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Ward C, Beharry A, Tennakoon R, Rozik P, Wilhelm SDP, Heinemann IU, O’Donoghue P. Mechanisms and Delivery of tRNA Therapeutics. Chem Rev 2024; 124:7976-8008. [PMID: 38801719 PMCID: PMC11212642 DOI: 10.1021/acs.chemrev.4c00142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/11/2024] [Accepted: 04/26/2024] [Indexed: 05/29/2024]
Abstract
Transfer ribonucleic acid (tRNA) therapeutics will provide personalized and mutation specific medicines to treat human genetic diseases for which no cures currently exist. The tRNAs are a family of adaptor molecules that interpret the nucleic acid sequences in our genes into the amino acid sequences of proteins that dictate cell function. Humans encode more than 600 tRNA genes. Interestingly, even healthy individuals contain some mutant tRNAs that make mistakes. Missense suppressor tRNAs insert the wrong amino acid in proteins, and nonsense suppressor tRNAs read through premature stop signals to generate full length proteins. Mutations that underlie many human diseases, including neurodegenerative diseases, cancers, and diverse rare genetic disorders, result from missense or nonsense mutations. Thus, specific tRNA variants can be strategically deployed as therapeutic agents to correct genetic defects. We review the mechanisms of tRNA therapeutic activity, the nature of the therapeutic window for nonsense and missense suppression as well as wild-type tRNA supplementation. We discuss the challenges and promises of delivering tRNAs as synthetic RNAs or as gene therapies. Together, tRNA medicines will provide novel treatments for common and rare genetic diseases in humans.
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Affiliation(s)
- Cian Ward
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Aruun Beharry
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Rasangi Tennakoon
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Peter Rozik
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Sarah D. P. Wilhelm
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Ilka U. Heinemann
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Patrick O’Donoghue
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
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2
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Ruan J, Yu X, Xu H, Cui W, Zhang K, Liu C, Sun W, Huang X, An L, Zhang Y. Suppressor tRNA in gene therapy. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-024-2613-y. [PMID: 38926247 DOI: 10.1007/s11427-024-2613-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 05/08/2024] [Indexed: 06/28/2024]
Abstract
Suppressor tRNAs are engineered or naturally occurring transfer RNA molecules that have shown promise in gene therapy for diseases caused by nonsense mutations, which result in premature termination codons (PTCs) in coding sequence, leading to truncated, often nonfunctional proteins. Suppressor tRNAs can recognize and pair with these PTCs, allowing the ribosome to continue translation and produce a full-length protein. This review introduces the mechanism and development of suppressor tRNAs, compares suppressor tRNAs with other readthrough therapies, discusses their potential for clinical therapy, limitations, and obstacles. We also summarize the applications of suppressor tRNAs in both in vitro and in vivo, offering new insights into the research and treatment of nonsense mutation diseases.
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Affiliation(s)
- Jingjing Ruan
- The Children's Hospital, National Clinical Research Center for Child Health, Zhejiang University School of Medicine, Liangzhu Laboratory, Hangzhou, 310000, China
- Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, 311121, China
| | - Xiaoxiao Yu
- Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, 311121, China
| | - Huixia Xu
- Department of Thoracic and Cardiovascular Surgery, Huaihe Hospital of Henan University, Henan University, Kaifeng, 475000, China
| | - Wenrui Cui
- Translational Medicine Center, Huaihe Hospital of Henan University, Henan University, Kaifeng, 475000, China
| | - Kaiye Zhang
- Eye Center, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310009, China
| | - Chenyang Liu
- Translational Medicine Center, Huaihe Hospital of Henan University, Henan University, Kaifeng, 475000, China
| | - Wenlong Sun
- Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, 311121, China
| | - Xiaodan Huang
- Eye Center, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310009, China
| | - Lei An
- Translational Medicine Center, Huaihe Hospital of Henan University, Henan University, Kaifeng, 475000, China.
| | - Yue Zhang
- The Children's Hospital, National Clinical Research Center for Child Health, Zhejiang University School of Medicine, Liangzhu Laboratory, Hangzhou, 310000, China.
- Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, 311121, China.
- Translational Medicine Center, Huaihe Hospital of Henan University, Henan University, Kaifeng, 475000, China.
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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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4
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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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5
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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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6
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Orenti A, Pranke I, Faucon C, Varilh J, Hatton A, Golec A, Dehillotte C, Durieu I, Reix P, Burgel PR, Grenet D, Tasset C, Gachelin E, Perisson C, Lepissier A, Dreano E, Tondelier D, Chevalier B, Weiss L, Kiefer S, Laurans M, Chiron R, Lemonnier L, Marguet C, Jung A, Edelman A, Kerem BS, Girodon E, Taulan-Cadars M, Hinzpeter A, Kerem E, Naehrlich L, Sermet-Gaudelus I. Nonsense mutations accelerate lung disease and decrease survival of cystic fibrosis children. J Cyst Fibros 2023; 22:1070-1079. [PMID: 37422433 DOI: 10.1016/j.jcf.2023.06.005] [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: 04/10/2023] [Revised: 06/11/2023] [Accepted: 06/12/2023] [Indexed: 07/10/2023]
Abstract
RATIONALE Limited information is available on the clinical status of people with Cystic Fibrosis (pwCF) carrying 2 nonsense mutations (PTC/PTC). The main objective of this study was to compare disease severity between pwCF PTC/PTC, compound heterozygous for F508del and PTC (F508del/PTC) and homozygous for F508del (F508del+/+). METHODS Based on the European CF Society Patient Registry clinical data of pwCF living in high and middle income European and neighboring countries, PTC/PTC (n = 657) were compared with F508del+/+ (n = 21,317) and F508del/PTC(n = 4254).CFTR mRNA and protein activity levels were assessed in primary human nasal epithelial (HNE) cells sampled from 22 PTC/PTC pwCF. MAIN RESULTS As compared to F508del+/+ pwCF; both PTC/PTC and F508del/PTC pwCF exhibited a significantly faster rate of decline in Forced Expiratory Volume in 1 s (FEV1) from 7 years (-1.33 for F508del +/+, -1.59 for F508del/PTC; -1.65 for PTC/PTC, p < 0.001) until respectively 30 years (-1.05 for F508del +/+, -1.23 for PTC/PTC, p = 0.048) and 27 years (-1.12 for F508del +/+, -1.26 for F508del/PTC, p = 0.034). This resulted in lower FEV1 values in adulthood. Mortality of pediatric pwCF with one or two PTC alleles was significantly higher than their F508del homozygous pairs. Infection with Pseudomonas aeruginosa was more frequent in PTC/PTC versus F508del+/+ and F508del/PTC pwCF. CFTR activity in PTC/PTC pwCF's HNE cells ranged between 0% to 3% of the wild-type level. CONCLUSIONS Nonsense mutations decrease the survival and accelerate the course of respiratory disease in children and adolescents with Cystic Fibrosis.
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Affiliation(s)
- Annalisa Orenti
- Department of Clinical Sciences and Community Health, Laboratory of Medical Statistics, Biometry and Epidemiology "G. A. Maccacaro", University of Milan, Milan, Italy
| | - Iwona Pranke
- Université de Paris, CNRS, INSERM U-1151, Institut Necker-Enfants Malades, Paris, France; Centre de Référence Maladies Rares, Mucoviscidose et affections liées à CFTR, Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Caroline Faucon
- Centre de Ressources et de Compétences de la Mucoviscidose, Centre Hospitalier Universitaire de Caen Normandie, Caen, France
| | - Jessica Varilh
- PhyMedExp, INSERM, CNRS UMR, Montpellier, France; Université de Montpellier, Montpellier, France
| | - Aurelie Hatton
- Université de Paris, CNRS, INSERM U-1151, Institut Necker-Enfants Malades, Paris, France; Centre de Référence Maladies Rares, Mucoviscidose et affections liées à CFTR, Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Anita Golec
- Université de Paris, CNRS, INSERM U-1151, Institut Necker-Enfants Malades, Paris, France; Centre de Référence Maladies Rares, Mucoviscidose et affections liées à CFTR, Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France
| | | | - Isabelle Durieu
- Centre de Référence Maladies Rares Mucoviscidose et affections liées à CFTR, Hospices Civils de Lyon, Pierre-Bénite, France; EA HESPER -Université Claude Bernard Lyon 1, Université de Lyon, France
| | - Philippe Reix
- Centre de Référence Maladies Rares Mucoviscidose et affections liées à CFTR, Hospices Civils de Lyon, Pierre-Bénite, France
| | - Pierre-Régis Burgel
- Department of Respiratory Medicine and National Reference Center for Cystic Fibrosis, Assistance Publique-Hôpitaux de Paris, Paris, France; Institut Cochin, Université Paris Cité and Inserm U1016, Paris, France; ERN-Lung CF network, France
| | - Dominique Grenet
- Centre de Ressources et de Compétences de la Mucoviscidose, Hôpital Foch, Suresnes, France
| | - Céline Tasset
- Centre de Ressources et de Compétences de la Mucoviscidose, Centre Hospitalier Universitaire Sud Reunion, Saint-Pierre, France
| | - Elsa Gachelin
- Centre de Ressources et de Compétences de la Mucoviscidose, Centre Hospitalier Universitaire Felix Guyon, Saint-Denis, France
| | - Caroline Perisson
- Centre de Ressources et de Compétences de la Mucoviscidose, Centre Hospitalier Universitaire Sud Reunion, Saint-Pierre, France
| | - Agathe Lepissier
- Université de Paris, CNRS, INSERM U-1151, Institut Necker-Enfants Malades, Paris, France; Centre de Référence Maladies Rares, Mucoviscidose et affections liées à CFTR, Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Elise Dreano
- Université de Paris, CNRS, INSERM U-1151, Institut Necker-Enfants Malades, Paris, France; Centre de Référence Maladies Rares, Mucoviscidose et affections liées à CFTR, Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Danielle Tondelier
- Université de Paris, CNRS, INSERM U-1151, Institut Necker-Enfants Malades, Paris, France; Centre de Référence Maladies Rares, Mucoviscidose et affections liées à CFTR, Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Benoit Chevalier
- Université de Paris, CNRS, INSERM U-1151, Institut Necker-Enfants Malades, Paris, France; Centre de Référence Maladies Rares, Mucoviscidose et affections liées à CFTR, Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Laurence Weiss
- Centre de Ressources et de Compétences de la Mucoviscidose, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Sébastien Kiefer
- Centre de Ressources et de Compétences de la Mucoviscidose, Centre Hospitalier Universitaire de Nancy, Nancy, France
| | - Muriel Laurans
- Centre de Ressources et de Compétences de la Mucoviscidose, Centre Hospitalier Universitaire de Caen Normandie, Caen, France
| | - Raphael Chiron
- Centre de Ressources et de Compétences de la Mucoviscidose, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | | | - Christophe Marguet
- Centre de Ressources et de Compétences de la Mucoviscidose, Centre Hospitalier Universitaire Charles Nicolle, Rouen, France
| | - Andreas Jung
- Pediatric Respiratory Medicine, Kinderspital, Zurich, Switzerland; European Cystic Fibrosis Society Patients Registry, France
| | - Aleksander Edelman
- Université de Paris, CNRS, INSERM U-1151, Institut Necker-Enfants Malades, Paris, France; Centre de Référence Maladies Rares, Mucoviscidose et affections liées à CFTR, Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Bat-Sheva Kerem
- Department of Genetics, The Life Science Institute, The Hebrew University, Jerusalem Israel
| | - Emmanuelle Girodon
- Molecular Genetics Laboratory, Cochin Hospital, Assistance Publique-Hôpitaux de Paris, Université de Paris, Paris, France
| | - Magali Taulan-Cadars
- PhyMedExp, INSERM, CNRS UMR, Montpellier, France; Université de Montpellier, Montpellier, France
| | - Alexandre Hinzpeter
- Université de Paris, CNRS, INSERM U-1151, Institut Necker-Enfants Malades, Paris, France; Centre de Référence Maladies Rares, Mucoviscidose et affections liées à CFTR, Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Eitan Kerem
- Division of Pediatrics, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Lutz Naehrlich
- European Cystic Fibrosis Society Patients Registry, France; Y Justus-Liebig-University Giessen, Department of Pediatrics, Giessen, Germany
| | - Isabelle Sermet-Gaudelus
- Université de Paris, CNRS, INSERM U-1151, Institut Necker-Enfants Malades, Paris, France; Centre de Référence Maladies Rares, Mucoviscidose et affections liées à CFTR, Hôpital Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France; ERN-Lung CF network, France.
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7
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Lau HH, Krentz NAJ, Abaitua F, Perez-Alcantara M, Chan JW, Ajeian J, Ghosh S, Lee Y, Yang J, Thaman S, Champon B, Sun H, Jha A, Hoon S, Tan NS, Gardner DSL, Kao SL, Tai ES, Gloyn AL, Teo AKK. PAX4 loss of function increases diabetes risk by altering human pancreatic endocrine cell development. Nat Commun 2023; 14:6119. [PMID: 37777536 PMCID: PMC10542369 DOI: 10.1038/s41467-023-41860-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: 06/26/2022] [Accepted: 09/20/2023] [Indexed: 10/02/2023] Open
Abstract
The coding variant (p.Arg192His) in the transcription factor PAX4 is associated with an altered risk for type 2 diabetes (T2D) in East Asian populations. In mice, Pax4 is essential for beta cell formation but its role on human beta cell development and/or function is unknown. Participants carrying the PAX4 p.His192 allele exhibited decreased pancreatic beta cell function compared to homozygotes for the p.192Arg allele in a cross-sectional study in which we carried out an intravenous glucose tolerance test and an oral glucose tolerance test. In a pedigree of a patient with young onset diabetes, several members carry a newly identified p.Tyr186X allele. In the human beta cell model, EndoC-βH1, PAX4 knockdown led to impaired insulin secretion, reduced total insulin content, and altered hormone gene expression. Deletion of PAX4 in human induced pluripotent stem cell (hiPSC)-derived islet-like cells resulted in derepression of alpha cell gene expression. In vitro differentiation of hiPSCs carrying PAX4 p.His192 and p.X186 risk alleles exhibited increased polyhormonal endocrine cell formation and reduced insulin content that can be reversed with gene correction. Together, we demonstrate the role of PAX4 in human endocrine cell development, beta cell function, and its contribution to T2D-risk.
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Affiliation(s)
- Hwee Hui Lau
- Stem Cells and Diabetes Laboratory, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Proteos, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Nicole A J Krentz
- Division of Endocrinology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Fernando Abaitua
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Jun-Wei Chan
- Stem Cells and Diabetes Laboratory, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Proteos, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Jila Ajeian
- Oxford Centre for Diabetes Endocrinology and Metabolism, University of Oxford, Oxford, UK
| | - Soumita Ghosh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Yunkyeong Lee
- Division of Endocrinology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Jing Yang
- Division of Endocrinology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Swaraj Thaman
- Division of Endocrinology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Benoite Champon
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Han Sun
- Division of Endocrinology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Alokkumar Jha
- Division of Endocrinology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Shawn Hoon
- Molecular Engineering Laboratory, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Proteos, Singapore
| | - Nguan Soon Tan
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | | | - Shih Ling Kao
- Department of Medicine, National University Hospital and National University Health System, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - E Shyong Tai
- Department of Medicine, National University Hospital and National University Health System, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Anna L Gloyn
- Division of Endocrinology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA.
| | - Adrian Kee Keong Teo
- Stem Cells and Diabetes Laboratory, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Proteos, Singapore.
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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8
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Osum SH, Oribamise EI, Corbière SM, Taisto M, Jubenville T, Coutts A, Kirstein MN, Fisher J, Moertel C, Du M, Bedwell D, Largaespada DA, Watson AL. Combining nonsense mutation suppression therapy with nonsense-mediated decay inhibition in neurofibromatosis type 1. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:227-239. [PMID: 37520682 PMCID: PMC10384610 DOI: 10.1016/j.omtn.2023.06.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 06/22/2023] [Indexed: 08/01/2023]
Abstract
Neurofibromatosis type 1 (NF1) results from germline mutations in the tumor-suppressor gene NF1 and predisposes patients to developing nervous system tumors. Twenty percent of NF1 patients harbor nonsense mutations resulting in premature termination codons (PTCs). Nonsense suppression therapies can facilitate ribosomal readthrough of PTCs to restore full-length protein, but their potential in NF1 is underexplored. We developed a minipig model of NF1 carrying a PTC to test whether nonsense suppression could restore expression of the NF1-encoded protein neurofibromin in vitro and in vivo. Nonsense suppression did not reliably increase neurofibromin in primary NF1-/- Schwann cells isolated from minipig neurofibromas but could reduce phosphorylated ERK. Gentamicin in vivo produced a similar plasma pharmacokinetic profile to humans and was detectable in clinically relevant tissues, including cerebral cortex, sciatic nerve, optic nerve, and skin. In gentamicin-treated animals, increased neurofibromin expression was seen in the optic nerve. Nonsense-mediated decay (NMD) causes degradation of transcripts with PTCs, which could impede nonsense suppression therapies. Nonsense suppression in combination with NMD inhibition restored neurofibromin protein expression in primary NF1-/- Schwann cells isolated from minipig neurofibromas. Thus, the effectiveness of nonsense suppression therapies can be improved in NF1 by the concurrent use of NMD inhibitors.
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Affiliation(s)
- Sara H. Osum
- Masonic Cancer Center, Department of Pediatrics, University of Minnesota, 2-191 Moos Tower, 515 Delaware Street SE, Minneapolis, MN 55455, USA
| | - Eunice I. Oribamise
- Masonic Cancer Center, Department of Pediatrics, University of Minnesota, 2-191 Moos Tower, 515 Delaware Street SE, Minneapolis, MN 55455, USA
| | | | - Mandy Taisto
- Recombinetics Inc., 3388 Mike Collins Drive, #1, Eagan, MN 55121, USA
| | - Tyler Jubenville
- Masonic Cancer Center, Department of Pediatrics, University of Minnesota, 2-191 Moos Tower, 515 Delaware Street SE, Minneapolis, MN 55455, USA
| | - Alex Coutts
- Recombinetics Inc., 3388 Mike Collins Drive, #1, Eagan, MN 55121, USA
| | - Mark N. Kirstein
- Masonic Cancer Center, Department of Pediatrics, University of Minnesota, 2-191 Moos Tower, 515 Delaware Street SE, Minneapolis, MN 55455, USA
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Room 459, 717 Delaware Street SE, Minneapolis, MN 55414, USA
| | - James Fisher
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Room 459, 717 Delaware Street SE, Minneapolis, MN 55414, USA
| | - Christopher Moertel
- Masonic Cancer Center, Department of Pediatrics, University of Minnesota, 2-191 Moos Tower, 515 Delaware Street SE, Minneapolis, MN 55455, USA
| | - Ming Du
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Bevill Biomedical Research Building Room 432A, 845 19 Street South, Birmingham, AL 35294, USA
| | - David Bedwell
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Bevill Biomedical Research Building Room 432A, 845 19 Street South, Birmingham, AL 35294, USA
| | - David A. Largaespada
- Masonic Cancer Center, Department of Pediatrics, University of Minnesota, 2-191 Moos Tower, 515 Delaware Street SE, Minneapolis, MN 55455, USA
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9
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Wong KM, Wegener E, Baradaran-Heravi A, Huppke B, Gärtner J, Huppke P. Evaluation of Novel Enhancer Compounds in Gentamicin-Mediated Readthrough of Nonsense Mutations in Rett Syndrome. Int J Mol Sci 2023; 24:11665. [PMID: 37511424 PMCID: PMC10380790 DOI: 10.3390/ijms241411665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Rett syndrome (RTT), a severe X-linked neurodevelopmental disorder, is primarily caused by mutations in the methyl CpG binding protein 2 gene (MECP2). Over 35% RTT patients carry nonsense mutation in MECP2, making it a suitable candidate disease for nonsense suppression therapy. In our previous study, gentamicin was found to induce readthrough of MECP2 nonsense mutations with modest efficiency. Given the recent discovery of readthrough enhancers, CDX compounds, we herein evaluated the potentiation effect of CDX5-1, CDX5-288, and CDX6-180 on gentamicin-mediated readthrough efficiency in transfected HeLa cell lines bearing the four most common MECP2 nonsense mutations. We showed that all three CDX compounds potentiated gentamicin-mediated readthrough and increased full-length MeCP2 protein levels in cells expressing the R168X, R255X, R270X, and R294X nonsense mutations. Among all three CDX compounds, CDX5-288 was the most potent enhancer and enabled the use of reduced doses of gentamicin, thus mitigating the toxicity. Furthermore, we successfully demonstrated the upregulation of full-length Mecp2 protein expression in fibroblasts derived from Mecp2R255X/Y mice through combinatorial treatment. Taken together, findings demonstrate the feasibility of this combinatorial approach to nonsense suppression therapy for a subset of RTT patients.
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Affiliation(s)
- Keit Men Wong
- Department of Neuropediatrics, Jena University Hospital, 07747 Jena, Germany
- Center for Rare Diseases, Jena University Hospital, 07747 Jena, Germany
| | - Eike Wegener
- Department of Pediatrics and Adolescent Medicine, Division of Neuropediatrics, Pediatric Neurology University Medical Center Göttingen, Georg August University Göttingen, 37075 Göttingen, Germany
| | - Alireza Baradaran-Heravi
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver BC V6T 1Z3, Canada
| | - Brenda Huppke
- Department of Neuropediatrics, Jena University Hospital, 07747 Jena, Germany
- Center for Rare Diseases, Jena University Hospital, 07747 Jena, Germany
| | - Jutta Gärtner
- Department of Pediatrics and Adolescent Medicine, Division of Neuropediatrics, Pediatric Neurology University Medical Center Göttingen, Georg August University Göttingen, 37075 Göttingen, Germany
| | - Peter Huppke
- Department of Neuropediatrics, Jena University Hospital, 07747 Jena, Germany
- Center for Rare Diseases, Jena University Hospital, 07747 Jena, Germany
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10
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Sun B, Chen L. Mapping genetic variants for nonsense-mediated mRNA decay regulation across human tissues. Genome Biol 2023; 24:164. [PMID: 37434206 PMCID: PMC10337212 DOI: 10.1186/s13059-023-03004-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 06/30/2023] [Indexed: 07/13/2023] Open
Abstract
BACKGROUND Nonsense-mediated mRNA decay (NMD) was originally conceived as an mRNA surveillance mechanism to prevent the production of potentially deleterious truncated proteins. Research also shows NMD is an important post-transcriptional gene regulation mechanism selectively targeting many non-aberrant mRNAs. However, how natural genetic variants affect NMD and modulate gene expression remains elusive. RESULTS Here we elucidate NMD regulation of individual genes across human tissues through genetical genomics. Genetic variants corresponding to NMD regulation are identified based on GTEx data through unique and robust transcript expression modeling. We identify genetic variants that influence the percentage of NMD-targeted transcripts (pNMD-QTLs), as well as genetic variants regulating the decay efficiency of NMD-targeted transcripts (dNMD-QTLs). Many such variants are missed in traditional expression quantitative trait locus (eQTL) mapping. NMD-QTLs show strong tissue specificity especially in the brain. They are more likely to overlap with disease single-nucleotide polymorphisms (SNPs). Compared to eQTLs, NMD-QTLs are more likely to be located within gene bodies and exons, especially the penultimate exons from the 3' end. Furthermore, NMD-QTLs are more likely to be found in the binding sites of miRNAs and RNA binding proteins. CONCLUSIONS We reveal the genome-wide landscape of genetic variants associated with NMD regulation across human tissues. Our analysis results indicate important roles of NMD in the brain. The preferential genomic positions of NMD-QTLs suggest key attributes for NMD regulation. Furthermore, the overlap with disease-associated SNPs and post-transcriptional regulatory elements implicates regulatory roles of NMD-QTLs in disease manifestation and their interactions with other post-transcriptional regulators.
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Affiliation(s)
- Bo Sun
- Department of Quantitative and Computational Biology, University of Southern California, 1050 Childs Way, Los Angeles, CA, 90089, USA
| | - Liang Chen
- Department of Quantitative and Computational Biology, University of Southern California, 1050 Childs Way, Los Angeles, CA, 90089, USA.
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11
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Friedman L, Avitzur OB, Galai EO, Ferrari N, Choen A, Dahan S, Mordechai T, Hart G. The safety and toxicity profile of SPL84, an inhaled antisense oligonucleotide for treatment of cystic fibrosis patients with the 3849 +10kb C->T mutation, supports a Phase 1/2 clinical study. Expert Opin Drug Metab Toxicol 2023; 19:709-720. [PMID: 37799089 DOI: 10.1080/17425255.2023.2266361] [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: 06/13/2023] [Accepted: 09/15/2023] [Indexed: 10/07/2023]
Abstract
INTRODUCTION SPL84 is an inhaled antisense oligonucleotide (ASO) in development for the treatment of cystic fibrosis (CF) patients carrying the 3849 + 10kb C->T (3849) mutation. To support the initiation of the first clinical study, a full battery of safety and toxicology studies were performed. RESEARCH DESIGN AND METHODS SPL84 was administered by inhalation to mice and monkeys to determine the no observed adverse effect level (NOAEL) and establish sufficient safety margins for the starting clinical dose. RESULTS There were no preclinical safety findings with SPL84; no related clinical signs, nor any effect on body weight, food consumption, or clinical pathology. The microscopic changes in the lungs were regarded as non-adverse and reflected a normal clearance process for inhaled compounds. Systemic exposure in both species was low. The NOAEL for mice and monkeys was the highest administered dose in both species, resulting in safety margins ~ 40X the proposed starting clinical dose. CONCLUSION These successful results supported the initiation of a phase 1/2 clinical study of SPL84 (ongoing), assessing the safety, tolerability, and pharmacokinetics of a single ascending dose in healthy subjects to be followed by assessment of safety, tolerability, pharmacokinetics, and preliminary efficacy of multiple ascending doses in CF patients carrying the 3849 mutation.
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Affiliation(s)
- Lital Friedman
- SpliSense, BiohouseLabs, Haddasah Ein Kerem, Jerusalem, Israel
| | | | | | | | - Asa Choen
- SpliSense, BiohouseLabs, Haddasah Ein Kerem, Jerusalem, Israel
| | - Sara Dahan
- SpliSense, BiohouseLabs, Haddasah Ein Kerem, Jerusalem, Israel
| | - Tamar Mordechai
- SpliSense, BiohouseLabs, Haddasah Ein Kerem, Jerusalem, Israel
| | - Gili Hart
- SpliSense, BiohouseLabs, Haddasah Ein Kerem, Jerusalem, Israel
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12
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Allaire NE, Griesenbach U, Kerem B, Lueck JD, Stanleigh N, Oren YS. Gene, RNA, and ASO-based therapeutic approaches in Cystic Fibrosis. J Cyst Fibros 2023; 22 Suppl 1:S39-S44. [PMID: 36658041 PMCID: PMC10012168 DOI: 10.1016/j.jcf.2022.12.016] [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: 09/12/2022] [Revised: 12/27/2022] [Accepted: 12/30/2022] [Indexed: 01/18/2023]
Abstract
Most people with Cystic Fibrosis (PwCF) harbor Cystic Fibrosis Transmembrane Conductance (CFTR) mutations that respond to highly effective CFTR modulators (HEM); however, a small fraction of non-responsive variants will require alternative approaches for treatment. Furthermore, the long-term goal to develop a cure for CF will require novel therapeutic strategies. Nucleic acid-based approaches offer the potential to address all CF-causing mutations and possibly a cure for all PwCF. In this minireview, we discuss current knowledge, recent progress, and critical questions surrounding the topic of Gene-, RNA-, and ASO-based therapies for the treatment of Cystic Fibrosis (CF).
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Affiliation(s)
| | - Uta Griesenbach
- National Heart and Lung Institute, Imperial College London and the UK Respiratory Gene Therapy Consortium, UK
| | - Batsheva Kerem
- Department of Genetics, The Life Sciences Institute, Hebrew University, Jerusalem, Israel
| | - John D Lueck
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY, USA
| | - Noemie Stanleigh
- Department of Genetics, The Life Sciences Institute, Hebrew University, Jerusalem, Israel
| | - Yifat S Oren
- SpliSenseTherapeutics, Biohouse Labs, Haddasah Ein Karem, Jerusalem, IL
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13
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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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14
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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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15
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Recoding of Nonsense Mutation as a Pharmacological Strategy. Biomedicines 2023; 11:biomedicines11030659. [PMID: 36979640 PMCID: PMC10044939 DOI: 10.3390/biomedicines11030659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/18/2023] [Accepted: 02/20/2023] [Indexed: 02/24/2023] Open
Abstract
Approximately 11% of genetic human diseases are caused by nonsense mutations that introduce a premature termination codon (PTC) into the coding sequence. The PTC results in the production of a potentially harmful shortened polypeptide and activation of a nonsense-mediated decay (NMD) pathway. The NMD pathway reduces the burden of unproductive protein synthesis by lowering the level of PTC mRNA. There is an endogenous rescue mechanism that produces a full-length protein from a PTC mRNA. Nonsense suppression therapies aim to increase readthrough, suppress NMD, or are a combination of both strategies. Therefore, treatment with translational readthrough-inducing drugs (TRIDs) and NMD inhibitors may increase the effectiveness of PTC suppression. Here we discuss the mechanism of PTC readthrough and the development of novel approaches to PTC suppression. We also discuss the toxicity and bioavailability of therapeutics used to stimulate PTC readthrough.
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16
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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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17
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Kim YJ, Krainer AR. Antisense Oligonucleotide Therapeutics for Cystic Fibrosis: Recent Developments and Perspectives. Mol Cells 2023; 46:10-20. [PMID: 36697233 PMCID: PMC9880599 DOI: 10.14348/molcells.2023.2172] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 11/22/2022] [Accepted: 11/23/2022] [Indexed: 01/27/2023] Open
Abstract
Antisense oligonucleotide (ASO) technology has become an attractive therapeutic modality for various diseases, including Mendelian disorders. ASOs can modulate the expression of a target gene by promoting mRNA degradation or changing pre-mRNA splicing, nonsense-mediated mRNA decay, or translation. Advances in medicinal chemistry and a deeper understanding of post-transcriptional mechanisms have led to the approval of several ASO drugs for diseases that had long lacked therapeutic options. For instance, an ASO drug called nusinersen became the first approved drug for spinal muscular atrophy, improving survival and the overall disease course. Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene cause cystic fibrosis (CF). Although Trikafta and other CFTR-modulation therapies benefit most CF patients, there is a significant unmet therapeutic need for a subset of CF patients. In this review, we introduce ASO therapies and their mechanisms of action, describe the opportunities and challenges for ASO therapeutics for CF, and discuss the current state and prospects of ASO therapies for CF.
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Affiliation(s)
- Young Jin Kim
- Department of Pediatrics, Mount Sinai Hospital, New York, NY 10029, USA
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18
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Egan ME. Non-Modulator Therapies: Developing a Therapy for Every Cystic Fibrosis Patient. Clin Chest Med 2022; 43:717-725. [PMID: 36344076 DOI: 10.1016/j.ccm.2022.06.011] [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] [Indexed: 11/06/2022]
Abstract
Cystic fibrosis transmembrane conductance regulator (CFTR) modulator therapy brings hope to most patients with cystic fibrosis (CF), but not all. For approximately 12% of CF patients with premature termination codon mutations, large deletions, insertions, and frameshifts, the CFTR modulator therapy is not effective. Many believe that genetic-based therapies such as RNA therapies, DNA therapies, and gene editing technologies will be needed to treat mutations that are not responsive to modulator therapy. Delivery of these therapeutic agents to affected cells is the major challenge that will need to be overcome if we are to harness the power of these emerging therapies for the treatment of CF.
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Affiliation(s)
- Marie E Egan
- Division of Pulmonary Allergy Immunology Sleep Medicine, Department of Pediatrics, Pediatric Pulmonary Allergy Immunology and Sleep Medicine, Yale Cystic Fibrosis Center, School of Medicine, Yale University, 333 Cedar Street, PO Box 208064, New Haven, CT 06520, USA.
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19
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Pranke IM, Varilh J, Hatton A, Faucon C, Girodon E, Dreano E, Chevalier B, Karri S, Reix P, Durieu I, Bidou L, Namy O, Taulan M, Hinzpeter A, Sermet-Gaudelus I. The U UGA C sequence provides a favorable context to ELX-02 induced CFTR readthrough. J Cyst Fibros 2022:S1569-1993(22)01392-3. [DOI: 10.1016/j.jcf.2022.10.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 09/22/2022] [Accepted: 10/24/2022] [Indexed: 11/18/2022]
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20
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Lee RE, Lewis CA, He L, Bulik-Sullivan EC, Gallant SC, Mascenik TM, Dang H, Cholon DM, Gentzsch M, Morton LC, Minges JT, Theile JW, Castle NA, Knowles MR, Kimple AJ, Randell SH. Small molecule eRF3a degraders rescue CFTR nonsense mutations by promoting premature termination codon readthrough. J Clin Invest 2022; 132:154571. [PMID: 35900863 PMCID: PMC9479597 DOI: 10.1172/jci154571] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 07/26/2022] [Indexed: 11/22/2022] Open
Abstract
The vast majority of people with cystic fibrosis (CF) are now eligible for CF transmembrane regulator (CFTR) modulator therapy. The remaining individuals with CF harbor premature termination codons (PTCs) or rare CFTR variants with limited treatment options. Although the clinical modulator response can be reliably predicted using primary airway epithelial cells, primary cells carrying rare CFTR variants are scarce. To overcome this obstacle, cell lines can be created by overexpression of mouse Bmi-1 and human TERT (hTERT). Using this approach, we developed 2 non-CF and 6 CF airway epithelial cell lines, 3 of which were homozygous for the W1282X PTC variant. The Bmi-1/hTERT cell lines recapitulated primary cell morphology and ion transport function. The 2 F508del-CFTR cell lines responded robustly to CFTR modulators, which was mirrored in the parent primary cells and in the cell donors’ clinical response. Cereblon E3 ligase modulators targeting eukaryotic release factor 3a (eRF3a) rescued W1282X-CFTR function to approximately 20% of WT levels and, when paired with G418, rescued G542X-CFTR function to approximately 50% of WT levels. Intriguingly, eRF3a degraders also diminished epithelial sodium channel (ENaC) function. These studies demonstrate that Bmi-1/hTERT cell lines faithfully mirrored primary cell responses to CFTR modulators and illustrate a therapeutic approach to rescue CFTR nonsense mutations.
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Affiliation(s)
- Rhianna E Lee
- Marsico Lung Institute/Cystic Fibrosis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - Catherine A Lewis
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - Lihua He
- Marsico Lung Institute/Cystic Fibrosis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - Emily C Bulik-Sullivan
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - Samuel C Gallant
- Marsico Lung Institute/Cystic Fibrosis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - Teresa M Mascenik
- Marsico Lung Institute/Cystic Fibrosis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - Hong Dang
- Marsico Lung Institute/Cystic Fibrosis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - Deborah M Cholon
- Marsico Lung Institute/Cystic Fibrosis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - Martina Gentzsch
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - Lisa C Morton
- Marsico Lung Institute/Cystic Fibrosis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - John T Minges
- Marsico Lung Institute/Cystic Fibrosis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | | | - Neil A Castle
- Research and Development, Icagen, Durham, United States of America
| | - Michael R Knowles
- Marsico Lung Institute/Cystic Fibrosis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - Adam J Kimple
- Department of Otolaryngology, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
| | - Scott H Randell
- Marsico Lung Institute/Cystic Fibrosis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, United States of America
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21
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Ma Y, Sun W, Zhao L, Yao M, Wu C, Su P, Yang L, Wang G. Generation of an mESC model with a human hemophilia B nonsense mutation via CRISPR/Cas9 technology. Stem Cell Res Ther 2022; 13:353. [PMID: 35883203 PMCID: PMC9327398 DOI: 10.1186/s13287-022-03036-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 07/06/2022] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Hemophilia B is a rare inherited genetic bleeding disorder caused by a deficiency or lack of coagulation factor IX, the gene for which (F9) is located on the X chromosome. Hemophilia B is currently incurable and the standard treatment is coagulation factor replacement therapy. Although gene therapy has the potential to cure hemophilia, significant barriers are still needed to be overcome, e.g., off-target effects and immunoreactivity, so new approaches must be explored. Nonsense mutations account for 8% of all the hemophilia B mutation types and can result in the development of coagulation factor inhibitors. In this study, CRISPR/Cas9 technology was used to construct a mouse embryonic stem cell model with a hemophilia B nonsense mutation (F9 c.223C > T) in humans to investigate the pathogenesis and treatment of nonsense mutations in hemophilia B. METHODS First, a donor plasmid with a mutation (F9 c.223 C > T) and sgRNAs were constructed. Second, both the donor plasmid and the px330-sgRNA were electroporated into mouse embryonic stem cell, and the mutant cells were then screened using puromycin and red fluorescence. Third, the mutant cell lines were tested for pluripotency and the ability to differentiate into three layers. Finally, the effect of mutation on gene function was studied in the differentiation system. RESULTS The mutant vector and effective sgRNA were constructed, and the mutant cell line was screened. This mutant cell line exhibited pluripotency and the ability to differentiate into three layers. This point mutation affects F9 expression at both the RNA and protein levels in the differentiation system. CONCLUSIONS The mutant cell line obtained in the current study had a single-base mutation rather than a base deletion or insertion in the exon, which is more similar to clinical cases. In addition, the mutant has the characteristics of mouse embryonic stem cells, and this point mutation affects F9 gene transcription and translation, which can be used as a disease model for studying the pathogenesis and treatment of hemophilia at the stem cell level.
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Affiliation(s)
- Yanchun Ma
- Department of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi Province, China
| | - Wenwen Sun
- Department of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi Province, China
| | - Lidong Zhao
- Department of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi Province, China
| | - Mingze Yao
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, 030006, Shanxi Province, China
| | - Changxin Wu
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, 030006, Shanxi Province, China
| | - Pengfei Su
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, 030006, Shanxi Province, China
| | - Linhua Yang
- Department of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi Province, China.
| | - Gang Wang
- Department of Hematology, The Second Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi Province, China.
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22
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Ensinck MM, Carlon MS. One Size Does Not Fit All: The Past, Present and Future of Cystic Fibrosis Causal Therapies. Cells 2022; 11:cells11121868. [PMID: 35740997 PMCID: PMC9220995 DOI: 10.3390/cells11121868] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 05/25/2022] [Accepted: 05/28/2022] [Indexed: 02/04/2023] Open
Abstract
Cystic fibrosis (CF) is the most common monogenic disorder, caused by mutations in the CF transmembrane conductance regulator (CFTR) gene. Over the last 30 years, tremendous progress has been made in understanding the molecular basis of CF and the development of treatments that target the underlying defects in CF. Currently, a highly effective CFTR modulator treatment (Kalydeco™/Trikafta™) is available for 90% of people with CF. In this review, we will give an extensive overview of past and ongoing efforts in the development of therapies targeting the molecular defects in CF. We will discuss strategies targeting the CFTR protein (i.e., CFTR modulators such as correctors and potentiators), its cellular environment (i.e., proteostasis modulation, stabilization at the plasma membrane), the CFTR mRNA (i.e., amplifiers, nonsense mediated mRNA decay suppressors, translational readthrough inducing drugs) or the CFTR gene (gene therapies). Finally, we will focus on how these efforts can be applied to the 15% of people with CF for whom no causal therapy is available yet.
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Affiliation(s)
- Marjolein M. Ensinck
- Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Flanders, Belgium;
| | - Marianne S. Carlon
- Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, 3000 Leuven, Flanders, Belgium;
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, 3000 Leuven, Flanders, Belgium
- Correspondence:
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23
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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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24
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DNA damage promotes HLA class I presentation by stimulating a pioneer round of translation-associated antigen production. Mol Cell 2022; 82:2557-2570.e7. [PMID: 35594857 DOI: 10.1016/j.molcel.2022.04.030] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 02/01/2022] [Accepted: 04/21/2022] [Indexed: 12/14/2022]
Abstract
Antigen presentation by the human leukocyte antigen (HLA) on the cell surface is critical for the transduction of the immune signal toward cytotoxic T lymphocytes. DNA damage upregulates HLA class I presentation; however, the mechanism is unclear. Here, we show that DNA-damage-induced HLA (di-HLA) presentation requires an immunoproteasome, PSMB8/9/10, and antigen-transporter, TAP1/2, demonstrating that antigen production is essential. Furthermore, we show that di-HLA presentation requires ATR, AKT, mTORC1, and p70-S6K signaling. Notably, the depletion of CBP20, a factor initiating the pioneer round of translation (PRT) that precedes nonsense-mediated mRNA decay (NMD), abolishes di-HLA presentation, suggesting that di-antigen production requires PRT. RNA-seq analysis demonstrates that DNA damage reduces NMD transcripts in an ATR-dependent manner, consistent with the requirement for ATR in the initiation of PRT/NMD. Finally, bioinformatics analysis identifies that PRT-derived 9-mer peptides bind to HLA and are potentially immunogenic. Therefore, DNA damage signaling produces immunogenic antigens by utilizing the machinery of PRT/NMD.
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25
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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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26
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Mosallaei D, Hao M, Antaya RJ, Levian B, Kwong A, Cogan J, Hamilton C, Schwieger-Briel A, Tan C, Tang X, Woodley DT, Chen M. Molecular and Clinical Outcomes After Intravenous Gentamicin Treatment for Patients With Junctional Epidermolysis Bullosa Caused by Nonsense Variants. JAMA Dermatol 2022; 158:366-374. [PMID: 35234826 PMCID: PMC8892363 DOI: 10.1001/jamadermatol.2021.5992] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
IMPORTANCE Junctional epidermolysis bullosa (JEB) is an incurable blistering skin disorder with high infant mortality often caused by nonsense variants in the genes that encode laminin 332. OBJECTIVE To evaluate the safety and outcomes following intravenous gentamicin readthrough therapy and subsequent laminin 332 expression in patients with JEB. DESIGN, SETTING, AND PARTICIPANTS This open-label, pilot nonrandomized clinical trial assessed 1 course of low- or high-dose intravenous gentamicin, including follow-up at 30 and 90 days after treatment. Five pediatric patients with JEB (2 with intermediate JEB and 3 with severe JEB) and confirmed nonsense variants in LAMA3 or LAMB3 in 1 or 2 alleles and decreased expression of laminin 332 at the dermal-epidermal junction of their skin participated in the study, which was performed at a single institution in collaboration with physicians and home infusion services near the patients from April 1, 2019, to February 28, 2021, with follow-up until May 31, 2021. INTERVENTIONS Three patients received gentamicin at 7.5 mg/kg daily for 14 days, and 2 patients received gentamicin at 10 mg/kg daily for 24 days. MAIN OUTCOMES AND MEASURES Primary outcomes were change in expression of laminin 332 in patients' skin and assessments for safety (ototoxic effects, nephrotoxic effects, and autoimmune response). Secondary outcomes included wound healing in monitored wounds and Epidermolysis Bullosa Disease Activity and Scarring Index (EBDASI) score. RESULTS After gentamicin treatment, all 5 patients (age range, 3 months to 10 years, 4 [80%] female) exhibited increased laminin 332 in the dermal-epidermal junction. By 1 month, 7 of 9 wounds in patients receiving low-dose intravenous gentamicin and all wounds in patients receiving high-dose intravenous gentamicin exhibited at least 50% wound closure. By 3 months, 8 of 9 wounds in patients receiving low-dose gentamicin and all wounds in patients receiving high-dose intravenous gentamicin exhibited greater than 85% closure. All 3 patients who were evaluated with EBDASI showed a decrease in total activity scores that met minimal clinically important differences 1 month after treatment. All 5 patients completed the study, and no ototoxic effects, nephrotoxic effects, or anti-laminin 332 antibodies were detected. CONCLUSIONS AND RELEVANCE In this nonrandomized clinical trial, intravenous gentamicin therapy was associated with induced readthrough of nonsense variants in patients with JEB, restored functional laminin 332 in their skin, and wound closure during the 3-month study period. Although long-term safety and efficacy requires further evaluation, a single cycle of intravenous gentamicin may be a safe and readily available therapy in the short term for this population of patients with JEB. TRIAL REGISTRATION ClinicalTrials.gov Identifiers: NCT03526159 and NCT04140786.
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Affiliation(s)
- Daniel Mosallaei
- Department of Dermatology, The Keck School of Medicine, University of Southern California, Los Angeles
| | - Michelle Hao
- Department of Dermatology, The Keck School of Medicine, University of Southern California, Los Angeles
| | - Richard J. Antaya
- Department of Dermatology and Pediatrics, Yale School of Medicine, New Haven, Connecticut
| | - Brandon Levian
- Department of Dermatology, The Keck School of Medicine, University of Southern California, Los Angeles
| | - Andrew Kwong
- Department of Dermatology, The Keck School of Medicine, University of Southern California, Los Angeles
| | - Jon Cogan
- Department of Dermatology, The Keck School of Medicine, University of Southern California, Los Angeles
| | - Claire Hamilton
- Department of Dermatology and Pediatrics, Yale School of Medicine, New Haven, Connecticut
| | - Agnes Schwieger-Briel
- Pediatric Skin Center, Division of Pediatric Dermatology, University Children’s Hospital Zurich, Zurich, Switzerland
| | - Calvin Tan
- Department of Dermatology, The Keck School of Medicine, University of Southern California, Los Angeles
| | - Xin Tang
- Department of Dermatology, The Keck School of Medicine, University of Southern California, Los Angeles
| | - David T. Woodley
- Department of Dermatology, The Keck School of Medicine, University of Southern California, Los Angeles
| | - Mei Chen
- Department of Dermatology, The Keck School of Medicine, University of Southern California, Los Angeles
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27
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Zhao J, Li Z, Puri R, Liu K, Nunez I, Chen L, Zheng S. Molecular profiling of individual FDA-approved clinical drugs identifies modulators of nonsense-mediated mRNA decay. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 27:304-318. [PMID: 35024243 PMCID: PMC8718828 DOI: 10.1016/j.omtn.2021.12.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 12/07/2021] [Indexed: 12/12/2022]
Abstract
Nonsense-mediated mRNA decay (NMD) degrades transcripts with premature stop codons. Given the prevalence of nonsense single nucleotide polymorphisms (SNPs) in the general population, it is urgent to catalog the effects of clinically approved drugs on NMD activity: any interference could alter the expression of nonsense SNPs, inadvertently inducing adverse effects. This risk is higher for patients with disease-causing nonsense mutations or an illness linked to dysregulated nonsense transcripts. On the other hand, hundreds of disorders are affected by cellular NMD efficiency and may benefit from NMD-modulatory drugs. Here, we profiled individual FDA-approved drugs for their impact on cellular NMD efficiency using a sensitive method that directly probes multiple endogenous NMD targets for a robust readout of NMD modulation. We found most FDA-approved drugs cause unremarkable effects on NMD, while many elicit clear transcriptional responses. Besides several potential mild NMD modulators, the anticancer drug homoharringtonine (HHT or omacetaxine mepesuccinate) consistently upregulates various endogenous NMD substrates in a dose-dependent manner in multiple cell types. We further showed translation inhibition mediates HHT's NMD effect. In summary, many FDA drugs induce transcriptional changes, and a few impact global NMD, and direct measurement of endogenous NMD substrate expression is robust to monitor cellular NMD.
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Affiliation(s)
- Jingrong Zhao
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA 91709, USA
| | - Zhelin Li
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA 91709, USA
| | - Ruchira Puri
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA 91709, USA
| | - Kelvin Liu
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA 91709, USA
| | - Israel Nunez
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA 91709, USA
| | - Liang Chen
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Sika Zheng
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA 91709, USA
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28
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Baradaran-Heravi A, Bauer CC, Pickles IB, Hosseini-Farahabadi S, Balgi AD, Choi K, Linley DM, Beech DJ, Roberge M, Bon RS. Nonselective TRPC channel inhibition and suppression of aminoglycoside-induced premature termination codon readthrough by the small molecule AC1903. J Biol Chem 2022; 298:101546. [PMID: 34999117 PMCID: PMC8808171 DOI: 10.1016/j.jbc.2021.101546] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/14/2021] [Accepted: 12/19/2021] [Indexed: 11/28/2022] Open
Abstract
Nonsense mutations, which occur in ∼11% of patients with genetic disorders, introduce premature termination codons (PTCs) that lead to truncated proteins and promote nonsense-mediated mRNA decay. Aminoglycosides such as G418 permit PTC readthrough and so may be used to address this problem. However, their effects are variable between patients, making clinical use of aminoglycosides challenging. In this study, we tested whether TRPC nonselective cation channels contribute to the variable PTC readthrough effect of aminoglycosides by controlling their cellular uptake. Indeed, a recently reported selective TRPC5 inhibitor, AC1903, consistently suppressed G418 uptake and G418-induced PTC readthrough in the DMS-114 cancer cell line and junctional epidermolysis bullosa (JEB) patient-derived keratinocytes. Interestingly, the effect of AC1903 in DMS-114 cells was mimicked by nonselective TRPC inhibitors, but not by well-characterized inhibitors of TRPC1/4/5 (Pico145, GFB-8438) or TRPC3/6/7 (SAR7334), suggesting that AC1903 may work through additional or undefined targets. Indeed, in our experiments, AC1903 inhibited multiple TRPC channels including TRPC3, TRPC4, TRPC5, TRPC6, TRPC4-C1, and TRPC5-C1, as well as endogenous TRPC1:C4 channels in A498 renal cancer cells, all with low micromolar IC50 values (1.8-18 μM). We also show that AC1903 inhibited TRPV4 channels, but had weak or no effects on TRPV1 and no effect on the nonselective cation channel PIEZO1. Our study reveals that AC1903 has previously unrecognized targets, which need to be considered when interpreting results from experiments with this compound. In addition, our data strengthen the hypothesis that nonselective calcium channels are involved in aminoglycoside uptake.
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Affiliation(s)
- Alireza Baradaran-Heravi
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada.
| | - Claudia C Bauer
- Discovery and Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds, UK
| | - Isabelle B Pickles
- Discovery and Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds, UK; School of Chemistry, University of Leeds, Leeds, UK
| | - Sara Hosseini-Farahabadi
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Aruna D Balgi
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Kunho Choi
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Deborah M Linley
- Discovery and Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds, UK
| | - David J Beech
- Discovery and Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds, UK
| | - Michel Roberge
- Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Robin S Bon
- Discovery and Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds, UK; Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK.
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29
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Kim YJ, Sivetz N, Layne J, Voss DM, Yang L, Zhang Q, Krainer AR. Exon-skipping antisense oligonucleotides for cystic fibrosis therapy. Proc Natl Acad Sci U S A 2022; 119:e2114858118. [PMID: 35017301 PMCID: PMC8784140 DOI: 10.1073/pnas.2114858118] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 11/16/2021] [Indexed: 11/25/2022] Open
Abstract
Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene cause cystic fibrosis (CF), and the CFTR-W1282X nonsense mutation causes a severe form of CF. Although Trikafta and other CFTR-modulation therapies benefit most CF patients, targeted therapy for patients with the W1282X mutation is lacking. The CFTR-W1282X protein has residual activity but is expressed at a very low level due to nonsense-mediated messenger RNA (mRNA) decay (NMD). NMD-suppression therapy and read-through therapy are actively being researched for CFTR nonsense mutants. NMD suppression could increase the mutant CFTR mRNA, and read-through therapies may increase the levels of full-length CFTR protein. However, these approaches have limitations and potential side effects: because the NMD machinery also regulates the expression of many normal mRNAs, broad inhibition of the pathway is not desirable, and read-through drugs are inefficient partly because the mutant mRNA template is subject to NMD. To bypass these issues, we pursued an exon-skipping antisense oligonucleotide (ASO) strategy to achieve gene-specific NMD evasion. A cocktail of two splice-site-targeting ASOs induced the expression of CFTR mRNA without the premature-termination-codon-containing exon 23 (CFTR-Δex23), which is an in-frame exon. Treatment of human bronchial epithelial cells with this cocktail of ASOs that target the splice sites flanking exon 23 results in efficient skipping of exon 23 and an increase in CFTR-Δex23 protein. The splice-switching ASO cocktail increases the CFTR-mediated chloride current in human bronchial epithelial cells. Our results set the stage for developing an allele-specific therapy for CF caused by the W1282X mutation.
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Affiliation(s)
- Young Jin Kim
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
- Graduate Program in Genetics, Stony Brook University, Stony Brook, NY 11794
- Medical Scientist Training Program, Stony Brook University School of Medicine, Stony Brook, NY 11794
| | - Nicole Sivetz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Jessica Layne
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Dillon M Voss
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
- Graduate Program in Genetics, Stony Brook University, Stony Brook, NY 11794
- Medical Scientist Training Program, Stony Brook University School of Medicine, Stony Brook, NY 11794
| | - Lucia Yang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
- Graduate Program in Genetics, Stony Brook University, Stony Brook, NY 11794
- Medical Scientist Training Program, Stony Brook University School of Medicine, Stony Brook, NY 11794
| | - Qian Zhang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
- Graduate Program in Molecular and Cell Biology, Stony Brook University, Stony Brook, NY 11794
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Kabadi AM, Machlin L, Dalal N, Lee RE, McDowell I, Shah NN, Drowley L, Randell SH, Reddy TE. Epigenome editing of the CFTR-locus for treatment of cystic fibrosis. J Cyst Fibros 2022; 21:164-171. [PMID: 34049825 PMCID: PMC8613331 DOI: 10.1016/j.jcf.2021.04.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 03/31/2021] [Accepted: 04/19/2021] [Indexed: 01/03/2023]
Abstract
BACKGROUND Mechanisms governing the diversity of CFTR gene expression throughout the body are complex. Multiple intronic and distal regulatory elements are responsible for regulating differential CFTR expression across tissues. METHODS Drawing on published data, 18 high-priority genomic regions were identified and interrogated for CFTR-enhancer function using CRISPR/dCas9-based epigenome editing tools. Each region was evaluated by dCas9p300 and dCas9KRAB for its ability to enhance or repress CFTR expression, respectively. RESULTS Multiple genomic regions were tested for enhancer activity using CRISPR/dCas9 epigenome editing. dCas9p300 mediates a significant increase in CFTR mRNA levels when targeted to the promoter and a region 44 kb upstream of the transcriptional start site in a CFTR-low expressing cell line. Multiple gRNAs targeting the promoter induced a robust increase in CFTR protein levels. In contrast, dCas9KRAB-mediated repression is much more robust with 10 of the 18 evaluated genomic regions inducing CFTR protein knockdown. To evaluate the therapeutic efficacy of modulating CFTR gene regulation, dCas9p300 was used to induce elevated levels of CFTR from the endogenous locus in ΔF508/ΔF508 human bronchial epithelial cells. Ussing chamber studies demonstrated a synergistic increase in ion transport in response to CRISPR-induced expression of ΔF508 CFTR mRNA along with VX809 treatment. CONCLUSIONS CRISPR/dCas9-based epigenome-editing provides a previously unexplored tool for interrogating CFTR enhancer function. Here, we demonstrate that therapeutic interventions that increase the expression of CFTR may improve the efficacy of CFTR modulators. A better understanding CFTR regulatory mechanisms could uncover novel therapeutic interventions for the development of cystic fibrosis therapies.
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Affiliation(s)
- Ami M Kabadi
- Element Genomics, a UCB Pharma company, Durham, NC, USA.
| | - Leah Machlin
- Element Genomics, a UCB Pharma company, Durham, NC, USA
| | - Nikita Dalal
- Element Genomics, a UCB Pharma company, Durham, NC, USA
| | - Rhianna E Lee
- Marsico Lung Institute, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ian McDowell
- Element Genomics, a UCB Pharma company, Durham, NC, USA
| | - Nirav N Shah
- Element Genomics, a UCB Pharma company, Durham, NC, USA
| | | | - Scott H Randell
- Marsico Lung Institute, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Timothy E Reddy
- Element Genomics, a UCB Pharma company, Durham, NC, USA; Department of Biostatistics and Bioinformatics, Duke University Medical School, Durham, NC, USA.
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Wang C, Luo X, Wang Y, Liu Z, Wu S, Wang S, Lan X, Xu Q, Xu W, Yuan F, Wang A, Zeng F, Jia J, Chen Y. Novel Mutations of the ALMS1 Gene in Patients with Alström Syndrome. Intern Med 2021; 60:3721-3728. [PMID: 34148947 PMCID: PMC8710367 DOI: 10.2169/internalmedicine.6467-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Objective Alström syndrome is an autosomal recessive genetic disease caused by a mutation in the ALMS1 gene. Alström syndrome is clinically characterized by multisystem involvement, including sensorineural deafness, cone-rod dystrophy, nystagmus, obesity, insulin resistance, type 2 diabetes and hypogonadism. The diagnosis is thus challenging for patients without this characteristic set of clinical symptoms. We explored the effectiveness of whole-exome sequencing in the diagnosis of Alström syndrome. Methods A girl with symptoms of Alström syndrome was tested and diagnosed with the disease by whole-exome sequencing. Results Whole-exome sequencing revealed two novel variants, c.6160_6161insAT: p.Lys2054Asnfs*21 (exon 8) and c.10823_10824 delAG:p.Glu 3608Alafs*9 (exon16) in the ALMS1 gene, leading to premature termination codons and the domain of ALMS1 protein. Blood sample testing of her asymptomatic parents revealed them to be heterozygous carriers of the same mutations. Assembly showed that the mutations on both alleles were located in conserved sequences. A review of the ALMS1 gene nonsense mutation status was performed. Conclusion We herein report two novel variants of the ALMS1 gene discovered in a Chinese Alström syndrome patient that expand the mutational spectrum of ALMS1 and provided new insight into the molecular mechanism underlying Alström syndrome. Our findings add to the current knowledge concerning the diagnosis and treatment of Alström syndrome.
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Affiliation(s)
- Chunmei Wang
- Department of Neurology, Children's Hospital of Shanghai, Shanghai JiaoTong University, China
| | - Xiaona Luo
- Department of Neurology, Children's Hospital of Shanghai, Shanghai JiaoTong University, China
| | - Yilin Wang
- Department of Neurology, Children's Hospital of Shanghai, Shanghai JiaoTong University, China
| | - Zhao Liu
- Division of Pediatric Neurology, Department of Pediatrics, University of Illinois and Children's Hospital of Illinois, USA
| | - Shengnan Wu
- Department of Neurology, Children's Hospital of Shanghai, Shanghai JiaoTong University, China
| | - Simei Wang
- Department of Neurology, Children's Hospital of Shanghai, Shanghai JiaoTong University, China
| | - Xiaoping Lan
- Department of Neurology, Children's Hospital of Shanghai, Shanghai JiaoTong University, China
| | - Quanmei Xu
- Department of Neurology, Children's Hospital of Shanghai, Shanghai JiaoTong University, China
| | - Wuhen Xu
- Department of Neurology, Children's Hospital of Shanghai, Shanghai JiaoTong University, China
| | - Fang Yuan
- Department of Neurology, Children's Hospital of Shanghai, Shanghai JiaoTong University, China
| | - Anqi Wang
- Department of Neurology, Children's Hospital of Shanghai, Shanghai JiaoTong University, China
| | - Fanyi Zeng
- NHC Key Laboratory of Medical Embryogenesis and Developmental Molecular Biology & Shanghai Key Laboratory of Embryo and Reproduction Engineering, China
| | - Jia Jia
- Fuxiang Gene Engineering Research Institute, China
| | - Yucai Chen
- Department of Neurology, Children's Hospital of Shanghai, Shanghai JiaoTong University, China
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Schneider N, Sundaresan Y, Gopalakrishnan P, Beryozkin A, Hanany M, Levanon EY, Banin E, Ben-Aroya S, Sharon D. Inherited retinal diseases: Linking genes, disease-causing variants, and relevant therapeutic modalities. Prog Retin Eye Res 2021; 89:101029. [PMID: 34839010 DOI: 10.1016/j.preteyeres.2021.101029] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 11/11/2021] [Accepted: 11/16/2021] [Indexed: 12/11/2022]
Abstract
Inherited retinal diseases (IRDs) are a clinically complex and heterogenous group of visual impairment phenotypes caused by pathogenic variants in at least 277 nuclear and mitochondrial genes, affecting different retinal regions, and depleting the vision of affected individuals. Genes that cause IRDs when mutated are unique by possessing differing genotype-phenotype correlations, varying inheritance patterns, hypomorphic alleles, and modifier genes thus complicating genetic interpretation. Next-generation sequencing has greatly advanced the identification of novel IRD-related genes and pathogenic variants in the last decade. For this review, we performed an in-depth literature search which allowed for compilation of the Global Retinal Inherited Disease (GRID) dataset containing 4,798 discrete variants and 17,299 alleles published in 31 papers, showing a wide range of frequencies and complexities among the 194 genes reported in GRID, with 65% of pathogenic variants being unique to a single individual. A better understanding of IRD-related gene distribution, gene complexity, and variant types allow for improved genetic testing and therapies. Current genetic therapeutic methods are also quite diverse and rely on variant identification, and range from whole gene replacement to single nucleotide editing at the DNA or RNA levels. IRDs and their suitable therapies thus require a range of effective disease modelling in human cells, granting insight into disease mechanisms and testing of possible treatments. This review summarizes genetic and therapeutic modalities of IRDs, provides new analyses of IRD-related genes (GRID and complexity scores), and provides information to match genetic-based therapies such as gene-specific and variant-specific therapies to the appropriate individuals.
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Affiliation(s)
- Nina Schneider
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel
| | - Yogapriya Sundaresan
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel
| | - Prakadeeswari Gopalakrishnan
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel
| | - Avigail Beryozkin
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel
| | - Mor Hanany
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Eyal Banin
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel
| | - Shay Ben-Aroya
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Dror Sharon
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel.
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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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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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Eintracht J, Forsythe E, May-Simera H, Moosajee M. Translational readthrough of ciliopathy genes BBS2 and ALMS1 restores protein, ciliogenesis and function in patient fibroblasts. EBioMedicine 2021; 70:103515. [PMID: 34365092 PMCID: PMC8353411 DOI: 10.1016/j.ebiom.2021.103515] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 07/13/2021] [Accepted: 07/19/2021] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Ciliary dysfunction underlies a range of genetic disorders collectively termed ciliopathies, for which there are no treatments available. Bardet-Biedl syndrome (BBS) is characterised by multisystemic involvement, including rod-cone dystrophy and renal abnormalities. Together with Alström syndrome (AS), they are known as the 'obesity ciliopathies' due to their common phenotype. Nonsense mutations are responsible for approximately 11% and 40% of BBS and AS cases, respectively. Translational readthrough inducing drugs (TRIDs) can restore full-length protein bypassing in-frame premature termination codons, and are a potential therapeutic approach for nonsense-mediated ciliopathies. METHODS Patient fibroblasts harbouring nonsense mutations from two different ciliopathies (Bardet-Biedl Syndrome and Alström Syndrome) were treated with PTC124 (ataluren) or amlexanox. Following treatment, gene expression, protein levels and ciliogenesis were evaluated. The expression of intraflagellar transport protein IFT88 and G-protein coupled receptor SSTR3 was investigated as a readout of ciliary function. FINDINGS mRNA expression was significantly increased in amlexanox-treated patient fibroblasts, and full-length BBS2 or ALMS1 protein expression was restored in PTC124- and amlexanox-treated fibroblasts. Treatment with TRIDs significantly improved ciliogenesis defects in BBS2Y24*/R275* fibroblasts. Treatment recovered IFT88 expression and corrected SSTR3 mislocalisation in BBS2Y24*/R275* and ALMS1S1645*/S1645* fibroblasts, suggesting rescue of ciliary function. INTERPRETATION The recovery of full-length BBS2 and ALMS1 expression and correction of anatomical and functional ciliary defects in BBS2Y24*/R275* and ALMS1S1645*/S1645* fibroblasts suggest TRIDs are a potential therapeutic option for the treatment of nonsense-mediated ciliopathies. FUNDING Wellcome Trust 205174/Z/16/Z, National Centre for the Replacement, Refinement & Reduction of Animals in Research. Deutsche Forschungsgemeinschaft SPP2127 (DFG Grant MA 6139/3-1).
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Affiliation(s)
| | - Elizabeth Forsythe
- Clinical Genetics Unit, Great Ormond Street Hospital; Genetics and Genomic Medicine Programme, Great Ormond Street Institute of Child Health
| | - Helen May-Simera
- Institute of Molecular Physiology, Johannes Gutenburg University, Mainz
| | - Mariya Moosajee
- UCL Institute of Ophthalmology, London, United Kingdom; The Francis Crick Institute, London, United Kingdom; Moorfields Eye Hospital NHS Foundation Trust, London, United Kingdom; Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom.
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Xie Z, Jiang J, Cao L, Jiang M, Yang F, Ma Z, Wang Z, Ruan C, Liu H, Zhou L. Nonsense-mediated mRNA decay efficiency influences bleeding severity in ITGA2B c.2659C > T (p.Q887X) knock-in mice. Clin Genet 2021; 100:213-218. [PMID: 33928629 DOI: 10.1111/cge.13975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 04/22/2021] [Accepted: 04/26/2021] [Indexed: 11/28/2022]
Abstract
Glanzmann's thrombasthenia (GT) is a severe hemorrhagic disease. It is caused by mutations in ITGA2B or ITGB3, which are the respective genes encoding integrin αIIb and β3. Despite widespread mutational analysis, the mechanisms underlying the extensive variability in bleeding severity observed among affected individuals remains poorly understood. In order to explore the mechanisms conferring for bleeding heterogeneity, three GT patients with ITGA2B c.2671C > T (p.Q891X) who possessed different bleeding scores were studied. Analysis showed that there was significant difference in nonsense-mediated mRNA decay (NMD) efficiency among the three patients. These differences positively correlated with their bleeding score. Next, a knock-in mouse model (KI mice) with the ITGA2B c.2659C > T (p.Q887X) was generated using CRISPR/Cas9. Importantly, this mutation is homologous to ITGA2B c.2671C > T (p.Q891X) in humans. The bleeding time of KI mice was significantly in comparison to the wide-type mice. Interestingly, bleeding was stopped after treatment with caffeine, which is a known NMD inhibitor. This suggests that NMD efficiency potentially influences bleeding severity in ITGA2B c.2659C > T (p.Q887X) KI mice.
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Affiliation(s)
- Zhanli Xie
- Department of Nuclear Medicine, Institute of Clinical Medicine Research, Suzhou Hospital (West District), Affiliated to Nanjing Medical University, Suzhou Science and Technology Town Hospital, Suzhou, China
- Hematology department, Affiliated Hospital of Nantong University, Nantong, China
| | - Jiang Jiang
- Department of Nuclear Medicine, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Lijuan Cao
- Jiangsu Institute of Hematology, Key Laboratory of Thrombosis & Hemostasis of Ministry of Health, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Miao Jiang
- Jiangsu Institute of Hematology, Key Laboratory of Thrombosis & Hemostasis of Ministry of Health, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Fei Yang
- Jiangsu Institute of Hematology, Key Laboratory of Thrombosis & Hemostasis of Ministry of Health, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Zhenni Ma
- Jiangsu Institute of Hematology, Key Laboratory of Thrombosis & Hemostasis of Ministry of Health, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Zhaoyue Wang
- Jiangsu Institute of Hematology, Key Laboratory of Thrombosis & Hemostasis of Ministry of Health, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Changgeng Ruan
- Jiangsu Institute of Hematology, Key Laboratory of Thrombosis & Hemostasis of Ministry of Health, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Hong Liu
- Hematology department, Affiliated Hospital of Nantong University, Nantong, China
| | - Lu Zhou
- Hematology department, Affiliated Hospital of Nantong University, Nantong, China
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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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Schilff M, Sargsyan Y, Hofhuis J, Thoms S. Stop Codon Context-Specific Induction of Translational Readthrough. Biomolecules 2021; 11:biom11071006. [PMID: 34356630 PMCID: PMC8301745 DOI: 10.3390/biom11071006] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/28/2021] [Accepted: 07/01/2021] [Indexed: 12/11/2022] Open
Abstract
Premature termination codon (PTC) mutations account for approximately 10% of pathogenic variants in monogenic diseases. Stimulation of translational readthrough, also known as stop codon suppression, using translational readthrough-inducing drugs (TRIDs) may serve as a possible therapeutic strategy for the treatment of genetic PTC diseases. One important parameter governing readthrough is the stop codon context (SCC)-the stop codon itself and the nucleotides in the vicinity of the stop codon on the mRNA. However, the quantitative influence of the SCC on treatment outcome and on appropriate drug concentrations are largely unknown. Here, we analyze the readthrough-stimulatory effect of various readthrough-inducing drugs on the SCCs of five common premature termination codon mutations of PEX5 in a sensitive dual reporter system. Mutations in PEX5, encoding the peroxisomal targeting signal 1 receptor, can cause peroxisomal biogenesis disorders of the Zellweger spectrum. We show that the stop context has a strong influence on the levels of readthrough stimulation and impacts the choice of the most effective drug and its concentration. These results highlight potential advantages and the personalized medicine nature of an SCC-based strategy in the therapy of rare diseases.
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Affiliation(s)
- Mirco Schilff
- Department of Child and Adolescent Health, University Medical Center, 37075 Göttingen, Germany; (M.S.); (Y.S.); (J.H.)
| | - Yelena Sargsyan
- Department of Child and Adolescent Health, University Medical Center, 37075 Göttingen, Germany; (M.S.); (Y.S.); (J.H.)
| | - Julia Hofhuis
- Department of Child and Adolescent Health, University Medical Center, 37075 Göttingen, Germany; (M.S.); (Y.S.); (J.H.)
- Department of Biochemistry and Molecular Medicine, Medical School, Bielefeld University, 33615 Bielefeld, Germany
| | - Sven Thoms
- Department of Child and Adolescent Health, University Medical Center, 37075 Göttingen, Germany; (M.S.); (Y.S.); (J.H.)
- Department of Biochemistry and Molecular Medicine, Medical School, Bielefeld University, 33615 Bielefeld, Germany
- Correspondence: ; Tel.: +49-521-106-86502
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Antisense oligonucleotide-based drug development for Cystic Fibrosis patients carrying the 3849+10 kb C-to-T splicing mutation. J Cyst Fibros 2021; 20:865-875. [PMID: 34226157 PMCID: PMC8464507 DOI: 10.1016/j.jcf.2021.06.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 06/09/2021] [Accepted: 06/10/2021] [Indexed: 01/24/2023]
Abstract
Background: Antisense oligonucleotide (ASO)-based drugs for splicing modulation were recently approved for various genetic diseases with unmet need. Here we aimed to develop an ASO-based splicing modulation therapy for Cystic Fibrosis (CF) patients carrying the 3849 + 10 kb C-to-T splicing mutation in the CFTR gene. Methods: We have screened, in FRT cells expressing the 3849 + 10 kb C-to-T splicing mutation, ~30 2ʹ-O-Methyl-modified phosphorothioate ASOs, targeted to prevent the recognition and inclusion of a cryptic exon generated due to the mutation. The effect of highly potent ASO candidates on the splicing pattern, protein maturation and CFTR function was further analyzed in well differentiated primary human nasal and bronchial epithelial cells, derived from patients carrying at least one 3849 + 10 kb C-to-T allele. Results: A highly potent lead ASO, efficiently delivered by free uptake, was able to significantly increase the level of correctly spliced mRNA and completely restore the CFTR function to wild type levels in cells from a homozygote patient. This ASO led to CFTR function with an average of 43% of wild type levels in cells from various heterozygote patients. Optimized efficiency of the lead ASO was further obtained with 2ʹ-Methoxy Ethyl modification (2ʹMOE). Conclusion: The highly efficient splicing modulation and functional correction, achieved by free uptake of the selected lead ASO in various patients, demonstrate the ASO therapeutic potential benefit for CF patients carrying splicing mutations and is aimed to serve as the basis for our current clinical development.
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Porter JJ, Heil CS, Lueck JD. Therapeutic promise of engineered nonsense suppressor tRNAs. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021; 12:e1641. [PMID: 33567469 PMCID: PMC8244042 DOI: 10.1002/wrna.1641] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 12/16/2020] [Accepted: 12/23/2020] [Indexed: 12/11/2022]
Abstract
Nonsense mutations change an amino acid codon to a premature termination codon (PTC) generally through a single-nucleotide substitution. The generation of a PTC results in a defective truncated protein and often in severe forms of disease. Because of the exceedingly high prevalence of nonsense-associated diseases and a unifying mechanism, there has been a concerted effort to identify PTC therapeutics. Most clinical trials for PTC therapeutics have been conducted with small molecules that promote PTC read through and incorporation of a near-cognate amino acid. However, there is a need for PTC suppression agents that recode PTCs with the correct amino acid while being applicable to PTC mutations in many different genomic landscapes. With these characteristics, a single therapeutic will be able to treat several disease-causing PTCs. In this review, we will focus on the use of nonsense suppression technologies, in particular, suppressor tRNAs (sup-tRNAs), as possible therapeutics for correcting PTCs. Sup-tRNAs have many attractive qualities as possible therapeutic agents although there are knowledge gaps on their function in mammalian cells and technical hurdles that need to be overcome before their promise is realized. This article is categorized under: RNA Processing > tRNA Processing Translation > Translation Regulation.
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Affiliation(s)
- Joseph J. Porter
- Department of Pharmacology and PhysiologyUniversity of Rochester Medical CenterRochesterNew YorkUSA
| | - Christina S. Heil
- Department of Pharmacology and PhysiologyUniversity of Rochester Medical CenterRochesterNew YorkUSA
| | - John D. Lueck
- Department of Pharmacology and PhysiologyUniversity of Rochester Medical CenterRochesterNew YorkUSA
- Department of NeurologyUniversity of Rochester Medical CenterRochesterNew YorkUSA
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41
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May HJ, Jeong J, Revah-Politi A, Cohen JS, Chassevent A, Baptista J, Baugh EH, Bier L, Bottani A, Carminho A Rodrigues MT, Conlon C, Fluss J, Guipponi M, Kim CA, Matsumoto N, Person R, Primiano M, Rankin J, Shinawi M, Smith-Hicks C, Telegrafi A, Toy S, Uchiyama Y, Aggarwal V, Goldstein DB, Roche KW, Anyane-Yeboa K. Truncating variants in the SHANK1 gene are associated with a spectrum of neurodevelopmental disorders. Genet Med 2021; 23:1912-1921. [PMID: 34113010 DOI: 10.1038/s41436-021-01222-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 05/07/2021] [Accepted: 05/10/2021] [Indexed: 11/09/2022] Open
Abstract
PURPOSE In this study, we aimed to characterize the clinical phenotype of a SHANK1-related disorder and define the functional consequences of SHANK1 truncating variants. METHODS Exome sequencing (ES) was performed for six individuals who presented with neurodevelopmental disorders. Individuals were ascertained with the use of GeneMatcher and Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources (DECIPHER). We evaluated potential nonsense-mediated decay (NMD) of two variants by making knock-in cell lines of endogenous truncated SHANK1, and expressed the truncated SHANK1 complementary DNA (cDNA) in HEK293 cells and cultured hippocampal neurons to examine the proteins. RESULTS ES detected de novo truncating variants in SHANK1 in six individuals. Evaluation of NMD resulted in stable transcripts, and the truncated SHANK1 completely lost binding with Homer1, a linker protein that binds to the C-terminus of SHANK1. These variants may disrupt protein-protein networks in dendritic spines. Dispersed localization of the truncated SHANK1 variants within the spine and dendritic shaft was also observed when expressed in neurons, indicating impaired synaptic localization of truncated SHANK1. CONCLUSION This report expands the clinical spectrum of individuals with truncating SHANK1 variants and describes the impact these variants may have on the pathophysiology of neurodevelopmental disorders.
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Affiliation(s)
- Halie J May
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, USA.
| | - Jaehoon Jeong
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Anya Revah-Politi
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, USA.,Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Julie S Cohen
- Department of Neurology and Developmental Medicine, Kennedy Krieger Institute, Baltimore, MD, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Anna Chassevent
- Department of Neurology and Developmental Medicine, Kennedy Krieger Institute, Baltimore, MD, USA
| | - Julia Baptista
- Exeter Genomics Laboratory, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK.,Institute of Biomedical & Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Evan H Baugh
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Louise Bier
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Armand Bottani
- Division of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | | | - Charles Conlon
- Department of Neurology and Developmental Medicine, Kennedy Krieger Institute, Baltimore, MD, USA
| | - Joel Fluss
- Pediatric Neurology Unit, Pediatrics Subspecialties Service, Geneva Children's Hospital, Geneva, Switzerland
| | - Michel Guipponi
- Division of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - Chong Ae Kim
- Genetics Unit, Instituto da Crianca, Hospital das Clinicas, Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Richard Person
- Clinical Genomics Program, GeneDx, Gaithersburg, MD, USA
| | - Michelle Primiano
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Julia Rankin
- Department of Clinical Genetics, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Marwan Shinawi
- Department of Pediatrics, Division of Genetics and Genomic Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Constance Smith-Hicks
- Department of Neurology and Developmental Medicine, Kennedy Krieger Institute, Baltimore, MD, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Aida Telegrafi
- Clinical Genomics Program, GeneDx, Gaithersburg, MD, USA
| | - Samantha Toy
- Department of Pediatrics, Division of Genetics and Genomic Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Rare Disease Genomics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Vimla Aggarwal
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Katherine W Roche
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Kwame Anyane-Yeboa
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, USA. .,Division of Clinical Genetics, Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA.
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42
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Bergeron C, Cantin AM. New Therapies to Correct the Cystic Fibrosis Basic Defect. Int J Mol Sci 2021; 22:ijms22126193. [PMID: 34201249 PMCID: PMC8227161 DOI: 10.3390/ijms22126193] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/31/2021] [Accepted: 06/04/2021] [Indexed: 12/24/2022] Open
Abstract
Rare diseases affect 400 million individuals worldwide and cause significant morbidity and mortality. Finding solutions for rare diseases can be very challenging for physicians and researchers. Cystic fibrosis (CF), a genetic, autosomal recessive, multisystemic, life-limiting disease does not escape this sad reality. Despite phenomenal progress in our understanding of this disease, treatment remains difficult. Until recently, therapies for CF individuals were focused on symptom management. The discovery of the cystic fibrosis transmembrane conductance regulator (CFTR) gene and its product, a protein present at the apical surface of epithelial cells regulating ion transport, allowed the scientific community to learn about the basic defect in CF and to study potential therapies targeting the dysfunctional protein. In the past few years, promising therapies with the goal to restore CFTR function became available and changed the lives of several CF patients. These medications, called CFTR modulators, aim to correct, potentialize, stabilize or amplify CFTR function. Furthermore, research is ongoing to develop other targeted therapies that could be more efficient and benefit a larger proportion of the CF community. The purpose of this review is to summarize our current knowledge of CF genetics and therapies restoring CFTR function, particularly CFTR modulators and gene therapy.
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Affiliation(s)
- Christelle Bergeron
- Department of Medicine, Respiratory Division, Faculty of Medicine and Health Sciences, University of Sherbrooke, Sherbrooke, QC J1H 5N4, Canada;
| | - André M. Cantin
- Department of Medicine, Respiratory Division, Faculty of Medicine and Health Sciences, University of Sherbrooke, Sherbrooke, QC J1H 5N4, Canada;
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Respiratory Division, Faculty of Medicine, University of Sherbrooke, 3001, 12e Avenue Nord, Sherbrooke, QC J1H 5N4, Canada
- Correspondence: ; Tel.: +1-819-346-1110 (ext. 14893); Fax: +1-819-564-5377
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43
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Santos L, Mention K, Cavusoglu-Doran K, Sanz DJ, Bacalhau M, Lopes-Pacheco M, Harrison PT, Farinha CM. Comparison of Cas9 and Cas12a CRISPR editing methods to correct the W1282X-CFTR mutation. J Cyst Fibros 2021; 21:181-187. [PMID: 34103250 DOI: 10.1016/j.jcf.2021.05.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 05/07/2021] [Accepted: 05/22/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND W1282X-CFTR variant (c.3846G>A) is the second most common nonsense cystic fibrosis (CF)-causing mutation in the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene. Even though remarkable breakthroughs have been done towards CF treatment with the approval of four CFTR protein modulators, none of these are approved for patients with nonsense mutations. CRISPR gene editing tools can be of great value to permanently correct the genetic defects caused by these mutations. METHODS We compared the capacity of homology-directed repair (HDR) mediated by Cas9 or Cas12a to correct W1282X CFTR mutation in the CFF-16HBEge W1282X CFTR cell line (obtained from CFF), using Cas9/gRNA and Cas12a/gRNA ribonucleoproteins (RNPs) and single strand DNA (ssODN) oligonucleotide donors. RESULTS Cas9 shows higher levels of correction than Cas12a as, by electroporating cells with Cas9 RNPs and ssODN donor, nearly 18% of precise editing was achieved compared to just 8% for Cas12a. Such levels of correction increase the abundance of CFTR mRNA and protein, and partially restore CFTR function in the pool of edited cells to 18% of WT CFTR function. Moreover, homozygous corrected clones produced levels of mRNA, protein, and function comparable to those of cells expressing WT CFTR. CONCLUSION Altogether, this work demonstrates the potential of gene editing as a therapeutic strategy for CF directly correcting the root cause of the disease.
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Affiliation(s)
- Lúcia Santos
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8 bdg, Lisboa 1749-016, Portugal; Department of Physiology, University College Cork, Cork T12 K8AF, Ireland
| | - Karen Mention
- Department of Physiology, University College Cork, Cork T12 K8AF, Ireland
| | | | - David J Sanz
- Department of Physiology, University College Cork, Cork T12 K8AF, Ireland
| | - Mafalda Bacalhau
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8 bdg, Lisboa 1749-016, Portugal
| | - Miquéias Lopes-Pacheco
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8 bdg, Lisboa 1749-016, Portugal
| | - Patrick T Harrison
- Department of Physiology, University College Cork, Cork T12 K8AF, Ireland
| | - Carlos M Farinha
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8 bdg, Lisboa 1749-016, Portugal.
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44
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Martins-Dias P, Romão L. Nonsense suppression therapies in human genetic diseases. Cell Mol Life Sci 2021; 78:4677-4701. [PMID: 33751142 PMCID: PMC11073055 DOI: 10.1007/s00018-021-03809-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 02/06/2021] [Accepted: 03/05/2021] [Indexed: 02/06/2023]
Abstract
About 11% of all human disease-associated gene lesions are nonsense mutations, resulting in the introduction of an in-frame premature translation-termination codon (PTC) into the protein-coding gene sequence. When translated, PTC-containing mRNAs originate truncated and often dysfunctional proteins that might be non-functional or have gain-of-function or dominant-negative effects. Therapeutic strategies aimed at suppressing PTCs to restore deficient protein function-the so-called nonsense suppression (or PTC readthrough) therapies-have the potential to provide a therapeutic benefit for many patients and in a broad range of genetic disorders, including cancer. These therapeutic approaches comprise the use of translational readthrough-inducing compounds that make the translational machinery recode an in-frame PTC into a sense codon. However, most of the mRNAs carrying a PTC can be rapidly degraded by the surveillance mechanism of nonsense-mediated decay (NMD), thus decreasing the levels of PTC-containing mRNAs in the cell and their availability for PTC readthrough. Accordingly, the use of NMD inhibitors, or readthrough-compound potentiators, may enhance the efficiency of PTC suppression. Here, we review the mechanisms of PTC readthrough and their regulation, as well as the recent advances in the development of novel approaches for PTC suppression, and their role in personalized medicine.
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Affiliation(s)
- Patrícia Martins-Dias
- Department of Human Genetics, Instituto Nacional de Saúde Doutor Ricardo Jorge, Av. Padre Cruz, 1649-016, Lisbon, Portugal
- Faculty of Sciences, BioISI-Biosystems and Integrative Sciences Institute, University of Lisboa, 1749-016, Lisbon, Portugal
| | - Luísa Romão
- Department of Human Genetics, Instituto Nacional de Saúde Doutor Ricardo Jorge, Av. Padre Cruz, 1649-016, Lisbon, Portugal.
- Faculty of Sciences, BioISI-Biosystems and Integrative Sciences Institute, University of Lisboa, 1749-016, Lisbon, Portugal.
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45
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Talebi S, Safarian M, Jaafari MR, Sayedi SJ, Abbasi Z, Ranjbar G, Kianifar HR. The effects of nano-curcumin as a nutritional strategy on clinical and inflammatory factors in children with cystic fibrosis: the study protocol for a randomized controlled trial. Trials 2021; 22:292. [PMID: 33879218 PMCID: PMC8056493 DOI: 10.1186/s13063-021-05224-6] [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: 09/14/2020] [Accepted: 03/25/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cystic fibrosis (CF) is a genetic disorder, which is caused by the CFTR protein defects. Along with CFTR dysfunction, inflammation plays a key role in the disease outcomes. Inflammation may develop due to the internal dysfunction of the CFTR protein or external factors. Curcumin affects the CFTR protein function primarily as a corrector and potentiator and secondary as an anti-inflammatory and antimicrobial agent. The present study aims to assess the impact of nano-curcumin on clinical and inflammatory markers in children with CF. METHODS This prospective, double blind control trial will be conducted at the Akbar Children's Hospital in Mashhad, Iran. Children with CF will be enrolled based on the eligibility criteria. Placebo and curcumin with the maximum dose of 80 mg considering the body surface of the patients will be administrated for 3 months. The primary outcome is to evaluate inflammation based on serum interleukin-6, interleukin-10, and hs-CRP, stool calprotectin, and neutrophil count of nasopharyngeal swab. The secondary outcome involved clinical assessment via spirometry, anthropometrics, and quality of life. They will be assessed before and after 3 months. DISCUSSION Due to the multifarious effects of curcumin on CF disease, it could be proposed as a nutritional strategy in the treatment of cystic fibrosis. TRIAL REGISTRATION Iranian Registry of Clinical Trials IRCT20200705048018N1 . Registered on July 10, 2020.
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Affiliation(s)
- Saeedeh Talebi
- Department of Nutrition, Faculty of medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahammad Safarian
- Department of Nutrition, Faculty of medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahmood Reza Jaafari
- Nanotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Javad Sayedi
- Department of Pediatrics, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Zahra Abbasi
- Akbar clinical research and development unit, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Golnaz Ranjbar
- Department of Nutrition, Faculty of Medicine, Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hamid Reza Kianifar
- Department of Pediatrics, Mashhad University of Medical Sciences, Mashhad, Iran.
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46
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Maule G, Ensinck M, Bulcaen M, Carlon MS. Rewriting CFTR to cure cystic fibrosis. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 182:185-224. [PMID: 34175042 DOI: 10.1016/bs.pmbts.2020.12.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Cystic fibrosis (CF) is an autosomal recessive monogenic disease caused by mutations in the Cystic Fibrosis Transmembrane conductance Regulator (CFTR) gene. Although F508del is the most frequent mutation, there are in total 360 confirmed disease-causing CFTR mutations, impairing CFTR production, function and stability. Currently, the only causal treatments available are CFTR correctors and potentiators that directly target the mutant protein. While these pharmacological advances and better symptomatic care have improved life expectancy of people with CF, none of these treatments provides a cure. The discovery and development of programmable nucleases, in particular CRISPR nucleases and derived systems, rekindled the field of CF gene therapy, offering the possibility of a permanent correction of the CFTR gene. In this review we will discuss different strategies to restore CFTR function via gene editing correction of CFTR mutations or enhanced CFTR expression, and address how best to deliver these treatments to target cells.
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Affiliation(s)
- Giulia Maule
- Department CIBIO, University of Trento, Trento, Italy; Institute of Biophysics, National Research Council, Trento, Italy
| | - Marjolein Ensinck
- Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Flanders, Belgium
| | - Mattijs Bulcaen
- Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Flanders, Belgium
| | - Marianne S Carlon
- Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Flanders, Belgium.
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47
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Sharma J, Abbott J, Klaskala L, Zhao G, Birket SE, Rowe SM. A Novel G542X CFTR Rat Model of Cystic Fibrosis Is Sensitive to Nonsense Mediated Decay. Front Physiol 2020; 11:611294. [PMID: 33391025 PMCID: PMC7772197 DOI: 10.3389/fphys.2020.611294] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 11/19/2020] [Indexed: 12/22/2022] Open
Abstract
Nonsense mutations that lead to the insertion of a premature termination codon (PTC) in the cystic fibrosis transmembrane conductance regulator (CFTR) transcript affect 11% of patients with cystic fibrosis (CF) worldwide and are associated with severe disease phenotype. While CF rat models have contributed significantly to our understanding of CF disease pathogenesis, there are currently no rat models available for studying CF nonsense mutations. Here we created and characterized the first homozygous CF rat model that bears the CFTR G542X nonsense mutation in the endogenous locus using CRISPR/Cas9 gene editing. In addition to displaying severe CF manifestations and developmental defects such as reduced growth, abnormal tooth enamel, and intestinal obstruction, CFTR G542X knockin rats demonstrated an absence of CFTR function in tracheal and intestinal sections as assessed by nasal potential difference and transepithelial short-circuit current measurements. Reduced CFTR mRNA levels in the model further suggested sensitivity to nonsense-mediated decay, a pathway elicited by the presence of PTCs that degrades the PTC-bearing transcripts and thus further diminishes the level of CFTR protein. Although functional restoration of CFTR was observed in G542X rat tracheal epithelial cells in response to single readthrough agent therapy, therapeutic efficacy was not observed in G542X knockin rats in vivo. The G542X rat model provides an invaluable tool for the identification and in vivo validation of potential therapies for CFTR nonsense mutations.
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Affiliation(s)
- Jyoti Sharma
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Joseph Abbott
- Horizon Discovery Group, PLC, St. Louis, MO, United States
| | | | - Guojun Zhao
- Horizon Discovery Group, PLC, St. Louis, MO, United States
| | - Susan E. Birket
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Steven M. Rowe
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL, United States
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Kondratyeva E, Efremova A, Melyanovskaya Y, Petrova N, Satsuk N, Bulatenko N, Bukharova T, Zodbinova A, Sherman V, Kashirskaya N, Zinchenko R, Kutsev S, Goldshtein D. Clinical and genetic characterization of patients with cystic fibrosis and functional assessment of the chloride channel with the pathogenic variant c.831G>A (p.Trp277*), described for the first time. Gene 2020; 761:145023. [PMID: 32758581 DOI: 10.1016/j.gene.2020.145023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 06/07/2020] [Accepted: 07/30/2020] [Indexed: 10/23/2022]
Abstract
The clinical pictures of the disease of two Russian patients with cystic fibrosis with a rare nonsense variant c.831G>A (p.Trp277*) are described. The first case is a patient with the genotype comprising variant c.54-5940_273+10250del21kb (CFTRdele2,3), and the genotype of the second case included variant c.1521_1523delCTT (F508del). Patient 1, whose genotype had two class I genetic variants, revealed severe violations of CFTR synthesis based on the intestinal current measurements (ICM) and results obtained in the intestinal organoids. In both cases of patients with genetic variant c.831G>A, a severe course of cystic fibrosis was observed.
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Affiliation(s)
- E Kondratyeva
- Research Centre for Medical Genetics, 115522, 1 Moskvorechye St., Moscow, Russia.
| | - A Efremova
- Research Centre for Medical Genetics, 115522, 1 Moskvorechye St., Moscow, Russia
| | - Yu Melyanovskaya
- Research Centre for Medical Genetics, 115522, 1 Moskvorechye St., Moscow, Russia.
| | - N Petrova
- Research Centre for Medical Genetics, 115522, 1 Moskvorechye St., Moscow, Russia
| | - N Satsuk
- Nizhnevartovsk Regional Clinical Children's Hospital, 628609, 30 Severnaya St., Nizhnevartovsk, Russia
| | - N Bulatenko
- Research Centre for Medical Genetics, 115522, 1 Moskvorechye St., Moscow, Russia
| | - T Bukharova
- Research Centre for Medical Genetics, 115522, 1 Moskvorechye St., Moscow, Russia
| | - A Zodbinova
- Research Centre for Medical Genetics, 115522, 1 Moskvorechye St., Moscow, Russia
| | - V Sherman
- Research Centre for Medical Genetics, 115522, 1 Moskvorechye St., Moscow, Russia
| | - N Kashirskaya
- Research Centre for Medical Genetics, 115522, 1 Moskvorechye St., Moscow, Russia
| | - R Zinchenko
- Research Centre for Medical Genetics, 115522, 1 Moskvorechye St., Moscow, Russia
| | - S Kutsev
- Research Centre for Medical Genetics, 115522, 1 Moskvorechye St., Moscow, Russia
| | - D Goldshtein
- Research Centre for Medical Genetics, 115522, 1 Moskvorechye St., Moscow, Russia
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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: 25] [Impact Index Per Article: 6.3] [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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50
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Joynt AT, Evans TA, Pellicore MJ, Davis-Marcisak EF, Aksit MA, Eastman AC, Patel SU, Paul KC, Osorio DL, Bowling AD, Cotton CU, Raraigh KS, West NE, Merlo CA, Cutting GR, Sharma N. Evaluation of both exonic and intronic variants for effects on RNA splicing allows for accurate assessment of the effectiveness of precision therapies. PLoS Genet 2020; 16:e1009100. [PMID: 33085659 PMCID: PMC7605713 DOI: 10.1371/journal.pgen.1009100] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 11/02/2020] [Accepted: 09/08/2020] [Indexed: 12/21/2022] Open
Abstract
Elucidating the functional consequence of molecular defects underlying genetic diseases enables appropriate design of therapeutic options. Treatment of cystic fibrosis (CF) is an exemplar of this paradigm as the development of CFTR modulator therapies has allowed for targeted and effective treatment of individuals harboring specific genetic variants. However, the mechanism of these drugs limits effectiveness to particular classes of variants that allow production of CFTR protein. Thus, assessment of the molecular mechanism of individual variants is imperative for proper assignment of these precision therapies. This is particularly important when considering variants that affect pre-mRNA splicing, thus limiting success of the existing protein-targeted therapies. Variants affecting splicing can occur throughout exons and introns and the complexity of the process of splicing lends itself to a variety of outcomes, both at the RNA and protein levels, further complicating assessment of disease liability and modulator response. To investigate the scope of this challenge, we evaluated splicing and downstream effects of 52 naturally occurring CFTR variants (exonic = 15, intronic = 37). Expression of constructs containing select CFTR intronic sequences and complete CFTR exonic sequences in cell line models allowed for assessment of RNA and protein-level effects on an allele by allele basis. Characterization of primary nasal epithelial cells obtained from individuals harboring splice variants corroborated in vitro data. Notably, we identified exonic variants that result in complete missplicing and thus a lack of modulator response (e.g. c.2908G>A, c.523A>G), as well as intronic variants that respond to modulators due to the presence of residual normally spliced transcript (e.g. c.4242+2T>C, c.3717+40A>G). Overall, our data reveals diverse molecular outcomes amongst both exonic and intronic variants emphasizing the need to delineate RNA, protein, and functional effects of each variant in order to accurately assign precision therapies. Genetic variants that impact pre-mRNA splicing are a common cause of genetic disease and have varying downstream molecular consequences. As a result, precision therapies that function at the protein level are not always effective for these variants and thus careful assessment is necessary. Here we evaluate RNA-level effects of 52 variants in the cystic fibrosis transmembrane conductance regulator (CFTR) gene and show that study of splicing and its consequences allows for more accurate assignment of precision therapies.
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Affiliation(s)
- Anya T. Joynt
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Taylor A. Evans
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Matthew J. Pellicore
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Emily F. Davis-Marcisak
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Melis A. Aksit
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Alice C. Eastman
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Shivani U. Patel
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, United States of America
| | - Kathleen C. Paul
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Derek L. Osorio
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Alyssa D. Bowling
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Calvin U. Cotton
- Departments of Pediatrics, Physiology and Biophysics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Karen S. Raraigh
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Natalie E. West
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, United States of America
| | - Christian A. Merlo
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, United States of America
| | - Garry R. Cutting
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- * E-mail: (GRC); (NS)
| | - Neeraj Sharma
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- * E-mail: (GRC); (NS)
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