three CoVs were virulence factors. SARS-CoV mutants in which the E protein PBM core was replaced by the E protein PBM core from virulent or attenuated CoVs were constructed. These mutants showed a gradient of virulence, depending on whether the alternative PBM core introduced was derived from a virulent or an attenuated CoV. Gene expression patterns in the lungs of mice infected with SARS-CoVs encoding each of the different PBMs were analyzed by RNA sequencing of infected lung tissues. E protein PBM of SARS-CoV and SARS-CoV-2 dysregulated gene expression related to ion transport and cell homeostasis. Decreased expression of cystic fibrosis transmembrane conductance regulator (CFTR) mRNA, essential for alveolar edema resolution, was shown. Reduced CFTR mRNA levels were associated with edema accumulation in the alveoli of mice infected with SARS-CoV and SARS-CoV-2. Compounds that increased CFTR expression and activity, significantly reduced SARS-CoV-2 growth in cultured cells and protected against mouse infection, suggesting that E protein virulence is mediated by a decreased CFTR expression. IMPORTANCE Three highly pathogenic human CoVs have been identified: SARS-CoV, MERS-CoV, and SARS-CoV-2. The E protein PBMs of these three CoVs were virulence factors. Gene expression patterns associated with the different PBM motifs in the lungs of infected mice were analyzed by deep sequencing. E protein PBM motif of SARS-CoV and SARS-CoV-2 dysregulated the expression of genes related to ion transport and cell homeostasis. A decrease in the mRNA expression of the cystic fibrosis transmembrane conductance regulator (CFTR), which is essential for edema resolution, was observed. The reduction of CFTR mRNA levels was associated with edema accumulation in the lungs of mice infected with SARS-CoV-2. Compounds that increased the expression and activity of CFTR drastically reduced the production of SARS-CoV-2 and protected against its infection in a mice model. These results allowed the identification of cellular targets for the selection of antivirals.
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Affiliation(s)
- Jose M. Honrubia
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Javier Gutierrez-Álvarez
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Alejandro Sanz-Bravo
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Ezequiel González-Miranda
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Diego Muñoz-Santos
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Carlos Castaño-Rodriguez
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Li Wang
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Marta Villarejo-Torres
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Jorge Ripoll-Gómez
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Ana Esteban
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Raul Fernandez-Delgado
- Department of Infectious Diseases and Global Health, Animal Health Research Center (CISA), National Institute of Research, Agricultural and Food Technology (INIA-CSIC), Valdeolmos, Madrid, Spain
| | - Pedro José Sánchez-Cordón
- Veterinary Pathology Department, Animal Health Research Center (CISA), National Institute of Research, Agricultural and Food Technology (INIA-CSIC), Valdeolmos, Madrid, Spain
| | - Juan Carlos Oliveros
- Bioinformatics for Genomics and Proteomics Unit, CNB-CSIC, Campus Universidad Autónoma de Madrid, Madrid, Spain
| | - Stanley Perlman
- Department of Microbiology, University of Iowa, Iowa City, USA
- Stead Family Department of Pediatrics, The University of Iowa, Iowa City, Iowa, USA
- Interdisciplinary Program in Immunology, University of Iowa, Iowa City, USA
| | - Paul B. McCray
- Stead Family Department of Pediatrics, The University of Iowa, Iowa City, Iowa, USA
- Pappajohn Biomedical Institute, The University of Iowa, Iowa City, Iowa, USA
- Center for Gene Therapy, The University of Iowa, Iowa City, Iowa, USA
| | - Isabel Sola
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Luis Enjuanes
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
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13
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Siddiqui A, Dundar H, Sharma J, Kaczmarczyk A, Echols J, Dai Y, Sun CR, Du M, Liu Z, Zhao R, Wood T, Sanders S, Rasmussen L, Bostwick JR, Augelli-Szafran C, Suto M, Rowe SM, Bedwell DM, Keeling KM. Triamterene Functions as an Effective Nonsense Suppression Agent for MPS I-H (Hurler Syndrome). Int J Mol Sci 2023; 24:4521. [PMID: 36901952 PMCID: PMC10003437 DOI: 10.3390/ijms24054521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 02/20/2023] [Accepted: 02/22/2023] [Indexed: 03/03/2023] Open
Abstract
Mucopolysaccharidosis I-Hurler (MPS I-H) is caused by the loss of α-L-iduronidase, a lysosomal enzyme that degrades glycosaminoglycans. Current therapies cannot treat many MPS I-H manifestations. In this study, triamterene, an FDA-approved, antihypertensive diuretic, was found to suppress translation termination at a nonsense mutation associated with MPS I-H. Triamterene rescued enough α-L-iduronidase function to normalize glycosaminoglycan storage in cell and animal models. This new function of triamterene operates through premature termination codon (PTC) dependent mechanisms that are unaffected by epithelial sodium channel activity, the target of triamterene's diuretic function. Triamterene represents a potential non-invasive treatment for MPS I-H patients carrying a PTC.
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Affiliation(s)
- Amna Siddiqui
- Department of Biochemistry & Molecular Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Halil Dundar
- Department of Biochemistry & Molecular Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Next Generation Sequencing Transplant Diagnostics, Thermo-Fisher Scientific, West Hills, CA 91304, USA
| | - Jyoti Sharma
- Cystic Fibrosis Research Center, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Division of Infectious Diseases, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Aneta Kaczmarczyk
- Department of Biochemistry & Molecular Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- ARUP Laboratories, Department of Pathology, University of Utah, Salt Lake City, UT 84112, USA
| | - Josh Echols
- Department of Biochemistry & Molecular Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Yanying Dai
- Department of Biochemistry & Molecular Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Chuanxi Richard Sun
- Department of Biochemistry & Molecular Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Ming Du
- Department of Biochemistry & Molecular Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Cystic Fibrosis Research Center, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Zhong Liu
- Department of Biochemistry & Molecular Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Rui Zhao
- Department of Biochemistry & Molecular Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Tim Wood
- Greenwood Genetic Center, Greenwood, SC 29646, USA
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | | | | | | | | | - Mark Suto
- Southern Research, Birmingham, AL 35205, USA
| | - Steven M. Rowe
- Cystic Fibrosis Research Center, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - David M. Bedwell
- Department of Biochemistry & Molecular Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Cystic Fibrosis Research Center, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Kim M. Keeling
- Department of Biochemistry & Molecular Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Cystic Fibrosis Research Center, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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14
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Adachi H, Pan Y, He X, Chen JL, Klein B, Platenburg G, Morais P, Boutz P, Yu YT. Targeted pseudouridylation: An approach for suppressing nonsense mutations in disease genes. Mol Cell 2023; 83:637-651.e9. [PMID: 36764303 PMCID: PMC9975048 DOI: 10.1016/j.molcel.2023.01.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/18/2022] [Accepted: 01/05/2023] [Indexed: 02/11/2023]
Abstract
Nonsense mutations create premature termination codons (PTCs), activating the nonsense-mediated mRNA decay (NMD) pathway to degrade most PTC-containing mRNAs. The undegraded mRNA is translated, but translation terminates at the PTC, leading to no production of the full-length protein. This work presents targeted PTC pseudouridylation, an approach for nonsense suppression in human cells. Specifically, an artificial box H/ACA guide RNA designed to target the mRNA PTC can suppress both NMD and premature translation termination in various sequence contexts. Targeted pseudouridylation exhibits a level of suppression comparable with that of aminoglycoside antibiotic treatments. When targeted pseudouridylation is combined with antibiotic treatment, a much higher level of suppression is observed. Transfection of a disease model cell line (carrying a chromosomal PTC) with a designer guide RNA gene targeting the PTC also leads to nonsense suppression. Thus, targeted pseudouridylation is an RNA-directed gene-specific approach that suppresses NMD and concurrently promotes PTC readthrough.
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Affiliation(s)
- Hironori Adachi
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, NY, USA
| | - Yi Pan
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, NY, USA
| | - Xueyang He
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, NY, USA
| | - Jonathan L Chen
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, NY, USA
| | - Bart Klein
- ProQR Therapeutics, Leiden, the Netherlands
| | | | | | - Paul Boutz
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, NY, USA; Center for Biomedical Informatics and Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY, USA.
| | - Yi-Tao Yu
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, NY, USA.
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15
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Bowling A, Eastman A, Merlo C, Lin G, West N, Patel S, Cutting G, Sharma N. Downstream Alternate Start Site Allows N-Terminal Nonsense Variants to Escape NMD and Results in Functional Recovery by Readthrough and Modulator Combination. J Pers Med 2022; 12:jpm12091448. [PMID: 36143233 PMCID: PMC9504986 DOI: 10.3390/jpm12091448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 08/26/2022] [Accepted: 08/31/2022] [Indexed: 11/23/2022] Open
Abstract
Genetic variants that introduce premature termination codons (PTCs) have remained difficult to therapeutically target due to lack of protein product. Nonsense mediated mRNA decay (NMD) targets PTC-bearing transcripts to reduce the potentially damaging effects of truncated proteins. Readthrough compounds have been tested on PTC-generating variants in attempt to permit translation through a premature stop. However, readthrough compounds have not proved efficacious in a clinical setting due to lack of stable mRNA. Here, we investigate N-terminal variants in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, which have been shown to escape NMD, potentially through a mechanism of alternative translation initiation at downstream AUG codons. We hypothesized that N-terminal variants in CFTR that evade NMD will produce stable transcript, allowing CFTR function to be restored by a combination of readthrough and protein modulator therapy. We investigate this using two cell line models expressing CFTR-expression minigenes (EMG; HEK293s and CFBEs) and primary human nasal epithelial (NE) cells, and we test readthrough compounds G418 and ELX-02 in combination with CFTR protein modulators. HEK293 cells expressing the variants E60X and L88X generate CFTR-specific core glycosylated products that are consistent with downstream translation initiation. Mutation of downstream methionines at codons 150 and 152 does not result in changes in CFTR protein processing in cells expressing L88X-CFTR-EMG. However, mutation of methionine at 265 results in loss of detectable CFTR protein in cells expressing E60X, L88X, and Y122X CFTR-EMGs, indicating that downstream translation initiation is occurring at the AUG codon at position M265. In HEK293 stable cells harboring L88X, treatment with readthrough compounds alone allows for formation of full-length, but misfolded CFTR protein. Upon addition of protein modulators in combination with readthrough, we observe formation of mature, complex-glycosylated CFTR. In CFBE and NE cells, addition of readthrough ELX-02 and modulator therapy results in substantial recovery of CFTR function. Our work indicates that N-terminal variants generate stable CFTR transcript due to translation initiation at a downstream AUG codon. Thus, individuals with CF bearing 5′ nonsense variants that evade NMD are ideal candidates for treatment with clinically safe readthrough compounds and modulator therapy.
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Affiliation(s)
- Alyssa Bowling
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Alice Eastman
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Christian Merlo
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins Hospital, Baltimore, MD 21205, USA
| | - Gabrielle Lin
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Natalie West
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins Hospital, Baltimore, MD 21205, USA
| | - Shivani Patel
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins Hospital, Baltimore, MD 21205, USA
| | - Garry Cutting
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Neeraj Sharma
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Correspondence:
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16
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Abreu RBV, Gomes TT, Nepomuceno TC, Li X, Fuchshuber-Moraes M, De Gregoriis G, Suarez-Kurtz G, Monteiro ANA, Carvalho MA. Functional Restoration of BRCA1 Nonsense Mutations by Aminoglycoside-Induced Readthrough. Front Pharmacol 2022; 13:935995. [PMID: 35837282 PMCID: PMC9273842 DOI: 10.3389/fphar.2022.935995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 06/01/2022] [Indexed: 11/13/2022] Open
Abstract
BRCA1 is a major tumor suppressor that functions in the accurate repair of DNA double-strand breaks via homologous recombination (HR). Nonsense mutations in BRCA1 lead to inactive truncated protein products and are associated with high risk of breast and ovarian cancer. These mutations generate premature termination codons (PTCs). Different studies have shown that aminoglycosides can induce PTC suppression by promoting stop codon readthrough and restoring full-length (FL) protein expression. The use of these compounds has been studied in clinical trials for genetic diseases such as cystic fibrosis and Duchenne muscular dystrophy, with encouraging results. Here we show proof-of-concept data demonstrating that the aminoglycoside G418 can induce BRCA1 PTC readthrough and restore FL protein synthesis and function. We first demonstrate that G418 treatment restores BRCA1 FL protein synthesis in HCC1395, a human breast tumor cell line carrying the R1751X mutation. HCC1395 cells treated with G418 also recover HR DNA repair and restore cell cycle checkpoint activation. A set of naturally occurring BRCA1 nonsense variants encoding different PTCs was evaluated in a GFP C-terminal BRCA1 construct model and BRCA1 PTC readthrough levels vary depending on the stop codon context. Because PTC readthrough could generate FL protein carrying pathogenic missense mutations, variants representing the most probable acquired amino acid substitutions in consequence of readthrough were functionally assessed by a validated transcription activation assay. Overall, this is the first study that evaluates the readthrough of PTC variants with clinical relevance in the breast and ovarian cancer-predisposing gene BRCA1.
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Affiliation(s)
- Renata B. V. Abreu
- Divisão de Pesquisa Clínica, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Thiago T. Gomes
- Divisão de Pesquisa Clínica, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Thales C. Nepomuceno
- Divisão de Pesquisa Clínica, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Xueli Li
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | | | | | | | - Alvaro N. A. Monteiro
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Marcelo A. Carvalho
- Divisão de Pesquisa Clínica, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
- Instituto Federal do Rio de Janeiro—IFRJ, Rio de Janeiro, Brazil
- *Correspondence: Marcelo A. Carvalho,
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17
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Ko W, Porter JJ, Sipple MT, Edwards KM, Lueck JD. Efficient suppression of endogenous CFTR nonsense mutations using anticodon-engineered transfer RNAs. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 28:685-701. [PMID: 35664697 PMCID: PMC9126842 DOI: 10.1016/j.omtn.2022.04.033] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 04/29/2022] [Indexed: 12/14/2022]
Abstract
Nonsense mutations or premature termination codons (PTCs) comprise ∼11% of all genetic lesions, which result in over 7,000 distinct genetic diseases. Due to their outsized impact on human health, considerable effort has been made to find therapies for nonsense-associated diseases. Suppressor tRNAs have long been identified as a possible therapeutic for nonsense-associated diseases; however, their ability to inhibit nonsense-mediated mRNA decay (NMD) and support significant protein translation from endogenous transcripts has not been determined in mammalian cells. Here, we investigated the ability of anticodon edited (ACE)-tRNAs to suppress cystic fibrosis (CF) causing PTCs in the cystic fibrosis transmembrane regulator (CFTR) gene in gene-edited immortalized human bronchial epithelial (16HBEge) cells. Delivery of ACE-tRNAs to 16HBEge cells harboring three common CF mutations G542XUGA-, R1162XUGA-, and W1282XUGA-CFTR PTCs significantly inhibited NMD and rescued endogenous mRNA expression. Furthermore, delivery of our highly active leucine-encoding ACE-tRNA resulted in rescue of W1282X-CFTR channel function to levels that significantly exceed the necessary CFTR channel function for therapeutic relevance. This study establishes the ACE-tRNA approach as a potential standalone therapeutic for nonsense-associated diseases due to its ability to rescue both mRNA and full-length protein expression from PTC-containing endogenous genes.
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Affiliation(s)
- Wooree Ko
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Joseph J. Porter
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Matthew T. Sipple
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Katherine M. Edwards
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - John D. Lueck
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY 14642, USA
- Department of Neurology, University of Rochester Medical Center, Rochester, NY 14642, USA
- Center for RNA Biology, University of Rochester Medical Center, Rochester, NY 14642, USA
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18
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Ensinck MM, Carlon MS. One Size Does Not Fit All: The Past, Present and Future of Cystic Fibrosis Causal Therapies. Cells 2022; 11:cells11121868. [PMID: 35740997 PMCID: PMC9220995 DOI: 10.3390/cells11121868] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 05/25/2022] [Accepted: 05/28/2022] [Indexed: 02/04/2023] Open
Abstract
Cystic fibrosis (CF) is the most common monogenic disorder, caused by mutations in the CF transmembrane conductance regulator (CFTR) gene. Over the last 30 years, tremendous progress has been made in understanding the molecular basis of CF and the development of treatments that target the underlying defects in CF. Currently, a highly effective CFTR modulator treatment (Kalydeco™/Trikafta™) is available for 90% of people with CF. In this review, we will give an extensive overview of past and ongoing efforts in the development of therapies targeting the molecular defects in CF. We will discuss strategies targeting the CFTR protein (i.e., CFTR modulators such as correctors and potentiators), its cellular environment (i.e., proteostasis modulation, stabilization at the plasma membrane), the CFTR mRNA (i.e., amplifiers, nonsense mediated mRNA decay suppressors, translational readthrough inducing drugs) or the CFTR gene (gene therapies). Finally, we will focus on how these efforts can be applied to the 15% of people with CF for whom no causal therapy is available yet.
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Affiliation(s)
- Marjolein M. Ensinck
- Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Flanders, Belgium;
| | - Marianne S. Carlon
- Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Flanders, Belgium;
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, 3000 Leuven, Flanders, Belgium
- Correspondence:
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19
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Kim YJ, Nomakuchi T, Papaleonidopoulou F, Yang L, Zhang Q, Krainer AR. Gene-specific nonsense-mediated mRNA decay targeting for cystic fibrosis therapy. Nat Commun 2022; 13:2978. [PMID: 35624092 PMCID: PMC9142507 DOI: 10.1038/s41467-022-30668-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 05/06/2022] [Indexed: 12/20/2022] Open
Abstract
Low CFTR mRNA expression due to nonsense-mediated mRNA decay (NMD) is a major hurdle in developing a therapy for cystic fibrosis (CF) caused by the W1282X mutation in the CFTR gene. CFTR-W1282X truncated protein retains partial function, so increasing its levels by inhibiting NMD of its mRNA will likely be beneficial. Because NMD regulates the normal expression of many genes, gene-specific stabilization of CFTR-W1282X mRNA expression is more desirable than general NMD inhibition. Synthetic antisense oligonucleotides (ASOs) designed to prevent binding of exon junction complexes (EJC) downstream of premature termination codons (PTCs) attenuate NMD in a gene-specific manner. We describe cocktails of three ASOs that specifically increase the expression of CFTR-W1282X mRNA and CFTR protein upon delivery into human bronchial epithelial cells. This treatment increases the CFTR-mediated chloride current. These results set the stage for clinical development of an allele-specific therapy for CF caused by the W1282X mutation. The W1282X nonsense mutation in the CFTR gene causes cystic fibrosis by reducing its mRNA and functional protein levels. Here the authors developed antisense-oligonucleotide cocktails that restore CFTR protein function by gene-specific stabilization of CFTR mRNA.
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Affiliation(s)
- Young Jin Kim
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.,Graduate Program in Genetics, Stony Brook University, Stony Brook, NY, 11794, USA.,Medical Scientist Training Program, Stony Brook University School of Medicine, Stony Brook, NY, 11794, USA
| | - Tomoki Nomakuchi
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.,Medical Scientist Training Program, Stony Brook University School of Medicine, Stony Brook, NY, 11794, USA.,Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Foteini Papaleonidopoulou
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.,Francis Crick Institute, London, 1140062, UK
| | - Lucia Yang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.,Graduate Program in Genetics, Stony Brook University, Stony Brook, NY, 11794, USA.,Medical Scientist Training Program, Stony Brook University School of Medicine, Stony Brook, NY, 11794, USA
| | - Qian Zhang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.,Graduate Program in Molecular and Cell Biology, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Adrian R Krainer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.
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20
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Sanderlin EJ, Keenan MM, Mense M, Revenko AS, Monia BP, Guo S, Huang L. CFTR mRNAs with nonsense codons are degraded by the SMG6-mediated endonucleolytic decay pathway. Nat Commun 2022; 13:2344. [PMID: 35487895 PMCID: PMC9054838 DOI: 10.1038/s41467-022-29935-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 03/24/2022] [Indexed: 12/22/2022] Open
Abstract
Approximately 10% of cystic fibrosis patients harbor nonsense mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene which can generate nonsense codons in the CFTR mRNA and subsequently activate the nonsense-mediated decay (NMD) pathway resulting in rapid mRNA degradation. However, it is not known which NMD branches govern the decay of CFTR mRNAs containing nonsense codons. Here we utilize antisense oligonucleotides targeting NMD factors to evaluate the regulation of nonsense codon-containing CFTR mRNAs by the NMD pathway. We observe that CFTR mRNAs with nonsense codons G542X, R1162X, and W1282X, but not Y122X, require UPF2 and UPF3 for NMD. Furthermore, we demonstrate that all evaluated CFTR mRNAs harboring nonsense codons are degraded by the SMG6-mediated endonucleolytic pathway rather than the SMG5-SMG7-mediated exonucleolytic pathway. Finally, we show that upregulation of all evaluated CFTR mRNAs with nonsense codons by NMD pathway inhibition improves outcomes of translational readthrough therapy.
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Affiliation(s)
| | | | - Martin Mense
- Cystic Fibrosis Foundation Therapeutics Lab, Cystic Fibrosis Foundation, Lexington, MA, USA
| | | | | | - Shuling Guo
- Ionis Pharmaceuticals, Inc., Carlsbad, CA, USA
| | - Lulu Huang
- Ionis Pharmaceuticals, Inc., Carlsbad, CA, USA.
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21
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AAV-delivered suppressor tRNA overcomes a nonsense mutation in mice. Nature 2022; 604:343-348. [PMID: 35322228 PMCID: PMC9446716 DOI: 10.1038/s41586-022-04533-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 01/05/2022] [Indexed: 12/19/2022]
Abstract
Gene therapy is a potentially curative medicine for many currently untreatable diseases, and recombinant adeno-associated virus (rAAV) is the most successful gene delivery vehicle for in vivo applications1-3. However, rAAV-based gene therapy suffers from several limitations, such as constrained DNA cargo size and toxicities caused by non-physiological expression of a transgene4-6. Here we show that rAAV delivery of a suppressor tRNA (rAAV.sup-tRNA) safely and efficiently rescued a genetic disease in a mouse model carrying a nonsense mutation, and effects lasted for more than 6 months after a single treatment. Mechanistically, this was achieved through a synergistic effect of premature stop codon readthrough and inhibition of nonsense-mediated mRNA decay. rAAV.sup-tRNA had a limited effect on global readthrough at normal stop codons and did not perturb endogenous tRNA homeostasis, as determined by ribosome profiling and tRNA sequencing, respectively. By optimizing the AAV capsid and the route of administration, therapeutic efficacy in various target tissues was achieved, including liver, heart, skeletal muscle and brain. This study demonstrates the feasibility of developing a toolbox of AAV-delivered nonsense suppressor tRNAs operating on premature termination codons (AAV-NoSTOP) to rescue pathogenic nonsense mutations and restore gene function under endogenous regulation. As nonsense mutations account for 11% of pathogenic mutations, AAV-NoSTOP can benefit a large number of patients. AAV-NoSTOP obviates the need to deliver a full-length protein-coding gene that may exceed the rAAV packaging limit, elicit adverse immune responses or cause transgene-related toxicities. It therefore represents a valuable addition to gene therapeutics.
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22
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Integrity and Stability of PTC Bearing CFTR mRNA and Relevance to Future Modulator Therapies in Cystic Fibrosis. Genes (Basel) 2021; 12:genes12111810. [PMID: 34828417 PMCID: PMC8621375 DOI: 10.3390/genes12111810] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/16/2021] [Accepted: 11/18/2021] [Indexed: 12/26/2022] Open
Abstract
Major advances have recently been made in the development and application of CFTR (cystic fibrosis transmembrane conductance regulator) mutation class-specific modulator therapies, but to date, there are no approved modulators for Class I mutations, i.e., those introducing a premature termination codon (PTC) into the CFTR mRNA. Such mutations induce nonsense-mediated decay (NMD), a cellular quality control mechanism that reduces the quantity of PTC bearing mRNAs, presumably to avoid translation of potentially deleterious truncated CFTR proteins. The NMD-mediated reduction of PTC-CFTR mRNA molecules reduces the efficacy of one of the most promising approaches to treatment of such mutations, namely, PTC readthrough therapy, using molecules that induce the incorporation of near-cognate amino acids at the PTC codon, thereby enabling translation of a full-length protein. In this study, we measure the effect of three different PTC mutations on the abundance, integrity, and stability of respective CFTR mRNAs, using CFTR specific RT-qPCR-based assays. Altogether, our data suggest that optimized rescue of PTC mutations has to take into account (1) the different steady-state levels of the CFTR mRNA associated with each specific PTC mutation; (2) differences in abundance between the 3' and 5' regions of CFTR mRNA, even following PTC readthrough or NMD inhibition; and (3) variable effects on CFTR mRNA stability for each specific PTC mutation.
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23
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Comprehensive Analysis of Combinatorial Pharmacological Treatments to Correct Nonsense Mutations in the CFTR Gene. Int J Mol Sci 2021; 22:ijms222111972. [PMID: 34769402 PMCID: PMC8584557 DOI: 10.3390/ijms222111972] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 10/29/2021] [Accepted: 11/02/2021] [Indexed: 12/11/2022] Open
Abstract
Cystic fibrosis (CF) is caused by loss of function of the CFTR chloride channel. A substantial number of CF patients carry nonsense mutations in the CFTR gene. These patients cannot directly benefit from pharmacological correctors and potentiators that have been developed for other types of CFTR mutations. We evaluated the efficacy of combinations of drugs targeting at various levels the effects of nonsense mutations: SMG1i to protect CFTR mRNA from nonsense-mediated decay (NMD), G418 and ELX-02 for readthrough, VX-809 and VX-445 to promote protein maturation and function, PTI-428 to enhance CFTR protein synthesis. We found that the extent of rescue and sensitivity to the various agents is largely dependent on the type of mutation, with W1282X and R553X being the mutations most and least sensitive to pharmacological treatments, respectively. In particular, W1282X-CFTR was highly responsive to NMD suppression by SMG1i but also required treatment with VX-445 corrector to show function. In contrast, G542X-CFTR required treatment with readthrough agents and VX-809. Importantly, we never found cooperativity between the NMD inhibitor and readthrough compounds. Our results indicate that treatment of CF patients with nonsense mutations requires a precision medicine approach with the design of specific drug combinations for each mutation.
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24
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Functional Restoration of CFTR Nonsense Mutations in Intestinal Organoids. J Cyst Fibros 2021; 21:246-253. [PMID: 34666947 DOI: 10.1016/j.jcf.2021.09.020] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 09/16/2021] [Accepted: 09/17/2021] [Indexed: 11/20/2022]
Abstract
BACKGROUND Pharmacotherapies for people with cystic fibrosis (pwCF) who have premature termination codons (PTCs) in the cystic fibrosis transmembrane conductance regulator (CFTR) gene are under development. Thus far, clinical studies focused on compounds that induce translational readthrough (RT) at the mRNA PTC location. Recent studies using primary airway cells showed that PTC functional restoration can be achieved through combining compounds with multiple mode-of-actions. Here, we assessed induction of CFTR function in PTC-containing intestinal organoids using compounds targeting RT, nonsense mRNA mediated decay (NMD) and CFTR protein modulation. METHODS Rescue of PTC CFTR protein was assessed by forskolin-induced swelling of 12 intestinal organoid cultures carrying distinct PTC mutations. Effects of compounds on mRNA CFTR level was assessed by RT-qPCRs. RESULTS Whilst response varied between donors, significant rescue of CFTR function was achieved for most donors with the quintuple combination of a commercially available pharmacological equivalent of the RT compound (ELX-02-disulfate or ELX-02ds), NMD inhibitor SMG1i, correctors VX-445 and VX-661 and potentiator VX-770. The quintuple combination of pharmacotherapies reached swelling quantities higher than the mean swelling of three VX-809/VX-770-rescued F508del/F508del organoid cultures, indicating level of rescue is of clinical relevance as VX-770/VX-809-mediated F508del/F508del rescue in organoids correlate with substantial improvement of clinical outcome. CONCLUSIONS Whilst variation in efficacy was observed between genotypes as well as within genotypes, the data suggests that strong pharmacological rescue of PTC requires a combination of drugs that target RT, NMD and protein function.
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25
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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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26
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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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27
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Sharma J, Du M, Wong E, Mutyam V, Li Y, Chen J, Wangen J, Thrasher K, Fu L, Peng N, Tang L, Liu K, Mathew B, Bostwick RJ, Augelli-Szafran CE, Bihler H, Liang F, Mahiou J, Saltz J, Rab A, Hong J, Sorscher EJ, Mendenhall EM, Coppola CJ, Keeling KM, Green R, Mense M, Suto MJ, Rowe SM, Bedwell DM. A small molecule that induces translational readthrough of CFTR nonsense mutations by eRF1 depletion. Nat Commun 2021; 12:4358. [PMID: 34272367 PMCID: PMC8285393 DOI: 10.1038/s41467-021-24575-x] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/22/2021] [Indexed: 11/09/2022] Open
Abstract
Premature termination codons (PTCs) prevent translation of a full-length protein and trigger nonsense-mediated mRNA decay (NMD). Nonsense suppression (also termed readthrough) therapy restores protein function by selectively suppressing translation termination at PTCs. Poor efficacy of current readthrough agents prompted us to search for better compounds. An NMD-sensitive NanoLuc readthrough reporter was used to screen 771,345 compounds. Among the 180 compounds identified with readthrough activity, SRI-37240 and its more potent derivative SRI-41315, induce a prolonged pause at stop codons and suppress PTCs associated with cystic fibrosis in immortalized and primary human bronchial epithelial cells, restoring CFTR expression and function. SRI-41315 suppresses PTCs by reducing the abundance of the termination factor eRF1. SRI-41315 also potentiates aminoglycoside-mediated readthrough, leading to synergistic increases in CFTR activity. Combining readthrough agents that target distinct components of the translation machinery is a promising treatment strategy for diseases caused by PTCs. Premature termination codons can cause early translation termination and lead to disease. Here the authors perform a screen to identify compounds with readthrough activity and show that these reduce eRF1 levels to suppress premature termination associated with cystic fibrosis.
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Affiliation(s)
- Jyoti Sharma
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham (UAB), Birmingham, AL, USA.,Department of Medicine, University of Alabama at Birmingham (UAB), Birmingham, AL, USA.,Department of Microbiology, University of Alabama at Birmingham (UAB), Birmingham, AL, USA
| | - Ming Du
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham (UAB), Birmingham, AL, USA.,Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham (UAB), Birmingham, AL, USA
| | - Eric Wong
- CFFT Lab, Cystic Fibrosis Foundation, Lexington, MA, USA
| | - Venkateshwar Mutyam
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham (UAB), Birmingham, AL, USA.,Department of Medicine, University of Alabama at Birmingham (UAB), Birmingham, AL, USA
| | - Yao Li
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham (UAB), Birmingham, AL, USA.,Department of Medicine, University of Alabama at Birmingham (UAB), Birmingham, AL, USA
| | - Jianguo Chen
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham (UAB), Birmingham, AL, USA.,Department of Medicine, University of Alabama at Birmingham (UAB), Birmingham, AL, USA
| | - Jamie Wangen
- Department of Molecular Biology and Genetics and Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kari Thrasher
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham (UAB), Birmingham, AL, USA.,Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham (UAB), Birmingham, AL, USA
| | - Lianwu Fu
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham (UAB), Birmingham, AL, USA.,Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham (UAB), Birmingham, AL, USA
| | - Ning Peng
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham (UAB), Birmingham, AL, USA.,Department of Medicine, University of Alabama at Birmingham (UAB), Birmingham, AL, USA
| | - Liping Tang
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham (UAB), Birmingham, AL, USA.,Department of Medicine, University of Alabama at Birmingham (UAB), Birmingham, AL, USA
| | - Kaimao Liu
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham (UAB), Birmingham, AL, USA.,Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham (UAB), Birmingham, AL, USA
| | | | | | | | - Hermann Bihler
- CFFT Lab, Cystic Fibrosis Foundation, Lexington, MA, USA
| | - Feng Liang
- CFFT Lab, Cystic Fibrosis Foundation, Lexington, MA, USA
| | - Jerome Mahiou
- CFFT Lab, Cystic Fibrosis Foundation, Lexington, MA, USA
| | - Josef Saltz
- CFFT Lab, Cystic Fibrosis Foundation, Lexington, MA, USA
| | - Andras Rab
- Department of Pediatrics, Emory University, Atlanta, Georgia
| | - Jeong Hong
- Department of Pediatrics, Emory University, Atlanta, Georgia
| | - Eric J Sorscher
- Department of Pediatrics, Emory University, Atlanta, Georgia
| | - Eric M Mendenhall
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL, USA
| | - Candice J Coppola
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL, USA
| | - Kim M Keeling
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham (UAB), Birmingham, AL, USA.,Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham (UAB), Birmingham, AL, USA
| | - Rachel Green
- Department of Molecular Biology and Genetics and Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Martin Mense
- CFFT Lab, Cystic Fibrosis Foundation, Lexington, MA, USA
| | | | - Steven M Rowe
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham (UAB), Birmingham, AL, USA.,Department of Medicine, University of Alabama at Birmingham (UAB), Birmingham, AL, USA.,Department of Pediatrics, University of Alabama at Birmingham (UAB), Birmingham, AL, USA
| | - David M Bedwell
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham (UAB), Birmingham, AL, USA. .,Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham (UAB), Birmingham, AL, USA.
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28
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Luna S, Torices L, Mingo J, Amo L, Rodríguez-Escudero I, Ruiz-Ibarlucea P, Erramuzpe A, Cortés JM, Tejada MI, Molina M, Nunes-Xavier CE, López JI, Cid VJ, Pulido R. A global analysis of the reconstitution of PTEN function by translational readthrough of PTEN pathogenic premature termination codons. Hum Mutat 2021; 42:551-566. [PMID: 33600059 DOI: 10.1002/humu.24186] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 01/15/2021] [Accepted: 02/14/2021] [Indexed: 12/29/2022]
Abstract
The PTEN tumor suppressor gene is mutated with high incidence in tumors and in the germline of patients with cancer predisposition or with macrocephaly associated with autism. PTEN nonsense mutations generating premature termination codons (PTC) and producing nonfunctional truncated PTEN proteins are frequent in association with human disease. However, there are no studies addressing the restoration of full-length PTEN proteins from the PTC-mutated PTEN gene by translational readthrough. Here, we have performed a global translational and functional readthrough analysis of the complete collection of PTEN PTC somatic or hereditary mutations found in tumors or in the germline of patients (disease-associated PTEN PTCome), and we set standards for the analysis of the potential of readthrough functional reconstitution in disease-relevant genes. Our analysis indicates that prevalent pathogenic PTEN PTC mutations are susceptible to PTEN functional restoration in response to readthrough-inducing compounds. Comprehensive readthrough analyses of disease-associated PTComes will be valuable tools for the implementation of readthrough-based precision interventions in specific groups of patients.
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Affiliation(s)
- Sandra Luna
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Leire Torices
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Janire Mingo
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Laura Amo
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Isabel Rodríguez-Escudero
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, UCM & Instituto Ramón y Cajal de Investigaciones Sanitarias (IRYCIS), Madrid, Spain
| | | | - Asier Erramuzpe
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Jesús M Cortés
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain.,Ikerbasque, The Basque Foundation for Science, Bilbao, Spain
| | - María I Tejada
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - María Molina
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, UCM & Instituto Ramón y Cajal de Investigaciones Sanitarias (IRYCIS), Madrid, Spain
| | - Caroline E Nunes-Xavier
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain.,Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - José I López
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain.,Department of Pathology, Cruces University Hospital, Barakaldo, Spain
| | - Víctor J Cid
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, UCM & Instituto Ramón y Cajal de Investigaciones Sanitarias (IRYCIS), Madrid, Spain
| | - Rafael Pulido
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain.,Ikerbasque, The Basque Foundation for Science, Bilbao, Spain
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29
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Targeting G542X CFTR nonsense alleles with ELX-02 restores CFTR function in human-derived intestinal organoids. J Cyst Fibros 2021; 20:436-442. [PMID: 33558100 DOI: 10.1016/j.jcf.2021.01.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/19/2020] [Accepted: 01/21/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND Promoting full-length protein production is a requisite step to address some of the remaining unmet medical need for those with Cystic Fibrosis (CF) nonsense alleles. ELX-02 promotes read-through of mRNA transcripts bearing nonsense mutations, including the most common CF nonsense allele G542X, in several different preclinical models including human bronchial epithelial cells. Here we evaluate ELX-02 mediated read-through using the CFTR-dependent Forskolin-induced swelling (FIS) assay across a selection of G542X genotype patient derived organoids (PDOs). METHODS CFTR functional restoration was evaluated in ELX-02 treated G542X homozygous and heterozygous PDOs in the CFTR-dependent FIS assay. CFTR mRNA abundance and integrity were evaluated by qPCR and Nanostring analysis while PDO protein was detected by capillary based size-exclusion chromatography. RESULTS PDOs homozygous for G542X or heterozygous with a second minimally functional allele had significantly increased CFTR activity with ELX-02 in a dose-dependent fashion across a variety of forskolin induction concentrations. The functional increases are similar to those obtained with tezacaftor/ivacaftor in F508del homozygous PDOs. Increased CFTR C- and B-band protein was observed in accordance with increased function. In addition, ELX-02 treatment of a G542X/G542X PDO results in a 5-fold increase in CFTR mRNA compared with vehicle treated, resulting in normalization of CFTR mRNA as measured via Nanostring. CONCLUSIONS These data with ELX-02 in PDOs are consistent with previous G542X model evaluations. These results also support the on-going clinical evaluation of ELX-02 as a read-through agent for CF caused by the G542X allele.
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30
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McHugh DR, Cotton CU, Hodges CA. Synergy between Readthrough and Nonsense Mediated Decay Inhibition in a Murine Model of Cystic Fibrosis Nonsense Mutations. Int J Mol Sci 2020; 22:ijms22010344. [PMID: 33396210 PMCID: PMC7794695 DOI: 10.3390/ijms22010344] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 12/17/2020] [Accepted: 12/29/2020] [Indexed: 12/15/2022] Open
Abstract
Many heritable genetic disorders arise from nonsense mutations, which generate premature termination codons (PTCs) in transcribed mRNA. PTCs ablate protein synthesis by prematurely terminating the translation of mutant mRNA, as well as reducing mutant mRNA quantity through targeted degradation by nonsense-mediated decay (NMD) mechanisms. Therapeutic strategies for nonsense mutations include facilitating ribosomal readthrough of the PTC and/or inhibiting NMD to restore protein function. However, the efficacy of combining readthrough agents and NMD inhibitors has not been thoroughly explored. In this study, we examined combinations of known NMD inhibitors and readthrough agents using functional analysis of the CFTR protein in primary cells from a mouse model carrying a G542X nonsense mutation in Cftr. We observed synergy between an inhibitor of the NMD component SMG-1 (SMG1i) and the readthrough agents G418, gentamicin, and paromomycin, but did not observe synergy with readthrough caused by amikacin, tobramycin, PTC124, escin, or amlexanox. These results indicate that treatment with NMD inhibitors can increase the quantity of functional protein following readthrough, and that combining NMD inhibitors and readthrough agents represents a potential therapeutic option for treating nonsense mutations.
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Affiliation(s)
- Daniel R. McHugh
- Department of Genetics and Genome Sciences, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH 44106, USA;
| | - Calvin U. Cotton
- Department of Pediatrics, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH 44106, USA;
- Department of Physiology and Biophysics, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH 44106, USA
| | - Craig A. Hodges
- Department of Genetics and Genome Sciences, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH 44106, USA;
- Department of Pediatrics, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH 44106, USA;
- Correspondence:
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31
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Palma M, Lejeune F. Deciphering the molecular mechanism of stop codon readthrough. Biol Rev Camb Philos Soc 2020; 96:310-329. [PMID: 33089614 DOI: 10.1111/brv.12657] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 09/23/2020] [Accepted: 09/26/2020] [Indexed: 12/11/2022]
Abstract
Recognition of the stop codon by the translation machinery is essential to terminating translation at the right position and to synthesizing a protein of the correct size. Under certain conditions, the stop codon can be recognized as a coding codon promoting translation, which then terminates at a later stop codon. This event, called stop codon readthrough, occurs either by error, due to a dedicated regulatory environment leading to generation of different protein isoforms, or through the action of a readthrough compound. This review focuses on the mechanisms of stop codon readthrough, the nucleotide and protein environments that facilitate or inhibit it, and the therapeutic interest of stop codon readthrough in the treatment of genetic diseases caused by nonsense mutations.
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Affiliation(s)
- Martine Palma
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR9020 - U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France
| | - Fabrice Lejeune
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR9020 - U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, F-59000 Lille, France
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32
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Wei T, Sui H, Su Y, Cheng W, Liu Y, He Z, Ji Q, Xu C. Research advances in molecular mechanisms underlying the pathogenesis of cystic fibrosis: From technical improvement to clinical applications (Review). Mol Med Rep 2020; 22:4992-5002. [PMID: 33173976 PMCID: PMC7646950 DOI: 10.3892/mmr.2020.11607] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 09/17/2020] [Indexed: 12/11/2022] Open
Abstract
Cystic fibrosis (CF) is a chronic disease causing severe impairment to the respiratory system and digestive tracts. Currently, CF is incurable. As an autosomal recessive disorder, the morbidity of CF is significantly higher among Caucasians of European descent, whereas it is less pervasive among African and Asian populations. The disease is caused by identical mutations (homozygosity) or different mutations (heterozygosity) of an autosomal recessive mutation at position 7q31.2-q31.1 of chromosome 7. Diagnostic criteria and guidelines work concurrently with laboratory detection to facilitate precise CF detection. With technological advances, the understanding of CF pathogenesis has reached an unprecedented level, allowing for increasingly precise carrier screening, more effective early stage CF intervention and improved prognostic outcomes. These advances significantly increase the life quality and expectancy of patients with CF. Given the numerous improvements in the field of CF, the current review summarized the technical advances in the study of the molecular mechanisms underlying CF, as well as how these improvements facilitate the clinical outcomes of CF. Furthermore, challenges and obstacles to overcome are discussed.
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Affiliation(s)
- Tao Wei
- Department of Histology and Embryology, Shandong First Medical University and Shandong Academy of Medical Sciences, Tai'an, Shandong 271000, P.R. China
| | - Hongshu Sui
- Department of Histology and Embryology, Shandong First Medical University and Shandong Academy of Medical Sciences, Tai'an, Shandong 271000, P.R. China
| | - Yanping Su
- Department of Histology and Embryology, Shandong First Medical University and Shandong Academy of Medical Sciences, Tai'an, Shandong 271000, P.R. China
| | - Wanjing Cheng
- Department of Histology and Embryology, Shandong First Medical University and Shandong Academy of Medical Sciences, Tai'an, Shandong 271000, P.R. China
| | - Yunhua Liu
- Department of Histology and Embryology, Shandong First Medical University and Shandong Academy of Medical Sciences, Tai'an, Shandong 271000, P.R. China
| | - Zilin He
- Department of Histology and Embryology, Shandong First Medical University and Shandong Academy of Medical Sciences, Tai'an, Shandong 271000, P.R. China
| | - Qingchao Ji
- Department of Histology and Embryology, Shandong First Medical University and Shandong Academy of Medical Sciences, Tai'an, Shandong 271000, P.R. China
| | - Changlong Xu
- Reproductive Medical Center, Nanning Second People's Hospital, Nanning, Guangxi Zhuang Autonomous Region 530031, P.R. China
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33
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Kerem E. ELX-02: an investigational read-through agent for the treatment of nonsense mutation-related genetic disease. Expert Opin Investig Drugs 2020; 29:1347-1354. [DOI: 10.1080/13543784.2020.1828862] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Eitan Kerem
- Department of Pediatrics and CF Center, Hadassah Hebrew University Medical Center, Jerusalem, Israel
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34
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Smith E, Dukovski D, Shumate J, Scampavia L, Miller JP, Spicer TP. Identification of Compounds That Promote Readthrough of Premature Termination Codons in the CFTR. SLAS DISCOVERY 2020; 26:205-215. [PMID: 33016182 PMCID: PMC7838340 DOI: 10.1177/2472555220962001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Cystic fibrosis (CF) is caused by a mutation of the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene, which disrupts an ion channel involved in hydration maintenance via anion homeostasis. Nearly 5% of CF patients possess one or more copies of the G542X allele, which results in a stop codon at residue 542, preventing full-length CFTR protein synthesis. Identifying small-molecule modulators of mutant CFTR biosynthesis that affect the readthrough of this and other premature termination codons to synthesize a fully functional CFTR protein represents a novel target area of drug discovery. We describe the implementation and integration for large-scale screening of a homogeneous, 1536-well functional G542X-CFTR readthrough assay. The assay uses HEK 293 cells engineered to overexpress the G542X-CFTR mutant, whose functional activity is monitored with a membrane potential dye. Cells are co-incubated with a CFTR amplifier and CFTR corrector to maximize mRNA levels and trafficking of CFTR to the cell surface. Compounds that allow translational readthrough and synthesis of functional CFTR chloride channels are reflected by changes in membrane potential in response to cAMP stimulation with forskolin and CFTR channel potentiation with genistein. Assay statistics yielded Z′ values of 0.69 ± 0.06. As further evidence of its suitability for high-throughput screening, we completed automated screening of approximately 666,000 compounds, identifying 7761 initial hits. Following secondary and tertiary assays, we identified 188 confirmed hit compounds with low and submicromolar potencies. Thus, this approach takes advantage of a phenotypic screen with high-throughput scalability to identify new small-molecule G542X-CFTR readthrough modulators.
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Affiliation(s)
- Emery Smith
- Department of Molecular Medicine, Scripps Florida, The Scripps Research Institute Molecular Screening Center, Jupiter, FL, USA
| | | | - Justin Shumate
- Department of Molecular Medicine, Scripps Florida, The Scripps Research Institute Molecular Screening Center, Jupiter, FL, USA
| | - Louis Scampavia
- Department of Molecular Medicine, Scripps Florida, The Scripps Research Institute Molecular Screening Center, Jupiter, FL, USA
| | | | - Timothy P Spicer
- Department of Molecular Medicine, Scripps Florida, The Scripps Research Institute Molecular Screening Center, Jupiter, FL, USA
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35
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Michaels WE, Bridges RJ, Hastings ML. Antisense oligonucleotide-mediated correction of CFTR splicing improves chloride secretion in cystic fibrosis patient-derived bronchial epithelial cells. Nucleic Acids Res 2020; 48:7454-7467. [PMID: 32520327 PMCID: PMC7367209 DOI: 10.1093/nar/gkaa490] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 05/22/2020] [Accepted: 06/05/2020] [Indexed: 12/27/2022] Open
Abstract
Cystic fibrosis (CF) is an autosomal recessive disorder caused by mutations in the CF transmembrane conductance regulator (CFTR) gene, encoding an anion channel that conducts chloride and bicarbonate across epithelial membranes. Mutations that disrupt pre-mRNA splicing occur in >15% of CF cases. One common CFTR splicing mutation is CFTR c.3718-2477C>T (3849+10 kb C>T), which creates a new 5′ splice site, resulting in splicing to a cryptic exon with a premature termination codon. Splice-switching antisense oligonucleotides (ASOs) have emerged as an effective therapeutic strategy to block aberrant splicing. We test an ASO targeting the CFTR c.3718-2477C>T mutation and show that it effectively blocks aberrant splicing in primary bronchial epithelial (hBE) cells from CF patients with the mutation. ASO treatment results in long-term improvement in CFTR activity in hBE cells, as demonstrated by a recovery of chloride secretion and apical membrane conductance. We also show that the ASO is more effective at recovering chloride secretion in our assay than ivacaftor, the potentiator treatment currently available to these patients. Our findings demonstrate the utility of ASOs in correcting CFTR expression and channel activity in a manner expected to be therapeutic in patients.
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Affiliation(s)
- Wren E Michaels
- Center for Genetic Diseases, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60064, USA.,School of Graduate and Postdoctoral Studies, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60064, USA
| | - Robert J Bridges
- Center for Genetic Diseases, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60064, USA
| | - Michelle L Hastings
- Center for Genetic Diseases, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60064, USA
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36
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Mall MA, Mayer-Hamblett N, Rowe SM. Cystic Fibrosis: Emergence of Highly Effective Targeted Therapeutics and Potential Clinical Implications. Am J Respir Crit Care Med 2020; 201:1193-1208. [PMID: 31860331 DOI: 10.1164/rccm.201910-1943so] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Cystic fibrosis (CF) remains the most common life-shortening hereditary disease in white populations, with high morbidity and mortality related to chronic airway mucus obstruction, inflammation, infection, and progressive lung damage. In 1989, the discovery that CF is caused by mutations in the CFTR (cystic fibrosis transmembrane conductance regulator) gene that encodes a cAMP-dependent anion channel vital for proper Cl- and HCO3- transport across epithelial surfaces provided a solid foundation for unraveling underlying disease mechanisms and the development of therapeutics targeting the basic defect in people with CF. In this review, we focus on recent advances in our understanding of the molecular defects caused by different classes of CFTR mutations, implications for pharmacological rescue of mutant CFTR, and insights into how CFTR dysfunction impairs key host defense mechanisms, such as mucociliary clearance and bacterial killing in CF airways. Furthermore, we review the path that led to the recent breakthrough in the development of highly effective CFTR-directed therapeutics, now applicable for up to 90% of people with CF who carry responsive CFTR mutations, including those with just a single copy of the most common F508del mutation. Finally, we discuss the remaining challenges and strategies to develop highly effective targeted therapies for all patients and the unprecedented potential of these novel therapies to transform CF from a fatal to a treatable chronic condition.
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Affiliation(s)
- Marcus A Mall
- Department of Pediatric Pulmonology, Immunology, and Intensive Care Medicine, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,German Center for Lung Research (DZL), Berlin, Germany
| | - Nicole Mayer-Hamblett
- Department of Pediatrics and.,Department of Biostatistics, University of Washington, Seattle, Washington.,Seattle Children's Hospital, Seattle, Washington
| | - Steven M Rowe
- Department of Medicine.,Department of Pediatrics, and.,Department of Cell, Developmental and Integrative Biology, Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama
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37
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Investigating REPAIRv2 as a Tool to Edit CFTR mRNA with Premature Stop Codons. Int J Mol Sci 2020; 21:ijms21134781. [PMID: 32640650 PMCID: PMC7369808 DOI: 10.3390/ijms21134781] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/03/2020] [Accepted: 07/04/2020] [Indexed: 12/21/2022] Open
Abstract
Cystic fibrosis (CF) is caused by mutations in the gene encoding the transmembrane conductance regulator (CFTR) protein. Some CF patients are compound heterozygous or homozygous for nonsense mutations in the CFTR gene. This implies the presence in the transcript of premature termination codons (PTCs) responsible for a truncated CFTR protein and a more severe form of the disease. Aminoglycoside and PTC124 derivatives have been used for the read-through of PTCs to restore the full-length CFTR protein. However, in a precision medicine framework, the CRISPR/dCas13b-based molecular tool “REPAIRv2” (RNA Editing for Programmable A to I Replacement, version 2) could be a good alternative to restore the full-length CFTR protein. This RNA editing approach is based on the targeting of the deaminase domain of the hADAR2 enzyme fused to the dCas13b protein to a specific adenosine to be edited to inosine in the mutant mRNA. Targeting specificity is allowed by a guide RNA (gRNA) complementarily to the target region and recognized by the dCas13b protein. Here, we used the REPAIRv2 platform to edit the UGA PTC to UGG in different cell types, namely IB3-1 cells, HeLa, and FRT cells engineered to express H2BGFPopal and CFTRW1282X, respectively.
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38
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Konstan MW, VanDevanter DR, Rowe SM, Wilschanski M, Kerem E, Sermet-Gaudelus I, DiMango E, Melotti P, McIntosh J, De Boeck K. Efficacy and safety of ataluren in patients with nonsense-mutation cystic fibrosis not receiving chronic inhaled aminoglycosides: The international, randomized, double-blind, placebo-controlled Ataluren Confirmatory Trial in Cystic Fibrosis (ACT CF). J Cyst Fibros 2020; 19:595-601. [PMID: 31983658 PMCID: PMC9167581 DOI: 10.1016/j.jcf.2020.01.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 01/17/2020] [Indexed: 12/18/2022]
Abstract
BACKGROUND Ataluren was developed for potential treatment of nonsense-mutation cystic fibrosis (CF). A previous phase 3 ataluren study failed to meet its primary efficacy endpoint, but post-hoc analyses suggested that aminoglycosides may have interfered with ataluren's action. Thus, this subsequent trial (NCT02139306) was designed to assess the efficacy and safety of ataluren in patients with nonsense-mutation CF not receiving aminoglycosides. METHODS Eligible subjects with nonsense-mutation CF (aged ≥6 years; percent predicted (pp) FEV1 ≥40 and ≤90) from 75 sites in 16 countries were randomly assigned in double-blinded fashion to receive oral ataluren or matching placebo thrice daily for 48 weeks. The primary endpoint was absolute change in average ppFEV1 from baseline to the average of Weeks 40 and 48. FINDINGS 279 subjects were enrolled; 138 subjects in the ataluren arm and 136 in the placebo arm were evaluable for efficacy. Absolute ppFEV1 change from baseline did not differ significantly between the ataluren and placebo groups at Week 40 (-0.8 vs -1.8) or Week 48 (-1.7 vs -2.4). Average ppFEV1 treatment difference from baseline to Weeks 40 and 48 was 0.6 (95% CI -1.3, 2.5; p = 0.54). Pulmonary exacerbation rate per 48 weeks was not significantly different (ataluren 0.95 vs placebo 1.13; rate ratio p = 0.40). Safety was similar between groups. No life-threatening adverse events or deaths were reported. INTERPRETATION Neither ppFEV1 change nor pulmonary exacerbation rate over 48 weeks were statistically different between ataluren and placebo groups. Development of a nonsense-mutation CF therapy remains elusive.
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Affiliation(s)
- M W Konstan
- Rainbow Babies and Children's Hospital, Cleveland, OH 44106 USA; Case Western Reserve University School of Medicine, Cleveland, OH 44106 USA.
| | - D R VanDevanter
- Case Western Reserve University School of Medicine, Cleveland, OH 44106 USA
| | - S M Rowe
- Pulmonary and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, AL 35249 USA
| | - M Wilschanski
- Center for Cystic Fibrosis, Hadassah Hebrew University Medical Center, Jerusalem, 91240, Israel
| | - E Kerem
- Center for Cystic Fibrosis, Hadassah Hebrew University Medical Center, Jerusalem, 91240, Israel
| | - I Sermet-Gaudelus
- Centre de Ressource et de Competence de la Mucoviscidose, Service de Pediatrie Generale, Service de Pneumologie Pediatrique, Service de Radiologie Pediatrique, Centre d'Investigation Clinique Hôpital Necker - Enfants Malades, 75015 Paris, France
| | - E DiMango
- Pulmonary, Allergy, and Critical Care Medicine, Columbia University, Department of Medicine, New York, NY 10032 USA
| | - P Melotti
- Centro Fibrosi Cistica, Azienda Ospedaliera Universitaria Integrata, Verona, Italy
| | - J McIntosh
- PTC Therapeutics, South Plainfield, NJ 07080 USA
| | - K De Boeck
- Pediatric Pulmonology and Infectious Diseases, University Hospital of Leuven, University of Leuven, Belgium
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Leier A, Bedwell DM, Chen AT, Dickson G, Keeling KM, Kesterson RA, Korf BR, Marquez Lago TT, Müller UF, Popplewell L, Zhou J, Wallis D. Mutation-Directed Therapeutics for Neurofibromatosis Type I. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 20:739-753. [PMID: 32408052 PMCID: PMC7225739 DOI: 10.1016/j.omtn.2020.04.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 04/20/2020] [Accepted: 04/23/2020] [Indexed: 02/07/2023]
Abstract
Significant advances in biotechnology have led to the development of a number of different mutation-directed therapies. Some of these techniques have matured to a level that has allowed testing in clinical trials, but few have made it to approval by drug-regulatory bodies for the treatment of specific diseases. While there are still various hurdles to be overcome, recent success stories have proven the potential power of mutation-directed therapies and have fueled the hope of finding therapeutics for other genetic disorders. In this review, we summarize the state-of-the-art of various therapeutic approaches and assess their applicability to the genetic disorder neurofibromatosis type I (NF1). NF1 is caused by the loss of function of neurofibromin, a tumor suppressor and downregulator of the Ras signaling pathway. The condition is characterized by a variety of phenotypes and includes symptoms such as skin spots, nervous system tumors, skeletal dysplasia, and others. Hence, depending on the patient, therapeutics may need to target different tissues and cell types. While we also discuss the delivery of therapeutics, in particular via viral vectors and nanoparticles, our main focus is on therapeutic techniques that reconstitute functional neurofibromin, most notably cDNA replacement, CRISPR-based DNA repair, RNA repair, antisense oligonucleotide therapeutics including exon skipping, and nonsense suppression.
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Affiliation(s)
- Andre Leier
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - David M Bedwell
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Ann T Chen
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
| | - George Dickson
- Centre of Biomedical Sciences, Department of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK
| | - Kim M Keeling
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Robert A Kesterson
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Bruce R Korf
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | | | - Ulrich F Müller
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
| | - Linda Popplewell
- Centre of Biomedical Sciences, Department of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK
| | - Jiangbing Zhou
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
| | - Deeann Wallis
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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40
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Wang X, Shan X, Gregory-Evans K, Gregory-Evans CY. RNA-based therapies in animal models of Leber congenital amaurosis causing blindness. PRECISION CLINICAL MEDICINE 2020; 3:113-126. [PMID: 35692607 PMCID: PMC8985810 DOI: 10.1093/pcmedi/pbaa009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/05/2020] [Accepted: 03/10/2020] [Indexed: 11/14/2022] Open
Abstract
Abstract
Leber congenital amaurosis (LCA) is a severe, genetically heterogeneous recessive eye disease in which ~ 35% of gene mutations are in-frame nonsense mutations coding for loss-of-function premature termination codons (PTCs) in mRNA. Nonsense suppression therapy allows read-through of PTCs leading to production of full-length protein. A limitation of nonsense suppression is that nonsense-mediated decay (NMD) degrades PTC-containing RNA transcripts. The purpose of this study was to determine whether inhibition of NMD could improve nonsense suppression efficacy in vivo. Using a high-throughput approach in the recessive cep290 zebrafish model of LCA (cep290;Q1223X), we first tested the NMD inhibitor Amlexanox in combination with the nonsense suppression drug Ataluren. We observed reduced retinal cell death and improved visual function. With these positive data, we next investigated whether this strategy was also applicable across species in two mammalian models: Rd12 (rpe65;R44X) and Rd3 (rd3;R107X) mouse models of LCA. In the Rd12 model, cell death was reduced, RPE65 protein was produced, and in vivo visual function testing was improved. We establish for the first time that the mechanism of action of Amlexanox in Rd12 retina was through reduced UPF1 phosphorylation. In the Rd3 model, however, no beneficial effect was observed with Ataluren alone or in combination with Amlexanox. This variation in response establishes that some forms of nonsense mutation LCA can be targeted by RNA therapies, but that this needs to be verified for each genotype. The implementation of precision medicine by identifying better responders to specific drugs is essential for development of validated retinal therapies.
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Affiliation(s)
- Xia Wang
- Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver BC V5Z 3N9, Canada
| | - Xianghong Shan
- Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver BC V5Z 3N9, Canada
| | - Kevin Gregory-Evans
- Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver BC V5Z 3N9, Canada
| | - Cheryl Y Gregory-Evans
- Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver BC V5Z 3N9, Canada
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41
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Sharma J, Keeling KM, Rowe SM. Pharmacological approaches for targeting cystic fibrosis nonsense mutations. Eur J Med Chem 2020; 200:112436. [PMID: 32512483 DOI: 10.1016/j.ejmech.2020.112436] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/04/2020] [Accepted: 05/06/2020] [Indexed: 12/11/2022]
Abstract
Cystic fibrosis (CF) is a monogenic autosomal recessive disorder. The clinical manifestations of the disease are caused by ∼2,000 mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) protein. It is unlikely that any one approach will be efficient in correcting all defects. The recent approvals of ivacaftor, lumacaftor/ivacaftor and elexacaftor/tezacaftor/ivacaftor represent the genesis of a new era of precision combination medicine for the CF patient population. In this review, we discuss targeted translational readthrough approaches as mono and combination therapies for CFTR nonsense mutations. We examine the current status of efficacy of translational readthrough/nonsense suppression therapies and their limitations, including non-native amino acid incorporation at PTCs and nonsense-mediated mRNA decay (NMD), along with approaches to tackle these limitations. We further elaborate on combining various therapies such as readthrough agents, NMD inhibitors, and corrector/potentiators to improve the efficacy and safety of suppression therapy. These mutation specific strategies that are directed towards the basic CF defects should positively impact CF patients bearing nonsense mutations.
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Affiliation(s)
- Jyoti Sharma
- Department of Medicine, University of Alabama at Birmingham (UAB), USA; Department of Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham (UAB), USA
| | - Kim M Keeling
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham (UAB), USA; Department of Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham (UAB), USA
| | - Steven M Rowe
- Department of Medicine, University of Alabama at Birmingham (UAB), USA; Department of Pediatrics, University of Alabama at Birmingham (UAB), USA; Department of Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham (UAB), USA.
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42
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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: 280] [Impact Index Per Article: 70.0] [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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43
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Wangen JR, Green R. Stop codon context influences genome-wide stimulation of termination codon readthrough by aminoglycosides. eLife 2020; 9:52611. [PMID: 31971508 PMCID: PMC7089771 DOI: 10.7554/elife.52611] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 01/22/2020] [Indexed: 12/14/2022] Open
Abstract
Stop codon readthrough (SCR) occurs when the ribosome miscodes at a stop codon. Such readthrough events can be therapeutically desirable when a premature termination codon (PTC) is found in a critical gene. To study SCR in vivo in a genome-wide manner, we treated mammalian cells with aminoglycosides and performed ribosome profiling. We find that in addition to stimulating readthrough of PTCs, aminoglycosides stimulate readthrough of normal termination codons (NTCs) genome-wide. Stop codon identity, the nucleotide following the stop codon, and the surrounding mRNA sequence context all influence the likelihood of SCR. In comparison to NTCs, downstream stop codons in 3′UTRs are recognized less efficiently by ribosomes, suggesting that targeting of critical stop codons for readthrough may be achievable without general disruption of translation termination. Finally, we find that G418-induced miscoding alters gene expression with substantial effects on translation of histone genes, selenoprotein genes, and S-adenosylmethionine decarboxylase (AMD1). Many genes provide a set of instructions needed to build a protein, which are read by structures called ribosomes through a process called translation. The genetic information contains a short, coded instruction called a stop codon which marks the end of the protein. When a ribosome finds a stop codon it should stop building and release the protein it has made. Ribosomes do not always stop at stop codons. Certain chemicals can actually prevent ribosomes from detecting stop codons correctly, and aminoglycosides are drugs that have exactly this effect. Aminoglycosides can be used as antibiotics at low doses because they interfere with ribosomes in bacteria, but at higher doses they can also prevent ribosomes from detecting stop codons in human cells. When ribosomes do not stop at a stop codon this is called readthrough. There are different types of stop codons and some are naturally more effective at stopping ribosomes than others. Wangen and Green have now examined the effect of an aminoglycoside called G418 on ribosomes in human cells grown in the laboratory. The results showed how ribosomes interacted with genetic information and revealed that certain stop codons are more affected by G418 than others. The stop codon and other genetic sequences around it affect the likelihood of readthrough. Wangen and Green also showed that sequences that encourage translation to stop are more common in the area around stop codons. These findings highlight an evolutionary pressure driving more genes to develop strong stop codons that resist readthrough. Despite this, some are still more affected by drugs like G418 than others. Some genetic conditions, like cystic fibrosis, result from incorrect stop codons in genes. Drugs that promote readthrough specifically in these genes could be useful new treatments.
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Affiliation(s)
- Jamie R Wangen
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Rachel Green
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, United States
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Screening Readthrough Compounds to Suppress Nonsense Mutations: Possible Application to β-Thalassemia. J Clin Med 2020; 9:jcm9020289. [PMID: 31972957 PMCID: PMC7073686 DOI: 10.3390/jcm9020289] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 01/08/2020] [Accepted: 01/13/2020] [Indexed: 02/07/2023] Open
Abstract
Several types of thalassemia (including β039-thalassemia) are caused by nonsense mutations in genes controlling globin production, leading to premature translation termination and mRNA destabilization mediated by the nonsense mediated mRNA decay. Drugs (for instance, aminoglycosides) can be designed to suppress premature translation termination by inducing readthrough (or nonsense suppression) at the premature termination codon. These findings have introduced new hopes for the development of a pharmacologic approach to cure this genetic disease. In the present review, we first summarize the principle and current status of the chemical relief for the expression of functional proteins from genes otherwise unfruitful for the presence of nonsense mutations. Second, we compare data available on readthrough molecules for β0-thalassemia. The examples reported in the review strongly suggest that ribosomal readthrough should be considered as a therapeutic approach for the treatment of β0-thalassemia caused by nonsense mutations. Concluding, the discovery of molecules, exhibiting the property of inducing β-globin, such as readthrough compounds, is of great interest and represents a hope for several patients, whose survival will depend on the possible use of drugs rendering blood transfusion and chelation therapy unnecessary.
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45
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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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46
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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. [PMID: 31570318 PMCID: PMC8862661 DOI: 10.1016/s2213-2600(19)30337-6] [Citation(s) in RCA: 563] [Impact Index Per Article: 140.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 07/19/2019] [Accepted: 08/14/2019] [Indexed: 02/06/2023]
Abstract
The past six decades have seen remarkable improvements in health outcomes for people with cystic fibrosis, which was once a fatal disease of infants and young children. However, although life expectancy for people with cystic fibrosis has increased substantially, the disease continues to limit survival and quality of life, and results in a large burden of care for people with cystic fibrosis and their families. Furthermore, epidemiological studies in the past two decades have shown that cystic fibrosis occurs and is more frequent than was previously thought in populations of non-European descent, and the disease is now recognised in many regions of the world. The Lancet Respiratory Medicine Commission on the future of cystic fibrosis care was established at a time of great change in the clinical care of people with the disease, with a growing population of adult patients, widespread genetic testing supporting the diagnosis of cystic fibrosis, and the development of therapies targeting defects in the cystic fibrosis transmembrane conductance regulator (CFTR), which are likely to affect the natural trajectory of the disease. The aim of the Commission was to bring to the attention of patients, health-care professionals, researchers, funders, service providers, and policy makers the various challenges associated with the changing landscape of cystic fibrosis care and the opportunities available for progress, providing a blueprint for the future of cystic fibrosis care. The discovery of the CFTR gene in the late 1980s triggered a surge of basic research that enhanced understanding of the pathophysiology and the genotype-phenotype relationships of this clinically variable disease. Until recently, available treatments could only control symptoms and restrict the complications of cystic fibrosis, but advances in CFTR modulator therapies to address the basic defect of cystic fibrosis have been remarkable and the field is evolving rapidly. However, CFTR modulators approved for use to date are highly expensive, which has prompted questions about the affordability of new treatments and served to emphasise the considerable gap in health outcomes for patients with cystic fibrosis between high-income countries, and low-income and middle-income countries (LMICs). Advances in clinical care have been multifaceted and include earlier diagnosis through the implementation of newborn screening programmes, formalised airway clearance therapy, and reduced malnutrition through the use of effective pancreatic enzyme replacement and a high-energy, high-protein diet. Centre-based care has become the norm in high-income countries, allowing patients to benefit from the skills of expert members of multidisciplinary teams. Pharmacological interventions to address respiratory manifestations now include drugs that target airway mucus and airway surface liquid hydration, and antimicrobial therapies such as antibiotic eradication treatment in early-stage infections and protocols for maintenance therapy of chronic infections. Despite the recent breakthrough with CFTR modulators for cystic fibrosis, the development of novel mucolytic, anti-inflammatory, and anti-infective therapies is likely to remain important, especially for patients with more advanced stages of lung disease. As the median age of patients with cystic fibrosis increases, with a rapid increase in the population of adults living with the disease, complications of cystic fibrosis are becoming increasingly common. Steps need to be taken to ensure that enough highly qualified professionals are present in cystic fibrosis centres to meet the needs of ageing patients, and new technologies need to be adopted to support communication between patients and health-care providers. In considering the future of cystic fibrosis care, the Commission focused on five key areas, which are discussed in this report: the changing epidemiology of cystic fibrosis (section 1); future challenges of clinical care and its delivery (section 2); the building of cystic fibrosis care globally (section 3); novel therapeutics (section 4); and patient engagement (section 5). In panel 1, we summarise key messages of the Commission. The challenges faced by all stakeholders in building and developing cystic fibrosis care globally are substantial, but many opportunities exist for improved care and health outcomes for patients in countries with established cystic fibrosis care programmes, and in LMICs where integrated multidisciplinary care is not available and resources are lacking at present. A concerted effort is needed to ensure that all patients with cystic fibrosis have access to high-quality health care in the future.
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Affiliation(s)
- Scott C Bell
- Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, QLD, Australia; QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.
| | - Marcus A Mall
- Charité - Universitätsmedizin Berlin, Berlin Institute of Health, Berlin, Germany; German Center for Lung Research, Berlin, Germany
| | | | - Milan Macek
- Department of Biology and Medical Genetics, Second Faculty of Medicine, Motol University Hospital, Charles University, Prague, Czech Republic
| | - Susan Madge
- Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Jane C Davies
- Royal Brompton and Harefield NHS Foundation Trust, London, UK; National Heart and Lung Institute, Imperial College, London, UK
| | - Pierre-Régis Burgel
- Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Paris, France; Université Paris Descartes, Institut Cochin, Paris, France
| | - Elizabeth Tullis
- St Michael's Hospital, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada
| | - Claudio Castaños
- Hospital de Pediatria "Juan P Garrahan", Buenos Aires, Argentina
| | - Carlo Castellani
- Cystic Fibrosis Centre, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Catherine A Byrnes
- Starship Children's Hospital, Auckland, New Zealand; University of Auckland, Auckland, New Zealand
| | - Fiona Cathcart
- Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | | | | | - Isabelle Fajac
- Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Paris, France; Université Paris Descartes, Institut Cochin, Paris, France
| | | | - Pavel Drevinek
- Department of Medical Microbiology, Second Faculty of Medicine, Motol University Hospital, Charles University, Prague, Czech Republic
| | | | - Anna M Gravelle
- Cystic Fibrosis Clinic, British Columbia Children's Hospital, Vancouver, BC, Canada
| | - Trudy Havermans
- Cystic Fibrosis Centre, University Hospital Leuven, Leuven, Belgium
| | - Nicole Mayer-Hamblett
- University of Washington, Seattle, WA, USA; Seattle Children's Research Institute, Seattle, WA, USA
| | | | | | - Joseph L Mathew
- Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Edward F McKone
- School of Medicine, St Vincent's University Hospital, Dublin, Ireland; University College Dublin School of Medicine, Dublin, Ireland
| | - Lutz Naehrlich
- Universities of Giessen and Marburg Lung Center, German Center of Lung Research, Justus-Liebig-University Giessen, Giessen, Germany
| | - Samya Z Nasr
- CS Mott Children's Hospital, Ann Arbor, MI, USA; University of Michigan, Ann Arbor, MI, USA
| | | | | | | | | | - Steven M Rowe
- University of Alabama at Birmingham, Birmingham, AL, USA
| | - Kevin W Southern
- Alder Hey Children's Hospital, Liverpool, UK; University of Liverpool, Liverpool, UK
| | - Sheila Sivam
- Royal Prince Alfred Hospital, Sydney, NSW, Australia; Woolcock Institute of Medical Research, Sydney, NSW, Australia
| | - Anne L Stephenson
- St Michael's Hospital, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada
| | - Marco Zampoli
- Division of Paediatric Pulmonology and MRC Unit for Child and Adolescent Health, University of Cape Town, Cape Town, South Africa; Red Cross War Memorial Children's Hospital, Cape Town, South Africa
| | - Felix Ratjen
- University of Toronto, Toronto, ON, Canada; Division of Respiratory Medicine, Department of Paediatrics, Translational Medicine Research Program, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada.
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47
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Hinzpeter A, Sermet-Gaudelus I, Sheppard DN. Suppressing 'nonsense' in cystic fibrosis. J Physiol 2019; 598:429-430. [PMID: 31869855 DOI: 10.1113/jp279267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Alexandre Hinzpeter
- INSERM U1151, Institut Necker Enfants Malades, Paris, France.,Université Paris Descartes, Paris, France
| | - Isabelle Sermet-Gaudelus
- INSERM U1151, Institut Necker Enfants Malades, Paris, France.,Université Paris Descartes, Paris, France
| | - David N Sheppard
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, UK
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48
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Phuan PW, Tan JA, Rivera AA, Zlock L, Nielson DW, Finkbeiner WE, Haggie PM, Verkman AS. Nanomolar-potency 'co-potentiator' therapy for cystic fibrosis caused by a defined subset of minimal function CFTR mutants. Sci Rep 2019; 9:17640. [PMID: 31776420 PMCID: PMC6881293 DOI: 10.1038/s41598-019-54158-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 11/07/2019] [Indexed: 12/11/2022] Open
Abstract
Available CFTR modulators provide no therapeutic benefit for cystic fibrosis (CF) caused by many loss-of-function mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) chloride channel, including N1303K. We previously introduced the concept of ‘co-potentiators’ (combination-potentiators) to rescue CFTR function in some minimal function CFTR mutants. Herein, a screen of ~120,000 drug-like synthetic small molecules identified active co-potentiators of pyrazoloquinoline, piperidine-pyridoindole, tetrahydroquinoline and phenylazepine classes, with EC50 down to ~300 nM following initial structure-activity studies. Increased CFTR chloride conductance by up to 8-fold was observed when a co-potentiator (termed ‘Class II potentiator’) was used with a classical potentiator (‘Class I potentiator’) such as VX-770 or GLPG1837. To investigate the range of CFTR mutations benefitted by co-potentiators, 14 CF-associated CFTR mutations were studied in transfected cell models. Co-potentiator efficacy was found for CFTR missense, deletion and nonsense mutations in nucleotide binding domain-2 (NBD2), including W1282X, N1303K, c.3700A > G and Q1313X (with corrector for some mutations). In contrast, CFTR mutations G85E, R334W, R347P, V520F, R560T, A561E, M1101K and R1162X showed no co-potentiator activity, even with corrector. Co-potentiator efficacy was confirmed in primary human bronchial epithelial cell cultures generated from a N1303K homozygous CF subject. The Class II potentiators identified here may have clinical benefit for CF caused by mutations in the NBD2 domain of CFTR.
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Affiliation(s)
- Puay-Wah Phuan
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
| | - Joseph-Anthony Tan
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Amber A Rivera
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Lorna Zlock
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Dennis W Nielson
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Walter E Finkbeiner
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Peter M Haggie
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Alan S Verkman
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.,Department of Physiology, University of California, San Francisco, San Francisco, CA, USA
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49
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Yeh JT, Hwang TC. Positional effects of premature termination codons on the biochemical and biophysical properties of CFTR. J Physiol 2019; 598:517-541. [PMID: 31585024 DOI: 10.1113/jp278418] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 09/16/2019] [Indexed: 12/14/2022] Open
Abstract
KEY POINTS Biochemical and biophysical characterizations of three nonsense mutations of cystic fibrosis transmembrane conductance regulator (CFTR) associated with a severe form of cystic fibrosis (CF) reveal the importance and heterogenous effects of the position of the premature termination codon (PTC) on the CFTR protein function. Electrophysiological studies of W1282X-CFTR, whose PTC is closer to the C-terminus of CFTR, suggest the presence of both C-terminus truncated CFTR proteins that are poorly functional and read-through, full-length products. For G542X- and E60X-CFTR, the only mechanism capable of generating functional proteins is the read-through, but the outcome of read-through products is highly variable depending on the interplay between the missense mutation caused by the read-through and the structural context of the protein. Pharmacological studies of these three PTCs with various CFTR modulators suggest position-dependent therapeutic strategies for these disease-inflicting mutations. ABSTRACT About one-third of genetic diseases and cancers are caused by the introduction of premature termination codons (PTCs). In theory, the location of the PTC in a gene determines the alternative mechanisms of translation, including premature cessation or reinitiation of translation, and read-through, resulting in differential effects on protein integrity. In this study, we used CFTR as a model system to investigate the positional effect of the PTC because of its well-understood structure-function relationship and pathophysiology. The characterization of three PTC mutations, E60X-, G542X- and W1282X-CFTR revealed heterogenous effects of these PTCs on CFTR function. The W1282X mutation results in both C-terminus truncated and read-through proteins that are partially or fully functional. In contrast, only the read-through protein is functional with E60X- and G542X-CFTR, although abundant N-terminus truncated proteins due to reinitiation of translation were detected in E60X-CFTR. Single-channel studies of the read-through proteins of E60X- and G542X-CFTR demonstrated that both mutations have a single-channel amplitude similar to wild type (WT), and good responses to high-affinity ATP analogues, suggesting intact ion permeation pathways and nucleotide binding domains (NBDs), albeit with reduced open probability (Po ). The comparison of the Po of these mutations with the proposed missense mutations revealed potential identities of the read-through products. Importantly, a majority of the functional protein studied responds to CFTR modulators like GLPG1837 and Lumacaftor. These results not only expand current understanding of the molecular (patho)physiology of CFTR, but also infer therapeutic strategies for different PTC mutations at large.
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Affiliation(s)
- Jiunn-Tyng Yeh
- Interdisciplinary Neuroscience Program, University of Missouri, Columbia, MO, 65211, USA.,Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO, 65211, USA
| | - Tzyh-Chang Hwang
- Interdisciplinary Neuroscience Program, University of Missouri, Columbia, MO, 65211, USA.,Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO, 65211, USA.,Department of Pharmacology and Physiology, School of Medicine, University of Missouri, Columbia, MO, 65211, USA
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50
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Huang L, Aghajan M, Quesenberry T, Low A, Murray SF, Monia BP, Guo S. Targeting Translation Termination Machinery with Antisense Oligonucleotides for Diseases Caused by Nonsense Mutations. Nucleic Acid Ther 2019; 29:175-186. [PMID: 31070517 PMCID: PMC6686700 DOI: 10.1089/nat.2019.0779] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Efforts to develop treatments for diseases caused by nonsense mutations have focused on identification of small molecules that promote translational read-through of messenger RNAs (mRNAs) harboring nonsense stop codons to produce full-length proteins. However, to date, no small molecule read-through drug has received FDA approval, probably because of a lack of balance between efficacy and safety. Depletion of translation termination factors eukaryotic release factor (eRF) 1 and eRF3a in cells was shown to promote translational read-through of a luciferase reporter gene harboring a nonsense mutation. In this study, we identified antisense oligonucleotides (ASOs) targeting translation termination factors and determined if ASO-mediated depletion of these factors could be a potentially effective and safe therapeutic approach for diseases caused by nonsense mutations. We found that ASO-mediated reduction of either eRF1 or eRF3a to 30%–40% of normal levels in the mouse liver is well tolerated. Hemophilia mice that express a mutant allele of human coagulation factor IX (FIX) containing nonsense mutation R338X were treated with eRF1- or eRF3a-ASO. We found that although eRF1- or eRF3a-ASO alone only elicited a moderate read-through effect on hFIX-R338X mRNA, both worked in synergy with geneticin, a small molecule read-through drug, demonstrating significantly increased production of functional full-length hFIX protein to levels that would rescue disease phenotypes in these mice. Overall our results indicate that modulating the translation termination pathway in the liver by ASOs may provide a novel approach to improving the efficacy of small molecule read-through drugs to treat human genetic diseases caused by nonsense mutations.
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Affiliation(s)
- Lulu Huang
- Ionis Pharmaceuticals, Carlsbad, California
| | | | | | - Audrey Low
- Ionis Pharmaceuticals, Carlsbad, California
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