1
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Toledano I, Supek F, Lehner B. Genome-scale quantification and prediction of pathogenic stop codon readthrough by small molecules. Nat Genet 2024:10.1038/s41588-024-01878-5. [PMID: 39174735 DOI: 10.1038/s41588-024-01878-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 07/23/2024] [Indexed: 08/24/2024]
Abstract
Premature termination codons (PTCs) cause ~10-20% of inherited diseases and are a major mechanism of tumor suppressor gene inactivation in cancer. A general strategy to alleviate the effects of PTCs would be to promote translational readthrough. Nonsense suppression by small molecules has proven effective in diverse disease models, but translation into the clinic is hampered by ineffective readthrough of many PTCs. Here we directly tackle the challenge of defining drug efficacy by quantifying the readthrough of ~5,800 human pathogenic stop codons by eight drugs. We find that different drugs promote the readthrough of complementary subsets of PTCs defined by local sequence context. This allows us to build interpretable models that accurately predict drug-induced readthrough genome-wide, and we validate these models by quantifying endogenous stop codon readthrough. Accurate readthrough quantification and prediction will empower clinical trial design and the development of personalized nonsense suppression therapies.
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Affiliation(s)
- Ignasi Toledano
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Fran Supek
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
| | - Ben Lehner
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
- University Pompeu Fabra (UPF), Barcelona, Spain.
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
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2
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Jover I, Ramos MC, Escámez MJ, Lozoya E, Tormo JR, de Prado-Verdún D, Mencía Á, Pont M, Puig C, Larraufie MH, Gutiérrez-Caballero C, Reyes F, Trincado JL, García-González V, Cerrato R, Andrés M, Crespo M, Vicente F, Godessart N, Genilloud O, Larcher F, Nueda A. Identification of novel small molecule-based strategies of COL7A1 upregulation and readthrough activity for the treatment of recessive dystrophic epidermolysis bullosa. Sci Rep 2024; 14:18969. [PMID: 39152155 PMCID: PMC11329504 DOI: 10.1038/s41598-024-67398-8] [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: 03/04/2024] [Accepted: 07/10/2024] [Indexed: 08/19/2024] Open
Abstract
Recessive dystrophic epidermolysis bullosa (RDEB) is a rare genetic disease caused by loss of function mutations in the gene coding for collagen VII (C7) due to deficient or absent C7 expression. This disrupts structural and functional skin architecture, leading to blistering, chronic wounds, inflammation, important systemic symptoms affecting the mouth, gastrointestinal tract, cornea, and kidney function, and an increased skin cancer risk. RDEB patients have an extremely poor quality of life and often die at an early age. A frequent class of mutations in RDEB is premature termination codons (PTC), which appear in homozygosity or compound heterozygosity with other mutations. RDEB has no cure and current therapies are mostly palliative. Using patient-derived keratinocytes and a library of 8273 small molecules and 20,160 microbial extracts evaluated in a phenotypic screening interrogating C7 levels, we identified three active chemical series. Two of these series had PTC readthrough activity, and one upregulated C7 mRNA, showing synergistic activity when combined with the reference readthrough molecule gentamicin. These compounds represent novel potential small molecule-based systemic strategies that could complement topical-based treatments for RDEB.
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Affiliation(s)
- Irene Jover
- R&D Centre, Almirall S.A., Laureà Miró 408-410, 08980, Sant Feliu de Llobregat, Barcelona, Spain
| | - Maria C Ramos
- Fundación MEDINA, Parque Tecnológico de La Salud, Av. Conocimiento 34, 18016, Granada, Spain
| | - María José Escámez
- Departamento de Bioingeniería E Ingeniería Aeroespacial (UC3M), División de Biomedicina Epitelial, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Centro de Investigación Biomédica en Red de Enfermedades Raras, Universidad Carlos III de Madrid (UC3M), Madrid, Spain
- Unidad de Innovación Biomédica. Centro de Investigaciones Energéticas, U714-CIBER de Enfermedades Raras (CIBERER-ISCIII), Madrid, Spain
- Instituto de Investigación Sanitaria, Fundación Jiménez Díaz (IISFJD), Madrid, Spain
- Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain
| | - Estrella Lozoya
- R&D Centre, Almirall S.A., Laureà Miró 408-410, 08980, Sant Feliu de Llobregat, Barcelona, Spain
| | - José R Tormo
- Fundación MEDINA, Parque Tecnológico de La Salud, Av. Conocimiento 34, 18016, Granada, Spain
| | - Diana de Prado-Verdún
- Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain
| | - Ángeles Mencía
- Departamento de Bioingeniería E Ingeniería Aeroespacial (UC3M), División de Biomedicina Epitelial, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Centro de Investigación Biomédica en Red de Enfermedades Raras, Universidad Carlos III de Madrid (UC3M), Madrid, Spain
- Unidad de Innovación Biomédica. Centro de Investigaciones Energéticas, U714-CIBER de Enfermedades Raras (CIBERER-ISCIII), Madrid, Spain
- Instituto de Investigación Sanitaria, Fundación Jiménez Díaz (IISFJD), Madrid, Spain
- Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain
| | - Mercè Pont
- R&D Centre, Almirall S.A., Laureà Miró 408-410, 08980, Sant Feliu de Llobregat, Barcelona, Spain
| | - Carles Puig
- R&D Centre, Almirall S.A., Laureà Miró 408-410, 08980, Sant Feliu de Llobregat, Barcelona, Spain
| | - Marie-Helene Larraufie
- R&D Centre, Almirall S.A., Laureà Miró 408-410, 08980, Sant Feliu de Llobregat, Barcelona, Spain
| | | | - Fernando Reyes
- Fundación MEDINA, Parque Tecnológico de La Salud, Av. Conocimiento 34, 18016, Granada, Spain
| | - Juan Luis Trincado
- R&D Centre, Almirall S.A., Laureà Miró 408-410, 08980, Sant Feliu de Llobregat, Barcelona, Spain
| | - Vicente García-González
- R&D Centre, Almirall S.A., Laureà Miró 408-410, 08980, Sant Feliu de Llobregat, Barcelona, Spain
| | - Rosario Cerrato
- R&D Centre, Almirall S.A., Laureà Miró 408-410, 08980, Sant Feliu de Llobregat, Barcelona, Spain
| | - Miriam Andrés
- R&D Centre, Almirall S.A., Laureà Miró 408-410, 08980, Sant Feliu de Llobregat, Barcelona, Spain
| | - Maribel Crespo
- R&D Centre, Almirall S.A., Laureà Miró 408-410, 08980, Sant Feliu de Llobregat, Barcelona, Spain
| | - Francisca Vicente
- Fundación MEDINA, Parque Tecnológico de La Salud, Av. Conocimiento 34, 18016, Granada, Spain
| | - Nuria Godessart
- R&D Centre, Almirall S.A., Laureà Miró 408-410, 08980, Sant Feliu de Llobregat, Barcelona, Spain
| | - Olga Genilloud
- Fundación MEDINA, Parque Tecnológico de La Salud, Av. Conocimiento 34, 18016, Granada, Spain
| | - Fernando Larcher
- Departamento de Bioingeniería E Ingeniería Aeroespacial (UC3M), División de Biomedicina Epitelial, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Centro de Investigación Biomédica en Red de Enfermedades Raras, Universidad Carlos III de Madrid (UC3M), Madrid, Spain.
- Unidad de Innovación Biomédica. Centro de Investigaciones Energéticas, U714-CIBER de Enfermedades Raras (CIBERER-ISCIII), Madrid, Spain.
- Instituto de Investigación Sanitaria, Fundación Jiménez Díaz (IISFJD), Madrid, Spain.
- Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain.
| | - Arsenio Nueda
- R&D Centre, Almirall S.A., Laureà Miró 408-410, 08980, Sant Feliu de Llobregat, Barcelona, Spain.
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3
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Liu Y, Hoskins I, Geng M, Zhao Q, Chacko J, Qi K, Persyn L, Wang J, Zheng D, Zhong Y, Rao S, Park D, Cenik ES, Agarwal V, Ozadam H, Cenik C. Translation efficiency covariation across cell types is a conserved organizing principle of mammalian transcriptomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.11.607360. [PMID: 39149359 PMCID: PMC11326257 DOI: 10.1101/2024.08.11.607360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Characterization of shared patterns of RNA expression between genes across conditions has led to the discovery of regulatory networks and novel biological functions. However, it is unclear if such coordination extends to translation, a critical step in gene expression. Here, we uniformly analyzed 3,819 ribosome profiling datasets from 117 human and 94 mouse tissues and cell lines. We introduce the concept of Translation Efficiency Covariation (TEC), identifying coordinated translation patterns across cell types. We nominate potential mechanisms driving shared patterns of translation regulation. TEC is conserved across human and mouse cells and helps uncover gene functions. Moreover, our observations indicate that proteins that physically interact are highly enriched for positive covariation at both translational and transcriptional levels. Our findings establish translational covariation as a conserved organizing principle of mammalian transcriptomes.
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Affiliation(s)
- Yue Liu
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Ian Hoskins
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Michael Geng
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Qiuxia Zhao
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Jonathan Chacko
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Kangsheng Qi
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Logan Persyn
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Jun Wang
- mRNA Center of Excellence, Sanofi, Waltham, MA 02451, USA
| | - Dinghai Zheng
- mRNA Center of Excellence, Sanofi, Waltham, MA 02451, USA
| | - Yochen Zhong
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Shilpa Rao
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Dayea Park
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Elif Sarinay Cenik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Vikram Agarwal
- mRNA Center of Excellence, Sanofi, Waltham, MA 02451, USA
| | - Hakan Ozadam
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
- Present address: Sail Biomedicines, Cambridge, MA, 02141, USA
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4
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Lakli M, Onnée M, Carrez T, Becq F, Thomas Falguières, Fanen P. ABC transporters involved in respiratory and cholestatic diseases: From rare to very rare monogenic diseases. Biochem Pharmacol 2024; 229:116468. [PMID: 39111603 DOI: 10.1016/j.bcp.2024.116468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 07/16/2024] [Accepted: 08/03/2024] [Indexed: 08/24/2024]
Abstract
ATP-binding cassette (ABC) transporters constitute a 49-member superfamily in humans. These proteins, most of them being transmembrane, allow the active transport of an important variety of substrates across biological membranes, using ATP hydrolysis as an energy source. For an important proportion of these ABC transporters, genetic variations of the loci encoding them have been correlated with rare genetic diseases, including cystic fibrosis and interstitial lung disease (variations in CFTR/ABCC7 and ABCA3) as well as cholestatic liver diseases (variations in ABCB4 and ABCB11). In this review, we first describe these ABC transporters and how their molecular dysfunction may lead to human diseases. Then, we propose a classification of the genetic variants according to their molecular defect (expression, traffic, function and/or stability), which may be considered as a general guideline for all ABC transporters' variants. Finally, we discuss recent progress in the field of targeted pharmacotherapy, which aim to correct specific molecular defects using small molecules. In conclusion, we are opening the path to treatment repurposing for diseases involving similar deficiencies in other ABC transporters.
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Affiliation(s)
- Mounia Lakli
- Inserm, Université Paris-Saclay, Physiopathogenèse et traitement des maladies du foie, UMR_S 1193, Hepatinov, 91400 Orsay, France
| | - Marion Onnée
- Univ Paris Est Creteil, INSERM, IMRB, F-94010, Créteil, France
| | - Thomas Carrez
- Université de Poitiers, Laboratoire Physiopathologie et Régulation des Transports Ioniques, Pôle Biologie Santé, 86000 Poitiers, France; ManRos Therapeutics, Hôtel de Recherche, Centre de Perharidy, 29680, Roscoff, France
| | - Frédéric Becq
- Université de Poitiers, Laboratoire Physiopathologie et Régulation des Transports Ioniques, Pôle Biologie Santé, 86000 Poitiers, France
| | - Thomas Falguières
- Inserm, Université Paris-Saclay, Physiopathogenèse et traitement des maladies du foie, UMR_S 1193, Hepatinov, 91400 Orsay, France
| | - Pascale Fanen
- Univ Paris Est Creteil, INSERM, IMRB, F-94010, Créteil, France; AP-HP, Département de Génétique Médicale, Hôpital Henri Mondor, F-94010, Créteil, France.
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5
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Karri S, Cornu D, Serot C, Biri L, Hatton A, Dréanot E, Rullaud C, Pranke I, Sermet-Gaudelus I, Hinzpeter A, Bidou L, Namy O. TLN468 changes the pattern of tRNA used to read through premature termination codons in CFTR. J Cyst Fibros 2024:S1569-1993(24)00802-6. [PMID: 39098506 DOI: 10.1016/j.jcf.2024.07.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 07/22/2024] [Accepted: 07/24/2024] [Indexed: 08/06/2024]
Abstract
Nonsense mutations account for 12 % of cystic fibrosis (CF) cases. The presence of a premature termination codon (PTC) leads to gene inactivation, which can be countered by the use of drugs stimulating PTC readthrough, restoring production of the full-length protein. We recently identified a new readthrough inducer, TLN468, more efficient than gentamicin. We measured the readthrough induced by these two drugs with different cystic fibrosis transmembrane conductance regulator (CFTR) PTCs. We then determined the amino acids inserted at the S1196X, G542X, W846X and E1417X PTCs of CFTR during readthrough induced by gentamicin or TLN468. TLN468 significantly promoted the incorporation of one specific amino acid, whereas gentamicin did not greatly modify the proportions of the various amino acids incorporated relative to basal conditions. The function of the engineered missense CFTR channels corresponding to these four PTCs was assessed with and without potentiator. For the recoded CFTR, except for E1417Q and G542W, the PTC readthrough induced by TLN468 allowed the expression of CFTR variants that were correctly processed and had significant activity that was enhanced by CFTR modulators. These results suggest that it would be relevant to assess the therapeutic benefit of TLN468 PTC suppression in combination with CFTR modulators in preclinical assays.
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Affiliation(s)
- Sabrina Karri
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette, 91198, France
| | - David Cornu
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette, 91198, France
| | - Claudia Serot
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette, 91198, France
| | - Lynda Biri
- CNRS, INSERM, Institut Necker Enfants Malades-INEM, Université Paris Cité, Paris, F-75015, France
| | - Aurélie Hatton
- CNRS, INSERM, Institut Necker Enfants Malades-INEM, Université Paris Cité, Paris, F-75015, France
| | - Elise Dréanot
- CNRS, INSERM, Institut Necker Enfants Malades-INEM, Université Paris Cité, Paris, F-75015, France
| | - Camille Rullaud
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette, 91198, France
| | - Iwona Pranke
- CNRS, INSERM, Institut Necker Enfants Malades-INEM, Université Paris Cité, Paris, F-75015, France
| | - Isabelle Sermet-Gaudelus
- CNRS, INSERM, Institut Necker Enfants Malades-INEM, Université Paris Cité, Paris, F-75015, France
| | - Alexandre Hinzpeter
- CNRS, INSERM, Institut Necker Enfants Malades-INEM, Université Paris Cité, Paris, F-75015, France
| | - Laure Bidou
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette, 91198, France; Sorbonne Université, 4 Place Jussieu, Paris, 75005, France
| | - Olivier Namy
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette, 91198, France.
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6
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Susorov D, Echeverria D, Khvorova A, Korostelev AA. mRNA-specific readthrough of nonsense codons by antisense oligonucleotides (R-ASOs). Nucleic Acids Res 2024:gkae624. [PMID: 39011883 DOI: 10.1093/nar/gkae624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 06/14/2024] [Accepted: 07/04/2024] [Indexed: 07/17/2024] Open
Abstract
Nonsense mutations account for >10% of human genetic disorders, including cystic fibrosis, Alagille syndrome, and Duchenne muscular dystrophy. A nonsense mutation results in the expression of a truncated protein, and therapeutic strategies aim to restore full-length protein expression. Most strategies under development, including small-molecule aminoglycosides, suppressor tRNAs, or the targeted degradation of termination factors, lack mRNA target selectivity and may poorly differentiate between nonsense and normal stop codons, resulting in off-target translation errors. Here, we demonstrate that antisense oligonucleotides can stimulate readthrough of disease-causing nonsense codons, resulting in high yields of full-length protein in mammalian cellular lysate. Readthrough efficiency depends on the sequence context near the stop codon and on the precise targeting position of an oligonucleotide, whose interaction with mRNA inhibits peptide release to promote readthrough. Readthrough-inducing antisense oligonucleotides (R-ASOs) enhance the potency of non-specific readthrough agents, including aminoglycoside G418 and suppressor tRNA, enabling a path toward target-specific readthrough of nonsense mutations in CFTR, JAG1, DMD, BRCA1 and other mutant genes. Finally, through systematic chemical engineering, we identify heavily modified fully functional R-ASO variants, enabling future therapeutic development.
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Affiliation(s)
- Denis Susorov
- RNA Therapeutics Institute, UMass Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, UMass Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Anastasia Khvorova
- RNA Therapeutics Institute, UMass Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Andrei A Korostelev
- RNA Therapeutics Institute, UMass Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA
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Loret C, Pauset A, Faye PA, Prouzet-Mauleon V, Pyromali I, Nizou A, Miressi F, Sturtz F, Favreau F, Turcq B, Lia AS. CRISPR Base Editing to Create Potential Charcot-Marie-Tooth Disease Models with High Editing Efficiency: Human Induced Pluripotent Stem Cell Harboring SH3TC2 Variants. Biomedicines 2024; 12:1550. [PMID: 39062123 PMCID: PMC11274897 DOI: 10.3390/biomedicines12071550] [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: 05/28/2024] [Revised: 07/05/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024] Open
Abstract
Human induced pluripotent stem cells (hiPSCs) represent a powerful tool to investigate neuropathological disorders in which the cells of interest are inaccessible, such as in the Charcot-Marie-Tooth disease (CMT), the most common inherited peripheral neuropathy. Developing appropriate cellular models becomes crucial in order to both study the disease's pathophysiology and test new therapeutic approaches. The generation of hiPS cellular models for disorders caused by a single nucleotide variation has been significantly improved following the development of CRISPR-based editing tools. In this study, we efficiently and quickly generated, by CRISPR editing, the two first hiPSCs cellular models carrying alterations involved in CMT4C, also called AR-CMTde-SH3TC2. This subtype of CMT is associated with alterations in the SH3TC2 gene and represents the most prevalent form of autosomal recessive demyelinating CMT. We aimed to develop models for two different SH3TC2 nonsense variants, c.211C>T, p.Gln71* and the most common AR-CMTde-SH3TC2 alteration, c.2860C>T, p.Arg954*. First, in order to determine the best CRISPR strategy to adopt on hiPSCs, we first tested a variety of sgRNAs combined with a selection of recent base editors using the conveniently cultivable and transfectable HEK-293T cell line. The chosen CRISPR base-editing strategy was then applied to hiPSCs derived from healthy individuals to generate isogenic CMT disease models with up to 93% editing efficiency. For point mutation generation, we first recommend to test your strategies on alternative cell line such as HEK-293T before hiPSCs to evaluate a variety of sgRNA-BE combinations, thus boosting the chance of achieving edited cellular clones with the hard-to-culture and to transfect hiPSCs.
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Affiliation(s)
- Camille Loret
- University of Limoges, NeurIT UR 20218, GEIST Institute, F-87000 Limoges, France; (P.-A.F.); (I.P.); (A.N.); (F.M.); (F.S.); (F.F.); (A.-S.L.)
| | - Amandine Pauset
- University of Bordeaux, CRISP'edit, TBMCore UAR CNRS 3427, US Inserm 005, F-33000 Bordeaux, France (V.P.-M.); (B.T.)
- University of Bordeaux, Modeling Transformation and Resistance in Leukemia, BRIC Inserm U1312, F-33000 Bordeaux, France
| | - Pierre-Antoine Faye
- University of Limoges, NeurIT UR 20218, GEIST Institute, F-87000 Limoges, France; (P.-A.F.); (I.P.); (A.N.); (F.M.); (F.S.); (F.F.); (A.-S.L.)
- CHU Limoges, Department of Biochemistry and Molecular Genetics, F-87000 Limoges, France
| | - Valérie Prouzet-Mauleon
- University of Bordeaux, CRISP'edit, TBMCore UAR CNRS 3427, US Inserm 005, F-33000 Bordeaux, France (V.P.-M.); (B.T.)
- University of Bordeaux, Modeling Transformation and Resistance in Leukemia, BRIC Inserm U1312, F-33000 Bordeaux, France
| | - Ioanna Pyromali
- University of Limoges, NeurIT UR 20218, GEIST Institute, F-87000 Limoges, France; (P.-A.F.); (I.P.); (A.N.); (F.M.); (F.S.); (F.F.); (A.-S.L.)
| | - Angélique Nizou
- University of Limoges, NeurIT UR 20218, GEIST Institute, F-87000 Limoges, France; (P.-A.F.); (I.P.); (A.N.); (F.M.); (F.S.); (F.F.); (A.-S.L.)
| | - Federica Miressi
- University of Limoges, NeurIT UR 20218, GEIST Institute, F-87000 Limoges, France; (P.-A.F.); (I.P.); (A.N.); (F.M.); (F.S.); (F.F.); (A.-S.L.)
| | - Franck Sturtz
- University of Limoges, NeurIT UR 20218, GEIST Institute, F-87000 Limoges, France; (P.-A.F.); (I.P.); (A.N.); (F.M.); (F.S.); (F.F.); (A.-S.L.)
- CHU Limoges, Department of Biochemistry and Molecular Genetics, F-87000 Limoges, France
| | - Frédéric Favreau
- University of Limoges, NeurIT UR 20218, GEIST Institute, F-87000 Limoges, France; (P.-A.F.); (I.P.); (A.N.); (F.M.); (F.S.); (F.F.); (A.-S.L.)
- CHU Limoges, Department of Biochemistry and Molecular Genetics, F-87000 Limoges, France
| | - Béatrice Turcq
- University of Bordeaux, CRISP'edit, TBMCore UAR CNRS 3427, US Inserm 005, F-33000 Bordeaux, France (V.P.-M.); (B.T.)
- University of Bordeaux, Modeling Transformation and Resistance in Leukemia, BRIC Inserm U1312, F-33000 Bordeaux, France
| | - Anne-Sophie Lia
- University of Limoges, NeurIT UR 20218, GEIST Institute, F-87000 Limoges, France; (P.-A.F.); (I.P.); (A.N.); (F.M.); (F.S.); (F.F.); (A.-S.L.)
- CHU Limoges, Department of Biochemistry and Molecular Genetics, F-87000 Limoges, France
- CHU Limoges, Department of Bioinformatics, F-87000 Limoges, France
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8
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Wang J, Gao G, Wang D. Developing AAV-delivered nonsense suppressor tRNAs for neurological disorders. Neurotherapeutics 2024; 21:e00391. [PMID: 38959711 PMCID: PMC11269797 DOI: 10.1016/j.neurot.2024.e00391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 05/29/2024] [Accepted: 06/19/2024] [Indexed: 07/05/2024] Open
Abstract
Adeno-associated virus (AAV)-based gene therapy is a clinical stage therapeutic modality for neurological disorders. A common genetic defect in myriad monogenic neurological disorders is nonsense mutations that account for about 11% of all human pathogenic mutations. Stop codon readthrough by suppressor transfer RNA (sup-tRNA) has long been sought as a potential gene therapy approach to target nonsense mutations, but hindered by inefficient in vivo delivery. The rapid advances in AAV delivery technology have not only powered gene therapy development but also enabled in vivo preclinical assessment of a range of nucleic acid therapeutics, such as sup-tRNA. Compared with conventional AAV gene therapy that delivers a transgene to produce therapeutic proteins, AAV-delivered sup-tRNA has several advantages, such as small gene sizes and operating within the endogenous gene expression regulation, which are important considerations for treating some neurological disorders. This review will first examine sup-tRNA designs and delivery by AAV vectors. We will then analyze how AAV-delivered sup-tRNA can potentially address some neurological disorders that are challenging to conventional gene therapy, followed by discussing available mouse models of neurological diseases for in vivo preclinical testing. Potential challenges for AAV-delivered sup-tRNA to achieve therapeutic efficacy and safety will also be discussed.
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Affiliation(s)
- Jiaming Wang
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Guangping Gao
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.
| | - Dan Wang
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.
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9
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Ojha R, Krug S, Jones P, Koestler BJ. Intact and mutated Shigella diguanylate cyclases increase c-di-GMP. J Biol Chem 2024; 300:107525. [PMID: 38960033 PMCID: PMC11327459 DOI: 10.1016/j.jbc.2024.107525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/31/2024] [Accepted: 06/21/2024] [Indexed: 07/05/2024] Open
Abstract
The intracellular human pathogen Shigella invades the colonic epithelium to cause disease. Prior to invasion, this bacterium navigates through different environments within the human body, including the stomach and the small intestine. To adapt to changing environments, Shigella uses the bacterial second messenger cyclic di-GMP (c di-GMP) signaling system, synthesized by diguanylate cyclases (DGCs) encoding GGDEF domains. Shigella flexneri encodes a total of 9 GGDEF or GGDEF-EAL domain enzymes in its genome, but five of these genes have acquired mutations that presumably inactivated the c-di-GMP synthesis activity of these enzymes. In this study, we examined individual S. flexneri DGCs for their role in c-di-GMP synthesis and pathogenesis. We individually expressed each of the four intact DGCs in a S. flexneri strain, where these four DGCs had been deleted (Δ4DGC). We found that the 4 S. flexneri intact DGCs synthesize c-di-GMP at different levels in vitro and during infection of tissue-cultured cells. We also found that dgcF and dgcI expression significantly reduces invasion and plaque formation, and dgcF expression increases acid sensitivity, and that these phenotypes did not correspond with measured c-di-GMP levels. However, deletion of these four DGCs did not eliminate S. flexneri c-di-GMP, and we found that dgcE, dgcQ, and dgcN, which all have nonsense mutations prior to the GGDEF domain, still produce c-di-GMP. These S. flexneri degenerate DGC pseudogenes are expressed as multiple proteins, consistent with multiple start codons within the gene. We propose that both intact and degenerate DGCs contribute to S. flexneri c-di-GMP signaling.
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Affiliation(s)
- Ruchi Ojha
- Department of Biological Sciences, Western Michigan University, Kalamazoo, Michigan, USA
| | - Stefanie Krug
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Prentiss Jones
- Department of Pathology, Western Michigan University Homer Stryker, M.D. School of Medicine, Kalamazoo, Michigan, USA
| | - Benjamin J Koestler
- Department of Biological Sciences, Western Michigan University, Kalamazoo, Michigan, USA.
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10
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Coelho JPL, Yip MCJ, Oltion K, Taunton J, Shao S. The eRF1 degrader SRI-41315 acts as a molecular glue at the ribosomal decoding center. Nat Chem Biol 2024; 20:877-884. [PMID: 38172604 PMCID: PMC11253071 DOI: 10.1038/s41589-023-01521-0] [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: 04/26/2023] [Accepted: 12/04/2023] [Indexed: 01/05/2024]
Abstract
Translation termination is an essential cellular process, which is also of therapeutic interest for diseases that manifest from premature stop codons. In eukaryotes, translation termination requires eRF1, which recognizes stop codons, catalyzes the release of nascent proteins from ribosomes and facilitates ribosome recycling. The small molecule SRI-41315 triggers eRF1 degradation and enhances translational readthrough of premature stop codons. However, the mechanism of action of SRI-41315 on eRF1 and translation is not known. Here we report cryo-EM structures showing that SRI-41315 acts as a metal-dependent molecular glue between the N domain of eRF1 responsible for stop codon recognition and the ribosomal subunit interface near the decoding center. Retention of eRF1 on ribosomes by SRI-41315 leads to ribosome collisions, eRF1 ubiquitylation and a higher frequency of translation termination at near-cognate stop codons. Our findings reveal a new mechanism of release factor inhibition and additional implications for pharmacologically targeting eRF1.
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Affiliation(s)
- João P L Coelho
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Matthew C J Yip
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Keely Oltion
- Chemistry and Chemical Biology Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Jack Taunton
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Sichen Shao
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
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11
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A molecular glue degrader of eRF1 on the ribosome. Nat Chem Biol 2024; 20:810-811. [PMID: 38287153 DOI: 10.1038/s41589-023-01522-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
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12
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Zhang C, Liu Y, Li G, Yang Z, Han C, Sun X, Sheng C, Ding K, Rao Y. Targeting the undruggables-the power of protein degraders. Sci Bull (Beijing) 2024; 69:1776-1797. [PMID: 38614856 DOI: 10.1016/j.scib.2024.03.056] [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: 01/27/2024] [Revised: 03/06/2024] [Accepted: 03/25/2024] [Indexed: 04/15/2024]
Abstract
Undruggable targets typically refer to a class of therapeutic targets that are difficult to target through conventional methods or have not yet been targeted, but are of great clinical significance. According to statistics, over 80% of disease-related pathogenic proteins cannot be targeted by current conventional treatment methods. In recent years, with the advancement of basic research and new technologies, the development of various new technologies and mechanisms has brought new perspectives to overcome challenging drug targets. Among them, targeted protein degradation technology is a breakthrough drug development strategy for challenging drug targets. This technology can specifically identify target proteins and directly degrade pathogenic target proteins by utilizing the inherent protein degradation pathways within cells. This new form of drug development includes various types such as proteolysis targeting chimera (PROTAC), molecular glue, lysosome-targeting Chimaera (LYTAC), autophagosome-tethering compound (ATTEC), autophagy-targeting chimera (AUTAC), autophagy-targeting chimera (AUTOTAC), degrader-antibody conjugate (DAC). This article systematically summarizes the application of targeted protein degradation technology in the development of degraders for challenging drug targets. Finally, the article looks forward to the future development direction and application prospects of targeted protein degradation technology.
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Affiliation(s)
- Chao Zhang
- Changping Laboratory, Beijing 102206, China
| | - Yongbo Liu
- State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Guangchen Li
- State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Zhouli Yang
- State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Chi Han
- State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Xiuyun Sun
- Changping Laboratory, Beijing 102206, China
| | - Chunquan Sheng
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China.
| | - Ke Ding
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China.
| | - Yu Rao
- State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China; Changping Laboratory, Beijing 102206, China.
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13
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Morais P, Zhang R, Yu YT. Therapeutic Nonsense Suppression Modalities: From Small Molecules to Nucleic Acid-Based Approaches. Biomedicines 2024; 12:1284. [PMID: 38927491 PMCID: PMC11201248 DOI: 10.3390/biomedicines12061284] [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: 05/02/2024] [Revised: 05/29/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024] Open
Abstract
Nonsense mutations are genetic mutations that create premature termination codons (PTCs), leading to truncated, defective proteins in diseases such as cystic fibrosis, neurofibromatosis type 1, Dravet syndrome, Hurler syndrome, Beta thalassemia, inherited bone marrow failure syndromes, Duchenne muscular dystrophy, and even cancer. These mutations can also trigger a cellular surveillance mechanism known as nonsense-mediated mRNA decay (NMD) that degrades the PTC-containing mRNA. The activation of NMD can attenuate the consequences of truncated, defective, and potentially toxic proteins in the cell. Since approximately 20% of all single-point mutations are disease-causing nonsense mutations, it is not surprising that this field has received significant attention, resulting in a remarkable advancement in recent years. In fact, since our last review on this topic, new examples of nonsense suppression approaches have been reported, namely new ways of promoting the translational readthrough of PTCs or inhibiting the NMD pathway. With this review, we update the state-of-the-art technologies in nonsense suppression, focusing on novel modalities with therapeutic potential, such as small molecules (readthrough agents, NMD inhibitors, and molecular glue degraders); antisense oligonucleotides; tRNA suppressors; ADAR-mediated RNA editing; targeted pseudouridylation; and gene/base editing. While these various modalities have significantly advanced in their development stage since our last review, each has advantages (e.g., ease of delivery and specificity) and disadvantages (manufacturing complexity and off-target effect potential), which we discuss here.
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Affiliation(s)
- Pedro Morais
- Drug Metabolism and Pharmacokinetics, Research and Development, Bayer Pharmaceuticals, 42113 Wuppertal, Germany
| | - Rui Zhang
- Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642, USA;
| | - Yi-Tao Yu
- Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642, USA;
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14
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Coatti GC, Vaghela N, Gillurkar P, Leir SH, Harris A. A promoter-dependent upstream activator augments CFTR expression in diverse epithelial cell types. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195031. [PMID: 38679287 DOI: 10.1016/j.bbagrm.2024.195031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/01/2024]
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) gene encodes an anion-selective channel found in epithelial cell membranes. Mutations in CFTR cause cystic fibrosis (CF), an inherited disorder that impairs epithelial function in multiple organs. Most men with CF are infertile due to loss of intact genital ducts. Here we investigated a novel epididymis-selective cis-regulatory element (CRE), located within a peak of open chromatin at -9.5 kb 5' to the CFTR gene promoter. Activation of the -9.5 kb CRE alone by CRISPRa had no impact on CFTR gene expression. However, CRISPRa co-activation of the -9.5 kb CRE and the CFTR gene promoter in epididymis cells significantly augmented CFTR mRNA and protein expression when compared to promoter activation alone. This increase was accompanied by enhanced chromatin accessibility at both sites. Furthermore, the combined CRISPRa strategy activated CFTR expression in other epithelial cells that lack open chromatin at the -9.5 kb site and in which the locus is normally inactive. However, the -9.5 kb CRE does not function as a classical enhancer of the CFTR promoter in transient reporter gene assays. These data provide a novel mechanism for activating/augmenting CFTR expression, which may have therapeutic utility for mutations that perturb CFTR transcription.
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Affiliation(s)
- Giuliana C Coatti
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Nirbhayaditya Vaghela
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Pulak Gillurkar
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Shih-Hsing Leir
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Ann Harris
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
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15
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Strandgren C, Wiman KG. Therapeutic targeting of TP53 nonsense mutations in cancer. Ups J Med Sci 2024; 129:10719. [PMID: 38863730 PMCID: PMC11165251 DOI: 10.48101/ujms.v129.10719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Revised: 04/23/2024] [Accepted: 04/23/2024] [Indexed: 06/13/2024] Open
Abstract
Mutations in the TP53 tumor suppressor gene occur with high prevalence in a wide range of human tumors. A significant fraction of these mutations (around 10%) are nonsense mutations, creating a premature termination codon (PTC) that leads to the expression of truncated inactive p53 protein. Induction of translational readthrough across a PTC in nonsense mutant TP53 allows the production of full-length protein and potentially restoration of normal p53 function. Aminoglycoside antibiotics and a number of novel compounds have been shown to induce full-length p53 in tumor cells carrying various TP53 nonsense mutations. Full-length p53 protein generated by translational readthrough retains the capacity to transactivate p53 target genes and trigger tumor cell death. These findings raise hopes for efficient therapy of TP53 nonsense mutant tumors in the future.
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Affiliation(s)
| | - Klas G Wiman
- Karolinska Institutet, Departement of Oncology-Pathology, Stockholm, Sweden
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16
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Ojha R, Krug S, Jones P, Koestler BJ. Intact and Degenerate Diguanylate Cyclases regulate Shigella Cyclic di-GMP. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.08.588579. [PMID: 38645013 PMCID: PMC11030455 DOI: 10.1101/2024.04.08.588579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
The intracellular human pathogen Shigella invades the colonic epithelium to cause disease. Prior to invasion, this bacterium navigates through different environments within the human body, including the stomach and the small intestine. To adapt to changing environments, Shigella uses the bacterial second messenger c-di-GMP signaling system, synthesized by diguanylate cyclases (DGCs) encoding GGDEF domains. Shigella flexneri encodes a total of 9 GGDEF or GGDEF-EAL domain enzymes in its genome, but 5 of these genes have acquired mutations that presumably inactivated the c-di-GMP synthesis activity of these enzymes. In this study, we examined individual S. flexneri DGCs for their role in c-di-GMP synthesis and pathogenesis. We individually expressed each of the 4 intact DGCs in an S. flexneri strain where these 4 DGCs had been deleted (Δ4DGC). We found that the 4 S. flexneri intact DGCs synthesize c-di-GMP at different levels in vitro and during infection of tissue-cultured cells. We also found that dgcF and dgcI expression significantly reduces invasion and plaque formation, and dgcF expression increases acid sensitivity, and that these phenotypes did not correspond with measured c-di-GMP levels. However, deletion of these 4 DGCs did not eliminate S. flexneri c-di-GMP, and we found that dgcE, dgcQ, and dgcN , which all have nonsense mutations prior to the GGDEF domain, still produce c-di-GMP. These S. flexneri degenerate DGC genes are expressed as multiple proteins, consistent with multiple start codons within the gene. We propose that both intact and degenerate DGCs contribute to S. flexneri c-di-GMP signaling.
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17
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Bharti N, Santos L, Davyt M, Behrmann S, Eichholtz M, Jimenez-Sanchez A, Hong JS, Rab A, Sorscher EJ, Albers S, Ignatova Z. Translation velocity determines the efficacy of engineered suppressor tRNAs on pathogenic nonsense mutations. Nat Commun 2024; 15:2957. [PMID: 38580646 PMCID: PMC10997658 DOI: 10.1038/s41467-024-47258-9] [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: 09/20/2023] [Accepted: 03/20/2024] [Indexed: 04/07/2024] Open
Abstract
Nonsense mutations - the underlying cause of approximately 11% of all genetic diseases - prematurely terminate protein synthesis by mutating a sense codon to a premature stop or termination codon (PTC). An emerging therapeutic strategy to suppress nonsense defects is to engineer sense-codon decoding tRNAs to readthrough and restore translation at PTCs. However, the readthrough efficiency of the engineered suppressor tRNAs (sup-tRNAs) largely varies in a tissue- and sequence context-dependent manner and has not yet yielded optimal clinical efficacy for many nonsense mutations. Here, we systematically analyze the suppression efficacy at various pathogenic nonsense mutations. We discover that the translation velocity of the sequence upstream of PTCs modulates the sup-tRNA readthrough efficacy. The PTCs most refractory to suppression are embedded in a sequence context translated with an abrupt reversal of the translation speed leading to ribosomal collisions. Moreover, modeling translation velocity using Ribo-seq data can accurately predict the suppression efficacy at PTCs. These results reveal previously unknown molecular signatures contributing to genotype-phenotype relationships and treatment-response heterogeneity, and provide the framework for the development of personalized tRNA-based gene therapies.
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Affiliation(s)
- Nikhil Bharti
- Institute of Biochemistry and Molecular Biology, University of Hamburg, 20146, Hamburg, Germany
| | - Leonardo Santos
- Institute of Biochemistry and Molecular Biology, University of Hamburg, 20146, Hamburg, Germany
| | - Marcos Davyt
- Institute of Biochemistry and Molecular Biology, University of Hamburg, 20146, Hamburg, Germany
| | - Stine Behrmann
- Institute of Biochemistry and Molecular Biology, University of Hamburg, 20146, Hamburg, Germany
| | - Marie Eichholtz
- Institute of Biochemistry and Molecular Biology, University of Hamburg, 20146, Hamburg, Germany
| | | | - Jeong S Hong
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, 30322, USA
- Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Andras Rab
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, 30322, USA
- Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Eric J Sorscher
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, 30322, USA
- Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Suki Albers
- Institute of Biochemistry and Molecular Biology, University of Hamburg, 20146, Hamburg, Germany.
| | - Zoya Ignatova
- Institute of Biochemistry and Molecular Biology, University of Hamburg, 20146, Hamburg, Germany.
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18
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Manjunath LE, Singh A, Devi Kumar S, Vasu K, Kar D, Sellamuthu K, Eswarappa SM. Transcript-specific induction of stop codon readthrough using a CRISPR-dCas13 system. EMBO Rep 2024; 25:2118-2143. [PMID: 38499809 PMCID: PMC11015002 DOI: 10.1038/s44319-024-00115-8] [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: 03/06/2023] [Revised: 02/23/2024] [Accepted: 02/28/2024] [Indexed: 03/20/2024] Open
Abstract
Stop codon readthrough (SCR) is the process where translation continues beyond a stop codon on an mRNA. Here, we describe a strategy to enhance or induce SCR in a transcript-selective manner using a CRISPR-dCas13 system. Using specific guide RNAs, we target dCas13 to the region downstream of canonical stop codons of mammalian AGO1 and VEGFA mRNAs, known to exhibit natural SCR. Readthrough assays reveal enhanced SCR of these mRNAs (both exogenous and endogenous) caused by the dCas13-gRNA complexes. This effect is associated with ribosomal pausing, which has been reported for several SCR events. Our data show that CRISPR-dCas13 can also induce SCR across premature termination codons (PTCs) in the mRNAs of green fluorescent protein and TP53. We demonstrate the utility of this strategy in the induction of readthrough across the thalassemia-causing PTC in HBB mRNA and hereditary spherocytosis-causing PTC in SPTA1 mRNA. Thus, CRISPR-dCas13 can be programmed to enhance or induce SCR in a transcript-selective and stop codon-specific manner.
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Affiliation(s)
- Lekha E Manjunath
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, 560012, India
| | - Anumeha Singh
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, 560012, India
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Sangeetha Devi Kumar
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, 560012, India
| | - Kirtana Vasu
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, 560012, India
| | - Debaleena Kar
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, 560012, India
| | - Karthi Sellamuthu
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, 560012, India
- University of Texas Medical Branch, Galveston, TX, USA
| | - Sandeep M Eswarappa
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, 560012, India.
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19
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Jia X, He X, Huang C, Li J, Dong Z, Liu K. Protein translation: biological processes and therapeutic strategies for human diseases. Signal Transduct Target Ther 2024; 9:44. [PMID: 38388452 PMCID: PMC10884018 DOI: 10.1038/s41392-024-01749-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 01/13/2024] [Accepted: 01/18/2024] [Indexed: 02/24/2024] Open
Abstract
Protein translation is a tightly regulated cellular process that is essential for gene expression and protein synthesis. The deregulation of this process is increasingly recognized as a critical factor in the pathogenesis of various human diseases. In this review, we discuss how deregulated translation can lead to aberrant protein synthesis, altered cellular functions, and disease progression. We explore the key mechanisms contributing to the deregulation of protein translation, including functional alterations in translation factors, tRNA, mRNA, and ribosome function. Deregulated translation leads to abnormal protein expression, disrupted cellular signaling, and perturbed cellular functions- all of which contribute to disease pathogenesis. The development of ribosome profiling techniques along with mass spectrometry-based proteomics, mRNA sequencing and single-cell approaches have opened new avenues for detecting diseases related to translation errors. Importantly, we highlight recent advances in therapies targeting translation-related disorders and their potential applications in neurodegenerative diseases, cancer, infectious diseases, and cardiovascular diseases. Moreover, the growing interest lies in targeted therapies aimed at restoring precise control over translation in diseased cells is discussed. In conclusion, this comprehensive review underscores the critical role of protein translation in disease and its potential as a therapeutic target. Advancements in understanding the molecular mechanisms of protein translation deregulation, coupled with the development of targeted therapies, offer promising avenues for improving disease outcomes in various human diseases. Additionally, it will unlock doors to the possibility of precision medicine by offering personalized therapies and a deeper understanding of the molecular underpinnings of diseases in the future.
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Affiliation(s)
- Xuechao Jia
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450000, China
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, 450000, China
| | - Xinyu He
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450000, China
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, 450000, China
| | - Chuntian Huang
- Department of Pathology and Pathophysiology, Henan University of Chinese Medicine, Zhengzhou, Henan, 450000, China
| | - Jian Li
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, 450000, China
| | - Zigang Dong
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450000, China.
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, 450000, China.
- Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou, Henan, 450052, China.
- Research Center for Basic Medicine Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, Henan, China.
- Provincial Cooperative Innovation Center for Cancer Chemoprevention, Zhengzhou University, Zhengzhou, Henan, 450000, China.
| | - Kangdong Liu
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450000, China.
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, 450000, China.
- Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou, Henan, 450052, China.
- Research Center for Basic Medicine Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, Henan, China.
- Provincial Cooperative Innovation Center for Cancer Chemoprevention, Zhengzhou University, Zhengzhou, Henan, 450000, China.
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, Henan, 450000, China.
- The Collaborative Innovation Center of Henan Province for Cancer Chemoprevention, Zhengzhou, Henan, 450000, China.
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20
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Cao L, Wu Y, Gong Y, Zhou Q. Small molecule modulators of cystic fibrosis transmembrane conductance regulator (CFTR): Structure, classification, and mechanisms. Eur J Med Chem 2024; 265:116120. [PMID: 38194776 DOI: 10.1016/j.ejmech.2023.116120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 12/28/2023] [Accepted: 12/31/2023] [Indexed: 01/11/2024]
Abstract
The advent of small molecule modulators targeting the cystic fibrosis transmembrane conductance regulator (CFTR) has revolutionized the treatment of persons with cystic fibrosis (CF) (pwCF). Presently, these small molecule CFTR modulators have gained approval for usage in approximately 90 % of adult pwCF. Ongoing drug development endeavors are focused on optimizing the therapeutic benefits while mitigating potential adverse effects associated with this treatment approach. Based on their mode of interaction with CFTR, these drugs can be classified into two distinct categories: specific CFTR modulators and non-specific CFTR modulators. Specific CFTR modulators encompass potentiators and correctors, whereas non-specific CFTR modulators encompass activators, proteostasis modulators, stabilizers, reader-through agents, and amplifiers. Currently, four small molecule modulators, all classified as potentiators and correctors, have obtained marketing approval. Furthermore, numerous novel small molecule modulators, exhibiting diverse mechanisms of action, are currently undergoing development. This review aims to explore the classification, mechanisms of action, molecular structures, developmental processes, and interrelationships among small molecule CFTR modulators.
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Affiliation(s)
- Luyang Cao
- China Pharmaceutical University, Nanjing, 210009, PR China
| | - Yong Wu
- Jiangsu Vcare PharmaTech Co., Ltd., Huakang Road 136, Biotech and Pharmaceutical Valley, Jiangbei New Area, Nanjing, 211800, PR China
| | - Yanchun Gong
- Jiangsu Vcare PharmaTech Co., Ltd., Huakang Road 136, Biotech and Pharmaceutical Valley, Jiangbei New Area, Nanjing, 211800, PR China.
| | - Qingfa Zhou
- China Pharmaceutical University, Nanjing, 210009, PR China.
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21
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Todaro AM, Radu CM, Ciccone M, Toffanin S, Serino ML, Campello E, Bulato C, Lunghi B, Gemmati D, Cuneo A, Hackeng TM, Simioni P, Bernardi F, Castoldi E. In vitro and ex vivo rescue of a nonsense mutation responsible for severe coagulation factor V deficiency. J Thromb Haemost 2024; 22:410-422. [PMID: 37866515 DOI: 10.1016/j.jtha.2023.10.007] [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: 08/01/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 10/24/2023]
Abstract
BACKGROUND Coagulation factor V (FV) deficiency is a rare bleeding disorder that is usually managed with fresh-frozen plasma. Patients with nonsense mutations may respond to treatment with readthrough agents. OBJECTIVES To investigate whether the F5 p.Arg1161Ter mutation, causing severe FV deficiency in several patients, would be amenable to readthrough therapy. METHODS F5 mRNA and protein expression were evaluated in a F5 p.Arg1161Ter-homozygous patient. Five readthrough agents with different mechanisms of action, i.e. G418, ELX-02, PTC-124, 2,6-diaminopurine (2,6-DAP), and Amlexanox, were tested in in vitro and ex vivo models of the mutation. RESULTS The F5 p.Arg1161Ter-homozygous patient showed residual F5 mRNA and functional platelet FV, indicating detectable levels of natural readthrough. COS-1 cells transfected with the FV-Arg1161Ter cDNA expressed 0.7% FV activity compared to wild-type. Treatment with 0-500 μM G418, ELX-02, and 2,6-DAP dose-dependently increased FV activity up to 7.0-fold, 3.1-fold, and 10.8-fold, respectively, whereas PTC-124 and Amlexanox (alone or in combination) were ineffective. These findings were confirmed by thrombin generation assays in FV-depleted plasma reconstituted with conditioned media of treated cells. All compounds except ELX-02 showed some degree of cytotoxicity. Ex vivo differentiated megakaryocytes of the F5 p.Arg1161Ter-homozygous patient, which were negative at FV immunostaining, turned positive after treatment with all 5 readthrough agents. Notably, they were also able to internalize mutant FV rescued with G418 or 2,6-DAP, which would be required to maintain the crucial platelet FV pool in vivo. CONCLUSION These findings provide in vitro and ex vivo proof-of-principle for readthrough-mediated rescue of the F5 p.Arg1161Ter mutation.
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Affiliation(s)
- Alice M Todaro
- Department of Biochemistry, Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, The Netherlands
| | - Claudia M Radu
- Department of Medicine, Thrombotic and Haemorrhagic Diseases Unit, Padua University Medical School, Padua, Italy
| | - Maria Ciccone
- Department of Medical Sciences, Section of Haematology, Sant'Anna Hospital, Ferrara University, Ferrara, Italy
| | - Serena Toffanin
- Department of Medicine, Thrombotic and Haemorrhagic Diseases Unit, Padua University Medical School, Padua, Italy
| | - M Luisa Serino
- Department of Medical Sciences, Section of Haematology, Sant'Anna Hospital, Ferrara University, Ferrara, Italy
| | - Elena Campello
- Department of Medicine, Thrombotic and Haemorrhagic Diseases Unit, Padua University Medical School, Padua, Italy
| | - Cristiana Bulato
- Department of Medicine, Thrombotic and Haemorrhagic Diseases Unit, Padua University Medical School, Padua, Italy
| | - Barbara Lunghi
- Department of Life Sciences and Biotechnology, Section of Biochemistry and Molecular Biology, Ferrara University, Ferrara, Italy
| | - Donato Gemmati
- Department of Translational Medicine, Haemostasis & Thrombosis Centre, Ferrara University, Ferrara, Italy
| | - Antonio Cuneo
- Department of Medical Sciences, Section of Haematology, Sant'Anna Hospital, Ferrara University, Ferrara, Italy
| | - Tilman M Hackeng
- Department of Biochemistry, Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, The Netherlands
| | - Paolo Simioni
- Department of Medicine, Thrombotic and Haemorrhagic Diseases Unit, Padua University Medical School, Padua, Italy
| | - Francesco Bernardi
- Department of Life Sciences and Biotechnology, Section of Biochemistry and Molecular Biology, Ferrara University, Ferrara, Italy
| | - Elisabetta Castoldi
- Department of Biochemistry, Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, The Netherlands.
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22
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Blomquist VG, Niu J, Choudhury P, Al Saneh A, Colecraft HM, Ahern CA. Transfer RNA-mediated restoration of potassium current and electrical correction in premature termination long-QT syndrome hERG mutants. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 34:102032. [PMID: 37842167 PMCID: PMC10568093 DOI: 10.1016/j.omtn.2023.102032] [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: 02/03/2023] [Accepted: 09/14/2023] [Indexed: 10/17/2023]
Abstract
Disease-causing premature termination codons (PTCs) individually disrupt the functional expression of hundreds of genes and represent a pernicious clinical challenge. In the heart, loss-of-function mutations in the hERG potassium channel account for approximately 30% of long-QT syndrome arrhythmia, a lethal cardiac disorder with limited treatment options. Premature termination of ribosomal translation produces a truncated and, for potassium channels, a potentially dominant-negative protein that impairs the functional assembly of the wild-type homotetrameric hERG channel complex. We used high-throughput flow cytometry and patch-clamp electrophysiology to assess the trafficking and voltage-dependent activity of hERG channels carrying patient PTC variants that have been corrected by anticodon engineered tRNA. Adenoviral-mediated expression of mutant hERG channels in cultured adult guinea pig cardiomyocytes prolonged action potential durations, and this deleterious effect was corrected upon adenoviral delivery of a human ArgUGA tRNA to restore full-length hERG protein. The results demonstrate mutation-specific, context-agnostic PTC correction and elevate the therapeutic potential of this approach for rare genetic diseases caused by stop codons.
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Affiliation(s)
- Viggo G. Blomquist
- Department of Physiology and Cellular Biophysics, Columbia University Medical Center, New York, NY 10032, USA
| | - Jacqueline Niu
- Department of Physiology and Cellular Biophysics, Columbia University Medical Center, New York, NY 10032, USA
| | - Papiya Choudhury
- Department of Physiology and Cellular Biophysics, Columbia University Medical Center, New York, NY 10032, USA
| | - Ahmad Al Saneh
- Department of Molecular Physiology and Biophysics, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Henry M. Colecraft
- Department of Physiology and Cellular Biophysics, Columbia University Medical Center, New York, NY 10032, USA
| | - Christopher A. Ahern
- Department of Molecular Physiology and Biophysics, University of Iowa Carver College of Medicine, Iowa City, IA, USA
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23
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Ford PW, Bennett EJ. How degrading! Trapped translation factors get trashed. Cell Rep 2023; 42:113278. [PMID: 37910507 DOI: 10.1016/j.celrep.2023.113278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 11/03/2023] Open
Abstract
Using small molecules that trap translation factors within translating ribosomes, Gurzeler et al.1 and Oltion et al.2 identify a new branch of the ribosome-associated quality-control (RQC) pathway. This mode of translation regulation expands the number of mechanistically distinct RQC pathways.
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Affiliation(s)
- Pierce W Ford
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093
| | - Eric J Bennett
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093.
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24
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Palomar-Siles M, Yurevych V, Bykov VJN, Wiman KG. Pharmacological induction of translational readthrough of nonsense mutations in the retinoblastoma (RB1) gene. PLoS One 2023; 18:e0292468. [PMID: 37917619 PMCID: PMC10621805 DOI: 10.1371/journal.pone.0292468] [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: 01/23/2023] [Accepted: 09/21/2023] [Indexed: 11/04/2023] Open
Abstract
The retinoblastoma protein (Rb) is encoded by the RB1 tumor suppressor gene. Inactivation of RB1 by inherited or somatic mutation occurs in retinoblastoma and various other types of tumors. A significant fraction (25.9%) of somatic RB1 mutations are nonsense substitutions leading to a premature termination codon (PTC) in the RB1 coding sequence and expression of truncated inactive Rb protein. Here we show that aminoglycoside G418, a known translational readthrough inducer, can induce full-length Rb protein in SW1783 astrocytoma cells with endogenous R579X nonsense mutant RB1 as well as in MDA-MB-436 breast carcinoma cells transiently transfected with R251X, R320X, R579X or Q702X nonsense mutant RB1 cDNA. Readthrough was associated with increased RB1 mRNA levels in nonsense mutant RB1 cells. Induction of full-length Rb protein was potentiated by the cereblon E3 ligase modulator CC-90009. These results suggest that pharmacological induction of translational readthrough could be a feasible strategy for therapeutic targeting of tumors with nonsense mutant RB1.
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Affiliation(s)
- Mireia Palomar-Siles
- Department of Oncology-Pathology, BioClinicum, Karolinska Institutet, Stockholm, Sweden
| | - Viktor Yurevych
- Department of Oncology-Pathology, BioClinicum, Karolinska Institutet, Stockholm, Sweden
| | - Vladimir J. N. Bykov
- Department of Oncology-Pathology, BioClinicum, Karolinska Institutet, Stockholm, Sweden
| | - Klas G. Wiman
- Department of Oncology-Pathology, BioClinicum, Karolinska Institutet, Stockholm, Sweden
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25
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de Oliveira ASLE, de Siqueira RC, Nait-Meddour C, Tricarico PM, Moura R, Agrelli A, d'Adamo AP, Jamain S, Crovella S, de Fátima Medeiros Brito M, Boniotto M, Brandão LAC. A loss-of-function NCSTN mutation associated with familial Dowling Degos disease and hidradenitis suppurativa. Exp Dermatol 2023; 32:1935-1945. [PMID: 37665193 DOI: 10.1111/exd.14919] [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: 05/04/2023] [Revised: 07/26/2023] [Accepted: 08/06/2023] [Indexed: 09/05/2023]
Abstract
Dowling Degos disease (DDD) is a rare autosomal dominant genodermatosis characterized by acquired, slowly progressive reticulated pigmented lesions primarily involving flexural skin areas. Mutations in KRT5, POGLUT-1 and POFUT-1 genes have been associated with DDD, and loss-of-function mutations in PSENEN, a subunit of the gamma-secretase complex, were found in patients presenting with DDD or DDD comorbid with hidradenitis suppurativa (HS). A nonsense mutation in NCSTN, another subunit of the gamma-secretase, was already described in a patient suffering from HS and DDD but whether NCSTN could be considered a novel gene for DDD is still debated. Here, we enrolled a four-generation family with HS and DDD. Through Whole Exome Sequencing (WES) we identified a novel nonsense mutation in the NCSTN gene in all the affected family members. To study the impact of this variant, we isolated outer root sheath cells from patients' hair follicles. We showed that this variant leads to a premature stop codon, activates a nonsense-mediated mRNA decay, and causes NCSTN haploinsufficiency in affected individuals. In fact, cells treated with gentamicin, a readthrough agent, had the NCSTN levels corrected. Moreover, we observed that this haploinsufficiency also affects other subunits of the gamma-secretase complex, possibly causing DDD. Our findings clearly support NCSTN as a novel DDD gene and suggest carefully investigating this co-occurrence in HS patients carrying a mutation in the NCSTN gene.
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Affiliation(s)
| | | | - Cécile Nait-Meddour
- Univ Paris Est Créteil, INSERM, IMRB, Translational Neuropsychiatry, Créteil, France
| | - Paola Maura Tricarico
- Institute for Maternal and Child Health-IRCCS "Burlo Garofolo", Department of Advanced Diagnostics, Trieste, Italy
| | - Ronald Moura
- Institute for Maternal and Child Health-IRCCS "Burlo Garofolo", Department of Advanced Diagnostics, Trieste, Italy
| | - Almerinda Agrelli
- Laboratory of Nanostructured Materials (LMNANO), Center for Strategic Technologies Northeastern (CETENE), Recife, Brazil
| | - Adamo Pio d'Adamo
- Institute for Maternal and Child Health-IRCCS "Burlo Garofolo", Department of Advanced Diagnostics, Trieste, Italy
- University of Trieste, Department of Medical Surgical and Health Sciences, Trieste, Italy
| | - Stéphane Jamain
- Univ Paris Est Créteil, INSERM, IMRB, Translational Neuropsychiatry, Créteil, France
| | - Sergio Crovella
- LARC Laboratory Animal Research Center, University of Qatar, Doha, Qatar
| | | | - Michele Boniotto
- Univ Paris Est Créteil, INSERM, IMRB, Translational Neuropsychiatry, Créteil, France
| | - Lucas André Cavalcanti Brandão
- Keizo Asami Institute-iLIKA, Federal University of Pernambuco, Recife, Brazil
- Department of Pathology, Federal University of Pernambuco, Recife, Brazil
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26
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Wittenstein A, Caspi M, Rippin I, Elroy-Stein O, Eldar-Finkelman H, Thoms S, Rosin-Arbesfeld R. Nonsense mutation suppression is enhanced by targeting different stages of the protein synthesis process. PLoS Biol 2023; 21:e3002355. [PMID: 37943958 PMCID: PMC10684085 DOI: 10.1371/journal.pbio.3002355] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 11/28/2023] [Accepted: 09/29/2023] [Indexed: 11/12/2023] Open
Abstract
The introduction of premature termination codons (PTCs), as a result of splicing defects, insertions, deletions, or point mutations (also termed nonsense mutations), lead to numerous genetic diseases, ranging from rare neuro-metabolic disorders to relatively common inheritable cancer syndromes and muscular dystrophies. Over the years, a large number of studies have demonstrated that certain antibiotics and other synthetic molecules can act as PTC suppressors by inducing readthrough of nonsense mutations, thereby restoring the expression of full-length proteins. Unfortunately, most PTC readthrough-inducing agents are toxic, have limited effects, and cannot be used for therapeutic purposes. Thus, further efforts are required to improve the clinical outcome of nonsense mutation suppressors. Here, by focusing on enhancing readthrough of pathogenic nonsense mutations in the adenomatous polyposis coli (APC) tumor suppressor gene, we show that disturbing the protein translation initiation complex, as well as targeting other stages of the protein translation machinery, enhances both antibiotic and non-antibiotic-mediated readthrough of nonsense mutations. These findings strongly increase our understanding of the mechanisms involved in nonsense mutation readthrough and facilitate the development of novel therapeutic targets for nonsense suppression to restore protein expression from a large variety of disease-causing mutated transcripts.
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Affiliation(s)
- Amnon Wittenstein
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Michal Caspi
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ido Rippin
- The Department of Human Molecular Genetics & Biochemistry School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Orna Elroy-Stein
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Hagit Eldar-Finkelman
- The Department of Human Molecular Genetics & Biochemistry School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Sven Thoms
- Biochemistry and Molecular Medicine, Medical School EWL, Bielefeld University, Bielefeld, Germany
| | - Rina Rosin-Arbesfeld
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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27
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Graeber SY, Mall MA. The future of cystic fibrosis treatment: from disease mechanisms to novel therapeutic approaches. Lancet 2023; 402:1185-1198. [PMID: 37699417 DOI: 10.1016/s0140-6736(23)01608-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/23/2023] [Accepted: 07/31/2023] [Indexed: 09/14/2023]
Abstract
With the 2019 breakthrough in the development of highly effective modulator therapy providing unprecedented clinical benefits for over 90% of patients with cystic fibrosis who are genetically eligible for treatment, this rare disease has become a front runner of transformative molecular therapy. This success is based on fundamental research, which led to the identification of the disease-causing CFTR gene and our subsequent understanding of the disease mechanisms underlying the pathogenesis of cystic fibrosis, working together with a continuously evolving clinical research and drug development pipeline. In this Series paper, we focus on advances since 2018, and remaining knowledge gaps in our understanding of the molecular mechanisms of CFTR dysfunction in the airway epithelium and their links to mucus dysfunction, impaired host defences, airway infection, and chronic inflammation of the lungs of people with cystic fibrosis. We review progress in (and the remaining obstacles to) pharmacological approaches to rescue CFTR function, and novel strategies for improved symptomatic therapies for cystic fibrosis, including how these might be applicable to common lung diseases, such as bronchiectasis and chronic obstructive pulmonary disease. Finally, we discuss the promise of genetic therapies and gene editing approaches to restore CFTR function in the lungs of all patients with cystic fibrosis independent of their CFTR genotype, and the unprecedented opportunities to transform cystic fibrosis from a fatal disease to a treatable and potentially curable one.
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Affiliation(s)
- Simon Y Graeber
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; Cystic Fibrosis Center, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; German Center for Lung Research, associated partner site, Berlin, Germany; Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Marcus A Mall
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; Cystic Fibrosis Center, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany; German Center for Lung Research, associated partner site, Berlin, Germany; Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany.
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28
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Gurzeler LA, Link M, Ibig Y, Schmidt I, Galuba O, Schoenbett J, Gasser-Didierlaurant C, Parker CN, Mao X, Bitsch F, Schirle M, Couttet P, Sigoillot F, Ziegelmüller J, Uldry AC, Teodorowicz W, Schmiedeberg N, Mühlemann O, Reinhardt J. Drug-induced eRF1 degradation promotes readthrough and reveals a new branch of ribosome quality control. Cell Rep 2023; 42:113056. [PMID: 37651229 DOI: 10.1016/j.celrep.2023.113056] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 06/15/2023] [Accepted: 08/16/2023] [Indexed: 09/02/2023] Open
Abstract
Suppression of premature termination codons (PTCs) by translational readthrough is a promising strategy to treat a wide variety of severe genetic diseases caused by nonsense mutations. Here, we present two potent readthrough promoters-NVS1.1 and NVS2.1-that restore substantial levels of functional full-length CFTR and IDUA proteins in disease models for cystic fibrosis and Hurler syndrome, respectively. In contrast to other readthrough promoters that affect stop codon decoding, the NVS compounds stimulate PTC suppression by triggering rapid proteasomal degradation of the translation termination factor eRF1. Our results show that this occurs by trapping eRF1 in the terminating ribosome, causing ribosome stalls and subsequent ribosome collisions, and activating a branch of the ribosome-associated quality control network, which involves the translational stress sensor GCN1 and the catalytic activity of the E3 ubiquitin ligases RNF14 and RNF25.
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Affiliation(s)
- Lukas-Adrian Gurzeler
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Marion Link
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Yvonne Ibig
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Isabel Schmidt
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Olaf Galuba
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | | | | | - Xiaohong Mao
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Francis Bitsch
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Markus Schirle
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Philipp Couttet
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | - Jana Ziegelmüller
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Anne-Christine Uldry
- Proteomics and Mass Spectrometry Core Facility, Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Wojciech Teodorowicz
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | | | - Oliver Mühlemann
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland.
| | - Jürgen Reinhardt
- Novartis Institutes for BioMedical Research, Basel, Switzerland.
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29
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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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30
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Joynt AT, Kavanagh EW, Newby GA, Mitchell S, Eastman AC, Paul KC, Bowling AD, Osorio DL, Merlo CA, Patel SU, Raraigh KS, Liu DR, Sharma N, Cutting GR. Protospacer modification improves base editing of a canonical splice site variant and recovery of CFTR function in human airway epithelial cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:335-350. [PMID: 37547293 PMCID: PMC10400809 DOI: 10.1016/j.omtn.2023.06.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 06/26/2023] [Indexed: 08/08/2023]
Abstract
Canonical splice site variants affecting the 5' GT and 3' AG nucleotides of introns result in severe missplicing and account for about 10% of disease-causing genomic alterations. Treatment of such variants has proven challenging due to the unstable mRNA or protein isoforms that typically result from disruption of these sites. Here, we investigate CRISPR-Cas9-mediated adenine base editing for such variants in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. We validate a CFTR expression minigene (EMG) system for testing base editing designs for two different targets. We then use the EMG system to test non-standard single-guide RNAs with either shortened or lengthened protospacers to correct the most common cystic fibrosis-causing variant in individuals of African descent (c.2988+1G>A). Varying the spacer region length allowed placement of the editing window in a more efficient context and enabled use of alternate protospacer adjacent motifs. Using these modifications, we restored clinically significant levels of CFTR function to human airway epithelial cells from two donors bearing the c.2988+1G>A variant.
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Affiliation(s)
- Anya T. Joynt
- Department of Genetic Medicine, Johns Hopkins University School of Medicine Baltimore, MD 21205, USA
| | - Erin W. Kavanagh
- Department of Genetic Medicine, Johns Hopkins University School of Medicine Baltimore, MD 21205, USA
| | - Gregory A. Newby
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Shakela Mitchell
- Department of Genetic Medicine, Johns Hopkins University School of Medicine Baltimore, MD 21205, USA
| | - Alice C. Eastman
- Department of Genetic Medicine, Johns Hopkins University School of Medicine Baltimore, MD 21205, USA
| | - Kathleen C. Paul
- Department of Genetic Medicine, Johns Hopkins University School of Medicine Baltimore, MD 21205, USA
| | - Alyssa D. Bowling
- Department of Genetic Medicine, Johns Hopkins University School of Medicine Baltimore, MD 21205, USA
| | - Derek L. Osorio
- Department of Genetic Medicine, Johns Hopkins University School of Medicine Baltimore, MD 21205, USA
| | - Christian A. Merlo
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins Hospital, Baltimore, MD 21287, USA
| | - Shivani U. Patel
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins Hospital, Baltimore, MD 21287, USA
| | - Karen S. Raraigh
- Department of Genetic Medicine, Johns Hopkins University School of Medicine Baltimore, MD 21205, USA
| | - David R. Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Neeraj Sharma
- Department of Genetic Medicine, Johns Hopkins University School of Medicine Baltimore, MD 21205, USA
| | - Garry R. Cutting
- Department of Genetic Medicine, Johns Hopkins University School of Medicine Baltimore, MD 21205, USA
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Baharara H, Kesharwani P, Johnston TP, Sahebkar A. Therapeutic potential of phytochemicals for cystic fibrosis. Biofactors 2023; 49:984-1009. [PMID: 37191383 DOI: 10.1002/biof.1960] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 05/01/2023] [Indexed: 05/17/2023]
Abstract
The aim of this review was to review and discuss various phytochemicals that exhibit beneficial effects on mutated membrane channels, and hence, improve transmembrane conductance. These therapeutic phytochemicals may have the potential to decrease mortality and morbidity of CF patients. Four databases were searched using keywords. Relevant studies were identified, and related articles were separated. Google Scholar, as well as gray literature (i.e., information that is not produced by commercial publishers), were also checked for related articles to locate/identify additional studies. The relevant databases were searched a second time to ensure that recent studies were included. In conclusion, while curcumin, genistein, and resveratrol have demonstrated effectiveness in this regard, it should be emphasized that coumarins, quercetin, and other herbal medicines also have beneficial effects on transporter function, transmembrane conductivity, and overall channel activity. Additional in vitro and in vivo studies should be conducted on mutant CFTR to unequivocally define the mechanism by which phytochemicals alter transmembrane channel function/activity, since the results of the studies evaluated in this review have a high degree of heterogenicity and discrepancy. Finally, continued research be undertaken to clearly define the mechanism(s) of action and the therapeutic effects that therapeutic phytochemicals have on the symptoms observed in CF patients in an effort to reduce mortality and morbidity.
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Affiliation(s)
- Hamed Baharara
- Department of Clinical Pharmacy, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Prashant Kesharwani
- Department of Pharmaceutics, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, India
- Center for Transdisciplinary Research, Department of Pharmacology, Saveetha Dental College, Saveetha Institute of Medical and Technical Science, Chennai, India
| | - Thomas P Johnston
- Division of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, Kansas City, Missouri, USA
| | - AmirHossein Sahebkar
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
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32
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Oliver KE, Carlon MS, Pedemonte N, Lopes-Pacheco M. The revolution of personalized pharmacotherapies for cystic fibrosis: what does the future hold? Expert Opin Pharmacother 2023; 24:1545-1565. [PMID: 37379072 PMCID: PMC10528905 DOI: 10.1080/14656566.2023.2230129] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/16/2023] [Accepted: 06/23/2023] [Indexed: 06/29/2023]
Abstract
INTRODUCTION Cystic fibrosis (CF), a potentially fatal genetic disease, is caused by loss-of-function mutations in the gene encoding for the CFTR chloride/bicarbonate channel. Modulator drugs rescuing mutant CFTR traffic and function are now in the clinic, providing unprecedented breakthrough therapies for people with CF (PwCF) carrying specific genotypes. However, several CFTR variants are unresponsive to these therapies. AREA COVERED We discussed several therapeutic approaches that are under development to tackle the fundamental cause of CF, including strategies targeting defective CFTR mRNA and/or protein expression and function. Alternatively, defective chloride secretion and dehydration in CF epithelia could be restored by exploiting pharmacological modulation of alternative targets, i.e., ion channels/transporters that concur with CFTR to maintain the airway surface liquid homeostasis (e.g., ENaC, TMEM16A, SLC26A4, SLC26A9, and ATP12A). Finally, we assessed progress and challenges in the development of gene-based therapies to replace or correct the mutant CFTR gene. EXPERT OPINION CFTR modulators are benefiting many PwCF responsive to these drugs, yielding substantial improvements in various clinical outcomes. Meanwhile, the CF therapy development pipeline continues to expand with the development of novel CFTR modulators and alternative therapeutic strategies with the ultimate goal of providing effective therapies for all PwCF in the foreseeable future.
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Affiliation(s)
- Kathryn E. Oliver
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
- Center for Cystic Fibrosis and Airways Disease Research, Emory University and Children’s Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Marianne S. Carlon
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
- Center for Molecular Medicine, KU Leuven, Leuven, Belgium
| | | | - Miquéias Lopes-Pacheco
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, Lisbon, Portugal
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Esposito C, Kamper M, Trentacoste J, Galvin S, Pfister H, Wang J. Advances in the Cystic Fibrosis Drug Development Pipeline. Life (Basel) 2023; 13:1835. [PMID: 37763239 PMCID: PMC10532558 DOI: 10.3390/life13091835] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 08/17/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
Cystic fibrosis is a genetic disease that results in progressive multi-organ manifestations with predominance in the respiratory and gastrointestinal systems. The significant morbidity and mortality seen in the CF population has been the driving force urging the CF research community to further advance treatments to slow disease progression and, in turn, prolong life expectancy. Enormous strides in medical advancements have translated to improvement in quality of life, symptom burden, and survival; however, there is still no cure. This review discusses the most current mainstay treatments and anticipated therapeutics in the CF drug development pipeline within the mechanisms of mucociliary clearance, anti-inflammatory and anti-infective therapies, restoration of the cystic fibrosis transmembrane conductance regulator (CFTR) protein (also known as highly effective modulator therapy (HEMT)), and genetic therapies. Ribonucleic acid (RNA) therapy, gene transfer, and gene editing are being explored in the hopes of developing a treatment and potential cure for people with CF, particularly for those not responsive to HEMT.
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Affiliation(s)
- Christine Esposito
- Division of Pulmonary, Critical Care and Sleep Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, New Hyde Park, New York, NY 11042, USA; (M.K.); (J.W.)
| | - Martin Kamper
- Division of Pulmonary, Critical Care and Sleep Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, New Hyde Park, New York, NY 11042, USA; (M.K.); (J.W.)
| | - Jessica Trentacoste
- Division of Pulmonary, Critical Care and Sleep Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, New Hyde Park, New York, NY 11042, USA; (M.K.); (J.W.)
| | - Susan Galvin
- Division of Pediatric Pulmonology, The Steven and Alexandra Cohen Children’s Medical Center, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Lake Success, New York, NY 11042, USA;
| | - Halie Pfister
- Manhasset Office of Clinical Research, The Feinstein Institutes for Medical Research, Lake Success, New York, NY 11042, USA;
| | - Janice Wang
- Division of Pulmonary, Critical Care and Sleep Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, New Hyde Park, New York, NY 11042, USA; (M.K.); (J.W.)
- Manhasset Office of Clinical Research, The Feinstein Institutes for Medical Research, Lake Success, New York, NY 11042, USA;
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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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35
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Li S, Li J, Shi W, Nie Z, Zhang S, Ma F, Hu J, Chen J, Li P, Xie X. Pharmaceuticals Promoting Premature Termination Codon Readthrough: Progress in Development. Biomolecules 2023; 13:988. [PMID: 37371567 DOI: 10.3390/biom13060988] [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: 04/25/2023] [Revised: 05/27/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
Around 11% of all known gene lesions causing human genetic diseases are nonsense mutations that introduce a premature stop codon (PTC) into the protein-coding gene sequence. Drug-induced PTC readthrough is a promising therapeutic strategy for treating hereditary diseases caused by nonsense mutations. To date, it has been found that more than 50 small-molecular compounds can promote PTC readthrough, known as translational readthrough-inducing drugs (TRIDs), and can be divided into two major categories: aminoglycosides and non-aminoglycosides. This review summarizes the pharmacodynamics and clinical application potential of the main TRIDs discovered so far, especially some newly discovered TRIDs in the past decade. The discovery of these TRIDs brings hope for treating nonsense mutations in various genetic diseases. Further research is still needed to deeply understand the mechanism of eukaryotic cell termination and drug-induced PTC readthrough so that patients can achieve the greatest benefit from the various TRID treatments.
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Affiliation(s)
- Shan Li
- School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Juan Li
- Central Laboratory, The First Hospital of Lanzhou University, Lanzhou 730000, China
- Gansu Key Laboratory of Genetic Study of Hematopathy, The First Hospital of Lanzhou University, Lanzhou 730000, China
| | - Wenjing Shi
- School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Ziyan Nie
- School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Shasha Zhang
- School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Fengdie Ma
- School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Jun Hu
- School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Jianjun Chen
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Peiqiang Li
- School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
| | - Xiaodong Xie
- School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China
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36
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Albers S, Allen EC, Bharti N, Davyt M, Joshi D, Perez-Garcia CG, Santos L, Mukthavaram R, Delgado-Toscano MA, Molina B, Kuakini K, Alayyoubi M, Park KJJ, Acharya G, Gonzalez JA, Sagi A, Birket SE, Tearney GJ, Rowe SM, Manfredi C, Hong JS, Tachikawa K, Karmali P, Matsuda D, Sorscher EJ, Chivukula P, Ignatova Z. Engineered tRNAs suppress nonsense mutations in cells and in vivo. Nature 2023; 618:842-848. [PMID: 37258671 PMCID: PMC10284701 DOI: 10.1038/s41586-023-06133-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 04/25/2023] [Indexed: 06/02/2023]
Abstract
Nonsense mutations are the underlying cause of approximately 11% of all inherited genetic diseases1. Nonsense mutations convert a sense codon that is decoded by tRNA into a premature termination codon (PTC), resulting in an abrupt termination of translation. One strategy to suppress nonsense mutations is to use natural tRNAs with altered anticodons to base-pair to the newly emerged PTC and promote translation2-7. However, tRNA-based gene therapy has not yielded an optimal combination of clinical efficacy and safety and there is presently no treatment for individuals with nonsense mutations. Here we introduce a strategy based on altering native tRNAs into efficient suppressor tRNAs (sup-tRNAs) by individually fine-tuning their sequence to the physico-chemical properties of the amino acid that they carry. Intravenous and intratracheal lipid nanoparticle (LNP) administration of sup-tRNA in mice restored the production of functional proteins with nonsense mutations. LNP-sup-tRNA formulations caused no discernible readthrough at endogenous native stop codons, as determined by ribosome profiling. At clinically important PTCs in the cystic fibrosis transmembrane conductance regulator gene (CFTR), the sup-tRNAs re-established expression and function in cell systems and patient-derived nasal epithelia and restored airway volume homeostasis. These results provide a framework for the development of tRNA-based therapies with a high molecular safety profile and high efficacy in targeted PTC suppression.
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Affiliation(s)
- Suki Albers
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | | | - Nikhil Bharti
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Marcos Davyt
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Disha Joshi
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA
- Children's Healthcare of Atlanta, Atlanta, GA, USA
| | | | - Leonardo Santos
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | | | | | | | | | | | | | | | | | - Amit Sagi
- Arcturus Therapeutics, San Diego, CA, USA
| | - Susan E Birket
- Pulmonary, Allergy, and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Guillermo J Tearney
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard-MIT Health Sciences and Technology, MA, Cambridge, USA
| | - Steven M Rowe
- Pulmonary, Allergy, and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Candela Manfredi
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA
- Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Jeong S Hong
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA
- Children's Healthcare of Atlanta, Atlanta, GA, USA
| | | | | | | | - Eric J Sorscher
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA.
- Children's Healthcare of Atlanta, Atlanta, GA, USA.
| | | | - Zoya Ignatova
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany.
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Birimberg-Schwartz L, Ip W, Bartlett C, Avolio J, Vonk AM, Gunawardena T, Du K, Esmaeili M, Beekman JM, Rommens J, Strug L, Bear CE, Moraes TJ, Gonska T. Validating organoid-derived human intestinal monolayers for personalized therapy in cystic fibrosis. Life Sci Alliance 2023; 6:e202201857. [PMID: 37024122 PMCID: PMC10079552 DOI: 10.26508/lsa.202201857] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 03/27/2023] [Accepted: 03/28/2023] [Indexed: 04/08/2023] Open
Abstract
Highly effective drugs modulating the defective protein encoded by the CFTR gene have revolutionized cystic fibrosis (CF) therapy. Preclinical drug-testing on human nasal epithelial (HNE) cell cultures and 3-dimensional human intestinal organoids (3D HIO) are used to address patient-specific variation in drug response and to optimize individual treatment for people with CF. This study is the first to report comparable CFTR functional responses to CFTR modulator treatment among patients with different classes of CFTR gene variants using the three methods of 2D HIO, 3D HIO, and HNE. Furthermore, 2D HIO showed good correlation to clinical outcome markers. A larger measurable CFTR functional range and access to the apical membrane were identified as advantages of 2D HIO over HNE and 3D HIO, respectively. Our study thus expands the utility of 2D intestinal monolayers as a preclinical drug testing tool for CF.
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Affiliation(s)
- Liron Birimberg-Schwartz
- Department of Paediatrics, Division of Gastroenterology, Hepatology and Nutrition, University of Toronto, Toronto, Canada
- Translational Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Wan Ip
- Translational Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Claire Bartlett
- Translational Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Julie Avolio
- Translational Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Annelotte M Vonk
- Regenerative Medicine Utrecht, University Medical Center, Utrecht University, Utrecht, The Netherlands
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Member of ERN-LUNG, Utrecht, The Netherland
| | - Tarini Gunawardena
- Programme in Molecular Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Kai Du
- Programme in Molecular Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Mohsen Esmaeili
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Jeffrey M Beekman
- Regenerative Medicine Utrecht, University Medical Center, Utrecht University, Utrecht, The Netherlands
- Department of Pediatric Pulmonology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Member of ERN-LUNG, Utrecht, The Netherland
| | - Johanna Rommens
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Lisa Strug
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
- Biostatistics Division, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
- Department of Statistical Sciences and Computer Science, University of Toronto, Toronto, Canada
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Canada
| | - Christine E Bear
- Programme in Molecular Medicine, The Hospital for Sick Children, Toronto, Canada
- Department of Physiology, University of Toronto, Toronto, Canada
- Department of Biochemistry, University of Toronto, Toronto, Canada
| | - Theo J Moraes
- Translational Medicine, The Hospital for Sick Children, Toronto, Canada
- Department of Paediatrics, Division of Respiratory Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Tanja Gonska
- Department of Paediatrics, Division of Gastroenterology, Hepatology and Nutrition, University of Toronto, Toronto, Canada
- Translational Medicine, The Hospital for Sick Children, Toronto, Canada
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38
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Spelier S, van Doorn EPM, van der Ent CK, Beekman JM, Koppens MAJ. Readthrough compounds for nonsense mutations: bridging the translational gap. Trends Mol Med 2023; 29:297-314. [PMID: 36828712 DOI: 10.1016/j.molmed.2023.01.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/28/2022] [Accepted: 01/19/2023] [Indexed: 02/24/2023]
Abstract
Approximately 10% of all pathological mutations are nonsense mutations that are responsible for several severe genetic diseases for which no treatment regimens are currently available. The most widespread strategy for treating nonsense mutations is by enhancing ribosomal readthrough of premature termination codons (PTCs) to restore the production of the full-length protein. In the past decade several compounds with readthrough potential have been identified. However, although preclinical results on these compounds are promising, clinical studies have not yielded positive outcomes. We review preclinical and clinical research related to readthrough compounds and characterize factors that contribute to the observed translational gap.
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Affiliation(s)
- Sacha Spelier
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584, EA, Utrecht, The Netherlands; Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584, CT, Utrecht, The Netherlands
| | - Eveline P M van Doorn
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584, EA, Utrecht, The Netherlands
| | - Cornelis K van der Ent
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584, EA, Utrecht, The Netherlands; Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584, CT, Utrecht, The Netherlands
| | - Jeffrey M Beekman
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584, EA, Utrecht, The Netherlands; Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584, CT, Utrecht, The Netherlands; Center for Living Technologies, Eindhoven-Wageningen-Utrecht Alliance, Utrecht, The Netherlands
| | - Martijn A J Koppens
- Department of Pediatric Respiratory Medicine, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584, EA, Utrecht, The Netherlands; Regenerative Medicine Utrecht, University Medical Center, Utrecht University, 3584, CT, Utrecht, The Netherlands; Department of Metabolic Diseases, Wilhelmina Children's Hospital, University Medical Center, Utrecht University, 3584, EA, Utrecht, The Netherlands.
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39
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Wagner RN, Wießner M, Friedrich A, Zandanell J, Breitenbach-Koller H, Bauer JW. Emerging Personalized Opportunities for Enhancing Translational Readthrough in Rare Genetic Diseases and Beyond. Int J Mol Sci 2023; 24:6101. [PMID: 37047074 PMCID: PMC10093890 DOI: 10.3390/ijms24076101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/17/2023] [Accepted: 03/21/2023] [Indexed: 04/14/2023] Open
Abstract
Nonsense mutations trigger premature translation termination and often give rise to prevalent and rare genetic diseases. Consequently, the pharmacological suppression of an unscheduled stop codon represents an attractive treatment option and is of high clinical relevance. At the molecular level, the ability of the ribosome to continue translation past a stop codon is designated stop codon readthrough (SCR). SCR of disease-causing premature termination codons (PTCs) is minimal but small molecule interventions, such as treatment with aminoglycoside antibiotics, can enhance its frequency. In this review, we summarize the current understanding of translation termination (both at PTCs and at cognate stop codons) and highlight recently discovered pathways that influence its fidelity. We describe the mechanisms involved in the recognition and readthrough of PTCs and report on SCR-inducing compounds currently explored in preclinical research and clinical trials. We conclude by reviewing the ongoing attempts of personalized nonsense suppression therapy in different disease contexts, including the genetic skin condition epidermolysis bullosa.
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Affiliation(s)
- Roland N. Wagner
- Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria
| | - Michael Wießner
- Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria
| | - Andreas Friedrich
- Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria
- Department of Biosciences, University of Salzburg, 5020 Salzburg, Austria
| | - Johanna Zandanell
- Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria
| | | | - Johann W. Bauer
- Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria
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40
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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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41
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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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42
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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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43
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Vijaykumar K, Rowe SM. Lessons from other fields of medicine, Part 2: Cystic fibrosis. HANDBOOK OF CLINICAL NEUROLOGY 2023; 192:119-130. [PMID: 36796937 DOI: 10.1016/b978-0-323-85538-9.00006-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Cystic fibrosis (CF), first described in 1938, is a common, life-limiting monogenetic disease. The discovery of the cystic fibrosis transmembrane conductance regulator (CFTR) gene in 1989 was crucial in advancing our understanding of disease pathogenesis and paving the road for treatment aimed at the fundamental molecular defect. With the delineation of over 2000 variations in the CFTR gene, a sound understanding of the individual variations in cell biology, and electrophysiological abnormalities conferred by the most common defects propelled the advent of targeted disease-modifying therapeutics beginning in 2012. Since then, CF care has transformed beyond just symptomatic treatment to include a variety of small-molecule therapies that address the basic electrophysiologic defect and cause profound improvements in physiology, clinical manifestations, and long-term outcomes, designed to differentially address six genetic/molecular subtypes. This chapter illustrates the progress made toward how fundamental science and translational initiatives enabled personalized, mutation specific treatment. We highlight the importance of preclinical assays and mechanistically-driven development strategies that were coupled with sensitive biomarkers and a clinical trial cooperative to provide a platform for successful drug development. This convergence of academic and private partnerships, and formation of multidisciplinary care teams directed by evidence-based initiatives provide a seminal example of addressing the needs of individuals with a rare, but fatal genetic disease.
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Affiliation(s)
- Kadambari Vijaykumar
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States; The 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; The Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL, United States.
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44
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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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45
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A High-Throughput Assay for In Vitro Determination of Release Factor-Dependent Peptide Release from a Pretermination Complex by Fluorescence Anisotropy-Application to Nonsense Suppressor Screening and Mechanistic Studies. Biomolecules 2023; 13:biom13020242. [PMID: 36830611 PMCID: PMC9953321 DOI: 10.3390/biom13020242] [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: 12/27/2022] [Revised: 01/23/2023] [Accepted: 01/25/2023] [Indexed: 02/03/2023] Open
Abstract
Premature termination codons (PTCs) account for ~12% of all human disease mutations. Translation readthrough-inducing drugs (TRIDs) are prominent among the several therapeutic approaches being used to overcome PTCs. Ataluren is the only TRID that has been approved for treating patients suffering from a PTC disease, Duchenne muscular dystrophy, but it gives variable readthrough results in cells isolated from patients suffering from other PTC diseases. We recently elucidated ataluren's mechanism of action as a competitive inhibitor of release factor complex (RFC) catalysis of premature termination and identified ataluren's binding sites on the ribosome responsible for such an inhibition. These results suggest the possibility of discovering new TRIDs, which would retain ataluren's low toxicity while displaying greater potency and generality in stimulating readthrough via the inhibition of termination. Here we present a detailed description of a new in vitro plate reader assay that we are using both to screen small compound libraries for the inhibition of RFC-dependent peptide release and to better understand the influence of termination codon identity and sequence context on RFC activity.
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46
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Oltion K, Carelli JD, Yang T, See SK, Wang HY, Kampmann M, Taunton J. An E3 ligase network engages GCN1 to promote the degradation of translation factors on stalled ribosomes. Cell 2023; 186:346-362.e17. [PMID: 36638793 PMCID: PMC9994462 DOI: 10.1016/j.cell.2022.12.025] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 11/29/2022] [Accepted: 12/13/2022] [Indexed: 01/14/2023]
Abstract
Ribosomes frequently stall during mRNA translation, resulting in the context-dependent activation of quality control pathways to maintain proteostasis. However, surveillance mechanisms that specifically respond to stalled ribosomes with an occluded A site have not been identified. We discovered that the elongation factor-1α (eEF1A) inhibitor, ternatin-4, triggers the ubiquitination and degradation of eEF1A on stalled ribosomes. Using a chemical genetic approach, we unveiled a signaling network comprising two E3 ligases, RNF14 and RNF25, which are required for eEF1A degradation. Quantitative proteomics revealed the RNF14 and RNF25-dependent ubiquitination of eEF1A and a discrete set of ribosomal proteins. The ribosome collision sensor GCN1 plays an essential role by engaging RNF14, which directly ubiquitinates eEF1A. The site-specific, RNF25-dependent ubiquitination of the ribosomal protein RPS27A/eS31 provides a second essential signaling input. Our findings illuminate a ubiquitin signaling network that monitors the ribosomal A site and promotes the degradation of stalled translation factors, including eEF1A and the termination factor eRF1.
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Affiliation(s)
- Keely Oltion
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jordan D Carelli
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Tangpo Yang
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Stephanie K See
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Hao-Yuan Wang
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases, Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Jack Taunton
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA.
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47
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Lin J, Gettings SM, Talbi K, Schreiber R, Taggart MJ, Preller M, Kunzelmann K, Althaus M, Gray MA. Pharmacological inhibitors of the cystic fibrosis transmembrane conductance regulator exert off-target effects on epithelial cation channels. Pflugers Arch 2023; 475:167-179. [PMID: 36205782 PMCID: PMC9849171 DOI: 10.1007/s00424-022-02758-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 09/28/2022] [Accepted: 10/03/2022] [Indexed: 02/01/2023]
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) anion channel and the epithelial Na+ channel (ENaC) play essential roles in transepithelial ion and fluid transport in numerous epithelial tissues. Inhibitors of both channels have been important tools for defining their physiological role in vitro. However, two commonly used CFTR inhibitors, CFTRinh-172 and GlyH-101, also inhibit non-CFTR anion channels, indicating they are not CFTR specific. However, the potential off-target effects of these inhibitors on epithelial cation channels has to date not been addressed. Here, we show that both CFTR blockers, at concentrations routinely employed by many researchers, caused a significant inhibition of store-operated calcium entry (SOCE) that was time-dependent, poorly reversible and independent of CFTR. Patch clamp experiments showed that both CFTRinh-172 and GlyH-101 caused a significant block of Orai1-mediated whole cell currents, establishing that they likely reduce SOCE via modulation of this Ca2+ release-activated Ca2+ (CRAC) channel. In addition to off-target effects on calcium channels, both inhibitors significantly reduced human αβγ-ENaC-mediated currents after heterologous expression in Xenopus oocytes, but had differential effects on δβγ-ENaC function. Molecular docking identified two putative binding sites in the extracellular domain of ENaC for both CFTR blockers. Together, our results indicate that caution is needed when using these two CFTR inhibitors to dissect the role of CFTR, and potentially ENaC, in physiological processes.
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Affiliation(s)
- JinHeng Lin
- grid.1006.70000 0001 0462 7212Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH UK ,grid.4991.50000 0004 1936 8948Present Address: Department of Pharmacology, University of Oxford, Oxford, OX1 3QT UK
| | - Sean M. Gettings
- grid.1006.70000 0001 0462 7212School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU UK
| | - Khaoula Talbi
- grid.7727.50000 0001 2190 5763Physiological Institute, University of Regensburg, 93053 Regensburg, Germany
| | - Rainer Schreiber
- grid.7727.50000 0001 2190 5763Physiological Institute, University of Regensburg, 93053 Regensburg, Germany
| | - Michael J. Taggart
- grid.1006.70000 0001 0462 7212Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH UK
| | - Matthias Preller
- grid.425058.e0000 0004 0473 3519Department of Natural Sciences/Institute for Functional Gene Analytics, Structural Biology Group, Bonn-Rhein-Sieg University of Applied Sciences, 53359 Rheinbach, Germany
| | - Karl Kunzelmann
- grid.7727.50000 0001 2190 5763Physiological Institute, University of Regensburg, 93053 Regensburg, Germany
| | - Mike Althaus
- grid.1006.70000 0001 0462 7212School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU UK ,grid.425058.e0000 0004 0473 3519Present Address: Department of Natural Sciences /Institute for Functional Gene Analytics, Ion Transport Physiology Group, Bonn-Rhein-Sieg University of Applied Sciences, 53359 Rheinbach, Germany
| | - Michael A. Gray
- grid.1006.70000 0001 0462 7212Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH UK
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Jackson JJ, Mao Y, White TR, Foye C, Oliver KE. Features of CFTR mRNA and implications for therapeutics development. Front Genet 2023; 14:1166529. [PMID: 37168508 PMCID: PMC10165737 DOI: 10.3389/fgene.2023.1166529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 03/27/2023] [Indexed: 05/13/2023] Open
Abstract
Cystic fibrosis (CF) is an autosomal recessive disease impacting ∼100,000 people worldwide. This lethal disorder is caused by mutation of the CF transmembrane conductance regulator (CFTR) gene, which encodes an ATP-binding cassette-class C protein. More than 2,100 variants have been identified throughout the length of CFTR. These defects confer differing levels of severity in mRNA and/or protein synthesis, folding, gating, and turnover. Drug discovery efforts have resulted in recent development of modulator therapies that improve clinical outcomes for people living with CF. However, a significant portion of the CF population has demonstrated either no response and/or adverse reactions to small molecules. Additional therapeutic options are needed to restore underlying genetic defects for all patients, particularly individuals carrying rare or refractory CFTR variants. Concerted focus has been placed on rescuing variants that encode truncated CFTR protein, which also harbor abnormalities in mRNA synthesis and stability. The current mini-review provides an overview of CFTR mRNA features known to elicit functional consequences on final protein conformation and function, including considerations for RNA-directed therapies under investigation. Alternative exon usage in the 5'-untranslated region, polypyrimidine tracts, and other sequence elements that influence splicing are discussed. Additionally, we describe mechanisms of CFTR mRNA decay and post-transcriptional regulation mediated through interactions with the 3'-untranslated region (e.g. poly-uracil sequences, microRNAs). Contributions of synonymous single nucleotide polymorphisms to CFTR transcript utilization are also examined. Comprehensive understanding of CFTR RNA biology will be imperative for optimizing future therapeutic endeavors intended to address presently untreatable forms of CF.
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Affiliation(s)
- JaNise J. Jackson
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, United States
- Center for Cystic Fibrosis and Airways Disease Research, Emory University and Children’s Healthcare of Atlanta, Atlanta, GA, United States
| | - Yiyang Mao
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, United States
- Center for Cystic Fibrosis and Airways Disease Research, Emory University and Children’s Healthcare of Atlanta, Atlanta, GA, United States
| | - Tyshawn R. White
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, United States
- Center for Cystic Fibrosis and Airways Disease Research, Emory University and Children’s Healthcare of Atlanta, Atlanta, GA, United States
| | - Catherine Foye
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, United States
- Center for Cystic Fibrosis and Airways Disease Research, Emory University and Children’s Healthcare of Atlanta, Atlanta, GA, United States
| | - Kathryn E. Oliver
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, United States
- Center for Cystic Fibrosis and Airways Disease Research, Emory University and Children’s Healthcare of Atlanta, Atlanta, GA, United States
- *Correspondence: Kathryn E. Oliver,
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Abstract
Cystic fibrosis (CF) is a multiorgan disease caused by a wide variety of mutations in the cystic fibrosis transmembrane conductance regulator gene. As treatment has progressed from symptom mitigation to targeting of specific molecular defects, genetics has played an important role in identifying the proper precision therapies for each individual. Novel therapeutic approaches are focused on expanding treatment to a greater number of individuals as well as working toward a cure. This review discusses the role of genetics in our understanding of CF with a particular emphasis on how genetics informs the exciting landscape of current and novel CF therapies.
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Affiliation(s)
- Anya T Joynt
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Garry R Cutting
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Neeraj Sharma
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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50
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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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